Monoclinic polymorph of 2-aza­niumylmethyl-1H-benzimidazol-3-ium dichloride monohydrate

Baskaran, M.D.; Jayaraman, S.; Hemamalini, M.; Elsegood, M.R.J.; Rajakannan, V.; Kavitha, S.J.

doi:10.1107/S2414314625008685

organic compounds

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Volume 10| Part 10| October 2025| x250868

https://doi.org/10.1107/S2414314625008685

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Monoclinic polymorph of 2-azaniumylmethyl-1H-benzimidazol-3-ium dichloride monohydrate

Manjula Devi Baskaran,^a Shanthini Jayaraman,^a Madhukar Hemamalini,^a Mark R. J. Elsegood,^b Venkatachalam Rajakannan ^c and Savaridasson Jose Kavitha ^a ^*

^aDepartment of Chemistry, Mother Teresa Women's University, Kodaikanal, Tamil Nadu, India, ^bChemistry Department, Loughborough University, Loughborough, Leicestershire, LE11 3TU, United Kingdom, and ^cDepartment of Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai-600 025, Tamil Nadu, India
^*Correspondence e-mail: [email protected]

Edited by W. T. A. Harrison, University of Aberdeen, United Kingdom (Received 15 September 2025; accepted 3 October 2025; online 7 October 2025)

The title hydrated salt, C₈H₁₁N₃²⁺·2Cl⁻·H₂O, is a monoclinic polymorph of the previously reported triclinic form. The compound crystallizes in space group P2₁/c with Z′ = 1. The crystal structure features N—H⋯O, N—H⋯Cl and O—H⋯Cl hydrogen bonds and aromatic π–π stacking interactions, forming a three-dimensional network.

Keywords: crystal structure; hydrogen bonding; polymorph.

CCDC reference: 2485331

Structure description

Benzimidazole-based systems have attracted attention as ligands for metal complexation owing to the desirable properties that are beneficial for biological applications such as anti-bacterial (Kankate et al., 2019 ) and anti-hypertensive (Sharma et al., 2013 ) effects. The materials applications of benzimidazole ligands include luminescent properties of their metal complexes, which can be applied in electroluminescent devices (Wu et al., 2008 ). The larger conjugated π-system and the nitrogen electron donor of the secondary amine group of the benzimidazole moiety play an important role in determining the properties of the complexes. As part of our work in this area, we now describe the synthesis and structure of the title benzimidazolium salt, C₈H₁₁N₃²⁺·2Cl⁻·H₂O.

A search of the Cambridge Structural Database (Version 6.00, update April 2025; Groom et al., 2016 ) for the 2-ammoniumylmethyl-1H -benzimidazol-3-ium (C₈H₁₁N₃²⁺) dication, generated three hits: a tetrachlorozinc(II) salt (CSD refcode COKXAC; Tapia-Benavides et al., 2008 ), the solvent-free dichloride salt (NEPKOK; Malecki, 2011 ) and the triclinic polymorph of the title compound (NINWIT; Sen et al., 2018 ).

The title compound crystallizes in a new monoclinic form in space group P2₁/c compared with the previously reported triclinic form, in space group P $[\overline{1}]$ (Sen et al., 2018). In the monoclinic polymorph, the asymmetric unit contains a benzimidazolium dication, two chloride ions, and a water molecule with Z′ = 1 (Fig. 1). In the more complex triclinic polymorph, the asymmetric unit contains three benzimidazolium dications, six chloride ions and three water molecules with Z′ = 3 (Sen et al., 2018). One notable feature is that in the solvent-free salt (Malecki, 2011), the pendant CH₂NH₃ moiety has a substantial torsion angle of ca. 59° relative to the plane of the fused rings, while in both monohydrate polymorphs, in all the unique molecules, that angle is < 10°, so that moiety is close to co-planar with the fused rings.

Figure 1
The asymmetric unit of the title compound with 50% probability ellipsoids showing hydrogen bonds as dashed lines.

In the monoclinic polymorph described here, all the N—H groups form strong, charge-assisted, hydrogen bonds to either chloride anions or the water oxygen atom (Table 1). The water molecule forms O—H⋯Cl links to two chloride ions. The molecules pack in sheets in the ab plane and these sheets are then hydrogen bonded to their neighbours, generating a three-dimensional network (Fig. 2), similar to that of the triclinic polymorph. The cations also display aromatic π–π stacking in the a-axis direction with alternate molecules anti-parallel, with a shortest centroid–centroid separation of 3.4071 (4) Å.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1C⋯Cl1	0.84 (1)	2.32 (1)	3.0898 (8)	152 (1)
N1—H1D⋯Cl2ⁱ	0.83 (1)	2.30 (1)	3.1262 (7)	177 (1)
N1—H1E⋯Cl2ⁱⁱ	0.86 (1)	2.41 (1)	3.2430 (7)	163 (1)
N2—H2⋯Cl2	0.866 (16)	2.259 (16)	3.1099 (6)	167.2 (14)
N3—H3⋯O1	0.812 (15)	1.911 (16)	2.7197 (9)	173.6 (15)
O1—H1A⋯Cl2ⁱⁱⁱ	0.80 (1)	2.59 (1)	3.3752 (7)	169 (2)
O1—H1B⋯Cl1^iv	0.81 (1)	2.31 (1)	3.1209 (7)	173 (2)
C1—H1F⋯Cl1^v	0.988 (13)	2.793 (13)	3.7079 (8)	154.2 (10)
C5—H5⋯Cl1ⁱⁱ	0.926 (13)	2.960 (13)	3.8515 (7)	162.1 (10)
Symmetry codes: (i) $[-x+2, y-{\script{1\over 2}}, -z+{\script{3\over 2}}]$ ; (ii) $[x, -y+{\script{1\over 2}}, z-{\script{1\over 2}}]$ ; (iii) $[x-1, -y+{\script{1\over 2}}, z-{\script{1\over 2}}]$ ; (iv) ; (v) .

Figure 2
Crystal packing of the title compound viewed down [100].

Synthesis and crystallization

The benzimidazolium cation was prepared following the reported procedure (Cescon & Day, 1962 ). About 1 mmol (5.46 g) of o-phenylenediamine and 1 mmol (5.68 g) of glycine were mixed and dissolved in 100 ml of hydrochloric acid (5 mol l⁻¹). The solution was refluxed for three days. The reaction mixture was cooled and placed in an ice bath overnight. The resulting purple crystals were isolated from the hydrochloric acid by filtration, and then recrystallized from ethanol solution, m.p. = 122 °C. From the same re-crystallization, some red crystals of the well known compound o-phenylenediamine dihydrochloride [CSD: PHNDMO; Stålhandske, 1974 ) were also identified. We have re-determined that structure to a slightly higher precision (Baskaran et al., 2025 )

Refinement

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

Table 2
Experimental details

Crystal data
Chemical formula	C₈H₁₁N₃²⁺·2Cl⁻·H₂O
M_r	238.11
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	100
a, b, c (Å)	6.81630 (11), 12.09585 (19), 12.5226 (2)
β (°)	90.7201 (14)
V (Å³)	1032.39 (3)
Z	4
Radiation type	Mo Kα
μ (mm⁻¹)	0.60
Crystal size (mm)	0.18 × 0.15 × 0.07

Data collection
Diffractometer	Rigaku FRE+ diffractometer with HF Varimax confocal mirrors, a UG2 goniometer and HyPix 6000HE detector
Absorption correction	Analytical (CrystalisPro; Rigaku OD, 2024 )
T_min, T_max	0.988, 0.994
No. of measured, independent and observed [I > 2σ(I)] reflections	49678, 5003, 4463
R_int	0.057
(sin θ/λ)_max (Å⁻¹)	0.833

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.029, 0.080, 1.06
No. of reflections	5003
No. of parameters	172
No. of restraints	5
H-atom treatment	Only H-atom coordinates refined
Δρ_max, Δρ_min (e Å⁻³)	0.72, −0.22
Computer programs: CrysAlis PRO (Rigaku OD, 2024), SHELXT2018/2 (Sheldrick, 2015a ), SHELXL2019/3 (Sheldrick, 2015b ) and SHELXTL (Sheldrick, 2008 ).

Structural data

CCDC reference: 2485331

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S2414314625008685/hb4537sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314625008685/hb4537Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2414314625008685/hb4537Isup3.cml

checkCIF report

Computing details top

2-Azaniumylmethyl-1H-benzimidazol-3-ium dichloride monohydrate top

Crystal data top

C₈H₁₁N₃²⁺·2Cl⁻·H₂O	F(000) = 496
M_r = 238.11	D_x = 1.532 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
a = 6.81630 (11) Å	Cell parameters from 29865 reflections
b = 12.09585 (19) Å	θ = 2.3–38.0°
c = 12.5226 (2) Å	µ = 0.60 mm⁻¹
β = 90.7201 (14)°	T = 100 K
V = 1032.39 (3) Å³	Block, colourless
Z = 4	0.18 × 0.15 × 0.07 mm

Data collection top

Rigaku FRE+ diffractometer with HF Varimax confocal mirrors, a UG2 goniometer and HyPix 6000HE detector	5003 independent reflections
Radiation source: Rotating Anode	4463 reflections with I > 2σ(I)
Detector resolution: 10 pixels mm^-1	R_int = 0.057
profile data from ω–scans	θ_max = 36.3°, θ_min = 2.3°
Absorption correction: analytical (CrystalisPro; Rigaku OD, 2024)	h = −11→11
T_min = 0.988, T_max = 0.994	k = −20→20
49678 measured reflections	l = −20→20

Refinement top

Refinement on F²	Primary atom site location: iterative
Least-squares matrix: full	Hydrogen site location: difference Fourier map
R[F² > 2σ(F²)] = 0.029	Only H-atom coordinates refined
wR(F²) = 0.080	w = 1/[σ²(F_o²) + (0.0466P)² + 0.1488P] where P = (F_o² + 2F_c²)/3
S = 1.06	(Δ/σ)_max = 0.002
5003 reflections	Δρ_max = 0.72 e Å⁻³
172 parameters	Δρ_min = −0.22 e Å⁻³
5 restraints

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. The H atoms atoms were located in a difference Fourier map and their coordinates allowed to refine freely. U_iso(H) values were also freely refined except for those on N1 and C5–C8, which were contstrained and tied to those of the carrier atom with U_iso(H) = 1.5 U_eq(N) and 1.2 U_eq(C).

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

	x	y	z	U_iso*/U_eq
N1	0.78913 (11)	0.09281 (6)	0.55978 (6)	0.01490 (11)
H1C	0.6658 (17)	0.0874 (11)	0.5557 (11)	0.022*
H1D	0.824 (2)	0.0323 (10)	0.5836 (11)	0.022*
H1E	0.839 (2)	0.0984 (11)	0.4968 (9)	0.022*
C1	0.84801 (12)	0.18467 (7)	0.63089 (6)	0.01495 (13)
H1F	0.991 (2)	0.1798 (11)	0.6436 (10)	0.019 (3)*
H1G	0.777 (2)	0.1781 (11)	0.6978 (11)	0.023 (3)*
C2	0.80152 (10)	0.29464 (6)	0.58338 (6)	0.01152 (11)
N2	0.83825 (10)	0.38973 (5)	0.63375 (5)	0.01193 (11)
H2	0.896 (2)	0.3946 (13)	0.6957 (13)	0.030 (4)*
C3	0.79320 (10)	0.47665 (6)	0.56549 (6)	0.01090 (11)
C4	0.72336 (10)	0.42885 (6)	0.47064 (6)	0.01071 (11)
N3	0.73024 (9)	0.31486 (5)	0.48549 (5)	0.01132 (10)
H3	0.682 (2)	0.2691 (12)	0.4455 (12)	0.026 (3)*
C5	0.66377 (11)	0.49262 (6)	0.38340 (6)	0.01216 (12)
H5	0.6100 (18)	0.4613 (10)	0.3222 (10)	0.015*
C6	0.67891 (11)	0.60627 (6)	0.39581 (6)	0.01288 (12)
H6	0.6386 (19)	0.6514 (11)	0.3388 (10)	0.015*
C7	0.74867 (11)	0.65425 (6)	0.49147 (6)	0.01293 (12)
H7	0.7560 (19)	0.7282 (11)	0.4942 (10)	0.016*
C8	0.80654 (11)	0.59081 (6)	0.57854 (6)	0.01269 (12)
H8	0.8465 (19)	0.6234 (11)	0.6454 (10)	0.015*
O1	0.54805 (9)	0.17363 (5)	0.34741 (5)	0.01701 (11)
H1A	0.431 (2)	0.1721 (15)	0.3536 (14)	0.043 (4)*
H1B	0.577 (2)	0.1084 (12)	0.3475 (13)	0.038 (4)*
Cl1	0.35804 (3)	0.07804 (2)	0.63181 (2)	0.01669 (5)
Cl2	1.05821 (3)	0.36655 (2)	0.85168 (2)	0.01277 (5)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N1	0.0179 (3)	0.0114 (3)	0.0153 (3)	0.0012 (2)	0.0001 (2)	0.0004 (2)
C1	0.0182 (3)	0.0123 (3)	0.0142 (3)	−0.0003 (2)	−0.0031 (2)	0.0022 (2)
C2	0.0113 (3)	0.0122 (3)	0.0110 (3)	−0.0004 (2)	−0.0012 (2)	0.0006 (2)
N2	0.0129 (2)	0.0126 (3)	0.0102 (2)	−0.00059 (19)	−0.00245 (19)	0.00026 (19)
C3	0.0108 (3)	0.0118 (3)	0.0101 (3)	−0.0005 (2)	−0.00105 (19)	−0.0002 (2)
C4	0.0107 (3)	0.0110 (3)	0.0104 (3)	0.0001 (2)	−0.0005 (2)	−0.0004 (2)
N3	0.0121 (2)	0.0108 (2)	0.0109 (2)	−0.00018 (19)	−0.00197 (18)	−0.00061 (19)
C5	0.0126 (3)	0.0134 (3)	0.0104 (3)	0.0005 (2)	−0.0013 (2)	0.0000 (2)
C6	0.0131 (3)	0.0131 (3)	0.0124 (3)	0.0003 (2)	−0.0001 (2)	0.0015 (2)
C7	0.0128 (3)	0.0118 (3)	0.0142 (3)	−0.0007 (2)	0.0003 (2)	−0.0001 (2)
C8	0.0127 (3)	0.0127 (3)	0.0126 (3)	−0.0016 (2)	−0.0008 (2)	−0.0017 (2)
O1	0.0162 (3)	0.0157 (3)	0.0190 (3)	0.00068 (19)	−0.0038 (2)	−0.0036 (2)
Cl1	0.01671 (9)	0.01516 (9)	0.01815 (9)	0.00088 (6)	−0.00154 (6)	−0.00008 (6)
Cl2	0.01447 (8)	0.01281 (8)	0.01098 (7)	0.00039 (5)	−0.00244 (5)	−0.00001 (5)

Geometric parameters (Å, º) top

N1—C1	1.4763 (10)	C4—N3	1.3920 (9)
N1—H1C	0.844 (12)	C4—C5	1.3938 (10)
N1—H1D	0.825 (11)	N3—H3	0.812 (15)
N1—H1E	0.864 (11)	C5—C6	1.3872 (11)
C1—C2	1.4896 (11)	C5—H5	0.926 (13)
C1—H1F	0.988 (13)	C6—C7	1.4085 (11)
C1—H1G	0.975 (14)	C6—H6	0.937 (13)
C2—N2	1.3340 (9)	C7—C8	1.3865 (10)
C2—N3	1.3355 (9)	C7—H7	0.897 (13)
N2—C3	1.3871 (9)	C8—H8	0.961 (13)
N2—H2	0.866 (16)	O1—H1A	0.802 (14)
C3—C8	1.3933 (10)	O1—H1B	0.813 (14)
C3—C4	1.3991 (10)

C1—N1—H1C	111.0 (9)	C8—C3—C4	122.02 (7)
C1—N1—H1D	111.9 (10)	N3—C4—C5	131.45 (6)
H1C—N1—H1D	103.9 (13)	N3—C4—C3	106.58 (6)
C1—N1—H1E	112.7 (9)	C5—C4—C3	121.96 (6)
H1C—N1—H1E	110.5 (13)	C2—N3—C4	108.38 (6)
H1D—N1—H1E	106.5 (13)	C2—N3—H3	125.4 (11)
N1—C1—C2	112.11 (6)	C4—N3—H3	125.4 (11)
N1—C1—H1F	108.2 (8)	C6—C5—C4	116.11 (7)
C2—C1—H1F	108.8 (8)	C6—C5—H5	121.8 (8)
N1—C1—H1G	108.9 (8)	C4—C5—H5	122.0 (8)
C2—C1—H1G	108.1 (8)	C5—C6—C7	121.83 (7)
H1F—C1—H1G	110.7 (11)	C5—C6—H6	118.1 (8)
N2—C2—N3	109.88 (6)	C7—C6—H6	120.1 (8)
N2—C2—C1	122.91 (6)	C8—C7—C6	122.04 (7)
N3—C2—C1	127.10 (6)	C8—C7—H7	120.5 (8)
C2—N2—C3	108.87 (6)	C6—C7—H7	117.5 (8)
C2—N2—H2	124.2 (11)	C7—C8—C3	116.02 (6)
C3—N2—H2	126.5 (11)	C7—C8—H8	122.2 (8)
N2—C3—C8	131.71 (7)	C3—C8—H8	121.7 (8)
N2—C3—C4	106.27 (6)	H1A—O1—H1B	102.8 (17)

N1—C1—C2—N2	178.82 (7)	C1—C2—N3—C4	−175.26 (7)
N1—C1—C2—N3	−5.29 (11)	C5—C4—N3—C2	179.19 (8)
N3—C2—N2—C3	−1.28 (8)	C3—C4—N3—C2	−0.44 (8)
C1—C2—N2—C3	175.23 (7)	N3—C4—C5—C6	−179.18 (7)
C2—N2—C3—C8	−179.35 (8)	C3—C4—C5—C6	0.40 (11)
C2—N2—C3—C4	0.97 (8)	C4—C5—C6—C7	−0.60 (11)
N2—C3—C4—N3	−0.32 (8)	C5—C6—C7—C8	0.14 (12)
C8—C3—C4—N3	179.96 (7)	C6—C7—C8—C3	0.54 (11)
N2—C3—C4—C5	−179.99 (7)	N2—C3—C8—C7	179.61 (7)
C8—C3—C4—C5	0.28 (11)	C4—C3—C8—C7	−0.74 (11)
N2—C2—N3—C4	1.07 (8)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1C···Cl1	0.84 (1)	2.32 (1)	3.0898 (8)	152 (1)
N1—H1D···Cl2ⁱ	0.83 (1)	2.30 (1)	3.1262 (7)	177 (1)
N1—H1E···Cl2ⁱⁱ	0.86 (1)	2.41 (1)	3.2430 (7)	163 (1)
N2—H2···Cl2	0.866 (16)	2.259 (16)	3.1099 (6)	167.2 (14)
N3—H3···O1	0.812 (15)	1.911 (16)	2.7197 (9)	173.6 (15)
O1—H1A···Cl2ⁱⁱⁱ	0.80 (1)	2.59 (1)	3.3752 (7)	169 (2)
O1—H1B···Cl1^iv	0.81 (1)	2.31 (1)	3.1209 (7)	173 (2)
C1—H1F···Cl1^v	0.988 (13)	2.793 (13)	3.7079 (8)	154.2 (10)
C5—H5···Cl1ⁱⁱ	0.926 (13)	2.960 (13)	3.8515 (7)	162.1 (10)

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

Acknowledgements

We thank the UK EPSRC National Crystallography Service at the University of Southampton for the X-ray data collection.

Funding information

>SJK thanks Tamil Nadu State Council for Higher Education (TANSCHE) for financial support (file No. RGP/2019–20/MTWU/HECP-0080).

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