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_4122353
_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 Pd2, 2(C34 H44 O10 S4), 8(F6 P)'
_chemical_formula_sum            'C114 H140 F48 N12 O20 P8 Pd2 S8'
_chemical_formula_weight         3627.41
_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             2012-11-09
_audit_creation_method
;
  Olex2 1.2
  (compiled Nov  5 2012 18:25:38, GUI svn.r4372)
;
_cell_angle_alpha                90
_cell_angle_beta                 100.002(4)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   35.8988(19)
_cell_length_b                   12.3423(6)
_cell_length_c                   39.878(2)
_cell_measurement_reflns_used    9622
_cell_measurement_temperature    100(2)
_cell_measurement_theta_max      54.20
_cell_measurement_theta_min      2.25
_cell_volume                     17400.4(15)
_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      99.99
_diffrn_detector_area_resol_mean 8
_diffrn_measured_fraction_theta_full 0.523
_diffrn_measured_fraction_theta_max 0.903
_diffrn_measurement_device_type  'Bruker Kappa APEX CCD area detector'
_diffrn_measurement_method       '\w and \f scans'
_diffrn_radiation_monochromator  'MX optics'
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54178
_diffrn_reflns_av_R_equivalents  0.0623
_diffrn_reflns_av_unetI/netI     0.0725
_diffrn_reflns_Laue_measured_fraction_full 0.523
_diffrn_reflns_Laue_measured_fraction_max 0.903
_diffrn_reflns_limit_h_max       35
_diffrn_reflns_limit_h_min       -34
_diffrn_reflns_limit_k_max       12
_diffrn_reflns_limit_k_min       -7
_diffrn_reflns_limit_l_max       39
_diffrn_reflns_limit_l_min       -39
_diffrn_reflns_number            24963
_diffrn_reflns_point_group_measured_fraction_full 0.523
_diffrn_reflns_point_group_measured_fraction_max 0.903
_diffrn_reflns_theta_full        67.679
_diffrn_reflns_theta_max         50.43
_diffrn_reflns_theta_min         2.25
_diffrn_source                   microsource
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    4.221
_exptl_absorpt_correction_T_max  0.7507
_exptl_absorpt_correction_T_min  0.5597
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
SADABS-2008/1 (Bruker,2008) was used for absorption correction.
wR2(int) was 0.1071 before and 0.0590 after correction.
The Ratio of minimum to maximum transmission is 0.7456.
The \l/2 correction factor is 0.0015.
;
_exptl_crystal_colour            green
_exptl_crystal_colour_primary    green
_exptl_crystal_density_diffrn    1.385
_exptl_crystal_description       plate
_exptl_crystal_F_000             7360
_exptl_crystal_size_max          0.258
_exptl_crystal_size_mid          0.109
_exptl_crystal_size_min          0.011
_refine_diff_density_max         3.266
_refine_diff_density_min         -1.336
_refine_diff_density_rms         0.171
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.541
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     1103
_refine_ls_number_reflns         8228
_refine_ls_number_restraints     1690
_refine_ls_restrained_S_all      1.499
_refine_ls_R_factor_all          0.1534
_refine_ls_R_factor_gt           0.1249
_refine_ls_shift/su_max          0.000
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
;
 w=1/[\s^2^(Fo^2^)+(0.2000P)^2^]
 where P=(Fo^2^+2Fc^2^)/3
;
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.3567
_refine_ls_wR_factor_ref         0.3771
_reflns_Friedel_coverage         0.000
_reflns_number_gt                5958
_reflns_number_total             8228
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            ja504662a_si_005.cif
_cod_data_source_block           n2246
_cod_depositor_comments
'Adding full bibliography for 4122349--4122355.cif.'
_cod_original_cell_volume        17400.5(16)
_cod_database_code               4122353
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  {H1A,H1B} of N1, {H2A,H2B} of N2, {H53A,H53B} of C53, {H54A,H54B} of C54,
  {H56A,H56B} of C56, {H55A,H55B} of C55, {H57A,H57B} of C57, H42 of C42, {H52A,
  H52B} of C52, {H50A,H50B} of C50, H45 of C45, H47 of C47, H46 of C46, {H49A,
  H49B} of C49, {H51A,H51B} of C51, {H32A,H32B} of C32, H28 of C28, H40 of C40,
  H25 of C25, {H37A,H37B} of C37, {H35A,H35B} of C35, {H33A,H33B} of C33, {H34A,
  H34B} of C34, {H38A,H38B} of C38, {H31A,H31B} of C31, {H30A,H30B} of C30, H41
  of C41, {H36A,H36B} of C36, H20 of C20, H23 of C23, H22 of C22, H15 of C15,
  H9 of C9, H21 of C21, H17 of C17, {H13A,H13B} of C13, H10 of C10, H7 of C7,
  H6 of C6, H12 of C12, H11 of C11, {H2C,H2D} of C2, H4 of C4, H3 of C3, H18 of
  C18, H14 of C14, {H2AA,H2AB} of C2A, {H1C,H1D} of C1, {H1AA,H1AB} of C1A
2. Restrained distances
 P5-F27 = P5-F30 = P5-F29 = P5-F25 = P5-F28 = P5A-F27A = P5A-F30A = P5A-F26A =
 P5A-F29A = P5A-F28A = P5A-F25A
 1.6 with sigma of 0.01
 P5-F25 ~ P5-F28 ~ P5-F27 ~ P5-F30 ~ P5-F29 ~ P2-F11 ~ P2-F12 ~ P2-F7 ~ P2-F9
 ~ P2-F10 ~ P2-F8 ~ P1-F6 ~ P1-F1 ~ P1-F4 ~ P1-F3 ~ P1-F2 ~ P1-F5 ~ P3-F18 ~ P3-
 F13 ~ P3-F15 ~ P3-F16 ~ P3-F14 ~ P3-F17 ~ P4-F19 ~ P4-F24 ~ P4-F20 ~ P4-F22 ~
 P4-F23 ~ P5A-F27A ~ P5A-F30A ~ P5A-F26A ~ P5A-F29A ~ P5A-F28A ~ P5A-F25A
 with sigma of 0.02
 F25-F28 ~ F27-F30 ~ F30-F27 ~ F28-F25 ~ F29-F28 ~ F27-F30 ~ F25A-F28A ~ F27A-
 F30A ~ F30A-F27A ~ F28A-F25A ~ F29A-F28A ~ F27A-F30A ~ F30A-F26A ~ F28A-F27A ~
 F25A-F29A
 with sigma of 0.01
 F26-F25 ~ F28-F30 ~ F27-F29 ~ F26A-F25A ~ F28A-F30A ~ F27A-F29A
 with sigma of 0.02
3. Uiso/Uaniso restraints and constraints
F28 ~ F25 ~ F26 ~ F27 ~ F29 ~ F30 ~ F26A ~ F25A ~ F27A ~ F28A ~ F29A ~ F30A: within 1.7A with sigma of 0.01 and sigma for terminal atoms of 0.02
4. Same fragment restrains
{P5, F25, F26, F27, F28, F29, F30}
as
{P5A, F25A, F26A, F27A, F28A, F29A, F30A}
5. Others
 1*[Sof(P5A)+Sof(F25A)+Sof(F26A)+Sof(F27A)+Sof(F28A)+Sof(F29A)+Sof(F30A)]+1*
 [Sof(P5)+Sof(F25)+Sof(F26)+Sof(F27)+Sof(F28)+Sof(F29)+Sof(F30)]+1*[Sof(P4)+
 Sof(F19)+Sof(F20)+Sof(F21)+Sof(F22)+Sof(F23)+Sof(F24)]=1 with esd of 0.0001
 Sof(P4)=Sof(F19)=Sof(F20)=Sof(F21)=Sof(F22)=Sof(F23)=Sof(F24)
 Sof(C1)=Sof(H1C)=Sof(H1D)=1-Sof(H1C)=1-Sof(H1C)=1-Sof(H1C)=Sof(C2)=Sof(H2C)=
 Sof(H2D)=1-Sof(H1C)=1-Sof(H1C)=1-Sof(H1C)
 Sof(P5)=Sof(F25)=Sof(F26)=Sof(F27)=Sof(F28)=Sof(F29)=Sof(F30)
 Sof(P5A)=Sof(F25A)=Sof(F26A)=Sof(F27A)=Sof(F28A)=Sof(F29A)=Sof(F30A)
6.a Secondary CH2 refined with riding coordinates:
 N1(H1A,H1B), N2(H2A,H2B), C1(H1C,H1D), C1A(H1AA,H1AB), C2(H2C,H2D), C2A(H2AA,
 H2AB), 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)
6.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)
;
_smtbx_masks_special_details
;
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.

Total solvent accessible volume / cell = 2735.0 Ang^3^ [15.7%]
Total electron count / cell = 616.5
;
_shelx_estimated_absorpt_t_max   0.955
_shelx_estimated_absorpt_t_min   0.409
_shelx_hkl_checksum              90631
_shelx_res_checksum              34525
_shelxl_version_number           2012-6