PUBLICATIONS: D. H. SMITH                     Page 2

11.

. 12.

13.

14. '

15.

16.

17.

18.

19.








20.

The Lunar Sample Preliminary Examination Team, "Preliminary Examination
of Lunar Samples from Apollo 12," Science, 167, 1325 (1970).

D. H. Smith, "Mass Spectrometry, " Chapter X in Guide to Modern
Methods of Instrumental Analysis, T. M. GOUW, Ed., Wiley-Interscience,
New York, 1972.

D. H. Smith, R. W. Olsen, F. C. Walls and A. L. Burlingame, "Real-time
Mass Spectrometry:  LOGOS--A Generalized Mass Spectrometry Computer
System for High and Low Resolution, GC/MS and Closed-Loop Applications,"
Anal. Chem., 43-, 1796 (1971).

A. L. Burlingame, J. S . Hauser, B. R. Simonei t, D. H. Smith, K .
Biemann, N. Mancuso, R. Murphy, D. A. Flory and M. A. Reynolds,
"Preliminary Organic Analysis of the Apollo 12 Cores," Proceedings of the
Apollo 12 Lunar Science Conference, E. Levinson, Ed., M.I.T. Press,
Cambridge, Mass., 1971, p. 1891.

D. H. Smith, "A Compound Classifier Based on Computer Analysis of Low
Resolution Mass Spectral Data,`! Anal. Chem., 44, 536 (1972).
                                                -

D. H. Smith and G. Eglinton, "Compound Classi fi cation by Computer
Treatment of Low Resolution Mass Spectra-Application to Geochemical and
Environmental Problems, " Nature, 235, 325 (1972).

D. H. Smith, N. A. B. Gray, C. T. Pillinger, B. J. Kimble and G.
Eglinton, "Complex Mixture Analysis - Geochemical and Environmental
Applications of a Compound Classifier Based on Computer Analysis of Low
Resolution Mass Spectra," Adv. in Org. Geochem., 1971, p. 249.

D. H. Smith, B. G. Buchanan, R. S. Engelmore, A, M. Duffield, A.
Yeo, E. A. Feigenbaum, J. Lederberg and C. Djerassi, "Applications of
Artificial Intelligence for Chemical Inference, VIII. An Approach to the
Computer Interpretation of the High Resolution Mass Spectra of Complex
Molecules.  Structure Elucidation of Estrogenic Steroids,"' J. Amer. Chem.
sot., 94, 5962 (1972).
--

D. H. Smith, A. M. Duffield and C. Djerassi, "Mass Spectrometry in
Structural and Stereochemical Problems, CCXXII. Delineation of
Competing Fragmentation Pathways of Complex Molecules from a Study of
Metastable Ion Transitions of Deuterated Derivatives," Org. Mass.
Spectrom., z, 367 (1973).

P. Longevial le, D. H. Smith, H. M. Fales, R. J. Highet and A. L.
Burlingame, "High Resolution Mass Spectrometry in Molecular Structure
Studies, V.  The Fragmentation of Amaryllis Alkaloids in the Crinine
Set-i-es, I' Org. Mass Spectrom., 7, 401 (1973).
                       --


PUBLICATIONS: D. H. SMITH

21.

22.

23.

24.

B. R. Simoneit, D. H. Smith, G. Eglinton and A. L. Burlingame.
"Applications of Real-time Mass Spectrometric Techniques to Environmental
Organic Geochemistry, I I.  San Francisco Bay Area Waters," Arch. Env.
Contam and Tox., 1, 193 (1973).

D. H. Smith, B. G. Buchanan, R. S. Engelmore, H. Adlercreutz and C.
Djerassi, "Applications of Artificial Intelligence for Chemical inference,
IX. Analysis of Mixtures Without Prior Separation as Illustrated for
Estrogens," J. Amer. Chem. Sot., 95, 6078 (1973).
                                    -

D. H. Smith, B. G. Buchanan, W. C. White, E. A. Feigenbaum, J.
Lederberg and C. Djerassi, "Applications of Artificial Intelligence for
Chemical Inference, X. INTSUM - A Data Interpretation and Summary
Program Applied to the Collected Mass Spectra of Estrogenic Steroids,"
Tetrahedron, 29, 3117 (1973).
             -

G. Loew, M. Chadwick and D. H. Smith, "Applications of Molecular
Orbital Theory to the Interpretation of Mass Spectra. Prediction of
Primary Fragmentation Sites' in Organic Molecules," Org. Mass Spectrom. f
z, 1241 (1973).

.

a7


SECTlON II -PRIVILEGED COMMUNICATION
                      BIOGRAPHICAL SKETCH

(Give the following information for ell professionel personnel listed on pege 3, bqinning with the Primipel Invartiptor.
       Use continuation pegar end follow the seme generel former for each psrronl

NAME                    ITITLE                  IBIRTHDATE ma, OW, rd

Sridharan, Natesa S.               Research Associate

10/2/46

PUCE OF BIRTH (City, Stete, Country)

PRESENT NATIONALITY (II nonUS citizen,    SEX
indicete kind of Vise and expiration data) India .

                                                                           ',
Madras, India              5/73-U.S. permanent residence     (g Male   0 Famals
              EDUCATION (&gin with baccelaurwte training end include postdoctorell
                                                                        SCIENTIFIC
          INSTITUTION AND LOCATION               DEGREE         YEAR
                                                    CONFERRED             FIELD
Indian Institute of Technology, Madras    Bachelor of
India                       Technology     1967    Electrical Engineering
State University of New York, Stony Brook M.S.          1969    Computer Science
                                Ph.D.          1971    Computer Science

HONORS
University Fellow - 1968-1971, SUNY Stony Brook; Graduate Assistant - 1967-1968, SUNY
Stony Brook; Siemens' Award (awarded for top rank in Electrical Engineering) - 1967, ITT
Madras; National Merit Scholarship - 1963-1967, ITT Madras                                   -
MAJOR RESEARCH INTEREST                    ROLE IN PROPOSED PROJECT
Computer Application in Chemistry

and MedicinL

RESEARCH SUPPORT (See instructions)

Research Associate

----

RESEARCH AND,QR PROFESSIONAL EXPERIENCE (Sterling with pfscent posidon,list end experience relevant to eree of p.ro@cl,  L!%t efi
or most representetivepublicetioru.  Do not exceed 3 peges for eech individual.)
1971-present Research Associate, Heuristic Programming Project, Stanford University

1970-1971    Consultant, IAC Computer Corp., Long Island, N.Y.

Sridharan, N.S., "An Application of Artificial Intelligence to Organic Chemical Synti-'esis"
Doctoral Thesis, State University of New York at StonyBrook, 1971.
Sridharan, N.S., "Search Strategies of Organic Chemical Synthesis", Third International
Joint Conference on Artificial Intelligence (3IJCAI), Stanford, 1973
Sridharan, N.S. (co-author), "Heuristic DENDRAL: Analysis of Molecular Structure", Proc.
NATO Advanced Study Institute, Amsterdam, 1973.
Sridharan, N.S. (co-author), "Heuristic Theory Formation", Machine Intelligence, Volume 7,
Edinburgh, 1972.


SECTION II - PRlVlLEGED COMMUNICATION
                        BIOGRAPHICAL SKETCH

NAME

(Give the following Inform&ion for sllprofessional pononnel listed on page 3, brginning w'th the Principal Invertlgator.
         Use continuetion pqm snd follow the snme genaruf format for eech person)
                           TITLE                        BIRTHDATE (Ma, Day, Yr.1

Brown, Harold D.                    Associate Professor        July 12,1934
PLACE OF BIRTH Kiry, Sate, Country)           PRESENT NATIONALITY f/f n0n.U.S citizen,     SEX
                                indicate kind of vis, and expiration date)
South Bend, Indiana                 u.s,               B Male Ofcrnale
                   EDUCATION f8eoin wirh bacce!auraate ttaining and include oostdoctorsll

lNSTlTUTlDN AND LOCATION

University of Notre Dame, Notre Dame,
Indiana

Ohio State University, Columbus, Ohio
       (No Baccalaureate Degree)

HONORS

Summa Cum Laude - Notre Dame

  YEAR            SCIENTIFIC
CONFERRED            FiELD
1963      Mathematics


1966      Mathamatics

MAJOR RESEARCH !NTEREST               %%k IN PROPOSEC) PROJECT
Applied Discrete Mathematics - Computer
   Science                              Research Associate
RESEARCH SUPPORT (See innrvctionrl

Principal Investigator, NSF-GP-16793 (Expires March, 1974)

Pending Proposal NSF (Proposed starting date September, 1974)

RESEARCH AND/OR PROFESSIONAL EXPERIENCE (Starting withprarent position,&J&(&gandexpetien&rel@vant tort-e* i,fproht L.tiz
or most representative publicetions.  Do not exceed 3 pages for each individual.)
Visiting Associate Professor, Computer Science, Stanford University , 1971-72, 1973-present
Associate Professor, Mathematics, Ohio State University, 1966-
Visitin.g Professor, Mathematics, Rhine,Westf. Tech. Hoch., Aachen, 1972 and 1973
Visiting Member, Courant Institute, New York University, 1967-65
Instructor/Assistant Professor, Assistant Chairman, Mathematics, Ohio State U.: 1963-65
Assistant to the Chairman, Mathematics, University of Notre Dame, 1960-63
Director or Associate Director, NSF-SSTP, 1964-70


Vitae   Pace 2

7Ciea.r A`l@'L)ras, Ill. J. Kath, 12(1968), Pg. 215.
Distrjbutor Theory in Rear AlZebras, Comm. Pure App. Eath.
  ??? ?o??O? ??? o ????

An Algorithm for the Determination of Space Groups, Ma& Comp.
  23(w59), Pg. 499.

Some Empirical Observations on Primitive Roots, with H. Zassenhaus,
  J, Number Theory 3(1971), Pg. 306.

A Generalization of Farey Sequences, with K. Eahler, J, Number
  Theory 3(1971), pg.364,

Basic Computations for tiders, Stanford CS Kemo STAN-CS-72-208.
An Application of Zassenhaus' Unit Theorem, Acta Arith. xX(1972),
  Pg, 154.

Integral Groups Tx The Reducible case, with J. Xeub:iser and
    II, Zassenhaus, Numer. Math. 19(i972), Pg. 3%.
Integral Groups II: The Irreducible Case, with J, Neubtiser and
   H. Zassenhaus, Numer. Math. ZO(l972), Pg. 22.
. Integral Groups IIIt Normalizers, with J. NeubGser and
    H, Zassenhaus, l-lath, Conp. 27(1973), PC;. 167.
Constructive Graph Labeling Via Dollble Cosets, with L. Hjelmeland
   and L. Mnsinter, Di&rete Wath, in press and Stanford CS I:e?lo
    STAN-E-72-318.

An Algorithm for the Construction of the Graphs of Organic liioiecljles,
  with I., Kasinter, Discrete Hatll. in press and Stariford CS E:eno
  STAN-G-73-261, )

The Crystallogaphic Groups of &-dimensional Space, with 2, Neubcser,
   H. Wondratschek and H. Zassenhaus, Wiley-Interscience in Fess.

30


SECTION II - PRIVILFtiEO COrulMUNICATlON
               ---         ------
                        8lOGRAPHICAL SKETCH

-II

{Give the following information forsllprofmsionel personnel listed on page 3, brglnning w'th the Princi@ Invartlpgtor.
         Use continuation moos end follow the s?rne aenerrtl former for eech person)

NAME

-
    TITLE                       BIRTHDATE (Ma, Day, Yr.)

DROMEY, Robert Geoffrey
PLACE OF BIRTH (Ciry, Stste, Countryj

Research Associate           11121146
PRESENT NATIONALITY (If non4.S citizen,    SEX
indicete kind of visa end expiration de tel

Castlemaine, Victoria, Australia   ustralian, J-l Visa, Exp. 10/8/74 ~~~~~ o>cms'a
              EDUCATION (Begin with baccelaureate training and include postdoctoralj
                                                                          SCIENTIFIC
         INSTITUTION AND LOCATION              DEGREE        YEAR
                                                      CONFERRED             FIELD
Swinburne College of Technology,       Diploma of     1968   Chemistry
Melbourne, Australia             Appl. Chem.
La Trobe University                     Ph.D.       1973    klolecular Science
Melbourne, Australia

HONORS CSIRO Postdoctoral Studentship
   Commonwealth Postgraduate Research Scholarship
    Walter Lindrum Memorial Scholarship

Artificial Intelligence Techniques to Bio
Medical and Chemical Problems.
RESEARCH SUPPORT (Sseinn~ctionrl

Research Associate

----

RESEARCH ANDjQR PROFESSIONAL EXPERIENCE (Starting withpracent positicn,~~sndexpen'sncerel#ent foor~s ofpmbt Lind
ormort mpnasntetivepublication+  Do not exceed 3pages for sach individual.)
1973   DENDRAL Project, Stanford University, Computer Science Department
1973   Software Development for Graphics Systems, LaTrobe University, Computer Centre
1969-73 Construction, development and applications of an on-line photoelectron spectrometer
     LaTrobe University, Chemistry Department
1569-73 Application of Deconvolution Techniques to the Processing of Experimental Data.

Publications:

"Deconvolution and Its Application to the Processing of Experimental Data", Intl. Journal,of
Mass Spectrometry and Ion Physics, 1970, 5. (co-author).

"Inverse Convolution in Mass Spectrometry", Intl. Jnl. Mass Spec. Ion Phys.,1971, 6. (co-

author).

"A Combined Time Averaging-Deconvolution Technique Applied to Electron Impact Ionization
Efficiency Curves", Internation Journal of Mass Spectrometry & Ion Physics, 1971, 5.
(co-author).

"The Perfect Direction and Velocity Focus at 254034' in a Cylindrical Electrostatic
Field", Reviews of Scientific Instruments, 1373, 44. (co-author).
                                                      -


R. G. Dromey

*'Detection of Spin-Orbit Splitting in the Photoelectron Spectrum of 02+ by Deconvolution",
Chem. Physics Letters (in press), 1973. (co-author)

"The Effect of Finite Line Widths on the Interpretation of Photoelectron Spectra", Journal
of Electron Spectroscopic (accepted for publication). (co-author).

"An On-line Ultraviolet Photoelectron Spectrometer for High-Resolution Studies o-f Molecular
Structure", Australian Journal of Chemistry (accepted for publication). (co-author).

"Photoelectron Spectroscopic Correlation of the Molecular Orbitals of the Alkanes and
Alkyliodides", Journal of Molecular Structure (submitted for publication). (coauthor).

"Comparison of the Photoelectron Spectra and the Photoionization EffFciency Curves for
the Alkyliodides", Transactions of the Faraday Society (submitted for publication).
(co-author).

"A Convolution-Deconvolution Algorithm Using Fast Fourier Transforms), Decuscope,
1973 (in press).


RESEARCH PIAN

33


  I.








rr,


ITT,


?? o


??


? ?? ?

PTOMOLECTJLAR CHARACTPFT7AfI3N:  AFTTFICTAL INTFLLIGENCE
     A Program of Fesource-!?elated 3esearch

A.  3bject.ivcs
n.  Backqround artd Rat ionale
C.  Pelationship to AIY-SUMFX and the Genetics Research Center

SPECIFIC AIFlS

t3FTH3DS


SIZNIFICANCE OF PROPOSED FESEARCE

FnCTLITIES 8 Z;QUIPI?FENT


ETBLIOGRAPHY

SahL~ 1
Fiqurps l-3
Appendix 4:   Letters of Interest
4op enlix R:   1973 Annual Report to the NTii


1.   INTFDDUCTION

Thi 3 r?czec3'L application is intended to susfain and augment the
zapabilities of the mass spectrometry (MS) program which has
;ecv~!il 3s 3 major insTitutional resource at Stanford for some
yp3rs.  Rith previous support from NASA and NSF it has made
oossible a hiqhly interdisciplinary set of research projects
r;tnqiPq ov2r:  artificial intelligence (AI) in biomolecular
~h3r3cterization,  natural product chemistry, clinical biochemical
sttl!ies on steroids,  and the mechanisms of molecular fragment
Formation in mass snectrometry.  While the facility equipment for
mass spectrometry has been funded mostly by other agencies,
cDnne!cted research proqrams embrace several NIY research projects
is wzll,  In addition, this activity was closely coupled with the
?,"FF Ye!ical school computer resource (1966-19731 and will have
sisflnr associations with the  new RI?!-S!JEl?X conputer resource
re:ontly flnded by the BP2 (see Section T.").

Previous support ref1ect.s the diversified facets of this
icperdisciplinacy research,  RASA has supported projects in new
i?:trunent3tion,  inclurlinq the initial mass spectrometer-computer
Ilnk,  gSF has supported chemical research,  and ARPA has supported
our artificial intelliqencc research and initial application to
nass spPctrometry,  Overall cutbacks have forced NASA to reduce
Ftinqinq for this area of research despite their interest.   Under
AFP.4 sunport to Drs. Feigecbaum an3 Lederherg for AI research, the
DENDPAL proqram became recoqnized as one of the most successful AI
3pplic3tions programs.   Eowevec *  ARPA is chartered to fund
Fr3nti~c computer science research and no longer provides funds
fnr the DENDRAL applications programs.   APPA has indicated a
relozt3nz~ to continue funding to this groun for the theory
fncmatior, work in chemistry, although we expect to continue to
receive AfiPA support for more theoretical aspects of OUT research
3r3ffr451  (e*q*,  3utomati.c  proqrarrming).

iJc previously submitted a comprehensive proposal to the NIH
(Rt?-~07SS,  3/25/73) which included an application for the
4fY -SUVEX zr>mputinq resource and a renewal  o f the existing DENDRAL
qrant IPP-00012) o  This proposal was approved for 5 years by the
Pational Advisory Researc+ Fes3urces Council.   Certain
reservations were,  however,  communicate3 to us:  they concerned
especially what we must aqree was an  ambitious effort to close the
control loop for  l'intelliqent. automationfi*  whose costs overreached
t he imme~i3~e utility of the expected result.  During subsequent
3iscussiDn? with the RioTechnDLoqy Resources Branch, takinq into
accnurt the council review aR.d a number of diverse policy issues,
we 37ceoit administratively to seqment the two components of the
3riqinaf proposal.  The ATPI-SU?!EX portion of the original proposal
(exclil3inq DI?F?DRAL) was recently funded for 5 years as a national
resource for artificial intelligence in medicine.  The present
~r~p~ri31 for resource-related research in hiomolecular
characterization and artificial intelliqence is an elaboration of
thz DEN?RAL portion incorporating intensive reexamination and
revision of the previous proposal.

Vith thr? differentiation of priorities represented by AItl-SUEEX,


th?  "tlnetizs  Fesearch Center (ZPC),  and continuinq work on
Irtifizial intelliqecce under Dr.  Feiqanbaum's leadership, the
Dresclt renewal application places more emphasis than heretofore
3n real-world oriented applic2t.ions.  Correspondingly, we have
sqceei that it is now more appropriate thst Dr. Djerassi should be
?ps!qn3ted as Principal Investiqatz)r in this phase of our work.

Fs outline3 in section 3.2, the interests 2nd responsibilities of
?r3f?ssors Djerassi (Chemis+ryl I Feiqenbaum (Computer Science) and
'_e?erberq (Genetics) have? been closely intordigitated.   With their
f!lrther connections with many colleagues,  these programs enjoy a
h irJh acqrs? of university-wide participation.  For example, the
?zRttics rtppartment is also closely affiliated with Biology,
Bi 3zhemis+.ry, Pediatrics, Psychiatry an3 xedicine through joint
lppointrnents or joint research projects or both.   This breadth
would be difficult to obtain except at a few institutions where
t5s medical. schDo3. is both aca4emicslly an3. qeoqraphically
inteqrlted with the university t:, the deqree that characterizes
the Stanford University envir0nmeF.t.

GLOFSARY !IF ABDREVIATIO?JS

AC"F    - Advanced Computer for Yedical Research {Nib-funded computer
           resource,  1968-1973)
91      - artificial intclliqencp
4 It!-S!Tr!??Y- A comprehensive computer resource jntended to serve

the n&iqnal requirement for artificial intelligence
in medicine.  This will be implevsnted at the Stanford
University facLlity called AIM-SVYEX
- Advanced Research Projects 4qency of the Department of
Defense.

- Biot?chngloqy Resources Rranch
- carhDn-l? saqr;etic resonance
- qas chroaatoqraphy or qas chromatoqraph
- Genetics Research Center (Stanford, J. Lederberg,

Principal Investiqator; NIGYS-approved and
awaitinq fundinq.  Grant #PDl-GY 20832-01)
- hiqh resolution mass spectrometry
- infra-red
- Tnstrumentation Research Laboratory

{Stanford Gene%ics Department)
- low resolution mass sppctrometry
- magnetic circular dichroism
- Mass spactronetry or mass sDectrometer
- National Aeronautics G Space Administration
- nuclear maqnetic resonance
- National Science Foilndation
- optinal rotatory dispersion
- a mo-lified version of the PL-1 computer language (for the

Stanford ACME computer fscility)
- Stanford University Eedical Experimental Computer Resource
(WIH funded computer resource, 1973-1978)
- ultra-violet

3&


A.   03JECTTVES:

Core Research.

"he fllnds now applied for would permit

1)  the continued fundinq of the ?!S laboratory as a biomolecular
oh3r37cerization resource;

?)  advancement of laboratory instrumentation capability in
specific areas of GC-HRMS and the exploitation of metastahle peak
linalvsis.

3)  the fucther development of AI computer techniques to match the
instranentation.  This work will emphasize practical utilization
for applications in biomolecular characterization connected with
other on-qoinq biomedical research programs.  It will include, for
3X3UP1, al   the analysis of mixtures by SC/MS; b) metastable peak
3n3lvsis f>r difficult problems of pure compounds and of mixtures
not rcalily separable by CC; c)  optimized data analysis for
zhsr3cterization of MS peaks an3 d) heuristic analysis of spectra
for the molecular ion composition.

?ur project is the only systematic effort, to our knowledge,
cl~rrently underway in this country for computer assisted structure
?licidation,  Subsequent to our early publications, an intensive
proqram has been mounted in Japan in similar areas.   This
situa+.lon may ho contrasted with computer assisted organic
synt.h,+sis, an area receiving considerable attention from several
ccse3rzh qroups,   The%? capabilities can be beneficially provided
t3 a wider community via the ATM-SUP?SX resource.   Research on the
?nulstion of human intellect by computer programs will undoubtedly
Influence the efficiency with which chemical research can be
soplied to ever more complex problems of health, e. q.,
intermediary metabolism and its pathologies; environmental
infl3F?n:a s on hea1t.h; the development and critical validation of
new therapeutic aqents.

"he a:Elevament of these nbjectiQeS depends on the continued
maintenance and development of the DENDP9L AI programming system
{see h313WI .  The advent of the ATM-StMEX facility will remove
some nf the serious computational limits on the exercise of this
system that have delayed recent progress.

Pduc3tion.
rn our university setting, pre-doctoral and post-doctoral
educa+_ion of course constitutes a part of our mission.   As far as
is practically possible, research participation in the DENDRAL
proqram has been couple3 with 3 issertation w3rk by graduate
stu??nts and post-doctoral research experience respectively.
Ex3 mplss of people (and their research area) whose education has
Seen enttan:e d in this way are the followinq:

Srad~late Students: J, Simek, padaqoqical aspects of the structure
qerlerstor;  Rai Lee Tan, synthesis of new estroqen compounds; H.
Fqqcrt,  13ZYYIR of amines and st?roidal ketones; C. Van Antwerp,
13CYR of steroidal alcohols; C. Farrell, theory formation from
~a3s spectral data; L. !!asint.cr, development of the structure
qnnnrator; Y. Stefik,  AI applications to chemistry.

37


F'nst3933rll Fcllous:   r,. Drr)mey,  theory formation f ram analytical
!3t3; P. Sritter, mass spectral  fragmentation of bioloqically
active steroids; R. Carhart, analysis of 13CI?R spectra by
DSNDRAL-like programs; 5, Hammerurn, development of better
fraqmcntation rules for proqesterones.

Fofmll orqlnization.
*his project has been a long-term commitment of Djerassi,
Lederberq and Feiqenbaum functioning in effect as
Jo-investigators,   We coordinate our activities with day-to-day
zDntlc?s i.1 the pursuit of converqent research objectives.   In the
light of the extension of our collaborative activity during the
1.3;t tdo years,  we are now orqanizinq a formal advisory group to
i ~cludp,  in addition to ourselves, H. Cann, J. Barchas, and E. Van
Tamelen,  This qroup will advise the principal investigators on
the direction of the proqram with respect to allocating available
facilities and seekinq out and helping other collaborators,   This
desiqlation simply recoqnizes the fact that many of our colleagues
haIre already been ecqaged in c. alevant collaborative research with

1s.  A '?S resource has recently been funded at the riniversity of
California/Berkeley,  under the direction of Dr. A.I..  Burlingane.
Drs.  Djerassi and Burlingame have recently engaqed in some
zollahorative research which was made more successful by the
sharinq of facilities ard expertise  available at or.e institution
but n?t at the other.  We would hope to maintain and strengthen
t hES2 contacts to avoid unnecessary duplication of effort.

U?  plan to discuss with Dr. A.L.  Burlinqamo the most appropriate
pr3c?Aures for coordinaticq the related activities of our
respect ivn proqrams at the 1Jni.versit.y of California/Berkeley and
!I?_?.   ?hi; may take the form of reciprocal membership in advisory
committees.

fhs
   '*hardware resource w to which this application is pegged has
333~ id entified as the MS facility.   ahile these  instruments alone
represent an investment of over 5`300,000, funded previously by
several aqencies, they do not represent the most important resource.
WC, would use this designation instead for the working team led by
th,e princioal and co-investiqators.  The skills embraced by this
group Fncllde, as mentioned, computer science, structural orqanic
zhemis+rv,  molecular biology,  instrumentation enqincering and a
wide ranqe of other disciplines,  They are represented not only in
tke princinal professors hut in a diversified and accomplished
orofessional research staff (SE?;? Bu3qet Justification).   The
proqrlm for which funds are now requested is the vital means by
which the interests of this qroup can he sustained in a
zn?r3inate? effort that would be very costly both in funds and in
tin4 if  it had to he reconstructed from scratch.   'dithout the
finanziatl support now requested, this line of collaborative
research will have to he abandoned,  with it a unique style of
interdisciplinary collaboration,  and the "1s facility will be
terminated.


9.   BACRGP3JJND AldD RATIOWALE

1,   Phe StrtlctVlre Elucidation Problem

    3)   The General Problem,  Analysis of molecular
structure is a major activity in our program of resource related
research.  For the speci.fic task of efuci3ating molecular
structures, i.e., the topoloqy of atom-to-atom connectivities,
analysts utilize a mixture of information derived from chemical
procedures and spectroscopic techniques.   Each item of
information,  if not red!lndant 3r uninterpretable, contributes to
t4e solution of the problem.  Chemists 3raw upon a tremendous body
7f snecific knowledge about the task area (e.q., clinical
chemistry,  biochemistry), molecular structure, spectroscopic
techniques, etc., in or3er to piece together this information and
l?fer the  structure of aolecules.  These features, and the
relative si!nplicity of the finai concept of a structure, make the
prohl?m particularly well-suited for applications of the
tec!iniqtles of AI to assis t research workers performing the task.

    bl  D-jerassF*s Laboratory.  Professor D jerassi has been concerned
with secncture elucidation problems since the beginning of his
-hamica research.
Y kL,d               His activities at Stanford have been concerned
heavily with the apnlication of particular spectroscopic
techniques to structural studios of biomedically important
~3nP3unas.  These techniques include optical rotatory dispersion
IoR?) and,  more recently,  maqnetic circular dichroism (BCD) (both
3f t.hem supported initially by the NIH),   Since 1961 he and his
?coun have also been concerned with MS because of the power of the
technique, in terms of specificity and sensitivity, as an
an3lyticsl tool for structllre elucidation.   Four books and
anproximately 250 articles on 9s have been published by him and
i i.s  zolIea7ues.

rha technique of E4S does not silffice for all structure
3zt~rminatio~ problems,  but it is a very powerful tool in areas
where thora exists a body of knowledge about the MS behavior of
related molecules,  Bhen sample size is limited MS may well be %he
only technique that tag be utilized.  The recent availability of
hiqh resolution mass spectrometers has madn HFMS the technique of
c: h 3 s z e four ntany applications because under ideal conditions the
exact mass number uniquely specifies the the empirical formula of
3 molecule or fraqraent.  nn a parallel course, the technique of
;:/?pS, routinely available with low resolution mass spectrometers
(r,C,'LRMS),  has revolutionized investigations wherever complex
aixtclrss ace encountered.  All of the above considerations argue
that an extension o f H,S at Stanford to provide routine GC/LRMS and
;C/!fRMS an.alyses would he the next logical step to assist
researcher; depending on this facility for solutions of their
structure elucidation problems.

2.   Aistorical Backqrnund

    91   Y3ss Spectrometry Laboratory.  Prior to the existing DENDHAL
7 r I c t ,  the qroundwork was laid for computerization of the existing
mass spectrometers, an Associated Electrical Industries MS-9 high
resolution mass spectrometer and an Atlas Z'i-4 low resolution mass
spectrometer.  This work, supported primarily by NASA via the


Tnstru~cntation Research Laboratory (T9L) in the Department of
:?r!etiZS, resulted in link-up to the then existinq ACME computer
facility via a PDP-11 mini-comolIter  which acted as a buffer
bctweon tha spectrometers and ACHE.  Initial data acquisition and
ceduztion proqrams were written for thz system and utilized on a
limitz?d basis,  The fundinq of the DENDRAL proposal, NIH qrant
PU-612 [May 7,1Q71-present)  in conjunction  with additional
resources provided by the IRL resulted in a major improvement to
these capabilities. The fruits  of these? efforts are described
un3et section T-B.3 [below).

    h)  Summary of Early DEYDRAL Development.
r? 1364, Lederberq devi.scd a notational algr,rithm for chemical
:):r!lz tllr?s  (termed DENDPAT,,f  that allowed questions of molecular
structure to b? framed in precise qraph-theoretic terms.   (Refs.
1,3-5,12)*  He also showed how to use the DENDPAL algorithm to
qenerate complete and irredundant lists of structural isomers.
(RCfS.  ???? o

Tn lQ65-66 Lederberq and Feiqc?nbaum began exploring the idea of
usin th: isomer qenerator in an artificial intelligence program -
searchinq the space of possible structures for plausible solutions
to a problem much as a chess-playinq program searches the space of
lesal moves for the best moves.   (Refs, 7,12).   This approach
qusrsnt??s that every possible sollfion to a problem is considered
- 2ith9r ianlicitly,  as when whole classes of unstable structures
are rz-jectsd, or explicitly, as when complnto molecules are tested
for plansibility,  In either case,  an investigator easily
?etPrmines the criteria for rejection and acceptance and knows
that no possibilities have been foryottpr.,  l!his approach also
guarantees that structures appear in the list only once - that
3utor3rphi.z representations of the Sam? corrplex molecule have not
h?en included.  In both these respects the computer proqram has an
advantaqe over manual approaches to structure elucidation.

    Cl  Initial collaboration with Djerassi.   (Refs.  14,15,19,
20,21,22,24).
Ledetberq and Feiqonbaum realized that (a) only throuqh
aaplicatio? to real problems could the AT approach be materially
l?v,ancad and critically evaluated, and (b)  MS appeared to be a
fruitful applications area.  MS appeared to be an excellent
orohlem area because of the close relationship between spectral
Tr3qmen+atiop patterns and molecular structure for many classes of
a?leculls*  Djerassigs interest and expertise - an3 daily
intpr3ctio2 between members of his qroup and the AI group - led to
9 seriF5 of joint publications describing the approach and initial
cesrllts of the programs.  The success of these collaborative
?)lf>rts led to the proposa?. to the NIH for initial fundinq to
ex+e?I these efforts.

    1)  Efforts Under NIH Funling for DENDRAL.   (3efs.  25-41).
?h? initial fundinq by NIH provided the opportunity to upgrade the
Fnstrument~tioc and computer pcoqr2ms.  In particular we were able
to !llnun+. a concerted project on both the analysis of mass spectra
of bioTedically important compounds and the mathematical aspects
of m31?cul3r structure.  Proqress reports  to the NIH describe this
research in detail.  The nest recent annual report appears in
4 r?pe!li?x 5.  R series of publications Sirccted to audiences both
in corsputer science and chemistry sre listed in the bibliography.
Ilh? followFnq section [Section 3) summarizes the capabilities for


-tcllcture elucidation which,
3                     in thsmselves, constitute an
impqrtnnt result of past wnrk.

    e)   Related Research.
Fr! important side effect of tha DEWDRAL project is the extent to
vhich additional research was inspired and carried out to fill
q3cIs in existinq knowledqe.  This research,  not supported by the
r)Srt'DRhL qrant, has been beneficial to or-qoicq DENDRAL work, and
vine-versa.  Publications whjch have arisen from this research are
listed in the hiblioqranhy (Pefs, 58-70).   A brief review of these
oublications should indicate the need for precise specification of
the kn7wledqe elicited from chemists and used in computer
Dr3nr3ms.  As an example, consider the description and application
>f an early alqorithm for qeneration of cyclic structural isomers
(311.  This paper considered the problem of spectroscopic
diffar?ntLation of isomers of Z6H100.   Unsaturated ethers fall in
3ne of the classes of isomeric compounds which must be considered,
but th? RS of unsaturated ethers had not been investigated
systematically.  This work WAS subsequently carried out in
Professor Djerassi's laboratory independently of DENDRAL support,
but of hen?Eit to DZ':NDRAL (62).  Other examples will be found in
t h3  Bihlioqraphy (Eefs. 58-70).

3.  Existinq Capabilities

an hlvp worked to develop distinctive capabilities for molecular
structure elucidation, bringing together a hiqh quality HRMS
svstea and AI programs applied to biomolecular characterization.
The feasibility of our analytical approach has been demonstrated
in saveral problem areas, base3 upon the development both of a MS
svst3v ;Init a qeneral se+  of computer proqrams for use in new
areas.

The princioal capabilities are summarized below.   These are now in
3pilq and Here developed primarily under NIH funding to this
pc3 jer=t, with additional support supplied by ARPA and NASA in
snecific areas.  (These agencies have reduced funding levels for
this work because overall cutbacks have forced NASA to cut out
this are3 3,f research despite their interest and ARPA is chartered
to provide funds for frontier coapllter science research but not
f9c 3pplic3tions.  Thus the NLH is the principal of support for
future development of anplications programs in the
interdisciplinary area of artifici31 intelliqence./health related
r:herrical problems.)

      3,  HRYS System and Coupled SC/LRMS System.
We h3ve coupled the PIH-supported Varian -YRT 711 High Resolution
Yass Spectrometer with a Hewlett Packard Gas Cbromatograph and
denonstratad its utility for GC/LR?!S analysis of such difficult
analytic problems as the free -;terols (i.e., not derivatized)
isolated from marine and other sources.   Advanced data reduction
techniques for this instrument Yere written for use with the ACME
conput er svstem  (36Q/50) and cow exist in Stanford's new 370/158
ihI. Ch  :Jnntinues to support the PL/ACNR lanquaqe.   nJC/HRMS scans on
extracts from urine and anniotiz flui demonstrated this system's
zapability to provide hiqh quality mass measurements on complex
nixtures obtained from biological sources.  An example of one
;t/fiRYS run on the amino acid fraction of amniotic fluid is
presented below (Sec. 1II.D).


      DEWDRAL Structure Generator (Refs.  1-6,14,31,37,38,40,41)
nhe D;iDRAL Structure Generator program accomplishes exhaustive
;   
an? irredundant generation of isomers,  with and without rings.
This pcoqram guarantees consideration of every candidate structure
- either implicitly,  as when whole  classes of structures are
focbi3"en, or explicitly, as when individual compounds in a class
-1ro  spec<,fied,  It corresponds to the "legal move generator" of
c3nnutcriz2d chess playinq and other heuris+ic programs.

      C.  DRNDRAL Planner (Refs. 25,28,33)
de have written a very qeneral set of computer proqrams for
determining structural features from analytical data in
well-defined areas.  Such qeneral planning programs have been
wri+t?n fo: low and hiqh resolution MS,  interpreted proton NJ4R
swectroscopy and 13CMR data,

    3,  INTSUM (ReFs. 26,29,34,35)
TNTS`JM ?s 3 computer proqram that aids in finding interpretive
rales for YS.  The proqraa interprets a larqcl collection of MS
data 1:: orjinq to criteria specified by the investiqator.   Then it
summarizes the data to show which of the possible interpretations
seen most plausible.

      P.  PllLEGEhr (Refs. 26,35)
RITLESEW is the current rule qeneration program that sugqests
various rules of interpretation for th? ES data summarized by
r NTS~JM.  Although not finished,  the program can provide useful
assistance in practical theory formation.

    f.  Ancillary Techniques
1.  The !!S facility provides other types of experiments in MS,
including ultra-high resolution measurements (masses determined
via peak matching),  defocussed metastahle ion determinations
(Barber-Rlliott technique) and low ionizing voltage experiments.
These data are utilized by both scientists and proqrams where
anpropriate.
2.   Additional computer proqraas provide added problem-
  solving assistance.
  3,  Predictor program for predicting major f.. eatures of mass spectra.
h.  Proqcams for drawinq and displayinq chemical structures.
  c.  Subroutines developed in conjunction with or existing as parts of
the Structure Generator for pr2bleol.s of partitioning, construction
>f vertex-graphs, and constructive graph labelling.   These can be
3nnlie? to answer certain questions of isomerism which do not
require the  complete generator.  For example,  the labelling
alqorithm can list alI structlrres resulting from substituting
sites of a carbocyclic skeleton  with stated numbers of different
fuactianal qrouns.

     9*  Other Spectroscopic Techniques
?vailahle to us are the facilities of Professor Djerassi's
Laboratory for work requiring Idditional spectroscopic data.   Also
Ivailahle on a fee for service basis are extensive spectroscopic
facilities (NMR, I.!?.,  3n.d V.V.) of the chemistry department.
These would be utilized for collecting additional data on
particular structure problems and gatherinq data on known
compounds [particularly in the area of 13CMR) as the AI programs
bec?me kn?zledqable about other spectrosconic information.


    h,   Chnaicsl Facilities
l-he  stsff and facilities of thP chemistry department represent
SubstaRt-la1 synthesis capabilities and gerieral chemical know-how.
This r?sollrce can be called upon to pr~vid? assistance i.~
5vnthesi.s of model or labelled cnmpounds, derivatization of
9ixCure9,  3nd so forth,  For example, a graduate student in
shemistry is presently engaqed in tfiesis research dealing with the
lahnratnry synthesis of a now s.strDgen metabolite stronqly
su~~3cte3 to be a component of certain preqnancy urines.   The
prsviously proposed structure 3f this compound was one of the
candidate structures inferred by the nlanner in a study of
?strDqen mixtures (Il-dehydroestradiol-17-alpha, ref. 33).

4.  !Js?r Community
RzDn3rnic utilization of existinq and proposed facilities can be
ce3ilized by sharinq them with 1 community of users.  Lacking
suppfcmentsry funds that would he needed for a comprehensive,
na!nr service facility, this =omaunity will include the following
7 r3'105,  hot will be informally available t.o others.
  A.   Stanford Eommunity
     if  Stanford Chemistry Department (except for Hodgson, all
      3re heavily supported by the hiT!i in their research efforts)
        Letters of interest are sttached to the proposal
       in Appendix A.

?rof. C. Djerassi - Steroids, marine sterols
Prof. W. Johnson - steroi3s
Prof. E.  Van Tamelen - steroids, triterpenoids, other
natural products

Prof. H. Mosher - natural products (e.g., marine toxins)
Prof. K, FIodqson - hiDlogical liqands, ligand-metal complexes
Prof. J. Collmnr. - cytDchrDme P450 models

ii)   Stanford ?ledical School Collaborators

The following research projects in the Stanford
Biomedical ComEunity will furnish samples for mass
eztrometric analysis under the present proposal.
it)tached to this proposal (Appendix A) are copies of
the letters of interest in the proposed facility
r?zzived from the principsl investFqators of these
arants.
    Dr.  James R. Trndell,  Department of Anesthesia,
  Stanford University School of Yedicinz.   Drug
   metabolite identification in humans.

Dr.  Irene S. Forrest, biomedical P,esearch Laboratory,
Veterans Administration i-I3spital, Palo Alto,   Drug
tnetabolite identification in bumar.s.

Dr. T.  Rabinowitz and D.I. Wilkinson, Department
of Dermatoloqy,  Stanford University School of
Medicine.  Prostaqlandins.

PrDf.  Fuqene D.  Eiohin,  Department of Respiratory Medicine,
Stanford Opiversity School of Tedicinc,   Ratio of
NAD+/WADH in cplls by measuring ratio of oxidized
to reduced redox plLrs.

Dr.  Leo E.  Holfister,  Veterans Administration

43


Hospital/Department of Medicine, Stanford 1Jniversity
School of Fedicine,   Mataholism of Marihuana.

Dr.  Hiram ??. Sern,  Pharmacy Deoartment, Stanford
University n0spita.l.  Drug Identification.

Dr.  Sumner p1. dalman,  Department of Pharmacology,
Stanford University School of Medicine.  Drug and
drug metabolitc identification.

Dr.  Jack Rarchas,  Department of Psychiatry, Stanford
University School of Yedicine.   Neurotransmitters
and- related compounds in m?n.

Dr.  Keith A.  Kvecvolden,  Chemical Evolution Branch,
YRSA Ames Research Center, Yountain View, Calif.
Amino acids, acids in geochemical samples, structure
of products formed from electrical discharges in gas
mixtures.

Dr.  William P. Fair,  Department of Urology, Stanford
University School of Medicine,   Identification of
the prostatic antibacterial factor; polyamines
fputrescine, spermnine,  spermidine) in body fluids
of patients with prostatic carcinoma,

R?sil,?s tha user projects just summarized, other major prospects
are in sight,  At the time of writing, the chair of pharmacology
is vacant.  Conversations uith the leadinq candidate have
ina icated a deep-seated interest in GC/HR?IS as the principal
analytical tool for broad ranging studies of drug metabolism in
nal.

     3.   Rxtramural Users
The development of the techniques of OP,D, MS and MCD at Stanford
has beer paralleled with extensive sharing of these resources
natian-  an1 world-wide 513 collaborative research efforts, without
anv ~~l~ditional funding.  Rather than provide routine service,
axneriance has shown th.at discretionary selection of problems
results in better utilization 3f our people an,d instrumentation
resource;.  we would extend this provision of services including
atr2ilablp computer programs,  to a limited number of extramural

IISerT,   vote, for example,  our successful collaboration with
?r?fassor Adlercreutz, Meilahti Hospital, University of Helsinki,
on th? identification of estrogens fron body fluids utilizing the
9X planning proqram {ref. 33).


".  Re?atiDnship to ATE-SrJMEY and the "Jenctics Research Center

I'he present application is strengthened by two research projects
related to,  but not overlapping, the proposed research of this
scant.

1)  RT"P-SUYEX (NIH RR-00785, Oct. 1, 1973, thru July 31, 1978,
prirlcipal Investigator, J. Lederberg).  This is a resource grant
co cst_3tbfi ,sh a national facility for applications of artificial
i?tslliqenzn in medicine (AI%).  Our own use of this facility will
inzlud? SUMEX PDP-10 computer time and file storage necessary to
run the DENDRAL artificial intelligence proyrnms.   This support
vi.11 he furnished without charge to the present proposal. It
represents an annual investmerzt of about R100,OOO in computer time
z?ui.valsnt value.

?he AT?!-SVEX computinq facility is shared equally between a
national user community {AIFP) and a Stanford fledicnl School
community.  The DENDRAL research will he supported out of the
Stanford portion.  The ATM service rill be administered under the
policg control of a national advisory committee and will be
imolemsnted over a national computer network.  AIM-SIIFIFX provides
tt?p W?3?lS for members of thm national user community interested in
?tr!lzt!lre elucidation to access the DSNDRAL programs.

2)  ;enetizs Research Center (NIH POl-SM 20832-01 - approved by
thP  NISMS Zouncil,  awaitinq fundinq,  Principal Investiqator, 3.
i~33tberq).  This research proposal is a comprehensive grant uhich
would support interdepartmentni research at the Stanford Eedical
3ch301 in Yedical Senetics,  Pe3irltrics and other clinical
an3lications.  .9 section of that proposal concerns the use of
SZ/LRMS for screening body fluids for evidence of inborn errors of
metabolism.  (This project qre% out of the initial DENDRAL grant,
one of the research qoals of nhich was the analysis of body fluids
using  ?????? o  This research on inborn metabolic errors will be
n~~?ii!~cted jointly in the Stanford Departments of Genetics and
Pediatrics using existing eguipment {Finniqan 1015 Quadrupole mass
spectrometer, Varian Aerograph GC and a PDP-11/20 based data
??????? o

k?? 3ppr?zisted the value of GC/HPYS analyses of selected extracts
3f ho4y ffjids (i.e., those containinq metaboli tes not identified
bv routine GC/LRMS data) when formulating the Senetics fiescarch
Lleater proposal.  Accordingly,  A small amount of funding was there
reg~lestad for recording selected GZ/HRYS data on the GC/Varian EAT
711 'Rass spectrometer in the Department of Chemistry.   If these
funds are awarded, we will noqotlate with YTH a suitable
elimination of this minor overlap with the present budget.


rr.   Sn'?CIFTC AIMS

1'52 spacj.fic aims enumerated in this section will be pursued in
tfi3 hiqhly inter-disciplinary manner that has characterized the
Ll)7NPRkL project from the start of its NIH support.   The aims are
not Iisjoint,but interactive and inter-dependent.  For example,
the pawor of P!S and, potentially,  other spactroscopic techniques,
z3tn h? enhanced by the use of computer proqrams to perform various
asnez+s of structure elucidation and thaory formation,   From the
star3point of computer science, one measure of the utility of
techniques of artifizi al intelligence is how well they perform in
r??l-v3rld 3Dplications. I+ is necessary in the development of
tFi3s2 proqrams to have a source  of data and informed, involved
teaB-mates able to  criticize methods and results.   The aims are
alaborsted in the methods section.

me have attempt28 tr, keep the proposal to a readable length.
rhF?r?fore,  some detail. has been omitted.   Houever,  many details
can be found in the bilioqraphy an? we are prepare3 to provide
3dditi onal information ;turinq t.he site visit.

1.  Enhance the power of the MS resource.

m he existinq MS resource, toqether with computer programs which
ixist Dr which are proposed (see Aim 2, below), is capable of
-olvinq sane of the structure
3                      zlucidat.ion problems of the user
community given computer supnort for data collection and
re3~lction.  We refer specifically to the areas of GC/LRMS and
ro:lt%ne,  b3tch HRYS samples.  We believe that many of the problems
of the user community require more powerful techniques  (see
YPction III) *  These techniques, specifically fJC/HRZS and
senl-automatic metastable defocussinq,  can be provided with a
minimum of cost and effort,  thus enhancing considerably the
capabilities of the resource.

Dur first aim is to provide the resource with adequate computer
3upp3rt (re placinq the previous ACZ!E system) to enable collection
In3 reduction of mass spectral data including low and high
resolution scans  and data or defocussed mctastable ions.

83 DrnDoSC to develop this computer support in the ways described
30131,  (those aims are writt.en to include the work necessary to
im3lencnt the extended PDP-11/20 computer system.  A description
of the rationale for this choice is provided in Section 1II.A and
tha  specific auqmentations in the Rudqet Justification).

    ,!I 1  Convert Pxistinq,  proven data acquisition and reduction
nc3qra?rs from the PL/ACME langllaqe into Fortran, consistent with
t; n3-:: rikizal assembly lanquaqz proqrams for data acquisition snd
instrument control.  These programs will be written in Fortran to
enhance comnatibility with %hc computer systems of other users of
3uch pzlcka~es*

    3)   Modify these proqrams,  3s requirej,  to handle acquisition and
ce?3u:tion of frequent or repetitive HRYS scans with selected
instLumen~ performance feedhsck to the operator, and to take
aqvantaqe of the cxpandcd canab<ilities of the extended 11/20
svstem.  Prototype GC/RRBS systems have  h eea developed at Stanford
1nd  els.ewhare, but this type :,f facility (in contrast to GC/LRVS)


is not n3ir available to the S+3nford community.  When this system
is d2vclopsd, service will- be available to the Stanford community
and research collaborators and,  if our resources permit, to any
szi.entist r?que!stinq assistance.  In many instances this type of
collaboration will require far more  involvement of convergent
interests,  efforts and skills than merely running samples on
requT?r;t o  me have in mind the chemical and eventually biological
internrotation of the analytical data as a matter of joint
concern,  as appropriate.

We have previously illus&.rated the advantages of high resolution
nass sncctral data in the computer analysis of mass spectra (e.g.,
ref. 29).  Also,  ue have previously shown that the same program
can deal with analyses of mixtures without prior separation
es~ecislly when additional data (e.g.* from selected metastable
lefoc*lssinq ?xporiments) were provided {Pef. 33).   We wish to use
the MS rslsaurce and the computer program in further studies of
nixtures of compounds which are difficult or impossible to
separate by GC. The advent of routine systems for high pressure
liquid chromatography have mado many of these separations
possible,  but the liquid chromatoqraph is not presently interfaced
to the TS.

Hany of +ha problems nf the user community require analysis of
complex mixtures which are amenable to treatment by K/MS
techniques.  We feel that where sample quantities permit,
acquisition of GC/HPMS data is highly desirable.   These data can
ho orovid+? by the resource supplemented width computer support
(abovzf .

Frs prDnose to continue tests of the GC/??S combination, operating
urler moderately high mass resolutions (5000-lOOOO), to define in
IPt3il. the optimum operating conditions of the GC/HRRS
sDmbinstion.   This will provide the necessary information on
maximum practical sensitivity to be expected.   This information
can then he used in collaboration with the user community for
:;9mpln  nrenaration.

r he 5:/H4MS system would normally be operated at reduced mass
sp2ctromzter resolutions to maximize sensitivity.   We have
Fxistinq multiplet resolution programs to increase the resolving
r3oyer of the MS.  We propose to provide the multiplet resolution
nrogram with heuristic quidance based on compositional variations
ir,fe,rred from molecular i0r.s or other singlet peaks,  For example,
a resolving power of 10,000 is barely sufficient. to resolve ions
which differ by CH2 vs. N (delta m = 0.012) for ions of about mass
133.  Alth3uqh it will resolve cH4 vs. 0 doublets (delta m =
3,037) at this mass,  it will c3t resolve closer doublets such as
:3?? vs.  H2o3 (delta m = 0.003).  'nle can prDvi.de exhaustive
tabulation; of multi.plPts by mass separations [based on ref. .?O)
which can be used by the multiplet resolution program.

We hive previously indicated the power of metastable ion
inf9rm3tion in the operation of our proqraas for structure
3117idItion fiefs, 28, 33),  We have extended one of our programs
(the ?IS predictor program)  to propose me%astable defocussing
axperiments in order to avoid collection of unnecessary data [see
Pin 2, bel3w).  Rlthouqh ye can collect these data (Barber-Elliott
technique) manually on our cxis+..ing Varian ??A??-771 YS, this is an


7xcnet4inqly wasteful operation,  both ir, terms of sample
consumption and timp.  we pr3p3s.e to implement som2 automation of
collecti3rt of these data on aetastahle ions.  We also propose to
Benin preliminary ipvestiqation of alternative rrodr?s of metastahle
F3n determination (see MP+hods (Sec. ITT), below).

    2
in thi*  Develop performance and theory formation programs to assist
     solution of structure elucidation problems in biomedicine.

TonDutzr programs have already been written for analysis of low
2ilnd hiqb resolution mass spectra,  for generation of acyclic and
zyz lit  molecular structures, f3r lsbellinq structural skeletons
with atoms,  for acalyzinq 13CMR spectra Df nmines and for
interpretation and summary of large volumes of da%a gathered on
!ilO1&?1 compounds (see Pxisting Capabilities above, for references).
Gr'e wish to increase the utility of these programs by providing
Lnt,eractive facilities +hat allow easier access to them, by
incrcn5inq their qenerallty an3 p3wer,  an? by supplementing them
with nBw rnasonlnq pr3qrams.

Parf9cmance Proqrams:

   The current structure qenerator proqrsm will be subjected to
further flitailed tests before usinq it for structure determination
nr7hlens.

   A n?w alqorithm for qencratinq cyclic skeletons (with
no multiple bonds) will be programBed and checked,  The algorithm
is written and informally prnv>d.   A formal proof will be devised
=ls W?ll.  This s'lqorithm represents one very powerful approach to
t hn problem of implementation 3f constraints, 3s discussed in the
f~3 ?.ovinq paraqraph.

   The qencratinq proqrams will be modified to allow isomer
qpnQr3tion within constraints,   Different kinds of constraints can
h? inferred from different kinds of spectroscopic data.   !?e intend
t7 qive thz  proqram knowledqe of 3 variety of these.

   Thp Planner proqrams that infer constraints from mass
sDectron?try data will be hrnadened to include additional
kn?wlerIqe shout the spectral behavior of classes of compounds of
r"levan~e to thcz NIH-sponsored research of the user community. In
3??i.i+i.on,  83 will add the capability for utilization of
izf3rma+t3n about chemical isolation procedures (e.q., one expects
scijic and neutral compounds in  solvent extraction of acidified
bo3v fluins) and relative GC retlntior! times (e.g., to admit the
possibility of homaloqous series).

     w F!  ~~303s~ to implement a more qeneral method for
ir,fsrrirq the i33ntity of thp mol?sular ion whether or not this
1!3pe1cs  explicitly in the spectrum,   This  information is important
f3r the Tuccessful operation of the structure qenerator and the
n?3rlrlf?r.  'de want the program to use whatever information is
3v3il3bl2  -Ind not depend,  as it ctlrrently does, on having
knowledqe 3f the structural slass together with inference rules
for that class.

   Tnt?rfsce routines will he written to mak? it easier for other
;nicntis?s to use tF.ese proqrans,   We have to wait for an


inker3ctivc system before startLng this:   AI!?-SI!MEX will he ideal.
rr.p'lf/output routines will he crucial to ~ssy use of the system.
u~u3vcc, WC als3 want t3 give users the facility to understand the
system's reasoning steps so they can t3k~ 34vantage of it.

Tn a4ditirn to makinq the compilter programs available through
4T"-TTJYEX, we w0da like to translate parts of the LISP code into
another 13nquaqe - for reasons of both efficiency and
?xp3rtability.  We have talked with computer professionals at IBM
Pesaaroh Canter about usinq the APL lanquaqe.   FORTRAN,  ALGOL and
PL/l arc other lanquages whose merits for our purposes we will
explor?.

   W? wish to continue a low-level of effort on computer
proqrams that interpret other kinds of spectroscopic data.
Plannicq proqrams similar to the ?IS Planner could be written for
automatic analysis of data fro3 3,ther spectroscopic
tc:hniques(e.q., IF, IJV) #  as we have illustrated for 13CMP (ref.
??? o

   Th? structure qenerator's view of chemical strlictlre is
topDloqizal and is presentlv unconstrained by bond lengths and
angles.  3ecauss stereochemjcal considerations are frequently
important in structure el.ucidation, we propose to begin
corsidsration of stereochemistry in the structure generation and
2vaLuation processes.

   !! nrolram with detailed knowledge about information
?htain?Sle from various spectroscopic techniques could be written
t3  C?X3Zli!l? a list Df candidate solutions and propose experiments
necessary and sufficient to distinquish among them.  The program
would represet?? an extended Predictor (e.q., ref. 27).   Be have a
Eir- ,t version of a program that suggests "crucial" metastable
pz3ks t.0 he snuqht in order to distinguish among car,didate
stru~tutz?s.  Work on this proqram will con%inuc at a fow level of
3ct!vity,  possibly expandinq  into areas other than ES.  One topic
we will continue to pursue is our collaborative effort uith Dr.
;iLd3 Loew,  Geneti.cs Department, on the potential application of
molez:rllar orbital theory to prediction of mass spectra (ref. 71).

Th33ry 3rnation Proqrams::

  The rile formation proqran (RtJLEGF:N) will he extended so that
i + car? search a larqer space of rules.  Present a priori
zo3str3int; on the rule qeneration qive us a search reduction from
te?s of millions to a thousand possihl? rules,  Even though search
heuristics now 3110~ efficient search of these possibilities, we
want to be able to deal with much larger spaces efficiently, as
wh?? the number of primitive predicates is drastically increased,

   The PULFGEN proqram will. be modified so th-at complex
Eraqmectation and rearranqement processes are manipulated nearly
3s easily 3s simple fraqmentations.  The program currently finds
frlqmentstion rules invnlvinq 3ne 3r two bonds, possibly followed
bv hydroqen miqration,   Ir. the case of cyclic systems such as
=S~CD~ZCS, however, the proqram must be able to work with sets of
. .
three or more bonds in some cleavages,

   Interactive proqrams will. be provided 3~ AIM-SUP!:EX for the
inv3stiqat3r to query the rule qeneration program.  For example,


msnv questions now arise about the proqram steps by which the
proqram Tnfer; the rules it suggests as explanations of the
re7l~larltins.  Why,  for example,  was some particular rule not
considered plausible?

   New d2it.a will have to be selected in order to test the rules
3nd to differentiate amnnq competinq rules.   Be will mite a
nroqram that suqqests new experiments (i.e., new data to obtain),
deosniinq on the nature of the existing rules,

   The t?st phase of the theory formation program will be
written as an evaluation function of each rule against new data.
Tn3;7f3r 3s 3ny new experiments are **crucialtl experiments,  the
evslu-ation function may merely reject a proposed rule.  Mostly,
13wevor , riles will have to be evaluated against new data along
3apv dimensions:  frequency,  strenqth of evidence,  uniqueness,
simplicity,  and the like.

   We wish to experiment with the whole theory formation program
to ,lztermi3e the critical aspects of our design.  For example, 11)
how sensitive is the proqram to discrepancies, inconsistencies and
ecr:>r5  in the data?   (2)  how well can the proqram find rules
within a sliqhtly different model of chemistry?  (3) how well can
the proqrsm perform w?%h one pass through the data, or several
passes? and (4) how critical are the principles of theory
Eormati~on?

    3.  Apply the structure plucidati3n techniques - both
i?;tcumsnt3tion and computer programs -  to hFomedically relevant
compounds.

3ur own interests are in elucidatinq the structures of, and
SnIerstandFnq the MS of, marine sterols, hormonal steroids, and
compounds isolated from human bofly fluids that can be associated
with qenatic disorders (from research in the GRC).  In addition,
W? riff be workinq closely with members of the Stanford Medical
School 3nd Chemistry Department  - in particular those mentioned
aih3ve fSect?.on 1.3.4) - on their structure elucidation problems in
which YS will be used.  Althouqh most users expect to require HRMS
3na  SZ/HRYS data,  some of their problems will be attacked
utilizicq SC/LRMS techniques and library search through (usually)
restricted libraries  of mass slnectral data,   We propose to
investiaate some extensions to the technique of library search
(SIP Methods) to complement our existinq and planned DENDRAL
prcqrams.  WE! plan to continue 3ur exchanqe of mass spectral data
an? library search information as we have previously done with Dr.
5, Uarkey (University of Colorado Medizsl School) and Dr. F. W.
YcLaffnrtv (Cornell Universi.tvI *

P.s !.n the Dast,  attention to new biomedFcnL research problems will
lead t-o increased capabilities in  the computer proqrams. We
rejuir? close communication with the people engaged in the
research so that the proqrams actually assist the researcher while
iycreasinq in power,   Collahor3 tive proposals have come out of
sjxzh past DENDRAL sponsored work, for exampl?, larqe portions of
t ?-lP ;9C Droposal apd a proposal. for 13CMH research.

k'3 2~visi.92  the interaction and collaboration with the user
zoamunity to involve the followinq: