1,1′-(4-Oxoheptane-1,7-di­yl)bis­(2-methyl-1H-benzimidazole) penta­hydrate

Lai-Ping Zhang; Ying-Ying Liu; Zhi-Fang Jia; Guo-Hua Wei

doi:10.1107/S1600536807063039

. 2007 Dec 6;64(Pt 1):o143. doi: 10.1107/S1600536807063039

1,1′-(4-Oxoheptane-1,7-diyl)bis(2-methyl-1H-benzimidazole) pentahydrate

Lai-Ping Zhang ^a, Ying-Ying Liu ^a,^*, Zhi-Fang Jia ^a, Guo-Hua Wei ^a

PMCID: PMC2915212 PMID: 21200708

Abstract

The title compound, C₂₃H₂₆N₄O·5H₂O, has noncrystallographic twofold rotation symmetry in the solid state. It crystallizes with five solvent water molecules in the asymmetric unit. Four of these water molecules are connected with each other via hydrogen-bonding interactions to form two types of centrosymmetric hexameric (H₂O)₆ rings. Via edge sharing of the hexamers, the water clusters thus build infinite chains that stretch parallel to the a axis. The fifth water molecule provides an additional connection between the two hexameric (H₂O)₆ units via hydrogen bonds to both rings. The water molecules in the channels along the a axis are also bonded via O—H⋯N hydrogen bonds to the organic units, and face-to-face π–π interactions [with centroid-to-centroid distances of 3.656 (1) Å and average face-to-face distances of 3.431 (5) Å] between the aromatic rings of adjacent molecules complete the intermolecular interactions in this structure.

Related literature

Hay et al. (1998 ▶) report the use of benzimidazole complexes to model the active site of a variety of metalloenzymes, such as carbonic anhydrase and carboxypeptidase.

Experimental

Crystal data

C₂₃H₂₆N₄O·5H₂O
M _r = 464.56
Monoclinic,
a = 8.814 (5) Å
b = 25.664 (13) Å
c = 11.635 (6) Å
β = 109.06 (1)°
V = 2488 (2) Å³
Z = 4
Mo Kα radiation
μ = 0.09 mm⁻¹
T = 293 (2) K
0.40 × 0.30 × 0.25 mm

Data collection

Bruker APEX CCD area-detector diffractometer
Absorption correction: multi-scan (SADABS; Sheldrick, 1996 ▶) T _min = 0.970, T _max = 0.982
12521 measured reflections
4424 independent reflections
2623 reflections with I > 2σ(I)
R _int = 0.109

Refinement

R[F ² > 2σ(F ²)] = 0.079
wR(F ²) = 0.222
S = 1.01
4424 reflections
311 parameters
15 restraints
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.33 e Å⁻³
Δρ_min = −0.27 e Å⁻³

Data collection: SMART (Bruker, 1997 ▶); cell refinement: SAINT (Bruker, 1999 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997 ▶); molecular graphics: SHELXTL-Plus (Sheldrick, 1990 ▶); software used to prepare material for publication: SHELXL97.

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536807063039/zl2082sup1.cif

e-64-0o143-sup1.cif^{(23.6KB, cif)}

Structure factors: contains datablocks I. DOI: 10.1107/S1600536807063039/zl2082Isup2.hkl

e-64-0o143-Isup2.hkl^{(211.1KB, 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
O1W—H1A⋯N4	0.93 (2)	1.95 (4)	2.758 (6)	144 (5)
O1W—H1B⋯O3Wⁱ	0.92 (4)	2.31 (5)	2.954 (5)	127 (5)
O2W—H2B⋯O4W	0.90 (5)	2.61 (6)	3.308 (7)	135 (7)
O2W—H2B⋯O5Wⁱⁱ	0.90 (5)	2.05 (7)	2.770 (6)	136 (8)
O3W—H3B⋯O1ⁱⁱⁱ	0.88 (5)	2.18 (5)	3.054 (6)	171 (7)
O4W—H4B⋯O1Wⁱ	0.92 (8)	2.00 (7)	2.900 (7)	166 (8)
O4W—H4A⋯O5Wⁱⁱ	0.92 (7)	2.33 (4)	3.200 (7)	157 (7)
O5W—H5B⋯N1^iv	0.90 (5)	1.93 (5)	2.822 (5)	175 (6)
O5W—H5A⋯O3W^v	0.90 (6)	1.92 (6)	2.811 (6)	167 (6)
O3W—H3A⋯O2Wⁱ	0.91 (2)	1.94 (2)	2.840 (7)	170 (6)
O2W—H2A⋯O1Wⁱ	0.90 (2)	2.14 (5)	2.823 (6)	132 (5)

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Symmetry codes: (i) Inline graphic ; (ii) ; (iii) ; (iv) ; (v) .

Acknowledgments

We thank the Science Foundation for Young Teachers of Northeast Normal University (No. 20070314) for support.

supplementary crystallographic information

Comment

Currently there is considerable interest in the use of benzimidazole complexes to model the active site of a variety of metalloenzymes such as carbonic anhydrase and carboxypeptidase (Hay et al., 1998). In this context we prepared (Fig 4) and analyzed the title benzimidazole compound, and its structure is described here.

The title molecule (Fig 1) has non-crystallographic two fold symmetry with an r.m.s. deviation for both halves of 0.066 Å. It crystallizes with five lattice water molecules in the asymmetric part of the unit cell. Four of these water molecules (O1W, O2W, O3W and O5W) are connected with each other via hydrogen bonding interactions to form two types of centrosymmetric hexameric (H₂O)₆ rings. Via edge sharing of the hexamers the water clusters thus build infinite chains that stretch parallel to the a axis. The fifth water molecule O4W provides an additional connection between the two hexameric (H₂O)₆ rings via hydrogen bonds to both units. Water molecules O1W and O5W in the channels along a axis are also bonded via O—H···N hydrogen bonds to N4 and N1 of the organic unit, and all water molecules act both as donors and acceptors (Fig. 2).

Face-to-face π-π interactions between adjacent benzimidazoles made up by the atoms C1—C7, N3 and N4 and their symmetry equivalents at 1 - x, -y, 2 - z (with centroid-to-centriod distances of 3.656 (1) Å and an average face-to-face distance of 3.431 (5) Å, Fig. 3) complete the intermolecular interactions in this structure and lead to the formation of a 1-D supramolecuar chain along the a axis.

Experimental

To a solution of 1,7-dichloro-4-oxoheptane (8.3 g, 47 mmol) and ethylene glycol (2.9 g, 47 mmol) in cyclohexane (35 ml) was added 0.024 g sodium bisulfate. The reaction mixture was refluxed for 3 h with azeotropic removal of water via a Dean–Stark trap, until there was no more water created. The resulting clear solution was cooled down, washed with water twice, and then distilled. The fraction distilling between 447 K and 453 K was collected to obtain 1,11-dichloro-(5,8-dioxaspiro[4.2]undecane) as a clear liquid (5.5 g, 25 mmol, 53%).

A mixture of 2-methyl-benzimidazole (6.6 g, 50 mmol) and NaOH (2.0 g, 50 mmol) in DMSO (10 ml) was stirred at 333 K for 1 h, and then the collected distillate (5.5 g, 25 mmol) from the previous step was added. The mixture was cooled to room temperature after stirring at 333 K for 2 h, then poured into 200 ml of water and a white solid formed immediately. The compound (5,8-dioxaspiro[4.2]undecyl)bis(2-methyl-benzimidazole) was obtained in 74% yield (7.6 g, 19 mmol).

After washing with 50 ml water, the solid was transfered into 150 ml water with 10 ml HCl (12 mol l^-1). The mixture was refluxed for 3.5 h, and then filtered. The obtained residue was dissolved in 100 ml me thanol, and colorless single crystals of the title compound were obtained after several days at room temperature (3.7 g, 10 mmol, 55%).