Highly selective acid-catalyzed olefin isomerization of limonene to terpinolene by kinetic suppression of overreactions in a confined space of porous metal–macrocycle frameworks
He, Wei; Tashiro, Shohei; Shionoya, Mitsuhiko; Chemical Science  (2022) –; doi:10.1039/D2SC01561G

data_1567106
_publ_section_title
;
 Highly selective acid-catalyzed olefin isomerization of limonene to
 terpinolene by kinetic suppression of overreactions in a confined space
 of porous metal--macrocycle frameworks
;
_journal_name_full               'Chemical Science'
_journal_paper_doi               10.1039/D2SC01561G
_journal_year                    2022
_chemical_formula_moiety         '2(C42 H42 Cl6 N6 Pd3), C2 H3 N, O'
_chemical_formula_sum            'C86 H87 Cl12 N13 O Pd6'
_chemical_formula_weight         2382.48
_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
_audit_creation_date             2021-10-06
_audit_creation_method
;
Olex2 1.5
(compiled 2021.08.20 svn.r13c46975 for OlexSys, GUI svn.r6405)
;
_audit_update_record
;
2022-01-10 deposited with the CCDC.	2022-06-13 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 90.6000(10)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   19.60170(10)
_cell_length_b                   52.3627(4)
_cell_length_c                   14.33970(10)
_cell_measurement_reflns_used    81574
_cell_measurement_temperature    93
_cell_measurement_theta_max      72.9860
_cell_measurement_theta_min      2.3020
_cell_volume                     14717.43(17)
_computing_cell_refinement       'CrysAlisPro 1.171.39.46e (Rigaku OD, 2018)'
_computing_data_collection       'CrysAlisPro 1.171.39.46e (Rigaku OD, 2018)'
_computing_data_reduction        'CrysAlisPro 1.171.39.46e (Rigaku OD, 2018)'
_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)'
_diffrn_ambient_temperature      93
_diffrn_detector                 'CCD plate'
_diffrn_measured_fraction_theta_full 0.978
_diffrn_measured_fraction_theta_max 0.956
_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    -88.00 -49.00   0.50    0.93    --    0.00 -82.00  60.00   78
  2  \w      1.00  89.00   0.50    0.93    --    0.00  38.00 -90.00  176
  3  \w    -22.00  27.00   0.50    0.93    --    0.00 -82.00  60.00   98
  4  \w     -8.00  53.00   0.50    0.93    --    0.00  19.00-180.00  122
  5  \w    -68.00  -4.00   0.50    0.93    --    0.00 -57.00-120.00  128
  6  \w      6.00  63.00   0.50    3.73    --   92.10 -15.00 -90.00  114
  7  \w    101.00 164.00   0.50    3.73    --   92.10  61.00 -30.00  126
  8  \w      3.00 103.00   0.50    3.73    --   92.10 -30.00-120.00  200
  9  \w     63.00 176.00   0.50    3.73    --   92.10  82.00 -90.00  226
 10  \w     25.00  96.00   0.50    3.73    --   92.10 -82.00  30.00  142
 11  \w     23.00 121.00   0.50    3.73    --   92.10 -82.00-120.00  196
 12  \w     85.00 170.00   0.50    3.73    --   92.10  15.00  90.00  170
 13  \w     65.00 102.00   0.50    3.73    --   92.10  77.00 -60.00   74
 14  \w    104.00 129.00   0.50    3.73    --   92.10  77.00 -60.00   50
 15  \w     68.00 109.00   0.50    3.73    --   92.10 -61.00-120.00   82
 16  \w     65.00  99.00   0.50    3.73    --   92.10  82.00 -60.00   68
 17  \w      3.00 108.00   0.50    3.73    --   92.10 -77.00-180.00  210
 18  \w     64.00 123.00   0.50    3.73    --   92.10  82.00  30.00  118
 19  \w      3.00  60.00   0.50    3.73    --   92.10 -15.00-180.00  114
 20  \w     84.00 109.00   0.50    3.73    --   92.10 -82.00 -60.00   50
 21  \w     31.00  60.00   0.50    3.73    --   92.10 -61.00-120.00   58
 22  \w     66.00 115.00   0.50    3.73    --   92.10  77.00 -30.00   98
 23  \w      7.00 101.00   0.50    3.73    --   92.10 -82.00-150.00  188
 24  \w     87.00 113.00   0.50    3.73    --   92.10  82.00   0.00   52
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'XtaLAB AFC12 (RINC): Kappa single'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      -0.0377948000
_diffrn_orient_matrix_UB_12      -0.0257708000
_diffrn_orient_matrix_UB_13      0.0028971000
_diffrn_orient_matrix_UB_21      0.0656605000
_diffrn_orient_matrix_UB_22      -0.0138079000
_diffrn_orient_matrix_UB_23      -0.0298839000
_diffrn_orient_matrix_UB_31      0.0209250000
_diffrn_orient_matrix_UB_32      -0.0032785000
_diffrn_orient_matrix_UB_33      0.1031646000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           'Cu K\a'
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0533
_diffrn_reflns_av_unetI/netI     0.0342
_diffrn_reflns_Laue_measured_fraction_full 0.978
_diffrn_reflns_Laue_measured_fraction_max 0.956
_diffrn_reflns_limit_h_max       24
_diffrn_reflns_limit_h_min       -23
_diffrn_reflns_limit_k_max       65
_diffrn_reflns_limit_k_min       -63
_diffrn_reflns_limit_l_max       17
_diffrn_reflns_limit_l_min       -17
_diffrn_reflns_number            173429
_diffrn_reflns_point_group_measured_fraction_full 0.978
_diffrn_reflns_point_group_measured_fraction_max 0.956
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         73.537
_diffrn_reflns_theta_min         2.254
_diffrn_source                   'Rotating-anode X-ray tube (dual wavelength)'
_diffrn_source_type              'Rigaku (Cu) X-ray DW Source'
_exptl_absorpt_coefficient_mu    8.056
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.36808
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.39.46e (Rigaku Oxford Diffraction, 2018)
Empirical absorption correction using spherical harmonics,
 implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            'clear yellowish yellow'
_exptl_crystal_colour_lustre     clear
_exptl_crystal_colour_modifier   yellowish
_exptl_crystal_colour_primary    yellow
_exptl_crystal_density_diffrn    1.075
_exptl_crystal_description       block
_exptl_crystal_F_000             4728
_exptl_crystal_size_max          0.02
_exptl_crystal_size_mid          0.01
_exptl_crystal_size_min          0.01
_refine_diff_density_max         4.228
_refine_diff_density_min         -2.216
_refine_diff_density_rms         0.250
_refine_ls_extinction_coef       0.00041(5)
_refine_ls_extinction_expression Fc^*^=kFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^
_refine_ls_extinction_method     'SHELXL-2018/3 (Sheldrick 2018)'
_refine_ls_goodness_of_fit_ref   1.546
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     1037
_refine_ls_number_reflns         28355
_refine_ls_number_restraints     357
_refine_ls_restrained_S_all      1.556
_refine_ls_R_factor_all          0.1213
_refine_ls_R_factor_gt           0.1080
_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^)+(0.2000P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.3449
_refine_ls_wR_factor_ref         0.3596
_reflns_Friedel_coverage         0.000
_reflns_number_gt                22853
_reflns_number_total             28355
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d2sc01561g2.cif
_cod_data_source_block           2NBSA@MMF-CHCl3
_cod_database_code               1567106
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         'C H N Cl Pd O S'
_chemical_oxdiff_usercomment     97-4-3
_shelx_estimated_absorpt_t_max   0.924
_shelx_estimated_absorpt_t_min   0.855
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups, All N(H) groups
 At 1.5 times of:
  All C(H,H,H) groups
2. Restrained distances
 C67-C70
 1.45 with sigma of 0.02
 C62-Pd5
 2.8 with sigma of 0.02
 Pd5-C57
 2.8 with sigma of 0.02
 C56-C53
 1.4 with sigma of 0.02
 Pd6-C76
 2.8 with sigma of 0.02
 N10-C62
 1.5 with sigma of 0.02
 Pd6-C71
 2.8 with sigma of 0.02
 C62-C57
 1.4 with sigma of 0.02
 C62-C63
 2.7 with sigma of 0.02
 N9-C57
 1.5 with sigma of 0.02
 C64-C63
 1.45 with sigma of 0.02
 N9-C56
 1.45 with sigma of 0.02
 C63-N10
 1.45 with sigma of 0.02
 C71-N11
 1.5 with sigma of 0.02
 C63-C64
 1.4 with sigma of 0.02
 N10-C63
 1.5 with sigma of 0.02
 C62-N10
 1.5 with sigma of 0.02
 C65-C63 \\sim C63-C69
 with sigma of 0.02
3. Restrained planarity
 C70, C67, C68, C66, C65, C69, C64, C63
 with sigma of 0.1
4. Rigid bond restraints
 C70, C67, C66, C68, C69, C65, C64, C63, N10, N11
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
 C56, C53, C54, C55, C50, C49, C51, C52
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
 Pd3, Cl6, Cl5, Pd1, Cl2, Cl1, Cl4, Cl3, Pd2, Cl7, Pd4, Cl8, Pd6, Cl11, Cl12,
 Pd5, Cl9, Cl10
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
5. Uiso/Uaniso restraints and constraints
N10 \\sim C63 \\sim C62 \\sim Pd5: within 2A with sigma of 0.01 and sigma for
terminal atoms of 0.02 within 2A
C71 \\sim C72 \\sim C73 \\sim C76: within 2A with sigma of 0.001 and sigma for
terminal atoms of 0.002 within 2A
C56 \\sim N9: within 2A with sigma of 0.001 and sigma for terminal atoms of
0.002 within 2A
N9 \\sim C57: within 2A with sigma of 0.0001 and sigma for terminal atoms of
0.0002 within 2A
C65 \\sim C64 \\sim C69 \\sim C68 \\sim C66 \\sim C67 \\sim C70 \\sim C63:
within 2A with sigma of 0.01 and sigma for terminal atoms of 0.02 within 2A
Uanis(C59) \\sim Ueq, Uanis(C58) \\sim Ueq, Uanis(C57) \\sim Ueq, Uanis(C60)
\\sim Ueq, Uanis(C61) \\sim Ueq, Uanis(C62) \\sim Ueq: with sigma of 0.01 and
sigma for terminal atoms of 0.02
Uanis(N9) \\sim Ueq, Uanis(N10) \\sim Ueq: with sigma of 0.001 and sigma for
terminal atoms of 0.002
Uanis(C63) \\sim Ueq, Uanis(C64) \\sim Ueq, Uanis(C69) \\sim Ueq, Uanis(C65)
\\sim Ueq: with sigma of 0.1 and sigma for terminal atoms of 0.2
Uanis(O1G) \\sim Ueq, Uanis(O2G) \\sim Ueq: with sigma of 0.01 and sigma for
terminal atoms of 0.02
6. Rigid body (RIGU) restrains
 C62, C57, C58, C59, C60, C61
 with sigma for 1-2 distances of 0.0001 and sigma for 1-3 distances of 0.0001
 C65, C64, C63, C69, C68, C67, C66
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 N11, N12, C76, C71
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
7. Others
 Fixed Sof: O1G(0.5) O2G(0.5)
8.a Ternary CH refined with riding coordinates:
 N4(H4), N5(H5), N2(H2), N6(H6), N3(H3), N8(H8), N7(H7), N1(H1), N12(H12A),
 N11(H11), N10(H10A), N9(H9A)
8.b Secondary CH2 refined with riding coordinates:
 C21(H21A,H21B), C7(H7A,H7B), C35(H35A,H35B), C42(H42A,H42B), C28(H28A,H28B),
 C14(H14A,H14B), C49(H49A,H49B), C84(H84A,H84B), C77(H77A,H77B), C70(H70A,H70B),
  C56(H56A,H56B), C63(H63A,H63B)
8.c Aromatic/amide H refined with riding coordinates:
 C23(H23), C26(H26), C13(H13), C24(H24), C27(H27), C10(H10), C16(H16), C9(H9),
 C37(H37), C38(H38), C41(H41), C12(H12), C40(H40), C44(H44), C19(H19), C17(H17),
  C18(H18), C2(H2A), C80(H80), C79(H79), C30(H30), C82(H82), C45(H45), C47(H47),
  C33(H33), C31(H31), C83(H83), C46(H46), C3(H3A), C72(H72), C73(H73), C74(H74),
  C75(H75), C5(H5A), C4(H4A), C32(H32), C55(H55), C51(H51), C54(H54), C52(H52),
 C66(H66), C68(H68), C69(H69), C65(H65), C60(H60), C59(H59), C58(H58), C61(H61)
8.d Fitted hexagon refined as free rotating group:
 C76(C71,C72,C73,C74,C75), C66(C67,C68,C69,C64,C65), C60(C59,C58,C57,C62,C61)
8.e Idealised Me refined with riding coordinates:
 C102(H10B,H10C,H10D)
;
_shelx_res_checksum              29583
_olex2_submission_special_instructions 'No special instructions were received'
_oxdiff_exptl_absorpt_empirical_details
;
Empirical correction (ABSPACK) includes:
- Absorption correction using spherical harmonics
- Frame scaling
;
_oxdiff_exptl_absorpt_empirical_full_max 2.565
_oxdiff_exptl_absorpt_empirical_full_min 0.544