1-(6-Chloro­pyridin-3-ylmeth­yl)-1H-benzimidazole

In the title compound, C₁₃H₁₀ClN₃, the benzimidazole and chloropyridyl groups are planar and make a dihedral angle of 68.01 (18)°. There are two weak C—H...N hydrogen bonds, producing sheets parallel to (100).

Key indicators

• Single-crystal X-ray study
• T = 298 K
• Mean [sigma](Wave) = 0.000 Å
• R factor = 0.037
• wR factor = 0.092
• Data-to-parameter ratio = 13.4

checkCIF/PLATON results

No syntax errors found



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           25.30
           From the CIF: _reflns_number_total               2063
           Count of symmetry unique reflns         1211
           Completeness (_total/calc)            170.36%
           TEST3: Check Friedels for noncentro structure
           Estimate of Friedel pairs measured       852
           Fraction of Friedel pairs measured     0.704
           Are heavy atom types Z>Si present        yes

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

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   0 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: XP (Bruker, 2002); software used to prepare material for publication: SHELXL97.

1-(6-Chloropyridin-3-ylmethyl)-1H-benzoimidazole

Crystal data

C13H10ClN3	F(000) = 504
Mr = 243.69	Dx = 1.424 Mg m^−3
Orthorhombic, P212121	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2ab	Cell parameters from 2063 reflections
a = 8.390 (5) Å	θ = 2.5–23.6°
b = 11.547 (7) Å	µ = 0.31 mm^−1
c = 11.737 (7) Å	T = 298 K
V = 1137.0 (12) Å^3	Rectangular, light yellow
Z = 4	0.50 × 0.20 × 0.08 mm

Data collection

Bruker SMART CCD area-detector diffractometer	2063 independent reflections
Radiation source: fine-focus sealed tube	1821 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.026
φ and ω scans	θmax = 25.3°, θmin = 2.5°
Absorption correction: multi-scan (SADABS; Bruker, 2002)	h = −10→9
Tmin = 0.859, Tmax = 0.975	k = −13→11
5749 measured reflections	l = −11→14

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.037	H-atom parameters constrained
wR(F^2) = 0.092	w = 1/[σ^2(Fo^2) + (0.0501P)^2] where P = (Fo^2 + 2Fc^2)/3
S = 1.04	(Δ/σ)max = 0.001
2063 reflections	Δρmax = 0.18 e Å^−3
154 parameters	Δρmin = −0.16 e Å^−3
0 restraints	Absolute structure: Flack (1983)
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: 0.10 (9)

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	0.1529 (3)	0.3689 (2)	0.2687 (2)	0.0677 (6)
H1	0.2320	0.3202	0.2407	0.081*
C2	0.1363 (3)	0.47508 (18)	0.21879 (18)	0.0538 (5)
C3	0.0191 (3)	0.5449 (2)	0.2620 (2)	0.0679 (7)
H3	0.0032	0.6182	0.2312	0.081*
C4	−0.0747 (3)	0.50794 (19)	0.3497 (2)	0.0674 (7)
H4	−0.1551	0.5545	0.3793	0.081*
C5	−0.0459 (3)	0.40041 (19)	0.39222 (19)	0.0583 (6)
C6	0.2372 (3)	0.5109 (2)	0.11923 (19)	0.0657 (6)
H6A	0.2506	0.5943	0.1203	0.079*
H6B	0.3418	0.4759	0.1263	0.079*
C7	0.0549 (3)	0.53523 (19)	−0.0483 (2)	0.0630 (6)
H7	0.0204	0.6089	−0.0279	0.076*
C8	0.0800 (2)	0.37626 (18)	−0.13498 (17)	0.0508 (5)
C9	0.0703 (3)	0.2828 (2)	−0.20891 (18)	0.0648 (6)
H9	0.0024	0.2846	−0.2716	0.078*
C10	0.1626 (3)	0.1885 (2)	−0.1872 (2)	0.0709 (7)
H10	0.1557	0.1243	−0.2348	0.085*
C11	0.2661 (3)	0.1865 (2)	−0.09606 (19)	0.0716 (7)
H11	0.3294	0.1214	−0.0845	0.086*
C12	0.2785 (3)	0.2774 (2)	−0.02219 (18)	0.0611 (6)
H12	0.3481	0.2756	0.0394	0.073*
C13	0.1834 (2)	0.37158 (16)	−0.04323 (16)	0.0461 (5)
Cl1	−0.16380 (9)	0.34813 (6)	0.50232 (5)	0.0861 (3)
N1	0.0636 (3)	0.33014 (16)	0.35478 (16)	0.0692 (5)
N2	0.16685 (19)	0.47658 (14)	0.01133 (14)	0.0514 (4)
N3	−0.0001 (2)	0.48047 (18)	−0.13569 (17)	0.0668 (5)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C1	0.0614 (14)	0.0762 (16)	0.0654 (14)	0.0193 (13)	−0.0054 (12)	−0.0104 (12)
C2	0.0517 (13)	0.0567 (13)	0.0530 (12)	−0.0067 (11)	−0.0117 (10)	−0.0123 (10)
C3	0.0762 (16)	0.0498 (13)	0.0777 (17)	0.0022 (12)	0.0071 (14)	−0.0045 (11)
C4	0.0707 (15)	0.0580 (13)	0.0735 (17)	0.0098 (12)	0.0122 (13)	−0.0024 (11)
C5	0.0593 (14)	0.0641 (14)	0.0517 (13)	0.0029 (11)	−0.0098 (11)	−0.0029 (10)
C6	0.0586 (14)	0.0714 (14)	0.0671 (14)	−0.0125 (11)	−0.0022 (12)	−0.0179 (12)
C7	0.0592 (14)	0.0523 (12)	0.0775 (17)	0.0023 (11)	0.0038 (13)	0.0136 (11)
C8	0.0414 (11)	0.0659 (12)	0.0451 (11)	−0.0106 (10)	0.0013 (9)	0.0124 (9)
C9	0.0562 (14)	0.0994 (18)	0.0387 (12)	−0.0266 (14)	0.0027 (10)	−0.0017 (12)
C10	0.0798 (17)	0.0737 (16)	0.0593 (15)	−0.0147 (14)	0.0149 (13)	−0.0181 (11)
C11	0.0841 (18)	0.0620 (15)	0.0686 (16)	0.0140 (13)	0.0142 (13)	−0.0053 (11)
C12	0.0628 (14)	0.0704 (14)	0.0502 (13)	0.0103 (11)	−0.0035 (11)	0.0006 (10)
C13	0.0428 (11)	0.0536 (12)	0.0419 (10)	−0.0046 (9)	0.0007 (8)	0.0038 (8)
Cl1	0.0889 (5)	0.0966 (5)	0.0727 (4)	0.0160 (4)	0.0108 (4)	0.0248 (4)
N1	0.0748 (13)	0.0693 (12)	0.0634 (12)	0.0202 (11)	−0.0021 (11)	0.0077 (10)
N2	0.0489 (9)	0.0527 (9)	0.0526 (10)	−0.0037 (8)	−0.0038 (9)	−0.0017 (8)
N3	0.0584 (11)	0.0768 (13)	0.0651 (13)	−0.0011 (10)	−0.0078 (10)	0.0184 (11)

Geometric parameters (Å, º)

C1—N1	1.335 (3)	C7—N2	1.353 (3)
C1—C2	1.366 (3)	C7—H7	0.9300
C1—H1	0.9300	C8—N3	1.378 (3)
C2—C3	1.369 (3)	C8—C13	1.383 (3)
C2—C6	1.501 (3)	C8—C9	1.387 (3)
C3—C4	1.364 (3)	C9—C10	1.360 (3)
C3—H3	0.9300	C9—H9	0.9300
C4—C5	1.360 (3)	C10—C11	1.379 (4)
C4—H4	0.9300	C10—H10	0.9300
C5—N1	1.302 (3)	C11—C12	1.366 (3)
C5—Cl1	1.736 (2)	C11—H11	0.9300
C6—N2	1.452 (3)	C12—C13	1.371 (3)
C6—H6A	0.9700	C12—H12	0.9300
C6—H6B	0.9700	C13—N2	1.378 (3)
C7—N3	1.291 (3)
N1—C1—C2	124.6 (2)	N3—C8—C13	110.15 (18)
N1—C1—H1	117.7	N3—C8—C9	130.3 (2)
C2—C1—H1	117.7	C13—C8—C9	119.6 (2)
C1—C2—C3	116.3 (2)	C10—C9—C8	118.2 (2)
C1—C2—C6	121.6 (2)	C10—C9—H9	120.9
C3—C2—C6	122.1 (2)	C8—C9—H9	120.9
C4—C3—C2	120.6 (2)	C9—C10—C11	121.2 (2)
C4—C3—H3	119.7	C9—C10—H10	119.4
C2—C3—H3	119.7	C11—C10—H10	119.4
C5—C4—C3	117.4 (2)	C12—C11—C10	121.8 (2)
C5—C4—H4	121.3	C12—C11—H11	119.1
C3—C4—H4	121.3	C10—C11—H11	119.1
N1—C5—C4	124.8 (2)	C11—C12—C13	116.8 (2)
N1—C5—Cl1	115.88 (18)	C11—C12—H12	121.6
C4—C5—Cl1	119.30 (19)	C13—C12—H12	121.6
N2—C6—C2	112.03 (18)	C12—C13—N2	132.26 (19)
N2—C6—H6A	109.2	C12—C13—C8	122.40 (19)
C2—C6—H6A	109.2	N2—C13—C8	105.33 (17)
N2—C6—H6B	109.2	C5—N1—C1	116.2 (2)
C2—C6—H6B	109.2	C7—N2—C13	105.67 (18)
H6A—C6—H6B	107.9	C7—N2—C6	126.6 (2)
N3—C7—N2	114.5 (2)	C13—N2—C6	127.17 (18)
N3—C7—H7	122.8	C7—N3—C8	104.37 (18)
N2—C7—H7	122.8

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
C3—H3···N1^i	0.93	2.71	3.634 (4)	176
C10—H10···N3^ii	0.93	2.60	3.457 (3)	153

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