Supercycloalkanes: dihydropyrazine-embedded macrocycles with flexible conformations resembling cycloalkanes
Qiu, Shuhai; Zhang, Li; Qu, Da-Hui; Wang, Zhaohui; Chemical Science 16 (2025) 20464–20472; doi:10.1039/D5SC06636K

data_1575898
_publ_section_title
;
 Supercycloalkanes: dihydropyrazine-embedded macrocycles with flexible
 conformations resembling cycloalkanes
;
_journal_issue                   43
_journal_name_full               'Chemical Science'
_journal_page_first              20464
_journal_page_last               20472
_journal_paper_doi               10.1039/D5SC06636K
_journal_volume                  16
_journal_year                    2025
_chemical_formula_moiety         'C300 H280 N10, 5(C9 H12)'
_chemical_formula_sum            'C345 H340 N10'
_chemical_formula_weight         4626.25
_chemical_name_systematic        DPP-P
_space_group_crystal_system      orthorhombic
_space_group_IT_number           62
_space_group_name_Hall           '-P 2ac 2n'
_space_group_name_H-M_alt        'P n m a'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     dual
_audit_creation_date             2024-04-26
_audit_creation_method
;
Olex2 1.5
(compiled 2024.02.16 svn.r378c4104 for OlexSys, GUI svn.r6928)
;
_audit_update_record
;
2025-01-18 deposited with the CCDC.	2025-09-26 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   31.155(3)
_cell_length_b                   37.425(4)
_cell_length_c                   33.005(3)
_cell_measurement_reflns_used    9920
_cell_measurement_temperature    193.00
_cell_measurement_theta_max      43.80
_cell_measurement_theta_min      2.66
_cell_volume                     38483(7)
_computing_cell_refinement       'SAINT V8.40B (Bruker, 2019)'
_computing_data_collection       'APEX5 V2023.9-2 (Bruker, 2023)'
_computing_data_reduction        'SAINT V8.40B (Bruker, 2019)'
_computing_molecular_graphics    'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2019/3 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXT 2018/2 (Sheldrick, 2018)'
_diffrn_ambient_temperature      193.00
_diffrn_detector                 CPAD
_diffrn_detector_area_resol_mean 7.41
_diffrn_detector_type            'Bruker PHOTON II'
_diffrn_measured_fraction_theta_full 0.998
_diffrn_measured_fraction_theta_max 0.998
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'Bruker D8 VENTURE MetalJet PHOTON II'
_diffrn_measurement_method       '\w and \f shutterless scans'
_diffrn_measurement_specimen_support 'nylon loop'
_diffrn_radiation_monochromator  'Helios Multi-layer Optic'
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           GaK\a
_diffrn_radiation_wavelength     1.34139
_diffrn_reflns_av_R_equivalents  0.1294
_diffrn_reflns_av_unetI/netI     0.0696
_diffrn_reflns_Laue_measured_fraction_full 0.998
_diffrn_reflns_Laue_measured_fraction_max 0.998
_diffrn_reflns_limit_h_max       27
_diffrn_reflns_limit_h_min       -36
_diffrn_reflns_limit_k_max       42
_diffrn_reflns_limit_k_min       -44
_diffrn_reflns_limit_l_max       37
_diffrn_reflns_limit_l_min       -38
_diffrn_reflns_number            295276
_diffrn_reflns_point_group_measured_fraction_full 0.998
_diffrn_reflns_point_group_measured_fraction_max 0.998
_diffrn_reflns_theta_full        52.097
_diffrn_reflns_theta_max         52.097
_diffrn_reflns_theta_min         1.553
_diffrn_source                   MetalJet
_diffrn_source_current           2.86
_diffrn_source_power             0.19937059999999998
_diffrn_source_type              'Liquid Metal source'
_diffrn_source_voltage           69.71
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    0.218
_exptl_absorpt_correction_T_max  0.7506
_exptl_absorpt_correction_T_min  0.6010
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
SADABS-2016/2 (Bruker,2016/2) was used for absorption correction.
wR2(int) was 0.1525 before and 0.0686 after correction.
The Ratio of minimum to maximum transmission is 0.8007.
The \l/2 correction factor is Not present.
;
_exptl_crystal_density_diffrn    0.798
_exptl_crystal_description       block
_exptl_crystal_F_000             9920
_exptl_crystal_size_max          0.13
_exptl_crystal_size_mid          0.12
_exptl_crystal_size_min          0.1
_refine_diff_density_max         0.369
_refine_diff_density_min         -0.216
_refine_diff_density_rms         0.058
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.080
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     1988
_refine_ls_number_reflns         33309
_refine_ls_number_restraints     3845
_refine_ls_restrained_S_all      1.040
_refine_ls_R_factor_all          0.2219
_refine_ls_R_factor_gt           0.1275
_refine_ls_shift/su_max          0.006
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0400P)^2^+80.0000P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.2731
_refine_ls_wR_factor_ref         0.3138
_reflns_Friedel_coverage         0.000
_reflns_number_gt                12659
_reflns_number_total             33309
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5sc06636k2.cif
_cod_data_source_block           a
_cod_depositor_comments
;
The following automatic conversions were performed:

data item '_diffrn_radiation_probe' value 'X-ray' was changed to
'x-ray' in accordance with the
/home/data/users/saulius/crontab/automatic-downloads/rss-feeds/RSC/lib/dictionaries/cif_core.dic
dictionary named 'cif_core.dic' version 2.4.2 last updated on
2011-04-26.

Automatic conversion script
Id: cif_fix_values 8170 2020-07-09 18:12:32Z antanas 

 Adding full bibliography for 1575895--1575899.cif.
;
_cod_original_cell_volume        38484(6)
_cod_database_code               1575898
_shelx_shelxl_version_number     2019/3
_shelx_estimated_absorpt_t_max   0.978
_shelx_estimated_absorpt_t_min   0.972
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups
 At 1.5 times of:
  All C(H,H,H) groups
2. Restrained distances
 C174-C173 = C169-C170 = C175-C176 = C180-C178 = C168-C163 = C160-C161 = C167-
 C165 = C189-C184 = C188-C186 = C181-C182 = C151-C152 = C154-C159 = C158-C156
 1.5 with sigma of 0.01
 C172-C173 = C172-C170 = C171-C170 = C178-C177 = C176-C177 = C178-C179
 1.39 with sigma of 0.01
 C173-C170
 2.4 with sigma of 0.01
 C172-C171
 2.4 with sigma of 0.01
 C172_$1-C172
 2.4 with sigma of 0.01
 C177-C179 = C178-C176
 2.4 with sigma of 0.01
 C157-C151 \\sim C153-C151
 with sigma of 0.02
 C15A-C10 \\sim C15-C10
 with sigma of 0.02
 C1A-C101 \\sim C102-C101 \\sim C190-C101 \\sim C104-C101 \\sim C1B-C101 \\sim
C103-C101
 with sigma of 0.02
 C191-C105 \\sim C107-C105 \\sim C1C-C105 \\sim C108-C105 \\sim C1D-C105 \\sim
C106-C105
 with sigma of 0.02
 C1E-C147 \\sim C149-C147 \\sim C1F-C147 \\sim C150-C147 \\sim C148-C147 \\sim
C192-C147
 with sigma of 0.02
3. Restrained planarity
 C151, C152, C153, C154, C155, C156, C157, C158, C159
 with sigma of 0.1
4. Uiso/Uaniso restraints and constraints
All non-hydrogen atoms have similar U: within 2A with sigma of 0.02 and sigma
for terminal atoms of 0.04 within 2A
5. Rigid body (RIGU) restrains
 All non-hydrogen atoms
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
6. Same fragment restrains
{C15A, C16A, C17A, C18A} sigma for 1-2: 0.02, 1-3: 0.04
as in
{C15, C16, C17, C18}
{C68A, C69A, C70A, C71A} sigma for 1-2: 0.02, 1-3: 0.04
as in
{C68, C69, C70, C71}
{C81A, C82A, C83A, C84A} sigma for 1-2: 0.02, 1-3: 0.04
as in
{C81, C82, C83, C84}
{C44A, C45A, C46A, C47A} sigma for 1-2: 0.02, 1-3: 0.04
as in
{C44, C45, C46, C47}
7. Others
 Sof(C15A)=Sof(C16A)=Sof(H16D)=Sof(H16E)=Sof(H16F)=Sof(C17A)=Sof(H17D)=
 Sof(H17E)=Sof(H17F)=Sof(C18A)=Sof(H18D)=Sof(H18E)=Sof(H18F)=1-FVAR(1)
 Sof(C15)=Sof(C16)=Sof(H16A)=Sof(H16B)=Sof(H16C)=Sof(C17)=Sof(H17A)=Sof(H17B)=
 Sof(H17C)=Sof(C18)=Sof(H18A)=Sof(H18B)=Sof(H18C)=FVAR(1)
 Sof(C44A)=Sof(C45A)=Sof(H45D)=Sof(H45E)=Sof(H45F)=Sof(C46A)=Sof(H46D)=
 Sof(H46E)=Sof(H46F)=Sof(C47A)=Sof(H47D)=Sof(H47E)=Sof(H47F)=1-FVAR(2)
 Sof(C44)=Sof(C45)=Sof(H45A)=Sof(H45B)=Sof(H45C)=Sof(C46)=Sof(H46A)=Sof(H46B)=
 Sof(H46C)=Sof(C47)=Sof(H47A)=Sof(H47B)=Sof(H47C)=FVAR(2)
 Sof(C68A)=Sof(C69A)=Sof(H69D)=Sof(H69E)=Sof(H69F)=Sof(C70A)=Sof(H70D)=
 Sof(H70E)=Sof(H70F)=Sof(C71A)=Sof(H71D)=Sof(H71E)=Sof(H71F)=1-FVAR(3)
 Sof(C68)=Sof(C69)=Sof(H69A)=Sof(H69B)=Sof(H69C)=Sof(C70)=Sof(H70A)=Sof(H70B)=
 Sof(H70C)=Sof(C71)=Sof(H71A)=Sof(H71B)=Sof(H71C)=FVAR(3)
 Sof(C81A)=Sof(C82A)=Sof(H82D)=Sof(H82E)=Sof(H82F)=Sof(C83A)=Sof(H83D)=
 Sof(H83E)=Sof(H83F)=Sof(C84A)=Sof(H84D)=Sof(H84E)=Sof(H84F)=1-FVAR(4)
 Sof(C81)=Sof(C82)=Sof(H82A)=Sof(H82B)=Sof(H82C)=Sof(C83)=Sof(H83A)=Sof(H83B)=
 Sof(H83C)=Sof(C84)=Sof(H84A)=Sof(H84B)=Sof(H84C)=FVAR(4)
 Sof(C190)=Sof(H19A)=Sof(H19B)=Sof(H19C)=Sof(C1A)=Sof(H1AA)=Sof(H1AB)=
 Sof(H1AC)=Sof(C1B)=Sof(H1BA)=Sof(H1BB)=Sof(H1BC)=1-FVAR(5)
 Sof(C102)=Sof(H10A)=Sof(H10B)=Sof(H10C)=Sof(C103)=Sof(H10D)=Sof(H10E)=
 Sof(H10F)=Sof(C104)=Sof(H10G)=Sof(H10H)=Sof(H10I)=FVAR(5)
 Sof(C191)=Sof(H19D)=Sof(H19E)=Sof(H19F)=Sof(C1C)=Sof(H1CA)=Sof(H1CB)=
 Sof(H1CC)=Sof(C1D)=Sof(H1DA)=Sof(H1DB)=Sof(H1DC)=1-FVAR(6)
 Sof(C106)=Sof(H10J)=Sof(H10K)=Sof(H10L)=Sof(C107)=Sof(H10M)=Sof(H10N)=
 Sof(H10O)=Sof(C108)=Sof(H10P)=Sof(H10Q)=Sof(H10R)=FVAR(6)
 Sof(C192)=Sof(H19G)=Sof(H19H)=Sof(H19I)=Sof(C1E)=Sof(H1EA)=Sof(H1EB)=
 Sof(H1EC)=Sof(C1F)=Sof(H1FA)=Sof(H1FB)=Sof(H1FC)=1-FVAR(7)
 Sof(C148)=Sof(H14A)=Sof(H14B)=Sof(H14C)=Sof(C149)=Sof(H14D)=Sof(H14E)=
 Sof(H14F)=Sof(C150)=Sof(H15A)=Sof(H15B)=Sof(H15C)=FVAR(7)
 Fixed Sof: C151(0.5) H15D(0.5) H15E(0.5) H15F(0.5) C153(0.5) H153(0.5)
 C152(0.5) C157(0.5) H157(0.5) C156(0.5) C155(0.5) H155(0.5) C154(0.5)
 C158(0.5) H15G(0.5) H15H(0.5) H15I(0.5) C159(0.5) H15J(0.5) H15K(0.5)
 H15L(0.5) C160(0.5) H16G(0.5) H16H(0.5) H16I(0.5) C162(0.5) H162(0.5)
 C161(0.5) C166(0.5) H166(0.5) C165(0.5) C164(0.5) H164(0.5) C163(0.5)
 C167(0.5) H16J(0.5) H16K(0.5) H16L(0.5) C168(0.5) H16M(0.5) H16N(0.5)
 H16O(0.5) H17G(0.5) H17H(0.5) H17I(0.5) H17J(0.5) H17K(0.5) H17L(0.5)
 C181(0.5) H18G(0.5) H18H(0.5) H18I(0.5) C182(0.5) C183(0.5) H183(0.5)
 C184(0.5) C185(0.5) H185(0.5) C186(0.5) C187(0.5) H187(0.5) C188(0.5)
 H18J(0.5) H18K(0.5) H18L(0.5) C189(0.5) H18M(0.5) H18N(0.5) H18O(0.5)
8.a Riding coordinates:
 C174(H17G,H17H,H17I)
8.b Aromatic/amide H refined with riding coordinates:
 C4(H4), C9(H9), C11(H11), C19(H19), C20(H20), C22(H22), C30(H30), C32(H32),
 C34(H34), C35(H35), C37(H37), C39(H39), C50(H50), C51(H51), C54(H54), C55(H55),
  C57(H57), C58(H58), C59(H59), C60(H60), C65(H65), C67(H67), C72(H72),
 C73(H73), C78(H78), C80(H80), C91(H91), C93(H93), C95(H95), C96(H96), C98(H98),
  C100(H100), C110(H110), C111(H111), C113(H113), C114(H114), C116(H116),
 C117(H117), C119(H119), C120(H120), C122(H122), C123(H123), C125(H125),
 C126(H126), C131(H131), C132(H132), C134(H134), C141(H141), C143(H143),
 C146(H146), C153(H153), C157(H157), C155(H155), C162(H162), C166(H166),
 C164(H164), C171(H171), C172(H172), C177(H177), C179(H179), C183(H183),
 C185(H185), C187(H187)
8.c Fitted hexagon refined as free rotating group:
 C153(C152,C157,C156,C155,C154), C162(C161,C166,C165,C164,C163), C182(C183,
 C184,C185,C186,C187)
8.d Idealised Me refined as rotating group:
 C1(H1A,H1B,H1C), C23(H23A,H23B,H23C), C24(H24A,H24B,H24C), C41(H41A,H41B,
 H41C), C42(H42A,H42B,H42C), C43(H43A,H43B,H43C), C102(H10A,H10B,H10C),
 C103(H10D,H10E,H10F), C104(H10G,H10H,H10I), C106(H10J,H10K,H10L), C107(H10M,
 H10N,H10O), C108(H10P,H10Q,H10R), C136(H13A,H13B,H13C), C137(H13D,H13E,H13F),
 C138(H13G,H13H,H13I), C148(H14A,H14B,H14C), C149(H14D,H14E,H14F), C150(H15A,
 H15B,H15C), C16(H16A,H16B,H16C), C17(H17A,H17B,H17C), C18(H18A,H18B,H18C),
 C45(H45A,H45B,H45C), C46(H46A,H46B,H46C), C47(H47A,H47B,H47C), C69(H69A,H69B,
 H69C), C70(H70A,H70B,H70C), C71(H71A,H71B,H71C), C82(H82A,H82B,H82C), C83(H83A,
 H83B,H83C), C84(H84A,H84B,H84C), C16A(H16D,H16E,H16F), C17A(H17D,H17E,H17F),
 C18A(H18D,H18E,H18F), C45A(H45D,H45E,H45F), C46A(H46D,H46E,H46F), C47A(H47D,
 H47E,H47F), C69A(H69D,H69E,H69F), C70A(H70D,H70E,H70F), C71A(H71D,H71E,H71F),
 C82A(H82D,H82E,H82F), C83A(H83D,H83E,H83F), C84A(H84D,H84E,H84F), C151(H15D,
 H15E,H15F), C158(H15G,H15H,H15I), C159(H15J,H15K,H15L), C160(H16G,H16H,H16I),
 C167(H16J,H16K,H16L), C168(H16M,H16N,H16O), C169(H16P,H16Q,H16R), C175(H17J,
 H17K,H17L), C180(H18P,H18Q,H18R), C181(H18G,H18H,H18I), C188(H18J,H18K,H18L),
 C189(H18M,H18N,H18O), C190(H19A,H19B,H19C), C1A(H1AA,H1AB,H1AC), C1B(H1BA,H1BB,
 H1BC), C191(H19D,H19E,H19F), C1C(H1CA,H1CB,H1CC), C1D(H1DA,H1DB,H1DC),
 C192(H19G,H19H,H19I), C1E(H1EA,H1EB,H1EC), C1F(H1FA,H1FB,H1FC)
;
_smtbx_masks_void_probe_radius   1.2
_smtbx_masks_void_truncation_radius 1.2
_shelx_res_checksum              23421
_shelx_fab_checksum              12991
_olex2_submission_special_instructions 'No special instructions were received'
_site                            XU