Literature DB >> 21579831

1-(2-Cyano-ethyl)-2-(2-pyrid-yl)-1H,3H-benzimidazol-3-ium perchlorate.

Yan Li, Xiaoliang Tang, Jiayu Chen, Daxiang Wu, Weisheng Liu.

Abstract

The title compound, C(15)H(13)N(4) (+)·ClO(4) (-), comprises a nonplanar 1-(2-cyano-ethyl)-2-(2-pyrid-yl)-1H,3H-benzimidazol-3-ium cation [dihedral angle between the imidazole and pyridine rings = 22.5 (8)°] and a perchlorate anion. The cation is formed by protonation of the N atom of the benzimidazole ring. A charged N-H⋯O hydrogen bond connects the anion and cation, and inter-molecular C-H⋯O and C-H⋯N inter-actions contribute to the crystal packing.

Entities: Chemical Disease Species

Year: 2010 PMID： 21579831 PMCID： PMC2979728 DOI： 10.1107/S1600536809055251

Source DB: PubMed Journal: Acta Crystallogr Sect E Struct Rep Online ISSN： 1600-5368

Related literature

For the pharmacological activity of benzimidazole and its derivatives, see: Feng & Xu (2001 ▶); Ferey (2001 ▶); Hossain et al. (2001 ▶); Howarth & Hanlon (2001 ▶); Kazak et al. (2006 ▶); Li et al. (1998 ▶).

Experimental

Crystal data

C15H13N4 +·ClO4 − M = 348.74 Triclinic, a = 8.788 (1) Å b = 9.4608 (10) Å c = 10.6013 (11) Å α = 69.690 (2)° β = 73.844 (2)° γ = 86.193 (2)° V = 793.52 (15) Å3 Z = 2 Mo Kα radiation μ = 0.27 mm−1 T = 296 K 0.22 × 0.21 × 0.19 mm

Data collection

Bruker SMART CCD area-detector diffractometer Absorption correction: multi-scan (SADABS; Bruker, 1997 ▶) T min = 0.940, T max = 0.955 4167 measured reflections 2924 independent reflections 2316 reflections with I > 2σ(I) R int = 0.013

Refinement

R[F 2 > 2σ(F 2)] = 0.047 wR(F 2) = 0.122 S = 1.01 2924 reflections 221 parameters 102 restraints H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.35 e Å−3 Δρmin = −0.24 e Å−3 Data collection: SMART (Bruker, 1997 ▶); cell refinement: SAINT (Bruker, 1997 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: SHELXTL (Sheldrick, 2008 ▶); software used to prepare material for publication: SHELXTL. Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536809055251/kp2242sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S1600536809055251/kp2242Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report

C₁₅H₁₃N₄⁺·ClO₄⁻	Z = 2
M_r = 348.74	F(000) = 360
Triclinic, P1	D_x = 1.460 Mg m⁻³
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 8.788 (1) Å	Cell parameters from 1758 reflections
b = 9.4608 (10) Å	θ = 2.4–26.4°
c = 10.6013 (11) Å	µ = 0.27 mm⁻¹
α = 69.690 (2)°	T = 296 K
β = 73.844 (2)°	Block, yellow
γ = 86.193 (2)°	0.22 × 0.21 × 0.19 mm
V = 793.52 (15) Å³

Bruker SMART CCD area-detector diffractometer	2924 independent reflections
Radiation source: fine-focus sealed tube	2316 reflections with I > 2σ(I)
graphite	R_int = 0.013
phi and ω scans	θ_max = 25.5°, θ_min = 2.1°
Absorption correction: multi-scan (SADABS; Bruker, 1997)	h = −10→10
T_min = 0.940, T_max = 0.955	k = −11→6
4167 measured reflections	l = −12→12

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)] = 0.047	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.122	H atoms treated by a mixture of independent and constrained refinement
S = 1.01	w = 1/[σ²(F_o²) + (0.043P)² + 0.670P] where P = (F_o² + 2F_c²)/3
2924 reflections	(Δ/σ)_max < 0.001
221 parameters	Δρ_max = 0.35 e Å⁻³
102 restraints	Δρ_min = −0.24 e Å⁻³

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.

	x	y	z	U_iso*/U_eq
C1	0.1586 (4)	−0.0845 (4)	0.8393 (4)	0.0755 (9)
H1	0.1941	−0.1600	0.9072	0.091*
C2	0.0604 (4)	−0.1248 (4)	0.7774 (4)	0.0781 (10)
H2	0.0314	−0.2256	0.8016	0.094*
C3	0.0053 (4)	−0.0148 (4)	0.6792 (4)	0.0797 (10)
H3	−0.0635	−0.0396	0.6369	0.096*
C4	0.0524 (4)	0.1333 (4)	0.6431 (3)	0.0657 (8)
H4	0.0168	0.2102	0.5762	0.079*
C5	0.1544 (3)	0.1638 (3)	0.7097 (3)	0.0469 (6)
C6	0.2150 (3)	0.3172 (3)	0.6751 (2)	0.0409 (6)
C7	0.3245 (3)	0.5180 (3)	0.6825 (2)	0.0402 (5)
C8	0.3956 (3)	0.6193 (3)	0.7178 (3)	0.0493 (6)
H8	0.4122	0.5949	0.8057	0.059*
C9	0.4403 (4)	0.7580 (3)	0.6163 (3)	0.0578 (7)
H9	0.4903	0.8288	0.6354	0.069*
C10	0.4127 (4)	0.7952 (3)	0.4854 (3)	0.0582 (7)
H10	0.4437	0.8908	0.4199	0.070*
C11	0.3412 (3)	0.6949 (3)	0.4506 (3)	0.0516 (7)
H11	0.3223	0.7203	0.3634	0.062*
C12	0.2988 (3)	0.5544 (3)	0.5516 (2)	0.0410 (6)
C13	0.2574 (3)	0.2959 (3)	0.9067 (2)	0.0437 (6)
H13A	0.1756	0.2165	0.9481	0.052*
H13B	0.2286	0.3688	0.9542	0.052*
C14	0.4152 (3)	0.2296 (3)	0.9245 (3)	0.0522 (7)
H14A	0.4470	0.1621	0.8715	0.063*
H14B	0.4953	0.3102	0.8880	0.063*
C15	0.4052 (4)	0.1470 (3)	1.0716 (3)	0.0591 (7)
Cl1	0.17292 (8)	0.51237 (8)	0.19213 (6)	0.0485 (2)
H5	0.207 (3)	0.416 (3)	0.491 (3)	0.044 (8)*
N1	0.2065 (3)	0.0574 (3)	0.8078 (3)	0.0601 (6)
N2	0.2311 (3)	0.4263 (2)	0.5520 (2)	0.0449 (5)
N3	0.2685 (2)	0.3697 (2)	0.75719 (19)	0.0399 (5)
N4	0.3982 (4)	0.0807 (4)	1.1839 (3)	0.0887 (10)
O1	0.0518 (3)	0.5091 (3)	0.1302 (3)	0.0896 (8)
O2	0.3196 (3)	0.4965 (3)	0.1030 (3)	0.0923 (8)
O3	0.1764 (4)	0.6462 (4)	0.2192 (4)	0.1268 (12)
O4	0.1453 (4)	0.3906 (4)	0.3209 (3)	0.1253 (12)

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.087 (2)	0.0490 (17)	0.080 (2)	−0.0088 (16)	−0.0136 (18)	−0.0141 (16)
C2	0.085 (2)	0.0587 (19)	0.081 (2)	−0.0247 (17)	0.0083 (18)	−0.0317 (17)
C3	0.084 (2)	0.088 (2)	0.075 (2)	−0.0308 (19)	−0.0067 (18)	−0.0423 (19)
C4	0.0707 (19)	0.073 (2)	0.0575 (18)	−0.0127 (16)	−0.0179 (15)	−0.0236 (15)
C5	0.0466 (14)	0.0479 (14)	0.0454 (14)	−0.0034 (11)	−0.0045 (11)	−0.0204 (12)
C6	0.0433 (14)	0.0456 (14)	0.0349 (13)	0.0033 (11)	−0.0098 (10)	−0.0159 (11)
C7	0.0443 (13)	0.0380 (13)	0.0352 (13)	0.0049 (10)	−0.0098 (10)	−0.0102 (10)
C8	0.0652 (17)	0.0459 (15)	0.0422 (14)	0.0035 (12)	−0.0224 (13)	−0.0159 (12)
C9	0.0699 (19)	0.0453 (16)	0.0621 (18)	−0.0032 (13)	−0.0218 (15)	−0.0192 (14)
C10	0.0704 (19)	0.0397 (15)	0.0507 (16)	−0.0021 (13)	−0.0122 (14)	−0.0012 (12)
C11	0.0604 (17)	0.0511 (16)	0.0360 (13)	0.0034 (13)	−0.0134 (12)	−0.0061 (12)
C12	0.0418 (13)	0.0454 (14)	0.0354 (13)	0.0038 (11)	−0.0104 (10)	−0.0139 (11)
C13	0.0563 (15)	0.0430 (14)	0.0286 (12)	0.0020 (11)	−0.0118 (11)	−0.0084 (10)
C14	0.0564 (16)	0.0528 (16)	0.0418 (14)	−0.0002 (13)	−0.0165 (12)	−0.0065 (12)
C15	0.0691 (19)	0.0531 (17)	0.0565 (18)	0.0111 (14)	−0.0295 (15)	−0.0124 (14)
Cl1	0.0493 (4)	0.0606 (4)	0.0450 (4)	−0.0011 (3)	−0.0169 (3)	−0.0257 (3)
N1	0.0657 (15)	0.0470 (13)	0.0656 (15)	−0.0028 (11)	−0.0196 (12)	−0.0149 (12)
N2	0.0534 (13)	0.0508 (13)	0.0340 (11)	0.0001 (10)	−0.0164 (10)	−0.0152 (10)
N3	0.0491 (12)	0.0382 (11)	0.0309 (10)	0.0014 (9)	−0.0115 (9)	−0.0096 (9)
N4	0.108 (2)	0.093 (2)	0.0539 (17)	0.0245 (18)	−0.0388 (16)	−0.0032 (16)
O1	0.0684 (15)	0.122 (2)	0.1015 (18)	0.0124 (14)	−0.0503 (14)	−0.0474 (16)
O2	0.0586 (14)	0.138 (2)	0.0961 (18)	0.0062 (14)	−0.0112 (13)	−0.0667 (17)
O3	0.139 (3)	0.116 (2)	0.172 (3)	0.0001 (19)	−0.041 (2)	−0.108 (2)
O4	0.173 (3)	0.129 (2)	0.0615 (16)	−0.058 (2)	−0.0465 (18)	0.0051 (16)

C1—N1	1.333 (4)	C9—H9	0.9300
C1—C2	1.361 (5)	C10—C11	1.373 (4)
C1—H1	0.9300	C10—H10	0.9300
C2—C3	1.365 (5)	C11—C12	1.382 (3)
C2—H2	0.9300	C11—H11	0.9300
C3—C4	1.377 (4)	C12—N2	1.382 (3)
C3—H3	0.9300	C13—N3	1.471 (3)
C4—C5	1.384 (4)	C13—C14	1.517 (4)
C4—H4	0.9300	C13—H13A	0.9700
C5—N1	1.335 (3)	C13—H13B	0.9700
C5—C6	1.465 (3)	C14—C15	1.462 (4)
C6—N2	1.330 (3)	C14—H14A	0.9700
C6—N3	1.336 (3)	C14—H14B	0.9700
C7—C8	1.381 (3)	C15—N4	1.123 (4)
C7—C12	1.389 (3)	Cl1—O3	1.396 (3)
C7—N3	1.393 (3)	Cl1—O1	1.404 (2)
C8—C9	1.374 (4)	Cl1—O2	1.404 (2)
C8—H8	0.9300	Cl1—O4	1.418 (3)
C9—C10	1.395 (4)	N2—H5	0.78 (3)

N1—C1—C2	123.6 (3)	C10—C11—H11	121.7
N1—C1—H1	118.2	C12—C11—H11	121.7
C2—C1—H1	118.2	C11—C12—N2	132.5 (2)
C1—C2—C3	118.8 (3)	C11—C12—C7	121.5 (2)
C1—C2—H2	120.6	N2—C12—C7	106.0 (2)
C3—C2—H2	120.6	N3—C13—C14	109.9 (2)
C2—C3—C4	119.5 (3)	N3—C13—H13A	109.7
C2—C3—H3	120.2	C14—C13—H13A	109.7
C4—C3—H3	120.2	N3—C13—H13B	109.7
C3—C4—C5	117.8 (3)	C14—C13—H13B	109.7
C3—C4—H4	121.1	H13A—C13—H13B	108.2
C5—C4—H4	121.1	C15—C14—C13	111.2 (2)
N1—C5—C4	123.1 (3)	C15—C14—H14A	109.4
N1—C5—C6	115.2 (2)	C13—C14—H14A	109.4
C4—C5—C6	121.7 (3)	C15—C14—H14B	109.4
N2—C6—N3	108.6 (2)	C13—C14—H14B	109.4
N2—C6—C5	124.6 (2)	H14A—C14—H14B	108.0
N3—C6—C5	126.7 (2)	N4—C15—C14	178.5 (3)
C8—C7—C12	121.9 (2)	O3—Cl1—O1	111.91 (19)
C8—C7—N3	131.6 (2)	O3—Cl1—O2	109.33 (18)
C12—C7—N3	106.5 (2)	O1—Cl1—O2	109.27 (15)
C9—C8—C7	116.5 (2)	O3—Cl1—O4	108.3 (2)
C9—C8—H8	121.8	O1—Cl1—O4	108.51 (17)
C7—C8—H8	121.8	O2—Cl1—O4	109.5 (2)
C8—C9—C10	121.7 (3)	C1—N1—C5	117.2 (3)
C8—C9—H9	119.2	C6—N2—C12	110.0 (2)
C10—C9—H9	119.2	C6—N2—H5	123 (2)
C11—C10—C9	121.9 (2)	C12—N2—H5	127 (2)
C11—C10—H10	119.1	C6—N3—C7	108.90 (19)
C9—C10—H10	119.1	C6—N3—C13	127.9 (2)
C10—C11—C12	116.6 (2)	C7—N3—C13	122.87 (19)

N1—C1—C2—C3	−1.0 (5)	N3—C13—C14—C15	−176.3 (2)
C1—C2—C3—C4	1.3 (5)	C13—C14—C15—N4	118 (13)
C2—C3—C4—C5	−0.3 (5)	C2—C1—N1—C5	−0.2 (5)
C3—C4—C5—N1	−1.1 (4)	C4—C5—N1—C1	1.3 (4)
C3—C4—C5—C6	178.0 (3)	C6—C5—N1—C1	−177.8 (3)
N1—C5—C6—N2	152.9 (2)	N3—C6—N2—C12	0.7 (3)
C4—C5—C6—N2	−26.3 (4)	C5—C6—N2—C12	−176.9 (2)
N1—C5—C6—N3	−24.3 (4)	C11—C12—N2—C6	179.1 (3)
C4—C5—C6—N3	156.6 (3)	C7—C12—N2—C6	0.2 (3)
C12—C7—C8—C9	−0.3 (4)	N2—C6—N3—C7	−1.3 (3)
N3—C7—C8—C9	178.5 (3)	C5—C6—N3—C7	176.3 (2)
C7—C8—C9—C10	1.1 (4)	N2—C6—N3—C13	172.2 (2)
C8—C9—C10—C11	−0.8 (5)	C5—C6—N3—C13	−10.3 (4)
C9—C10—C11—C12	−0.4 (4)	C8—C7—N3—C6	−177.6 (3)
C10—C11—C12—N2	−177.5 (3)	C12—C7—N3—C6	1.4 (3)
C10—C11—C12—C7	1.3 (4)	C8—C7—N3—C13	8.6 (4)
C8—C7—C12—C11	−0.9 (4)	C12—C7—N3—C13	−172.5 (2)
N3—C7—C12—C11	180.0 (2)	C14—C13—N3—C6	102.0 (3)
C8—C7—C12—N2	178.1 (2)	C14—C13—N3—C7	−85.3 (3)
N3—C7—C12—N2	−1.0 (3)

D—H···A	D—H	H···A	D···A	D—H···A
N2—H5···O4	0.77 (3)	2.11 (3)	2.885 (4)	179 (4)
C11—H11···O3	0.93	2.54	3.343 (5)	145
C4—H4···O4	0.93	2.62	3.347 (4)	135
C13—H13A···N1	0.97	2.41	2.903 (4)	111
C10—H10···N4ⁱ	0.93	2.64	3.423 (4)	142
C13—H13B···O2ⁱⁱ	0.97	2.60	3.427 (4)	144
C14—H14B···O2ⁱⁱⁱ	0.97	2.57	3.483 (4)	157
C2—H2···O1^iv	0.93	2.62	3.552 (4)	180

Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N2—H5⋯O4	0.77 (3)	2.11 (3)	2.885 (4)	179 (4)
C11—H11⋯O3	0.93	2.54	3.343 (5)	145
C4—H4⋯O4	0.93	2.62	3.347 (4)	135
C13—H13A⋯N1	0.97	2.41	2.903 (4)	111
C10—H10⋯N4ⁱ	0.93	2.64	3.423 (4)	142
C13—H13B⋯O2ⁱⁱ	0.97	2.60	3.427 (4)	144
C14—H14B⋯O2ⁱⁱⁱ	0.97	2.57	3.483 (4)	157
C2—H2⋯O1^iv	0.93	2.62	3.552 (4)	180

Symmetry codes: (i) ; (ii) ; (iii) ; (iv) .

2 in total

1. New materials in hydrothermal synthesis.

Authors: S Feng; R Xu
Journal: Acc Chem Res Date: 2001-03 Impact factor: 22.384

2. A short history of SHELX.

Authors: George M Sheldrick
Journal: Acta Crystallogr A Date: 2007-12-21 Impact factor: 2.290

2 in total