3-Isopropyl-1-[2-(pyrrolidinium-1-yl)­eth­yl]benzimidazolium diodide

Akkurt, M.; Türktekin, S.; Şireci, N.; Küçükbay, H.; Büyükgüngör, O.

doi:10.1107/S1600536805041280

3-Isopropyl-1-[2-(pyrrolidinium-1-yl)ethyl]benzimidazolium diodide

M. Akkurt, S. Türktekin, N. Şireci, H. Küçükbay and O. Büyükgüngör

In the molecule of the title compound, C₁₆H₂₅N₃²⁺·2I⁻, the pyrrolidine ring has an envelope conformation. The crystal structure has been determined at room temperature and exhibits intermolecular N—H

I and C—H

I interactions.

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536805041280/dn6284sup1.cif Contains datablocks global, I
	Structure factor file (CIF format) https://doi.org/10.1107/S1600536805041280/dn6284Isup2.hkl Contains datablock I

CCDC reference: 296557

checkCIF report

Key indicators

Single-crystal X-ray study
T = 296 K
Mean (C-C) = 0.005 Å
R factor = 0.030
wR factor = 0.066
Data-to-parameter ratio = 24.2

checkCIF/PLATON results

No syntax errors found



Alert level C
RINTA01_ALERT_3_C  The value of Rint is greater than 0.10
            Rint given   0.115
PLAT020_ALERT_3_C The value of Rint is greater than 0.10 .........       0.12
PLAT042_ALERT_1_C Calc. and Rep. MoietyFormula Strings Differ ....          ?
PLAT063_ALERT_3_C Crystal Probably too Large for Beam Size .......       0.70 mm
PLAT066_ALERT_1_C Predicted and Reported Transmissions Identical .          ?
PLAT241_ALERT_2_C Check High      Ueq as Compared to Neighbors for        C14

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

   2 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
   3 ALERT type 3 Indicator that the structure quality may be low
   0 ALERT type 4 Improvement, methodology, query or suggestion

Comment top

There is a considerable interest in the pharmacology of heterocyclic compounds and their derivatives (Mishra & Yadaw, 2000). Particularly, benzimidazole ring systems are an important pharmacophore in modern drug discovery (Tebbe et al., 1997). Benzimidazole derivatives generally exhibit versatile pharmacological activity, such as antitumor, diuretic, fungicidal, bactericidal, antihelmintic, antiallergic, vasodilator, antihistaminic, anti-ulcer and local analgesic. We have also reported the syntheses and antimicrobial activities of many benzimidazole derivatives (Küçükbay et al., 2003, 2004; Küçükbay & Durmaz, 1997). Therefore, the preparation of benzimidazole derivatives has gained considerable attention, particularly in recent years. The objective of this study was then to synthesize and elucidate the crystal structure of a new benzimidazole compound having a pyrolidine ring.

The molecular structure of (I) is shown in Fig. 1. The geometric parameters of (I) are in good agreement with the results obtained in our previous studies of related benzimidazole derivatives (Akkurt, Yıldırım et al.., 2005; Yıldırım et al., 2005; Akkurt, Türktekin et al., 2005). The nine-membered benzimidazole ring system (N1/N2/C1–C7) of (I) is essentially planar, the maximum deviations from planarity being −0.038 (2) Å at atom C1. The conformation of the five-membered pyrrolidine ring (N3/C13–C16) is close to an envelope at N3, the puckering parameters are Q(2) = 0.310 (4) Å and ϕ(2) = 6.2 (9)° (Cremer & Pople, 1975). The details of the C–H···I and N–H···I hydrogen-bonding interactions are given in Table 1 (Fig. 2).

Experimental top

To a solution of 1-(2-pyrolidinium-1-yl)ethylbenzimidazole iodide (2.86 g, 8.33 mmol) in dimethylformamide (5 ml) was added isopropyl iodide (1.42 g, 8.33 mmol) and the mixture was heated under reflux for 8 h. The mixture was then cooled and the solvent was removed in vacuo. The residue was crystallized from EtOH (15 ml). Yield 3.50 g, 82%. M.p. 494–495 K. ¹H NMR (DMSO-d₆): δ 1.67 (d, CH₃, 6H), 1.87 (m, ring methylene, 2H), 2.08 (t, ring methylene, 2H), 3.24 (m, ring methylene, 2H), 3.70 (t, ring methylene, 2H), 3.92 (t, CH₂CH₂-pyrolidine, 2H), 4.91 (t, CH₂CH₂-pyrolidine, 2H), 7.74 (m, Ar—H, 2H), 8.19 (m, Ar—H, 2H), 9.58 (s, 2-CH, 1H), 10.01 (s, pyolidine-1H, 1H). ¹³C NMR (DMSO-d₆): δ 22.07, 23.16, 43.53, 51.35, 52.08, 54.31, 114.49, 114.64, 127.14, 127.23, 131.03, 131.73, 132.04. Analysis calculated for C₁₆H₂₅N₃I₂: C 37.42, H 4.87, N 8.18%; found: C 37.71, H 4.87, N 8.24%.

Computing details top

Data collection: X-AREA (Stoe & Cie, 2002); cell refinement: X-AREA; data reduction: X-RED32 (Stoe & Cie, 2002); program(s) used to solve structure: SIR97 (Altomare et al., 1999); 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).

Figures top

	Fig. 1. An ORTEP-3 (Farrugia, 1997) plot of (I), with the atom-numbering scheme. Displacement ellipsoids for non-H atoms are drawn at the 30% probability level.
	Fig. 2. The packing and hydrogen-bonding interactions (dashed lines) of (I), shown down the c axis. H atoms not involved in hydrogen bonding have been omitted.

3-Isopropyl-1-[2-(pyrrolidinium-1-yl)ethyl]benzimidazolium diodide top

Crystal data top

C₁₆H₂₅N₃²⁺·2I⁻	F(000) = 992
M_r = 513.19	D_x = 1.720 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 47374 reflections
a = 11.639 (5) Å	θ = 2.2–28.0°
b = 12.945 (5) Å	µ = 3.17 mm⁻¹
c = 13.192 (5) Å	T = 296 K
β = 94.349 (5)°	Prism, yellow
V = 1981.9 (14) Å³	0.70 × 0.47 × 0.32 mm
Z = 4

Data collection top

Stoe IPDS-II diffractometer	4649 independent reflections
Radiation source: sealed X-ray tube, 12 x 0.4 mm long-fine focus	3867 reflections with I > 2σ(I)
Plane graphite monochromator	R_int = 0.115
Detector resolution: 6.67 pixels mm^-1	θ_max = 27.9°, θ_min = 2.2°
ω scans	h = −15→15
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	k = −16→16
T_min = 0.181, T_max = 0.362	l = −17→17
32700 measured reflections

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)] = 0.030	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.066	H-atom parameters constrained
S = 1.03	w = 1/[σ²(F_o²) + (0.0183P)² + 1.4496P] where P = (F_o² + 2F_c²)/3
4649 reflections	(Δ/σ)_max = 0.002
192 parameters	Δρ_max = 0.55 e Å⁻³
0 restraints	Δρ_min = −0.47 e Å⁻³

Crystal data top

C₁₆H₂₅N₃²⁺·2I⁻	V = 1981.9 (14) Å³
M_r = 513.19	Z = 4
Monoclinic, P2₁/c	Mo Kα radiation
a = 11.639 (5) Å	µ = 3.17 mm⁻¹
b = 12.945 (5) Å	T = 296 K
c = 13.192 (5) Å	0.70 × 0.47 × 0.32 mm
β = 94.349 (5)°

Data collection top

Stoe IPDS-II diffractometer	4649 independent reflections
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	3867 reflections with I > 2σ(I)
T_min = 0.181, T_max = 0.362	R_int = 0.115
32700 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.030	0 restraints
wR(F²) = 0.066	H-atom parameters constrained
S = 1.03	Δρ_max = 0.55 e Å⁻³
4649 reflections	Δρ_min = −0.47 e Å⁻³
192 parameters

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
N1	0.84375 (17)	0.47989 (19)	0.65470 (17)	0.0496 (5)
N2	0.78661 (18)	0.41067 (18)	0.50849 (18)	0.0474 (5)
N3	0.54418 (19)	0.2897 (2)	0.4476 (2)	0.0562 (6)
H3	0.5473	0.3237	0.5081	0.067*
C1	0.8675 (2)	0.5516 (2)	0.5799 (2)	0.0486 (6)
C2	0.9227 (2)	0.6463 (2)	0.5865 (3)	0.0584 (7)
H2	0.9483	0.6752	0.6487	0.070*
C3	0.9374 (3)	0.6951 (3)	0.4965 (3)	0.0647 (8)
H3A	0.9745	0.7587	0.4975	0.078*
C4	0.8980 (3)	0.6520 (3)	0.4028 (3)	0.0669 (9)
H4	0.9088	0.6885	0.3435	0.080*
C5	0.8439 (2)	0.5577 (2)	0.3954 (2)	0.0571 (7)
H5	0.8181	0.5290	0.3332	0.069*
C6	0.8302 (2)	0.5080 (2)	0.4871 (2)	0.0486 (6)
C7	0.7970 (2)	0.3980 (2)	0.6092 (2)	0.0500 (6)
H7	0.7743	0.3391	0.6428	0.060*
C8	0.8688 (3)	0.4959 (3)	0.7655 (2)	0.0603 (7)
H8	0.9464	0.5251	0.7763	0.072*
C9	0.8677 (4)	0.3951 (3)	0.8211 (3)	0.0859 (11)
H9A	0.9216	0.3485	0.7937	0.129*
H9B	0.7918	0.3658	0.8132	0.129*
H9C	0.8890	0.4064	0.8919	0.129*
C10	0.7852 (4)	0.5727 (3)	0.8042 (3)	0.0833 (11)
H10A	0.7079	0.5480	0.7900	0.125*
H10B	0.7939	0.6379	0.7709	0.125*
H10C	0.8007	0.5812	0.8762	0.125*
C11	0.7548 (2)	0.3295 (2)	0.4340 (2)	0.0519 (6)
H11A	0.7649	0.2630	0.4674	0.062*
H11B	0.8078	0.3323	0.3808	0.062*
C12	0.6333 (2)	0.3354 (3)	0.3852 (2)	0.0570 (7)
H12A	0.6142	0.4073	0.3718	0.068*
H12B	0.6305	0.2999	0.3203	0.068*
C13	0.4247 (3)	0.3020 (3)	0.3977 (3)	0.0772 (10)
H13A	0.3945	0.3701	0.4106	0.093*
H13B	0.4243	0.2918	0.3248	0.093*
C14	0.3561 (3)	0.2210 (4)	0.4447 (4)	0.1068 (16)
H14A	0.3005	0.1916	0.3942	0.128*
H14B	0.3147	0.2504	0.4988	0.128*
C15	0.4371 (3)	0.1394 (4)	0.4862 (4)	0.0940 (13)
H15A	0.4216	0.0745	0.4511	0.113*
H15B	0.4289	0.1292	0.5581	0.113*
C16	0.5564 (3)	0.1768 (3)	0.4693 (3)	0.0647 (8)
H16A	0.6081	0.1652	0.5295	0.078*
H16B	0.5865	0.1410	0.4124	0.078*
I1	0.508777 (19)	0.395704 (18)	0.679775 (17)	0.06756 (8)
I2	0.837046 (18)	0.115434 (19)	0.646326 (17)	0.06782 (8)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N1	0.0419 (11)	0.0600 (14)	0.0470 (12)	−0.0061 (10)	0.0031 (9)	0.0014 (11)
N2	0.0426 (11)	0.0522 (13)	0.0478 (13)	−0.0002 (9)	0.0058 (9)	0.0003 (10)
N3	0.0450 (11)	0.0630 (15)	0.0596 (15)	0.0060 (10)	−0.0022 (10)	−0.0090 (12)
C1	0.0352 (11)	0.0564 (16)	0.0545 (16)	0.0007 (11)	0.0061 (10)	0.0025 (13)
C2	0.0437 (14)	0.0593 (17)	0.073 (2)	−0.0042 (12)	0.0076 (13)	−0.0002 (15)
C3	0.0525 (16)	0.0589 (18)	0.084 (2)	−0.0031 (13)	0.0135 (15)	0.0098 (17)
C4	0.0609 (17)	0.066 (2)	0.076 (2)	0.0079 (15)	0.0205 (16)	0.0245 (18)
C5	0.0587 (16)	0.0631 (18)	0.0509 (16)	0.0069 (14)	0.0130 (13)	0.0044 (14)
C6	0.0380 (12)	0.0544 (15)	0.0543 (15)	0.0030 (11)	0.0099 (11)	0.0042 (12)
C7	0.0441 (13)	0.0556 (16)	0.0509 (15)	−0.0025 (11)	0.0075 (11)	0.0027 (13)
C8	0.0551 (15)	0.076 (2)	0.0485 (16)	−0.0132 (14)	−0.0035 (12)	−0.0027 (15)
C9	0.112 (3)	0.089 (3)	0.056 (2)	−0.002 (2)	−0.003 (2)	0.0138 (19)
C10	0.099 (3)	0.090 (3)	0.062 (2)	−0.001 (2)	0.0090 (19)	−0.022 (2)
C11	0.0522 (14)	0.0532 (15)	0.0506 (15)	0.0030 (12)	0.0064 (12)	−0.0039 (13)
C12	0.0581 (15)	0.0616 (17)	0.0507 (16)	0.0033 (13)	−0.0003 (12)	0.0007 (14)
C13	0.0482 (16)	0.080 (2)	0.101 (3)	0.0141 (16)	−0.0113 (17)	−0.010 (2)
C14	0.0461 (18)	0.109 (3)	0.165 (5)	0.001 (2)	0.003 (2)	−0.001 (3)
C15	0.064 (2)	0.098 (3)	0.121 (4)	−0.006 (2)	0.013 (2)	0.020 (3)
C16	0.0538 (16)	0.0674 (19)	0.072 (2)	0.0048 (14)	0.0005 (14)	0.0085 (17)
I1	0.07027 (14)	0.07263 (15)	0.06063 (14)	0.01439 (10)	0.01047 (10)	0.00271 (10)
I2	0.06355 (13)	0.08111 (16)	0.05814 (14)	0.01448 (10)	0.00036 (9)	0.01609 (11)

Geometric parameters (Å, º) top

N1—C7	1.315 (4)	C8—H8	0.9800
N1—C1	1.397 (4)	C9—H9A	0.9600
N1—C8	1.483 (4)	C9—H9B	0.9600
N2—C7	1.336 (4)	C9—H9C	0.9600
N2—C6	1.396 (3)	C10—H10A	0.9600
N2—C11	1.467 (4)	C10—H10B	0.9600
N3—C12	1.494 (4)	C10—H10C	0.9600
N3—C16	1.494 (4)	C11—C12	1.510 (4)
N3—C13	1.501 (4)	C11—H11A	0.9700
N3—H3	0.9100	C11—H11B	0.9700
C1—C2	1.384 (4)	C12—H12A	0.9700
C1—C6	1.388 (4)	C12—H12B	0.9700
C2—C3	1.366 (5)	C13—C14	1.482 (6)
C2—H2	0.9300	C13—H13A	0.9700
C3—C4	1.402 (5)	C13—H13B	0.9700
C3—H3A	0.9300	C14—C15	1.492 (6)
C4—C5	1.373 (5)	C14—H14A	0.9700
C4—H4	0.9300	C14—H14B	0.9700
C5—C6	1.389 (4)	C15—C16	1.503 (5)
C5—H5	0.9300	C15—H15A	0.9700
C7—H7	0.9300	C15—H15B	0.9700
C8—C9	1.496 (5)	C16—H16A	0.9700
C8—C10	1.507 (5)	C16—H16B	0.9700

C7—N1—C1	108.1 (2)	H9B—C9—H9C	109.5
C7—N1—C8	127.2 (2)	C8—C10—H10A	109.5
C1—N1—C8	124.7 (2)	C8—C10—H10B	109.5
C7—N2—C6	107.8 (2)	H10A—C10—H10B	109.5
C7—N2—C11	125.3 (2)	C8—C10—H10C	109.5
C6—N2—C11	126.1 (2)	H10A—C10—H10C	109.5
C12—N3—C16	115.6 (2)	H10B—C10—H10C	109.5
C12—N3—C13	112.0 (3)	N2—C11—C12	115.5 (2)
C16—N3—C13	105.0 (2)	N2—C11—H11A	108.4
C12—N3—H3	107.9	C12—C11—H11A	108.4
C16—N3—H3	107.9	N2—C11—H11B	108.4
C13—N3—H3	107.9	C12—C11—H11B	108.4
C2—C1—C6	121.8 (3)	H11A—C11—H11B	107.5
C2—C1—N1	131.3 (3)	N3—C12—C11	114.3 (2)
C6—C1—N1	106.7 (2)	N3—C12—H12A	108.7
C3—C2—C1	116.3 (3)	C11—C12—H12A	108.7
C3—C2—H2	121.8	N3—C12—H12B	108.7
C1—C2—H2	121.8	C11—C12—H12B	108.7
C2—C3—C4	121.9 (3)	H12A—C12—H12B	107.6
C2—C3—H3A	119.1	C14—C13—N3	104.6 (3)
C4—C3—H3A	119.1	C14—C13—H13A	110.8
C5—C4—C3	122.3 (3)	N3—C13—H13A	110.8
C5—C4—H4	118.9	C14—C13—H13B	110.8
C3—C4—H4	118.9	N3—C13—H13B	110.8
C4—C5—C6	115.6 (3)	H13A—C13—H13B	108.9
C4—C5—H5	122.2	C13—C14—C15	108.0 (3)
C6—C5—H5	122.2	C13—C14—H14A	110.1
C1—C6—C5	122.1 (3)	C15—C14—H14A	110.1
C1—C6—N2	106.4 (2)	C13—C14—H14B	110.1
C5—C6—N2	131.4 (3)	C15—C14—H14B	110.1
N1—C7—N2	110.9 (2)	H14A—C14—H14B	108.4
N1—C7—H7	124.5	C14—C15—C16	106.5 (3)
N2—C7—H7	124.5	C14—C15—H15A	110.4
N1—C8—C9	110.7 (3)	C16—C15—H15A	110.4
N1—C8—C10	110.0 (3)	C14—C15—H15B	110.4
C9—C8—C10	112.3 (3)	C16—C15—H15B	110.4
N1—C8—H8	107.9	H15A—C15—H15B	108.6
C9—C8—H8	107.9	N3—C16—C15	105.5 (3)
C10—C8—H8	107.9	N3—C16—H16A	110.6
C8—C9—H9A	109.5	C15—C16—H16A	110.6
C8—C9—H9B	109.5	N3—C16—H16B	110.6
H9A—C9—H9B	109.5	C15—C16—H16B	110.6
C8—C9—H9C	109.5	H16A—C16—H16B	108.8
H9A—C9—H9C	109.5

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3···I1	0.91	2.52	3.410 (3)	166
C7—H7···I2	0.93	2.98	3.715 (3)	136
C8—H8···I2ⁱ	0.98	2.89	3.856 (3)	168
C12—H12A···I1ⁱⁱ	0.97	2.98	3.921 (3)	164

Symmetry codes: (i) −x+2, y+1/2, −z+3/2; (ii) −x+1, −y+1, −z+1.

Experimental details

Crystal data
Chemical formula	C₁₆H₂₅N₃²⁺·2I⁻
M_r	513.19
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	296
a, b, c (Å)	11.639 (5), 12.945 (5), 13.192 (5)
β (°)	94.349 (5)
V (Å³)	1981.9 (14)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	3.17
Crystal size (mm)	0.70 × 0.47 × 0.32

Data collection
Diffractometer	Stoe IPDS-II diffractometer
Absorption correction	Multi-scan (SADABS; Sheldrick, 1996)
T_min, T_max	0.181, 0.362
No. of measured, independent and observed [I > 2σ(I)] reflections	32700, 4649, 3867
R_int	0.115
(sin θ/λ)_max (Å⁻¹)	0.658

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.030, 0.066, 1.03
No. of reflections	4649
No. of parameters	192
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.55, −0.47

Computer programs: X-AREA (Stoe & Cie, 2002), X-AREA, X-RED32 (Stoe & Cie, 2002), SIR97 (Altomare et al., 1999), SHELXL97 (Sheldrick, 1997), ORTEP-3 for Windows (Farrugia, 1997), WinGX (Farrugia, 1999).