Mechanical bonds and topological effects in radical dimer stabilization.
Frasconi, Marco; Kikuchi, Takashi; Cao, Dennis; Wu, Yilei; Liu, Wei-Guang; Dyar, Scott M.; Barin, Gokhan; Sarjeant, Amy A.; Stern, Charlotte L.; Carmieli, Raanan; Wang, Cheng; Wasielewski, Michael R.; Goddard, 3rd, William A; Stoddart, J. Fraser; Journal of the American Chemical Society 136 (2014) 11011–11026; doi:10.1021/ja504662a

data_4122352
_publ_section_title
;
 Mechanical bonds and topological effects in radical dimer stabilization.
;
_journal_issue                   31
_journal_name_full               'Journal of the American Chemical Society'
_journal_page_first              11011
_journal_page_last               11026
_journal_paper_doi               10.1021/ja504662a
_journal_volume                  136
_journal_year                    2014
_chemical_formula_moiety
'C46 H52 N12 Pt2, 2(C34 H44 O10 S4), 8(F6 P), 2(C2 H3 N)'
_chemical_formula_sum            'C118 H146 F48 N14 O20 P8 Pt2 S8'
_chemical_formula_weight         3886.90
_chemical_name_systematic
;
 ?
;
_space_group_crystal_system      monoclinic
_space_group_IT_number           15
_space_group_name_Hall           '-C 2yc'
_space_group_name_H-M_alt        'C 1 2/c 1'
_symmetry_space_group_name_Hall  '-C 2yc'
_symmetry_space_group_name_H-M   'C 1 2/c 1'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     direct
_audit_creation_date             2012-10-31
_audit_creation_method
;
  Olex2 1.2
  (compiled Oct 26 2012 17:09:49, GUI svn.r4371)
;
_cell_angle_alpha                90
_cell_angle_beta                 99.3191(19)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   35.6937(10)
_cell_length_b                   12.3490(4)
_cell_length_c                   39.6287(11)
_cell_measurement_reflns_used    9938
_cell_measurement_temperature    100(2)
_cell_measurement_theta_max      64.88
_cell_measurement_theta_min      2.51
_cell_volume                     17237.1(9)
_computing_cell_refinement       'SAINT V7.23A (Bruker, 2005)'
_computing_data_collection       'APEX2 V2.1-4 (Bruker, 2007)'
_computing_data_reduction        'Bruker SAINT'
_computing_molecular_graphics
;
O. V. Dolomanov, L. J. Bourhis, R. J. Gildea, J. A. K. Howard and H. Puschmann,
OLEX2: a complete structure solution, refinement and analysis program.
J. Appl. Cryst. (2009). 42, 339-341.
;
_computing_publication_material
;
O. V. Dolomanov, L. J. Bourhis, R. J. Gildea, J. A. K. Howard and H. Puschmann,
OLEX2: a complete structure solution, refinement and analysis program.
J. Appl. Cryst. (2009). 42, 339-341.
;
_computing_structure_refinement
;
SHELXL, G.M. Sheldrick, Acta Cryst.
(2008). A64, 112-122
;
_computing_structure_solution
;
XS, G.M. Sheldrick, Acta Cryst.
(2008). A64, 112-122
;
_diffrn_ambient_temperature      100.05
_diffrn_detector_area_resol_mean 8
_diffrn_measured_fraction_theta_full 0.989
_diffrn_measured_fraction_theta_max 0.990
_diffrn_measurement_device_type  'Bruker Kappa APEX CCD area detector'
_diffrn_measurement_method       '\w and \f scans'
_diffrn_radiation_monochromator  'Quazar optics'
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54178
_diffrn_reflns_av_R_equivalents  0.0605
_diffrn_reflns_av_unetI/netI     0.0603
_diffrn_reflns_Laue_measured_fraction_full 0.989
_diffrn_reflns_Laue_measured_fraction_max 0.990
_diffrn_reflns_limit_h_max       40
_diffrn_reflns_limit_h_min       -40
_diffrn_reflns_limit_k_max       9
_diffrn_reflns_limit_k_min       -14
_diffrn_reflns_limit_l_max       45
_diffrn_reflns_limit_l_min       -45
_diffrn_reflns_number            46063
_diffrn_reflns_point_group_measured_fraction_full 0.989
_diffrn_reflns_point_group_measured_fraction_max 0.990
_diffrn_reflns_theta_full        62.400
_diffrn_reflns_theta_max         62.38
_diffrn_reflns_theta_min         2.26
_diffrn_source                   microsource
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    5.586
_exptl_absorpt_correction_T_max  0.7526
_exptl_absorpt_correction_T_min  0.5428
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
SADABS-2008/1 (Bruker,2008) was used for absorption correction.
wR2(int) was 0.0997 before and 0.0656 after correction.
The Ratio of minimum to maximum transmission is 0.7212.
The \l/2 correction factor is 0.0015.
;
_exptl_crystal_colour            green
_exptl_crystal_colour_primary    green
_exptl_crystal_density_diffrn    1.498
_exptl_crystal_description       plate
_exptl_crystal_F_000             7792
_exptl_crystal_size_max          0.105
_exptl_crystal_size_mid          0.043
_exptl_crystal_size_min          0.006
_refine_diff_density_max         2.776
_refine_diff_density_min         -2.277
_refine_diff_density_rms         0.229
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.168
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     929
_refine_ls_number_reflns         13568
_refine_ls_number_restraints     949
_refine_ls_restrained_S_all      1.141
_refine_ls_R_factor_all          0.1332
_refine_ls_R_factor_gt           0.1208
_refine_ls_shift/su_max          0.003
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
;
 w=1/[\s^2^(Fo^2^)+(0.1147P)^2^+866.4355P]
 where P=(Fo^2^+2Fc^2^)/3
;
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.3123
_refine_ls_wR_factor_ref         0.3193
_reflns_Friedel_coverage         0.000
_reflns_number_gt                11425
_reflns_number_total             13568
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            ja504662a_si_002.cif
_cod_data_source_block           n2260
_cod_depositor_comments
'Adding full bibliography for 4122349--4122355.cif.'
_cod_database_code               4122352
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  {H57A,H57B} of C57, {H1A,H1B} of N1, {H2A,H2B} of N2, {H1C,H1D} of C1, {H2C,
  H2D} of C2, H3 of C3, H4 of C4, H6 of C6, H7 of C7, H9 of C9, H10 of C10, H11
  of C11, H12 of C12, {H33A,H33B} of C33, {H32A,H32B} of C32, {H31A,H31B} of
  C31, {H30A,H30B} of C30, H28 of C28, H25 of C25, H23 of C23, H22 of C22, H21
  of C21, H20 of C20, H18 of C18, H17 of C17, H15 of C15, H14 of C14, {H13A,
  H13B} of C13, {H38A,H38B} of C38, {H37A,H37B} of C37, {H34A,H34B} of C34,
  {H36A,H36B} of C36, {H35A,H35B} of C35, {H56A,H56B} of C56, {H55A,H55B} of
  C55, {H54A,H54B} of C54, {H53A,H53B} of C53, {H52A,H52B} of C52, {H51A,H51B}
  of C51, {H50A,H50B} of C50, {H49A,H49B} of C49, H47 of C47, H46 of C46, H45
  of C45, H42 of C42, H41 of C41, H40 of C40
 At 1.5 times of:
  {H59A,H59B,H59C} of C59
2. Restrained distances
 F25-F30 ~ F29-F28 ~ F27-F26 ~ F27-F30 ~ F29-F25 ~ F28-F26 ~ F25-F27 ~ F28-F29
 ~ F30-F26
 with sigma of 0.02
 F28-F27 ~ F25-F29 ~ F26-F30
 with sigma of 0.02
3. Uiso/Uaniso restraints and constraints
Uanis(F23) = Uanis(P4) = Uanis(F19) = Uanis(F24) = Uanis(F20) = Uanis(F21) = Uanis(F22) = Uanis(F11) = Uanis(P2) = Uanis(F12) = Uanis(F9) = Uanis(F10) = Uanis(F8) = Uanis(F7) = Uanis(F28) = Uanis(P5) = Uanis(F25) = Uanis(F27) = Uanis(F29) = Uanis(F26) = Uanis(F30)
4. Others
 1*[Sof(P5)+Sof(F28)+Sof(F25)+Sof(F27)+Sof(F29)+Sof(F26)+Sof(F30)]+1*[Sof(P4)+
 Sof(F22)+Sof(F23)+Sof(F19)+Sof(F24)+Sof(F20)+Sof(F21)]+1*[Sof(P2)+Sof(F12)+
 Sof(F9)+Sof(F10)+Sof(F8)+Sof(F7)+Sof(F11)]=2 with esd of 0.0001
 Sof(P4)=Sof(F22)=Sof(F23)=Sof(F19)=Sof(F24)=Sof(F20)=Sof(F21)
 Sof(P2)=Sof(F12)=Sof(F9)=Sof(F10)=Sof(F8)=Sof(F7)=Sof(F11)
 Sof(P5)=Sof(F28)=Sof(F25)=Sof(F27)=Sof(F29)=Sof(F26)=Sof(F30)
5.a Secondary CH2 refined with riding coordinates:
 N1(H1A,H1B), N2(H2A,H2B), C1(H1C,H1D), C2(H2C,H2D), C13(H13A,H13B), C30(H30A,
 H30B), C31(H31A,H31B), C32(H32A,H32B), C33(H33A,H33B), C34(H34A,H34B),
 C35(H35A,H35B), C36(H36A,H36B), C37(H37A,H37B), C38(H38A,H38B), C49(H49A,H49B),
  C50(H50A,H50B), C51(H51A,H51B), C52(H52A,H52B), C53(H53A,H53B), C54(H54A,
 H54B), C55(H55A,H55B), C56(H56A,H56B), C57(H57A,H57B)
5.b Aromatic/amide H refined with riding coordinates:
 C3(H3), C4(H4), C6(H6), C7(H7), C9(H9), C10(H10), C11(H11), C12(H12),
 C14(H14), C15(H15), C17(H17), C18(H18), C20(H20), C21(H21), C22(H22), C23(H23),
  C25(H25), C28(H28), C40(H40), C41(H41), C42(H42), C45(H45), C46(H46), C47(H47)
5.c Idealised Me refined as rotating group:
 C59(H59A,H59B,H59C)
;
_smtbx_masks_special_details
;
Total solvent accessible volume / cell = 2456.4 Ang^3^ [14.2%]
Total electron count / cell = 496.0

The solvent masking procedure as implemented in Olex2 was used to remove the
electronic contribution of solvent molecules from the refinement.  As the exact
solvent content is not known, only the atoms used in the refinement model are
reported in the formula here.
;
_shelx_estimated_absorpt_t_max   0.967
_shelx_estimated_absorpt_t_min   0.592
_shelx_hkl_checksum              32102
_shelx_res_checksum              19981
_shelxl_version_number           2012-6