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COMMUNICATIONS
ISSN: 2056-9890
Volume 74| Part 3| March 2018| Pages 380-384
https://doi.org/10.1107/S2056989018002876

Different mol­ecular conformations in the crystal structures of three 5-nitro­imidazolyl derivatives

CROSSMARK_Color_square_no_text.svg
Luis F. B. Osorio,a Samir A. Carvalho,a Edson F. da Silva,a Carlos A. M. Fraga,b Solange M. S. V. Wardell,c Bruce F. Milne,d James L. Wardelle and William T. A. Harrisone*

aInstituto de Tecnologia em Fármacos e Farmanguinhos, Fundação Oswaldo Cruz, 21041-250 Rio de Janeiro, RJ, Brazil, bPrograma de Pesquisa em Desenvolvimento de Fármacos, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, PO Box 68023, 21941-902 Rio de Janeiro, RJ, Brazil, cCHEMSOL, 1 Harcourt Road, Aberdeen AB15 5NY, Scotland, dCFisUC, Physics Department, University of Coimbra, Rua Larga 3004–516, Coimbra, Portugal, and eDepartment of Chemistry, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland
*Correspondence e-mail: w.harrison@abdn.ac.uk

Edited by J. T. Mague, Tulane University, USA (Received 1 February 2018; accepted 19 February 2018; online 23 February 2018)

The crystal structures of (E)-1-methyl-5-nitro-1H-imidazole-2-carbaldehyde O-benzyl­oxime, C12H12N4O3, (I), (E)-1-methyl-5-nitro-1H-imidazole-2-carb­alde­hyde O-(4-fluoro­benz­yl) oxime, C12H11FN4O3, (II), and (E)-1-methyl-5-nitro-1H-imidazole-2-carbaldehyde O-(4-bromo­benz­yl) oxime, C12H11BrN4O3, (III), are described. The dihedral angle between the ring systems in (I) is 49.66 (5)° and the linking Nm—C—C=N (m = methyl­ated) bond shows an anti conformation [torsion angle = 175.00 (15)°]. Compounds (II) and (III) are isostructural [dihedral angle between the aromatic rings = 8.31 (5)° in (II) and 5.34 (15)° in (III)] and differ from (I) in showing a near-syn conformation for the Nm—C—C=N linker [torsion angles for (II) and (III) = 17.64 (18) and 8.7 (5)°, respectively], which allows for the occurrence of a short intra­molecular C—H⋯N contact. In the crystal of (I), C—H⋯N hydrogen bonds link the mol­ecules into [010] chains, which are cross-linked by very weak C—H⋯O bonds into (100) sheets. Weak aromatic π–π stacking inter­actions occur between the sheets. The extended structures of (II) and (III) feature several C—H⋯N and C—H⋯O hydrogen bonds, which link the mol­ecules into three-dimensional networks, which are consolidated by aromatic π–π stacking inter­actions. Conformational energy calculations and Hirshfeld fingerprint analyses for (I), (II) and (III) are presented and discussed.

CCDC references: 1486983; 1486982; 1486987

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1. Chemical context

Trypanosomes infect a variety of hosts and cause various serious illnesses, including sleeping sickness (transmitted by Trypanosoma brucei) and Chagas' disease. The infectious agent of Chagas' disease is the protozoan parasite Trypanosoma cruzi, which produces progressive symptoms from mild swelling to intestinal disease and ultimately heart failure (Rassi et al., 2010[Rassi, A. Jr, Rassi, A. & Marin-Neto, J. A. (2010). Lancet, 375, 1388-1402.]). New effective drugs are urgently required for the treatment of Chagas' disease, which infects an estimated 6.6 million people worldwide (Rassi et al., 2010[Rassi, A. Jr, Rassi, A. & Marin-Neto, J. A. (2010). Lancet, 375, 1388-1402.]): benznidazole and nifurtimox have been the only recognised treatments for over 40 years and both drugs present variable results and undesirable side effects (Soeiro & Castro, 2011[Soeiro, M. de N. C. & de Castro, S. L. (2011). Open Med. Chem. J. 5, 21-30.]). Megazol, while active, also has serious side effects (Poli et al. 2002[Poli, P., Aline de Mello, M., Buschini, A., Mortara, R. A., Northfleet de Albuquerque, C., da Silva, S., Rossi, C. & Zucchi, T. M. (2002). Biochem. Pharmacol. 64, 1617-1627.]).

We have recently described (Carvalho et al., 2017[Carvalho, S. A., Osorio, L. F. B., Salomão, K., de Castro, S. L., Wardell, S. M. S. V., Wardell, J. L., da Silva, E. F. & Fraga, C. A. M. (2017). J. Heterocycl. Chem. 54, 3626-3631.]) the syntheses and biological activities of a family of 5-nitro­imidazolyl-O-benzyl­oxime ethers, which displayed moderate anti­trypanosidal activity. We now report the crystal structures, Hirshfeld surface analyses and conformational energy calculations for three compounds from that study, viz. (E)-1-methyl-5-nitro-1H-imidazole-2-carbaldehyde O-benzyl­oxime, C12H12N4O3 (I)[link], (E)-1-methyl-5-nitro-1H-imidazole-2-carb­al­de­hyde O-(4-fluoro­benz­yl) oxime C12H11FN4O3 (II)[link] and (E)-1-methyl-5-nitro-1H-imidazole-2-carbaldehyde O-(4-bromo­benz­yl) oxime, C12H11BrN4O3 (III)[link].

[Scheme 1]

2. Structural commentary

Compound (I)[link] crystallizes in space group P21/c with one mol­ecule in the asymmetric unit (Fig. 1 and Table 1[link][link]). The dihedral angle between the imidazole ring (C1/C2/C3/N1/N2) and phenyl group (C7–C12) is 49.66 (5)°. The N4/O2/O3 nitro group is approximately coplanar with its attached ring [dihedral angle = 7.87 (17)°]. The C—C and C—N bond lengths within the heterocyclic ring show typical values and N2 is statistically planar (bond-angle sum = 359.7°). The angle C1—N2—C4 [129.47 (13)°] is significantly greater than C3—N2—C4 [126.14 (14)°] perhaps because of steric repulsion between the C4 methyl group and the nitro group. The key parameter defining the conformation of the mol­ecule of (I)[link] is the N2—C3—C5=N3 torsion angle: the value of 175.00 (15)° indicates an anti conformation for these atoms. The rest of the chain linking the rings can be described as extended in terms of the C3—C5=N3—O1, C5=N3—O1—C6 and N3—O1—C6—C7 torsion angles of 175.55 (14), −172.50 (15) and 172.62 (14)°, respectively. The major twist in the mol­ecule of (I)[link] occurs about the C6—C7 bond as indicated by the O1—C6—C7—C12 torsion angle of −45.5 (2)°. Assuming that the rotating-group refinement model for the C4 methyl group is reliable, it may be seen that this group has twisted about the N2—C4 bond to reduce steric repulsion with H5, although a rather short intra­molecular contact (H5⋯H4C = 2.12 Å) is still present.

Table 1
Hydrogen-bond geometry (Å, °) for (I)[link]

D—H⋯A D—H H⋯A D⋯A D—H⋯A
C4—H4B⋯N3i 0.98 2.51 3.466 (2) 165
C5—H5⋯O3ii 0.95 2.65 3.175 (2) 115
Symmetry codes: (i) [-x, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]; (ii) [x, -y+{\script{1\over 2}}, z+{\script{1\over 2}}].
[Figure 1]
Figure 1
The mol­ecular structure of (I)[link] showing 50% displacement ellipsoids.

Compounds (II)[link] and (III)[link] are isostructural, crystallizing in P21/n with one mol­ecule in the asymmetric unit (Figs. 2[link] and 3[link]). The dihedral angles between the aromatic rings for (II)[link] and (III)[link] are 8.31 (5) and 5.34 (15)°, respectively, whereas the dihedral angles for the nitro group and its attached ring are 2.83 (11) and 5.9 (30)°, respectively. The geometrical data for the imidazole rings in (II)[link] and (III)[link] show no significant differences compared to (I)[link] but a major conformational difference is seen in terms of the N2—C3—C5=N3 torsion angles of 17.64 (18) for (II)[link] and 8.7 (5)° for (III)[link], indicating an approximate syn conformation, as opposed to anti for (I)[link]. This reorientation facilitates the formation of an intra­molecular C4—H4C⋯N3 hydrogen bond in both (II)[link] (Table 2[link]) and (III)[link] (Table 3[link]). The rest of the linking chain displays an extended conformation in both (II)[link] and (III)[link] with respective C3—C5=N3—O1, C5=N3—O1—C6 and N3—O1—C6—C7 torsion angles of 179.79 (9), −173.96 (9) and 175.61 (8)° in (II)[link] and 179.2 (2), −171.8 (2) and 179.7 (2)° in (III)[link]. The C6—C7 bond in (II)[link] and (III)[link] is somewhat less twisted than in (I)[link], with O1—C6—C7—C8 torsion angles of −30.95 (14) and −23.1 (4)° for (II)[link] and (III)[link], respectively.

Table 2
Hydrogen-bond geometry (Å, °) for (II)[link]

D—H⋯A D—H H⋯A D⋯A D—H⋯A
C4—H4C⋯N3 0.98 2.29 3.0184 (15) 131
C4—H4A⋯N1i 0.98 2.63 3.5693 (16) 160
C9—H9⋯N1ii 0.95 2.58 3.4973 (16) 163
C2—H2⋯O3iii 0.95 2.49 3.3165 (15) 145
C5—H5⋯O2iv 0.95 2.63 3.1676 (14) 116
C6—H6A⋯O2v 0.99 2.54 3.1376 (14) 119
C4—H4C⋯F1vi 0.98 2.77 3.353 (2) 119
Symmetry codes: (i) [-x+{\script{1\over 2}}, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]; (ii) [x-{\script{1\over 2}}, -y+{\script{1\over 2}}, z+{\script{1\over 2}}]; (iii) -x+1, -y+1, -z; (iv) [-x+{\script{1\over 2}}, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]; (v) [x-{\script{1\over 2}}, -y+{\script{3\over 2}}, z+{\script{1\over 2}}]; (vi) [-x+{\script{1\over 2}}, y+{\script{1\over 2}}, -z+{\script{3\over 2}}].

Table 3
Hydrogen-bond geometry (Å, °) for (III)[link]

D—H⋯A D—H H⋯A D⋯A D—H⋯A
C4—H4C⋯N3 0.98 2.24 2.997 (4) 133
C4—H4A⋯N1i 0.98 2.62 3.499 (4) 149
C9—H9⋯N1ii 0.95 2.77 3.681 (4) 160
C2—H2⋯O3iii 0.95 2.44 3.282 (4) 148
C5—H5⋯O2iv 0.95 2.64 3.341 (4) 131
C6—H6A⋯O2v 0.99 2.63 3.254 (4) 121
C4—H4C⋯Br1vi 0.98 2.85 3.491 (3) 124
Symmetry codes: (i) [-x+{\script{1\over 2}}, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]; (ii) [x-{\script{1\over 2}}, -y+{\script{1\over 2}}, z+{\script{1\over 2}}]; (iii) -x+1, -y+1, -z; (iv) [-x+{\script{1\over 2}}, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]; (v) [x-{\script{1\over 2}}, -y+{\script{3\over 2}}, z+{\script{1\over 2}}]; (vi) [-x+{\script{1\over 2}}, y+{\script{1\over 2}}, -z+{\script{3\over 2}}].
[Figure 2]
Figure 2
The mol­ecular structure of (II)[link] showing 50% displacement ellipsoids.
[Figure 3]
Figure 3
The mol­ecular structure of (III)[link] showing 50% displacement ellipsoids.

3. Computational calculations

The different conformations of (I)[link] compared to (II)[link] and (III)[link] were investigated by computational means. All calculations were performed with the Orca software package version 4.0.0.2 (Neese, 2012[Neese, F. (2012). WIREs Comput. Mol. Sci. 2, 73-78.]). Geometry optimizations were performed at the spin-component-scaled MP2 (SCS-MP2) level (Grimme, 2003[Grimme, S. (2003). J. Chem. Phys. 118, 9095-9102.]) using the Def2-TZVP (Hellweg et al., 2007[Hellweg, A., Hättig, C., Höfener, S. & Klopper, W. (2007). Theor. Chem. Acc. 117, 587-597.]) basis set. Optimized geometries were then subjected to single-point energy calculations at the SCS-MP2 level with the larger Def2-QZVPP basis set to obtain final relative conformational energies. Geometry optimizations and single point energies were repeated using the SMD method to model the methanol solvent environment (Marenich et al., 2009[Marenich, A. V., Cramer, C. J. & Truhlar, D. G. (2009). J. Phys. Chem. B, 113, 6378-6396.]) used in the crystallization experiments. The results (Table 4[link]) show that the syn conformation [i.e. that found for (II)[link] and (III)] is favoured for all substituents by roughly the same energy (with the energy of the syn conformer arbitrarily defined to be zero in each case) either in vacuo or in a methanol solvent environment, although the differences in the latter case are quite small.

Table 4
Relative conformational energies (kJ mol−1)

The two values refer to a vacuum and methanol solvation, respectively. The energy of the syn conformer is arbitrarily set to zero in each case.
Substituent Compound anti syn
H (I) 14.90/5.91 0
CH3 Carvalho et al. (2017[Carvalho, S. A., Osorio, L. F. B., Salomão, K., de Castro, S. L., Wardell, S. M. S. V., Wardell, J. L., da Silva, E. F. & Fraga, C. A. M. (2017). J. Heterocycl. Chem. 54, 3626-3631.]) 14.90/6.84 0
F (II) 17.12/6.17 0
Br (III) 16.84/6.17 0

4. Supra­molecular features

In the crystal of (I)[link], the mol­ecules are linked by C—H⋯N hydrogen bonds (Table 1[link]) to generate [010] C(6) chains, with adjacent mol­ecules related by the 21 screw axis (Fig. 4[link]). The C5—H5⋯O3 contact is long and the angle is small, but if it is regarded as significant, it serves to cross-link the chains into (100) sheets. Weak aromatic π–π stacking inter­actions arise between the sheets, such that each imidazole ring is sandwiched by two phenyl groups and vice versa [centroid–centroid separations = 3.7355 (10) and 4.1184 (10) Å; corres­ponding slippages = 1.35 and 2.25 Å, respectively].

[Figure 4]
Figure 4
Fragment of an [010] hydrogen-bonded chain in the crystal of (I)[link]. Symmetry codes: (i) –x, [{1\over 2}] + y, 1/2 – z; (iii) x, y + 1, z.

There are a number of inter­molecular inter­actions in (II)[link] (Table 2[link]) and (III)[link] (Table 3[link]) and together they lead to three-dimensional networks in each case. It is inter­esting that the C9—H9⋯N1 inter­action in (II)[link] is clearly a directional bond [H⋯N = 2.58 Å compared to a van der Waals contact distance (Bondi, 1964[Bondi, A. (1964). J. Phys. Chem. 68, 441-451.]) of 2.75 Å for these atoms] whereas the equivalent contact in (III)[link], included in Table 3[link] for completeness, has an H⋯N separation of 2.77 Å and, by itself, would be very doubtful as a bond, which shows that isostructural crystals can show distinct variations in their weak inter­actions. This is supported by the presence of a weak C4—H4C⋯Br1 bond in (III)[link] (H⋯Br = 2.85 Å, van der Waals contact distance = 3.05 Å) whilst the equivalent link in (II)[link] has H⋯F = 2.77 Å, significantly greater than the van der Waals contact distance of 2.67 Å and would not be regarded as a significant bond. As in (I)[link], π–π stacking appears to consolidate the crystals of (II)[link] and (III)[link], in which the imidazole rings and phenyl rings form alternating stacks, which propagate in [100]. In (II)[link], the imidazole ring faces phenyl rings with centroid–centroid (slippage) distances of 3.7297 (7) (1.23) and 3.9323 (7) Å (1.64 Å). Equivalent data for (III)[link] are 3.7664 (18) (1.47) and 3.9698 (18) Å (1.82 Å).

5. Hirshfeld surface analysis

Hirshfeld surface fingerprint plots for (I)[link], (II)[link] and (III)[link] (supplementary Figs. 1[link], 2[link] and 3[link], respectively) were calculated with CrystalExplorer17 (Turner et al., 2017[Turner, M. J., McKinnon, J. J., Wolff, S. K., Grimwood, D. J., Spackman, P. R., Jayatilaka, D. & Spackman, M. A. (2017). CrystalExplorer17. University of Western Australia, Nedlands, Western Australia; https://hirshfeldsurface.net.]). When the fingerprint plots are decomposed into the separate types of inter­molecular contacts (McKinnon et al., 2007[McKinnon, J. J., Jayatilaka, D. & Spackman, M. A. (2007). Chem. Commun. 3814-3816.]), it may be seen (Table 5[link]) that as a percentage of surface inter­actions, H⋯H contacts (i.e. van der Waals inter­actions) are the most significant in each structure, followed by O⋯H/H⋯O contacts. It is inter­esting the percentage of the latter for (I)[link] is slightly higher than for (II)[link], despite the fact that (I)[link] features one weak C—H⋯O bond at best whilst (II)[link] features three such bonds. The C⋯C contacts (associated with aromatic π–π stacking) contribute a very small percentage in each structure, which is slightly surprising given the significant π–π stacking inter­actions noted above. Finally, it may be noted that the C⋯H/H⋯C and N⋯N/H⋯N contributions for (I)[link] and the C⋯H/H⋯C, N⋯N/H⋯N and X—H/H⋯X contributions for (II)[link] and (III)[link] sum to approximately the same amount.

Table 5
Hirshfeld contact inter­actions (%)

Contact type (I) (II) (III)
H⋯H 34.6 30.3 28.3
O⋯H/H⋯O 24.6 24.4 23.2
N⋯H/H⋯N 14.7 9.4 8.1
C⋯H/H⋯C 12.4 6.0 6.5
C⋯C 4.6 5.8 5.9
X⋯H/H⋯X – 11.7 15.0

Beyond a vague appeal to `packing forces', we find it difficult to explain why (I)[link] forms the energetically disfavoured anti conformation in the crystal: it allows the C5—H5 group to form a weak hydrogen bond (Table 1[link]) to a nitro group oxygen atom but it should be noted that the same grouping forms a similar bond in the opposite direction (i.e. pointing away from C4) in both (II)[link] and (III)[link]. The syn conformation for (II)[link] and (III)[link] seems to be favoured in terms of the occurrence of an intra­molecular C—H⋯N link and it is possible that weak C—H⋯X (X = F, Br) inter­actions in the crystals of (II)[link] and (III)[link] provide some stabilization not possible in (I)[link], although they are at the opposite end of the mol­ecule. The Hirshfeld fingerprint data (Table 5[link]) show that N⋯H/H⋯N and C⋯H/H⋯C contacts are somewhat more significant in the crystal of (I)[link] but the energetic consequences of these are not clear. We cannot rule out the posssibility that a polymorph of (I)[link] may exist in which the Nm—C—C=N grouping has a syn conformation but with a different overall packing motif to (II)[link] and (III)[link].

6. Database survey

A survey of of the Cambridge Structural Database (Groom et al., 2016[Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171-179.]: updated to January 2018) for the 1-methyl 5-nitro imidazole fragment revealed 33 hits. The 4-methyl-substituted analogue of the title compounds, N-[(4-methyl­benz­yl)­oxy]-1-(1-methyl-5-nitro-1H-imidazol-2-yl)methanimine (refcode: TEVGAF), has been reported by Carvalho et al. (2017[Carvalho, S. A., Osorio, L. F. B., Salomão, K., de Castro, S. L., Wardell, S. M. S. V., Wardell, J. L., da Silva, E. F. & Fraga, C. A. M. (2017). J. Heterocycl. Chem. 54, 3626-3631.]): its Nm—C—C=N torsion angle is −30.7 (2)°, i.e. somewhat twisted from syn.

7. Synthesis and crystallization

The syntheses and spectroscopic data of the title compounds have already been described (Carvalho et al., 2017[Carvalho, S. A., Osorio, L. F. B., Salomão, K., de Castro, S. L., Wardell, S. M. S. V., Wardell, J. L., da Silva, E. F. & Fraga, C. A. M. (2017). J. Heterocycl. Chem. 54, 3626-3631.]). The crystals used for data collections in this study were recrystallized from methanol solution in each case as colourless plates of (I)[link], orange blocks of (II)[link] and yellow blocks of (III)[link].

8. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 6[link]. The hydrogen atoms were geometrically placed (C—H = 0.95–0.99Å) and refined as riding atoms. The constraint Uiso(H) = 1.2Ueq(carrier) or 1.5Ueq(methyl carrier) was applied in all cases. The methyl groups were allowed to rotate, but not to tip, to best fit the electron density.

Table 6
Experimental details

  (I) (II) (III)
Crystal data
Chemical formula C12H12N4O3 C12H11FN4O3 C12H11BrN4O3
Mr 260.26 278.25 339.16
Crystal system, space group Monoclinic, P21/c Monoclinic, P21/n Monoclinic, P21/n
Temperature (K) 100 120 120
a, b, c (Å) 7.6399 (5), 10.5071 (7), 14.9243 (11) 7.5484 (2), 12.6442 (4), 13.4150 (9) 7.6024 (2), 12.7526 (3), 13.8954 (5)
β (°) 97.942 (3) 102.988 (7) 104.869 (2)
V (Å3) 1186.53 (14) 1247.62 (10) 1302.05 (7)
Z 4 4 4
Radiation type Mo Kα Mo Kα Mo Kα
μ (mm−1) 0.11 0.12 3.17
Crystal size (mm) 0.11 × 0.07 × 0.03 0.19 × 0.13 × 0.10 0.66 × 0.52 × 0.24
 
Data collection
Diffractometer Rigaku Saturn724+ CCD Rigaku Saturn724+ CCD Rigaku Mercury CCD
Absorption correction Multi-scan (FS_ABSCOR; Rigaku, 2013[Rigaku (2013). FS_ABSCOR. Rigaku Corporation, Tokyo, Japan.]) Multi-scan (FS_ABSCOR; Rigaku, 2013[Rigaku (2013). FS_ABSCOR. Rigaku Corporation, Tokyo, Japan.]) Multi-scan (FS_ABSCOR; Rigaku, 2013[Rigaku (2013). FS_ABSCOR. Rigaku Corporation, Tokyo, Japan.])
Tmin, Tmax 0.618, 1.000 0.802, 1.000 0.438, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections 7757, 2705, 1891 8522, 2848, 2292 16791, 2974, 2835
Rint 0.055 0.021 0.065
(sin θ/λ)max (Å−1) 0.649 0.649 0.650
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.047, 0.126, 0.95 0.034, 0.094, 1.09 0.051, 0.140, 1.11
No. of reflections 2705 2848 2974
No. of parameters 173 182 182
H-atom treatment H-atom parameters constrained H-atom parameters constrained H-atom parameters constrained
Δρmax, Δρmin (e Å−3) 0.24, −0.22 0.29, −0.18 1.78, −1.03
Computer programs: CrystalClear (Rigaku, 2012[Rigaku (2012). CrystalClear. Rigaku Corporation, Tokyo, Japan.]), SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]), SHELXL2014 (Sheldrick, 2015[Sheldrick, G. M. (2015). Acta Cryst. C71, 3-8.]), ORTEP-3 for Windows (Farrugia, 2012[Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849-854.]) and publCIF (Westrip, 2010[Westrip, S. P. (2010). J. Appl. Cryst. 43, 920-925.]).

Supporting information

CCDC references: 1486983; 1486982; 1486987

Crystal structure: contains datablocks I, II, III, global. DOI: https://doi.org/10.1107/S2056989018002876/mw2136sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989018002876/mw2136Isup2.hkl

Structure factors: contains datablock II. DOI: https://doi.org/10.1107/S2056989018002876/mw2136IIsup3.hkl

Structure factors: contains datablock III. DOI: https://doi.org/10.1107/S2056989018002876/mw2136IIIsup4.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2056989018002876/mw2136Isup5.cml

Supporting information file. DOI: https://doi.org/10.1107/S2056989018002876/mw2136IIsup6.cml

Supporting information file. DOI: https://doi.org/10.1107/S2056989018002876/mw2136IIIsup7.cml

Supplementary Figures 1, 2 and 3: Hirshfeld fingerprint plots. DOI: https://doi.org/10.1107/S2056989018002876/mw2136sup8.pdf

checkCIF report


Computing details top

For all structures, data collection: CrystalClear (Rigaku, 2012); cell refinement: CrystalClear (Rigaku, 2012); data reduction: CrystalClear (Rigaku, 2012); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012); software used to prepare material for publication: publCIF (Westrip, 2010).

(E)-1-Methyl-5-nitro-1H-imidazole-2-carbaldehyde O-benzyloxime (I) top
Crystal data top
C12H12N4O3F(000) = 544
Mr = 260.26Dx = 1.457 Mg m−3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
a = 7.6399 (5) ÅCell parameters from 7971 reflections
b = 10.5071 (7) Åθ = 2.4–27.5°
c = 14.9243 (11) ŵ = 0.11 mm−1
β = 97.942 (3)°T = 100 K
V = 1186.53 (14) Å3Plate, colourless
Z = 40.11 × 0.07 × 0.03 mm
Data collection top
Rigaku Saturn724+ CCD
diffractometer		1891 reflections with I > 2σ(I)
ω scansRint = 0.055
Absorption correction: multi-scan
(FS_ABSCOR; Rigaku, 2013)		θmax = 27.5°, θmin = 2.4°
Tmin = 0.618, Tmax = 1.000h = −9→6
7757 measured reflectionsk = −13→13
2705 independent reflectionsl = −19→18
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.047H-atom parameters constrained
wR(F2) = 0.126 w = 1/[σ2(Fo2) + (0.0674P)2]
where P = (Fo2 + 2Fc2)/3
S = 0.95(Δ/σ)max < 0.001
2705 reflectionsΔρmax = 0.24 e Å−3
173 parametersΔρmin = −0.22 e Å−3
0 restraints
Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
C1−0.2026 (2)0.18424 (17)0.08287 (11)0.0272 (4)
C2−0.1242 (2)0.06989 (17)0.10516 (11)0.0302 (4)
H2−0.11770.00100.06460.036*
C3−0.0953 (2)0.18453 (17)0.22478 (11)0.0262 (4)
C4−0.2593 (2)0.38590 (16)0.17211 (11)0.0295 (4)
H4A−0.37800.39180.13780.044*
H4B−0.18320.45120.15080.044*
H4C−0.26610.39910.23650.044*
C5−0.0422 (2)0.23260 (16)0.31595 (11)0.0277 (4)
H5−0.06100.31930.33000.033*
C60.1846 (3)0.13647 (17)0.51983 (12)0.0353 (5)
H6A0.27940.09690.49030.042*
H6B0.10690.06800.53720.042*
C70.2641 (2)0.20824 (16)0.60261 (11)0.0275 (4)
C80.2637 (2)0.15343 (17)0.68727 (11)0.0296 (4)
H80.20390.07510.69270.036*
C90.3508 (2)0.21295 (18)0.76444 (12)0.0328 (4)
H90.35220.17390.82200.039*
C100.4346 (2)0.32796 (18)0.75770 (12)0.0336 (4)
H100.49430.36800.81030.040*
C110.4313 (2)0.38490 (17)0.67342 (12)0.0327 (4)
H110.48650.46520.66860.039*
C120.3475 (2)0.32503 (17)0.59602 (11)0.0293 (4)
H120.34710.36390.53850.035*
N1−0.05705 (18)0.06958 (14)0.19410 (9)0.0292 (4)
N2−0.18520 (17)0.25946 (13)0.15896 (9)0.0257 (3)
N30.03028 (18)0.15619 (14)0.37682 (9)0.0287 (3)
N4−0.28663 (19)0.22404 (14)−0.00435 (9)0.0308 (4)
O10.08352 (16)0.22291 (11)0.45775 (7)0.0304 (3)
O2−0.33264 (17)0.33549 (12)−0.01644 (8)0.0382 (3)
O3−0.30669 (18)0.14106 (13)−0.06357 (8)0.0402 (4)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0262 (8)0.0346 (9)0.0192 (8)−0.0040 (7)−0.0031 (6)0.0003 (7)
C20.0309 (9)0.0354 (9)0.0224 (9)−0.0024 (8)−0.0026 (7)−0.0007 (7)
C30.0231 (8)0.0319 (9)0.0215 (8)−0.0024 (7)−0.0038 (6)0.0032 (7)
C40.0303 (9)0.0299 (8)0.0257 (9)0.0015 (7)−0.0055 (7)0.0003 (7)
C50.0276 (9)0.0319 (8)0.0215 (8)−0.0012 (7)−0.0033 (7)0.0000 (7)
C60.0412 (10)0.0328 (9)0.0270 (9)0.0019 (8)−0.0131 (8)0.0024 (8)
C70.0243 (8)0.0320 (9)0.0232 (8)0.0031 (7)−0.0070 (6)0.0001 (7)
C80.0266 (8)0.0335 (9)0.0272 (9)0.0006 (7)−0.0018 (7)0.0034 (7)
C90.0328 (9)0.0427 (10)0.0211 (9)0.0104 (8)−0.0030 (7)0.0024 (8)
C100.0305 (9)0.0404 (10)0.0263 (9)0.0069 (8)−0.0090 (7)−0.0072 (8)
C110.0271 (9)0.0317 (9)0.0366 (10)−0.0005 (7)−0.0049 (7)−0.0031 (8)
C120.0285 (9)0.0344 (9)0.0230 (9)0.0024 (8)−0.0031 (7)0.0037 (7)
N10.0306 (7)0.0339 (8)0.0212 (7)−0.0019 (6)−0.0033 (6)0.0012 (6)
N20.0247 (7)0.0305 (7)0.0197 (7)−0.0012 (6)−0.0049 (6)0.0002 (6)
N30.0282 (7)0.0355 (8)0.0203 (7)−0.0027 (6)−0.0040 (6)−0.0042 (6)
N40.0321 (8)0.0374 (8)0.0202 (7)−0.0036 (7)−0.0054 (6)0.0002 (7)
O10.0334 (7)0.0358 (6)0.0185 (6)0.0028 (5)−0.0087 (5)−0.0025 (5)
O20.0460 (8)0.0378 (7)0.0271 (7)0.0049 (6)−0.0085 (6)0.0048 (6)
O30.0500 (8)0.0428 (7)0.0236 (7)−0.0058 (6)−0.0097 (6)−0.0054 (6)
Geometric parameters (Å, º) top
C1—C21.363 (2)C6—H6A0.9900
C1—N21.375 (2)C6—H6B0.9900
C1—N41.432 (2)C7—C81.389 (2)
C2—N11.355 (2)C7—C121.392 (2)
C2—H20.9500C8—C91.396 (2)
C3—N11.338 (2)C8—H80.9500
C3—N21.368 (2)C9—C101.378 (3)
C3—C51.456 (2)C9—H90.9500
C4—N21.468 (2)C10—C111.390 (3)
C4—H4A0.9800C10—H100.9500
C4—H4B0.9800C11—C121.391 (2)
C4—H4C0.9800C11—H110.9500
C5—N31.279 (2)C12—H120.9500
C5—H50.9500N3—O11.4071 (16)
C6—O11.4428 (19)N4—O21.2287 (18)
C6—C71.502 (2)N4—O31.2359 (18)
C2—C1—N2108.43 (14)C12—C7—C6121.42 (15)
C2—C1—N4127.30 (16)C7—C8—C9120.27 (17)
N2—C1—N4124.26 (15)C7—C8—H8119.9
N1—C2—C1109.59 (15)C9—C8—H8119.9
N1—C2—H2125.2C10—C9—C8120.40 (16)
C1—C2—H2125.2C10—C9—H9119.8
N1—C3—N2112.68 (14)C8—C9—H9119.8
N1—C3—C5125.95 (14)C9—C10—C11119.54 (16)
N2—C3—C5121.28 (15)C9—C10—H10120.2
N2—C4—H4A109.5C11—C10—H10120.2
N2—C4—H4B109.5C10—C11—C12120.36 (17)
H4A—C4—H4B109.5C10—C11—H11119.8
N2—C4—H4C109.5C12—C11—H11119.8
H4A—C4—H4C109.5C11—C12—C7120.16 (16)
H4B—C4—H4C109.5C11—C12—H12119.9
N3—C5—C3118.90 (15)C7—C12—H12119.9
N3—C5—H5120.5C3—N1—C2105.18 (14)
C3—C5—H5120.5C3—N2—C1104.12 (14)
O1—C6—C7109.39 (14)C3—N2—C4126.14 (14)
O1—C6—H6A109.8C1—N2—C4129.47 (13)
C7—C6—H6A109.8C5—N3—O1110.01 (13)
O1—C6—H6B109.8O2—N4—O3124.23 (14)
C7—C6—H6B109.8O2—N4—C1119.68 (14)
H6A—C6—H6B108.2O3—N4—C1116.09 (14)
C8—C7—C12119.23 (15)N3—O1—C6107.65 (12)
C8—C7—C6119.24 (16)
N2—C1—C2—N10.2 (2)C1—C2—N1—C3−0.16 (19)
N4—C1—C2—N1178.92 (15)N1—C3—N2—C10.01 (19)
N1—C3—C5—N3−8.6 (3)C5—C3—N2—C1176.86 (15)
N2—C3—C5—N3175.00 (15)N1—C3—N2—C4174.49 (15)
O1—C6—C7—C8138.31 (16)C5—C3—N2—C4−8.7 (2)
O1—C6—C7—C12−45.5 (2)C2—C1—N2—C3−0.11 (18)
C12—C7—C8—C9−2.0 (3)N4—C1—N2—C3−178.90 (15)
C6—C7—C8—C9174.21 (16)C2—C1—N2—C4−174.33 (16)
C7—C8—C9—C101.4 (3)N4—C1—N2—C46.9 (3)
C8—C9—C10—C110.3 (3)C3—C5—N3—O1175.55 (14)
C9—C10—C11—C12−1.5 (3)C2—C1—N4—O2−171.21 (18)
C10—C11—C12—C70.9 (3)N2—C1—N4—O27.4 (3)
C8—C7—C12—C110.9 (3)C2—C1—N4—O38.3 (3)
C6—C7—C12—C11−175.28 (16)N2—C1—N4—O3−173.14 (16)
N2—C3—N1—C20.09 (19)C5—N3—O1—C6−172.50 (15)
C5—C3—N1—C2−176.59 (16)C7—C6—O1—N3172.62 (14)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C4—H4B···N3i0.982.513.466 (2)165
C5—H5···O3ii0.952.653.175 (2)115
Symmetry codes: (i) −x, y+1/2, −z+1/2; (ii) x, −y+1/2, z+1/2.
(E)-1-Methyl-5-nitro-1H-imidazole-2-carbaldehyde O-(4-fluorobenzyl) oxime (II) top
Crystal data top
C12H11FN4O3F(000) = 576
Mr = 278.25Dx = 1.481 Mg m−3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
a = 7.5484 (2) ÅCell parameters from 7472 reflections
b = 12.6442 (4) Åθ = 3.1–27.5°
c = 13.4150 (9) ŵ = 0.12 mm−1
β = 102.988 (7)°T = 120 K
V = 1247.62 (10) Å3Block, orange
Z = 40.19 × 0.13 × 0.10 mm
Data collection top
Rigaku Saturn724+ CCD
diffractometer		2292 reflections with I > 2σ(I)
ω scansRint = 0.021
Absorption correction: multi-scan
(FS_ABSCOR; Rigaku, 2013)		θmax = 27.5°, θmin = 3.1°
Tmin = 0.802, Tmax = 1.000h = −9→9
8522 measured reflectionsk = −14→16
2848 independent reflectionsl = −14→17
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.034H-atom parameters constrained
wR(F2) = 0.094 w = 1/[σ2(Fo2) + (0.0501P)2 + 0.1808P]
where P = (Fo2 + 2Fc2)/3
S = 1.09(Δ/σ)max < 0.001
2848 reflectionsΔρmax = 0.29 e Å−3
182 parametersΔρmin = −0.18 e Å−3
0 restraints
Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
C10.40044 (15)0.59196 (9)0.16775 (9)0.0177 (2)
C20.38559 (16)0.48697 (9)0.14129 (9)0.0192 (3)
H20.39230.45900.07650.023*
C30.35720 (15)0.49975 (9)0.29626 (9)0.0160 (2)
C40.40828 (17)0.69554 (9)0.33328 (9)0.0213 (3)
H4A0.32040.74990.30250.032*
H4B0.53200.72280.34010.032*
H4C0.38920.67690.40100.032*
C50.32784 (15)0.46335 (9)0.39394 (9)0.0176 (2)
H50.34570.39060.41090.021*
C60.18665 (15)0.54029 (9)0.60895 (9)0.0185 (2)
H6A0.07180.57160.56970.022*
H6B0.27370.59840.63300.022*
C70.15188 (14)0.47943 (9)0.69873 (9)0.0175 (2)
C80.10500 (15)0.37210 (9)0.69078 (9)0.0201 (3)
H80.10180.33540.62860.024*
C90.06311 (16)0.31892 (10)0.77312 (10)0.0238 (3)
H90.03280.24590.76840.029*
C100.06662 (16)0.37454 (11)0.86169 (10)0.0249 (3)
C110.11210 (17)0.48020 (11)0.87283 (9)0.0250 (3)
H110.11320.51650.93500.030*
C120.15620 (16)0.53179 (10)0.79027 (9)0.0210 (3)
H120.19000.60430.79650.025*
N10.36001 (13)0.42969 (8)0.22186 (7)0.0187 (2)
N20.38326 (12)0.60100 (7)0.26758 (7)0.0160 (2)
N30.27904 (12)0.52518 (8)0.45773 (7)0.0180 (2)
N40.42710 (14)0.67827 (8)0.10515 (8)0.0225 (2)
O10.26029 (11)0.46915 (6)0.54488 (6)0.01878 (19)
O20.44180 (14)0.76801 (7)0.14148 (7)0.0315 (2)
O30.43216 (14)0.65795 (8)0.01587 (7)0.0338 (2)
F10.02098 (11)0.32309 (7)0.94206 (6)0.0378 (2)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0181 (5)0.0188 (6)0.0166 (6)0.0022 (4)0.0048 (4)0.0022 (5)
C20.0219 (6)0.0197 (6)0.0162 (6)0.0018 (4)0.0051 (4)−0.0009 (5)
C30.0138 (5)0.0155 (5)0.0181 (6)0.0007 (4)0.0022 (4)0.0002 (5)
C40.0275 (6)0.0157 (6)0.0215 (6)−0.0017 (4)0.0071 (5)−0.0037 (5)
C50.0177 (5)0.0164 (6)0.0184 (6)−0.0011 (4)0.0030 (4)0.0005 (5)
C60.0188 (5)0.0187 (6)0.0185 (6)0.0011 (4)0.0055 (4)−0.0031 (5)
C70.0121 (5)0.0208 (6)0.0189 (6)0.0023 (4)0.0022 (4)0.0004 (5)
C80.0180 (5)0.0211 (6)0.0206 (6)0.0016 (4)0.0031 (4)−0.0007 (5)
C90.0214 (6)0.0211 (6)0.0286 (7)0.0017 (5)0.0049 (5)0.0053 (5)
C100.0212 (6)0.0328 (7)0.0217 (6)0.0045 (5)0.0067 (5)0.0111 (5)
C110.0237 (6)0.0342 (7)0.0174 (6)0.0031 (5)0.0053 (5)−0.0008 (5)
C120.0188 (6)0.0221 (6)0.0218 (6)0.0010 (4)0.0037 (4)−0.0012 (5)
N10.0203 (5)0.0175 (5)0.0181 (5)0.0003 (4)0.0042 (4)−0.0013 (4)
N20.0164 (4)0.0146 (5)0.0172 (5)0.0012 (4)0.0041 (4)0.0005 (4)
N30.0170 (5)0.0200 (5)0.0167 (5)−0.0001 (4)0.0032 (4)0.0030 (4)
N40.0237 (5)0.0212 (5)0.0243 (6)0.0027 (4)0.0092 (4)0.0038 (4)
O10.0230 (4)0.0186 (4)0.0164 (4)0.0026 (3)0.0077 (3)0.0022 (3)
O20.0468 (6)0.0176 (5)0.0332 (6)−0.0032 (4)0.0158 (4)0.0013 (4)
O30.0537 (6)0.0307 (5)0.0217 (5)0.0033 (4)0.0182 (4)0.0037 (4)
F10.0437 (5)0.0446 (5)0.0286 (4)0.0027 (4)0.0158 (4)0.0162 (4)
Geometric parameters (Å, º) top
C1—C21.3721 (16)C6—H6A0.9900
C1—N21.3789 (15)C6—H6B0.9900
C1—N41.4187 (15)C7—C121.3890 (16)
C2—N11.3506 (15)C7—C81.4005 (17)
C2—H20.9500C8—C91.3890 (17)
C3—N11.3382 (15)C8—H80.9500
C3—N21.3636 (15)C9—C101.3757 (18)
C3—C51.4522 (16)C9—H90.9500
C4—N21.4721 (15)C10—F11.3679 (14)
C4—H4A0.9800C10—C111.3791 (19)
C4—H4B0.9800C11—C121.3888 (17)
C4—H4C0.9800C11—H110.9500
C5—N31.2731 (15)C12—H120.9500
C5—H50.9500N3—O11.4012 (12)
C6—O11.4393 (13)N4—O21.2301 (14)
C6—C71.5013 (16)N4—O31.2339 (14)
C2—C1—N2108.14 (10)C8—C7—C6121.49 (11)
C2—C1—N4127.25 (11)C9—C8—C7120.48 (11)
N2—C1—N4124.60 (10)C9—C8—H8119.8
N1—C2—C1109.26 (10)C7—C8—H8119.8
N1—C2—H2125.4C10—C9—C8118.41 (12)
C1—C2—H2125.4C10—C9—H9120.8
N1—C3—N2112.56 (10)C8—C9—H9120.8
N1—C3—C5119.63 (10)F1—C10—C9118.57 (12)
N2—C3—C5127.81 (10)F1—C10—C11118.42 (12)
N2—C4—H4A109.5C9—C10—C11123.01 (12)
N2—C4—H4B109.5C10—C11—C12117.84 (12)
H4A—C4—H4B109.5C10—C11—H11121.1
N2—C4—H4C109.5C12—C11—H11121.1
H4A—C4—H4C109.5C11—C12—C7121.26 (11)
H4B—C4—H4C109.5C11—C12—H12119.4
N3—C5—C3122.53 (11)C7—C12—H12119.4
N3—C5—H5118.7C3—N1—C2105.71 (10)
C3—C5—H5118.7C3—N2—C1104.31 (9)
O1—C6—C7108.62 (9)C3—N2—C4126.92 (10)
O1—C6—H6A110.0C1—N2—C4128.42 (10)
C7—C6—H6A110.0C5—N3—O1110.43 (9)
O1—C6—H6B110.0O2—N4—O3123.85 (11)
C7—C6—H6B110.0O2—N4—C1119.16 (10)
H6A—C6—H6B108.3O3—N4—C1116.99 (10)
C12—C7—C8118.98 (11)N3—O1—C6107.89 (8)
C12—C7—C6119.43 (10)
N2—C1—C2—N1−0.16 (13)C5—C3—N1—C2178.73 (10)
N4—C1—C2—N1−179.62 (11)C1—C2—N1—C30.72 (13)
N1—C3—C5—N3−162.10 (10)N1—C3—N2—C10.95 (12)
N2—C3—C5—N317.64 (18)C5—C3—N2—C1−178.81 (11)
O1—C6—C7—C12152.70 (10)N1—C3—N2—C4−172.71 (10)
O1—C6—C7—C8−30.95 (14)C5—C3—N2—C47.53 (18)
C12—C7—C8—C90.13 (16)C2—C1—N2—C3−0.46 (12)
C6—C7—C8—C9−176.23 (10)N4—C1—N2—C3179.02 (10)
C7—C8—C9—C100.82 (17)C2—C1—N2—C4173.07 (10)
C8—C9—C10—F1178.37 (10)N4—C1—N2—C4−7.45 (18)
C8—C9—C10—C11−0.87 (18)C3—C5—N3—O1179.79 (9)
F1—C10—C11—C12−179.30 (10)C2—C1—N4—O2−178.34 (11)
C9—C10—C11—C12−0.05 (18)N2—C1—N4—O22.29 (17)
C10—C11—C12—C71.06 (18)C2—C1—N4—O32.41 (18)
C8—C7—C12—C11−1.10 (17)N2—C1—N4—O3−176.96 (11)
C6—C7—C12—C11175.34 (10)C5—N3—O1—C6−173.96 (9)
N2—C3—N1—C2−1.05 (13)C7—C6—O1—N3175.61 (8)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C4—H4C···N30.982.293.0184 (15)131
C4—H4A···N1i0.982.633.5693 (16)160
C9—H9···N1ii0.952.583.4973 (16)163
C2—H2···O3iii0.952.493.3165 (15)145
C5—H5···O2iv0.952.633.1676 (14)116
C6—H6A···O2v0.992.543.1376 (14)119
C4—H4C···F1vi0.982.773.353 (2)119
Symmetry codes: (i) −x+1/2, y+1/2, −z+1/2; (ii) x−1/2, −y+1/2, z+1/2; (iii) −x+1, −y+1, −z; (iv) −x+1/2, y−1/2, −z+1/2; (v) x−1/2, −y+3/2, z+1/2; (vi) −x+1/2, y+1/2, −z+3/2.
(E)-1-Methyl-5-nitro-1H-imidazole-2-carbaldehyde O-(4-bromobenzyl) oxime (III) top
Crystal data top
C12H11BrN4O3F(000) = 680
Mr = 339.16Dx = 1.730 Mg m−3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
a = 7.6024 (2) ÅCell parameters from 6837 reflections
b = 12.7526 (3) Åθ = 2.2–27.5°
c = 13.8954 (5) ŵ = 3.17 mm−1
β = 104.869 (2)°T = 120 K
V = 1302.05 (7) Å3Block, yellow
Z = 40.66 × 0.52 × 0.24 mm
Data collection top
Rigaku Mercury CCD
diffractometer		2835 reflections with I > 2σ(I)
ω scansRint = 0.065
Absorption correction: multi-scan
(FS_ABSCOR; Rigaku, 2013)		θmax = 27.5°, θmin = 2.2°
Tmin = 0.438, Tmax = 1.000h = −8→9
16791 measured reflectionsk = −16→16
2974 independent reflectionsl = −18→16
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.051H-atom parameters constrained
wR(F2) = 0.140 w = 1/[σ2(Fo2) + (0.0837P)2 + 1.3179P]
where P = (Fo2 + 2Fc2)/3
S = 1.11(Δ/σ)max = 0.001
2974 reflectionsΔρmax = 1.78 e Å−3
182 parametersΔρmin = −1.03 e Å−3
0 restraints
Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
C10.4010 (4)0.5860 (2)0.1628 (2)0.0210 (6)
C20.3825 (4)0.4812 (2)0.1385 (2)0.0227 (6)
H20.39020.45170.07690.027*
C30.3498 (4)0.4984 (2)0.2868 (2)0.0201 (6)
C40.3974 (5)0.6933 (2)0.3184 (3)0.0281 (7)
H4A0.31080.74570.28270.042*
H4B0.52140.72100.33080.042*
H4C0.37040.67700.38210.042*
C50.3150 (4)0.4652 (2)0.3803 (2)0.0221 (6)
H50.31200.39220.39320.026*
C60.2011 (4)0.5460 (2)0.5916 (2)0.0227 (6)
H6A0.08940.58330.55540.027*
H6B0.29820.59860.61590.027*
C70.1655 (4)0.4863 (2)0.6778 (2)0.0203 (6)
C80.1233 (4)0.3798 (2)0.6718 (2)0.0229 (6)
H80.12070.34220.61240.027*
C90.0849 (4)0.3284 (2)0.7522 (2)0.0237 (6)
H90.05610.25580.74810.028*
C100.0890 (4)0.3840 (2)0.8382 (2)0.0224 (6)
C110.1292 (4)0.4900 (2)0.8463 (2)0.0232 (6)
H110.13000.52750.90550.028*
C120.1683 (4)0.5400 (2)0.7656 (2)0.0232 (6)
H120.19770.61260.77020.028*
N10.3517 (4)0.42704 (18)0.21619 (19)0.0233 (5)
N20.3819 (3)0.59752 (17)0.25814 (18)0.0191 (5)
N30.2882 (3)0.52867 (18)0.44583 (19)0.0219 (5)
N40.4338 (4)0.6687 (2)0.1020 (2)0.0234 (5)
O10.2561 (3)0.47297 (15)0.52654 (16)0.0239 (5)
O20.4605 (4)0.75804 (16)0.13734 (19)0.0325 (5)
O30.4324 (4)0.64727 (19)0.01529 (19)0.0343 (6)
Br10.04121 (4)0.31299 (2)0.94938 (2)0.02821 (16)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0257 (14)0.0171 (12)0.0208 (14)0.0008 (10)0.0071 (11)−0.0021 (10)
C20.0304 (15)0.0168 (12)0.0214 (15)0.0020 (10)0.0076 (12)−0.0035 (10)
C30.0216 (13)0.0147 (11)0.0239 (15)0.0002 (10)0.0058 (11)−0.0007 (10)
C40.0431 (19)0.0137 (13)0.0295 (18)−0.0020 (11)0.0132 (15)−0.0045 (10)
C50.0241 (14)0.0144 (11)0.0284 (16)0.0010 (10)0.0078 (12)0.0019 (10)
C60.0284 (15)0.0165 (12)0.0237 (15)0.0008 (10)0.0079 (12)0.0004 (10)
C70.0198 (13)0.0173 (12)0.0231 (15)0.0017 (10)0.0042 (11)0.0025 (10)
C80.0259 (14)0.0168 (12)0.0256 (15)0.0013 (10)0.0058 (11)−0.0016 (10)
C90.0279 (15)0.0140 (11)0.0291 (17)0.0004 (10)0.0072 (12)0.0008 (11)
C100.0218 (14)0.0196 (13)0.0262 (15)0.0019 (10)0.0069 (11)0.0052 (10)
C110.0275 (15)0.0202 (13)0.0221 (15)0.0010 (11)0.0067 (12)−0.0016 (10)
C120.0290 (15)0.0141 (12)0.0269 (16)−0.0015 (10)0.0082 (12)0.0000 (10)
N10.0305 (13)0.0144 (10)0.0255 (13)−0.0002 (9)0.0083 (10)−0.0035 (9)
N20.0261 (12)0.0126 (10)0.0195 (12)−0.0001 (8)0.0071 (9)−0.0015 (9)
N30.0263 (12)0.0176 (10)0.0227 (13)−0.0007 (9)0.0079 (10)0.0041 (9)
N40.0268 (13)0.0188 (11)0.0257 (14)0.0005 (9)0.0090 (11)0.0011 (10)
O10.0328 (12)0.0170 (9)0.0253 (12)0.0019 (8)0.0137 (9)0.0027 (8)
O20.0485 (14)0.0161 (10)0.0357 (13)−0.0055 (9)0.0158 (11)−0.0015 (9)
O30.0536 (15)0.0290 (12)0.0251 (13)0.0010 (11)0.0190 (11)−0.0004 (10)
Br10.0366 (2)0.0231 (2)0.0267 (2)0.00051 (10)0.01133 (17)0.00691 (10)
Geometric parameters (Å, º) top
C1—C21.377 (4)C6—H6A0.9900
C1—N21.378 (4)C6—H6B0.9900
C1—N41.413 (4)C7—C81.393 (4)
C2—N11.352 (4)C7—C121.394 (4)
C2—H20.9500C8—C91.389 (4)
C3—N11.341 (4)C8—H80.9500
C3—N21.366 (3)C9—C101.383 (4)
C3—C51.453 (4)C9—H90.9500
C4—N21.468 (3)C10—C111.384 (4)
C4—H4A0.9800C10—Br11.905 (3)
C4—H4B0.9800C11—C121.387 (4)
C4—H4C0.9800C11—H110.9500
C5—N31.273 (4)C12—H120.9500
C5—H50.9500N3—O11.401 (3)
C6—O11.433 (4)N4—O31.232 (4)
C6—C71.502 (4)N4—O21.237 (3)
C2—C1—N2108.0 (3)C12—C7—C6118.9 (2)
C2—C1—N4126.9 (3)C9—C8—C7120.3 (3)
N2—C1—N4125.1 (2)C9—C8—H8119.8
N1—C2—C1109.1 (3)C7—C8—H8119.8
N1—C2—H2125.4C10—C9—C8119.4 (3)
C1—C2—H2125.4C10—C9—H9120.3
N1—C3—N2112.2 (3)C8—C9—H9120.3
N1—C3—C5119.7 (2)C9—C10—C11121.8 (3)
N2—C3—C5128.1 (3)C9—C10—Br1119.4 (2)
N2—C4—H4A109.5C11—C10—Br1118.8 (2)
N2—C4—H4B109.5C10—C11—C12118.1 (3)
H4A—C4—H4B109.5C10—C11—H11120.9
N2—C4—H4C109.5C12—C11—H11120.9
H4A—C4—H4C109.5C11—C12—C7121.5 (3)
H4B—C4—H4C109.5C11—C12—H12119.2
N3—C5—C3123.6 (3)C7—C12—H12119.2
N3—C5—H5118.2C3—N1—C2105.9 (2)
C3—C5—H5118.2C3—N2—C1104.7 (2)
O1—C6—C7108.3 (2)C3—N2—C4126.7 (3)
O1—C6—H6A110.0C1—N2—C4128.6 (2)
C7—C6—H6A110.0C5—N3—O1110.1 (2)
O1—C6—H6B110.0O3—N4—O2123.5 (3)
C7—C6—H6B110.0O3—N4—C1117.4 (2)
H6A—C6—H6B108.4O2—N4—C1119.1 (3)
C8—C7—C12118.9 (3)N3—O1—C6108.3 (2)
C8—C7—C6122.2 (3)
N2—C1—C2—N10.2 (3)C5—C3—N1—C2178.5 (3)
N4—C1—C2—N1−179.8 (3)C1—C2—N1—C30.5 (3)
N1—C3—C5—N3−170.9 (3)N1—C3—N2—C11.3 (3)
N2—C3—C5—N38.7 (5)C5—C3—N2—C1−178.3 (3)
O1—C6—C7—C8−23.1 (4)N1—C3—N2—C4−177.1 (3)
O1—C6—C7—C12159.4 (3)C5—C3—N2—C43.3 (5)
C12—C7—C8—C9−0.1 (4)C2—C1—N2—C3−0.9 (3)
C6—C7—C8—C9−177.7 (3)N4—C1—N2—C3179.2 (3)
C7—C8—C9—C100.0 (5)C2—C1—N2—C4177.4 (3)
C8—C9—C10—C110.5 (5)N4—C1—N2—C4−2.5 (5)
C8—C9—C10—Br1−178.8 (2)C3—C5—N3—O1179.2 (2)
C9—C10—C11—C12−0.9 (4)C2—C1—N4—O36.0 (5)
Br1—C10—C11—C12178.4 (2)N2—C1—N4—O3−174.0 (3)
C10—C11—C12—C70.8 (4)C2—C1—N4—O2−174.7 (3)
C8—C7—C12—C11−0.3 (4)N2—C1—N4—O25.3 (4)
C6—C7—C12—C11177.3 (3)C5—N3—O1—C6−171.8 (2)
N2—C3—N1—C2−1.2 (3)C7—C6—O1—N3179.7 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C4—H4C···N30.982.242.997 (4)133
C4—H4A···N1i0.982.623.499 (4)149
C9—H9···N1ii0.952.773.681 (4)160
C2—H2···O3iii0.952.443.282 (4)148
C5—H5···O2iv0.952.643.341 (4)131
C6—H6A···O2v0.992.633.254 (4)121
C4—H4C···Br1vi0.982.853.491 (3)124
Symmetry codes: (i) −x+1/2, y+1/2, −z+1/2; (ii) x−1/2, −y+1/2, z+1/2; (iii) −x+1, −y+1, −z; (iv) −x+1/2, y−1/2, −z+1/2; (v) x−1/2, −y+3/2, z+1/2; (vi) −x+1/2, y+1/2, −z+3/2.
Relative conformational energies (kJ mol-1) top
The two values refer to a vacuum and methane solvation, respectively. The energy of the syn conformer is arbitrarily set to zero in each case.
SubstituentCompoundantisyn
H(I)14.90/5.910
CH3Carvalho et al. (2017)14.90/6.840
F(II)17.12/6.170
Br(III)16.84/6.170
Hirshfeld contact interactions (%) top
Contact type(I)(II)(III)
H···H34.630.328.3
O···H/H···O24.624.423.2
N···H/H···N14.79.48.1
C···H/H···C12.46.06.5
C···C4.65.85.9
X···H/H···X–11.715.0
 

Acknowledgements

We thank the EPSRC National Crystallography Service (University of Southampton) for the X-ray data collections.

References

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Journal logoCRYSTALLOGRAPHIC
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ISSN: 2056-9890
Volume 74| Part 3| March 2018| Pages 380-384
https://doi.org/10.1107/S2056989018002876
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