Rotaxane synthesis via a dynamic [2]catenane-ring-opening, axle-cleaving double cross metathesis
Cetin, M. Mustafa; Mazumdar, Arindam; Cordes, David B.; Fidan, Vahap Gazi; Yang, Zhen; Mayer, Michael F.; RSC Advances 15 (2025) 47117–47127; doi:10.1039/D5RA07142A

data_7251385
_publ_section_title
;
 Rotaxane synthesis via a dynamic [2]catenane-ring-opening, axle-cleaving
 double cross metathesis
;
_journal_issue                   55
_journal_name_full               'RSC Advances'
_journal_page_first              47117
_journal_page_last               47127
_journal_paper_doi               10.1039/D5RA07142A
_journal_volume                  15
_journal_year                    2025
_chemical_formula_moiety         'C62 H58 Cu N4 O8, F6 P'
_chemical_formula_sum            'C62 H58 Cu F6 N4 O8 P'
_chemical_formula_weight         1195.63
_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   geom
_atom_sites_solution_primary     dual
_audit_creation_date             2025-10-28
_audit_creation_method
;
Olex2 1.5
(compiled 2025.07.13 svn.rb7424aed for OlexSys, GUI svn.r7314)
;
_audit_update_record
;
2025-10-28 deposited with the CCDC.	2025-11-13 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 96.345(5)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   16.7265(8)
_cell_length_b                   7.8498(4)
_cell_length_c                   43.035(2)
_cell_measurement_reflns_used    15018
_cell_measurement_temperature    173
_cell_measurement_theta_max      27.9520
_cell_measurement_theta_min      2.3520
_cell_volume                     5615.9(5)
_computing_cell_refinement       'CrysAlisPro 1.171.43.126a (Rigaku OD, 2024)'
_computing_data_collection
'CrystalClear-SM Expert 2.1 b45 (Rigaku OD, 2015)'
_computing_data_reduction        'CrysAlisPro 1.171.43.126a (Rigaku OD, 2024)'
_computing_molecular_graphics    'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2025/1 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXT 2018/2 (Sheldrick, 2018)'
_diffrn_ambient_temperature      173
_diffrn_detector                 CCD
_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   -120.00  60.00   1.00  200.00    --  -29.00  54.00   0.00  180
  2  \w   -120.00  60.00   1.00  200.00    --  -29.00  54.00 120.00  180
  3  \w   -120.00  60.00   1.00  200.00    --  -29.00  54.00 240.00  180
;
_diffrn_measurement_device       'Fixed \c 2 circle'
_diffrn_measurement_device_type  'Rigaku SCXMini'
_diffrn_measurement_method       '\w scans'
_diffrn_measurement_specimen_support Loop
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      0.0270413000
_diffrn_orient_matrix_UB_12      -0.0068313000
_diffrn_orient_matrix_UB_13      -0.0115289000
_diffrn_orient_matrix_UB_21      -0.0328409000
_diffrn_orient_matrix_UB_22      0.0035646000
_diffrn_orient_matrix_UB_23      -0.0119120000
_diffrn_orient_matrix_UB_31      0.0033532000
_diffrn_orient_matrix_UB_32      0.0900338000
_diffrn_orient_matrix_UB_33      -0.0004285000
_diffrn_radiation_monochromator  'SHINE graphite Monochromator'
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           'Mo K\a'
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.0900
_diffrn_reflns_av_unetI/netI     0.0644
_diffrn_reflns_Laue_measured_fraction_full 0.999
_diffrn_reflns_Laue_measured_fraction_max 0.999
_diffrn_reflns_limit_h_max       17
_diffrn_reflns_limit_h_min       -17
_diffrn_reflns_limit_k_max       8
_diffrn_reflns_limit_k_min       -8
_diffrn_reflns_limit_l_max       45
_diffrn_reflns_limit_l_min       -45
_diffrn_reflns_number            33616
_diffrn_reflns_point_group_measured_fraction_full 0.999
_diffrn_reflns_point_group_measured_fraction_max 0.999
_diffrn_reflns_theta_full        21.963
_diffrn_reflns_theta_max         21.963
_diffrn_reflns_theta_min         1.905
_diffrn_source                   'Sealed Tube'
_diffrn_source_type              'Sealed tube'
_exptl_absorpt_coefficient_mu    0.498
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.88529
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.43.126a (Rigaku Oxford Diffraction, 2024)
Empirical absorption correction using spherical harmonics,
implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            red
_exptl_crystal_colour_primary    red
_exptl_crystal_density_diffrn    1.414
_exptl_crystal_description       plate
_exptl_crystal_F_000             2480
_exptl_crystal_recrystallization_method
'Re-crystallisation from solvent: Methanol'
_exptl_crystal_size_max          0.42
_exptl_crystal_size_mid          0.12
_exptl_crystal_size_min          0.02
_refine_diff_density_max         0.753
_refine_diff_density_min         -1.188
_refine_diff_density_rms         0.121
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.259
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     834
_refine_ls_number_reflns         6867
_refine_ls_number_restraints     420
_refine_ls_restrained_S_all      5.864
_refine_ls_R_factor_all          0.1679
_refine_ls_R_factor_gt           0.1472
_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^)+139.0982P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.3117
_refine_ls_wR_factor_ref         0.3205
_reflns_Friedel_coverage         0.000
_reflns_number_gt                5478
_reflns_number_total             6867
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5ra07142a2.cif
_cod_data_source_block           7-p2
_cod_depositor_comments
;
The following automatic conversions were performed:

data item '_diffrn_radiation_probe' value 'X-ray' was changed to
'x-ray' in accordance with the
/home/data/users/saulius/crontab/automatic-downloads/rss-feeds/RSC/lib/dictionaries/cif_core.dic
dictionary named 'cif_core.dic' version 2.4.2 last updated on
2011-04-26.

Automatic conversion script
Id: cif_fix_values 8170 2020-07-09 18:12:32Z antanas 
;
_cod_original_cell_volume        5615.8(5)
_cod_original_sg_symbol_H-M      P21/c
_cod_database_code               7251385
_shelx_shelxl_version_number     2025/1
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups, All C(H,H,H,H) groups
 At 1.5 times of:
  All C(H,H,H) groups
2. Restrained distances
 O2-C28 = O2A-C28 = O2A-C29A = O2-C29
 1.45 with sigma of 0.01
 C29A-C30 = C29-C30
 1.55 with sigma of 0.01
 O7-C52 = O7A-C52A
 1.37 with sigma of 0.02
 O7-C55 = O7A-C55A
 1.43 with sigma of 0.02
 P1-F6A = P1-F5 = P1-F5A = P1-F4 = P1-F4A = P1-F3 = P1-F3A = P1-F6
 1.55 with sigma of 0.02
 C54A-C49 = C54-C49 = C54-C53 = C54A-C53A = C52-C51 = C52A-C51A = C51-C50 =
 C51A-C50A = C53-C52 = C53A-C52A = C50-C49 = C50A-C49
 1.39 with sigma of 0.001
 C49-C51 = C50-C52 = C51-C53 = C52-C54 = C53-C49 = C54-C51 = C49-C51A = C50A-
 C52A = C51A-C53A = C52A-C54A = C53A-C49 = C54A-C51A
 2.42 with sigma of 0.001
3. Restrained planarity
 C49, C54, C53, C52, O7, C51, C50
 with sigma of 0.01
 C49, C54A, C53A, C52A, O7A, C51A, C50A
 with sigma of 0.01
4. Uiso/Uaniso restraints and constraints
O2 \\sim O2A \\sim C29 \\sim C29A: within 2A with sigma of 0.04 and sigma for
terminal atoms of 0.08 within 2A
F3 \\sim F4 \\sim F5 \\sim F6 \\sim F3A \\sim F4A \\sim F5A \\sim F6A: within
2A with sigma of 0.04 and sigma for terminal atoms of 0.08 within 2A
O7 \\sim O7A \\sim C50 \\sim C51 \\sim C52 \\sim C53 \\sim C54 \\sim C55 \\sim
C50A \\sim C51A \\sim C52A \\sim C53A \\sim C54A \\sim C55A: within 2A with
sigma of 0.04 and sigma for terminal atoms of 0.08 within 2A
Uanis(C12) \\sim Ueq, Uanis(C14) \\sim Ueq, Uanis(C15) \\sim Ueq, Uanis(C17)
\\sim Ueq, Uanis(C25) \\sim Ueq, Uanis(C56) \\sim Ueq, Uanis(C61) \\sim Ueq:
with sigma of 0.01 and sigma for terminal atoms of 0.02
5. Rigid body (RIGU) restrains
 P1, F1, F2, F3, F4, F5, F6
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
6. Others
 Sof(O2A)=Sof(H28C)=Sof(H28D)=Sof(C29A)=Sof(H29C)=Sof(H29D)=Sof(H30C)=
 Sof(H30D)=1-FVAR(1)
 Sof(O2)=Sof(H28A)=Sof(H28B)=Sof(C29)=Sof(H29A)=Sof(H29B)=Sof(H30A)=Sof(H30B)=
 FVAR(1)
 Sof(F3A)=Sof(F4A)=Sof(F5A)=Sof(F6A)=1-FVAR(2)
 Sof(F3)=Sof(F4)=Sof(F5)=Sof(F6)=FVAR(2)
 Sof(O7A)=Sof(C50A)=Sof(H50A)=Sof(C51A)=Sof(H51A)=Sof(C52A)=Sof(C53A)=
 Sof(H53A)=Sof(C54A)=Sof(H54A)=Sof(C55A)=Sof(H55D)=Sof(H55E)=Sof(H55F)=1-FVAR(3)
 Sof(O7)=Sof(C55)=Sof(H55A)=Sof(H55B)=Sof(H55C)=Sof(C52)=Sof(C53)=Sof(H53)=
 Sof(C54)=Sof(H54)=Sof(C50)=Sof(H50)=Sof(C51)=Sof(H51)=FVAR(3)
7.a Secondary CH2 refined with riding coordinates:
 C27(H27A,H27B), C28(H28A,H28B), C28(H28C,H28D), C29(H29A,H29B), C29A(H29C,
 H29D), C30(H30A,H30B), C30(H30C,H30D), C31(H31A,H31B), C32(H32A,H32B),
 C33(H33A,H33B), C34(H34A,H34B), C35(H35A,H35B), C36(H36A,H36B)
7.b Aromatic/amide H refined with riding coordinates:
 C2(H2), C3(H3), C5(H5), C6(H6), C8(H8), C9(H9), C14(H14), C17(H17), C18(H18),
 C21(H21), C24(H24), C25(H25), C38(H38), C39(H39), C41(H41), C42(H42), C44(H44),
  C45(H45), C50A(H50A), C51A(H51A), C53A(H53A), C54A(H54A), C57(H57), C58(H58),
 C60(H60), C61(H61), C53(H53), C54(H54), C50(H50), C51(H51)
7.c Idealised Me refined as rotating group:
 C19(H19A,H19B,H19C), C26(H26A,H26B,H26C), C55(H55A,H55B,H55C), C55A(H55D,H55E,
 H55F), C62(H62A,H62B,H62C)
;
_shelx_res_checksum              31439