Reverse Turn and Loop Secondary Structures in Stereodefined Cyclic Peptoid Scaffolds.
D'Amato, Assunta; Pierri, Giovanni; Tedesco, Consiglia; Della Sala, Giorgio; Izzo, Irene; Costabile, Chiara; De Riccardis, Francesco; The Journal of organic chemistry 84 (2019) 10911–10928; doi:10.1021/acs.joc.9b01509

data_4033871
_publ_section_title
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 Reverse Turn and Loop Secondary Structures in Stereodefined Cyclic
 Peptoid Scaffolds.
;
_journal_issue                   17
_journal_name_full               'The Journal of organic chemistry'
_journal_page_first              10911
_journal_page_last               10928
_journal_paper_doi               10.1021/acs.joc.9b01509
_journal_volume                  84
_journal_year                    2019
_chemical_absolute_configuration syn
_chemical_formula_moiety         'C38 H40 N4 O4'
_chemical_formula_sum            'C38 H40 N4 O4'
_chemical_formula_weight         616.74
_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
_audit_creation_date             2019-01-22
_audit_creation_method
;
Olex2 1.2
(compiled 2018.05.29 svn.r3508 for OlexSys, GUI svn.r5506)
;
_cell_angle_alpha                90
_cell_angle_beta                 93.945(12)
_cell_angle_gamma                90
_cell_formula_units_Z            2
_cell_length_a                   8.9528(11)
_cell_length_b                   11.419(3)
_cell_length_c                   15.863(2)
_cell_measurement_reflns_used    9904
_cell_measurement_temperature    296(2)
_cell_measurement_theta_max      73.72
_cell_measurement_theta_min      2.80
_cell_volume                     1617.9(5)
_computing_cell_refinement       'Bruker SAINT'
_computing_data_collection       'Bruker APEX2'
_computing_data_reduction        'Bruker SAINT'
_computing_molecular_graphics    'Olex2 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL-2014 (Sheldrick 2014)'
_computing_structure_solution    'SHELXS-97 (Sheldrick 2008)'
_diffrn_ambient_temperature      296.15
_diffrn_measured_fraction_theta_full 0.982
_diffrn_measured_fraction_theta_max 0.951
_diffrn_measurement_device_type  'Bruker APEX-II CCD'
_diffrn_measurement_method       '\f and \w scans'
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54178
_diffrn_reflns_av_R_equivalents  0.0406
_diffrn_reflns_av_unetI/netI     0.0253
_diffrn_reflns_Laue_measured_fraction_full 0.982
_diffrn_reflns_Laue_measured_fraction_max 0.951
_diffrn_reflns_limit_h_max       9
_diffrn_reflns_limit_h_min       -10
_diffrn_reflns_limit_k_max       14
_diffrn_reflns_limit_k_min       -14
_diffrn_reflns_limit_l_max       19
_diffrn_reflns_limit_l_min       -19
_diffrn_reflns_number            34032
_diffrn_reflns_point_group_measured_fraction_full 0.982
_diffrn_reflns_point_group_measured_fraction_max 0.934
_diffrn_reflns_theta_full        67.679
_diffrn_reflns_theta_max         74.970
_diffrn_reflns_theta_min         2.792
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    0.661
_exptl_absorpt_correction_T_max  0.7538
_exptl_absorpt_correction_T_min  0.6994
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
SADABS-2014/5 (Bruker,2014/5) was used for absorption correction.
wR2(int) was 0.1401 before and 0.0611 after correction.
The Ratio of minimum to maximum transmission is 0.9278.
The \l/2 correction factor is Not present.
;
_exptl_crystal_colour            colorless
_exptl_crystal_density_diffrn    1.266
_exptl_crystal_description       prism
_exptl_crystal_F_000             656
_exptl_crystal_size_max          0.46
_exptl_crystal_size_mid          0.12
_exptl_crystal_size_min          0.06
_refine_diff_density_max         0.174
_refine_diff_density_min         -0.163
_refine_diff_density_rms         0.026
_refine_ls_abs_structure_details
;
 Flack x determined using 2189 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   -0.02(8)
_refine_ls_extinction_coef       0.0121(15)
_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   1.015
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     470
_refine_ls_number_reflns         6225
_refine_ls_number_restraints     97
_refine_ls_restrained_S_all      1.013
_refine_ls_R_factor_all          0.0513
_refine_ls_R_factor_gt           0.0420
_refine_ls_shift/su_max          0.000
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0554P)^2^+0.2517P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1052
_refine_ls_wR_factor_ref         0.1116
_reflns_Friedel_coverage         0.865
_reflns_Friedel_fraction_full    0.981
_reflns_Friedel_fraction_max     0.914
_reflns_number_gt                5364
_reflns_number_total             6225
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            jo9b01509_si_002.cif
_cod_data_source_block           tbe243_1_a
_cod_original_cell_volume        1617.8(5)
_cod_database_code               4033871
_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
 At 1.5 times of:
  All C(H,H,H) groups
2. Rigid bond restraints
 C9B, C7B, C8B, C10B, C6B, C5B
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 C6A, C5A, C10A, C7A, C8A, C9A
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
3. Uiso/Uaniso restraints and constraints
C9B \\sim C7B \\sim C8B \\sim C10B \\sim C6B \\sim C5B: within 2A with sigma of
0.04 and sigma for terminal atoms of 0.08
C6A \\sim C5A \\sim C10A \\sim C7A \\sim C8A \\sim C9A: within 2A with sigma of
0.04 and sigma for terminal atoms of 0.08
4. Others
 Sof(C4B)=Sof(H4BA)=Sof(H4BB)=Sof(H4BC)=Sof(C9B)=Sof(H9B)=Sof(C7B)=Sof(H7B)=
 Sof(C8B)=Sof(H8B)=Sof(C10B)=Sof(H10B)=Sof(C5B)=Sof(C6B)=Sof(H6B)=1-FVAR(1)
 Sof(C6A)=Sof(H6A)=Sof(C5A)=Sof(C10A)=Sof(H10A)=Sof(C9A)=Sof(H9A)=Sof(C8A)=
 Sof(H8A)=Sof(C7A)=Sof(H7A)=Sof(C4A)=Sof(H4AA)=Sof(H4AB)=Sof(H4AC)=FVAR(1)
5.a Ternary CH refined with riding coordinates:
 C22(H22), C3(H3)
5.b Secondary CH2 refined with riding coordinates:
 C1(H1A,H1B), C32(H32A,H32B), C11(H11A,H11B), C20(H20A,H20B), C13(H13A,H13B),
 C30(H30A,H30B)
5.c Me refined with riding coordinates:
 C4B(H4BA,H4BB,H4BC)
5.d Aromatic/amide H refined with riding coordinates:
 C15(H15), C6A(H6A), C10A(H10A), C9A(H9A), C8A(H8A), C7A(H7A), C26(H26),
 C29(H29), C38(H38), C25(H25), C28(H28), C18(H18), C36(H36), C35(H35), C34(H34),
  C16(H16), C19(H19), C27(H27), C17(H17), C37(H37), C9B(H9B), C7B(H7B),
 C8B(H8B), C10B(H10B), C6B(H6B)
5.e Fitted hexagon refined as free rotating group:
 C6A(C5A,C10A,C9A,C8A,C7A)
5.f Idealised Me refined as rotating group:
 C23(H23A,H23B,H23C), C4A(H4AA,H4AB,H4AC)
;
_shelx_res_checksum              35506
_shelx_hkl_checksum              73201
_olex2_submission_special_instructions 'No special instructions were received'