The Supertristeroids: Large, Chiral, Molecular Bowls Prepared by Trimerization of Pentacyclic Steroidal Ketones
Qiuling Song; Douglas M. Ho; Robert A. Pascal Jr.; Journal of Organic Chemistry 72 (2007) 4449–4453; doi:10.1021/jo070458k

data_4022954
_publ_contact_author_address
;
Princeton University
Department of Chemistry
Princeton, NJ   08544-1009
USA
;
_publ_contact_author_email       rpascal@princeton.edu
_publ_contact_author_fax         '(609) 258 6746'
_publ_contact_author_name        'Professor Robert A. Pascal, Jr.'
_publ_contact_author_phone       '(609) 258 5417'
_publ_section_title
;
 The Supertristeroids: Large, Chiral, Molecular Bowls Prepared
 by Trimerization of Pentacyclic Steroidal Ketones
;
_journal_name_full               'Journal of Organic Chemistry'
_journal_page_first              4449
_journal_page_last               4453
_journal_paper_doi               10.1021/jo070458k
_journal_volume                  72
_journal_year                    2007
_chemical_absolute_configuration rm
_chemical_compound_source        'chemical synthesis'
_chemical_formula_iupac          'C31 H52 O'
_chemical_formula_moiety         'C31 H52 O'
_chemical_formula_structural     'C31 H52 O'
_chemical_formula_sum            'C31 H52 O'
_chemical_formula_weight         440.73
_chemical_name_systematic
;
4alpha,3beta-(3'-oxocyclohexano)-5beta-cholestane
;
_space_group_IT_number           5
_symmetry_cell_setting           monoclinic
_symmetry_Int_Tables_number      5
_symmetry_space_group_name_Hall  'C 2y'
_symmetry_space_group_name_H-M   'C 1 2 1'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     direct
_atom_sites_solution_secondary   difmap
_audit_creation_date             'November 22, 2006'
_audit_creation_method
;
SHELXL and manual editing of form.cif
;
_audit_update_record
;
Nov. 22, 2006  rap124f.cif        Initial CIF created by DMH.

Nov. 22, 2006  README sections    See _exptl_special_details for a brief
                                  discussion of the data collection and
                                  data reduction procedures and results.
                                  (Located about a third of the way from
                                  the begin of this file.)

                                  See _refine_special_details for a brief
                                  discussion of the structure solution
                                  and refinement, disorder treatment, etc.
                                  (Located about a third-to-halfway from
                                  the begin of this file.)
                                  
                                  See _geom_special_details for a brief
                                  discussion of miscellaneous structural
                                  features.  (Located at the bottom of
                                  this file.)

Nov. 22, 2006  Sent to Checkcif.  See rap124f_checkcif.pdf for
                                  the alerts that were generated.
                                  Selected responses follow.

Nov. 28, 2006  Updates.           A few fixes were made to the responses
                                  to the CheckCIF alerts.

-------------------------------------------------------------------------

THETM01_ALERT_3_A The value of sine(theta_max)/wavelength is      < 0.550
                  Calculated sin(theta_max)/wavelength =           0.5391
PLAT027_ALERT_3_A _diffrn_reflns_theta_full (too) Low ........ 22.53 Deg.

                  The alerts THETM01_ALERT_3_A and PLAT027_ALERT_3_A are
                  not a problem.  They simply reflect the fact that the
                  crystal available for the experiment was not of
                  sufficient quality to provide usable data to higher
                  angles.  Also, there is extensive disorder in the
                  aliphatic side chain in this molecule.  It is not
                  uncommon to find that extensive disorder will diminish
                  the effective resolution of a data set.  Therefore,
                  only a 0.93 Angstrom resolution data set was targeted.
                  Nevertheless, such a data set is still considered to
                  be of "atomic resolution", and still meets the
                  community's standards of acceptability in such severe
                  disorder cases.

PLAT024_ALERT_4_B Merging of Friedel Pairs is STRONGLY Indicated ...... !
REFLT03_ALERT_4_G MoKa measured Friedel data cannot be used to determine
                  absolute structure in a light-atom study EXCEPT under
                  VERY special conditions. It is preferred that Friedel
                  data is merged in such cases.

                  PLAT024_ALERT_4_B and REFLT03_ALERT_4_G are the same,
                  and is only a recommendation.  In truth and on theoret-
                  ical grounds, Friedel data are unique and should not be
                  merged.  Therefore, it is not wrong to ignore this
                  CheckCif recommendation, and to exercise our right to
                  retain the data as unmerged.

PLAT222_ALERT_3_A Large Non-Solvent H Ueq(max)/Ueq(min) ...... 5.16 Ratio
PLAT220_ALERT_2_B Large Non-Solvent C Ueq(max)/Ueq(min) ...... 4.18 Ratio
PLAT242_ALERT_2_C Check Low Ueq as Compared to Neighbors for ....... C25
PLAT242_ALERT_2_B Check Low Ueq as Compared to Neighbors for ....... C25*
PLAT242_ALERT_2_C Check Low Ueq as Compared to Neighbors for ....... C25'
PLAT242_ALERT_2_C Check Low Ueq as Compared to Neighbors for ....... C25"
PLAT432_ALERT_2_B Short Inter X...Y Contact C26* .. C26* ...... 3.09 Ang.
PLAT432_ALERT_2_B Short Inter X...Y Contact C27" .. C27" ...... 3.07 Ang.
PLAT305_ALERT_2_A Isolated Hydrogen Atom (Outside Bond Range ??) .. <H24A
PLAT305_ALERT_2_A Isolated Hydrogen Atom (Outside Bond Range ??) .. <H24B
PLAT305_ALERT_2_A Isolated Hydrogen Atom (Outside Bond Range ??) .. <H24C
PLAT305_ALERT_2_A Isolated Hydrogen Atom (Outside Bond Range ??) .. <H24D
PLAT305_ALERT_2_A Isolated Hydrogen Atom (Outside Bond Range ??) .. <H24E
PLAT305_ALERT_2_A Isolated Hydrogen Atom (Outside Bond Range ??) .. <H24F
PLAT305_ALERT_2_A Isolated Hydrogen Atom (Outside Bond Range ??) .. <H24G
PLAT305_ALERT_2_A Isolated Hydrogen Atom (Outside Bond Range ??) .. <H24H
PLAT301_ALERT_3_C Main Residue Disorder ..................... 14.00 Perc.
PLAT720_ALERT_4_C Number of Unusual/Non-Standard Label(s) ............. 8

                  PLAT222_ALERT_3_A to PLAT720_ALERT_4_C are the result
                  of extensive disorder in 14.00 percent of the molecule.
                  The disorder was modelled as well as might be expected
                  (see _refine_special_details).  The validation routine
                  is apparently having some difficulties with correctly
                  grouping the partial atoms of each component of the
                  disorder together.  All eight C-H distances for H24A
                  to H24H are 0.99 Angstroms, i.e., within bond range
                  (see _geom_bond_distance).  The atoms for the minor
                  components of the disorder were given labels ending
                  with *, ', or ".  The validation routine considers the
                  eight partial atoms with labels ending with * to be
                  unusual.  That is of course just a subjective
                  preference in the validation software, i.e., there is
                  no hard rule that says that * may not be used.

STRVA01_ALERT_4_C Flack test results are meaningless.
                  From the CIF: _refine_ls_abs_structure_Flack      0.180
                  From the CIF: _refine_ls_abs_structure_Flack_su   2.340
PLAT032_ALERT_4_C Std. Uncertainty in Flack Parameter too High ..... 2.00
PLAT850_ALERT_2_C Check Flack Parameter Exact Value 0.00 and su .. 2.00

                  STRVA01_ALERT_4_C, PLAT032_ALERT_4_C and PLAT850_ALERT_
                  2_C are obviously all saying the same thing.  Yes, we
                  agree that the absolute structure cannot be determined
                  based on the intensity data.  However, the compound is
                  derived from a steroid, and hence, contains centers of
                  known chirality to begin with.  Since the chemical
                  procedures used in synthesizing the compound do not
                  involve bond making or breaking at those centers of
                  known chirality, the absolute structure of the compound
                  remains fully discernible and unequivocal based on the
                  pre-existing internal chiral labels within the molecule
                  itself.

PLAT791_ALERT_1_G Confirm the Absolute Configuration of ....... C3  =  S
PLAT791_ALERT_1_G Confirm the Absolute Configuration of ....... C4  =  R
PLAT791_ALERT_1_G Confirm the Absolute Configuration of ....... C5  =  R
PLAT791_ALERT_1_G Confirm the Absolute Configuration of ....... C8  =  R
PLAT791_ALERT_1_G Confirm the Absolute Configuration of ....... C9  =  S
PLAT791_ALERT_1_G Confirm the Absolute Configuration of ....... C10 =  R
PLAT791_ALERT_1_G Confirm the Absolute Configuration of ....... C13 =  R
PLAT791_ALERT_1_G Confirm the Absolute Configuration of ....... C14 =  S
PLAT791_ALERT_1_G Confirm the Absolute Configuration of ....... C17 =  S

                  The CheckCif recommendation for the assignment of the
                  chiral centers in 4alpha,3beta-(3'-oxocyclohexano)-
                  5beta-cholestane is (3S,4R,5R,8R,9S,10R,13R,14S,17S).
                  In truth, steroids are rather notoriously difficult
                  when it comes to R/S assignments, and we believe that
                  the validation routine has not only missed C20 (i.e.,
                  there are 10 stereocenters), but has misassigned 4 of
                  the 9 stereocenters that it did find.  We believe that
                  the correct assignment is (3S,4S,5R,8S,9S,10S,13R,14S,
                  17R,20R).  Regardless, by visual inspection of the
                  molecule with any molecular viewer, it is obvious that
                  the standard correct hand for steroids is depicted,
                  and any discrepancy between the CheckCif assigments
                  and our own is merely book-keeping, i.e., the refined
                  absolute structure is correct as stands.
;
_cell_angle_alpha                90.00
_cell_angle_beta                 91.180(2)
_cell_angle_gamma                90.00
_cell_formula_units_Z            4
_cell_length_a                   11.3299(7)
_cell_length_b                   7.5129(4)
_cell_length_c                   32.620(2)
_cell_measurement_reflns_used    14706
_cell_measurement_temperature    200(2)
_cell_measurement_theta_max      22.53
_cell_measurement_theta_min      1.25
_cell_volume                     2776.0(3)
_computing_cell_refinement       'DENZO-SMN (Otwinowski & Minor, 1997)'
_computing_data_collection       'COLLECT (Nonius, 1998)'
_computing_data_reduction        'DENZO-SMN (Otwinowski & Minor, 1997)'
_computing_molecular_graphics    'Siemens SHELXTL (Sheldrick, 1996)'
_computing_publication_material  'Siemens SHELXTL (Sheldrick, 1996)'
_computing_structure_refinement  'Siemens SHELXTL (Sheldrick, 1996)'
_computing_structure_solution    'Siemens SHELXTL (Sheldrick, 1996)'
_diffrn_ambient_temperature      200(2)
_diffrn_measured_fraction_theta_full 0.998
_diffrn_measured_fraction_theta_max 0.998
_diffrn_measurement_device       'Nonius KappaCCD'
_diffrn_measurement_method       '\w scans, 1720 0.5\% rotations'
_diffrn_radiation_monochromator  graphite
_diffrn_radiation_source         'fine-focus sealed tube'
_diffrn_radiation_type           'Mo K\a'
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.0730
_diffrn_reflns_av_sigmaI/netI    0.0559
_diffrn_reflns_limit_h_max       11
_diffrn_reflns_limit_h_min       -12
_diffrn_reflns_limit_k_max       8
_diffrn_reflns_limit_k_min       -8
_diffrn_reflns_limit_l_max       34
_diffrn_reflns_limit_l_min       -35
_diffrn_reflns_number            14706
_diffrn_reflns_theta_full        22.53
_diffrn_reflns_theta_max         22.53
_diffrn_reflns_theta_min         1.25
_diffrn_standards_decay_%        0
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    0.061
_exptl_absorpt_correction_type   none
_exptl_crystal_colour            Colorless
_exptl_crystal_density_diffrn    1.055
_exptl_crystal_density_method    'not measured'
_exptl_crystal_description       Plate
_exptl_crystal_F_000             984
_exptl_crystal_size_max          0.30
_exptl_crystal_size_mid          0.19
_exptl_crystal_size_min          0.05
_refine_diff_density_max         0.094
_refine_diff_density_min         -0.124
_refine_diff_density_rms         0.026
_refine_ls_abs_structure_details 'Flack H D (1983), Acta Cryst. A39, 876-881'
_refine_ls_abs_structure_Flack   0.18(234)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_all   1.071
_refine_ls_goodness_of_fit_ref   1.099
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     400
_refine_ls_number_reflns         3635
_refine_ls_number_restraints     369
_refine_ls_restrained_S_all      1.209
_refine_ls_restrained_S_obs      1.062
_refine_ls_R_factor_all          0.0606
_refine_ls_R_factor_gt           0.0478
_refine_ls_shift/su_max          0.000
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0371P)^2^+0.9453P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_all         0.1300
_refine_ls_wR_factor_ref         0.1046
_reflns_number_gt                3109
_reflns_number_total             3636
_reflns_threshold_expression     I>2\s(I)
_cod_data_source_file            jo070458ksi20070305_110730.cif
_cod_data_source_block           rap124f
_cod_depositor_comments
;
The following automatic conversions were performed:
'_symmetry_cell_setting' value 'Monoclinic' changed to 'monoclinic'
according to '/home/saulius/struct/CIF-dictionaries/cif_core.dic'
dictionary named 'cif_core.dic' version 2.4.1 from 2010-06-29.

Automatic conversion script
Id: cif_fix_enum 1527 2010-12-29 10:47:43Z saulius 
;
_cod_original_sg_symbol_H-M      'C 2'
_cod_database_code               4022954