Polarization-dependent second harmonic generation in peptide crystals: effects of molecular packing.
Nandi, Sujay Kumar; Roy, Samrat; Pal, Bipul; Haldar, Debasish; Physical chemistry chemical physics : PCCP 25 (2023) 5849–5856; doi:10.1039/d2cp05462k

data_7246212
_publ_section_title
;
 Polarization-dependent second harmonic generation in peptide crystals:
 effects of molecular packing.
;
_journal_issue                   7
_journal_name_full               'Physical chemistry chemical physics : PCCP'
_journal_page_first              5849
_journal_page_last               5856
_journal_paper_doi               10.1039/d2cp05462k
_journal_volume                  25
_journal_year                    2023
_chemical_absolute_configuration s
_chemical_formula_moiety         'C14 H12 N2 O7, 0.25(C H Cl3)'
_chemical_formula_sum            'C14.25 H12.25 Cl0.75 N2 O7'
_chemical_formula_weight         350.10
_space_group_crystal_system      monoclinic
_space_group_IT_number           4
_space_group_name_Hall           'P 2yb'
_space_group_name_H-M_alt        'P 1 21 1'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     dual
_audit_creation_date             2021-10-28
_audit_creation_method
;
Olex2 1.3
(compiled 2020.11.12 svn.r5f609507 for OlexSys, GUI svn.r6272)
;
_audit_update_record
;
2022-05-26 deposited with the CCDC.	2023-01-30 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 101.7300(10)
_cell_angle_gamma                90
_cell_formula_units_Z            8
_cell_length_a                   13.94710(10)
_cell_length_b                   13.69170(10)
_cell_length_c                   16.76920(10)
_cell_measurement_reflns_used    16449
_cell_measurement_temperature    293(2)
_cell_measurement_theta_max      67.9510
_cell_measurement_theta_min      2.6900
_cell_volume                     3135.36(4)
_computing_cell_refinement       'CrysAlisPro 1.171.40.84a (Rigaku OD, 2020)'
_computing_data_collection       'CrysAlisPro 1.171.40.84a (Rigaku OD, 2020)'
_computing_data_reduction        'CrysAlisPro 1.171.40.84a (Rigaku OD, 2020)'
_computing_molecular_graphics    'Olex2 1.3 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.3 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2014/7 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXT 2014/5 (Sheldrick, 2014)'
_diffrn_ambient_temperature      293(2)
_diffrn_detector                 'Hybrid Pixel Array Detector'
_diffrn_detector_area_resol_mean 10.0000
_diffrn_detector_type            HyPix3000
_diffrn_measured_fraction_theta_full 0.998
_diffrn_measured_fraction_theta_max 0.994
_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    -28.00 118.00   0.50    0.24    --   40.33   7.00  47.00  292
  2  \w     85.00 164.00   0.50    1.10    --   96.67  33.00 -60.00  158
  3  \w    100.00 125.00   0.50    1.10    --   96.67 117.00 -30.00   50
  4  \w     79.00 159.00   0.50    1.10    --   96.67  50.00  60.00  160
  5  \w     59.00 161.00   0.50    1.10    --   96.67   7.00  47.00  204
  6  \w      0.00  29.00   0.50    0.24    --   40.33 -38.00  30.00   58
  7  \w    -22.00  29.00   0.50    0.24    --   40.33 -38.00 -30.00  102
  8  \w    -37.00  28.00   0.50    0.24    --   40.33  -7.00-127.00  130
  9  \w     44.00  99.00   0.50    0.24    --   40.33-138.00 -60.00  110
 10  \w     45.00  71.00   0.50    1.10    --   96.67-145.00-120.00   52
 11  \w     83.00 127.00   0.50    1.10    --   96.67-145.00-120.00   88
 12  \w     30.00 108.00   0.50    1.10    --   96.67-117.00-120.00  156
 13  \w     32.00  78.00   0.50    1.10    --   96.67 -96.00 -30.00   92
 14  \w     23.00 101.00   0.50    1.10    --   96.67 -96.00-120.00  156
 15  \w     32.00  57.00   0.50    1.10    --   96.67 -50.00-120.00   50
 16  \w     30.00  83.00   0.50    1.10    --   96.67 -68.00 -30.00  106
 17  \w     68.00  95.00   0.50    1.10    --   96.67 -77.00  90.00   54
 18  \w     40.00  66.00   0.50    1.10    --   96.67 -77.00  90.00   52
 19  \w     39.00  65.00   0.50    1.10    --   96.67 -59.00 120.00   52
 20  \w     39.00  65.00   0.50    1.10    --   96.67 -59.00  90.00   52
 21  \w     29.00  54.00   0.50    1.10    --   96.67 -59.00 -30.00   50
 22  \w     30.00  55.00   0.50    1.10    --   96.67 -50.00 -60.00   50
 23  \w     31.00  57.00   0.50    1.10    --   96.67 -50.00 -90.00   52
 24  \w     29.00  54.00   0.50    1.10    --   96.67 -59.00-120.00   50
 25  \w     30.00  56.00   0.50    1.10    --   96.67 -50.00-150.00   52
 26  \w    -67.00 -11.00   0.50    0.24    --  -40.33  77.00  90.00  112
 27  \w    -57.00  26.00   0.50    0.24    --  -40.33  50.00 -30.00  166
 28  \w     -4.00  26.00   0.50    0.24    --  -40.33  77.00  90.00   60
 29  \w    -28.00  37.00   0.50    0.24    --  -40.33   7.00  47.00  130
 30  \w    -67.00 -18.00   0.50    0.24    --  -40.33  77.00-150.00   98
 31  \w     -4.00  28.00   0.50    0.24    --  -40.33  77.00-150.00   64
 32  \w    -52.00 -25.00   0.50    1.10    --  -82.50  68.00-180.00   54
 33  \w    -47.00 -21.00   0.50    1.10    --  -82.50  42.00 -90.00   52
 34  \w    -55.00 -15.00   0.50    1.10    --  -82.50  59.00  90.00   80
 35  \w    -41.00 -15.00   0.50    1.10    --  -82.50  42.00  30.00   52
 36  \w    -45.00 -18.00   0.50    1.10    --  -82.50  42.00   0.00   54
 37  \w    -46.00 -21.00   0.50    1.10    --  -82.50  42.00 -30.00   50
 38  \w   -160.00 -51.00   0.50    1.10    --  -82.50  -7.00-127.00  218
 39  \w   -113.00 -21.00   0.50    0.24    --  -40.33  -7.00-127.00  184
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'XtaLAB Synergy, Dualflex, HyPix3000'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      -0.1041976000
_diffrn_orient_matrix_UB_12      -0.0084205000
_diffrn_orient_matrix_UB_13      0.0169336000
_diffrn_orient_matrix_UB_21      0.0419846000
_diffrn_orient_matrix_UB_22      0.0069605000
_diffrn_orient_matrix_UB_23      0.0921914000
_diffrn_orient_matrix_UB_31      -0.0104485000
_diffrn_orient_matrix_UB_32      0.1119639000
_diffrn_orient_matrix_UB_33      -0.0044608000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           'Cu K\a'
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0278
_diffrn_reflns_av_unetI/netI     0.0257
_diffrn_reflns_Laue_measured_fraction_full 0.998
_diffrn_reflns_Laue_measured_fraction_max 0.994
_diffrn_reflns_limit_h_max       16
_diffrn_reflns_limit_h_min       -16
_diffrn_reflns_limit_k_max       16
_diffrn_reflns_limit_k_min       -10
_diffrn_reflns_limit_l_max       19
_diffrn_reflns_limit_l_min       -20
_diffrn_reflns_number            22225
_diffrn_reflns_point_group_measured_fraction_full 0.673
_diffrn_reflns_point_group_measured_fraction_max 0.669
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         68.197
_diffrn_reflns_theta_min         2.691
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'PhotonJet (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    2.154
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.55714
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.40.84a (Rigaku Oxford Diffraction, 2020)
Empirical absorption correction using spherical harmonics,
implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            'light yellow'
_exptl_crystal_density_diffrn    1.483
_exptl_crystal_description       block
_exptl_crystal_F_000             1444
_exptl_crystal_size_max          0.2487
_exptl_crystal_size_mid          0.2149
_exptl_crystal_size_min          0.1895
_refine_diff_density_max         0.820
_refine_diff_density_min         -0.601
_refine_diff_density_rms         0.144
_refine_ls_abs_structure_details
;
 Flack x determined using 1457 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   0.020(14)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.075
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     873
_refine_ls_number_reflns         7678
_refine_ls_number_restraints     1
_refine_ls_restrained_S_all      1.075
_refine_ls_R_factor_all          0.0711
_refine_ls_R_factor_gt           0.0679
_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^)+(0.1371P)^2^+0.9245P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1967
_refine_ls_wR_factor_ref         0.2019
_reflns_Friedel_coverage         0.000
_reflns_number_gt                7028
_reflns_number_total             7678
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d2cp05462k2.cif
_cod_data_source_block           sn-couala1
_cod_depositor_comments
;
Adding full bibliography for 7246211--7246213.cif.

2024-12-16
Z value and formula fixed to values more according to usual
chemical conventions.                 miguel
;
_cod_original_formula_sum            'C57 H49 Cl3 N8 O28'
_cod_original_formula_weight         1400.39
_cod_original_formula_moiety         '4(C14 H12 N2 O7), C H Cl3'
_cod_original_formula_units_Z            2
_cod_original_sg_symbol_H-M      'P 21'
_cod_database_code               7246212
_shelx_shelxl_version_number     2014/7
_chemical_oxdiff_formula         'C H N O'
_chemical_oxdiff_usercomment     @RT
_reflns_odcompleteness_completeness 99.98
_reflns_odcompleteness_iscentric 1
_reflns_odcompleteness_theta     66.97
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All N(H) groups
 At 1.5 times of:
  All C(H,H,H) groups
2.a Ternary CH refined with riding coordinates:
 C39(H39), C25(H25), C53(H53), C11(H11), C57(H57)
2.b Aromatic/amide H refined with riding coordinates:
 N8(H8), N6(H6), N2(H2), N4(H4), C35(H35), C44(H44), C2(H2A), C49(H49),
 C19(H19), C21(H21), C33(H33), C47(H47), C7(H7), C5(H5), C17(H17), C30(H30),
 C16(H16), C45(H45), C3(H3), C31(H31)
2.c Idealised Me refined as rotating group:
 C54(H54A,H54B,H54C), C26(H26A,H26B,H26C), C40(H40A,H40B,H40C), C12(H12A,H12B,
 H12C), C56(H56A,H56B,H56C), C42(H42A,H42B,H42C), C14(H14A,H14B,H14C), C28(H28A,
 H28B,H28C)
;
_shelx_res_checksum              69963
_shelx_hkl_checksum              97287
_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 1.686
_oxdiff_exptl_absorpt_empirical_full_min 0.692