Unveiling protonated form of 2,6-di-m-phenylpyridine embedded isosmaragdyrin analogue and its organo-Pd(ii) complex
Pradhan, Sourav Ranjan; Murugavel, M.; Chitranshi, Sangya; Kim, Gakhyun; Kim, Dongho; Das, Mainak; Srinivasan, A.; New Journal of Chemistry 47 (2023) 19987–19992; doi:10.1039/D3NJ03432A

data_7062813
_publ_section_title
;
 Unveiling protonated form of 2,6-di-m-phenylpyridine embedded
 isosmaragdyrin analogue and its organo-Pd(ii) complex
;
_journal_issue                   43
_journal_name_full               'New Journal of Chemistry'
_journal_page_first              19987
_journal_page_last               19992
_journal_paper_doi               10.1039/D3NJ03432A
_journal_volume                  47
_journal_year                    2023
_chemical_formula_moiety
'C52 H40 F5 N3, 2(C2 F3 O2), 2(C0.458 F0.688 O), 1.542(C2 F3 O), 0.458(O), 2.5[CH2Cl2]'
_chemical_formula_sum            'C62.5 H45 Cl5 F17 N3 O8'
_chemical_formula_weight         1466.26
_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
_audit_creation_date             2023-09-26
_audit_creation_method
;
Olex2 1.5-dev
(compiled 2023.09.12 svn.re1ec1418 for OlexSys, GUI svn.r6697)
;
_audit_update_record
;
2023-10-01 deposited with the CCDC.	2023-10-03 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 97.8318(19)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   17.3774(4)
_cell_length_b                   19.4464(3)
_cell_length_c                   20.1641(4)
_cell_measurement_reflns_used    27067
_cell_measurement_temperature    293(2)
_cell_measurement_theta_max      76.2260
_cell_measurement_theta_min      3.4620
_cell_volume                     6750.5(2)
_computing_cell_refinement       'CrysAlisPro 1.171.39.46b (Rigaku OD, 2018)'
_computing_data_collection       'CrysAlisPro 1.171.39.46b (Rigaku OD, 2018)'
_computing_data_reduction        'CrysAlisPro 1.171.39.46b (Rigaku OD, 2018)'
_computing_molecular_graphics    'Olex2 1.5-dev (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5-dev (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2018/3 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXT 2014/5 (Sheldrick, 2014)'
_diffrn_ambient_temperature      293(2)
_diffrn_detector_type            'Pilatus 200K'
_diffrn_measured_fraction_theta_full 0.998
_diffrn_measured_fraction_theta_max 0.998
_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     -4.00  67.00   0.50    1.00    --    0.00  11.00 -91.00  142
  2  \w     98.00 169.00   0.50    4.00    --  102.09  11.00 -91.00  142
  3  \w     35.00 106.00   0.50    4.00    --  102.09 -11.00  95.00  142
  4  \w    -67.00   4.00   0.50    1.00    --    0.00 -11.00  95.00  142
  5  \w    -22.00  62.00   0.50    1.00    --    0.00  77.00-180.00  168
  6  \w     -1.00  67.00   0.50    1.00    --    0.00  19.00  60.00  136
  7  \w    -62.00  22.00   0.50    1.00    --    0.00 -77.00 -60.00  168
  8  \w    -65.00   1.00   0.50    1.00    --    0.00 -37.00  30.00  132
  9  \w     34.00 104.00   0.50    4.00    --  102.09 -15.00-150.00  140
 10  \w    100.00 170.00   0.50    4.00    --  102.09  15.00-180.00  140
 11  \w     39.00 118.00   0.50    4.00    --  102.09-125.00  60.00  158
 12  \w    101.00 169.00   0.50    4.00    --  102.09  30.00  60.00  136
 13  \w     40.00 114.00   0.50    4.00    --  102.09 -61.00 -60.00  148
 14  \w     34.00 109.00   0.50    4.00    --  102.09 -94.00 120.00  150
 15  \w     36.00 103.00   0.50    4.00    --  102.09 -30.00 -30.00  134
 16  \w    100.00 170.00   0.50    4.00    --  102.09  15.00-150.00  140
 17  \w     40.00 124.00   0.50    4.00    --  102.09 -77.00-150.00  168
 18  \w     91.00 164.00   0.50    4.00    --  102.09  61.00 120.00  146
 19  \w     34.00 109.00   0.50    4.00    --  102.09 -94.00-150.00  150
 20  \w     34.00 109.00   0.50    4.00    --  102.09 -94.00-180.00  150
 21  \w     94.00 166.00   0.50    4.00    --  102.09 125.00  60.00  144
 22  \w     34.00 109.00   0.50    4.00    --  102.09 -94.00   0.00  150
 23  \w     34.00 109.00   0.50    4.00    --  102.09 -94.00  90.00  150
 24  \w    100.00 165.00   0.50    4.00    --  102.09  45.00  30.00  130
 25  \w     39.00 105.00   0.50    4.00    --  102.09 -45.00  60.00  132
 26  \w     80.00 164.00   0.50    4.00    --  102.09  77.00  90.00  168
 27  \w     39.00 105.00   0.50    4.00    --  102.09 -45.00 -90.00  132
 28  \w     39.00 105.00   0.50    4.00    --  102.09 -45.00   0.00  132
 29  \w    -22.00  62.00   0.50    1.00    --    0.00  77.00 -30.00  168
 30  \w    -22.00  62.00   0.50    1.00    --    0.00  77.00 120.00  168
 31  \w     -1.00  67.00   0.50    1.00    --    0.00  19.00 -60.00  136
 32  \w     -1.00  67.00   0.50    1.00    --    0.00  19.00 150.00  136
 33  \w     -1.00  65.00   0.50    1.00    --    0.00  37.00 120.00  132
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type
'SuperNova, Dual, Cu at home/near, Pilatus 200K'
_diffrn_measurement_method       '\w scans'
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0796
_diffrn_reflns_av_unetI/netI     0.0244
_diffrn_reflns_Laue_measured_fraction_full 0.998
_diffrn_reflns_Laue_measured_fraction_max 0.998
_diffrn_reflns_limit_h_max       20
_diffrn_reflns_limit_h_min       -20
_diffrn_reflns_limit_k_max       22
_diffrn_reflns_limit_k_min       -22
_diffrn_reflns_limit_l_max       19
_diffrn_reflns_limit_l_min       -23
_diffrn_reflns_number            45950
_diffrn_reflns_point_group_measured_fraction_full 0.998
_diffrn_reflns_point_group_measured_fraction_max 0.998
_diffrn_reflns_theta_full        64.995
_diffrn_reflns_theta_max         64.995
_diffrn_reflns_theta_min         3.429
_exptl_absorpt_coefficient_mu    2.860
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.78589
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.39.46b (Rigaku Oxford Diffraction, 2018)
Empirical absorption correction using spherical harmonics,
 implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            blue
_exptl_crystal_colour_primary    blue
_exptl_crystal_density_diffrn    1.443
_exptl_crystal_description       block
_exptl_crystal_F_000             2972
_exptl_crystal_size_max          0.2
_exptl_crystal_size_mid          0.1
_exptl_crystal_size_min          0.1
_refine_diff_density_max         0.230
_refine_diff_density_min         -0.232
_refine_diff_density_rms         0.043
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.050
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     531
_refine_ls_number_reflns         5733
_refine_ls_number_restraints     210
_refine_ls_restrained_S_all      1.090
_refine_ls_R_factor_all          0.0784
_refine_ls_R_factor_gt           0.0732
_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^)+(0.1102P)^2^+6.0417P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.2160
_refine_ls_wR_factor_ref         0.2201
_reflns_Friedel_coverage         0.000
_reflns_number_gt                4973
_reflns_number_total             5733
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d3nj03432a2.cif
_cod_data_source_block           as-py-ism-tfa
_cod_depositor_comments
'Adding full bibliography for 7062813--7062814.cif.'
_cod_original_cell_volume        6750.4(2)
_cod_original_formula_sum        'C62.50 H45 Cl5 F17 N3 O8'
_cod_database_code               7062813
_shelx_shelxl_version_number     2018/3
_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. Restrained distances
 O3-C56 \\sim O3A-C56A
 with sigma of 0.02
 O4-C56 \\sim O4A-C56A
 with sigma of 0.02
 F8-C55 \\sim F8A-C55A
 with sigma of 0.02
 C56-C55 \\sim C56A-C55A
 with sigma of 0.02
 C55-F7 \\sim C55A-F7A
 with sigma of 0.02
 C55-F9 \\sim C55A-F9A
 with sigma of 0.02
 O3-O4 \\sim O3A-O4A
 with sigma of 0.04
 O3-C55 \\sim O3A-C55A
 with sigma of 0.04
 O4-C55 \\sim O4A-C55A
 with sigma of 0.04
 F8-C56 \\sim F8A-C56A
 with sigma of 0.04
 F8-F7 \\sim F8A-F7A
 with sigma of 0.04
 F8-F9 \\sim F8A-F9A
 with sigma of 0.04
 C56-F7 \\sim C56A-F7A
 with sigma of 0.04
 C56-F9 \\sim C56A-F9A
 with sigma of 0.04
 F7-F9 \\sim F7A-F9A
 with sigma of 0.04
 O1-C54 \\sim O1A-C54A
 with sigma of 0.02
 F5-C53 \\sim F5A-C53A
 with sigma of 0.02
 C54-O2 \\sim C54A-O2A
 with sigma of 0.02
 C54-C53 \\sim C54A-C53A
 with sigma of 0.02
 F4-C53 \\sim F4A-C53A
 with sigma of 0.02
 C53-F6 \\sim C53A-F6A
 with sigma of 0.02
 O1-O2 \\sim O1A-O2A
 with sigma of 0.04
 O1-C53 \\sim O1A-C53A
 with sigma of 0.04
 F5-C54 \\sim F5A-C54A
 with sigma of 0.04
 F5-F4 \\sim F5A-F4A
 with sigma of 0.04
 F5-F6 \\sim F5A-F6A
 with sigma of 0.04
 C54-F4 \\sim C54A-F4A
 with sigma of 0.04
 C54-F6 \\sim C54A-F6A
 with sigma of 0.04
 F4-F6 \\sim F4A-F6A
 with sigma of 0.04
 O2-C53 \\sim O2A-C53A
 with sigma of 0.04
3. Uiso/Uaniso restraints and constraints
Uanis(O3A) \\sim Ueq, Uanis(O4) \\sim Ueq: with sigma of 0.01 and sigma for
terminal atoms of 0.02
4. Rigid body (RIGU) restrains
 O4A, O3, C56A, C55A, F8A, F7A, F9A
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 F9, O4, C56, C55, F8, F7
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 F9A, O3, C56A, C55A, O4A, F8A, F7A
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
 F7, O4, C56, C55, F8, F9
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
 O2, O1, C54, C53, F5, F4, F6
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
 O2A, C54A, O1A, C53A, F5A, F4A, F6A
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
5. Others
 Sof(C55A)=Sof(O3A)=Sof(C56A)=Sof(O4A)=Sof(F8A)=Sof(F7A)=Sof(F9A)=1-FVAR(1)
 Sof(O3)=Sof(O4)=Sof(F8)=Sof(C56)=Sof(C55)=Sof(F7)=Sof(F9)=FVAR(1)
 Sof(C54A)=Sof(O1A)=Sof(O2A)=Sof(C53A)=Sof(F5A)=Sof(F4A)=Sof(F6A)=1-FVAR(2)
 Sof(O1)=Sof(F5)=Sof(C54)=Sof(F4)=Sof(O2)=Sof(C53)=Sof(F6)=FVAR(2)
6.a Aromatic/amide H refined with riding coordinates:
 N2(H2), N3(H3), C27(H27), C8(H8), C9(H9), C4(H4), C2(H2A), C25(H25), C31(H31),
  C33(H33), C24(H24), C3(H3A)
6.b Idealised Me refined as rotating group:
 C35(H35A,H35B,H35C), C37(H37A,H37B,H37C), C36(H36A,H36B,H36C)
;
_smtbx_masks_special_details
'A solvent mask was calculated and 456 electrons were found in a volume of 1204\%A^3^ in 1 void per unit cell. This is consistent with the presence of  1.25[CH2Cl2] per Asymmetric Unit which account for 420 electrons per unit cell.'
_shelx_res_checksum              94837
_shelx_fab_checksum              12394
_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
;