(1H-Benzo­diazol-2-ylmeth­yl)di­ethyl­amine

Khamrang, T.; Kannan, A.; Hemamalini, M.; Tahir, M.N.; Antony, G.J.M.; Saravanan, D.

doi:10.1107/S241431462401006X

organic compounds

IUCrDATA

ISSN: 2414-3146

Volume 9| Part 10| October 2024| x241006

https://doi.org/10.1107/S241431462401006X

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(1H-Benzodiazol-2-ylmethyl)diethylamine

Themmila Khamrang,^a A. Kannan,^b Madhukar Hemamalini,^c Muhammad Nawaz Tahir,^d G. Jerald Maria Antony ^e ^* and Dhandayutham Saravanan ^e

^aDepartment of Chemistry, Dhanamanjuri University, Manipur 795 001, India, ^bDepartment of Chemistry, Anjalai Ammal Mahalingam Engineering College, Kovilvenni, Tiruvarur 614 403, Tamil Nadu, India, ^cDepartment of Chemistry, Mother Teresa Women's University, Kodaikanal, Tamil Nadu, India, ^dDepartment of Physics, University of Sargodha, Sargodha, 40100, Punjab, Pakistan, and ^eDepartment of Chemistry, National College, Tiruchirappalli, Tamil Nadu, India
^*Correspondence e-mail: jerelewin.mine@gmail.com

Edited by W. T. A. Harrison, University of Aberdeen, United Kingdom (Received 27 September 2024; accepted 15 October 2024; online 31 October 2024)

In the crystal of the title compound, C₁₂H₁₇N₃, the molecules are linked by N—H⋯N hydrogen bonds, generating a C(4) chain extending along the c-axis direction. One of the ethyl groups is disordered over two sets of sites with a refined occupancy ratio of 0.582 (15):0.418 (15).

Keywords: crystal structure; benzimidazole; hydrogen bonding.

CCDC reference: 2376300

Structure description

Benzimidazole and its derivatives show a wide range of pharmacological activities including antimicrobial, antifungal, antihistaminic, anti-inflammatory, antiviral, and antioxidant effects (e.g., Walia et al., 2011 ; Navarrete-Vazquez et al., 2001 ). The present research focuses on elucidating the hydrogen-bonding patterns exhibited by the title compound, C₁₂H₁₇N₃.

The asymmetric unit is shown in Fig. 1. As expected, the benzimidazole (N2,N3,C6–C12) ring system is almost planar with a maximum deviation of 0.022 (8) Å for C6. The N2—C7—C8—N3 torsion angle is −155.9 (5)° and the C11/C12 ethyl group is disordered over two sets of sites with a refined occupancy ratio of 0.582 (15):0.418 (15). In the extended structure (Fig. 2), the molecules are connected by N1—H1⋯N2 hydrogen bonds (Table 1) to form C(4) chains propagating along the c-axis direction.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1⋯N2ⁱ	0.86	2.06	2.873 (4)	157
Symmetry code: (i) $[-x+{\script{1\over 2}}, y, z+{\script{1\over 2}}]$ .

Figure 1
The asymmetric unit of the title compound with displacement ellipsoids drawn at the 30% probability level.

Figure 2
The crystal packing of the title compound.

There are thousands of benzimidazole derivatives in the Cambridge Structural Database (CSD; Version 5.43, update to November 2022; Groom et al., 2016 ) with three examples being methyl 2-[(1H-benzimidazol-2-ylmethyl)amino]benzoate (CSD refcode VARDEZ; Ghani et al., 2011 ), 1-(1H-benzimidazol-2-yl)-N,N-bis[(1H-benzimidazol-2-yl)methyl]methanamine methanol solvate (IHILIX; Anzaldo-Olivares et al., 2020 ) and 1-(1-methyl-1H-benzimidazol-2-yl)-N-[(1-methyl-1H-benzimidazol-2-yl)methyl]methanamine (TAZJIR; Gaoxiang et al., 2022 ).

Synthesis and crystallization

The title compound was prepared according to the literature method (Lingala et al., 2011). Single crystals were obtained by slowly evaporating a dichloromethane solution of the title compound.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2.

Table 2
Experimental details

Crystal data
Chemical formula	C₁₂H₁₇N₃
M_r	203.28
Crystal system, space group	Orthorhombic, Pca2₁
Temperature (K)	293
a, b, c (Å)	7.9290 (7), 15.3027 (15), 10.0486 (6)
V (Å³)	1219.25 (18)
Z	4
Radiation type	Mo Kα
μ (mm⁻¹)	0.07
Crystal size (mm)	0.36 × 0.33 × 0.30

Data collection
Diffractometer	Agilent Xcalibur, Atlas, Gemini
Absorption correction	Analytical (SADABS; Krause et al., 2015 )
T_min, T_max	0.507, 0.578
No. of measured, independent and observed [I > 2σ(I)] reflections	3304, 2135, 1138
R_int	0.036
(sin θ/λ)_max (Å⁻¹)	0.675

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.066, 0.130, 1.18
No. of reflections	2135
No. of parameters	158
No. of restraints	41
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.11, −0.10
Absolute structure	Flack x determined using 249 quotients [(I⁺)−(I⁻)]/[(I⁺)+(I⁻)] (Parsons et al., 2013 )
Absolute structure parameter	−1.1 (10)
Computer programs: CrysAlis PRO (Agilent, 2012 ), SHELXT2014/5 (Sheldrick, 2015a ), SHELXL2018/3 (Sheldrick, 2015b ) and PLATON (Spek, 2020 ).

Structural data

CCDC reference: 2376300

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S241431462401006X/hb4488sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S241431462401006X/hb4488Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S241431462401006X/hb4488Isup3.cml

checkCIF report

Computing details top

(1H-Benzodiazol-2-ylmethyl)diethylamine top

Crystal data top

C₁₂H₁₇N₃	D_x = 1.107 Mg m⁻³
M_r = 203.28	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, Pca2₁	Cell parameters from 9307 reflections
a = 7.9290 (7) Å	θ = 3.5–26.4°
b = 15.3027 (15) Å	µ = 0.07 mm⁻¹
c = 10.0486 (6) Å	T = 293 K
V = 1219.25 (18) Å³	Block, colouress
Z = 4	0.36 × 0.33 × 0.30 mm
F(000) = 440

Data collection top

Agilent Xcalibur, Atlas, Gemini diffractometer	1138 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	R_int = 0.036
ω scans	θ_max = 28.7°, θ_min = 3.5°
Absorption correction: analytical (SADABS; Krause et al., 2015)	h = −10→8
T_min = 0.507, T_max = 0.578	k = −8→20
3304 measured reflections	l = −8→13
2135 independent reflections

Refinement top

Refinement on F²	Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: full	H-atom parameters constrained
R[F² > 2σ(F²)] = 0.066	w = 1/[σ²(F_o²) + (0.0388P)²] where P = (F_o² + 2F_c²)/3
wR(F²) = 0.130	(Δ/σ)_max < 0.001
S = 1.18	Δρ_max = 0.11 e Å⁻³
2135 reflections	Δρ_min = −0.10 e Å⁻³
158 parameters	Absolute structure: Flack x determined using 249 quotients [(I⁺)-(I^-)]/[(I⁺)+(I^-)] (Parsons et al., 2013)
41 restraints	Absolute structure parameter: −1.1 (10)
Primary atom site location: dual

Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Refinement. All the H atoms were positioned geometrically (C—H = 0.96–0.97 A°) and refined using a riding model with U_iso(H) = 1.2 U_eq(C) or 1.5 U_eq(methyl C).

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq	Occ. (<1)
N1	0.2389 (4)	0.3102 (2)	0.0373 (3)	0.0597 (10)
H1	0.284732	0.301682	0.113816	0.072*
N2	0.1987 (4)	0.3027 (3)	−0.1813 (3)	0.0659 (11)
N3	0.5022 (5)	0.1850 (4)	0.0249 (4)	0.0951 (15)
C1	0.0952 (5)	0.3570 (3)	0.0120 (3)	0.0515 (11)
C2	−0.0116 (6)	0.4053 (3)	0.0930 (4)	0.0648 (13)
H2	0.005609	0.408829	0.184357	0.078*
C3	−0.1425 (6)	0.4474 (3)	0.0331 (5)	0.0761 (14)
H3	−0.216070	0.480461	0.084546	0.091*
C4	−0.1685 (6)	0.4418 (3)	−0.1041 (4)	0.0791 (15)
H4	−0.259316	0.471219	−0.141747	0.095*
C5	−0.0640 (6)	0.3942 (3)	−0.1845 (4)	0.0739 (14)
H5	−0.083221	0.390253	−0.275557	0.089*
C6	0.0716 (5)	0.3521 (3)	−0.1255 (3)	0.0570 (13)
C7	0.2952 (5)	0.2799 (3)	−0.0819 (4)	0.0643 (12)
C8	0.4587 (6)	0.2325 (4)	−0.0949 (4)	0.0909 (17)
H8A	0.451582	0.191793	−0.168709	0.109*
H8B	0.547429	0.274120	−0.114689	0.109*
C9	0.3974 (11)	0.1078 (5)	0.0413 (6)	0.131 (2)
H9A	0.436683	0.062760	−0.019218	0.158*
H9B	0.282447	0.122226	0.016695	0.158*
C10	0.3979 (10)	0.0716 (5)	0.1815 (7)	0.165 (3)
H10A	0.386626	0.118764	0.243885	0.248*
H10B	0.502133	0.041431	0.197381	0.248*
H10C	0.305414	0.031777	0.192073	0.248*
C11A	0.6923 (15)	0.1942 (10)	0.0568 (12)	0.099 (5)	0.582 (15)
H11A	0.722510	0.255582	0.058529	0.118*	0.582 (15)
H11B	0.714977	0.169826	0.144064	0.118*	0.582 (15)
C12A	0.797 (2)	0.1479 (12)	−0.0451 (15)	0.136 (6)	0.582 (15)
H12A	0.756247	0.089389	−0.056573	0.205*	0.582 (15)
H12B	0.912622	0.146040	−0.015698	0.205*	0.582 (15)
H12C	0.790966	0.178585	−0.128247	0.205*	0.582 (15)
C11B	0.6574 (15)	0.1307 (12)	0.0073 (17)	0.096 (6)	0.418 (15)
H11C	0.664688	0.106808	−0.081926	0.116*	0.418 (15)
H11D	0.662348	0.083481	0.071549	0.116*	0.418 (15)
C12B	0.793 (3)	0.1976 (13)	0.032 (3)	0.121 (8)	0.418 (15)
H12D	0.789364	0.241313	−0.036326	0.181*	0.418 (15)
H12E	0.901286	0.169560	0.031495	0.181*	0.418 (15)
H12F	0.774788	0.224638	0.117173	0.181*	0.418 (15)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N1	0.0612 (18)	0.085 (3)	0.0325 (16)	0.003 (2)	−0.0023 (16)	−0.0003 (19)
N2	0.074 (2)	0.093 (3)	0.0311 (17)	0.014 (2)	−0.0006 (17)	0.0026 (19)
N3	0.078 (3)	0.131 (4)	0.076 (2)	0.027 (3)	0.008 (2)	0.032 (3)
C1	0.057 (2)	0.059 (3)	0.039 (2)	−0.002 (2)	0.0025 (18)	0.004 (2)
C2	0.073 (3)	0.074 (3)	0.048 (2)	−0.001 (3)	0.010 (2)	−0.003 (2)
C3	0.075 (3)	0.078 (4)	0.075 (3)	0.010 (3)	0.021 (3)	0.003 (3)
C4	0.075 (3)	0.093 (4)	0.070 (3)	0.017 (3)	−0.003 (2)	0.020 (3)
C5	0.073 (3)	0.093 (4)	0.056 (3)	0.001 (3)	−0.008 (2)	0.008 (3)
C6	0.061 (3)	0.071 (4)	0.040 (2)	0.000 (3)	0.0020 (18)	0.004 (2)
C7	0.067 (2)	0.086 (3)	0.040 (2)	0.011 (2)	0.0071 (19)	0.001 (2)
C8	0.084 (3)	0.136 (5)	0.053 (3)	0.039 (3)	0.013 (2)	0.012 (3)
C9	0.190 (7)	0.100 (6)	0.104 (5)	0.027 (5)	0.003 (5)	0.005 (5)
C10	0.234 (9)	0.131 (6)	0.130 (6)	0.009 (6)	0.029 (6)	0.039 (5)
C11A	0.070 (8)	0.105 (12)	0.120 (10)	0.009 (10)	−0.007 (7)	0.007 (8)
C12A	0.107 (11)	0.139 (14)	0.163 (14)	0.027 (11)	0.024 (11)	0.012 (11)
C11B	0.070 (9)	0.121 (16)	0.098 (10)	0.006 (10)	0.000 (8)	0.014 (10)
C12B	0.066 (11)	0.121 (19)	0.18 (2)	−0.007 (15)	−0.020 (16)	0.022 (16)

Geometric parameters (Å, º) top

N1—C7	1.360 (5)	C8—H8A	0.9700
N1—C1	1.369 (5)	C8—H8B	0.9700
N1—H1	0.8600	C9—C10	1.513 (8)
N2—C7	1.306 (5)	C9—H9A	0.9700
N2—C6	1.379 (5)	C9—H9B	0.9700
N3—C8	1.448 (6)	C10—H10A	0.9600
N3—C9	1.453 (8)	C10—H10B	0.9600
N3—C11B	1.496 (15)	C10—H10C	0.9600
N3—C11A	1.547 (13)	C11A—C12A	1.498 (10)
C1—C2	1.388 (5)	C11A—H11A	0.9700
C1—C6	1.396 (4)	C11A—H11B	0.9700
C2—C3	1.362 (6)	C12A—H12A	0.9600
C2—H2	0.9300	C12A—H12B	0.9600
C3—C4	1.396 (6)	C12A—H12C	0.9600
C3—H3	0.9300	C11B—C12B	1.505 (11)
C4—C5	1.367 (6)	C11B—H11C	0.9700
C4—H4	0.9300	C11B—H11D	0.9700
C5—C6	1.387 (5)	C12B—H12D	0.9600
C5—H5	0.9300	C12B—H12E	0.9600
C7—C8	1.491 (6)	C12B—H12F	0.9600

C7—N1—C1	106.7 (3)	N3—C9—C10	113.6 (6)
C7—N1—H1	126.7	N3—C9—H9A	108.8
C1—N1—H1	126.7	C10—C9—H9A	108.8
C7—N2—C6	105.3 (3)	N3—C9—H9B	108.8
C8—N3—C9	111.5 (5)	C10—C9—H9B	108.8
C8—N3—C11B	112.1 (7)	H9A—C9—H9B	107.7
C9—N3—C11B	91.9 (7)	C9—C10—H10A	109.5
C8—N3—C11A	111.0 (6)	C9—C10—H10B	109.5
C9—N3—C11A	127.4 (7)	H10A—C10—H10B	109.5
N1—C1—C2	132.6 (4)	C9—C10—H10C	109.5
N1—C1—C6	105.6 (3)	H10A—C10—H10C	109.5
C2—C1—C6	121.8 (4)	H10B—C10—H10C	109.5
C3—C2—C1	117.2 (4)	C12A—C11A—N3	111.0 (13)
C3—C2—H2	121.4	C12A—C11A—H11A	109.4
C1—C2—H2	121.4	N3—C11A—H11A	109.4
C2—C3—C4	121.3 (4)	C12A—C11A—H11B	109.4
C2—C3—H3	119.3	N3—C11A—H11B	109.4
C4—C3—H3	119.3	H11A—C11A—H11B	108.0
C5—C4—C3	121.8 (5)	C11A—C12A—H12A	109.5
C5—C4—H4	119.1	C11A—C12A—H12B	109.5
C3—C4—H4	119.1	H12A—C12A—H12B	109.5
C4—C5—C6	117.7 (4)	C11A—C12A—H12C	109.5
C4—C5—H5	121.1	H12A—C12A—H12C	109.5
C6—C5—H5	121.1	H12B—C12A—H12C	109.5
N2—C6—C5	130.4 (3)	N3—C11B—C12B	101.0 (16)
N2—C6—C1	109.5 (4)	N3—C11B—H11C	111.6
C5—C6—C1	120.2 (4)	C12B—C11B—H11C	111.6
N2—C7—N1	113.0 (3)	N3—C11B—H11D	111.6
N2—C7—C8	124.9 (3)	C12B—C11B—H11D	111.6
N1—C7—C8	121.9 (4)	H11C—C11B—H11D	109.4
N3—C8—C7	112.2 (3)	C11B—C12B—H12D	109.5
N3—C8—H8A	109.2	C11B—C12B—H12E	109.5
C7—C8—H8A	109.2	H12D—C12B—H12E	109.5
N3—C8—H8B	109.2	C11B—C12B—H12F	109.5
C7—C8—H8B	109.2	H12D—C12B—H12F	109.5
H8A—C8—H8B	107.9	H12E—C12B—H12F	109.5

C7—N1—C1—C2	−176.9 (4)	C6—N2—C7—C8	−174.1 (5)
C7—N1—C1—C6	0.1 (5)	C1—N1—C7—N2	−0.6 (5)
N1—C1—C2—C3	177.3 (4)	C1—N1—C7—C8	174.5 (4)
C6—C1—C2—C3	0.7 (6)	C9—N3—C8—C7	73.2 (6)
C1—C2—C3—C4	0.2 (7)	C11B—N3—C8—C7	174.5 (8)
C2—C3—C4—C5	−0.1 (8)	C11A—N3—C8—C7	−138.7 (6)
C3—C4—C5—C6	−0.9 (7)	N2—C7—C8—N3	−155.9 (5)
C7—N2—C6—C5	178.8 (4)	N1—C7—C8—N3	29.6 (7)
C7—N2—C6—C1	−0.7 (5)	C8—N3—C9—C10	−162.1 (5)
C4—C5—C6—N2	−177.7 (5)	C11B—N3—C9—C10	83.2 (9)
C4—C5—C6—C1	1.8 (7)	C11A—N3—C9—C10	56.2 (10)
N1—C1—C6—N2	0.4 (5)	C8—N3—C11A—C12A	−68.0 (13)
C2—C1—C6—N2	177.8 (4)	C9—N3—C11A—C12A	73.8 (14)
N1—C1—C6—C5	−179.2 (4)	C8—N3—C11B—C12B	83.4 (15)
C2—C1—C6—C5	−1.8 (7)	C9—N3—C11B—C12B	−162.5 (14)
C6—N2—C7—N1	0.8 (5)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···N2ⁱ	0.86	2.06	2.873 (4)	157

Symmetry code: (i) −x+1/2, y, z+1/2.

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