Confinement-Driven Photophysics in Cages, Covalent-Organic Frameworks, Metal-Organic Frameworks, and DNA.
Dolgopolova, Ekaterina A.; Berseneva, Anna A.; Faillace, Martín S; Ejegbavwo, Otega A.; Leith, Gabrielle A.; Choi, Seok W.; Gregory, Haley N.; Rice, Allison M.; Smith, Mark D.; Chruszcz, Maksymilian; Garashchuk, Sophya; Mythreye, Karthikeyan; Shustova, Natalia B.; Journal of the American Chemical Society  (2020) –; doi:10.1021/jacs.9b13505

data_4134305
_publ_section_title
;
 Confinement-Driven Photophysics in Cages, Covalent-Organic Frameworks,
 Metal-Organic Frameworks, and DNA.
;
_journal_name_full               'Journal of the American Chemical Society'
_journal_paper_doi               10.1021/jacs.9b13505
_journal_year                    2020
_chemical_formula_moiety
'C108 H144 N36 Pd6, C12 H10 Cl N2 O2, 2(O4.49)'
_chemical_formula_sum            'C120 H154 Cl N38 O10.97 Pd6'
_chemical_formula_weight         2978.21
_space_group_crystal_system      tetragonal
_space_group_IT_number           88
_space_group_name_Hall           '-I 4ad'
_space_group_name_H-M_alt        'I 41/a :2'
_atom_sites_solution_hydrogens   geom
_audit_creation_date             2019-01-13
_audit_creation_method
;
Olex2 1.2
(compiled 2018.05.29 svn.r3510 for OlexSys, GUI svn.r5506)
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   26.0645(9)
_cell_length_b                   26.0645(9)
_cell_length_c                   31.6937(13)
_cell_measurement_reflns_used    9704
_cell_measurement_temperature    100(2)
_cell_measurement_theta_max      25.005
_cell_measurement_theta_min      2.430
_cell_volume                     21531.4(14)
_computing_cell_refinement       'SAINT+ Ver. 8.38A (Bruker-AXS, 2016)'
_computing_data_collection       'Bruker APEX3 v2016.5-0 (Bruker, 2016)'
_computing_data_reduction        'SAINT+ Ver. 8.38A (Bruker-AXS, 2016)'
_computing_molecular_graphics    'Olex2 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 (Dolomanov et al., 2009)'
_computing_structure_refinement  'ShelXL (Sheldrick, 2015)'
_computing_structure_solution    'ShelXT (Sheldrick, 2015)'
_diffrn_ambient_temperature      100(2)
_diffrn_detector_area_resol_mean 10.4
_diffrn_detector_type            'CMOS area detector'
_diffrn_measured_fraction_theta_full 0.998
_diffrn_measured_fraction_theta_max 0.997
_diffrn_measurement_device       'three-circle diffractometer'
_diffrn_measurement_device_type  'Bruker D8 QUEST'
_diffrn_measurement_method       '\w and \f scans'
_diffrn_radiation_type           MoK\a
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.0718
_diffrn_reflns_av_unetI/netI     0.0247
_diffrn_reflns_Laue_measured_fraction_full 0.998
_diffrn_reflns_Laue_measured_fraction_max 0.997
_diffrn_reflns_limit_h_max       31
_diffrn_reflns_limit_h_min       -30
_diffrn_reflns_limit_k_max       31
_diffrn_reflns_limit_k_min       -31
_diffrn_reflns_limit_l_max       37
_diffrn_reflns_limit_l_min       -37
_diffrn_reflns_number            142485
_diffrn_reflns_point_group_measured_fraction_full 0.998
_diffrn_reflns_point_group_measured_fraction_max 0.997
_diffrn_reflns_theta_full        25.080
_diffrn_reflns_theta_max         25.082
_diffrn_reflns_theta_min         1.861
_exptl_absorpt_coefficient_mu    0.546
_exptl_absorpt_correction_T_max  0.6193
_exptl_absorpt_correction_T_min  0.5226
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
SADABS-2016/2 (Bruker,2016/2) was used for absorption correction.
wR2(int) was 0.1699 before and 0.0663 after correction.
The Ratio of minimum to maximum transmission is 0.8439.
The \l/2 correction factor is Not present.
;
_exptl_crystal_colour            yellow
_exptl_crystal_colour_primary    yellow
_exptl_crystal_density_diffrn    0.919
_exptl_crystal_description       plate
_exptl_crystal_F_000             6083
_exptl_crystal_size_max          0.46
_exptl_crystal_size_mid          0.24
_exptl_crystal_size_min          0.05
_platon_squeeze_details          )
_refine_diff_density_max         0.535
_refine_diff_density_min         -0.483
_refine_diff_density_rms         0.075
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.027
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     445
_refine_ls_number_reflns         9537
_refine_ls_number_restraints     95
_refine_ls_restrained_S_all      1.031
_refine_ls_R_factor_all          0.0634
_refine_ls_R_factor_gt           0.0450
_refine_ls_shift/su_max          0.005
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0667P)^2^+79.5630P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1196
_refine_ls_wR_factor_ref         0.1346
_reflns_Friedel_coverage         0.000
_reflns_number_gt                7053
_reflns_number_total             9537
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            ja9b13505_si_003.cif
_cod_data_source_block           eadclohbi_sqz
_cod_original_cell_volume        21531.4(17)
_cod_original_sg_symbol_H-M      'I 41/a'
_cod_database_code               4134305
_shelx_shelxl_version_number     2014/7
_shelx_estimated_absorpt_t_max   0.973
_shelx_estimated_absorpt_t_min   0.787
_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
2. Restrained distances
 Cl31-C39
 1.75 with sigma of 0.02
 C31-O31
 1.22 with sigma of 0.015
 C31-C32
 1.48 with sigma of 0.015
 C33-N32
 1.32 with sigma of 0.01
 N32-C32
 1.4 with sigma of 0.015
 C33-N31
 1.38 with sigma of 0.01
 N31-C31
 1.39 with sigma of 0.015
 C33-C34
 1.48 with sigma of 0.01
 N31-C35
 1.46 with sigma of 0.015
 C32-C36
 1.35 with sigma of 0.02
 C36-C37
 1.45 with sigma of 0.02
 N31-N32
 2.24 with sigma of 0.02
 N31-C32
 2.25 with sigma of 0.02
 C31-C33
 2.255 with sigma of 0.02
 C31-N32
 2.344 with sigma of 0.02
 O32-C42
 1.4 with sigma of 0.02
 H24F-H23A
 -2.1 with sigma of 0.02
 H24E-H23B
 -2.1 with sigma of 0.02
 C37-O32 \\sim C41-O32
 with sigma of 0.02
 N32-C34 \\sim N31-C34
 with sigma of 0.01
 C31-C35 \\sim C33-C35
 with sigma of 0.01
 N31-O31 \\sim C32-O31
 with sigma of 0.01
 N8-C20B \\sim N8-C20A \\sim N7-C19A \\sim N7-C19B
 with sigma of 0.01
 C20B-C19B \\sim C20A-C19A
 with sigma of 0.01
 N8-C24A \\sim N8-C24B \\sim N8-C23 \\sim N7-C21 \\sim N7-C22
 with sigma of 0.01
3. Restrained planarity
 C40, Cl31, C39, C38, C37, C41, C36, C42, C32, O32, C31, N32, O31, N31, C33,
 C35, C34
 with sigma of 0.015
4. Uiso/Uaniso restraints and constraints
Uanis(C20A) \\sim Ueq, Uanis(C20B) \\sim Ueq: with sigma of 0.01 and sigma for
terminal atoms of 0.02
Uanis(C20A) = Uanis(C20B)
Uanis(C19B) = Uanis(C19A)
Uiso(C34) = Uiso(C35) = Uiso(N31) = Uiso(N32) = Uiso(C33) = Uiso(C32) =
Uiso(C31) = Uiso(C36) = Uiso(C37) = Uiso(C42) = Uiso(O31) = Uiso(O32) =
Uiso(C41) = Uiso(C40) = Uiso(C39) = Uiso(C38)
Uanis(C24A) = Uanis(C24B)
5. Rigid body (RIGU) restrains
 N7, C19A, C19B, C20A, C20B, N8
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
6. Others
 Sof(C19B)=Sof(H19C)=Sof(H19D)=Sof(C20B)=Sof(H20C)=Sof(H20D)=Sof(C24B)=
 Sof(H24D)=Sof(H24E)=Sof(H24F)=1-FVAR(1)
 Sof(C19A)=Sof(H19A)=Sof(H19B)=Sof(C20A)=Sof(H20A)=Sof(H20B)=Sof(C24A)=
 Sof(H24A)=Sof(H24B)=Sof(H24C)=FVAR(1)
 Fixed Sof: Cl31(0.25) O31(0.25) O32(0.25) N31(0.25) C31(0.25) C32(0.25)
 N32(0.25) C33(0.25) C34(0.25) H34A(0.25) H34B(0.25) H34C(0.25) C35(0.25)
 H35A(0.25) H35B(0.25) H35C(0.25) C36(0.25) H36(0.25) C37(0.25) C38(0.25)
 H38(0.25) C39(0.25) C40(0.25) H40(0.25) C41(0.25) H41(0.25) C42(0.25)
 Fixed Uiso: O1S(0.1) O2S(0.1) O3S(0.1) O4S(0.1) O5S(0.1) O6S(0.1) O7S(0.1)
 O8S(0.1) O9S(0.1) O10S(0.1) O11S(0.1) O12S(0.1)
7.a Secondary CH2 refined with riding coordinates:
 C19A(H19A,H19B), C20A(H20A,H20B), C19B(H19C,H19D), C20B(H20C,H20D), C25(H25A,
 H25B)
7.b Aromatic/amide H refined with riding coordinates:
 C1(H1), C2(H2), C4(H4), C5(H5), C9(H9), C10(H10), C12(H12), C13(H13),
 C14(H14), C15(H15), C17(H17), C18(H18), C36(H36), C38(H38), C40(H40), C41(H41)
7.c Fitted hexagon refined as free rotating group:
 C37(C38,C39,C40,C41,C42)
7.d Idealised Me refined with riding coordinates:
 C34(H34A,H34B,H34C), C35(H35A,H35B,H35C)
7.e Idealised Me refined as rotating group:
 C21(H21A,H21B,H21C), C22(H22A,H22B,H22C), C23(H23A,H23B,H23C), C24A(H24A,H24B,
 H24C), C24B(H24D,H24E,H24F), C26(H26A,H26B,H26C), C27(H27A,H27B,H27C)
;
_platon_squeeze_void_probe_radius 1.20
_olex2_submission_special_instructions 'No special instructions were received'