Synthesis of compact water-soluble bioconjugatable porphyrins for life sciences applications
Ngo, Quang-Thien; Cao, Phuong-Lien Doan; Wu, Zhiyuan; Siwawannapong, Kittipan; Ntim, Thomas; Nalaoh, Phattananawee; Lindsey, Jonathan S.; New Journal of Chemistry 49 (2025) 15584–15611; doi:10.1039/D5NJ02077H

data_7063903
_publ_section_title
;
 Synthesis of compact water-soluble bioconjugatable porphyrins for life
 sciences applications
;
_journal_issue                   36
_journal_name_full               'New Journal of Chemistry'
_journal_page_first              15584
_journal_page_last               15611
_journal_paper_doi               10.1039/D5NJ02077H
_journal_volume                  49
_journal_year                    2025
_chemical_formula_moiety         'C44 H36 N4 O5 Zn, 1[C4H8O]'
_chemical_formula_sum            'C48 H44 N4 O6 Zn'
_chemical_formula_weight         838.24
_space_group_crystal_system      monoclinic
_space_group_IT_number           14
_space_group_name_Hall           '-P 2yn'
_space_group_name_H-M_alt        'P 1 21/n 1'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     dual
_audit_creation_date             2025-07-07
_audit_creation_method
;
Olex2 1.5
(compiled 2025.05.31 svn.r86d253d1 for OlexSys, GUI svn.r7254)
;
_audit_update_record
;
2025-07-08 deposited with the CCDC.	2025-07-15 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 90.476(3)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   9.8497(8)
_cell_length_b                   32.182(3)
_cell_length_c                   12.7803(9)
_cell_measurement_reflns_used    9696
_cell_measurement_temperature    100.00
_cell_measurement_theta_max      27.06
_cell_measurement_theta_min      2.48
_cell_volume                     4051.0(6)
_computing_cell_refinement       'SAINT V8.40B (?, 2016)'
_computing_data_collection       'APEX4 and SAINT (Bruker, 2021)'
_computing_data_reduction        'SAINT V8.40B (?, 2016)'
_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_detector                 'Bruker APEX2 area detector'
_diffrn_detector_area_resol_mean 7.9
_diffrn_detector_type            'CCD area detector'
_diffrn_measured_fraction_theta_full 0.999
_diffrn_measured_fraction_theta_max 0.998
_diffrn_measurement_device       'three-circle diffractometer'
_diffrn_measurement_device_type  'Bruker SMART APEX2 area detector'
_diffrn_measurement_method       '\w and \f scans'
_diffrn_radiation_monochromator  'mirror optics'
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           MoK\a
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.0481
_diffrn_reflns_av_unetI/netI     0.0272
_diffrn_reflns_Laue_measured_fraction_full 0.999
_diffrn_reflns_Laue_measured_fraction_max 0.998
_diffrn_reflns_limit_h_max       12
_diffrn_reflns_limit_h_min       -12
_diffrn_reflns_limit_k_max       40
_diffrn_reflns_limit_k_min       -40
_diffrn_reflns_limit_l_max       15
_diffrn_reflns_limit_l_min       -15
_diffrn_reflns_number            67105
_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         26.376
_diffrn_reflns_theta_min         2.162
_diffrn_source                   'microfocus sealed X-ray tube'
_diffrn_source_type              'Incoatec I\ms'
_exptl_absorpt_coefficient_mu    0.663
_exptl_absorpt_correction_T_max  0.7455
_exptl_absorpt_correction_T_min  0.6231
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
SADABS-2016/2 (Bruker,2016/2) was used for absorption correction.
wR2(int) was 0.0963 before and 0.0575 after correction.
The Ratio of minimum to maximum transmission is 0.8358.
The \l/2 correction factor is Not present.
;
_exptl_crystal_colour            'clear dark red'
_exptl_crystal_colour_lustre     clear
_exptl_crystal_colour_modifier   dark
_exptl_crystal_colour_primary    red
_exptl_crystal_density_diffrn    1.374
_exptl_crystal_description       plate
_exptl_crystal_F_000             1752
_exptl_crystal_recrystallization_method
'Re-crystallisation from solvent: tetrahydrofuran'
_exptl_crystal_size_max          0.612
_exptl_crystal_size_mid          0.432
_exptl_crystal_size_min          0.13
_refine_diff_density_max         1.255
_refine_diff_density_min         -1.155
_refine_diff_density_rms         0.076
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.024
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     545
_refine_ls_number_reflns         8273
_refine_ls_number_restraints     8
_refine_ls_restrained_S_all      1.024
_refine_ls_R_factor_all          0.0625
_refine_ls_R_factor_gt           0.0569
_refine_ls_shift/su_max          0.004
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0598P)^2^+9.3919P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1392
_refine_ls_wR_factor_ref         0.1434
_reflns_Friedel_coverage         0.000
_reflns_number_gt                7370
_reflns_number_total             8273
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5nj02077h2.cif
_cod_data_source_block           mo_ncsu_pn44_a
_cod_depositor_comments
'Adding full bibliography for 7063903--7063904.cif.'
_cod_database_code               7063903
_shelx_shelxl_version_number     2018/3
_shelx_estimated_absorpt_t_max   0.919
_shelx_estimated_absorpt_t_min   0.687
_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,H) groups
2. Restrained distances
 C5-C6 \\sim C5-C6A
 with sigma of 0.02
 C5-C10 \\sim C5-C10A
 with sigma of 0.02
 C6-C7 \\sim C6A-C7A
 with sigma of 0.02
 C7-C8 \\sim C7A-C8
 with sigma of 0.02
 C8-C9 \\sim C8-C9A
 with sigma of 0.02
 C9-C10 \\sim C9A-C10A
 with sigma of 0.02
 C5-C7 \\sim C5-C7A
 with sigma of 0.04
 C5-C9 \\sim C5-C9A
 with sigma of 0.04
 C6-C8 \\sim C6A-C8
 with sigma of 0.04
 C8-C10 \\sim C8-C10A
 with sigma of 0.04
 O3-C4 \\sim O3A-C4A
 with sigma of 0.02
 O6-C49 \\sim O6A-C1A
 with sigma of 0.02
 C49-C51 \\sim C1A-C51
 with sigma of 0.02
 C51-C4 \\sim C51-C4A
 with sigma of 0.02
 O3-C51 \\sim O3A-C51
 with sigma of 0.04
 O6-C51 \\sim O6A-C51
 with sigma of 0.04
 C51-C12 \\sim C51-C12A
 with sigma of 0.02
 C5-C6 \\sim C5A-C6
 with sigma of 0.02
 C5-C10 \\sim C5A-C10
 with sigma of 0.02
 C5-C10A \\sim C5A-C10A
 with sigma of 0.02
 C5-C6A \\sim C5A-C6A
 with sigma of 0.02
 C5-C47A \\sim C5A-C47A
 with sigma of 0.02
 C5-C44 \\sim C5A-C44
 with sigma of 0.02
 Zn2-H2A \\sim Zn2-H2B
 with sigma of 0.02
3. Uiso/Uaniso restraints and constraints
Uanis(O6) = Uanis(O3A)
Uanis(C4A) = Uanis(C4)
Uanis(O6) = Uanis(O6A)
Uanis(C5A) = Uanis(C5)
Uanis(C8) = Uanis(C5A) = Uanis(C5)
Uanis(C47A) = Uanis(C44)
Uanis(C12) = Uanis(C12A)
Uanis(C13) = Uanis(C47A) = Uanis(C44)
Uanis(C23) = Uanis(C4A) = Uanis(C4)
Uanis(C49) = Uanis(C1A)
Uanis(C45) = Uanis(C51)
4. Others
 Fixed Sof: O3(0.5) O6(0.5) C49(0.5) H49A(0.5) H49B(0.5) C51(0.5) C4(0.5)
 H4A(0.5) H4B(0.5) C5(0.5) C6(0.5) H6(0.5) C7(0.5) H7(0.5) C9(0.5) H9(0.5)
 C10(0.5) H10(0.5) C11(0.5) H11A(0.5) H11B(0.5) H11C(0.5) C12(0.5) H12A(0.5)
 H12B(0.5) H12C(0.5) C9A(0.5) H9A(0.5) C10A(0.5) H10A(0.5) C7A(0.5) H7A(0.5)
 C6A(0.5) H6A(0.5) O3A(0.5) O6A(0.5) C1A(0.5) H1AA(0.5) H1AB(0.5) C4A(0.5)
 H4AA(0.5) H4AB(0.5) C12A(0.5) H12D(0.5) H12E(0.5) H12F(0.5) C47A(0.5)
 H47A(0.5) C44(0.5) H44(0.5) C45(0.5) C46(0.5) H46A(0.5) H46B(0.5) H46C(0.5)
 C5A(0.5)
5.a Free rotating group:
 O2(H2A,H2B)
5.b Ternary CH refined with riding coordinates:
 C47A(H47A), C44(H44)
5.c Secondary CH2 refined with riding coordinates:
 C49(H49A,H49B), C50(H50A,H50B), C4(H4A,H4B), C39(H39A,H39B), C1A(H1AA,H1AB),
 C4A(H4AA,H4AB)
5.d Aromatic/amide H refined with riding coordinates:
 C6(H6), C7(H7), C9(H9), C10(H10), C15(H15), C16(H16), C20(H20), C21(H21),
 C22(H22), C24(H24), C25(H25), C28(H28), C29(H29), C31(H31), C35(H35), C36(H36),
  C37(H37), C9A(H9A), C10A(H10A), C7A(H7A), C6A(H6A)
5.e Idealised Me refined as rotating group:
 C11(H11A,H11B,H11C), C12(H12A,H12B,H12C), C12A(H12D,H12E,H12F), C46(H46A,H46B,
 H46C)
5.f :
 C41(H41), C43(H43)
;
_smtbx_masks_special_details
;
A solvent mask was calculated and 190 electrons were 
found in a volume of 614\%A^3^ in 1 void per unit cell. 
This is consistent with the presence of 
1[C4H8O] per Formula Unit 
which account for 160 electrons 
per unit cell.
;
_smtbx_masks_void_probe_radius   1.2
_smtbx_masks_void_truncation_radius 1.2
_shelx_res_checksum              5568
_shelx_fab_checksum              70142
_olex2_submission_special_instructions 'No special instructions were received'