2,2′-(Imino­dimethyl­ene)dibenz­imid­azol­ium bis­(perchlorate) methanol solvate

Chun-Shan Zhou; Xue-Ying Huang; Xiang-Gao Meng

doi:10.1107/S1600536808008519

. 2008 Apr 2;64(Pt 5):o791–o792. doi: 10.1107/S1600536808008519

2,2′-(Iminodimethylene)dibenzimidazolium bis(perchlorate) methanol solvate

Chun-Shan Zhou ^a, Xue-Ying Huang ^a, Xiang-Gao Meng ^a,^*

PMCID: PMC2961233 PMID: 21202284

Abstract

In the title compound, C₁₆H₁₇N₅ ²⁺·2ClO₄ ⁻·CH₃OH, the dihedral angle between the two benzimidazolium ring systems is 34.6 (1)°. The anions and solvent molecules are linked to the cation by N—H⋯O hydrogen bonds. In the crystal structure, the combination of N—H⋯O and O—H⋯O hydrogen bonds results in two-dimensional layers running parallel to the (010) plane; these are in turn linked by π–π interactions, forming a three-dimensional network.

Related literature

For related literature, see: Adams et al. (1990 ▶); Allen (2002 ▶); Berends & Stephan (1984 ▶); Bernstein et al. (1995 ▶); Bruno et al. (2002 ▶); Girasolo et al. (2000 ▶); Liao et al. (2001 ▶); Liu et al. (2004 ▶); Meng et al. (2005 ▶, 2006a ▶,b ▶); Spek (2003 ▶); Tarazon Navarro & McKee (2003 ▶); Xu et al. (2007 ▶); Young et al. (1995 ▶); Zheng et al. (2005 ▶).

Experimental

Crystal data

C₁₆H₁₇N₅ ²⁺·2ClO₄ ⁻·CH₄O
M _r = 510.29
Monoclinic,
a = 8.3359 (4) Å
b = 18.0323 (8) Å
c = 14.8532 (7) Å
β = 102.944 (1)°
V = 2175.89 (18) Å³
Z = 4
Mo Kα radiation
μ = 0.36 mm⁻¹
T = 295 (2) K
0.30 × 0.20 × 0.20 mm

Data collection

Bruker SMART APEX CCD area-detector diffractometer
Absorption correction: multi-scan (SADABS; Sheldrick, 1997 ▶) T _min = 0.900, T _max = 0.932
24553 measured reflections
4957 independent reflections
3479 reflections with I > 2σ(I)
R _int = 0.069

Refinement

R[F ² > 2σ(F ²)] = 0.057
wR(F ²) = 0.169
S = 1.02
4957 reflections
317 parameters
5 restraints
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.26 e Å⁻³
Δρ_min = −0.23 e Å⁻³

Data collection: SMART (Bruker, 2001 ▶); cell refinement: SAINT-Plus (Bruker, 2001 ▶); data reduction: SAINT-Plus; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: PLATON (Spek, 2003 ▶); software used to prepare material for publication: PLATON.

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536808008519/wn2246sup1.cif

e-64-0o791-sup1.cif^{(22.6KB, cif)}

Structure factors: contains datablocks I. DOI: 10.1107/S1600536808008519/wn2246Isup2.hkl

e-64-0o791-Isup2.hkl^{(242.8KB, hkl)}

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1⋯O7ⁱ	0.86 (3)	2.42 (3)	3.200 (3)	150 (2)
N2—H2A⋯O8	0.831 (16)	2.15 (2)	2.895 (3)	150 (3)
N2—H2A⋯O9	0.831 (16)	2.489 (19)	3.233 (3)	150 (2)
N3—H3A⋯O1	0.831 (16)	1.996 (17)	2.799 (3)	162 (2)
N4—H4A⋯O1	0.857 (16)	1.985 (17)	2.823 (3)	166 (2)
N5—H5A⋯O4	0.824 (16)	2.46 (2)	3.197 (4)	150 (2)
N5—H5A⋯O5	0.824 (16)	2.21 (2)	2.939 (3)	147 (2)
O1—H1C⋯O6ⁱⁱ	0.805 (17)	2.00 (2)	2.765 (3)	159 (3)

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Symmetry codes: (i) Inline graphic ; (ii) .

Table 2. Table 2 π–π Stacking interactions (°, Å).

Cg_i	Cg_j	Dihedral angle	CCD	Interplanar spacing
Cg1	Cg2^iv	0.42	3.854 (2)	3.349 (2)
Cg1	Cg4^iv	0.35	3.557 (2)	3.354 (2)
Cg3	Cg2^iv	0.85	3.612 (2)	3.360 (2)
Cg3	Cg4^v	0.36	3.929 (2)	3.453 (2)

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CCD is the centroid-to-centroid distance; Cg1 is the centroid of atoms N2/N3/C2/C3/C8; Cg2 is the centroid of atoms N4/N5/C10/C11/C16; Cg3 is the centroid of atoms C3–C8; Cg4 is the centroid of atoms C11–C16. Symmetry codes: (iv) Inline graphic ; (v) .

Acknowledgments

This work received financial support mainly from the National Key Fundamental Project (No. 2002CCA00500).

supplementary crystallographic information

Comment

Bis[N-(benzimidazol-2-ylmethyl)]amine (IDB) and its analogs have been utilized extensively in the synthesis of various metal complexes to mimic certain biological activities; these include superoxide dismutase (Liao et al., 2001), DNA probe (Girasolo et al., 2000), alkaline phosphatase (Young et al., 1995). In IDB, each benzimidazole (bzim) arm possesses one imine N atom, one amine NH group and, at the centre, an NH group. The two imine N atoms can chelate metal ions, while the three NH groups can act as hydrogen bond donors. In the absence of metal coordination, the two imine N atoms can also act as hydrogen bond acceptors. The easily formed coordination and hydrogen-bonding interactions allow the central acyclic —CH₂—NH—CH₂– unit to possess various steric arrangements. In our and other reported organic complex analogs (Meng et al., 2006a; Meng et al., 2006b; Meng et al., 2005; Zheng et al., 2005; Liu et al., 2004; Tarazon Navarro et al., 2003) we find that IDB preferentially adopts a more extended conformation, with the two bzim groups pointing away from each other. However, in most examples of metal-complexes it adopts a more crowded conformation, with the two bzim units bending towards the same side of the central acyclic linkage (Berends & Stephan, 1984; Xu et al., 2007; Adams et al., 1990). With the aim of gaining more insight into the influence of solvents and anions on the crystal structure, we have synthesized H₂IDB²⁺.2ClO₄^-.CH₃OH and report its molecular and supramolecular structure in this communication.

The two imine N atoms on both bzim arms are protonated, as confirmed by the residual electron peaks around the imine N atoms during the structure refinement. The positive charge on each imine N atom is delocalized in the imidazole ring, as evidenced by the near equivalence of bonds C2—N2/C2—N3 [1.323 (3)/1.320 (3) Å] and C10—N4/C10—N5 [1.330 (3)/1.32 6(3) Å]. These values lie within the range of C—N single bond [1.357 (2) Å] and C═N double bond [1.318 (2) Å] determined at low temperature by Tarazon Navarro & McKee (2003). In the title compound, the dication adopts a somewhat folded conformation and the dihedral angle between two bzim groups is 34.6 (1)°. This angle is comparable with those in (IDB).(H₂O)₄ [36.2 (1)° and 39.7 (1) °; Meng et al. (2006a)] and (IDB)₂.(H₂O)₂.C₂H₅OH [26.8 (1)° and 25.8 (1)°; Meng et al. (2006b)], but considerably larger those in IDB [0.0°; Tarazon Navarro & McKee (2003)], HIDB⁺.Cl^- [5.4 (1)°; Zheng et al. (2005)], HIDB⁺.ClO₄^- [3.7 (1)°; Liu et al. (2004)] and H₂IDB²⁺.SO₄^2- [3.3 (1)°; Meng et al. (2005)].

Two imine N atoms (N2 and N5) act as hydrogen bond donors, via atoms H2A and H5A, respectively, to atoms O8/O9 and O4/O5, thereby generating four hydrogen bonds, each two forming an R²₁(4) (Fig.1) motif (Bernstein et al., 1995). The other two N atoms (N3 and N4) on bzim also act as hydrogen bond donors, forming intermolecular hydrogen bonds of R¹₂(10) motif, to the methanol solvent molecule. The methanol molecule donates its hydroxyl H atom to atom O6, forming a relatively strong O—H···O hydrogen bond. There is a pseudo-mirror plane passing through the central NH group and the solvent C and O atoms.

In the crystal structure, the component ions are assembled into a three-dimensional network by a combination of N—H···O, O—H···O hydrogen bonds and π-π interactions which can be analyzed in terms of several substructures. Firstly, by the six cooperative hydrogen-bonding interactions (Table 1), the discrete dications, anions and methanol molecules are joined together, forming a relatively independent neutral unit. These neutral units are linked together by N1···O7 (-1/2 + x,1/2 - y,-1/2 + z) and O1···O6 (1/2 + x,1/2 - y,-1/2 + z) hydrogen bonds related by the n-glide plane at y =1/4, forming a two-dimensional layer parallel to the (010) plane in the domain of -0.259 < y < 0.759 (Fig.2). Secondly, by π–π stacking interactions, adjacent two-dimensional layers are interlinked into a simple three-dimensional network. The geometric details of the π–π stacking interactions are listed in Table 2. A CSD (Version 1.9, September 2006 release; Allen, 2002; Bruno et al., 2002) study indicates that π–π stacking interactions play a critical role in stabilizing the crystal structures of organic and metal-organic compounds containing poly-bzim groups. For instance, in HIDB⁺.ClO₄^- (Liu et al., 2004), the N—H···N and N—H···O hydrogen bonds link the component ions into one-dimensional chains. However, π–π stacking interactions between adjacent bzim groups link the molecules into a three-dimensional network.

Experimental

All the reagents and solvents were used as obtained without further purification. Bis(benzimidazol-2-yl-methyl)amine (IDB) was prepared according to the method described by Adams et al. (1990). 2 g of the powdered title compound were dissolved in 15 ml methanol and adjusted to pH 5 using HClO₄. Colorless crystals were obtained as blocks by slowly evaporating the solvent over a period of several days.