The curious case of proton migration under pressure in the malonic acid and 4,4'-bipyridine cocrystal.
Patyk-Kaźmierczak, Ewa; Izquierdo-Ruiz, Fernando; Lobato, Alvaro; Kaźmierczak, Michał; Moszczyńska, Ida; Olejniczak, Anna; Recio, J. Manuel; IUCrJ 11 (2024) 168–181; doi:10.1107/S2052252524000344

data_1571138
_publ_section_title
;
 The curious case of proton migration under pressure in the malonic acid
 and 4,4'-bipyridine cocrystal.
;
_journal_coeditor_code           YC5045
_journal_issue                   2
_journal_name_full               IUCrJ
_journal_page_first              168
_journal_page_last               181
_journal_paper_doi               10.1107/S2052252524000344
_journal_volume                  11
_journal_year                    2024
_chemical_formula_moiety         'C3 H3.414 O4, C10 H8.586 N2'
_chemical_formula_sum            'C13 H12 N2 O4'
_chemical_formula_weight         260.25
_chemical_name_systematic        'Malonic acid 4,4'-bipyridyl'
_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'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     dual
_audit_creation_date             2022-08-08
_audit_creation_method
;
Olex2 1.5
(compiled 2022.04.07 svn.rca3783a0 for OlexSys, GUI svn.r6498)
;
_cell_angle_alpha                90
_cell_angle_beta                 106.12(4)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   19.647(6)
_cell_length_b                   3.7375(4)
_cell_length_c                   15.222(6)
_cell_measurement_reflns_used    576
_cell_measurement_temperature    298(2)
_cell_measurement_theta_max      21.2710
_cell_measurement_theta_min      4.4250
_cell_volume                     1073.8(6)
_computing_cell_refinement       'CrysAlisPro 1.171.41.93a (Rigaku OD, 2020)'
_computing_data_collection       'CrysAlisPro 1.171.41.93a (Rigaku OD, 2020)'
_computing_data_reduction        'CrysAlisPro 1.171.41.93a (Rigaku OD, 2020)'
_computing_molecular_graphics    'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2014/7 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXT 2014/4 (Sheldrick, 2014)'
_diffrn_ambient_pressure         1830000(20000)
_diffrn_ambient_temperature      298(2)
_diffrn_detector                 'CCD plate'
_diffrn_detector_area_resol_mean 16.1544
_diffrn_detector_type            Eos
_diffrn_measured_fraction_theta_full 0.568
_diffrn_measured_fraction_theta_max 0.479
_diffrn_measurement_details
;
List of Runs (angles in degrees, time in seconds):

  # Type    Start    End  Width  t~exp~   \w     \q     \k     \f   Frames
--------------------------------------------------------------------------
  1  \f    -45.00  24.60   0.80   30.00   0.00 -25.00   0.00    --    87
  2  \f    135.00 204.60   0.80   30.00   0.00 -25.00   0.00    --    87
  3  \f    155.00 221.40   0.80   30.00   0.00  25.00   0.00    --    83
  4  \f    -25.00  39.80   0.80   30.00   0.00  25.00   0.00    --    81
  5  \w    -29.00  28.60   0.80   30.00    --   30.00  39.46 -12.90   72
  6  \w    -29.00  28.60   0.80   30.00    --   30.00  39.46 167.10   72
  7  \w    -60.00  20.00   0.80   30.00    --  -30.00  39.46 167.10  100
  8  \w    -55.00  14.60   0.80   30.00    --  -30.00  39.46 -12.90   87
  9  \w    -69.00  -3.40   0.80   30.00    --  -30.00  81.40 -28.90   82
 10  \w    -69.00  -3.40   0.80   30.00    --  -30.00  81.40 151.10   82
 11  \w    -23.00  14.60   0.80   30.00    --   25.00  81.40 151.10   47
 12  \w    -23.00  14.60   0.80   30.00    --   25.00  81.40 -28.90   47
 13  \w    -48.00 -16.00   0.80   30.00    --   25.00 134.60 -56.90   40
 14  \w    -48.00 -15.20   0.80   30.00    --   25.00 134.60 123.10   41
 15  \w    -96.00 -30.40   0.80   30.00    --  -25.00 134.60 123.10   82
 16  \w    -96.00 -30.40   0.80   30.00    --  -25.00 134.60 -56.90   82
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'Xcalibur, Eos'
_diffrn_measurement_method       '\w and \f scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      0.0283201000
_diffrn_orient_matrix_UB_12      -0.0034145000
_diffrn_orient_matrix_UB_13      0.0408103000
_diffrn_orient_matrix_UB_21      0.0211729000
_diffrn_orient_matrix_UB_22      0.1013057000
_diffrn_orient_matrix_UB_23      -0.0217865000
_diffrn_orient_matrix_UB_31      -0.0127372000
_diffrn_orient_matrix_UB_32      0.1604227000
_diffrn_orient_matrix_UB_33      0.0146256000
_diffrn_radiation_monochromator  graphite
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           'Mo K\a'
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.1287
_diffrn_reflns_av_unetI/netI     0.1681
_diffrn_reflns_Laue_measured_fraction_full 0.568
_diffrn_reflns_Laue_measured_fraction_max 0.479
_diffrn_reflns_limit_h_max       24
_diffrn_reflns_limit_h_min       -22
_diffrn_reflns_limit_k_max       4
_diffrn_reflns_limit_k_min       -4
_diffrn_reflns_limit_l_max       17
_diffrn_reflns_limit_l_min       -17
_diffrn_reflns_number            3130
_diffrn_reflns_point_group_measured_fraction_full 0.568
_diffrn_reflns_point_group_measured_fraction_max 0.479
_diffrn_reflns_theta_full        25.242
_diffrn_reflns_theta_max         28.318
_diffrn_reflns_theta_min         4.443
_diffrn_source                   'fine-focus sealed X-ray tube'
_diffrn_source_type              'Enhance (Mo) X-ray Source'
_exptl_absorpt_coefficient_mu    0.122
_exptl_absorpt_correction_T_max  0.575
_exptl_absorpt_correction_T_min  0.449
_exptl_absorpt_correction_type   gaussian
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.41.93a (Rigaku Oxford Diffraction, 2020)
Numerical absorption correction based on gaussian integration over
a multifaceted crystal model (Absorb Angel (2004) J. Appl. Cryst. 37:486-492)
;
_exptl_crystal_colour            colourless
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.610
_exptl_crystal_description       plate
_exptl_crystal_F_000             544
_exptl_crystal_preparation       'mounted in a diamond-anvil cell '
_exptl_crystal_recrystallization_method
; Single crystal grown at ambient conditions from EtOH:DMSO (1:1 vol. ratio) 
mounted in diamond anvil cell
;
_exptl_crystal_size_max          0.328
_exptl_crystal_size_mid          0.153
_exptl_crystal_size_min          0.026
_refine_diff_density_max         0.201
_refine_diff_density_min         -0.237
_refine_diff_density_rms         0.058
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.047
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     89
_refine_ls_number_reflns         633
_refine_ls_number_restraints     47
_refine_ls_restrained_S_all      1.030
_refine_ls_R_factor_all          0.2104
_refine_ls_R_factor_gt           0.0665
_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^)+(0.0248P)^2^+2.6453P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1012
_refine_ls_wR_factor_ref         0.1544
_reflns_Friedel_coverage         0.000
_reflns_number_gt                247
_reflns_number_total             633
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            yc5045.cif
_cod_data_source_block           BIPYMA_183
_cod_database_code               1571138
_shelx_shelxl_version_number     2014/7
_chemical_oxdiff_formula         'C10H8N4, C9H16O4'
_shelx_estimated_absorpt_t_max   0.997
_shelx_estimated_absorpt_t_min   0.961
_exptl_oxdiff_absorpt_process_details
;
Gaussian integration over a grid
of 16 x 16 x 16 points =  4096 total grid points
  Based upon method of Burnham (1966)

 Data corrected for diamond-anvil cell absorption
 Note that exptl_absorpt_correction_tmin and _tmax
 the total correction factors applied to the intensities
 The individual factors are: 
         range of dac transmission factors (min-max)      0.451     0.578
         range of gasket transmission (min-max)           1.000     1.000
         range of P media transmission (min-max)          1.000     1.000

 thickness of diamond anvil 1: 13.500 mm, mu =  0.0202 mm-1
       thickness of platten 1:  0.000 mm, mu =  0.0000 mm-1

 thickness of diamond anvil 2: 13.500 mm, mu =  0.0202 mm-1
       thickness of platten 2:  0.000 mm, mu =  0.0000 mm-1

    Gasket shadowing corrections were made based upon
    Gasket thickness = 200.0 microns, radius = 191.0 microns
    Gasket absorption coeff =         0.00 mm-1
    REFLECTION WAS CONSIDERED TOTALLY OBSCURED IF 
 FRACTION CRYSTAL ILLUMINATED WAS LESS THAN 0.00

    Non-absorbing pressure medium
;
_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 O(H) groups
2. Restrained distances
 C8-C7
 1.5 with sigma of 0.002
3. Rigid bond restraints
 C6, N1, C2, C3, C4, C5
 with sigma for 1-2 distances of 0.005 and sigma for 1-3 distances of 0.005
 O2, C7, O1
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 C7, C8
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
4. Uiso/Uaniso restraints and constraints
C2 \\sim C3 \\sim C4 \\sim C5 \\sim C6: within 2A with sigma of 0.005 and sigma
for terminal atoms of 0.1 within 2A
C7 \\sim C8: within 2A with sigma of 0.04 and sigma for terminal atoms of 0.08
within 2A
5. Others
 Sof(H1)=1-FVAR(1)
 Sof(H1A)=FVAR(1)
 Fixed Sof: H8A(0.5) H8B(0.5)
6.a Secondary CH2 refined with riding coordinates:
 C8(H8A,H8B)
6.b Aromatic/amide H refined with riding coordinates:
 N1(H1), C3(H3), C6(H6), C5(H5), C2(H2)
6.c Idealised tetrahedral OH refined as rotating group:
 O1(H1A)
;
_shelx_res_checksum              30931
_shelx_hkl_checksum              32340
_ins_header
;
TITL BIPYMA_182_final_56 in C2/c 
REM C2/c (#15 in standard setting)
CELL 0.71073  19.646950   3.737527  15.221554  90.0000 106.1174  90.0000
ZERR    2.00   0.005892   0.000366   0.006155   0.0000   0.0441   0.0000
LATT  7
SYMM -x, y,-z+1/2 
SFAC C H N O
UNIT 38.00 48.00 8.00 8.00
SIZE 0.03 0.15 0.33
TREF
HKLF 4
END
;
_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
;
_oxdiff_exptl_absorpt_empirical_full_max 2.385
_oxdiff_exptl_absorpt_empirical_full_min 0.797