Mutually antagonistic molecular clips: symmetry-breaking non-covalent bonds at the chiral-nonchiral interface.
Bae, Sungryul; Jeong, Younjae; Lee, Dongwhan; Chemical science 16 (2025) 3459–3469; doi:10.1039/d4sc07655a

data_1573598
_publ_section_title
;
 Mutually antagonistic molecular clips: symmetry-breaking non-covalent
 bonds at the chiral-nonchiral interface.
;
_journal_issue                   8
_journal_name_full               'Chemical science'
_journal_page_first              3459
_journal_page_last               3469
_journal_paper_doi               10.1039/d4sc07655a
_journal_volume                  16
_journal_year                    2025
_chemical_formula_moiety         'C40 H33 N5 O5, C44 H36 N4 O3'
_chemical_formula_sum            'C84 H69 N9 O8'
_chemical_formula_weight         1332.48
_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
_audit_creation_date             2024-07-05
_audit_creation_method
;
Olex2 1.5
(compiled 2024.02.16 svn.r378c4104 for OlexSys, GUI svn.r6928)
;
_audit_update_record
;
2024-07-10 deposited with the CCDC.	2025-01-07 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   14.434(3)
_cell_length_b                   15.041(3)
_cell_length_c                   30.493(6)
_cell_measurement_reflns_used    115024
_cell_measurement_temperature    100
_cell_measurement_theta_max      30.000
_cell_measurement_theta_min      0.401
_cell_volume                     6620(2)
_computing_cell_refinement       'HKL3000sm (Otwinowski & Minor, 1997)'
_computing_data_collection       'PAL BL2D-SMDC Program (Shin et. al, 2016)'
_computing_data_reduction        'HKL3000sm (Otwinowski & Minor, 1997)'
_computing_molecular_graphics    'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2018/3 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXT 2018/2 (Sheldrick, 2018)'
_diffrn_ambient_temperature      100.00
_diffrn_measured_fraction_theta_full 0.960
_diffrn_measured_fraction_theta_max 0.967
_diffrn_measurement_device_type  'Rayonix MX225HS CCD area detector'
_diffrn_measurement_method       'omega scan'
_diffrn_radiation_type           synchrotron
_diffrn_radiation_wavelength     0.700
_diffrn_reflns_av_R_equivalents  0.1244
_diffrn_reflns_av_unetI/netI     0.0911
_diffrn_reflns_Laue_measured_fraction_full 0.960
_diffrn_reflns_Laue_measured_fraction_max 0.967
_diffrn_reflns_limit_h_max       20
_diffrn_reflns_limit_h_min       -20
_diffrn_reflns_limit_k_max       21
_diffrn_reflns_limit_k_min       -21
_diffrn_reflns_limit_l_max       43
_diffrn_reflns_limit_l_min       -43
_diffrn_reflns_number            66130
_diffrn_reflns_point_group_measured_fraction_full 0.947
_diffrn_reflns_point_group_measured_fraction_max 0.954
_diffrn_reflns_theta_full        24.835
_diffrn_reflns_theta_max         29.731
_diffrn_reflns_theta_min         1.487
_diffrn_source                   'PLSII 2D bending magnet'
_exptl_absorpt_coefficient_mu    0.085
_exptl_absorpt_correction_T_max  1.000
_exptl_absorpt_correction_T_min  0.820
_exptl_absorpt_correction_type   empirical
_exptl_absorpt_process_details   'HKL3000sm Scalepack(Otwinowski et.al,2003)'
_exptl_crystal_colour            yellow
_exptl_crystal_density_diffrn    1.337
_exptl_crystal_description       plate
_exptl_crystal_F_000             2800
_exptl_crystal_size_max          0.271
_exptl_crystal_size_mid          0.221
_exptl_crystal_size_min          0.065
_refine_diff_density_max         0.275
_refine_diff_density_min         -0.249
_refine_diff_density_rms         0.060
_refine_ls_abs_structure_details
;
 Flack x determined using 4039 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   -0.1(6)
_refine_ls_extinction_coef       0.0138(11)
_refine_ls_extinction_expression Fc^*^=kFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^
_refine_ls_extinction_method     'SHELXL-2018/3 (Sheldrick 2018)'
_refine_ls_goodness_of_fit_ref   1.036
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     923
_refine_ls_number_reflns         18822
_refine_ls_number_restraints     2
_refine_ls_restrained_S_all      1.037
_refine_ls_R_factor_all          0.1040
_refine_ls_R_factor_gt           0.0682
_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^)+(0.0728P)^2^+1.2518P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1569
_refine_ls_wR_factor_ref         0.1789
_reflns_Friedel_coverage         0.816
_reflns_Friedel_fraction_full    0.931
_reflns_Friedel_fraction_max     0.939
_reflns_number_gt                12876
_reflns_number_total             18822
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d4sc07655a4.cif
_cod_data_source_block           nip2cross
_cod_depositor_comments
'Adding full bibliography for 1573595--1573598.cif.'
_cod_database_code               1573598
_shelx_shelxl_version_number     2018/3
_shelx_estimated_absorpt_t_max   0.995
_shelx_estimated_absorpt_t_min   0.977
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups, All C(H,H,H,H) groups, All N(H) groups
 At 1.5 times of:
  All C(H,H,H) groups
2. Restrained distances
 C02I-C02O \\sim C02I-C1
 with sigma of 0.02
 C02O-C02Q \\sim C1-C02Q
 with sigma of 0.02
3. Others
 Sof(H02D)=Sof(H02E)=Sof(H02R)=Sof(H02S)=Sof(C1)=Sof(H1A)=Sof(H1B)=1-FVAR(1)
 Sof(H02A)=Sof(H02B)=Sof(C02O)=Sof(H02K)=Sof(H02L)=Sof(H02P)=Sof(H02Q)=FVAR(1)
4.a Secondary CH2 refined with riding coordinates:
 C010(H01A,H01B), C01A(H01C,H01D), C01E(H01F,H01I), C01N(H01L,H01N), C024(H02X,
 H02Y), C02E(H2,H), C02I(H02A,H02B), C02I(H02D,H02E), C02K(H5,HA), C02L(H02F,
 H02G), C02M(H02H,H02I), C02O(H02K,H02L), C02Q(H02P,H02Q), C02Q(H02R,H02S),
 C02R(H02T,H02U), C02S(H02V,H02W), C1(H1A,H1B)
4.b Aromatic/amide H refined with riding coordinates:
 N009(H009), N00C(H00C), C00U(H00U), C015(H015), C018(H018), C019(H019),
 C01D(H01E), C01F(H01J), C01G(H01G), C01H(H01H), C01K(H01K), C01M(H01M),
 C01O(H01O), C01P(H01P), C01S(H01S), C01T(H01T), C01U(H01U), C01V(H01V),
 C01X(H01X), C01Y(H01Y), C01Z(H01Z), C020(H020), C022(H022), C023(H023),
 C025(H025), C026(H026), C028(H028), C02A(H02Z), C02B(H02), C02C(H02C),
 C02D(H1), C02G(H3), C02H(H4), C02J(H02J), C02N(H6)
4.c Idealised Me refined as rotating group:
 C02P(H02M,H02N,H02O), C02T(H7,HB,HC)
;
_shelx_res_checksum              14045
_olex2_submission_special_instructions 'No special instructions were received'