Bilirubin and its crystal forms
Bracken, Matthew L.; Fernandes, Manuel A.; Mathura, Sadhna; CrystEngComm 26 (2024) 2136–2142; doi:10.1039/D4CE00123K

data_7248346
_publ_section_title
;
 Bilirubin and its crystal forms
;
_journal_issue                   16
_journal_name_full               CrystEngComm
_journal_page_first              2136
_journal_page_last               2142
_journal_paper_doi               10.1039/D4CE00123K
_journal_volume                  26
_journal_year                    2024
_chemical_formula_moiety         'C33 H36 N4 O6'
_chemical_formula_sum            'C33 H36 N4 O6'
_chemical_formula_weight         584.66
_space_group_crystal_system      triclinic
_space_group_IT_number           2
_space_group_name_Hall           '-P 1'
_space_group_name_H-M_alt        'P -1'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     dual
_audit_creation_date             2024-02-06
_audit_creation_method
;
Olex2 1.5
(compiled 2023.08.24 svn.re1ec1418 for OlexSys, GUI svn.r6817)
;
_audit_update_record
;
2024-02-06 deposited with the CCDC.	2024-03-25 downloaded from the CCDC.
;
_cell_angle_alpha                73.515(2)
_cell_angle_beta                 81.274(3)
_cell_angle_gamma                82.823(3)
_cell_formula_units_Z            4
_cell_length_a                   11.6630(7)
_cell_length_b                   15.3457(8)
_cell_length_c                   17.2204(10)
_cell_measurement_reflns_used    9927
_cell_measurement_temperature    173.00
_cell_measurement_theta_max      24.09
_cell_measurement_theta_min      2.35
_cell_volume                     2910.2(3)
_computing_cell_refinement       'SAINT V8.40B (?, 2016)'
_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      173.00
_diffrn_measured_fraction_theta_full 1.000
_diffrn_measured_fraction_theta_max 1.000
_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  0.0904
_diffrn_reflns_av_unetI/netI     0.0594
_diffrn_reflns_Laue_measured_fraction_full 1.000
_diffrn_reflns_Laue_measured_fraction_max 1.000
_diffrn_reflns_limit_h_max       13
_diffrn_reflns_limit_h_min       -13
_diffrn_reflns_limit_k_max       18
_diffrn_reflns_limit_k_min       -18
_diffrn_reflns_limit_l_max       20
_diffrn_reflns_limit_l_min       -20
_diffrn_reflns_number            127211
_diffrn_reflns_point_group_measured_fraction_full 1.000
_diffrn_reflns_point_group_measured_fraction_max 1.000
_diffrn_reflns_theta_full        24.999
_diffrn_reflns_theta_max         24.999
_diffrn_reflns_theta_min         1.594
_diffrn_source_current           1.4
_diffrn_source_power             0.07
_diffrn_source_voltage           50.0
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    0.093
_exptl_absorpt_correction_T_max  0.7454
_exptl_absorpt_correction_T_min  0.6299
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
SADABS-2016/2 (Bruker,2016/2) was used for absorption correction.
wR2(int) was 0.0958 before and 0.0742 after correction.
The Ratio of minimum to maximum transmission is 0.8450.
The \l/2 correction factor is Not present.
;
_exptl_crystal_colour            Orange
_exptl_crystal_density_diffrn    1.334
_exptl_crystal_description       block
_exptl_crystal_F_000             1240
_exptl_crystal_recrystallization_method
'Vapour diffusion of diethyl ether into pyridine'
_exptl_crystal_size_max          0.225
_exptl_crystal_size_mid          0.156
_exptl_crystal_size_min          0.154
_refine_diff_density_max         0.476
_refine_diff_density_min         -0.271
_refine_diff_density_rms         0.051
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.084
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     1519
_refine_ls_number_reflns         10254
_refine_ls_number_restraints     1355
_refine_ls_restrained_S_all      1.024
_refine_ls_R_factor_all          0.1243
_refine_ls_R_factor_gt           0.0851
_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^)+(0.1029P)^2^+3.1601P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.2280
_refine_ls_wR_factor_ref         0.2681
_reflns_Friedel_coverage         0.000
_reflns_number_gt                6779
_reflns_number_total             10254
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d4ce00123k3.cif
_cod_data_source_block           Form_1_23mbb_sadhna18_ns18_bilpyether
_cod_depositor_comments
'Adding full bibliography for 7248346--7248347.cif.'
_cod_database_code               7248346
_shelx_shelxl_version_number     2018/3
_shelx_estimated_absorpt_t_max   0.986
_shelx_estimated_absorpt_t_min   0.979
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups, All N(H) groups
 At 1.5 times of:
  All C(H,H,H) groups, All O(H) groups
2. Restrained distances
 C32A-C31A = C2A-C1A = C35A-C34A = C65A-C64A
 1.3 with sigma of 0.005
 C64A-C61A = C28A-C31A
 1.55 with sigma of 0.005
3. Uiso/Uaniso restraints and constraints
O7A \\sim O8A \\sim O9A \\sim O10A \\sim O11A \\sim O12A \\sim N6A \\sim N7A
\\sim C34A \\sim C35A \\sim N5A \\sim C38A \\sim C37A \\sim C36A \\sim C39A
\\sim C40A \\sim C41A \\sim C42A \\sim C43A \\sim C44A \\sim C45A \\sim C46A
\\sim C47A \\sim C48A \\sim C49A \\sim C50A \\sim C51A \\sim C52A \\sim C53A
\\sim C54A \\sim C55A \\sim C56A \\sim C57A \\sim C58A \\sim C59A \\sim N8A
\\sim C60A \\sim C61A \\sim C62A \\sim C63A \\sim C64A \\sim C65A \\sim C66A:
within 2A with sigma of 0.02 and sigma for terminal atoms of 0.04 within 2A
O1A \\sim O2A \\sim O3A \\sim O4A \\sim O5A \\sim O6A \\sim N2A \\sim N3A \\sim
C1A \\sim C2A \\sim N1A \\sim C5A \\sim C4A \\sim C3A \\sim C6A \\sim C7A \\sim
C8A \\sim C9A \\sim C10A \\sim C11A \\sim C12A \\sim C13A \\sim C14A \\sim C15A
\\sim C16A \\sim C17A \\sim C18A \\sim C19A \\sim C20A \\sim C21A \\sim C22A
\\sim C23A \\sim C24A \\sim C25A \\sim C26A \\sim N4A \\sim C27A \\sim C28A
\\sim C29A \\sim C30A \\sim C31A \\sim C32A \\sim C33A: within 2A with sigma of
0.02 and sigma for terminal atoms of 0.04 within 2A
Uanis(C62A) \\sim Ueq: with sigma of 0.05 and sigma for terminal atoms of 0.1
4. Rigid body (RIGU) restrains
 O7A, O8A, O9A, O10A, O11A, O12A, N6A, N7A, C34A, C35A, N5A, C38A, C37A, C36A,
 C39A, C40A, C41A, C42A, C43A, C44A, C45A, C46A, C47A, C48A, C49A, C50A, C51A,
 C52A, C53A, C54A, C55A, C56A, C57A, C58A, C59A, N8A, C60A, C61A, C62A, C63A,
 C64A, C65A, C66A
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 O1A, O2A, O3A, O4A, O5A, O6A, N2A, N3A, C1A, C2A, N1A, C5A, C4A, C3A, C6A,
 C7A, C8A, C9A, C10A, C11A, C12A, C13A, C14A, C15A, C16A, C17A, C18A, C19A,
 C20A, C21A, C22A, C23A, C24A, C25A, C26A, N4A, C27A, C28A, C29A, C30A, C31A,
 C32A, C33A
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
5. Same fragment restrains
{O1A, O2A, O3A, O4A, O5A, O6A, N2A, N3A, C1A, C2A, N1A, C5A, C4A, C3A, C6A,
C7A, C8A, C9A, C10A, C11A, C12A, C13A, C14A, C15A, C16A, C17A, C18A, C19A,
C20A, C21A, C22A, C23A, C24A, C25A, C26A, N4A, C27A, C28A, C29A, C30A, C31A,
C32A, C33A} sigma for 1-2: 0.005, 1-3: 0.04
as in
{O7A, O8A, O9A, O10A, O11A, O12A, N6A, N7A, C34A, C35A, N5A, C38A, C37A, C36A,
C39A, C40A, C41A, C42A, C43A, C44A, C45A, C46A, C47A, C48A, C49A, C50A, C51A,
C52A, C53A, C54A, C55A, C56A, C57A, C58A, C59A, N8A, C60A, C61A, C62A, C63A,
C64A, C65A, C66A}
{O7A, O8A, O9A, O10A, O11A, O12A, N6A, N7A, C34A, C35A, N5A, C38A, C37A, C36A,
C39A, C40A, C41A, C42A, C43A, C44A, C45A, C46A, C47A, C48A, C49A, C50A, C51A,
C52A, C53A, C54A, C55A, C56A, C57A, C58A, C59A, N8A, C60A, C61A, C62A, C63A,
C64A, C65A, C66A} sigma for 1-2: 0.005, 1-3: 0.04
as in
{O1A, O2A, O3A, O4A, O5A, O6A, N2A, N3A, C1A, C2A, N1A, C5A, C4A, C3A, C6A,
C7A, C8A, C9A, C10A, C11A, C12A, C13A, C14A, C15A, C16A, C17A, C18A, C19A,
C20A, C21A, C22A, C23A, C24A, C25A, C26A, N4A, C27A, C28A, C29A, C30A, C31A,
C32A, C33A}
6. Others
 Sof(O1A)=Sof(O2A)=Sof(O3A)=Sof(H3AA)=Sof(O4A)=Sof(O5A)=Sof(O6A)=Sof(H6A)=
 Sof(N2A)=Sof(H2AA)=Sof(N3A)=Sof(H3AB)=Sof(C1A)=Sof(H1AA)=Sof(H1AB)=Sof(C2A)=
 Sof(H2AB)=Sof(N1A)=Sof(H1AC)=Sof(C5A)=Sof(C4A)=Sof(C3A)=Sof(C6A)=Sof(C7A)=
 Sof(H7AA)=Sof(H7AB)=Sof(H7AC)=Sof(C8A)=Sof(H8A)=Sof(C9A)=Sof(C10A)=Sof(C11A)=
 Sof(C12A)=Sof(C13A)=Sof(H13D)=Sof(H13E)=Sof(H13F)=Sof(C14A)=Sof(H14C)=
 Sof(H14D)=Sof(C15A)=Sof(H15C)=Sof(H15D)=Sof(C16A)=Sof(C17A)=Sof(H17C)=
 Sof(H17D)=Sof(C18A)=Sof(C19A)=Sof(C20A)=Sof(C21A)=Sof(C22A)=Sof(H22C)=
 Sof(H22D)=Sof(C23A)=Sof(H23C)=Sof(H23D)=Sof(C24A)=Sof(C25A)=Sof(H25D)=
 Sof(H25E)=Sof(H25F)=Sof(C26A)=Sof(H26A)=Sof(N4A)=Sof(H4A)=Sof(C27A)=Sof(C28A)=
 Sof(C29A)=Sof(C30A)=Sof(C31A)=Sof(H31A)=Sof(C32A)=Sof(H32C)=Sof(H32D)=
 Sof(C33A)=Sof(H33D)=Sof(H33E)=Sof(H33F)=1-FVAR(1)
 Sof(O1)=Sof(O2)=Sof(O3)=Sof(H3)=Sof(O4)=Sof(O5)=Sof(O6)=Sof(H6)=Sof(N1)=
 Sof(H1)=Sof(N2)=Sof(H2)=Sof(N3)=Sof(H3A)=Sof(N4)=Sof(H4)=Sof(C1)=Sof(H1A)=
 Sof(H1B)=Sof(C2)=Sof(H2A)=Sof(C3)=Sof(C4)=Sof(C5)=Sof(C6)=Sof(C7)=Sof(H7A)=
 Sof(H7B)=Sof(H7C)=Sof(C8)=Sof(H8)=Sof(C9)=Sof(C10)=Sof(C11)=Sof(C12)=Sof(C13)=
 Sof(H13A)=Sof(H13B)=Sof(H13C)=Sof(C14)=Sof(H14A)=Sof(H14B)=Sof(C15)=Sof(H15A)=
 Sof(H15B)=Sof(C16)=Sof(C17)=Sof(H17A)=Sof(H17B)=Sof(C18)=Sof(C19)=Sof(C20)=
 Sof(C21)=Sof(C22)=Sof(H22A)=Sof(H22B)=Sof(C23)=Sof(H23A)=Sof(H23B)=Sof(C24)=
 Sof(C25)=Sof(H25A)=Sof(H25B)=Sof(H25C)=Sof(C26)=Sof(H26)=Sof(C27)=Sof(C28)=
 Sof(C29)=Sof(C30)=Sof(C31)=Sof(H31)=Sof(C32)=Sof(H32A)=Sof(H32B)=Sof(C33)=
 Sof(H33A)=Sof(H33B)=Sof(H33C)=FVAR(1)
 Sof(O7A)=Sof(O8A)=Sof(O9A)=Sof(H9A)=Sof(O10A)=Sof(O11A)=Sof(O12A)=Sof(H12A)=
 Sof(N6A)=Sof(H6AA)=Sof(N7A)=Sof(H7AD)=Sof(C34A)=Sof(H34C)=Sof(H34D)=Sof(C35A)=
 Sof(H35A)=Sof(N5A)=Sof(H5A)=Sof(C38A)=Sof(C37A)=Sof(C36A)=Sof(C39A)=Sof(C40A)=
 Sof(H40D)=Sof(H40E)=Sof(H40F)=Sof(C41A)=Sof(H41A)=Sof(C42A)=Sof(C43A)=
 Sof(C44A)=Sof(C45A)=Sof(C46A)=Sof(H46D)=Sof(H46E)=Sof(H46F)=Sof(C47A)=
 Sof(H47C)=Sof(H47D)=Sof(C48A)=Sof(H48C)=Sof(H48D)=Sof(C49A)=Sof(C50A)=
 Sof(H50C)=Sof(H50D)=Sof(C51A)=Sof(C52A)=Sof(C53A)=Sof(C54A)=Sof(C55A)=
 Sof(H55C)=Sof(H55D)=Sof(C56A)=Sof(H56C)=Sof(H56D)=Sof(C57A)=Sof(C58A)=
 Sof(H58D)=Sof(H58E)=Sof(H58F)=Sof(C59A)=Sof(H59A)=Sof(N8A)=Sof(H8AA)=Sof(C60A)=
 Sof(C61A)=Sof(C62A)=Sof(C63A)=Sof(C64A)=Sof(H64C)=Sof(C65A)=Sof(H65A)=
 Sof(H65B)=Sof(C66A)=Sof(H66D)=Sof(H66E)=Sof(H66F)=1-FVAR(2)
 Sof(O7)=Sof(O8)=Sof(O9)=Sof(H9)=Sof(O10)=Sof(O11)=Sof(O12)=Sof(H12)=Sof(N5)=
 Sof(H5)=Sof(N6)=Sof(H6B)=Sof(N7)=Sof(H7)=Sof(N8)=Sof(H8B)=Sof(C34)=Sof(H34A)=
 Sof(H34B)=Sof(C35)=Sof(H35)=Sof(C36)=Sof(C37)=Sof(C38)=Sof(C39)=Sof(C40)=
 Sof(H40A)=Sof(H40B)=Sof(H40C)=Sof(C41)=Sof(H41)=Sof(C42)=Sof(C43)=Sof(C44)=
 Sof(C45)=Sof(C46)=Sof(H46A)=Sof(H46B)=Sof(H46C)=Sof(C47)=Sof(H47A)=Sof(H47B)=
 Sof(C48)=Sof(H48A)=Sof(H48B)=Sof(C49)=Sof(C50)=Sof(H50A)=Sof(H50B)=Sof(C51)=
 Sof(C52)=Sof(C53)=Sof(C54)=Sof(C55)=Sof(H55A)=Sof(H55B)=Sof(C56)=Sof(H56A)=
 Sof(H56B)=Sof(C57)=Sof(C58)=Sof(H58A)=Sof(H58B)=Sof(H58C)=Sof(C59)=Sof(H59)=
 Sof(C60)=Sof(C61)=Sof(C62)=Sof(C63)=Sof(C64)=Sof(H64A)=Sof(H64B)=Sof(C65)=
 Sof(H65)=Sof(C66)=Sof(H66A)=Sof(H66B)=Sof(H66C)=FVAR(2)
7.a Secondary CH2 refined with riding coordinates:
 C14(H14A,H14B), C15(H15A,H15B), C17(H17A,H17B), C22(H22A,H22B), C23(H23A,
 H23B), C14A(H14C,H14D), C15A(H15C,H15D), C17A(H17C,H17D), C22A(H22C,H22D),
 C23A(H23C,H23D), C47(H47A,H47B), C48(H48A,H48B), C50(H50A,H50B), C55(H55A,
 H55B), C56(H56A,H56B), C47A(H47C,H47D), C48A(H48C,H48D), C50A(H50C,H50D),
 C55A(H55C,H55D), C56A(H56C,H56D)
7.b Me refined with riding coordinates:
 C7(H7A,H7B,H7C), C13(H13A,H13B,H13C), C25(H25A,H25B,H25C), C33(H33A,H33B,
 H33C), C7A(H7AA,H7AB,H7AC), C13A(H13D,H13E,H13F), C25A(H25D,H25E,H25F),
 C33A(H33D,H33E,H33F), C40(H40A,H40B,H40C), C46(H46A,H46B,H46C), C58(H58A,H58B,
 H58C), C66(H66A,H66B,H66C), C40A(H40D,H40E,H40F), C46A(H46D,H46E,H46F),
 C58A(H58D,H58E,H58F), C66A(H66D,H66E,H66F)
7.c Aromatic/amide H refined with riding coordinates:
 N1(H1), N2(H2), N3(H3A), N4(H4), C2(H2A), C8(H8), C26(H26), C31(H31),
 N2A(H2AA), N3A(H3AB), C2A(H2AB), N1A(H1AC), C8A(H8A), C26A(H26A), N4A(H4A),
 C31A(H31A), N5(H5), N6(H6B), N7(H7), N8(H8B), C35(H35), C41(H41), C59(H59),
 C65(H65), N6A(H6AA), N7A(H7AD), C35A(H35A), N5A(H5A), C41A(H41A), C59A(H59A),
 N8A(H8AA), C64A(H64C)
7.d Fitted pentagon refined as free rotating group:
 N1A(C5A,C4A,C3A,C6A), N4A(C27A,C28A,C29A,C30A), N5A(C38A,C37A,C36A,C39A),
 N8A(C60A,C61A,C62A,C63A)
7.e Tetrahedral OH refined with riding coordinates:
 O3A(H3AA), O6A(H6A), O9A(H9A), O12A(H12A)
7.f X=CH2 refined with riding coordinates:
 C1(H1A,H1B), C32(H32A,H32B), C1A(H1AA,H1AB), C32A(H32C,H32D), C34(H34A,H34B),
 C64(H64A,H64B), C34A(H34C,H34D), C65A(H65A,H65B)
7.g Idealised tetrahedral OH refined as rotating group:
 O3(H3), O6(H6), O9(H9), O12(H12)
;
_shelx_res_checksum              45347
_olex2_submission_special_instructions 'No special instructions were received'