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organic compounds
The benzimidazole and pyridyl portions of the molecule of the title compound, C12H9N3·3H2O are essentially co-planar; the three N atoms interact with the water molecules, forming a three-dimensional hydrogen-bonded network structure.
Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536804010244/ww6198sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536804010244/ww6198Isup2.hkl |
CCDC reference: 242302
Key indicators
- Single-crystal X-ray study
- T = 293 K
- Mean (C-C) = 0.003 Å
- R factor = 0.050
- wR factor = 0.142
- Data-to-parameter ratio = 15.3
checkCIF/PLATON results
No syntax errors found
Alert level C PLAT042_ALERT_1_C Calc. and Rep. MoietyFormula Strings Differ .... ? PLAT230_ALERT_2_C Hirshfeld Test Diff for N3 - C10 .. 5.47 su PLAT720_ALERT_4_C Number of Unusual/Non-Standard Label(s) ........ 6
0 ALERT level A = In general: serious problem 0 ALERT level B = Potentially serious problem 3 ALERT level C = Check and explain 0 ALERT level G = General alerts; check 1 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 1 ALERT type 4 Improvement, methodology, query or suggestion
Computing details top
Data collection: SMART (Bruker, 2002); cell refinement: SAINT (Bruker, 2002); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEPII (Johnson, 1976); software used to prepare material for publication: SHELXL97.
2-(4-Pyridyl)-1H-benzimidazole trihydrate top
Crystal data top
C12H9N3·3H2O | F(000) = 528 |
Mr = 249.27 | Dx = 1.290 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 1887 reflections |
a = 7.3913 (6) Å | θ = 2.4–23.9° |
b = 9.3377 (8) Å | µ = 0.10 mm−1 |
c = 18.643 (2) Å | T = 293 K |
β = 94.209 (2)° | Block, colorless |
V = 1283.3 (2) Å3 | 0.20 × 0.16 × 0.13 mm |
Z = 4 |
Data collection top
Bruker APEX area-detector diffractometer | 1910 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.027 |
Graphite monochromator | θmax = 27.5°, θmin = 2.2° |
φ and ω scans | h = −9→9 |
10725 measured reflections | k = −12→12 |
2925 independent reflections | l = −24→24 |
Refinement top
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)] = 0.050 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.142 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.01 | w = 1/[σ2(Fo2) + (0.0733P)2 + 0.0813P] where P = (Fo2 + 2Fc2)/3 |
2925 reflections | (Δ/σ)max = 0.001 |
191 parameters | Δρmax = 0.18 e Å−3 |
7 restraints | Δρmin = −0.21 e Å−3 |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
x | y | z | Uiso*/Ueq | ||
O1 | 0.6728 (2) | 0.8842 (2) | 0.5528 (1) | 0.0670 (4) | |
O2 | 0.7129 (2) | 0.0856 (2) | 0.4451 (1) | 0.0724 (4) | |
O3 | 1.0025 (2) | 0.5604 (2) | 0.1385 (1) | 0.0760 (5) | |
N1 | 0.7260 (2) | 0.5922 (1) | 0.5419 (1) | 0.0468 (4) | |
N2 | 0.7339 (2) | 0.3591 (2) | 0.5182 (1) | 0.0482 (4) | |
N3 | 0.9012 (2) | 0.5914 (2) | 0.2818 (1) | 0.0605 (4) | |
C1 | 0.7535 (2) | 0.4939 (2) | 0.4933 (1) | 0.0421 (4) | |
C2 | 0.6862 (2) | 0.5162 (2) | 0.6028 (1) | 0.0459 (4) | |
C3 | 0.6484 (2) | 0.5649 (2) | 0.6708 (1) | 0.0595 (5) | |
C4 | 0.6149 (3) | 0.4647 (2) | 0.7214 (1) | 0.0667 (6) | |
C5 | 0.6193 (3) | 0.3196 (3) | 0.7063 (1) | 0.0686 (6) | |
C6 | 0.6560 (3) | 0.2686 (2) | 0.6402 (1) | 0.0628 (5) | |
C7 | 0.6899 (2) | 0.3699 (2) | 0.5884 (1) | 0.0471 (4) | |
C8 | 0.8037 (2) | 0.5266 (2) | 0.4202 (1) | 0.0423 (4) | |
C9 | 0.8400 (3) | 0.4201 (2) | 0.3718 (1) | 0.0581 (5) | |
C10 | 0.8866 (3) | 0.4579 (2) | 0.3044 (1) | 0.0646 (5) | |
C11 | 0.8683 (3) | 0.6926 (2) | 0.3287 (1) | 0.0652 (5) | |
C12 | 0.8197 (3) | 0.6659 (2) | 0.3973 (1) | 0.0573 (5) | |
HO11 | 0.692 (3) | 0.794 (1) | 0.547 (1) | 0.09 (1)* | |
HO12 | 0.566 (2) | 0.892 (3) | 0.567 (2) | 0.12 (1)* | |
HO21 | 0.717 (3) | 0.019 (2) | 0.477 (1) | 0.10 (1)* | |
HO22 | 0.793 (3) | 0.074 (3) | 0.415 (1) | 0.10 (1)* | |
HO31 | 0.982 (3) | 0.582 (2) | 0.182 (1) | 0.09 (1)* | |
HO32 | 0.901 (2) | 0.571 (3) | 0.114 (1) | 0.11 (1)* | |
H2 | 0.743 (3) | 0.279 (1) | 0.496 (1) | 0.07 (1)* | |
H3 | 0.6461 | 0.6622 | 0.6814 | 0.071* | |
H4 | 0.5885 | 0.4945 | 0.7671 | 0.080* | |
H5 | 0.5964 | 0.2546 | 0.7423 | 0.082* | |
H6 | 0.6581 | 0.1710 | 0.6304 | 0.075* | |
H9 | 0.8330 | 0.3242 | 0.3848 | 0.070* | |
H10 | 0.9093 | 0.3846 | 0.2724 | 0.077* | |
H11 | 0.8785 | 0.7875 | 0.3145 | 0.078* | |
H12 | 0.7978 | 0.7414 | 0.4280 | 0.069* |
Atomic displacement parameters (Å2) top
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.087 (1) | 0.049 (1) | 0.067 (1) | 0.002 (1) | 0.019 (1) | 0.005 (1) |
O2 | 0.096 (1) | 0.053 (1) | 0.072 (1) | 0.007 (1) | 0.035 (1) | 0.007 (1) |
O3 | 0.088 (1) | 0.095 (1) | 0.048 (1) | 0.003 (1) | 0.024 (1) | 0.005 (1) |
N1 | 0.057 (1) | 0.047 (1) | 0.038 (1) | 0.004 (1) | 0.010 (1) | 0.002 (1) |
N2 | 0.057 (1) | 0.045 (1) | 0.044 (1) | 0.000 (1) | 0.014 (1) | 0.001 (1) |
N3 | 0.062 (1) | 0.081 (1) | 0.041 (1) | −0.004 (1) | 0.013 (1) | 0.003 (1) |
C1 | 0.043 (1) | 0.046 (1) | 0.037 (1) | 0.002 (1) | 0.006 (1) | 0.004 (1) |
C2 | 0.047 (1) | 0.054 (1) | 0.038 (1) | 0.005 (1) | 0.010 (1) | 0.005 (1) |
C3 | 0.068 (1) | 0.069 (1) | 0.044 (1) | 0.009 (1) | 0.017 (1) | −0.002 (2) |
C4 | 0.068 (1) | 0.093 (2) | 0.041 (1) | 0.012 (1) | 0.021 (1) | 0.008 (1) |
C5 | 0.066 (1) | 0.088 (2) | 0.054 (1) | 0.005 (1) | 0.022 (1) | 0.026 (1) |
C6 | 0.070 (1) | 0.059 (1) | 0.062 (1) | 0.001 (1) | 0.020 (1) | 0.015 (1) |
C7 | 0.045 (1) | 0.05 (1) | 0.042 (1) | 0.003 (1) | 0.011 (1) | 0.006 (1) |
C8 | 0.040 (1) | 0.052 (1) | 0.035 (1) | 0.001 (1) | 0.006 (1) | 0.002 (1) |
C9 | 0.072 (1) | 0.056 (1) | 0.049 (1) | −0.004 (1) | 0.019 (1) | −0.005 (1) |
C10 | 0.073 (1) | 0.077 (1) | 0.046 (1) | −0.004 (1) | 0.020 (1) | −0.015 (1) |
C11 | 0.083 (1) | 0.066 (1) | 0.049 (1) | 0.002 (1) | 0.019 (1) | 0.011 (1) |
C12 | 0.078 (1) | 0.053 (1) | 0.043 (1) | 0.004 (1) | 0.018 (1) | 0.002 (1) |
Geometric parameters (Å, º) top
N1—C1 | 1.316 (2) | C11—C12 | 1.377 (2) |
N1—C2 | 1.388 (2) | O1—HO11 | 0.86 (1) |
N2—C1 | 1.354 (2) | O1—HO12 | 0.86 (1) |
N2—C7 | 1.376 (2) | O2—HO21 | 0.85 (1) |
N3—C11 | 1.323 (2) | O2—HO22 | 0.86 (1) |
N3—C10 | 1.324 (2) | O3—HO31 | 0.85 (1) |
C1—C8 | 1.470 (2) | O3—HO32 | 0.86 (1) |
C2—C7 | 1.393 (2) | N2—H2 | 0.86 (1) |
C2—C3 | 1.396 (2) | C3—H3 | 0.93 |
C3—C4 | 1.363 (3) | C4—H4 | 0.93 |
C4—C5 | 1.385 (3) | C5—H5 | 0.93 |
C5—C6 | 1.367 (3) | C6—H6 | 0.93 |
C6—C7 | 1.387 (2) | C9—H9 | 0.93 |
C8—C12 | 1.376 (2) | C10—H10 | 0.93 |
C8—C9 | 1.382 (2) | C11—H11 | 0.93 |
C9—C10 | 1.374 (3) | C12—H12 | 0.93 |
C1—N1—C2 | 105.0 (1) | C8—C12—C11 | 119.6 (2) |
C1—N2—C7 | 107.2 (1) | HO11—O1—HO12 | 107 (2) |
C10—N3—C11 | 116.0 (2) | HO21—O2—HO22 | 112 (2) |
N1—C1—N2 | 112.8 (1) | HO31—O3—HO32 | 106 (2) |
N1—C1—C8 | 123.8 (1) | C1—N2—H2 | 129 (1) |
N2—C1—C8 | 123.5 (1) | C7—N2—H2 | 124 (1) |
N1—C2—C7 | 109.7 (1) | C4—C3—H3 | 121.2 |
N1—C2—C3 | 130.2 (2) | C2—C3—H3 | 121.2 |
C3—C2—C7 | 120.1 (2) | C3—C4—H4 | 119.2 |
C2—C3—C4 | 117.7 (2) | C5—C4—H4 | 119.2 |
C3—C4—C5 | 121.5 (2) | C6—C5—H5 | 118.9 |
C4—C5—C6 | 122.2 (2) | C4—C5—H5 | 118.9 |
C5—C6—C7 | 116.6 (2) | C5—C6—H6 | 121.7 |
N2—C7—C6 | 132.8 (2) | C7—C6—H6 | 121.7 |
N2—C7—C2 | 105.3 (1) | C10—C9—H9 | 120.4 |
C2—C7—C6 | 121.9 (2) | C8—C9—H9 | 120.4 |
C9—C8—C12 | 116.9 (2) | N3—C10—H10 | 117.8 |
C1—C8—C9 | 122.0 (2) | C9—C10—H10 | 117.8 |
C1—C8—C12 | 121.1 (1) | N3—C11—H11 | 118.0 |
C8—C9—C10 | 119.1 (2) | C12—C11—H11 | 118.0 |
N3—C10—C9 | 124.4 (2) | C8—C12—H12 | 120.2 |
N3—C11—C12 | 124.0 (2) | C11—C12—H12 | 120.2 |
C2—N1—C1—N2 | 0.2 (2) | C3—C2—C7—N2 | −178.9 (2) |
C2—N1—C1—C8 | −178.7 (1) | N1—C2—C7—C6 | 179.6 (2) |
C7—N2—C1—N1 | 0.1 (2) | C3—C2—C7—C6 | 0.3 (3) |
C7—N2—C1—C8 | 179.0 (1) | N1—C1—C8—C12 | −2.1 (2) |
C1—N1—C2—C7 | −0.4 (2) | N2—C1—C8—C12 | 179.2 (2) |
C1—N1—C2—C3 | 178.8 (2) | N1—C1—C8—C9 | 176.8 (2) |
N1—C2—C3—C4 | −179.5 (2) | N2—C1—C8—C9 | −1.9 (2) |
C7—C2—C3—C4 | −0.4 (3) | C12—C8—C9—C10 | −0.9 (3) |
C2—C3—C4—C5 | 0.4 (3) | C1—C8—C9—C10 | −179.9 (2) |
C3—C4—C5—C6 | −0.4 (3) | C11—N3—C10—C9 | 0.1 (3) |
C4—C5—C6—C7 | 0.3 (3) | C8—C9—C10—N3 | 0.6 (3) |
C1—N2—C7—C6 | −179.3 (2) | C10—N3—C11—C12 | −0.6 (3) |
C1—N2—C7—C2 | −0.4 (2) | C9—C8—C12—C11 | 0.6 (3) |
C5—C6—C7—N2 | 178.6 (2) | C1—C8—C12—C11 | 179.5 (2) |
C5—C6—C7—C2 | −0.2 (3) | N3—C11—C12—C8 | 0.2 (3) |
N1—C2—C7—N2 | 0.5 (2) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
O1—HO11···N1 | 0.86 (1) | 1.91 (1) | 2.764 (2) | 175 (2) |
O1—HO12···O2i | 0.86 (1) | 2.07 (2) | 2.868 (2) | 155 (3) |
O2—HO21···O1ii | 0.85 (1) | 1.94 (1) | 2.782 (2) | 167 (2) |
O2—HO22···O3iii | 0.86 (1) | 1.87 (1) | 2.719 (2) | 170 (2) |
O3—HO31···N3 | 0.85 (1) | 2.01 (1) | 2.841 (2) | 167 (2) |
O3—HO32···O1iv | 0.86 (1) | 2.01 (1) | 2.862 (2) | 174 (2) |
N2—H2···O2 | 0.86 (1) | 2.05 (1) | 2.892 (2) | 169 (2) |
Symmetry codes: (i) −x+1, −y+1, −z+1; (ii) x, y−1, z; (iii) −x+2, y−1/2, −z+1/2; (iv) x, −y+3/2, z−1/2. |
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