Download citation
Download citation
link to html
A novel three-dimensional framework of 2-[(1H-imidazol-1-yl)meth­yl]-1H-benzimidazole dihydrate, C11H10N4·2H2O or L·2H2O, (I), in which L acts as both hydrogen-bond acceptor and donor in the supra­molecular construction with water, has been obtained by self-assembly reaction of L with H2O. The two independent water mol­ecules are hydrogen bonded alternately with each other to form a one-dimensional infinite zigzag water chain. These water chains are linked by the benzimidazole mol­ecules into a three-dimensional framework, in which each organic mol­ecule is hydrogen bonded by three water mol­ecules. This study shows that the diversity of hydrogen-bonded patterns plays a crucial role in the formation of the three-dimensional framework. More significantly, as water mol­ecules are important in contributing to the conformation, stability, function and dynamics of biomacromolecules, the infinite chains of hydrogen-bonded water mol­ecules seen in (I) may be a useful model for water in other chemical and biological processes.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270109001814/sq3184sup1.cif
Contains datablocks global, I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S0108270109001814/sq3184Isup2.hkl
Contains datablock I

CCDC reference: 728207

Comment top

Research on supramolecular compounds has become popular because of their potential applications in areas such as gas storage (Rowsell et al., 2005), selective absorption (Dong et al., 2007), catalysis (Wu et al., 2007), magnetics (Zhao et al., 2003; Wang et al., 2006; Neville et al., 2008) and optics (Huang et al., 2007). Many strategies have been developed to achieve supramolecular compounds with predefined structures (Yaghi et al., 1998; Cho et al., 2006; Ma et al., 2008). Among these strategies, the choice and design of organic molecules as hydrogen-bond acceptors or donors are undoubtedly a key part of the construction of intriguing frameworks driven by hydrogen-bonding interactions (Albrecht, 2001; Telfer et al., 2004; Burchell et al., 2006). Imidazole or benzimidazole derivatives have been widely used in supramolecular chemistry and numerous coordination polymers with versatile structures and potential properties have been reported (Chen et al., 2005; Zheng et al., 2007). It is well known that imidazole-containing molecules can easily coordinate to metal ions as well as act as hydrogen-bond acceptors or donors in supramolecular assembly reactions. Although much effort has been put in the study of supramolecular chemistry based on imidazole-containing ligands, benzimidazole-functionalized imidazole ligands are less well studied (Li et al., 2008). The inclusion of both benzimidazole and imidazole functional groups can lead to different coordination modes and may play a crucial role in the construction of supramolecular compounds driven by hydrogen-bonding interactions.

The study of lattice water molecules has also attracted much attention because of their fundamental importance in chemical and biological processes (Mascal et al., 2006). Some hydrogen-bonded water molecules, such as water clusters (Ghosh et al., 2005; Dai et al., 2008), one-dimensional water chains (Sreenivasulu et al., 2004) and two-dimensional water layers (Janiak et al., 2002), have been found. However, infinite chains of hydrogen-bonded water molecules in abiological molecules, especially in supramolecular compounds, are still rare (Wang et al., 2007; Mukherjee et al., 2004; Neogi et al., 2005). Herein we report the synthesis and characterization of a novel three-dimensional hydrogen-bonded framework of 2-[(1H-imidazol-1-yl)methyl]-1H-benzimidazole dihydrate, (C11H10N4).2H2O (L.2H2O), (I), which contains infinite chains of hydrogen-bonded water molecules.

(I) was found to crystallize in the acentric orthorhombic space group Pna21. The asymmetric unit contains one L molecule and two inequivalent water molecules (Fig. 1). The benzimidazole ring and imidazole ring of the L ligand are not coplanar but rather have a dihedral angle of 70.233 (89)°. The two types of water molecules are linked alternately into a one-dimensional zigzag water chain (Fig. 2) via O—H···O hydrogen bonds (Table 1) along the crystallogrophic c axis. As shown in Fig. 2, the first O—H···O hydrogen bond consists of atom O1 and bond O2—H2A. The second O—H···O hydrogen bond involves atom O2i [symmetry code: (i) x, y , z - 1] and bond O1—H1A . The O atoms of water molecules in the chain are coplanar, which finding agrees with one literature report (Wang et al., 2007), but disagrees with another report (Neogi et al., 2005), in which the O atoms of water molecules in the chain are not coplanar. As shown in Fig. 2, atom O1 of the water molecule and atom N4iii [symmetry code: (iii) -x + 0.5, y + 0.5, z - 0.5] of L are connected together via an O—H···N hydrogen bond while atom O2 of the water molecule is linked by two N atoms [N1iv and N2; symmetry code: (iv) x - 0.5, -y + 3/2, z] from two benzimidazole molecules via O—H···N and N—H···O hydrogen bonds (Table 1). Thus, in this water chain, atom O1 is in a three-coordinate configuration by coordinating to two water molecules and one benzimidazole molecule, while atom O2 is in a four-coordinate configuration with two interactions with water molecules and two with benzimidazole molecules. This is different from the reported one-dimensional water chains (Wang et al., 2007) in which all the O atoms are in a three-coordinate configuration with two bonds with water molecules and one bond with a ligand.

As illustrated above, L acts as both hydrogen-bond acceptor and donor and is connected to the water chains. Each benzimidazole molecule is totally linked by three water molecules from three water chains. The infinite chains of hydrogen-bonded water molecules further extend to a three-dimensional framework via the connection of ligands and water chains (Fig. 3). As a result, all the organic molecules in the framework are surrounded by one-dimensional water chains along the crystallographic c axis. It is the first example of one-dimensional water chains located in a three-dimensional framework based on an imidazole-rich organic ligand. In summary, a novel three-dimensional hydrogen-bonded supramolecular framework has been synthesized. The benzimidazole-functionalized imidazole organic molecule 2-[(1H-imidazol-1-yl)methyl]-1H-benzimidazole plays a crucial role in the construction of the framework by acting as both hydrogen-bond acceptor and donor. More importantly, one-dimensional water chains are found in this framework. As water molecules play an important role in contributing to the conformation, stability, function and dynamics of biomacromolecules (Luan et al., 2006), the new one-dimensional water chain may provide new insight into the hydrogen-bonding motif of the aqueous environment in living systems.

Related literature top

For related literature, see: Albrecht (2001); Burchell et al. (2006); Chen et al. (2005); Cho et al. (2006); Dai et al. (2008); Dong et al. (2007); Ghosh & Bharadwaj (2005); Huang et al. (2007); Janiak et al. (2002); Li et al. (2008); Luan et al. (2006); Ma & Lin (2008); Mascal et al. (2006); Mukherjee et al. (2004); Neogi & Bharadwaj (2005); Neville et al. (2008); Rowsell & Yaghi (2005); Sreenivasulu & Vittal (2004); Telfer & Kuroda (2004); Wang et al. (2006, 2007); Wu & Lin (2007); Yaghi et al. (1998); Zhao et al. (2003); Zheng et al. (2007).

Experimental top

All solvents and reagents used for the synthesis were commercially available and used as received.

Under a nitrogen atmosphere, 2-(1H-imidazol-1-yl)acetic acid (0.80 g, 6.3 mmol), benzene-1,2-diamine (0.68 g, 6.3 mmol) and polyphosphoric acid (10 ml) were combined and stirred at 443 K for 3 h. After cooling to room temperature, the reaction mixture was poured into ice water and aqueous ammonia was added until the pH value of the system was adjusted to about 7. The system was filtered and subsequently washed by water to provide the white precipitate L.2H2O, (I). Yield: 82.6%. 1H NMR (300 MHz, DMSO-d6, p.p.m): δ = 12.44 (s, 1H, NH), 7.76 (s, 1H, CH), 7.52 (d, 2H, o-C6H4), 7.22 (d, 1H, CH), 7.16 (d, 2H, o-C6H4), 6.91 (d, 1H, CH), 5.43 (s, 2H, CH2). IR (KBr, cm-1): ν = 3371, 3325, 3130, 2977, 2836, 2674, 1787, 1616, 1439, 1324, 1291, 1270, 1079, 917, 833, 754, 655, 615. (I) was dissolved in methanol solution and colourless crystals were obtained after slow evaporation of the solvent.

Refinement top

The Friedel pairs were merged prior to final refinement and the absolute configuration was not determined. The absolute enantiomer was chosen randomly. Water H atoms were located in the difference map and refined with isotropic displacement parameters subject to an O—H = 0.84 (2) Å distance restraint. Other H atoms were placed in idealized positions and treated as riding, with C—H = 0.97 (CH2) or 0.93 Å (CH), N—H = 0.86 Å and Uiso(H) = 1.2 Ueq(C, N).

Computing details top

Data collection: SMART (Bruker, 2000); cell refinement: SMART (Bruker, 2000); data reduction: SAINT (Bruker, 2000); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. The molecular structure of (I) (displacement ellipsoids drawn at the 30% probability level).
[Figure 2] Fig. 2. The one-dimensional water chain in (I). [Symmetry codes: (i) x, y, z - 1; (iii) -x + 1/2, y + 1/2, z - 1/2; (iv) x - 1/2, -y + 3/2, z.]
[Figure 3] Fig. 3. Perspective view of the three-dimensional hydrogen-bonded framework in (I). (Hydrogen-bonding interactions are shown as dashed lines.)
2-[(1H-imidazol-1-yl)methyl]-1H-benzimidazole dihydrate top
Crystal data top
C11H10N4·2H2OF(000) = 496
Mr = 234.26Dx = 1.254 Mg m3
Orthorhombic, Pna21Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P2c-2nCell parameters from 1702 reflections
a = 14.030 (2) Åθ = 2.6–21.2°
b = 19.121 (3) ŵ = 0.09 mm1
c = 4.6240 (8) ÅT = 298 K
V = 1240.5 (4) Å3Block, colourless
Z = 40.30 × 0.27 × 0.25 mm
Data collection top
CCD area-detector
diffractometer
1117 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.055
Graphite monochromatorθmax = 25.5°, θmin = 1.8°
ϕ and ω scansh = 1616
6623 measured reflectionsk = 2319
1313 independent reflectionsl = 54
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.035Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.079H-atom parameters constrained
S = 1.03 w = 1/[σ2(Fo2) + (0.0373P)2]
where P = (Fo2 + 2Fc2)/3
1313 reflections(Δ/σ)max < 0.001
154 parametersΔρmax = 0.10 e Å3
5 restraintsΔρmin = 0.11 e Å3
Crystal data top
C11H10N4·2H2OV = 1240.5 (4) Å3
Mr = 234.26Z = 4
Orthorhombic, Pna21Mo Kα radiation
a = 14.030 (2) ŵ = 0.09 mm1
b = 19.121 (3) ÅT = 298 K
c = 4.6240 (8) Å0.30 × 0.27 × 0.25 mm
Data collection top
CCD area-detector
diffractometer
1117 reflections with I > 2σ(I)
6623 measured reflectionsRint = 0.055
1313 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0355 restraints
wR(F2) = 0.079H-atom parameters constrained
S = 1.03Δρmax = 0.10 e Å3
1313 reflectionsΔρmin = 0.11 e Å3
154 parameters
Special details top

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

Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) 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
xyzUiso*/Ueq
O10.11409 (11)0.88152 (7)0.1260 (4)0.0689 (6)
N40.36690 (16)0.52524 (10)0.6793 (7)0.0862 (8)
C10.41716 (19)0.57195 (13)0.5387 (8)0.0750 (9)
H10.47400.56230.44320.090*
C20.2916 (2)0.56111 (15)0.7866 (8)0.0862 (10)
H20.24330.54160.89860.103*
C30.29626 (18)0.62851 (13)0.7091 (9)0.0757 (9)
H30.25300.66360.75560.091*
C40.41240 (17)0.69948 (11)0.4174 (6)0.0572 (7)
H4A0.36580.71660.27970.069*
H4B0.47050.68920.31210.069*
C50.43209 (15)0.75491 (10)0.6344 (6)0.0469 (5)
C60.41751 (16)0.84206 (11)0.9242 (6)0.0477 (6)
C70.38681 (18)0.89936 (12)1.0828 (7)0.0598 (7)
H70.32450.91561.06770.072*
C80.45102 (19)0.93126 (12)1.2620 (7)0.0672 (7)
H80.43210.97011.36830.081*
C90.54399 (19)0.90689 (13)1.2890 (7)0.0679 (8)
H90.58550.92941.41520.082*
C100.57598 (17)0.85021 (12)1.1333 (7)0.0607 (7)
H100.63820.83401.15080.073*
C110.51115 (16)0.81846 (11)0.9492 (5)0.0469 (6)
N10.51804 (12)0.76285 (8)0.7624 (4)0.0500 (5)
H1C0.56790.73770.73240.060*
N20.36886 (12)0.80074 (9)0.7246 (5)0.0507 (5)
N30.37666 (13)0.63523 (9)0.5495 (5)0.0534 (5)
O20.17694 (10)0.81693 (8)0.6079 (5)0.0707 (5)
H2A0.16290.83390.44550.085*
H2B0.23470.81300.65190.085*
H1A0.13760.87100.03640.085*
H1B0.11950.92550.12590.085*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0790 (11)0.0582 (9)0.0695 (14)0.0014 (8)0.0074 (11)0.0079 (10)
N40.0940 (16)0.0537 (12)0.111 (2)0.0114 (12)0.0227 (18)0.0028 (16)
C10.0734 (16)0.0540 (15)0.098 (3)0.0003 (14)0.0231 (18)0.0025 (16)
C20.0823 (19)0.077 (2)0.099 (3)0.0288 (16)0.028 (2)0.003 (2)
C30.0638 (15)0.0642 (17)0.099 (3)0.0120 (12)0.0259 (19)0.0109 (18)
C40.0636 (14)0.0553 (14)0.0526 (17)0.0034 (12)0.0065 (14)0.0051 (13)
C50.0541 (13)0.0429 (12)0.0438 (14)0.0050 (10)0.0040 (14)0.0082 (11)
C60.0512 (13)0.0428 (12)0.0491 (16)0.0033 (10)0.0043 (12)0.0085 (12)
C70.0621 (15)0.0520 (14)0.0653 (19)0.0021 (11)0.0060 (15)0.0027 (14)
C80.0867 (19)0.0512 (14)0.0636 (19)0.0070 (13)0.0085 (18)0.0009 (15)
C90.086 (2)0.0638 (16)0.0537 (18)0.0246 (14)0.0031 (17)0.0017 (15)
C100.0562 (14)0.0670 (16)0.0588 (17)0.0085 (12)0.0016 (15)0.0110 (16)
C110.0497 (13)0.0451 (12)0.0459 (14)0.0040 (10)0.0043 (13)0.0073 (12)
N10.0465 (10)0.0511 (10)0.0526 (14)0.0042 (8)0.0037 (11)0.0055 (11)
N20.0486 (10)0.0470 (10)0.0565 (14)0.0012 (8)0.0009 (11)0.0057 (11)
N30.0547 (11)0.0479 (11)0.0576 (14)0.0071 (9)0.0050 (10)0.0037 (10)
O20.0511 (9)0.0909 (12)0.0700 (13)0.0061 (8)0.0025 (10)0.0192 (12)
Geometric parameters (Å, º) top
O1—H1A0.8446C6—C71.387 (3)
O1—H1B0.8441C6—N21.393 (3)
N4—C11.311 (3)C6—C111.394 (3)
N4—C21.354 (4)C7—C81.368 (4)
C1—N31.338 (3)C7—H70.9300
C1—H10.9300C8—C91.391 (3)
C2—C31.339 (3)C8—H80.9300
C2—H20.9300C9—C101.376 (4)
C3—N31.354 (3)C9—H90.9300
C3—H30.9300C10—C111.386 (3)
C4—N31.461 (3)C10—H100.9300
C4—C51.485 (3)C11—N11.373 (3)
C4—H4A0.9700N1—H1C0.8600
C4—H4B0.9700O2—H2A0.8412
C5—N21.315 (3)O2—H2B0.8381
C5—N11.352 (3)
H1A—O1—H1B101.7C8—C7—C6117.9 (2)
C1—N4—C2104.9 (2)C8—C7—H7121.0
N4—C1—N3111.7 (2)C6—C7—H7121.0
N4—C1—H1124.2C7—C8—C9121.5 (3)
N3—C1—H1124.2C7—C8—H8119.2
C3—C2—N4110.6 (3)C9—C8—H8119.2
C3—C2—H2124.7C10—C9—C8121.5 (3)
N4—C2—H2124.7C10—C9—H9119.2
C2—C3—N3106.1 (2)C8—C9—H9119.2
C2—C3—H3126.9C9—C10—C11116.9 (2)
N3—C3—H3126.9C9—C10—H10121.6
N3—C4—C5112.4 (2)C11—C10—H10121.6
N3—C4—H4A109.1N1—C11—C10132.8 (2)
C5—C4—H4A109.1N1—C11—C6105.4 (2)
N3—C4—H4B109.1C10—C11—C6121.8 (2)
C5—C4—H4B109.1C5—N1—C11107.42 (18)
H4A—C4—H4B107.9C5—N1—H1C126.3
N2—C5—N1112.8 (2)C11—N1—H1C126.3
N2—C5—C4124.4 (2)C5—N2—C6104.92 (18)
N1—C5—C4122.81 (19)C1—N3—C3106.8 (2)
C7—C6—N2130.2 (2)C1—N3—C4126.8 (2)
C7—C6—C11120.3 (2)C3—N3—C4126.4 (2)
N2—C6—C11109.5 (2)H2A—O2—H2B118.5
C2—N4—C1—N30.7 (4)N2—C6—C11—C10179.9 (2)
C1—N4—C2—C30.5 (4)N2—C5—N1—C110.5 (2)
N4—C2—C3—N30.1 (4)C4—C5—N1—C11180.0 (2)
N3—C4—C5—N288.6 (3)C10—C11—N1—C5179.5 (3)
N3—C4—C5—N190.8 (3)C6—C11—N1—C50.2 (2)
N2—C6—C7—C8178.9 (2)N1—C5—N2—C60.6 (2)
C11—C6—C7—C80.0 (4)C4—C5—N2—C6179.9 (2)
C6—C7—C8—C90.8 (4)C7—C6—N2—C5178.5 (3)
C7—C8—C9—C101.0 (4)C11—C6—N2—C50.5 (2)
C8—C9—C10—C110.2 (4)N4—C1—N3—C30.7 (4)
C9—C10—C11—N1179.0 (2)N4—C1—N3—C4179.9 (3)
C9—C10—C11—C60.7 (4)C2—C3—N3—C10.3 (3)
C7—C6—C11—N1178.9 (2)C2—C3—N3—C4179.8 (3)
N2—C6—C11—N10.2 (2)C5—C4—N3—C1119.4 (3)
C7—C6—C11—C100.8 (3)C5—C4—N3—C360.0 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1A···O2i0.842.022.836 (3)162
N1—H1C···O2ii0.861.942.794 (2)172
O1—H1B···N4iii0.841.932.772 (2)173
O2—H2A···O10.841.872.696 (3)169
O2—H2B···N20.841.932.764 (2)176
Symmetry codes: (i) x, y, z1; (ii) x+1/2, y+3/2, z; (iii) x+1/2, y+1/2, z1/2.

Experimental details

Crystal data
Chemical formulaC11H10N4·2H2O
Mr234.26
Crystal system, space groupOrthorhombic, Pna21
Temperature (K)298
a, b, c (Å)14.030 (2), 19.121 (3), 4.6240 (8)
V3)1240.5 (4)
Z4
Radiation typeMo Kα
µ (mm1)0.09
Crystal size (mm)0.30 × 0.27 × 0.25
Data collection
DiffractometerCCD area-detector
diffractometer
Absorption correction
No. of measured, independent and
observed [I > 2σ(I)] reflections
6623, 1313, 1117
Rint0.055
(sin θ/λ)max1)0.606
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.035, 0.079, 1.03
No. of reflections1313
No. of parameters154
No. of restraints5
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.10, 0.11

Computer programs: SMART (Bruker, 2000), SAINT (Bruker, 2000), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1A···O2i0.842.022.836 (3)162.4
N1—H1C···O2ii0.861.942.794 (2)172.0
O1—H1B···N4iii0.841.932.772 (2)172.6
O2—H2A···O10.841.872.696 (3)168.7
O2—H2B···N20.841.932.764 (2)175.6
Symmetry codes: (i) x, y, z1; (ii) x+1/2, y+3/2, z; (iii) x+1/2, y+1/2, z1/2.
 

Follow Acta Cryst. C
Sign up for e-alerts
Follow Acta Cryst. on Twitter
Follow us on facebook
Sign up for RSS feeds