research communications
H-benzimidazole
Hirshfeld surface analysis and density functional theory study of 6-methyl-2-[(5-methylisoxazol-3-yl)methyl]-1aLaboratory of Heterocyclic Organic Chemistry URAC 21, Pharmacochemistry Competence Center, Av. Ibn Battouta, BP 1014, Faculty of Sciences, Mohammed V University, Rabat, Morocco, bDepartment of Biochemistry, Faculty of Education & Science, Al-Baydha University, Yemen, and cKU Leuven, Chemistry Department, Celestijnenlaan 200F box 2404, Leuven, (Heverlee), B-3001, Belgium
*Correspondence e-mail: abadnadeem3@gmail.com
In the title molecule, C13H13N3O, the isoxazole ring is inclined to the benzimidazole ring at a dihedral angle of 69.28 (14)°. In the crystal, N—H⋯N hydrogen bonds between neighboring benzimidazole rings form chains along the a-axis direction. Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from H⋯H (48.8%), H⋯C/C⋯H (20.9%) and H⋯N/N⋯H (19.3%) interactions. The optimized structure calculated using density functional theory at the B3LYP/6–311 G(d,p) level is compared with the experimentally determined structure in the solid state. The calculated highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energy gap is 4.9266 eV.
Keywords: crystal structure; density functional theory; benzimidazole; hydrogen bond; Hirshfeld surface analysis.
CCDC reference: 2048487
1. Chemical context
Nitrogen-based structures have attracted increased attention in structural and inorganic chemistry in recent years because of their interesting properties (Lahmidi et al., 2018; Chkirate et al., 2020a; Taia et al., 2020; Al Ati et al., 2021). The benzimidazole family, particularly compounds containing the 2-methyl benzimidazole moiety, is important in medicinal chemistry because of their wide range of pharmacological applications including as antimicrobial and antitubercular agents (Ranjith et al., 2013), potential urease enzyme inhibitors (Menteşe et al., 2019) and antibacterial agents (Chkirate et al., 2020b). In particular, isoxazolyl benzimidazole derivatives are used as analgesic and anti-inflammatory agents (Kankala et al., 2013). They are also potent and orally bioavailable bromodomain BET inhibitors (Sperandio et al., 2019). Given the wide range of therapeutic applications for such compounds, and in a continuation of the work already carried out on the synthesis of compounds resulting from 1,5-benzodiazepine (Chkirate et al., 2001, 2018, 2019a,b,c, 2021), a similar approach gave the title compound, 6-methyl-2-[(5-methylisoxazol-3-yl)methyl]-1H-benzimidazole C13H13N3O (I).
Besides the synthesis, we also report the molecular and crystal structures along with the results of a Hirshfeld surface analysis and density functional theory computational calculations carried out at the B3LYP/6– 311 G(d,p) level.
2. Structural commentary
The title compound crystallizes in the orthorhombic Pbca with one molecule in the (Fig. 1). The molecule is not planar, as indicated by the torsion angles C4—C3—C6—C7 [−40.4 (4)°] and C3—C6—C7—N15 [−46.0 (4)°]. The best plane of the isoxazole ring (O1/N2/C3–C5; r.m.s. deviation = 0.003 Å) makes a dihedral angle of 69.28 (14)° with the best plane of the benzimidazole ring (C7/N8/C9–C14/N15; r.m.s. deviation = 0.015 Å). Both methyl groups are in the same plane as the ring to which they are attached [deviation of C17 from the isoxazole plane = 0.016 (6) Å, deviation of C16 from the benzimidazole ring = 0.067 (4) Å].
3. Supramolecular features
The crystal packing is characterized by N—H⋯N and C—H⋯N interactions (Fig. 2, Table 1). Chains of molecules running in the a-axis direction are formed by N8—H8⋯N15i hydrogen bonds between neighboring benzimidazole rings [symmetry code: (i) − + x, y, 3/2 – z]. Parallel chains interact through C4—H4⋯N2ii hydrogen bonds between neighboring isoxazole rings [symmetry code: (ii) 3/2 – x, + y, z] resulting in the three-dimensional structure. The crystal packing contains no voids.
4. Hirshfeld surface analysis
The CrystalExplorer program (Turner et al., 2017) was used to investigate and visualize the intermolecular interactions of (I). The Hirshfeld surface plotted over dnorm in the range −0.61 49 to 1.3177 a.u. is shown in Fig. 3a. The red spots are close contacts with a negative dnorm value and represent N—H⋯N and C—H⋯N interactions. The white regions representing contacts equal to the van der Waals separation and a dnorm value of zero are indicative of the H⋯H interactions. The electrostatic potential using the STO-3G basis set at the Hartree–Fock level of theory and mapped on the Hirshfeld surface over the range ± 0.05 a.u. clearly shows the positions of close intermolecular contacts in the compound (Fig. 3b). The positive electrostatic potential (blue region) over the surface indicates hydrogen-donor potential, whereas the hydrogen-bond acceptors are represented by negative electrostatic potential (red region). The shape-index (Fig. 4) generated in the ranges −1 to 1 Å reveals that there are no significant π–π interactions (normally indicated by adjacent red and blue triangles).
The overall two-dimensional fingerprint plot (McKinnon et al., 2007) is shown in Fig. 5a, while those delineated into H⋯H, H⋯C/C⋯H, H⋯N/N⋯H, H⋯O/O⋯H, C⋯C and C⋯N/N⋯C contacts are illustrated in Fig. 5b–g, respectively, together with their relative contributions to the Hirshfeld surface (HS). The most important interaction is H⋯H, contributing 48.8% to the overall crystal packing, which is reflected in Fig. 5b as widely scattered points of high density due to the large hydrogen content of the molecule, with the tip at de = di = 1.28 Å. In the presence of C—H interactions, the pair of characteristic wings in the fingerprint plot delineated into H⋯C/C⋯H contacts (20.9% contribution to the HS), Fig. 5c, has the tips at de + di = 2.69 Å. The pair of scattered points of spikes in the fingerprint plot delineated into H⋯N/N⋯H, Fig. 5d (19.3%), have the tips at de + di = 1.81 Å. The H⋯O/O⋯H contacts, Fig. 5e (9.6%), have the tips at de + di = 2.65 Å. The C⋯C contacts, Fig. 5f, contribute 0.9% to the HS and appear as a pair of scattered points of spikes with the tips at de + di = 3.60 Å. Finally, the C⋯N/N⋯C contacts, Fig. 5g, make only a 0.5% contribution to the HS and have a low-density distribution of points.
5. Density Functional Theory calculations
The structure in the gas phase of the title compound was optimized by means of density functional theory. The density functional theory calculation was performed by the hybrid B3LYP method and the 6–311 G(d,p) basis-set, which is based on Becke's model (Becke, 1993) and considers a mixture of the exact (Hartree–Fock) and density functional theory exchange utilizing the B3 functional, together with the LYP correlation functional (Lee et al., 1988). After obtaining the converged geometry, the harmonic vibrational frequencies were calculated at the same theoretical level to confirm that the number of imaginary frequencies is zero for the stationary point. Both the geometry optimization and harmonic vibrational frequency analysis of the title compound were performed with the GAUSSIAN 09 program (Frisch et al., 2009). The theoretical and experimental results related to bond lengths and angles are in good agreement, as well as with the results of the previous structural study of 5,6-dimethyl-2-[(5-methyl-1,2-oxazol-3-yl)methyl]-1-(prop-2-en-1-yl)-1H-benzimidazole, (III) (Benyahya et al., 2017) and 5-methyl-3-(1-(2-pyridylmethyl)-1H-benzimidazol-2-ylmethyl)isoxazole, (IV) (Doumbia et al., 2009), which are summarized in Table 2. Calculated numerical values for title compound including (χ), hardness (η), (I), (μ), (A), (ω) and softness (σ) are collated in Table 3. The electron transition from the highest occupied molecular orbital (HOMO) to the lowest unoccupied molecular orbital (LUMO) energy level is shown in Fig. 6. The HOMO and LUMO are localized in the plane extending over the whole 6-methyl-2-[(5-methylisoxazol-3-yl)methyl]-1H-benzimidazole system. The energy band gap [ΔE = ELUMO - EHOMO] of the molecule is 4.9266 eV, and the frontier molecular orbital energies, EHOMO and ELUMO, are −5.8170 and −0.8904 eV, respectively.
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6. Database survey
A search of the Cambridge Structural Database (CSD version 5.40, updated March 2020; Groom et al., 2016) with the 2-methylbenzimidazole fragment yielded multiple matches. Of these, three had an isoxazol-3-yl substituent comparable to (I) and they are shown in Fig. 7. The first compound (II) (refcode REQZIW; Attar et al., 2001) has no substituent on the phenyl ring. For the second one (III) (refcode FECPIP; Benyahya et al., 2017) the phenyl ring is disubstituted with an allyl substituent on nitrogen 1. The third one (IV) (refcode PUGLAF; Doumbia et al., 2009) carries pyridin-2-ylmethyl on nitrogen 1. The benzimidazole and isoxazole moieties are planar and make a dihedral angle of 76,15 (4)° in REQZIW. In FECPIP, the benzimidazole moiety is slightly non-planar, as indicated by the dihedral angle of 1.3 (1)° between the five- and six-membered rings. The isoxazole ring is planar to within 0.005 (1) Å and makes a dihedral angle of 89.78 (8)° with the benzimidazole ring. On the other hand, in PUGLAF, the fused-ring system is essentially planar, with a maximum deviation of 0.019 (1) Å. It forms interplanar angles of 70.03 (7)° with the isoxazole ring and 81.68 (7)° with the pyridine ring. The two latter rings are also planar, the maximum deviations from the mean planes being 0.0028 (15) and 0.0047 (12) Å. In (I), The isoxazole ring is inclined to the mean plane of the benzimidazole ring by 69.28 (14)° which is approximately the same as in PUGLAF, but less tilted than in REQZIW and FECPIP.
7. Synthesis and crystallization
(Z)-7-Methyl-4-(2-oxopropylidene)-1,5-benzodiazepin-2-one (2.3 g, 0.01 mol) and hydroxylamine hydrochloride (0.7 g, 0.01 mol) were brought to reflux in 40 ml of methanol for 2 h. After neutralization with NaHCO3, the compound that precipitated was filtered and recrystallized from ethyl acetate. The product was dissolved to saturation in ethyl acetate and crystals were obtained by evaporation at room temperature. yield: 70%; m.p. 465–467 K; IR [KBr, γ(cm−1)]: γNH = 3416; γCH = 3012–3263; γC=N–C=C= 1525–1672; 1H NMR [300MHz, DMSO-d6, δ(ppm)]: 2.32 (s, 3H, CH3 isoxazole); 2.57 (s, 3H, CH3 benzimidazole); 4.23 (s, 2H, CH2); 6.22 (s, 1H, CH isoxazole); 7.00–7.60 (m, 3H, CHar); 5.0 (s, 1H, NH). 13C NMR [75MHz, DMSO-d6, δ(ppm)]: 13.2 (CH3 isoxazole); 24.3 (CH3 benzimidazole); 26.7 (CH2); 101.8 (CH isoxazole); 115.2–125.8 (CH aryl); 132.7–169.6 (C quaternary).
8. Refinement
Crystal data, data collection and structure details . Hydrogen atoms were located in the first difference-Fourier map. C-bound H atoms were positioned geometrically (C—H = 0.93–0.97 Å) and included as riding contributions with Uiso(H) = 1.2Ueq(C) (1.5 for methyl groups). At the end of the the final difference Fourier map showed no residual peaks of chemical significance.
are given in Table 4
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Supporting information
CCDC reference: 2048487
https://doi.org/10.1107/S2056989021002723/tx2037sup1.cif
contains datablock I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989021002723/tx2037Isup2.hkl
Data collection: CrysAlis PRO (Rigaku OD, 2018); cell
CrysAlis PRO (Rigaku OD, 2018); data reduction: CrysAlis PRO (Rigaku OD, 2018); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2016/4 (Sheldrick, 2015b); molecular graphics: OLEX2 (Dolomanov et al., 2009); software used to prepare material for publication: OLEX2 (Dolomanov et al., 2009).C13H13N3O | Dx = 1.214 Mg m−3 |
Mr = 227.26 | Mo Kα radiation, λ = 0.71073 Å |
Orthorhombic, Pbca | Cell parameters from 3531 reflections |
a = 9.6545 (6) Å | θ = 2.9–23.3° |
b = 11.2437 (6) Å | µ = 0.08 mm−1 |
c = 22.9108 (14) Å | T = 294 K |
V = 2487.0 (3) Å3 | Prism, brown |
Z = 8 | 0.35 × 0.2 × 0.2 mm |
F(000) = 960 |
Rigaku Oxford Diffraction SuperNova, Single source at offset/far, Eos diffractometer | 2519 independent reflections |
Radiation source: micro-focus sealed X-ray tube, SuperNova (Mo) X-ray Source | 1723 reflections with I > 2σ(I) |
Mirror monochromator | Rint = 0.024 |
Detector resolution: 15.9631 pixels mm-1 | θmax = 26.4°, θmin = 2.8° |
ω scans | h = −10→12 |
Absorption correction: multi-scan (CrysAlisPro; Rigaku OD, 2018) | k = −14→13 |
Tmin = 0.883, Tmax = 1.000 | l = −28→28 |
13352 measured reflections |
Refinement on F2 | Primary atom site location: dual |
Least-squares matrix: full | Hydrogen site location: mixed |
R[F2 > 2σ(F2)] = 0.064 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.203 | w = 1/[σ2(Fo2) + (0.0963P)2 + 0.6658P] where P = (Fo2 + 2Fc2)/3 |
S = 1.05 | (Δ/σ)max < 0.001 |
2519 reflections | Δρmax = 0.33 e Å−3 |
160 parameters | Δρmin = −0.26 e Å−3 |
0 restraints |
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 | ||
O1 | 0.8450 (3) | 0.0193 (2) | 0.57078 (9) | 0.1116 (8) | |
N2 | 0.7873 (3) | −0.0264 (2) | 0.62282 (11) | 0.0916 (8) | |
C3 | 0.7336 (2) | 0.0646 (2) | 0.64943 (11) | 0.0649 (6) | |
C4 | 0.7542 (3) | 0.1693 (2) | 0.61779 (12) | 0.0852 (9) | |
H4 | 0.726197 | 0.245615 | 0.628050 | 0.102* | |
C5 | 0.8227 (4) | 0.1368 (3) | 0.56964 (12) | 0.0962 (10) | |
C6 | 0.6621 (3) | 0.0459 (3) | 0.70624 (12) | 0.0802 (8) | |
H6A | 0.562991 | 0.042286 | 0.699489 | 0.096* | |
H6B | 0.690721 | −0.030027 | 0.722308 | 0.096* | |
C7 | 0.6914 (2) | 0.1410 (2) | 0.74970 (10) | 0.0628 (6) | |
N8 | 0.5894 (2) | 0.19185 (18) | 0.78133 (8) | 0.0616 (5) | |
C9 | 0.6490 (2) | 0.2765 (2) | 0.81631 (9) | 0.0578 (6) | |
C10 | 0.5943 (3) | 0.3565 (2) | 0.85619 (10) | 0.0727 (7) | |
H10 | 0.499999 | 0.357606 | 0.864518 | 0.087* | |
C11 | 0.6850 (3) | 0.4350 (3) | 0.88328 (11) | 0.0815 (8) | |
C12 | 0.8243 (3) | 0.4291 (3) | 0.87071 (12) | 0.0855 (9) | |
H12 | 0.883742 | 0.481816 | 0.889438 | 0.103* | |
C13 | 0.8799 (3) | 0.3491 (3) | 0.83190 (11) | 0.0785 (8) | |
H13 | 0.974628 | 0.347148 | 0.824563 | 0.094* | |
C14 | 0.7902 (2) | 0.2713 (2) | 0.80401 (10) | 0.0615 (6) | |
N15 | 0.81476 (19) | 0.18510 (19) | 0.76175 (9) | 0.0678 (6) | |
C16 | 0.6344 (5) | 0.5270 (4) | 0.92565 (15) | 0.1269 (13) | |
H16A | 0.638258 | 0.604086 | 0.907763 | 0.190* | |
H16B | 0.691872 | 0.526214 | 0.959831 | 0.190* | |
H16C | 0.540500 | 0.509387 | 0.936487 | 0.190* | |
C17 | 0.8775 (7) | 0.2031 (4) | 0.51859 (15) | 0.174 (2) | |
H17A | 0.975882 | 0.191938 | 0.516094 | 0.261* | |
H17B | 0.857462 | 0.286270 | 0.523070 | 0.261* | |
H17C | 0.834513 | 0.174111 | 0.483589 | 0.261* | |
H8 | 0.501 (3) | 0.182 (2) | 0.7723 (11) | 0.079 (8)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.153 (2) | 0.0868 (15) | 0.0948 (15) | −0.0016 (13) | 0.0324 (14) | −0.0116 (12) |
N2 | 0.118 (2) | 0.0609 (13) | 0.0961 (16) | 0.0068 (12) | 0.0172 (14) | 0.0016 (12) |
C3 | 0.0657 (15) | 0.0504 (12) | 0.0785 (15) | −0.0017 (10) | −0.0074 (12) | −0.0070 (11) |
C4 | 0.121 (2) | 0.0538 (14) | 0.0809 (18) | −0.0009 (14) | −0.0090 (17) | −0.0022 (12) |
C5 | 0.150 (3) | 0.0717 (18) | 0.0673 (17) | −0.0246 (18) | −0.0082 (17) | −0.0019 (14) |
C6 | 0.0720 (17) | 0.0801 (18) | 0.0885 (18) | −0.0208 (13) | 0.0074 (13) | −0.0092 (14) |
C7 | 0.0463 (13) | 0.0698 (14) | 0.0724 (14) | −0.0068 (11) | 0.0015 (10) | 0.0054 (11) |
N8 | 0.0404 (11) | 0.0732 (13) | 0.0711 (12) | −0.0031 (9) | −0.0037 (9) | 0.0051 (10) |
C9 | 0.0494 (12) | 0.0671 (14) | 0.0569 (12) | 0.0038 (10) | −0.0035 (10) | 0.0105 (10) |
C10 | 0.0704 (16) | 0.0799 (17) | 0.0678 (14) | 0.0137 (13) | −0.0001 (12) | 0.0093 (13) |
C11 | 0.103 (2) | 0.0806 (18) | 0.0608 (15) | 0.0105 (16) | −0.0089 (14) | 0.0014 (12) |
C12 | 0.094 (2) | 0.093 (2) | 0.0687 (16) | −0.0185 (16) | −0.0220 (15) | 0.0013 (14) |
C13 | 0.0649 (16) | 0.099 (2) | 0.0717 (15) | −0.0169 (14) | −0.0119 (13) | 0.0017 (15) |
C14 | 0.0528 (13) | 0.0738 (15) | 0.0580 (12) | −0.0059 (10) | −0.0080 (10) | 0.0101 (11) |
N15 | 0.0453 (11) | 0.0817 (14) | 0.0763 (13) | −0.0062 (9) | 0.0034 (9) | −0.0031 (10) |
C16 | 0.157 (3) | 0.126 (3) | 0.097 (2) | 0.025 (3) | −0.003 (2) | −0.029 (2) |
C17 | 0.311 (7) | 0.140 (3) | 0.072 (2) | −0.080 (4) | 0.008 (3) | 0.011 (2) |
O1—N2 | 1.413 (3) | C9—C14 | 1.393 (3) |
O1—C5 | 1.339 (4) | C10—H10 | 0.9300 |
N2—C3 | 1.299 (3) | C10—C11 | 1.390 (4) |
C3—C4 | 1.396 (4) | C11—C12 | 1.377 (4) |
C3—C6 | 1.488 (4) | C11—C16 | 1.500 (4) |
C4—H4 | 0.9300 | C12—H12 | 0.9300 |
C4—C5 | 1.337 (4) | C12—C13 | 1.374 (4) |
C5—C17 | 1.485 (4) | C13—H13 | 0.9300 |
C6—H6A | 0.9700 | C13—C14 | 1.386 (3) |
C6—H6B | 0.9700 | C14—N15 | 1.391 (3) |
C6—C7 | 1.488 (4) | C16—H16A | 0.9600 |
C7—N8 | 1.349 (3) | C16—H16B | 0.9600 |
C7—N15 | 1.320 (3) | C16—H16C | 0.9600 |
N8—C9 | 1.371 (3) | C17—H17A | 0.9600 |
N8—H8 | 0.88 (3) | C17—H17B | 0.9600 |
C9—C10 | 1.387 (3) | C17—H17C | 0.9600 |
C5—O1—N2 | 108.2 (2) | C9—C10—C11 | 117.8 (3) |
C3—N2—O1 | 105.5 (2) | C11—C10—H10 | 121.1 |
N2—C3—C4 | 111.3 (2) | C10—C11—C16 | 121.4 (3) |
N2—C3—C6 | 118.9 (2) | C12—C11—C10 | 119.4 (3) |
C4—C3—C6 | 129.7 (2) | C12—C11—C16 | 119.2 (3) |
C3—C4—H4 | 127.2 | C11—C12—H12 | 118.4 |
C5—C4—C3 | 105.6 (3) | C13—C12—C11 | 123.3 (3) |
C5—C4—H4 | 127.2 | C13—C12—H12 | 118.4 |
O1—C5—C17 | 117.0 (3) | C12—C13—H13 | 121.1 |
C4—C5—O1 | 109.5 (3) | C12—C13—C14 | 117.8 (3) |
C4—C5—C17 | 133.5 (3) | C14—C13—H13 | 121.1 |
C3—C6—H6A | 108.9 | C13—C14—C9 | 119.5 (2) |
C3—C6—H6B | 108.9 | C13—C14—N15 | 130.8 (2) |
H6A—C6—H6B | 107.7 | N15—C14—C9 | 109.67 (19) |
C7—C6—C3 | 113.3 (2) | C7—N15—C14 | 104.72 (19) |
C7—C6—H6A | 108.9 | C11—C16—H16A | 109.5 |
C7—C6—H6B | 108.9 | C11—C16—H16B | 109.5 |
N8—C7—C6 | 121.7 (2) | C11—C16—H16C | 109.5 |
N15—C7—C6 | 125.6 (2) | H16A—C16—H16B | 109.5 |
N15—C7—N8 | 112.7 (2) | H16A—C16—H16C | 109.5 |
C7—N8—C9 | 107.59 (19) | H16B—C16—H16C | 109.5 |
C7—N8—H8 | 121.4 (17) | C5—C17—H17A | 109.5 |
C9—N8—H8 | 129.2 (17) | C5—C17—H17B | 109.5 |
N8—C9—C10 | 132.5 (2) | C5—C17—H17C | 109.5 |
N8—C9—C14 | 105.29 (19) | H17A—C17—H17B | 109.5 |
C10—C9—C14 | 122.2 (2) | H17A—C17—H17C | 109.5 |
C9—C10—H10 | 121.1 | H17B—C17—H17C | 109.5 |
O1—N2—C3—C4 | −0.7 (3) | N8—C7—N15—C14 | −0.4 (3) |
O1—N2—C3—C6 | 179.3 (2) | N8—C9—C10—C11 | −177.5 (2) |
N2—O1—C5—C4 | 0.0 (4) | N8—C9—C14—C13 | 178.6 (2) |
N2—O1—C5—C17 | 179.1 (3) | N8—C9—C14—N15 | 0.5 (2) |
N2—C3—C4—C5 | 0.7 (3) | C9—C10—C11—C12 | −1.3 (4) |
N2—C3—C6—C7 | 139.7 (3) | C9—C10—C11—C16 | 178.2 (3) |
C3—C4—C5—O1 | −0.4 (4) | C9—C14—N15—C7 | −0.1 (3) |
C3—C4—C5—C17 | −179.3 (4) | C10—C9—C14—C13 | −0.6 (3) |
C3—C6—C7—N8 | 133.7 (2) | C10—C9—C14—N15 | −178.7 (2) |
C3—C6—C7—N15 | −46.0 (4) | C10—C11—C12—C13 | 0.5 (4) |
C4—C3—C6—C7 | −40.4 (4) | C11—C12—C13—C14 | 0.3 (4) |
C5—O1—N2—C3 | 0.4 (3) | C12—C13—C14—C9 | −0.3 (4) |
C6—C3—C4—C5 | −179.3 (3) | C12—C13—C14—N15 | 177.4 (2) |
C6—C7—N8—C9 | −179.1 (2) | C13—C14—N15—C7 | −177.9 (3) |
C6—C7—N15—C14 | 179.3 (2) | C14—C9—C10—C11 | 1.4 (3) |
C7—N8—C9—C10 | 178.4 (2) | N15—C7—N8—C9 | 0.7 (3) |
C7—N8—C9—C14 | −0.7 (2) | C16—C11—C12—C13 | −179.0 (3) |
D—H···A | D—H | H···A | D···A | D—H···A |
N8—H8···N15i | 0.89 (3) | 1.96 (3) | 2.830 (3) | 167 (2) |
C4—H4···N2ii | 0.93 | 2.57 | 3.447 (3) | 157 |
Symmetry codes: (i) x−1/2, y, −z+3/2; (ii) −x+3/2, y+1/2, z. |
X-ray | B3LYP/6–311G(d,p) | (III)a | (IV)b | |
O1—N2 | 1.413 (3) | 1.3949 | 1.417 | 1.4100 |
O1—C5 | 1.339 (4) | 1.3481 | 1.356 | 1.3526 |
N2—C3 | 1.299 (3) | 1.3115 | 1.304 | 1.3044 |
C3—C6 | 1.488 (4) | 1.5065 | 1.501 | 1.504 |
C5—C17 | 1.485 (4) | 1.4868 | 1.476 | 1.478 |
C6—C7 | 1.488 (4) | 1.5026 | 1.498 | 1.494 |
C7—N8 | 1.349 (3) | 1.3755 | 1.377 | 1.3720 |
C7—N15 | 1.320 (3) | 1.3092 | 1.312 | 1.3079 |
N8—C9 | 1.371 (3) | 1.3814 | 1.386 | 1.3840 |
C11—C16 | 1.500 (4) | 1.5112 | 1.504 | – |
C14—N15 | 1.391 (3) | 1.388 | 1.400 | 1.3880 |
C5—O1—N2 | 108.2 (2) | 109.1398 | 108.37 | 108.57 |
C3—N2—O1 | 105.5 (2) | 106.0707 | 105.15 | 105.28 |
N2—C3—C4 | 111.3 (2) | 111.0906 | 112.00 | 111.51 |
N2—C3—C6 | 118.9 (2) | 120.8172 | 120.16 | 119.88 |
O1—C5—C17 | 117.0 (3) | 116.8621 | 116.33 | 115.90 |
C4—C5—O1 | 109.5 (3) | 109.3513 | 109.34 | 109.15 |
N8—C7—C6 | 121.7 (2) | 122.8089 | 123.02 | 122.62 |
N15—C7—C6 | 125.6 (2) | 123.8733 | 123.28 | 124.10 |
N15—C7—N8 | 112.7 (2) | 113.2373 | 113.69 | 113.28 |
C7—N8—C9 | 107.59 (19) | 106.9514 | 106.09 | 106.49 |
N8—C9—C14 | 105.29 (19) | 104.6015 | 105.63 | 105.05 |
C13—C14—N15 | 130.8 (2) | 130.4265 | 129.98 | 129.63 |
N15—C14—C9 | 109.67 (19) | 110.2891 | 110.23 | 110.42 |
C7—N15—C14 | 104.72 (19) | 104.9141 | 104.36 | 104.75 |
Notes: (a) Results of the previous DFT-optimized geometry of 5,6-dimethyl-2-[(5-methyl-1,2-oxazol-3-yl)methyl]-1-(prop-2-en-1-yl)-1H-benzimidazole (Benyahya et al., 2017); () results of the previous crystallographic study of 5-methyl-3-(1-(2-pyridylmethyl)-1H-benzimidazol-2-ylmethyl)isoxazole (Doumbia et al., 2009) |
Molecular Energy | Title Compound |
Total Energy TE (eV) | -20214.1624 |
EHOMO (eV) | -5.8170 |
ELUMO (eV) | -0.8904 |
Gap, ΔE (eV) | 4.9266 |
Dipole moment, µ (Debye) | 4.4403 |
Ionization potential, I (eV) | 5.8170 |
Electron affinity, A | 0.8904 |
Electronegativity, χ | 3.3537 |
Hardness, η | 2.4633 |
Electrophilicity, index ω | 2.2830 |
Softness, σ | 0.4060 |
Fraction of electron transferred, ΔN | 0.7401 |
Acknowledgements
LVM thanks the Hercules Foundation for supporting the purchase of the diffractometer through project AKUL/09/0035. Authors contributions are as follows. Conceptualization, AI; methodology, AI; investigation, KC and NA; theoretical calculations, KC; writing (original draft) KC; writing (review and editing of the manuscript), NA; formal analysis, BD; supervision, EME and RA; crystal-structure determination and validation, LVM.
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