Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270109001814/sq3184sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S0108270109001814/sq3184Isup2.hkl |
CCDC reference: 728207
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.
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).
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).
C11H10N4·2H2O | F(000) = 496 |
Mr = 234.26 | Dx = 1.254 Mg m−3 |
Orthorhombic, Pna21 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P2c-2n | Cell parameters from 1702 reflections |
a = 14.030 (2) Å | θ = 2.6–21.2° |
b = 19.121 (3) Å | µ = 0.09 mm−1 |
c = 4.6240 (8) Å | T = 298 K |
V = 1240.5 (4) Å3 | Block, colourless |
Z = 4 | 0.30 × 0.27 × 0.25 mm |
CCD area-detector diffractometer | 1117 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.055 |
Graphite monochromator | θmax = 25.5°, θmin = 1.8° |
ϕ and ω scans | h = −16→16 |
6623 measured reflections | k = −23→19 |
1313 independent reflections | l = −5→4 |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.035 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.079 | H-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 parameters | Δρmax = 0.10 e Å−3 |
5 restraints | Δρmin = −0.11 e Å−3 |
C11H10N4·2H2O | V = 1240.5 (4) Å3 |
Mr = 234.26 | Z = 4 |
Orthorhombic, Pna21 | Mo Kα radiation |
a = 14.030 (2) Å | µ = 0.09 mm−1 |
b = 19.121 (3) Å | T = 298 K |
c = 4.6240 (8) Å | 0.30 × 0.27 × 0.25 mm |
CCD area-detector diffractometer | 1117 reflections with I > 2σ(I) |
6623 measured reflections | Rint = 0.055 |
1313 independent reflections |
R[F2 > 2σ(F2)] = 0.035 | 5 restraints |
wR(F2) = 0.079 | H-atom parameters constrained |
S = 1.03 | Δρmax = 0.10 e Å−3 |
1313 reflections | Δρmin = −0.11 e Å−3 |
154 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
O1 | 0.11409 (11) | 0.88152 (7) | 0.1260 (4) | 0.0689 (6) | |
N4 | 0.36690 (16) | 0.52524 (10) | 0.6793 (7) | 0.0862 (8) | |
C1 | 0.41716 (19) | 0.57195 (13) | 0.5387 (8) | 0.0750 (9) | |
H1 | 0.4740 | 0.5623 | 0.4432 | 0.090* | |
C2 | 0.2916 (2) | 0.56111 (15) | 0.7866 (8) | 0.0862 (10) | |
H2 | 0.2433 | 0.5416 | 0.8986 | 0.103* | |
C3 | 0.29626 (18) | 0.62851 (13) | 0.7091 (9) | 0.0757 (9) | |
H3 | 0.2530 | 0.6636 | 0.7556 | 0.091* | |
C4 | 0.41240 (17) | 0.69948 (11) | 0.4174 (6) | 0.0572 (7) | |
H4A | 0.3658 | 0.7166 | 0.2797 | 0.069* | |
H4B | 0.4705 | 0.6892 | 0.3121 | 0.069* | |
C5 | 0.43209 (15) | 0.75491 (10) | 0.6344 (6) | 0.0469 (5) | |
C6 | 0.41751 (16) | 0.84206 (11) | 0.9242 (6) | 0.0477 (6) | |
C7 | 0.38681 (18) | 0.89936 (12) | 1.0828 (7) | 0.0598 (7) | |
H7 | 0.3245 | 0.9156 | 1.0677 | 0.072* | |
C8 | 0.45102 (19) | 0.93126 (12) | 1.2620 (7) | 0.0672 (7) | |
H8 | 0.4321 | 0.9701 | 1.3683 | 0.081* | |
C9 | 0.54399 (19) | 0.90689 (13) | 1.2890 (7) | 0.0679 (8) | |
H9 | 0.5855 | 0.9294 | 1.4152 | 0.082* | |
C10 | 0.57598 (17) | 0.85021 (12) | 1.1333 (7) | 0.0607 (7) | |
H10 | 0.6382 | 0.8340 | 1.1508 | 0.073* | |
C11 | 0.51115 (16) | 0.81846 (11) | 0.9492 (5) | 0.0469 (6) | |
N1 | 0.51804 (12) | 0.76285 (8) | 0.7624 (4) | 0.0500 (5) | |
H1C | 0.5679 | 0.7377 | 0.7324 | 0.060* | |
N2 | 0.36886 (12) | 0.80074 (9) | 0.7246 (5) | 0.0507 (5) | |
N3 | 0.37666 (13) | 0.63523 (9) | 0.5495 (5) | 0.0534 (5) | |
O2 | 0.17694 (10) | 0.81693 (8) | 0.6079 (5) | 0.0707 (5) | |
H2A | 0.1629 | 0.8339 | 0.4455 | 0.085* | |
H2B | 0.2347 | 0.8130 | 0.6519 | 0.085* | |
H1A | 0.1376 | 0.8710 | −0.0364 | 0.085* | |
H1B | 0.1195 | 0.9255 | 0.1259 | 0.085* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0790 (11) | 0.0582 (9) | 0.0695 (14) | 0.0014 (8) | 0.0074 (11) | 0.0079 (10) |
N4 | 0.0940 (16) | 0.0537 (12) | 0.111 (2) | −0.0114 (12) | 0.0227 (18) | 0.0028 (16) |
C1 | 0.0734 (16) | 0.0540 (15) | 0.098 (3) | −0.0003 (14) | 0.0231 (18) | −0.0025 (16) |
C2 | 0.0823 (19) | 0.077 (2) | 0.099 (3) | −0.0288 (16) | 0.028 (2) | −0.003 (2) |
C3 | 0.0638 (15) | 0.0642 (17) | 0.099 (3) | −0.0120 (12) | 0.0259 (19) | −0.0109 (18) |
C4 | 0.0636 (14) | 0.0553 (14) | 0.0526 (17) | −0.0034 (12) | 0.0065 (14) | 0.0051 (13) |
C5 | 0.0541 (13) | 0.0429 (12) | 0.0438 (14) | −0.0050 (10) | 0.0040 (14) | 0.0082 (11) |
C6 | 0.0512 (13) | 0.0428 (12) | 0.0491 (16) | −0.0033 (10) | 0.0043 (12) | 0.0085 (12) |
C7 | 0.0621 (15) | 0.0520 (14) | 0.0653 (19) | 0.0021 (11) | 0.0060 (15) | 0.0027 (14) |
C8 | 0.0867 (19) | 0.0512 (14) | 0.0636 (19) | −0.0070 (13) | 0.0085 (18) | 0.0009 (15) |
C9 | 0.086 (2) | 0.0638 (16) | 0.0537 (18) | −0.0246 (14) | −0.0031 (17) | 0.0017 (15) |
C10 | 0.0562 (14) | 0.0670 (16) | 0.0588 (17) | −0.0085 (12) | −0.0016 (15) | 0.0110 (16) |
C11 | 0.0497 (13) | 0.0451 (12) | 0.0459 (14) | −0.0040 (10) | 0.0043 (13) | 0.0073 (12) |
N1 | 0.0465 (10) | 0.0511 (10) | 0.0526 (14) | 0.0042 (8) | 0.0037 (11) | 0.0055 (11) |
N2 | 0.0486 (10) | 0.0470 (10) | 0.0565 (14) | 0.0012 (8) | 0.0009 (11) | 0.0057 (11) |
N3 | 0.0547 (11) | 0.0479 (11) | 0.0576 (14) | −0.0071 (9) | 0.0050 (10) | −0.0037 (10) |
O2 | 0.0511 (9) | 0.0909 (12) | 0.0700 (13) | −0.0061 (8) | −0.0025 (10) | 0.0192 (12) |
O1—H1A | 0.8446 | C6—C7 | 1.387 (3) |
O1—H1B | 0.8441 | C6—N2 | 1.393 (3) |
N4—C1 | 1.311 (3) | C6—C11 | 1.394 (3) |
N4—C2 | 1.354 (4) | C7—C8 | 1.368 (4) |
C1—N3 | 1.338 (3) | C7—H7 | 0.9300 |
C1—H1 | 0.9300 | C8—C9 | 1.391 (3) |
C2—C3 | 1.339 (3) | C8—H8 | 0.9300 |
C2—H2 | 0.9300 | C9—C10 | 1.376 (4) |
C3—N3 | 1.354 (3) | C9—H9 | 0.9300 |
C3—H3 | 0.9300 | C10—C11 | 1.386 (3) |
C4—N3 | 1.461 (3) | C10—H10 | 0.9300 |
C4—C5 | 1.485 (3) | C11—N1 | 1.373 (3) |
C4—H4A | 0.9700 | N1—H1C | 0.8600 |
C4—H4B | 0.9700 | O2—H2A | 0.8412 |
C5—N2 | 1.315 (3) | O2—H2B | 0.8381 |
C5—N1 | 1.352 (3) | ||
H1A—O1—H1B | 101.7 | C8—C7—C6 | 117.9 (2) |
C1—N4—C2 | 104.9 (2) | C8—C7—H7 | 121.0 |
N4—C1—N3 | 111.7 (2) | C6—C7—H7 | 121.0 |
N4—C1—H1 | 124.2 | C7—C8—C9 | 121.5 (3) |
N3—C1—H1 | 124.2 | C7—C8—H8 | 119.2 |
C3—C2—N4 | 110.6 (3) | C9—C8—H8 | 119.2 |
C3—C2—H2 | 124.7 | C10—C9—C8 | 121.5 (3) |
N4—C2—H2 | 124.7 | C10—C9—H9 | 119.2 |
C2—C3—N3 | 106.1 (2) | C8—C9—H9 | 119.2 |
C2—C3—H3 | 126.9 | C9—C10—C11 | 116.9 (2) |
N3—C3—H3 | 126.9 | C9—C10—H10 | 121.6 |
N3—C4—C5 | 112.4 (2) | C11—C10—H10 | 121.6 |
N3—C4—H4A | 109.1 | N1—C11—C10 | 132.8 (2) |
C5—C4—H4A | 109.1 | N1—C11—C6 | 105.4 (2) |
N3—C4—H4B | 109.1 | C10—C11—C6 | 121.8 (2) |
C5—C4—H4B | 109.1 | C5—N1—C11 | 107.42 (18) |
H4A—C4—H4B | 107.9 | C5—N1—H1C | 126.3 |
N2—C5—N1 | 112.8 (2) | C11—N1—H1C | 126.3 |
N2—C5—C4 | 124.4 (2) | C5—N2—C6 | 104.92 (18) |
N1—C5—C4 | 122.81 (19) | C1—N3—C3 | 106.8 (2) |
C7—C6—N2 | 130.2 (2) | C1—N3—C4 | 126.8 (2) |
C7—C6—C11 | 120.3 (2) | C3—N3—C4 | 126.4 (2) |
N2—C6—C11 | 109.5 (2) | H2A—O2—H2B | 118.5 |
C2—N4—C1—N3 | −0.7 (4) | N2—C6—C11—C10 | 179.9 (2) |
C1—N4—C2—C3 | 0.5 (4) | N2—C5—N1—C11 | −0.5 (2) |
N4—C2—C3—N3 | −0.1 (4) | C4—C5—N1—C11 | −180.0 (2) |
N3—C4—C5—N2 | −88.6 (3) | C10—C11—N1—C5 | −179.5 (3) |
N3—C4—C5—N1 | 90.8 (3) | C6—C11—N1—C5 | 0.2 (2) |
N2—C6—C7—C8 | −178.9 (2) | N1—C5—N2—C6 | 0.6 (2) |
C11—C6—C7—C8 | 0.0 (4) | C4—C5—N2—C6 | −179.9 (2) |
C6—C7—C8—C9 | −0.8 (4) | C7—C6—N2—C5 | 178.5 (3) |
C7—C8—C9—C10 | 1.0 (4) | C11—C6—N2—C5 | −0.5 (2) |
C8—C9—C10—C11 | −0.2 (4) | N4—C1—N3—C3 | 0.7 (4) |
C9—C10—C11—N1 | 179.0 (2) | N4—C1—N3—C4 | −179.9 (3) |
C9—C10—C11—C6 | −0.7 (4) | C2—C3—N3—C1 | −0.3 (3) |
C7—C6—C11—N1 | −178.9 (2) | C2—C3—N3—C4 | −179.8 (3) |
N2—C6—C11—N1 | 0.2 (2) | C5—C4—N3—C1 | −119.4 (3) |
C7—C6—C11—C10 | 0.8 (3) | C5—C4—N3—C3 | 60.0 (3) |
D—H···A | D—H | H···A | D···A | D—H···A |
O1—H1A···O2i | 0.84 | 2.02 | 2.836 (3) | 162 |
N1—H1C···O2ii | 0.86 | 1.94 | 2.794 (2) | 172 |
O1—H1B···N4iii | 0.84 | 1.93 | 2.772 (2) | 173 |
O2—H2A···O1 | 0.84 | 1.87 | 2.696 (3) | 169 |
O2—H2B···N2 | 0.84 | 1.93 | 2.764 (2) | 176 |
Symmetry codes: (i) x, y, z−1; (ii) x+1/2, −y+3/2, z; (iii) −x+1/2, y+1/2, z−1/2. |
Experimental details
Crystal data | |
Chemical formula | C11H10N4·2H2O |
Mr | 234.26 |
Crystal system, space group | Orthorhombic, Pna21 |
Temperature (K) | 298 |
a, b, c (Å) | 14.030 (2), 19.121 (3), 4.6240 (8) |
V (Å3) | 1240.5 (4) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.09 |
Crystal size (mm) | 0.30 × 0.27 × 0.25 |
Data collection | |
Diffractometer | CCD area-detector diffractometer |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 6623, 1313, 1117 |
Rint | 0.055 |
(sin θ/λ)max (Å−1) | 0.606 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.035, 0.079, 1.03 |
No. of reflections | 1313 |
No. of parameters | 154 |
No. of restraints | 5 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.10, −0.11 |
Computer programs: SMART (Bruker, 2000), SAINT (Bruker, 2000), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).
D—H···A | D—H | H···A | D···A | D—H···A |
O1—H1A···O2i | 0.84 | 2.02 | 2.836 (3) | 162.4 |
N1—H1C···O2ii | 0.86 | 1.94 | 2.794 (2) | 172.0 |
O1—H1B···N4iii | 0.84 | 1.93 | 2.772 (2) | 172.6 |
O2—H2A···O1 | 0.84 | 1.87 | 2.696 (3) | 168.7 |
O2—H2B···N2 | 0.84 | 1.93 | 2.764 (2) | 175.6 |
Symmetry codes: (i) x, y, z−1; (ii) x+1/2, −y+3/2, z; (iii) −x+1/2, y+1/2, z−1/2. |
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.