Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536805030229/cv6580sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536805030229/cv6580Isup2.hkl |
CCDC reference: 283811
Key indicators
- Single-crystal X-ray study
- T = 298 K
- Mean (C-C) = 0.003 Å
- R factor = 0.042
- wR factor = 0.130
- Data-to-parameter ratio = 13.4
checkCIF/PLATON results
No syntax errors found
Alert level C PLAT241_ALERT_2_C Check High Ueq as Compared to Neighbors for C5
0 ALERT level A = In general: serious problem 0 ALERT level B = Potentially serious problem 1 ALERT level C = Check and explain 0 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 0 ALERT type 3 Indicator that the structure quality may be low 0 ALERT type 4 Improvement, methodology, query or suggestion
The title compound can be synthesized from 1,2-phenylenediamine and malonic acid in ethylene glycol as solvent at reflux for 24 h (Lane, 1953), in a yield of 56%, or in PPA (poly phosphorous acid) as solvent at 453 K for 2.5–4 h (Vyas et al., 1980), in a yield of 85%. However, we used 1,2-phenylenediamine (0.02 mol) and malonamide (0.01 mol) at 453–463 K under solvent-free conditions for 1 h, providing a convenient protocol for the preparation of this class of heterocycles. Purification was achieved by recrystallization from methanol in 92% isolated yield. Crystals of (I) suitable for X-ray diffraction analysis were obtained by slow evaporation from methanol at room temperature over two weeks.
All H atoms were placed in calculated positions, with C—H = 0.93–0.97 Å and N—H = 0.86 Å, and were included in the final cycles of refinement using a riding model, with Uiso(H) = 1.2Ueq of the parent atom.
Data collection: SMART (Bruker, 1998); cell refinement: SAINT (Bruker, 1999); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL (Bruker, 1999); software used to prepare material for publication: SHELXTL.
C15H12N4 | Dx = 1.253 Mg m−3 |
Mr = 248.29 | Mo Kα radiation, λ = 0.71073 Å |
Tetragonal, I41/a | Cell parameters from 4441 reflections |
Hall symbol: -I 4ad | θ = 2.2–25.8° |
a = 18.296 (4) Å | µ = 0.08 mm−1 |
c = 15.728 (3) Å | T = 298 K |
V = 5264.6 (18) Å3 | Block, orange |
Z = 16 | 0.40 × 0.31 × 0.27 mm |
F(000) = 2080 |
Bruker SMART CCD area-detector diffractometer | 2307 independent reflections |
Radiation source: fine-focus sealed tube | 1798 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.035 |
ϕ and ω scans | θmax = 25.1°, θmin = 2.8° |
Absorption correction: multi-scan (SADABS; Sheldrick, 1996) | h = −15→21 |
Tmin = 0.950, Tmax = 0.979 | k = −17→21 |
10662 measured reflections | l = −18→18 |
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)] = 0.042 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.130 | H-atom parameters constrained |
S = 1.00 | w = 1/[σ2(Fo2) + (0.075P)2 + 1.5659P] where P = (Fo2 + 2Fc2)/3 |
2307 reflections | (Δ/σ)max < 0.001 |
172 parameters | Δρmax = 0.20 e Å−3 |
0 restraints | Δρmin = −0.16 e Å−3 |
C15H12N4 | Z = 16 |
Mr = 248.29 | Mo Kα radiation |
Tetragonal, I41/a | µ = 0.08 mm−1 |
a = 18.296 (4) Å | T = 298 K |
c = 15.728 (3) Å | 0.40 × 0.31 × 0.27 mm |
V = 5264.6 (18) Å3 |
Bruker SMART CCD area-detector diffractometer | 2307 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 1996) | 1798 reflections with I > 2σ(I) |
Tmin = 0.950, Tmax = 0.979 | Rint = 0.035 |
10662 measured reflections |
R[F2 > 2σ(F2)] = 0.042 | 0 restraints |
wR(F2) = 0.130 | H-atom parameters constrained |
S = 1.00 | Δρmax = 0.20 e Å−3 |
2307 reflections | Δρmin = −0.16 e Å−3 |
172 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 | ||
N1 | 0.57166 (10) | 0.30536 (8) | 0.09757 (10) | 0.0708 (5) | |
N2 | 0.58129 (8) | 0.42431 (7) | 0.11565 (8) | 0.0560 (4) | |
H2A | 0.5790 | 0.4704 | 0.1049 | 0.067* | |
N3 | 0.41074 (8) | 0.42962 (7) | −0.06625 (8) | 0.0578 (4) | |
N4 | 0.41095 (8) | 0.32348 (7) | 0.00088 (8) | 0.0563 (4) | |
H4A | 0.4271 | 0.2856 | 0.0273 | 0.068* | |
C1 | 0.60520 (9) | 0.39271 (9) | 0.18957 (11) | 0.0563 (4) | |
C2 | 0.63143 (12) | 0.42248 (11) | 0.26529 (12) | 0.0767 (6) | |
H2 | 0.6354 | 0.4727 | 0.2728 | 0.092* | |
C3 | 0.65094 (15) | 0.37490 (13) | 0.32774 (14) | 0.0954 (8) | |
H3 | 0.6693 | 0.3931 | 0.3786 | 0.114* | |
C4 | 0.64421 (17) | 0.30066 (14) | 0.31753 (17) | 0.1144 (10) | |
H4 | 0.6575 | 0.2699 | 0.3620 | 0.137* | |
C5 | 0.61850 (17) | 0.27091 (12) | 0.24371 (17) | 0.1101 (10) | |
H5 | 0.6142 | 0.2206 | 0.2372 | 0.132* | |
C6 | 0.59899 (11) | 0.31847 (10) | 0.17871 (12) | 0.0669 (5) | |
C7 | 0.56216 (9) | 0.37014 (8) | 0.06352 (10) | 0.0514 (4) | |
C8 | 0.53220 (10) | 0.38310 (11) | −0.02331 (10) | 0.0635 (5) | |
H8A | 0.5526 | 0.3470 | −0.0617 | 0.076* | |
H8B | 0.5481 | 0.4309 | −0.0427 | 0.076* | |
C9 | 0.45082 (9) | 0.37953 (8) | −0.02848 (9) | 0.0511 (4) | |
C10 | 0.33919 (10) | 0.40476 (9) | −0.06135 (10) | 0.0557 (4) | |
C11 | 0.27477 (12) | 0.43470 (11) | −0.09232 (13) | 0.0752 (6) | |
H11 | 0.2745 | 0.4795 | −0.1203 | 0.090* | |
C12 | 0.21142 (12) | 0.39574 (13) | −0.08007 (14) | 0.0813 (6) | |
H12 | 0.1675 | 0.4146 | −0.1000 | 0.098* | |
C13 | 0.21165 (12) | 0.32914 (13) | −0.03878 (14) | 0.0782 (6) | |
H13 | 0.1679 | 0.3040 | −0.0321 | 0.094* | |
C14 | 0.27489 (11) | 0.29906 (11) | −0.00732 (12) | 0.0699 (5) | |
H14 | 0.2748 | 0.2544 | 0.0208 | 0.084* | |
C15 | 0.33900 (9) | 0.33830 (9) | −0.01940 (9) | 0.0538 (4) |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.1020 (12) | 0.0503 (8) | 0.0599 (9) | 0.0033 (8) | −0.0166 (8) | −0.0050 (7) |
N2 | 0.0746 (9) | 0.0432 (7) | 0.0503 (8) | −0.0022 (6) | −0.0062 (6) | 0.0046 (6) |
N3 | 0.0764 (10) | 0.0527 (8) | 0.0442 (7) | −0.0072 (7) | −0.0072 (6) | 0.0067 (6) |
N4 | 0.0748 (9) | 0.0468 (7) | 0.0472 (8) | 0.0037 (6) | 0.0050 (6) | 0.0072 (6) |
C1 | 0.0640 (10) | 0.0522 (9) | 0.0527 (10) | −0.0008 (7) | −0.0092 (8) | 0.0029 (7) |
C2 | 0.0981 (15) | 0.0647 (11) | 0.0672 (12) | −0.0069 (10) | −0.0244 (11) | −0.0038 (9) |
C3 | 0.126 (2) | 0.0895 (16) | 0.0703 (14) | −0.0084 (14) | −0.0436 (13) | 0.0050 (11) |
C4 | 0.172 (3) | 0.0834 (16) | 0.0881 (17) | −0.0068 (16) | −0.0636 (18) | 0.0252 (13) |
C5 | 0.173 (3) | 0.0557 (12) | 0.1017 (19) | −0.0041 (13) | −0.0560 (18) | 0.0158 (12) |
C6 | 0.0873 (13) | 0.0515 (10) | 0.0618 (11) | 0.0012 (8) | −0.0199 (9) | 0.0017 (8) |
C7 | 0.0573 (9) | 0.0510 (9) | 0.0460 (9) | 0.0001 (7) | 0.0037 (7) | −0.0005 (7) |
C8 | 0.0739 (11) | 0.0769 (12) | 0.0398 (9) | −0.0046 (9) | 0.0032 (8) | 0.0018 (8) |
C9 | 0.0706 (10) | 0.0504 (9) | 0.0324 (7) | −0.0023 (7) | 0.0006 (7) | −0.0002 (6) |
C10 | 0.0725 (11) | 0.0548 (9) | 0.0397 (8) | −0.0040 (8) | −0.0025 (7) | −0.0037 (7) |
C11 | 0.0876 (14) | 0.0743 (12) | 0.0639 (12) | 0.0041 (10) | −0.0142 (10) | 0.0057 (9) |
C12 | 0.0713 (13) | 0.1036 (17) | 0.0690 (13) | 0.0044 (11) | −0.0093 (10) | −0.0094 (12) |
C13 | 0.0715 (13) | 0.0945 (15) | 0.0686 (13) | −0.0101 (11) | 0.0116 (10) | −0.0168 (11) |
C14 | 0.0827 (13) | 0.0652 (11) | 0.0618 (11) | −0.0112 (9) | 0.0167 (10) | −0.0051 (9) |
C15 | 0.0702 (11) | 0.0519 (9) | 0.0393 (8) | −0.0007 (8) | 0.0067 (7) | −0.0075 (7) |
N1—C7 | 1.312 (2) | C4—H4 | 0.9300 |
N1—C6 | 1.391 (2) | C5—C6 | 1.389 (3) |
N2—C7 | 1.333 (2) | C5—H5 | 0.9300 |
N2—C1 | 1.370 (2) | C7—C8 | 1.491 (2) |
N2—H2A | 0.8600 | C8—C9 | 1.493 (2) |
N3—C9 | 1.315 (2) | C8—H8A | 0.9700 |
N3—C10 | 1.388 (2) | C8—H8B | 0.9700 |
N4—C9 | 1.340 (2) | C10—C15 | 1.384 (2) |
N4—C15 | 1.381 (2) | C10—C11 | 1.388 (3) |
N4—H4A | 0.8600 | C11—C12 | 1.374 (3) |
C1—C6 | 1.374 (2) | C11—H11 | 0.9300 |
C1—C2 | 1.395 (2) | C12—C13 | 1.381 (3) |
C2—C3 | 1.360 (3) | C12—H12 | 0.9300 |
C2—H2 | 0.9300 | C13—C14 | 1.373 (3) |
C3—C4 | 1.373 (3) | C13—H13 | 0.9300 |
C3—H3 | 0.9300 | C14—C15 | 1.388 (2) |
C4—C5 | 1.366 (4) | C14—H14 | 0.9300 |
C7—N1—C6 | 105.43 (14) | N2—C7—C8 | 122.81 (15) |
C7—N2—C1 | 106.98 (13) | C7—C8—C9 | 114.19 (14) |
C7—N2—H2A | 126.5 | C7—C8—H8A | 108.7 |
C1—N2—H2A | 126.5 | C9—C8—H8A | 108.7 |
C9—N3—C10 | 105.81 (13) | C7—C8—H8B | 108.7 |
C9—N4—C15 | 106.79 (13) | C9—C8—H8B | 108.7 |
C9—N4—H4A | 126.6 | H8A—C8—H8B | 107.6 |
C15—N4—H4A | 126.6 | N3—C9—N4 | 112.65 (15) |
N2—C1—C6 | 106.58 (14) | N3—C9—C8 | 123.38 (14) |
N2—C1—C2 | 132.04 (16) | N4—C9—C8 | 123.89 (15) |
C6—C1—C2 | 121.38 (16) | C15—C10—C11 | 120.81 (17) |
C3—C2—C1 | 117.20 (19) | C15—C10—N3 | 108.47 (14) |
C3—C2—H2 | 121.4 | C11—C10—N3 | 130.70 (16) |
C1—C2—H2 | 121.4 | C12—C11—C10 | 117.53 (19) |
C2—C3—C4 | 121.7 (2) | C12—C11—H11 | 121.2 |
C2—C3—H3 | 119.2 | C10—C11—H11 | 121.2 |
C4—C3—H3 | 119.2 | C11—C12—C13 | 121.4 (2) |
C5—C4—C3 | 121.6 (2) | C11—C12—H12 | 119.3 |
C5—C4—H4 | 119.2 | C13—C12—H12 | 119.3 |
C3—C4—H4 | 119.2 | C14—C13—C12 | 121.72 (19) |
C4—C5—C6 | 117.7 (2) | C14—C13—H13 | 119.1 |
C4—C5—H5 | 121.2 | C12—C13—H13 | 119.1 |
C6—C5—H5 | 121.2 | C13—C14—C15 | 117.08 (19) |
C1—C6—C5 | 120.44 (18) | C13—C14—H14 | 121.5 |
C1—C6—N1 | 108.32 (14) | C15—C14—H14 | 121.5 |
C5—C6—N1 | 131.25 (18) | N4—C15—C10 | 106.27 (14) |
N1—C7—N2 | 112.69 (14) | N4—C15—C14 | 132.23 (17) |
N1—C7—C8 | 124.49 (15) | C10—C15—C14 | 121.46 (17) |
C7—N2—C1—C6 | −0.26 (19) | C10—N3—C9—N4 | 0.06 (17) |
C7—N2—C1—C2 | −179.9 (2) | C10—N3—C9—C8 | 176.91 (14) |
N2—C1—C2—C3 | 179.9 (2) | C15—N4—C9—N3 | −0.03 (17) |
C6—C1—C2—C3 | 0.3 (3) | C15—N4—C9—C8 | −176.87 (14) |
C1—C2—C3—C4 | −1.0 (4) | C7—C8—C9—N3 | 131.44 (16) |
C2—C3—C4—C5 | 0.9 (5) | C7—C8—C9—N4 | −52.1 (2) |
C3—C4—C5—C6 | −0.2 (5) | C9—N3—C10—C15 | −0.06 (17) |
N2—C1—C6—C5 | −179.3 (2) | C9—N3—C10—C11 | −178.29 (18) |
C2—C1—C6—C5 | 0.4 (3) | C15—C10—C11—C12 | −0.3 (3) |
N2—C1—C6—N1 | 0.4 (2) | N3—C10—C11—C12 | 177.74 (17) |
C2—C1—C6—N1 | −179.91 (18) | C10—C11—C12—C13 | −0.2 (3) |
C4—C5—C6—C1 | −0.4 (4) | C11—C12—C13—C14 | 0.7 (3) |
C4—C5—C6—N1 | 179.9 (3) | C12—C13—C14—C15 | −0.5 (3) |
C7—N1—C6—C1 | −0.4 (2) | C9—N4—C15—C10 | −0.01 (16) |
C7—N1—C6—C5 | 179.3 (3) | C9—N4—C15—C14 | 177.71 (17) |
C6—N1—C7—N2 | 0.2 (2) | C11—C10—C15—N4 | 178.48 (15) |
C6—N1—C7—C8 | −178.84 (16) | N3—C10—C15—N4 | 0.04 (17) |
C1—N2—C7—N1 | 0.0 (2) | C11—C10—C15—C14 | 0.5 (2) |
C1—N2—C7—C8 | 179.10 (15) | N3—C10—C15—C14 | −177.98 (14) |
N1—C7—C8—C9 | 81.0 (2) | C13—C14—C15—N4 | −177.49 (17) |
N2—C7—C8—C9 | −97.94 (19) | C13—C14—C15—C10 | −0.1 (2) |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2A···N3i | 0.86 | 1.94 | 2.7869 (18) | 169 |
N4—H4A···N1ii | 0.86 | 2.00 | 2.823 (2) | 160 |
Symmetry codes: (i) −x+1, −y+1, −z; (ii) −x+1, −y+1/2, z. |
Experimental details
Crystal data | |
Chemical formula | C15H12N4 |
Mr | 248.29 |
Crystal system, space group | Tetragonal, I41/a |
Temperature (K) | 298 |
a, c (Å) | 18.296 (4), 15.728 (3) |
V (Å3) | 5264.6 (18) |
Z | 16 |
Radiation type | Mo Kα |
µ (mm−1) | 0.08 |
Crystal size (mm) | 0.40 × 0.31 × 0.27 |
Data collection | |
Diffractometer | Bruker SMART CCD area-detector diffractometer |
Absorption correction | Multi-scan (SADABS; Sheldrick, 1996) |
Tmin, Tmax | 0.950, 0.979 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 10662, 2307, 1798 |
Rint | 0.035 |
(sin θ/λ)max (Å−1) | 0.596 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.042, 0.130, 1.00 |
No. of reflections | 2307 |
No. of parameters | 172 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.20, −0.16 |
Computer programs: SMART (Bruker, 1998), SAINT (Bruker, 1999), SAINT, SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), SHELXTL (Bruker, 1999), SHELXTL.
N1—C7 | 1.312 (2) | N3—C10 | 1.388 (2) |
N1—C6 | 1.391 (2) | N4—C9 | 1.340 (2) |
N2—C7 | 1.333 (2) | N4—C15 | 1.381 (2) |
N2—C1 | 1.370 (2) | C7—C8 | 1.491 (2) |
N3—C9 | 1.315 (2) | C8—C9 | 1.493 (2) |
C7—N1—C6 | 105.43 (14) | C9—N4—C15 | 106.79 (13) |
C7—N2—C1 | 106.98 (13) | C7—C8—C9 | 114.19 (14) |
C9—N3—C10 | 105.81 (13) |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2A···N3i | 0.86 | 1.94 | 2.7869 (18) | 169 |
N4—H4A···N1ii | 0.86 | 2.00 | 2.823 (2) | 160 |
Symmetry codes: (i) −x+1, −y+1, −z; (ii) −x+1, −y+1/2, z. |
Bis(benzimidazol-2-yl)methane and its derivatives are the subject of intensive study because they exhibit antimicrobial activities (Agh-Atabay et al., 2003), execute control of liver diseases (Kotomo et al., 1992), and may serve as inhibitors of cell death (Bitler et al., 2000) and HCV NS3 serine protease (Yeung et al., 2001). They are also employed as ligands (Gupta et al., 2001). In this paper, we report the crystal structure of the title compound, (I) (Fig. 1).
In (I), the bond lengths and angles of the benzimidazole moieties (Table 1) are in agreement with published values (Eryigit & Kendi, 1998; Chen et al., 2002). The benzimidazolyl moieties C1–C7/N1/N2 and C9–C15/N3/N4 are essentially planar, making a dihedral angle of 63.53 (2)°.
The crystal packing of (I) (Fig. 2) is stabilized by intermolecular N—H···N hydrogen-bond interactions (Table 2).