The preservation of sarin and O,O’-diisopropyl fluorophosphate inside coordination cage hosts
Dorrat, Jack C.; Young, Rosemary J.; Taylor, Christopher; Tipping, Max B.; Blok, Andrew James; Turner, David Roger; McKay, Alasdair I.; Ovenden, Simon; Ward, Michael D.; Dennison, Genevieve Helen; Tuck, Kellie; Dalton Transactions  (2023) –; doi:10.1039/D3DT01378B

data_7713202
_publ_section_title
;
 The preservation of sarin and O,O&#x2019;-diisopropyl fluorophosphate
 inside coordination cage hosts
;
_journal_name_full               'Dalton Transactions'
_journal_paper_doi               10.1039/D3DT01378B
_journal_year                    2023
_chemical_formula_moiety
'1(C336 H258.94 Co8 N72), 11.63(Cl), 0.32(F O3 P), 1.14(C F O3 P), 11.71(O), 28(O H2), 10(C4 O H8), 4.37(Cl)'
_chemical_formula_sum            'C376 H394.942 Cl16 Co8 F1.46 N72 O54.09 P1.46'
_chemical_formula_weight         7899.375
_space_group_crystal_system      orthorhombic
_space_group_IT_number           56
_space_group_name_Hall           '-P 2ab 2ac'
_space_group_name_H-M_alt        'P c c n'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     iterative
_audit_creation_date             2023-01-20
_audit_creation_method
;
Olex2 1.5
(compiled 2022.04.07 svn.rca3783a0 for OlexSys, GUI svn.r6498)
;
_audit_update_record
;
2023-01-20 deposited with the CCDC.	2023-05-24 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   40.097(8)
_cell_length_b                   42.347(9)
_cell_length_c                   27.540(6)
_cell_measurement_reflns_used    8723
_cell_measurement_temperature    100(2)
_cell_measurement_theta_max      20.91
_cell_measurement_theta_min      0.72
_cell_volume                     46763(17)
_computing_cell_refinement       'XDS (Kabsch, 2010)'
_computing_data_collection       'AS QEGUI'
_computing_data_reduction        'XDS (Kabsch, 2010)'
_computing_molecular_graphics    'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2018/3 (Sheldrick, 2015)'
_computing_structure_solution    'olex2.solve 1.5 (Bourhis et al., 2015)'
_diffrn_ambient_temperature      100(2)
_diffrn_detector_area_resol_mean 13.3
_diffrn_measured_fraction_theta_full 0.990
_diffrn_measured_fraction_theta_max 0.844
_diffrn_measurement_device_type  'MX1 Beamline Australian Synchrotron'
_diffrn_measurement_method       'Omega Scan'
_diffrn_radiation_monochromator  'Silicon Double Crystal'
_diffrn_radiation_type           Synchrotron
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.0400
_diffrn_reflns_av_unetI/netI     0.0185
_diffrn_reflns_Laue_measured_fraction_full 0.990
_diffrn_reflns_Laue_measured_fraction_max 0.844
_diffrn_reflns_limit_h_max       50
_diffrn_reflns_limit_h_min       -51
_diffrn_reflns_limit_k_max       49
_diffrn_reflns_limit_k_min       -49
_diffrn_reflns_limit_l_max       37
_diffrn_reflns_limit_l_min       -36
_diffrn_reflns_number            579461
_diffrn_reflns_point_group_measured_fraction_full 0.990
_diffrn_reflns_point_group_measured_fraction_max 0.844
_diffrn_reflns_theta_full        25.242
_diffrn_reflns_theta_max         28.681
_diffrn_reflns_theta_min         0.699
_diffrn_source                   'MX1 Beamline Australian Synchrotron'
_exptl_absorpt_coefficient_mu    0.399
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details   'XDS (Kabsch, 2010)'
_exptl_crystal_colour            'clear orange'
_exptl_crystal_density_diffrn    1.122
_exptl_crystal_description       rhombohedral
_exptl_crystal_F_000             13484
_exptl_crystal_recrystallization_method
'Re-crystallisation from solvent: Water/THF'
_exptl_crystal_size_max          0.2
_exptl_crystal_size_mid          0.2
_exptl_crystal_size_min          0.1
_exptl_transmission_factor_max   0.4314
_exptl_transmission_factor_min   0.3440
_platon_squeeze_details
;
The structure contains solvent accessible voids filled with THF
and water solvent molecules as well as disordered chloride anions. Electron density equating to approximately 
28 water molecules, 10 THF molecules and 4.37 chloride anions per asymmetric unit was removed by the 
SQUEEZE routine.
;
_refine_diff_density_max         1.662
_refine_diff_density_min         -1.470
_refine_diff_density_rms         0.121
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.070
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     2208
_refine_ls_number_reflns         50926
_refine_ls_number_restraints     466
_refine_ls_restrained_S_all      1.072
_refine_ls_R_factor_all          0.1557
_refine_ls_R_factor_gt           0.1337
_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^)+(0.4000P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.4398
_refine_ls_wR_factor_ref         0.4733
_reflns_Friedel_coverage         0.000
_reflns_number_gt                34420
_reflns_number_total             50926
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d3dt01378b2.cif
_cod_data_source_block           HaDFP
_cod_original_cell_volume        46763(16)
_cod_database_code               7713202
_shelx_shelxl_version_number     2018/3
_shelx_estimated_absorpt_t_max   0.961
_shelx_estimated_absorpt_t_min   0.924
_diffrn_measurement_detector_type 'Dectris Eiger2 9M'
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups
2. Restrained distances
 O3DB-C1DB
 1.33 with sigma of 0.02
 P1DA-O5DA
 1.5 with sigma of 0.02
 P1DB-O3DB
 1.536 with sigma of 0.02
 C2DB-C1DB
 1.53 with sigma of 0.02
3. Uiso/Uaniso restraints and constraints
N2A \\sim N2B \\sim N3A \\sim N3B \\sim Co3 \\sim N5 \\sim N4: within 2A with
sigma of 0.04 and sigma for terminal atoms of 0.08 within 2A
N36 \\sim Co2 \\sim N31 \\sim N30 \\sim N32 \\sim N33 \\sim N35: within 2A with
sigma of 0.04 and sigma for terminal atoms of 0.08 within 2A
N25 \\sim Co10 \\sim N27 \\sim N26 \\sim N24: within 2A with sigma of 0.04 and
sigma for terminal atoms of 0.08 within 2A
N16 \\sim Co1 \\sim N12 \\sim N10 \\sim N7 \\sim N8 \\sim N14: within 2A with
sigma of 0.04 and sigma for terminal atoms of 0.08 within 2A
P1DB \\sim F2DB \\sim O3DB \\sim O4DB \\sim O5DB \\sim C1DB \\sim C2DB: within
2A with sigma of 0.04 and sigma for terminal atoms of 0.08 within 2A
4. Rigid body (RIGU) restrains
 P1DB, F2DB, O3DB, O4DB, O5DB
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 P1DA, F3DA, O2DA, O4DA, O5DA
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 N20, N21, N22, C86, C87, C88, C89, C90, C91, C92, C93
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 N1A, N1B, N2A, N2B, N3A, N3B, C2A, C2B, C3A, C3B, C4A, C4B, C5A, C5B, C6A,
 C6B, C7A, C7B, C8A, C8B, C9A, C9B
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 O3DB
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 O3DB, C1DB
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 P1DB, F2DB
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C66, N31, C70, C69, C67, C68
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C71, C72, C73, N29, N30
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 N4, C10, C11, C12, C13, C14
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
5. Others
 Sof(P1DB)=Sof(F2DB)=Sof(O3DB)=Sof(O4DB)=Sof(O5DB)=1-FVAR(1)
 Sof(N1A)=Sof(N2A)=Sof(N3A)=Sof(C1A)=Sof(H1AA)=Sof(H1AB)=Sof(C2A)=Sof(H2A)=
 Sof(C3A)=Sof(H3A)=Sof(C4A)=Sof(C5A)=Sof(C6A)=Sof(H6A)=Sof(C7A)=Sof(H7A)=
 Sof(C8A)=Sof(H8A)=Sof(C9A)=Sof(H9A)=1-FVAR(2)
 Sof(N1B)=Sof(N2B)=Sof(N3B)=Sof(C1B)=Sof(H1BA)=Sof(H1BB)=Sof(C2B)=Sof(H2B)=
 Sof(C3B)=Sof(H3B)=Sof(C4B)=Sof(C5B)=Sof(C6B)=Sof(C7B)=Sof(H7B)=Sof(C8B)=
 Sof(H8B)=Sof(C9B)=Sof(H9B)=FVAR(2)
 Sof(P1DA)=Sof(F3DA)=Sof(O2DA)=Sof(O4DA)=Sof(O5DA)=0.15*FVAR(4)
 Sof(Cl5D)=1-FVAR(4)
 Sof(Cl5C)=FVAR(4)
 Fixed Sof: Cl1C(0.82727) Cl2C(0.45036) Cl3C(0.69696) Cl4C(0.77292)
 Cl6C(0.60576) Cl7C(0.68187) Cl8C(0.7772) C1DB(0.57) C2DB(0.57) O6DB(0.85)
 Fixed Uiso: C2DB(0.3)
 Fixed X: O4DA(0.5496) P1DB(0.584579)
 Fixed Y: O4DA(0.4958) P1DB(0.52618)
 Fixed Z: O4DA(0.321301) P1DB(0.26981)
6.a Riding coordinates:
 C87(H87)
6.b Secondary CH2 refined with riding coordinates:
 C1A(H1AA,H1AB), C1B(H1BA,H1BB), C18(H18A,H18B), C29(H29A,H29B), C46(H46A,
 H46B), C57(H57A,H57B), C74(H74A,H74B), C102(H10A,H10B), C130(H13A,H13B),
 C141(H14A,H14B), C158(H15A,H15B)
6.c Aromatic/amide H refined with riding coordinates:
 C2A(H2A), C2B(H2B), C3A(H3A), C3B(H3B), C6A(H6A), C7A(H7A), C7B(H7B),
 C8A(H8A), C8B(H8B), C9A(H9A), C9B(H9B), C10(H10), C11(H11), C12(H12), C13(H13),
  C16(H16), C17(H17), C20(H20), C21(H21), C22(H22), C25(H25), C26(H26),
 C27(H27), C30(H30), C31(H31), C34(H34), C35(H35), C36(H36), C37(H37), C38(H38),
  C39(H39), C40(H40), C41(H41), C44(H44), C45(H45), C47(H47), C51(H51),
 C52(H52), C53(H53), C54(H54), C55(H55), C58(H58), C59(H59), C62(H62), C63(H63),
  C64(H64), C65(H65), C66(H66), C67(H67), C68(H68), C69(H69), C72(H72),
 C73(H73), C76(H76), C77(H77), C78(H78), C81(H81), C82(H82), C83(H83), C85(H85),
  C86(H86), C90(H90), C91(H91), C92(H92), C93(H93), C94(H94), C95(H95),
 C96(H96), C97(H97), C100(H100), C101(H101), C104(H104), C105(H105), C106(H106),
  C109(H109), C110(H110), C111(H111), C113(H113), C114(H114), C115(H115),
 C118(H118), C119(H119), C120(H120), C121(H121), C122(H122), C123(H123),
 C124(H124), C125(H125), C128(H128), C129(H129), C132(H132), C133(H133),
 C134(H134), C137(H137), C138(H138), C139(H139), C142(H142), C143(H143),
 C146(H146), C147(H147), C148(H148), C149(H149), C150(H150), C151(H151),
 C152(H152), C153(H153), C156(H156), C157(H157), C160(H160), C161(H161),
 C162(H162), C165(H165), C166(H166), C167(H167)
;
_platon_squeeze_void_probe_radius 1.20