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_7251384
_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      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_block_doi                 10.5517/ccdc.csd.cc11gksv
_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                115.129(11)
_cell_angle_beta                 114.546(10)
_cell_angle_gamma                92.324(8)
_cell_formula_units_Z            2
_cell_length_a                   14.7809(14)
_cell_length_b                   14.8375(16)
_cell_length_c                   15.4905(18)
_cell_measurement_reflns_used    3972
_cell_measurement_temperature    173
_cell_measurement_theta_max      30.1280
_cell_measurement_theta_min      1.5520
_cell_volume                     2698.9(7)
_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  300.00    --  -29.00  54.00   0.00  180
  2  \w   -120.00  60.00   1.00  300.00    --  -29.00  54.00 120.00  180
  3  \w   -120.00  60.00   1.00  300.00    --  -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      0.0359034000
_diffrn_orient_matrix_UB_12      -0.0291677000
_diffrn_orient_matrix_UB_13      -0.0060254000
_diffrn_orient_matrix_UB_21      -0.0077866000
_diffrn_orient_matrix_UB_22      -0.0210012000
_diffrn_orient_matrix_UB_23      0.0306105000
_diffrn_orient_matrix_UB_31      -0.0405089000
_diffrn_orient_matrix_UB_32      -0.0412813000
_diffrn_orient_matrix_UB_33      -0.0484066000
_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  0.1299
_diffrn_reflns_av_unetI/netI     0.1944
_diffrn_reflns_Laue_measured_fraction_full 0.999
_diffrn_reflns_Laue_measured_fraction_max 0.999
_diffrn_reflns_limit_h_max       15
_diffrn_reflns_limit_h_min       -15
_diffrn_reflns_limit_k_max       15
_diffrn_reflns_limit_k_min       -15
_diffrn_reflns_limit_l_max       16
_diffrn_reflns_limit_l_min       -16
_diffrn_reflns_number            16972
_diffrn_reflns_point_group_measured_fraction_full 0.999
_diffrn_reflns_point_group_measured_fraction_max 0.999
_diffrn_reflns_theta_full        21.967
_diffrn_reflns_theta_max         21.967
_diffrn_reflns_theta_min         1.907
_diffrn_source                   'Sealed Tube'
_diffrn_source_type              'Sealed tube'
_exptl_absorpt_coefficient_mu    0.518
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.94952
_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    1.471
_exptl_crystal_description       prism
_exptl_crystal_F_000             1240
_exptl_crystal_recrystallization_method
'Re-crystallisation from solvent: Methanol'
_exptl_crystal_size_max          0.09
_exptl_crystal_size_mid          0.06
_exptl_crystal_size_min          0.02
_refine_diff_density_max         0.589
_refine_diff_density_min         -0.460
_refine_diff_density_rms         0.073
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.004
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     801
_refine_ls_number_reflns         6604
_refine_ls_number_restraints     441
_refine_ls_restrained_S_all      1.007
_refine_ls_R_factor_all          0.1699
_refine_ls_R_factor_gt           0.0754
_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^)+(0.0151P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1168
_refine_ls_wR_factor_ref         0.1541
_reflns_Friedel_coverage         0.000
_reflns_number_gt                3313
_reflns_number_total             6604
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5ra07142a2.cif
_cod_data_source_block           7-p1
_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        2698.9(6)
_cod_original_sg_symbol_H-M      P-1
_cod_database_code               7251384
_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
 C28-C27 = C30-C29 = C31-C32 = C34-C33 = C35-C36
 1.55 with sigma of 0.01
 O1-C27 = O2-C28 = O2-C29 = O3-C30 = O3-C31 = O4-C32 = O4-C33 = O5-C34 = O5-
 C35 = O6-C36
 1.45 with sigma of 0.01
 O1-C28 = O2-C30 = O3-C32 = O4-C34 = O5-C36 = O6-C35 = O5-C33 = O4-C31 = O3-
 C29 = O2-C27
 2.45 with sigma of 0.02
 C28-C29 = C30-C31 = C32-C33 = C34-C35
 2.29 with sigma of 0.02
 C28A-C27A = C30A-C29A = C31A-C32A = C33A-C34
 1.55 with sigma of 0.01
 O1-C27A = O2A-C28A = O2A-C29A = O3A-C30A = O3A-C31A = C32A-O4A = O4A-C33A
 1.45 with sigma of 0.01
 O1-C28A = O2A-C30A = O2A-C27A = O3A-C32A = O3A-C29A = C31A-O4A = O4A-C34
 2.45 with sigma of 0.001
 C28A-C29A = C30A-C31A = C32A-C33A
 2.29 with sigma of 0.001
 P1-F6A = P1-F6 = P1-F3A = P1-F3 = P1-F4A = P1-F4 = P1-F5A = P1-F5
 1.55 with sigma of 0.01
 F3A-F2
 2.19 with sigma of 0.01
3. Restrained planarity
 F4A, P1, F6A, F2, F1
 with sigma of 0.01
 F3A, P1, F6A, F4A, F5A
 with sigma of 0.01
4. Uiso/Uaniso restraints and constraints
C27A \\sim C27 \\sim C28 \\sim C28A \\sim O2 \\sim O2A \\sim C29 \\sim C29A
\\sim C30 \\sim C30A \\sim O3 \\sim O3A \\sim C31 \\sim C32 \\sim C31A \\sim
C32A \\sim O4 \\sim O4A \\sim C33 \\sim C33A: within 2A with sigma of 0.04 and
sigma for terminal atoms of 0.08 within 2A
F6A \\sim F6 \\sim F3A \\sim F3 \\sim F4A \\sim F4 \\sim F5A \\sim F5: within
2A with sigma of 0.04 and sigma for terminal atoms of 0.08 within 2A
Uanis(C33) \\sim Ueq, Uanis(C39) \\sim Ueq: with sigma of 0.005 and sigma for
terminal atoms of 0.2
5. Rigid body (RIGU) restrains
 O6, C36, C35, O5, C34, C33, O4, C32, C31, O3, C30, C29, O2, C28, C27, O1
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
6. Others
 Sof(H34C)=Sof(H34D)=Sof(O4A)=Sof(C32A)=Sof(H32C)=Sof(H32D)=Sof(O3A)=Sof(C33A)=
 Sof(H33C)=Sof(H33D)=Sof(C27A)=Sof(H27C)=Sof(H27D)=Sof(C29A)=Sof(H29C)=
 Sof(H29D)=Sof(O2A)=Sof(C30A)=Sof(H30C)=Sof(H30D)=Sof(C28A)=Sof(H28C)=Sof(H28D)=
 Sof(C31A)=Sof(H31C)=Sof(H31D)=1-FVAR(1)
 Sof(C29)=Sof(H29A)=Sof(H29B)=Sof(O4)=Sof(C33)=Sof(H33A)=Sof(H33B)=Sof(C30)=
 Sof(H30A)=Sof(H30B)=Sof(C32)=Sof(H32A)=Sof(H32B)=Sof(O2)=Sof(O3)=Sof(H34A)=
 Sof(H34B)=Sof(C31)=Sof(H31A)=Sof(H31B)=Sof(C27)=Sof(H27A)=Sof(H27B)=Sof(C28)=
 Sof(H28A)=Sof(H28B)=FVAR(1)
 Sof(F4A)=Sof(F3A)=Sof(F5A)=Sof(F6A)=1-FVAR(2)
 Sof(F3)=Sof(F4)=Sof(F5)=Sof(F6)=FVAR(2)
7.a Secondary CH2 refined with riding coordinates:
 C36(H36A,H36B), C35(H35A,H35B), C29(H29A,H29B), C33(H33A,H33B), C30(H30A,
 H30B), C32(H32A,H32B), C34(H34A,H34B), C34(H34C,H34D), C31(H31A,H31B),
 C27(H27A,H27B), C28(H28A,H28B), C32A(H32C,H32D), C33A(H33C,H33D), C27A(H27C,
 H27D), C29A(H29C,H29D), C30A(H30C,H30D), C28A(H28C,H28D), C31A(H31C,H31D)
7.b Aromatic/amide H refined with riding coordinates:
 C24(H24), C25(H25), C21(H21), C58(H58), C61(H61), C60(H60), C57(H57),
 C14(H14), C8(H8), C3(H3), C54(H54), C9(H9), C45(H45), C2(H2), C5(H5), C18(H18),
  C6(H6), C50(H50), C38(H38), C42(H42), C53(H53), C39(H39), C41(H41), C44(H44),
 C51(H51), C17(H17)
7.c Idealised Me refined as rotating group:
 C26(H26A,H26B,H26C), C19(H19A,H19B,H19C), C62(H62A,H62B,H62C), C55(H55A,H55B,
 H55C)
;
_shelx_res_checksum              21389