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The title compound, C
14H
18N
4O
2, 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.
Supporting information
CCDC reference: 601183
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
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)-1
H-benzimidazole
top
Crystal data top
C14H18N4O2 | Z = 2 |
Mr = 274.32 | F(000) = 292 |
Triclinic, P1 | Dx = 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 | Rint = 0.041 |
Graphite monochromator | θmax = 27.5°, θmin = 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(Fo2) + (0.1044P)2 + 0.199P] where P = (Fo2 + 2Fc2)/3 |
3272 reflections | (Δ/σ)max < 0.001 |
253 parameters | Δρmax = 0.41 e Å−3 |
0 restraints | Δρmin = −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 | Uiso*/Ueq | |
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···N3iv | 2.82 (3) |
O2···H7ii | 2.43 (3) | H7···O2ix | 2.43 (3) |
O2···H14Aii | 2.82 (4) | H7···H8B | 2.38 (4) |
N2···N3 | 2.239 (3) | H8A···N3viii | 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···O1vi | 2.69 (3) |
N4···N2 | 2.954 (3) | H8B···C14 | 2.90 (2) |
N4···C7 | 3.405 (3) | H8B···H7 | 2.38 (4) |
N3···H5iv | 2.82 (3) | H8B···H14A | 2.31 (5) |
N3···H2v | 2.72 (3) | H9A···H14B | 2.39 (6) |
N3···H8Av | 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···H11Bvii | 2.48 (8) |
C5···C2iii | 3.573 (3) | H11A···C6vii | 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···H10Bvii | 2.48 (8) |
C8···O1vi | 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···H11Avii | 2.85 (5) | H14A···O1vi | 2.90 (4) |
C8···H2 | 2.99 (3) | H14A···O2ix | 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···N3viii | 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···O2ix | 1.00 (3) | 2.43 (3) | 3.425 (4) | 174 (2) |
Symmetry code: (ix) x, y−1, z. |
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