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_1567107
_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_absolute_configuration rmad
_chemical_formula_moiety
'4(C42 H42 Cl6 N6 Pd3), 2(O), C2 H3 N, 0.91(C10 H16)'
_chemical_formula_sum            'C179.1 H185.56 Cl24 N25 O2 Pd12'
_chemical_formula_weight         4847.88
_space_group_crystal_system      monoclinic
_space_group_IT_number           4
_space_group_name_Hall           'P 2yb'
_space_group_name_H-M_alt        'P 1 21 1'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     iterative
_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                 91.6790(10)
_cell_angle_gamma                90
_cell_formula_units_Z            2
_cell_length_a                   14.32050(10)
_cell_length_b                   50.1973(12)
_cell_length_c                   19.4935(3)
_cell_measurement_reflns_used    45829
_cell_measurement_temperature    93
_cell_measurement_theta_max      71.8000
_cell_measurement_theta_min      2.5190
_cell_volume                     14006.9(4)
_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    'olex2.solve 1.5 (Bourhis et al., 2015)'
_diffrn_ambient_temperature      93
_diffrn_detector                 'Hybrid Pixel Array Detector'
_diffrn_detector_area_resol_mean 5.8140
_diffrn_measured_fraction_theta_full 0.998
_diffrn_measured_fraction_theta_max 0.983
_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    -20.00  85.00   0.50    0.61    --    0.00  38.00 -30.00  210
  2  \w    -26.00  73.00   0.50    0.61    --    0.00  38.00-120.00  198
  3  \w    -27.00  -2.00   0.50    0.61    --    0.00  77.00  60.00   50
  4  \w    -19.00   7.00   0.50    0.61    --    0.00 -38.00 150.00   52
  5  \w      7.00  87.00   0.50    0.61    --    0.00  77.00  60.00  160
  6  \w     17.00 125.00   0.50    2.43    --   95.70 -61.00  60.00  216
  7  \w     59.00 104.00   0.50    2.43    --   95.70  82.00-180.00   90
  8  \w      7.00 118.00   0.50    2.43    --   95.70 -77.00  60.00  222
  9  \w     72.00  99.00   0.50    2.43    --   95.70 -82.00  90.00   54
 10  \w    125.00 151.00   0.50    2.43    --   95.70  61.00-120.00   52
 11  \w     76.00 184.00   0.50    2.43    --   95.70  45.00  60.00  216
 12  \w     61.00  87.00   0.50    2.43    --   95.70  77.00-180.00   52
 13  \w     25.00  51.00   0.50    2.43    --   95.70 -77.00-120.00   52
 14  \w     79.00 104.00   0.50    2.43    --   95.70 -82.00 120.00   50
 15  \w     13.00 123.00   0.50    2.43    --   95.70 -15.00  60.00  220
 16  \w     59.00 185.00   0.50    2.43    --   95.70  82.00 150.00  252
 17  \w      8.00 117.00   0.50    2.43    --   95.70 -61.00-180.00  218
 18  \w      6.00  32.00   0.50    2.43    --   95.70 -82.00-120.00   52
 19  \w      6.00 100.00   0.50    2.43    --   95.70 -82.00 -30.00  188
 20  \w     83.00 185.00   0.50    2.43    --   95.70  45.00  30.00  204
 21  \w     61.00 148.00   0.50    2.43    --   95.70  77.00-150.00  174
 22  \w     79.00 105.00   0.50    2.43    --   95.70 -82.00 -90.00   52
 23  \w     11.00 125.00   0.50    2.43    --   95.70 -82.00-180.00  228
;
_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      -0.0032539000
_diffrn_orient_matrix_UB_12      -0.0297605000
_diffrn_orient_matrix_UB_13      -0.0189134000
_diffrn_orient_matrix_UB_21      0.1072799000
_diffrn_orient_matrix_UB_22      -0.0003992000
_diffrn_orient_matrix_UB_23      -0.0036215000
_diffrn_orient_matrix_UB_31      0.0074383000
_diffrn_orient_matrix_UB_32      -0.0074463000
_diffrn_orient_matrix_UB_33      0.0767235000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           'Cu K\a'
_diffrn_radiation_wavelength     1.54187
_diffrn_reflns_av_R_equivalents  0.0849
_diffrn_reflns_av_unetI/netI     0.0631
_diffrn_reflns_Laue_measured_fraction_full 0.998
_diffrn_reflns_Laue_measured_fraction_max 0.983
_diffrn_reflns_limit_h_max       17
_diffrn_reflns_limit_h_min       -17
_diffrn_reflns_limit_k_max       61
_diffrn_reflns_limit_k_min       -61
_diffrn_reflns_limit_l_max       23
_diffrn_reflns_limit_l_min       -23
_diffrn_reflns_number            147264
_diffrn_reflns_point_group_measured_fraction_full 0.987
_diffrn_reflns_point_group_measured_fraction_max 0.958
_diffrn_reflns_theta_full        67.687
_diffrn_reflns_theta_max         72.559
_diffrn_reflns_theta_min         2.268
_diffrn_source                   'Rotating-anode X-ray tube (dual wavelength)'
_diffrn_source_type              'Rigaku (Cu) X-ray DW Source'
_exptl_absorpt_coefficient_mu    8.472
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.33410
_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    1.149
_exptl_crystal_description       block
_exptl_crystal_F_000             4822
_exptl_crystal_size_max          0.05
_exptl_crystal_size_mid          0.02
_exptl_crystal_size_min          0.01
_refine_diff_density_max         4.349
_refine_diff_density_min         -3.053
_refine_diff_density_rms         0.301
_refine_ls_abs_structure_details
;
 Refined as an inversion twin.
;
_refine_ls_abs_structure_Flack   0.23(3)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.795
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     2016
_refine_ls_number_reflns         53297
_refine_ls_number_restraints     2069
_refine_ls_restrained_S_all      1.788
_refine_ls_R_factor_all          0.1966
_refine_ls_R_factor_gt           0.1752
_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          0.4605
_refine_ls_wR_factor_ref         0.4764
_reflns_Friedel_coverage         0.926
_reflns_Friedel_fraction_full    0.975
_reflns_Friedel_fraction_max     0.933
_reflns_number_gt                37640
_reflns_number_total             53297
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d2sc01561g2.cif
_cod_data_source_block           b-pinene@MMF
_cod_original_formula_sum        'C179.10 H185.56 Cl24 N25 O2 Pd12'
_cod_database_code               1567107
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         'C46 H46 N6 Pd3 Cl6'
_chemical_oxdiff_usercomment     1802
_shelx_estimated_absorpt_t_max   0.920
_shelx_estimated_absorpt_t_min   0.677
_olex2_refinement_description
;
1. Twinned data refinement
 Scales: 0.77(3)
 0.23(3)
2. 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
3. Restrained distances
 Pd8-N16
 2.1 with sigma of 0.02
 C5G-C4G
 1.5 with sigma of 0.02
 C4G-C9G
 1.5 with sigma of 0.02
 C3G-C4G
 1.5 with sigma of 0.02
 C7G-C6G
 1.5 with sigma of 0.02
 N7-Pd4
 2 with sigma of 0.02
 C6G-C10G
 1.5 with sigma of 0.02
 C8G-C7G
 1.5 with sigma of 0.02
 C43-N7
 1.5 with sigma of 0.02
 C10G-C3G
 1.5 with sigma of 0.02
 C3G-C2G
 1.5 with sigma of 0.02
 N7-C84
 1.5 with sigma of 0.02
 C2G-C8G
 1.5 with sigma of 0.02
 C80-C84
 1.5 with sigma of 0.02
 C4G-C6G
 1.5 with sigma of 0.02
 C2G-C1G
 1.4 with sigma of 0.02
 C6G-C3G
 -2.1 with sigma of 0.02
 C141-N21
 1.5 with sigma of 0.02
 C140-N21
 1.5 with sigma of 0.02
 N21-Pd11
 2 with sigma of 0.02
 C7-N2
 1.5 with sigma of 0.02
 N2-C6
 1.5 with sigma of 0.02
 N2-Pd1
 2.8 with sigma of 0.02
 C8-C7
 1.4 with sigma of 0.02
 Pd1-N2
 2 with sigma of 0.02
 C120-C119
 1.4 with sigma of 0.02
 C133-C134
 1.4 with sigma of 0.02
 C132-N20
 1.5 with sigma of 0.02
 C148-C147
 1.5 with sigma of 0.02
 C128-H15B
 -2 with sigma of 0.02
 C133-N20
 1.5 with sigma of 0.02
 N16-C105
 1.5 with sigma of 0.02
 C151-C154
 1.4 with sigma of 0.02
 N23-C154
 1.5 with sigma of 0.02
 N14-C91
 1.5 with sigma of 0.02
 C98-N15
 1.5 with sigma of 0.02
 C95-C98
 1.4 with sigma of 0.02
 C91-C92
 1.4 with sigma of 0.02
 C150-C154 \\sim C154-C152
 with sigma of 0.01
4. Restrained planarity
 C91, C92, C97, C93, C96, C94, C95, C98
 with sigma of 0.1
 C154, C151, C152, C153, C148, C149, C150, C147
 with sigma of 0.01
5. Rigid bond restraints
 C12, N3, C7, C3, C2, C47, C77, C76, Cl8, Cl7, N4
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
 C47, C76, C77
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
6. Uiso/Uaniso restraints and constraints
N1 \\sim C1 \\sim N2 \\sim C6 \\sim C102 \\sim C103 \\sim C104 \\sim C99 \\sim
C100 \\sim C101: within 2A with sigma of 0.001 and sigma for terminal atoms of
0.002 within 2A
Uanis(O3G) \\sim Ueq, Uanis(O1G) \\sim Ueq, Uanis(O2G) \\sim Ueq, Uanis(O3H)
\\sim Ueq: with sigma of 0.001 and sigma for terminal atoms of 0.002
Uanis(N3) \\sim Ueq, Uanis(C15) \\sim Ueq, Uanis(C18) \\sim Ueq, Uanis(C17)
\\sim Ueq, Uanis(C16) \\sim Ueq, Uanis(C19) \\sim Ueq, Uanis(C20) \\sim Ueq,
Uanis(N4) \\sim Ueq, Uanis(C28) \\sim Ueq, Uanis(N5) \\sim Ueq, Uanis(C29)
\\sim Ueq, Uanis(C34) \\sim Ueq, Uanis(N6) \\sim Ueq: with sigma of 0.01 and
sigma for terminal atoms of 0.02
Uanis(C21) \\sim Ueq, Uanis(C24) \\sim Ueq, Uanis(C26) \\sim Ueq, Uanis(C27)
\\sim Ueq, Uanis(C25) \\sim Ueq, Uanis(C23) \\sim Ueq, Uanis(C22) \\sim Ueq,
Uanis(C7) \\sim Ueq, Uanis(C8) \\sim Ueq, Uanis(C9) \\sim Ueq, Uanis(C10) \\sim
Ueq, Uanis(C11) \\sim Ueq, Uanis(C12) \\sim Ueq, Uanis(C14) \\sim Ueq: with
sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(N1G) \\sim Ueq, Uanis(C11G) \\sim Ueq, Uanis(C12G) \\sim Ueq, Uanis(C42)
\\sim Ueq, Uanis(C39) \\sim Ueq: with sigma of 0.01 and sigma for terminal
atoms of 0.02
Uanis(C77) \\sim Ueq, Uanis(C50) \\sim Ueq, Uanis(C48) \\sim Ueq, Uanis(C57)
\\sim Ueq, Uanis(C62) \\sim Ueq, Uanis(C76) \\sim Ueq, Uanis(C67) \\sim Ueq,
Uanis(C68) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
7. Rigid body (RIGU) restrains
 O1G, O2G
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C1G, C10G, C6G, C3G, C4G, C7G, C2G, C5G, C9G, C8G, C11G, N1G, C12G
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
 C127, Pd12, N23, N24, Cl24, Cl23, C155, C154, C161, C160, C156, C151, C162,
 C159, C157, C152, C150, C163, C167, C158, C153, C149, C164, C166, C148, C165,
 C147, C168, N22, N19, Pd11, C146, Pd10, Cl21, Cl22, N21, C141, C145, Cl20,
 Cl19, N20, C132, C128, C140, C142, C144, C133, C131, C129, C137, C143, C134,
 C130, C138, C136, C139, C135
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
 C86, Pd7, N13, N14, Cl14, Cl13, C85, C126, C90, C91, C123, C89, C92, C87,
 C124, C122, C88, C97, C93, C125, C121, C96, C94, C120, C95, C119, C98, N18,
 N15, Pd9, C118, Pd8, C99, Cl17, Cl18, N17, C113, C117, Cl16, Cl15, N16, C100,
 C104, C112, C114, C116, C105, C101, C103, C109, C115, C106, C102, C108, C110,
 C107, C111
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
 C73, Pd4, N7, N8, Cl8, Cl7, C84, C43, C49, C48, C80, C44, C50, C47, C81, C83,
 C45, C55, C51, C46, C79, C82, C54, C52, C78, C53, C77, C56, N12, N9, Pd6, C76,
 Pd5, C57, N11, Cl12, Cl11, C75, C71, N10, Cl9, Cl10, C62, C58, C70, C74, C72,
 C63, C61, C59, C67, C64, C60, C66, C68, C69, C65
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
 C25, C27, C26, C24, C22, C23, C34, C29, C30, C31, C32, N6, C33, N5, C6, C1,
 C2, C3, C4, C5, C39, C38, C37, C36, C41, C40, C14, C11, C12, C13, C8, C9, C10
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
8. Others
 Sof(O3H)=1-FVAR(1)
 Sof(C10G)=Sof(H10D)=Sof(H10E)=Sof(C4G)=Sof(C5G)=Sof(H5GA)=Sof(H5GB)=Sof(H5GC)=
 Sof(C6G)=Sof(H6G)=Sof(O3G)=Sof(C3G)=Sof(H3G)=Sof(C9G)=Sof(H9GA)=Sof(H9GB)=
 Sof(H9GC)=Sof(C2G)=Sof(C7G)=Sof(H7GA)=Sof(H7GB)=Sof(C8G)=Sof(H8GA)=Sof(H8GB)=
 Sof(C1G)=Sof(H1GA)=Sof(H1GB)=FVAR(1)
 Fixed Sof: O2G(0.5) O1G(0.5)
9.a Ternary CH refined with riding coordinates:
 N6(H6), N9(H9A), N1(H1), N2(H2), N5(H5), N23(H23A), N11(H11), N24(H24),
 N12(H12A), N13(H13C), N3(H3), N14(H14), N10(H10A), N8(H8), N19(H19A),
 N17(H17A), N18(H18A), N20(H20), N22(H22A), N4(H4A), N15(H15), N16(H16E),
 N7(H7), C6G(H6G), C3G(H3G), N21(H21)
9.b Secondary CH2 refined with riding coordinates:
 C21(H21A,H21B), C35(H35A,H35B), C42(H42A,H42B), C56(H56A,H56B), C161(H16A,
 H16B), C7(H7A,H7B), C70(H70A,H70B), C91(H91A,H91B), C84(H84A,H84B), C77(H77A,
 H77B), C49(H49A,H49B), C28(H28A,H28B), C14(H14A,H14B), C154(H15A,H15B),
 C119(H11A,H11B), C63(H63A,H63B), C126(H12B,H12C), C112(H11C,H11D), C140(H14C,
 H14D), C168(H16C,H16D), C133(H13A,H13B), C147(H14E,H14F), C98(H98A,H98B),
 C105(H10B,H10C), C10G(H10D,H10E), C7G(H7GA,H7GB), C8G(H8GA,H8GB)
9.c Aromatic/amide H refined with riding coordinates:
 C128(H128), C129(H129), C130(H130), C131(H131), C54(H54), C38(H38), C51(H51),
 C30(H30), C66(H66), C65(H65), C69(H69), C68(H68), C22(H22), C2(H2A), C3(H3A),
 C4(H4), C5(H5A), C26(H26), C19(H19), C18(H18), C17(H17), C16(H16), C72(H72),
 C73(H73), C74(H74), C75(H75), C23(H23), C41(H41), C33(H33), C124(H124),
 C156(H156), C157(H157), C158(H158), C159(H159), C86(H86), C31(H31), C37(H37),
 C40(H40), C87(H87), C32(H32), C125(H125), C52(H52), C59(H59), C164(H164),
 C166(H166), C167(H167), C163(H163), C58(H58), C12(H12), C13(H13), C9(H9),
 C10(H10), C60(H60), C44(H44), C79(H79), C81(H81), C83(H83), C82(H82), C61(H61),
  C46(H46), C88(H88), C27(H27), C122(H122), C45(H45), C149(H149), C153(H153),
 C152(H152), C150(H150), C97(H97), C96(H96), C94(H94), C93(H93), C121(H121),
 C145(H145), C144(H144), C143(H143), C142(H142), C89(H89), C47(H47), C55(H55),
 C107(H107), C108(H108), C110(H110), C111(H111), C117(H117), C116(H116),
 C115(H115), C114(H114), C100(H100), C101(H101), C102(H102), C103(H103),
 C138(H138), C139(H139), C135(H135), C136(H136)
9.d Fitted hexagon refined as free rotating group:
 C132(C127,C128,C129,C130,C131), C66(C65,C64,C69,C68,C67), C1(C2,C3,C4,C5,C6),
 C15(C20,C19,C18,C17,C16), C76(C71,C72,C73,C74,C75), C160(C155,C156,C157,C158,
 C159), C164(C165,C166,C167,C162,C163), C12(C13,C8,C9,C10,C11), C79(C81,C80,C83,
 C82,C78), C149(C148,C153,C152,C151,C150), C92(C97,C96,C95,C94,C93), C141(C146,
 C145,C144,C143,C142), C106(C107,C108,C109,C110,C111), C113(C118,C117,C116,C115,
 C114), C100(C101,C102,C103,C104,C99), C137(C138,C139,C134,C135,C136)
9.e X=CH2 refined with riding coordinates:
 C1G(H1GA,H1GB)
9.f Idealised Me refined with riding coordinates:
 C12G(H12D,H12E,H12F), C5G(H5GA,H5GB,H5GC), C9G(H9GA,H9GB,H9GC)
;
_shelx_res_checksum              75366
_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 2.694
_oxdiff_exptl_absorpt_empirical_full_min 0.467