5-Nitro-1-(2-piperidinoeth­yl)-1H-benzimidazole

Akkurt, M.; Yıldırım, S.O.; Küçükbay, H.; Şireci, N.; Fun, H.-K.

doi:10.1107/S1600536806003758

5-Nitro-1-(2-piperidinoethyl)-1H-benzimidazole

M. Akkurt, S. O. Yıldırım, H. Küçükbay, N. Şireci and H.-K. Fun

The title compound, C₁₄H₁₈N₄O₂, was synthesized from 5-nitrobenzimidazolium nitrate and N-(2-chloroethyl)piperidine hydrochloride in KOH/EtOH solution. The piperidine ring has a chair conformation. The structure is stabilized by intra- and intermolecular C—H

O hydrogen bonds.

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536806003758/hg6295sup1.cif Contains datablocks global, I
	Structure factor file (CIF format) https://doi.org/10.1107/S1600536806003758/hg6295Isup2.hkl Contains datablock I

CCDC reference: 601183

checkCIF report

Key indicators

Single-crystal X-ray study
T = 273 K
Mean (C-C) = 0.005 Å
R factor = 0.072
wR factor = 0.219
Data-to-parameter ratio = 12.9

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT063_ALERT_3_C Crystal Probably too Large for Beam Size .......       0.76 mm
PLAT220_ALERT_2_C Large Non-Solvent    C     Ueq(max)/Ueq(min) ...       2.85 Ratio
PLAT222_ALERT_3_C Large Non-Solvent    H     Ueq(max)/Ueq(min) ...       3.48 Ratio
PLAT241_ALERT_2_C Check High      Ueq as Compared to Neighbors for        C11
PLAT242_ALERT_2_C Check Low       Ueq as Compared to Neighbors for         N1
PLAT242_ALERT_2_C Check Low       Ueq as Compared to Neighbors for         N4
PLAT340_ALERT_3_C Low Bond Precision on C-C bonds (x 1000) Ang ...          5

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   7 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
   4 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
   0 ALERT type 4 Improvement, methodology, query or suggestion

Computing details top

Data collection: SMART (Siemens, 1996); cell refinement: SAINT (Siemens, 1996); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997); software used to prepare material for publication: WinGX (Farrugia, 1999).

5-Nitro-1-(2-piperidinoethyl)-1H-benzimidazole top

Crystal data top

C₁₄H₁₈N₄O₂	Z = 2
M_r = 274.32	F(000) = 292
Triclinic, P1	D_x = 1.271 Mg m⁻³
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 6.3202 (2) Å	Cell parameters from 2162 reflections
b = 10.1321 (4) Å	θ = 3.2–24.9°
c = 12.4362 (5) Å	µ = 0.09 mm⁻¹
α = 104.109 (3)°	T = 273 K
β = 103.953 (2)°	Needle, colorless
γ = 102.546 (2)°	0.76 × 0.23 × 0.19 mm
V = 716.61 (5) Å³

Data collection top

Siemens SMART CCD area-detector diffractometer	2158 reflections with I > 2σ(I)
Radiation source: sealed tube	R_int = 0.041
Graphite monochromator	θ_max = 27.5°, θ_min = 1.8°
φ and ω scans	h = −7→8
9940 measured reflections	k = −13→13
3272 independent reflections	l = −16→16

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)] = 0.072	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.219	All H-atom parameters refined
S = 1.06	w = 1/[σ²(F_o²) + (0.1044P)² + 0.199P] where P = (F_o² + 2F_c²)/3
3272 reflections	(Δ/σ)_max < 0.001
253 parameters	Δρ_max = 0.41 e Å⁻³
0 restraints	Δρ_min = −0.30 e Å⁻³

Special details top

Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All su's are estimated from the variances of the (full) variance-covariance matrix. The cell e.s.d.'s are taken into account in the estimation of distances, angles and torsion angles

Refinement. Refinement on F² for ALL reflections except those flagged by the user for potential systematic errors. Weighted R-factors wR and all goodnesses of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The observed criterion of F² > σ(F²) is used only for calculating -R-factor-obs 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 (Å²) top

	x	y	z	U_iso*/U_eq
O1	0.5400 (5)	1.4151 (3)	0.1259 (3)	0.1288 (13)
O2	0.2147 (6)	1.4509 (2)	0.1255 (3)	0.1162 (13)
N1	0.3450 (5)	1.3771 (3)	0.1301 (2)	0.0835 (10)
N2	0.0507 (3)	0.83331 (18)	0.14889 (16)	0.0483 (6)
N3	0.3842 (3)	0.8900 (2)	0.1135 (2)	0.0666 (8)
N4	0.0840 (4)	0.7633 (2)	0.36832 (18)	0.0620 (7)
C1	0.0927 (3)	0.9724 (2)	0.15094 (18)	0.0453 (6)
C2	−0.0315 (4)	1.0688 (3)	0.1683 (2)	0.0574 (8)
C3	0.0553 (5)	1.2022 (3)	0.1620 (2)	0.0628 (8)
C4	0.2613 (5)	1.2344 (2)	0.1375 (2)	0.0610 (8)
C5	0.3875 (4)	1.1413 (3)	0.1201 (2)	0.0605 (8)
C6	0.3008 (4)	1.0069 (2)	0.1277 (2)	0.0517 (7)
C7	0.2315 (4)	0.7916 (3)	0.1272 (2)	0.0604 (9)
C8	−0.1420 (4)	0.7480 (3)	0.1717 (2)	0.0578 (8)
C9	−0.1170 (5)	0.7873 (3)	0.2996 (3)	0.0665 (10)
C10	0.1623 (7)	0.8536 (4)	0.4889 (3)	0.0922 (14)
C11	0.3823 (11)	0.8374 (6)	0.5542 (5)	0.129 (2)
C12	0.3623 (10)	0.6850 (5)	0.5494 (4)	0.117 (2)
C13	0.2623 (11)	0.5892 (6)	0.4252 (4)	0.1121 (19)
C14	0.0474 (7)	0.6150 (3)	0.3638 (4)	0.0838 (11)
H2	−0.169 (5)	1.041 (3)	0.178 (2)	0.076 (8)*
H3	−0.011 (4)	1.295 (2)	0.1742 (18)	0.046 (6)*
H5	0.523 (5)	1.160 (3)	0.101 (2)	0.071 (8)*
H7	0.236 (4)	0.693 (3)	0.124 (2)	0.063 (7)*
H8A	−0.284 (5)	0.767 (3)	0.133 (2)	0.058 (6)*
H8B	−0.140 (4)	0.647 (3)	0.138 (2)	0.063 (7)*
H9A	−0.254 (5)	0.733 (3)	0.308 (3)	0.084 (9)*
H9B	−0.107 (4)	0.886 (3)	0.323 (2)	0.055 (6)*
H10A	0.043 (6)	0.816 (4)	0.532 (3)	0.103 (11)*
H10B	0.196 (7)	0.946 (5)	0.480 (4)	0.126 (14)*
H11A	0.448 (8)	0.907 (5)	0.631 (4)	0.134 (15)*
H11B	0.477 (9)	0.860 (6)	0.510 (5)	0.16 (2)*
H12A	0.497 (7)	0.670 (4)	0.587 (4)	0.118 (13)*
H12B	0.259 (8)	0.656 (5)	0.586 (4)	0.126 (17)*
H13A	0.352 (8)	0.614 (5)	0.386 (4)	0.130 (19)*
H13B	0.224 (7)	0.498 (5)	0.425 (3)	0.113 (13)*
H14A	−0.003 (6)	0.558 (4)	0.286 (3)	0.097 (11)*
H14B	−0.067 (8)	0.594 (5)	0.405 (4)	0.133 (16)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.105 (2)	0.0880 (17)	0.176 (3)	−0.0157 (14)	0.0318 (19)	0.0612 (18)
O2	0.171 (3)	0.0606 (13)	0.142 (2)	0.0506 (16)	0.063 (2)	0.0465 (14)
N1	0.105 (2)	0.0538 (14)	0.0785 (16)	0.0045 (14)	0.0197 (14)	0.0229 (12)
N2	0.0425 (9)	0.0481 (10)	0.0594 (11)	0.0144 (7)	0.0152 (8)	0.0252 (8)
N3	0.0548 (12)	0.0734 (13)	0.0946 (16)	0.0302 (10)	0.0347 (11)	0.0450 (12)
N4	0.0659 (13)	0.0634 (12)	0.0634 (13)	0.0189 (10)	0.0228 (10)	0.0287 (10)
C1	0.0399 (10)	0.0464 (11)	0.0474 (11)	0.0093 (8)	0.0072 (8)	0.0201 (9)
C2	0.0522 (13)	0.0560 (13)	0.0660 (15)	0.0191 (11)	0.0165 (11)	0.0216 (11)
C3	0.0719 (16)	0.0476 (13)	0.0645 (15)	0.0184 (11)	0.0129 (12)	0.0172 (11)
C4	0.0716 (16)	0.0432 (12)	0.0555 (13)	0.0054 (11)	0.0030 (11)	0.0198 (10)
C5	0.0482 (13)	0.0643 (15)	0.0652 (15)	0.0042 (11)	0.0118 (11)	0.0302 (12)
C6	0.0439 (11)	0.0564 (13)	0.0568 (13)	0.0128 (9)	0.0126 (9)	0.0259 (10)
C7	0.0599 (14)	0.0600 (14)	0.0781 (17)	0.0291 (12)	0.0271 (12)	0.0353 (12)
C8	0.0435 (12)	0.0573 (14)	0.0732 (16)	0.0071 (10)	0.0160 (11)	0.0305 (12)
C9	0.0606 (15)	0.0721 (18)	0.0853 (19)	0.0240 (13)	0.0364 (14)	0.0395 (15)
C10	0.115 (3)	0.082 (2)	0.072 (2)	0.024 (2)	0.0207 (19)	0.0232 (17)
C11	0.139 (4)	0.115 (4)	0.087 (3)	0.009 (3)	−0.017 (3)	0.027 (3)
C12	0.123 (4)	0.132 (4)	0.093 (3)	0.042 (3)	0.003 (3)	0.056 (3)
C13	0.137 (4)	0.106 (3)	0.103 (3)	0.059 (3)	0.016 (3)	0.050 (3)
C14	0.098 (2)	0.0671 (18)	0.084 (2)	0.0245 (17)	0.0152 (19)	0.0323 (17)

Geometric parameters (Å, º) top

O1—N1	1.227 (5)	C12—C13	1.503 (7)
O2—N1	1.227 (5)	C13—C14	1.499 (8)
N1—C4	1.461 (4)	C2—H2	0.90 (3)
N2—C1	1.369 (3)	C3—H3	1.10 (2)
N2—C7	1.364 (3)	C5—H5	0.94 (3)
N2—C8	1.463 (3)	C7—H7	1.00 (3)
N3—C6	1.388 (3)	C8—H8A	0.99 (3)
N3—C7	1.303 (4)	C8—H8B	1.01 (3)
N4—C9	1.454 (4)	C9—H9A	0.96 (3)
N4—C10	1.452 (4)	C9—H9B	0.95 (3)
N4—C14	1.455 (4)	C10—H10A	1.08 (4)
C1—C2	1.389 (3)	C10—H10B	0.95 (5)
C1—C6	1.403 (3)	C11—H11A	0.97 (5)
C2—C3	1.373 (4)	C11—H11B	0.94 (6)
C3—C4	1.396 (4)	C12—H12A	0.93 (5)
C4—C5	1.372 (4)	C12—H12B	0.92 (5)
C5—C6	1.388 (4)	C13—H13A	0.87 (5)
C8—C9	1.502 (4)	C13—H13B	0.90 (5)
C10—C11	1.496 (8)	C14—H14A	0.93 (4)
C11—C12	1.507 (8)	C14—H14B	1.00 (5)

O1···C8ⁱ	3.363 (4)	H2···C8	2.99 (3)
O1···H5	2.50 (3)	H2···H8A	2.59 (4)
O1···H8Bⁱ	2.69 (3)	H3···O2	2.19 (2)
O1···H14Aⁱ	2.90 (4)	H5···O1	2.50 (3)
O2···H3	2.19 (2)	H5···N3^iv	2.82 (3)
O2···H7ⁱⁱ	2.43 (3)	H7···O2^ix	2.43 (3)
O2···H14Aⁱⁱ	2.82 (4)	H7···H8B	2.38 (4)
N2···N3	2.239 (3)	H8A···N3^viii	2.66 (3)
N2···N4	2.954 (3)	H8A···C2	3.00 (3)
N2···C4ⁱⁱⁱ	3.447 (3)	H8A···H2	2.59 (4)
N3···N2	2.239 (3)	H8B···O1^vi	2.69 (3)
N4···N2	2.954 (3)	H8B···C14	2.90 (2)
N4···C7	3.405 (3)	H8B···H7	2.38 (4)
N3···H5^iv	2.82 (3)	H8B···H14A	2.31 (5)
N3···H2^v	2.72 (3)	H9A···H14B	2.39 (6)
N3···H8A^v	2.66 (3)	H9B···C1	2.95 (3)
C1···C4ⁱⁱⁱ	3.563 (3)	H9B···C2	3.03 (3)
C2···C6ⁱⁱⁱ	3.474 (3)	H9B···H10B	2.23 (5)
C2···C5ⁱⁱⁱ	3.573 (3)	H10A···H12B	2.45 (7)
C3···C6ⁱⁱⁱ	3.582 (3)	H10A···H14B	2.26 (6)
C4···N2ⁱⁱⁱ	3.447 (3)	H10B···H9B	2.23 (5)
C4···C1ⁱⁱⁱ	3.563 (3)	H10B···H11B^vii	2.48 (8)
C5···C2ⁱⁱⁱ	3.573 (3)	H11A···C6^vii	2.85 (5)
C6···C2ⁱⁱⁱ	3.474 (3)	H11B···C14	3.06 (6)
C6···C3ⁱⁱⁱ	3.582 (3)	H11B···H13A	2.43 (8)
C7···N4	3.405 (3)	H11B···H10B^vii	2.48 (8)
C8···O1^vi	3.363 (4)	H12B···H10A	2.45 (7)
C1···H9B	2.95 (3)	H12B···H14B	2.49 (7)
C2···H8A	3.00 (3)	H13A···C10	3.08 (5)
C2···H9B	3.03 (3)	H13A···H11B	2.43 (8)
C6···H11A^vii	2.85 (5)	H14A···O1^vi	2.90 (4)
C8···H2	2.99 (3)	H14A···O2^ix	2.82 (4)
C8···H14A	2.82 (4)	H14A···C8	2.82 (4)
C10···H13A	3.08 (5)	H14A···H8B	2.31 (5)
C14···H8B	2.90 (2)	H14B···H9A	2.39 (6)
C14···H11B	3.06 (6)	H14B···H10A	2.26 (6)
H2···N3^viii	2.72 (3)	H14B···H12B	2.49 (7)

O1—N1—O2	123.6 (3)	N3—C7—H7	126.9 (16)
O1—N1—C4	118.1 (3)	N2—C8—H8A	109.2 (18)
O2—N1—C4	118.3 (3)	N2—C8—H8B	103.3 (16)
C1—N2—C7	106.1 (2)	C9—C8—H8A	106.6 (15)
C1—N2—C8	127.3 (2)	C9—C8—H8B	112.8 (14)
C7—N2—C8	126.5 (2)	H8A—C8—H8B	113 (2)
C6—N3—C7	104.5 (2)	N4—C9—H9A	111 (2)
C9—N4—C10	112.2 (3)	N4—C9—H9B	110.2 (15)
C9—N4—C14	112.2 (3)	C8—C9—H9A	108 (2)
C10—N4—C14	109.8 (3)	C8—C9—H9B	105.4 (15)
N2—C1—C2	131.9 (2)	H9A—C9—H9B	110 (3)
N2—C1—C6	105.68 (18)	N4—C10—H10A	108.6 (19)
C2—C1—C6	122.5 (2)	N4—C10—H10B	101 (3)
C1—C2—C3	117.9 (3)	C11—C10—H10A	104 (2)
C2—C3—C4	119.0 (3)	C11—C10—H10B	107 (3)
N1—C4—C3	117.0 (3)	H10A—C10—H10B	125 (4)
N1—C4—C5	118.7 (3)	C10—C11—H11A	112 (3)
C3—C4—C5	124.3 (2)	C10—C11—H11B	102 (4)
C4—C5—C6	116.6 (2)	C12—C11—H11A	116 (3)
N3—C6—C1	109.59 (19)	C12—C11—H11B	107 (4)
N3—C6—C5	130.7 (2)	H11A—C11—H11B	107 (5)
C1—C6—C5	119.7 (2)	C11—C12—H12A	115 (3)
N2—C7—N3	114.1 (2)	C11—C12—H12B	109 (3)
N2—C8—C9	111.7 (2)	C13—C12—H12A	112 (3)
N4—C9—C8	113.0 (3)	C13—C12—H12B	105 (3)
N4—C10—C11	110.9 (4)	H12A—C12—H12B	106 (4)
C10—C11—C12	111.9 (5)	C12—C13—H13A	109 (3)
C11—C12—C13	110.2 (4)	C12—C13—H13B	109 (2)
C12—C13—C14	111.6 (5)	C14—C13—H13A	102 (3)
N4—C14—C13	111.6 (4)	C14—C13—H13B	107 (3)
C1—C2—H2	120 (2)	H13A—C13—H13B	119 (4)
C3—C2—H2	122 (2)	N4—C14—H14A	109 (3)
C2—C3—H3	130.4 (13)	N4—C14—H14B	107 (3)
C4—C3—H3	110.6 (13)	C13—C14—H14A	109 (2)
C4—C5—H5	125.4 (19)	C13—C14—H14B	109 (3)
C6—C5—H5	117.9 (19)	H14A—C14—H14B	112 (4)
N2—C7—H7	119.0 (16)

O1—N1—C4—C5	−10.6 (4)	C10—N4—C9—C8	155.0 (3)
O2—N1—C4—C5	167.6 (3)	C2—C1—C6—C5	−0.8 (3)
O1—N1—C4—C3	169.5 (3)	N2—C1—C2—C3	−178.3 (2)
O2—N1—C4—C3	−12.3 (4)	C2—C1—C6—N3	−179.5 (2)
C7—N2—C1—C6	1.0 (2)	N2—C1—C6—C5	178.0 (2)
C7—N2—C8—C9	100.9 (3)	C6—C1—C2—C3	0.1 (3)
C8—N2—C1—C6	177.9 (2)	N2—C1—C6—N3	−0.8 (3)
C1—N2—C8—C9	−75.4 (3)	C1—C2—C3—C4	0.6 (3)
C1—N2—C7—N3	−0.9 (3)	C2—C3—C4—C5	−0.8 (4)
C8—N2—C7—N3	−177.8 (2)	C2—C3—C4—N1	179.2 (2)
C8—N2—C1—C2	−3.6 (4)	C3—C4—C5—C6	0.1 (4)
C7—N2—C1—C2	179.5 (2)	N1—C4—C5—C6	−179.8 (2)
C7—N3—C6—C5	−178.3 (3)	C4—C5—C6—C1	0.7 (3)
C6—N3—C7—N2	0.4 (3)	C4—C5—C6—N3	179.2 (2)
C7—N3—C6—C1	0.3 (3)	N2—C8—C9—N4	−61.5 (3)
C14—N4—C10—C11	60.3 (5)	N4—C10—C11—C12	−57.0 (5)
C9—N4—C14—C13	174.4 (3)	C10—C11—C12—C13	51.5 (7)
C14—N4—C9—C8	−80.8 (3)	C11—C12—C13—C14	−50.8 (7)
C9—N4—C10—C11	−174.2 (4)	C12—C13—C14—N4	55.9 (6)
C10—N4—C14—C13	−60.1 (5)

Symmetry codes: (i) x+1, y+1, z; (ii) x, y+1, z; (iii) −x, −y+2, −z; (iv) −x+1, −y+2, −z; (v) x+1, y, z; (vi) x−1, y−1, z; (vii) −x+1, −y+2, −z+1; (viii) x−1, y, z; (ix) x, y−1, z.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C3—H3···O2	1.10 (2)	2.19 (2)	2.692 (4)	104.8 (16)
C7—H7···O2^ix	1.00 (3)	2.43 (3)	3.425 (4)	174 (2)

Symmetry code: (ix) x, y−1, z.

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5-Nitro-1-(2-piperidinoeth­yl)-1H-benzimidazole

Supporting information

Key indicators

checkCIF/PLATON results

5-Nitro-1-(2-piperidinoethyl)-1H-benzimidazole