I'm having trouble obtaining a 'molecular view' from a CIF (attached) -
seems very difficult to obtain a connected molecule for one of the moities
(as well as jmols 'molecular load', I've tried various unit-cell loads
coupled with scripts to find and display the connected molecules).
Any help or pointers would be greatly appreciated.
Cheers
Simon Westrip
##############################################################################
### ###
### Electronic paper (Acta Crystallographica Section E) ###
### ###
##############################################################################
# #
# This CIF contains the data in a paper accepted for publication in Acta #
# Crystallographica Section E. It conforms to the requirements of Notes #
# for Authors for Section E, and has been peer reviewed under the auspices #
# of the IUCr Commission on Journals. #
# #
# Full details of the Crystallographic Information File format #
# are given in the paper "The Crystallographic Information File (CIF): #
# a New Standard Archive File for Crystallography" by S. R. Hall, F. H. #
# Allen and I. D. Brown [Acta Cryst. (1991), A47, 655-685]. #
# #
# The current version of the core CIF dictionary is obtainable from #
# ftp://ftp.iucr.org/pub/cif_core.dic. The current version number is 2.4. #
# #
# Software is freely available for graphical display of the structure(s) in #
# this CIF. For information consult the CIF home page http://www.iucr.org/ #
# cif/home.html #
# #
# This file may be used for bona fide research purposes within the #
# scientific community so long as proper attribution is given to the journal #
# article from which it was obtained. #
# #
##############################################################################
data_global
_audit_creation_method 'form.cif (version 2.0)'
_journal_data_validation_number ?
_journal_date_recd_electronic 2010-12-06
_journal_date_accepted 2010-12-19
_journal_name_full 'Acta Crystallographica, Section E'
_journal_year 2011
_journal_volume 67
_journal_issue 2
_journal_page_first o263
_journal_page_last o263
_journal_paper_category QO
_journal_coeditor_code DS2078
_publ_contact_author_name 'Ren, Chun-Xia; Shang, Shao-Ming'
_publ_contact_author_address
;
School of Chemical and Material Engineering
Jiangnan University
1800 Lihu Road
Wuxi
Jiangsu Province 214122
People's Republic of China
;
_publ_contact_author_email '[email protected], [email protected]'
_publ_contact_author_phone '0086-13382888962'
_publ_section_title
;
2,2'-(<i>p</i>-Phenylene)bis(4,5-dihydro-1<i>H</i>-imidazol-3-ium)
bis(3-nitrobenzoate)
;
loop_
_publ_author_name
_publ_author_address
'Xiu-Mei Song'
;
School of Chemical and Material Engineering
Jiangnan University
1800 Lihu Road
Wuxi
Jiangsu Province 214122
People's Republic of China
;
'Jun-Jun Li'
;
College of Pharmacy
GuangDong Pharmaceutical University
Guangzhou
Guangdong Province 510006
People's Republic of China
;
'Xin-Hua Liu'
;
School of Chemical and Material Engineering
Jiangnan University
1800 Lihu Road
Wuxi
Jiangsu Province 214122
People's Republic of China
;
'Chun-Xia Ren'
;
School of Chemical and Material Engineering
Jiangnan University
1800 Lihu Road
Wuxi
Jiangsu Province 214122
People's Republic of China
;
'Shao-Ming Shang'
;
School of Chemical and Material Engineering
Jiangnan University
1800 Lihu Road
Wuxi
Jiangsu Province 214122
People's Republic of China
;
data_I
_audit_creation_method SHELXL-97
_chemical_name_systematic
;
2,2'-(<i>p</i>-Phenylene)bis(4,5-dihydro-1<i>H</i>-imidazol-3-ium)
bis(3-nitrobenzoate)
;
_chemical_name_common ?
_chemical_formula_moiety 'C12 H16 N4 2+, 2(C7 H4 N O4 -)'
_chemical_formula_sum 'C26 H24 N6 O8'
_chemical_formula_iupac 'C12 H16 N4 2+, 2C7 H4 N O4 -'
_chemical_formula_weight 548.51
_chemical_melting_point ?
_symmetry_cell_setting triclinic
_symmetry_space_group_name_H-M 'P -1'
_symmetry_space_group_name_Hall '-P 1'
loop_
_symmetry_equiv_pos_as_xyz
'x, y, z'
'-x, -y, -z'
_cell_length_a 6.9882(12)
_cell_length_b 7.4165(12)
_cell_length_c 13.233(2)
_cell_angle_alpha 81.343(3)
_cell_angle_beta 82.443(3)
_cell_angle_gamma 62.699(2)
_cell_volume 600.96(17)
_cell_formula_units_Z 1
_cell_measurement_reflns_used ?
_cell_measurement_theta_min ?
_cell_measurement_theta_max ?
_cell_measurement_temperature 273(2)
_exptl_crystal_description block
_exptl_crystal_colour colorless
_exptl_crystal_size_max 0.67
_exptl_crystal_size_mid 0.55
_exptl_crystal_size_min 0.42
_exptl_crystal_density_diffrn 1.516
_exptl_crystal_density_meas ?
_exptl_crystal_density_method 'not measured'
_exptl_crystal_F_000 286
_exptl_absorpt_coefficient_mu 0.115
_exptl_absorpt_correction_type multi-scan
_exptl_absorpt_process_details '(SADABS; Bruker, 1998)'
_exptl_absorpt_correction_T_min 0.9269
_exptl_absorpt_correction_T_max 0.9533
_exptl_special_details
;
;
_diffrn_ambient_temperature 273(2)
_diffrn_radiation_type MoK\a
_diffrn_radiation_wavelength 0.71073
_diffrn_radiation_source 'fine-focus sealed tube'
_diffrn_radiation_monochromator graphite
_diffrn_measurement_device_type 'Bruker SMART APEX CCD area-detector'
_diffrn_measurement_method '\f and \w'
_diffrn_detector_area_resol_mean ?
_diffrn_reflns_number 3714
_diffrn_reflns_av_R_equivalents 0.0161
_diffrn_reflns_av_sigmaI/netI 0.0345
_diffrn_reflns_theta_min 1.56
_diffrn_reflns_theta_max 27.01
_diffrn_reflns_theta_full 27.01
_diffrn_measured_fraction_theta_max 0.982
_diffrn_measured_fraction_theta_full 0.982
_diffrn_reflns_limit_h_min -8
_diffrn_reflns_limit_h_max 8
_diffrn_reflns_limit_k_min -9
_diffrn_reflns_limit_k_max 9
_diffrn_reflns_limit_l_min -16
_diffrn_reflns_limit_l_max 8
_diffrn_standards_number ?
_diffrn_standards_interval_count ?
_diffrn_standards_interval_time ?
_diffrn_standards_decay_% ?
_refine_special_details
;
Refinement of <i>F</i>^2^ against ALL reflections. The weighted <i>R</i>-factor
<i>wR</i> and goodness of fit <i>S</i> are based on <i>F</i>^2^, conventional
<i>R</i>-factors <i>R</i> are based on <i>F</i>, with <i>F</i> set to zero for
negative <i>F</i>^2^. The threshold expression of <i>F</i>^2^ >
\s(<i>F</i>^2^) is used only for calculating <i>R</i>-factors(gt) <i>etc</i>.
and is not relevant to the choice of reflections for refinement.
<i>R</i>-factors based on <i>F</i>^2^ are statistically about twice as large
as those based on <i>F</i>, and <i>R</i>- factors based on ALL data will be
even larger.
;
_reflns_number_total 2575
_reflns_number_gt 1676
_reflns_threshold_expression I>2sigma(I)
_refine_ls_structure_factor_coef Fsqd
_refine_ls_matrix_type full
_refine_ls_R_factor_all 0.0839
_refine_ls_R_factor_gt 0.0534
_refine_ls_wR_factor_gt 0.1291
_refine_ls_wR_factor_ref 0.1510
_refine_ls_goodness_of_fit_ref 1.067
_refine_ls_restrained_S_all 1.067
_refine_ls_number_reflns 2575
_refine_ls_number_parameters 181
_refine_ls_number_restraints 1
_refine_ls_hydrogen_treatment constr
_refine_ls_weighting_scheme calc
_refine_ls_weighting_details
'calc w=1/[\s^2^(Fo^2^)+(0.0613P)^2^+0.1694P] where P=(Fo^2^+2Fc^2^)/3'
_atom_sites_solution_hydrogens geom
_atom_sites_solution_primary direct
_atom_sites_solution_secondary difmap
_refine_ls_shift/su_max 0.000
_refine_ls_shift/su_mean 0.000
_refine_diff_density_max 0.197
_refine_diff_density_min -0.284
_refine_ls_extinction_method none
_refine_ls_extinction_coef ?
loop_
_atom_type_symbol
_atom_type_description
_atom_type_scat_dispersion_real
_atom_type_scat_dispersion_imag
_atom_type_scat_source
'C' 'C' 0.0033 0.0016
'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
'H' 'H' 0.0000 0.0000
'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
'N' 'N' 0.0061 0.0033
'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
'O' 'O' 0.0106 0.0060
'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
_computing_data_collection '<i>SMART</i> (Bruker, 1998)'
_computing_cell_refinement '<i>SAINT-Plus</i> (Bruker, 1998)'
_computing_data_reduction '<i>SAINT-Plus</i> (Bruker, 1998)'
_computing_structure_solution '<i>SHELXS97</i> (Sheldrick, 2008)'
_computing_structure_refinement '<i>SHELXL97</i> (Sheldrick, 2008)'
_computing_molecular_graphics '<i>SHELXTL</i> (Sheldrick, 2008)'
_computing_publication_material '<i>SHELXTL</i> (Sheldrick, 2008)'
loop_
_atom_site_type_symbol
_atom_site_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_U_iso_or_equiv
_atom_site_adp_type
_atom_site_calc_flag
_atom_site_refinement_flags
_atom_site_occupancy
_atom_site_disorder_assembly
_atom_site_disorder_group
C C1 0.7607(4) 0.1903(4) 0.18562(17) 0.0483(6) Uani d . 1 . .
H H1A 0.7398 0.2592 0.2458 0.058 Uiso calc R 1 . .
H H1B 0.6839 0.1075 0.1981 0.058 Uiso calc R 1 . .
C C2 0.6871(4) 0.3430(3) 0.09029(18) 0.0492(6) Uani d . 1 . .
H H2A 0.5961 0.3147 0.0521 0.059 Uiso calc R 1 . .
H H2B 0.6093 0.4820 0.1083 0.059 Uiso calc R 1 . .
C C3 1.0544(3) 0.1481(3) 0.07401(15) 0.0383(5) Uani d . 1 . .
C C4 1.2831(3) 0.0707(3) 0.03509(15) 0.0373(5) Uani d . 1 . .
C C5 1.3404(3) 0.1420(3) -0.06192(15) 0.0414(5) Uani d . 1 . .
H H5 1.2337 0.2373 -0.1034 0.050 Uiso calc R 1 . .
C C6 1.5554(4) 0.0716(3) -0.09660(15) 0.0416(5) Uani d . 1 . .
H H6 1.5925 0.1195 -0.1615 0.050 Uiso calc R 1 . .
C C7 0.1900(4) 0.5421(5) 0.2448(2) 0.0620(8) Uani d . 1 . .
C C8 0.2163(3) 0.3932(3) 0.33993(16) 0.0437(5) Uani d . 1 . .
C C9 0.1925(4) 0.2191(4) 0.33805(19) 0.0529(6) Uani d . 1 . .
H H9 0.1691 0.1887 0.2765 0.064 Uiso calc R 1 . .
C C10 0.2027(4) 0.0885(4) 0.4264(2) 0.0639(7) Uani d . 1 . .
H H10 0.1849 -0.0275 0.4239 0.077 Uiso calc R 1 . .
C C11 0.2391(4) 0.1307(4) 0.5170(2) 0.0620(7) Uani d . 1 . .
H H11 0.2445 0.0452 0.5769 0.074 Uiso calc R 1 . .
C C12 0.2671(3) 0.3009(4) 0.51797(16) 0.0507(6) Uani d U 1 . .
C C13 0.2561(3) 0.4345(3) 0.43168(17) 0.0462(5) Uani d . 1 . .
H H13 0.2750 0.5497 0.4350 0.055 Uiso calc R 1 . .
N N1 0.8925(3) 0.3081(3) 0.03187(14) 0.0482(5) Uani d . 1 . .
H H1 0.9055 0.3822 -0.0226 0.058 Uiso calc R 1 . .
N N2 0.9901(3) 0.0671(3) 0.15833(13) 0.0438(5) Uani d . 1 . .
H H2 1.0721 -0.0439 0.1930 0.053 Uiso calc R 1 . .
N N3 0.3060(4) 0.3471(5) 0.61616(18) 0.0776(8) Uani d U 1 . .
O O1 0.1555(3) 0.4959(3) 0.16467(14) 0.0884(7) Uani d . 1 . .
O O2 0.2025(3) 0.7013(3) 0.25649(18) 0.0916(8) Uani d . 1 . .
O O3 0.3241(4) 0.5037(6) 0.6153(2) 0.1100(10) Uani d . 1 . .
O O4 0.3135(4) 0.2288(5) 0.69216(16) 0.1205(11) Uani d . 1 . .
loop_
_atom_site_aniso_label
_atom_site_aniso_U_11
_atom_site_aniso_U_22
_atom_site_aniso_U_33
_atom_site_aniso_U_12
_atom_site_aniso_U_13
_atom_site_aniso_U_23
C1 0.0495(13) 0.0543(13) 0.0410(12) -0.0242(11) -0.0023(10) -0.0025(10)
C2 0.0456(13) 0.0468(12) 0.0473(13) -0.0152(10) -0.0034(10) -0.0009(10)
C3 0.0477(12) 0.0387(10) 0.0286(10) -0.0187(9) -0.0089(9) -0.0010(8)
C4 0.0446(12) 0.0356(10) 0.0298(10) -0.0160(9) -0.0068(8) -0.0011(8)
C5 0.0472(12) 0.0380(11) 0.0323(11) -0.0142(9) -0.0099(9) 0.0053(8)
C6 0.0516(13) 0.0424(11) 0.0273(10) -0.0197(10) -0.0045(9) 0.0040(8)
C7 0.0410(13) 0.0717(18) 0.0494(16) -0.0137(12) -0.0021(11) 0.0233(13)
C8 0.0359(11) 0.0477(12) 0.0367(12) -0.0129(9) -0.0031(9) 0.0074(9)
C9 0.0513(14) 0.0599(15) 0.0463(14) -0.0226(11) -0.0085(11) -0.0052(11)
C10 0.0610(16) 0.0510(14) 0.080(2) -0.0292(13) -0.0097(14) 0.0104(13)
C11 0.0513(15) 0.0686(17) 0.0530(16) -0.0235(13) -0.0059(12) 0.0225(13)
C12 0.0350(12) 0.0701(16) 0.0336(12) -0.0131(11) -0.0033(9) -0.0013(11)
C13 0.0362(11) 0.0487(12) 0.0484(13) -0.0153(10) -0.0014(9) -0.0037(10)
N1 0.0481(11) 0.0478(10) 0.0372(10) -0.0146(9) -0.0047(8) 0.0072(8)
N2 0.0464(10) 0.0434(10) 0.0365(10) -0.0181(8) -0.0060(8) 0.0062(8)
N3 0.0438(13) 0.124(2) 0.0481(14) -0.0212(14) -0.0029(10) -0.0174(15)
O1 0.0837(14) 0.1023(16) 0.0365(10) -0.0115(12) -0.0080(9) 0.0177(10)
O2 0.0766(14) 0.0759(14) 0.1167(19) -0.0418(12) -0.0346(12) 0.0561(13)
O3 0.0816(17) 0.173(3) 0.0934(19) -0.0593(18) 0.0042(13) -0.0671(19)
O4 0.0984(18) 0.183(3) 0.0363(12) -0.0305(18) -0.0134(11) 0.0122(15)
_geom_special_details
;
All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes)
are estimated using the full covariance matrix. The cell e.s.d.'s are taken
into account individually in the estimation of e.s.d.'s in distances, angles
and torsion angles; correlations between e.s.d.'s in cell parameters are only
used when they are defined by crystal symmetry. An approximate (isotropic)
treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s.
planes.
;
loop_
_geom_bond_atom_site_label_1
_geom_bond_atom_site_label_2
_geom_bond_site_symmetry_2
_geom_bond_distance
_geom_bond_publ_flag
C1 N2 . 1.462(3) ?
C1 C2 . 1.531(3) ?
C1 H1A . 0.9700 ?
C1 H1B . 0.9700 ?
C2 N1 . 1.468(3) ?
C2 H2A . 0.9700 ?
C2 H2B . 0.9700 ?
C3 N2 . 1.312(3) ?
C3 N1 . 1.317(3) ?
C3 C4 . 1.476(3) ?
C4 C6 2_855 1.393(3) ?
C4 C5 . 1.394(3) ?
C5 C6 . 1.383(3) ?
C5 H5 . 0.9300 ?
C6 C4 2_855 1.393(3) ?
C6 H6 . 0.9300 ?
C7 O1 . 1.246(4) ?
C7 O2 . 1.257(4) ?
C7 C8 . 1.514(3) ?
C8 C9 . 1.380(3) ?
C8 C13 . 1.387(3) ?
C9 C10 . 1.388(3) ?
C9 H9 . 0.9300 ?
C10 C11 . 1.367(4) ?
C10 H10 . 0.9300 ?
C11 C12 . 1.366(4) ?
C11 H11 . 0.9300 ?
C12 C13 . 1.380(3) ?
C12 N3 . 1.481(3) ?
C13 H13 . 0.9300 ?
N1 H1 . 0.8600 ?
N2 H2 . 0.8600 ?
N3 O4 . 1.221(3) ?
N3 O3 . 1.222(4) ?
loop_
_geom_angle_atom_site_label_1
_geom_angle_atom_site_label_2
_geom_angle_atom_site_label_3
_geom_angle_site_symmetry_1
_geom_angle_site_symmetry_3
_geom_angle
_geom_angle_publ_flag
N2 C1 C2 . . 102.53(17) ?
N2 C1 H1A . . 111.3 ?
C2 C1 H1A . . 111.3 ?
N2 C1 H1B . . 111.3 ?
C2 C1 H1B . . 111.3 ?
H1A C1 H1B . . 109.2 ?
N1 C2 C1 . . 102.37(17) ?
N1 C2 H2A . . 111.3 ?
C1 C2 H2A . . 111.3 ?
N1 C2 H2B . . 111.3 ?
C1 C2 H2B . . 111.3 ?
H2A C2 H2B . . 109.2 ?
N2 C3 N1 . . 111.85(19) ?
N2 C3 C4 . . 122.98(18) ?
N1 C3 C4 . . 125.13(18) ?
C6 C4 C5 2_855 . 119.30(19) ?
C6 C4 C3 2_855 . 119.93(18) ?
C5 C4 C3 . . 120.75(18) ?
C6 C5 C4 . . 120.20(19) ?
C6 C5 H5 . . 119.9 ?
C4 C5 H5 . . 119.9 ?
C5 C6 C4 . 2_855 120.50(19) ?
C5 C6 H6 . . 119.7 ?
C4 C6 H6 2_855 . 119.7 ?
O1 C7 O2 . . 127.2(2) ?
O1 C7 C8 . . 117.2(3) ?
O2 C7 C8 . . 115.6(3) ?
C9 C8 C13 . . 118.9(2) ?
C9 C8 C7 . . 120.8(2) ?
C13 C8 C7 . . 120.2(2) ?
C8 C9 C10 . . 121.2(2) ?
C8 C9 H9 . . 119.4 ?
C10 C9 H9 . . 119.4 ?
C11 C10 C9 . . 119.9(2) ?
C11 C10 H10 . . 120.1 ?
C9 C10 H10 . . 120.1 ?
C12 C11 C10 . . 118.7(2) ?
C12 C11 H11 . . 120.7 ?
C10 C11 H11 . . 120.7 ?
C11 C12 C13 . . 122.8(2) ?
C11 C12 N3 . . 118.7(2) ?
C13 C12 N3 . . 118.4(3) ?
C12 C13 C8 . . 118.5(2) ?
C12 C13 H13 . . 120.7 ?
C8 C13 H13 . . 120.7 ?
C3 N1 C2 . . 110.95(18) ?
C3 N1 H1 . . 124.5 ?
C2 N1 H1 . . 124.5 ?
C3 N2 C1 . . 111.14(17) ?
C3 N2 H2 . . 124.4 ?
C1 N2 H2 . . 124.4 ?
O4 N3 O3 . . 124.9(3) ?
O4 N3 C12 . . 117.8(3) ?
O3 N3 C12 . . 117.3(3) ?
loop_
_geom_hbond_atom_site_label_D
_geom_hbond_atom_site_label_H
_geom_hbond_atom_site_label_A
_geom_hbond_site_symmetry_A
_geom_hbond_distance_DH
_geom_hbond_distance_HA
_geom_hbond_distance_DA
_geom_hbond_angle_DHA
C6 H6 O2 2_765 0.93 2.48 3.283(3) 144
N1 H1 O1 2_665 0.86 1.97 2.763(3) 153
N2 H2 O2 1_645 0.86 1.80 2.646(3) 166
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