Full elucidation of the transmembrane anion transport mechanism of squaramides using in silico investigations.
Marques, Igor; Costa, Pedro M. R.; Q Miranda, Margarida; Busschaert, Nathalie; Howe, Ethan N. W.; Clarke, Harriet J.; Haynes, Cally J. E.; Kirby, Isabelle L.; Rodilla, Ananda M.; Pérez-Tomás, Ricardo; Gale, Philip A.; Félix, Vítor; Physical chemistry chemical physics : PCCP 20 (2018) 20796–20811; doi:10.1039/c8cp02576b

data_7231074
_publ_section_title
;
 Full elucidation of the transmembrane anion transport mechanism of
 squaramides using in silico investigations.
;
_journal_issue                   32
_journal_name_full               'Physical chemistry chemical physics : PCCP'
_journal_page_first              20796
_journal_page_last               20811
_journal_paper_doi               10.1039/c8cp02576b
_journal_volume                  20
_journal_year                    2018
_chemical_formula_moiety
'3(C26 H18 N4 O4), 3(C16 H36 N), O4 P, C2 H6 O S'
_chemical_formula_sum            'C128 H168 N15 O17 P S'
_chemical_formula_weight         2251.79
_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             2016-03-08
_audit_creation_method
;
Olex2 1.2-alpha
(compiled 2016.02.24 svn.r3266 for OlexSys, GUI svn.r5155)
;
_audit_update_record
;
2017-12-11 deposited with the CCDC.
2018-06-29 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 91.1396(14)
_cell_angle_gamma                90
_cell_formula_units_Z            8
_cell_length_a                   28.4389(4)
_cell_length_b                   15.9129(2)
_cell_length_c                   56.0834(9)
_cell_measurement_reflns_used    53533
_cell_measurement_temperature    100(2)
_cell_measurement_theta_max      69.5670
_cell_measurement_theta_min      3.1600
_cell_volume                     25375.3(6)
_computing_cell_refinement
;
'CrysAlisPro 1.171.38.41 (Rigaku OD, 2015)'
;
_computing_data_collection       'CrystalClear-SM Expert 3.1 b27 (Rigaku, 2013)'
_computing_data_reduction
;
'CrysAlisPro 1.171.38.41 (Rigaku OD, 2015)'
;
_computing_molecular_graphics    'Olex2 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 (Dolomanov et al., 2009)'
_computing_structure_refinement  'ShelXL (Sheldrick, 2015)'
_computing_structure_solution    'ShelXT (Sheldrick, 2015)'
_diffrn_ambient_temperature      100(2)
_diffrn_detector                 'CCD area detector'
_diffrn_detector_area_resol_mean 22.2222
_diffrn_detector_type            'Rigaku HG Saturn944+ (2x2 bin mode)'
_diffrn_measured_fraction_theta_full 0.993
_diffrn_measured_fraction_theta_max 0.993
_diffrn_measurement_details
;
List of Runs (angles in degrees, time in seconds):

  # Type    Start    End  Width  t~exp~   \w     \q     \k     \f   Frames
  1  \w    -94.00  77.00   1.00   10.00    --  -13.00  30.00  30.00  171
  2  \w    -72.00 -52.00   1.00   10.00    --  -13.00   7.00-120.00   20
  3  \w   -179.00   0.00   1.00   60.00    --  -90.00  60.00-180.00  179
  4  \w   -179.00 -17.00   1.00   60.00    --  -90.00  60.00 -30.00  162
  5  \w   -179.00   0.00   1.00   60.00    --  -90.00  22.00-120.00  179
  6  \w   -155.00   0.00   1.00   60.00    --  -90.00  60.00   0.00  155
  7  \w   -147.00 -60.00   1.00   60.00    --  -90.00  30.00 -60.00   87
  8  \w   -120.00  -8.00   1.00   60.00    --  -90.00  15.00 -90.00  112
  9  \w   -158.00-112.00   1.00   60.00    --  -90.00  45.00 -30.00   46
 10  \w   -147.00 -79.00   1.00   60.00    --  -90.00  60.00  30.00   68
 11  \w   -133.00-113.00   1.00   60.00    --  -90.00  37.00  90.00   20
;
_diffrn_measurement_device       'three-circle quarter \c goniometer'
_diffrn_measurement_device_type
'dtrek-CrysAlisPro-abstract goniometer imported rigaku-d*trek images'
_diffrn_measurement_method       'profile data from \w-scans'
_diffrn_measurement_specimen_support 'MiTeGen MicroMesh'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      -0.0476267000
_diffrn_orient_matrix_UB_12      -0.0253412000
_diffrn_orient_matrix_UB_13      -0.0114308000
_diffrn_orient_matrix_UB_21      0.0174117000
_diffrn_orient_matrix_UB_22      0.0283580000
_diffrn_orient_matrix_UB_23      -0.0245576000
_diffrn_orient_matrix_UB_31      0.0190205000
_diffrn_orient_matrix_UB_32      -0.0891094000
_diffrn_orient_matrix_UB_33      -0.0045890000
_diffrn_radiation_collimation    0.3
_diffrn_radiation_monochromator  'Confocal mirrors, Varimax'
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0392
_diffrn_reflns_av_unetI/netI     0.0185
_diffrn_reflns_Laue_measured_fraction_full 0.993
_diffrn_reflns_Laue_measured_fraction_max 0.993
_diffrn_reflns_limit_h_max       34
_diffrn_reflns_limit_h_min       -34
_diffrn_reflns_limit_k_max       16
_diffrn_reflns_limit_k_min       -19
_diffrn_reflns_limit_l_max       68
_diffrn_reflns_limit_l_min       -63
_diffrn_reflns_number            129166
_diffrn_reflns_point_group_measured_fraction_full 0.993
_diffrn_reflns_point_group_measured_fraction_max 0.993
_diffrn_reflns_theta_full        66.601
_diffrn_reflns_theta_max         66.601
_diffrn_reflns_theta_min         6.332
_diffrn_source                   'Rotating Anode'
_diffrn_source_current           30.0
_diffrn_source_power             1.2
_diffrn_source_target            Cu
_diffrn_source_type              'Rotating Anode'
_diffrn_source_voltage           40.0
_exptl_absorpt_coefficient_mu    0.890
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.72514
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
'CrysAlisPro 1.171.38.41 (Rigaku Oxford Diffraction, 2015) Empirical absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm.'
_exptl_crystal_colour            'clear light yellow'
_exptl_crystal_colour_lustre     clear
_exptl_crystal_colour_modifier   light
_exptl_crystal_colour_primary    yellow
_exptl_crystal_density_diffrn    1.179
_exptl_crystal_description       prism
_exptl_crystal_F_000             9664
_exptl_crystal_recrystallization_method
'The material was recrystallised from DMSO by slow evaporation'
_exptl_crystal_size_max          0.36
_exptl_crystal_size_mid          0.24
_exptl_crystal_size_min          0.22
_refine_diff_density_max         1.366
_refine_diff_density_min         -0.988
_refine_diff_density_rms         0.092
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.869
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     1485
_refine_ls_number_reflns         22270
_refine_ls_number_restraints     1302
_refine_ls_restrained_S_all      1.856
_refine_ls_R_factor_all          0.1164
_refine_ls_R_factor_gt           0.1102
_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^)+(0.2000P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.3782
_refine_ls_wR_factor_ref         0.3924
_reflns_Friedel_coverage         0.000
_reflns_number_gt                19664
_reflns_number_total             22270
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            c8cp02576b7.cif
_cod_data_source_block           2016sot0012_d_100k
_cod_depositor_comments
'Adding full bibliography for 7231074--7231075.cif.'
_cod_original_cell_volume        25375.3(7)
_cod_database_code               7231074
_diffrn_measurement_device_type2 'Rigaku AFC11'
_reflns_odcompleteness_completeness 98.58
_reflns_odcompleteness_iscentric 1
_reflns_odcompleteness_theta     70.49
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups, All N(H) groups
 At 1.5 times of:
  All C(H,H,H) groups
2. Restrained distances
 C65A-C64A
 1.54 with sigma of 0.02
 C64A-C63A
 1.54 with sigma of 0.02
 C611-C612
 1.54 with sigma of 0.02
 N601-C63B
 1.4 with sigma of 0.02
 N601-C63A
 1.4 with sigma of 0.02
 C63B-C64B
 1.54 with sigma of 0.02
 C63A-C64A
 1.54 with sigma of 0.02
 C64B-C65B
 1.54 with sigma of 0.02
 C64A-C65A
 1.54 with sigma of 0.02
 C66A-C65A
 1.54 with sigma of 0.02
 C65A-C66A
 1.54 with sigma of 0.02
 C65B-C66B
 1.54 with sigma of 0.02
 C65A-C63A
 2.5 with sigma of 0.04
 C66A-C64A
 2.5 with sigma of 0.04
3. Uiso/Uaniso restraints and constraints
Uanis(C66A) \\sim Ueq, Uanis(C65A) \\sim Ueq, Uanis(C64A) \\sim Ueq,
Uanis(C608) \\sim Ueq, Uanis(C607) \\sim Ueq, Uanis(C606) \\sim Ueq,
Uanis(C63A) \\sim Ueq, Uanis(N601) \\sim Ueq, Uanis(C609) \\sim Ueq,
Uanis(C610) \\sim Ueq, Uanis(C611) \\sim Ueq, Uanis(C612) \\sim Ueq,
Uanis(C601) \\sim Ueq, Uanis(C602) \\sim Ueq, Uanis(C603) \\sim Ueq,
Uanis(C604) \\sim Ueq: with sigma of 0.1 and sigma for terminal atoms of 0.2
Uanis(C63A) = Uanis(C63B)
Uanis(C64A) = Uanis(C64B)
Uanis(C65A) = Uanis(C65B)
Uanis(C66A) = Uanis(C66B)
4. Rigid body (RIGU) restrains
 All non-hydrogen atoms
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
5. Others
 Sof(C63B)=Sof(H63C)=Sof(H63D)=Sof(C64B)=Sof(H64C)=Sof(H64D)=Sof(C65B)=
 Sof(H65C)=Sof(H65D)=Sof(C66B)=Sof(H66D)=Sof(H66E)=Sof(H66F)=1-FVAR(1)
 Sof(C63A)=Sof(H63A)=Sof(H63B)=Sof(C64A)=Sof(H64A)=Sof(H64B)=Sof(C65A)=
 Sof(H65A)=Sof(H65B)=Sof(C66A)=Sof(H66A)=Sof(H66B)=Sof(H66C)=FVAR(1)
6.a Secondary CH2 refined with riding coordinates:
 C401(H40A,H40B), C402(H40C,H40D), C403(H40E,H40F), C405(H40J,H40K), C406(H40L,
 H40M), C407(H40N,H40O), C409(H40S,H40T), C410(H41A,H41B), C411(H41C,H41D),
 C413(H41H,H41I), C414(H41J,H41K), C415(H41L,H41M), C501(H50A,H50B), C502(H50C,
 H50D), C503(H50E,H50F), C505(H50J,H50K), C506(H50L,H50M), C507(H50N,H50O),
 C509(H50S,H50T), C510(H51A,H51B), C511(H51C,H51D), C513(H51H,H51I), C514(H51J,
 H51K), C515(H51L,H51M), C601(H60A,H60B), C602(H60C,H60D), C603(H60E,H60F),
 C605(H60J,H60K), C606(H60L,H60M), C607(H60N,H60O), C609(H60S,H60T), C610(H61A,
 H61B), C611(H61C,H61D), C63A(H63A,H63B), C64A(H64A,H64B), C65A(H65A,H65B),
 C63B(H63C,H63D), C64B(H64C,H64D), C65B(H65C,H65D)
6.b Me refined with riding coordinates:
 C66A(H66A,H66B,H66C), C66B(H66D,H66E,H66F)
6.c Aromatic/amide H refined with riding coordinates:
 N101(H101), N102(H102), N103(H103), N104(H104), C101(H10A), C102(H10B),
 C103(H10C), C104(H10D), C105(H105), C112(H112), C113(H113), C114(H114),
 C115(H115), C122(H122), C123(H123), C124(H124), C125(H125), C126(H126),
 N201(H201), N202(H202), N203(H203), N204(H204), C201(H20A), C202(H20B),
 C203(H20C), C204(H20D), C205(H205), C212(H212), C213(H213), C214(H214),
 C215(H215), C222(H222), C223(H223), C224(H224), C225(H225), C226(H226),
 N301(H301), N302(H302), N303(H303), N304(H304), C301(H30A), C302(H30B),
 C303(H30C), C304(H30D), C305(H305), C312(H312), C313(H313), C314(H314),
 C315(H315), C322(H322), C323(H323), C324(H324), C325(H325), C326(H326)
6.d Idealised Me refined as rotating group:
 C404(H40G,H40H,H40I), C408(H40P,H40Q,H40R), C412(H41E,H41F,H41G), C416(H41N,
 H41O,H41P), C504(H50G,H50H,H50I), C508(H50P,H50Q,H50R), C512(H51E,H51F,H51G),
 C516(H51N,H51O,H51P), C604(H60G,H60H,H60I), C608(H60P,H60Q,H60R), C612(H61E,
 H61F,H61G), C701(H70A,H70B,H70C), C702(H70D,H70E,H70F)
;
_shelx_res_checksum              12410
_shelx_shelxl_version_number     2014/7
_olex2_date_sample_submission    2016-02-16
_olex2_diffrn_ambient_temperature_device 'Oxford Cryosystems'
_olex2_exptl_crystal_mounting_method
'The crystal was mounted on a mylar loop in perfluoroether oil'
_olex2_submission_original_sample_id S60
_olex2_submission_special_instructions 'No special instructions were received'
_oxdiff_exptl_absorpt_empirical_details
;
Empirical correction (ABSPACK) includes:
- Absorption correction using spherical harmonics
- Frame scaling
- Detector area scaling
;
_oxdiff_exptl_absorpt_empirical_full_max 2.124
_oxdiff_exptl_absorpt_empirical_full_min 0.482