Heterocyclic 1,3-diazepine-based thiones and selones as versatile halogen-bond acceptors
Ragusa, Arianna C.; Peloquin, Andrew J.; Shahani, Marjan M.; Dowling, Keri N.; Golen, James A.; McMillen, Colin D.; Rabinovich, Daniel; Pennington, William T.; Acta Crystallographica Section B 78 (2022) –; doi:10.1107/S2052520622008150

data_2109058
_publ_section_title
;
 Heterocyclic 1,3-diazepine-based thiones and selones as versatile
 halogen-bond acceptors
;
_journal_coeditor_code           RM5061
_journal_issue                   5
_journal_name_full               'Acta Crystallographica Section B'
_journal_page_first
;
;
_journal_paper_doi               10.1107/S2052520622008150
_journal_volume                  78
_journal_year                    2022
_chemical_formula_moiety         'C6 F4 I2, C23 H30 N2 Se'
_chemical_formula_sum            'C29 H30 F4 I2 N2 Se'
_chemical_formula_weight         815.31
_space_group_crystal_system      orthorhombic
_space_group_IT_number           19
_space_group_name_Hall           'P 2ac 2ab'
_space_group_name_H-M_alt        'P 21 21 21'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     dual
_atom_sites_solution_secondary   difmap
_audit_creation_date             2021-06-24
_audit_creation_method
;
Olex2 1.3
(compiled 2020.11.12 svn.r5f609507 for OlexSys, GUI svn.r6272)
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   8.2583(2)
_cell_length_b                   12.9953(4)
_cell_length_c                   27.2240(7)
_cell_measurement_reflns_used    9905
_cell_measurement_temperature    99.99
_cell_measurement_theta_max      29.13
_cell_measurement_theta_min      2.74
_cell_volume                     2921.65(14)
_computing_cell_refinement       'SAINT V8.38A (Bruker AXS Inc., 2017)'
_computing_data_collection       'APEX3 v2017.3-0 (Bruker AXS Inc., 2017)'
_computing_data_reduction        'SAINT V8.38A (Bruker AXS Inc., 2017)'
_computing_molecular_graphics    'Mercury (Macrae <i>et al.</i>, 2008)'
_computing_publication_material  'Olex2 1.5 (Dolomanov <i>et al.</i>, 2009)'
_computing_structure_refinement  'SHELXL 2018/3 (Sheldrick, 2015<i>b</i>)'
_computing_structure_solution    'SHELXT 2018/2 (Sheldrick, 2015<i>a</i>)'
_diffrn_ambient_temperature      99.99
_diffrn_measured_fraction_theta_full 0.998
_diffrn_measured_fraction_theta_max 0.997
_diffrn_measurement_device_type  'Bruker D8 Venture Photon 2'
_diffrn_measurement_method       '\f and \w scans'
_diffrn_radiation_type           MoK\a
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.0468
_diffrn_reflns_av_unetI/netI     0.0225
_diffrn_reflns_Laue_measured_fraction_full 0.998
_diffrn_reflns_Laue_measured_fraction_max 0.997
_diffrn_reflns_limit_h_max       11
_diffrn_reflns_limit_h_min       -11
_diffrn_reflns_limit_k_max       17
_diffrn_reflns_limit_k_min       -17
_diffrn_reflns_limit_l_max       37
_diffrn_reflns_limit_l_min       -37
_diffrn_reflns_number            85940
_diffrn_reflns_point_group_measured_fraction_full 0.998
_diffrn_reflns_point_group_measured_fraction_max 0.997
_diffrn_reflns_theta_full        25.242
_diffrn_reflns_theta_max         29.166
_diffrn_reflns_theta_min         2.167
_diffrn_source                   'Incoatec I\mS'
_diffrn_source_current           1.0
_diffrn_source_power             0.05
_diffrn_source_voltage           50.0
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    3.446
_exptl_absorpt_correction_T_max  0.7458
_exptl_absorpt_correction_T_min  0.4936
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details   'SADABS v2016/2 (Bruker AXS Inc., 2017)'
_exptl_crystal_colour            yellow
_exptl_crystal_colour_primary    yellow
_exptl_crystal_density_diffrn    1.854
_exptl_crystal_density_meas      ?
_exptl_crystal_density_method    'not measured'
_exptl_crystal_description       needle
_exptl_crystal_F_000             1576
_exptl_crystal_size_max          0.291
_exptl_crystal_size_mid          0.081
_exptl_crystal_size_min          0.067
_exptl_transmission_factor_max   'not measured'
_exptl_transmission_factor_min   'not measured'
_refine_diff_density_max         0.991
_refine_diff_density_min         -0.935
_refine_diff_density_rms         0.085
_refine_ls_abs_structure_details
;
 Flack x determined using 3173 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   0.003(4)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.126
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     386
_refine_ls_number_reflns         7878
_refine_ls_number_restraints     96
_refine_ls_restrained_S_all      1.139
_refine_ls_R_factor_all          0.0253
_refine_ls_R_factor_gt           0.0219
_refine_ls_shift/su_max          0.002
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0030P)^2^+3.3501P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0423
_refine_ls_wR_factor_ref         0.0443
_reflns_Friedel_coverage         0.779
_reflns_Friedel_fraction_full    0.999
_reflns_Friedel_fraction_max     0.997
_reflns_number_gt                7491
_reflns_number_total             7878
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            rm5061sup1.cif
_cod_data_source_block           SDiazMesSe_13F4DIB
_cod_depositor_comments
;
The following automatic conversions were performed:

data item '_exptl_crystal_density_meas' value 'not measured' was
changed to '?' -- the value is perceived as not measured.

Automatic conversion script
Id: cif_fix_values 7556 2019-12-06 15:28:31Z antanas 
;
_cod_original_cell_volume        2921.66(14)
_cod_database_code               2109058
_shelx_shelxl_version_number     2016/6
_shelx_estimated_absorpt_t_max   0.802
_shelx_estimated_absorpt_t_min   0.434
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups
 At 1.5 times of:
  All C(H,H,H) groups
2. Uiso/Uaniso restraints and constraints
C2 \\sim C2B \\sim C3 \\sim C3B \\sim C4 \\sim C4B \\sim C5 \\sim C5B: within
2A with sigma of 0.01 and sigma for terminal atoms of 0.02 within 2A
Uanis(C23) \\sim Ueq: with sigma of 0.003 and sigma for terminal atoms of 0.006
3. Others
 Sof(C2B)=Sof(H2BA)=Sof(H2BB)=Sof(C3B)=Sof(H3BA)=Sof(H3BB)=Sof(C4B)=Sof(H4BA)=
 Sof(H4BB)=Sof(C5B)=Sof(H5BA)=Sof(H5BB)=1-FVAR(1)
 Sof(C2)=Sof(H2A)=Sof(H2B)=Sof(C3)=Sof(H3A)=Sof(H3B)=Sof(C4)=Sof(H4A)=Sof(H4B)=
 Sof(C5)=Sof(H5A)=Sof(H5B)=FVAR(1)
4.a Secondary CH2 refined with riding coordinates:
 C2(H2A,H2B), C2B(H2BA,H2BB), C3(H3A,H3B), C3B(H3BA,H3BB), C4(H4A,H4B),
 C4B(H4BA,H4BB), C5(H5A,H5B), C5B(H5BA,H5BB)
4.b Aromatic/amide H refined with riding coordinates:
 C8(H8), C10(H10), C17(H17), C19(H19)
4.c Idealised Me refined as rotating group:
 C12(H12A,H12B,H12C), C13(H13A,H13B,H13C), C14(H14A,H14B,H14C), C21(H21A,H21B,
 H21C), C22(H22A,H22B,H22C), C23(H23A,H23B,H23C)
;
_shelx_res_checksum              61486
_shelx_hkl_checksum              74359
_olex2_submission_special_instructions 'No special instructions were received'
_cod_database_fobs_code 2109058