#------------------------------------------------------------------------------
#$Date: 2024-09-06 02:55:23 +0300 (Fri, 06 Sep 2024) $
#$Revision: 294483 $
#$URL: file:///home/coder/svn-repositories/cod/cif/1/57/20/1572001.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_1572001
loop_
_publ_author_name
'Prajapati, Dharmraj'
'Clegg, Jack K.'
'Mukherjee, Partha Sarathi'
_publ_section_title
;
Formation of a low-symmetry Pd8 molecular barrel employing a
hetero donor tetradentate ligand, and its use in the binding and
extraction of C70.
;
_journal_issue 31
_journal_name_full 'Chemical science'
_journal_page_first 12502
_journal_page_last 12510
_journal_paper_doi 10.1039/d4sc01332h
_journal_volume 15
_journal_year 2024
_chemical_formula_moiety '2(C78 H101 N22 Pd4), 16[NO3H2OH2O]'
_chemical_formula_sum 'C156 H266 N60 O80 Pd8'
_chemical_formula_weight 5113.47
_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 geom
_atom_sites_solution_primary dual
_audit_creation_date 2023-12-18
_audit_creation_method
;
Olex2 1.5
(compiled 2023.08.24 svn.re1ec1418 for OlexSys, GUI svn.r6817)
;
_audit_update_record
;
2023-12-17 deposited with the CCDC. 2024-06-23 downloaded from the CCDC.
;
_cell_angle_alpha 87.8618(14)
_cell_angle_beta 77.0258(15)
_cell_angle_gamma 82.1629(14)
_cell_formula_units_Z 2
_cell_length_a 21.8333(4)
_cell_length_b 21.8629(3)
_cell_length_c 30.2029(6)
_cell_measurement_reflns_used 60434
_cell_measurement_temperature 150(2)
_cell_measurement_theta_max 28.2120
_cell_measurement_theta_min 1.8440
_cell_volume 13917.4(4)
_computing_cell_refinement 'CrysAlisPro 1.171.42.78a (Rigaku OD, 2022)'
_computing_data_collection 'CrysAlisPro 1.171.42.78a (Rigaku OD, 2022)'
_computing_data_reduction 'CrysAlisPro 1.171.42.78a (Rigaku OD, 2022)'
_computing_molecular_graphics 'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_publication_material 'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_structure_refinement 'SHELXL 2018/3 (Sheldrick, 2015)'
_computing_structure_solution 'SHELXT (Sheldrick, 2015)'
_diffrn_ambient_environment N~2~
_diffrn_ambient_temperature 150(2)
_diffrn_detector 'Hybrid Pixel Array Detector'
_diffrn_detector_area_resol_mean 5.8140
_diffrn_detector_type 'Pilatus 300K'
_diffrn_measured_fraction_theta_full 0.999
_diffrn_measured_fraction_theta_max 0.999
_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 -45.00 -12.00 0.50 180.00 -- -4.80 124.00 162.00 66
2 \w -71.00 -32.00 0.50 180.00 -- -4.80 147.00 -33.00 78
3 \w 51.00 77.00 0.50 180.00 -- 3.16 57.00-120.00 52
4 \w -18.00 40.00 0.50 180.00 -- 3.16 57.00-120.00 116
5 \w 41.00 74.00 0.50 180.00 -- 3.16 57.00 -30.00 66
6 \w -1.00 37.00 0.50 180.00 -- 3.16 -99.00 120.00 76
7 \w -17.00 39.00 0.50 180.00 -- 3.16 57.00 -30.00 112
8 \w -66.00 29.00 0.50 180.00 -- 3.16 -77.00 150.00 190
9 \w 1.00 39.00 0.50 180.00 -- 3.16 -99.00 -60.00 76
10 \w -25.00 31.00 0.50 180.00 -- 3.16 19.00 -60.00 112
11 \w 60.00 85.00 0.50 180.00 -- 3.16 19.00 -60.00 50
12 \w 17.00 43.00 0.50 180.00 -- 3.16 -99.00 0.00 52
13 \w -53.00 33.00 0.50 180.00 -- 3.16 -77.00 -90.00 172
14 \w -72.00 3.00 0.50 180.00 -- 3.16 -57.00 30.00 150
15 \w -5.00 20.00 0.50 180.00 -- -4.80 57.00 120.00 50
;
_diffrn_measurement_device 'four-circle diffractometer'
_diffrn_measurement_device_type 'XtaLAB Synergy, Dualflex, Pilatus 300K'
_diffrn_measurement_method '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11 0.0256708000
_diffrn_orient_matrix_UB_12 0.0143115000
_diffrn_orient_matrix_UB_13 -0.0128072000
_diffrn_orient_matrix_UB_21 0.0094364000
_diffrn_orient_matrix_UB_22 0.0056717000
_diffrn_orient_matrix_UB_23 0.0203002000
_diffrn_orient_matrix_UB_31 0.0195687000
_diffrn_orient_matrix_UB_32 -0.0289061000
_diffrn_orient_matrix_UB_33 -0.0021684000
_diffrn_radiation_monochromator mirror
_diffrn_radiation_probe x-ray
_diffrn_radiation_type 'Mo K\a'
_diffrn_radiation_wavelength 0.71073
_diffrn_reflns_av_R_equivalents 0.0876
_diffrn_reflns_av_unetI/netI 0.0591
_diffrn_reflns_Laue_measured_fraction_full 0.999
_diffrn_reflns_Laue_measured_fraction_max 0.999
_diffrn_reflns_limit_h_max 26
_diffrn_reflns_limit_h_min -26
_diffrn_reflns_limit_k_max 26
_diffrn_reflns_limit_k_min -26
_diffrn_reflns_limit_l_max 36
_diffrn_reflns_limit_l_min -36
_diffrn_reflns_number 269222
_diffrn_reflns_point_group_measured_fraction_full 0.999
_diffrn_reflns_point_group_measured_fraction_max 0.999
_diffrn_reflns_theta_full 25.123
_diffrn_reflns_theta_max 25.123
_diffrn_reflns_theta_min 1.901
_diffrn_source 'micro-focus sealed X-ray tube'
_diffrn_source_type 'PhotonJet (Mo) X-ray Source'
_exptl_absorpt_coefficient_mu 0.584
_exptl_absorpt_correction_T_max 1.00000
_exptl_absorpt_correction_T_min 0.95483
_exptl_absorpt_correction_type multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.42.78a (Rigaku Oxford Diffraction, 2022)
Empirical absorption correction using spherical harmonics,
implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour yellow
_exptl_crystal_colour_primary yellow
_exptl_crystal_density_diffrn 1.220
_exptl_crystal_description block
_exptl_crystal_F_000 5260
_exptl_crystal_size_max 0.1
_exptl_crystal_size_mid 0.05
_exptl_crystal_size_min 0.05
_refine_diff_density_max 2.647
_refine_diff_density_min -1.339
_refine_diff_density_rms 0.152
_refine_ls_extinction_method none
_refine_ls_goodness_of_fit_ref 1.037
_refine_ls_hydrogen_treatment constr
_refine_ls_matrix_type full
_refine_ls_number_parameters 1903
_refine_ls_number_reflns 49608
_refine_ls_number_restraints 1253
_refine_ls_restrained_S_all 1.034
_refine_ls_R_factor_all 0.1302
_refine_ls_R_factor_gt 0.0979
_refine_ls_shift/su_max 0.005
_refine_ls_shift/su_mean 0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.1768P)^2^+62.9791P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme calc
_refine_ls_wR_factor_gt 0.2843
_refine_ls_wR_factor_ref 0.3153
_reflns_Friedel_coverage 0.000
_reflns_number_gt 31518
_reflns_number_total 49608
_reflns_threshold_expression 'I > 2\s(I)'
_cod_data_source_file d4sc01332h2.cif
_cod_data_source_block spm23jc04
_cod_depositor_comments 'Adding full bibliography for 1572001.cif.'
_cod_database_code 1572001
_shelx_shelxl_version_number 2018/3
_chemical_oxdiff_formula 'C50 N12 H30 Pd O6'
_chemical_oxdiff_usercomment 'DRP 235 NO3'
_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.
;
_shelx_estimated_absorpt_t_max 0.971
_shelx_estimated_absorpt_t_min 0.944
_olex2_refinement_description
;
1. Fixed Uiso
At 1.2 times of:
All C(H) groups, All C(H,H) groups
At 1.5 times of:
All C(H,H,H) groups
2. Restrained distances
C15-C21
2.5 with sigma of 0.02
H7B-H26B
1.6 with sigma of 0.02
N192-C7
1.43 with sigma of 0.02
N192-C26
1.58 with sigma of 0.02
N192-C31
1.58 with sigma of 0.02
3. Uiso/Uaniso restraints and constraints
All non-hydrogen atoms restrained to be isotropic: with sigma of 0.02 and sigma
for terminal atoms of 0.04
4.a Secondary CH2 refined with riding coordinates:
C44(H44A,H44B), C179(H17D,H17E), C180(H18A,H18B), C45(H45A,H45B), C163(H16G,
H16H), C164(H16L,H16M), C160(H16Q,H16R), C197(H19D,H19E), C2(H2A,H2B),
C14(H14A,H14B), C3(H3A,H3B), C1(H1A,H1B), C7(H7A,H7B), C28(H28A,H28B),
C23(H23A,H23B), C102(H10D,H10E)
4.b Me refined with riding coordinates:
C4(H4A,H4B,H4C), C6(H6A,H6B,H6C)
4.c Aromatic/amide H refined with riding coordinates:
C22(H22), C90(H90), C62(H62), C125(H125), C86(H86), C84(H84), C107(H107),
C109(H109), C147(H147), C94(H94), C75(H75), C70(H70), C56(H56), C63(H63),
C12(H12), C99(H99), C33(H33), C60(H60), C103(H103), C17(H17), C146(H146),
C10(H10), C106(H106), C19(H19), C110(H110), C92(H92), C143(H143), C81(H81),
C73(H73), C132(H132), C27(H27), C112(H112), C38(H38), C104(H104), C115(H115),
C141(H141), C41(H41), C97(H97), C52(H52), C121(H121), C24(H24), C58(H58),
C127(H127), C50(H50), C78(H78), C113(H113), C67(H67), C124(H124), C82(H82),
C72(H72), C32(H32), C116(H116), C39(H39), C65(H65), C64(H64), C30(H30),
C29(H29), C25(H25), C130(H130), C119(H119), C136(H136), C144(H144), C68(H68),
C42(H42), C96(H96), C138(H138), C150(H150), C128(H128), C149(H149), C36(H36),
C79(H79), C134(H134), C139(H139), C35(H35)
4.d Idealised Me refined as rotating group:
C47(H47A,H47B,H47C), C48(H48A,H48B,H48C), C168(H16A,H16B,H16C), C152(H15A,
H15B,H15C), C202(H20A,H20B,H20C), C167(H16D,H16E,H16F), C159(H15D,H15E,H15F),
C171(H17A,H17B,H17C), C185(H18C,H18D,H18E), C161(H16I,H16J,H16K), C184(H18F,
H18G,H18H), C183(H18I,H18J,H18K), C153(H15G,H15H,H15I), C195(H19A,H19B,H19C),
C169(H16N,H16O,H16P), C182(H18L,H18M,H18N), C196(H19F,H19G,H19H), C166(H16S,
H16T,H16U), C8(H8A,H8B,H8C), C5(H5A,H5B,H5C), C15(H15J,H15K,H15L), C54(H54A,
H54B,H54C), C43(H43A,H43B,H43C), C21(H21A,H21B,H21C), C31(H31A,H31B,H31C),
C66(H66A,H66B,H66C), C69(H69A,H69B,H69C), C40(H40A,H40B,H40C), C100(H10A,H10B,
H10C), C26(H26A,H26B,H26C)
;
_smtbx_masks_special_details
;
A solvent mask was calculated and 1905 electrons were
found per unit cell.
This was included in the formula as
16NO3 anions and 32 H2O solvent molecules per Asymmetric Unit.
;
_smtbx_masks_void_probe_radius 1.2
_smtbx_masks_void_truncation_radius 1.2
_shelx_res_file
;
TITL spm23jc04_a.res in P-1
spm23jc04.res
created by SHELXL-2018/3 at 09:38:27 on 18-Dec-2023
REM Old TITL Spm23jc04 in P-1
REM SHELXT solution in P-1: R1 0.308, Rweak 0.034, Alpha 0.120
REM 0.000 for 0 systematic absences, Orientation as input
REM Formula found by SHELXT: C190 N66 O22 Pd8
CELL 0.71073 21.833264 21.862857 30.202904 87.8618 77.0258 82.1629
ZERR 2 0.000379 0.000348 0.000568 0.0014 0.0015 0.0014
LATT 1
SFAC C H N O Pd
UNIT 312 532 120 160 16
DFIX 2.5 C15 C21
ISOR 0.02 0.04
DFIX 1.6 H7b H26b
DFIX 1.43 N192 C7
DFIX 1.58 N192 C26
DFIX 1.58 N192 C31
L.S. 12
PLAN 245
SIZE 0.1 0.05 0.05
TEMP -123(2)
CONF
ABIN
MORE -1
BOND $H
fmap 2
acta
SHEL 20 0.837
OMIT -8 -2 1
OMIT -3 -2 2
OMIT -3 2 5
OMIT -2 -4 5
OMIT -1 -5 10
OMIT -1 1 7
OMIT -1 5 1
OMIT 0 3 7
OMIT 1 -3 5
OMIT 1 4 0
OMIT 2 -1 6
OMIT 2 1 6
OMIT 2 8 1
OMIT 4 -4 2
OMIT 4 2 2
OMIT 5 5 1
REM
REM
REM