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Acta Crystallogr Sect E Struct Rep Online. 2009 June 1; 65(Pt 6): m672.
Published online 2009 May 23. doi:  10.1107/S1600536809018704
PMCID: PMC2969820

Penta­aqua­(1H-benzimidazole-5,6-dicarboxyl­ato-κN 3)nickel(II) penta­hydrate

Abstract

In the title mononuclear complex, [Ni(C9H4N2O4)(H2O)5]·5H2O, the NiII atom is six-coordinated by one N atom from a 1H-benzimidazole-5,6-dicarboxyl­ate ligand and by five O atoms from five water mol­ecules and displays a distorted octa­hedral geometry. Inter­molecular O—H(...)O hydrogen-bonding inter­actions among the coordinated water mol­ecules, solvent water mol­ecules and carboxyl O atoms of the organic ligand and additional N—H(...)O hydrogen bonding lead to the formation of a three-dimensional supra­molecular network.

Related literature

For background information on 1H-benzimidazole-5,6-dicarboxyl­ate complexes, see: Lo et al. (2007 [triangle]); Yao et al. (2008 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-0m672-scheme1.jpg

Experimental

Crystal data

  • [Ni(C9H4N2O4)(H2O)5]·5H2O
  • M r = 443.01
  • Triclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-0m672-efi1.jpg
  • a = 6.8436 (14) Å
  • b = 11.434 (2) Å
  • c = 12.344 (3) Å
  • α = 78.29 (3)°
  • β = 78.65 (3)°
  • γ = 74.92 (3)°
  • V = 902.6 (3) Å3
  • Z = 2
  • Mo Kα radiation
  • μ = 1.15 mm−1
  • T = 293 K
  • 0.31 × 0.25 × 0.21 mm

Data collection

  • Rigaku Mercury CCD diffractometer
  • Absorption correction: multi-scan (REQAB; Jacobson, 1998 [triangle]) T min = 0.725, T max = 0.793
  • 7176 measured reflections
  • 3228 independent reflections
  • 2851 reflections with I > 2σ(I)
  • R int = 0.048

Refinement

  • R[F 2 > 2σ(F 2)] = 0.056
  • wR(F 2) = 0.167
  • S = 1.14
  • 3228 reflections
  • 235 parameters
  • 30 restraints
  • H-atom parameters constrained
  • Δρmax = 1.53 e Å−3
  • Δρmin = −0.60 e Å−3

Data collection: RAPID-AUTO (Rigaku, 1998 [triangle]); cell refinement: RAPID-AUTO; data reduction: CrystalStructure (Rigaku/MSC, 2002 [triangle]); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: ORTEPII (Johnson, 1976 [triangle]); software used to prepare material for publication: SHELXL97.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536809018704/zl2208sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809018704/zl2208Isup2.hkl

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

Acknowledgments

The authors acknowledge Guang Dong Ocean University for supporting this work.

supplementary crystallographic information

Comment

In the structural investigation of 1H-benzimidazole-5,6-dicarboxylate complexes, it has been found that the 1H-benzimidazole-5,6-dicarboxylic acid can function as a multidentate ligand (Lo et al., 2007; Yao et al., 2008), with versatile binding and coordination modes. In this paper, we report the crystal structure of the title compound, a new Ni complex obtained by the reaction of 1H-benzimidazole-5,6-dicarboxylic acid with nickel chloride in an alkaline aqueous solution.

As illustrated in Fig. 1, the NiII atom exhibits a slightly distorted octahedral coordination sphere, defined by one N atom from the 1H-benzimidazole-5,6-dicarboxylate ligand and five coordinated water molecules. The five non-bonded solvent water molecules are located in cavities of the three-dimensional framework, allowing them to participate in various O—H···O hydrogen bonds (Table 1) with the coordinated water molecules, non-coordinated water molecules and carboxylate O atoms of the organic ligand. The hydrogen bonds are in the normal range (Table 1, Fig. 2).

Experimental

A mixture of nickel chloride (1 mmol), 1H-benzimidazole-5,6-dicarboxylic acid (1 mmol), NaOH (1.5 mmol) and H2O (12 ml) was placed in a 23 ml Teflon reactor, which was heated to 433 K for three days and then cooled to room temperature at a rate of 10 K h-1. The crystals obtained were washed with water and dryed in air.

Refinement

Carbon and nitrogen bound H atoms were placed at calculated positions and were treated as riding on the parent C or N atoms with C—H = 0.93 Å, N—H = 0.86 Å, and with Uiso(H) = 1.2 Ueq(C, N). The water H atoms were located in a difference map, and were refined with a distance restraint of O—H = 0.84 Å; their Uiso values were refined.

Figures

Fig. 1.
The structure of the title compound, showing the atomic numbering scheme. Non-H atoms are shown with 30% probability displacement ellipsoids.
Fig. 2.
A packing view of the title compound. The intermolecular hydrogen bonds are shown as dashed lines.

Crystal data

[Ni(C9H4N2O4)(H2O)5]·5H2OZ = 2
Mr = 443.01F(000) = 464
Triclinic, P1Dx = 1.630 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 6.8436 (14) ÅCell parameters from 3600 reflections
b = 11.434 (2) Åθ = 1.4–28°
c = 12.344 (3) ŵ = 1.15 mm1
α = 78.29 (3)°T = 293 K
β = 78.65 (3)°Block, blue
γ = 74.92 (3)°0.31 × 0.25 × 0.21 mm
V = 902.6 (3) Å3

Data collection

Rigaku Mercury CCD diffractometer3228 independent reflections
Radiation source: fine-focus sealed tube2851 reflections with I > 2σ(I)
graphiteRint = 0.048
ω scansθmax = 25.2°, θmin = 3.1°
Absorption correction: multi-scan (REQAB; Jacobson, 1998)h = −8→8
Tmin = 0.725, Tmax = 0.793k = −13→13
7176 measured reflectionsl = −14→13

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.056Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.167H-atom parameters constrained
S = 1.14w = 1/[σ2(Fo2) + (0.0905P)2 + 1.2897P] where P = (Fo2 + 2Fc2)/3
3228 reflections(Δ/σ)max = 0.001
235 parametersΔρmax = 1.53 e Å3
30 restraintsΔρmin = −0.60 e Å3

Special details

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)

xyzUiso*/Ueq
C10.3714 (6)0.5621 (4)0.7112 (3)0.0205 (8)
N10.3498 (6)0.3063 (3)0.9967 (3)0.0272 (8)
H10.30740.30781.06690.033*
Ni10.59930 (7)0.09723 (4)0.74101 (4)0.0200 (2)
O10.2171 (5)0.6926 (3)0.5614 (3)0.0379 (8)
C20.4484 (6)0.4375 (3)0.7118 (3)0.0210 (8)
H20.51060.40680.64600.025*
N20.4903 (5)0.2318 (3)0.8396 (3)0.0224 (7)
O20.5536 (5)0.6543 (3)0.5459 (2)0.0346 (8)
C30.4301 (6)0.3595 (3)0.8136 (3)0.0209 (8)
O30.0491 (5)0.7830 (3)0.8792 (3)0.0346 (8)
C40.3381 (6)0.4072 (4)0.9121 (3)0.0230 (8)
O40.3074 (5)0.8139 (3)0.7441 (3)0.0328 (7)
C50.2592 (6)0.5316 (4)0.9124 (3)0.0253 (9)
H50.19730.56170.97850.030*
C60.2755 (6)0.6096 (4)0.8113 (3)0.0222 (8)
C70.4385 (7)0.2068 (4)0.9496 (3)0.0258 (9)
H70.46180.12770.98980.031*
C80.2025 (6)0.7459 (4)0.8107 (3)0.0243 (9)
C90.3812 (6)0.6449 (3)0.5979 (3)0.0217 (8)
O1W0.3920 (4)0.1803 (3)0.6302 (2)0.0284 (7)
H2W0.43030.22720.57270.043*
H1W0.35130.12370.61380.043*
O2W0.8180 (4)0.1821 (3)0.6393 (2)0.0274 (6)
H3W0.86970.22730.66560.041*
H4W0.79250.21290.57440.041*
O3W0.7170 (6)−0.0427 (3)0.6518 (3)0.0463 (10)
H5W0.7472−0.11640.68230.070*
H6W0.7539−0.03440.58220.070*
O4W0.7928 (5)0.0082 (3)0.8549 (3)0.0313 (7)
H7W0.8647−0.05960.83910.047*
H8W0.86180.04750.87650.047*
O5W0.3802 (5)0.0021 (3)0.8336 (2)0.0285 (7)
H9W0.27340.04890.86070.043*
H10W0.3518−0.05250.80720.043*
O6W0.8012 (5)0.9831 (3)0.4213 (2)0.0340 (7)
H11W0.76151.04200.37170.051*
H12W0.92570.94990.40490.051*
O7W0.2893 (5)0.2719 (3)0.2313 (3)0.0372 (8)
H14W0.41280.25540.23980.056*
H13W0.22010.33170.26240.056*
O8W0.9187 (5)0.5590 (3)0.6314 (3)0.0431 (8)
H16W0.82000.57770.59520.065*
H15W1.01370.59320.59820.065*
O9W−0.0044 (5)0.8476 (3)0.0863 (3)0.0378 (8)
H18W0.01840.78950.13950.057*
H17W0.00750.82200.02570.057*
O10W0.0100 (5)0.3191 (3)0.7221 (3)0.0406 (8)
H19W−0.00440.39500.70060.061*
H20W0.12570.28000.69580.061*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
C10.0213 (19)0.021 (2)0.0181 (18)−0.0063 (15)−0.0026 (15)0.0000 (15)
N10.041 (2)0.0185 (17)0.0163 (16)−0.0034 (14)−0.0012 (15)0.0021 (13)
Ni10.0245 (3)0.0148 (3)0.0184 (3)−0.0027 (2)−0.0024 (2)−0.00091 (19)
O10.0319 (17)0.0426 (19)0.0323 (16)−0.0088 (14)−0.0108 (13)0.0156 (14)
C20.025 (2)0.0178 (19)0.0179 (18)−0.0028 (15)−0.0014 (15)−0.0019 (14)
N20.0285 (18)0.0143 (16)0.0211 (16)−0.0028 (13)−0.0034 (14)0.0013 (12)
O20.0295 (16)0.0383 (18)0.0272 (16)−0.0074 (13)−0.0024 (13)0.0123 (13)
C30.0221 (19)0.0179 (19)0.0218 (19)−0.0035 (15)−0.0035 (15)−0.0023 (15)
O30.0371 (17)0.0234 (16)0.0344 (17)0.0036 (13)0.0036 (14)−0.0068 (12)
C40.028 (2)0.021 (2)0.0189 (19)−0.0063 (16)−0.0015 (16)−0.0002 (14)
O40.0382 (18)0.0188 (15)0.0391 (17)−0.0077 (12)−0.0007 (14)−0.0031 (12)
C50.031 (2)0.021 (2)0.0205 (19)−0.0028 (16)−0.0002 (16)−0.0037 (15)
C60.023 (2)0.017 (2)0.024 (2)−0.0018 (15)−0.0034 (16)−0.0027 (15)
C70.035 (2)0.0179 (19)0.022 (2)−0.0049 (16)−0.0046 (17)0.0015 (15)
C80.030 (2)0.018 (2)0.024 (2)−0.0036 (16)−0.0074 (17)−0.0021 (15)
C90.030 (2)0.0166 (19)0.0192 (19)−0.0058 (16)−0.0053 (16)−0.0015 (14)
O1W0.0327 (16)0.0282 (16)0.0246 (14)−0.0124 (12)−0.0063 (12)0.0039 (11)
O2W0.0297 (15)0.0283 (16)0.0238 (14)−0.0103 (12)−0.0053 (12)0.0023 (11)
O3W0.081 (3)0.0219 (16)0.0287 (17)−0.0075 (16)0.0088 (17)−0.0086 (13)
O4W0.0315 (16)0.0221 (15)0.0396 (17)0.0020 (12)−0.0139 (13)−0.0052 (12)
O5W0.0327 (16)0.0227 (15)0.0292 (15)−0.0092 (12)0.0025 (12)−0.0053 (11)
O6W0.0355 (18)0.0310 (17)0.0306 (16)−0.0042 (13)−0.0035 (13)0.0006 (12)
O7W0.0381 (18)0.0401 (19)0.0320 (17)−0.0067 (14)−0.0040 (14)−0.0067 (14)
O8W0.0349 (18)0.039 (2)0.052 (2)−0.0080 (15)−0.0099 (15)0.0024 (15)
O9W0.0462 (19)0.0365 (18)0.0310 (16)−0.0061 (15)−0.0090 (15)−0.0077 (13)
O10W0.0358 (18)0.0334 (18)0.051 (2)−0.0075 (14)−0.0088 (15)−0.0022 (15)

Geometric parameters (Å, °)

C1—C21.383 (5)C5—H50.9300
C1—C61.422 (6)C6—C81.506 (5)
C1—C91.522 (5)C7—H70.9300
N1—C71.332 (5)O1W—H2W0.8400
N1—C41.387 (5)O1W—H1W0.8400
N1—H10.8600O2W—H3W0.8400
Ni1—O3W2.029 (3)O2W—H4W0.8400
Ni1—O4W2.053 (3)O3W—H5W0.8400
Ni1—N22.052 (3)O3W—H6W0.8400
Ni1—O2W2.069 (3)O4W—H7W0.8400
Ni1—O1W2.078 (3)O4W—H8W0.8400
Ni1—O5W2.099 (3)O5W—H9W0.8400
O1—C91.242 (5)O5W—H10W0.8400
C2—C31.390 (5)O6W—H11W0.8400
C2—H20.9300O6W—H12W0.8400
N2—C71.325 (5)O7W—H14W0.8400
N2—C31.398 (5)O7W—H13W0.8400
O2—C91.247 (5)O8W—H16W0.8400
C3—C41.400 (6)O8W—H15W0.8400
O3—C81.250 (5)O9W—H18W0.8400
C4—C51.384 (6)O9W—H17W0.8400
O4—C81.263 (5)O10W—H19W0.8400
C5—C61.383 (5)O10W—H20W0.8400
C2—C1—C6121.3 (3)C6—C5—H5121.1
C2—C1—C9117.1 (3)C4—C5—H5121.1
C6—C1—C9121.5 (3)C5—C6—C1120.4 (4)
C7—N1—C4107.6 (3)C5—C6—C8118.6 (3)
C7—N1—H1126.2C1—C6—C8120.9 (3)
C4—N1—H1126.2N2—C7—N1113.3 (3)
O3W—Ni1—O4W88.73 (14)N2—C7—H7123.4
O3W—Ni1—N2176.19 (13)N1—C7—H7123.4
O4W—Ni1—N287.52 (13)O3—C8—O4124.7 (4)
O3W—Ni1—O2W86.14 (14)O3—C8—C6118.0 (4)
O4W—Ni1—O2W92.83 (12)O4—C8—C6117.1 (3)
N2—Ni1—O2W94.75 (13)O1—C9—O2124.9 (4)
O3W—Ni1—O1W90.63 (14)O1—C9—C1117.3 (3)
O4W—Ni1—O1W176.58 (11)O2—C9—C1117.7 (4)
N2—Ni1—O1W93.07 (13)Ni1—O1W—H2W117.9
O2W—Ni1—O1W90.49 (11)Ni1—O1W—H1W106.6
O3W—Ni1—O5W89.34 (13)H2W—O1W—H1W111.6
O4W—Ni1—O5W88.84 (13)Ni1—O2W—H3W119.4
N2—Ni1—O5W89.88 (13)Ni1—O2W—H4W115.2
O2W—Ni1—O5W175.15 (11)H3W—O2W—H4W111.6
O1W—Ni1—O5W87.79 (12)Ni1—O3W—H5W122.7
C1—C2—C3118.0 (4)Ni1—O3W—H6W125.1
C1—C2—H2121.0H5W—O3W—H6W111.9
C3—C2—H2121.0Ni1—O4W—H7W113.0
C7—N2—C3104.9 (3)Ni1—O4W—H8W119.4
C7—N2—Ni1122.5 (3)H7W—O4W—H8W111.4
C3—N2—Ni1132.1 (3)Ni1—O5W—H9W112.7
C2—C3—N2130.8 (4)Ni1—O5W—H10W119.8
C2—C3—C4120.3 (4)H9W—O5W—H10W111.1
N2—C3—C4108.9 (3)H11W—O6W—H12W111.6
N1—C4—C5132.6 (4)H14W—O7W—H13W111.7
N1—C4—C3105.3 (3)H16W—O8W—H15W111.6
C5—C4—C3122.2 (4)H18W—O9W—H17W111.7
C6—C5—C4117.8 (4)H19W—O10W—H20W111.4

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
O10W—H20W···O1W0.842.002.836 (4)176
O10W—H19W···O8Wi0.841.882.703 (5)166
O9W—H17W···O3ii0.841.902.733 (5)172
O9W—H18W···O10Wiii0.841.912.720 (5)163
O8W—H15W···O1iv0.841.952.765 (5)163
O8W—H16W···O20.841.962.775 (5)162
O7W—H13W···O8Wv0.841.932.754 (5)165
O7W—H14W···O4v0.841.912.734 (5)169
O6W—H12W···O2Wvi0.842.062.857 (4)159
O6W—H11W···O4vii0.841.972.808 (4)174
O5W—H10W···O4viii0.841.962.800 (4)176
O5W—H9W···O9Wiii0.841.982.817 (4)173
O4W—H8W···O9Wv0.841.902.736 (5)173
O4W—H7W···O3ix0.841.942.709 (4)151
O3W—H6W···O6Wviii0.841.932.761 (4)172
O3W—H5W···O7Wx0.841.932.729 (5)159
O2W—H4W···O1v0.841.802.620 (4)164
O2W—H3W···O10Wiv0.841.902.734 (5)175
O1W—H1W···O6Wv0.841.962.783 (5)168
O1W—H2W···O2v0.841.792.612 (4)166
N1—H1···O7Wxi0.861.972.803 (5)162

Symmetry codes: (i) x−1, y, z; (ii) x, y, z−1; (iii) −x, −y+1, −z+1; (iv) x+1, y, z; (v) −x+1, −y+1, −z+1; (vi) −x+2, −y+1, −z+1; (vii) −x+1, −y+2, −z+1; (viii) x, y−1, z; (ix) x+1, y−1, z; (x) −x+1, −y, −z+1; (xi) x, y, z+1.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: ZL2208).

References

  • Jacobson, R. (1998). REQAB Molecular Structure Corporation, The Woodlands, Texas, USA.
  • Johnson, C. K. (1976). ORTEPII Report ORNL-5138. Oak Ridge National Laboratory, Tennessee, USA.
  • Lo, Y.-L., Wang, W.-C., Lee, G.-A. & Liu, Y.-H. (2007). Acta Cryst. E63, m2657–m2658.
  • Rigaku (1998). RAPID-AUTO Rigaku Corporation, Tokyo, Japan.
  • Rigaku/MSC (2002). CrystalStructure Rigaku/MSC, The Woodlands, Texas, USA.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Yao, Y. L., Che, Y. X. & Zheng, J. M. (2008). Cryst. Growth Des.8, 2299–2306.

Articles from Acta Crystallographica Section E: Structure Reports Online are provided here courtesy of International Union of Crystallography