research communications
N-[(E)-(5-nitrothiophen-2-yl)methylidene]aniline
and Hirshfeld surface analysis of 2-methyl-3-nitro-aSamsun University, Faculty of Engineering, Department of Fundamental Sciences, Samsun, 55420, Turkey, bOndokuz Mayıs University, Faculty of Arts and Sciences, Department of Physics, 55139, Samsun, Turkey, cOndokuz Mayıs University, Faculty of Arts and Sciences, Department of Chemistry, 55139, Samsun, Turkey, dAmasya University, Faculty of Arts and Sciences, Department of Chemistry, Amasya, Turkey, eKocaeli University, Faculty of Arts and Sciences, Department of Physics, 41100, Kocaeli, Turkey, fDepartment of Computer and Electronic Engineering Technology, Sana'a Community College, Sana'a, Yemen, and gOndokuz Mayıs University, Faculty of Engineering, Department of Electrical and Electronic Engineering, 55139, Samsun, Turkey
*Correspondence e-mail: sevgi.kansiz@samsun.edu.tr, eiad.saif@scc.edu.tr
The title compound, C12H9N3O4S, synthesized by condensation of 5-nitrothiophene-2-carbaldehyde and 2-methyl-3-nitroaniline, crystallizes in the orthorhombic P212121. In the molecule, the aromatic benzene and thiophene rings are twisted with respect to each other, making a dihedral angle of 23.16 (7)°. In the crystal, molecules are linked by intermolecular C—H⋯O hydrogen bonds into chains extending along the c-axis direction. Weak π–π stacking interactions along the a-axis direction provide additional stabilization of the The roles of the various intermolecular interactions were clarified by Hirshfeld surface analysis, which reveals that the crystal packing is dominated by O⋯H (39%) and H⋯H (21.3%) contacts. The crystal studied was refined as a two-component inversion twin.
Keywords: crystal structure; thiophene; 5-nitrothiophen-2-yl; Schiff base; Hirshfeld surface analysis; hydrogen bonding.
CCDC reference: 2055920
1. Chemical context
Bioactivity is an important topic, which includes many areas such as the synthesis of new drugs, creams, agricultural products and so on. In this respect, et al., 2008). can include heterocycles or amino acid residues and can be easily obtained by the condensation of primary with or without by-products, thus giving the pure product for biological treatments (Yu et al., 2009; Lobana et al., 2009). Many natural products contain thiophene groups, which lead to pharmacological properties. Thiophene-containing molecules are used in medicinal chemistry for therapeutic applications (Mishra et al., 2011). 5-Nitrothiophene-2-carboxaldehyde derivatives exhibit antibacterial properties (Foroumadi et al., 2003). This highly reactive molecule has been used in chemosensor applications (Ye et al., 2019). In the present study, a new Schiff base, 2-methyl-3-nitro-N-[(E)-(5-nitrothiophen-2-yl)methylidene]aniline (I), was obtained in crystalline form from the reaction of 5-nitrothiophene-2-carbaldehyde with 2-methyl-3-nitroaniline.
are organic molecules suitable for bioactivity applications because of the imine bond that increases the lipophilic character of the molecule. The imine bond provides a synthetic route to structural changes the electronic properties and leads to solubility in different media (Tarafder2. Structural commentary
The molecular structure of the title compound is shown in Fig. 1. The molecule adopts the E configuration with respect to the C=N bond and the benzene and thiophene rings form a dihedral angle of 23.16 (7)°. The deviation from planarity can be attributed to packing forces. The nitro group attached to the thiophene ring is strongly conjugated with the π-system of this ring, as evident from the short N2—C7 distance (see Table 1). As a result, this nitro group is almost coplanar with the thiophene ring. The nitro group attached to the benzene ring is twisted by 48.4 (2)° with respect to this ring, and thus the π-conjugation is much weaker in this case. The length of the C8=N2 bond is 1.277 (4) Å, which is consistent with those in the related structures 4-(naphthalen-2-yl)-N-[(Z)-4-propoxybenzylidene]-1,3-thiazol-2-amine [1.284 (3) Å; Sheakh Mohamad et al., 2020] and (E)-2,4-di-tert-butyl-6-[(3-chloro-4-methylphenylimino)methyl]phenol [1.278 (4) Å; Kansiz et al., 2018]. The C9—S1 and C12—S1 bonds in the thiophene ring are slightly shorter than a standard Csp2—S single bond (1.76 Å; Allen et al., 1987) as a result of the π-conjugation with the double bonds. At the same time, these S—C bonds are longer than those in the structure of 6-[(E)-2-(thiophen-2-yl)ethenyl]-4,5-dihydropyridazin-3(2H)-one [1.691 (3) Å; Daoui et al., 2019].
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3. Supramolecular features
In the i hydrogen bonds into chains stretched along the c-axis direction (Table 2; Fig. 2). As a result, the molecules form stacks extended along the a-axis direction. The shortest intercentroid separation of 3.603 (2) Å within the stack indicates π–π stacking interactions between the benzene and thiophene rings, which are, however, very weak, since intermolecular contacts shorter than the sum of van der Waals radii are absent from these stacks.
molecules are connected by weak intermolecular C8—H8⋯O44. Database survey
A search of the Cambridge Structural Database (CSD, version 5.41, update of November 2019; Groom et al., 2016) for (E)-N-[(5-nitrothiophen-2-yl)methylene]aniline gave 15 hits including 4-methyl-N-[(5-nitrothiophen-2-yl)methylidene]aniline (EXIWIS; Cai et al., 2011), N-(2-chlorophenyl)-1-(5-nitrothiophen-2-yl)methanimine (FIBKUZ; Tari et al., 2018) and 1-(5-nitro-2-thienyl)-N-(2-phenoxyphenyl)methanimine (TONBAB; Tanak et al., 2014). In FIBKUZ and TONBAB, intermolecular C—H⋯O hydrogen bonds are important features in the crystal packing, as in the structure of the title compound. In EXIWIS, the C=N bond length [1.277 (2) Å] is the same as in the title compound and longer than in both FIBKUZ [1.265 (6) Å] and in TONBAB [1.261 (4) Å]. The N—O bond lengths in the nitro groups in the title compound are the same within standard deviations as the corresponding bond lengths in all of the reference structures. The C—S bond lengths in EXIWIS, FIBKUZ and TONBAB range from 1.694 (3) to 1.730 (2) Å. The corresponding bond lengths in the title compound fall within these limits.
5. Hirshfeld surface analysis
The Hirshfeld surface analysis (Spackman & Jayatilaka, 2009) was carried out using the CrystalExplorer17.5 (Turner et al., 2017). The Hirshfeld surface and the associated two-dimensional fingerprint plots were used to quantify the various intermolecular interactions in the title compound. The Hirshfeld surfaces mapped over dnorm and electrostatic potential are illustrated in Fig. 3. In Fig. 3a, the red spots correspond to the O⋯H contacts. The electrostatic potential (Fig. 3b) shows donor (red) and acceptor (blue) regions. The percentage contribution of various interactions is shown in the fingerprint plot (Fig. 4). The most important interactions for determining the morphology of the crystal are H⋯H, O⋯H and S⋯H contacts, their individual contributions being 39%, 21.3% and 5.9%, respectively. C⋯N/N⋯C (5.8%) and C⋯H/H⋯C (5.4%) contacts are also observed. The Hirshfeld surface analysis confirms the importance of H-atom contacts in establishing the crystal packing.
6. Synthesis and crystallization
The title compound was prepared by refluxing a solution containing 5-nitrothiophene-2-carbaldehyde (0,07 mmol) and 2-methyl-3-nitroaniline (0,07 mmol) in ethanol (40 ml) for 5 h under stirring. The obtained yellow crystalline material was washed with ethanol and dried at room temperature (yield: 78%, m.p. 433 K). Crystals were grown from a solution in ethanol.
7. Refinement
Crystal data, data collection and structure . The C-bound H atoms were placed in idealized positions and refined using a riding model with C—H = 0.93–0.96 Å and Uiso(H) = 1.5Ueq(C-methyl) and 1.2Ueq(C) for other C-bound H atoms. The structure was refined as a two-component inversion twin.
details are summarized in Table 3Supporting information
CCDC reference: 2055920
https://doi.org/10.1107/S2056989021000529/yk2142sup1.cif
contains datablock I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989021000529/yk2142Isup2.hkl
Supporting information file. DOI: https://doi.org/10.1107/S2056989021000529/yk2142Isup3.cml
Data collection: X-AREA (Stoe & Cie, 2002); cell
X-AREA(Stoe & Cie, 2002); data reduction: X-RED32 (Stoe & Cie, 2002); program(s) used to solve structure: SHELXT2017/1 (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2017/1 (Sheldrick, 2015b); molecular graphics: PLATON (Spek, 2020); software used to prepare material for publication: WinGX (Farrugia, 2012).C12H9N3O4S | Dx = 1.496 Mg m−3 |
Mr = 291.28 | Mo Kα radiation, λ = 0.71073 Å |
Orthorhombic, P212121 | Cell parameters from 6261 reflections |
a = 7.1335 (4) Å | θ = 2.2–30.9° |
b = 11.7297 (6) Å | µ = 0.27 mm−1 |
c = 15.4593 (7) Å | T = 293 K |
V = 1293.54 (11) Å3 | Stick, yellow |
Z = 4 | 0.75 × 0.39 × 0.14 mm |
F(000) = 600 |
Stoe IPDS 2 diffractometer | 3930 independent reflections |
Radiation source: sealed X-ray tube, 12 x 0.4 mm long-fine focus | 2258 reflections with I > 2σ(I) |
Detector resolution: 6.67 pixels mm-1 | Rint = 0.049 |
rotation method scans | θmax = 30.5°, θmin = 2.2° |
Absorption correction: integration (X-RED32; Stoe & Cie, 2002) | h = −8→10 |
Tmin = 0.839, Tmax = 0.966 | k = −16→12 |
6707 measured reflections | l = −22→20 |
Refinement on F2 | Hydrogen site location: mixed |
Least-squares matrix: full | H atoms treated by a mixture of independent and constrained refinement |
R[F2 > 2σ(F2)] = 0.053 | w = 1/[σ2(Fo2) + (0.063P)2] where P = (Fo2 + 2Fc2)/3 |
wR(F2) = 0.129 | (Δ/σ)max < 0.001 |
S = 0.91 | Δρmax = 0.33 e Å−3 |
3930 reflections | Δρmin = −0.19 e Å−3 |
186 parameters | Absolute structure: Refined as an inversion twin. |
0 restraints | Absolute structure parameter: 0.59 (15) |
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. |
Refinement. Refined as a two-component inversion twin |
x | y | z | Uiso*/Ueq | ||
S1 | 0.63801 (15) | 0.83820 (8) | 0.62698 (6) | 0.0504 (3) | |
N2 | 0.6540 (5) | 0.6808 (2) | 0.47460 (18) | 0.0437 (7) | |
N1 | 0.7061 (6) | 0.2794 (3) | 0.3994 (3) | 0.0637 (10) | |
O2 | 0.8371 (6) | 0.2537 (3) | 0.4460 (2) | 0.0886 (11) | |
O1 | 0.5937 (6) | 0.2119 (3) | 0.3708 (3) | 0.0988 (13) | |
C8 | 0.7015 (6) | 0.7831 (3) | 0.4567 (2) | 0.0432 (8) | |
C7 | 0.6589 (5) | 0.5963 (3) | 0.4097 (2) | 0.0397 (7) | |
C9 | 0.6899 (5) | 0.8708 (3) | 0.5213 (2) | 0.0431 (8) | |
C6 | 0.6287 (6) | 0.6186 (3) | 0.3229 (2) | 0.0487 (9) | |
H6 | 0.610040 | 0.693392 | 0.304891 | 0.058* | |
C3 | 0.6828 (5) | 0.4000 (3) | 0.3749 (3) | 0.0474 (8) | |
N3 | 0.6315 (7) | 1.0145 (4) | 0.7400 (3) | 0.0756 (12) | |
C2 | 0.6860 (5) | 0.4834 (3) | 0.4389 (2) | 0.0423 (8) | |
C4 | 0.6524 (7) | 0.4210 (3) | 0.2888 (2) | 0.0549 (9) | |
H4 | 0.649811 | 0.361601 | 0.249035 | 0.066* | |
O3 | 0.5983 (7) | 0.9420 (5) | 0.7941 (2) | 0.1054 (15) | |
C12 | 0.6570 (6) | 0.9799 (3) | 0.6526 (2) | 0.0537 (10) | |
C11 | 0.7002 (6) | 1.0482 (3) | 0.5853 (3) | 0.0575 (11) | |
H11 | 0.714508 | 1.126873 | 0.589073 | 0.069* | |
O4 | 0.6437 (7) | 1.1168 (4) | 0.7564 (3) | 0.1149 (15) | |
C10 | 0.7204 (6) | 0.9856 (3) | 0.5095 (3) | 0.0520 (10) | |
H10 | 0.751275 | 1.017854 | 0.456431 | 0.062* | |
C1 | 0.7131 (7) | 0.4585 (4) | 0.5333 (3) | 0.0559 (10) | |
H1A | 0.710488 | 0.528510 | 0.565450 | 0.084* | |
H1B | 0.614362 | 0.409413 | 0.553194 | 0.084* | |
H1C | 0.831809 | 0.421538 | 0.541751 | 0.084* | |
C5 | 0.6258 (7) | 0.5321 (4) | 0.2626 (2) | 0.0573 (10) | |
H5 | 0.606041 | 0.548561 | 0.204434 | 0.069* | |
H8 | 0.747 (5) | 0.807 (3) | 0.403 (2) | 0.034 (9)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
S1 | 0.0561 (5) | 0.0487 (5) | 0.0465 (4) | −0.0019 (5) | −0.0005 (5) | −0.0003 (4) |
N2 | 0.0474 (16) | 0.0390 (15) | 0.0448 (15) | −0.0002 (14) | 0.0051 (14) | −0.0033 (12) |
N1 | 0.075 (3) | 0.0406 (18) | 0.075 (3) | 0.0010 (19) | 0.002 (2) | −0.0039 (17) |
O2 | 0.110 (3) | 0.0465 (17) | 0.109 (3) | 0.012 (2) | −0.021 (3) | 0.0103 (18) |
O1 | 0.120 (3) | 0.0470 (17) | 0.130 (3) | −0.0226 (19) | −0.015 (3) | −0.009 (2) |
C8 | 0.052 (2) | 0.0367 (18) | 0.0407 (18) | 0.0013 (15) | 0.0051 (16) | 0.0002 (14) |
C7 | 0.0433 (19) | 0.0334 (15) | 0.0424 (17) | −0.0017 (16) | 0.0050 (16) | −0.0029 (13) |
C9 | 0.042 (2) | 0.0383 (17) | 0.0490 (19) | 0.0033 (14) | −0.0003 (15) | −0.0014 (15) |
C6 | 0.062 (2) | 0.0445 (18) | 0.0400 (18) | 0.007 (2) | −0.0010 (19) | 0.0059 (14) |
C3 | 0.050 (2) | 0.0368 (17) | 0.055 (2) | 0.0010 (15) | 0.0040 (19) | 0.0005 (17) |
N3 | 0.070 (2) | 0.093 (3) | 0.063 (2) | 0.006 (3) | −0.006 (2) | −0.032 (2) |
C2 | 0.045 (2) | 0.0399 (18) | 0.0423 (18) | −0.0028 (15) | 0.0037 (15) | −0.0006 (15) |
C4 | 0.064 (3) | 0.050 (2) | 0.050 (2) | 0.002 (2) | 0.005 (2) | −0.0148 (17) |
O3 | 0.131 (4) | 0.134 (4) | 0.052 (2) | 0.012 (3) | 0.006 (2) | −0.010 (2) |
C12 | 0.050 (2) | 0.056 (2) | 0.055 (2) | 0.004 (2) | −0.0073 (19) | −0.0194 (18) |
C11 | 0.064 (3) | 0.038 (2) | 0.070 (3) | 0.0038 (18) | −0.004 (2) | −0.0101 (19) |
O4 | 0.141 (4) | 0.101 (3) | 0.102 (3) | 0.004 (3) | −0.007 (3) | −0.063 (3) |
C10 | 0.061 (2) | 0.0366 (19) | 0.058 (2) | −0.0001 (17) | −0.0024 (19) | 0.0013 (17) |
C1 | 0.073 (3) | 0.046 (2) | 0.048 (2) | 0.000 (2) | 0.002 (2) | 0.0085 (17) |
C5 | 0.073 (3) | 0.063 (2) | 0.0361 (18) | 0.002 (3) | −0.001 (2) | −0.0028 (17) |
S1—C12 | 1.714 (4) | C3—C2 | 1.392 (5) |
S1—C9 | 1.718 (4) | N3—O3 | 1.216 (6) |
N2—C8 | 1.277 (4) | N3—O4 | 1.230 (6) |
N2—C7 | 1.411 (4) | N3—C12 | 1.423 (5) |
N1—O1 | 1.211 (5) | C2—C1 | 1.501 (5) |
N1—O2 | 1.218 (5) | C4—C5 | 1.377 (6) |
N1—C3 | 1.474 (5) | C4—H4 | 0.9300 |
C8—C9 | 1.435 (5) | C12—C11 | 1.349 (6) |
C8—H8 | 0.93 (4) | C11—C10 | 1.391 (6) |
C7—C6 | 1.384 (5) | C11—H11 | 0.9300 |
C7—C2 | 1.412 (5) | C10—H10 | 0.9300 |
C9—C10 | 1.376 (5) | C1—H1A | 0.9600 |
C6—C5 | 1.378 (5) | C1—H1B | 0.9600 |
C6—H6 | 0.9300 | C1—H1C | 0.9600 |
C3—C4 | 1.371 (5) | C5—H5 | 0.9300 |
C12—S1—C9 | 89.25 (18) | C3—C2—C1 | 123.8 (3) |
C8—N2—C7 | 120.0 (3) | C7—C2—C1 | 120.8 (3) |
O1—N1—O2 | 124.3 (4) | C3—C4—C5 | 118.6 (3) |
O1—N1—C3 | 117.3 (4) | C3—C4—H4 | 120.7 |
O2—N1—C3 | 118.4 (4) | C5—C4—H4 | 120.7 |
N2—C8—C9 | 120.5 (3) | C11—C12—N3 | 126.4 (4) |
N2—C8—H8 | 124 (2) | C11—C12—S1 | 114.6 (3) |
C9—C8—H8 | 115 (2) | N3—C12—S1 | 119.0 (3) |
C6—C7—N2 | 123.5 (3) | C12—C11—C10 | 111.1 (4) |
C6—C7—C2 | 120.6 (3) | C12—C11—H11 | 124.5 |
N2—C7—C2 | 115.8 (3) | C10—C11—H11 | 124.5 |
C10—C9—C8 | 126.9 (4) | C9—C10—C11 | 112.9 (4) |
C10—C9—S1 | 112.2 (3) | C9—C10—H10 | 123.5 |
C8—C9—S1 | 120.9 (3) | C11—C10—H10 | 123.6 |
C5—C6—C7 | 121.3 (3) | C2—C1—H1A | 109.5 |
C5—C6—H6 | 119.4 | C2—C1—H1B | 109.5 |
C7—C6—H6 | 119.4 | H1A—C1—H1B | 109.5 |
C4—C3—C2 | 124.5 (3) | C2—C1—H1C | 109.5 |
C4—C3—N1 | 116.1 (3) | H1A—C1—H1C | 109.5 |
C2—C3—N1 | 119.4 (4) | H1B—C1—H1C | 109.5 |
O3—N3—O4 | 123.7 (5) | C4—C5—C6 | 119.7 (4) |
O3—N3—C12 | 118.6 (4) | C4—C5—H5 | 120.2 |
O4—N3—C12 | 117.7 (5) | C6—C5—H5 | 120.2 |
C3—C2—C7 | 115.4 (3) | ||
C7—N2—C8—C9 | 177.5 (3) | N2—C7—C2—C3 | 177.4 (3) |
C8—N2—C7—C6 | −30.4 (6) | C6—C7—C2—C1 | −178.2 (4) |
C8—N2—C7—C2 | 153.2 (4) | N2—C7—C2—C1 | −1.7 (6) |
N2—C8—C9—C10 | −173.9 (4) | C2—C3—C4—C5 | 1.0 (7) |
N2—C8—C9—S1 | 7.5 (5) | N1—C3—C4—C5 | 178.7 (4) |
C12—S1—C9—C10 | 0.4 (3) | O3—N3—C12—C11 | −177.8 (5) |
C12—S1—C9—C8 | 179.2 (3) | O4—N3—C12—C11 | 2.5 (8) |
N2—C7—C6—C5 | −176.7 (4) | O3—N3—C12—S1 | 0.6 (7) |
C2—C7—C6—C5 | −0.5 (7) | O4—N3—C12—S1 | −179.2 (4) |
O1—N1—C3—C4 | −47.0 (6) | C9—S1—C12—C11 | 0.0 (4) |
O2—N1—C3—C4 | 132.2 (4) | C9—S1—C12—N3 | −178.6 (4) |
O1—N1—C3—C2 | 130.8 (4) | N3—C12—C11—C10 | 178.1 (4) |
O2—N1—C3—C2 | −50.0 (6) | S1—C12—C11—C10 | −0.3 (5) |
C4—C3—C2—C7 | −1.2 (6) | C8—C9—C10—C11 | −179.3 (4) |
N1—C3—C2—C7 | −178.8 (3) | S1—C9—C10—C11 | −0.7 (4) |
C4—C3—C2—C1 | 177.9 (4) | C12—C11—C10—C9 | 0.6 (5) |
N1—C3—C2—C1 | 0.3 (6) | C3—C4—C5—C6 | −0.5 (7) |
C6—C7—C2—C3 | 0.9 (6) | C7—C6—C5—C4 | 0.3 (7) |
D—H···A | D—H | H···A | D···A | D—H···A |
C8—H8···O4i | 0.93 (4) | 2.56 (4) | 3.492 (5) | 176 (3) |
Symmetry code: (i) −x+3/2, −y+2, z−1/2. |
Funding information
This study was supported by Ondokuz Mayıs University under Project No. PYO·FEN.1906.19.001.
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