Competing hydrogen bonding and acyclic π-stacking between hydrogen-bridged quasi-rings in Z- and E-methyl pyruvate semicarbazone: a quantitative interaction energy analysis
Raičević, Vidak; Radulović, Niko S.; Banić, Nemanja; Leovac, Vukadin M.; Rodić, Marko V.; CrystEngComm 27 (2025) 7721–7733; doi:10.1039/D5CE00911A

data_7251407
_publ_section_title
;
 Competing hydrogen bonding and acyclic \p-stacking between
 hydrogen-bridged quasi-rings in Z- and E-methyl pyruvate semicarbazone: a
 quantitative interaction energy analysis
;
_journal_issue                   47
_journal_name_full               CrystEngComm
_journal_page_first              7721
_journal_page_last               7733
_journal_paper_doi               10.1039/D5CE00911A
_journal_volume                  27
_journal_year                    2025
_chemical_formula_moiety         'C5 H9 N3 O3'
_chemical_formula_sum            'C5 H9 N3 O3'
_chemical_formula_weight         159.15
_chemical_melting_point          471
_chemical_name_common            ' (E)-methyl pyruvate semicarbazone'
_chemical_name_systematic
' methyl (E)-2-(2-carbamoylhydrazineylidene)propanoate'
_chemical_properties_physical    Photo-sensitive
_chemical_temperature_decomposition 471
_space_group_crystal_system      triclinic
_space_group_IT_number           2
_space_group_name_Hall           '-P 1'
_space_group_name_H-M_alt        'P -1'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     dual
_audit_creation_method           SHELXL-2018/3
_audit_update_record
;
2025-08-05 deposited with the CCDC.	2025-11-04 downloaded from the CCDC.
;
_cell_angle_alpha                90.144(10)
_cell_angle_beta                 97.506(9)
_cell_angle_gamma                91.316(10)
_cell_formula_units_Z            2
_cell_length_a                   4.1764(4)
_cell_length_b                   7.4068(10)
_cell_length_c                   12.2230(13)
_cell_measurement_reflns_used    879
_cell_measurement_temperature    295(2)
_cell_measurement_theta_max      70.9580
_cell_measurement_theta_min      9.4520
_cell_volume                     374.76(7)
_computing_cell_refinement       'CrysAlisPro 1.171.38.41 (Rigaku OD, 2015)'
_computing_data_collection       'CrysAlisPro 1.171.38.41 (Rigaku OD, 2015)'
_computing_data_reduction        'CrysAlisPro 1.171.38.41 (Rigaku OD, 2015)'
_computing_molecular_graphics
' Mercury (Macrae et. al., 2020) and VESTA (Momma & Izumi, 2011)'
_computing_publication_material
' PLATON (Spek, 2009) and Huebschle et al., 2011'
_computing_structure_refinement  'SHELXL-2018/3 (Sheldrick, 2018)'
_computing_structure_solution    'SHELXT 2014/5 (Sheldrick, 2014)'
_diffrn_ambient_temperature      295(2)
_diffrn_detector                 'CCD plate'
_diffrn_detector_area_resol_mean 16.3280
_diffrn_detector_type            Sapphire3
_diffrn_measured_fraction_theta_full 0.990
_diffrn_measured_fraction_theta_max 0.961
_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    -31.00  53.00   1.00    1.50    --   36.00 -57.00  30.00   84
  2  \w     44.00  75.00   1.00    1.50    --   36.00 -99.00 -60.00   31
  3  \w     58.00  87.00   1.00    1.50    --   36.00-178.00 -90.00   29
  4  \w     49.00 124.00   1.00    6.00    --  108.00 -77.00 -60.00   75
  5  \w     69.00  98.00   1.00    6.00    --  108.00 -45.00-150.00   29
  6  \w     90.00 154.00   1.00    6.00    --  108.00  30.00-150.00   64
  7  \w    132.00 159.00   1.00    6.00    --  108.00 111.00 -30.00   27
  8  \w    102.00 174.00   1.00    6.00    --  108.00 111.00  30.00   72
  9  \w    143.00 176.00   1.00    6.00    --  108.00  45.00 120.00   33
 10  \w    113.00 165.00   1.00    6.00    --  108.00  15.00 -30.00   52
 11  \w     91.00 136.00   1.00    6.00    --  108.00  45.00 120.00   45
 12  \w     61.00 126.00   1.00    6.00    --  108.00 -61.00  60.00   65
 13  \w     84.00 109.00   1.00    6.00    --  108.00 -94.00  90.00   25
 14  \w     70.00  97.00   1.00    6.00    --  108.00-111.00  90.00   27
 15  \w     42.00  69.00   1.00    6.00    --  108.00 -94.00  90.00   27
 16  \w     40.00 129.00   1.00    6.00    --  108.00 -30.00 -60.00   89
 17  \w     71.00 110.00   1.00    6.00    --  108.00  15.00 -30.00   39
 18  \w     65.00  92.00   1.00    1.50    --   36.00  77.00-120.00   27
 19  \w     61.00 101.00   1.00    1.50    --   36.00 178.00-150.00   40
 20  \w     66.00  97.00   1.00    6.00    --  108.00 178.00-150.00   31
 21  \w     73.00 146.00   1.00    6.00    --  108.00 178.00 -30.00   73
 22  \w     71.00  96.00   1.00    1.50    --   36.00 178.00 120.00   25
 23  \w     42.00 107.00   1.00    1.50    --   36.00  19.00  30.00   65
 24  \w     12.00  63.00   1.00    1.50    --   36.00  77.00-120.00   51
 25  \w    -31.00  26.00   1.00    1.50    --   36.00 -37.00 -90.00   57
;
_diffrn_measurement_device       '\k-geometry diffractometer'
_diffrn_measurement_device_type  'Gemini S (Oxford Diffraction)'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      0.0075430000
_diffrn_orient_matrix_UB_12      0.0777153000
_diffrn_orient_matrix_UB_13      -0.1164509000
_diffrn_orient_matrix_UB_21      0.0761766000
_diffrn_orient_matrix_UB_22      -0.1881979000
_diffrn_orient_matrix_UB_23      -0.0424478000
_diffrn_orient_matrix_UB_31      -0.3642098000
_diffrn_orient_matrix_UB_32      -0.0427493000
_diffrn_orient_matrix_UB_33      -0.0282707000
_diffrn_radiation_monochromator  graphite
_diffrn_radiation_probe          x-ray
_diffrn_radiation_source         'fine-focus sealed X-ray tube'
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0182
_diffrn_reflns_av_unetI/netI     0.0312
_diffrn_reflns_Laue_measured_fraction_full 0.990
_diffrn_reflns_Laue_measured_fraction_max 0.961
_diffrn_reflns_limit_h_max       3
_diffrn_reflns_limit_h_min       -5
_diffrn_reflns_limit_k_max       9
_diffrn_reflns_limit_k_min       -9
_diffrn_reflns_limit_l_max       13
_diffrn_reflns_limit_l_min       -14
_diffrn_reflns_number            2123
_diffrn_reflns_point_group_measured_fraction_full 0.990
_diffrn_reflns_point_group_measured_fraction_max 0.961
_diffrn_reflns_theta_full        67.885
_diffrn_reflns_theta_max         71.139
_diffrn_reflns_theta_min         3.647
_exptl_absorpt_coefficient_mu    1.007
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.89364
_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. 

Empirical correction (ABSPACK) includes:
- Absorption correction using spherical harmonics
- Frame scaling
;
_exptl_crystal_colour            colourless
_exptl_crystal_density_diffrn    1.410
_exptl_crystal_description       prism
_exptl_crystal_F_000             168
_exptl_crystal_recrystallization_method
'Re-crystallisation from solvent: aqueous ethanol'
_exptl_crystal_size_max          0.63
_exptl_crystal_size_mid          0.32
_exptl_crystal_size_min          0.21
_refine_diff_density_max         0.166
_refine_diff_density_min         -0.177
_refine_diff_density_rms         0.035
_refine_ls_extinction_coef       0.042(7)
_refine_ls_extinction_expression Fc^*^=kFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^
_refine_ls_extinction_method     'SHELXL-2018/3 (Sheldrick 2018)'
_refine_ls_goodness_of_fit_ref   1.087
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     114
_refine_ls_number_reflns         1393
_refine_ls_number_restraints     1
_refine_ls_restrained_S_all      1.086
_refine_ls_R_factor_all          0.0423
_refine_ls_R_factor_gt           0.0384
_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^)+(0.0659P)^2^+0.0225P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1099
_refine_ls_wR_factor_ref         0.1160
_reflns_Friedel_coverage         0.000
_reflns_number_gt                1238
_reflns_number_total             1393
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5ce00911a2.cif
_cod_data_source_block           1-E
_cod_database_code               7251407
_shelx_shelxl_version_number     2018/3
_shelx_estimated_absorpt_t_min   0.906
_shelx_estimated_absorpt_t_max   0.906
_shelx_res_checksum              39951