Structural variety in calcium metal–organic frameworks with a tetratopic carboxylate ligand
Zhao, Baiwen; Clarkson, Guy J.; Liu, Jie; Le, Thi Huong; Marrot, Jérôme; Millange, Franck; Frigoli, Michel; Walton, Richard I.; CrystEngComm 27 (2025) 2830–2840; doi:10.1039/D5CE00145E

data_7250207
_publ_section_title
;
 Structural variety in calcium metal--organic frameworks with a tetratopic
 carboxylate ligand
;
_journal_issue                   18
_journal_name_full               CrystEngComm
_journal_page_first              2830
_journal_page_last               2840
_journal_paper_doi               10.1039/D5CE00145E
_journal_volume                  27
_journal_year                    2025
_chemical_formula_moiety         'C114 H62 Ca5 O29, 0.5[]'
_chemical_formula_sum            'C114 H62 Ca5 O29'
_chemical_formula_weight         2096.03
_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   mixed
_atom_sites_solution_primary     dual
_audit_creation_date             2025-03-14
_audit_creation_method
;                                                                               
Olex2 1.5                                                                       
(compiled 2025.03.06 svn.red2d20d0 for OlexSys, GUI svn.r7188)                  
;
_audit_update_record
;
2025-03-14 deposited with the CCDC.	2025-03-31 downloaded from the CCDC.
;
_cell_angle_alpha                66.031(4)
_cell_angle_beta                 67.392(3)
_cell_angle_gamma                85.309(3)
_cell_formula_units_Z            2
_cell_length_a                   18.6030(6)
_cell_length_b                   19.2334(7)
_cell_length_c                   20.9801(7)
_cell_measurement_reflns_used    12154
_cell_measurement_temperature    100(2)
_cell_measurement_theta_max      71.6360
_cell_measurement_theta_min      2.4710
_cell_volume                     6307.6(5)
_computing_molecular_graphics    'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2019/3 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXT  (Sheldrick, 2015)'
_diffrn_ambient_temperature      100(2)
_diffrn_measured_fraction_theta_full 0.999
_diffrn_measured_fraction_theta_max 0.995
_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     35.00 122.00   0.50   20.00    --   47.75  32.00 -96.00  174        
  2  \w    -26.00  36.00   0.50   20.00    --   47.75 -32.00 104.00  124        
  3  \w   -165.00 -79.00   0.50   80.00    --  -91.75 -32.00 104.00  172        
  4  \w    100.00 178.00   0.50   80.00    --  113.25  32.00 -96.00  156        
  5  \w    -23.00  28.00   0.50   20.00    --  -47.75  19.00  60.00  102        
  6  \w    -23.00  28.00   0.50   20.00    --  -47.75  19.00-180.00  102        
  7  \w   -119.00 -73.00   0.50   20.00    --  -47.75-125.00-180.00   92        
  8  \w   -119.00 -73.00   0.50   20.00    --  -47.75-125.00  60.00   92        
  9  \w    -36.00  27.00   0.50   20.00    --  -47.75  32.00 -96.00  126        
 10  \w   -121.00 -35.00   0.50   20.00    --  -47.75 -32.00 104.00  172        
 11  \w   -119.00 -73.00   0.50   20.00    --  -47.75-125.00-150.00   92        
 12  \w    -23.00  28.00   0.50   20.00    --  -47.75  19.00 -60.00  102        
 13  \w     34.00  96.00   0.50   20.00    --   47.75-125.00 -30.00  124        
 14  \w    -24.00  71.00   0.50   20.00    --   47.75 -77.00  90.00  190        
 15  \w    -72.00 -19.00   0.50   80.00    --  -91.75  61.00 -60.00  106        
 16  \w    -50.00 -20.00   0.50   80.00    --  -91.75  45.00-120.00   60        
 17  \w    -85.00 -19.00   0.50   80.00    --  -91.75 125.00 -30.00  132        
 18  \w     42.00 106.00   0.50   80.00    --  113.25 -97.00 -40.62  128        
 19  \w    100.00 178.00   0.50   80.00    --  113.25  15.00  60.00  156        
 20  \w    101.00 178.00   0.50   80.00    --  113.25  45.00 -60.00  154        
 21  \w     42.00  72.00   0.50   80.00    --  113.25 -61.00-180.00   60        
 22  \w    101.00 178.00   0.50   80.00    --  113.25  45.00  60.00  154        
 23  \w     91.00 178.00   0.50   80.00    --  113.25  77.00-180.00  174        
 24  \w     42.00  72.00   0.50   80.00    --  113.25 -61.00  30.00   60        
 25  \w     42.00 106.00   0.50   80.00    --  113.25 -94.00 150.00  128        
 26  \w    101.00 178.00   0.50   80.00    --  113.25  30.00   0.00  154        
 27  \w     95.00 178.00   0.50   80.00    --  113.25 125.00-120.00  166        
 28  \w     42.00 106.00   0.50   80.00    --  113.25 -94.00-120.00  128        
 29  \w     42.00 106.00   0.50   80.00    --  113.25 -94.00 -90.00  128        
 30  \w     42.00  72.00   0.50   80.00    --  113.25 -61.00 -30.00   60        
 31  \w     42.00 106.00   0.50   80.00    --  113.25 -94.00   0.00  128        
 32  \w     42.00  72.00   0.50   80.00    --  113.25 -61.00 -90.00   60        
 33  \w     42.00 136.00   0.50   80.00    --  113.25 -77.00-180.00  188        
 34  \w    101.00 178.00   0.50   80.00    --  113.25  30.00-120.00  154        
 35  \w     42.00 106.00   0.50   80.00    --  113.25 -94.00 -30.00  128        
 36  \w     42.00 111.00   0.50   80.00    --  113.25-125.00 150.00  138        
 37  \w    101.00 178.00   0.50   80.00    --  113.25  45.00 150.00  154        
 38  \w     42.00 106.00   0.50   80.00    --  113.25 -94.00  30.00  128        
 39  \w     42.00 106.00   0.50   80.00    --  113.25 -94.00  60.00  128        
 40  \w     42.00 106.00   0.50   80.00    --  113.25 -94.00  90.00  128        
 41  \w    101.00 178.00   0.50   80.00    --  113.25  45.00 -90.00  154        
 42  \w     42.00  72.00   0.50   80.00    --  113.25 -61.00   0.00   60        
 43  \w     42.00 136.00   0.50   80.00    --  113.25 -77.00-180.00  188        
 44  \w     42.00 106.00   0.50   80.00    --  113.25 -94.00 120.00  128        
 45  \w     42.00 107.00   0.50   80.00    --  113.25-105.00-174.24  130        
 46  \w    101.00 168.00   0.50   80.00    --  113.25  45.00   0.00  134        
 47  \w    104.00 176.00   0.50   80.00    --  113.25  45.00 -30.00  144        
 48  \w     79.00 106.00   0.50   80.00    --  113.25 -97.00-169.81   54        
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'XtaLAB Synergy, Dualflex, HyPix'
_diffrn_measurement_method       '\w scan'
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.1301
_diffrn_reflns_av_unetI/netI     0.0813
_diffrn_reflns_Laue_measured_fraction_full 0.999
_diffrn_reflns_Laue_measured_fraction_max 0.995
_diffrn_reflns_limit_h_max       22
_diffrn_reflns_limit_h_min       -22
_diffrn_reflns_limit_k_max       23
_diffrn_reflns_limit_k_min       -23
_diffrn_reflns_limit_l_max       25
_diffrn_reflns_limit_l_min       -25
_diffrn_reflns_number            121764
_diffrn_reflns_point_group_measured_fraction_full 0.999
_diffrn_reflns_point_group_measured_fraction_max 0.995
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         72.112
_diffrn_reflns_theta_min         2.734
_exptl_absorpt_coefficient_mu    2.397
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.86368
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;                                                                               
 CrysAlisPro 1.171.41.94a (Rigaku Oxford Diffraction, 2021) Empirical           
 absorption correction using spherical harmonics, implemented in                
 SCALE3 ABSPACK scaling algorithm.                                              
;
_exptl_crystal_colour            colourless
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.104
_exptl_crystal_description       block
_exptl_crystal_F_000             2156
_exptl_crystal_size_max          0.05
_exptl_crystal_size_mid          0.02
_exptl_crystal_size_min          0.01
_platon_squeeze_details
;
Electron density in the voids were initially modelled as up to 15 partially
occupied water molecules with no major improvement in the refinement R values 
so the refinement was eventually completed using the Squeeze algorithm in
Platon giving the details in the table below.

Taking the volume of H20 to be about 40 and the number of electrons as 18 

31 waters would be 31 x 18 = 558 electrons
31 waters have a volume of 31 x 40 = 1240

The unit cell contains 31 water molecules which have been treated as a diffuse 
contribution to the overall scattering without specific atom positions as 
calculated by SQUEEZE routine in PLATON then the structure refined with Olex2. 
;
_refine_diff_density_max         0.884
_refine_diff_density_min         -1.134
_refine_diff_density_rms         0.090
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.006
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     1463
_refine_ls_number_reflns         24708
_refine_ls_number_restraints     172
_refine_ls_restrained_S_all      1.012
_refine_ls_R_factor_all          0.1399
_refine_ls_R_factor_gt           0.0902
_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^)+(0.1935P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.2623
_refine_ls_wR_factor_ref         0.3028
_reflns_Friedel_coverage         0.000
_reflns_number_gt                13438
_reflns_number_total             24708
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5ce00145e2.cif
_cod_data_source_block           bwx2new_sq
_cod_depositor_comments
'Adding full bibliography for 7250204--7250207.cif.'
_cod_original_cell_volume        6307.5(4)
_cod_database_code               7250207
_shelx_shelxl_version_number     2019/3
_shelx_estimated_absorpt_t_max   0.976
_shelx_estimated_absorpt_t_min   0.890
_olex2_refinement_description
;     
The asymmetric unit contains two complete ligands and two half ligands 
that sit on inversion centres and 5 calcium ions.
I think that works out OK considering charge balance. Based on this I 
believe that the coordinated oxygens O1, O2, O3A, O3B and O5 are waters. 
Hydrogens were located on water O3B where they form hydrogen bonds with 
the oxygens of neighbouring ligands. 
No hydrogens were located on the other coordinated waters which must be 
interacting with diffuse solvent in the voids in the structure.

Two of the terminal benzoic acid legs were modelled as disordered over 
two closely related positions.
The occupancy of benzoic acid leg C119 to O125 and its associated 
component C1 to O8 were linked to a free variable which refined to 62:38
The occupancy of benzoic acid leg C314 to O321 and its associated component 
C14 to O21 were linked to a free variable which refined close to 50:50 but 
was then fixed at this value for the remainder of the refinement. 
Several DFIX and SIMU restraints were used to give the disordered components 
reasonably bond lengths and thermal parameters.
Electron density in the voids were initially modelled as up to 15 partially 
occupied water molecules with no major improvement in the refinement R values.
The refinement was eventually completed using the Squeeze algorithm in Platon.
See Squeeze details at the end of the file.
                                                                          
1. Fixed Uiso                                                                   
 At 1.2 times of:                                                               
  All C(H) groups                                                               
 At 1.5 times of:                                                               
  All O(H,H) groups                                                             
2. Restrained distances                                                         
 C222-C225                                                                      
 1.3 with sigma of 0.008                                                        
 C122-C125                                                                      
 1.3 with sigma of 0.008                                                        
 C1-C7 = C17-C20                                                                
 1.3 with sigma of 0.01                                                         
 O7-C7 = O8-C7 = O126-C125 = C20-O20 = C20-O21                                  
 1.25 with sigma of 0.008                                                       
 Ca3-H3BA \\sim Ca3-H3BB                                                        
 with sigma of 0.02                                                             
3. Uiso/Uaniso restraints and constraints                                       
C1 \\sim C2 \\sim C3 \\sim C4 \\sim C5 \\sim C6 \\sim C7 \\sim O7 \\sim O8:     
within 2A with sigma of 0.008 and sigma for terminal atoms of 0.016 within 2A   
C14 \\sim C15 \\sim C16 \\sim C17 \\sim C18 \\sim C19 \\sim C20 \\sim O20 \\sim 
O21: within 2A with sigma of 0.004 and sigma for terminal atoms of 0.008 within 
2A                                                                              
C314 \\sim C315 \\sim C316 \\sim C317 \\sim C318 \\sim C319 \\sim O320 \\sim    
C320 \\sim O321 \\sim O5: within 2A with sigma of 0.004 and sigma for terminal  
atoms of 0.008 within 2A                                                        
4. Others                                                                       
 Sof(C1)=Sof(C3)=Sof(H3)=Sof(C2)=Sof(H2)=Sof(C4)=Sof(C5)=Sof(H5)=Sof(C6)=       
 Sof(H6)=Sof(C7)=Sof(O7)=Sof(O8)=1-FVAR(1)                                      
 Sof(C119)=Sof(C120)=Sof(H120)=Sof(C121)=Sof(H121)=Sof(C122)=Sof(C123)=         
 Sof(H123)=Sof(C124)=Sof(H124)=Sof(C125)=Sof(O125)=Sof(O126)=FVAR(1)            
 Fixed Sof: C14(0.5) C15(0.5) H15(0.5) C16(0.5) H16(0.5) C17(0.5) C18(0.5)      
 H18(0.5) C19(0.5) H19(0.5) C20(0.5) O20(0.5) O21(0.5) C314(0.5) C319(0.5)      
 H319(0.5) C318(0.5) H318(0.5) C317(0.5) C316(0.5) H316(0.5) C315(0.5)          
 H315(0.5) C320(0.5) O320(0.5) O321(0.5)                                        
5.a Free rotating group:                                                        
 O3B(H3BA,H3BB)                                                                 
5.b Aromatic/amide H refined with riding coordinates:                           
 C3(H3), C2(H2), C5(H5), C6(H6), C15(H15), C16(H16), C18(H18), C19(H19),        
 C104(H104), C105(H105), C107(H107), C108(H108), C110(H110), C112(H112),        
 C115(H115), C117(H117), C130(H130), C131(H131), C133(H133), C134(H134),        
 C138(H138), C139(H139), C141(H141), C142(H142), C204(H204), C205(H205),        
 C207(H207), C208(H208), C210(H210), C212(H212), C215(H215), C217(H217),        
 C220(H220), C221(H221), C223(H223), C224(H224), C230(H230), C231(H231),        
 C233(H233), C234(H234), C238(H238), C239(H239), C241(H241), C242(H242),        
 C304(H304), C305(H305), C307(H307), C308(H308), C310(H310), C312(H312),        
 C404(H404), C405(H405), C407(H407), C408(H408), C410(H410), C412(H412),        
 C415(H415), C416(H416), C418(H418), C419(H419), C120(H120), C121(H121),        
 C123(H123), C124(H124), C319(H319), C318(H318), C316(H316), C315(H315)         
5.c Fitted hexagon refined as free rotating group:                              
 C1(C3,C2,C4,C5,C6), C14(C15,C16,C17,C18,C19), C314(C319,C318,C317,C316,C315)   
;
_shelx_res_checksum              70081
_shelx_fab_checksum              49995
_platon_squeeze_void_probe_radius 1.20
_olex2_submission_special_instructions 'No special instructions were received'