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_7251408
_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          404
_chemical_name_common            ' (Z)-methyl pyruvate semicarbazone'
_chemical_name_systematic
' Methyl (Z)-2-(2-carbamoylhydrazineylidene)propanoate'
_chemical_temperature_decomposition 404
_space_group_crystal_system      orthorhombic
_space_group_IT_number           43
_space_group_name_Hall           'F 2 -2d'
_space_group_name_H-M_alt        'F d d 2'
_atom_sites_solution_hydrogens   mixed
_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
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            32
_cell_length_a                   36.4109(10)
_cell_length_b                   23.9057(9)
_cell_length_c                   7.0463(2)
_cell_measurement_reflns_used    5435
_cell_measurement_temperature    295(2)
_cell_measurement_theta_max      26.9800
_cell_measurement_theta_min      2.7910
_cell_volume                     6133.3(3)
_computing_cell_refinement       'CrysAlisPro 1.171.40.53 (Rigaku OD, 2019)'
_computing_data_collection       'CrysAlisPro 1.171.40.53 (Rigaku OD, 2019)'
_computing_data_reduction        'CrysAlisPro 1.171.40.53 (Rigaku OD, 2019)'
_computing_structure_refinement  'SHELXL-2018/3 (Sheldrick, 2018)'
_computing_structure_solution    'SHELXT 2018/2 (Sheldrick, 2018)'
_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 0.999
_diffrn_measured_fraction_theta_max 0.914
_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    -21.00   7.00   1.00   10.00    --  -16.67 -99.00  90.00   28
  2  \w    -11.00  22.00   1.00   10.00    --  -16.67 -99.00-180.00   33
  3  \w      2.00  67.00   1.00   10.00    --   17.53  57.00   0.00   65
  4  \w     43.00  75.00   1.00   10.00    --   17.53 178.00-150.00   32
  5  \w    -50.00  34.00   1.00   10.00    --   17.53 -57.00 -90.00   84
  6  \w    -45.00  37.00   1.00   10.00    --   17.53 -77.00-180.00   82
  7  \w      7.00  80.00   1.00   10.00    --   17.53  37.00  90.00   73
  8  \f     90.00 360.00   1.00    0.50   0.00   0.00   0.00    --   270
;
_diffrn_measurement_device       '\k-geometry diffractometer'
_diffrn_measurement_device_type  'Gemini S (Oxford Diffraction)'
_diffrn_measurement_method       '\w and \f scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      -0.0057117000
_diffrn_orient_matrix_UB_12      -0.0237073000
_diffrn_orient_matrix_UB_13      0.0528051000
_diffrn_orient_matrix_UB_21      -0.0177002000
_diffrn_orient_matrix_UB_22      0.0119897000
_diffrn_orient_matrix_UB_23      0.0108868000
_diffrn_orient_matrix_UB_31      -0.0058119000
_diffrn_orient_matrix_UB_32      -0.0131878000
_diffrn_orient_matrix_UB_33      -0.0850159000
_diffrn_radiation_monochromator  graphite
_diffrn_radiation_probe          x-ray
_diffrn_radiation_source         'fine-focus sealed X-ray tube'
_diffrn_radiation_type           'Mo K\a'
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.0194
_diffrn_reflns_av_unetI/netI     0.0186
_diffrn_reflns_Laue_measured_fraction_full 0.999
_diffrn_reflns_Laue_measured_fraction_max 0.914
_diffrn_reflns_limit_h_max       46
_diffrn_reflns_limit_h_min       -49
_diffrn_reflns_limit_k_max       30
_diffrn_reflns_limit_k_min       -30
_diffrn_reflns_limit_l_max       8
_diffrn_reflns_limit_l_min       -9
_diffrn_reflns_number            12757
_diffrn_reflns_point_group_measured_fraction_full 0.994
_diffrn_reflns_point_group_measured_fraction_max 0.875
_diffrn_reflns_theta_full        25.242
_diffrn_reflns_theta_max         29.252
_diffrn_reflns_theta_min         2.813
_exptl_absorpt_coefficient_mu    0.114
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.95474
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
; 
CrysAlisPro 1.171.40.53 (Rigaku Oxford Diffraction, 2019) 
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    1.379
_exptl_crystal_description       prism
_exptl_crystal_F_000             2688
_exptl_crystal_recrystallization_method
'Re-crystallisation from solvent: ethyl acetate'
_refine_diff_density_max         0.113
_refine_diff_density_min         -0.170
_refine_diff_density_rms         0.036
_refine_ls_abs_structure_details
; 
 Flack x determined using 1043 quotients [(I+)-(I-)]/[(I+)+(I-)] 
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259). 
;
_refine_ls_abs_structure_Flack   0.3(4)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.036
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     223
_refine_ls_number_reflns         3654
_refine_ls_number_restraints     1
_refine_ls_restrained_S_all      1.036
_refine_ls_R_factor_all          0.0541
_refine_ls_R_factor_gt           0.0383
_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^)+(0.0500P)^2^+0.1485P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0851
_refine_ls_wR_factor_ref         0.0929
_reflns_Friedel_coverage         0.778
_reflns_Friedel_fraction_full    0.988
_reflns_Friedel_fraction_max     0.830
_reflns_number_gt                2871
_reflns_number_total             3654
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5ce00911a2.cif
_cod_data_source_block           1-Z
_cod_database_code               7251408
_shelx_shelxl_version_number     2018/3
_shelx_res_checksum              85463