research communications
a]pyridin-3-yl)ethan-1-one
and Hirshfeld surface analysis of 2,2,2-trifluoro-1-(7-methylimidazo[1,2-aKosygin State University of Russia, 117997 Moscow, Russian Federation, bN. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russian Federation, cDepartment of Aircraft Electrics and Electronics, School of Applied Sciences, Cappadocia University, Mustafapaşa, 50420 Ürgüp, Nevşehir, Turkey, dDepartment of Physics, Faculty of Sciences, Erciyes University, 38039 Kayseri, Turkey, and eDepartment of Chemistry, M.M.A.M.C (Tribhuvan University) Biratnagar, Nepal
*Correspondence e-mail: bkajaya@yahoo.com
The bicyclic imidazo[1,2-a]pyridine core in the molecule of the title compound, C10H7F3N2O, is planar within 0.004 (1) Å. In the crystal, the molecules are linked by pairs of C—H⋯N and C—H⋯O hydrogen bonds, forming strips. These strips are connected by the F⋯F contacts into layers, which are further joined by π–π stacking interactions. The Hirshfeld surface analysis and fingerprint plots reveal that molecular packing is governed by F⋯H/H⋯F (31.6%), H⋯H (16.8%), C⋯H/H⋯C (13.8%) and O⋯H/H⋯O (8.5%) contacts.
Keywords: crystal structure; imidazo[1,2-a]pyridine; hydrogen bonds; F⋯F contacts; Hirshfeld surface analysis.
CCDC reference: 2124974
1. Chemical context
The imidazo[1,2-a]pyridine synthon is one of the important fused bicyclic 5–6 heterocycles and it is recognized as a `drug prejudice' scaffold because of its wide range of applications in medicinal chemistry (Bagdi et al., 2015). This synthon is also useful in coordination chemistry and catalysis because of its coordination ability and non-covalent donor–acceptor bonding (Guseinov et al., 2022; Ma et al., 2020, 2021; Mahmudov et al., 2020, 2021). Synthesis of this synthon from easily available chemicals is desirable due to its importance in the various branches of chemistry (Bagdi et al., 2015). Along with this, intermolecular interactions organize molecular architectures, which play a crucial role in synthesis, catalysis, micellization, etc. (Gurbanov et al., 2020a,b; Kopylovich et al., 2011; Ma et al., 2017a,b). The non-covalent bond–acceptor ability of both nitrogen atoms in the imidazo[1,2-a]pyridine synthon can be used in crystal engineering and in the design of dyes and other materials (Maharramov et al., 2018; Mizar et al., 2012; Shixaliyev et al., 2014; Shikhaliyev et al., 2018, 2019). Herein, we report a one-pot synthesis of 2,2,2-trifluoro-1-(7-methylimidazo[1,2-a]pyridin-3-yl)ethan-1-one (I) from (E/Z)-3-bromo-1,1,1-trifluoro-4-isopropoxybut-3-en-2-one and 4-methylpyridin-2-amine, which provides multiple intermolecular non-covalent interactions.
2. Structural commentary
In the molecule of the title compound (Fig. 1), the fused bicyclic imidazo[1,2-a]pyridine core is planar within 0.004 (1) Å, with a dihedral angle of 0.34 (6)° between the mean planes of the five- and six-membered rings. The C2—C1—C8—C9 and N2—C1—C8—O1 torsion angles of 1.04 (18) and 1.14 (19)°, respectively, show that the ethanone group lies near the plane of the bicycle. The bond lengths N1—C2, C2—C1 and C1—C8 of 1.3367 (16), 1.3987 (16) and 1.4247 (16) Å, respectively, indicate strong π-conjugation in the N1–O1 chain.
3. Supramolecular features and Hirshfeld surface analysis
In the crystal, the molecules are linked by pairs of C—H⋯N and C—H⋯O hydrogen bonds into strips elongated along the [210] direction (Figs. 2 and 3, Table 1). These strips are joined into layers parallel to (12) by F⋯F contacts (Figs. 3–5, Table 2). The layers are connected by F⋯H contacts (Fig. 5, Table 2) and π–π interactions with a shortest intercentroid separation of 3.6395 (7) Å [Cg1⋯Cg1(1 − x, 1 − y, 1 − z); Cg1 is the centroid of the imidazole ring].
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To visualize the intermolecular interactions in the title compound, the 3D Hirshfeld surfaces and two-dimensional fingerprint plots were computed using Crystal Explorer 17 (Turner et al., 2017). The Hirshfeld surface plotted over dnorm in the range −0.3137 to 1.1314 a.u. is shown in Fig. 6. The intense red spots with negative dnorm values represent C—H⋯O and C—H⋯N hydrogen bonds. Pale red spots correspond to π–π interactions, which are also seen in the shape-index surface (Fig. 7) generated in the range −1 to 1 Å, where they are indicated by adjacent red and blue triangles. The Hirshfeld surface mapped over the electrostatic potential is shown in Fig. 8, where the hydrogen-bond acceptors are represented as red regions. The overall two-dimensional fingerprint plot, and those delineated into F⋯H/H⋯F (31.6%), H⋯H (16.8%), C⋯H/H⋯C (13.8%) and O⋯H/H⋯O (8.5%) contacts are illustrated in Fig. 9. Other minor contributions to the Hirshfeld surface are from N⋯H/H⋯N (7.7%), F⋯F (6.1%), O⋯C/C⋯O (4.2%), N⋯C/C⋯N (3.8%), C⋯C (2.4%), F⋯C/C⋯F (1.7%), F⋯N/N⋯F (1.4%), N⋯N (1.1%) and O⋯N/N⋯O (0.9%) contacts.
4. Database survey
The most closely related compounds containing a similar imidazo[1,2-a]pyridine skeleton, but with different substituents on the amide N atom are: N-t-butyl-2-(phenylethynyl)imidazo[1,2-a]pyridin-3-amine (XOWVOX; Tber et al., 2019), 6-bromo-2-(4-bromophenyl)imidazo[1,2-a]pyridine (KOXGEM; Khamees et al., 2019), N-t-butyl-2-(2-nitrophenyl)imidazo[1,2-a]pyridin-3-amine (PILGAV01; Dhanalakshmi et al., 2019), 2-(4-methoxyphenyl)-6-nitroimidazo[1,2-a]pyridine-3-carbaldehyde (DABTEI; Koudad et al., 2015), 2-(ethylsulfinyl)imidazo[1,2-a]pyridine-3-sulfonamide (ZAPJAD; Gong et al., 2012) and 2-methyl-6-(trifluoromethyl)imidazo[1,2-a]pyridine-3-carbonitrile (ULEGOI; Fun et al., 2011). In the crystal of XOWVOX, molecules are linked by N—H⋯H hydrogen bonds, forming chains along the c-axis direction. The chains are linked by C—H⋯π interactions, forming slabs parallel to the ac plane. In the structure of KOXGEM, an intramolecular C—H⋯N hydrogen bond forms an S(5) ring motif. In the crystal, a short H⋯H contact links adjacent molecules into centrosymmetric dimers. The dimers are joined by weak C—H⋯π and slipped π–π stacking interactions, forming layers parallel to (110), which are connected into a three-dimensional network by short Br⋯H contacts. In the crystal of PILGAV01, N—H⋯N hydrogen bonds link the molecules into [010] chains. The cohesion of the of DABTEI is ensured by C—H⋯N and C—H⋯O hydrogen bonds, forming layers parallel to the ac plane. In ZAPJAD, the supramolecular structure is defined by two kinds of intermolecular hydrogen bonds. Pairs of N—H⋯N hydrogen bonds link the molecules into centrosymmetric dimers and N—H⋯O hydrogen bonds link the dimers into tubular chains running along the a-axis direction. In the crystal of ULEGOI, molecules are linked into chains through pairs of C—H⋯N interactions, forming R22(12) and R22(8) hydrogen-bond ring motifs. These chains are stacked along the a axis.
5. Synthesis and crystallization
A mixture of (E/Z)-3-bromo-1,1,1-trifluoro-4-isopropoxybut-3-en-2-one (0.522 mg, 2 mmol) and 4-methylpyridin-2-amine (0.216 mg, 2 mmol) in dry isopropyl alcohol (15 mL) was refluxed for 4 h. Then the solvent was removed on a rotary evaporator under reduced pressure. The residue was recrystallized from methanol. Crystals suitable for X-ray analysis were obtained by slow evaporation of a methanol solution. Colourless solid (yield 94%), m.p. 405–406 K. Analysis calculated for C10H7F3N2O (M = 228.17): C 52.64, H 3.09, N 12.28; found: C 52.55, H 3.07, N 12.19%. 1H NMR (300 MHz, CDCl3) δ 2.48 (3H, CH3), 7.32–8.60 (3H, Ar), 9.32 (1H, CH). 13C NMR (75 MHz, CDCl3) δ 174.45, 150.22, 141.32, 135.67, 131.04, 123.55, 118.66, 118.21, 116.32 and 21.56. ESI–MS: m/z: 229.18 [M + H]+.
6. Refinement
Crystal data, data collection and structure . Hydrogen atoms were positioned geometrically (C—H = 0.95–0.98 Å) and refined as riding, with Uiso(H) = 1.2Ueq(C) for CH hydrogen atoms and Uiso(H) = 1.5Ueq(C) for CH3 hydrogen atoms.
details are summarized in Table 3Supporting information
CCDC reference: 2124974
https://doi.org/10.1107/S2056989021012676/yk2161sup1.cif
contains datablock I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989021012676/yk2161Isup2.hkl
Supporting information file. DOI: https://doi.org/10.1107/S2056989021012676/yk2161Isup3.cml
Data collection: CrysAlis PRO (Rigaku OD, 2021); cell
CrysAlis PRO (Rigaku OD, 2021); data reduction: CrysAlis PRO (Rigaku OD, 2021); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL (Sheldrick, 2015b); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012); software used to prepare material for publication: PLATON (Spek, 2020).C10H7F3N2O | Z = 2 |
Mr = 228.18 | F(000) = 232 |
Triclinic, P1 | Dx = 1.618 Mg m−3 |
a = 5.4384 (1) Å | Cu Kα radiation, λ = 1.54184 Å |
b = 8.8298 (2) Å | Cell parameters from 11472 reflections |
c = 10.0744 (2) Å | θ = 4.5–79.1° |
α = 102.501 (2)° | µ = 1.30 mm−1 |
β = 96.764 (2)° | T = 100 K |
γ = 91.415 (2)° | Block, colorless |
V = 468.39 (2) Å3 | 0.15 × 0.06 × 0.02 mm |
XtaLAB Synergy, Dualflex, HyPix diffractometer | 2006 independent reflections |
Radiation source: micro-focus sealed X-ray tube, PhotonJet (Cu) X-ray Source | 1927 reflections with I > 2σ(I) |
Mirror monochromator | Rint = 0.050 |
Detector resolution: 10.0000 pixels mm-1 | θmax = 79.5°, θmin = 4.5° |
ω scans | h = −6→6 |
Absorption correction: multi-scan (CrysAlis PRO; Rigaku OD, 2021) | k = −11→10 |
Tmin = 0.323, Tmax = 1.000 | l = −12→12 |
14165 measured reflections |
Refinement on F2 | Hydrogen site location: inferred from neighbouring sites |
Least-squares matrix: full | H-atom parameters constrained |
R[F2 > 2σ(F2)] = 0.037 | w = 1/[σ2(Fo2) + (0.0617P)2 + 0.1479P] where P = (Fo2 + 2Fc2)/3 |
wR(F2) = 0.105 | (Δ/σ)max = 0.001 |
S = 1.09 | Δρmax = 0.37 e Å−3 |
2006 reflections | Δρmin = −0.26 e Å−3 |
147 parameters | Extinction correction: SHELXL2018/3 (Sheldrick 2015b), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
0 restraints | Extinction coefficient: 0.0061 (14) |
Primary atom site location: dual |
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. |
x | y | z | Uiso*/Ueq | ||
F3 | 0.83669 (15) | 0.51338 (8) | 0.12281 (8) | 0.0298 (2) | |
F1 | 1.03655 (15) | 0.72062 (9) | 0.10632 (8) | 0.0306 (2) | |
F2 | 0.63947 (16) | 0.69737 (10) | 0.05569 (8) | 0.0352 (2) | |
O1 | 0.94235 (16) | 0.85798 (10) | 0.34833 (9) | 0.0231 (2) | |
N2 | 0.53525 (17) | 0.75163 (11) | 0.47862 (10) | 0.0178 (2) | |
N1 | 0.25848 (19) | 0.55184 (12) | 0.38082 (11) | 0.0224 (2) | |
C3 | 0.3285 (2) | 0.66590 (13) | 0.49404 (12) | 0.0195 (3) | |
C7 | 0.6410 (2) | 0.87311 (13) | 0.57981 (12) | 0.0199 (3) | |
H7 | 0.783693 | 0.930322 | 0.567582 | 0.024* | |
C6 | 0.5364 (2) | 0.90977 (14) | 0.69840 (12) | 0.0214 (3) | |
H6 | 0.608051 | 0.993640 | 0.769395 | 0.026* | |
C4 | 0.2206 (2) | 0.70392 (14) | 0.61568 (13) | 0.0214 (3) | |
H4 | 0.077951 | 0.646052 | 0.626999 | 0.026* | |
C5 | 0.3224 (2) | 0.82541 (14) | 0.71850 (13) | 0.0211 (3) | |
C2 | 0.4210 (2) | 0.56623 (14) | 0.29402 (12) | 0.0210 (3) | |
H2 | 0.416403 | 0.500889 | 0.205342 | 0.025* | |
C1 | 0.5986 (2) | 0.68799 (13) | 0.34799 (12) | 0.0191 (3) | |
C9 | 0.8297 (2) | 0.66755 (14) | 0.14284 (13) | 0.0231 (3) | |
C8 | 0.7991 (2) | 0.74800 (13) | 0.29223 (12) | 0.0190 (3) | |
C10 | 0.2118 (2) | 0.87010 (16) | 0.85047 (13) | 0.0267 (3) | |
H10A | 0.336148 | 0.863035 | 0.927312 | 0.040* | |
H10B | 0.068569 | 0.799545 | 0.848113 | 0.040* | |
H10C | 0.158430 | 0.976875 | 0.862058 | 0.040* |
U11 | U22 | U33 | U12 | U13 | U23 | |
F3 | 0.0391 (5) | 0.0189 (4) | 0.0298 (4) | −0.0012 (3) | 0.0086 (3) | −0.0001 (3) |
F1 | 0.0318 (4) | 0.0315 (4) | 0.0291 (4) | −0.0052 (3) | 0.0120 (3) | 0.0047 (3) |
F2 | 0.0349 (5) | 0.0452 (5) | 0.0241 (4) | 0.0054 (4) | −0.0037 (3) | 0.0081 (3) |
O1 | 0.0223 (4) | 0.0190 (4) | 0.0270 (4) | −0.0048 (3) | 0.0026 (3) | 0.0037 (3) |
N2 | 0.0161 (5) | 0.0153 (5) | 0.0222 (5) | −0.0015 (3) | 0.0010 (4) | 0.0058 (4) |
N1 | 0.0197 (5) | 0.0184 (5) | 0.0280 (5) | −0.0036 (4) | 0.0008 (4) | 0.0044 (4) |
C3 | 0.0158 (5) | 0.0162 (5) | 0.0272 (6) | −0.0019 (4) | 0.0002 (4) | 0.0079 (4) |
C7 | 0.0180 (5) | 0.0167 (5) | 0.0241 (6) | −0.0029 (4) | −0.0006 (4) | 0.0051 (4) |
C6 | 0.0208 (6) | 0.0192 (6) | 0.0231 (6) | −0.0002 (4) | −0.0002 (4) | 0.0044 (4) |
C4 | 0.0177 (5) | 0.0206 (6) | 0.0282 (6) | −0.0006 (4) | 0.0026 (4) | 0.0110 (5) |
C5 | 0.0201 (6) | 0.0203 (6) | 0.0250 (6) | 0.0029 (4) | 0.0023 (4) | 0.0098 (5) |
C2 | 0.0196 (6) | 0.0180 (6) | 0.0240 (6) | −0.0017 (4) | 0.0000 (4) | 0.0034 (4) |
C1 | 0.0191 (6) | 0.0167 (5) | 0.0213 (6) | −0.0006 (4) | 0.0008 (4) | 0.0046 (4) |
C9 | 0.0228 (6) | 0.0225 (6) | 0.0244 (6) | −0.0014 (4) | 0.0025 (5) | 0.0065 (5) |
C8 | 0.0186 (5) | 0.0162 (5) | 0.0227 (6) | 0.0010 (4) | 0.0009 (4) | 0.0063 (4) |
C10 | 0.0278 (6) | 0.0282 (7) | 0.0264 (6) | 0.0017 (5) | 0.0054 (5) | 0.0097 (5) |
F3—C9 | 1.3345 (14) | C6—H6 | 0.9500 |
F1—C9 | 1.3292 (14) | C6—C5 | 1.4245 (17) |
F2—C9 | 1.3453 (14) | C4—H4 | 0.9500 |
O1—C8 | 1.2208 (15) | C4—C5 | 1.3728 (18) |
N2—C3 | 1.3827 (14) | C5—C10 | 1.5028 (17) |
N2—C7 | 1.3706 (15) | C2—H2 | 0.9500 |
N2—C1 | 1.4011 (15) | C2—C1 | 1.3987 (16) |
N1—C3 | 1.3571 (16) | C1—C8 | 1.4247 (16) |
N1—C2 | 1.3367 (16) | C9—C8 | 1.5489 (17) |
C3—C4 | 1.3997 (17) | C10—H10A | 0.9800 |
C7—H7 | 0.9500 | C10—H10B | 0.9800 |
C7—C6 | 1.3629 (17) | C10—H10C | 0.9800 |
C3—N2—C1 | 106.60 (10) | N1—C2—C1 | 112.65 (11) |
C7—N2—C3 | 122.01 (10) | C1—C2—H2 | 123.7 |
C7—N2—C1 | 131.39 (10) | N2—C1—C8 | 123.53 (11) |
C2—N1—C3 | 105.23 (10) | C2—C1—N2 | 104.25 (10) |
N2—C3—C4 | 119.63 (11) | C2—C1—C8 | 132.19 (11) |
N1—C3—N2 | 111.28 (10) | F3—C9—F2 | 106.95 (10) |
N1—C3—C4 | 129.10 (11) | F3—C9—C8 | 113.36 (9) |
N2—C7—H7 | 120.8 | F1—C9—F3 | 107.82 (10) |
C6—C7—N2 | 118.35 (11) | F1—C9—F2 | 107.29 (10) |
C6—C7—H7 | 120.8 | F1—C9—C8 | 110.72 (10) |
C7—C6—H6 | 119.2 | F2—C9—C8 | 110.45 (10) |
C7—C6—C5 | 121.61 (11) | O1—C8—C1 | 126.81 (11) |
C5—C6—H6 | 119.2 | O1—C8—C9 | 117.43 (10) |
C3—C4—H4 | 120.2 | C1—C8—C9 | 115.72 (10) |
C5—C4—C3 | 119.55 (11) | C5—C10—H10A | 109.5 |
C5—C4—H4 | 120.2 | C5—C10—H10B | 109.5 |
C6—C5—C10 | 119.98 (11) | C5—C10—H10C | 109.5 |
C4—C5—C6 | 118.86 (11) | H10A—C10—H10B | 109.5 |
C4—C5—C10 | 121.17 (11) | H10A—C10—H10C | 109.5 |
N1—C2—H2 | 123.7 | H10B—C10—H10C | 109.5 |
F3—C9—C8—O1 | 130.29 (11) | C3—N1—C2—C1 | 0.16 (13) |
F3—C9—C8—C1 | −51.85 (14) | C3—C4—C5—C6 | −0.07 (16) |
F1—C9—C8—O1 | 8.98 (15) | C3—C4—C5—C10 | 179.86 (10) |
F1—C9—C8—C1 | −173.16 (10) | C7—N2—C3—N1 | −179.78 (10) |
F2—C9—C8—O1 | −109.71 (12) | C7—N2—C3—C4 | 0.59 (16) |
F2—C9—C8—C1 | 68.15 (13) | C7—N2—C1—C2 | 179.87 (11) |
N2—C3—C4—C5 | −0.35 (17) | C7—N2—C1—C8 | −2.02 (19) |
N2—C7—C6—C5 | −0.07 (17) | C7—C6—C5—C4 | 0.29 (17) |
N2—C1—C8—O1 | 1.14 (19) | C7—C6—C5—C10 | −179.65 (10) |
N2—C1—C8—C9 | −176.48 (9) | C2—N1—C3—N2 | −0.18 (13) |
N1—C3—C4—C5 | −179.91 (11) | C2—N1—C3—C4 | 179.41 (11) |
N1—C2—C1—N2 | −0.09 (13) | C2—C1—C8—O1 | 178.67 (12) |
N1—C2—C1—C8 | −177.96 (12) | C2—C1—C8—C9 | 1.04 (18) |
C3—N2—C7—C6 | −0.37 (16) | C1—N2—C3—N1 | 0.13 (13) |
C3—N2—C1—C2 | −0.03 (12) | C1—N2—C3—C4 | −179.50 (9) |
C3—N2—C1—C8 | 178.08 (10) | C1—N2—C7—C6 | 179.75 (11) |
D—H···A | D—H | H···A | D···A | D—H···A |
C2—H2···F3 | 0.95 | 2.53 | 2.9876 (14) | 110 |
C4—H4···N1i | 0.95 | 2.48 | 3.4139 (16) | 167 |
C7—H7···O1 | 0.95 | 2.43 | 2.9864 (14) | 117 |
C7—H7···O1ii | 0.95 | 2.30 | 3.1464 (14) | 147 |
Symmetry codes: (i) −x, −y+1, −z+1; (ii) −x+2, −y+2, −z+1. |
Contact | Distance | Symmetry operation |
O1···C3 | 3.1574 (15) | 1 + x, y, z |
F1···H10B | 2.86 | 1 + x, y, -1 + z |
F3···F1 | 2.9074 (11) | 2 - x, 1 - y, -z |
H10C···O1 | 2.83 | 1 - x, 2 - y, 1 - z |
F2···H10A | 2.64 | x, y, -1 + z |
H2···F2 | 2.80 | 1 - x, 1 - y, -z |
C3···N1 | 3.3055 (16) | 1 - x, 1 - y, 1 - z |
Acknowledgements
The author's contributions are as follows. Conceptualization, FIG, MA and AB; synthesis, FIG and KIK; X-ray analysis, BIU, ZA and MA; writing (review and editing of the manuscript), FIG, ZA, MA and AB.
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