C5-pyrimidine-functionalized morpholino oligonucleotides exhibit differential binding affinity, target specificity and lipophilicity.
Das, Arnab; Ghosh, Atanu; Sinha, Surajit; Organic & biomolecular chemistry 21 (2023) 1242–1253; doi:10.1039/d2ob01759h

data_7159056
_publ_section_title
;
 C5-pyrimidine-functionalized morpholino oligonucleotides exhibit
 differential binding affinity, target specificity and lipophilicity.
;
_journal_issue                   6
_journal_name_full               'Organic &amp; biomolecular chemistry'
_journal_page_first              1242
_journal_page_last               1253
_journal_paper_doi               10.1039/d2ob01759h
_journal_volume                  21
_journal_year                    2023
_chemical_absolute_configuration rmad
_chemical_formula_moiety
'C38 H32 N3 O4, C4 H8 O2, 0.05[C4H6O3], 0.5[C4H6O3]'
_chemical_formula_sum            'C42 H41 N3 O6'
_chemical_formula_weight         683.77
_space_group_crystal_system      orthorhombic
_space_group_IT_number           18
_space_group_name_Hall           'P 2 2ab'
_space_group_name_H-M_alt        'P 21 21 2'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     iterative
_audit_creation_date             2022-09-14
_audit_creation_method
;
Olex2 1.5
(compiled 2022.04.07 svn.rca3783a0 for OlexSys, GUI svn.r6498)
;
_audit_update_record
;
2022-09-13 deposited with the CCDC.	2022-12-23 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   15.094(3)
_cell_length_b                   18.129(3)
_cell_length_c                   14.040(2)
_cell_measurement_reflns_used    7933
_cell_measurement_temperature    144.98
_cell_measurement_theta_max      24.88
_cell_measurement_theta_min      2.28
_cell_volume                     3841.9(11)
_computing_cell_refinement       'SAINT V8.38A (Bruker, 2018)'
_computing_data_reduction        'SAINT V8.38A (Bruker, 2018)'
_computing_molecular_graphics    'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_structure_refinement  'XL  (Sheldrick, 2008)'
_computing_structure_solution    'olex2.solve 1.5 (Bourhis et al., 2015)'
_diffrn_ambient_temperature      144.98
_diffrn_measured_fraction_theta_full 0.996
_diffrn_measured_fraction_theta_max 0.996
_diffrn_measurement_device_type  'Bruker APEX-III CCD'
_diffrn_measurement_method       '\f and \w scans'
_diffrn_radiation_type           MoK\a
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.0913
_diffrn_reflns_av_unetI/netI     0.0857
_diffrn_reflns_Laue_measured_fraction_full 0.996
_diffrn_reflns_Laue_measured_fraction_max 0.996
_diffrn_reflns_limit_h_max       17
_diffrn_reflns_limit_h_min       -17
_diffrn_reflns_limit_k_max       21
_diffrn_reflns_limit_k_min       -21
_diffrn_reflns_limit_l_max       16
_diffrn_reflns_limit_l_min       -14
_diffrn_reflns_number            25718
_diffrn_reflns_point_group_measured_fraction_full 0.993
_diffrn_reflns_point_group_measured_fraction_max 0.993
_diffrn_reflns_theta_full        25.062
_diffrn_reflns_theta_max         25.062
_diffrn_reflns_theta_min         2.247
_diffrn_source_current           1.0
_diffrn_source_power             0.05
_diffrn_source_voltage           50.0
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    0.079
_exptl_absorpt_correction_T_max  0.7452
_exptl_absorpt_correction_T_min  0.4991
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
SADABS-2016/2 (Bruker,2016/2) was used for absorption correction.
wR2(int) was 0.1463 before and 0.1033 after correction.
The Ratio of minimum to maximum transmission is 0.6698.
The \l/2 correction factor is Not present.
;
_exptl_crystal_colour            'clear whiteish white'
_exptl_crystal_colour_lustre     clear
_exptl_crystal_colour_modifier   whiteish
_exptl_crystal_colour_primary    white
_exptl_crystal_density_diffrn    1.182
_exptl_crystal_description       needle
_exptl_crystal_F_000             1448
_exptl_crystal_preparation       'Slow evaporation'
_exptl_crystal_size_max          0.035
_exptl_crystal_size_mid          0.032
_exptl_crystal_size_min          0.028
_refine_diff_density_max         0.328
_refine_diff_density_min         -0.190
_refine_diff_density_rms         0.044
_refine_ls_abs_structure_details
;
 Flack x determined using 1728 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   -0.5(10)
_refine_ls_extinction_coef       0.0125(14)
_refine_ls_extinction_expression Fc^*^=kFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^
_refine_ls_extinction_method     'SHELXL-2016/6 (Sheldrick 2016)'
_refine_ls_goodness_of_fit_ref   1.026
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     472
_refine_ls_number_reflns         6777
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.026
_refine_ls_R_factor_all          0.0805
_refine_ls_R_factor_gt           0.0493
_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^)+(0.0463P)^2^+0.7263P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1117
_refine_ls_wR_factor_ref         0.1314
_reflns_Friedel_coverage         0.784
_reflns_Friedel_fraction_full    0.989
_reflns_Friedel_fraction_max     0.988
_reflns_number_gt                4953
_reflns_number_total             6777
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d2ob01759h2.cif
_cod_data_source_block           mo_ss290422_0ma_a
_cod_depositor_comments
;
          Adding full bibliography for 7159056.cif.

2025-04-01
Z value and formula fixed to values more according to usual
chemical conventions.                 miguel
;
_cod_original_formula_sum            'C168 H164 N12 O24'
_cod_original_formula_weight         2735.10
_cod_original_formula_moiety
'4(C38 H32 N3 O4), 4(C4 H8 O2), 0.2[C4H6O3], 2[C4H6O3]'
_cod_original_formula_units_Z            1
_cod_original_cell_volume        3841.9(12)
_cod_database_code               7159056
_shelx_shelxl_version_number     2016/6
_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, All O(H) groups
2.a Ternary CH refined with riding coordinates:
 C2(H2), C3(H3A)
2.b Secondary CH2 refined with riding coordinates:
 C1(H1A,H1B), C4(H4A,H4B), C5(H5A,H5B), C01E(H01A,H01B)
2.c Aromatic/amide H refined with riding coordinates:
 C6(H6A), C10(H10), C22(H22), C9(H9), C33(H33), C39(H39), C26(H26), C11(H11),
 C28(H28), C38(H38), C37(H37), C16(H16), C35(H35), C23(H23), C13(H13), C30(H30),
  C32(H32), C25(H25), C31(H31), C14(H14), C15(H15), C24(H24)
2.d Idealised Me refined as rotating group:
 C01G(H01C,H01D,H01E), C01H(H01F,H01G,H01H)
2.e Idealised tetrahedral OH refined as rotating group:
 O6(H6)
;
_smtbx_masks_special_details
;
A solvent mask was calculated and 112 electrons were found in a volume of 464\%A^3^ in 2 voids per unit cell. 
This is consistent with the presence of [+ solvents]2[C4H6O3] per Asymmetric Unit 
which account for 108 electrons 
per unit cell.
;
_smtbx_masks_void_probe_radius   1.2
_smtbx_masks_void_truncation_radius 1.2
_shelx_res_checksum              77228
_shelx_fab_checksum              26632
_olex2_submission_special_instructions 'No special instructions were received'