Programmable synthesis of organic cages with reduced symmetry.
Andrews, Keith G.; Horton, Peter N.; Coles, Simon J.; Chemical science 15 (2024) 6536–6543; doi:10.1039/d4sc00889h

data_1571316
_publ_section_title
;
 Programmable synthesis of organic cages with reduced symmetry.
;
_journal_issue                   17
_journal_name_full               'Chemical science'
_journal_page_first              6536
_journal_page_last               6543
_journal_paper_doi               10.1039/d4sc00889h
_journal_volume                  15
_journal_year                    2024
_chemical_formula_moiety         'C122 H110 N12 O10, 6[C4H8O2], 9[C4H8O]'
_chemical_formula_sum            'C182 H230 N12 O31'
_chemical_formula_weight         3081.77
_space_group_crystal_system      monoclinic
_space_group_IT_number           7
_space_group_name_Hall           'P -2yac'
_space_group_name_H-M_alt        'P 1 n 1'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     dual
_audit_creation_date             2023-09-08
_audit_creation_method
;
Olex2 1.5
(compiled 2023.08.24 svn.re1ec1418 for OlexSys, GUI svn.r6817)
;
_audit_update_record
;
2023-11-29 deposited with the CCDC.	2024-04-01 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 91.715(2)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   20.2715(6)
_cell_length_b                   42.387(3)
_cell_length_c                   25.2850(7)
_cell_measurement_reflns_used    12561
_cell_measurement_temperature    100(2)
_cell_measurement_theta_max      73.5200
_cell_measurement_theta_min      2.4090
_cell_volume                     21716.4(18)
_computing_cell_refinement       'CrysAlisPro 1.171.41.105a (Rigaku OD, 2021)'
_computing_data_collection       'CrysAlisPro 1.171.41.105a (Rigaku OD, 2021)'
_computing_data_reduction        'CrysAlisPro 1.171.41.105a (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 2018/2 (Sheldrick, 2018)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_temperature      100(2)
_diffrn_detector                 'hybrid pixel array detector'
_diffrn_detector_area_resol_mean 10.0000
_diffrn_detector_dtime           0.000
_diffrn_detector_type            'Rigaku, HyPix 6000HE'
_diffrn_measured_fraction_theta_full 0.593
_diffrn_measured_fraction_theta_max 0.593
_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    -95.00 -18.00   0.50   20.00    --  -46.36 127.00 -88.00  154
  2  \w   -119.00 -64.00   0.50   20.00    --  -46.36-143.00  25.00  110
  3  \w     25.00  95.00   0.50   20.00    --   46.36-127.00-165.00  140
  4  \w     32.00 105.00   0.50   20.00    --   46.36-143.00  25.00  146
  5  \w     70.00 119.00   0.50   20.00    --   46.36 143.00  80.00   98
  6  \w     42.00 107.00   0.50   80.00    --  101.75-127.00-165.00  130
  7  \w    104.00 129.00   0.50   80.00    --  101.75 127.00 -88.00   50
  8  \w     99.00 125.00   0.50   80.00    --  101.75-143.00  25.00   52
  9  \w    128.00 171.00   0.50   80.00    --  101.75 143.00  80.00   86
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_details 'Rigaku, UG2 \k goniometer'
_diffrn_measurement_device_type
'Rigaku 007HF diffractometer equipped with Arc)Sec VHF Varimax confocal mirrors and a UG2 goniometer and HyPix 6000HE detector'
_diffrn_measurement_method       'profile data from \w-scans'
_diffrn_measurement_specimen_support 'MiTeGen MicroLoop'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      -0.0486861000
_diffrn_orient_matrix_UB_12      0.0218952000
_diffrn_orient_matrix_UB_13      -0.0302012000
_diffrn_orient_matrix_UB_21      0.0332178000
_diffrn_orient_matrix_UB_22      0.0289205000
_diffrn_orient_matrix_UB_23      0.0263939000
_diffrn_orient_matrix_UB_31      0.0480572000
_diffrn_orient_matrix_UB_32      0.0022275000
_diffrn_orient_matrix_UB_33      -0.0458866000
_diffrn_radiation_collimation    'Arc)Sec VHF Varimax focusing mirrors'
_diffrn_radiation_monochromator  'Confocal mirrors, Arc)Sec VHF Varimax'
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           'Cu K\a'
_diffrn_radiation_wavelength     1.54178
_diffrn_radiation_xray_symbol    K-L~3~
_diffrn_reflns_av_R_equivalents  0.0420
_diffrn_reflns_av_unetI/netI     0.0370
_diffrn_reflns_Laue_measured_fraction_full 0.593
_diffrn_reflns_Laue_measured_fraction_max 0.593
_diffrn_reflns_limit_h_max       20
_diffrn_reflns_limit_h_min       -15
_diffrn_reflns_limit_k_max       21
_diffrn_reflns_limit_k_min       -21
_diffrn_reflns_limit_l_max       18
_diffrn_reflns_limit_l_min       -25
_diffrn_reflns_number            47982
_diffrn_reflns_point_group_measured_fraction_full 0.304
_diffrn_reflns_point_group_measured_fraction_max 0.304
_diffrn_reflns_theta_full        50.432
_diffrn_reflns_theta_max         50.432
_diffrn_reflns_theta_min         2.417
_diffrn_source                   'Rotating anode'
_diffrn_source_current           30.0
_diffrn_source_power             1.2
_diffrn_source_target            Cu
_diffrn_source_type              'Rigaku 007 HF'
_diffrn_source_voltage           40.0
_exptl_absorpt_coefficient_mu    0.516
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.39482
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.41.105a (Rigaku Oxford Diffraction, 2021)
Empirical absorption correction using spherical harmonics,
implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            colourless
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    0.943
_exptl_crystal_description       plate
_exptl_crystal_F_000             6616
_exptl_crystal_recrystallization_method
'The material was recrystallised by vapour diffusion of n-pentane from a mixture of THF and ethyl acetate'
_exptl_crystal_size_max          0.36
_exptl_crystal_size_mid          0.14
_exptl_crystal_size_min          0.03
_refine_diff_density_max         0.396
_refine_diff_density_min         -0.270
_refine_diff_density_rms         0.045
_refine_ls_abs_structure_details
;
 Classical Flack method preferred over Parsons because s.u. lower.
;
_refine_ls_abs_structure_Flack   -0.2(3)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.070
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     2233
_refine_ls_number_reflns         13807
_refine_ls_number_restraints     5843
_refine_ls_restrained_S_all      1.052
_refine_ls_R_factor_all          0.1101
_refine_ls_R_factor_gt           0.0898
_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          0.2452
_refine_ls_wR_factor_ref         0.2739
_reflns_Friedel_coverage         0.023
_reflns_Friedel_fraction_full    0.013
_reflns_Friedel_fraction_max     0.013
_reflns_number_gt                8716
_reflns_number_total             13807
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d4sc00889h3.cif
_cod_data_source_block           KGAcage2
_cod_depositor_comments
'Adding full bibliography for 1571314--1571316.cif.'
_cod_original_cell_volume        21716.5(18)
_cod_database_code               1571316
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         'C122 H110 N12 O10'
_chemical_oxdiff_usercomment     k51_409
_shelx_estimated_absorpt_t_max   0.985
_shelx_estimated_absorpt_t_min   0.836
_reflns_odcompleteness_completeness 41.83
_reflns_odcompleteness_iscentric 1
_reflns_odcompleteness_theta     69.95
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All N(H) groups
 At 1.5 times of:
  All C(H,H,H) groups
2. Restrained distances
 C50-C49
 1.5 with sigma of 0.02
 O205-C221
 -1.25 with sigma of 0.01
 C100-C102 \\sim C100-C101 \\sim C100-C96 \\sim C102-C101 \\sim C102-C96 \\sim
C101-C96
 with sigma of 0.04
 C99-C100 \\sim C99-C102 \\sim C99-C101 \\sim C99-C96
 with sigma of 0.02
 C26-C32 \\sim C26-C30 \\sim C26-C31 \\sim C32-C30 \\sim C32-C31 \\sim C30-C31
 with sigma of 0.04
 C29-C26 \\sim C29-C32 \\sim C29-C30 \\sim C29-C31
 with sigma of 0.02
 C111-C106 \\sim C111-C110 \\sim C111-C112 \\sim C106-C110 \\sim C106-C112
\\sim C110-C112
 with sigma of 0.04
 C109-C111 \\sim C109-C106 \\sim C109-C110 \\sim C109-C112
 with sigma of 0.02
 C42-C41 \\sim C42-C40 \\sim C41-C40
 with sigma of 0.04
 C39-C42 \\sim C39-C41 \\sim C39-C40
 with sigma of 0.02
 C121-C116 \\sim C121-C120 \\sim C121-C122 \\sim C116-C120 \\sim C116-C122
\\sim C120-C122
 with sigma of 0.04
 C119-C121 \\sim C119-C116 \\sim C119-C120 \\sim C119-C122
 with sigma of 0.02
 C46-C50 \\sim C46-C52 \\sim C46-C51 \\sim C50-C52 \\sim C50-C51 \\sim C52-C51
 with sigma of 0.04
 C49-C46 \\sim C49-C50 \\sim C49-C52 \\sim C49-C51
 with sigma of 0.02
 C236-C241 \\sim C236-C240 \\sim C236-C242 \\sim C241-C240 \\sim C241-C242
\\sim C240-C242
 with sigma of 0.04
 C239-C236 \\sim C239-C241 \\sim C239-C240 \\sim C239-C242
 with sigma of 0.02
 C302-C301 \\sim C302-C296 \\sim C302-C300 \\sim C301-C296 \\sim C301-C300
\\sim C296-C300
 with sigma of 0.04
 C299-C302 \\sim C299-C301 \\sim C299-C296 \\sim C299-C300
 with sigma of 0.02
 C312-C311 \\sim C312-C306 \\sim C312-C310 \\sim C311-C306 \\sim C311-C310
\\sim C306-C310
 with sigma of 0.04
 C309-C312 \\sim C309-C311 \\sim C309-C306 \\sim C309-C310
 with sigma of 0.02
 C232-C226 \\sim C232-C230 \\sim C232-C231 \\sim C230-C231
 with sigma of 0.04
 C229-C232 \\sim C229-C230 \\sim C229-C231
 with sigma of 0.02
 C316-C321 \\sim C316-C322 \\sim C316-C320 \\sim C321-C322 \\sim C321-C320
\\sim C322-C320
 with sigma of 0.04
 C319-C316 \\sim C319-C321 \\sim C319-C322 \\sim C319-C320
 with sigma of 0.02
 C252-C251 \\sim C252-C250 \\sim C252-C246 \\sim C250-C246
 with sigma of 0.04
 C249-C252 \\sim C249-C250 \\sim C249-C246
 with sigma of 0.02
 C246-C252 \\sim C246-C251 \\sim C246-C250 \\sim C252-C251 \\sim C252-C250
\\sim C251-C250
 with sigma of 0.04
 C249-C246 \\sim C249-C252 \\sim C249-C251 \\sim C249-C250
 with sigma of 0.02
 O210-C291 \\sim O209-C291 \\sim O205-C221 \\sim O204-C221 \\sim O4-C21 \\sim
O5-C21 \\sim O10-C91 ~
 O9-C91
 with sigma of 0.04
 O5-O4 \\sim O10-O9 \\sim O210-O209 \\sim O205-O204
 with sigma of 0.06
 C48-C65 \\sim C118-C68 \\sim C62-C108 \\sim C38-C59 \\sim C53-C28 \\sim
C98-C56 \\sim C318-C268 ~
 C265-C248 \\sim C259-C238 \\sim C308-C262 \\sim C253-C228 \\sim C256-C298
 with sigma of 0.02
 N203-C219 \\sim N202-C213 \\sim N201-C207 \\sim N209-C289 \\sim N207-C277
\\sim N208-C283 \\sim N3-
 C19 \\sim N2-C13 \\sim N1-C7 \\sim N9-C89 \\sim N8-C83 \\sim N7-C77
 with sigma of 0.02
 N201-C223 \\sim N202-C233 \\sim N203-C243 \\sim N209-C313 \\sim N208-C303
\\sim N207-C293 \\sim N3-
 C43 \\sim N2-C33 \\sim N1-C23 \\sim N9-C113 \\sim N8-C103 \\sim N7-C93
 with sigma of 0.02
3. Restrained planarity
 O209, O210, C271, C291
 with sigma of 0.01
 O204, O205, C201, C221
 with sigma of 0.01
 O4, O5, C1, C21
 with sigma of 0.01
 O9, O10, C71, C91
 with sigma of 0.01
4. Rigid bond restraints
 All non-hydrogen atoms
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
5. Uiso/Uaniso restraints and constraints
All non-hydrogen atoms have similar U: within 2A with sigma of 0.01 and sigma
for terminal atoms of 0.02 within 2A
6. Rigid body (RIGU) restrains
 All non-hydrogen atoms
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
7.a Ternary CH refined with riding coordinates:
 C2(H2A), C72(H72), C202(H20A), C272(H272)
7.b Me refined with riding coordinates:
 C22(H22A,H22B,H22C), C30(H30A,H30B,H30C), C31(H31A,H31B,H31C), C32(H32A,H32B,
 H32C), C40(H40A,H40B,H40C), C41(H41A,H41B,H41C), C42(H42A,H42B,H42C), C50(H50A,
 H50B,H50C), C51(H51A,H51B,H51C), C52(H52A,H52B,H52C), C92(H92A,H92B,H92C),
 C100(H10A,H10B,H10C), C101(H10D,H10E,H10F), C102(H10G,H10H,H10I), C110(H11A,
 H11B,H11C), C111(H11D,H11E,H11F), C112(H11G,H11H,H11I), C120(H12A,H12B,H12C),
 C121(H12D,H12E,H12F), C122(H12G,H12H,H12I), C222(H22D,H22E,H22F), C230(H23A,
 H23B,H23C), C231(H23D,H23E,H23F), C232(H23G,H23H,H23I), C240(H24A,H24B,H24C),
 C241(H24D,H24E,H24F), C242(H24G,H24H,H24I), C250(H25A,H25B,H25C), C251(H25D,
 H25E,H25F), C252(H25G,H25H,H25I), C292(H29A,H29B,H29C), C300(H30D,H30E,H30F),
 C301(H30G,H30H,H30I), C302(H30J,H30K,H30L), C310(H31D,H31E,H31F), C311(H31G,
 H31H,H31I), C312(H31J,H31K,H31L), C320(H32D,H32E,H32F), C321(H32G,H32H,H32I),
 C322(H32J,H32K,H32L)
7.c Aromatic/amide H refined with riding coordinates:
 N1(H1), N2(H2), N3(H3), N7(H7), N8(H8), N9(H9), C8(H8A), C6(H6), C5(H5),
 C11(H11), C12(H12), C14(H14), C17(H17), C18(H18), C20(H20), C27(H27), C25(H25),
  C37(H37), C35(H35), C45(H45), C47(H47), C54(H54), C55(H55), C57(H57),
 C58(H58), C64(H64), C63(H63), C61(H61), C60(H60), C66(H66), C67(H67), C69(H69),
  C70(H70), C75(H75), C76(H76), C78(H78), C84(H84), C82(H82), C81(H81),
 C90(H90), C88(H88), C87(H87), C95(H95), C97(H97), C107(H107), C105(H105),
 C115(H115), C117(H117), N201(H201), N202(H202), N203(H203), C247(H247),
 C245(H245), N207(H207), N208(H208), N209(H209), C205(H205), C206(H206),
 C208(H20B), C214(H214), C212(H212), C211(H211), C220(H220), C218(H218),
 C217(H217), C225(H225), C227(H227), C235(H235), C237(H237), C254(H254),
 C258(H258), C257(H257), C255(H255), C263(H263), C264(H264), C260(H260),
 C261(H261), C266(H266), C267(H267), C269(H269), C270(H270), C278(H278),
 C276(H276), C275(H275), C281(H281), C282(H282), C284(H284), C290(H290),
 C288(H288), C287(H287), C297(H297), C295(H295), C307(H307), C305(H305),
 C317(H317), C315(H315)
7.d Fitted hexagon refined as free rotating group:
 C3(C8,C7,C6,C5,C4), C9(C10,C11,C12,C13,C14), C15(C16,C17,C18,C19,C20), C24(N4,
 C28,C27,C26,C25), C34(N5,C38,C37,C36,C35), C48(N6,C44,C45,C46,C47), C53(C54,
 C55,C56,C57,C58), C59(C64,C63,C62,C61,C60), C65(C66,C67,C68,C69,C70), C73(C74,
 C75,C76,C77,C78), C79(C84,C83,C82,C81,C80), C85(C90,C89,C88,C87,C86), C94(C95,
 C96,C97,C98,N10), C104(N11,C108,C107,C106,C105), C114(C115,C116,C117,C118,N12),
  N206(C248,C247,C246,C245,C244), C203(C204,C205,C206,C207,C208), C209(C214,
 C213,C212,C211,C210), C215(C220,C219,C218,C217,C216), C224(C225,C226,C227,C228,
 N204), C234(C235,C236,C237,C238,N205), C254(C253,C258,C257,C256,C255),
 C262(C263,C264,C259,C260,C261), C265(C266,C267,C268,C269,C270), C273(C278,C277,
 C276,C275,C274), C279(C280,C281,C282,C283,C284), C285(C290,C289,C288,C287,
 C286), C294(N210,C298,C297,C296,C295), C308(C307,C306,C305,C304,N211),
 C314(N212,C318,C317,C316,C315)
;
_smtbx_masks_special_details
;
A solvent mask was calculated and 2588 electrons were 
found in a volume of 13790\%A^3^ in 1 void per unit cell. 
This is consistent with the presence of 
6[C4H8O2], 9[C4H8O] per Asymmetric Unit 
which account for 2592 electrons 
per unit cell.
;
_smtbx_masks_void_probe_radius   1.2
_smtbx_masks_void_truncation_radius 1.2
_shelx_res_checksum              22663
_shelx_fab_checksum              86974
_olex2_diffrn_ambient_temperature_device 'Oxford Cryosystems'
_olex2_exptl_crystal_mounting_method
'The crystal was mounted on a MITIGEN holder in oil'
_olex2_submission_original_sample_id k51_409
_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
- Detector area scaling
;
_oxdiff_exptl_absorpt_empirical_full_max 1.918
_oxdiff_exptl_absorpt_empirical_full_min 0.535