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_1571143
_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 O4, C10 H9 N2'
_chemical_formula_sum            'C13 H12 N2 O4'
_chemical_formula_weight         260.25
_chemical_name_systematic        '4,4'-bipyridine hydrogen malonate'
_space_group_crystal_system      monoclinic
_space_group_IT_number           14
_space_group_name_Hall           '-P 2ybc'
_space_group_name_H-M_alt        'P 1 21/c 1'
_atom_sites_solution_hydrogens   geom
_audit_creation_date             2023-07-05
_audit_creation_method
;
Olex2 1.5
(compiled 2023.03.06 svn.rbb2c1857 for OlexSys, GUI svn.r6748)
;
_cell_angle_alpha                90
_cell_angle_beta                 103.33(6)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   8.412(4)
_cell_length_b                   7.9665(11)
_cell_length_c                   15.576(9)
_cell_measurement_reflns_used    1058
_cell_measurement_temperature    298(5)
_cell_measurement_theta_max      25.9230
_cell_measurement_theta_min      3.1530
_cell_volume                     1015.7(8)
_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_temperature      298(5)
_diffrn_detector                 'CCD plate'
_diffrn_detector_area_resol_mean 16.1544
_diffrn_detector_type            Eos
_diffrn_measured_fraction_theta_full 0.475
_diffrn_measured_fraction_theta_max 0.400
_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      0.0660098000
_diffrn_orient_matrix_UB_12      0.0000922000
_diffrn_orient_matrix_UB_13      0.0378483000
_diffrn_orient_matrix_UB_21      0.0177082000
_diffrn_orient_matrix_UB_22      -0.0845120000
_diffrn_orient_matrix_UB_23      -0.0084870000
_diffrn_orient_matrix_UB_31      0.0533956000
_diffrn_orient_matrix_UB_32      0.0277474000
_diffrn_orient_matrix_UB_33      -0.0262443000
_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  0.0815
_diffrn_reflns_av_unetI/netI     0.1272
_diffrn_reflns_Laue_measured_fraction_full 0.475
_diffrn_reflns_Laue_measured_fraction_max 0.400
_diffrn_reflns_limit_h_max       10
_diffrn_reflns_limit_h_min       -10
_diffrn_reflns_limit_k_max       10
_diffrn_reflns_limit_k_min       -10
_diffrn_reflns_limit_l_max       15
_diffrn_reflns_limit_l_min       -16
_diffrn_reflns_number            4177
_diffrn_reflns_point_group_measured_fraction_full 0.475
_diffrn_reflns_point_group_measured_fraction_max 0.400
_diffrn_reflns_theta_full        25.242
_diffrn_reflns_theta_max         28.153
_diffrn_reflns_theta_min         2.889
_diffrn_source                   'fine-focus sealed X-ray tube'
_diffrn_source_type              'Enhance (Mo) X-ray Source'
_exptl_absorpt_coefficient_mu    0.128
_exptl_absorpt_correction_T_max  0.990
_exptl_absorpt_correction_T_min  0.987
_exptl_absorpt_correction_type   analytical
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.41.93a (Rigaku Oxford Diffraction, 2020)
Analytical numeric absorption correction using a multifaceted crystal
model based on expressions derived by R.C. Clark & J.S. Reid.
(Clark, R. C. & Reid, J. S. (1995). Acta Cryst. A51, 887-897)
Empirical absorption correction using spherical harmonics,
implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            colourless
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.702
_exptl_crystal_description       block
_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          0.335
_exptl_crystal_size_mid          0.171
_exptl_crystal_size_min          0.08
_refine_diff_density_max         0.187
_refine_diff_density_min         -0.206
_refine_diff_density_rms         0.047
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.023
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     173
_refine_ls_number_reflns         998
_refine_ls_number_restraints     83
_refine_ls_restrained_S_all      0.982
_refine_ls_R_factor_all          0.1954
_refine_ls_R_factor_gt           0.0617
_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^)+(0.0498P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1093
_refine_ls_wR_factor_ref         0.1621
_reflns_Friedel_coverage         0.000
_reflns_number_gt                409
_reflns_number_total             998
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            yc5045.cif
_cod_data_source_block           BIPYMA_276
_cod_database_code               1571143
_shelx_shelxl_version_number     2014/7
_chemical_oxdiff_formula         'C3O4H4, N2C10H8'
_shelx_estimated_absorpt_t_max   0.990
_shelx_estimated_absorpt_t_min   0.958
_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. Rigid bond restraints
 N2, N1, C5, C9, C2, C3, C4, C10, C6, C11, C8, C7
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
3. Uiso/Uaniso restraints and constraints
C5 \\sim C9 \\sim C2 \\sim C3 \\sim C4 \\sim C10 \\sim C6 \\sim C11 \\sim C8
\\sim C7: within 2A with sigma of 0.04 and sigma for terminal atoms of 0.08
within 2A
4.a Secondary CH2 refined with riding coordinates:
 C13(H13A,H13B)
4.b Aromatic/amide H refined with riding coordinates:
 N2(H2), C5(H5), C9(H9), C2(H2A), C3(H3), C10(H10), C6(H6), C11(H11), C8(H8)
4.c Idealised tetrahedral OH refined as rotating group:
 O1(H1)
;
_shelx_res_checksum              7699
_shelx_hkl_checksum              65552
_ins_header
;
TITL BIPYMA_276_FINAL in P2(1)/c 
REM P2(1)/c (#14 in standard setting)
CELL 0.71073   8.411695   7.966464  15.576343  90.0000 103.3271  90.0000
ZERR    3.00   0.004216   0.001065   0.008546   0.0000   0.0619   0.0000
LATT  1
SYMM -x, y+1/2,-z+1/2 
SFAC C H N O
UNIT 39.00 36.00 6.00 12.00
SIZE 0.08 0.17 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 2.774
_oxdiff_exptl_absorpt_empirical_full_min 0.656