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_4122350
_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, C68 H88 O20 S8, 6(C2 H3 N), C2 F3 O2, 7(F6 P)'
_chemical_formula_sum            'C128 H158 F45 N18 O22 P7 Pd2 S8'
_chemical_formula_weight         3841.78
_chemical_name_systematic
;
 ?
;
_space_group_crystal_system      triclinic
_space_group_IT_number           2
_space_group_name_Hall           '-P 1'
_space_group_name_H-M_alt        'P -1'
_symmetry_space_group_name_Hall  '-P 1'
_symmetry_space_group_name_H-M   'P -1'
_atom_sites_solution_hydrogens   geom
_audit_creation_date             2014-04-01
_audit_creation_method
;
Olex2 1.2
(compiled 2014.03.20 svn.r2914 for OlexSys, GUI svn.r4816)
;
_cell_angle_alpha                105.106(2)
_cell_angle_beta                 92.137(2)
_cell_angle_gamma                103.604(2)
_cell_formula_units_Z            2
_cell_length_a                   13.7152(5)
_cell_length_b                   20.7673(7)
_cell_length_c                   33.7422(10)
_cell_measurement_reflns_used    9413
_cell_measurement_temperature    100(2)
_cell_measurement_theta_max      63.72
_cell_measurement_theta_min      2.31
_cell_volume                     8968.4(5)
_computing_molecular_graphics    'Olex2 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 (Dolomanov et al., 2009)'
_computing_structure_refinement  'ShelXL (Sheldrick, 2008)'
_diffrn_ambient_temperature      100.04
_diffrn_measured_fraction_theta_full 0.888
_diffrn_measured_fraction_theta_max 0.952
_diffrn_measurement_device_type  'Bruker APEX-II CCD'
_diffrn_measurement_method       '\f and \w scans'
_diffrn_radiation_monochromator  graphite
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54178
_diffrn_reflns_av_unetI/netI     0.0652
_diffrn_reflns_Laue_measured_fraction_full 0.888
_diffrn_reflns_Laue_measured_fraction_max 0.952
_diffrn_reflns_limit_h_max       16
_diffrn_reflns_limit_h_min       -16
_diffrn_reflns_limit_k_max       23
_diffrn_reflns_limit_k_min       -24
_diffrn_reflns_limit_l_max       39
_diffrn_reflns_limit_l_min       0
_diffrn_reflns_number            28846
_diffrn_reflns_point_group_measured_fraction_full 0.888
_diffrn_reflns_point_group_measured_fraction_max 0.952
_diffrn_reflns_theta_full        67.679
_diffrn_reflns_theta_max         64.718
_diffrn_reflns_theta_min         2.308
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    4.040
_exptl_absorpt_correction_T_max  0.7524
_exptl_absorpt_correction_T_min  0.5878
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
SADABS-2008/1 (Bruker,2008) was used for absorption correction.
wR2(int) was 0.0653 before and 0.0361 after correction.
The Ratio of minimum to maximum transmission is 0.7812.
The \l/2 correction factor is 0.0000.
;
_exptl_crystal_colour            green
_exptl_crystal_density_diffrn    1.423
_exptl_crystal_description       block
_exptl_crystal_F_000             3916
_exptl_crystal_size_max          0.344
_exptl_crystal_size_mid          0.184
_exptl_crystal_size_min          0.154
_platon_squeeze_details
;
 Diffuse, disordered solvent molecules could not be adequately modeled.  The
 bypass procedure in Platon (Spek, 1990) was used to remove the electronic
 contribution from these solvents. The total potential solvent accessible void
 volume was 1259.5 Ang^3^ and the electron count / cell = 265. As the exact
 solvent content is not known, the reported formula reflects only the atoms
 used in the refinement.

;
_refine_diff_density_max         6.277
_refine_diff_density_min         -1.244
_refine_diff_density_rms         0.151
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.609
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     2071
_refine_ls_number_reflns         28846
_refine_ls_number_restraints     2325
_refine_ls_restrained_S_all      1.572
_refine_ls_R_factor_all          0.1481
_refine_ls_R_factor_gt           0.1274
_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^)+(0.2000P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.3750
_refine_ls_wR_factor_ref         0.3933
_reflns_Friedel_coverage         0.000
_reflns_number_gt                21997
_reflns_number_total             28846
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            ja504662a_si_006.cif
_cod_data_source_block           n1345
_cod_depositor_comments
'Adding full bibliography for 4122349--4122355.cif.'
_cod_database_code               4122350
_shelxl_version_number           2013-4
_shelx_estimated_absorpt_t_max   0.575
_shelx_estimated_absorpt_t_min   0.337
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups, All C(H,H,H,H) groups, All N(H,H) groups
 At 1.5 times of:
  All C(H,H,H) groups
2. Restrained distances
 C111-C110
 1.45 with sigma of 0.01
 C110-O18
 1.45 with sigma of 0.01
 C109-O18
 1.45 with sigma of 0.01
 C108-O17
 1.45 with sigma of 0.01
 C109-C108
 1.45 with sigma of 0.01
 C2S-C1S \\sim C2SA-C1SA
 with sigma of 0.01
 F37A-C1SA \\sim F39A-C1SA \\sim F38A-C1SA \\sim F38-C1S \\sim F39-C1S \\sim
F37-C1S
 with sigma of 0.01
 O21A-C2SA \\sim O22A-C2SA \\sim O22-C2S \\sim O21-C2S
 with sigma of 0.01
3. Rigid bond restraints
 All non-hydrogen atoms
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
4. Uiso/Uaniso restraints and constraints
All non-hydrogen atoms have similar U: within 1.7A with sigma of 0.04 and sigma
for terminal atoms of 0.08
Uanis(O18) \\sim Ueq, Uanis(C109) \\sim Ueq, Uanis(C110) \\sim Ueq, Uanis(C111)
\\sim Ueq: with sigma of 0.005 and sigma for terminal atoms of 0.01
Uanis(F40) = Uanis(F41) = Uanis(F42) = Uanis(F43) = Uanis(F44) = Uanis(F45) =
Uanis(F40A) = Uanis(F41A) = Uanis(F42A) = Uanis(F43A) = Uanis(F44B) =
Uanis(F45A)
Uanis(O21) = Uanis(O22) = Uanis(O21A) = Uanis(O22A) = Uanis(C1S) = Uanis(C1SA)
= Uanis(C2S) = Uanis(C2SA) = Uanis(F37) = Uanis(F38) = Uanis(F39) = Uanis(F37A)
= Uanis(F38A) = Uanis(F39A)
5. Same fragment restrains
{P1, F1, F2, F3, F4, F5, F6}
as
{P6, F31, F32, F33, F34, F35, F36}
{P1, F1, F2, F3, F4, F5, F6}
as
{P7, F40, F41, F42, F43, F44, F45}
{P1, F1, F2, F3, F4, F5, F6}
as
{P7B, F40A, F41A, F42A, F43A, F44B, F45A}
6. Others
 Sof(P7B)=Sof(F40A)=Sof(F41A)=Sof(F42A)=Sof(F43A)=Sof(F44B)=Sof(F45A)=1-FVAR(1)
 Sof(P7)=Sof(F40)=Sof(F41)=Sof(F42)=Sof(F43)=Sof(F44)=Sof(F45)=FVAR(1)
 Sof(F37A)=Sof(F38A)=Sof(F39A)=Sof(C1SA)=Sof(C2SA)=Sof(O21A)=Sof(O22A)=1-FVAR(2)
 Sof(F37)=Sof(F38)=Sof(F39)=Sof(C1S)=Sof(C2S)=Sof(O21)=Sof(O22)=FVAR(2)
 Sof(O1A)=Sof(H53A)=Sof(H53B)=Sof(H54A)=Sof(H54B)=1-FVAR(3)
 Sof(O1B)=Sof(H53C)=Sof(H53D)=Sof(H54C)=Sof(H54D)=FVAR(3)
7.a Secondary CH2 refined with riding coordinates:
 N1(H1A,H1B), N2(H2A,H2B), N7(H7A,H7B), N8(H8A,H8B), C1(H1C,H1D), C2(H2C,H2D),
 C13(H13A,H13B), C24(H24A,H24B), C25(H25A,H25B), C36(H36A,H36B), C53(H53A,H53B),
  C53(H53C,H53D), C54(H54A,H54B), C54(H54C,H54D), C55(H55A,H55B), C56(H56A,
 H56B), C57(H57A,H57B), C58(H58A,H58B), C59(H59A,H59B), C60(H60A,H60B),
 C61(H61A,H61B), C72(H72A,H72B), C73(H73A,H73B), C74(H74A,H74B), C75(H75A,H75B),
  C76(H76A,H76B), C77(H77A,H77B), C78(H78A,H78B), C79(H79A,H79B), C80(H80A,
 H80B), C87(H87A,H87B), C88(H88A,H88B), C89(H89A,H89B), C90(H90A,H90B),
 C91(H91A,H91B), C92(H92A,H92B), C93(H93A,H93B), C94(H94A,H94B), C95(H95A,H95B),
  C106(H10A,H10B), C107(H10C,H10D), C108(H10E,H10F), C109(H10G,H10H), C110(H11A,
 H11B), C111(H11C,H11D), C112(H11E,H11F), C113(H11G,H11H), C114(H11I,H11J)
7.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),
  C26(H26), C27(H27), C29(H29), C30(H30), C32(H32), C33(H33), C34(H34),
 C35(H35), C37(H37), C38(H38), C40(H40), C41(H41), C43(H43), C44(H44), C45(H45),
  C46(H46), C48(H48), C51(H51), C63(H63), C64(H64), C65(H65), C68(H68),
 C69(H69), C70(H70), C82(H82), C85(H85), C97(H97), C98(H98), C99(H99),
 C102(H102), C103(H103), C104(H104)
7.c Idealised Me refined as rotating group:
 C116(H11K,H11L,H11M), C118(H11N,H11O,H11P), C120(H12A,H12B,H12C), C122(H12D,
 H12E,H12F), C124(H12G,H12H,H12I), C126(H12J,H12K,H12L)

 Rigid bond restraints (esd 0.01) were imposed on the displacement parameters
 as well as restraints on similar amplitudes (esd 0.05) separated by less than
 1.7 Ang. Group anisotropic displacement parameters were refined for the disordered
 TFA and fluorine atoms.  O18, C109-C111 were restrained esd (0.005) that their
 Uij components approximate to isotropic and respective distances between these
 positions were restrained to 1.45 (esd 0.01).  Indicating disorder that was not
 modeled.

;
_shelx_res_checksum              13268
_shelx_hkl_checksum              6774