Crystal structure, DFT calculation, Hirshfeld surface analysis and energy framework study of 6-bromo-2-(4-bromo­phen­yl)imidazo[1,2-a]pyridine

Khamees, H.A.; Chaluvaiah, K.; El-khatatneh, N.A.; Swamynayaka, A.; Chong, K.H.; Dasappa, J.P.; Madegowda, M.

doi:10.1107/S2056989019013410

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ISSN: 2056-9890

Volume 75| Part 11| November 2019| Pages 1620-1626

https://doi.org/10.1107/S2056989019013410

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Crystal structure, DFT calculation, Hirshfeld surface analysis and energy framework study of 6-bromo-2-(4-bromophenyl)imidazo[1,2-a]pyridine

Hussien Ahmed Khamees,^a Kumara Chaluvaiah,^b Nasseem Ahmed El-khatatneh,^a Ananda Swamynayaka,^a Kwong Huey Chong,^c Jagadeesh Prasad Dasappa ^b and Mahendra Madegowda ^a ^*

^aDepartment of Studies in Physics, Manasagangotri, University of Mysore, Mysuru 570 006, Karnataka, India, ^bDepartment of Chemistry, Mangalore University, Mangalagangothri, Mangaluru 574 199, Karnataka, India, and ^cDepartment of Chemistry, Faculty of Science, Universiti Putra Malaysia 43400, UPM Serdang, Selangor Darul Ehsan, Malaysia
^*Correspondence e-mail: mahendra@physics.uni-mysore.ac.in

Edited by M. Weil, Vienna University of Technology, Austria (Received 18 September 2019; accepted 30 September 2019; online 3 October 2019)

The title imidazo[1,2-a] pyridine derivative, C₁₃H₈Br₂N₂, was synthesized via a single-step reaction method. The title molecule is planar, showing a dihedral angle of 0.62 (17)° between the phenyl and the imidazo[1,2-a] pyridine rings. An intramolecular C—H⋯N hydrogen bond with an S(5) ring motif is present. In the crystal, a short H⋯H contact links adjacent molecules into inversion-related dimers. The dimers are linked in turn by weak C—H⋯π and slipped π–π stacking interactions, forming layers parallel to (110). The layers are connected into a three-dimensional network by short Br⋯H contacts. Two-dimensional fingerprint plots and three-dimensional Hirshfeld surface analysis of the intermolecular contacts reveal that the most important contributions for the crystal packing are from H⋯Br/Br⋯H (26.1%), H⋯H (21.7%), H⋯C/C⋯H (21.3%) and C⋯C (6.5%) interactions. Energy framework calculations suggest that the contacts formed between molecules are largely dispersive in nature. Analysis of HOMO–LUMO energies from a DFT calculation reveals the pure π character of the aromatic rings with the highest electron density on the phenyl ring, and σ character of the electron density on the Br atoms. The HOMO–LUMO gap was found to be 4.343 eV.

Keywords: crystal structure; imidazole-pyridine derivative; π–π interactions; DFT calculation; Hirshfeld surface analysis; energy framework; frontier molecular orbitals.

CCDC references: 1914069; 1914069

1. Chemical context

Five-membered heterocyclic compounds comprising a nitrogen atom and at least one other non-carbon atom (i.e. nitrogen, sulfur, or oxygen) as part of the ring are known as azoles. To date, numerous azoles have found a wide range of applications in various fields, including agriculture (Berger et al., 2017 ), and because of their biological activities (Pozharskii et al., 2011 ; Kumbar et al., 2018 ). Among the various classes of azoles, the imidazole moiety with two nitrogen atoms is extremely common in nature and forms the core of many biomolecules (Chopra & Sahu, 2019 ) and synthetic drugs (Pozharskii et al., 2011). Furthermore, pyridine and its derivatives are present in many important compounds, including pharmaceuticals, vitamins (Al-Ghorbani et al., 2016 ) and drugs, acting as antimicrobial, antiviral, antioxidants, antidiabetic, anti-malarial, anti-inflammatory or antiamoebic agents, as well as psychopharmacological antagonists (Altaf et al., 2015 ). Hence, the combination of pyridine and imidazole derivatives has been proven to result in highly active agents in diverse biological fields that include anticancer (Kamal et al., 2014 ; Mantu et al., 2016 ), anti-HIV (Bode et al., 2011 ), antibacterial (Rival et al., 1992 ) and anti-inflammatory (Rupert et al., 2003 ) properties. In addition, such a combination showed significant activity against the human cytomegalo virus and the varicella-zoster virus (Gueiffier et al., 1998 ; Mavel et al., 2002 ).

In this context, we synthesized a new imidazo[1,2-a] pyridine derivative, C₁₃H₈Br₂N₂, and report herein its molecular and crystal structure, as well as the quantification of supramolecular interactions by Hirshfeld surface analysis. This study is supplemented by DFT calculations and a comparison of structural details with related compounds.

2. Structural commentary

The molecular structure of the title compound is depicted in Fig. 1. The molecular system is planar, showing a dihedral angle of 0.62 (17)° between the phenyl ring (C1–C6) and the imidazo[1,2-a] pyridine ring system (C7–C13,N1,N2). The torsion angles about the terminal bromine atoms, Br1 and Br2, are 177.3 (3)° (Br1—C1—C6—C5) and −178.9 (4)° (Br2—C11—C12—C13), respectively. The planar arrangement between the two rings enables an intramolecular C—H⋯N interaction (Fig. 1, Table 1) forming an S(5) ring motif (Tan & Tiekink, 2019 ). The Br1—C1 and Br2—C11 bond lengths are 1.886 (4) Å and 1.880 (4) Å, respectively, in good agreement with structures comprising bromophenyl moieties (Zhang & Hu, 2005 ; Arif Tawfeeq et al., 2019 ). The N1=C9 bond is slightly longer than similar bonds of reported imidazo[1,2-a] pyridine structures (see §7 for a listing of these structures), which may be attributed to the presence of the intramolecular bond (H5⋯N1). Overall, the bond lengths and angles of the phenyl ring and the imidazo[1,2-a]pyridine ring system are in normal ranges and compare well with those of other imidazo[1,2-a]pyridine derivatives (Zhang et al., 2005; Dhanalakshmi et al., 2018 ).

Table 1
Hydrogen-bond geometry (Å, °)

Cg3 is the centroid of C1–C6 ring

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C5—H5⋯N1	0.93	2.47	2.827 (5)	103
C3—H3⋯Cg3ⁱ	0.93	2.91	3.5670 (1)	129
Symmetry code: (i) $[x, -y-{\script{3\over 2}}, z-{\script{1\over 2}}]$ .

Figure 1
The molecular structure of the title compound with displacement ellipsoids drawn at the 50% probability level. The intramolecular C—H⋯N hydrogen bond forming an S(5) ring motif is shown with dashed lines.

3. Supramolecular features

The crystal packing is mainly based on short contacts and weak π–π interactions, similar to reported structures with the same kind of terminal bromine atoms (Arif Tawfeeq et al., 2019). In the title compound, two inversion-related molecules are linked by a short H5⋯H5(1 − x, 2 − y, z) contact (Fig. 2). These dimers are connected to each other through C—H⋯π interactions (Table 1), forming sheets propagating parallel to (110). Slipped π–π stacking interactions [Cg3⋯Cg1(−x, 1 − y, −z) = 3.655 (2) Å, slippage of 0.885 Å; Cg3⋯Cg2(−x, 1 − y, −z) = 3.819 (2) Å, slippage of 1.473 Å], where Cg1, Cg2 and Cg3 are the centroids of the imidazole, pyridine and phenyl rings, respectively, are also present within these sheets (Fig. 2). Adjacent sheets are linked along [001] into a three-dimensional network through short contacts of 3.01 Å between Br1 and H12(x, $[{3\over 2}]$ − y, $[{1\over 2}]$ + z), forming S(11) chain motifs (Fig. 3).

Figure 2
The crystal packing of the title compound in a view along [001], showing interactions in the sheets. H5⋯H5 short contacts are represented as blue dashed lines, C3—H3⋯Cg3 interactions as red dashed lines (slippage 1.676 Å) and Cg3⋯Cg1 and Cg3⋯Cg2 interactions as light-green dashed lines.

Figure 3
The three-dimensional supramolecular network of the title compound viewed approximately along [010].

4. DFT study and FMOs

Density functional theory (DFT) calculations were carried out by using the B3LYP basis set (Becke, 1993 ) at the highest basis set level of 6-311 ++G(d,p) in the GAUSSIAN09 program (Frisch et al., 2009 ). The DFT-optimized structure of the title compound is generally found to be in good agreement with the experimental data for all bond lengths and angles.

Frontier molecular orbitals (FMOs) are useful to specify the distribution of electronic densities and other quantum chemical parameters including hardness (η), softness (ζ), chemical potential (μ), electrophilicity (ψ) and electronegativity (χ) by foreseeing the highest occupied molecular orbitals (HOMO) and the lowest-unoccupied molecular orbitals (LUMO), as well as the energy gap (E_g = E_H - E_L) (Khamees et al., 2018 ). The results of these calculations are compiled in Table 2, and orbital energy plots of (E_H, E_H-1) and (E_L, E_L+1) are depicted in Fig. 4. The HOMO (ground state) manifests the highest π characterization for phenyl ring (C1–C6) that displays bifurcated π–π stacking interactions as well as C—H⋯π interactions in the supramolecular network, as discussed in Section 3. Pronounced σ character of the electron density is located on the two Br atoms, with the higher amount located on Br1. The other FMOs orbitals, i.e. HOMO-1, LUMO and LUMO+1, exhibit a mix of π and σ character on the rings with variations of the electron density distribution (Fig. 4). The HOMO–LUMO gap is 4.343 eV for the title compound.

Table 2
HUMO–LUMO energies and values of quantum chemical parameters (eV)

Property	Symbol and formula	Value
HOMO energy	E_H (eV)	−6.234
LUMO energy	E_L (eV)	−1.891
HOMO-1 energy	E_H-1 (eV)	−6.552
LUMO+1 energy	E_L+1 (eV)	−1.156
Energy gap 1	E_g1 = (E_H - E_L) (eV)	4.343
Energy gap 2	E_g2 = (E_H-1 - E_L+1) (eV)	5.397
Global hardness	η = (E_L - E_H)/2	2.172
Softness	ζ = 1/ 2η	0.230
Chemical potential	μ = (E_L + E_H)/2	4.062
Electrophilicity	ψ = μ²/2η	3.799
Electronegativity	χ = -μ	−4.062

Figure 4
Electron distribution and molecular orbital energies of HOMO-1, HOMO, LUMO and LUMO+1 of the title compound.

5. Hirshfeld surface analysis

The nature of intermolecular interactions in the title compound has been computed by CrystalExplorer17.5 (Turner et al., 2017 ), using Hirshfeld surface analysis (Spackman & Jayatilaka, 2009 ) and two-dimensional fingerprint plots (McKinnon et al., 2007 ). The d_norm plot was estimated via calculations of the external (d_e) and internal (d_i) distances to the nearest nucleus and built over the volume of 363.34 Å³ and an area of 339.81 Å², with scaled colour of −0.1544 (red) a.u. to 1.0479 (blue) a.u. (Fig. 5a). The plots of shape-index and curvedness were generated in the range of −4.0 to 4.0 a.u. and −1.00 to 1.00 a.u., respectively, (Fig. 5b,c). The medium dark and side pale-red spots on the Hirshfeld surface (Fig. 5a) symbolize the H5⋯H5 and Br1⋯H12 short contacts, respectively. The two-dimensional fingerprint plot for all contacts is depicted in Fig. 6a. The H⋯Br/Br⋯H contacts make the largest contribution (26.1%) to the Hirshfeld surface (Fig. 6b). These contacts also make a significant contribution to the crystal packing as the distance between the atoms involved is slightly less than their van der Waals radii (d_i + d_e ≃ 3.01 Å). The interatomic contacts of H⋯H interactions generated 22.7% of the Hirshfeld surface (Fig. 6c), showing a short spike at diagonal axes d_i + d_e ≃ 2.24 Å < 2.4 Å, denoting H⋯H short contacts with another significant effect on the molecular packing. The two symmetrical broad wings in Fig. 6d belong to H⋯C/C⋯H contacts that represent 21.3% of total surface and indicate the presence of C—H⋯π interactions in the crystal packing, where d_i + d_e ≃ 2.77 Å < 2.90 Å. The proportion of H⋯N/N⋯H contacts is 7.9% of the Hirshfeld surface (Fig. 6e) and they appear as two close wings pointing at a distance greater than the van der Waals radii of N and H atoms (d_i + d_e > 2.75Å), with no significant contribution towards the crystal packing of the title molecule. The small contribution of the C⋯C contacts (6.5%) to the Hirshfeld surface appears as an intense triangle (Fig. 6f) at d_i + d_e ≃ 3.6 Å, indicating π–π stacking interactions in the crystal packing. This type of stacking interaction appears as a flat region on the curvedness (Fig. 5c) and also on the shape-index as red and blue triangles on the rings (Fig. 5b), in particular on the phenyl ring (C1–C6). The contributions from other contacts have negligible effects on the packing.

Figure 5
(a) Hirshfeld surface mapped over d_norm showing short contacts as green dashed lines, (b) shape-index map and (c) curvedness map showing regions of π–π interactions.

Figure 6
Two-dimensional fingerprint plots of the title molecule with their relative contributions to the Hirshfeld surface.

6. Energy framework

Quantification of energy framework energies is considered a powerful method for understanding the topology of the overall interactions of molecules in the crystal. This method allowed us to calculate and compare different energy components, i.e. repulsion (E_rep), electric (E_ele), dispersion (E_dis), polarization (E_pol) and total (E_tot) energy based on the anisotropy of the topology of pairwise intermolecular interaction energies. CrystalExplorer17.5 (Turner et al., 2017) was used to calculate the energy framework of the title compound by generating new wave functions using the DFT method under 3-21G basis set with exchange and potential functions (B3LYP) for a molecular cluster environment for a 1×1×1 unit cell. The thickness of the cylinder radius indicates the grade of interactions and is directly related to the energy magnitude and offers information about the stabilization of the crystal packing. In order to avoid the crowdedness of less significant interaction energies, we set the cylindrical radii with a cut-off value of 5 kJ mol⁻¹ and a scale factor of 50 to all energy components. The benchmarked energies were scaled according to Mackenzie et al. (2017 ) while E_rep, E_ele, E_dis and E_pol were scaled as 0.618, 1.057, 0.740, 0.871, respectively (Edwards et al., 2017 ). The results of the calculations revealed that dispersion interactions exhibit approximately chair-shaped energy topologies through the rings, having a maximum energy value of −180.558 kJ mol⁻¹ (Fig. 7). The other energy components have values of 62.232 kJ mol⁻¹, −29.38 kJ mol⁻¹ and −9.176 kJ mol⁻¹ for repulsion, electrostatic and polarization energies, respectively. The small value of electrostatic energy is attributed to the absence of classical hydrogen bonds. The total interaction energy that resulted from all four main components is −156.886 kJ mol⁻¹ (Fig. 7d).

Figure 7
Energy framework of the title molecules viewed along [001], showing: (a) electrostatic, (b) dispersion, (c) total energy force diagrams and (d) the details of interaction with colour-coded, symmetry operation (Symop) and distances between molecular centroids (R) in Å.

7. Database survey

36 structures containing the 2-phenylimidazo[1,2-a]pyridine moiety with different substituents were found in a search of the Cambridge Structural Database (CSD, version 5.40, last update May 2019; Groom et al., 2016 ). The different substituents R₁ (on the imidazo[1,2-a]pyridinyl ring) and R₂ (on the phenyl ring) together with the dihedral angles between the mean planes of the corresponding imidazo[1,2-a]pyridinyl and phenyl rings (dihedral angle 1) are compiled in Table 3. By comparing the substitution positions, the structures can be divided into `3-(substituted)imidazo[1,2-a]pyridinyl' compounds and `non-3-(substituted)imidazo[1,2-a]pyridinyl' compounds. In general, the 3-(substituted)imidazo[1,2-a]pyridinyl compounds have a greater dihedral angle 1 values (12.0–47.5°). This may arise from steric repulsion between the 3-(substituted) group and the phenyl ring. However, there are four outliers (KABMIM, MIXZOJ, MONREO and ZUSSAJ) whose dihedral angle 1 values are lower than 10°. Most of the non-3-(substituted)imidazo[1,2-a]pyridinyl compounds have dihedral angle 1 values between 0.7 and 12.5°, which indicates that the imidazo[1,2-a]pyridinyl rings are close to coplanar to their attached phenyl rings. Here, the outlier is JEBZEY where the imidazo[1,2-a]pyridinyl ring is attached to a di-ortho-substituted isophthalonitrile ring. The dihedral angle 1 is 46.4° in this structure.

Table 3
Comparison of structural details in related imidazo[1,2-a]pyridinyl derivatives containing phenyl rings

Dihedral angle 1 is the angle between the mean planes of imidazo[1,2-a]pyridinyl and phenyl rings. Two sets of dihedral angles 1 are stated for compounds HURZOL, MONREO, OMIDEV, RUJNEQ, TUZYEU, ZUSSAJ and VEGKAU because there are two molecules in their asymmetric units.

Compound	R₁	R₂	Dihedral angle 1
3-(Substituted)imidazo[1,2-a]pyridinyl
AHOMIV (Liu et al., 2015 )	6-iodo-3-(methylsulfanyl)-imidazo[1,2-a]pyridinyl	phenyl	27.0
BEGTUE (Nair et al., 2012 )	ethyl (imidazo[1,2-a]pyridin-3-yl)acetate	phenyl	38.6
DABTEI (Koudad et al., 2015 )	6-nitroimidazo[1,2-a]pyridinyl-3-carbaldehyde	4-methoxyphenyl	34.0
DIDZUO (Dey et al., 2018 )	3-chloro-7-methyl-imidazo[1,2-a]pyridinyl	phenyl	28.0
ECEGEA (Ma et al., 2011 )	ethyl 8-methyl-imidazo[1,2-a]pyridinyl-3-carboxylate	phenyl	44.2
HUPWIZ01 (Vega et al., 2011 )	N,N-dimethyl-2-(6-methyl-imidazo[1,2-a]pyridin-3-yl)acetamide	4-methylphenyl	24.6
HURZOL (Yang et al., 2015 )	6-methylimidazo[1,2-a]pyridin-3-yl thiocyanate	3-chlorophenyl	33.8, 27.7
KABMIM (Yang et al., 2016 )	6-methyl-3-nitrosoimidazo[1,2-a]pyridinyl	3-chlorophenyl	6.8
MIXZOJ (Anaflous et al., 2008a )	N-(imidazo[1,2-a]pyridin-3-yl)acetamide	phenyl	9.0
MIXZUP (Anaflous et al., 2008b )	imidazo[1,2-a]pyridinyl-3-carbaldehyde	phenyl	28.6
MONREO (Velázquez-Ponce et al., 2013 )	3-nitrosoimidazo[1,2-a]pyridinyl	phenyl	17.4, 4.9
NOGRIM (Marandi et al., 2014 )	3-(t-butylamino)-imidazo[1,2-a]pyridinyl-8-carboxylic acid	3-nitrophenyl	16.8
OMIDEV (Samanta et al., 2016 )	3-iodo-8-methyl-imidazo[1,2-a]pyridinyl	phenyl	36.1, 34.4
QUQSEC (Ravi et al., 2016 )	6-methyl-3-(methylsulfanyl)imidazo[1,2-a]pyridinyl	4-chlorophenyl	38.1
RELQUW (Yan et al., 2012 )	8-methyl-3-nitroimidazo[1,2-a]pyridinyl	phenyl	47.5
RUJNEQ (Li et al., 2009 )	imidazo[1,2-a]pyridinyl-3-carbaldehyde	4-chlorophenyl	34.6, 33.5
TUZYEU (Zhang et al., 2016 )	6-fluoro-3-nitro-imidazo[1,2-a]pyridinyl	phenyl	43.8, 37.9
UTITEX (Chunavala et al., 2011 )	ethyl 7-methylimidazo[1,2-a]pyridinyl-3-carboxylate	phenyl	39.6
YEDHIY (Georges et al., 1993 )	6-chloro-N,N-dipropylimidazo[1,2-a] pyridinyl-3-acetamide	4-chlorophenyl	15.2
ZUSSAJ (Xiao et al., 2015 )	3-chloro-imidazo[1,2-a]pyridinyl	4-methylphenyl	12.0, 0.3
Non-3-(substituted)imidazo[1,2-a]pyridinyl
BISDUF (Kutniewska et al., 2018 )	imidazo[1,2-a]pyridinyl	2-hydroxy-5-methoxyphenyl	6.0
BISFAN (Kutniewska et al., 2018)	imidazo[1,2-a]pyridinyl	2-hydroxy-4-bromophenyl	4.2
CAJTIQ (Aslanov et al., 1983 )	6-nitro-imidazo[1,2-a]pyridinyl	phenyl	3.3
FEMQOF (Kurteva et al. 2012 )	imidazo[1,2-a]pyridinyl	4-methoxyphenyl	12.5
JEBZEY (Zhu et al., 2017 )	imidazo[1,2-a]pyridinyl	isophthalonitrile	46.4
MIQSUD (Jin et al., 2019 )	2-(imidazo[1,2-a]pyridin-5-yl)propan-2-ol	phenyl	2.7
NAGGEH (Tafeenko et al., 1996 )	imidazo[1,2-a]pyridinyl	phenyl	4.4
NONFOM (Mutai et al., 2008 )	imidazo[1,2-a]pyridinyl	2-hydroxyphenyl	6.7
NUBVUD (Seferoğlu et al., 2015 )	7-methylimidazo[1,2-a]pyridinyl	4-methoxyphenyl	0.7
NUBWAK (Seferoğlu et al., 2015)	7-methyl-imidazo[1,2-a]pyridinyl	phenyl	5.3
QODZUG (Mutai et al., 2014 )	imidazo[1,2-a]pyridinyl-6-carbonitrile	2-hydroxyphenyl	2.8
TIDVIN (Donohoe et al., 2012 )	6-bromo-imidazo[1,2-a]pyridinyl	phenyl	2.4
VEGKAU (Duan et al., 2006 )	imidazo[1,2-a]pyridinyl	3-bromo-4-methoxyphenyl	12.2, 2.7
WUHKER (Aydıner et al., 2015 )	7-methylimidazo[1,2-a]pyridinyl	4-chlorophenyl	9.1
ZUNVOV (Stasyuk et al., 2016 )	imidazo[1,2-a]pyridinyl	2-hydroxy-4-florophenyl	3.2
ZUPCOE (Stasyuk et al., 2016)	imidazo[1,2-a]pyridinyl	2-hydroxy-4-methoxyphenyl	5.8

8. Synthesis and crystallization

5-Bromopyridin-2-amine (1.211 g, 0.007 mol) and phenacyl bromide (0.007 mol) were refluxed for 14 h in 50 ml of absolute ethanol. The progress of the reaction was monitored by thin layer chromatography using Merck alumina backed silica gel 60 F254. After completion of the reaction, the resulting product was poured into crushed ice to obtain a fine grained solid product that was filtered off, separated and dried. The crude product was then recrystallized from hot ethanol with a yield of ∼70%. The melting point of 345 K was determined in an open capillary and is uncorrected. IR (KBr, cm⁻¹): 3080 (Ar C—H stretch), 2918 (aliphatic C—H stretch, 4-bromophenyl moiety), 1587 (C=N stretch), 1332 (C—N), 792 and 595 (C—Br). ¹H NMR (400 MHz, DMSO, δ ppm): 7.37 (d, 1H, 5-bromopyridine moiety), 7.55 (d, 2H, 4-bromophenyl moiety), 7.56 (d, 1H, 5-bromopyridine moiety), 7.78 (d, 2H, 4-bromophenyl moiety), 8.37 (s, 1H, imidazole ring), 8.87 (s, 1H, 5-bromopyridine moiety).¹³C NMR (400 MHz, δ ppm): 145.13 (imidazopyridine carbon atom), 110.24, 119.82, 125.12 and 132.14 (four carbon atoms of 5-bromopyridine moiety), 123.12, 128.30, 132.11, and 132.32 (six carbon atoms of 4-bromophenyl moiety), 113.13 and 130.10 (two carbon atoms of imidazole ring). LC–Mass m/z 350 [M+], 352 [M+2], 354 [M+4]. Analysis calculated for C₁₃H₈Br₂N₂ (350): C, 44.36; H, 2.29; N, 7.96. Found: C, 44.31; H, 2.23; N, 7.92%.

9. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 4. Hydrogen atoms were placed in calculated positions (C—H = 0.93 Å) and were included in the refinement in the riding-model approximation, with U_iso(H) set to 1.2U_eq(C). The reflection (002) was affected by the beam-stop and was removed from the refinement

Table 4
Experimental details

Crystal data
Chemical formula	C₁₃H₈Br₂N₂
M_r	352.03
Crystal system, space group	Orthorhombic, Pbca
Temperature (K)	293
a, b, c (Å)	14.1711 (4), 6.0546 (2), 27.7102 (8)
V (Å³)	2377.54 (12)
Z	8
Radiation type	Mo Kα
μ (mm⁻¹)	6.80
Crystal size (mm)	0.15 × 0.14 × 0.14

Data collection
Diffractometer	Bruker Kappa APEXII CCD
No. of measured, independent and observed [I > 2σ(I)] reflections	41143, 3485, 1726
R_int	0.100
(sin θ/λ)_max (Å⁻¹)	0.704

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.047, 0.118, 1.00
No. of reflections	3485
No. of parameters	154
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.88, −0.49
Computer programs: APEX2 and SAINT (Bruker, 2016 ), SHELXT (Sheldrick, 2015a ), SHELXL (Sheldrick, 2015b ), Mercury (Macrae et al., 2008 ), PLATON (Spek, 2009 ) and publCIF (Westrip, 2010 ).

Supporting information

CCDC references: 1914069; 1914069

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2056989019013410/wm5525sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989019013410/wm5525Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2056989019013410/wm5525Isup3.cml

checkCIF report

Computing details top

Data collection: APEX2 (Bruker, 2016); cell refinement: SAINT (Bruker, 2016); data reduction: SAINT (Bruker, 2016); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL (Sheldrick, 2015b); molecular graphics: Mercury (Macrae et al., 2008) and PLATON (Spek, 2009); software used to prepare material for publication: publCIF (Westrip, 2010).

6-Bromo-2-(4-bromophenyl)imidazo[1,2-a]pyridine top

Crystal data top

C₁₃H₈Br₂N₂	D_x = 1.967 Mg m⁻³
M_r = 352.03	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, Pbca	Cell parameters from 3485 reflections
a = 14.1711 (4) Å	θ = 2.1–30.1°
b = 6.0546 (2) Å	µ = 6.80 mm⁻¹
c = 27.7102 (8) Å	T = 293 K
V = 2377.54 (12) Å³	Block, colourless
Z = 8	0.15 × 0.14 × 0.14 mm
F(000) = 1360

Data collection top

Bruker Kappa APEXII CCD diffractometer	R_int = 0.100
ω and φ scan	θ_max = 30.1°, θ_min = 2.1°
41143 measured reflections	h = −19→19
3485 independent reflections	k = −8→8
1726 reflections with I > 2σ(I)	l = −39→38

Refinement top

Refinement on F²	0 restraints
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.047	H-atom parameters constrained
wR(F²) = 0.118	w = 1/[σ²(F_o²) + (0.0442P)² + 2.6166P] where P = (F_o² + 2F_c²)/3
S = 1.00	(Δ/σ)_max = 0.002
3485 reflections	Δρ_max = 0.88 e Å⁻³
154 parameters	Δρ_min = −0.49 e Å⁻³

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

	x	y	z	U_iso*/U_eq
Br2	0.15325 (4)	0.05914 (9)	0.27691 (2)	0.0700 (2)
Br1	0.12673 (4)	0.88905 (10)	0.68410 (2)	0.0740 (2)
N2	0.1377 (2)	0.3517 (6)	0.40975 (12)	0.0449 (8)
N1	0.0885 (2)	0.6735 (6)	0.44091 (12)	0.0484 (9)
C7	0.1238 (3)	0.5400 (6)	0.47646 (14)	0.0401 (9)
C1	0.1234 (3)	0.7762 (8)	0.62067 (15)	0.0482 (11)
C11	0.1297 (3)	0.2554 (7)	0.32808 (15)	0.0498 (11)
C4	0.1241 (3)	0.6173 (7)	0.52687 (15)	0.0424 (9)
C12	0.0872 (3)	0.4597 (8)	0.31737 (16)	0.0571 (12)
H12	0.070603	0.493692	0.285760	0.069*
C8	0.1549 (3)	0.3438 (8)	0.45819 (15)	0.0479 (10)
H8	0.182324	0.228190	0.475266	0.058*
C3	0.1597 (3)	0.4933 (7)	0.56424 (16)	0.0495 (10)
H3	0.185335	0.355055	0.557750	0.059*
C6	0.0866 (3)	0.9064 (7)	0.58414 (16)	0.0539 (11)
H6	0.061410	1.044944	0.590752	0.065*
C13	0.0707 (3)	0.6058 (8)	0.35300 (15)	0.0561 (12)
H13	0.041977	0.740195	0.346048	0.067*
C2	0.1582 (3)	0.5687 (8)	0.61068 (16)	0.0532 (11)
H2	0.180652	0.480001	0.635558	0.064*
C5	0.0885 (3)	0.8244 (7)	0.53745 (15)	0.0479 (10)
H5	0.065063	0.911265	0.512485	0.057*
C9	0.0968 (3)	0.5559 (7)	0.40055 (15)	0.0442 (10)
C10	0.1555 (3)	0.2005 (7)	0.37352 (15)	0.0492 (11)
H10	0.184202	0.065712	0.380142	0.059*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Br2	0.0853 (4)	0.0701 (4)	0.0545 (3)	0.0001 (3)	0.0150 (3)	−0.0104 (2)
Br1	0.0737 (4)	0.1022 (4)	0.0460 (3)	−0.0056 (3)	0.0062 (2)	−0.0110 (3)
N2	0.039 (2)	0.047 (2)	0.049 (2)	−0.0024 (16)	0.0010 (15)	0.0053 (16)
N1	0.051 (2)	0.050 (2)	0.044 (2)	0.0047 (17)	0.0001 (16)	0.0062 (17)
C7	0.032 (2)	0.042 (2)	0.045 (2)	0.0013 (19)	−0.0038 (17)	0.0074 (18)
C1	0.041 (2)	0.063 (3)	0.040 (2)	−0.008 (2)	0.0008 (18)	0.004 (2)
C11	0.051 (3)	0.052 (3)	0.046 (2)	−0.002 (2)	0.007 (2)	−0.002 (2)
C4	0.030 (2)	0.047 (2)	0.051 (2)	−0.0038 (18)	−0.0002 (18)	0.005 (2)
C12	0.070 (3)	0.060 (3)	0.041 (2)	0.002 (2)	0.007 (2)	0.013 (2)
C8	0.043 (2)	0.055 (3)	0.046 (2)	0.002 (2)	−0.0061 (19)	0.006 (2)
C3	0.046 (2)	0.045 (2)	0.058 (3)	0.008 (2)	−0.001 (2)	0.008 (2)
C6	0.051 (3)	0.049 (3)	0.062 (3)	0.003 (2)	0.004 (2)	−0.001 (2)
C13	0.067 (3)	0.057 (3)	0.044 (2)	0.009 (2)	0.005 (2)	0.008 (2)
C2	0.047 (3)	0.066 (3)	0.046 (2)	0.007 (2)	−0.0042 (19)	0.008 (2)
C5	0.044 (2)	0.051 (3)	0.048 (2)	0.006 (2)	−0.0076 (19)	0.013 (2)
C9	0.044 (2)	0.041 (2)	0.048 (2)	0.0035 (19)	0.0013 (18)	0.0050 (19)
C10	0.047 (3)	0.042 (2)	0.059 (3)	0.002 (2)	0.002 (2)	0.000 (2)

Geometric parameters (Å, º) top

Br2—C11	1.880 (4)	C4—C5	1.383 (6)
Br1—C1	1.886 (4)	C12—C13	1.346 (6)
N2—C8	1.365 (5)	C12—H12	0.9300
N2—C10	1.382 (5)	C8—H8	0.9300
N2—C9	1.389 (5)	C3—C2	1.366 (6)
N1—C9	1.331 (5)	C3—H3	0.9300
N1—C7	1.369 (5)	C6—C5	1.386 (6)
C7—C8	1.364 (6)	C6—H6	0.9300
C7—C4	1.473 (6)	C13—C9	1.401 (6)
C1—C2	1.378 (6)	C13—H13	0.9300
C1—C6	1.385 (6)	C2—H2	0.9300
C11—C10	1.353 (6)	C5—H5	0.9300
C11—C12	1.407 (6)	C10—H10	0.9300
C4—C3	1.375 (6)

C8—N2—C10	131.2 (4)	C2—C3—C4	121.4 (4)
C8—N2—C9	106.6 (3)	C2—C3—H3	119.3
C10—N2—C9	122.2 (4)	C4—C3—H3	119.3
C9—N1—C7	104.8 (3)	C1—C6—C5	118.1 (4)
C8—C7—N1	111.4 (4)	C1—C6—H6	120.9
C8—C7—C4	128.9 (4)	C5—C6—H6	120.9
N1—C7—C4	119.7 (4)	C12—C13—C9	120.1 (4)
C2—C1—C6	120.5 (4)	C12—C13—H13	119.9
C2—C1—Br1	120.6 (3)	C9—C13—H13	119.9
C6—C1—Br1	119.0 (4)	C3—C2—C1	120.0 (4)
C10—C11—C12	121.9 (4)	C3—C2—H2	120.0
C10—C11—Br2	119.9 (3)	C1—C2—H2	120.0
C12—C11—Br2	118.2 (3)	C4—C5—C6	122.0 (4)
C3—C4—C5	118.0 (4)	C4—C5—H5	119.0
C3—C4—C7	122.8 (4)	C6—C5—H5	119.0
C5—C4—C7	119.2 (4)	N1—C9—N2	111.0 (3)
C13—C12—C11	119.8 (4)	N1—C9—C13	130.6 (4)
C13—C12—H12	120.1	N2—C9—C13	118.3 (4)
C11—C12—H12	120.1	C11—C10—N2	117.6 (4)
C7—C8—N2	106.1 (4)	C11—C10—H10	121.2
C7—C8—H8	127.0	N2—C10—H10	121.2
N2—C8—H8	127.0

C9—N1—C7—C8	0.9 (5)	C6—C1—C2—C3	2.4 (7)
C9—N1—C7—C4	−178.9 (4)	Br1—C1—C2—C3	−176.7 (3)
C8—C7—C4—C3	1.1 (6)	C3—C4—C5—C6	−1.0 (6)
N1—C7—C4—C3	−179.1 (4)	C7—C4—C5—C6	179.9 (4)
C8—C7—C4—C5	−179.8 (4)	C1—C6—C5—C4	1.2 (6)
N1—C7—C4—C5	0.0 (6)	C7—N1—C9—N2	−0.7 (4)
C10—C11—C12—C13	−0.5 (7)	C7—N1—C9—C13	178.7 (5)
Br2—C11—C12—C13	−178.9 (4)	C8—N2—C9—N1	0.3 (5)
N1—C7—C8—N2	−0.8 (5)	C10—N2—C9—N1	−178.8 (4)
C4—C7—C8—N2	179.0 (4)	C8—N2—C9—C13	−179.2 (4)
C10—N2—C8—C7	179.3 (4)	C10—N2—C9—C13	1.7 (6)
C9—N2—C8—C7	0.3 (4)	C12—C13—C9—N1	179.3 (5)
C5—C4—C3—C2	1.5 (6)	C12—C13—C9—N2	−1.4 (7)
C7—C4—C3—C2	−179.4 (4)	C12—C11—C10—N2	0.8 (6)
C2—C1—C6—C5	−1.8 (6)	Br2—C11—C10—N2	179.2 (3)
Br1—C1—C6—C5	177.3 (3)	C8—N2—C10—C11	179.8 (4)
C11—C12—C13—C9	0.8 (7)	C9—N2—C10—C11	−1.4 (6)
C4—C3—C2—C1	−2.2 (7)

Hydrogen-bond geometry (Å, º) top

Cg3 is the centroid of C1–C6 ring

D—H···A	D—H	H···A	D···A	D—H···A
C5—H5···N1	0.93	2.47	2.827 (5)	103
C3—H3···Cg3ⁱ	0.93	2.91	3.5670 (1)	129

Symmetry code: (i) x, −y−3/2, z−1/2.

HUMO–LUMO energies and values of quantum chemical parameters (eV) top

Property	Symbol and formula	Value
HOMO energy	E_H (eV)	-6.234
LUMO energy	E_L (eV)	-1.891
HOMO-1 energy	E_H-1 (eV)	-6.552
LUMO+1 energy	E_L+1 (eV)	-1.156
Energy gap 1	E_g1 = (E_H - E_L) (eV)	4.343
Energy gap 2	E_g2 = (E_H-1 - E_L+1) (eV)	5.397
Global hardness	η = (E_L - E_H)/2	2.172
Softness	ζ = 1/ 2η	0.230
Chemical potential	µ = (E_L + E_H)/2	4.062
Electrophilicity	ψ = µ²/2η	3.799
Electronegativity	χ = -µ	-4.062

Comparison of structural details in related imidazo[1,2-a]pyridinyl derivatives containing phenyl rings top

Compound	R₁	R₂	Dihedral angle 1
3-(Substituted)imidazo[1,2-a]pyridinyl
AHOMIV (Liu et al., 2015)	6-iodo-3-(methylsulfanyl)-imidazo[1,2-a]pyridinyl	phenyl	27.0
BEGTUE (Nair et al., 2012)	ethyl (imidazo[1,2-a]pyridin-3-yl)acetate	phenyl	38.6
DABTEI (Koudad et al., 2015)	6-nitroimidazo[1,2-a]pyridinyl-3-carbaldehyde	4-methoxyphenyl	34.0
DIDZUO (Dey et al., 2018)	3-chloro-7-methyl-imidazo[1,2-a]pyridinyl	phenyl	28.0
ECEGEA (Ma et al., 2011)	ethyl 8-methyl-imidazo[1,2-a]pyridinyl-3-carboxylate	phenyl	44.2
HUPWIZ01 (Vega et al., 2011)	N,N-dimethyl-2-(6-methyl-imidazo[1,2-a]pyridin-3-yl)acetamide	4-methylphenyl	24.6
HURZOL (Yang et al., 2015)	6-methylimidazo[1,2-a]pyridin-3-yl thiocyanate	3-chlorophenyl	33.8, 27.7
KABMIM (Yang et al., 2016)	6-methyl-3-nitrosoimidazo[1,2-a]pyridinyl	3-chlorophenyl	6.8
MIXZOJ (Anaflous et al., 2008a)	N-(imidazo[1,2-a]pyridin-3-yl)acetamide	phenyl	9.0
MIXZUP (Anaflous et al., 2008b)	imidazo[1,2-a]pyridinyl-3-carbaldehyde	phenyl	28.6
MONREO (Velázquez-Ponce et al., 2013)	3-nitrosoimidazo[1,2-a]pyridinyl	phenyl	17.4, 4.9
NOGRIM (Marandi et al., 2014)	3-(t-butylamino)-imidazo[1,2-a]pyridinyl-8-carboxylic acid	3-nitrophenyl	16.8
OMIDEV (Samanta et al., 2016)	3-iodo-8-methyl-imidazo[1,2-a]pyridinyl	phenyl	36.1, 34.4
QUQSEC (Ravi et al., 2016)	6-methyl-3-(methylsulfanyl)imidazo[1,2-a]pyridinyl	4-chlorophenyl	38.1
RELQUW (Yan et al., 2012)	8-methyl-3-nitroimidazo[1,2-a]pyridinyl	phenyl	47.5
RUJNEQ (Li et al., 2009)	imidazo[1,2-a]pyridinyl-3-carbaldehyde	4-chlorophenyl	34.6, 33.5
TUZYEU (Zhang et al., 2016)	6-fluoro-3-nitro-imidazo[1,2-a]pyridinyl	phenyl	43.8, 37.9
UTITEX (Chunavala et al., 2011)	ethyl 7-methylimidazo[1,2-a]pyridinyl-3-carboxylate	phenyl	39.6
YEDHIY (Georges et al., 1993)	6-chloro-N,N-dipropylimidazo[1,2-a] pyridinyl-3-acetamide	4-chlorophenyl	15.2
ZUSSAJ (Xiao et al., 2015)	3-chloro-imidazo[1,2-a]pyridinyl	4-methylphenyl	12.0, 0.3
Non-3-(substituted)imidazo[1,2-a]pyridinyl
BISDUF (Kutniewska et al., 2018)	imidazo[1,2-a]pyridinyl	2-hydroxy-5-methoxyphenyl	6.0
BISFAN (Kutniewska et al., 2018)	imidazo[1,2-a]pyridinyl	2-hydroxy-4-bromophenyl	4.2
CAJTIQ (Aslanov et al., 1983)	6-nitro-imidazo[1,2-a]pyridinyl	phenyl	3.3
FEMQOF (Kurteva et al. 2012)	imidazo[1,2-a]pyridinyl	4-methoxyphenyl	12.5
JEBZEY (Zhu et al., 2017)	imidazo[1,2-a]pyridinyl	isophthalonitrile	46.4
MIQSUD (Jin et al., 2019)	2-(imidazo[1,2-a]pyridin-5-yl)propan-2-ol	phenyl	2.7
NAGGEH (Tafeenko et al., 1996)	imidazo[1,2-a]pyridinyl	phenyl	4.4
NONFOM (Mutai et al., 2008)	imidazo[1,2-a]pyridinyl	2-hydroxyphenyl	6.7
NUBVUD (Seferoğlu et al., 2015)	7-methylimidazo[1,2-a]pyridinyl	4-methoxyphenyl	0.7
NUBWAK (Seferoğlu et al., 2015)	7-methyl-imidazo[1,2-a]pyridinyl	phenyl	5.3
QODZUG (Mutai et al., 2014)	imidazo[1,2-a]pyridinyl-6-carbonitrile	2-hydroxyphenyl	2.8
TIDVIN (Donohoe et al., 2012)	6-bromo-imidazo[1,2-a]pyridinyl	phenyl	2.4
VEGKAU (Duan et al., 2006)	imidazo[1,2-a]pyridinyl	3-bromo-4-methoxyphenyl	12.2, 2.7
WUHKER (Aydıner et al., 2015)	7-methylimidazo[1,2-a]pyridinyl	4-chlorophenyl	9.1
ZUNVOV (Stasyuk et al., 2016)	imidazo[1,2-a]pyridinyl	2-hydroxy-4-florophenyl	3.2
ZUPCOE (Stasyuk et al., 2016)	imidazo[1,2-a]pyridinyl	2-hydroxy-4-methoxyphenyl	5.8

Summary of short interatomic contacts (Å) top

Contact	Distance	symmetry
H5···H5	2.24	1-x,2-y,-z
Br1···H12	3.01	x,3/2-y,-1/2+z

Acknowledgements

The authors thank the Sophisticated Analytical Instruments Facility (SAIF), IIT Madras, for providing single-crystal and spectroscopic data.

References

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