SECTION I

Form APProvd
O.Y.B. 6e-R0.249

       DEPARTMENT OF
HEALTH. EDU~TION. AND WELFARE
    PUELIC HEALTH SERVICE

                 LEAVE BLANK
TYPE `PROGRAM           NUMBER

GRANT APPLICATION

REVIEW GROUP

COUNCIL (Monrh, Yew/

FORMERLY

DATE RECEIVED

TO BE COMPLETED BY PRINCIPAL INVESTIGATOR (/terns 7 thro~#~ 7and ISA)
1. TITLE OF PROPOSAL (Do nor cxcccd 5.3 rypJwrirJrzp~cJd
  Resource-Related Research - Computer in Chemistry (RR-00612 renewal)

           2. PRINCIPAL INVESTIGATOR
ZA. NAME ILasr. Fim, Iniridl
D jerassi, Carl

13.DATES OF ENTIRE PROPOSED PROJECT PERIOD (Thts roplicdrion
FROM                   THROUGH
May 1, 1980      April 30, 1985

28. TITLE OF POSITION

Professor of Chemistry

4. TOTAL DIRECT COSTS RE-   5. DIRECT COSTS REQUESTED
QUESTED FOR PERIOD IN     FOR FIRST 12-MONTH PERIOC
ITEM 3
$1,611,719         $511,400

2C. MAILING AODR ESS LSrre-* Cirv, Srare, Z';p &de)

6. PERFORMANCE SITEIS) l&e /nsrrucr;ons/

Department of Chemistry
Stanford University
Stanford, CA 94305

?D. DEGREE

2G. DEPARTMENT, SERVICE. LABORATORY OR EOUIVALENT
  ISew lmrrucdonsl

Chemistry Department

2H. MAJOR SUB01 VISION ISee lnsrrucriond

Stanford University
Stanford, CA 94305

School of Humanities and Sciences

`1. Resarrch involving Human Subjects (See lnsrrucrions/

A.m NO l3.0 YES Approved:                  A.m NO  6.0 YES - Not prwiously reperred
C.0 YES - Pending R-i&w              oatm          C. 0YE.S - Prsv~ously reportm
TO BE COMPLETED BY RESPONSiBLE ADMINISTRATIVE AUTHORITY (Irems 8 rhmwh 13 dnd 1581
9. APPLICANT ORGANIZATIONIS) (See Imrrucrronsl             1

Stanford University
Stanford, CA 94305
IRS No. 94-1156365
Congressional District 12

,l. TYPE OF ORGANIZATION {Check dpplkdbk Mernj
0 FEDERAL 0 SATE 0 LOCAL m OTHER fsprC;fY~
      Private, non-a&t univeni tv
12. NAME, TITLE, ADDRESS, AND TELEPHONE NUMBER OF
  OFFICIAL IN BUSINE.SS OFFICE WHO SHOULD ALSO BE
  NOTIFIED IF AN AWARD IS MADE

10. NAME. TITLE. AND TEiEPHONE NUMBER OF OFFICIAL(S)
SIGNING FOR APPLICANT ORGANIZATIONIS)
  Larry J. Lollar
  Sponsored Projects Officer

T@lephono Number (8)  415-497-2883

14.  EtiTITY SUYBER (Formerly PHS Account Number)
       IRS No. 94-1156365

15. CERTIFICATION AND ACCEPTANCE. We, thm undcrzignd, cwtii
knowledge wd nxrpt, 8s to o ny gfant mw.wded, the obiimtion to comply with Public Hcalt? Service trrmr rnd conditions in cffm at the timeof the

K. D. Creighton
Assoc. Vice President-Controller
Stanford University

   s'""f"r(r$ho~)N,5 415-497-2251
3. IDENTIFY ORtANlZATlONAL COMPONENTTO RECEIVE CREDlf
FOR INSTITUTIONAL GRANT PURPOSES f.%e lnrrrucrionr~

wrd.

   SIGNATURES      A. >I~,,~-QN NAMED IN ITEM 2A                        DATE

lSign*lurM rcquifd on
original copy only.       8. SIGNATURE(S) OF PERSON(S) NAMED IN ITEM 10        I DATE
USJ mk. "Per" rigtwursr

  nor acrerrnblrl      I                                           I

HIM 398 (FCFMiRLI PnS 398)                  1
Rev. `173


SECTION 1

DEPARTMENT OF HEALTH. EDUCATION. ANO WELFARE
          PUBLIC HEALTH SERVICE

I        LEAVE BUNK

1 PROXCT NUMBER

RESEARCH OBJECTIVES

NAME AND AODRESS OF APPLICANT ORGANIZATION
Stanford University, Stanford, CA 94305

NAME, SOCIAL SECURITY NUMBER, OFFICIAL TITLE, AN0 DEPARTMENT OF ALL PROFESSIONAL PERSONNEL ENGAGED ON
PROJECT, BEGINNING WITH PRINCIPAL INVESTIGATOR

Carl Djerassi
Dennis H. Smith
Bruce G. Buchanan

Professor of Chemistry
Senior Research Associate
Adjunct Professor

Department of Chemistry
Department of Chemistry
Department of Computer

James G. Nourse
Neil A. B. Gray

-                     Science
          Research Associate      Department of Chemistry
     --       Research Associate      Department of Computer
                            Science

Resource-Related Research - Computen in Chemistry
u THIS SPACE TO ABSTRACT YOUR PROPOSED RESEARCH. OUTLINE OBJECTIVES ANO METHOOS. UNOERSCORE THE KEY WORDS
(NOT TO EXCEED 10) IN YOUR ABSTRACT.
Our proposed research concerns computer-assisted structure elucidation of organic compounds of
biological importance.  W propose to make a quantum jump in both performance of existing and new
programs and their availab.1 % `ity to a nat@n WI e community of biomedical scientists. We will build more
                           `d
wrful programs (basing our efforts on the solid foundation of programs developed under earlier grant
support by:  a) assembling a Semi-Automated Structure Elucidation System (SASES) which will act
as a computer-based "laboratory" for carrying out experiments involving computer representation and
manipulation of chemical structures, including structure elucidation , spectral data interpretation
and prediction and conformational analysis to establish relationships between three-dimensional
structures and their biological and chemical properties (structure/property relationships); b) develop-
ing at the heart of SASES the GENOA program, a method for structure Generation with Overlapping
Atoms, which will include as a component our existing CONGEN program; c) developing a method
for constrained generation of molecular conformations; and d) extending our topological structure
representations to include both configurational and conformational stereochemistry and infusing
proper treatment of stereochemistry throughout our computer programs.  We will increase the avail -
ability of our programs to the outside community through resource sharing in the foll.owing ways:
a) through a dedicated computer system which will exploit the proposed relationship of our work
to the S UMEX-AIM computer resource; b) by continuing to develop exportable versions of our
programs; and, c) by holding intensive workshops to introduce other research groups to our tech-
niques.

MlH 398 (FOMRLT PHS 398)
Rev. l/73

PAGE 2


SECTION II - PSIVILEGE.0 COMMUNICATION

   BUDGET ESTIMATES FOR ALL YEARS OF SUPPORT REQUESTED FROM PUBLIC HEALTH SERVICE
                    OlRECTCOSTSONLY(OmitCentr)

                       157 PERlOO
    DESCRIPTION         Is., ME AS OE   ADDITIONAL YEARS SUPPORT REQUESTED /This ap~li;af/on only/
                      TAILED BUDGETI   2ND YEAR    JR0 YEAR    4TH YEAR    5TH YEAR    6TH YEAR    7TH YEAR

PERSONNEL
COSTS          190,586   204,704 220,459 229,843 247,511

CONSULTANT COSTS                       i
(Include fea, tmvel, etc.1             `A .
                             '            a

EQUIPMENT        265,674   11,460. -

SUPPLIES          2,600    2,782   2,977   3,185   3,408

            DOMESTI c   1,500    1,500   1,500   1,500   1,500
TRAVEL .
            FOREIGN

PATIENT COSTS

ALTERATIONS ANb
RENOVATIONS

OTHER EXPENSES      51,040   37,836  40,483   43,320   46,351

TOTAL DIRECT COSTS

511,400   258,282 265,419 277,848 298,770

TOTAL FOR ENTIRE PROPOSED PROJECT PERIOD (Enruon &e 1, /ten 41  -  s 1,611,719

REMARUS: Justify 811 costs for the fiat ywr for which the nd nuy nor be o&viwr For fufure WV=, junify equipment car=, es well es eny
s*nifiont incr-a in o ny other catsgory. If o rawring o mud imm in pmonnd CQCP is mquated, give pucenrapa  /Use conrinu~rion
pmp if needed.)

Salary increases, and increases in other categories figured at 7% per year.

Staff benefits determined according to the following:

5/l/80 - g/31/80     21.6%
9/l/80 - 8/31/81     22.4%
9/l/81  - g/31/82     23.2%
9/l/82 - g/31/83     24.0%
9/l/83  - 8/3J/84     24.8%
9/l/84 - 4/30/85     25.6%

(see attached)

`NIH 398 (FOFw?LT PHS 398)
Rev. 1179                         4


Budget Remarks

Personnel

    Professor Djerassi will continue in  his role as principal investigator,
providing overall scientific direction to the project, Dr. Smith acting as co-
investigator. Drs.  Smith, Nourse, Gray and Buchanan will be responsible for the
design, implementation and application of the programs which we propose to develop,
including representing the scientific  interface to the outside community of
collaborators.

   Two programmers, Mr. Terry and a person to be appointed, will provide
scientific  vxv-~ing   support   for the  project  incluaing  the following
responsibilities. Mr.  Terry will have primary responsibility for maintenance and
documentation of application programs, with the assistance of other members of the
scientific and technical staff,  He will share responsibility for design and
progrannning of new algorithms with the scientific staff. Together with the second
programmer, he will provide  technical support for collaborators and be responsible
for developing versions of CCNGEN and newer programs  for other computer systems.
The second programmer,to be named,  will have primary responsibility for the
dedicated computer  system (the DEC VAX) requested in this proposal, including
interfaces t0 the SUMEX PDP-10 system,  and all other necessary system support
functions including obtaining and implementing new languages, text editors and so
forth.

   The pre- and postdoctoral fellows supported by the grant will be involved in
applications of the programs to chemical problems in our own laboratories or in
research involving development of new computer techniques in collaboration with the
professional staff.

    The secretarial responsibilities (105 percent of a full time person) are
distributed among three persons, reflecting our best estimates of actual time spent
on this grant and other grants,  to myself or  Prof. Feigenbaum, which support the
remainder of their salaries (Ms. Learned-Driscoll is supported for the remainder of
her time by the Chemistry Department).

Equipment

.

A Dedicated Computer System - the DEC VAX-11/780
                               ---

    We have requested funds in  the first year of the proposal to purchase a
dedicated computer system for our project.   The reasons for this approach are
discussed in detail in Section A.2.c, Relationship to the SUMEX-AIM Resource, and in
Section C.5.a.  Brieflyti the implementation  of this machine as an adjunct to the
SDMEX resource is a research study in itself, namely, how best to provide access to
computational resources  in a computing environment where  heavy demands are being
made on both development and application of  software tools for solving biomedical
problems.  We intend to make the dedicated system available for production use of
our applications programs,  assuring high quality interactive service to our
collaborators.  We cannot get such additional capacity for  this mrk from SDMEX
which is already overcrowded and committed to new program development rather than
production use.  We will exploit our  close relationship with SUMEX for the
development  of new programs, for continued close contact with the AI community
centered there, as a gateway to  communication facilities allowing remote terminal

5


Djerassi, Carl

access and for sharing of peripheral equipment and operations support so far  as is
possible.  At the end of this section we ccmment on our situation were the dedicated
machine not approved as part of this proposal.

    In considering  the type of machine which could provide the needed,
additional capacity, we  have focussed our attention on the qualities we muld
require in  a machine, letting  these considerations guide our choice.  We require
high quality, interactive service to  support our programs in a reasonable way. An
interactive program must provide rapid  response to the scientist using it. This
means we need a system with a good time-sharing operating system.  Our programs tend
to be larger than can fit comfortably on mini-computers, and certainly the more
complex programs which we propose  to develop will only grow larger.   This
requirement suggests a  system.which possesses a large address space,  large enough
that space  is not a limiting factor.   The combination of time sharing and large
address space  suggests a virtual memory machine with demand paging.  Finally, we
want a machine that will maximize long-term compatibilities with the SUMEX AI
community and other biochemical and chemical computing resources and laboratory
systems.

    We have considered several alternative computers which might meet the above
qualities and would provide the needed computational power to support our community.
We have rejected all 16-bit (or fewer) mini-computers on the basis of address space
limitations which are too restrictive for the size of our programs. Although it is
possible in principle to fit our new programs such as the exportable version of
CCNGEN into such a small machine using extensive overlays, the prcgramming effort
would be prohibitive.

    One plausible alternative  is to purchase a computer compatible with the
existing DE-10 or DE-20 systems at SDMEX and Rutgers on which our new software
such as CCNGEN will run without change.  There are only tkX)  reasonable alternatives
here,  the DEC-20 family or  the Foonly F-2 (a DEC-10 compatible machine being
developed by a Pay-area company).  The higher end of the DEC line is prohibitively
expensive (e.g.,  the 2040 or 2050), leaving the DEC-2020 as the only reasonable
choice.  These systems have  the advantage of running the  highly developed
interactive monitors (TENEX or TOPS-20) now used at SUMEX and other AI resources.
This would maximize near-term compatibility and minimize operational costs. The
2020 (and the F-2) are ccnnputationally quite slow, however, particularly for
arithmetic processing since they do not have a floating point processor.   We expect
our new research will make significant demands in this area.

    There are several other negative-factors about selecting either the 2020 or
the F-2.  The current price-performance index of the DE-2020 is quite poor: no
price advantage per user is achieved over the much more complex (and expensive) DEC-
20's.  Foonly is a very  anal1 company whose  future is insecure.  Only a few
laboratories to which we might export software and collaborate   on program
developments and applications operate  DEC-10 or -20 compatible machines. Finally,
this class of machines is rapidly becoming obsolete.  DEC appears to be directing
their future developments toward VAX-like machines.

    In parallel with this, the ARPANET AI coannunity has been investigating long-
term alternatives for INTERLISP support given the address space limitations of the
DEC-10.  A nlnnber of alternatives are under consideration including a "personal"
LISP machine being developed at MIT, a PRIME system being considered by BB and N
(Bolt Beranek and Newman Inc.) and the DEC-VAX.  It appears that a consensus is
developing around VAX given its attractive architecture, good interactive operating
systems (UNIX or perhaps V?4S) and vendor support.  The DEC-VAX also appears to be

6


Djerassi, Carl

increasingly popular in  scientific laboratories, including  labs of several of our
mrkshop attendees  (see Annual Report, Appendix I).   As another example, the
National Resource for Computation in Chemistry will  soon take delivery of a VAX
system,  meaning that additional, chemistry related software will soon become
available on the VAX.  (We note that similarly configured VAX's and 2020's have
similar prices;  the VAX will deliver considerably more computational power,
however).

     In su~~pnary,  purchase of a  2020 or similar machine muld be an expedient,
short-term option to pursue in  terms of our compatibility with ourselves.   We feel
strongly, however, that this would be short sighted. We must look further into the
future in our propsal to make the best estimate possible on the trends in computer
developments followed by both manufacturers and users.  We are already seeing shifts
in DEC, the AI community and, most importantly, computational chemists with whom we
interact, toward VAX and similar machines,   It is becoming  clear that VAX or its
equivalent is the machine to obtain, especially as a medium for providing high
quality,  interactive service to our collaborators, whether by network access to
Stanford or programs exported to other sites. We have, therefore, tentatively
decided to purchase a VAX as the dedicated machine to support applications of our
programs.  The configuration of the VAX as we propose it would include:

    1) Basic system, including 512 KByte memory, one RR06 disc drive, one TE16
  tape drive, VW operating system, LA120 operator console, DZ-11A for eight
  terminal lines ($185,000);

2) 1 MByte additional memory ($35,000);

  3) Either 1 Mbyte additional memory ($35,000) or one additional RR06 disc
drive ($34,000) ($35,000 figured in the total appearing on the budget)

4) FORTRAN compiler ($3,300);

5) Floating point accelerator ($9,900).

    Item (2) is strongly recommended by DEC in order to support more than two or
three concurrent users.  The choice in item (3) remains to be made,   The tradeoff
here is whether or not support for  a larger complement of users (8 - 12) is best
handled by a separate disc system for paging, or by additional memory. Further
discussions with other VAX users will be required to reach a final conclusion. The
final budget figure ($254,214) was obtained by swing the above figures, taking an
11 percent educational discount and adding 6-l/2 percent California State sales tax.

    We are currently evaluating the various operating systems available for the
VAX, including VMS from DEC, T.,JNIX from Bell Laboratories or the Interactive Systems
Corp.  UNIX version which couples both VMS and UNIX in one package. Choice of one
of the non-DEC operating systems will add an additional increment to our budget. In
addition, new software from DEC, such as new compilers, will represent additional
costs.  Given the price of the FORTRAN compiler, we can estimate other languages to
cost about the same.  We have requested funds in  the budget to cover sortware
purchases, with the greatest expense in year one.

    We have also budgeted, as a one-time cost , our best estimates of the expnse
required to implement the SlJMEX/vpx link (see Section C.5). This figure, $15,000,
will cover communications  interfaces,  circuit boards,  cabling and  integrated
circuits.

7


D-jerassi, Carl

    As a final note, the rapidly changing situation with respect to new machines
and cheaper prices for existing machines may allow us to reduce these  estimates in
the coming months. We are making  every effort to find more cost-effective  ways to
meet our basic goals for the dedicated ccxnputer.

   We believe that a DEC maintenance contract to support the hardware is the
most cost-effective way  to ensure maximum computer availability for our outside
collaborators.  Based on the hardware cited above and DEC's standard contract
prices,  the cost for year one (nine-month basis, three months covered under
warranty) is $13,450, including a maintenance contract on the existing GT40.

    If this propxal is approved and funded without the proposed computer, we
will be forced to provide .access to our programs,
applications,                           for both development and
        to SDMEX alone, i.e.,
an important experiment in resource perpetuate the current situation. Not only will

COlhbOratOrS (see Section F)    access and resource sharing be lost, but our
                  will become increasingly impatient at the slow
response time of SUMEX,  We know from past experience that if respnse time in a
highly interactive program beccnnes too long, scientists will simply find more
productive uses for their time and will cease to use the computer. It also must be
recognized that, because SDMEX is funded separately from our grant, we must also try
to ensure  long-term computational support   for our research.    The machine
configuration requested is , alone, insufficient to meet our needs in the absence of
SUMEX, but muld do so with augmentation (additional peripheral equipment, memory,
network interface, additional terminal ports and perhaps additional personnel).

Graphics Terminals

    The goals of our proposed research are heavily involved with stereochemical
representations of molecular structure.  The requirements  for visualizing these
structures plus our desires to seek improvements in the interactive  capabilities of
our programs (most of our collaborators have
and output) have led us to propose       requested some form of graphic input
                     a low-cost alternative to expensive graphics
systems (Evans and Sutherland, Vector-General) or even expensive graphics terminals
like the DEC GT-40.  We are currently examining alternative display systems which
represent new technology and provide graphics capabilities together in sane
instances with capabilities
information.            for input of graphic (in our   case structural)

     We have  examined several display  systems so far,  including those
manufactured by Grinnel Systems (Santa Clara, CA), DeAnza Systems (Santa Clara, CA)
and Tektronix,  At this time, the Tektronix 4025 appears to have a better set of
desirable features,  including capacity for pseudo-rotation of structures  based on
sequential display of stored  images, programmable  functions for special graphics
such as automatic construction of ring systems, and cursor control for structure
input.  The budget figure requested inclties the basic terminal plus additional
display and graphics memory (to a total of 32K and 64K bytes, respectively) to allow
storage of sufficient multiple images for pseudo-rotation (to add three-dimensional
characteristics to the visualized structures).  We will continue to search for other
low-cost graphics terminal which would meet our needs together with the needs of our
collaborators.

    A second terminal has been requested  in the second year of the btiget. By
that time we should be heavily involved in representation and manipulation of three-
dimensional representations  of structure and would require
terminal support for program developnent and application.     additional graphics

8


SECTION II - PRIVILEGED COMMUNICATION
                        BIOGRAPHICAL SKETCH

       (Give fhe lo/lowing infornution for rll profsrsional psrsonnd l&ad on pag# 3. beginning m'th the Principrl Investigstof.
                Usa continuation pap and folIow the same gmrrwl format for each panod
NAME                       TITLE -                    BIRTHDATE IMa, Day. Yr.)
Carl D jerassi             Professor of Chemi&y         1 O/29/23

PLACE OF BIRTH (City, State, Country)           PRESENT NATIONALITY (If non-US citizen,

Vienna, Austria

I indicate kind of visa md expire tion ah to)
U. S. Citizen

I

EDUCATION (Begin with b.xc8kurem mining ma

INSTITUTION AND LOCATION              DEGREE

                                                   lclude postdoctorr Ill

                                                             YEAR           SCIENTIFIC
                                                        CONFERRED             FIELD
Kenyon College                 A. 6. (summa   1942     Chemistry, Biology
                       cum laude)
University of Wisconsin                Ph.D.      1945     Organic Chemistry
                                             Biochemistrv (minor)
HoNoRs National Medal of Science (`73); Perkin Medal (`75); Am. Chem. Sot. Awards: Pure Chemistry
(`58), Baekeland Medal (`59), Fritzsche Award (`&I), Award for Creative Invention (`73); Freedman Four
dation Patent Award
Centenary Lecturer, k `71) and Chem. Pioneer Award `73) of Am. Inst. Chem. * Han, Member and
            hem. Sot . (London); Member o f National Academy of Sciences, American
MAJOR RESEARCH INTEREST                      ROLE IN PROPOSED PROJECT

HONORS (continued)
Academy of Arts and Sciences, Royal Swedish Academy of Sciences, Leopoldina, Bulgarian Academy of
Sciences. Honorary D. SC. Kenyon College, Nat. Univ. of Mexico, Federal Univ. of Rio de Janeiro,
Worcester Polytechnic Inst., Wayne State, Columbia, Uppsala, Coe College, University of Geneva.
Wolf Prize in Chemistry (1978), National Inventors Hall of Fame (1978).

RESEARCH ANODR PROFESSIONAL EXPERIENCE IStarting with prunt position. -and rxpbtiencr rrlnmt to se-m of Proict  List &I
or mm mpnwnaoiw publkationa  Do mt ucad 3 pr011 for mch individwll

Academic Experience
Professor of Chemistry, Stanford University, 1959 - present
Assoc. Professor (`52:`54) and Professor (`%-`59), Wayne State University
Industrial Experience

Zoecon Corp., Palo Alto, CA, Chairman of the Board and Chief Exec. Officer, `68 - present.
Syntex Corp. : Various positions in Mexico City (`49-`52, `57-`60) and Palo Alto, CA (`&`72) ranging from
ASSOC. Director of Chemical Research to President of Syntex Research.
Ciba Pharmaceutical Co., Summit, NJ, Research Chemist, `42-`43, `4%`49.
Miscellaneous
Chairman of AAAS Gordon Res. Conf. on Steroids and Nat. Prod. (`52-`54); Member Amer. Pugwash Comm.
(`68-`75); Chairman, Latin American Science Board of National Academy of Sciences (`66-`68); Member (`68
`72) and Chairman (`73-`75) of Board on Science and Technology for international Development of National
Academy of Sciences; Member, President's Advisory Group on Contributions of Technology to Economic Streng
(`75-76); Comm. on National Medal of Science; NAS Institute of Medicine (Member of Membership Comm. ar
Comm. on International Health).

Publications

Author or co-author of six books (four dealing with organic mass spectrometry( and over 930 scientific publica-
tions. The most recent publications (since Janua x 1978) are listed here, with papers Nos. 927, 925, 924,
915, 907 and 906 being particularly relevant to t is application.

Mill 39.9 (FORMERLY PHS 39)
Rev. 1173                         9              lr"S GOVERNUENT PRINTING CF:EE. 1977-241~1619C24


RESEARCH SUPPORT: CARL DJERASSI

Since essentially all of my research is supported by the NIH, it is important for the
reviewers to undentand what each grant actually covers in terms of personnel, equip-
ment, etc., and how the present renewal application of RR-00612 fits into this overall
picture.  Therefore, I am going into somewhat more detail than is generally required for
this section.

GM-06840 (20-23): "Marine Chemistry with Special Emphasis on Steroids" 5/l/78 - 4/30/82.
Current annual budget $133,042.  This grant supports the bulk (equivalent to three predoctorate
and five postdoctorate fellows) of my collaborators who are working on the isolation, structure
elucidation, biosynthesis and possible biological function of marine steroids.

GM-20276 (05): "Magnetic Circular Dichroism of Cytochromes P-450" 7/l/78 - 6/30/79.
Current budget $38,201.  Aside from equipment maintenance and liquid helium, this grant
supports partial salaries of two postdoctorate research associates.  A renewal application,
entitled "MCD of Porphyrins and Artificial Heme Proteins" has been submitted.

RR-00612 (09-10):  "Resource Related Research - Computers in Chemistry" 5/l/78 - 4/30/80.
Current budget $144,051 (5/l/79 - 1 l/30/79).  The current application is for renewal of
this project.  The renewal represents a significant change in emphasis from the current
proposal in that the SUMEX-AIM computer resource is the resource to which our research
will be related in the future, rather than the mass spectrometry laboratory.  For this reason,
the following two (partially overlapping) applications were submitted (and are pending) for
support of personnel and supplies and purchase of new equipment to maintain and upgrade
the mass spectrometry laboratory.  Because of this shift in emphasis, the current proposal
requests no funds for support of the laboratory and does not overlap in any way with the follow-
ing two proposals.

M-04257:  "Mass Spectrometry in Organic and Biochemistry" 12/l/76 - 11/30/79.
Current annual budget $74,800.  This grant currently supports one mass spectrometer,
a senior technician to opemte the instrument, one postdoctoral fellow and three predoctoral
fellows, who are engaged in isolation and synthetic work related to interpretation of frag-
mentation patterns of known and unknown molecular structures.

A renewal application has been submitted for this grant and is currently pending. This
renewal is designed to support the mass spectrometer, personnel and supplies currently
supported under RR-006 12.  In addition funds were requested to upgrade the mass spectrometer
facilities.  No action has as yet been taken on this application.

Pending Application: A NIGMS Shared Instrumentation Resource proposal entitled "A Shared
Mass Spectrometry Resource" h*as been submitted for the period 9/l/79 to 8/30/82. The
first year budget is $145,046, including $130,850 of capital equipment.  This proposal re-
quests support for equipment similar to that requested in the renewal of AM-04257, with
some differences reflecting the resource sharing aspects of the NIGMS program.  The only
personnel for whom support is requested under this proposal include 10 percent of Dr. Smith
and 10 percent of a senior technicial.  No action has yet been taken on this application.
If AM-04257 is approved then only $18,500 is requested from NIGMS for a chemical ionization
act essory .

10


RESEARCH SUPPORT: CARL DJERASSI (continued)

Pending Application:  An application entitled "Circular Dichroism of Cyclic Ketones -
Conformational Isotope Effects" with an annual budget of $55,782 for the period 4/l/79
to 3/31/81 has been submitted to the National Science Foundation.  In terms of personnel,
it covers the salaries of one postdoctorate and two  redoctorate fellows for synthetic work
on chiral ketones, whose chirality is only due to l$ or deuterium.  No action has as yet
been taken on this application.

RECENT PUBLICATIONS

900. Magnetic Circular Dichroism Studies LII.  Magnetic Circular Dichroism of Purified Forms
of Rabbit Liver Cytochromes P-450 and P-420. Biochemistry 17, 33 (1978), by J. H. Dawson,
J. R. Trudell, R. E. Linder, G. Barth, E. Bunnenberg and CTD jerassi.

901.  Optical Rotatory Dispersion Studies CXXI I.  Synthesis and Circular Dichroism of (3S)-
Deuteriocyclohexanone.  Tetrahedron Letters, 535 (1978), by C. Djerassi, C. L. VanAntwerp
and P. Sundararaman.

902.  Hommes Affamei, Parasites Affamej. Prospective et Sante', No. 4, 87-91 (1978), by
Carl D jerassi .

903. Marine Natural Products.  Synthesis of Four Naturally Occurring 20B-H Cholanic Acid
Derivatives.  J. Org. Chem. 43, 1442 (1978), by D. J. Vanderah and C. Djerassi.

904. One Step Conversion of Aldehydes to Esters.  Tetrahedron Letters, 1627 (1978), by
P. Sundararaman, E. C. Walker and C. Djerassi.

905.  Terpenoids LXXV. A9(12)-Capnel lene, A New Sesquiterpene Hydrocarbon from the
Soft Coral Capnel la Imbricata.  Tetrahedron Letters, 1671 (1978), by E. Ayanoglu, T.
Gebreyesus, C. M. Beechan, C. Djerassi and M. Kaisin

906. Applications of Artificial Intelligence for Chemical Inference XXVI I. Computer-Assisted
Structure Manipulation.  Studies in the Biosynthesis of Natural Products. Tetrahedron 34,
                                                                           -
841 (1978), by T. H. Varkony, D. H Smith and C. Djerassi

907. Recent Advances in the Mass Spectrometry of Steroids. Pure and Appl. Chem. 50,
177 (1978), by C. Djerassi.

11


RECENT PUBLICATIONS - Carl Djerassi

908.

909.

910.

911.

912.

913.

914.

Optical Rotatory Dispersion Studies CXXI I I.  Experimental
Evidence for Preference of Axial Deuterium over Axial Hydrogen.
    J. Amer. Chem. Sot. 100, 3965 (1978)
  by S.-F. Lee, G. BarthTK. Kieslich and C. Djerassi

Optical Rotatory Dispersion Studies CXXIV. Synthesis and
Circular Dichroism of 3(S)a- and 3(R)e-Deuterio-4(R)-+ktyl-
cyclohexanone and 2(R)a- and 2(S)e-Deuterio-4(R)-Isopropyl-

cyclohexanone.

Tetrahedron Letters, 2457 (1978)
by P. Sundararaman and C. Djerassi

Minor and Trace Sterols in Marine Invertebrates IV. ldentifica-
tion of Sterols with Short Side Chains in the Sponge Damiriana
hawaiiana.

Helv. Chim. Acta 61, 1470 (1978)
by C. Delseth, R.KK. Carlson, C. Dierassi, T.
Erdman and P. J. Scheuer

"Copjng with Interdependence: The Population Problem':, in
Proceedings of the Symposium on Energy, Food, Population and
World Interdependence, Committee on Chemistry and Public
Affairs, American Chemical Society, Washington, D.C., 1978,
pp. 40-43; 53-55. By Carl Djerassi .

Minor and Trace Sterols in Marine Invertebrates V. Isolation,
Structure Elucidation and Synthesis of 3/3-Hydroxy-26,27-
Bisnorcholest-5-en-24-o n e from the Sponge Psammaplysilla
purpurea

Steroids 31, 815 (1978)
byyzoglu, C. Djerassi, T. R. Erdman and P.J.
Scheuer

Terpenoids LXXIV.  The Sesquiterpenes from the Soft Cd
Sinularia movi.

Dral

Tetrahedron 34, 2503 (1978)
by C. M. Gchan, C. Djemssi and H. Eggert

24-Ethyl-A5~24!28)~28-cholestatrien-3P-ol - a Natural
Occurring Allenic Marine Sterol.
   J. Amer.Chem. Sot. 100, 5574 (1978)

IY

by N. Theobald, J. NY?hoolery, C. Djerassi f T. R.
irdman and P. J. Scheuer

12


RECENT PUBLICATIONS - Carl Djerassi

915.

916.

917.

918.

919.

920.

Applications of Artificial Intelligence for Chemical Inference
XXVIII.  Computer-Assisted Simulation of Chemical Reaction
Sequences. Applications to Problems of Structure Elucidation.
   J. Chem. Inf. Comput. Sci. 18, 168 (1978)
   by T.H. Varkony, R. E. Carhz, D. H. Smith and
   C. D jerassi

Birth Control after 1984 Revisited.
   Bull. Amer. Acad. of Arts and Sciences 32, No. 1,
   (1978)
   by C. Djemssi

Determination of the Absolute Configuration of Stelliferasterol
and Strongylosterol - Two Marine Stemls with " Extended"
Side Chains.

Tetrohedron Letters, 4369 (1978)
by N. Theobald and C. Djerassi

Minor and Trace Stemls in Marine Invertebrates IX.
Vemngulasterol - a Marine Sterol with a Novel Side Chain
Al kylation Pattern.

Tetrahedron Letters, 4373 (1978)
by W .C.M.C. Kokke, W. H. Fenical, C. S. Pak
and C. Djerassi

Optical Rotatory Dispersion Studies CXXVI. Synthesis and
Chiroptical Properties of Cyclohexanones with Chimlity Solely
Due to Isotopic Substitution: 12CH3 vs *3CH3 and CH3 vs
CD3

Tetrahedron Letters, 4377 (1978)
by C. 5. Pak and C. Djerassi

Isolation and Structure of 26,27-Cycloaplysterol (Petmsterol): /
Cyclopropane-Containing Marine Steml.
   Tet'rahedmn Letters, 4379 (1978)
   by B. N. Ravi, W.C.M.C. Kokke, C. Delseth and
   C. D jerassi

13


RECENT PUBLICATIONS - Carl Djerassi

921.

922.

Minor and Trace Sterols in Marine Invertebrates VIII.
Isolation, Structure Elucidation and Partial Synthesis of
Two Novel C30 Marine Sterols - Stelliferasterol and
lsostel Ii ferasterol .

J. Amer. Chem. Sot., 100, 7677 (1978)
by N. Theobald, R.J. Wells and C. Djerassi

Optical Rotatory Dispersion Studies CXXV. Independent Evi-
dence for Preference of Axial Deuterium vs. Axial Hydrogen
through Variable Temperature Circular Dichroism Spectra of
(4?)-2,2 -d imethyl-4-deuteriocyclohexanone and (3S)-3-
deuterio-4,4-dimethylcyclohexanone.
   J. Amer. Chem. Sot., 100, 8010 (1978)
   by S.F. Lee, G. Barth and C. Djerassi

923 .Partial Reduction of Aquomethemoglobin on a Sephadex G-25
  Column as Detected by Magnetic Circular Dichroism
  Spectmscopy and Revised ktinction Coefficients for Aquo-
   methemoglobin.

Analytical Biochemistry, 90, 474 (1978)
by R. E. Linder, R. Records, G. Barth, E. Bunnen-
berg, C. Djerassi, B. E. Hedlund, A. Rosenberg,
E. S. Benson, L. Seamans and A. Moscowi tz

924.  Minor and Trace Sterols in Marine Invertebrates VI.
  Occurrence and Possible Origins of Sterols Possessing
   Unusually Short Hydrocarbon Side Chains
     Bioorganic Chemistry, 7, 453 (1978)
     by R.M. K . Carfson, S . Popov, I. Massey, C.
     Delseth, E. Ayanoglu, T. H, Varkony and C. Djerassi

13a


RECENT PUBLICATIONS - Carl Djerasse

925.  A Novel Role of Computers in the Natural Products Field.
       Naturwissenschaften, 66, 9 (1979)
       by C. Djerassi, D. HTSmith and T. H . Varkony

926.  The Synthesis of Demethylgorgosterol.
       Tetrahedron Letters, 767 (1979)
      by R. D. Walkup, G. D. Anderson and C. Djerassi

927. Applications of Artificial Intelligence for Chemical Inference
     XXIX.  Exhaustive Generation of Stereoisomers for Structure
    Elucidation.

J. Amer. Chem. Sot., 101, 1216 (1979)
by J. G. Nourse, R. E.-&hart, D. H. Smith and
C. Djerassi

928.

Minor and Trace Sterols in Marine Invertebrates Xl. 5a-24-
Norcholestan-38-I and (24Z)-Stigmasta-5,7,24(28)-trien-3B-
01, Two New Marine Stemls from the Pacific Sponges Terpios
Zeteki and Dysidea Herbacea.
   Helv. Chim. Acta, 62, 101 (1979)
   by C. Delseth, L. TTela, P. J. Scheuer, R. J. Wells
   and C. Djerassi

13b


SECTION II - PRIVILEGED COMMUNICATION
                        BIOGRAPHICAL SKETCH
       (Give the follorinp inf~mnbon /or all profarsio~l pwsonnd lirted on pago 3. beginning m'th the Princiml Invatiptor.
                   us8 continw tion -4% rd lolluw th8 am8 pl8d forrmt for e&h pmonl
NAME                       TiTLE -                      BIRTHDATE /Ma. Dw. Yr.1
    Dennis H. Smith                 Research Associate           11-12-42

PLACE OF BIRTH ICify. State. Cbun~yl           PRESENT NATIONALITY /If non-U.S citirm,     SEX
                                 indict h kind of via #rrd srpit-8 tion date)
    New York                      USA                  El Mslr   0 Fernal.
                 EDUCATION (Bc+n tirh bmxalaurrwtr fnining and include por?doctorwll

           INSTITUTION AND LOCATION

Massachusetts Institute of Technology
Cambridge, MA
University of California
Berkeley , CA

DEGREE

S.B.

Ph.D.

  YEAR            SCIENTIFIC
CONFERRED            FIELD

  1964    Chemistry

  1967    Chemistry

HONORS

Alfred P. Sloan Foundation Scholarship, NASA Predoctoral Traineeship, Phi Lambda Upsilon,

Sigma Xi, Editorial Board of Journal of Chemical Information and Computer Science. .

MAJOR RESEARCH INTEREST                      ROLE IN PROPOSED PROJECT
Mass Spectrometry and Computer Applications
in Chemistry                     Senior Research Associate

RESEARCH SUPPORT ISn innnrca'onrl

.

RESEARCH ANOmR PROFESSIONAL EXPERIENCE (Spying wirhprwnt polio'on,liR~ndexp~~~n~r~u~n( toema ofprojat Lin ~11
or mart npraunmdv8 publiatiorr  DO not UC& 3 pros for mh individwl)

197 1 -present  Research Associate, Stanford University, Stanford, CA
1970-1971    Visiting Scientist, University of Bristol, Bristol, England
1967-1970   Assistant Research Chemist, University of California at Berkeley, Berkeley, CA
19651967   NASA Pre-Doctoral Traineeship, University of Colifomia at Berkeley, Berkeley, CA

Publications:  See attached list.


RECENT PUBLICATIONS - Dennis H. Smith

    (32) R.E. Carhart, D.H. Smith, H. Brown, and N.S. Sridharan,
"Applications of Artificial Intelligence for Chemical Inference. XVI.
Computer Generation of Vertex-Graphs and Ring Systems," J. Chem. Inf.
Comp. Sci
   ., 2, 124 (1975); Erratum, Ibid
                ., 16, 125 (197n.-
    (33) R.E. Car-hart, S.M. Johnson, D.H. Smith, B.G. Buchanan, R.G.
Dromey, and J. Lederberg, "Networking and a Collaborative Research
Community: A Case Study Using the DENDRAL Programs," in Computer
NettYDrking and Chemistry, P. Lykos, Ed., American Chemical Society,
Washmgton,D,C., 1975.

   (34) R.E. Carhart, DIH. Smith, H. Brown, and C. Djerassi,
"Applications of Artificial Intelligence for Chemical Inference. XVII.
An Approach to Computer-Assisted Elucidation of Molecular Structure," J.
Amer. Chem. Sot
      ., 97, 5755 (1975).                                         -
--

     (35) D.H. Smith,
Inf. Coma. Sci       "The Scope of Structural Isomerism," J. Chem.
          15 203 (1975).                                  --
-.-'I-'

    (36) D.H. Smith, J.P. Konopelski, and C. Djerassi, "Applications
of Artificial Intelligence for Chemical Inference. XIX.  Computer
Generation of Ion Structures," Org. Mass Spectrom., 11, 86 (1976).
                                  --              -
    (37) B.R. Simoneit, D.H. Smith, and G. Fglinton, "Application of
Real-Time Mass Spectrometric Techniques to Environmental Organic
Geochemistry. I. Computerized High Resolution Mass Spectrometry and Gas
Chromatography-Low Resolution Mass Spectrometry," Arch. Environ. Cont.
==*I 2, 385 (1976).

    (38) R.E. Carhart and D.H. Smith, "Applications of Artificial
Intelligence for Chemical Inference. XX. *Intelligent' Use of
Constraints in Computer-Assisted Structure Elucidation," Computers in
Chemistry, I, 79 (1976).                                                 -

.

    (39) C. Cheer, D.H. Smith, C. Djerassi, B. Tursch, J.C.
Braekman, and D. Daloze, "Applications of Artifical Intelligence for
Chemical Inference. XXI. Chemical Studies of Marine Invertebrates. XVII.
The Computer-Assisted Identification of [+I-Palustrol in the Marine
Organism Cespitularia sp., aff. Subvirdis," Tetrahedron, 32 1807
(1976).                                                 -'

    (40) B.G. Buchanan, D.H. Smith, W.C. White, R. Gritter, E.A.
Feigenbam, J. Lederberg, and C. Djerassi, "Applications of Artificial
Intelligence for Chemical Inference. XXII. Automatic Rule Formation in
Mass Spectrometry by Means of the Meta-DENDRAL Program," J. Amer. Chem.
tic., 9&, 6168 (1976).                                        ---

    (41) D.H. Smith and R. E. Carhart, "Structural Isomerism of
Mono- and Sesquiterpenoid Skeletons," Tetrahedron, 32, 2513 (1976).
                                                        -
    (42) L.L. Dunham, C.A. Henrick, D.H. Smith, and C. Djerassi,
"Mass Spectrometry in Structural and Stereochemical Problems. CCXLUI.

15


RECENT PUBLICATIONS - Dennis H. Smith

Electron Impact Induced Fragmentation of Juvenile Hormone Analogs," Org.
Mass Spectrom., 11, 1120 (1976).
                 -

    (43) T.H. Varkony, R.E. Carhart, and D.H. Smith, "Computer-
Assisted Structure Elucidation.  Mcdelling Chemical Reaction Sequences
Used in Molecular Structure Problems,"
Synthesis,"                in "Computer-Assisted Organic
     W.T. Wipke and J. Howe, Eds., American Chemical Society,
Washington, D.C., 1977, p. 188.

   (44) "Computer-Assisted Structure Elucidation," D.H. Smith, Ed.,
American Chemical Society, Washington, D.C., 1977.

   (45) R.E. Carhart, T,H:Varkony, and D.H. Smith, "Computer
Assistance for the Structural Chemist,"
Elucidation,"                in "Computer-Assisted Structure
        D.H. Smith, Ed.,
D.C., 1977, p. 126.       American Chemical Society, Washington,

    (46) D.H. Smith, M. Achenbach, W.J. Yeager, P.J. Anderson, W.L.
Fitch, and T.C. Rindfleisch, "Quantitative Comparison of Combined Gas
Chromatographic/Mass Spectrometric Profiles of Complex Mixtures," Anal.
Chem., 49, 1623 (1977).

    (47) B.G. Buchanan and D.H. Smith,
Reasoning,"                   "Computer Assisted Chemical
     in "Computers in Chemical Education and Research," E.V.
Ludena, N.H. Sabelli, and A.C. Wahl, Eds.,
1977, p. 401.                  Plenum Press, New York, N.Y.,

    (48) D.H. Smith and R.E. Carhart, "Structure Elucidation Based
on Computer Analysis of High and Iow Resolution Mass Spectral Data," in
"High Performance Mass Spectrometry: Chemical Aplications," M.L. Gross,
a., Z4nerican Chemical Society, 1978, p. 325.

   (49) T.H. Varkony, D.H. Smith, and C. D-jerassi, "Computer-
Assisted Structure Manipulation:
Products,"             Studies in the Biosynthesis of Natural
      Tetrahedron, 34, 841 (1978).
                          -
  (50);.H&gitkrd P.C. Jurs, "Prediction of 13C NMR Chemical
Shifts," . . . ., 100, 3316 (1978).
   (51) T.H. Varkony, R.E. Carhart, D.H. Smith, and C. Djerassi,
"Computer-Assisted Simulation of Chemical Reaction Sequences.
Applications to Problems of Structure Elucidation," J, Chem, Inf. Comp.
., 18, 168 (1978).
Sci                                                       W-P

   (52) D.H. Smith, 'r.C. Rindfleisch, and W.J. Yeager, "Exchange of
Comments: Analysis of Complex Volatile Mixtures by a Combined Gas
Chromatography-Yass Spectrometry System," Anal. Chem
                       ., 50, 1585 (1978).

\       (53) W.L. Fitch, P.J. Anderson, and D-H. Smith, "Isolation,
  Identification and Quantitation of Urinary Organic Acids," J. Chrom.,
   162, 249 (1979).                                                 -

16


RECENT PUBLICATIONS - Dennis Smith

    (54) W.L. Fitch, E.T. Everhart, and D.H. Smith,
"Characterization of Carbon Black Msorbates and Artifacts Formed During
Extraction," Anal. Chem
         ., 5GJ 2122 (1978').
    (55) W.L. Fitch and D.H. Smith, "Analysis of Adsorption
Properties and Adsorbed Species on Commercial Polymeric Carbons,"
Environ. Sci. Tech
       .I 2, 341 (1979).
    (56) J.G. Course, R.E. Carhart, D.H. Smith, and C. Djerassi,
'*Exhaustive Generation of Stereoisomers for Structure Elucidation," J.
Am, Chem. Sot.,
--    181, 1216 (1979).                                        -

    (57) C. Djerassi, D.H. Smith, and T.H. Varkony, "A Novel F&le of
Computers in the Natural Products Field," Naturwiss., 66, 9 (1979).
                                                            -
    (58) N.A.B. Gray, D.H. Smith, T.H. Varkony, R.E. Carhart, and
B.G. Buchanan, "Use of a Computer to Identify Unknown Compounds. The
Automation of Scientific Inference," Chapter 7 in "Biomedical
Applications of Mass Spectrometry," G.R. Wailer, Ed., in press.

    (59) T.C. Rindfleisch and D.H. Smith, in Chapter 3 of
"Bicmedical Applications of Mass Spectrometry," G.R. Waller, Ed., in
press.

    (60) T.H. Varkony, Y. Shiloach, and D.H. Smith, "Computer-
Assisted Examination of Chemical Compounds for Structural Similarities,"
J. Chem. Inf. Comp. Sci., in press.
m-p

17


>`L I I'JN II -PRIVILEGED COMf.W:JICAl-ION
---

.    . .

BIOGRAPHICAL SKETCH

(Give ;he following information for afIprofrJsionsl penonnef lined on page 3, bqinniw tiith the Principef Invcariptor.
        Use continuation pp end follow the =me gsnerel former for ouch person)
                                            BIRTHDATE Ma. Dar, Yr.1

PUCE OF BIRTH Icky, Stste. Country)

PRESENT NATIONALITY (If non-U.S citizen,
indicate kind of vise end erpimtion date)

     I    U.S.          I   XXI Msls   0 Female
EDUCATION (Beyin with baccelaorwte training nnd include postdocroral)

         INSTITUTION AND LOCATION

Ohio Wesleyan University, Delaware, Ohio
Michigan State University

DEGREE

6.A.
M.A.
Ph.D.

  YEAR            SCIENTIFIC
CONFERRED            FIELD
1961       Mathematics                -.
1966      Philosophy

#OeN?$ent of National Institutes of Health Career Development Award (1971-1976).
contitiued on attached sheet

MAJOR RESEARCH INTEREST
Artificial Intel 1 igence

RESEARCH SU??ORT (Sue instructions)

ROLE IN PROPOSED PROJECT
Principal tnvestigator

NlH `jR24 RR 00612-09 Resource Related Research:
  Time presently committed-: 20%          Computers and Chemistry 5/l/77 to.9//30/79

Dept. of Defense kIA W3-77-C-03X% Heuristic Programming 8/l/77 to y/30/79. Time presently
  ;Commi tted:  45%

National Science Foundation MCS 7702712 Knowledge-Based Intelligent Systems 6/l/77 to
  5130179 *  Time presently committed: 10%
National Science Foundation MCS 7S-02777; MOLGEN:
  Molecular Genetics .               A Computer Science Application to
              T,ime piesently committed: 25%

RESEARCH ANDDR PROFESSIONAL EXPERIENCE (Starting withprasentporition,&&&&trsinin.?and8xperienc8r8kvant toorea ofprojecL Lirlsll
ar mmt reprssantatke publications  00 not 8xceed 3 pages for aech individual.)
                           .

1976 - present

1972-1976

rY66-lP71

Adjunct Professor; Computer Science Department,
Stanford University, Stanford, CA 94305.
Research Computer Scientist, Computer Science Department,
Stanford University.
Research Associate, Artificial Intelligence Project,
Stanford University.

Selected Pub,l ications -   See attached

WIH 396 (FORWILY PHS 393)
Rev. 1173


Biographical Sketch
Page 2

Eruce G. Buchanan

Recent Honors

Editorial Board, Artificial Intelligence:  An International
      Journal.

Chairman of IJCAI-79 Program Committee (.International Joint
    Conference on Artificial Intelligence, Tokyo, 1979).
Invited Speaker, Workshop on The Logic of Discovery & Diagnosis
    in Medicine (Pittsburgh, October 1978).
Invited Speaker, Douglass College Seminars for Faculty,
    (Rutgers University, 1078).

Selected Publications

Bruce G. Buchanan, G.L. Sutherland, E.A. Feigenbaum, "Toward an
    Understanding of Information Processes of Scientific
    Inference in the Context of Organic Chemistry." in
    B. Meltzer and D. Michie (eds.), Machine Intelligence, 5,
     Edinburgh:  Edinburgh University Press, 1970.

Jo Lederberg, G.L. Sutherland, B.C. Buchanan, E.A. Feigenbaum, A.V.
    Robertson, A.M. Duffield, and C. Djerassi, "Applications
    of Artificial Intelligence for Chemical Inference I. The
    Number of Possible Organic Compounds:  Acyclic Structures
    Containing C,H,O and N," Journal of the Am. Chem. Society,
    91, 2973, 1969.

COW. Churchman and B.G. Buchanan,  "On the Design of the Inductive
     Systems:  Some Philosophical Problems," British Journal for the
    Philosophy of Science, 20., 311, 1969.

B.G. Buchanan, E.A. Feigenbaum, and N.S. Sridharan,
    "Heuristic Theory Formation:  Data Interpretation
    and Rule Formation," in B. Meltzer and D. Michie
    (eds.), Machine Intelligence 7, Edinburgh:
    Edinburgh University Press, 1972.

D. Michie and B.G. Buchanan, "The Scientist's Apprentice,"
    in R.A.G. Carrington (ed.), Computers for Spectroscopy,
      London:  Adam Hilger, 1974.

E.H. Shortliffe and B.G. Buchanan, "A Model of Inexact Reasoning in
    Medicine,"  Mathematical Biosciences, 23, 351,1975.

19


Biographical Sketch
Page 3

Bruce G. Buchanan

Selected Publications (continued)

E.H. Shortliffe, R. Davis, S.G. Axline, B.G. Buchanan, C.C. Green,
     S.N. Cohen, "Computer-Based Consultations in Clinical
     Therapeutics:  Explanation and Rule Acquisition Capabilities
    of the MYCIN System,"  Computers and Biomedical Research,
     8, 303, 1975.

Randall Davis, Bruce Buchanan, Edward Shortliffe, "Production Rules
    as a Representation of a Knowledge-Based Consultation Program,"
     Artificial Intelligence, 8,1,1?77.

B.G. Buchanan, D.H. Smith, W.C. White, R.J. Gritter, E.A. Feigenbaum,
     J. Lederberg, and Carl Djerassi,  "Application of Artificial
     Intelligence for Chemical Inference XXII.  Automatic Rule
     Formation in Mass Spectrometry by Means of the Meta-DENDPAL
    Program,"  Journal of the American Chemical Society, 98,
     6168, 1976.

B.G. Buchanan, R. Davis,  V. Yu and S. Cohen,  "Rule Based Medical Decision
    Making by Computer,"  Proceedings of MEDIhFO77, Toronto, 1977.

Bruce G. Buchanan and Tom Mitchell,  "Model-Directed Learning of Production
     Rules,"  in D.A. Waterman and F. Hayes-Roth teds.), Pattern
     Directed Inference Systems, New York:  Academic Press, 1978.

Randall Davis and Bruce G. Buchanan, 'Meta-Level Knowledge: Overview and
    Applications,"  Proceedings of the Fifth IJCAI,1,920, August 1977.

Victor L. Yu, Bruce G. Buchanan, Edward H. Shortliffe, Sharon M. Wraith,
     Randall Davis, A. Carlisle Scott, Stanley N. Cohen,  "Evaluating
    the Performance of a Computer-Based Consultant."  Forthcoming,
     Computer Programs in Biomedicine, Amsterdam.

Bruce G. Buchanan, Tom M. Mitchell, Reid G. Smith and C. Richard
     Johnson, Dr., "Models of Learning Systems,"   in J. Belzer
     (ed.), Encyclopedia of Computer Sciences and Technology,
      New York:  Marcel Dekker, Inc., 1978, Vol 11.
Bruce G. Buchanan and Edward A. Feigenbaum, 'DEh?RAL and Meta-DEh?)RAL:
    Their Applications Dimension,' to appear in Artificial
     Intelligence, Fall 1978.

20


SECTION II -PRIVILEGED COMMUNICATION
                        BIOGRAPHICAL SKETCH

!fAME

IGive the following information for ail professional personnel listed on WI 3, beginning *n'rh the Principal Inveti~tor.
         US* continuation pa06 and follow th# mme general format for mch psrson]
                 TITLE -                    BIRTHOATE &la. Day, Yf.)

James G. Nourse                 Research Associate

December 14, 1947

PLACE OF BIRTH (City, State, Country/

PRESENT NATIONALITY l/f non-US citizen.    SEX

Buffalo, NY

I                                -
indican kind of visa amI expiration danl
   U.S. citizen             pJ Mai.   0 Female

              f
EDUCATION (Eegin tith bsccc

rurwte twining and include portdoctoral~

INSTITUTION AN0 LOCATION

  Columbia University, New York, NY
  California Inst. of Tech., Pasadena, CA
  UCLA, Los Angeles, CA
  Princeton University, Princeton, NJ
HONORS

DEGREE        YEAR            SCIENTIFIC
          CONFERRED            FIELD

B.S.
Ph.D.
Post Dot
Post Dot

1969    Chemical Engineering
1974    Organic Chemistry
1973-74  Organic Chemistry
1974-76   Organic Chemistry

Sigma Xi, Invited Lecturer 1978 Conference on the Permutation and its Application to Chemistry
and Physics, Bielefeld, Germany

MAJOR RESEARCH INTEREST                       ROLE IN PROPOSED PROJECT
  Stereochemistry, Computer Applications     Research Associate

                                               I
RESEARCH SUPPORT (SH insvutiom~

RESEARCH ANOnOR PROFESSIONAL EXPERIENCE (S&rtiq m'thpruntporidoq~~nduparimnr~ff~nt tomva ofpmjrt iktaff
or mat qlunadvo publiutiom  Do not UC& 3 p10rr for mch individwk)

Research Associate, Department of Chemistry, Stanford University, 5/79 -
Research Affiliate, Department of Computer Science, Stanford University, 8/76 to 4/79
Postdoctoral Research Associate, Department of Chemistry, Princeton hiversily, 2/74 to 7/76
Postdoctoral Research Associate, Department of Chemistry, UCLA, lo/73 to l/74

NIH 39s (FORMERLY pna 398)
Rev. J/73

21         oUJ GOVERHYENTPRlNT!NCOFFrE 1977-241 ;~~Joz,


Publications- James C. l!ourse

Y. G. Putchings, J. G. Course, and K. ?:i.slo\T, "P First Approach to the
Stereochemical knalysis of Tetraarylmethanes", Tetrahedron, 30, 1535, 1074.

J. G. Yourse, "An Algebraic Pescr!ption of Ptrreochemical Correspondence",
Proceedings cf the Katiooal ~carlerry of Sciences, 72, 23P5, 1975.

.J. C. I.!ourse and K. i!islol7, "Pynanic Ptercochcr!istry of Tetraarylrethanes
and Cognate Systccs. .The Pole of the Permtatioc Subgroup Lattice", Journal
of the knwrican Clerical Society, 97, 45?1, 1075.

J. c. Course and J. D. Roberts, Ul:uclear P'ngnetic Pesonencc Spectroscopy.
Carbon-13 Spectra of Sonc Yncrolide Antibiotics and ??crivztives. Pubstituent
an+ Confornational Effects", Journal of the Anerican Cherr.ical Society, $7,
45F4, 1975.

J. C. I?ourse, "Tscudochirality", Journal of the Pmerican Checical Society, C?,
45?.4, 1475.

J. G.  Y'ovrse,  "Ccnerali zed Stereolsonerizat?on Yodes", Journal of the Pmrican
Chenical Society, o", 2063, 1077.

J. C. Course, "The Coaffgurction Pyrretry Croup and its Application to
Stcreoisocer C-meration, Specification, and Enuceration", Journal of the
$reri,can Chenical Society, lcI1, 121C, lP70.

J. G. ?:ourse, P. E. Carhart, C. I?. Zsith, and C. Pjerassi, "Exhrustive
Cmeration of Stsreoiscrr.ers for Structure ?Zlucidation", Journal of the
Ecerican Chemical Society, lG1, 1216, lo:?.

J. G. Yourse, " PpplFcation of the Pcrr.utation Croup in FvnaFtc Stercochcrristry"
                                                               A
to appear in the Proceedings of the Conference oT the Perrutetion Croup and its
hpplication to Chcrl'strp ard Fhysics, !lelc! at Ficlcfeld, Ccrnnny, 2-l" July
lT:7?.

J. C. E'ourse, "AppI.icatFon of the ?Prrutation Crcrlp to Stereoiconcr Cer.eration
for Coppcter Assisted Structure Elucidation", to appear ir. the Proceed'ngs of
the Conference on the Pcrc:ut~tZon Group 2nd its l*pplicatlon to Chcrnistry znd
P!-ys!cs, held at Pielefled, Cercany, 3-12 July, lF7r.

22


SECTION II - PRIVILEGED COMMUNICATION
                       BIOGRAPHICAL SKETCH

(Give the following information for xllprofarional personnel listed on pago 3, beginning m`th thhr PrimiDa/ Invlatigltor.

               Use continuation WB and foIlow the mms general format for mch perronl
ffAME                      TITLE -
  Neil A. B. Gray            Research Associate

PLACE OF BIRTH (City, Stare, Country)             PRESEr
                                     indian
  Edinburgh, Scotland, UK    g!~
                 EDUCATION Bepin with bsc,

NATIONALITY (If non-US citizen,     SEX

?d of vis and expin tion & td
Jcyo7eg!y, on J-l visa,

lNSTlTUTlON AND LOCATION              DEGREE

imperial College, London
University of Cambridge

Wude pactdoctorr

   YEAP
CONFERRED

B. S.
M. S.
M. S.
Ph.D.

1968
1970
1971
1977

iIRTHOATE (Ma. Day. Yd
September 5, 1947

g.l Male   0 Female

SCIENTIFIC
  FIELD

Chemistry
Theoretical Chemistry
Computer Science
Comouter Sciexe

Applications of Computers to Chemistry

RESEARCH SUPPORT ISu instmtions)

RESEARCH ANDmA PROFESSIONALEXPERIENCE /Smrri~withpr~nt~ition,~xnd~xpa~n'mnr~mnt toamaofpmjct L*aff
of mat mpnwnatfve publiutiorr  Do not UC& 3 P+OII for a?h i&%dual.)

Science Research Counci f/NATO research fellow.  Development of programs for structure
generation and analysis including new approaches to the processing of high and low
resolution mass spectral data and to handling magnetic resonance data.  Stanford University,
1977-1979.

Junior Research Fellowship at King's College. Work on various computer-assisted approaches to
chemical structure elucidation ,including both rule-based and pattern-recognition methods. Part
of this work being incorporated into a Ph.D. thesis for the Computer Science Department.  University
of Cambridge, 1973-1977.

Research Assistant in Professor Eglinton's Organic Geochemistry Unit in the School of Chemistry on
an OSTI-grant (Office for Scientific and Technical Information). Design and implementation of
file-search and interpretive schemes for processing low-resolution mass spectral data, work on data-
communications software and creation of small, dedicated data-acquisition system on PDP-8 mini-
computers. Univenity of Bristol, 1971-1973.
M.Sc. thesis on limitations of CNDO-type semi-empirical quantum mechanical calculations.
University of Cambridge, 1968-1970.

rln 39s (FORMERLY PI6 39a)
Rev. 1173

23          oUS COVERHYENTPRlNTlNGOFFEE i377-i41.]61 3024


Publications:

N.A.B. Gray and A.J. Stone.
    "Justifiability of the ZDO Approximation in Terms of a
     Power Series Expansion."
     Theoret. Chim. Acta, 18, 389 (1970).

D. Field, N*A.B.Gray and P.F. Knewstubb.
    "Computational Study of the Reactions between CH4 and CH4+."
    J.Chem.Soc., Faraday II, 68, 852 (1972).

D.H. Smith, N.A.B. Gray, C.T. Pillinger, B.J. Kimble and G. Eglinton.
    "Geochemical and environmental applications of a compound
     classifier based on computer analysis of low resolution
     mass spectra."

Advances in Organic Geochemisty 1971.
H.R.V. Gaertner and H. Nehner (Eds).
Pergammon (1972).

T.O. Gronneberg, N.A.B. Gray and G. Eglinton.
    'Computer based search and retrieval system for rapid mass
     spectral screening of samples.'
     Anal. Chem., 47, 415 (1975).

N.A.B. Gray and T.O. Gronneberg.
    'Programs for spectrum classification and screening of
     gas-chromatographic/mass-spectrometric data on a laboratory
     mini-computer."
     Anal.Chem., 47, 419 (1975).

N.A.B. Gray.

"A program for generating empirical spectrum classification
schemes."

Org. Mass Spectrom., 10, 507 (1975).

N.A.B. Gray, J.A. Zoro, T.O. Gronneberg, S.J. Gaskell, J-N. Cardoso
     and G. Eglinton.
    'Automatic classification of mass spectra by a laboratory
     computer system."

Analyt. Letters, 8, 461 (1975).

N.A.B. Gray.
    "Structural Interpretation of spectra."
     Anal. Chem., 47, 2426 (1975).

N.A.B. Gray.

"Similarity measures for binary coded mass spectral data."
Anal. Chem.,  48, 1420 (1976).

24


N.A.B. Gray.

"Constraints on learning machine classification methods."
Anal. Chem., 48, 2426 (1976).

N-A-B. Gray, D.H. Smith, T.H. Varkony, R.E. Carhart
    and B.G. Buchanan.

"Use of a Computer to Identify Unknown Compounds:
The Automation of Scientific Inference."
Biochemical Applications of Mass Spectrometry-
G-R. Wailer (Ed).

Interscience (1979 ?).

25


Dierassi, Carl

Table of Contents

Section

    Subsection

  List of Figures             .

A.    INTRODUCTION.            .

     A.1   Objective. .

     A.2   Background. .

     A.3   Rationale. .

B.    SPECIFIC AIMS.           .

C.    METBODSOFPROXDDRE. .

C.l    SASES - A Semi-Automatic Structure Elucidation System.

c.2   The GENOA Program: Structure Generation with Overlapping
       Atoms           . . . . . . . . . . . . . .

.

.

o

?

?

?

?

?

?

c.3   Development of Automated -roaches to the Exploitation of
     Spectroscopic Data. . . . . . . W . . . . . .

c.4   Conformation Generator for CCNGEN. . . . . . . . .

     c.5   Resource Sharing. . . .

D.    SIGNIFICANCE             . . * .

E.    FACILITIES AVAILABLE. . . . .

F.    COLLABORATIVE ARRANGEMENTS. . .

G.    PRINCIPAL INVESTIGATOR ASSURANCE

H.    REFERENCES.               . . . .

..........

..........

..........

..........

s .   ??????   ???

??????????

.

.

o

?

?

?

?

?

?

?

?

?

?

?

?

?

?

.

.

o

?

?

?

?

?

?

?

?

?

?

?

?

?

?

Page

27

28

28

29

37

40

42

. 42

44

51

62

70

77

79

81

87

88

26


Djerassi, Carl

List of Figures
-m

1.  Block Diagram of the SASES system. . . . . . . . . . . . . . 43

2.  Current Status of GENOA and its Interface to the CONGEN Program. . . . . 45

3.   Illustration of the Use of GENOA in the Step-By-Step Specification of
Overlapping Structural Information for the Structure of Palustrol [17A]. . . . 48

4.  Meta-DENDFW C-13 Spectrum Interpretation Rule . . . . . . . . . 52

5.

6.

Isoterpinolene -+ example structure for C-13 interpretation functions . . 53

Spectral data input for Isoterpinolene . . . . . . . . . . . . 54

7.  Adjacency matrix derived for Isoterpinolene using Alpha-neighbors . . . 55

8.  Adjacency matrix derived for Isoterpinolene using Beta-neighbors . . . . 56

9.

10.

11.

Proposed Link of CONGEN to existing coordinate-based methods . . . . . 63

Access to DENDPALprogramsonSUMEX, . . . . . . . . . . . . 71

SUMEX hardware

? ? ? ? ? ? ? ? ? ? ? ? ? o ? ? ?   80
                                             -

27


Djerassi, Carl

RESEARCH PLAN
         -.

A    lINlEQWCTION.

A.1   Objective.

The overall objective of our research is to develop and apply computational

techniques to the procedures of structural analysis of known and unknown organic
compounds based on  structural information obtained from physical and chemical
methods and to place these techniques in  the hands of a wide corrmunity of
collaborators to help them solve questions of structure of important biomolecules.
These techniques  are embodied in interactive computer programs  which place
structural analysis under  the complete control of the scientist working on his or
her own structural problem.  Thus, we stress the word assist& in computer-assisted
structure elucidation or analysis.

    Cur principal. objective in this proposal  is to extend our existing
techniques for computer assistance in the representation and manipulation of
chemical structures along two complementary, interdigitated lines. We propose to
put together a comprehensive, interactive system to assist scientists in all phases
of structural analysis (SASES, or Semi-Automated Structure Elucidation System) from
data interpretation  through structure generation to data prediction.  This system
will act as a computer-based laboratory in which complex structural questions can be
posed and answered quickly, thereby conserving time and smle. In a complementary
development we will extend our techniques from the current emphasis on topological,
or  constitutional,  representations   of structure   to detailed   treatment of
conformational and configurational stereochemical aspects of structure.

    We will make our programs available to a community of collaborators through
network access to a dedicated machine requested  in this proposal, exportable
versions of our software and workshops held to introduce others to our computational
methods.

    By meeting our objectives we  will fill in the "missing link"  in computer
assistance in structural analysis.  Our capabilities for structural analysis based
on the three-dimensional nature of molecules is an absolute necessity for relating
structural characteristics of molecules to their observed biological, chemical or
spectroscopic behavior,  These capabilities will represent a quanta leap beyond our
current techniques  and open new vistas in applications of our programs,  both of
which will attract new applications  among a broad ccnmnunity of structural chemists
and biochemists who will have'access to our techniques.

28


Djerassi, Carl

A.2   Background.                               ?.

    There are three convergent aspects to  the background of this renewal
propsal which are important to discuss in some detail. This discussion will serve
to set the context of our proposed research in  the framework of: a) our past work
under this grant; b) the work of other research groups on problems related to past
and proposed research: and 3) the relationship of our research effort to the SUMEX-
AIM computer resource to which our research will be related.

A.2.a   Background of the DENDRAL Project.
                      --

    The problem of exploiting modern computer  hardware and novel computer
science techniques for the purpse of structure determination of organic compounds
was initially addressed in the mid-1960's under the collaborative direction of
Professors Edward Feigenbaum  in Computer Science and Joshua Lederberg  in the
Department of Genetics.  Among the results of this collaboration was an algorithm
called DENDPAL (for DENDritic ALgorithm) and a computer program, given the same
name,  based on thiagorithK  The program was capable of constructing or
"generating" all structural iscnners of molecular formulas corresponding to acyclic
organic compounds [1,2].  (Although this program now exists only in greatly modified
form as one of the kernel techniques in the CCBJGEN program [3], the term DENDRAL has
remained as an informal name for the project.)

    It was obvious from the outset that such a program must be constrained to
produce only plausible structural  isomers when applied to generating candidate
isomers for an unknown structure.  Although constraints can, and do, come from a
variety of sources including chemical and physical methods and chemical intuition,
initial- efforts were on use of mass spectral data as a source of constraints, and
collaboration with Professor Djerassi's group in the Department of Chemistry was
begun, this group acting as a source of expertise in mass spactrometry. The results
of this expanded collaboration were embodied in  the Heuristic DENDRAL program, in
which structural candidates were generated under heuristics, or rules, relating
observed mass spectral data to plausible structural constraints,  to yield a much
smaller set of plausible structures than the total allowed by the molecular formula
alone.  Initial success with acyclic ketones [4]  led eventually to a more general
program for saturated, monofunctional compounds [S].

    At about this time, financial support from the NIH was sought and funding
for further work was begun in 1971.  The project continued to be guided by the same
general philosophy (which continues in only slightly modified form into the present
proposal), namely,  structure determination via constrained generation of isomers,
each isomer representing a candidate structure for an unknown compound.  However, in
1971 this work was pursued on two related, but somewhat divergent, courses which are
only now beginning to converge again.  Cne course  involved advances  in structure
generation.  Work on molecules of sufficient complexity to be of interest in
biomedical research requires the capability for generating cyclic structures. tie
early approach [6] proved only a temporary stopgap and  it was not until 1974 that
the general problem was finally solved [7] and proven mathematically [8,9,101.

    During this period  interpretation of mass  spectral data obtained from
complex molecules was pursued successfully for  comIpunds in specific chemical
classes [ll] for which detailed rules of mass spectral fragmentation were available
in the literature or could be obtained by automated methods (the Meta-DENDRAL
program [12,13]).  This work utilized only a very primitive scheme for structure
generation of representatives of a given class because the general cyclic structure
generator was unavailable.
                              29


Djerassi, Carl

   At the end of this period we possessed a complete .structure generator,
without constraints, and knowledge of how to use mass spectral data to provide
constraints.  It would have been possible at that point to  integrate the
interpretive program with the structure generator.  This was not done because of the
reliance, in most structure determination problems involving complex, polyfunctiondl
molecules,  on data from several physical  and chemical methods besides mass
spectrcmetry.  Mass spectral data by themselves are insufficient to solve structural
problems in the absence of knowledge of the chemical class to which the unknown
belongs and detailed knowledge of the modes of mass spectral fragmentation for that
class.  However, at that time, with the limited computational tools available, it
was not possible to develop a system  for complex molecules which was capable of
constraining   the structure  generator   based on  interpretation   of diverse
spectroscopic or chemical data.  In addition, we did not feel such an automated
approach, which largely excluded the chemist from the computations, was  the proper
way to utilize the computer in structural problems.  For these reasons we developed
mechanisms for constraining  the structure generator  with various substructural
constraints [3,14],  independent of the source  of such substructural information.
The resulting program (called CONGEN, for CONstrained structure GENeration) was made
highly interactive and designed  specifizly to stand by iElf as an aid in
structure determination [3], performing only the structure generation aspects of the
problem.  At the same time,  work on data interpretation, especia 13 y  automated rule
formation, continued separately, both for mass spectral [13] and   CMR [15,16] data.
During this period CCNGEN was utilized to solve a variety of structural problems in
our own laboratories [17] and initial experiments with network availability of
CONGEN via the SUMEX resource were carried out [18].

    More recently, our  efforts have concentrated on increasing the power of
CCNGEN in a ncrmber of ways and increasing its availability. We added the capability
for computer simulation of chemical reaction sequences as a separate program (called
REACT [19]), interfaced to CCNGEN via structure files, and applied REACT to several
problems involving reaction mechanisms [19],  simulation of biochemical reactions
[20] and applications  to structure elucidation problems  [211.   We have taken
preliminary steps to provide assistance  to the structural chemist after CONGEN has
been used to propose structures , including automated examination of large nunbers of
structures to constrain or rank-order the structures based on combinations of
desired and undesired structural features, and to assist in planning new experiments
to differentiate among the candidates [22].  We have also been developing methods
for prediction of mass spectra  and ranking candidate structures based on  extent of
a~$;~;;~~ne~~~ ~ed~ste& ~cb;;mil spectra [23]. We have made some-progress
                      In addition we now have the capability for
general treatment of configurational 'stereoisomerism in the SIEPDC program [24,251
as the first step in developing stereochemical extensions to CCR?GEN.

    To increase accessibility, we have recently completed an exportable version
of the CONGEN program, held an intensive series of workshops here at Stanford on the
use of the new version and have begun exporting CONGEN to several sites around the
country, including both academic  and industrial laboratories whose work is heavily
concerned with structure elucidation of cconpounds of biological importance.   We are
in the process  of arranging for wider  availability through network access here at
=I  and exploring the utility of access through the National E&source for
Computation in Chemistry (NRCC) and the NIH/EPA Chemical Information System. These
recent developments are  described in detail in the accompanying Annual Report,
AppendixI.

    Achieving the goals of our last proposal period has left us in the following
position.  We have a very efficient, interactive program, CCNGEN, for suggesting
structural isomers as candidates for an unknown structure.   We have ancillary
                               30


Djerassi, Carl

programs (e.g., REACT, SURVEY, EXAMINE,  MSANUYZE, WK) to assist chemists in the
evaluation of the candidates. We have studied automatic rule formation  (the Meta-
DENDRALprcgram)  to determine relationships among known structures and associated
spectral data.   We have used such
spectrometry and,         relationshipf3 to interpret data in mass
           in much less general ways,   CMR spectroscopy.    We have
demonstrated the utility of spectral prediction and ranking as a method for
evaluating large number of candidate structures, again in the area of mass
spectrometry. We have developed the capability for generation of stereoisomers in
the STEREO program as a first step toward consideration of three dimensional aspects
of molecular structure.

    We are now prepared to make a concerted effort toward representation and
manipulation of structures in.three  dimensions. In many ways this is the logical
next step in development of techniques for computer-assisted structure elucidation.
By removing the current limitation, in all of the programs summarized above, of
treatment of only structural isomers,  we can consider a much more detailed and
comprehensive approach to the use of computers  in structure elucidation.   Such an
approach could utilize computational procedures throughout the entire procedure of
structural assignment, including: 1) interpretation of diverse spectroscopic data to
obtain substructural information; 2) postulating structural candidates based on the
inferred substructures;  and 3)  evaluating those candidates by prediction of
spectroscopic properties.  The key to success of this approach is the capability for
representing configurational and conformational stereochemistry.  For example, data
from many spectroscopic techniques are  sensitive to molecular  stereochemistry and
such sensitivity must be taken into account to analyze adequately or  to predict
spectral data.  Ibe Specific Aims,  Section B of the &search Plan, represent a
logical set of steps to achieve these new objectives.

     A.2.b   Background of Proposed Research.
                              -

    The preceding discussion  has reflected only the development of our own
research over the past few years.  Our past efforts  and our new proposals are
obviously influenced by work of others in the field.  This section is meant to
provide a brief history of the use of computer techniques in structure elucidation
(excluding of course, X-ray crystallography)  to illustrate how our work is related
to that of other groups. Although this review is not exhaustive, the important
milestones are mentioned and references within the important papers referenced in
this section can be used as a more detailed guide to relevant literature.

A.2.b.i   Data interpretation and Prediction.

Early work on use of computers specifically for structure elucidation

involved library search techniques,  whereby a match of observed data, e.g., a
spectrum, is sought in collection  of spectra of known compounds.  Mass spectrometry
received (and still receives) the most attention due to the relative  specificity of
mass spectral fragmentations patterns, the sensitivity of the technique and the lack
of direct relationships between functionalities in a compound and  its fragmentation
pattern (relationships provided much more explicitly by other methods such as iV$?).
Over the years several groups  have have worked intensively on mass spectral search
techniques;  these efforts have been reviewed recently 126,271. Sophisticated
systems such as that developed by McLafferty and co-workers  [28] now attempt to
correlate several features of fragmentation patterns with structure  to obtain
substructural information from a library.   Interest in such  techniques has
stimulated development of interactive systems to  allow computer netxxk access to
large libraries on  central computers from most areas of the US and some parts Of
                               31


Djerassi, Carl

Europe [29].  More recently. collections of spectral data from o
been utilized in library search systems, notably IR [30]  and rs r techniques have
                                                    CMR  [31]. Other
groups have developed computer-based systems for simultaneous search of several
spectroscopic data bases (MS, II?, NMR) to attapt to derive structural information
from close matches [32].

    In our own mrk involving mass spectral analyses 1331 we have made extensive
use of library search techniques.  Our goal has always been to identify using such
techniques as many unknowns (in a complex mixture analyzed by Gc/MS, for example) as
possible before  turning to   more  sophisticated procedures   to aid   in the
identification of the remaining unknowns.  This two-stage approach will be followed
in the future wherever possible.  In our own experience existing libraries, even the
extensive collections of mass spectral data, are of limited utility in the natural
products field where our computer techniques , especially CONGEN, have found the most
application.

    Computer approaches  to the interpretation of spectroscopic  data, in
particular mass spectra data, were  introduced even before computerized library
search techniques.  Initially,  high resolution mass spectral data acquired on a
specific compund class, the peptides, were  analyzed by special-purpose programs
[341*  Note that such.a precise definition of compound class largely removes the
requirement for  a complete and  irredundant structure generator.  Although similar
methods were proposed for other classes such as ketones [35], even the next step to
low resolution spectra of aliphatic molecules required a structure generator for any
generality [2,4,5] (obviously, special purpse programs cannot be written for every
compound  class!).   Subsequently,  we proposed    a more  general   method for
interpretation of high resolution mass spectral data [ll] which could be applied in
principle to any compound class, but could only be used under the asscPnption that
the class of the unknown structure was known.  Other programs have been proposed for
analysis of mass spectral data,  again in rather narrowly defined chemical contexts
C361-  These efforts have not led to a general interpretive program for mass spectra
primarily because of the difficulty in establishing the fragmentation rules, neded
by such programs, for complex, polyfunctional molecules.

    More recently, computational techniques have been applied to interpretation
of other types of spectral data, where the goal of the interpretive procedure  is to
determine plausible substructures present in an unknoy3molecule. Methods have been
developed for partial interpretation of IR [37] and   CMR [38,39] data and in tm
systems,  use of data from a variety of spectroscopic  techniques as an aid in
substructural assignment '[40,41,42] and in one of the systems eventual automatic
generation of candidate structures [41,42].  These methods are currently little more
than automated look-up procedures, where positions of observed resonances or
absorptions are compared to tables relating position to substructure. In a method
which consider data from several techniques [41,42] there is no systematic procedure
to verify or  assign plausibilities  to the inferences from one technique by
examination of relevant data from other, complementary techniques.

    Pattern recognition procedures have been  applied to diverse spectroscopic
data in attempts to determine
references 26, 271 IR [43] and 12ubstructural information from mass [see reviews,
                  CMR [38,44] spectral data. These approaches have
been the subject of recent reviews [26,27,45].  In most pattern recognition mrk in
this area, a program is "trained" to determine spectroscopic signatures which permit
yes or no  answers to specific questions  about the presence   of selected
functionalities.  Known structures and associated spectra are utilized in the
training.   These methods have been successful in areas where table look-up
procedures also meet with some success, i.e., where the signatures   for a
functionality display little variation among a set of diverse structures.   Such is
                              32


Djerassi, Carl

                                                                       z
not the case for either mass or 13CMP data and, although such programs can be
trained to answer questions correctly among the training sets of structures, there
have been no reported instances, to our knowledge, where the techniques have been
applied successfully to prospective analysis of spectral data in terms of structure
for actual unknowns of biological importance.

    Our work has involved primarily symbolic, rather than numeric, calculations,
based on strong mOdels, e.g.,  of a spectroscopic technique like mass spectrcznetry,
in order to relate structural features to observed data.  Because of this emphasis
we have not utilized statistical procedures.  We still feel that, particularly in
spectral interpretation,  rule-based systems which are based on strong models and
which can take advantage of the wealth of chemical information  which has been
collected in the past, stands .a better chance of success in  determining structural
features from spectral data.

    We also note that pattern recognition approaches have been used in
prediction of spectral data, especially mass spectral data [46]. This approach is
clearly an alternative to our past [11,13,23] and proposed developments  in spectral
prediction;  no attempt has been made so  far to compare the  results of the two
techniques because the applications have been so far been quite different.

    Pattern recognition procedures have sometimes taken into account geometrical
descriptions  of molecular structure 1471 based on manually selected molecular
features deemed important or interesting in a particular investigation. In our past
[24,25] and proposed studies relating to stereochemical descriptions of structure we
have taken a more general approach describing configurations and conformations,
again because in our applications
to structure, e.g.,       there exist strfng models relating observed data
           vicinal coupling constants in HMR.

A.2.b.ii   Topological Structure Generation.

    In conjunction  with the above interpretive procedures,  systematic methods
for structure generation have been developed. Given computer programs which can
propose partial structures, it is only logical to consider how these partial
structures can be assembled into complete structures.  The first computer program
for exhaustive,  irredundant structure generation dealt with acyclic structural
isomers,  with or without multiple bonds [1,21. Subsequently, groups headed by
Sasaki [411, Munk [48a] and our own group [7] proposed methods for construction of
structures  including those with ring systems. Since that time, these groups,
including more recent efforts of DuEois [49] and Gribov [50], have concentrated on
increasing the repertoire of constraints
improve performance              and chemical knowledge of the programs to
             [3,14,42,48b].  Of these systems, the work of Sasaki and co-
workers on the CHEMICS program [41,42]  is the most ambitious in that an attempt is
made to automate the entire procedure  of structure elucidation from spectral
interpretation through to proposal of final structures.

    The work of Munk and co-workers,  and to a lesser extent that of Gribov and
DuEois, is most closely related to our past goals.  In fact,  we have on several
occasions cooperated with Munk's group on both conceptual matters and specific
approaches.  For example, his group employs our teletype structure drawing program
as one method for output of structures.  We have adopted some of their ideas on user
interaction in our CCNGEN program.  Both CBXXN and their program, CASE, are
designed for the same task.   There are, however,  substantial differences in
computational procedures  and user interaction;  which approaches are preferable is
arguable.  We feel our methods rest on a firmer, mathematically proven, foundation.
However, past comparisons of results of solved structural problems have so far been

33


D-ierassi, Carl

in agreement.  Our proposals  to extend our efforts into spectral
                                                                   . . _

interpretation,
representations

structure gqneration and spectrum prediction based on stereochemical
of structure,  and our proposed capabilities  for structure  generation given
overlapping  structural units,  discussed -subsequently,  represent fundamental
departures from the similarities among the research efforts mentioned above.

   The work of Sasaki and co-workers bears most closely on our own proposals
for more automated systems for structure elucidation. We feel their approach is
limited in several ways which our proposed research is designed to overcOme: 1) the
concept of total automation has so far been demons rated  successfully only for
relatively simple structures [41,42], e.g., where f HMR  spectra are essentially
first-order.  We feel that the chemist, with his or her specific knowledge about
what is probably a much more complicated unknown, must remain for the near future,
at least,  an integral part of a system  for structure elucidation which may
nevertheless be highly automated but which still retains its interactive nature in
order to guide and control  the procedures; 2) there is no   treatment of
stereochemistry in their approach, a necessity, we feel, for a more useful program;
and 3) structures must be built in CHDlICS from a library of small structural
fragments, in part because CHEMICS cannot perform structure generation with
overlapping  substructures.  This leads to considerable inefficiency for larger
structures.  Cur new methods for structure generation are designed to overcOme this
limitation.

     A.2.b.iii   Conformational Structure Generation.
  The problems of the generation and/or enumeration of the conformag;:
pssible for a given chemical structure have been approached in several ways.
are approaches which do not specifically compute energies for the conformations. An
energy calculation is often done after the geometric coordinates of the conformation
have been determined.  Representatives of these approaches will be divided into
three classes:

1) Studies related to properties of polymers

2) Studies related to conformational analysis of single cyclic structures

2) Exhaustive computerized methods using coordinate representations.

   Approaches to conformation enmeration and/or generation related to the
study of polymeric properties are  often concerned with the study of linear acyclic
structures.  Anong the  properties studied are cyclization  equilibria which
necessitates consideration of the possible cyclic or near-cyclic structures of a
linear chain.  R. P. Smith [Sl] did early calculations which enumerated the possible
conformations of a linear molecule.  These were all the pssible conformations which
could be imbedded in a diamond lattice of carbon atoms.  This is a simple geometric
model since there are only four possible bond directions on a diamond  lattice. He
also enumerated the possible cyclic structures up to ring size 18, also on a diamond
lattice. A large amount of work has been done by P. J. Flory on the statistical
properties of chain molecules [52]. The method used assumes a discrete number of
rotarneric states for a single bond, usually three (trans, gauche(+), gauche(-)).
The methcd is used to compute average end-to-end distances of chains among other
properties.  These end to end distances can be used to study cyclization equilibria.
In these studies conformations are rarely explicitly constructed, but are instead
studied as statistical averages because of their enormous number.  Computations of
the number of conformations of linear chains which can close to form rings have been
done by Semlyen [53].  This is a geometrical method which explicitly considers bond
                              34


Djerassi, Carl

lengths and angles.  In general these studies primarily en,runerate conformations
rather than generate  them explicitly since the number of conformations, or the
average   number,  with  a particular  property are the  principle interest.
Conformations are only rarely constructed, and then by Monte Carlo methods rather
than exhaustively.

    Approaches to conformation  enumeration and/or generation   related to
conformational analysis are generally concerned with monocyclic structures. To
determine the conformations of cyclic molecules it is necessary to know the
theoretical Ipssibilities.  Hendrickson [54] was one of the first to deal with this
problem  by determining the  possible symmetrical   conformations  of cyclic
hydrocarbons.  This was done by labelling the bonds of the ring with the possible
signs of the dihedral. angle. for that bond.   There were conditions on allowed
sequences of  signs which were considered energetically unfeasible and conditions
which maintained symmetry as no unsyrrunetrical conformations were considered. These
conformations were  "processed" by doing empirical energy calculations.   This work
provided a useful enumeration  and classification of these syrmnetrical cyclic
conformations.  More recently,  Scheraga [55] has approached the  problem of
determining  the possible conformations of cyclic peptides with  emphasis on
symmetrical structures.  This was a geometrical approach with postulated cycle
closure conditions which was used eventually to examine the energy space for each
molecule considered.  Dale [56] has done a systematic manual construction of
possible conformations for cyclic molecules for ring sizes 9-16.   There was no
comment on the completeness of the resulting list.  Conformations were generated by
labelling bonds as either gauche or trans subject to a n&r of heuristic rules on
allowed sequences of signs.  An interesting representation of the resulting
conformations was given which involved considering the ring as a polygon. The
processing of the resulting conformations was again an energy calculation. Saunders
[57] has attempted to generate  all possible diamond lattice conformations of rings
up to 24 atoms.  This approach relies on  the restricted number of bond directions
possible on a diamond lattice and several heuristic rules for disallowed situations.
only even ntiered rings larger than 4 atoms can be fit onto a diamond lattice.

    Another approach has been taken  by Strauss [58], which generalizes mrk of
Pitzer [59] on the pseudorotation of a S-membered ring. A reference plane is chosen
and the z-coordinates of atoms with respect to that plane are considered. The
possible conformations can be classified by their syn'metry properties with respect
to the symmetry group of the ring.   This method is restricted to "convex"
conformations, so is not exhaustive, but has the advantage of providing a convenient
representation of pseudorotation processes.  A somewhat similar approach has been
taken by Cramer [60] to describe puckering coordinates of a ring. These can be used
to construct possible conformations. A similar approach has been us& by Altona
1611 to analyze the conformations of some five-membered ring sugars.

    Computer programs  have been written to generate exhaustively possible
conformations which use coordinate representations and vary torsional angles by
increments.  Cne such program has  been recently described by Dirkx [62] for cyclic
molecules.  Different programs were used  to treat different molecules as a general
program was not thought reasonable.  When cyclic peptides were considered, only a
very few torsional states were allowed  to reduce the magnitude of the problem. No
problems with syrrunetry were considered. A similar  idea has been used by Murakami
[63] for acyclic conformations. This program has been applied to the side chain
conformations of prostaglandins allowing three  rotational states per  side chain
bond.  A more general program has been described by Marshall and Barry [64,651.
This program  is coordinate based and generates  conformations by varying some
coordinates (which are input to the program and may or may not be  torsional angles)
by very small increments.  The conformations are checked for various constraints

                             35


Diersssi, Carl

. while they are being generated.  Symmetrical  structures are  not explicitly
  considered.  The program is used in part for determining drug receptor sites.

     Much can be done  in structure elucidation with knowledge of conformational
properties of molecules.  In particular, it is necessary to get  information about
atomic coordinates and possible conformations.  The problem of generating the
possible conformations (based on discrete values for sane internal coordinates such
as torsional angles) for an organic chemical structure of given constitution and
configuration  has only been addressed for several special cases and a general
solution for any possible structure is lacking. Such a general solution would have
to consider acyclic, cyclic , and polycyclic structures of any possible qmnnetry. We
propse (Section C.4) to develop such a solution.

A.2.c  Relationship to the !TUMEX-AIM I&source.
                        --

The pursuit of our research goals over the past few years and continuing

through this proposal has involved a slow but steady shift away fram initial
reliance on mass spectral data as  a source of constraints for our structure
generation procedures.  We now are proposing to embark on much more general
approaches to computer  applications in  structural analysis  including, but not
limited to,  analysis of mass spectral data.  This shift in emphasis has prompted
important changes in  the nature of the btiget in the current proposal and in the
nature of the resource to which our proposal is related.  In the past,  the resource
to which our research was related was the mass spectrometry laboratory in the
Department of Chemistry.  We will continue to analyze mass spectral data provided by
the mass spectrometry laboratory as part of our  work on spectral prediction.
I-kwever, funds to support the laboratory personnel and operations and to maintain
the instrumentation are now being requestd  from other sources (see Research
Support) v  Wow, however, our computational approaches are beccming much more general
and we plan wide dissemination of the programs resulting from our work.   These more
general approaches  to aids for the structural biochemist will yield computer
programs with much wider applicability than, for example, the existing CCIGEN
program.  We expect that this will create a significant increase in requests for
access to our programs, placing heavy emphasis on our relationship with SUMEX to
provide this access.

    For the above reasons, we identify the Stanford  University Medical
Experimental computer facility for research in Artific'-ial Intelliqence in Me&ine,
s@lEX-AIM, as the resource to which our proposa research-is related.  (A plan for
resource management is presented  in Section C.5, Resource Sharing).   The SDMEX-AIM
resource has provided the computational basis for our past program developments and
for initial exposure  of the scientific community to these programs.   The resource
is, however, funded completely separately from our own research; we are only one of
a nationwide comnunity of users of the SUMEX-AIM facility.  In a sense, then,
relating our new research to  'SUMEX formalizes a relationship which already exists.
However, such a formalization seems much more relevant now than in the past because
of our broader emphasis on  software tools and new capabilities for  sharing the
results of our research.  The relationship which we propose (and discuss more fully
in Section C, Methods of Procedure) is one which goes far beyond mere consumption of
cycles on the SUMEX machine.  It has been the goal of the SUMEX project  [183 to
provide a computational resource for research in symbolic computational procedures
applied to health-related problems,  As such research matures, it produces results,
among which are computer programs, of potential  utility to a broad community of
scientists.  A second goal of SUMEX has been to promote dissemination of useful
results to that community, in part by providing network access to programs running
on the SUMEX-AIM facility during their development phases.  SUMEX does not, however,

                           36
. .


Djerassi, Carl

have the capacity to support extensive operational use of such programs.   It was
eXpeCted from the beginning  that user projects would develop alternative computing
resources as operational demands for  their programs grew.   Such a state has been
reached for the CONGEN program and future developments to yield more generally
useful programs will simply magnify the problem.

We have proposed, therefore, under  the new relationship between SUMEX-AlI4

and our project,-to-
methods and results
addition, wa plan to
extensive operational
a test environment
computing environment

participate as-before in the SUMEX-AIM c&unity in sharing
with other groups  during development of new programs. In
purchase a small machine which will allow us to provide more
access to our existing and developing programs, and to provide
for adapting our programs  to a more realistic laboratory
than the. special-puqose SUMEX resource. Ihis facility will
  -. -                           

derive substantial benefit from its relationship with SUMEX including sharing of
network gateways, some peripheral equipment and operational supFort. ti the other
side of the coin,  SUMEX benefits by moving a substantial part of the DENDRAL
production load to a more cost-effective system, thereby freeing the SUMFX resource
for new program development.  Also, working with the proposed new machine (DSC-VAX,
see Budget Remarks) will be advantageous as a model for !SDMEX*s future development.
Collaborators who wish to use existing programs for specific problems would access
SUMEX via the network-as before, but now would be routed to the new machine. New
developments, such as those we propose , would be carried out on SUMEX itself, taking
advantage of the much more extensive  repertoire of peripheral devices, languages,
debugging tools and text editors, i.e., precisely the tasks for which that system
was designed.

   Our proposed relationship to STJMEX-AIM has important implications beyond the
practical considerations mentioned above.  There is a significant research component
to our proposal to.make the dedicated computer as integral part of the resource
sharing aspects of our relationship to SUMEX.  If our propsal is approved and
funded, the DENDRAL project muld be the first of the SUMEX-AIM projects to have
developed sufficient maturity to  request and obtain additional computer facilities
to support production  use of its programs in real-world, biomedical applications.
In a sense, then, we will be acting in a pathfinding role for the rest of the SDMEX-
AIM community as  other projects reach maturity and seek additional computing
resources to support the needs of their collaborators.   Our
interfacing                                   approaches to
      with SLJMEX with the dedicated machine,  implementing  new software,
regulating access to divert development and applications to the appropriate machine
are all experiments which we are willing to undertake together 4th SUMBX, knowing
that wa will be providing direction to future efforts along similar lines.   We will
also be in a pathfinding role for a
involved in computing,          large segment of the biochemical community
                    as we move to  a machine which will be much more widely
available in Department and laboratory environments than DEC-10-s and -20's. There
are currently no widely available computing resources which provide  access to
symbolic,  problem solving programs oprating in an interactive environment. We
would be able to fulfill that need to the extent that applications  have direct,
biomedical relevance, to the limits of our available computing resources.

A.3   Rationale.

We have initiated

this propsal at what we feel is a particularly opprtune

time in the developnent of computer aids to structure elucidation. We are beginning
to push our  techniques for spectral interpretation,  structure generation (e.g.,
CONGEN) and spectral prediction to  their limits within the confines of topological
representations of molecular structure.  Even so, these techniques are perceived to

37


Djerassi, Carl

be of significant utility in the scientific community as evidenced by our wrkshops,
the demand for the exportable version of CCNGEN and the nmer of persons requesting
collaborative or guest access  to our programs at Stanford.  In order to proceed
further in providing to the comnunity programs which are more generally applicable
to biological structure problems and more easily accessible we must address squarely
the limitations inherent in existing  approaches and search for ways to solve them.
The major objectives of our proposal are addressed to these issues in the following
-ys*

   None of the techniques for computer-assisted structure elucidation of
unknown molecular structures described in the previous section, including Our Own,
make full use of stereochemical information.  As existing programs were being
developed this limitation was. less important.  The first step in many structure
determinations is to establish the constitution of the structure, or the topological
structure,  and that is what CONGEN, for example,  was designed to accomplish.
However, most spectroscopic behavior  and certainly most biological activities of
molecules are due to their three-dimensional nature. For ~=pj~ &c;r;y;;;
program for prediction of the n&r of resonances observed in
the topological syrmnetry group of a molecule is used in prediction.   However, in
reality it is the synnnetry group of the stereoisomer that must be used.   This group
reflects the usually lower symmetry of molecules possessing chiral centers and which
generally exist in fewer than the total pssible nlsnber of conformations. This will
increase  the number of carbon resonances observed over that predicted by the
to@ogical syrfmetry group alone. More generally, few of the techniques described in
the background section  can be used in accurate prediction of structure/property
relationships, whether the  properties be spectral resonances  or biological
activities.

    A structure is not, in fact,  considered to be established until its
configuration, at least, has been determined.  Its conformational behavior may then
be important to determine its spectroscopic or biological behavior.   For these
reasons we emphasize  in this proposal developnent of stereochemical extensions to
CONGEN, existing related programs and  the proposed new programs GENOA and SASES,
inclllaing   machine  representations and  manipulations of  configuration and
conformation and constrained generators for both aspects of stereochemistry.

   None of the existing techniques for computer-assisted structure elucidation
of unknown molecules, excepting very recent developments in our own  laboratory, are
capable of structure generation based on inferred partial  structures which may
overlap to any extent.  Such a capability is a critical element in a computer-based
system, such as we propose, for automated inference of substructures and subsequent
structure generation based on  what is frequently highly redundant structural
information including many overlapping part structures.  Important elements of our
propsal are concerned with further developments of such a capability for structure
generation (the GENOA program).

   Given the above tools for structure representation and generation, we can
consider, and have proposed, new interpretive and predictive techniques for relating
spectroscopic data (or other properties) to molecular structure. Ihe capability for
representation of stereochemistry is required for any comprehensive treatment of: 1)
interpretation of spectroscopic data; 2) prediction of spectroscopic data: 3)
induction of rules (Meta-DENDFW-like rule formation [13,15,16]) relating known
molecular structures to observed chemical or biological properties.  These elements,
taken together, will yield a general system for computer aided structural analysis
(the SASES system) with potential  for applications far beyond the specific task of
structure elucidation.

38


Djerassi, Carl

   Parallel to our program development we will embark on a concerted effort to
extend to the scientific comnunity access to our prqrams, and critical parts of our
proposal are devoted to methods for promoting this resource sharing.   Cur rationale
for this effort is that the techniques must be readily accessible in order to be
U=d,  and that development of useful programs such as we propose can only be
accomplished by an extended period of testing and refinement based on results
obtained in analysis of a variety of structural problems,  analyzed by those
scientists actively involved in solutions to those problems.

     To this end,  we have proposed to purchase a dedicated computer  system for
applications of our programs.  Our current collaborators (Section F) will obtain
much better computational support by accessing the proposed system than the can
obtain currently via SDMEX, which is very heavily loaded.  Programs developed on the
new machine will enjoy wider exportability.   In addition,  by offering better
service, through both netmrk access and export, we can attract new applications and
make firm guarantees of computational  support with fast response   time for
interactive programs, something we cannot do at the present time.

     The overall   rationale for all  our developments is   that structure
determination of unknown structures and relationship of known structures to observed
data are complex  and time-consuming tasks.  We know from our past experience that
computer programs can complement the chemist*s knowledge and  reasoning-power,
thereby acting as valuable assistants.  If we meet our present objectives, we feel
strongly that our programs  will become essential tools in the repertoire of
techniques available to the structural chemist or biochemist.

39


Djerassi, Carl

--

      B    SPECIFIC AIMS.

    The specific objectives for the requested five year period' of support
include the following:

1) Develop SASES (Semi-Automated Structure Elucidation System) as a general
system for computer  -aidea structEti analy%.s,  utilizing stereochemical
structural representations as the fundamental structural description. SASES will
represent a computer-based  "laboratory" for detailed exploration of structural
questions on the computer.  It will have as key components the following:
     a) Capabilities for interpretation of spectral data which, together
     with inferences from chemical or other data,  would be use? for
    determination of (possibly overlapping) substructures;

b) The GENOA (structure Generation with Overlapping Atoms) program
which will have the capability of exhaustive generation of (topological
and stereochemical)  structural candidates and include as an essential
component the existing CCNGEN program;

  c) Capabilities for  prediction of spectral   (and biological)
properties to  rank-order candidates on the basis of agreement between
predicted and observed properties.

  2) Develop the GENOA program and integrate it with CONGEN.   GENOA will
represent the heart of SASES for exploration of structures of unknown compounds,
or  configurations  or conformations of known compounds.   GENOA will be a
completely general method for  construction of structural candidates for an
unknown based on redundant,  overlappinq substructural information, and it will
include capabilities for generation of topological and stereochemical isomers.

  3) Develop automated approaches to both  interpretation and prediction of
spectroscopic data,  including but not limited  to the following spectroscopic
techniques:

4  carbon-13 magnetic resonance ( 13CMR) ;

b) proton magnetic resonance (%MR);

4  infrared spectroscopy (IR);

d) mass spectrometry (MS)

  e)  chiroptical methods including circular dichroism  (CD), magnetic
circular dichroism (MCD).

The interpretive procedures will yield  substructural information, including
stereochemical features,  which can be used to construct structural candidates
using GENOA. The predictive procedures will be designed to provide approximate
but rapid predictions of expect4 spectroscopic behavior of large numbers of
structural candidates,  including various  conformers of particular structures.
Such procedures can be used to rank-order candidates and/or conformers. The
predictive procedures will also be designed to provide more detailed predictions
of structure/property relationships  for known or candidate structures in
specific biological applications.

4) Develop a constrained generator of stereoisomers, including:

40


Djerassi, Carl

  a) design and implement a complete  and irredundant generator of
pssible conformations for a given known , or a candidate for an unknown,
structure;

  b) provide constraints  for the conformation generator so that
proposed structures for a  known or unknown compound pssess only those
features allowed by: i)  intrinsic structural features such as ring
closure and dynamics of the chemical structure; and ii)  data sensitive
to molecular conformations (e.g., MCD, NMR);

  cl  integrate the stereochemical developments with the GENOA program
as a final, comprehensive  solution to the structure generation problem
and allow for interface of the program with other methods dependent on
atomic coordinates.

  5)  Promote applications of these new techniques to structural problems of a
conrnunity of collaborators, i.nclUairq improved methods for structure elucidation
and potential new biomedical applications, through resource sharing involving
the following methods of access to our facilities and personnel;

  4  nationwide computer network access, via the SDMEX computer
resource and the dedicated machine requested in the first year of the
current proposal;

  b) exportable versions  of programs to specific sites and via the
National Resource for Computation in Chemistry and the NIH/EPA Chemical
Information System;

  d  war kshops at  Stanford to provide  collaborators with access to
existing and new developments in computer-assisted structure elucidation
in an environment where complex questions of utility and application can
be answered directly by our own scientific staff;

  d) interface to a commercially available graphics terminal for
structural input and output, at  as low a cost as possible,  so that
chemists can draw or visualize structures more simply and intuitively
than with our current, teletype-oriented interfaces.

41


     Djerassi, Carl
. -

C   METHODS OF PROCEDURE.
              -

      c.1    SASES - A Semi-Automatic Structure Elucidation System.
                -e-
   A long term aim of our research is the development of a system which
performs  automated data  analysis
ranking of candidate-Z&ctures.  in
of the system ("SASES"), and in the following three  sections we will discuss the
proposed development of the component parts.
   
   There are tm important themes underlying the system. The first is that, in
our opinion,  the task of structure elucidation is sufficiently complex that the
chemist must remain an integral part of the system.
for +ni-$utomated Structure Elucidation %&em,  !Ihe name for the system, SASES,
                            reflects our judgment that at

several places throughout the @stem the chemist must be able to examine  the status
of the computations and express his/her own judgments on how best to proceed. This
will be an interactive system and not a black box with data input and structure
output.  The chemist will be able to exercise the various aspects of structure
determination (data interpretation,
prediction,  structure ranking)     constrained structure generation,
                 throughout the process.            spectral
                                       The second theme is the

reliance on stereochemical representations of structures throughout SASES. This
capability will make component parts of SASES applicable to several other problems,
such as structure/property relationships, besides
elucidation.                            the central task of structure

features The novelty of this proposed system for structure elucidation, and the
    which set it apart from other  current systems (including our present

   The SASES system is described in block diagram form in Figure 1 The solid
lines connecting the chemist to various programs
capability for interacting with the procedures.  or output from SASES imply the
                         The dashed lines simply indicate

that both "INTERP" and "PREDICICR" modules can access the same data.

     The " INTERP"
combine a number  module, shown in Figure 1, represents a program which will
               of  existing and proposed functions
information from diverse data (See Section C.3).       for inferring structural
                              The chemist will interact with the

interpretive procedures in at least tm ways. He will be able to add substructural
inferences to the growing. list based on his own jtigements, or data from other
techniques (e.g. chemical behavior, UV spectroscopy etc).  In addition, he will be
capable of examining (perhaps in question/answer mode with the program)
list of substructures thereby noting                     the growing
                   extensions to them or new experiments (e.g.

proton decoupling) to be performed. Tne output of "INTERP" will be in the form of a
file of computer representations  of substructures, containing both topological and
stereochemical information (possibly with associated plausibility ratings).

42


Djerassi, Carl

      Spectroscopic Data

0 /'(C-13 and 1-H nmr, MS, IR, CD) ',
                   \
                                       ,    \         ,
                      > "PREDICT0R"

structures

Chemist User

Figure 1.  Block Diagram of the SASES system,

   The GENOA program (for GENeration of structures with Overlapping Atoms) will
include:

  1) The current CONGEN program  for generation of constitutional (i.e. bond
connectivity) and configurational stereoisomers;

2) The current preliminary version of GENOA;

3) The proposed conformation generator (Section C.4);

4) The proposed developments to GENOA (Section C.2).

    GENOA will build structures incrementally, with the chemist able to exert as
much (or as little) control as desired. In particular, the chemist will be able to
add additional constraints as required as the  individual structures take shape in
the stepwise generation procedure. The chemist will also have control over the
extent to which stereochemistry is considered.  For example, early in structure
generation problems, when.the number of candidates is large, topological generation
may be sufficient to guide  the next step with details  of stereochemistry
incorporated as detailed knowledge about the structure becomes available (the number
of topological representatives thereby decreasing).

    The output of GENOA will be a file of structures which can be examined by
the chemist,  and more importantly, saved away for further processing at a later
time. Such facilities are extremely important at intermediate stages of a complex
structure problem. Analysis can proceed  utilizing the set of structures which were
plausible based on previous  data, thereby avoiding time-consuming recomputation of
the problem. These  interactive facilities are an integral part of the existing
CONGEN and GENOA programs and will certainly be included in all subsequent
developments.

    The "PREDICIt7R" functions will communicate with GENOA through the structure
file, and will be capable of sharing observed data with the interpretive procedures
(Figure 1). These functions will be used to predict spectral properties for GEN0A.s
candidate structures.  As discussed in Section C.3, the "PREDICTOR" functions are

                             43


Djerassi, Carl

intended to utilize more precise models of spectroscopic behavior, that relate to
total molecular conformation, as opposed  to the simpler models used in "IMCEXP",
which relate primarily to local, topological structure. The "PREDICTOR" functions
will also rank order structures based on agreement between observed  and computed
spectroscopic data. Ihe output will be a rank-ordered structure file, which can be
used subsequently in GENOA for further pruning, use of the EXAMINE/SURVEY functions
and so forth.

    The structure of SASES will be designed to be completely modular in that
each of the three major portions can be run  independently. In this way, we can
provide a computer-based "chemical laboratory" in which "experiments" can be
performed on the computer to help save time and valuable sample. Links between the
modules will be files of structural information, further contributing to the
modularity. This modularity will increase the-utility of SASES in a number of ways.
For example, it will be desirable to run the "INTERP" module on existing data as a
stand-alone early in a structure elucidation problem in order to develop ideas about
what additional information muld be required before attempting to construct
structures. The GENOA module will continue to  find extensive use as a stand-alone
structure generator for many problems where structural inferences have been
determined by other methods. In addition,  the combined structure generator and
predictor will be used for several studies on structures whose topology is known but
whose stereochemistry remains imprecisely defined. In Section F, Collaborative
Arrangements, we discuss two  collaborative projects where our techniques will find
application  to known structures  in attempts to relate observed properties (NMR
couplings, biological activity) to computed conformers.

c.2  The GENOA Program: Structure Generation with
        e-                     Overlapping Atoms

    As discussed in Section A.2,  one of the significant limitations of current
approaches to  structure generation is  the requirement for  disjoint substructures.
In other wOrds,  substructures and atoms input to a structure generator  such as
CONGEN must not overlap; the total number of atoms of each type in the collection of
substructures and remaining atoms must agree with the molecular formula.  Cne of the
aims of the previous proposal was to develop an  approach which muld remove this
limitation.  This mrk was characterized as "constructive substructure search" or
"constraints interpretation/translation." Together, these names are suggestive of a
procedure whereby inferred substructures are built from  previously inferred
components (atoms and substructures),  considering all possible overlaps.   Such a
procedure removes the requirement for non-overlapping components and allows the
chemist to input what are  usually7redundant structural data, obtained from various
spectroscopic techniques, in a completely natural way.  This makes the program much
easier to use, an  important consideration for any program to be used by a wide
community of persons.

   Our initial work on such a program led to a version based on the INTERLISP
version of CONGEN (hereafter referred-  to as old CCNGEN, or OCOHGEN).  This program
[661 accomplished its designed goal, of taking VOODLIST," or desired, substructures
and incorporating them into the  structure generation problem in all possible ways.
The program was, howver, quite limited in that it had no mechanism for elimination
of undesired structural features,   nor  was it interfaced to CCCNGEN for final
construction of structures.  It was also very inefficient.

    This approach was  set aside for several months as we emphasized the
development and initial export of the new CCNW program. Although we believed that
an approach to structure aeration with Overlapping Atoms (hereafter referred to as

44


Djerassi, Carl

GENOA) was an ultimately desirable goal, frankly it was not until the series of
workshops late last year (see attached Annual Report, Appendix I) on the use of the
new CONGEN program that be  realized both the practical and conceptual potential of
GENOA.  Workshop participants were spending more time to analyze and decompose their
existing substructural information into non-overlapping substructures than they used
in actually solving  the problem with CCWEN.   The statement,  made to mrkshop
participants, that it is difficult to handle, completely and irredundantly, problems
expressed with overlapping substructures was accepted but hardly understood. After
all, they are forced to consider structural information in that way when solving the
problems manually; a decent computer program ought to do the same.

     As a result,  during the past  three months we have assembled, in the BCPL
language utilizing portions of CCWEN and extensive new code, a much more efficient
version of GENOA based in part on the earlier  INTERLISP concepts but improved by
experience and by removing some of the limitations.  The current status of GENOA is
summarized in Figure 2.

    Briefly, GENOA obtains  the molecular formula for an unknown compound, and
the ntier (may be an integer , a range or zero) and name of inferred substructures,
one at a time.  For each new substructure, GENOA builds the requested ncrmber and
ensures that the required number of all previous substructures is met.  Utility
functions allow definition of substructures, and visualizing and saving all
intermediate results.  As an example of use of GENOA with overlapping substructural
information,  we present in Figure 3 one of the many possible ways to supply
substructural information for the structure of palustrol  Wal ,  together with
examples of intermediate problems.

I           .

MOLECULAR     ,,GENA                     CONGEN
FORMULA             \SIMPLE
                 GENERATOR'

.

Utility Functions

   DRAW .
  SAVE/RESTORE
   DEFINE
   etc.

Utility Functions

   PRUNE
   STEREO
   MSANALYZE
   SURVEY
   ETC.

Figure 2.  Current Status of GENOA and its Interface to the CONGEN Program.

    'Ihis example (Figure 3) is shown to illustrate several points about the use
of GENOA in a structural problem.  One can, as was done in this problem using CCWEN
Wal I  wait until many of the data are gathered, determine non-overlapping
substructures and use constraints to  test for those substructures which might
overlap, at the end of the problem.  Using GENOA, however, yields greater efficiency
through use of data and inferred  substructures as they are gathered and applied to
the problem.  From the very beginning of the problem one can examine the
implications of the next piece of information and, interactively,  remove structures
with undesirable features early in the problem.  Because only those substructures

45


Djerassi, Carl

are constructed which have been supplied to GENOA, i.e., no-;-attempt is made to
generate complete structures until the user wishes, problems remain very small in
terms of numbers of possibilities which must be considered at each step, even when
very little information is known  about the structure.  To illustrate these pints,
consider the steps  in Figure 3 (The sequence of steps parallels approximately the
order in which data were collected on the structure) .

  Aftef3definition of the molecular formula (Step 1) , GENOA was given the
results of   CMR analysis summarized in Step 2,  thereby specifying the number of
carbons of each degree  (the alcohol functionality had been previously determined) .
The result is a single problem for GENOA, which looks exactly like the input data.
Step 3 specified the presence of tm tertiary methyl groups from 1HMFL  Three
problems result Figure  3, each representing one way of obtaining two such groups.
Examination of these three problems at the computer terminal and consideration of
data obtained from use of shift reagent allowed Step 4, specifying no methyls
attached to the carbinol carbon, thereby removing tm of the previous problems. The
cyclopropyl ring with two, vicinal hydrogens, was specified in Step 5.   Ther are
tm ways to construct that substructure from the previous problem, as shown. f blR
data allowed rejection of the case  in which the carbinol carbon is in the three-
membered ring,  Step 6.   In Step 7, two secordary methyls,  from proton NMR, are
specified,  resulting in  three problems,  one of which is removed in Step 8, no
isopropyl groups,  In Step 9,  the environment of the cyclopropyl ring is specified
in more detail, and,  finally,  in Step 10,  more detail based on decoupling
experiments is provided,  resulting in two problems.   Note that at each step there
was no concern over what atoms might overlap, and at each step examination of the
results yielded additional constraints which had been overlooked up to that point,
The final generation of structures, Step 11, yields 81 complete structures from the
two problems.  At any point throughout the procedure, the problem can be saved and
then recalled at a later time when additional data are available.  Thus, GENOA-s
analysis of a problem can work hand in hand with laboratory experimentation.

   GENOA-s method of construction of overlapping substructures is completely
general  in that any substructure of any size (not, of course,  exceeding the
molecular formula) can be specified. For example, if prior to Step 11, Figure 3,
one wished to construct only those structures which obeyed the head-to-tail isoprene
rule, one could define the fifteen carbon substructure representing that linkage and
supply it to GENOA, which muld then construct alternatives based on  the problems
already specified through Step 10.  Subsequent generation muld then be only of
structures obeying that form of the isoprene rule.  Note that the program determines
not only how the required substructures can be built,  but also makes structural
inferences concerning  the imp1 ications  of each statement.   For example, the
characteristics of this problem force two of the methyl groups to be geminal and on
the cyclopropyl ring ,  even though no explicit  statement of that partial structure
was made.

46


Djerassi, Carl

SIEP               RESULTS AND EXAMPLES

1. DEFINE MOLECULAR FORMULA       C15H260

2. (1) HO+ (1) -+         lPROBLEt4, EXACTLY AS INPUT DATA

(5) TH- (4) --.(4) CHy-
3. (2) cH&

3 PROBLEMS:
1) (CH&- ; HO-+ ; 5 X -bH-;

4. (0) CH3-C+H

  4x -2 -;2xcH-.
            3
2) CH3+- ; 2 C +-OH; 5 X -dH-;

  4x 3 -;2x Qs -.
3) (CH&T-oH ; + ; 5 X -kH-;

  4x -2 -:2x 9 -*
lPROBLEM,ql, PREVIOUS STEP.

5.  (1)                       2 PROBLEMS:
          1) (CH&- ; 3 X-&H ; 4 X -CHA- ;
                2 X CHg- ;         OH
          2) Ho+ ;  rP
                  3 X AH-; 4 x -a-IL- ;
               2x9-i ID<
                  1 PROBKEM,$2, PREVIOUS STEP.

6. (0)  HO
7. (2) CH3TH-

3 PROBLEMS:

1)

2)

3)

HO+: CH &H-O
      3 -I 2 X dH-;
4 x -u-If f
HO+;  lx
  (CH&'+H ; 2 X --hH-;

4 X -CHZ- ; P


Dierassi, Carl

8. (0) ,CH,2&-
9. (1)    CH2-
% H-
        A

2 PROBLEMS, *1,*3, PREVIOUS STEP.

2 PROBLEMS;

H-; 3 X-CH- ;
      2

3X-CH-;
    2

2 PROBLEMS:

10. (1)

           H-
           2
     HOW3
         A A

11. -RATE STRUCTURES:          81CCKPLETESTRUCTURESFOR~

(0) c=c; (1) a
(0) EC

    Figure 3.  Illustration of the Use of GENOA in the Step-By-Step
Specification of Overlapping Structural Information for the Structure of Palustrol
                        [17A].

    After the last known substructure is specified,  a simplified structure
generator,  not the one utilized in CCNGEN,  is used currently to build complete
structures. Ihe generator .is quite inefficient and creates many duplicate structures
which must be removed (automatically).  Control is then passed directly to the
CONGEN program where all the currently available utilities for further processing,
egg., STEREO,  MSANALYZE, may be used to prune or explore further the structural
candidates.

    Our proposals to extend the current version of GENOA include the following
steps, which  we feel represent a logical course  to pursue in the context of our
other goals.  We will expend  this effort because GENOA will be the heart of the
proposed SASES program. We will:

  4  evaluate the existing program with selected collaborators to determine
strengths and weaknesses on actual problems;

  b) extend   the   current  version,  applicable  only to  topological
representations of structure, to make a complete, stand-alone version of GENOA
integrated completely with CONGEN including:

i) greater user control over allowed overlaps of substructures:
                 48


Djerassi, Carl

  ii)  integrate the output   of GENOA with  CUNGEN's efficient,
interactive method for structure generation.

  cl  commence work on a version of GENOA which incorprates stereochemical
constraints during generation;

Each of these proposals is now explained in more detail.

     C.2.a   Evaluate Current Version of GENOA.

    Even though the current version has significant limitations,  it possesses
all the desirable interactive characteristics of CCNGEN and has so far proven robust
(error-free).  In order to guide  further development we  will begin evaluation of
GENOA by allowing selected collaborators to make use of the program in parallel with
CONGEN.  This will give us important measures of utility in real applications and
allow us to correct obvious deficiencies as we proceed with further developnents,
and to produce a better program for wider distribution.  Collaborators such as Lynn
in Nakanishi's group at Columbia and Dreiding  in Zurich muld be among those
selected for such an evaluation.

    We will complement these  evaluations with extensive tests among members of
our own group and other SUMEX users who deal in one way or another with structure
manipulations , including persons such as Wipke  at Santa Cruz (SECS project) and
members of the MOKXN (molecular genetics) project at Stanford.   We have begun
evaluations in our own group, trying selected structural problems solved previously
by CaGE%   In addition, we have in El e  past few weeks  evaluated GENOA  usi
input  substructures  inferred from    CMR  data of ethers and al kanes.  59 as
                                                                 CMR
represents a fertile area for GENOA applications because of detailed structural
information which can be obtained on the environment of a given carbon atom.
obviously, such information is highly redundant.

     C.2.b   Integration of GENOA with CONGEN.
                               ---

    Initially,  we will complete the development  of GENOA with regards to
topological representations of structure.  Although the current version incorporates
some considerations of symmetry of input substructures and of the representation of
the problem itself, the construction procedure  itself requires more development,
primarily directed toward efficiency.

C.2.b.i   Greater User Control of Overlaps.
                                   -

    The current version has an important limitation which needs to be overcome
both for the propsed topological and stereochemical versions of GENOA. There is no
control over which atoms in which substructures may (or may not)  overlap, even
though such information is frequently available from spectroscopic data. The
flexibility of input permits one to work around some of these problems (for example,
substructures known to be non-overlapping can be input to GENOA as a single
substructure composed of several disjoint units), but a more general  approach is
required to prevent building undesired structures.  We will accomplish this by
associating with each atom a "uniqueness"  tag which will declare that it is  (or is
not) to be considered in overlaps.  Further work will permit one to allow designated
sets of atoms to overlap with one another but not with another designated set.  This
capability will also be  important in developing the  automated inference/generation
procedures described below.

49


Djerassi, Carl

C.2.b.ii   Integration.

    The next step will be to remove the generator/CONGEN separation of Figure 2
by integrating the output of GENOA with CCNGEN itself to perform the final step Of
structure generation.  The output of GENOA is a set of problems (see Figure 3), each
of which is composed of non-overlapping structural fragments and can,  therefore, be
treated as a separate CONGEN problem.  I'he combined results of all problems
represent the complete and irredundant final set of structures. We will perform
this integration by taking each individual problem from GENOA and casting it into
the standard CONGEN superatom/atom framework.

    This integration presents a  n&er of potential difficulties which we have
already recognized and will attempt to overcome.  The set of CONGEYN problems from
GENOA may incltie problems which ',contain" other problems. That is, the entire set
of final structures fram one CCNGEN problem will be entirely contained in the final
structures from another CONGEN problem.  This sort of duplication will have to be
recognized at this stage and the "contained" problem eliminated.  Another potential
difficulty is that some of the CONGEN problems will have identical superatoms and
might give  identical unimbedded structures after generation.   These identical
superatoms in separate problems will have to be recognized so that duplicates can be
eliminated after generation but before imbedding,  Some constraint information will
have to be carried through and tested during generation and imbedding to free the
user from having to input different constraints at different times.  The final GENOA
program will simply require as many statements (in a prescribed format) about the
overall problem as the user  wishes to input  at the beginning  and will apply the
information throughout.

c.2.c   A Stereochemical Version of GENOA.
                                     -

The next steo in develounent of GENOA will be to produce a version which

                      b
generates   structures  consist&t with both
constraints.  It is particularly important that

and stereochemical
full recognition of

stereochemistry (both configurational and conformational).  For many conceivable
applications of stereochemical constraints it will be necessary to allow overlapping
substructures.  An example muld be the substructures deduced from long-range
couplings which will  a Ii!? st certainly contain substructures involved in short-range
couplings. Data from  CMR will likely yield substructures which overlap those from
proton NMR or CD spectra, etc.  Ihis effort to incorporate the stereochemical
developnents  into the GENOA program will bring together two of   the novel
developnents in our structure elucidation programs.

    The exact method chosen for this development will probably depnd on the
current form of GENOA and the stereochemical programs at that time.  However, a
likely development %oul.d be in two stages.   In the first version the user would
input constraints with and without stereochemical information.  ?he programmuld
recognize the stereochemical constraints  and save them until complete structures
(topological) were generated.  At this time the STEREO programs muld be called and
the constraints applied.  After sufficient use and testing of this first version,
the second version muld be develom.   The novel feature of this version would be
the a lication of stereochemical constraints at the earliest possible time and in
=-T--                                                                   --
the most ef lclent way.                           -e
             This WUld necessitate some modification of tiztructure
T+Zitation now used  in GENOA and a  "smart" constraints translator which muld
recognize   those stereochemical   constraints which   affect  pssibilities for
toplogical structures.  An example of such a constraint would be the requirement of
only trans double bonds eliminating structures  with small rings  containing double
bonds.  This final version FJould merge the stereochemical developments in such a way
                               50


Dierassi, Carl

that the user need not be concerned with any differences between topological and
stereochemical constraints.

     c.3
Spectroscopic

Development   of Automated
                -         Approaches to the
Data.                                           --  Exploitation of

   Research will be undertaken into the developnent both of methods for
deriving structural constraints for GENOA by automated spectral interpretation, and
of methods for evaluatmg genera= candldate structures by comparative analysis of
predlcted & observed spectral propartles.                                            -

   Spectral interpretation,
only for those techniques     to derive structural constraints, is appropriate
              in which, at least to a first approximation, spectral

features can be correlated with fairly localized structural environments. Some
spectrum/structure correlations are relatively weak:  these can only be taken as
suggestions, and not as absolute constraints. An example of such weak correlation
                                    -7
would be any association of a particular group with an II? absorption below 1500cm
(for that region of the IR spectrum is usually dominated by combination and overtone
bands due to vibrations of the entire molecule that render reliable interpretation
difficult). Generally, inferences based on such weak spectrum/structure correlations
should not be employ&I as constraints prior  to structure generation but can be
exploited when ranking structures subsequent to generation.
inferring                               In our propsed mrk on
     structural constraints from spectral data, we shall be concentrating

mainly on magnetic resonance techniques in which spectrum/substructure correlations
are usually well defined.

   Once structures have been generated, it is possible to exploit spectral data
that relates more to the complete molecular structure than to any isolated subpart.
We have already developed functions  for predicting mass spectra using models,
"theories", of how a given molecular structure might fragment [23,67]. Functions
that predict magnetic resonance spectra,  using a model of a complete molecular
conformation, will in general be more accurate than those based purely on localized
substructures,  and consequently, will permit  finer discriminations to be made
between different candidate structures. Other post-testing of generated structures
can exploit the suggestive evidence of spectrum/structure correlations
evidence  for or against particular                      that yield

definitive tests.             structural features but are not absolutely

     C.3.a   Carbon-13 Magnetic Resonance.
   The chemical shift of a given carbon atom is sensitive to features of its
local environment up to, and sometimes including, delta-neighbors. For some
molecules, with rigid conformations,
produce significan           topologically more remote neighbors may also
       i shifts `through steric  crowding. Although there is a  great
       3CMR data, frequently structure elucidation studies use the   eal
of information in                   &lR
results just to determine gross features  of the carbons in the structure  such as
their hybridization,  degree of substitution and pssible bonds to electronegative
atoms.  We intend to explore  more constructive uses
inference of substructural parts prior         of CMR including both the
                         to structure generation, and spectrum

prediction and evaluation for complete, generated structures.

51


Dierassi. Carl

C.3.a.i   Carbon-13 Spectrum Interpretation.

One aspect of the Meta-DENDF?AL project in recent years was

by Mitchell and Schwnzer, of a system         the develoqn&
                       for the structural interpretation of
spectra [16].  The Mitchell/Schwenzer system utilized rules   that correlated
particular resonance values with substructures;
defining a fairly precise range          each rule involved a main prediction
                 in which a particular carbon in &-&structure

should resonate and a nlrmber of secondary and support predictions defining ranges in
which the resonances should occur for the other constituent atoms   of the
substructure. An example of the type of rule used  is shown in Figure 4.   The rule
is interpreted to mean that if a resonance is observed in the range 44.7-44.9, and
if appropriate  secondary/support  predictions  are satisfied,  then  the given
substructure can be taken as a.Ipssible explanation for the resonance.   These rules
were abstracted fram a set of spectra of standard alkanes and alkylamines and could
be used for the identification of additional alkanes and amines not present in the
training set.

44.7 ppn < delta(3) < 44.9 ppn =>

Node

1
2

3
4

5
7
8

atomtype

secondary
prediction

C
C

CH2
CH2

C
C
C

29.7<delta(2)
<35.6

17.9<delta(4)
X56.9

      1
     I
5-4-3-2-7
     I
      8
support
prediction

27.1 < delta(l) (34.9
30.7 < delta(2) (33.4

17.9 < delta($) (27.6

15.4 < delta(5) <24.3
27.1 < delta(7) (34.9
27.1 < delta(8) <34.9

Figure 4.  Meta-DENDRAL C-13 Spectrum Interpretation Rule

    Structure elucidation was accomplished by determining the rules, and
consequently the substructures,  that could be associated with each individual
resonance and then, in a complex search scheme, determining allowed combinations of
these separate substructures. .The Mitchell/Schwenzer system involved a heuristically
guided, depth first search  in which substructures were combined and expanded by
identifying their allowed partial overlaps. The method has been  illustrated through
its analysis of a fully+lecoupled spectrum of 3-3Aimethylhexane [16].

    Methods of spectrum interpretation using data bases of 13CMR spectra have
been reprted by both Bremser and Jezl [68,69,70,71].
number of search options;                  These two systems allow for a
                  the data base can be searched in a conventional manner to
identify reference  compounds with spectra similar  to that for an unknown, or
individual resonances may be entered and the data base  searched to retrieve all
substructures showing similar shifts, or the data base may be searched to  find the
range of shifts associated with some given substructure (i.e.  spectrum prediction).
Bremser has  illustrated how results of a standard  file search may be interpreted

                             52


Djerassi, Carl

manually to yield information on substructural commnents of a compound not  in fact
present in his reference file.

    In these two systems, the data. characterizing each reference compound
consists of atom-centered codes,  (describing the  topological environment of each
carbon with an assigned shift),  and associated shifts. Originally, both systems
defined atam-centered codes that represented a tree-structure grown through the
molecule from the central atom; tags were used in the Jezl system to indicate ring-
membership and similar properties.  These codes were ambiguous in that quite
distinct, cyclic  sub-structures could yield the same code. The Jezl scheme also
suffered from the disadvantage  that the codes were derived through relatively
complex rules,  handling many special cases, and the coding process could not be
automated.  The Bremser  "HOSE".code was more simply defined as a Hierarchically
Ordered description of an atom's Spherical Environment; generation of the code could
be completely automatic.  Bremser.s original code had problems of ambiguity similar
to those of the Jezl code;  Bremser has subsequently modified his coding scheme but
problems, such as truncation after a certain number of characters, remain.

   We have started to develop a system for 13CMR spectra interpretation that
is an extension of the second-type of search option in the Bremser and Jezl schemes.
Our program takes, as input, the individual resonances of all carbon atoms in the
unknown structure and searches a reference file to identify all atom-centered.codes
associated with similar resonances.  Unlike the Jezl and Bremser systems, these
retrieved codes are not the program's output, but are  in fact the input to a more
detailed stage of analysis  in which the results for individual resonances are
combined to ield much larger substructu=.
    53              In esseG, the subsequent process=
steps c0rres.p  to the structure building procedures of the Mitchell/Schwenzer
system; however, in this context it is possible to avoid some of their complexities
relating to graph matching of possibly partially overlapping structures.

    The current implementation of these algorithms is incomplete.   We have
systems for generating atom-centered codes and creating reference libraries of codes
and shifts, and we have preliminary versions  of functions for exploiting such
reference libraries. The atom-centered code that we employ is a complete, canonical
description of an atom's topological environment (out to a distance of three bonds).
The coding system will be extended to include stereochemical information once such
data has been incorporated into our standard structure definitions.

The following example is derived from data on isoterpinolene Figure 5:
      C
     I
  A
    c c
  s   I
  \ /"
      C
  c=
    /\
    c c

Figure 5.  Isoterpinolene - example structure for C-13 interpretation
                      functions

53


Djerassi, Carl

The program requires  the shift, multiplicity and allowed error in shift for every
carbon in the structure.

I  C-resonance  :  21.4 4 0~5
I  C-resonance  : 30.6 10.5
I                   --e
C-resonance  :  133.1 2 0.5
I  C-resonance  : 125.15 Z 0,5
I  C-resonance  : 127,7 ii3
I  C-resonance  : 125.7 ii3
I C-resonance : 25.7"-'"
                       5 1.10
I  C-resonance  :  31.7
I  C-resonance  : 20.5
I  C-resonance  : 19,6
I Cl3 reference XiZ

G-
3 1.0
--
4 0.5
--
4 0.5
-e
: crsncs

Figure  6.  Spectral data input for Isoterpinolene

    The program searches  the file of substructures and associated shifts,
retrieving those substructures with appropriate shifts and multiplicities.   In this
first pass through the reference file , each shift is considered individually.

I 3565 references read, 280 references written.
I

I allo& atom codes are :
I   -CH3 -CH2- >CH- <H= >C=   <*Hz >c*=

1 LINETYPE .
I 1 -CH3
I 2 XH-
I 3 -CH= -C*H=
1 4 -CH= -C*H=
I 5 >c= >c*=
I 6 >C= >C*=
1 7 -CH2-
I 8 -CH2-
I 9 -cH3
I 10 -CH3

(The symbol c* indicates an aromatic atom type). In a subsequent checks, through the
reduced reference file,  the program utilizes existing partial results regarding
possible alpha-neighbors for each atom. Such checks are able to derive the following
information:

54


Djerassi, Carl

I

I allowed atom codes are :
I   -CH3 -CH2- >CH- -CB= >C=

I

1  LINETYF'E
I  1 -cH3
I  2 XH-
I  3 -cH=
I  4 -CH=
I  5 >c=
I  6 X=
I  7 <H2-
I  8 -CH2-
I  9 -CH3
1  10 -CH3

Current partial adjacency matrix:
   Hetero 1 2 3 4 5 6    7    8    9   10
   1     . ? . ? ?
   2   .; ;
    ..; ; 3 ;  ;  i  ;  3
   3                                                          .      .
   4   . ;
5 .;:+3    ?    ?  ;  ;
                                             *
                   ;        ?    ?  ;  ;
   6 .?        ?    ?                    ?    ?
7 ..3.??::;..
   8     ..?.??
    ..?..?3    ?     t      .      .
   9                                               .      .      .      .
  18     ? o ? . . ? ?     ?      o      .      o

Figure 7.  Adjacency matrix derived for Isoterpinolene using Alpha-
                 neighbors

(In the adjacency matrix, the "."s  indicate no bond possible,  '*?"s indicate
~ssibility of a bond and "*"s show where the program finds bonds to have been
definitely established),  The program has been able  to determine that the none of
the methyls can bond to the methylene groups, has established that the sole methine
carbon must bond to one of the alkene units and identified the other alkene part..
These restrictions could be input to GENOA (see Section C.2) and muld considerably
reduce the size of the structure generation problem. However, in this example, it
was possible to derive  further constraints by utilizing data on beta-neighbors
provided by the retrieved codes.  Using beta-neighbors leads to the following final
connectivity matrix of Figure. 8.  Tfie only uncertainty remaining concerns which of
the methyl groups is attached to the methine and which are substituted onto the
alkene Because the methyl groups exhibit different shifts, they are distinct within
this program. As far as they are defined, these results do correspnd to the correct
structure,

55


Djerassi, 'Carl

Current partial adjacency matrix:
    Hetero 1 2 3 4
   1     . ? .
   2   .; ;
   3   ..; ;
   4   ,..;
   5   . ;
   6   :;::.
   7        . .
   8   ..;::
   9     ..?..
  10     . . ? . o

7 8 9 18

.   ;
.     s  ;

o      ?      ?      ?
?     ?      ?      ?

     ?

?    ?
  ? ?  ?

                 ?
? ? o ?

?      ?      ?      ?

?      ?      ?      ?

  Figure 8.  Adjacency matrix derived for Isoterpinolene using Beta-neighbors

    The current program has several limitations (apart from the fact that the
structure codes are purely topological with no stereochemical data). The major
limitation is in the reference file which is derived from data on rather less than
500 compounds (standard alkanes, alkenes, terpenes, diterpenes and a few other
natural products such as coumarins).  Very frequently, the file does not contain any
substructure equivalent, out to beta neighbors, to scme feature in a new unknown
compound. In such cases, attempts to utilize beta-neighbors will lead to a situation
where no complete structure may be generated.  However,  matching alpha-neighbors
does still provide a few usable constraints. We proposf3to obtain from other
sources computer readable files of extensive collections of  CMR spectra. me such
file is available through the NIH/EpA Chemical Information System. However,
although most of the spectra are assigned,  structures are not associated with the
spectra.  We are exploring ways to obtain the structures (in computer readable form)
and integrate them with the spectra themselves. Bremser [70] has available a large
collection of assigned spectra with associated structures.  The charge  is, however,
DM 1.75 per spectrum (approximately 14,000 spectra are available) .  If we are mable
to obtain the required data from the ND/EPA system we will be forced to submit a
supplementary application for funds to purchase Bremser's collection.

    The current program is not interfaced to the rest of the CCNGEN system, and
some of the constraints that it can identify cannot be expressed in terms of the
substructures that may be  input to the current GENOA program. We propose to buf3:
those interfaces and to develop ways to translate constraints derived from the
analysis into a form usable by GENOA.  This mrk will initially relate only to the
topological representations of structure. 'We will at the same time, however, begin
a design of the required stereochemical extensions to both the interpretive aspects
of the program and the interfaces to the structure generators.

     C.3.a.ii  Prediction of C-13 Spectra.
                                 --

    Several approaches to the computerized prediction of 13CMR data have been
reported. The CARBON-13 program of Munk, et al,  [39] is concerned solely  wi   the
                                              --

prediction of the ntier of distinct resonances that might be expected in  the tp 3CMR
spectrum.  Their prediction method is based on identifying topolcqically equivalent
atoms with a few,  ad hoc, extensions  to identify anisochronous methyl groups in
those diasterotopically related geminal methyls which are a commonly encountered
feature of organic molecules. Our algorithms for determining the true stereochemical
symmetry group would permit the correct enmeration of such resonance counts.

Other programs reported  in the literature have been concerned with the

                        56


Djerassi, Carl

prediction of approximate resonance shifts for eat P carbon nucleus.   Some attempts
have been made to utilize additivffy rules for  3CMR spectrum prediction. Thus,
Clerc has a program for estimating  CMR shifts of singly bonded carbons in acyclic
structures  containing   combinations of  non-cyclic   functional  groups [721.
Predictions for more complex cyclized  structures generally require parameter ized
schemes devised especially for sets of related structures.  While topological
descriptors may suffice for certain applications, geometrical descf$ptors are also
of value.  Some advances in the computerized derivation of   CMR prediction
functions, based on both toplogical and geometrical descriptors, have recently been
reported [73].

    Spectrum/substructure correlation rules of course provide another method of
spectra prediction. The spectrcan prediction system of Mitchell [15] employs a
slightly unusual representation  of such a correlation table.  III this system, 138
rules of the form "substructure -> shift range" were abstracted from a set of alkane
and amine spectra.  Spectrum prediction  was achieved by graph matching each
substructure to the given structure, and assigning  to each carbon a shift range
representing the  cormnon range of shifts predicted by each applicable rule. The
interactive NIH 13CMR system [74] can mrk in a somewhat similar manner; it differs
in that the range of shifts,  and details of their distribution, are derived from
data base as required,. rather than being  abstracted into a "prediction rule". The
substructure of interest is defined and then the program retrieves the shifts of all
instances of that substructure in the current data base. (This has the advantage
that expansion  of the data base does not require re-analysis to derive new
prediction rules),  The search of the potentially large data base is made efficient
by the use of fragment codes,  bit screens etc; the final steps do, like Mitchell's
system, require some graph matching,

    Bremser has noted the use of his library of atom-centered codes and related
shifts for spectral prediction;  a paper with more  details is due to be published.
Essentially the same Mitchell/NIH correlation methods are us&i; atom-centered codes
are generated for each atom in the given structure and the data base is  searched to
retrieve shifts associated with these codes. The graph-matching processes  are here
replaced by the string comparisons on the atom-centered codes.  The Jezl/balrymple
RACES system may be used for spectrum prediction in exactly similar fashion.

    Currently, we have a similar spectrum prediction capability. `We are choosing
to concentrate at present on deriving substructural constraints   from these
spectru&tructure correlations, rather th
schemes.  If the methods of interpreting v explore spectrum prediction and ranking
                               CMR data in terms of substructures are
successful (and used to derive constraints for a structure generator) , then spectrum
prediction based on  this type of model would not serve as a basis for further
discrimination between structures.   We will consider the use of more elaborate
approaches to spectra prediction that might be applicable once the CCNGEN programs
have   been   extended to  provide  complete   conformational,   stereochemical
representations of structures. The conformations could be used as input to a force-
field structure modeler and the resulting configurations analyzed to derive both
topological and steric contributions to chemical shifts (as in the mrk of Smith and
Jurs noted earlier).

     C.3.b   Proton magnetic resonance.

    The chemical shift of a proton is, like a carbon nucleus, determined largely
by features of its local environment. However, the13factors determining the shift
tend to be somewhat shorter range than those for   CMR. Not all influences on a
resonance can be   correlated   with the   immediate  topological neighbors;

57


Djerassi, Carl

steric/conformation   effects can   result in
shielding/deshielding                     protons   experiencing   strong
        bv e to topologically remote, but sterically close, pi-systems.
Consequently, as with  CMR, much prelim'
structure generation,  by interpreting r ary information can be derived, prior to
                          ,@!R in terms of local environments but
sensitive discrimination between related structures may require spectrum prediction
based on accurate models of molecular conformations.

    Some attempts have been made to derive structural information from the
coupling pattern exhibited in a proton spectrum either independently of [75], or in
association with chemical shift data [76]. These methods assume well resolved,
first order spectra. It is rare for comIpunds of bio chemical interest to show such
simple spectral characteristics,  and these interpretation methods are mainly of
educational rather than practical interest.

     Sasaki  [41] uses conventional correlation chart approaches to derive
structural data from the 1m spectrum.  He employs a table of about 200 standard
fragments, each defined by the n&r of protons that should resonate in particular
spectral regions.  Analysis of a spectra, by referencing this table, identifies
maxima and minima for the numbers of group  of different types. For moderately large
structures, the results from this type of B HMR interpretation are generally somewhat
ambiguous; usually, many different combinations of substructures can be found that
would satisfy  these weak spectral   constraints.  However, even  this simple
interpretive process does capture the kind of negative evidence that chemists
frequently fail to provide to CCNGEN and other structure generating programs; the
absence of required resonances will lead to the prohibition of the generation of
certain substructures - a prohibition  that the chemist will typically only apply
after seeing the generation of invalid structures.

   We have made some preliminary experiments, within the TXERLISP version of
CaGEN,  on the use of additivity rules for  the prediction  of proton resonance
spectra.  This lHMJ3 system consisted of functions for predicting  the resonance
values of protons attached to alkyl and alkene carbons, and functions allowing the
user to define constraints on the number and type of protons in particular regions
of the spectrum.
formulae using   The proton shifts were predicted by conventional additivity
        incremental shifts due to alpha-functional groups   with some
corrections for beta-groups and membership of small rings. The performance of this
spectrum-prediction/structure-pruning system was erratic when applied to typical
CCNGEN problems.  In some cases, more than 80% of generated candidate structures
could be successfully eliminated using relatively weak constraints. More frequently,
within the accuracy of the model, there  were no significant differences  in the
spectra predicted for different candidate structures and pruning of the structure
list was not possible. In a few cases,  there ware sufficiently large differences
between the observed and predicted spectra of the true structure that pruning on the
basis of what might have been  assumed to be reasonable constraints would in fact
have eliminated the correct structure. Prediction performance appeared to be poorest
for protons on di- and tri-substituted alkenes;  but, the scope and limitations of
the additivity rules could not be clearly defined. Consequently, this proton
magnetic resonance system was not made routinely available to CONGEN users.

investigated for

lack of suitable, mach&-readable collections of assigned proton spectra.

Spectral-structure correlations based on infra-red data have been exploited

58


Djerassi, Carl

in a number of other structure elucidation programs. Thus, both Sasaki [41,421 and
Gribov [50] employ what are essentially correlation tables, while Munk has a system
for inferring substructures  by either  "Pattern Recognition" or "Artificial
Intel1 igence" IR-classif ication functions [ 371.

    However, these IR interpretation schemes are limited. For example, Sasaki's
system attempts merely to determine  minima and maxima constraints on the number of
oxygens in carbonyl , hydroxy and ether groups. Other groups with absorptions above
1500~6~ might be characterizable by similar correlation rules.  However, reliable
identification is frequently not possible.  Problems of interpretation result from
extreme variability in  intensity of  "character istic" absorption bands  (e .g . the
absence of a nitrile absorption  in many alpha-hydroxy-nitr i f es) , and from the fact
that m_apy of these absorptions _ lie in the same 1500-1700cm-
1500cm                                region. Spectra below
    are frequently dominated by combination and overtone bands characteristic
of the molecule as a whole rather than any isolated subparts; while such spectral
data are valuable in file search oriented methods of identifying structures, they
are of limited diagnostic value offering suggestive rather than definitive evidence.
The same qualification - suggestive rather than definitive evidence - has to be
applied to attempts to derive additional structural information from  the particular
position of absorption of a befter characterized group such as a carbonyl. A
carbonyl absorption around 1770cm-  is suggestive of a five-membered lactone ring,
but presumption of such a substructure,  and its use as a constraint on a structure
generator, muld be ill-advised (similar absorption also characterize vinyl esters
and several other substructures).

    Since the identification of principal
completed long before                 functionality has normally been
             a structure-elucidation problem is given to CONGEN, there
appears to be relatively limited use for
association with coNGEN/GENoA.         this type of IR-interpretive scheme in
                                                   .

   Gribov has mrked on the evaluation of candidate structures using predicted
IR spectra.  The spectrlnn prediction
analyzing the vibrational        is based on conventional approaches for
               frequencies pf a molecule using parameterized bond
strengths etc. As noted by Gribov, this approach is really only applicable to fairly
small molecules. Conceivably,
molecules analyzed by CONGEN.  such an approach might be tried with the larger

   The only use for IR currently envisaged is in a very simple ranking scheme.
In the LISP version of CCNGEN,  functions were available that allowed the user to
associate positive and negative scores with particular substructures and to  let the
program rank candidate molecules by combining scores associated   with their
constituent substructures. It is possible to implement a scheme that muld derive
scores for different substructures through the suggestive, but not definitive, IR-
interpretation  rules   noted earlier.   This   would allow the   association of
plausibility values
ranking functions.  for each structure which might then be used with the simple

     C. 3.d   Mass Spectrometry.

    Interpretive processing of mass spectral data by means of spectrum/structure
correlations is of limited utility, These correlations, e.g. ( M-44 <=> anhydride) ,
generally only provide tweak evidence for, or against, the presence of functional
groups more readily identified by other spectral/chemical techniques. This type of
mass spectral processing is available as a minor component in Gribov's
may yet be incorporated in Sasaki's programs.                 system, and
                                However,  it is not considered to be
of value in the type of structure elucidation problem generally given to CCNGEN.

59


Djerassi, Carl

    The Mass Distribution Graph method does constitute a more general model for
mass spectrcPn interpretation  [671.  HOwever,  the applicability of the method to
large structures is limited by the combinatorial nature of the algorithms.   We have
no plans currently to develop further this,approach;
conceptual base,                      in spite of the elegance of its
         a practical, useful program seems extremely difficult to develop.

    Some of the more sophisticated mass spectral  file search systems have the
capability of identifying constituent substructures of molecules not actually
present in the reference file [28]. McLafferty's group is exploring the possibility
of using CCWEN in
ZiterpretatEi+tZ.  association with their STIRS file-based    mass
                                         ---           spectral

    While methods for interpretation of mass spectra are still of limited
applicability, our algorithms for mass spectrum prediction and structure ranki
seem well pro&- [67,23].     e-
--          For mass spectral predictions, the use of  p+,MIw
model of a chemical structure,                         a topo ogical
                  as produced by current Cm, is generally quite

satisfactory. The mass spectral processing algoriths can employ models, "theories",
of fragmentation processes of varying degrees of specificity as may be appropriate
to a particular application.

C.3.e  Circular Dichroism and Magnetic Circular Dichroism
Circular Dichroism (CD) and Magnetic Circular Dichroism (MCD) are spectral

techniques particularly useful in structural/stereochemical studies.   E&cause of
their strong  dependence on  stereochemistry, these techniques have heretofore not
found much use in CONGEN and this represents a serious deficiency.   With the
addition of conformation information to CONGEN it will now be possible to
incorporate  structural and stereochemical information from these sources into
computer-assisted structure elucidation using CONGEN and GENOA.

    The interpretation and prediction of CD spectra based on substructural
hyIptheses is well established. Kxaples are
derived for ketones [77],             the familiar octant rule originally
              Brewster's rules for parrafinic hydrocarbons [781, and

extensions to sector rules such as those of Kirk and Klyne [79]. In all cases the
substructure considered must include both configurational   and conformational
information.  The general method is to associate with each substructure an intensity
(either positive or negative) tiich contributes to the overall observed intensity of
the spectrum.  The assmption  is often made of additivity, but not always.
Interpretation of CD spectra makes primary use of the observd sign and intensity of
the spectra.  First of all, the fact that a CD spectra was observed at all says
that the molecule is chiral, which is a very useful constraint for CONGEN*s
structure generation.  Rationalization of the observed intensity is best made with
respect to pssible structures, i.e.,
structures and their conformations.   after a CONGEN generation of possible chiral
structural hypotheses by itself since The observed spectra will not usually lead to
                      the (usually single) intensity can be caused

by any number of substituents around the chromophore involved. The real use of the
method is to rule out possible structures with specified conformation.

    Useful, but somewhat coarse, predictions of CD and MCD spectra can be made
with the use of a number of models proposed which correlate spectral
substituents,                                   intensity with
         Among these  are the octant rule [80] and the 'zig-zag" model which
are most useful for the CD spectra of saturated ketones.  A simple model has also
been propxed for MCD spectra of saturated ketones [al]. These models generally are
gused for predicting  spectra of structures having idealized
substituents in nearby or well-defined locations            geometries with

These methods can therefore be applied      with respect to the chromophore.
                         to structures output from the propsed

60


Djerassi, Carl

conformation generator.  We propse to develop a program which will allow us to
discriminate between candidate conformations using these models and experimentally
obtained CD or MCD spectra.                                       $ :
                                                                     .I

    A more precise prediction of CD spectra  requires a refined geometry and a
more detailed energy calculation.  If a flexible structure is in an equilibrium
between two or more conformations, relative energies are needed to determine
ppulations before computation of spectra.   To make use of these methods, an
interface between the output of CONGEN and the input to these already existing
energy programs will be required.  This work will be the second stage of this effort
and will be guided by results of the first stage using the simpler models.

    While CD spectroscopy in the  ultraviolet region is long established as a
useful tool for structure elucidation, recent work on KD (Magnetic Circular
Dichroism),  VUVCD (Vacuum Ultraviolet Circular Dichroism) , and VCD (Vibrational
Circular Dichroim) indicate considerable promise for structure elucidation. While
the methods of interpretation for these spectra differ, the end result is usually a
correlation of substructure (including stereochemistry) with observed intensity and
sign.  We feel our propsed system for  CD spectra will incorporate, with modest
modification, substructural information from these newer methods as they become more
conanon in biomedical structure elucidation.

C.3.f  Combined Spectral Interpretation.

   As we mentioned previously, structural information from different physical
techniques is often complementary.  Any program seeking to perform automated
analysis of data from different  techniques must eventually be capable of examining
the data and resulting inferences  from each technique in light of what has been
learned from other techniques. We illustfgte& p;e;~;~~s~im;; example of this
approach in the example on interpretation of                 The assignment
of specific substructures to observed resonances implies additional assignments,
which can be made on the basis of further data analysis or logically, to cite the
trivial example that assignment of one carbon  to a C=C functionality means that
another carbon must also be assigned to the double bond. We propse to generalize
this method,  perhaps using an adjacency matrix representation for the growing
structure,  with a program which acquires  inferences from each technique and
automatically searches data from other techniques for confirmation or denial of the
inferred substructure.  This approach will be complicated by the fact that sOme of
the inferences will be tentative.  We will evaluate schemes for assigning certainty
factors to each inference to explore the Epssibility of generating structures with
associated plausibilities  (determined by appropriate  combination of the certainty
factors for each component part).

    There is another useful application of methods for  considering the
collection of available data.  As noted earlier, chemists using CGNGEN frequently
fail to specify all the structural constraints that, in fact, they know. For the
mst part, it is negative constraints that are forgotten. Because such constraints
are neglected, some problems appear to be too large and many others are solved
extremely inefficiently with the chemist generating and then Fruning away large
classes of structures.  If some convenient method of entering spectral data can be
devised, then relatively unsophisticated spectral interpretation techniques could be
used to derive such negative constraints,  e ffectively prohibiting the generation of
particular substructures.

61


Djerassi, Carl

      c.4   Conformation Generator for CGNGEN.

   A great deal of the information input to a structure elucidation problem is
conformational in nature. Examples af  such information are vicinal and long range
couplings in NMR, steric shifts in  CMR such as the differentiation between axial
and equatorial substituents,  Circular Dichroism spectra, etc.  At present, this
information can be used indirectly in CCNGEN only as it pertains to the constitution
(bond-connectivity) or configuration (chiral centers and double bonds) of a proposed
structure.

    RI eliminate this deficiency and  enhance the value and scope of CC?!JGEN, we
propose to provide CCNGEN with an exhaustive and irredundant  generator of
conformations based on a chosen discrete set of possible torsional  states (i.e.,
positions of rotation) around rotatable bonds.  The input to such a generator muld
be a CONGEN stereoisomer  (specified constitution and configuration) and the chosen
set of torsional states  ( which might be a default set contained in the program).
The output would be the possible conformations based on these possible torsional
states.  Only torsional angles will be considered as variables for the conformation
generation, the bond lengths and bond angles will be considered fixed.

    While the conformation generator will indeed be exhaustive and irredundant,
special attention will be given  to conmon conformational situations such as six-
membered rings.  This will be done to improve the efficiency of the program for
coxmnon problems while retaining the desired assurance for more complex problems (see
Sec. C.4.b.i).

    A conformation generator will provide the necessary link from CONGEN to
existing computer methods which require input structures with coordinates. This
link is shown schematically in Figure 9.  Examples of such methods are molecular
mechanics energy calculations, quantum mechanical  energy calculations, graphics
display programs, and  finer grid (torsional angles) conformation generation. A
conformation generator would also allow CCNGEN to be applied  in confonnational
analysis, another form of structure elucidation.  We propose to develop this link to
existing methods and applications.

    We feel the proposed   investment of resources into  developing this
conformation generator will be repaid many times over because:

  1) The added versatility it will provide CON- to deal with all facets of
conformational information in structure elucidation:

  2) It will allow development of links to existing atomic coordinate based
methods which permit many potential new biomedical applications.   (See Sections
C.4.C, F),

62


Djerassi, Carl

Molecular Formula
     !
      !
     !                              !
       V                              !
Constitutional Isomers                  !
(Topological Isomers,              CONGEN now
Bond-connectivity)                       !
      !                              !
      !                              !
      !                              !

       V                               !
Configurational Stereoisomers                V
(Chiral centers, double bonds)
      !
      !
      !                     Proposed link
       V                                 !
Conformations                                       V
(Single bond rotation).                             -
      !
     !           7
      !              Extensive existing methods
       V                               !
Refined Structure                             V
(Atomic coordinates, energetics)

Figure 9.  Proposed Link of CONGEN to existing coordinate-based methods

C.4.a   Total Conformation Generation.

    In its current state of developnent, CONGEN will generate, if desired, all
possible configurational stereoisomers from  an input molecular formula (Figure 9).
This generation is complete  and irredundant, that is, all possibilities consistent
with chemical valence are included without duplication.  We feel that complete and
irredundant generation is one of CONGEN's strongest selling points as it assures no
possibilities  are overlooked in a structure elucidation problem.  We propse to
provide the same  assurance for conformation generation.  However, since there are
infinitely many conformations possible for most structures, as torsional angles vary
continuously, a complete and irredundant generation is possible only if a finite
number of discrete values are, allowed for the torsional angles. To accomplish the
desired total conformation*generation it will be necessary to develop:

i)  a generation algorithm,

ii)  a means of representing conformations,

iii)  an assurance of irredundance.

C.4,a.i   Generation Algorithm.

We propose to generate conformations for a CCNGEW stereoisomer by labelling

63


Djerassi, Carl

the bonds (edges) of the graph representing the stereoisomer with the possible bond
torsional states.  The algorithm will be developed. so that any number of possible
torsional states can be specified.  'Ihe possible torsional states might be the
familiar trans, gauche (+), and gauche (-) states which correspond to the minima of-
the torsional potential for single carbon-carbon bonds (e.g., the central bond of n-
butane).  Alternatively,  the states might be the six (three staggered, three
eclipsed) possible for a single carbon-carbon bond.  The former choice might be made
in cases where only local bond potentials are considered important, while the latter
might be made when global potentials are  important.  The point here is that the
algorithm would have to handle either case or any other choice of pssible torsional
states 1821.

    Part of the algorithm FJould involve recognizing the various kinds of
rotatable bonds   (e.g. sp3-sp3, sp3-sp2,  sp2-sp2, etc.) and  treating each
accordingly.  The problem of deciding which are rotatable bonds muld be handled in
a manner analogous to that used for determining stereocenters in the algorithm for
configurational stereoisomer generation  1251.  This method would start out by
assuming every bond is rotatable and then proceed to reject those known to be fixed
by intrinsic or input constraints (section C.4.b, below). Generation would proceed
on the remaining bonds with further testing done as the conformations are generated.
This method is similar to that used successfully for other structural generation
problems in CONGE'N.

    We propose to do the generation of conformations as a labelling since our
extensive experience with such algorithms suggests  that these are very fast and
efficient algorithms for problems of this kind.  In particular, we believe that this
method would be faster than an algorithm based entirely on atomic coordinates. The
result of such a labelling muld be a CCNGEN structure represented as a graph with
labels on some of the edges (bonds).  The result of a generation of this kind would
be a list of structures with bonds labelled in all possible ways and including
structures not consistent with constraints (such as those imposed by intrinsic
structural features such as ring closure).  Labelling algorithms assure completeness
since the labels are distributed in all possible ways.  In our experience they are
also constrainable, a particularly important consideration for conformations.

     C.4.a.ii   Canonical Representation.

    In order to deal with conformations in the computer, some canonical (unique)
representation for each conformation is  required.  We will likely construct such a
canonical representation by making use  of the atom numbering of the input
stereoisomer.  This is in analogy to the canonical representation used for the
configuration of the stereocenters in the stereoisomer [24]. For example, consider
the problem of uniquely describing  the three staggered rotamers of a structure
numbered as:

   2            6             4
l!    3     1    !    3     l!    3
\    /      \    /      \    /
\ /        \  /        \ /
   C             C             C
    !              !              !
/ !  \      /   !  \      / !  \
6 !    4     4    !    2     2 !    6
   5             5             5

A method which muld give unique representations  for each of these three rotamers

                              64


Djerassi, Carl

would be to choose the lowest numbered substituent on each of t&' two atoms involved
in the bond and express the bond state in term of them.
be 1,2qauche(+), 1,2-trans,                In the example, this would

designating clockwise      and 1,2-gauche(-) respectively.   The convention of
           rotation with a positive sign was used.  If any or all of
these were equivalent by symmetry, an ordering of the torsional states would be
required, and the canonical representative would be the lowest.  For example, if the
ordering based on torsional angle wzre used: gauche(+) < trans < gauche(-), and all
three were equivalent in the above case (because of equivalent substituents) the
canonical representative  would  be 1,2-gauche(+).   This method   of canonical
representation assumes that the numbering  of the atoms was determined before the
edge labels are added.  This sequence correspnds  to that which will be used in
CCNGEN since the atom numbering is done when the constitution (bond to bond
connectivity) is determined.

C.4.a.iii   Irredundance.

   Assuring irredundance (no duplicate structures generated) in the labelling
algorithm being proposed for conformation generation requires the proper use of the
symmetries involved in the problem.
arbitrary symmetry,            Since CCNGEN can produce structures of
           the conformation generator

pssible symmetrical structure.           must be able to deal with any

with so generally,       It is for this reason that symmetry must be dealt
          not because of any claim of preponderance

structures in biomedical problems.                    of symmetrical
considering arbitrary symmetry in    To our knowledge,  this general problem of
                 conformation generation has not yet been solved.

The problems for which conformation generation has been treated either have no
symmetry at all or synnnetry of just one type (such as that in cyclic hydrocarbons).
This problem can be solved by using a method similar to that used to irredundantly
generate the configuration stereoisomers [24].  For the conformation generation
problem, the symmetry group of the input CONGEN stereoisomer is represented by its
effect on the possible torsional states for each rotatable bond.
classes of this group on                         The equivalence

distinct conformations.   the set of all possible conformations are the symmetry
            A lowest representative of each class will be the canonical
representative.  This method will also readily give an enclmeration formula for
conformations which will be of use to the program since  it will provide an
independent check of the conformation generator and will allow faster computation of
the number of conformations.

   The method for irredundant generation of conformations will be illustrated
on tetrachloromethylmethane  (ClCH ),C.
             f     The objective  is to find the distinct
rotamers of this structure with on y perfectly staggered rotamers allowed.   'Ib do
this it is necessary to represent the synnnetry group of the structure by its effect
on the pssible torsional states of the rotatable bonds. The symmetry group of this
structure is its Configuration
tetrahedral pint group.     Sytnnetry Group [24] and is isomorphic to the

generator in CNXN.      This group is  computed by the current stereoisomer
          It is this group which must be represented on the possible

torsional states of the bonds. This group has five
the identity, eight C3 rotation axes,         "kinds" of symmetry operations:

and six S4 alternating axes.     three C2 rotation axes, six reflection planes,
                   Each of these five will be considered in turn to
ascertain their effect on the pssible torsional states.
no effect on the possible torsional states.         The identity operation has

effect.                      The C3 operations, however, do have an
    Each C3 axis is colinear with one of the C-C bond axes.   Rotation about
this axis has the effect of interchanging the three pssible torsional positions
about that axis.  It has no effect on the torsional positions about the other three
axes.  Each C2 axis interchanges pairs of bonds and the torsional states around
each. With this much information it is pssible to compute the number of possible
rotamers using the method of Kerber [83]. The identity operation can be expressed

65


Djerassi, Carl

by the permutation (l)(2)(3)(4) of- atoms. The C3 operations can be expressed as
permutations like (123) (4). There are eight of these.  The C2 operations can be
expressed as permutations (12)(34) and there are three of these.  The number of
rotamers can be computed by substituting .3 for each orbit in the permutation and
multiplying by the number of permutations, summing  over all types of permutations
and dividing by the order of the group.  This is done as stated for the identity and
the C2 axes.  However, because the C3 axes interconvert the pssible rotamers about
one axis, this term contributes zero  to the total.  This conclusion can be reached
without rationalization by simply using the formula derived by Kerber  [83]. This
yields (1/12)*((3)*(3)*(3)*(3)+3*(3)*(3))  =(1/12)*(81+27)=9 which is the correct
number of rotamers for this structure [84].  The number of enantiomeric pairs can be
computed by following through the procedure for the other synnnetry operations.  This
procedure has computed the n&r of equivalence classes for this permutation group.
A generation algorithm can be developed by simply taking each possible rotamer in
turn and letting the symmetry group represented in this manner act on it. This
process will  actually construct the equivalence classes and the lowest member Of
each class is the canonical representative.  While this is not the most efficient
algorithm, it serves to illustrate the method.

     C.4.b   Constrained Generation of Conformations.
                                            -

    As in the previous  efforts to develop generators of constitutional isomers
and configurational stereoisomers, once a total generator  is devised,  it is
necessary to mcdify it so that constrained generation can be done.  We propose to
develop a constrained generator of conformations in this manner. Constraints
relevant to conformation generation include 1) intrinsic structural constraints such
as that imposed by ring closure,  2) constraints input by the user based on partial
structural information, and 3) constraints impsed by dynamics since most chemical
structures exist in several conformations in rapid eguilibrim.

C.4.b.i    Intrinsic constraints.

    The intrinsic constraints on conformation generation imposed by ring closure
in polycyclic  structures are probably the most difficult problem  facing a
conformation generation program of the type proposed here.  Not all possible values
of torsional angles  for bonds are consistent with ring closure in these cyclic
systems.  For a polycyclic structure,  the conformations pssible for each ring are
constrained by the conformations of adjacent rings, in addition to the constraint of
ring closure.  The relative constraints of overlapping rings can be determined by
establishing the overlapping bonds and the configurations of any stereocenters
involved.  For example, in cisaecalin the common bond to the tm six-membered rings
has the same signed torsional angle (with respect to the ring carbons)  inboth
rings.  In trans-decalin,  the common bond has opposite signed torsional angles in
the two rings.  For a given polycyclic structure these relationships can be computed
by finding all rings in  the structure and establishing the relative configurations
of the stereocenters involved.  The ring-finding can be done using a currently
available function in CCNGEN.   Hence,  the general problem reduces to that of
determining the pssible conformations for a single ring with constraints on the
values for the torsional angles of some bonds.  'Ihe ring-finding muld have to be
done only once  for all the stereoisomers of given constitution.   This is an
efficiency because the list of structures coming out of CONEEN has all stereoisomers
of the same constitution together.  Another efficiency would be to consider only
nonenveloping rings (those which do not "contain" smaller rings).

The process of generating  conformations for a single ring with constraints

                       66


Djerassi, Carl

will be the "unit operation" of the conformation generator and will have to be
optimized for efficiency besides belong complete and irredui&nt.  Six possible
methods can be suggested based in part on the work of others.

  1)  The most direct method would be to systematically vary each bond in turn
and check for end-to-end distance and overlapping atoms trigonometrically using
coordinates.  This muld be a depth first generation with pruning when atoms
overlap or the end-to-end distance becomes to large to allow closure.

  2) A variation on this approach successfully used by Barry [64] would be to
vary "fold axes" or dihedral angles which have as their axis the line connecting
two nonbonded atoms.  This method is more efficient because ring closure is more
easily maintained but is  not always exhaustive for one set of fold axes. The
same distance checking would be done here.

  3) A different method muld be to use internal coordinates which measure
the "pucker" of the ring and directly take account of the ring syzrnetry. These
coordinates are usually based on displacement from a reference plane of the ring
but could probably be expressed in terms of torsional angles. This method would
probably have to be modified to assure exhaustion for large rings.   This method
also requires coordinates, but in a somewhat simpler fashion [58,60,611.

  4)  Another method makes use of ideas developed by workers in conformational
analysis 1851.  Families of conformations can be differentiated by the sequence
of the signs of the bond torsional angles.  For example, the chair conformation
of cyclohexane has six torsional angle sign changes as one goes around the ring.
The boat-twist family has  four torsional angle sign changes.   Similar patterns
are evident for families of conformations of larger rings.   This observation
suggests that conformations might be generated by first discerning such families
and then generating within each family.  The families might be generated by
first labelling the atoms with locations of torsional angle sign changes (only
an even ntier of these are possible for any size ring) and then labelling the
bonds with the values of the torsional angles, The first labelling reduces the
number of possibilities for  the second labelling.   This is a reductionist
approach which resembles the vertex graph method used so successfully in the
first version of the COJ%EN cyclic structure generator.

  5) A related labelling method FJould make use of the plygon classification
method for conformations developed by Dale [56]. Conformations are considered
as polygons made of straight chain edges of varying lengths. This has the
effect of reducing a ring of n atoms to a polygon of mtn sides.  Generation with
a method like this tJould involve generating the possible polygons and labelling
the edges in all possible consistent ways with numbers of bonds. This is also a
reductionist approach similar to the one above.

  6) A different method would be to make use of a "catalog" of the possible
conformations for each ring size  with a backup generator for cases involving
rings larger than those in the catalog.  Each ring in the structure would then
be labelled with each of the pssible conformations consistent with any
constraints,  This method effectively trades faster runtimes for a larger
storage requirement.

    These six possibilities  have been ordered by their probable speed. The
choice of one of these, a combinat-ion of them, or  another method entirely will
depend on speed,  programmability, and constrainability along with an assurance of
completeness and irredundance.


    Particular attention will be paid to common conformational features such as
six-membered rings.  This will probably be done most efficiently by making use Of a
"catalog"  of six-membered ring conformations  (item 6 above).  The possible six-
membered ring conformations  will be generated by reference to the catalog and any
current constraints.  This method will simplify the interpretation of conformational
observations in this cornnon case and will easily permit use of notions most familiar
to chemists (chair, twist, axial, equatorial, etc.).

    Other common intrinsic constraints involve rigid substructures such as
multiple bonds and three-membered rings.  These features are easily recognized with
currently available parts of CCNGEN which will simply be used in the conformation
generator as well.

C.4.b.ii   Constraints.
       Input

These are the constraints which will be input by the user when solving a

particular structural problem.  Common constraints of this type will arise from
interpretation of NMR coupling d&a (vicinal and longrange), steric effects on Cl3
NMR (e.g. axial vs. equatorial substituent shifts) and interpretation of CD or OFU2
spectra (sector rules, Brewster's rules, etc.).  Such constraints will be expressed
as desired or undesired substructures which include designations for absolute
configurations  and bond torsional angles.  They will be dealt with in a manner
similar to that in C@GEN now,  that is, by graph matching and pruning. Particular
interest will be directed toward expressing constraints dealing with CD spectra
because of ongoing efforts in Prof. Djerassi's research group on this topic and
because of recent developments in new methods  such as Magnetic Circular Dichroisn
(-) tw ,  Vacuum ultraviolet Circular Dichroism (VUVCD)[87]   and Vibrational
Circular Dichroism (VCD)[88].  The latter (VCD) is particularly interesting because
this method will likely provide direct evidence about individual chiral environments
of many chromophores.  Some or all of these new methods will be particularly useful
to structure determination of bicmedically relevant molecules because almost all
such structures are chiral.  Another type of input constraint   arises  from
observations about synnnetrically equivalent atoms.  The symmetry of conformations
will always be less  than or equal to the symmetry of the configurational
stereoisomer from which they are generated.  Thus, to take proper account of
observations about the symmetry of a unknown structure, consideration of the
possible conformations is crucial.

C.4.b.iii  Dynamics.

A different sort of constraint arises in the conformation generation problem

since most flexible molecules are in rapid equilibrium among several different
conformations.  Thus a structure determination of the type discussed here which
includes conformations may  lead to several final structures rather than just one.
This sort of information could be expressed as a constraint which requires at least
n conformations' or requires only one be present.   Alternatively, there may be an
zbservation tiich requires that  there be interconversion between tm known partial
substructures (chair-chair interconversion in cyclohexane for example).  To make use
of this information  it will be necessary  to predict flexibility in conformations.
For certain situations such a prediction is fairly simple.   For example, most
acyclic  substructures are flexible if not too heavily substituted.   In many
structure determination problems there may be no interest in flexibility of acyclic
substructures, hence these could be recognized and ignored in  further conformation
generation leading to a savings in time and storage.  Other kinds of flexibility
which are fairly easily recognized involve ring pseudorotation, large unconstrained

68


Djerassi, Carl

rings or parts of rings, chair-chair interconversion, etc.  However,  predictions of
flexibility in this way can only go so far since this property depends strongly on
energetics.  A typical structure elucidation problem might end with the observation
of several final structures and the question  of whether or not they can be
interconverted and their relative populations.  Resolution of this question would
require an energy calculation of some type. The conformation generator will allow
computation of.all the possibilities, an important piece of information  in problems
of this kind.

c.4.c   Interface and Applications.

CCNGEN Interface.

    The conformation generator program will eventually become part of the CONGEN
program.  Conformation generation will take place after configuration stereoisomer
generation.  Information will flow to the conformation generator which describes the
constitution and configuration of the stereoisomer for which conformation generation
is to be done.  The conformation generator  will construct a list of possible
conformations subject to  input constraints and will return information about
continued candidacy of the input structure in the ongoing structure elucidation
problem.  Thus it may be possible to eliminate a stereoisomer or    even a
constitutional isomer   from further consideration   based on results   of the
conformation generation.  The user interface will resemble that currently in CCNGEN
and in fact will use many of the program sections already written for this purpose.

Other Applications.

    Besides improving CONGEN as a tool for structure elucidation, this proposed
addition of a conformation generator  will lead to ptential new biomedical
applications.  The CONGEN program with a conformation generator will output
structures complete with internal  (torsional angle) coordinates.   Since many
existing programs require as input a structure with coordinates,  the opportunity
exists to interface CONGEN with these programs.   Examples of such programs are
empirical force-field energy calculations (molecular mechanics), quantum mechanical
energy calculations (probably semi-empirical), graphics programs, and finer grid
conformation generation. (smaller torsional angle  increments with van der Waals
checking).  These programs and methods frequently see bioanedical applications: an
example is in the determination of structure-activity relationships. By interfacing
CCNGED to these existing  programs, the opportunity for new biamedical applications
will be expanded.  Since these programs have been extensively developed by others,
it will not be necessary  for us to spend the time to develop them.   Instead, we
propose to use collaborative efforts to take advantage of these very interesting new
applications.  (See Section F, Collaborative Arrangements, section C.5.d Graphics
Interface).

    Another application would be to the field of conformational analysis. The
conformation generator  would be useful to such efforts by exhaustively and
irredundantly generating the Ipssible conformations which must be considered in such
a study.  'We propose to explore this possibility collaboratively as well (Section
?? o

    The conformation generator program will  also be written to exist by itself
(besides being a part of CONGD\J) by providing a mechanism for inputting structures

69


Djerassi, Carl

from other sources.  Since we expect this program to be fast and efficient and able
to deal with large  lists of structures,  it is conceivable that the conformation
generator could be used on lists of structures from other data bases to "upgrade" a
list of structures which do not yet contain any conformational information. This
could lead to applications in pharmacology or toxicology and other areas which make
use of large chemical structure data bases.

c.5   Resource Sharing.

     C.5.a   Access to Programs via SDMEX and Local Dedicated Computer and
Resource Management. -                  .- --

    In Section A.2, Background, we discussed the relationship of our project to
the SUMEX resource.  In that discussion we outlined the conflicts between program
development and extensive "production"  use of resulting applications programs by
collaborators both within and outside of the SUMEX community. We propose  to resolve
these conflicts by providing separate machines for development and production uses,
each available to local and network users.

    We propose that program development take place, as it has in the past, on
the SUMEX RDP-10 system. This system provides  the requisite facilities for
languages,  editors, message  handling and so forth, to support effectively such
development. In addition,  SUMEX will provide the gateway for access to production
use the proposed dedicated computer (see Figure 10). In the past, few collaborators
have participated directly in program development. Their contributions have been,
for the most part, indirect in that many suggestions  resulting from trial use of
CONGEN were incorporated by our group into programs, resulting in improved
performance and greater  chemical  "intelligence".  Now that more chemical and
biochemical research groups are becoming sophisticated in their use of computers, we
expect that, during this proposal period, our collaborators may desire more direct
involvement,  Cowburn   at Rockefeller  for example.   We will  encourage such
collaboration and will carry out such work on SUMEZL

70


Local TTY
Scanner

TYMNET
Interface

c    I

4 IO
Peripherals
(LPT, PLT, )

CSD Machines
HPP TTY Clusters
Quality Printing

  Stanford
r-l
  Campus
Gateway

ETHERNET -

ETIIERNET

---+-l
50K bit/set
  Lines

cl
ARPANET
Link

SUM-EX 2020

Figure 10.  Access to DENDRAL programs on SUMEX

DENDRAL/SUMEX
    VAX
(Proposed)


Djerassi, Carl

    The production machine will provide more  routine access to programs whose
development and testing has progressed  to the point where outside use of the
programs by a wide community can be encouraged.  Currently, COKEN and auxiliary
programs or functions,  (STEREO for unconstrained generation of configurational
isomers, SURVEY for examining structures, MSANAL,YZE for mass spectral prediction and
ranking and REACT for simulation of chemical reaction sequences) are in this
category. This use of our programs may involve local users, i.e. persons in our own
group or local colldborators,  or remote users accessing programs via TYMNET and
SUMEX. We propose that access for applications, or production, use be handled by a
computer linked to, but separate from the SUMEX system, specifically a Digital
Equipnent Corporation  VAX-11/780. Ihe schematic diagram of Figure 10 conveys our
proposed design  to allow users to access either machine, taking advantage of all
existing network communications- facilities on SUMEX.  Whether qutations will be
carried out on SUMEX or the VAX will depend on the users and the program to be run.
Only SUMEX users  involved in DENDRAL will be enabled to run on the VAX and Vice-
versa. By exercising such administrative controls we will assure allocation of the
DENDRAL machine for biochemical work while maintaining flexibility for network mail
routing and approved file transfers.  The VAX will have its own disc system, for
system programs and page-swapping in the time sharing system of the VAX. The netmrk
configuration does not make the DENDRAL VAX dependent on SclMM being up for access,
yet still takes advantage of existing SUMM cormmmications hardware and other
selected peripheral  equipment (e.g., printer,  plotter, TTY  ports)  without
duplicating them.

    We have discussed previously (see Budget Remarks)  the reasons for our
preliminary selection of the VAX computer. Briefly, in our opinion, it represents an
optimum trade-off of several factors including interactive computing, large address
space r  compatibility with the biochemical and computer  science communities with
which we interact,  long-term trends within the computing industry and cost-
effectiveness.  Several of the persons attending our workshops last year (see Annual
Report, Appendix I) have, or soon will have, a VAX system. The National Resource for
Computation in Chemistry will soon obtain a VAX. Taken together, these factors point
towards the VAX as at least a good representative of the future shape of scientific
computing appropriate to our applications.

    The implementation of the VAX system as a part of the SUMEX resource, to be
used as discussed above, will involve primarily the efforts of the two scientific
programmers identified in the btiget, under the guidance of the scientific staff and
the Advisory Committee (see below). Their responsibilities, outlined in the Budget
Remarks, are discussed here in more detail,  We identify these programmers in the
following discussion `as befits their responsibilities, "systems progranxner" and
"applications programmer."  Although we will be able to call upon the advice and
expertise of the existing  SUMEX staff in the implementation   and continued
maintenance and support of the VAX, in our opinion a full-time  systems programmer
and a full-time applications programmer (concerned primarily with the VAX) represent
the minimum staffing  required to support our VAX system. Initial  implemetation of
the VAX will include the following:

  0  select either DEC's, or Bell Lab's UNIX, operating  system (the
responsibility of the entire staff).

  ii) together with the SUMEX staff,  make the necessary operating system
modifications to allow access as outlined in Figure 10 (systems prcqramner).

  iii)  obtain, (or write) a BCPL compiler for the VAX in order to run the
current CCNGEN,  GENOA and related programs  written in BCPL (applications
programmer).

72


Dierassi, Carl

While (i-iii) are being carried out, SUMEX will be used for applications under
community controls in effect at the present time (GUEST access, strict control over
SUMEX resource allocation (computer cycles) for local users).  The applications
programmer will coordinate this access and provide required documentation.

    Once the PCPL compiler has been brought up, our next step will be to put the
current production versions of CONGEN and GENOA on the VAX. At this stage we will
have full availability of these programs and  the system to the outside cormunity,
thereby relieving SDMEX of the bulk of the current production use (only programs in
INTERLISP and experimental versions of new programs open for testing will be on
SDMEX at this stage) (applications programmer).

   At this time we will schedule a workshop, aggressively inform outside users
of the system's availability and encourage them to thoroughly test  the current
versions of the programs and the VAX system.  Based on our past experience with
workshops and outside users we expect, because of a responsive system and many newly
enthusiastic users (workshop participants),  to have an active community of outside
collaborators using our programs on the VAX.  We expect this situation to occur in
approximately late 1980 to early 1981 depending on the delivery time of the new
system.

    Following this initial period we will enter a phase of stepise development
of new programs on SUMEX,  experimental testing of new applications programs by
selected outside collaborators on the VAX and, finally,  community-wide announcement
of production versions of these programs on the VAX.  (The scientific staff will be
responsible for most of the new program development.  The applications programmer,
with the aid of the scientific staff and the systems programmer, will have important
responsibilties in the resource sharing of experimental and production versions.)

    Future DENDRAL program developments on SUMEX will be in languages for which
compilers exist,  or will soon exist, on VAX e.g.   PASCAL, FORTRAN, MAINSAIL and
BCPL. obtaining  these languages,  and other system support packages such as text
editors, will be the responsibility of the systems programmer. It should be noted
that these efforts plus maintenance  of the operating system and ancillary progrms
is a full-time, continuing job for a system of the complexity of the VAX.

    There are proposals  for an INTEFUJSP on VAX, which is probably a year or
more away from implementation.  Therefore, DENDRAL programs, such as REACT, MAX!%0
and so forth, which are in INTERLISP and which we do not propose to convert to an
exportable, algorithmic language,- will remain accessible solely through SUMEX until
an INTERLISP for VAX is available.

    We plan,  with the aid of the programmers  requested in the budget, to
implement on  the VAX a number of chemistry-related programs which will directly
support our  new research and. the work of our collaborators.  We are particularly
interested in molecular modelling programs such as MMI, CAMSEQ and PCILO,   as an
example.  We plan to modify or adapt CMNIGPAPH to simplify our program developments
for graphical input and output of structural information. We will mrk closely with
others possessing VAX systems in order to  share software and avoid duplication of
effort as far as possible (e.g., VAX systems are being obtained by the National
Resource for Computation  in Chemistry with whom we are  in contact, and Dr. David
Pensak at DuPont who.has been a collaborator wi+h us in the past).

    In a sense, we will be acting as brokers of some chemistry-related programs
for the new generation of computers  such as the VAX, for which little applications
software exists currently.  Our responsibilities as brokers nould extend only to
providing network access by qualified collaborators using our programs on the VAX,

73


and exporting applications programs to other VAX or VAX-compatible sites working on
bianedically-relevant problems.  we do not plan to compete with the quantum
chemistry program exchange (QCPE), which distributes primarily programs that perform
numerical computations. Our
computations.           programs' are primarily involved  with symbolic
      Also, wz specifically do not intend to embark on language development

for the VAX (e.g., INTERLISP), or to implement
related to our goals or               software which is not directly
            the goals of our collaborators. Although we may well

utilize such programs and languages, such efforts are best done by other groups. We
will monitor these efforts closely in order  to take advantage of new software.
Further into the grant period (two to three years)  we expect that VAX and similar
machines will be widely utilized within the biomedical connnunity and that,   as a
result, we will be able to exploit the software available from the work of others.

Resource Management

   To promote an orderly implementation of the dedicated computer system and to
ensure that the respective goals of SUMEX-AIM and DENDFUU are being met,
to establish an Advisory Committee.                             we propose

persons:               This Committee will consist of the following
Professor Edward Feigenbalpn (chairman) - Principal Investigator - SUMEX
Professor Carl Djerassi - Principal Investigator - DENDRAL
Thomas Pindfleisch - Resource Manager - SUMEX
Dennis EL 3nith - Co-Investigator - DENDRAL
Bruce G. Buchanan - Mjunct Professor, Computer Science - DENDRAL,MYCIN

   The persons making up the
for the conduct of both the SUMEX
knowledge and expertise, with
guidance on the computer science
-.

committee are those with primary responsibilities
and DENDW efforts.
Feigenbaum,       They represent complementary
      Rindfleisch and Buchanan providing
aspects of our research and on specific questions
                                                    .-

of the hardware and software interface with SUMEX and the dedicated machine, while
Djerassi and Smith bring to the committee a strong emphasis on specific chemical and
biochemical research problems of our group and those of our collaborators. Persons
named above have worked extremely closely in the past (Prof. Feigenbaun, for
example, was at one time PI on the DENDRAL grant); this committee will formalize an
already existing close working relationship and focus attention on the specific area
of resource sharing of our results.

   This connnittee will advise on: a) planning the purchase, installation and
development of the dedicated computer system; b) planning the hardware and software
interfaces providing access
priorities         to either the SUMEX or DENDBAL machines: c) assigning
     for development of applications software on the VAX; d) pranoting
resource sharing  activities such as lectures and mrkshops;
equitable access to the computer                     and e) ensuring
                  resources at Stanford by our collaborators.  This
con'rnittee will meet at tm week intervals during
and once per month thereafter.           the initial phases of the grant,

     C.5.b   Exportable Programs.
   To meet one of the goals of our present research, we have recently completed
and begun distribution of an exportable version  of CCNGEN (see attached Annual
Report). As we develop GENOA and the complete SASES system, we will ensure that they
retain at least the same degree  of exportability. The proposed version for  the VAX
computer will certainly improve the likelihood that outside scientists will be able
to run the program in their own laboratories.

74


Djerassi, Carl

    An intriguing philosophical question is why produce exportable versions for
different machines when the program can be run at one site, accessible nationwide by
computer  networks. There are some practical reasons  for this.   Industrial firms
require a high degree of secrecy for key structural problems and feel strongly that,
to retain control and guarantee secrecy, they n& a version operating on their own
computers. Same academic laboratories have free access to mini/midi computer systems
and cannot afford conununication and comercial network/computer costs. When these
practical reasons are  exhausted, there remains a significant group of persons who
simply want a version on their own machine under their own control

    There is, however, another practical reason and that is, despite our efforts
over the past few months, we  have been unable to provide even experimental network
access to CONGEN except the restricted access at SUMI%. There are two likely sites
to which CaJGEN can in principle be exported, both of which are easily accessible by
computer network. The first is the NIH/EPA Chemical Information System  (CIS), which
operates a PDP-10 system on  which CCNGEN in its current form can be run without
modification. For a year of more we have been negotiating, with persons responsible
for CIS, for funds to support the conversion required to integrate CONGEN into CIS.
Such funding  has, we  understand,   received favorable Division   of Research
Resources/NIH review. However, we have  recently learned that such funding will not
occur now, and the future seems to be in question.  It is unlikely that this
situation will be resolved before the current proposal is submitted.

    Another possible site is the  Control Data (CDC) 6600 system, accessible at
the Lawrence Radiation Laboratory  (LDL) in Berkeley, through the National Resource
for Computation  in Chemistry (NPCC). We have arranged for some trials of the
interactive E?CPL system existing there  to explore how CONGEN might operate in that
environment. We do not expect these experiments to be fruitful because CONGEN relies
heavily  on intermediate files (to and from which structural information is
comnunlcated many hundreds of times during a problem); access to the file system is
one of the primary bottlenecks of the LBL CDC system , access times being up to many
seconds during heavy use of.the system.  However, the imminent purchase of a VAX
system by the NRCC would change the situation dramatically. This factor, plus the
uncertainties of the CIS lend considerable emphasis to our desires  to implement
readily-accessible versions of our programs on our own VAX system, with distribution
to a wider community of persons handled eventually by the NRCC or the CIS.

c.5.c   Workshops.

    Our successful experience with workshops on the use of the new CCNGEN
program prompts us to propose a continuing series of such workshops designed to
serve purposes  similar to the  previous effort. We want to   introduce new
collaborators to applications programs as  they are developed,  and to promote new
applications  and wider use of the programs. We want both new and current
collaborators to evaluatqnew programs so that bugs, and clumsy or  unclear aspects
of the interaction can be resolved before development of the final version for
application.  Most importantly, these workshops will provide a mechanisn for keeping
our group up-to-date on requirements of the community for computer assistance in
their efforts and provide a  far more diverse set of structural problems than we
would encounter in work here at Stanford. We have budgeted funds for one workshop
w ye=, to be .organized by our personnel and held here at Stanford University (or
possibly elsewhere, the netmrk providing access to the system).

75


Djerassi, Carl

C.5.d   Graphics Interface.
We have invested a great deal of time and effort in the interface to CCNGEN

(and GEXCA) with the lowest cormnon denominator terminal, a teletype!, in mind. This
proved to be a wise decision because many collaborators have only teletypes, or
teletype-like hard copy terminals with which to access our programs. However, many
structure drawings suffer in teletype form.  Some can simply not be laid out within
the confines of the teletype grid. In addition, the interface lacks characteristics
enjoyed by most chemists,
information.           namely the capability actually to draw structural
       Elegant graphics interfaces have been produced for other systems,

including Corey's [89] and Wipke's [90] organic synthesis programs, and the NIB
Prophet system.   In fact,  OCCNGEN offers capabilities for structure output to a
variety of graphics terminals, taking
things are                 advantage of NIH's Cknnigraph package. '!%o
      clear from this experience.  Few potential  users can afford currently
available terminals, such as the (XC-40 series,  even though graphical  input and
output would add considerably to the perceived utility of our programs. It would be
out of the question  to produce a useful graphics package for a wide variety of
terminals, most of which will soon be obsolete.

     Yet,  we can hardly emphasize  three-dimensional aspects   of molecular
structure and   not  provide  capabilities   for  visualizing the  resulting
representations. At Stanford we can utilize the a-40 purchased under the current
grant for some of our work. We do not, however,
effort into                      wish to put a great deal of time and
        interfaces for that terminal.  It is nearly obsolete and compatible,
newer versions are simply too expensive for mot research groups. We have requested
funds to purchase one
proposed grant.    new graphics terminal in each of the first two years of the
          The terminal market is changing
storage displays,                     rapidly with plasma displays,
           and raster displays,  potential alternatives to the refresh
displays such as the the m-40.  We will seek to purchase a display which is likely
to become widely available at relatively low cost and invest our programming in that
display.

76


Djerassi, Carl

D    SIGNIFICANCE

    There are several aspects of our proposed research which we feel are novel
and especially significant  including not only specific computer programs but also
the methods by which they are shared.

    Cne significant aspect of the proposed mrk, and a primary novelty, lies in
the comprehensive c stereochemical aspects
        omputer treatment of both topological and                  c
ofmolecular structures In methods to assist scientists Glucldation of important
Eomolecular structures. By developing  these method to include stereochemistry, we
will have extended our approaches to computer-assisted structure elucidation to
cover the key missing link of determining the actual spatial relationships of atoms
in a structure rather than their mere connectivity.  Our proposed methods for data
interpretation and prediction applied to data collected on unknown structures offer
several new treatments of toIplogical representations of structure:  the proposed
stereochemical efforts, however, are certainly novel because no other similar system
for structure elucidation utilizes stereochemistry in comprehensive form. The
efforts are also necessary given the strong dependence of spectral properties on
molecular configuration and conformation.

    The proposed generator of conformers  will be a novel solution to a long-
standing problem in structural chemistry.  Successful completion of a general
constrained generator  of conformation will be an important result in itself.
However, its applications both to candidates for an unknown structure and to studies
of conformations of (topologically) known structures will be a more important and
novel result. In addition to the proposed collaborative efforts, we  foresee several
applications  to problems relating  structure to observed properties, including
structure/biological activity relationships.  We have not proposed such studies
ourselves, but will collaborate with others who can make use of our  results, under
the resource sharing aspects of our proposal. The investment of resources into
developing this program will be repaid many times over by increasing the versatility
of C@JGEN (as a tool for structure elucidation)  and its scope of potential
biomedical applications  (by providing a link to existing methods based on atomic
coordinates),

    The GENOA program developnent, culminating in the SASES system, represents a
general,  and novel approach,  to construction of structures with overlapping
substructures,  eventually constrained not  only by topological but  also by
stereochemical constraints. These programs will be novel in:

  a their modularity, so  that they can be  used alone or in concert with
related programs,  of our group or of our collaborators,  via shared files of

data,

   b

their comprehensive treatment of stereochemistry,

    C  the close invovlement of the scientist in the problem solving processes
of the programs.

'Ihe last point perhaps deserves some more emphasis.  me most interesting novel
result of the proposed mrk lies in  the use to which a well-designed system can be
put in the hands of a well-trained chemist. The synergism of man and machine can be
a powerful problem solving combination. The structure manipulations embodied in the
SASES system represent a  "dry" laboratory of functions for manipulating structures
and associated data. Many aspects of structural chemistry besides the central task
Of structure elucidation can be studied utilizing comIpnent parts of SASES.  In this
way, complex questions can be  posed and answered on the computer, before execution
of actual laboratory experiments.

77


Djerassi, Carl

    We feel that these features of our proposed research offer scientists
capabilities for solving structures more  accurately (in the sense of ensuring that
all plausible alternatives have been considered) and in less time. In an era where
detection and identification of trace-level organic compounds in environmental and
biological milieus is  of critical importance, new capabilities such as we propose
can be of tremendous value.

    We feel that the interest shown by structural chemists in our work,
especially the CCNGEN program,  is already significant.
workshops, to persons requesting access              We can point to the
                      to the programs at Stanford and to persons

interested in the exportable version of CCNGEN (see Section  F, Collaborative
Arrangements, and the Annual Report,' 'Appendix I). However, we have been unable to
meet the needs of many of the persons requesting access for the simple reason that
methods of access have been limited.  Some structural chemists and biochemists,
because of personal preference or industrial secrecy,
reasons,  desire programs                   to name only tm pzssible

Limitations          in their own laboratories on their own computers.
      in laboratory computers and CaJGEN's currently limited exportability

make export non-trivial.  Those who access programs
dozens of other persons for                at STJMEX must compete with
                 access to the machine and therefore obtain poor
interactive service during normal working hours.  me significant aspect of our

propsal is to promote
export becomes simpler
(and less expensive)
computer  environment
interaction for those
institutions.

resource sharing in such a way (the dedicated computer) that
by utilizing exportable languages and more commonly available
computers,  while at the same time providing a networked
which greatly facilitates  remote access and provides good
who do not have access to suitable computers in their own

78


Djerassi, Ca
-

rl

E    FACILITIES AVAILABLE.

    This research will be carried out in our well-equipped laboratories in the
Department of Chemistry and on the existing SDMEX-AIM computer resource at Stanford,
supplemented by the dedicated machine requested in this proposal. We are able to
support the proposed mrk within existing space allocations.  Our primary equipment
needs, besides the computer, are terminals.   We have three character-oriented CRT
display terminals, a.Tektronix 4012 storage terminal and a GT-40 graphics terminal,
plus access to various hard copy terminals when required. The additional terminals
requested in the first tm years of our grant will provide the required support for
visualization of three-dimensional representations of molecular structure, currently
~ssible in very limited ways with the existing  Tektronix 4012 and GI'-40 display
terminals.

    The SUMEX computer facilities, which will provide the support for the
majority of our development efforts,  are shown in Figure 11.   This system has a
complete complement of peripheral devices to suprt our needs and to interface with
the dedicated system we propose.  The system also provides extensive software
support which is more than adequate for our proposed program developnents, including
text editors, a variety of languages, debugging facilities and an excellent staff to
assist us  in complicated problems  related to the SUMEX system or one of its
supported pieces of software.

    Our personnel will become involved, as they have in the past, with
structural problems related to  research in my group or in the groups of our
collaborators.  Many of these problems will require chemical and spectroscopic data
to be obtained at Stanford or elsewhere.  Any costs associated with collection of
these data will be borne by the individual research groups.   However, it is
important to note that Stanford has well-equipped chemical and spectroscopic
laboratories  in the Chemistry Department which will enable collection of high
quality data in support of these structural studies.

79


AMPEX Mewr y

DEC Central

`I'otdl 156M Words

Figure 11.  SUMEX hardware

1          1

-I

DEC Drum
Controller
RES-10

Dig Dev     018 Drv
Fix Disk     Fix Disk
A-7312118     A-7312D8
*

-   _ . -.. . . rds
                   -/

SUMEX-AIEI COM-PUTER CONFICIJRATION (5/79)


Djerassi, Carl

      F    COILABORATIVE ARRANGENENTS.

    The proposed  improvements to  our structure elucidation programs  will, in
addition, create the possibility of new biomedical applications which make use of
existing methods and programs.  We propose to promote  these new applications via
collaborative arrangements.

Collaboration with Prof. David Cowburn.
               ---
A very likely application for CONGEN enhanced with a conformation generator

would be to the field of conformational analysis.  This is the problem of
determining the   conformation of a structure   with known   constitution and
configuration and is  a general problem in describing the structures of molecules.
The description of the conformation(s) of molecules of biological origin or of those
possessing biological activity is of considerable importance in establishing more
clearly the relationship of structure to function in the actions of drugs,hormones,
and neurotransmitters on their natural receptors,  the mechanisn of enzyme action,
and the rational design of new drugs. We propose to develop this application by
collaboration with Professor David Cowburn and his coworkers at the Rockefeller
University in New York.  Professor Cowburn is actively engaged in determining
peptide conformations  using principally nuclear magnetic   resonance  studies of
specifically designed and synthesized isotopic isomers of peptide hormones. These
studies use the stable isotopes  - deuterim, carbon-13, and nitrogen-15 [91]. Dr.
Cowburn now has an account at SUMFX and muld use the program remotely, at least at
first.  It is hoped that an effective collaboration  can be developed in which Dr.
Cowburn   will  investigate techniques   for  effectively  rejecting chemically
unreasonable conformations as they are generated.  Those strategies that may be
generally useful will then be adapted for CONGEN and incorlprated. These techniques
will be related either to general considerations(e.g.   insufficient degrees of
freedom for cyclization of a particular ring system, from a partially generated
conformational state)   or to  the specific  molecules being   examined (e.g.
restrictions stemming from experimental data such as nmr vicinal coupling constants
1.  Some research using small programs outside CONGEN would be expected to be useful
in investigating this area,  and some possible techniques are outlined in Dr.
Cowburn's letter (p. - ).  CCNGEN equipped with a conformation generator,
would likely be useful to Prof.  Cowburn's research in at least three ways:

  1)  The program would be able to generate all the possible conformations for
a given problem with input  constraints based on NMR couplings.   Such a
generation is a difficult task for,e.g, compounds containing large rings. The
value of CCNG!ZN would be to provide  assurance of exhaustion and to explicitly
construct all the possibilities.

  2) The program muld be able to generate all possible isotopic isomers for
a given constitution and configuration.  if a pruning technique was available,
then the generated list would be extremely useful to Dr. Cowburn in considering
the strategies of synthesis and nmr experimentation. The   avoidance of
particularly costly or time consming steps is of considerable importance in
that experimental work.

  3) In conjunction with the spectral  interpretation and planning modules
proposed, CCNGENmaybe able  to generate strategies for patterns of enrichment
or for nmr experiments which are optimum for conformational determination.   Some
additional programming would probably be necessary to accomplish this.

81


Djerassi, Carl

Collaboration with Prof. Gilda Loew.
               ---

   Since our proposed conformation generator will output structures with
internal (torsional angle) coordinates, it is possible to obtain further information
about these structures by doing quanUn  mechanical energy calculations. By
developing a link to these methods, the usefulness of CCNGEN should be considerably
increased.  Since a great deal of mrk has been done by others on such methods it is
not necessary for our group to develop programs of this kind.  Instead we propose to
develop this link by collaborating with Prof. Gilda Loew and her group in the Dept.
of Genetics at Stanford Medical School.  Professor Koew's mrk has involved the use
of semi-empirical quantum mechanical energy calculations to derive structure-
activity for a variety of drug types [92].  The first step in such a collaboration
would be to construct the interface necessary to link the CCNGEN output structures
with the input for the PCILC (Perturbation Configuration Interaction using I.localized
Orbitals) program.  This program requires as input, structures with internal
coordinates.  This will be the form of the output from the proposed conformation
generator with an assmption of bond lengths and angles. mce this link has been
made then we see at least t:FFD areas where CONGEN might be helpful to Professor
Loew's ongoing research.

  1) It will be possible to generate systematically variants of a structure
with respect to its constitution, configuration, and conformation.   Each such
structure muld then be given to PCILC for an energy calculation, the results 6f
which are used to help explain potency variations [92]. The advantage of using
CONGEN in this way  is that an exhaustive generation can be guaranteed which
assures no possibilities are overlooked.

  2)  Professor I;oew has been considering the conformational variations caused
by the intercalation  of ethidium into nucleic  acids [93].   The observed
stability of such intercalated  structures has been related to conformational
changes in parts of the DNA structure, in particular, the sugar moieties. The
application of CONGEN to such a  study would again be a systematic variation of
possibilities with particular emphasis on the more difficult cyclic structures.

GUEST Access.

    We currently provide  access to new users of our programs via  the GUEST
account at SUMEX.  In addition,  we have provided GUEST access to several of our
recent workshop participants.  A list of these participants appears in our annual
report (Appendix I).  We-receive many inquiries about our programs and access to
them, far in excess of the current capacity at SUMEX. A list of persons to whom

such access has been granted in the past year appears in our annual report
?? o  More recent inquiries have been received from (and GUEST access given
     Prof. Glenn D. Prestwich
    Dept. of Chemistry
   State University of New York at Stony Brook
    Stony Brook, New York 11794

(Wndk
to) :

Dr. Andrew Stuper
RCG Group
IUnn and Haas
Norristown and McKean F&ads
Springhouse, Pa. 19477

Prof. E. F. Domino
Department of Pharmacology
M6322 Medical Sciences Building
Ann Arbor, Michigan 48109    82


Djerassi, Carl

Prof. John D. mberts
Div. of Chem. and Chem. Engr.
Calif. Inst. of Tech.
Pasadena, Calif. 91125

83


THE ROCKEFELLER UNIVERSITY

1250 YORK AVENUE NEW YORK, NEW YORK 13:21

10 May 1979

Dr. J. Nourse
Department of Chemistry
Stanford University
Stanford, California 94305

Dear Dr. Nourse:

GENERATION OF CONFORMATIONS BY CONGEE

In the past, you and the other members of the Dendral group at Stanford have
produced a unique tool for assisting chemists in the interpretation of data,
principally in the area of organic structure determination.   This tool, the
program CONGEN, has recently been augmented by your inclusion of configuration
in the descriptive quantities that the program can accept and process.

The possible extension of CONGEN to include conformational values is then the
next logical step in the development of this system.   In addition to the
potential uses of conformer generations in the area of organic structure
determination - e.g. inclusion of structural constraints based on experimental
observations from NMR or Mass Spectrometric studies, such a program would be of
considerable use as a research tool in the applications of conformational analysis
in a number of areas.  The program would be very useful in exhaustively and
precisely defining conformational states in small molecules.   In larger molecules
(molecular weight >300) the description of standard states (Dunitz 72) and the
conformational features associated with certain kinds of rings or regularly
repeating substructure are areas of active and significant research endeavor
(e.g. [Anet 781, [Dale 751, [Cremer 751).   For polymers, particularly biopolymers,
the assumption that a somewhat irregular structure (e.g. a protein) can be
described by the cataloguing of standard conformational states associated with
the substructures has been widely made (IDesantis 651, [Zimmerman 771).   This
assumption has been tested to some degree in a few highly - resolved crystal
structures.  It has not been tested widely with respect to structuresin solution,
or to those dynamic structures interconverting relatively rapidly.   Such struc-
tures, and their analysis, are of very considerable importance in understanding
more thoroughly the structure/function relationships of hormones, neurotransmitters
and drugs.

It is probable that an enhanced.CONGEN could be a very effective tool in these
developing fields, for several purposes.   For a set of standard states, the program
will be able to completely generate all the possible combinations of the conformers
of the substructures.   This is of considerable importance when a number of rather
different substructures are considered in any one molecule, where the permutational
task is not straightforward.   The powerful features of CONGEN in creating positive
and negative conditions for an allowed structure during its generation will provide
an exceptionally sound base for testing selections of standard conformational states,
for generating a restricted list of possible conformers, and for investigating

84


-2-

Dr. 3. Nourse                        10 May 1979

conformational classes in sets of related molecules.

The enhanced CONGEN would be useful to our research in all the above ways.
I hope that during the period of introducing these enhancements, it will be
possible for us to cooperate and collaborate in testing various algorithms
that might be incorporated into the final product.   These algorithms include
various standard modules concerning generation of Cartesian coordinates, forced
cyclization of coordinates of end groups in rings systems, empirical energy
calculations, etc., and modules concerning less well known problems.   In this
latter area, we are particularly interested in developing techniques for effec-
tively reducing the number of produced conformers during a constrained genera-
tion.  Methods for doing this may be of a quite general nature.   For example,
a technique for selection based on the ability of a growning structure to
correctly refold to permit cyclization has been described [Dirkx 791. Exact
descriptions for certain regular rings are also possible [Cremer 751.   These
pruning techniques may, alternatively, be quite specific to the structure under
consideration, e.g. incorporation of known conformational features, or restrictions
based on maxima or minima for certain interatomic distances, or restrictions of
torsion angles based on predicted effects or specific neighboring groups.

We look forward to being able to pursue this area of research with you, while
specifically applying these techniques to the studies of the dynamic conforma-
tions of peptide hormones currently under investigation here.   The people
associated with this research here include Professors William C. Agosta, and

David H. Live, Mr. William Wittbold, and myself.   Our research
is supported by NIH AM-20357.
                          I

                                 Sincerely,

in this area

DC:mmh

85

David Cowbum
Associate Professor


[Anet 781 Anet F. A. L.; Rawdah T. N.  "The conformational energy surface

      of trans,trans,trans-1,5,9-cyclodecatriene. n JACS, 1978, 100, 5003-5007.

[Cremer 751 Cremer D.; Pople J. A. JACS 1975, 97, 1358.

[Dale 751 Dale J.  "Multistep conformational interconversion mechanisms." Topics

      in stereochemistry, 1975, 9, 199-270.

[DeSantis 651 DeSantis P.: Giglio E.; Liquori A. M.; Ripamonti A. Nature,

1965, 206, 456-461.

[Dirkx 791 Dirkx J.; Rnappenburg El.; Dufour P. "A .progrsm for generation of
     possible conformations of cyclic molecules." Comp. Prog. Biomed.

       1979, 9, 63-68.

[Dunitz 721 Dunitz J. D.; Waser J.  "Geometric constraints in six and eight

       membered rings."  JACS 1972, 94, 5645-5650.

[Zimmerman 791 Zimmerman S. S.; Pottle M. S.; Nemethy G.; Scheraga H. A.

        "Conformational analysis of the 20 naturally occurring amino
       acid residues using ECEPP"  Macromolecules 1977, 10, l-9.

86


Djerassi, Carl

G   PRINCIPAL INVESTIGA~R ASSURANCE

    The undersigned agrees to
technical conduct. of the research  accept responsibility for  the scientific and
                 project and for provision of required progress
reports if a grant is awarded as the result of this application.
                                     I '
                                         :
                      i I                       i
                                      _!
                                     - '_
            Date    Principal Inv&gator

87


Djerassi, Carl

H    REFERENCES.

1) J. merberg,

"DENDRAL-64-A System for Computer Construction,
Enumeration and Notation of Organic Molecules
as Three Structures and Cyclic Graphs,"
(technical reports to NASA)
(la) Part I. Notational algorithm for tree
  structures, 1964, CR.57029
(lb) Part II. Tbpology of cyclic graphs, 1965, CR.68898
(lc) Part III. Complete chemical graphs; embedding
  rings in trees, 1969,

2) J. Lederberg, G.L. Sutherland, B.G. Buchanan, E.A. Feigenbaum,
    A.V. Robertson, A.M. Duffield, and C. Djerassi,
    J.kn.Chem.Soc.,  91, 2973, (1969).
                           -
3) R.E. Carhart, D.H. Smith, H. Brown and C. Djerassi,
    J.Am.Chem.Soc., 97, 5755, (1975).
                          -

4) A.M. Duffield, A.V. Robertson, C. Djerassi, B.G. Buchanan,
    G.L. Sutherland, E.A. Feigenbam, and J. Lederberg,
     J.Am.Chem.Soc., 91, 2977, (1969).
5) A. Buchs, A.B. Delfino, A.M. Duffield, C. Djerassi, B.G. Buchanan,
    E.A. Feigenbaum and J. Lederberg,
   Helv.Chim.Acta, 53, 1394, (1970).

6) Y.M. Sheikh, A. Buchs, A.B. Delfino, G. Schroll, A.M. Duffield,
   C. Djerassi, B.G. Buchanan, G.L. Sutherland, E.A. Feigenbaum,
    and J. Lederberg,

org.Mass &, 4, 493, (1970).

7) (a) L.M. Masinter, N.S. Sridharan, J. Lederberg and D.H. Smith.

J.Amer.Chem.Soc., 9&, 7702, (1974).
(b) L.M. Masinter, N.S. Sridharan, R.E. Carhart and D.H. .Smith,
ibid, 96, 7714, (1974).

8) H. Brown, L. Hjelmeland, and L. Masinter,
   Discrete Mathematics, 1, 1, (1974).

9) H. Brown and L. Masinter,
   Discrete Mathematics, S, 227, (1974).

10) H. Brown,

   SIAM Journal of Applied LMath, 32, 534, (1977).
11) D.H. Snith, B.G. Buchanan, R.S. Engelmore, A.M. Duffield, A. Yeo,
    E.A. Feigenbaum, J. Lederberg, and C. Djerassi,
    J.Am.Chem.sOc., 94, 5962, (1972).
                          -
12) D.H. Smith, B.G. Buchanan, W.C. White, E.A. Feigenbaum,
    C.Djerassi , and J. Lederberg,
    Tetrahedron, 29, 3117, (1973).
                       -

88


Djerassi, Carl

13) B.G. Buchanan, D.H. Smith, W.C. White, R.J. Gritter,
    E.A. Feigenbam, J. Lederberg, and Carl Djerassi,
     J.Am.Chem.Soc., 98, 6168, (1976).
                          -

14) R.E. Carhart and D.H. Smith,
   Computers in Chemistry, I, 79, (1976).
                   -

15) T.M. Mitchell and G.M. Schwenzer
   Organic Magnetic Resonance, 11, 378, (1978).
                                       -

16) G.M. Schwenzer and T.M. Mitchell,
    in D. Smith, (ed.), Computer Assisted Structure Elucidation,
   ACS Symposium Series, 2,
    Washington, D.C., 1977, ~58.

17) (a) C.J. Cheer, D.H. Smith, and C. Djerassi, B. Tursch,
     J.C. Braekman, and D, Daloze,
   Tetrahedron, 32, 1807, (1976).
   (b) D.H. Smith,
     Anal.Chem.,
   (c) D.H. .Smith, 47, 1176, (1975).
   J.Chem.Inf.Comp.Sci., 15, 203, (1975).
  (d) D.H. smith, J.P.. KonoFlski and C. Djerassi,
    Org.Mass Spectrom., 11, 86, (1976).
                               -

18) R.E. Carhart, S,M. Johnson, D.H. Smith, B,G. Buchanan, R.G Dromey,
    J. Lederberg,
    in P. Lykos (ed.),
   Computer Networking and Chemistry,
   American Chemistry SZXety Symposium Series, 19,
    Washington, D.C., 1975, p192.

19) T.H. Varkony, R.E. Carhart and D.H. Smith,
    in W.T. Wipke and T. Howe, (Eds) ,
    American Chemical Society Symposium Series, 66,
    Washington, D.C., 1977, ~188.

20) (a) T.H. Varkony, D.H. Smith, and C. Djerassi,
    Tetrahedron, 34, 841, (1978).
  (b) R.M.K.Carlsoc S; Popov, I. Massey, C Delseth, E. Ayanoglu,
     T.H. Varkony, and C.Djerassi,
    Bioorg.Chem., 1, 453, (1978).

21) T.H. Varkony, R.E. Carhart, D.H. Smith, C. Djerassi,
   J.Chem.Inf.Comp.Sci.,.~, 168, (1978).
22) C. Djerassi, D.H. Smith and T.H. Varkony,
    Naturwissenschaften, 66, 9 (1979).
23) N.A.B. Gray, D.H. Smith, FH. Varkony, R.E. Carhart,
     and B.G. Buchanan.
    "Use of a Computer to Identify Unknown Compounds.
     The Automation of Scientific Inference,"
    Chapter 7 in "Biomedical Applications of Mass Spectrometry,"
    -G.R. Waller (Ed.),
    in press.

89


Djerassi, Carl

24) James G. Nourse,
    J.Am.Chem.Soc., Ml, 1210 (1979)
25) James G. Nourse, Raymond E. Carhart, Dennis H. Smith, and
    Carl Djerassi,
    J.Am.Chem.Soc., 101, 1216 (1979).

26) (a) M. Bachiri and G. Mouvier,
   Org.Mass Spectrom., 11, 1271, (1976).
  (b) G-M. Pesyna and F.WFMcLafferty,
Determination of Organic Structures by Physical Methods",Vol 6,
    F.C. Nachod, J.J. Zuchermann, and E.W. Randall (Fds),
    Academic Press, New York, N.Y., 1976, p91.

27) F.W. Mellon,
    in "Mass Spectrometry",Vol 4,
    R.A.W. Johnstone, Sr. Reporter,
    The Chemical Society,
    Burlington House, 1977, p89.

28) (a) K.S. Kwk, R. Venkataraghavan, and F.W. McLafferty,
    J.Am.Chem.Soc., 95, 4185 (1973).
  (b) H.E. Dayringer,G.M. Pesyna, R. Venkataraghavan,
    and F.W. McLafferty.
   Org.Mass Spectrom., 2, 529, (1976).

29) S.R. Heller, G.W.A. Milne and R.J. Feldmann,
    Science, 195, 253 (1977).                    .
30) R.C. Fox,
    AnalXhem., 48, 717 (1976).
                      -

31) D.L. Dalrymple, C.L. Wilkins, G.W.A. Milne, and S.R. Heller,
    Org.Magn.Fes., 11, 535, (1978).
                         -

32) (a) P.R. Naegli and J.T. Clerc,
    Anal.chem., 46, 739a, (1974).
   (b) J. Zupan, M. Penca, D. Hadzl and J. Marcel,
    Anal.chem., 49, 2141, (1977).
                     -

33) D.H. Snith, M. Achenbach, W.J. Yeager, P.J. Anderson, W.L. Fitch,
     and T.C. Rindfleisch.
    Anal.chem., 49, 1623, (1977).
                      -

34) (a) M. Senn, R. Venkataraghavan, and F.W. McLafferty,
    J.Am.Chem.Soc., 88, 5593, (1966).

   (b) K.Biemann, C.Cone, B.R. Webster and G,P. Arsenault,
    J.Am.Chem.Soc,, 88, 5598, (1966).

35) A. Mandelbaum, P.V. FeMessey and K.Biemann,
  Proc.Ann,Conf.Mass Spectrom and Allied Topics, 15th, 111, (1967).

36) A. Kundered, R.B. Spencer, and W.L. Budde,
    Anal.chem., <43>, 1086, (1971).

90


Djerassi, Carl

37) H.B. Woodruff and M.E. Munk.

Anal.Chim. Acta, 95, 13 (1977).
            --

38) H.L. Surprennant and C.N. Reilley,

in "Computer Assisted Structure Elucidation",
D.H. Smith (Ed.),                        .*
ACS Symposilpn Series, 54,
American Chemical SociXy (1977).

39) C.A. Shelley and M.E. Munk,
     Anal.chem., 50, 1522, (1978).
                      -

40) C.A. Shelley, H.B. Woodruff., C.R. Snelling, and M.E. Munk.
    in "Computer Assisted Structure Elucidation",
    D.H. Smith (Ed.),

ACS Symposium Series, 54,
American Chemical SociXy (1977).

41) S. Sasaki, Y. Kudo, S. Ochiai and H. Abe,
    Mikrochim.Acta, 726 (1971).

42) S. Sasaki, H. Abe, Y. Hirota, Y. Ishida, Y. Kudo, Si Ochiai,
    K. Saito, and T. Yamasaki,
    J.Chem.Inf.Comp.Sci.,l8, 211, (1978).
                                -

43) (a) B.R. Kowalski, P.C. Jurs, T.L. Isenhour, and C.N. Reilley,
     Anal .chem., 41, 1945, (1969).
   (b) H.B. Woodrzf, G.L. Ritter, S.R. Lowry, and T.L. Isenhour,
    Appl.Spectrosc., 30, 213, (1976).
                           -

44) C.L.Wilkins, R.C. Williams, T.R. Brunner and P.J. McCombie,
     J.Am.Chem.Soc., 96, 4182, (1974).

45) P.C. Jurs and T.L. Isenhour,
    "Chemical Applications of Pattern Recognition",
    Wiley-Inter-science,
     New York, N.Y., (1975).

46) J. Schechter and P.C. Jurs,
    Appl.Spectrosc., 2, 30 (1973).

47) W.E. Brugger, A.J. Stuper, and P.C. Jurs,
    J.Chem.Inf.Comp.Sci., 16, 105 (1976).
                                 -

48) (a) M.E. Munk, C.S. Sodano,, R.L. McLean, and T.H. Haskell,
     J.Am.Chem.Soc., !30, 1087, (1968).
   (b) C.A. Shelley, T.R. Hays, M.E. Munk and R.V. FUrnan,
    Anal.Chim. Acta, 103, 121 (1978).
                    --

49) J.E. Dubois,

in "Computer Representation and Manipulation of
Chemical Information",
W.T. Wipke, S.R. Heller, R.J. Feldmann and E. Hyde, (Eds.),
Wiley-Interscience,

New York, N.Y., 1974, p239.

91


50) L.A. Gfikmv, M.E. Elyashberg and V.V. Serov,
   Anal.Chi.m.Acta, 95, 97, (1977).

51) R. P. Smith,
   J. Chem. Phys., 42, li62 (1965).
        --

52) P. J. Florv, U. W. Suter, and M. Mutter,
   J. Am.-ChemSoc., 98, 5733, (1976).
        --
    and earXG-c?GZ references.

53) L.

54) J.

55) M.

56) J.

57) M,

58) D.

59) J.

60) D.

61) C.

62) J.

63) A.

64) C.

65) F.

E. Scales and J. A. Semlyen,
Polymer, 17, 601, (1976).

B. Hendrickson,
J.Am.Chem.Soc., 86, 4854, (1964)w

Dygert, N. Go, H. A. Scheraga,
Macromolecules, i, 750, (1975).

Dale,

Acta. Chem. Scand., 27, 1115, (1973).
--          -

Saunders,
Tetrahedron, 23, 2105, (1967).
               -

F. Bocian, H. M. Pickett, T. C. Ebunds, H. L. Strauss,
J.Am.Chem.Soc., 97, 687, (1975).

E. Kilpatrick, K. S. Pitzer, R. Spitzer,
J.Am.Chem.Soc., 69, 2483, (1947).
                  -

Crmer and J. A. Pople,
J.Am.Chem.Soc., 97, 1354, (1975).

Altona and M. Sundaralingam,
J.Am.ChemSoc., 95, 2333, (1975).

Dirkx, M. Knappenburg, P. DuFour,
Camp. Prog. Bicmed., 2, 63, (1979).

Murakami and Y. Akahori,
Chem.Pharm. Bull
      ., 2, 2870, (1977).

D. Barry, J..A. Glasel, R. J. P. Williams, A. V. Xavier,
J. Mol. Biol
-- ., 84, 471, (1974).

A. Gor in and G. R. brshall,
Proc.Nat. Acad. Sci., 74, 5179, (1977).

66) R.E. Carhart, T.H. Varkony and D.H. Smith,
    in "Computer Assist& Structure Elucidation",
    D.H. Smith (Ed),
    American Chemical Society Sympsium Series, 54,
    Washington, D.C., 1977, ~126.

92


Djerassi, Carl

67) Dennis H. Smith and Raymond E. Carhart,

68) W.

Bremser, M. Klier and E. Meyer,
        , 1, 97, (1975) .

69) W. Bremser,
    Fesenius Z.Anal.Chem., 286, 1, (1977).

70) W.

Bremser,
Anal.Chim. Acta, 103, 355, (1978).
             --

in "High Performance Mass Spectrom&ry: Chemi&al Applications",
M.L. Gross, (Ed.),
American Chemical Society Symposium Series, 70,
Washington, D.C., 1978, ~325.

71) B.A. Jezl and D.L. Dalrymple,
     Anal.Chem., 47, 203, (1975).
                      -

72) J.T.Clerc and H.Sonunerauer,
    Anal.Chim. Acta, 95, 33, (1977).
                    --

73) D.H.Smith and P.C.Jurs,
     J.Am.Chem.Soc., 100, 3316, (1978).

74) J. Zupan, S.R. Heller, G.W.A. Milne and J.A. Miller,
    Anal.Chim. Acta, 103, 141, (1978).
                     --

75) D.H. Sleeman,

Int.J.Man Machine Studies, 1, 183, (1975).

76) G. Beech, R.T. Jones and K. Miller,
     AEIl.CheITl., 46, 714, (1974).

77) W. Moffitt, R. B. Woodward, A. Moscowitz, W. Klyne,
    and C. D-jerassi.
     J.Am.Chem.Soc,, 83, 4013, (1961).

78) J.H. Brewster,

Tetrahedron, 30-, 1807, 1974.

79) D.N. Kirk and W. Klyne,

80) L.

81) R.

82) W.

83) A.

J.Chem.Soc. Perkin.2, 1076, (1974).

Seamans, A. Xoscowitz, G. Barth, E. Bunnenberg, C. Djerassi,
J.Am.Chem.soC,, 94-, 6464, (1972).

E. Linder, R. Morrill, J. S. Dixon, G. Barth,
E. Bunnenberg, C. D-jerassi, L. Seamans, and A. Moscowitz,
J.Am.Chem.Soc., 2, 727, (1977).

D. Hounshell, D. A. Dxugherty, and K. Mislow,
J.Am.Ch~.Soc., 100, 3149, (1978).

Kerber,
"Representations of Permutation Groups", Vol II,
Springer-Verlag, N. Y., 1975.

93


Djerassi, Carl
:i 0

84) R.S. Cahn, C. Ingold, and v. Prelog,
    Agnew.Chem.Int.Ed.Eng, 57, 385 (1966).
                                  -

85) F. A. L. Anet,
    Fort. Ch. Forsch., 45, 169, (1974).
        --           -

86) J. H. Dawson, J. R. Trudell, R. E. Linder, G. Barth,
    E. Bunnenberg , and C. Djerassi,
   Biochemistry, 17, 33, (1978).

87) W. C. Johnson,
   Ann. Rev. Phys. Chem., 2, 93, (1978).
        --

-88) C. Marcott, H. A. Havel, J. Overend, A. Moscowitz,
     J.ILn.Chem.soC., 100, 7088, (1978).

89) E.J. Corey and W.T. Wipke,
    Science, 166,178 (1969).

90) W.T. Wipke, H. Braun, G. SMith, F. Choplin, and W. Sielser,

91) (4

in "Computer Assisted Organic Synthesis",
W.T. Wipke and J. Howe, Eds.,
American Chemical Society Symposium Series, 61,
Washington D.C., 1977, p97,

D. Cowburn, A.J. Fischman, D.H. Live, W.C. Mosta,
H.R. Wvssbrod,
Proc.Fifth Amer.
Ed. M. Go&ari%?%eBir, 322, (1977).

(b) A. J. Fischman, M. Rieman, D. A. Cowburn,
Febs. Letts., 94, 236, (1978).
(c) D. H. Live, a 5 authors ,
J. Am. Chem. Sot., 101, 474, (1979).
  a--

92) (a) G. I;oew and J.R. Jester,
   J. Med. Chem., lf& 1051, (1975).
  (brG=ew, D.S. Berkowitz, and R.C. Newth,
     J. Med. Chem., 19, 863, (1976).
   (c)G.xwandR.%hakian,

      J, Med. Chem .,
         --    28, 103, (1977).

93) G.R. Pack and G. Uew,
   Biochim. et Biophys. Acta, 519, 163, (1978).
                  -           --

94


APPENDIX I

DENDRAL 1978-1979 ANNUAL REPORT

95


Table of Contents

Section

     Subsection

1.

2.

3.     SIGNIFICANCE

Cbjectives               . . .

1.1   CWerall Cbjectives . .

1.2   Goals for Current Year

STUDIES and RESULTS . . .

2.1

2.2

2.3

2,4

2.5

2.6

2.7

2.8

2.9

CO?SGEN            * . .

CDNGEN Developments 4

RESOURCESHARING . .

Stereochemistry . . .

Structure checking functions for CONGEN .

Meta-DEINDPAL . . . . . . . . .

REACTand MAXSUBPrograms . . . . .

High Resolution GC/MS System . . . .

References        . . . . . . . . .

. . . . . . , . .

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

Page

. 97

.  97

.  97

. 99

o ??

' 103

,107

- 110

. 112

. 121

o 123

. 124

. 125

. 127

4.    RESEARCH GDALS 1979-1980 . . . . . . . . . . .   o 128

96


1   Objectives

1.1   Overall Objectives

  This progress report covers the second year of our three year
grant on computer  applications in chemistry, with particular emphasis
on  techniques of  computer-assisted   structure   elucidation and
applications of these techniques to problems of biomolecular structure
characterization.  To meet this primary objective we have focussed our
attention on development of interactive
designed to act as chemists'         computer programs which are
              assistants in exploration of the potential

structures for unknown compounds.  These programs take into account
structural information derived from a variety of sources including both
physical and chemical methods.  We are focussing our research on those
aspects of structural analysis which are most difficult to perform
manually.  We are extending the interpretive power of these programs to
enable them to draw meaningful structural conclusions  from chemical
data.  To meet these objectives we are developing a series of computer
yogr=ns, described in more detail below, which emulate several
important aspects of manual approaches to structure elucidation, We are
applying these programs to structural problems in our own laboratories
and laboratories   of others  incltiing   utilization of   the mass
spectrometry resource supported under,'ISis grant   for  structural
assignment based on mass spectral data.

  In order to promote dissemination of the results of our research
to the biomedical comnunity, we  are developing methods for better
access  to our programs,  including both remote access  to theSUMEX
resource via nationwide computer netmrks  and exportable versions of
important programs including just recently the CONGEN program discussed
below.

1.2   Coals for Current Year
       --

- Our goals for the current year includ&I the' following:

  i) develop and test an exprtable version of the
CONGEN program and begin investigation   of actual
exprt;

  ii) develop' CCJNGEN   to utilize  techniques of
constraint interpretation  developed in year 1 and to
incorprate   other   features   useful   in structure
elucidation (see below);

97


  iii) promote resource sharing utilizing SUMEX,
through export of programs and through workshops held
at Stanford;

  iv)  interface  the stereochemistry  package to
CCNGEN and provide useful output of the STFXEO program
to

  v) the  chemist:   under   Meta-DEND
automated rule formation for both mass and %  explore
                i spectra,
and use such rules to predict spectra   and rank
candidate structures for an unknown compound based on
agreement between predicted and  observed spectral
properties;

  vi)  to develop approaches to automated examination
of large numbers  of candidate structures to aid in
experiment planning;

  vii)  apply the REACT program to  investigation of
biosynthetic pathways in the marine sterol field;

  viii) develop a   program   for   detection of
structural similarities in a set of diverse structures;

  ix) exploit the high resolution,  cbmbined gas
chromatography/mass    spectrometry    system     for
identification of new natural products.

  We have met these goals during the past year, although the methods
used and the programs  which resulted reflect some changes  in emphasis
based on requirements  of our own applications  and those of outside
parsons using the programs.  We have endeavored to place our emphasis
on those aspects of  the campltational methods which were required for
certain key structural problems AND which appeared to be of sufficient
generality to warrant including inthe programs for future use by other
persons.    Our  approaches to  experiment  planning,    use of
stereochemistry, definition of aromaticity and mass spectral prediction
and ranking all reflect such exposure to real problems and the results
represent what we think are generally useful solutions.

98


2   STUDIES and RESULTS

2.1    COESGEN

2.1.1   Exportable CONGEN

2.1.1.1   Reprogrming CONGEN

  Our previous annuals report discussed preliminary development of
scme portions of CCNGEN in the BCPL programming language, specifically
the structure generation algorithm. This early experience showed ECPL
to be a compact and efficient  language containing all of the basic
features needed   for the  full reprogramming   effort.   Continued
development has produced a version of CONGEN in PCPL which contains
nearly all of the features of the INTERLISP/SAIL/FORTRAN version.  'Ihe
primary exception is the perception of aromaticity, and this feature is
currently being  implemented.
advantages over the previous one; The !3CPL version has the following

  4  It requires less than 10% as much computer
m-w  due partly to the more compact coding and
partly to the use of an overlay structure;

  b) It uses about 2-5 times less computer time on
typical cases   than the most  highly-tuned (block
compiled) previous version of CONGEN;

c) The redesigned front-end provides significantly
more error checking , a simpler and more flexible input
format, and a more thorough "help" facility;

  d) It can easily deal with problems an order of
magnitude larger.

  4  It is exportable to  a variety of different
computers.

2.1.1.2   Overlay structure

  As portions of CONGEN were developed in 2CPL, estimates of its
eventual size could be made and it became obvious  that the entire
program would occupy a somewhat larger amount of memory than is usually
available at many installations (on the order of 100-200 K words, still
much smaller +&an the roughly 450 K mrds needed by the prior version).

99


Because  the processing  in CONGEN falls naturally   into  several
independent activities (generating intermediate  structures, imbedding,
defining substructures, etc.), the program 'can easily be broken into
separate overlay segments which need to communicate only relatively
small amounts of information.  In the interest of transportability,
though, it was decided not to rely upon the overlay mechanimn provided
by any particular oper'at.ing system or language. The safest approach
seemed to be to divide the overall program into completely injependent,
separately runnable modules capable of starting one  another and
comnunicating with one  another via disk files.  The drawback of this
approach is that there may be a significant overhead in creating and
reading files,  and in switching  from one module to another. But
because all information needed to describe a CCNGEN session is
maintained on file, the program  is unusually robust: even if an error
causes the program to crash, CCXEN can simply be restarted and it will
restore the complete  environment which existed before the erroneous
comnand was issued.  Also, a particular operating system may offer some
means of accomplishing overlays efficiently, and by interfacing the
modules through a small control program, it should be possible to take
advantage of such facilities. Under TENEX on the PDP-10, for example,
a program may control a large number of forks  (independent virtual
address spaces)  .each containing a   separate  program.    We have
successfully interfaced  the CCNGEN modules through a small fork-
manipulating program so  that the overhead of starting a particular
module is paid only once for each CCNGEN session.

  'The current CCNGEN is composed of  eight modules, the largest of
which occupies about 46 K words of memory and the rest of which fall in
the range 15-36 K words.  We are exploring ways of reducing the size of
this largest module (SURVEY - see below) to bring it into this range
also.  The modules and their functions are as follows:

  a) cmm (35 K)  - Main control module, user
interaction, error checking;

  b) EDITS (19 K) -  User interaction for defining
substructures;

.   cl GENERA (26 K)  - Generation of intermediate
structures:

  d) PRUNE (15 K)  - Elimination of structures based
on structural features;

e) IMBELD (36' K)
intermediate structures; - Expansion of superatoms in

  f) DF@JN (26 K)
the user's terminal; - Output of structural drawings to

100


  g,          - Examination of large structur?
lists      frequency of    occurrence   of standard
structural features; and

h) STEREO (24 K)  - Generation of stereoisomers.

2.1.1.3   status
      Exqrt

  We are concentrating  our export effort on machines which have a
significant number of users in the chemical comnunity. We decided to
pay special attention to machines which our CCXEN users have access to
now and to those which they have indicated to us that they will have
access  to in the near future.  We are also strongly guided by the
persons attending the workshops  (see Section ???) and the machines to
which they have ready access.

'Since many of our users have Digital Quipnent Coqoration RDP-10
computers this was our first priority. The program was designed to run
on the Pops-10 oprating system since there is a
which allows programs                 compatibility package
             which run under 'Fops-10 to also r*un without
change on Tops-20 and the Tenex operating systems. We got a version
running on the Tops-10 and exprted  it to Rutgers where it ran  on the
Tops-20 system,  and to two different Tops-10 sites: Slnith,Kline
Research and Ely Lilly Research. Since we have a Tenex operating system
at Stanford we have now verified that CCNGEN does run on all three and
that the compatibility package is robust.

  We are continuing negotiatio;ls for a contract, separate from this
propsal, to provide a version of CONGEN accessible through the NIH/EPA
Chemical Information System (CIS). That system is currently operating
on DEC equipment so that direct export of the current version of the
program to CIS will be simple.  Complete integration of the program
into the CIS framework of programs and their  interconanunication is,
however, a much more difficult task.  'Ibis task will be pursued and
funded separately from the current grant
mechanical programming and documentation  because it is essentially a
                             effort with little research
content.  However,  the resulting doccanentation will be available for
all persons to who we exTprt the program, thus benefitting our DENDRAL
work.

  We decideci on two other machines with their associated operating
systems for reasons that will be discussed briefly below.   The two
machines are the IBM 370 running the new Virtual Machine Conversational
Monitor  System Operating System (VM/XS) (CCNGEN running on this
system will also run on the next generation of IBM machines  the 3100
and the 3300 because they will run an identical (to the user) version
of VM/CXS ), and the Control Data Corporation  6600 computer at the
National Resource for Computation in Chemistry at the Lawrence Berkeley
Laboratory. .

101


  A study was made of all of the different operating systems for IBM
370 series computers.
with virtual memory.  We looked carefully at those operating systems
          Of these, only VM/CNS seemed to be a reasonable
short range possibility since  its interactive, time sharing  system is
very similar to the PDP-10 Tenex system. We applied and were admitted
as a project to a Stanford/IBY Joint Sttiy project. This project is
slated to provide us with access to a IBM 370 computer some time in the
spring. After we get CCNGEN running on VM/CMS we plan to investigate in
mre detail.the other 370 virtual memory operating systems and also to
investigate the IBM series  1 mini-computer which has a virtual memory
operating system. We estimate that
project.                3 man month.3 will be spent on this

  The NRCC currently has a computer complex consisting of a Ccc
7600,6600, and 6400 together with a PDP-8E mini-computer. The 6600 has
been dedicated to interactive computing consisting of both interactive
programs and an interactive system for preparing batch programs for the
7600.  The 6400 serves as an input / output machine and the PDP-BE
manages the terminals and teletypes for the 6600. A project at LJ3L
called the real time systems group has brought up a version of BCPL on
the 6600 and they have expressed interest in helping us bring CCNGEN. ,
We did a detailed calculation and determined that an average CONGEN
session on the 6600 conducted over the Tymnet network muld cost about
100 dollars at normal priority at week day rates. This seem&
reasonable to us and we will be applying to NRCC for a grant for the
computer time necessary to bring up CCNGEN. We estimate the task to be
about one and a half man months.

  During our discussion and research we considered a significant
number of other machines and other prograrmning languages. We have so
far been unable to find any solution to the problem of a version of
CCNGEN for a mini-computer  system such as the DEC PDP-11 series
machines.  Address space  limitations of 32X words make the task
proh.ibitive  in terms of effort.  Even with systems with memory
management, the job of rewriting CONGEN to fit into 64K 16 bit words is
probably beyond our present means in terms of prograrruning time
required.

  We are discussing with VarZan Associates, Palo Alto, the prospects
for a mini-computer version of CCNGEN in the PASCAL language.  If they
decide to undertake such an effort we may have access to a mini-
computer version in a language which is rapidly gaining popularity and
already enjoys significant transportability among machines.

  Several other computer systems and languages have been explored
for suitability for CCNGEN.  So far all have suffered from language
deficiencies which do not allow the
CCNGEN's basic algorithms (e.g. FOKTRAN), heavy  recursion required for
                      from lack of transportability

(the BLISS and C languages), or from being implemented on a machine

102


which is not widely available in the chemical and biochemical communitv
t-3., Honeywell, Hewlett Packard).  These investigations will continue
because new machines like the DEC VAX-11/70 will have an increasing
number of users in the future and versions of the BCPL compiler will be
available for popular systems.

   2.2   Developments
        CCNGEN

  The reprcyrming effort has been far from a transliteration of
existing algorithms into BCPL. In many portions, the basic algorithmic
approach taken in the previous version was reformulated to allow for a
more effective representation and solution of the problem.   Aside from
the development of and proof of correctness for a new structure-
generation technique (related to that of Sasaki) which we discussed in
last year's report, and aside from the work described elsewhere in this
report on  stereochemistry (Section 2.4) and the SUPXEY function
(Section 2.5),  the major milestones  in CCNGEN development which have
paralleled the reprogramming are as follows:

  1) Imbedder.    The mathematical
expanding                   technique for
       superatoms in   intermediate   structures
developed by Brown was reexamined and reformulated to
allow for a more compact representation.  The primary
difference in our new approach is that the to@cqical
syimnetry group of the atoms, rather than the free
valences, is used in the computation.  For exmle, the
superatom A below,  with twelve free valences, has
twelve torplogical syrranetry operations

\/
\ A /
-c c-
l I
;"\A
A

A

interchanging its atoms,
interchanges between    but because of the pairwise
            free valences on each atom, the
free-valence group has  64x12=768 syrnnetry elements.
The BCPL version of the tiedder carries the synanetry
information as 11  permutations of 6 objects
identity permutation                     ( tie
            is not explicitly represented)

103


requiring  66 words of memory,  rather than as 768
permutations of 12 objects requiring 9216 words of
memory.   BY  implicitly  representing  interchange
qmnetry among free valences, among the termini of
internal bonds being allocated to the superatom and
among monovalent atoms being attached to the superatom,
the new version is able to use a drastically smaller
amount of  space for the   storage
information.                  of synunetry

  Neither of these approaches to  imbedding can
perceive all possible sources of duplicate structures,
so  it was necessary also to develop a final filter
package to canonicalize the imbedded structures and
compare them for duplicates.  EIowever, the new version
stores  the structure representations on an external
random-access file rather than in the computer-s memory
as was done before, and only a list of pointers to
these filed  structures is  stored internally. As a
result, the new imbedder.can deal with thousands rather
than hundreds of imbedded structures using only a
modest amount of memory.

  2) Constraints.  The basic structure generation
and imbedding algorithms are of little practical use
without the ability to constrain their output based on
the presence  or absence of structural features. The
graph matcher and cycle finder,  which accomplish
constraint testing,
from their     were translated with little change
        INTERLISP counterparts.    Inclusion of
constraints in the imbedder, where they serve only as a
filter on the   final   output   structures,    was
straightforward.  In the structure generator, however,
the constraint-testing mechanism was merged much more
intimately with the generation process.   The main
aspects of this merging are as follows:

  a) As soon as hydrogen atoms are
distributed   among  the non-hydrogen
atoms (the  first activity   of the
generator) , the   distributions    are
checked   against the   constraint
substructures to    determine   which
distributions can   be ruled   out a
priori. . If a substructure is required
to be  present and   contains three
methine carbons (CEI), for example, the
generator   will  ixnnediately discard
hy?rcgen distributions which do not

104


contain  at least three such carbons.
WY   constraints  supplied   to the
generator place  restrictions on the
possible   distributions
atoms,  and by this    of hydrogen
               mechanism such
constraints      are    tested    inost
efficiently.

  b) The   order in   which   the
generator   assembles   its   atoms is
influenced by which atoms appear in the
constraints.    If a   substructure
forbidding        construction   of
peroxides  (0% is   present, the
generator   will be
consider          encouraged to
       possible   interconnections
among oxygen atoms first so that the
presence of peroxides can be avoided
early in the  computation.   Because
different constraints  may encourage
different starting atoms, a. scoring
scheqe has been developed which is used
to establish the overall order of atom
assembly,  taking all constraints into
account.

  3) Interactive   aids.   Much   effort  has been
directed toward the development of a robust and helpful
interactive system to allow a user easily to define a
CONGEN problem and to make use of the basic algorithmic
tools.  The primary accomplishments in this direction
have been as follows:

  a) The developnent of LINSTR, a
package of   ECPL   functions   for
interactive  input   from  the user,
accessed by all of the interactive
CONGEN modules.  The line-input and
prompting functions in LINSTR provide
for three levels of help information
which can easily be passe? from the
main program.  The first level consists
of prompts which are typed to the user
when  information  is required by the
program.  The novice may step through
the prompting sequences supplying one
piece of information at a time in
response to these prompts, while the
expert user may anticipate  the prompts

105


and type ahead his responses on the
line to avoid the   prompts.   This,
together with the ability of the LINSTR
functions to   accept  unambigwus
abbreviations for keywords, allows a
great deal of flexibility in the form
of  the input.    For  example, the
following tm sequences accomplish the
same effect in the program (user's
inputs are underlined):

Step-by-step input:

DEFINE
DEFINITION TYPE:SDBSTRUCTURE
NAME:R6 .

>RING6
>ENE-
RT-B&NED

Condensed input;

DE S R6;R 6;DO
@mEwBsm~RE)

R6 DEFINED

  A second level of help is provided
by the o ?* facility which can can be
evoked at any prompt in the program.
At these pints, the '?'  input will
cause helpful information oassed by the
main program to LINSTR to be typed to
the user.  The third level of help is
provided by a similar '??' facility,
which will cause the program to refer
to a much more extensive on-line help
document to give a full description of
the  expected  information,   and the
context in which it will be used. This
third level is still under development;
the basic mechanism has been developed
but we have not yet constructed the on-
line documentation.

.

  b) The    simplification
extension of the basic ccrrmands. The

106


number of basic CONGEN commands has
been reduced from 29. to 14 by the
consolidation of commands with similar
function (e.g., SHCW is now a general-
purpse method of obtaining information
about the session and replaces six
previous  commands)   and eliminating
littlwed options (e.g., TREEGEN).
The nmber of EDITXRUC  commands has
likewise been reduced from 23 to 17.
a=,  previous concepts   which were
somewhat artificial have been removed.
For example, a user does not now need
to distinguish between superatoms and
patterns    when he    defines
substructure. The representations fo:
these &u types of substructure have

     consolidated and a   defined
substructure can be used in either
context.  As another example, the user
does not need to place substructures on
BADLIST any more - the  new input
sequence  allows him to express the
presence or absence of substructural
features in a natural statement such as
'exactly 3' or  #at imst 1' or *none'.
The new command structure seems easier
for users to remember and work with.

2.3   RESCURCE SHARING

2.3.1   CONGEN Workshops

In early December, 1978, we held at Stanford a series of mini-

workshops on the  use of an exportable version of the CCWEN program.
Invitees included members of the chemical and biochemical community who
are actively engaged in solving  the structures of unknown chemical
compounds encountered   in research in  industrial,   academic and
government  research laboratories.  The primary purpose   of these
workshops was to introduce  experts  in the field   of structure
elucidation to the first version of the exportable program.  These
persons were chosen for. their chemical and biochemical expertise; few
had significant experience  with computers previously.   Thus, they
represented what we think is  a good cross-section of the community of
potential users of CCXEN.  We held three three-day sessions of the
workshop so that we could offer access to a computer terminal  for all

107


the parsons at one  session and so that we could provide close
supervision and assistance as they  began to learn and use CCNGEN. We
also implemented a recording  scheme so that an interactive session at
the terminal could be recorded as a text file arxl available after the
problem was completed for close  scrutiny for  the chemist and for
ourselves.  Such scrutiny reveals, for example, cCBIPnOn difficulties in
certain Fortions of the user interaction thereby pointing out areas for
improving the interaction.

  The prsons who attended the workshops, their affiliation and a
s-y of their reactions to the program are surnnarized in Appendix I.
We also include in that Appendix parsons who were not able to attend
the workshops but desire, on  the basis of our contacts with them with
regards to the workshops, a  copy of the exprtable CONGEN. A copy of
the original letter sent to one of the invited persons is included as
Appendix II to describe our purpses in more detail.

  Although the version  of CCNGEB used in the workshops was not
complete, enough of-the program existed in close to final form to allow
us to fulfill our other purwses.  We wanted to ensure that any
remaining program errors could be detected and fixed prior  to making
the program more widely available. The best way we have found to do
this once a program is essentially debugged is to confront the prcqrm
with a wide variety of problems from many different users.   we also
wanted to determine if there were major deficiencies in any part of the
program which made it difficult to understand or use. Eliminating such
deficiencies muld ensure that an exported version muld meet the needs
of the persons  attending the workshop, i.e., that some minimum
standards of acceptability could be determined and met.  Finally, we
needed to determine the coquting facilities available to this group
and in detailed discussions to explore omrtunities for export to
their own laboratories.  This allows us to set some priorities on
developing versions for various makes of computers. The facilities of
each attendee and the current and future state of export to each
laboratory are summarized in Appendix I.

   2.3.2   Conclusions from the Workshop
                            --
  There are several conclusions which can be drawn from the workshop
experience.  The reaction of all r;ersons attending the workshop was
very psitive,  not only concerning organization and intellectual
stimulation,  but also with the problem-solving capabilities of the
program.  The following
expr ience:         are major psitive aspects of the workshop

  a)  we were able to meet our goal of demonstration
of exprtability by utilizing CCNCZXJ on two different
comwters during the workshop;

108


  b) every  participant   found the  program of
sufficient utility to express an interest in obtaining
a version in some way for his or her own laboratory:

  c) the interface to CCNGEN, extensively modified
based on experience  with the old version of the
p-3-b  proved much  simpler to use,   much more
chemically logical and consistent and much more helpful
to the user in providing guidance and error checking;

  d) several new problems were analyzed successfully
at the workshops,  either by verification   of the
unambiguous nature of the structural assignment or by
obtaining  a list of candidate solutions  to guide
further experimentation;

        0)  installation of the exportable version has been
    completed successfully at two different sites, Lilly
    Research and Smith, Kline and French Research, and
     several more will follow in the next two months.
There are some common criticisms expressed by the persons attending the
workshop which, in  our opinion, represent points of focus  for the
remainder of the grant period and for a renewal application.
the major deficiencies were as follows:               Briefly,

  a) The requirement of specifying non-overlapping
structural units is non-intuitive and thus unnatural.
Other programs, like CONGEN, share this difficulty, but
we are in a position to remedy it based on recent
research so that future versions may be easier to use;

  b) The   prog-  is very  complex   and lacks
sufficient documentation or internal 'help' facilities.
We recognize this and to same extent it is a reflection
of the lack of maturity of the new version.  We plan to
provide better on-line help facilities accessible from
within the program and a much more comprehensive
program guide with exaE?iies.

  c) The teletype oriented drawing program produces
some drawings which are difficult (if not impossible)
to interpret.  Providing the chemist with a connection
table of such drawings, as we can do currently,  is no
long-term solution,  Here we face the problem of
diminishing the exportability of the progra if we
restrict its use to certain types of graphics terminals
(there are  maw types,  each  requiring different
programs to operate). Currently there is no graphics
terminal which is competitive in price to character-

109


oriented terminals.  One way to solve this problem is
to encourage  collaborators to provide   their own
graphics packages  which we can then in turn offer to
others.

2.4   Stereochemistry

2.4.1   SAIL Program
The stereoisomer generator program written in SAIL and discussed

in last year's annual report has been improved in several ways. The
program has been modified to-process lists of structures to count
and/or generate the possible stereoisaners.  Thus with the existing
CONGEN structure generator it is now possible for the first time to
generate all the possible stereoisomers for a given empirical formula
completely and irredundantly.  These stereoisomers are represented in a
compact canonical form and are written onto a disk file by the program
along with other  information about the structure.   Three additional
features which were proposed in the last annual report have been added     .
to this program. First,  at the user*s discretion, the program will
compute cis and trans double bond designations for the stereoisomers
and write these on the file.  Second R and S designations for
tetravalent stereocenters based on the C&n-Ingold-Prelog conventions
are ccnnputed for stereocenters which are  not fixed by any nontrivial
syrmnetry element.  These designations were thought to be the most
useful and most stable with respect to future changes of the R/S
nomenclature system.  Third,  the ability to handle stereochemistry of
conxnon heteroatoms with valence less than 5 has been added.   Asmall
interactive package  has been added for deciding whether trivalent
nitrogen atoms are free to invert.  The user is given a choice for each
such nitrogen atom.

  This program has been included with the current LISP version of
CCNGEN (it runs as a separate  fork) and is available to all users who
can access SUMEX.  It has been extensively tested on well over 1000
structures.  Further details can be found in the publications citti in
this report.(EIPP-78-B,RPP-78-9)

   2.4.2   ECPLprogram
  Since the CONGEN program has been recently reprogrammed into EYCPL
to create an exportable version,  it was decided to also reprogram the
STEREO program into ECPL and carry on further developments in that
language to ensure compatibility and exportability. With the exception
of the parts of the program which compute R/S symbols and handle

110


heteratoms  interactively,  this reprogramming has been accomplished.
Further developments on this program include a fairly extensive
interactive package which allows the user to obtain  information about
the generated stereoisaners.  The user may obtain drawings of projected
stereocenters showing  absolute configurations of stereocenters (e.g.,
Fischer ,projections, Newman projections,  double bards) or obtain
drawings of   linear  segments of .structures  showing   all the
configurations of the included stereocenters.  The user may also obtain
information   about the  symneW  and equivalent   atoms  in any
stereoisomer.  This program is currently running with the ECPL version
of CCNGEN and was available and tested during the recent series of
mrkshops.  This program has been exported with this version of CCNGEN.

  The experimental version of the ECPL program has been modified to

allow for some constrained generation of stereoisomers as proposed in
the last annual report.  The algorithm and program for exhaustive
generation were written with this eventuality in mird.   An'additional
interactive session has been added to the stereoisomer generator which
allows the user to add constraints before generating the stereoisomers.
At present, the user may.input constraints on the absolute or relative
stereochemistry  of any   stereocenters.    Thus if   part   of the
stereochemistry of a structure is known,  it is possible to constrain
the stereoimer generator to produce just those isomers consistent
with the known stereochemistry.  This parallels the procedure in the
structure generator of CCNGEN.

.

   2.4.3   European speaking trip

   At the   invitation   (ad  expense) of the    Center   for
Interdisciplinary Research at  the University of Bielefeld in West
G-=nY I  one of our group, J. G.  Nourse, talked   about recent
developments in the CCNGEN program. Besides the lecture at Bielefold
at a conference on the applications of permutation group theory to
Chemistry, Physics, and Biolcgy, a lecture was given at the University
of Bremen (also W. Germany) to a conference on applications of graph
theory to Chemistry.  In addition invited lectures were given in Berlin
(Free University) and twice in Zurich (ETH and University).   A great
deal was learned about current efforts by others in both the US and
Europe on computer applications  to chemical structure elucidation,
synthesis,  and data bases.  Considerable interest in our programs
resulted.  Besides continuing correspondence, this is evidenced in part
by the presence of Prof. Andre Dreidinq of the University of Zurich at
one of our recent CONGEN 'mrkshops.   The contents to some of these
lectures are includti iri references 14 and 20.

111


2.5   Structure checking functions for CCNGEX

2.5.1    Introduction

   A program, YZRUCC", has been developed to provide functions for
checking sets of structures  for desired substructural features or for
compatibility with recorded mass-spectral or nmr data. While primarily
devised for processing sets of structural isomers produced by means of
ccNGEN  , STRUCC can also take as input sets of structures created
through the REACT program or defined though an extension of CCNG&*s
EDITST'fUJC function.

The main structure checking functions currently available'through
STRUCC are:

  1) EXAMINE: This EXAMINE function is an extended
version bf available in standard CUNGEN. -Amongst
other extensions are facilities for  checking for
specified  ring-fusions or  spire-junctions within
structures.

  2) NSA:   The ?ISA  ("Mass Spectral Analysis")
funcfion=rovide a means for using mass spectral data
to rank candidate structures.   The MSA functions can
employ either ordinary "half-order theory", or a model'
of fragmentation in which bond break plausibilities are
related to specified substructural features.

  3) LI=oK: The UXJK (1) functions are intended to
assist aYiE& in investigating the utility of proposed
experiments  for differentiating   between candidate
structures. LCOK provides a mechanism  for determining
the   various different  ways in  which particular
superatom  parts are.  incorporated   into candidate
structures.

  4) TSYM: The ISYM function allows some simple
forms o?-&nnnetry constraint to be defined. These
constraints use only topological symmetry.

  5) REWNANCBCHEK: The RESCNANCECHECX function is
intended for checking that all constraints  have been
given  to the structure generator. The function can
identify differences in candidate structures that muld
be associated w.ith features in the lHnmr or 13Cnmr that

  (1) (The LGCK functions incormrate some of the features of the
PLAN functions described in last year's reprt).

112


one might reasonably expect to be fairly obvious (e.g.
different n&rs of hydroxy protons, different n&zers
of carbonyl carbons etc). Generally,  such differences
are foti in cases where the user has forgotten to
specify substructural features incompatible with the
observed data, or has misapplied the constraints so
that not all instances of unwanted   features are
eliminated .

  6) NMRFLT: The NMRE'LT functions represent a first
attempt at developing a system for predicting proton
             of candidate structures,  and for

resonance spectra
using differences
spectra as a basis

between predicted  and. observed
for pruning the structure list.

  The SRUCC system is
evaluation functions. When

also used as a test-bed for new structure
functions are considered to be sufficiently

developed to be of use, top-level calls to those functions are added to
SIWCC's repertoire of commands.

  STRUCC has a user-interface similar to that of CCNGEN and
incorporates many of the same subsystems (e.g. SDITSTRUC and DRAW.

2.5.2'  The Ebrmof the STRDCC Program-
               ----
m
  The following diagram indicates schematically the overall form of
STRUCC :

          - I Executive I                    ITSYMI
                         \ \
   ,' ,' I I \\ -- \ \    \-
                                     \
                       \ --
Status I / /' IESI I            Ii&
~~sl---/ / - I I \           - -
      IDRI 1 -
           IMSAI ILCOKI
                          -   I - -
    I File
I ManipulationI          -
                  IDSI
                               -

1) Status commands:

  i AR?:   Lists the   "aromatics
templats used in  CCNGEN*s last
GENEPATE or IMBED step.

113


ii CLEAR: Restarts the program.

  iii CM?:   Gives the   structure
compositiZK

  iv CN?: Lists the contents of the
"Global Constraint   list"   used in
CoNGEN's last GENENQE,IMBED orPRUNE
step.

  v CT?: Gives the current number of
structu??.

  vi EF?:   Gives the
formula maefined).      empirical

vii EXIT: Erads the program.

  viii UA?:  Displays all user
defined seaatoms and patterns.

2) File Manipulation:

  i RESIQRE: E&ads in aCONGEI+file
(or a REACT-file) containing defined
superatoms,  composition,  constraints
and structures.

  ii ECPL:  Reads in a   file of
structur=reated through the new ECPL
version of the CONGEN program  in order
that they may be analyzed through &A,
EXAMINE etc.

  iii APPEND:  Adds all structures
from a Ct?NGEN save-file to the set
currently in memory and then eliminates
any duplicates.  This option is useful
for combining results from problems
where the structure generation process
WaS  performed   several   times with
different assumptions about starting
superatoms etc.

  iv .SAVE:  Creates   a CCNGEN-file
containi@-    current    superatoms,
structures etc.

3) FDITSIRTJC (ES):  CONGEN's standard FDITSTRUC

114


function is available. See the CZGEN user's manual for:
details of this function.

  4) DRAW (DR) :  CCNGEN's standard DRAW function is
availabl~~e CCNGEN user's manual for details of
this function.

  5) DEFINE-STRIJCTDRES   (DS) : The DS   function
provides various extensions tostandard RDITSTRDC that
are useful when creating  sets of related structures.
The IX function is used when the structures to be
processed by one of the analysis functions (e.g. MSA)
have not been created by REACT or CCNGEN.

6) MSA: Mass spectral analysis.

  7) LGCK:
etc). -  (for assistance in experiment planning

  8) RESCMNCKCRKCK (RC): (Simple checks for omitted
constraints).

9) EXAMINE @MN): Extended version of EXANINE.

  10) NMPFLT (NMR): Prediction and checks on proton
resonance spectrXcandidate structures.

  11) TOPSYM (TSYM): TSYM will prune the structure
list to retain only those structures in which some,
user defined, substructure has a given minimum number
of syrnnetrically eqikvalent images.

  Cn starting,  or on restarting subsequent to a 'CLEAR" command,
STRUCC first lists any news bulletins  about new options/bugs etc and
then asks whether the structures might vary in composition. Many of the
processing functions use checks on composition and have to be informed
as to whether these checks have to be performed just once, or, for each
structure being processed. If the structures were generated by CCNGEN
then all will have the same composition but structures produced by
REACT or entered manually throwh DEFINE-STRLJCTDRES may vary in
composition.

   2.5.3  STRUCC'S HELP system

   STRXC has a  primitive on-line doczumentation   .qystem.  This
subsystem is invoked by giving the ccrranand "HELP" in reply to a prompt
from the program. If the command %ELP" is used alone, then the program
retrieves  information supposedly useful within the current context.


hrguments can be used with the YELP" command, e.g. "HELP TAG UNTAG"
kfould result in HELP trying to find information on the DDITSTRUC TAG
ard LJNx!AG commands.  The HELe files do contain some cozrnented examples
of the more complex functions.

   2.5.4   DEFINE-D

   The DEFINE-m S (DS) cod allows you to define complete
structures by means of an extended EDITSlXDC system. Typically, the IX-
command would be used to enter a set of structures that are to be
processed by one of the analysis routines - such as MSA - but which
have not been generated by c3xQz-i.

  Generally, sets of structures that are being entered by means of
the DS-system will share ccrnnon substructures. For exmle, the
structures might consist of steroidal compounds based on one or &u
nuclear skeletons and half a dozen sidechains. The ES-system allows you
to use substructures, (previously defined as Pattern-type Superatoms in
EDITSITRUC) when creating new structures.

   2.5.5  MSA, The Mass Spectral Analysis Functions.
               --
  The MSA functions utilize an extended version of DENDRAL's "half-
order theory of mass spectrometry",  (aescribed in previous reports),
and can provide the following forms of mass-spectral analysis:

1) PREDICTION: prediction of spectra on the basis
"half order theory".  The program has to be given:

       i Parameters   controlling the
    fragmentation process

ii A minimum plausibility value
for ions to be listed

       iii The minimrnn mass of interest.
-All structures on the structure list are processed and
their spectra are listed at the terminal.

  2) ANALYSIS: In this mode, MSA can be used to list
all possible rationalisations for observed ions. The
program lists, for each ion, the breaks, neutral losses
and H-transfers*necessary for it to be generated from a
given structure. In general, this is a large amount of
data: consequently, the program only processes a user-
defined subset of the structures. Each structure in
the subset is processed in txn with the fragmentation

116


.

analysis being listed at the terminal.  The program has
to be given:

  i) The index   numbers   of the
structures to be processed

ii) The observed spectrcpn

  iii) Fragmentation
parameters.

control

  iv) A minims plausibility value
on processes that are to be reported.

3) RANKING: For ranking structures, the program
has to brq5EE:

i) The observed spectrum.

  ii)  Fragmentation
parameters.

control

  iii) The   form of
function. The       the scoring
          contribttion to o a
structures' score from a recorded ion
being predicted is given as the product
of the predicted plausibility and one
of:

  a) 1
(presence/absence of
ion    is    all   that
matters)

b) The ion's mass

  c) The     ion's
observed intensity

  d) The product of
the   ion's   mass and
intensity.

All structures are processed; optionally, their scores
can be listed as they are processed. Once all have been
processed, the program produces a ranked listing of the
structures. It is then pssible either to simply prune
away those with inadequate scores, or to  enter EXAMINE
with these scores. Within EXAMINE, the results of MSA-
scoring can be combined with substructural features to

117


form selection criterion based on overall agreement
with the qectrm and presence of desired features.

  4) EXAMINE: In this mode, the program identifies
all structures for   which the observed   ions are
predicted.  The information is converted into a form
that can be used by EXAMINE. The observed ions can then
be   used as   EXAUNE-selection  keys I  just like
substructural features;  so, one can select structures
with
X8H6Ol AND C6H10N103 AND C4H8N102
The n-r of ions that can be rationalized in terms of
a given structure  is used as a score   for that
structure. This score is available in EXAMINE.  So, as
well as checking  for structures that can explain
particular ions, it is possible to request those which
can explain a given number of the observed  ions. In
EX?MINE mode,  MSA requires the same data as when in
RANKING mode.

The basic set of parameters which may have plausibilities adjusted

-

in the "half order theory" are:

  1) the plausibility of single bond
1)

2) the plausibilTty of aromatic bond
0)

  3) the plausibility of double bond
0)

  4) the plausibility of bonds of
breaking, (e.g. 0)

breaks, (e.g.

breaks, (e.g.

.

breaks, (e.g.

higher order

  5) the plausibility of adjacent breaks, (e.g.
0.25)

  6) the plausibility of the molecular ion being
observed, (? class depndent)

  7) if multi-step processes are permitted, then
taking the plausibility of single step processes as 1,
values must be. given for  relative plausibilities of
more complex pFocesses
      e.g.   two step processes (e.g. 0.7)
        three step processes (e.g. 0.4)

8) if H-transfers or neutral losses are specified

118


then plausibility values must be given   for each
transfer/loss.

   M!34 functions allow  substructural patterns   (created using
EDIITSTRX) to be used to define borxd environments to which special
break plausibilities.are to be assigned. The program works by checking
whether any of these  substructural patterns match a structure,  and if
so which bonds in the structure correspond to those for which special
break plausibilities have been designated. Then, when the program is
fragmenting that structure to predict ions , it can check if any of the
bonds it has broken are in the list of those having special break
plausibilities.

  As well as allowing these more general mechanisms for defining the
plausibility of bond breaks,  the %A functions let the plausibility
assigned to a predicted ion to be adjusted according to how well it is
likely to localize charge. The basic "half order theory does not make
allowance for factors such as Nitrogen being able to better stabilize a
charge than Carbon and,  consequently, Nitrogen-containing ions being
more plausible than those without Nitrogen. In M!SA,  relative charge-
localization.plausibilities may be defined for different atom-types.
The plausibility assigned to a predicted ion is then modified by the
mairmzn charge-localization plausibility of any of its constituent
atoms.

2.5.6 LCCIK

  Frequently, a chemist can conceive of additional experiments that
could serve to probe the structural environment of one of the spratam
parts that he has used in defining a CCNGEN problem. Such experiments
might involve a reaction at the site of the suparatom part or a series
of proton decoupling .measurements for "walking along alkyl chains" from
some identifiable starting point. Generally,  the utility of such
expriments depends on  there being some  significant structural
difference between candidates within scme relatively small radius of
the already known superatom part. The LOOK functions are intended to
assist the chemist in finding such differences.

  Basically,  LOOK takes the starting superatom (or any other
substructural pattern that the user may wish to define), maps  it into
each structure,  expands it by including neighboring atoms, creates a
canonical representation of  the expanded part and groups candidates
according to these canonical representations. LOOK then reports on the
different exmti features that have been identified and allows the
user to further inspect these larger features. The user can choose for
a part to be further  expanded to achieve sme finer discrimination or
can investigate differences relating to ring-systems involving the new
feature etc.  In I%oK, the substructure expansion process is controlled
through user specified options.

119


   2.5.7   The Proton NMR Functions
  Some simple functions are  now available that can be used to
specify features in the proton resonance spectra and prune the
slmxture list to obtain only those candidates that appear to provide a
rational for the selected features.

  These functions use an "additivity of shifts" model for predicting
the proton resonance spectrum of a candidate structure. This model
ignores all steric effects;  including such imprtant influences as
shielding/deshielding through close proximity to an unsaturated system.
Further, as shift values in reference tables represent averages over
many different types of (usually acyclic) compounds, they can provide
but a poor model for any given structure. Cne can hope that the
predicted resonances of methylene groups will generally be within about
0.6ppm of the observed values while methines should be within 1.5ppn.

The formulae used are:

k1t%i2 = 0.2 + Cl + c2

De1t* = 0.2 + Cl + c2 + c3
6

DeltaCa = 5.2 + 2 gem + zcis + Ztrans

where the Ci and Zi values are supposedly additive constants.

  The resonances of methyl, aromatic, alkyne, aldehydic, hydroxy and
some other classes of protons are not computed but taken from standard
tables. For some of these classes, e.g. hydroxy and aromatic protons,
the resonance values are given as a range rather than any typical
VdlW.

  If the approximate prediction methods appear tolerably accurate
for a given class of candidate structures, then the functions can be
used for pruning the structure list by tests that predicted spectra
satisfy user-defined constraints. !&ese constraints take the form of
requirements for specified (minixn~) nmbers of protons  resonating in
(possibly overlapping) regions of the spectrum.

2.5.8    E!CPL versions of SfWXC
                        -

  The more useful .-components of the SEUJCC system are being
converted to BCPL so that they may be available to future users Of the
BCPL-CONGEN system.

120


2.6    Neta-DESDRAL

2.6.1    MErA-DENDRAL

2.6.1.1 INISB

  The DITSUM program for
  The DITSUM program for  the analysis of spectra has been improved
                the analysis of spectra has been improved
by using confidence
by using confidence  factors in the place
             factors in the place  of many of the original
                         of many of the original
program constraints. This feature allows association of liklihoods with
program constraints. This feature allows association of liklihoods with
fragmentations.
fragmentations.  It thus allows consideration of a much wider range of
         It thus allows consideration of a much wider range of
Possible processes while limiting the final explanations for spectrum
Possible processes while limiting the final explanations for spectrum
peaks to the most plausible explanations.
peaks to the most plausible explanations.

  Additional improvement of the program allows logical separation of
the concepts of H-transfers and neutral composition transfers. This
provides a better correlation between the explanations provided by the
program and those expected by the chemist.

   2.6.1.2   RUIJBN
A significant problem in generalizing  the INT!XlM explanations has
always been reducing the size of the search space so as to be able to
produce interestmg rules in a reasonable amount of time.   In addition
to the constraints already provided, the RULE= program now allows use
of existing rules to filter the peak explanations to be considered.
This is an important step  in allowing the program to focus on rules
which account for peak explanations not yet encompassed by existing
rules.  As an aid in better understanding the process of rule
formation,  the program is now capable of  generating additional
information about the search space. This information serves as data for
other programs whichcan then  analyze and present to the user compact
descriptions of the rule search done by RULEGEN.

   2.6.1.3    EDIT!SRlX INTEBFACE
The latest versions of the structure editor, EDITSTRUC, and the
structure drawing programs have  been interfaced to allow their use in
all appropriate places in  lmsm and RULEGEN. The newest programs for
conversion of EDITSIRUC structures recognize a larger subset of the
structural features which may be specified within ELXTSTNC.  This
allows   the user  greater flexibility   in the  specification of
substructures in user-created rules.

2.6.1.4    PREDICTICNandRANKING

The programs allowing the entry and use of user-defined rules have

121


been extended to allow prediction of-the molecular ion and inclusion of
confidence factors in the rules.

  The process of spectrum prediction from Meta-DENDRAL rules has
previously involved the matching of rules against only those sites in
the molecules considered as possible breaks. With the use of user-
entered rules,  and program  developed rules  containing greater
structural detail, the program was generalized to allow prediction
based on graph matching alone, without the prior generation of possible
break sites.

   2.6.1.5    HUMAN ENGINEERING
Manyminor  improvements have been made in the program-s interaction
with the user.  In general,  these improvements have been designed
according to the following criteria: 1. Messages should be informative
yet not excessively long or wordy; 2.  User typing should be kept to a
minimum; 3.  Programs should behave in ways which  people find
understandable; 4.   During execution,   progr-  should provide
occasional information concerning their progress.

   2.6.2    REsuLTs
The practical value and cawility of new programs are best evaluate
by applying them to real, non-trivial problems. In our case, we have
chosen the biologically mrtant marine sterol comp~imds. Their mass
q5ctra are predominant in . the structure elucidation of new compounds
in spite of the fact that relatively few of the fragmentation
mechanisms are known.  Often very similar spectra are recorded due to
the great similarity of cormnon skeletons. Our study involves the
comparison of predicted spectra of known structures with the observed
spectra of unknown compounds. We want to compare the usefulness of
different methods of forming the rules used for spectrum prediction.
We distinguish 3 methods: 1) Half+rder theory (can be supplemented by
functional group rules).  2) Class-specific rules (selected by the
chemist) 3) Corrquter-generated rules Our  results were obtained using
nine selected 4-demethylsterols (six  isomers of compsition C29H480,
~PRJ C28H460 and one C27H440). Each spectrum of the nine selected marine
sterols was considered to be the observed spectra and ranked against
23 candidate structures (the.23 candidates contained 17 different C7 -
Cl1 sidechains and three 4-demethylsterol skeletons). For the half-
order theory an overall average performance of (2.4 0.9) was obtained.
The first number gives the nLPnber of candidates ranked better than the
correct one, the second represents  the nmber of candidates rankd
equally with the correct one.  In this case the average value is not
very representative,
which          as its value is strongly reduced by a cornpond
        was   ranked '    17th  place.   This   comcound    the 23-
demethylgorgosterol, cogains a cyclopropane in the s&chain for which
no special fragmentation processes  are considered in the simple half-

122


order  theory.  The ranking can be greatly improved by providing
fragmentation rules for cyclopropane rings. The results of the second
method (class specific rules),  depends on the quality and ntznber of
selected rules.  For this study we selected about 17 skeleton breaks
(observed in more then 70 percent of the structures) from the INTSUM
results of 23 marine sterolk to which we added 13 known fragmentation
processes.   These  processes (associated with neutral transfers,
intensity range, and  a confidence factor)  were entered using the new
rule editor program.  The overall performance of these rules was (0.3
0) which means that, with the exception of three compounds, which were
ranked in the second psition, the correct structure was always ranked

first.  A further improvement is  seen when the distribution of the
scoring values is considered. For these rules, much better-separations
were observed than with the half-order theory. Also, the quality of
the predicted etra are sufficient to consider the creation of a
library which could be visually compared without the need of a
computer.  For the third method no results can be surnnarized here, as
the computer generated rules are still being developed. The improvement
of this last step will be a main goal of the next year.

2.7   REACTand MAXSUB Programs
       --

2.7.1 FUZAC!r

  During the last year there have been no additional detelopnents in
the REACT   program.   Rather, it   has been used  extensively in
applications  to both  structure elucidation problems, and, more
effectively,  in mechanistic sttiies involving plausible biochemical
cyclization and rearrangement pathways.

  A major palpr describing the REACT program and the underlying
algorithms which allow it to interpret  automatically structural

constraints applied to reaction products appeared this year  ??? o  This
paper was concerned more with describing the program for iiiterested
persons, but did include a simple example application involving the
persons, but did include a simple example application involving the
structure elucidation.of a sesquiterpenoid alcohol
structure elucidation.of a sesquiterpenoid alcohol  isolated from a
                                        isolated from a
marine organisn.
marine organisn.  The program was also described in more "chemical"
          The program was also described in more "chemical"
terms for a general atiience in a review pa-r which will appear
terms for a general atiience in a review pa-r which will appear
shortly (I.J. -                                   - -

   In conjunction with the work on Meta-DENDRAL  and spectrm
prediction and ranking applied to analysis of marine sterols (see
Section 2.f), we have  employed the F6ACT program   to generate
biochemically plausible sterol side chains. As -we described in the
previous annual reprt, reaction mechanisms thought to be applicable to
side chain modification, incltiing cyclizations,  rearrangements and

123


degradations, were  supplied to REACT as, effectively,  constraints on
the variety of side chains  which are theoretically ossible. For
example, CONGEN can be used to generate isomeric C-11 sterol side
chains pssessirq one double bond.  There are 7769 (!) of them. Using
mm,  however, only 76,  less than one percent, are predicted as
plausible.

  Went papers have illustrated this approach for both extended (z)
and tirtened (19) side chains.  Recently we showed (15) that seven new
structures were21 predictedbythe program,addesorne suprtto
the hypotheses of biochemical transformations.

2.7.2    MAXSUH Program

  The function of the MAXSUB program is to detect common structural
features in a potentially diverse but related set of compunds. This
problem is one faced by chemists engaged in structure/activity studies,
particularly in design of new, biologically active coqounds based on
known coqounds with known activities.  However, any problem involving
an "activity" related to structure , including spectral signatures, is
in principle amenable to analysis by MAXSUB. M?USJB, by determining
ccnnnon features of  structures displaying cornnon   activities, is
presumably focussing on  those aspect of the structures which are
related to the activity.  However, in its current state, the program is
only experimental.  Many types of activity are intimately connected
with stereochemical aspects of structure arxd MAXSUB does not include
any stereochemistry.  It does represent a foundation for further study
of the problem because the algorithms can in principle deal with three-
dimensional descriptors of atoms and bonds. Some mrk may be done on
this program in  the nextgrantpariod.  The existing program will be
described in detail in a ,wblication which will appear.soon (18).

   2.8  Bigh Resolution CC/MS System
For the current grant pericdxeemphasized further develorment of our
CC/MS and CC/& q&.&n as requested by the study section -and focussed
our attention on maintenance of the existing system and applications of
the system to a variety of mass spectral and structural problems of
ourselves and our collaborators.  In addition * have in press  a major
paper describing in detail our approach to both CC/low resolution mass
spectrometry and CC/high resolution mass qectrometry (17) o   In this
paper ~   describe methods of  data acquisition,  reduction and
preliminary analysis, a description which includes all  major elements
of   our mass  spectrometer/com+er  systems and    a  variety of
computational details where our  approaches differ from those of other
workers in the field.  In a companion paper we describe how resulting
mass spectral data have been  utilized in computer-assisted structure

124


elucidation (16).  The following list sunnnarizes the samples we have
analyzed in vzious operating &es of the instrument during  the past

year:

  1) High

i',
2) High

E&solution analyses:

DEWDRAL-related
Outside collaborators
Resolution GC/MS

134
45

DENIXAL-related            86
Outside collaborators       13

3) Low resolution Gc/MS            45
(these samples were primarily
  marine sterol mixtures from our
  laboratory and from several other
  groups, which did not require ERMS
  analysis)

   2.9   References                 6
In this section we summarizi recent publications supported wholly in
part bythe current grant.  This list includes a few publications
published at the end of 1977 to help set the context for more recent
publications which build on the previous results.

  (1) T.H. Varkony, R.E. Carhart, and D.H. Smith, "Computer-Assisted
Structure Elucidation.  Helling Chemical Reaction Sequences Used in
Molecular   Structure  Problems," in   '*Computer-Assisted
Synthesis," W.T. Wipke, Ed.,                     Organic
                American Chemical Society, Washington,
D.C., 1977, p. 188.

   (2)  "Computer-Assisted Structure Elucidation," D.H. Smith, Ed.,
American Chemical Society, Washington, D.C., 1977.

  (3) R.E. Carhart, T.H. Varkony, and D.H.   aith,
Assistance for the Structural Chemist,"              'Computer

Elucidation," D.H. Smith, a.,      in "Computer-Assisted Structure
                 American Chemical Society, Washington,
D.C., 1977, p. 126.

   (4) D.H.  Smith, M.  Achenbach, W.J. Yeager, P.J. Anderson, W.L.
Fitch, and T.C. Rindfleitih, "Quantitative Comparison of Combined Gas
Chromatographic/Nass Sp&ctrometric Profiles of Complex titures," anal.
Chem., 49, 1623 (1977).

(5) B.G. Buchanan and D.H. Smith,  "Coquter Assisted Chemical

125


Reasoning,"  in "Computers  in Chemical Education and Research," E.V.
Ludena,  N.H. Sabelli, and A.C. Wahl, Eds., Plenum Press, yew York,
N.Y., 1977, p. 401.

   (6) D-H. Smith and R.E. Carhart, "Structure Elucidation Based on

Computer Analysis of High and Low Resolution Mass Spectral Data," in
"High Performance Mass Spectrometry: Chemical Applications," M.L.
Gross, a., ZQnerican chemical Society, 1978, p. 325.

  (7) T.H. Varkony, D.H. Smith, and C. Djerassi, "Computer-Assisted
Structure Manipulation: Studies  in the Biosynthesis   of Natural
Products," Tetrahedron; 34, 841 (1978).

   (8) D.H. Smith and P.C. JUTS, "Prediction of 13C NMR Chemical
Shifts," J. Am. C&m. Sot.,
         -m-     100, 3316 (1978).

   (9) T.H. Varkony, R.E.  Carhart,  D.H. Smith,  and C. Djerassi,
"Computer-Assisted Simulation of Chemical Reaction Sequences.
Applications to Problems of Structure Elucidation," J. Chem. Inf. Comp.
Sci., 2, 168 (1978).                                   ---

   (10) D.H. Smith, T.C.
Comments :           Rindfleisch, and W.J. Yeager, "Exchange of
     Analysis of Complex Volatile Mix&es by  a Combined Gas
Chromatography+lass Spectrometry System," Anal. Chem
                         . , 50, 1585 (1978).
  (11) W.L. Fitch,. P.J. tierson, arb D.H. Smith, "Isolation,
Identification and Quantitation of Urinary Organic Acids," J. Chrcm.,
in press.                                                          -

   (12) W.L. Fitch, E.T. Everhart, and D.H. Smith, "Characterization
of Carbon Black Adsorbates and Artifacts Formed During Extraction,'*
Anal. chem., in press.

   (13) W.L. Fitch and D.H. Smith, "Analysis of Adsorption Properties
and Adsorbed Species on Canmercial Polymeric Carhons," Environ. Sci.
T-h., in press.

   (14) J.G.  Nourse, R.E. Carhart, D.H. Smith, and C. Djerassi,
"Exhaustive Generation of Stereoisomers for Structure Elucidation," J,
Am. a-ml. sot., in press.                                             e
--

  (15) C. Djerassi, D.H. Smith, and T.H. Varkony, "A Novel Role of
Computers in the Natural Products Field," Naturwiss., in press.

  (16) N.A.B. Gray, D.H.' Smith, T.H. Varkony, R.E. Carhart, and B.G.
Buchanan,  "Use of a Computer to Identify Unknown Compounds. The
Automation of  Scientific Inference,"  Chapter 7 in "Biomedical
Applications of Mass Spectranetry," G.R. Waller, Ed., in press.

126


   (17) T.C. Rindfleisch and D.H. Smith, in Chapter 3 of "Biomedical
Applications of Mass Spectrcmetry," G.R. Waller, Ed., in press.

  (18) T.H. Varkony, Y. Sbiloach, and D.H. Smith, "Cosquter-Assisted
Examination of Chemical Compounds for Structural Similarities," J.
Chem. Inf. Camp. Sci., in press.
--

(19) R. Carlson, et al., m., 1, in press.

   (20) J.G. Nourse,  "The Configuration Syrsnetry Group and its
Application to Stereoisomer Generation, Specification and mumeration,"
J.*chem. sac., in press.

3    SIGNIFICANCE

  There are several results obtained during the past year which are
especially significant for both the advancement of our  techniques for
biomolecular structure elucidation and the dissemination of results of
our research.  Perhaps the most significant result is in the category
of dissemination because for the first time we can offer directly to
the biomedical commmity the results of our research in the form of
exprtable   computer   software   for   camplter-assisted   structure
elucidation.  We have discussed in the past the differences between our
work and many other  forms of health-related research. The latter can
generally be described in the literature in sufficient detail for
others to duplicate the procedures and results and, more importantly,
build on those results in extensions of the work.   When one of the
primary "results" of research is a set of complex computer programs,
transfer of these results becanes a formidable task.   Certainly the
programs and even some  of the algorithms can be described in the
literature.  We have done so,  and the recent references at the end of
the previous section  represent such publications.  Bowever,  unless an
interested person  can actually gain access  to a program in an
executable, or runnable, form, such descriptions are  inadequate. We
now have the capability of offering the new, smaller, faster version of
CONGENtothe community at SUMM on a trial basis and qrted to their
own computers for those who wish to make more extensive use of the
program.  Therefore,  we can share our results with our collaborators
much more easily now than in the past and persons receiving the program
have a foundation on which to build.

  The workshops  w&e also significant   in that   we received
constructive suggestions and criticisms from a   cross-section of
Iptential users of our computational techniques, while at the same time
exposing a variety of persons active in structure elucidation to CONGEN
working on real problems. The success of this effort has encouraged us

127


to make available in the exportable CBJGEN a variety of other structure
manipulation tools which we and the persons at the workshop perceive as
useful as adjuncts to CONGEN.  Thus, as we have developed capabilities
for exploration of large numbers of structures in the STRUCC program,
and new ways to use and display the results of the STEREO program, we
have begun incorporating these capabilities into CCNGEN.   This effort
will continue, using CCNGEN as the focal Ipint for further developments
in the area (see next section).

  Other significant advances have been smarized in the sections
outlining various aspects of our research, above.  These incllde new
mathematical developments which made possible the reduced size and
increased efficiency of CCNGEN, completion of the STEREO program and
integration of it  into CONGEN,  new approaches  to rule formation in
Meta-DEBDRAL and better methods for predicting mass spectra and ranking
structures based on those predictions. The last item deserves further
comment,  because it represents a general approach to structural
analysis of which we can now take advantage because of the efficiency
of the newC6JGEN.  Spectrums prediction for a variety of spectroscopic
techniques,  inclawng mass, NMR, m,  etc.,  iIX2lLdiIlg    now even
chiroptical methods for future  work , represents a valuable method for
structure determination.  Now that e can deal with hundreds or even
thousands of structures ,in intermediate stages of a problem, such
spectrum prediction techniques provide powerful filters to separate
plausible from implausible structures.

.

4    RESEARCH GOALS 1979-1980

  We have several goals for CCNGE3 development and export during the
nextgrantyear.  Because several were summarized previously, we give
only a brief list here.  The reprogramming effort will continue, first
to incorporate amnaticity into the program and second to include
capabilities  for constraints interpretation and translation. These
capabilities have been experimental efforts in the old, LISP version of
CONGEN.  Some additional development must be done and the BCPL version
brought up to date with these features.  Such developments will allow
much more intuitive use of the program (see section on Conclusions from
the Workshops)  and greatly improve  the ease with which structural
problems can be specified to CCNGEN.

  We will be pushing .very hard for further export of CCNm either
by developments here  at Stanford or by assisting others  at remote
sites.  We can now supply version for DEC-10 and DEC-20 under TOPS-10
or 20 or TENEX operating systems.   The contract  for an XIH/EPA CIS
version will make CONGEN available on that system soon.   Cur Joint
Study project will hopefully allow us  to develop an IBM version at

128


minimal cost.  A version for the Ccc svstems at the National Resource

for Computation in Chemistry is under Gttiy. The whole area of mini-
computer versions is under investigation.  We expect that these efforts
will make the current version widely available. However, it does leave
open the question of long-term maintenance and, particularly, upgrading
older versions as new developments ensue.  These issues will bedealt
with at length in our reneti proposal for funding subsequent to the
coming year.

  In further response  to the workshop requests, we   will be
developing an extended "help" facility for the program which, together
with improved documentation, will  improve the ease with which new
persons can become familiar with CCNGEX  We have alreadybegun
investigations of how to improve  the current  structure drawing
facilities in CONGEN,  with our first goal to improve  the teletype
drawings so that all users can benefit.  We will also be considering
methods for aiding those with graphics terminals to exploit the
improved structure input and output possible with such devices.

  E'urther work on the SITERED program will be to develop further the
constrained stereoisomer generator and to improve interaction with the
main CCWEN program and the user.  Specifically,  constraints involving
the chirality of structures, patterns  of equivalent atoms based on
either stereoisomer or topological syrmnetry, and undesirable structural
features such as trans double bonds in small rings will be implemented.
The flowof information within the programwillbecome two-waybetween
CWGES and the stereoisomer generator.   At present,  this information
only flows to the stereoisomer generator.  The user interaction will be
improved so the user can more easily visualize the stereoisomers and
the stereochemistry of substructures  and can input stereochemical
information more intuitively.

  We will emphasize several  lines of investigation with regards to
examination and evaluation of structural candidates from CONGEX,
through the SIRE program.  Experiment planning will be approached
from the current PUN and UXX comnands, which search the environment
of program- or  user-specified structural features and  give the
experimentalist information on how the structural candidates vary with
respect to those environments.  The mass spectrum prediction and
ranking functions will be completed and transferred to BCPL versions
running as part of the CCNGENprcgram.  The concept of prediction and
ranking will be extended to proton and carbon NMR data using, first,
simple additivity rules and,  later, refining the predictions based on
more detailed examination of the structural relationships  among the
protons and carbons whose signals are being predicted. We hope that
this approach will be effective in choosing a small subset of highly
plausible structures based on agreement between predicted and observed
spectra,  just as the mass spectrum analysis functions have proven
useful.

129


  We plan no further development of the GC/MS/Comouter system, or
the REACT and MAXSUB programs.   Rather,  these will be used in
applications  to current structural problems in  conjunction with
compounds or data from other sources.  Incremental improvements will be
He as necessary if a particular new application demarads it.

130


  I.
  Apndix     CONGEN Worksho
Interests, CommZits on Program

Affiliation, Research

  1) Dr.  Henry Stoklosa, E.I. DuPont de Nemours.
Dr. Stoklosa has been affiliated with a group at DuPont
involved  with canputer  applications  to chemical
problaTls,  inc1tii.q computer-aided organic synthesis.
He will soon be involved in another group which might
also be able to make useof the REACT prugra in
addition to his more general interest in CCXEN.

  2) Dr. G.W.A.   Milne,  National   Institutes of
Health. Dr.  Milne is currently in charge of the
National Institutes of Health contribution to the
NM/EPA Chemical Information System.   His interests
included not only evaluation of the utility of the
program but also exploration of ways in which CfXGEN
might be interfaced to the Chemical Information System.
This effort-is described in more detail in Section 2.3.
Dr.  Milne offered both praise and criticism. He
praised the program itself but wants good user-level
docmentation and a large number of sample problems for
future wDr kshops.

  We are currently exploring with him the interest of
NIH in obtaining a version of the current program for
use on the NIH PDP-10 facility.

  3) Dr. William Brugger, International Flavors and
Fragrances. Dr.  Brugger represents the key person at
IE'F Research responsible for computer applications in
their laboratories.  Structure elucidation is a major
activity of this company not only in analysis of
natural and synthetic products but also in assessing
the relationships between chemical structure and toxic
properties affecting human health. Dr.  Brugger has
access to both DEC VAX and IBM computers,  the former
representing the laboratory computer.  The status of a
version of CCNGEN for these machines has been discussed
previously.  Meanwhile Dr. Brugger and his colleagues
are evaluating CONGEN at SUMEX via the GUEST access
facility.

  4) Dr.  Douglas   Dorman is   head of   the NMH
laboratory at .Lilly &search Laboratories and works
closely with mass spectroscopists and other chemists in
solving structures of a variety of compounds related to
existing or new products.  Dr. Norman has been familiar
with the "old" (non-exprtable) version of CCNGEN and

131


thus was able to critique the new program not only on
its merits but also on comparison with the old version.
His detailed critique is included in Appendix III. It
is worthwhile to point out that we are in the process
of implementing two of the important new features he
mentions because of their general importance. The
suRvm and EXAMINE  commands will allow both user-
specified   features used to  explore   structural
possibilities and Boolean statements used to select
structures with combinations of features.   The MSRANK
facility will perform the- selection  of plausible
structures based on agreement of predicted and observed
spectra. Dr.  Dorman has access to a PDF-10 computer
operating tier the TOPS-10 operating system.  About
&o weeks ago he received acopy of the exportable
CCNGEN and is now using the program in his own
laboratory. He  has agreed  to provide   us with
continuing caxments and criticism in exchange for
receiving updated versions of the program.

  5) Dr. Jon Clardy, Cornell University. Dr. Clardy
is a recognized leader in development and applications
of the technique of X-ray crystallography in structure
elucidation.  His attendance of the FForkshop was based
on an interest in learning about alternative, computer-
based approaches to the problem. As his letter points
out, the ability to use CCNGEN to help solve structures
before expenditure of time and effort in X-ray analysis
muld be an important benefit.  A more important
outcome of the workshop for  future research were
discussions on the possibility of coupling CONGEE-
suggested structures to Patterson search techniques.
In principle,  each of the candidates suggested by
CONGEN could be used in turn to guide the search of the
electron density maps for a fitting of the structure to
the maps.  The correct structure should yield the least
ambiguous fit.  Dr. Clardy will access CCNGEN at SUMEX
via the GUEST facility.  His ability to use CCN- at
Cornell depends on the success of the efforts of Mr. In
Ki Mun (next section).

  6) Mr.  In Hi Mun, Cornell University. Mr. Mun
attended the  workshop  representing   Prof.   Fred
McLafferty at Cornell.  Prof. McLafferty's group has
had for manyyears an  interest in use of computer
tec.hniques to help`solve structures, based primarily on
mass spectral d&a.  His research in this area has ld
to   programs   which  suggest the   presence of
functionalities in an unknown molecule. CCNGEN can, in

132


principle,  complete such a schema for. analysis by
piecing together the inferred functionalities. Mr. Mun
attended to explore the  feasibility of this approach
and tolearnhowbest to useCCXEXon the IBMsystem
at Cornell.  He is currently evaluating the effort of
modifying CCNGEN for an IBM version of BCPL. If
successful then this version should be available for
other persons who have good   interactive services
available at their IBM installations.

  7) Dr.  Mmar Breuning, Munich. Dr. Breuning
learned of the   existence of the  mrkshops from
discussions with Prof. Djerassi at the IDPAC meeting on
natural products.  Dr. Breuning had the opportunity to
attend as he was in the process of arranging a post-
doctoral appointment with Prof. Nakanishi (see next
section).  He is actively involved in natural products
structure elucidation at Munich and expects these
interests to continue.  Dr. Breuning can access (3XGEN
via Guest for the near future frun Munich.  At Columbia
he will h&e the opportunity to take advantage of
access to the facility there.

  8) Dr. David Lynn, Colmia University. Dr. Lynn
attended the  workshop  representing   Prof.  Koji
Nakanishi, the latter a recognized expert in the area
of structure elucidation of a n&r of classes of
natural products of relevance to human health. Dr.
Lynn is to act aS the focal point for introduction of
the computer methods to that research group. Prof.
Nakanishi's group has access to a  DEXZ-20 system
operating under the IUPS- operating system.   We are
currently arranging  for a version of CCXEN to be
installed there.  We anticipate no problems because of
our successful experiment during the  workshop of
running CONGEN on a DE-20 system at Rutgers.

  9) Dr. Y. Gopichand, University of Oklahoma. Dr.
Gopichand attended the mrkshop representing the marine
natural products group of Prof. Francis Schlitz. This
group  specializes in   structure   elucidation of
halogenated terpenoid molecules possessing a variety of
biological activities  and marine sterols representing
intermediates or end products in steroid biosynthesis.
As evidenced by the letter of critique, this group
represents an excellent example of classical approaches
to structure elucidation; sufficient data are collected
such that the n&r of structural possibilities is
reduced to a very small n&r.   As the letter also

133


indicates, CUNQN should be useful at least to check
the rigor of their structural assignment.   What should
prove more interesting is whether or not such a group,
with little computer expertise, can use CCNGEN earlier
on in the process of structure elucidation to guide
subsequent collection of data.

  l0) Ms. Wendy Harrison, University of Hawaii. Ms.
Harrison attended the workshop representing the marine
natural prcducts group of Prof. Paul Scheuer at Hawaii.
This group is engaged in structure elucidation problems
similar to   those encountered in   Prof.  Schmitz's
laboratory, although focus is on different classes of
organisms.  Their letter of critique mentioned that due
to   absence of   critical  high   resolution mass
spectrometric data to establish molecular formulas,
theyhavebeen unable to useCm this past month to
help on their problems.  This situation is expected to
be resolved soon.   Prof.  Scheuer plans to useCCNGEN
as an aid in a course  in structure elucidation this
caning  semester.  One difficulty is that this group
only has access   to a DEC PDP-11  system.   This
introduces all of the problems mentioned earlier on a
version of the program for mini-computers, inclLlaing
proliferation of manufacturers and operating systems.
For example, there  is a version of BCPL for PDP-11
series machines, but only uxx3er the m-11 operating
system, whereas the Hawaii group runs under The PSX-11
operating system.  For the near future, access from
Hawaii will be to CCNGEN at SUMEX running under the
GUEST directory.

  11) Dr.  Laszlo Takes and Dr. Michael Maddox,
syntex   F&search.    Drs.   Tokes and   Maddox are,
respectively, in  charge of themass spectrometryand
NMR laboratories at  Syntex Research.   They are
responsible for the majority of structure elucidation
problems which  rely on physical   methods.   Their
interest in CONGEN is that it might help them solve
certain problems in less time than required by manual
methods.  a'iyntex research has access only to laboratory
mini-ccmputers such as the DEC PDP-11 series machines.
They, too,  must await a smaller version of CCXGEN
suitable for mini-computers before being able to use
the program in their own laboratory.

  12) Dr. John Figueras, Kodak Research Laboratory.
Dr.  Figueras atteIlded representing  the Analytical
Sciences Division of Kodak's Research Laboratory. This

134


.

division is   responsible for data   collection and
analysis in supp&t of the   structure elucidation
activities of the Laboratoryincllding not `only new
developments in the photographic process but also the
new technology of thin-film bound enzymes systems for
clinical analyses.  His role was to evaluate what part
m could play in the on-going automation of of the
Division,  The Division will be obtainirq a DEC-20
system in the near future on which CCNGEN will run
directly.  MeamMle we have offered GUEST access in
return for continuing critique on utility of CCNGEN for
. large,  poly-heteroatanic,  aromatic molecules of the
types encountered in their research.

  13) Dr. Charles Snelling, University of Illinois.
Dr. Snelling attended the workshop representing Prof.
Kenneth Rinehart in the Chemistry Dept. at Illinois.
Prof.  Rinehart is also an acknowledged expert in
structure elucidation  with emphasis   on macrolide
antibiotics, halogenated terpenoids and other classes
of natural and synthetic products of relevance to hman
health problm.  Dr. Snelling had several cQnments and
criticisms about the difficulties facing a novice user
of such a'complicated system.  Althoughhe found the
program useful and wishes to get it  running at
Illinois, he would like to see sane changes made to
simplify use of the program for the chemist. There are
many canputer systems available at Illinois and choice .
of which system on which to mount cQEK;EN will depend on
the ease of the task and access to a ,oarticular system.
This is currently under study by them.

  14) Dr. Gilles Wreau, F&ussel LXX?@.   Dr. Moreau
attended the  workshop  representing the   French
pharmaceutical concern mussel UCIAF.  This ccxnpany
maintains an active group in computer applications in
chemistry and wished to evaluate CCNGEN for its use in
their structural problems.  me company  is quite
interested and will explore use of the program via
GUEST access.  They are concerned about issues of
secrecy for new problems and we have made it quite
clear that GUEST access represents public knowltige of
their problems.  Therefore, assming their interest
continues,  we will be arranging sune alternative to
SUMEX for use of CONGEN. They have access to IEM
equipment and we are awaiting further description of
the form of access possible.

15) Prof.  Andre Dreiding, Zurich.  Dr. Dreiding

135


has been interested in both the problem-solving and the
pedagogical aspects of CCBJGEN for scane time.   He had
previously used the old version and was gratified to
see the improvements in the new version.  He would like
to see much  more attention paid to   the actual
structures (i.e.,  in three dimensions)  of molecules
rather than simply their constitutions as CONGEN, with
the  exception of  the STE!RUl canard, currently
represents structures.  We are, of course, working very
hard to introduce concepts of stereochemistry into our
cmputational procedures.  Prof. Dreiding will probably
be able to access CCNGEN at Zurich on an existing PDP-
10 installation.  If so, export to his group will be
trivial.

  16) Dr.  James Shoolery and Dr. Michael Gross,
Varian Associates. Dr.  Shmlery is in charge of
Varian's W application laboratory and Dr. Gross is in
charge of computer software for Varianas NMR/computer
systems.   Their  respective  interests   match their
responsibilities.  Dr. Shoolery feels that CCNGENcould
be a valuable assistant in helping solve structures
based primarily on proton and carbon XMR data. In
fact, he has been able to demonstrate such an approach
on some recent problems of persons outside Varian. Dr.
Gross is interested in a mhi-computer version of
CCNGEN for incorpxation  into their existing data
system.  Although we cannot ourselves support such an
effort,  we have agreed to prwide them withprogram
listings and documentation to explore the feasibility
of a small machine version.

  17) Dr.  Daniel F. Chodosh, .Bnith,   Kline and
French. Dr.  Chodosh was not actually invited to the
workshop, but happened to visit our group during one of
the sessions.  He was sufficiently impressed that he
procured a tape to carry away a copyof the program
with him. He has now been supplied with a version of
CCXGEN for the PDP-10 and as of last wek has it
running at the SKJ?   research   laboratories in
Philadelphia.   This   is an  interesting experiment
because as an informal attendee of a small portion of
the wxkshop,  he is learning  the program almost from
scratch   based  on existing  help   facilities and
documentation. .He will begin introducing others to the
program when he has developed sufficient familiarity to
be comfortable with the program.     -

In addition, the following persons during the past year have asked

136


for information about and access to CCWGEN. For the most part we have
granted access through the GUEST directory, setting up an account only
for those users with n0re than occasional log-ins.

Dr. David Cowburn
Physical Biochemistry
The Rockefeller University
New York City

We have sent Dr. Cowburn information on access to CCNGEN and are.
currently discussing how to use same of our computational methods
or extensions to them for assistance in his problems of elucidating
peptide conformations.

Douglas Henry
School of Pharmacy

Oregon State University
Corvallis, Oregon

He has been sent o& Fograms for structure drawing for use
on his own computer.

The following have asked for and received information on access to
CCNGEN at SUMEX via the GUEST facility.

Dr. H. Kating         .
Institut fur Pharmazeutische Biologie
Der Universitat
Bonn, Germany

Dr. Kerber
Lehrstuhl D fur `Yathematik
Aachen,Germany

Dr. Brenda J. Kimble
Radiobiology Laboratory
University of California
Davis, California

Dr. J. Neubuser
Lehrstuhl D fur Mathematic
Aachen, Germany

Dr. George Padfila
Dept. of Physiology *
Duke University-Medical Center
Durham, N.C.

Dr. W. Sieber
sad02 Ltd.

137


Basel, Switzerland

Dr. Babu Venkataraghavan
Merle Laboratories
Pearl River, New York

We also helm him bring up the Fortran draw program on the DEC-10
system at Merle

Dr. Stephen Wilson
Dept. of Chemistry
Indiana University
Bloomington, Indiana

138


Le;Le~;fAgitation
Sent
        ?o???? o

139


DEPARTMEST Of CFIEMLSTRI

STANFORD UNIVERSIT:
STANFORD. CALIFORNIA 9430?

August 24, 1978

Professor Kenneth Rinehart
Department of Chemical Science
University of Illinois
Urbana, Illinois 61801

Dear Professor Rinehart:

I am writing to determine  your interest in a mini-workshop we plan to
hold at Stanford on use of computer programs  for computer-assisted
structure elucidation.  Over the past three years we have been involved
in a research effort directed in part to exploring the  feasibility and
utility  of interactive  computer programs  as tools  to help chemists
solve unknown structures.  The most highly developed of these research
tools is the CONGEN program, and I know that you  have in one way or
another been exposed to this program.

We have made CONGEN available on the SUMEX computer here at Stanford
via communications networks to a selected group of chemists  because we
know that the only way to improve the program and to make it useful is
to apply it to a variety of real structural problems in chemistry. We
have learned a great deal from this experience and have designed a
production version of CONGEN with th? primary goal of eliminating the
deficiencies in the research version.  In particular the new program is.
much simpler to use, much  qpaller and faster and can be exported to
certain other computers.

There is a significant amount of work which remains to be done to make
the exportable version of CONGEN a truly useful chemist's "assistant".
Some of this work is underway now.  But before investing a great deal
of time and effort in polishing a new  version to make it more useful
and acceptable,  we would like to expose a  group of  several chemists
experienced in structure elucidation to 'this version of the program and
base future  research and development  efforts on their perceptions of
deficiencies remaining in the program and its ultimate utility. We
feel its usefulness can   be significant in terms   of exploring
alternative structural possibilities  and in guaranteeing  no plausible
alternative has been overlooked.  However, in order to demonstrate that
utility we need assistance in developing a version which  large numbers
of chemists can use  easily and productively in their  own laboratories
and on  their own  computers.  We feel that by participating in this
workshop you can contribute in an important way.

We plan  an approximately four to five day  informal workshop here at
Stanford, to be attended by you or one of your experienced co-workers.
During this time you would  be able to use the exportable  version of
CONGEN here at SUMEX to work on recent structural problems encountered
in Your laboratory, which we hope will include  some which  would be

140


unknowns.  In turn, we would be learning how to finish development .of
the first  vergion of the program for export  to your laboratory with
some guarantee that major problems or deficiencies would  be eliminated
based on the experience of the workshop,  We have not yet established a
time for the workshop,  but we are tentatively considering a date
between October and December, 1978. We are also trying to arrange for
travel support for non-industrial persons.  We are seeking now only an
expression of interest on your part.

There are only two requirements on your part, other than your expressed
interest in participating.  The first requirement is that you must be
capable  of accessing CONGEN at SUMEX or preferably be capable of
running CONGEN on your own computer system.  The second  requirement is
that you .actually be  interested in using the program in  the future
-  (assuming the workshop was worthwhile) to provide us with some feedback
on whether improvements meet your criteria for acceptance.

Currently' the new  version of CONGEN can be used on Digital Equipment
Corp. PDP-10's and 20's with little problem. We are now exploring use
of IBM 360 and 370 series machines.  We have already demonstrated that
small segments of the program run on suitably configured IBM computers.
However, for CONGEN to be used interactively requires a time-sharing
operating  system.  If you have access  to an IBM computer but are
uncertain  about  the operating system,  find out from your computer
systems people the name of the operating system and call or write to u3
with that information.

While at Stanford you would also  be able to take a close look at some
of our other  research effort3  which are  not quite  so far  along as
CONGEN,   including a   recently finished   stereochemical structure
generator,  the REACT program and a variety of  tools for ranking
structures based on  comparison of predicted  and  observed spectra,
facile examination of large sets  of structural candidates for common
and unique features and methods for assistance in  experiment planning.
We would appreciate your evaluation of these effort3 also.   The main
emphasis, however, will be on CONGEN.

Obviously we do not expect a firm commitment for attendance at this
time, but if at  all possible I would appreciate a reply.  Indication3
of your interest are important in this regard.

Your3 sincerely,

Carl Djerassi
Professor of Chemistry