2-(4-Pyridyl)-1H-benz­imidazole trihydrate

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.

Key indicators

• Single-crystal X-ray study
• T = 293 K
• Mean [sigma](C-C) = 0.003 Å
• R factor = 0.050
• wR factor = 0.142
• Data-to-parameter ratio = 15.3

checkCIF/PLATON results

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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

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Computing details

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

Crystal data

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) Å^3	0.20 × 0.16 × 0.13 mm
Z = 4

Data collection

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

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)] = 0.050	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.142	H atoms treated by a mixture of independent and constrained refinement
S = 1.01	w = 1/[σ^2(Fo^2) + (0.0733P)^2 + 0.0813P] where P = (Fo^2 + 2Fc^2)/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 (Ų)

	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 (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
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)

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)

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···O2^i	0.86 (1)	2.07 (2)	2.868 (2)	155 (3)
O2—HO21···O1^ii	0.85 (1)	1.94 (1)	2.782 (2)	167 (2)
O2—HO22···O3^iii	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···O1^iv	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.