Diverse tetracyanodihydrodipyrazinopyrazine clathrate crystals assembled from weak intermolecular interactions
Watanabe, Kosuke; Sugiyama, Haruki; Segawa, Yasutomo; CrystEngComm 27 (2025) 3552–3559; doi:10.1039/D5CE00289C

data_7250303
_publ_section_title
;
 Diverse tetracyanodihydrodipyrazinopyrazine clathrate crystals assembled
 from weak intermolecular interactions
;
_journal_issue                   21
_journal_name_full               CrystEngComm
_journal_page_first              3552
_journal_page_last               3559
_journal_paper_doi               10.1039/D5CE00289C
_journal_volume                  27
_journal_year                    2025
_chemical_formula_moiety         'C30 H22 N10, C7 H8'
_chemical_formula_sum            'C37 H30 N10'
_chemical_formula_weight         614.71
_space_group_crystal_system      monoclinic
_space_group_IT_number           14
_space_group_name_Hall           '-P 2ybc'
_space_group_name_H-M_alt        'P 1 21/c 1'
_atom_sites_solution_hydrogens   geom
_audit_creation_date             2024-12-20
_audit_creation_method
;
Olex2 1.5
(compiled 2023.08.24 svn.re1ec1418 for OlexSys, GUI svn.r6817)
;
_audit_update_record
;
2025-03-10 deposited with the CCDC.	2025-04-23 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 103.377(2)
_cell_angle_gamma                90
_cell_formula_units_Z            6
_cell_length_a                   11.6712(2)
_cell_length_b                   18.7282(3)
_cell_length_c                   24.0317(4)
_cell_measurement_reflns_used    23638
_cell_measurement_temperature    113.15
_cell_measurement_theta_max      30.9540
_cell_measurement_theta_min      2.5020
_cell_volume                     5110.35(15)
_computing_cell_refinement       'CrysAlisPro 1.171.39.43c (Rigaku OD, 2018)'
_computing_data_collection       'CrysAlisPro 1.171.39.43c (Rigaku OD, 2018)'
_computing_data_reduction        'CrysAlisPro 1.171.39.43c (Rigaku OD, 2018)'
_computing_molecular_graphics    'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2019/3 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXT  (Sheldrick, 2015)'
_diffrn_ambient_temperature      113.15
_diffrn_detector                 'CCD plate'
_diffrn_detector_type            HyPix
_diffrn_measured_fraction_theta_full 0.999
_diffrn_measured_fraction_theta_max 0.998
_diffrn_measurement_details
;
List of Runs (angles in degrees, time in seconds):

  # Type    Start    End  Width  t~exp~   \w     \q     \k     \f   Frames
  1  \w    -60.00  14.00   0.50   20.98    --    7.34 -37.00  60.00  148
  2  \w    -12.00  18.00   0.50   20.98    --    7.34 -99.00  90.00   60
  3  \w     -3.00  22.00   0.50   20.98    --    7.34-105.00 140.00   50
  4  \w    -11.00  29.00   0.50   20.98    --    7.34 -99.00 -60.00   80
  5  \w      0.00  25.00   0.50   20.98    --    7.34 -99.00 -90.00   50
  6  \w    -77.00   3.00   0.50   20.98    --   -5.93 -57.00-180.00  160
  7  \w     -1.00  35.00   0.50   20.98    --    7.34  37.00-150.00   72
  8  \w     55.00  80.00   0.50   20.98    --    7.34  37.00-150.00   50
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'ROD, Synergy Custom system, HyPix'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      0.0161091000
_diffrn_orient_matrix_UB_12      -0.0359873000
_diffrn_orient_matrix_UB_13      -0.0033519000
_diffrn_orient_matrix_UB_21      0.0008853000
_diffrn_orient_matrix_UB_22      -0.0067142000
_diffrn_orient_matrix_UB_23      0.0291405000
_diffrn_orient_matrix_UB_31      -0.0603716000
_diffrn_orient_matrix_UB_32      -0.0096758000
_diffrn_orient_matrix_UB_33      -0.0077242000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           'Mo K\a'
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.0329
_diffrn_reflns_av_unetI/netI     0.0236
_diffrn_reflns_Laue_measured_fraction_full 0.999
_diffrn_reflns_Laue_measured_fraction_max 0.998
_diffrn_reflns_limit_h_max       15
_diffrn_reflns_limit_h_min       -14
_diffrn_reflns_limit_k_max       24
_diffrn_reflns_limit_k_min       -24
_diffrn_reflns_limit_l_max       31
_diffrn_reflns_limit_l_min       -31
_diffrn_reflns_number            58548
_diffrn_reflns_point_group_measured_fraction_full 0.999
_diffrn_reflns_point_group_measured_fraction_max 0.998
_diffrn_reflns_theta_full        25.242
_diffrn_reflns_theta_max         27.878
_diffrn_reflns_theta_min         2.106
_diffrn_source                   'Rotating-anode X-ray tube'
_diffrn_source_type              'Rigaku (Mo) X-ray Source'
_exptl_absorpt_coefficient_mu    0.075
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.76101
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.39.43c (Rigaku Oxford Diffraction, 2018)
Empirical absorption correction using spherical harmonics,
 implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            yellow
_exptl_crystal_colour_primary    yellow
_exptl_crystal_density_diffrn    1.198
_exptl_crystal_description       block
_exptl_crystal_F_000             1932
_exptl_crystal_size_max          0.15
_exptl_crystal_size_mid          0.1
_exptl_crystal_size_min          0.08
_refine_diff_density_max         0.629
_refine_diff_density_min         -0.423
_refine_diff_density_rms         0.040
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.021
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     791
_refine_ls_number_reflns         12179
_refine_ls_number_restraints     205
_refine_ls_restrained_S_all      1.044
_refine_ls_R_factor_all          0.0625
_refine_ls_R_factor_gt           0.0502
_refine_ls_shift/su_max          0.001
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0691P)^2^+1.5946P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1309
_refine_ls_wR_factor_ref         0.1382
_reflns_Friedel_coverage         0.000
_reflns_number_gt                9879
_reflns_number_total             12179
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5ce00289c2.cif
_cod_data_source_block           TCDP-PhMe
_cod_depositor_comments
'Adding full bibliography for 7250300--7250316.cif.'
_cod_database_code               7250303
_shelx_shelxl_version_number     2019/3
_chemical_oxdiff_formula         'C H O '
_chemical_oxdiff_usercomment     'C N O H'
_shelx_estimated_absorpt_t_max   0.994
_shelx_estimated_absorpt_t_min   0.989
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups
 At 1.5 times of:
  All C(H,H,H) groups
2. Restrained distances
 C7-C23
 1.51 with sigma of 0.02
 N5-C44 \\sim N5-C44A
 with sigma of 0.02
 C44-C45 \\sim C44A-C45A
 with sigma of 0.02
 C44-C49 \\sim C44A-C49A
 with sigma of 0.02
 C45-C51 \\sim C45A-C51A
 with sigma of 0.02
 C45-C46 \\sim C45A-C46A
 with sigma of 0.02
 C49-C48 \\sim C49A-C48A
 with sigma of 0.02
 C49-C52 \\sim C49A-C52A
 with sigma of 0.02
 C48-C47 \\sim C48A-C47A
 with sigma of 0.02
 C46-C47 \\sim C46A-C47A
 with sigma of 0.02
 C47-C50 \\sim C47A-C50A
 with sigma of 0.02
 N5-C45 \\sim N5-C45A
 with sigma of 0.04
 N5-C49 \\sim N5-C49A
 with sigma of 0.04
 C44-C48 \\sim C44A-C48A
 with sigma of 0.04
 C44-C51 \\sim C44A-C51A
 with sigma of 0.04
 C44-C46 \\sim C44A-C46A
 with sigma of 0.04
 C44-C52 \\sim C44A-C52A
 with sigma of 0.04
 C45-C49 \\sim C45A-C49A
 with sigma of 0.04
 C45-C47 \\sim C45A-C47A
 with sigma of 0.04
 C49-C47 \\sim C49A-C47A
 with sigma of 0.04
 C48-C46 \\sim C48A-C46A
 with sigma of 0.04
 C48-C52 \\sim C48A-C52A
 with sigma of 0.04
 C48-C50 \\sim C48A-C50A
 with sigma of 0.04
 C51-C46 \\sim C51A-C46A
 with sigma of 0.04
 C46-C50 \\sim C46A-C50A
 with sigma of 0.04
3. Uiso/Uaniso restraints and constraints
Uanis(C17) \\sim Ueq, Uanis(C7) \\sim Ueq, Uanis(C14) \\sim Ueq, Uanis(C10)
\\sim Ueq, Uanis(C21) \\sim Ueq, Uanis(C68) \\sim Ueq: with sigma of 0.01 and
sigma for terminal atoms of 0.02
Uanis(C44) \\sim Ueq, Uanis(C45) \\sim Ueq, Uanis(C49) \\sim Ueq, Uanis(C48)
\\sim Ueq, Uanis(C46) \\sim Ueq, Uanis(C52) \\sim Ueq, Uanis(C47) \\sim Ueq,
Uanis(C50) \\sim Ueq, Uanis(C45A) \\sim Ueq, Uanis(C46A) \\sim Ueq, Uanis(C47A)
\\sim Ueq, Uanis(C50A) \\sim Ueq, Uanis(C48A) \\sim Ueq, Uanis(C49A) \\sim Ueq,
Uanis(C44A) \\sim Ueq, Uanis(C52A) \\sim Ueq, Uanis(C51) \\sim Ueq, Uanis(C51A)
\\sim Ueq: with sigma of 0.005 and sigma for terminal atoms of 0.01
4. Rigid body (RIGU) restrains
 C68, C17, C7, C14, C10, C21
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
5. Others
 Sof(C66A)=Sof(H66D)=Sof(H66E)=Sof(H66F)=Sof(C62A)=Sof(C67A)=Sof(H67A)=
 Sof(C61A)=Sof(H61A)=Sof(C65A)=Sof(H65A)=Sof(C64A)=Sof(H64A)=Sof(C63A)=
 Sof(H63A)=1-FVAR(1)
 Sof(C62)=Sof(C67)=Sof(H67)=Sof(C61)=Sof(H61)=Sof(C65)=Sof(H65)=Sof(C64)=
 Sof(H64)=Sof(C63)=Sof(H63)=Sof(C66)=Sof(H66A)=Sof(H66B)=Sof(H66C)=FVAR(1)
 Fixed Sof: C44(0.5) C45(0.5) C49(0.5) C48(0.5) H48(0.5) C51(0.5) H51A(0.5)
 H51B(0.5) H51C(0.5) C46(0.5) H46(0.5) C52(0.5) H52A(0.5) H52B(0.5) H52C(0.5)
 C47(0.5) C50(0.5) H50A(0.5) H50B(0.5) H50C(0.5) C7(0.5) C14(0.5) H14(0.5)
 C10(0.5) H10(0.5) C21(0.5) H21(0.5) C68(0.5) H68(0.5) C17(0.5) H17(0.5)
 C23(0.5) H23A(0.5) H23B(0.5) H23C(0.5) C51A(0.5) H51D(0.5) H51E(0.5) H51F(0.5)
 C45A(0.5) C46A(0.5) H46A(0.5) C47A(0.5) C50A(0.5) H50D(0.5) H50E(0.5)
 H50F(0.5) C48A(0.5) H48A(0.5) C49A(0.5) C44A(0.5) C52A(0.5) H52D(0.5)
 H52E(0.5) H52F(0.5)
6.a Aromatic/amide H refined with riding coordinates:
 C39(H39), C37(H37), C5(H5), C3(H3), C48(H48), C46(H46), C67(H67), C61(H61),
 C65(H65), C64(H64), C63(H63), C67A(H67A), C61A(H61A), C65A(H65A), C64A(H64A),
 C63A(H63A), C14(H14), C10(H10), C21(H21), C68(H68), C17(H17), C46A(H46A),
 C48A(H48A)
6.b Fitted hexagon refined as free rotating group:
 C62(C67,C61,C65,C64,C63), C62A(C67A,C61A,C65A,C64A,C63A), C7(C14,C10,C21,C68,
 C17)
6.c Idealised Me refined as rotating group:
 C18(H18A,H18B,H18C), C42(H42A,H42B,H42C), C19(H19A,H19B,H19C), C41(H41A,H41B,
 H41C), C43(H43A,H43B,H43C), C51(H51A,H51B,H51C), C52(H52A,H52B,H52C), C20(H20A,
 H20B,H20C), C50(H50A,H50B,H50C), C66(H66A,H66B,H66C), C66A(H66D,H66E,H66F),
 C23(H23A,H23B,H23C), C51A(H51D,H51E,H51F), C50A(H50D,H50E,H50F), C52A(H52D,
 H52E,H52F)
;
_shelx_res_checksum              1783
_olex2_submission_special_instructions 'No special instructions were received'
_oxdiff_exptl_absorpt_empirical_details
;
Empirical correction (ABSPACK) includes:
- Absorption correction using spherical harmonics
- Frame scaling
;
_oxdiff_exptl_absorpt_empirical_full_max 1.118
_oxdiff_exptl_absorpt_empirical_full_min 0.777