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_4134303
_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, 1.23(C12 H11 Cl N2 O), 51.58(O), 12.02(N O3)'
_chemical_formula_sum
'C122.73 H157.5 Cl1.23 D103.13 N50.47 O88.88 Pd6'
_chemical_formula_weight         4651.49
_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
_atom_sites_solution_primary     dual
_audit_creation_date             2016-09-28
_audit_creation_method
;
Olex2 1.2
(compiled 2016.09.09 svn.r3337 for OlexSys, GUI svn.r5227)
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   26.1739(14)
_cell_length_b                   26.1739(14)
_cell_length_c                   31.8805(18)
_cell_measurement_reflns_used    9949
_cell_measurement_temperature    100(2)
_cell_measurement_theta_max      28.124
_cell_measurement_theta_min      2.420
_cell_volume                     21840(2)
_computing_cell_refinement       'SAINT v8.34A (Bruker, 2013)'
_computing_data_collection       'Bruker APEX3 v2016.5-0 (Bruker, 2016)'
_computing_data_reduction        'SAINT v8.34A (Bruker, 2013)'
_computing_molecular_graphics    'Olex2 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 (Dolomanov et al., 2009)'
_computing_structure_refinement  'XL (Sheldrick, 2008)'
_computing_structure_solution    'ShelXT (Sheldrick, 2015)'
_diffrn_ambient_temperature      100(2)
_diffrn_detector                 'Bruker PHOTON-100 area detector'
_diffrn_detector_area_resol_mean 10.4
_diffrn_detector_type            'CMOS area detector'
_diffrn_measured_fraction_theta_full 0.999
_diffrn_measured_fraction_theta_max 0.999
_diffrn_measurement_device       'three-circle diffractometer'
_diffrn_measurement_device_type  'Bruker D8 QUEST'
_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  0.0465
_diffrn_reflns_av_unetI/netI     0.0169
_diffrn_reflns_Laue_measured_fraction_full 0.999
_diffrn_reflns_Laue_measured_fraction_max 0.999
_diffrn_reflns_limit_h_max       34
_diffrn_reflns_limit_h_min       -34
_diffrn_reflns_limit_k_max       34
_diffrn_reflns_limit_k_min       -34
_diffrn_reflns_limit_l_max       42
_diffrn_reflns_limit_l_min       -42
_diffrn_reflns_number            436796
_diffrn_reflns_point_group_measured_fraction_full 0.999
_diffrn_reflns_point_group_measured_fraction_max 0.999
_diffrn_reflns_theta_full        28.350
_diffrn_reflns_theta_max         28.351
_diffrn_reflns_theta_min         2.068
_diffrn_source                   'microfocus sealed X-ray tube'
_diffrn_source_type              'Incoatec I\ms'
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    0.594
_exptl_absorpt_correction_T_max  0.4920
_exptl_absorpt_correction_T_min  0.4560
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
SADABS-2014/4 (Bruker,2014/4) was used for absorption correction.
wR2(int) was 0.0979 before and 0.0451 after correction.
The Ratio of minimum to maximum transmission is 0.9268.
The \l/2 correction factor is 0.00150.
;
_exptl_crystal_colour            yellow
_exptl_crystal_colour_primary    yellow
_exptl_crystal_density_diffrn    1.415
_exptl_crystal_description       prism
_exptl_crystal_F_000             9433
_exptl_crystal_size_max          0.4
_exptl_crystal_size_mid          0.34
_exptl_crystal_size_min          0.2
_refine_diff_density_max         0.736
_refine_diff_density_min         -0.774
_refine_diff_density_rms         0.099
_refine_ls_extinction_coef       0.00011(2)
_refine_ls_extinction_expression Fc^*^=kFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^
_refine_ls_extinction_method     'SHELXL-2014/7 (Sheldrick 2014'
_refine_ls_goodness_of_fit_ref   1.062
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     795
_refine_ls_number_reflns         13647
_refine_ls_number_restraints     109
_refine_ls_restrained_S_all      1.076
_refine_ls_R_factor_all          0.0748
_refine_ls_R_factor_gt           0.0523
_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^)+(0.0813P)^2^+79.3074P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1443
_refine_ls_wR_factor_ref         0.1654
_reflns_Friedel_coverage         0.000
_reflns_number_gt                10332
_reflns_number_total             13647
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            ja9b13505_si_002.cif
_cod_data_source_block           ead_83_3
_cod_original_cell_volume        21840(3)
_cod_original_sg_symbol_H-M      'I 41/a'
_cod_original_formula_sum
'C122.73 H157.50 Cl1.23 D103.13 N50.47 O88.88 Pd6'
_cod_database_code               4134303
_shelx_estimated_absorpt_t_max   0.890
_shelx_estimated_absorpt_t_min   0.797
_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
 C39-Cl1
 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
 1.31 with sigma of 0.015
 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
 1.46 with sigma of 0.02
 O101-N101 = O102-N101 = O103-N101
 1.23 with sigma of 0.02
 O101-O102 = O102-O103 = O103-O101
 2.1 with sigma of 0.02
 O104-N102 = O105-N102 = O106-N102
 1.23 with sigma of 0.02
 O104-O105 = O105-O106 = O106-O104
 2.1 with sigma of 0.02
 O107-N103 = O108-N103 = O109-N103
 1.23 with sigma of 0.02
 O107-O108 = O108-O109 = O109-O107
 2.1 with sigma of 0.02
 O110-N104 = O111-N104 = O112-N104
 1.23 with sigma of 0.02
 O110-O111 = O111-O112 = O112-O110
 2.1 with sigma of 0.02
 O113-N105 = O114-N105 = O115-N105
 1.23 with sigma of 0.02
 O113-O114 = O114-O115 = O115-O113
 2.1 with sigma of 0.02
 O116-N106 = O117-N106 = O118-N106
 1.23 with sigma of 0.02
 O116-O117 = O117-O118 = O118-O116
 2.1 with sigma of 0.02
 O119-N107 = O120-N107 = O121-N107
 1.23 with sigma of 0.02
 O119-O120 = O120-O121 = O121-O119
 2.1 with sigma of 0.02
 O122-N108 = O123-N108 = O124-N108
 1.23 with sigma of 0.02
 O122-O123 = O123-O124 = O124-O122
 2.1 with sigma of 0.02
 O125-N109 = O126-N109 = O127-N109
 1.23 with sigma of 0.02
 O125-O126 = O126-O127 = O127-O125
 2.1 with sigma of 0.02
 O128-N110 = O129-N110 = O130-N110
 1.23 with sigma of 0.02
 O128-O129 = O129-O130 = O130-O128
 2.1 with sigma of 0.02
 O131-N111 = O132-N111 = O133-N111
 1.23 with sigma of 0.02
 O131-O132 = O132-O133 = O133-O131
 2.1 with sigma of 0.02
 N7-C19A = N7-C19B = N8-C20A = N8-C20B
 1.5 with sigma of 0.008
 C19A-C20A = C19B-C20B
 1.5 with sigma of 0.008
 N8-C23A = N8-C23B = N8-C24A = N8-C24B = N7-C21A = N7-C21B = N7-C22A = N7-C22B
 1.5 with sigma of 0.008
 O31-N31 \\sim O31-C32
 with sigma of 0.02
3. Restrained planarity
 C32, Cl1, C39, C38, C40, C37, C41, C36, C42, N32, C31, C33, O31, N31, C34, C35
 with sigma of 0.1
 O128, N110, O129, O130
 with sigma of 0.1
 O111, O110, N104, O112
 with sigma of 0.1
 O131, O132, N111, O133
 with sigma of 0.1
4. Uiso/Uaniso restraints and constraints
Uiso(O102) = Uiso(O104)
Uiso(C32) = Uiso(C39) = Uiso(C38) = Uiso(C40) = Uiso(C37) = Uiso(C41) =
Uiso(C36) = Uiso(C42) = Uiso(N32) = Uiso(C31) = Uiso(C33) = Uiso(O31) =
Uiso(N31) = Uiso(C34) = Uiso(C35)
Uiso(O101) = Uiso(O105)
Uiso(O125) = Uiso(N109) = Uiso(O127) = Uiso(O126)
Uanis(C24A) = Uanis(C24B)
Uanis(C23A) = Uanis(C23B)
Uiso(O111) = Uiso(N104) = Uiso(O110) = Uiso(O112)
Uanis(C22B) = Uanis(C22A)
Uanis(C21A) = Uanis(C21B)
Uiso(O131) = Uiso(O132) = Uiso(O133) = Uiso(N111)
Uiso(O107) = Uiso(O108) = Uiso(O109) = Uiso(N103)
Uiso(O123) = Uiso(N108) = Uiso(O124)
Uanis(O122) = Uanis(O8S)
5. Others
 1*[Sof(O107)+Sof(O108)+Sof(O109)+Sof(N103)]+1*[Sof(O122)+Sof(O123)+Sof(O124)+
 Sof(N108)]+1*[Sof(O8S)]=1 with esd of 0.0001
 Sof(Cl1)=Sof(O31)=Sof(N31)=Sof(N32)=Sof(C31)=Sof(C32)=Sof(C33)=Sof(C34)=
 Sof(H34A)=Sof(H34B)=Sof(H34C)=Sof(C35)=Sof(H35A)=Sof(H35B)=Sof(H35C)=Sof(C36)=
 Sof(H36)=Sof(C37)=Sof(C38)=Sof(H38)=Sof(C39)=Sof(C40)=Sof(H40)=Sof(C41)=
 Sof(H41)=Sof(C42)=Sof(H42)=FVAR(1)
 Sof(O107)=Sof(O108)=Sof(O109)=Sof(N103)=FVAR(2)
 Sof(O110)=Sof(O111)=Sof(O112)=Sof(N104)=FVAR(3)
 Sof(O113)=Sof(O114)=Sof(O115)=Sof(N105)=FVAR(4)
 Sof(O116)=Sof(O117)=Sof(O118)=Sof(N106)=FVAR(5)
 Sof(O119)=Sof(O120)=Sof(O121)=Sof(N107)=FVAR(6)
 Sof(O122)=Sof(O123)=Sof(O124)=Sof(N108)=FVAR(7)
 Sof(O125)=Sof(O126)=Sof(O127)=Sof(N109)=FVAR(8)
 Sof(O128)=Sof(O129)=Sof(O130)=Sof(N110)=FVAR(9)
 Sof(C19B)=Sof(H19C)=Sof(H19D)=Sof(C20B)=Sof(H20C)=Sof(H20D)=Sof(C21B)=
 Sof(H21D)=Sof(H21E)=Sof(H21F)=Sof(C22B)=Sof(H22D)=Sof(H22E)=Sof(H22F)=
 Sof(C23B)=Sof(H23D)=Sof(H23E)=Sof(H23F)=Sof(C24B)=Sof(H24D)=Sof(H24E)=
 Sof(H24F)=1-FVAR(10)
 Sof(C19A)=Sof(H19A)=Sof(H19B)=Sof(C20A)=Sof(H20A)=Sof(H20B)=Sof(C21A)=
 Sof(H21A)=Sof(H21B)=Sof(H21C)=Sof(C22A)=Sof(H22A)=Sof(H22B)=Sof(H22C)=
 Sof(C23A)=Sof(H23A)=Sof(H23B)=Sof(H23C)=Sof(C24A)=Sof(H24A)=Sof(H24B)=
 Sof(H24C)=FVAR(10)
 Sof(O131)=Sof(O132)=Sof(O133)=Sof(N111)=FVAR(11)
 Fixed Sof: O101(0.33333) O102(0.33333) O103(0.33333) N101(0.33333)
 O104(0.33333) O105(0.33333) O106(0.33333) N102(0.33333) O17S(0.33333)
 Fixed Uiso: O32(0.1) O33(0.1) O34(0.1) O119(0.1) O120(0.1) O121(0.1)
 N107(0.1) O128(0.1) O129(0.1) O130(0.1) N110(0.1) O131(0.1) O132(0.1)
 O133(0.1) N111(0.1) O4S(0.1) O5S(0.1) O6S(0.1) O7S(0.1) O9S(0.1) O10S(0.1)
 O11S(0.1) O12S(0.1) O13S(0.1) O14S(0.1) O15S(0.1) O16S(0.1) O18S(0.1)
 O20S(0.1) O21S(0.1) O22S(0.1) O23S(0.1) O24S(0.1) O25S(0.1) O26S(0.1)
 O27S(0.1) O28S(0.1) O29S(0.1) O30S(0.1) O31S(0.1) O32S(0.1) O33S(0.1)
 O34S(0.1) O35S(0.1) O36S(0.1) O37S(0.1) O38S(0.1) O39S(0.1) O40S(0.1)
 O41S(0.1) O42S(0.1) O43S(0.1) O44S(0.1) O45S(0.1)
6.a Secondary CH2 refined with riding coordinates:
 C19A(H19A,H19B), C20A(H20A,H20B), C19B(H19C,H19D), C20B(H20C,H20D), C25(H25A,
 H25B)
6.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),
  C42(H42)
6.c Fitted hexagon refined as free rotating group:
 C37(C38,C39,C40,C41,C42)
6.d Idealised Me refined as rotating group:
 C21A(H21A,H21B,H21C), C22A(H22A,H22B,H22C), C23A(H23A,H23B,H23C), C24A(H24A,
 H24B,H24C), C21B(H21D,H21E,H21F), C22B(H22D,H22E,H22F), C23B(H23D,H23E,H23F),
 C24B(H24D,H24E,H24F), C26(H26A,H26B,H26C), C27(H27A,H27B,H27C), C34(H34A,H34B,
 H34C), C35(H35A,H35B,H35C)
;
_shelx_res_checksum              67192
_shelx_hkl_checksum              66505
_shelx_shelxl_version_number     2014/7
_olex2_submission_special_instructions 'No special instructions were received'