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_1567104
_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
'C42 H42 Cl6 N6 Pd3, C42 H41 Cl6 N6 Pd3, C2 H3 N, 0.866(O), 0.366(C6 H4 N O5 S)'
_chemical_formula_sum            'C88.2 H87.46 Cl12 N13.37 O2.7 Pd6 S0.37'
_chemical_formula_weight         2453.43
_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             2021-10-18
_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                 90.5870(10)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   19.5405(2)
_cell_length_b                   51.9315(5)
_cell_length_c                   14.31520(10)
_cell_measurement_reflns_used    75684
_cell_measurement_temperature    93
_cell_measurement_theta_max      72.9120
_cell_measurement_theta_min      3.2280
_cell_volume                     14525.8(2)
_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 0.995
_diffrn_measured_fraction_theta_max 0.967
_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     11.00  83.00   0.50    1.20    --    0.00  19.00 120.00  144
  2  \w    -23.00  17.00   0.50    1.20    --    0.00  77.00 150.00   80
  3  \w    -10.00  17.00   0.50    1.20    --    0.00 -57.00 -90.00   54
  4  \w    -19.00  89.00   0.50    1.20    --    0.00  57.00 -60.00  216
  5  \w    -16.00  41.00   0.50    1.20    --    0.00  57.00  60.00  114
  6  \w    -83.00 -57.00   0.50    1.20    --    0.00 -57.00 -90.00   52
  7  \w     14.00 101.00   0.50    4.80    --   92.10 -15.00 -60.00  174
  8  \w     22.00  50.00   0.50    4.80    --   92.10 -45.00-150.00   56
  9  \w    138.00 168.00   0.50    4.80    --   92.10  45.00 -30.00   60
 10  \w     83.00 176.00   0.50    4.80    --   92.10  15.00-180.00  186
 11  \w     70.00 122.00   0.50    4.80    --   92.10 -82.00  90.00  104
 12  \w     83.00 178.00   0.50    4.80    --   92.10  15.00 120.00  190
 13  \w     10.00 122.00   0.50    4.80    --   92.10 -82.00-150.00  224
 14  \w     43.00 116.00   0.50    4.80    --   92.10 -82.00 -30.00  146
 15  \w     12.00 107.00   0.50    4.80    --   92.10 -61.00 -30.00  190
 16  \w     66.00 115.00   0.50    4.80    --   92.10  77.00 -60.00   98
 17  \w     13.00 113.00   0.50    4.80    --   92.10 -61.00-150.00  200
 18  \w     35.00  66.00   0.50    4.80    --   92.10 -82.00  90.00   62
 19  \w      4.00  53.00   0.50    4.80    --   92.10 -15.00-120.00   98
 20  \w     71.00 181.00   0.50    4.80    --   92.10  61.00 -60.00  220
 21  \w      3.00  74.00   0.50    4.80    --   92.10 -77.00 150.00  142
 22  \w     48.00  74.00   0.50    4.80    --   92.10 -15.00-150.00   52
 23  \w     12.00  37.00   0.50    4.80    --   92.10 -15.00-150.00   50
;
_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      -0.0290301000
_diffrn_orient_matrix_UB_12      0.0259442000
_diffrn_orient_matrix_UB_13      -0.0345248000
_diffrn_orient_matrix_UB_21      0.0676124000
_diffrn_orient_matrix_UB_22      0.0133626000
_diffrn_orient_matrix_UB_23      0.0275205000
_diffrn_orient_matrix_UB_31      0.0283084000
_diffrn_orient_matrix_UB_32      -0.0053565000
_diffrn_orient_matrix_UB_33      -0.0981320000
_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  0.0517
_diffrn_reflns_av_unetI/netI     0.0346
_diffrn_reflns_Laue_measured_fraction_full 0.995
_diffrn_reflns_Laue_measured_fraction_max 0.967
_diffrn_reflns_limit_h_max       23
_diffrn_reflns_limit_h_min       -24
_diffrn_reflns_limit_k_max       63
_diffrn_reflns_limit_k_min       -64
_diffrn_reflns_limit_l_max       16
_diffrn_reflns_limit_l_min       -17
_diffrn_reflns_number            168241
_diffrn_reflns_point_group_measured_fraction_full 0.995
_diffrn_reflns_point_group_measured_fraction_max 0.967
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         74.322
_diffrn_reflns_theta_min         2.261
_diffrn_source                   'Rotating-anode X-ray tube (dual wavelength)'
_diffrn_source_type              'Rigaku (Cu) X-ray DW Source'
_exptl_absorpt_coefficient_mu    8.234
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.40031
_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    1.122
_exptl_crystal_description       block
_exptl_crystal_F_000             4871
_exptl_crystal_size_max          0.22
_exptl_crystal_size_mid          0.15
_exptl_crystal_size_min          0.14
_refine_diff_density_max         4.108
_refine_diff_density_min         -1.696
_refine_diff_density_rms         0.238
_refine_ls_extinction_coef       0.00026(4)
_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   1.665
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     1131
_refine_ls_number_reflns         28625
_refine_ls_number_restraints     491
_refine_ls_restrained_S_all      1.670
_refine_ls_R_factor_all          0.1377
_refine_ls_R_factor_gt           0.1209
_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          0.3815
_refine_ls_wR_factor_ref         0.3983
_reflns_Friedel_coverage         0.000
_reflns_number_gt                21899
_reflns_number_total             28625
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d2sc01561g2.cif
_cod_data_source_block           2NBSA@MMF-CH3CN
_cod_original_formula_sum        'C88.20 H87.46 Cl12 N13.37 O2.70 Pd6 S0.37'
_cod_database_code               1567104
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         'C100 H100 N12 Cl12 Pd6 O4 S'
_chemical_oxdiff_usercomment     97-5
_shelx_estimated_absorpt_t_max   0.392
_shelx_estimated_absorpt_t_min   0.265
_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
 1.5 with sigma of 0.02
 C6G-O4G
 2.7 with sigma of 0.02
 S1G-O4G
 1.45 with sigma of 0.02
 O3G-O4G
 2.4 with sigma of 0.02
 O4G-O5G
 2.4 with sigma of 0.02
 N10-C62
 1.7 with sigma of 0.02
 C50-C49
 1.5 with sigma of 0.02
 C2G-C1G = C6G-C5G = C4G-C3G
 1.43 with sigma of 0.02
 C71-N11
 1.55 with sigma of 0.02
 N11-C71
 1.5 with sigma of 0.01
 C62-N10
 1.5 with sigma of 0.02
 C2G-C1G
 1.55 with sigma of 0.02
 C63-N10
 1.55 with sigma of 0.02
 C1G-C6G
 1.55 with sigma of 0.02
 C5G-C4G
 1.55 with sigma of 0.02
 N10-C63
 1.5 with sigma of 0.01
 C4G-C3G
 1.55 with sigma of 0.02
 C2G-C3G
 1.55 with sigma of 0.02
 S1G-C6G
 1.8 with sigma of 0.02
 C6G-O5G
 2.7 with sigma of 0.02
 C6G-O3G
 2.7 with sigma of 0.02
 S1G-O5G
 1.5 with sigma of 0.02
 S1G-O3G
 1.45 with sigma of 0.02
 O3G-O5G
 2.4 with sigma of 0.02
 N9-C57
 1.5 with sigma of 0.02
 Pd06-C62
 2.9 with sigma of 0.02
 Pd06-C57
 2.9 with sigma of 0.02
 C62-C57
 1.4 with sigma of 0.02
 C63-C64
 1.5 with sigma of 0.02
 C64-C63
 1.5 with sigma of 0.01
 Pd06-C63
 -2.7 with sigma of 0.02
 N11-Pd05
 1.9 with sigma of 0.02
 C29-C34
 1.4 with sigma of 0.02
 C1G-S1G \\sim S1G-C5G
 with sigma of 0.02
 C2G-N1G \\sim N1G-C6G
 with sigma of 0.02
 C69-C63 \\sim C63-C65
 with sigma of 0.02
3. Restrained planarity
 S1G, N1G, C1G, C6G, C5G, C4G, C3G, C2G
 with sigma of 0.1
 C1G, N1G, O1G, O2G
 with sigma of 0.1
 C63, C68, C69, C64, C65, C66, C67, C70
 with sigma of 0.1
4. Rigid bond restraints
 Cl9, Pd06, Cl10, Cl11, Cl12, Pd05, Pd04, Cl8, Cl7, Cl3, Pd01, Cl4, Pd03, Cl6,
 Cl5, Cl2, Pd02, Cl1
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
 C62, C61, C60, C57, C58, C59, N9, C56
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 N10
 with sigma for 1-2 distances of 0.00001 and sigma for 1-3 distances of 0.00001
5. Uiso/Uaniso restraints and constraints
C2G \\sim C3G \\sim C1G \\sim C65 \\sim C64 \\sim C62 \\sim C60 \\sim C59 \\sim
C58 \\sim C57: within 2A with sigma of 0.01 and sigma for terminal atoms of
0.02 within 2A
C6 \\sim C1 \\sim C2 \\sim C3 \\sim C4 \\sim C5: within 2A with sigma of 0.001
and sigma for terminal atoms of 0.0002 within 2A
C63 \\sim N10: within 2A with sigma of 0.0005 and sigma for terminal atoms of
0.001 within 2A
N10 \\sim C62 \\sim C57 \\sim C63 \\sim C61 \\sim C60 \\sim C59 \\sim C58 \\sim
N9 \\sim C76 \\sim C71 \\sim C72 \\sim C73 \\sim C74 \\sim C75 \\sim N11 \\sim
N12: within 2A with sigma of 0.001 and sigma for terminal atoms of 0.002 within
2A
C53 \\sim C54 \\sim C55: within 2A with sigma of 0.001 and sigma for terminal
atoms of 0.002 within 2A
Uanis(C63) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(C71) \\sim Ueq, Uanis(C76) \\sim Ueq: with sigma of 0.1 and sigma for
terminal atoms of 0.2
Uanis(C64) \\sim Ueq, Uanis(N10) \\sim Ueq, Uanis(C65) \\sim Ueq: with sigma of
0.01 and sigma for terminal atoms of 0.2
Uanis(C69) \\sim Ueq, Uanis(N10) \\sim Ueq, Uanis(N9) \\sim Ueq, Uanis(C76)
\\sim Ueq: with sigma of 0.001 and sigma for terminal atoms of 0.002
6. Rigid body (RIGU) restrains
 O5G, O3G, O4G
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C53, C56, C50, C49, C70, N11, N12, O4G, S1G, C6G, O3G, O5G, C1G, C5G, C2G,
 N1G, C4G, C3G, O1G, O2G, C63, C64, C65, C66, C67, C70, C68, C69
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
 C72, C73, C74, C75, C70, C76, C71, Cl12, Cl11, Cl8, Cl7
 with sigma for 1-2 distances of 0.0001 and sigma for 1-3 distances of 0.0001
 N10, N8, N7, C62, C61, C60, C59, C58, C57, N9
 with sigma for 1-2 distances of 0.00001 and sigma for 1-3 distances of 0.00001
7. Others
 Sof(O6G)=Sof(C1G)=Sof(C6G)=Sof(C5G)=Sof(H5G)=Sof(C4G)=Sof(H4G)=Sof(C3G)=
 Sof(H3G)=Sof(C2G)=Sof(H2G)=Sof(S1G)=Sof(O1G)=Sof(N1G)=Sof(O2G)=Sof(O4G)=
 Sof(O3G)=Sof(O5G)=FVAR(1)
 Fixed Sof: O7G(0.5)
8.a Ternary CH refined with riding coordinates:
 N4(H4), N5(H5), N2(H2), N3(H3), N6(H6), N7(H7), N1(H1), N8(H8), N12(H12A),
 N11(H11), N9(H9A), N10(H10A)
8.b Secondary CH2 refined with riding coordinates:
 C21(H21A,H21B), C7(H7A,H7B), C42(H42A,H42B), C35(H35A,H35B), C14(H14A,H14B),
 C28(H28A,H28B), 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:
 C26(H26), C40(H40), C23(H23), C16(H16), C27(H27), C10(H10), C13(H13),
 C41(H41), C9(H9), C44(H44), C12(H12), C24(H24), C37(H37), C19(H19), C38(H38),
 C18(H18), C17(H17), C82(H82), C30(H30), C45(H45), C79(H79), C80(H80), C33(H33),
  C2(H2A), C47(H47), C5(H5A), C83(H83), C31(H31), C46(H46), C3(H3A), C32(H32),
 C51(H51), C52(H52), C54(H54), C55(H55), C4(H4A), C66(H66), C68(H68), C69(H69),
 C58(H58), C59(H59), C60(H60), C61(H61), C5G(H5G), C4G(H4G), C3G(H3G), C2G(H2G),
  C72(H72), C73(H73), C74(H74), C75(H75)
8.d Fitted hexagon refined as free rotating group:
 C50(C51,C52,C53,C54,C55), C66(C67,C68,C69,C64,C65), C62(C57,C58,C59,C60,C61),
 C1G(C6G,C5G,C4G,C3G,C2G), C71(C72,C73,C74,C75,C76)
8.e Idealised Me refined with riding coordinates:
 C8G(H8GA,H8GB,H8GC)
;
_shelx_res_checksum              5064
_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 2.255
_oxdiff_exptl_absorpt_empirical_full_min 0.651
_publcif_funding_html
;
;