Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807023483/hb2413sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536807023483/hb2413Isup2.hkl |
CCDC reference: 651486
Key indicators
- Single-crystal X-ray study
- T = 295 K
- Mean (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
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).
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 Uiso(H) = 1.2Ueq(C) or 1.5Ueq(methyl C).
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).
For related literature, see: Chen et al. (2005)(please provide reference); Teng et al. (2005); Benkli (2004); Frank (2006).
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).
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) Å3 | 0.20 × 0.10 × 0.02 mm |
Z = 2 |
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 on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.047 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.147 | H-atom parameters constrained |
S = 1.10 | w = 1/[σ2(Fo2) + (0.0821P)2] where P = (Fo2 + 2Fc2)/3 |
1518 reflections | (Δ/σ)max < 0.001 |
164 parameters | Δρmax = 0.23 e Å−3 |
1 restraint | Δρmin = −0.19 e Å−3 |
C13H12N4O | V = 600.23 (4) Å3 |
Mr = 240.27 | Z = 2 |
Monoclinic, P21 | Mo Kα radiation |
a = 4.5880 (1) Å | µ = 0.09 mm−1 |
b = 8.1255 (2) Å | T = 295 K |
c = 16.1240 (8) Å | 0.20 × 0.10 × 0.02 mm |
β = 93.074 (1)° |
Bruker SMART 4K CCD area detector diffractometer | 1143 reflections with I > 2σ(I) |
5797 measured reflections | Rint = 0.037 |
1518 independent reflections |
R[F2 > 2σ(F2)] = 0.047 | 1 restraint |
wR(F2) = 0.147 | H-atom parameters constrained |
S = 1.10 | Δρmax = 0.23 e Å−3 |
1518 reflections | Δρmin = −0.19 e Å−3 |
164 parameters |
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. |
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) |
U11 | U22 | U33 | U12 | U13 | U23 | |
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) |
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) |
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···N2i | 0.93 | 2.39 | 3.302 (5) | 165 |
C7—H7A···N4ii | 0.97 | 2.61 | 3.533 (5) | 158 |
Symmetry codes: (i) −x+3, y−1/2, −z+1; (ii) x−1, y+1, z. |
Experimental details
Crystal data | |
Chemical formula | C13H12N4O |
Mr | 240.27 |
Crystal system, space group | Monoclinic, P21 |
Temperature (K) | 295 |
a, b, c (Å) | 4.5880 (1), 8.1255 (2), 16.1240 (8) |
β (°) | 93.074 (1) |
V (Å3) | 600.23 (4) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.09 |
Crystal size (mm) | 0.20 × 0.10 × 0.02 |
Data collection | |
Diffractometer | Bruker SMART 4K CCD area detector |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 5797, 1518, 1143 |
Rint | 0.037 |
(sin θ/λ)max (Å−1) | 0.660 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.047, 0.147, 1.10 |
No. of reflections | 1518 |
No. of parameters | 164 |
No. of restraints | 1 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.23, −0.19 |
Computer programs: SMART (Bruker, 2001), SAINT (Bruker, 2001), SAINT, SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), PLATON (Spek, 2003), SHELXTL (Bruker, 2001).
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···N2i | 0.93 | 2.39 | 3.302 (5) | 165 |
C7—H7A···N4ii | 0.97 | 2.61 | 3.533 (5) | 158 |
Symmetry codes: (i) −x+3, y−1/2, −z+1; (ii) x−1, y+1, z. |
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).