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#$Date: 2026-02-19 03:45:32 +0100 (Thu, 19 Feb 2026) $
#$Revision: 304543 $
#$URL: svn://saulius.grazulis.lt/cod-secondary/cif/7/25/16/7251641.cif $
#------------------------------------------------------------------------------
#
# This file is available in the Crystallography Open Database (COD),
# http://www.crystallography.net/
#
# All data on this site have been placed in the public domain by the
# contributors.
#
data_7251641
loop_
_publ_author_name
'Kodrin, Ivan'
'Rodríguez, Maricel Gabriela'
'Politeo, Nives'
'Soldin, Željka'
'Kerš, Igor'
'Rončević, Tomislav'
'Čikeš Čulić, Vedrana'
'Sokol, Vesna'
'Doctorovich, Fabio'
'Kukovec, Boris-Marko'
_publ_section_title
;
 The influence of the substituent type and position on the topology of 2-D
 heterometallic sodium--palladium(ii) coordination networks with
 substituted nicotinate ligands
;
_journal_issue                   11
_journal_name_full               'RSC Advances'
_journal_page_first              9520
_journal_page_last               9529
_journal_paper_doi               10.1039/D5RA08782A
_journal_volume                  16
_journal_year                    2026
_chemical_formula_sum            'C12 H22 Cl2 F2 N2 Na2 O12 Pd'
_chemical_formula_weight         647.59
_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   mixed
_audit_creation_method           SHELXL-2018/3
_audit_update_record
;
2025-11-13 deposited with the CCDC.	2026-01-27 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 102.535(2)
_cell_angle_gamma                90
_cell_formula_units_Z            2
_cell_length_a                   8.4926(2)
_cell_length_b                   25.4917(5)
_cell_length_c                   5.49290(10)
_cell_measurement_reflns_used    10395
_cell_measurement_temperature    296(2)
_cell_measurement_theta_max      28.4690
_cell_measurement_theta_min      4.0220
_cell_volume                     1160.82(4)
_computing_structure_refinement  'SHELXL-2018/3 (Sheldrick, 2018)'
_computing_structure_solution    'SHELXT 2018/2 (Sheldrick, 2018)'
_diffrn_ambient_temperature      296(2)
_diffrn_measured_fraction_theta_full 0.995
_diffrn_measured_fraction_theta_max 0.995
_diffrn_measurement_device_type  'Xcalibur, Eos, Gemini'
_diffrn_measurement_method       'ω scans'
_diffrn_radiation_type           MoK\a
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.0582
_diffrn_reflns_av_unetI/netI     0.0236
_diffrn_reflns_Laue_measured_fraction_full 0.995
_diffrn_reflns_Laue_measured_fraction_max 0.995
_diffrn_reflns_limit_h_max       10
_diffrn_reflns_limit_h_min       -10
_diffrn_reflns_limit_k_max       30
_diffrn_reflns_limit_k_min       -30
_diffrn_reflns_limit_l_max       6
_diffrn_reflns_limit_l_min       -6
_diffrn_reflns_number            20797
_diffrn_reflns_point_group_measured_fraction_full 0.995
_diffrn_reflns_point_group_measured_fraction_max 0.995
_diffrn_reflns_theta_full        24.999
_diffrn_reflns_theta_max         24.999
_diffrn_reflns_theta_min         3.433
_exptl_absorpt_coefficient_mu    1.143
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.72351
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.41.95a (Rigaku Oxford Diffraction, 2021)
Empirical absorption correction using spherical harmonics,
implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            light-yellow
_exptl_crystal_density_diffrn    1.853
_exptl_crystal_description       plate
_exptl_crystal_F_000             648
_exptl_crystal_size_max          0.05
_exptl_crystal_size_mid          0.01
_exptl_crystal_size_min          0.01
_refine_diff_density_max         0.408
_refine_diff_density_min         -0.308
_refine_diff_density_rms         0.054
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.060
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     175
_refine_ls_number_reflns         2033
_refine_ls_number_restraints     12
_refine_ls_restrained_S_all      1.058
_refine_ls_R_factor_all          0.0274
_refine_ls_R_factor_gt           0.0239
_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/[σ²(Fo²)+(0.0204P)²+0.7147P] where P=(Fo²+2Fc²)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0528
_refine_ls_wR_factor_ref         0.0545
_reflns_Friedel_coverage         0.000
_reflns_number_gt                1878
_reflns_number_total             2033
_reflns_threshold_expression     'I > 2σ(I)'
_cod_data_source_file            d5ra08782a2.cif
_cod_data_source_block           2
_cod_original_sg_symbol_H-M      'P 21/c'
_cod_database_code               7251641
_shelx_shelxl_version_number     2018/3
_shelx_space_group_comment
;
The symmetry employed for this shelxl refinement is uniquely defined
by the following loop, which should always be used as a source of
symmetry information in preference to the above space-group names.
They are only intended as comments.
;
loop_
_space_group_symop_operation_xyz
'x, y, z'
'-x, y+1/2, -z+1/2'
'-x, -y, -z'
'x, -y-1/2, z-1/2'
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_U_iso_or_equiv
_atom_site_adp_type
_atom_site_occupancy
_atom_site_site_symmetry_order
_atom_site_calc_flag
_atom_site_refinement_flags_posn
_atom_site_refinement_flags_adp
_atom_site_refinement_flags_occupancy
_atom_site_disorder_assembly
_atom_site_disorder_group
Pd1 Pd 0.500000 0.500000 0.500000 0.02977(10) Uani 1 2 d S . P . .
Na1 Na 0.49909(11) 0.29409(4) 0.89859(17) 0.0335(2) Uani 1 1 d . . . . .
F1 F 0.18232(19) 0.49968(7) 0.1574(3) 0.0635(5) Uani 1 1 d . . . . .
Cl1 Cl 0.40341(8) 0.56679(3) 0.70651(13) 0.04579(18) Uani 1 1 d . . . . .
N1 N 0.2992(2) 0.45788(7) 0.5073(3) 0.0296(4) Uani 1 1 d . . . . .
O1 O 0.28602(19) 0.34026(7) 1.0226(3) 0.0365(4) Uani 1 1 d . . . . .
O2 O 0.01781(19) 0.33698(7) 0.9127(3) 0.0390(4) Uani 1 1 d . . . . .
O3 O 0.3425(2) 0.28624(7) 0.4788(3) 0.0355(4) Uani 1 1 d D . . . .
H31 H 0.332(3) 0.3067(8) 0.363(4) 0.043 Uiso 1 1 d D U . . .
H32 H 0.2503(16) 0.2780(10) 0.482(5) 0.043 Uiso 1 1 d D U . . .
O4 O 0.6570(2) 0.28221(7) 1.3092(3) 0.0360(4) Uani 1 1 d D . . . .
H41 H 0.7524(14) 0.2788(10) 1.313(5) 0.043 Uiso 1 1 d D U . . .
H42 H 0.653(3) 0.3034(8) 1.418(4) 0.043 Uiso 1 1 d D U . . .
O5 O 0.6817(2) 0.34956(8) 0.7488(4) 0.0471(5) Uani 1 1 d D . . . .
H51 H 0.660(3) 0.3770(7) 0.674(5) 0.057 Uiso 1 1 d D U . . .
H52 H 0.7792(14) 0.3509(11) 0.805(5) 0.057 Uiso 1 1 d D U . . .
O6 O -0.0113(2) 0.27552(7) 1.3098(3) 0.0383(4) Uani 1 1 d D . . . .
H61 H -0.001(3) 0.2915(9) 1.185(3) 0.046 Uiso 1 1 d D U . . .
H62 H -0.003(3) 0.2449(5) 1.272(5) 0.046 Uiso 1 1 d D U . . .
C1 C 0.2922(3) 0.42247(9) 0.6867(4) 0.0279(5) Uani 1 1 d . . . . .
H1 H 0.383462 0.417044 0.812528 0.033 Uiso 1 1 calc R U . . .
C2 C 0.1550(3) 0.39400(8) 0.6907(4) 0.0248(5) Uani 1 1 d . . . . .
C3 C 0.0201(3) 0.40274(10) 0.5030(4) 0.0334(6) Uani 1 1 d . . . . .
H3 H -0.074578 0.384281 0.501548 0.040 Uiso 1 1 calc R U . . .
C4 C 0.0258(3) 0.43871(11) 0.3185(5) 0.0421(6) Uani 1 1 d . . . . .
H4 H -0.063525 0.445209 0.190735 0.051 Uiso 1 1 calc R U . . .
C5 C 0.1680(3) 0.46444(10) 0.3309(5) 0.0369(6) Uani 1 1 d . . . . .
C6 C 0.1539(3) 0.35395(8) 0.8932(4) 0.0272(5) Uani 1 1 d . . . . .
loop_
_atom_type_symbol
_atom_type_description
_atom_type_scat_dispersion_real
_atom_type_scat_dispersion_imag
_atom_type_scat_source
C C 0.0033 0.0016 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
H H 0.0000 0.0000 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
Pd Pd -0.9988 1.0072 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
Na Na 0.0362 0.0249 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
F F 0.0171 0.0103 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
Cl Cl 0.1484 0.1585 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
N N 0.0061 0.0033 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
O O 0.0106 0.0060 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
loop_
_geom_angle_atom_site_label_1
_geom_angle_atom_site_label_2
_geom_angle_atom_site_label_3
_geom_angle
_geom_angle_site_symmetry_1
_geom_angle_site_symmetry_3
_geom_angle_publ_flag
N1 Pd1 N1 180.0 3_666 . ?
N1 Pd1 Cl1 90.54(6) 3_666 . ?
N1 Pd1 Cl1 89.46(6) . . ?
N1 Pd1 Cl1 89.46(6) 3_666 3_666 ?
N1 Pd1 Cl1 90.54(6) . 3_666 ?
Cl1 Pd1 Cl1 180.0 . 3_666 ?
O5 Na1 O1 113.53(7) . . ?
O5 Na1 O4 97.35(7) . . ?
O1 Na1 O4 95.68(6) . . ?
O5 Na1 O3 89.10(7) . . ?
O1 Na1 O3 91.08(6) . . ?
O4 Na1 O3 167.89(8) . . ?
O5 Na1 O4 88.64(7) . 4_565 ?
O1 Na1 O4 157.76(7) . 4_565 ?
O4 Na1 O4 82.51(6) . 4_565 ?
O3 Na1 O4 87.43(6) . 4_565 ?
O5 Na1 O3 161.70(8) . 4_566 ?
O1 Na1 O3 83.65(6) . 4_566 ?
O4 Na1 O3 86.64(6) . 4_566 ?
O3 Na1 O3 84.13(6) . 4_566 ?
O4 Na1 O3 74.12(6) 4_565 4_566 ?
O5 Na1 Na1 89.96(5) . 4_565 ?
O1 Na1 Na1 131.51(5) . 4_565 ?
O4 Na1 Na1 123.92(6) . 4_565 ?
O3 Na1 Na1 45.49(4) . 4_565 ?
O4 Na1 Na1 41.99(5) 4_565 4_565 ?
O3 Na1 Na1 73.18(5) 4_566 4_565 ?
O5 Na1 Na1 139.04(5) . 4_566 ?
O1 Na1 Na1 87.94(4) . 4_566 ?
O4 Na1 Na1 44.01(4) . 4_566 ?
O3 Na1 Na1 126.57(6) . 4_566 ?
O4 Na1 Na1 75.31(5) 4_565 4_566 ?
O3 Na1 Na1 42.68(5) 4_566 4_566 ?
Na1 Na1 Na1 101.40(5) 4_565 4_566 ?
C5 N1 C1 117.27(19) . . ?
C5 N1 Pd1 119.96(15) . . ?
C1 N1 Pd1 122.77(15) . . ?
C6 O1 Na1 128.65(15) . . ?
Na1 O3 Na1 91.83(6) . 4_565 ?
Na1 O3 H31 129.8(19) . . ?
Na1 O3 H31 110.7(19) 4_565 . ?
Na1 O3 H32 109.4(18) . . ?
Na1 O3 H32 109.8(19) 4_565 . ?
H31 O3 H32 104(2) . . ?
Na1 O4 Na1 94.00(7) . 4_566 ?
Na1 O4 H41 113.1(19) . . ?
Na1 O4 H41 119.6(19) 4_566 . ?
Na1 O4 H42 120(2) . . ?
Na1 O4 H42 105.5(19) 4_566 . ?
H41 O4 H42 105(2) . . ?
Na1 O5 H51 127(2) . . ?
Na1 O5 H52 125(2) . . ?
H51 O5 H52 105(3) . . ?
H61 O6 H62 103(2) . . ?
N1 C1 C2 122.5(2) . . ?
N1 C1 H1 118.8 . . ?
C2 C1 H1 118.8 . . ?
C1 C2 C3 118.1(2) . . ?
C1 C2 C6 120.55(19) . . ?
C3 C2 C6 121.39(19) . . ?
C4 C3 C2 120.0(2) . . ?
C4 C3 H3 120.0 . . ?
C2 C3 H3 120.0 . . ?
C5 C4 C3 117.2(2) . . ?
C5 C4 H4 121.4 . . ?
C3 C4 H4 121.4 . . ?
N1 C5 F1 114.6(2) . . ?
N1 C5 C4 125.0(2) . . ?
F1 C5 C4 120.3(2) . . ?
O1 C6 O2 125.9(2) . . ?
O1 C6 C2 117.54(19) . . ?
O2 C6 C2 116.5(2) . . ?
loop_
_geom_bond_atom_site_label_1
_geom_bond_atom_site_label_2
_geom_bond_distance
_geom_bond_site_symmetry_2
_geom_bond_publ_flag
Pd1 N1 2.0230(18) 3_666 ?
Pd1 N1 2.0231(18) . ?
Pd1 Cl1 2.2940(7) . ?
Pd1 Cl1 2.2940(7) 3_666 ?
Na1 O5 2.374(2) . ?
Na1 O1 2.3788(18) . ?
Na1 O4 2.380(2) . ?
Na1 O3 2.4070(19) . ?
Na1 O4 2.472(2) 4_565 ?
Na1 O3 2.532(2) 4_566 ?
Na1 Na1 3.5490(12) 4_565 ?
Na1 Na1 3.5490(12) 4_566 ?
F1 C5 1.334(3) . ?
N1 C5 1.319(3) . ?
N1 C1 1.347(3) . ?
O1 C6 1.241(3) . ?
O2 C6 1.261(3) . ?
O3 H31 0.812(10) . ?
O3 H32 0.815(10) . ?
O4 H41 0.810(10) . ?
O4 H42 0.812(10) . ?
O5 H51 0.813(10) . ?
O5 H52 0.819(10) . ?
O6 H61 0.820(10) . ?
O6 H62 0.815(10) . ?
C1 C2 1.377(3) . ?
C1 H1 0.9300 . ?
C2 C3 1.383(3) . ?
C2 C6 1.511(3) . ?
C3 C4 1.375(3) . ?
C3 H3 0.9300 . ?
C4 C5 1.363(3) . ?
C4 H4 0.9300 . ?
loop_
_geom_hbond_atom_site_label_D
_geom_hbond_atom_site_label_H
_geom_hbond_atom_site_label_A
_geom_hbond_distance_DH
_geom_hbond_distance_HA
_geom_hbond_distance_DA
_geom_hbond_angle_DHA
_geom_hbond_site_symmetry_A
_geom_hbond_publ_flag
O3 H31 O1 0.812(10) 2.017(12) 2.808(2) 165(3) 1_554 yes
O3 H32 O6 0.815(10) 2.219(16) 2.958(3) 151(2) 1_554 yes
O4 H41 O6 0.810(10) 2.013(10) 2.821(2) 176(3) 1_655 yes
O4 H42 O5 0.812(10) 2.134(12) 2.933(3) 168(3) 1_556 yes
O5 H51 Cl1 0.813(10) 2.493(16) 3.247(2) 155(3) 3_666 yes
O5 H52 O2 0.819(10) 2.016(12) 2.818(3) 167(3) 1_655 yes
O6 H61 O2 0.820(10) 1.925(10) 2.740(2) 173(3) . yes
O6 H62 O2 0.815(10) 2.220(17) 2.923(3) 145(2) 4_566 yes
O6 H62 O6 0.815(10) 2.58(2) 3.0390(16) 117(2) 4_565 yes
C1 H1 Cl1 0.93 2.89 3.758(2) 156.0 3_667 yes
C4 H4 F1 0.93 2.41 3.228(3) 146.6 3_565 yes
loop_
_geom_torsion_atom_site_label_1
_geom_torsion_atom_site_label_2
_geom_torsion_atom_site_label_3
_geom_torsion_atom_site_label_4
_geom_torsion
_geom_torsion_site_symmetry_1
_geom_torsion_site_symmetry_2
_geom_torsion_site_symmetry_3
_geom_torsion_site_symmetry_4
_geom_torsion_publ_flag
C5 N1 C1 C2 -0.4(3) . . . . ?
Pd1 N1 C1 C2 179.89(17) . . . . ?
N1 C1 C2 C3 -0.3(3) . . . . ?
N1 C1 C2 C6 178.8(2) . . . . ?
C1 C2 C3 C4 0.5(4) . . . . ?
C6 C2 C3 C4 -178.7(2) . . . . ?
C2 C3 C4 C5 0.1(4) . . . . ?
C1 N1 C5 F1 -179.5(2) . . . . ?
Pd1 N1 C5 F1 0.2(3) . . . . ?
C1 N1 C5 C4 1.0(4) . . . . ?
Pd1 N1 C5 C4 -179.3(2) . . . . ?
C3 C4 C5 N1 -0.8(4) . . . . ?
C3 C4 C5 F1 179.7(2) . . . . ?
Na1 O1 C6 O2 114.0(2) . . . . ?
Na1 O1 C6 C2 -65.1(3) . . . . ?
C1 C2 C6 O1 -14.1(3) . . . . ?
C3 C2 C6 O1 165.1(2) . . . . ?
C1 C2 C6 O2 166.8(2) . . . . ?
C3 C2 C6 O2 -14.1(3) . . . . ?
