Mimic uracil–uracil base pairing: self-assembly and single crystal structure
Zhang, Menglei; Li, Zhongkui; Zhu, Yanhong; Yan, Li; Zhong, Xue; Zhang, Yijie; Li, Ziyao; Bai, Yixiang; Li, Hui; CrystEngComm 26 (2024) 261–267; doi:10.1039/D3CE01056B

data_7247826
_publ_section_title
;
 Mimic uracil--uracil base pairing: self-assembly and single crystal
 structure
;
_journal_issue                   3
_journal_name_full               CrystEngComm
_journal_page_first              261
_journal_page_last               267
_journal_paper_doi               10.1039/D3CE01056B
_journal_volume                  26
_journal_year                    2024
_chemical_absolute_configuration ad
_chemical_formula_moiety         'C27 H29 Cd N8 O11 P, 3(H2 O)'
_chemical_formula_sum            'C27 H35 Cd N8 O14 P'
_chemical_formula_weight         839.00
_space_group_crystal_system      orthorhombic
_space_group_IT_number           20
_space_group_name_Hall           'C 2c 2'
_space_group_name_H-M_alt        'C 2 2 21'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     direct
_audit_creation_date             2023-06-26
_audit_creation_method
;
Olex2 1.5
(compiled 2023.03.06 svn.rbb2c1857 for OlexSys, GUI svn.r6748)
;
_audit_update_record
;
2023-08-16 deposited with the CCDC.	2023-12-01 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            8
_cell_length_a                   10.7744(4)
_cell_length_b                   25.5061(11)
_cell_length_c                   31.6431(12)
_cell_measurement_reflns_used    9861
_cell_measurement_temperature    296.15
_cell_measurement_theta_max      27.03
_cell_measurement_theta_min      2.42
_cell_volume                     8695.9(6)
_computing_cell_refinement       'SAINT v8.34A (Bruker, 2013)'
_computing_data_reduction        'SAINT v8.34A (Bruker, 2013)'
_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    'SHELXS  (Sheldrick, 2008)'
_diffrn_ambient_temperature      296.15
_diffrn_detector_area_resol_mean 7.9
_diffrn_detector_type            'CCD area detector'
_diffrn_measured_fraction_theta_full 1.000
_diffrn_measured_fraction_theta_max 0.998
_diffrn_measurement_device       'three-circle diffractometer'
_diffrn_measurement_device_type  'Bruker APEX-II CCD'
_diffrn_measurement_method       '\f and \w scans'
_diffrn_radiation_type           MoK\a
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.0503
_diffrn_reflns_av_unetI/netI     0.0454
_diffrn_reflns_Laue_measured_fraction_full 1.000
_diffrn_reflns_Laue_measured_fraction_max 0.998
_diffrn_reflns_limit_h_max       13
_diffrn_reflns_limit_h_min       -13
_diffrn_reflns_limit_k_max       32
_diffrn_reflns_limit_k_min       -32
_diffrn_reflns_limit_l_max       40
_diffrn_reflns_limit_l_min       -40
_diffrn_reflns_number            49298
_diffrn_reflns_point_group_measured_fraction_full 1.000
_diffrn_reflns_point_group_measured_fraction_max 0.998
_diffrn_reflns_theta_full        25.242
_diffrn_reflns_theta_max         27.134
_diffrn_reflns_theta_min         1.287
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    0.601
_exptl_absorpt_correction_T_max  0.7455
_exptl_absorpt_correction_T_min  0.5337
_exptl_absorpt_correction_type   none
_exptl_absorpt_process_details
;
SADABS-2014/5 (Bruker,2014/5) was used for absorption correction.
wR2(int) was 0.0757 before and 0.0493 after correction.
The Ratio of minimum to maximum transmission is 0.7159.
The \l/2 correction factor is 0.00150.
;
_exptl_crystal_colour            yellow
_exptl_crystal_colour_primary    yellow
_exptl_crystal_density_diffrn    1.282
_exptl_crystal_description       plate
_exptl_crystal_F_000             3424
_exptl_crystal_size_max          0.26
_exptl_crystal_size_mid          0.24
_exptl_crystal_size_min          0.04
_refine_diff_density_max         0.990
_refine_diff_density_min         -0.954
_refine_diff_density_rms         0.073
_refine_ls_abs_structure_details
;
 Flack x determined using 2894 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   0.000(9)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.032
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     486
_refine_ls_number_reflns         9610
_refine_ls_number_restraints     118
_refine_ls_restrained_S_all      1.032
_refine_ls_R_factor_all          0.0601
_refine_ls_R_factor_gt           0.0407
_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^)+(0.0496P)^2^+5.6080P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0922
_refine_ls_wR_factor_ref         0.0994
_reflns_Friedel_coverage         0.829
_reflns_Friedel_fraction_full    1.000
_reflns_Friedel_fraction_max     0.997
_reflns_number_gt                7596
_reflns_number_total             9610
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d3ce01056b2.cif
_cod_data_source_block           00
_cod_depositor_comments
'Adding full bibliography for 7247822--7247826.cif.'
_cod_database_code               7247826
_shelx_shelxl_version_number     2018/3
_shelx_estimated_absorpt_t_max   0.976
_shelx_estimated_absorpt_t_min   0.859
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All N(H) groups
 At 1.5 times of:
  All O(H) groups, All O(H,H) groups
2. Restrained distances
 H13b-O5
 1.95 with sigma of 0.02
3. Uiso/Uaniso restraints and constraints
Uanis(O14) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
4. Rigid body (RIGU) restrains
 N2, N6, N9, N10, C13, C14, C15, C16, C17, C18, C19, C20, C21, C22, C23, C24
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
5. Others
 Fixed Sof: N6(0.5) N9(0.5) C14(0.5) H14(0.5) C13(0.5) H13(0.5) N2(0.5)
 C17(0.5) H17(0.5) C16(0.5) H16(0.5) C15(0.5) C18(0.5) H18(0.5) C21(0.5)
 C20(0.5) H20(0.5) C19(0.5) H19(0.5) N10(0.5) C23(0.5) H23(0.5) C22(0.5)
 H22(0.5) C24(0.5) H24(0.5)
6.a Free rotating group:
 O13(H13a,H13b), O14(H14a,H14b), O12(H12a,H12b)
6.b Rotating group:
 O1(H1a,H1b), O3(H3a,H3b)
6.c Ternary CH refined with riding coordinates:
 C26(H26), C27(H27), C28(H28), C29(H29)
6.d Aromatic/amide H refined with riding coordinates:
 C2(H2), C1(H1), C5(H5), C4(H4), C6(H6), C7(H7), C8(H8a), C10(H10), C11(H11),
 C12(H12), C25(H25), N8(H8b), C32(H32), C33(H33), C14(H14), C13(H13), C17(H17),
 C16(H16), C18(H18), C20(H20), C19(H19), C23(H23), C22(H22), C24(H24)
6.e Fitted hexagon refined as free rotating group:
 C2(C1,N1,C5,C4,C3), C7(C8,C9,C10,C11,N5), C30(N8,C31,C32,C33,N7), C14(C13,N2,
 C17,C16,C15), C21(C20,C19,N10,C23,C22)
6.f Idealised tetrahedral OH refined as rotating group:
 O8(H8), O9(H9)
;
_smtbx_masks_void_probe_radius   1.2
_smtbx_masks_void_truncation_radius 1.2
_shelx_res_checksum              61238
_shelx_fab_checksum              79484
_olex2_submission_special_instructions 'No special instructions were received'