Crystal Structure Prediction of Aminols: Advantages of a Supramolecular Synthon Approach with Experimental Structures
Archan Dey; Michael T. Kirchner; Venu R. Vangala; Gautam R. Desiraju; Raju Mondal; Judith A. K. Howard; Journal of the American Chemical Society 127 (2005) 10545–10559; doi:10.1021/ja042738c

data_4111831
_publ_contact_author_address
;
School of Chemistry
University of Hyderabad
Hyderabad 500 046
India
;
_publ_contact_author_email       desiraju@uohyd.ernet.in
_publ_contact_author_fax         '91 40 23010567'
_publ_contact_author_name        'Professor Gautam R. Desiraju'
_publ_contact_author_phone       '91 40 23134828'
_publ_section_title
;
 Crystal Structure Prediction of Aminols: Advantages of a Supramolecular
 Synthon Approach with Experimental Structures
;
_journal_name_full               'Journal of the American Chemical Society'
_journal_page_first              10545
_journal_page_last               10559
_journal_paper_doi               10.1021/ja042738c
_journal_volume                  127
_journal_year                    2005
_chemical_formula_moiety         'C6 H13 N O'
_chemical_formula_sum            'C6 H13 N O'
_chemical_formula_weight         115.17
_chemical_melting_point          384
_chemical_name_common            trans-4-Amino-cyclohexanol
_chemical_name_systematic
; 
  trans-4-Amino-cyclohexanol
;
_space_group_IT_number           14
_symmetry_cell_setting           monoclinic
_symmetry_space_group_name_Hall  '-P 2yn'
_symmetry_space_group_name_H-M   'P 1 21/n 1'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     direct
_atom_sites_solution_secondary   difmap
_audit_creation_method           SHELXL-97
_cell_angle_alpha                90.00
_cell_angle_beta                 95.486(8)
_cell_angle_gamma                90.00
_cell_formula_units_Z            4
_cell_length_a                   5.259(2)
_cell_length_b                   11.954(5)
_cell_length_c                   11.730(4)
_cell_measurement_reflns_used    877
_cell_measurement_temperature    298(2)
_cell_measurement_theta_max      22.65
_cell_measurement_theta_min      2.44
_cell_volume                     734.0(5)
_computing_cell_refinement       'Bruker SMART'
_computing_data_collection       'Bruker SMART'
_computing_data_reduction        'Bruker SAINT'
_computing_molecular_graphics    'Bruker SHELXTL'
_computing_publication_material  'Bruker SHELXTL'
_computing_structure_refinement  'SHELXL-97 (Sheldrick, 1997)'
_computing_structure_solution    'SHELXS-97 (Sheldrick, 1990)'
_diffrn_ambient_temperature      298(2)
_diffrn_detector_area_resol_mean 512
_diffrn_measured_fraction_theta_full 0.969
_diffrn_measured_fraction_theta_max 0.969
_diffrn_measurement_details
;
The crystal is multiply twinned. The nature of the twinning was not
established before measurement, instead a general hemisphere data
collection was used.
600 Frames from the first run were thresholded with a lower I/sigma of 4.
907 centered reflections were obtained and further analysed first manually
using RLATT3, then by CELL_NOW V2. Four domains could be identified with
375 (375 exclusive), 297 (231 exclusive), 88 (70 exclusive) and 69 (63
exclusive) reflections respective, leaving 168 unassigned.
The second domain is rotated from the first domain by   2.3 degrees about
reciprocal axis  0.623  1.000  0.358  and real axis  1.000  0.301  0.154.
The third domain is rotated from the first domain by  57.5 degrees about
reciprocal axis -0.037 -0.004  1.000  and real axis  0.029 -0.010  1.000.
The fourth domain is rotated from the first domain by  64.1 degrees about
reciprocal axis  0.013  0.079  1.000  and real axis  0.274  0.069  1.000.

SAINT6.45A was used to simultaneously reduce the data of the four domains
including overlap. The box size optimization had to be disabled and a fixed
box of 0.8 \% in each direction was set. Data reduction with SAINT was
repeated once with the orientation matrices of the first reduction runs as
starting point.
13424 spots were found, 11539 without overlap. Due to the small rotation
law between components 1 and 2, there were 1280 overlaps between these two.
The volumes of the global unconstrained cells of each component match
within 3 esd to the single unit cell of all component data. (i.e. no
polymorphs)
Absorption correction was performed by TWINABS V1.05.
The mean I/sigma for components 1-4 was found to be 5.6, 5.2, 0.8, 0.7.
A single parameter set was refined to fit all single and composite
reflections that contained at least one contribution from domains 1 and 2.

For parameter refinement a cutoff of 1.1 Angstrom was used.
A restraint of 0.001 is put on the scale factor esd.
Maximum odd and even orders for spherical harmonics are 1 and 4.
R(int) drops from 3.82% to 3.44%.
The scale factor is between 0.945 and 1.019.
In the best error model factor g was 0.1134 and was once refinded manually.
All three runs are similar in R(int) and k-scale factor for each compound.
R(int)-values for each run are:
single 1 : 0.0532   0.0595   0.0720   
single 2 : 0.0664   0.0606   0.0818   
single 3 : 0.3824   0.3106   0.2159   
single 4 : 0.4049   0.4117   0.3260   
composite: 0.0200   0.0259   0.0240   
all      : 0.0437   0.0537   0.0525   

A hkl-file with all spots that contained contributions from components 1
and 2 was created manually.

The transmission ratio is 0.771181 (based on component 1) and a spherical
absorbtion correction was applied as mu*r=0.02.

Theoretical values for minimum and maximum transmission based
on the size of the crystal are 0.9677 and 0.9874.
;
_diffrn_measurement_device_type  'Bruker Nonius SMART APEX CCD area detector'
_diffrn_measurement_method
;
Run  Frame1  2Theta  Omega   Phi     Chi    Axis Width   Frames  Time
1    001     -28.00  -28.00    0.00   54.74  2  -0.300    600    5.00
2    001     -28.00  -28.00   90.00   54.74  2  -0.300    435    5.00
3    001     -28.00  -28.00  180.00   54.74  2  -0.300    230    5.00
;
_diffrn_radiation_monochromator  graphite
_diffrn_radiation_source         'fine-focus sealed tube'
_diffrn_radiation_type           MoK\a
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.0000
_diffrn_reflns_av_sigmaI/netI    0.0473
_diffrn_reflns_limit_h_max       6
_diffrn_reflns_limit_h_min       -6
_diffrn_reflns_limit_k_max       14
_diffrn_reflns_limit_k_min       0
_diffrn_reflns_limit_l_max       14
_diffrn_reflns_limit_l_min       0
_diffrn_reflns_number            3661
_diffrn_reflns_theta_full        26.33
_diffrn_reflns_theta_max         26.33
_diffrn_reflns_theta_min         2.44
_exptl_absorpt_coefficient_mu    0.070
_exptl_absorpt_correction_T_max  0.9874
_exptl_absorpt_correction_T_min  0.7615
_exptl_absorpt_correction_type   empirical
_exptl_absorpt_process_details
;
The transmission ratio is 0.771181 (based on component 1) and a spherical
absorbtion correction was applied as mu*r=0.02.
Theoretical values for minimum and maximum transmission based
on the size of the crystal are 0.9677 and 0.9874.
For further details see _diffrn_measurement_details
;
_exptl_crystal_colour            colorless
_exptl_crystal_density_diffrn    1.042
_exptl_crystal_description       block
_exptl_crystal_F_000             256
_exptl_crystal_size_max          0.47
_exptl_crystal_size_mid          0.32
_exptl_crystal_size_min          0.18
_refine_diff_density_max         0.198
_refine_diff_density_min         -0.168
_refine_diff_density_rms         0.036
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   0.951
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     91
_refine_ls_number_reflns         3683
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      0.951
_refine_ls_R_factor_all          0.1289
_refine_ls_R_factor_gt           0.0660
_refine_ls_shift/su_max          0.055
_refine_ls_shift/su_mean         0.007
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'calc w=1/[\s^2^(Fo^2^)+(0.0766P)^2^+0.0000P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1430
_refine_ls_wR_factor_ref         0.1697
_reflns_number_gt                1853
_reflns_number_total             3683
_reflns_threshold_expression     >2sigma(I)
_cod_data_source_file            ja042738csi20050407_114233_01.cif
_cod_data_source_block           6
_cod_original_cell_volume        734.1(5)
_cod_original_sg_symbol_H-M      'P 1 21/n 1 '
_cod_database_code               4111831