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_1567105
_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), 3.25(C H Cl3), C2 H3 N, 2(O)'
_chemical_formula_sum            'C89.25 H90.25 Cl21.75 N13 O2 Pd6'
_chemical_formula_weight         2786.43
_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             2021-10-07
_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                 90.7060(10)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   19.4857(2)
_cell_length_b                   51.8380(7)
_cell_length_c                   14.31670(10)
_cell_measurement_reflns_used    68278
_cell_measurement_temperature    93
_cell_measurement_theta_max      72.9800
_cell_measurement_theta_min      2.8720
_cell_volume                     14460.2(3)
_computing_cell_refinement       'CrysAlisPro 1.171.41.104a (Rigaku OD, 2021)'
_computing_data_collection       'CrysAlisPro 1.171.41.104a (Rigaku OD, 2021)'
_computing_data_reduction        'CrysAlisPro 1.171.41.104a (Rigaku OD, 2021)'
_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)'
_computing_structure_solution    'SHELXT 2014/5 (Sheldrick, 2014)'
_diffrn_ambient_temperature      93
_diffrn_detector_area_resol_mean 5.8140
_diffrn_measured_fraction_theta_full 0.993
_diffrn_measured_fraction_theta_max 0.971
_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    -69.00  20.00   0.50    0.61    --    0.00 -77.00  30.00  178
  2  \w    -17.00   9.00   0.50    0.61    --    0.00  77.00 150.00   52
  3  \w    -73.00  16.00   0.50    0.61    --    0.00 -38.00 120.00  178
  4  \w    -64.00  14.00   0.50    0.61    --    0.00 -57.00 -90.00  156
  5  \w      5.00 110.00   0.50    2.46    --   93.00 -61.00-150.00  210
  6  \w      9.00 118.00   0.50    2.46    --   93.00 -77.00  90.00  218
  7  \w     64.00 180.00   0.50    2.46    --   93.00  76.00 -35.89  232
  8  \w     82.00 181.00   0.50    2.46    --   93.00  45.00  30.00  198
  9  \w     75.00 182.00   0.50    2.46    --   93.00  45.00  60.00  214
 10  \w     62.00  87.00   0.50    2.46    --   93.00  82.00 -90.00   50
 11  \w     29.00 110.00   0.50    2.46    --   93.00 -82.00-150.00  162
 12  \w      6.00  89.00   0.50    2.46    --   93.00 -45.00 -60.00  166
 13  \w     10.00 116.00   0.50    2.46    --   93.00 -61.00 -60.00  212
 14  \w     64.00  89.00   0.50    2.46    --   93.00  77.00 -60.00   50
 15  \w     89.00 115.00   0.50    2.46    --   93.00  30.00 -60.00   52
 16  \w    114.00 165.00   0.50    2.46    --   93.00  30.00  90.00  102
 17  \w    136.00 162.00   0.50    2.46    --   93.00  30.00 -60.00   52
 18  \w     64.00 180.00   0.50    2.46    --   93.00  77.00 -90.00  232
 19  \w     63.00 107.00   0.50    2.46    --   93.00  82.00 -60.00   88
 20  \w     70.00 178.00   0.50    2.46    --   93.00  63.00 -48.65  216
 21  \w     79.00 104.00   0.50    2.46    --   93.00 -82.00-180.00   50
 22  \w     77.00 110.00   0.50    2.46    --   93.00 -82.00 -75.87   66
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'XtaLAB AFC12 (RINC): Kappa single'
_diffrn_measurement_method       '\w scans'
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54187
_diffrn_reflns_av_R_equivalents  0.0971
_diffrn_reflns_av_unetI/netI     0.0547
_diffrn_reflns_Laue_measured_fraction_full 0.993
_diffrn_reflns_Laue_measured_fraction_max 0.971
_diffrn_reflns_limit_h_max       23
_diffrn_reflns_limit_h_min       -23
_diffrn_reflns_limit_k_max       60
_diffrn_reflns_limit_k_min       -63
_diffrn_reflns_limit_l_max       17
_diffrn_reflns_limit_l_min       -17
_diffrn_reflns_number            175959
_diffrn_reflns_point_group_measured_fraction_full 0.993
_diffrn_reflns_point_group_measured_fraction_max 0.971
_diffrn_reflns_theta_full        67.687
_diffrn_reflns_theta_max         73.384
_diffrn_reflns_theta_min         2.268
_exptl_absorpt_coefficient_mu    9.899
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.08262
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.41.104a (Rigaku Oxford Diffraction, 2021)
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    1.280
_exptl_crystal_description       block
_exptl_crystal_F_000             5514
_exptl_crystal_size_max          0.02
_exptl_crystal_size_mid          0.01
_exptl_crystal_size_min          0.01
_refine_diff_density_max         3.142
_refine_diff_density_min         -1.949
_refine_diff_density_rms         0.208
_refine_ls_extinction_coef       0.000110(19)
_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   1.084
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     1262
_refine_ls_number_reflns         28222
_refine_ls_number_restraints     368
_refine_ls_restrained_S_all      1.082
_refine_ls_R_factor_all          0.1527
_refine_ls_R_factor_gt           0.1322
_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^)+(0.1458P)^2^+256.2788P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.3489
_refine_ls_wR_factor_ref         0.3637
_reflns_Friedel_coverage         0.000
_reflns_number_gt                21454
_reflns_number_total             28222
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d2sc01561g2.cif
_cod_data_source_block           terpinolene@MMF
_cod_database_code               1567105
_shelx_shelxl_version_number     2018/3
_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
 Pd2-C20
 2.88 with sigma of 0.02
 C6G-Cl15
 1.7 with sigma of 0.02
 Pd2-C15
 2.88 with sigma of 0.02
 C6G-Cl14
 1.7 with sigma of 0.02
 C6G-Cl16
 1.7 with sigma of 0.02
 Pd5-C57
 2.88 with sigma of 0.02
 Pd5-C62
 2.88 with sigma of 0.02
 Cl14-Cl15
 2.7 with sigma of 0.02
 N9-C57
 1.5 with sigma of 0.02
 Cl14-Cl16
 2.7 with sigma of 0.02
 N10-Pd5
 2 with sigma of 0.02
 Cl15-Cl16
 2.7 with sigma of 0.02
 N9-Pd5
 2 with sigma of 0.02
 C62-N10
 1.5 with sigma of 0.02
 N10-C63
 1.5 with sigma of 0.02
 C63-C64
 1.5 with sigma of 0.02
 C3G-Cl3G
 1.7 with sigma of 0.02
 C3G-Cl1G
 1.7 with sigma of 0.02
 Cl2G-C3G
 1.7 with sigma of 0.02
 C4G-Cl6G
 1.7 with sigma of 0.02
 C8G-Cl19
 1.7 with sigma of 0.02
 C4G-Cl21
 1.7 with sigma of 0.02
 Cl7G-C5G
 1.7 with sigma of 0.02
 C4G-Cl4G
 1.7 with sigma of 0.02
 C5G-Cl9G
 1.7 with sigma of 0.02
 C8G-Cl18
 1.7 with sigma of 0.02
 C8G-Cl17
 1.7 with sigma of 0.02
 C5G-Cl8G
 1.7 with sigma of 0.02
 Cl1B-C7G
 1.7 with sigma of 0.02
 C7G-Cl1A
 1.7 with sigma of 0.02
 Cl13-C7G
 1.7 with sigma of 0.02
 Cl1A-Cl13
 2.7 with sigma of 0.02
 Cl1B-Cl1A
 2.7 with sigma of 0.02
 Cl13-Cl1B
 2.7 with sigma of 0.02
3. Rigid bond restraints
 C6, C1
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
4. Uiso/Uaniso restraints and constraints
O3G \\sim O1G \\sim O2G: within 2A with sigma of 0.001 and sigma for terminal
atoms of 0.02 within 2A
N2 \\sim C6 \\sim C5 \\sim C4 \\sim C3 \\sim C2 \\sim C1 \\sim N1: within 2A
with sigma of 0.001 and sigma for terminal atoms of 0.002 within 2A
Uanis(C76) \\sim Ueq, Uanis(N12) \\sim Ueq, Uanis(N10) \\sim Ueq, Uanis(C62)
\\sim Ueq, Uanis(N9) \\sim Ueq: with sigma of 0.1 and sigma for terminal atoms
of 0.2
Uanis(N11) \\sim Ueq, Uanis(N12) \\sim Ueq: with sigma of 0.01 and sigma for
terminal atoms of 0.01
Uanis(C59) \\sim Ueq, Uanis(C60) \\sim Ueq, Uanis(C61) \\sim Ueq, Uanis(C62)
\\sim Ueq, Uanis(C57) \\sim Ueq, Uanis(C58) \\sim Ueq: with sigma of 0.05 and
sigma for terminal atoms of 0.1
Uanis(O2G) \\sim Ueq, Uanis(O1G) \\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 0.01 and sigma for
terminal atoms of 0.02
5. Rigid body (RIGU) restrains
 C72, C71, C76, C75, C74, C73
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C60, C61, C62, C57, C58, C59, N10, N9, C63, C56, C7G, Cl1A
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
 C5G, Cl9G, Cl18, C8G, Cl14, C6G, C2G, O1G, Cl13, Cl1A, Cl16, Cl1B, N1G, C3G,
 Cl2G, Cl21, Cl7G, Cl4G, O3G, Cl6G, Cl15, C7G, Cl17, Cl3G, C1G, Cl8G, Cl1G, C4G,
  Cl19
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 Cl15, C6G, Cl18, Cl16, Cl1A, C8G, Cl3G, Cl21, Cl7G, O2G, Cl13, C4G, O3G, C2G,
 Cl14, O1G, Cl2G, Cl4G, Cl17, Cl19, C3G, C5G, Cl1B, Cl1G, C7G, N1G, Cl6G, Cl8G,
 Cl9G, C1G
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
6. Others
 Fixed Sof: Cl21(0.5) Cl4G(0.5) Cl6G(0.5) Cl8G(0.5) Cl9G(0.5) Cl7G(0.5)
 Cl13(0.5) Cl14(0.25) Cl15(0.25) Cl16(0.25) Cl17(0.5) Cl18(0.5) Cl19(0.5)
 C4G(0.5) H4G(0.5) C5G(0.5) H5G(0.5) C8G(0.5) H8G(0.5) C6G(0.25) H6G(0.25)
 O1G(0.5) Cl1A(0.5) Cl1B(0.5) C7G(0.5) H7G(0.5) O2G(0.5)
7.a Ternary CH refined with riding coordinates:
 N6(H6), N4(H4), N1(H1), N8(H8), N2(H2), N7(H7), N3(H3), N019(H019), N12(H12A),
  N11(H11), N9(H9A), N10(H10A), C3G(H3G), C4G(H4G), C5G(H5G), C8G(H8G),
 C6G(H6G), C7G(H7G)
7.b Secondary CH2 refined with riding coordinates:
 C35(H35A,H35B), C14(H14A,H14B), C21(H21A,H21B), C7(H7A,H7B), C42(H42A,H42B),
 C84(H84A,H84B), C28(H28A,H28B), C77(H77A,H77B), C49(H49A,H49B), C70(H70A,H70B),
  C56(H56A,H56B), C63(H63A,H63B)
7.c Aromatic/amide H refined with riding coordinates:
 C75(H75), C74(H74), C73(H73), C72(H72), C26(H26), C37(H37), C23(H23),
 C38(H38), C40(H40), C24(H24), C27(H27), C41(H41), C30(H30), C12(H12), C3(H3A),
 C13(H13), C45(H45), C2(H2A), C44(H44), C16(H16), C17(H17), C18(H18), C19(H19),
 C10(H10), C33(H33), C9(H9), C32(H32), C80(H80), C31(H31), C47(H47), C5(H5),
 C82(H82), C46(H46), C83(H83), C79(H79), C4(H4A), C55(H55), C51(H51), C52(H52),
 C54(H54), C69(H69), C68(H68), C61(H61), C60(H60), C59(H59), C58(H58), C66(H66),
  C65(H65)
7.d Fitted hexagon refined as free rotating group:
 C71(C76,C75,C74,C73,C72), C20(C15,C16,C17,C18,C19), C57(C62,C61,C60,C59,C58)
7.e Idealised Me refined with riding coordinates:
 C2G(H2GA,H2GB,H2GC)
;
_shelx_res_checksum              75592
_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
;