2-(1-Benzyl-5-methyl-1H-imidazol-4-yl)-1,3,4-oxadiazole

In the title imidazole derivative, C₁₃H₁₂N₄O, the two heterocyclic rings are almost coplanar [dihedral angle = 0.9 (2)°]. The phenyl ring, however, is almost perpendicular to the central ring [dihedral angle = 75.8 (2)°]. The crystal packing is consolidated by weak C—H...N inter­actions.

Key indicators

• Single-crystal X-ray study
• T = 295 K
• Mean [sigma](C-C) = 0.006 Å
• R factor = 0.047
• wR factor = 0.147
• Data-to-parameter ratio = 9.3

checkCIF/PLATON results

No syntax errors found



Alert level B
PLAT230_ALERT_2_B Hirshfeld Test Diff for    C2     -   C3      ..       7.38 su

Alert level C
PLAT180_ALERT_3_C Check Cell Rounding: # of Values Ending with 0 =          3
PLAT340_ALERT_3_C Low Bond Precision on C-C Bonds (x 1000) Ang ...          6

Alert level G
REFLT03_ALERT_4_G Please check that the estimate of the number of Friedel pairs is
            correct. If it is not, please give the correct count in the
            _publ_section_exptl_refinement section of the submitted CIF.
           From the CIF: _diffrn_reflns_theta_max           27.98
           From the CIF: _reflns_number_total               1518
           Count of symmetry unique reflns         1544
           Completeness (_total/calc)             98.32%
           TEST3: Check Friedels for noncentro structure
           Estimate of Friedel pairs measured         0
           Fraction of Friedel pairs measured     0.000
           Are heavy atom types Z>Si present         no
PLAT860_ALERT_3_G Note: Number of Least-Squares Restraints .......          1

   0 ALERT level A = In general: serious problem
   1 ALERT level B = Potentially serious problem
   2 ALERT level C = Check and explain
   2 ALERT level G = General alerts; check

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   1 ALERT type 2 Indicator that the structure model may be wrong or deficient
   3 ALERT type 3 Indicator that the structure quality may be low
   1 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

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S1. Comment

Imidazole derivatives have many biological properties, such as antibacterial and antifungal activities (Frank et al., 2006; Benkli, 2004). Our group has synthesized a novel class of 2-(1-benzyl-4-methyl-1H-imidazol-4-yl)-1,3,4-oxadiazole analogues. In this paper, we present the structure of one such analogue, the title compound (I).

Rings A (O1/N3–4/C12–13) and ring B (N1–2/C8—C10) are almost coplanar with a dihedral angle of 0.9 (2)°. The dihedral angle between the central ring and the terminal aromatic ring (C1—C6) is 75.8 (2)°. The weak C—H···N intramolecular and intermolecular hydrogen bonds (Table 1) give rise to a three dimensional network (Fig. 2).

Related literature

For related literature, see: Chen et al. (2005)(please provide reference); Teng et al. (2005); Benkli (2004); Frank (2006).

S2. Experimental

2-(4-methyl-1H-imidazol-4-yl)-1,3,4-oxadiazole (0.18 g, 1.2 mmol) was dissolved in DMF (2 ml), then 60% sodium hydride (58 mg, 1.44 mmol), was added, and after stirring for 30 minutes at room temperature, benzyl bromide (0.31 g, 1.8 mmol) was added dropwise. The reaction mixture was poured into water until the consumption of the starting material, as monitored by TLC. Then, the product was extracted with ethyl acetate, whcih was dried and concentrated. The reside was chromatographed (acetone/petroleum ether, 1:5 v/v). The yield of the title compound is 43%. Colourless plates of (I) were grown from an acetone solution at 288 K (r.t.).¹H NMR (CDCl3, 400 MHz): σ 8.43 (s, 1 H), 7.68 (s, 1 H), 7.39 - 7.11 (m, 5 H), 5.18 (s, 2 H), 2.57 (s, 3 H).

S3. Refinement

Anomalous dispersion was negligible and Friedel pairs were merged before refinement. All H atoms were positioned geometrically (C—H = 0.93–0.97 Å) and refined as riding with U_iso(H) = 1.2U_eq(C) or 1.5U_eq(methyl C).

Computing details

Data collection: SMART (Bruker, 2001); cell refinement: SAINT (Bruker, 2001); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 2003); software used to prepare material for publication: SHELXTL (Bruker, 2001).

Figures

	Fig. 1. The molecular structure of (I). Displacement ellipsoids are drawn at the 50% probability level (arbitrary spheres for the H atoms).
	Fig. 2. A packing diagram for (I). Hydrogen bonds are shown as dashed lines.

2-(1-benzyl-5-methyl-1H-imidazol-4-yl)-1,3,4-oxadiazole

Crystal data

C13H12N4O	F(000) = 252
Mr = 240.27	Dx = 1.329 Mg m^−3
Monoclinic, P21	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2yb	Cell parameters from 1201 reflections
a = 4.5880 (1) Å	θ = 2.5–20.4°
b = 8.1255 (2) Å	µ = 0.09 mm^−1
c = 16.1240 (8) Å	T = 295 K
β = 93.074 (1)°	Plate, colorless
V = 600.23 (4) Å^3	0.20 × 0.10 × 0.02 mm
Z = 2

Data collection

Bruker SMART 4K CCD area detector diffractometer	1143 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.037
Graphite monochromator	θmax = 28.0°, θmin = 1.3°
ω scans	h = −6→6
5797 measured reflections	k = −10→10
1518 independent reflections	l = −20→21

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.047	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.147	H-atom parameters constrained
S = 1.10	w = 1/[σ^2(Fo^2) + (0.0821P)^2] where P = (Fo^2 + 2Fc^2)/3
1518 reflections	(Δ/σ)max < 0.001
164 parameters	Δρmax = 0.23 e Å^−3
1 restraint	Δρmin = −0.19 e Å^−3

Special details

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

Refinement. Refinement of F² against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The threshold expression of F² > σ(F²) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F² are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
C1	0.5507 (9)	0.3950 (6)	0.0930 (2)	0.0671 (11)
H1	0.4139	0.3110	0.0860	0.081*
C2	0.6742 (13)	0.4632 (8)	0.0241 (2)	0.0899 (17)
H2	0.6190	0.4262	−0.0290	0.108*
C3	0.8794 (11)	0.5866 (8)	0.0352 (3)	0.0865 (16)
H3	0.9645	0.6323	−0.0106	0.104*
C4	0.9576 (10)	0.6415 (6)	0.1133 (3)	0.0809 (14)
H4	1.0963	0.7245	0.1206	0.097*
C5	0.8343 (8)	0.5759 (5)	0.1802 (2)	0.0596 (10)
H5	0.8879	0.6155	0.2329	0.072*
C6	0.6298 (7)	0.4511 (4)	0.17146 (19)	0.0460 (7)
C7	0.4958 (7)	0.3825 (5)	0.2474 (2)	0.0544 (9)
H7A	0.4159	0.4722	0.2787	0.065*
H7B	0.3362	0.3098	0.2301	0.065*
C8	0.8387 (8)	0.3479 (5)	0.3730 (2)	0.0570 (9)
H8	0.8008	0.4508	0.3952	0.068*
C9	0.8167 (7)	0.1368 (4)	0.28808 (19)	0.0452 (7)
C10	1.0097 (7)	0.1096 (4)	0.35461 (19)	0.0450 (7)
C11	0.7285 (10)	0.0334 (5)	0.2150 (2)	0.0672 (11)
H11A	0.8162	0.0757	0.1667	0.101*
H11B	0.5199	0.0353	0.2063	0.101*
H11C	0.7925	−0.0778	0.2248	0.101*
C12	1.1856 (7)	−0.0360 (4)	0.37196 (17)	0.0460 (7)
C13	1.4927 (9)	−0.1875 (5)	0.4375 (2)	0.0623 (10)
H13	1.6279	−0.2270	0.4777	0.075*
N4	1.4110 (8)	−0.2676 (4)	0.3739 (2)	0.0716 (10)
N1	0.7076 (6)	0.2910 (4)	0.30149 (15)	0.0474 (7)
N2	1.0229 (7)	0.2439 (4)	0.40749 (16)	0.0547 (8)
O1	1.3644 (5)	−0.0374 (3)	0.44171 (13)	0.0549 (7)
N3	1.2055 (7)	−0.1670 (4)	0.3294 (2)	0.0680 (10)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C1	0.078 (2)	0.060 (2)	0.062 (2)	0.012 (2)	−0.013 (2)	−0.0128 (19)
C2	0.118 (4)	0.109 (4)	0.0416 (19)	0.057 (4)	−0.001 (2)	0.002 (2)
C3	0.089 (3)	0.094 (4)	0.079 (3)	0.035 (3)	0.025 (3)	0.035 (3)
C4	0.077 (3)	0.066 (3)	0.101 (4)	0.003 (2)	0.013 (2)	0.026 (3)
C5	0.065 (2)	0.048 (2)	0.065 (2)	0.0077 (19)	−0.0021 (18)	0.0040 (18)
C6	0.0452 (17)	0.0394 (16)	0.0530 (17)	0.0101 (15)	−0.0011 (13)	0.0027 (15)
C7	0.0487 (17)	0.053 (2)	0.0606 (19)	0.0103 (17)	−0.0013 (16)	0.0051 (18)
C8	0.078 (2)	0.0463 (19)	0.0473 (17)	0.0119 (18)	0.0054 (17)	−0.0060 (15)
C9	0.0501 (17)	0.0390 (17)	0.0466 (17)	−0.0021 (15)	0.0040 (14)	0.0018 (14)
C10	0.0547 (18)	0.0402 (17)	0.0403 (15)	−0.0029 (15)	0.0031 (14)	0.0006 (13)
C11	0.086 (3)	0.054 (2)	0.060 (2)	0.001 (2)	−0.0166 (19)	−0.0090 (18)
C12	0.0536 (19)	0.0443 (17)	0.0399 (15)	−0.0010 (15)	0.0008 (13)	−0.0009 (15)
C13	0.074 (2)	0.054 (2)	0.058 (2)	0.017 (2)	−0.0033 (18)	0.0089 (18)
N4	0.089 (3)	0.0551 (19)	0.069 (2)	0.0212 (18)	−0.0092 (18)	−0.0049 (17)
N1	0.0526 (15)	0.0486 (15)	0.0411 (13)	0.0041 (13)	0.0039 (11)	0.0025 (12)
N2	0.072 (2)	0.0455 (18)	0.0456 (15)	0.0060 (15)	−0.0034 (13)	−0.0047 (13)
O1	0.0716 (16)	0.0500 (13)	0.0419 (11)	0.0056 (13)	−0.0074 (10)	0.0031 (11)
N3	0.081 (2)	0.055 (2)	0.0664 (19)	0.0147 (18)	−0.0152 (17)	−0.0173 (16)

Geometric parameters (Å, º)

C1—C6	1.376 (5)	C8—N1	1.353 (4)
C1—C2	1.388 (7)	C8—H8	0.9300
C1—H1	0.9300	C9—N1	1.371 (4)
C2—C3	1.380 (8)	C9—C10	1.372 (5)
C2—H2	0.9300	C9—C11	1.485 (5)
C3—C4	1.366 (7)	C10—N2	1.384 (4)
C3—H3	0.9300	C10—C12	1.452 (5)
C4—C5	1.353 (6)	C11—H11A	0.9600
C4—H4	0.9300	C11—H11B	0.9600
C5—C6	1.384 (5)	C11—H11C	0.9600
C5—H5	0.9300	C12—N3	1.272 (5)
C6—C7	1.506 (5)	C12—O1	1.356 (4)
C7—N1	1.472 (4)	C13—N4	1.254 (5)
C7—H7A	0.9700	C13—O1	1.357 (5)
C7—H7B	0.9700	C13—H13	0.9300
C8—N2	1.299 (5)	N4—N3	1.414 (4)
C6—C1—C2	120.3 (5)	N1—C8—H8	123.5
C6—C1—H1	119.9	N1—C9—C10	104.4 (3)
C2—C1—H1	119.9	N1—C9—C11	123.8 (3)
C3—C2—C1	119.4 (4)	C10—C9—C11	131.8 (3)
C3—C2—H2	120.3	C9—C10—N2	111.1 (3)
C1—C2—H2	120.3	C9—C10—C12	127.6 (3)
C4—C3—C2	120.0 (4)	N2—C10—C12	121.2 (3)
C4—C3—H3	120.0	C9—C11—H11A	109.5
C2—C3—H3	120.0	C9—C11—H11B	109.5
C5—C4—C3	120.4 (4)	H11A—C11—H11B	109.5
C5—C4—H4	119.8	C9—C11—H11C	109.5
C3—C4—H4	119.8	H11A—C11—H11C	109.5
C4—C5—C6	121.2 (4)	H11B—C11—H11C	109.5
C4—C5—H5	119.4	N3—C12—O1	112.5 (3)
C6—C5—H5	119.4	N3—C12—C10	129.3 (3)
C1—C6—C5	118.7 (4)	O1—C12—C10	118.2 (3)
C1—C6—C7	121.8 (4)	N4—C13—O1	113.3 (3)
C5—C6—C7	119.5 (3)	N4—C13—H13	123.3
N1—C7—C6	112.5 (3)	O1—C13—H13	123.3
N1—C7—H7A	109.1	C13—N4—N3	106.1 (3)
C6—C7—H7A	109.1	C8—N1—C9	107.3 (3)
N1—C7—H7B	109.1	C8—N1—C7	125.6 (3)
C6—C7—H7B	109.1	C9—N1—C7	127.1 (3)
H7A—C7—H7B	107.8	C8—N2—C10	104.1 (3)
N2—C8—N1	113.1 (3)	C12—O1—C13	102.1 (3)
N2—C8—H8	123.5	C12—N3—N4	105.9 (3)
C6—C1—C2—C3	0.7 (7)	O1—C13—N4—N3	−0.5 (5)
C1—C2—C3—C4	−0.6 (7)	N2—C8—N1—C9	−0.2 (4)
C2—C3—C4—C5	−0.2 (7)	N2—C8—N1—C7	−178.1 (3)
C3—C4—C5—C6	0.8 (6)	C10—C9—N1—C8	0.5 (3)
C2—C1—C6—C5	−0.1 (6)	C11—C9—N1—C8	−179.4 (3)
C2—C1—C6—C7	178.7 (4)	C10—C9—N1—C7	178.4 (3)
C4—C5—C6—C1	−0.6 (5)	C11—C9—N1—C7	−1.5 (5)
C4—C5—C6—C7	−179.5 (3)	C6—C7—N1—C8	102.4 (4)
C1—C6—C7—N1	113.2 (4)	C6—C7—N1—C9	−75.1 (4)
C5—C6—C7—N1	−68.0 (4)	N1—C8—N2—C10	−0.2 (4)
N1—C9—C10—N2	−0.7 (4)	C9—C10—N2—C8	0.5 (4)
C11—C9—C10—N2	179.3 (4)	C12—C10—N2—C8	−179.6 (3)
N1—C9—C10—C12	179.5 (3)	N3—C12—O1—C13	−1.2 (4)
C11—C9—C10—C12	−0.5 (6)	C10—C12—O1—C13	−179.5 (3)
C9—C10—C12—N3	1.8 (6)	N4—C13—O1—C12	1.0 (4)
N2—C10—C12—N3	−178.0 (4)	O1—C12—N3—N4	0.9 (4)
C9—C10—C12—O1	179.8 (3)	C10—C12—N3—N4	179.0 (3)
N2—C10—C12—O1	0.0 (5)	C13—N4—N3—C12	−0.3 (5)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
C11—H11C···N3	0.96	2.57	3.226 (6)	126
C13—H13···N2^i	0.93	2.39	3.302 (5)	165
C7—H7A···N4^ii	0.97	2.61	3.533 (5)	158

Symmetry codes: (i) −x+3, y−1/2, −z+1; (ii) x−1, y+1, z.