Synthesis of a visibly emissive 9-nitro-2,3-dihydro-1H-pyrimido[1,2-a]quinoxalin-5-amine scaffold with large stokes shift and live cell imaging
Kanungo, Ajay; Patra, Dipendu; Mukherjee, Sanghamitra; Mahata, Tridib; Maulik, Prakas R.; Dutta, Sanjay; RSC Adv. 5 (2015) 70958–; doi:10.1039/C5RA12960E

data_7221836
_publ_section_title
;
 Synthesis of a visibly emissive
 9-nitro-2,3-dihydro-1H-pyrimido[1,2-a]quinoxalin-5-amine scaffold with
 large stokes shift and live cell imaging
;
_journal_issue                   87
_journal_name_full               'RSC Adv.'
_journal_page_first              70958
_journal_paper_doi               10.1039/C5RA12960E
_journal_volume                  5
_journal_year                    2015
_chemical_formula_moiety         'C16 H15 N5 O3'
_chemical_formula_sum            'C16 H15 N5 O3'
_chemical_formula_weight         325.33
_chemical_name_systematic
'(E)-methyl 2-(4-benzyl-1-(3-(dimethylamino)propyl)-8-nitro-3-oxo-3,4-dihydropyrazino[2,3-b]quinoxalin-2(1H)-ylidene)acetate '
_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'
_symmetry_space_group_name_Hall  'P 2yb'
_symmetry_space_group_name_H-M   'P 1 21 1'
_atom_sites_solution_hydrogens   geom
_audit_creation_date             2015-08-04
_audit_creation_method
;
Olex2 1.2-alpha
(compiled 2015.07.23 svn.r3196 for OlexSys, GUI svn.r5077)
;
_audit_update_record
;
2015-08-10 deposited with the CCDC.
2015-08-11 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 100.189(7)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   8.4267(9)
_cell_length_b                   10.4362(12)
_cell_length_c                   17.949(2)
_cell_measurement_reflns_used    3583
_cell_measurement_temperature    296.15
_cell_measurement_theta_max      25.26
_cell_measurement_theta_min      2.27
_cell_volume                     1553.6(3)
_computing_cell_refinement       'SAINT v8.34A (Bruker, 2013)'
_computing_data_reduction        'SAINT v8.34A (Bruker, 2013)'
_computing_molecular_graphics    'Olex2 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 (Dolomanov et al., 2009)'
_computing_structure_refinement  'ShelXL (Sheldrick, 2015)'
_computing_structure_solution    'ShelXT (Sheldrick, 2015)'
_diffrn_ambient_temperature      296.15
_diffrn_measured_fraction_theta_full 0.994
_diffrn_measured_fraction_theta_max 0.990
_diffrn_measurement_device_type  'Bruker APEX-II CCD'
_diffrn_measurement_method       '\f and \w scans'
_diffrn_radiation_type           MoK\a
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.0438
_diffrn_reflns_av_unetI/netI     0.0612
_diffrn_reflns_Laue_measured_fraction_full 0.994
_diffrn_reflns_Laue_measured_fraction_max 0.990
_diffrn_reflns_limit_h_max       10
_diffrn_reflns_limit_h_min       -10
_diffrn_reflns_limit_k_max       13
_diffrn_reflns_limit_k_min       -13
_diffrn_reflns_limit_l_max       23
_diffrn_reflns_limit_l_min       -23
_diffrn_reflns_number            15689
_diffrn_reflns_point_group_measured_fraction_full 0.992
_diffrn_reflns_point_group_measured_fraction_max 0.984
_diffrn_reflns_theta_full        26.000
_diffrn_reflns_theta_max         27.464
_diffrn_reflns_theta_min         2.306
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    0.100
_exptl_absorpt_correction_T_max  0.7456
_exptl_absorpt_correction_T_min  0.6803
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
SADABS-2014/5 (Bruker,2014/5) was used for absorption correction.
wR2(int) was 0.0735 before and 0.0529 after correction.
The Ratio of minimum to maximum transmission is 0.9124.
The \l/2 correction factor is 0.00150.
;
_exptl_crystal_colour            yellow
_exptl_crystal_density_diffrn    1.391
_exptl_crystal_description       needle
_exptl_crystal_F_000             680
_exptl_crystal_preparation       Luminescent
_exptl_crystal_recrystallization_method
'Re-crystallisation from solvent: chloroform, methanol'
_exptl_crystal_size_max          0.72
_exptl_crystal_size_mid          0.34
_exptl_crystal_size_min          0.1
_refine_diff_density_max         0.182
_refine_diff_density_min         -0.156
_refine_diff_density_rms         0.032
_refine_ls_abs_structure_details
;
 Flack x determined using 1400 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   -0.1(8)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   0.958
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     498
_refine_ls_number_reflns         6998
_refine_ls_number_restraints     239
_refine_ls_restrained_S_all      0.954
_refine_ls_R_factor_all          0.1039
_refine_ls_R_factor_gt           0.0451
_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^)+(0.0576P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0985
_refine_ls_wR_factor_ref         0.1245
_reflns_Friedel_coverage         0.885
_reflns_Friedel_fraction_full    0.988
_reflns_Friedel_fraction_max     0.978
_reflns_number_gt                3929
_reflns_number_total             6998
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            c5ra12960e2.cif
_cod_data_source_block           sd_ak2786ond2_1058070
_cod_database_code               7221836
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups, All C(H,H,H,H) groups, All N(H) groups
2. Restrained distances
 C13B_1-C12_1 \\sim C13A_1-C12_1
 with sigma of 0.02
 C14B_1-C13B_1 \\sim C14A_1-C13A_1
 with sigma of 0.02
 C15B_1-C14B_1 \\sim C15A_1-C14A_1
 with sigma of 0.02
 C16A_1-C15A_1 \\sim C16B_1-C15B_1
 with sigma of 0.02
 O3B_1-C16B_1 \\sim O3A_1-C16A_1
 with sigma of 0.02
 O3B_1-C13B_1 \\sim O3A_1-C13A_1
 with sigma of 0.02
3. Uiso/Uaniso restraints and constraints
C13B_1 \\sim C14B_1 \\sim C15B_1 \\sim C16B_1 \\sim O3B_1 \\sim C13A_1 \\sim
C14A_1 \\sim C15A_1 \\sim C16A_1 \\sim O3A_1: within 2A with sigma of 0.02 and
sigma for terminal atoms of 0.04
C3A_2 \\sim C4B_2: within 2A with sigma of 0.02 and sigma for terminal atoms of
0.04
C4A_2 \\sim C3B_2: within 2A with sigma of 0.02 and sigma for terminal atoms of
0.04
4. Rigid body (RIGU) restrains
 C3A_2, C4B_2
 with sigma for 1-2 distances of 0.02 and sigma for 1-3 distances of 0.02
 C4A_2, C3B_2
 with sigma for 1-2 distances of 0.02 and sigma for 1-3 distances of 0.02
 C13B_1, C14B_1, C15B_1, C16B_1, O3B_1, C13A_1, C14A_1, C15A_1, C16A_1, O3A_1
 with sigma for 1-2 distances of 0.02 and sigma for 1-3 distances of 0.02
5. Same fragment restrains
{N3_1, C3_1, C4_1, C5_1} sigma for 1-2: 0.02, 1-3: 0.04
as
{N3_2, C3A_2, C4A_2, C3B_2}
6. Others
 Sof(H12C)=Sof(H12D)=Sof(C13B)=Sof(O3B)=Sof(C16B)=Sof(H16B)=Sof(C15B)=
 Sof(H15B)=Sof(C14B)=Sof(H14B)=1-FVAR(1)
 Sof(H12A)=Sof(H12B)=Sof(C13A)=Sof(O3A)=Sof(C14A)=Sof(H14A)=Sof(C15A)=
 Sof(H15A)=Sof(C16A)=Sof(H16A)=FVAR(1)
 Sof(C3B)=Sof(H3BA)=Sof(H3BB)=Sof(C4B)=Sof(H4BA)=Sof(H4BB)=Sof(H5BC)=Sof(H5BD)=
 1-FVAR(2)
 Sof(C3A)=Sof(H3AA)=Sof(H3AB)=Sof(C4A)=Sof(H4AA)=Sof(H4AB)=Sof(H5AA)=Sof(H5AB)=
 FVAR(2)
7.a Secondary CH2 refined with riding coordinates:
 C3(H3A,H3B), C4(H4A,H4B), C5(H5A,H5B), C12(H12A,H12B), C12(H12C,H12D),
 C3A(H3AA,H3AB), C4A(H4AA,H4AB), C3B(H3BA,H3BB), C4B(H4BA,H4BB), C5(H5AA,H5AB),
 C5(H5BC,H5BD), C12(H12A,H12B)
7.b Aromatic/amide H refined with riding coordinates:
 N4(H4), C7(H7), C9(H9), C10(H10), C14A(H14A), C15A(H15A), C16A(H16A),
 C16B(H16B), C15B(H15B), C14B(H14B), N4(H4), C7(H7), C9(H9), C10(H10), C14(H14),
  C15(H15), C16(H16)
;
_shelx_res_checksum              11295
_shelx_shelxl_version_number     2014/7
_olex2_submission_special_instructions 'No special instructions were received'