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Acta Crystallogr Sect E Struct Rep Online. 2008 July 1; 64(Pt 7): m928.
Published online 2008 June 19. doi:  10.1107/S1600536808017595
PMCID: PMC2961800

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

Abstract

The title compound, [Cu(C9H4N2O4)(H2O)5]·5H2O, contains one crystallographically independent CuII atom and one 1H-benzimidazole-5,6-dicarboxyl­ate (bdc) ligand, along with five coordinated and five uncoordinated water mol­ecules. The CuII atom is six-coordinated by one N atom from the bdc ligand and five O atoms from water mol­ecules, giving an octa­hedral coordination geometry. Hydrogen bonds link the mononuclear complex and uncoordinated water mol­ecules into a three-dimensional network.

Related literature

For related literature, see: Lemos et al. (2004 [triangle]); Park et al. (2006 [triangle]); Zhang et al. (2007 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-64-0m928-scheme1.jpg

Experimental

Crystal data

  • [Cu(C9H4N2O4)(H2O)5]·5H2O
  • M r = 447.84
  • Triclinic, An external file that holds a picture, illustration, etc.
Object name is e-64-0m928-efi1.jpg
  • a = 6.8449 (5) Å
  • b = 11.4381 (8) Å
  • c = 12.3549 (9) Å
  • α = 78.1549 (1)°
  • β = 78.6224 (1)°
  • γ = 74.8804 (1)°
  • V = 903.29 (11) Å3
  • Z = 2
  • Mo Kα radiation
  • μ = 1.28 mm−1
  • T = 296 (2) K
  • 0.24 × 0.24 × 0.24 mm

Data collection

  • Bruker SMART CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 1998 [triangle]) T min = 0.748, T max = 0.748
  • 4648 measured reflections
  • 3164 independent reflections
  • 2774 reflections with I > 2σ(I)
  • R int = 0.018

Refinement

  • R[F 2 > 2σ(F 2)] = 0.034
  • wR(F 2) = 0.092
  • S = 1.05
  • 3164 reflections
  • 295 parameters
  • 20 restraints
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.32 e Å−3
  • Δρmin = −0.54 e Å−3

Data collection: SMART (Bruker, 1998 [triangle]); cell refinement: SAINT (Bruker, 1998 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: SHELXTL (Sheldrick, 2008 [triangle]); software used to prepare material for publication: SHELXTL.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536808017595/kj2082sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536808017595/kj2082Isup2.hkl

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

Acknowledgments

This work was supported by the Funding Project for Academic Human Resources Development in Institutions of Higher Learning under the Jurisdiction of Beijing Municipality.

supplementary crystallographic information

Comment

Several coordination polymers formed by the ligand 1H-benzoimidazole-5,6-dicarboxylic acid have been reported recently: µ2-2,2'-Bibenzimidazolato-N',N'',N''')tetrakis (triphenylphosphine)-di-copper(I) dichloromethane solvate (Lemos et al., 2004), catena-poly [tetrakis(µ2Benzimidazolato-N,N')-di-Co(II) unknown clathrate hydrate] (Park et al., 2006), and catena-poly [bis (µ5Benzotriazole-5-carboxylate) -bis(µ2-hydroxo)-tri-Co(II)] (Zhang et al., 2007) The first complex is a binuclear structure and the latter two are 3D porous metal-organic frameworks. However, up to now, the CuII complex of the 1H-benzoimidazole-5,6-dicarboxylic acid ligand (H2L), has not been reported.

As shown in Figure 1, the title compound has a mononuclear structure, in which there exists only one crystallographically independent Cu (II) atom and only one 1H-benzoimidazole-5,6-dicarboxylate ligand, along with five coordinated and five uncoordinated water. Each Cu (II) is six-coordinated with one N atom from the ligand, and five O atoms from water molecules, giving an octahedral coordination geometry. Hydrogen bonds link the mononuclear complex and uncoordinated water molecules into a three-dimensional network.

Experimental

The title complex was synthesized by carefully layering a solution of Cu(NO3)2.3H2O (24 mg, 0.1 mmol) in MeOH (10 ml) on top of a solution of H2L (27 mg, 0.1 mmol) and LiOH (8.4 mg, 0.2 mmol) in H2O (10 ml) in a test-tube. After about several months at room temperature, green block-shaped single crystals suitable for X-ray investigation appeared at the boundary between MeOH and H2O with a yield of 25%.

Refinement

H atoms of C were included in calculated positions and treated in the subsequent refinement as riding atoms, with C—H = 0.93 Å and Uiso(H) = 1.2 Ueq(C,N). The H atoms of the water molecules were located in Fourier difference maps and refined with isotropic displacement parameters set at 1.5 times those of the parent O atoms.

Figures

Fig. 1.
Structure of the title complex, showing displacement ellipsoids at the 30% probability level.

Crystal data

[Cu(C9H4N2O4)(H2O)5]·5H2OZ = 2
Mr = 447.84F000 = 466
Triclinic, P1Dx = 1.647 Mg m3
Hall symbol: -P 1Mo Kα radiation λ = 0.71073 Å
a = 6.8449 (5) ÅCell parameters from 2164 reflections
b = 11.4381 (8) Åθ = 2.7–27.7º
c = 12.3549 (9) ŵ = 1.28 mm1
α = 78.1549 (1)ºT = 296 (2) K
β = 78.6224 (1)ºBlock, green
γ = 74.8804 (1)º0.24 × 0.24 × 0.24 mm
V = 903.29 (11) Å3

Data collection

Bruker SMART CCD area-detector diffractometer3164 independent reflections
Radiation source: fine-focus sealed tube2774 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.018
T = 296(2) Kθmax = 25.0º
[var phi] and ω scansθmin = 1.7º
Absorption correction: multi-scan(SADABS; Bruker, 1998)h = −8→7
Tmin = 0.748, Tmax = 0.748k = −13→9
4648 measured reflectionsl = −14→13

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.034H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.092  w = 1/[σ2(Fo2) + (0.0394P)2 + 1.2855P] where P = (Fo2 + 2Fc2)/3
S = 1.05(Δ/σ)max = 0.001
3164 reflectionsΔρmax = 0.32 e Å3
295 parametersΔρmin = −0.53 e Å3
20 restraintsExtinction correction: none
Primary atom site location: structure-invariant direct methods

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
Cu20.40064 (5)0.90276 (3)0.25900 (3)0.01956 (13)
C10.5610 (5)0.7927 (3)0.0504 (2)0.0208 (6)
H1B0.53720.87190.01000.025*
C20.5701 (4)0.6408 (2)0.1857 (2)0.0155 (6)
C30.5523 (4)0.5625 (2)0.2878 (2)0.0164 (6)
H3A0.49080.59330.35350.020*
C40.6288 (4)0.4374 (2)0.2891 (2)0.0164 (6)
C50.7248 (4)0.3904 (3)0.1890 (2)0.0174 (6)
C60.7410 (5)0.4686 (3)0.0879 (2)0.0209 (6)
H6A0.80360.43850.02200.025*
C70.6613 (4)0.5927 (3)0.0878 (2)0.0188 (6)
C80.6183 (4)0.3556 (2)0.4017 (2)0.0181 (6)
C90.7972 (5)0.2539 (3)0.1890 (2)0.0200 (6)
N10.6497 (4)0.6937 (2)0.0032 (2)0.0232 (6)
H1A0.69210.6925−0.06700.028*
N20.5095 (4)0.7684 (2)0.16013 (19)0.0178 (5)
O10.7832 (3)0.3070 (2)0.43846 (19)0.0333 (6)
O1W0.1811 (3)0.8182 (2)0.36057 (18)0.0231 (5)
H1D0.206 (6)0.780 (3)0.418 (2)0.035*
H1C0.145 (6)0.774 (3)0.331 (3)0.035*
O20.4460 (3)0.3461 (2)0.45410 (18)0.0296 (5)
O2W0.2065 (4)0.9916 (2)0.14521 (19)0.0267 (5)
H2B0.151 (6)0.950 (3)0.122 (3)0.040*
H2A0.119 (5)1.055 (3)0.154 (3)0.040*
O30.6926 (3)0.18604 (18)0.25581 (18)0.0281 (5)
O3W0.6198 (3)0.9979 (2)0.16683 (18)0.0236 (5)
H3B0.652 (6)1.045 (3)0.196 (3)0.035*
H3C0.719 (5)0.957 (3)0.139 (3)0.035*
O40.9510 (3)0.21717 (19)0.12100 (18)0.0296 (5)
O4W0.2824 (5)1.0432 (2)0.3484 (2)0.0410 (7)
H4B0.255 (7)1.113 (3)0.320 (4)0.061*
H4A0.275 (7)1.030 (4)0.416 (2)0.061*
O5W0.6079 (3)0.8194 (2)0.36953 (18)0.0241 (5)
H5B0.647 (6)0.873 (3)0.385 (3)0.036*
H5A0.579 (6)0.775 (3)0.424 (2)0.036*
O6W0.0815 (4)0.4415 (2)0.3683 (2)0.0397 (6)
H6B−0.005 (6)0.402 (4)0.403 (4)0.060*
H6C0.164 (6)0.421 (4)0.410 (3)0.060*
O7W0.2891 (4)0.2718 (2)0.2314 (2)0.0330 (5)
H7A0.406 (4)0.257 (4)0.244 (4)0.050*
H7B0.224 (6)0.331 (3)0.262 (3)0.050*
O8W0.9900 (4)0.6813 (2)0.2776 (2)0.0353 (6)
H8B0.874 (4)0.710 (4)0.303 (3)0.053*
H8A1.008 (7)0.609 (3)0.303 (4)0.053*
O9W−0.0044 (4)0.8476 (2)0.0862 (2)0.0339 (6)
H9B0.018 (7)0.825 (4)0.027 (3)0.051*
H9A0.013 (7)0.789 (3)0.133 (3)0.051*
O10W0.8011 (4)0.9835 (2)0.4212 (2)0.0312 (5)
H10B0.779 (6)1.053 (3)0.387 (3)0.047*
H10A0.919 (4)0.953 (4)0.402 (3)0.047*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Cu20.0244 (2)0.0145 (2)0.0180 (2)−0.00297 (14)−0.00237 (14)−0.00150 (14)
C10.0287 (16)0.0122 (14)0.0197 (15)−0.0042 (12)−0.0049 (12)0.0018 (11)
C20.0185 (14)0.0112 (13)0.0165 (14)−0.0022 (11)−0.0039 (11)−0.0021 (11)
C30.0208 (15)0.0161 (14)0.0120 (13)−0.0041 (11)−0.0004 (11)−0.0040 (11)
C40.0193 (14)0.0141 (14)0.0159 (14)−0.0041 (11)−0.0056 (11)0.0005 (11)
C50.0193 (14)0.0140 (14)0.0183 (14)−0.0022 (11)−0.0033 (11)−0.0031 (11)
C60.0280 (16)0.0184 (15)0.0141 (14)−0.0040 (12)0.0024 (12)−0.0046 (11)
C70.0242 (15)0.0157 (14)0.0146 (14)−0.0038 (12)−0.0028 (11)0.0010 (11)
C80.0270 (16)0.0118 (14)0.0153 (14)−0.0054 (12)−0.0039 (12)0.0000 (11)
C90.0253 (16)0.0148 (14)0.0203 (15)−0.0010 (12)−0.0084 (12)−0.0037 (12)
N10.0372 (15)0.0161 (13)0.0117 (12)−0.0040 (11)0.0002 (11)0.0016 (10)
N20.0240 (13)0.0106 (12)0.0168 (12)−0.0022 (10)−0.0031 (10)−0.0002 (9)
O10.0296 (13)0.0388 (14)0.0270 (12)−0.0103 (10)−0.0113 (10)0.0145 (10)
O1W0.0278 (12)0.0234 (12)0.0173 (11)−0.0090 (9)−0.0051 (9)0.0038 (9)
O20.0263 (12)0.0315 (13)0.0239 (12)−0.0079 (10)−0.0016 (9)0.0111 (10)
O2W0.0290 (13)0.0182 (12)0.0315 (12)0.0036 (9)−0.0134 (10)−0.0038 (10)
O30.0342 (13)0.0142 (11)0.0338 (13)−0.0069 (9)−0.0013 (10)−0.0013 (9)
O3W0.0270 (12)0.0193 (11)0.0253 (12)−0.0088 (9)0.0003 (9)−0.0050 (9)
O40.0333 (13)0.0177 (11)0.0302 (12)0.0044 (9)0.0016 (10)−0.0061 (9)
O4W0.0744 (19)0.0175 (12)0.0255 (13)−0.0081 (12)0.0065 (13)−0.0079 (11)
O5W0.0322 (12)0.0231 (12)0.0182 (11)−0.0122 (10)−0.0075 (9)0.0053 (9)
O6W0.0334 (15)0.0358 (15)0.0475 (17)−0.0081 (12)−0.0107 (12)0.0035 (12)
O7W0.0357 (14)0.0362 (14)0.0265 (12)−0.0074 (12)−0.0041 (11)−0.0054 (10)
O8W0.0307 (13)0.0291 (13)0.0446 (15)−0.0055 (11)−0.0069 (11)−0.0029 (11)
O9W0.0407 (14)0.0334 (14)0.0280 (13)−0.0050 (11)−0.0076 (11)−0.0080 (11)
O10W0.0313 (13)0.0268 (13)0.0305 (13)−0.0033 (11)−0.0033 (11)0.0007 (10)

Geometric parameters (Å, °)

Cu2—O4W2.037 (2)C9—O41.248 (4)
Cu2—O2W2.055 (2)C9—O31.261 (4)
Cu2—N22.055 (2)N1—H1A0.8600
Cu2—O1W2.070 (2)O1W—H1D0.78 (2)
Cu2—O5W2.076 (2)O1W—H1C0.80 (2)
Cu2—O3W2.097 (2)O2W—H2B0.80 (3)
C1—N21.322 (4)O2W—H2A0.82 (3)
C1—N11.328 (4)O3W—H3B0.81 (2)
C1—H1B0.9300O3W—H3C0.78 (2)
C2—C31.393 (4)O4W—H4B0.79 (3)
C2—N21.396 (3)O4W—H4A0.81 (3)
C2—C71.397 (4)O5W—H5B0.80 (2)
C3—C41.387 (4)O5W—H5A0.78 (2)
C3—H3A0.9300O6W—H6B0.84 (3)
C4—C51.420 (4)O6W—H6C0.79 (3)
C4—C81.510 (4)O7W—H7A0.81 (3)
C5—C61.382 (4)O7W—H7B0.83 (3)
C5—C91.510 (4)O8W—H8B0.80 (3)
C6—C71.381 (4)O8W—H8A0.81 (3)
C6—H6A0.9300O9W—H9B0.81 (3)
C7—N11.387 (4)O9W—H9A0.79 (3)
C8—O21.248 (4)O10W—H10B0.81 (3)
C8—O11.249 (4)O10W—H10A0.80 (3)
O4W—Cu2—O2W88.82 (10)C6—C7—C2122.3 (3)
O4W—Cu2—N2176.07 (10)N1—C7—C2105.0 (2)
O2W—Cu2—N287.32 (9)O2—C8—O1124.5 (3)
O4W—Cu2—O1W86.06 (10)O2—C8—C4118.2 (2)
O2W—Cu2—O1W92.49 (9)O1—C8—C4117.3 (3)
N2—Cu2—O1W94.83 (9)O4—C9—O3125.0 (3)
O4W—Cu2—O5W90.71 (11)O4—C9—C5117.9 (3)
O2W—Cu2—O5W176.77 (9)O3—C9—C5117.0 (3)
N2—Cu2—O5W93.11 (9)C1—N1—C7107.4 (2)
O1W—Cu2—O5W90.66 (9)C1—N1—H1A126.3
O4W—Cu2—O3W89.28 (10)C7—N1—H1A126.3
O2W—Cu2—O3W89.14 (9)C1—N2—C2104.4 (2)
N2—Cu2—O3W89.94 (9)C1—N2—Cu2122.93 (19)
O1W—Cu2—O3W175.03 (9)C2—N2—Cu2132.25 (19)
O5W—Cu2—O3W87.67 (9)Cu2—O1W—H1D118 (3)
N2—C1—N1113.8 (2)Cu2—O1W—H1C113 (3)
N2—C1—H1B123.1H1D—O1W—H1C106 (4)
N1—C1—H1B123.1Cu2—O2W—H2B117 (3)
C3—C2—N2130.6 (3)Cu2—O2W—H2A123 (3)
C3—C2—C7120.0 (3)H2B—O2W—H2A105 (4)
N2—C2—C7109.4 (2)Cu2—O3W—H3B118 (3)
C4—C3—C2118.3 (3)Cu2—O3W—H3C115 (3)
C4—C3—H3A120.8H3B—O3W—H3C109 (4)
C2—C3—H3A120.8Cu2—O4W—H4B123 (3)
C3—C4—C5120.9 (3)Cu2—O4W—H4A120 (3)
C3—C4—C8117.1 (2)H4B—O4W—H4A116 (5)
C5—C4—C8121.9 (2)Cu2—O5W—H5B107 (3)
C6—C5—C4120.5 (3)Cu2—O5W—H5A122 (3)
C6—C5—C9118.4 (3)H5B—O5W—H5A109 (4)
C4—C5—C9121.0 (3)H6B—O6W—H6C100 (5)
C7—C6—C5117.9 (3)H7A—O7W—H7B107 (4)
C7—C6—H6A121.0H8B—O8W—H8A104 (5)
C5—C6—H6A121.0H9B—O9W—H9A108 (4)
C6—C7—N1132.7 (3)H10B—O10W—H10A107 (4)
N2—C2—C3—C4−179.4 (3)C4—C5—C9—O4−148.5 (3)
C7—C2—C3—C40.6 (4)C6—C5—C9—O3−141.7 (3)
C2—C3—C4—C50.7 (4)C4—C5—C9—O333.8 (4)
C2—C3—C4—C8176.6 (3)N2—C1—N1—C7−0.4 (4)
C3—C4—C5—C6−1.1 (4)C6—C7—N1—C1−178.6 (3)
C8—C4—C5—C6−176.7 (3)C2—C7—N1—C11.0 (3)
C3—C4—C5—C9−176.4 (3)N1—C1—N2—C2−0.5 (3)
C8—C4—C5—C97.9 (4)N1—C1—N2—Cu2172.7 (2)
C4—C5—C6—C70.1 (4)C3—C2—N2—C1−178.9 (3)
C9—C5—C6—C7175.5 (3)C7—C2—N2—C11.1 (3)
C5—C6—C7—N1−179.2 (3)C3—C2—N2—Cu28.8 (5)
C5—C6—C7—C21.3 (5)C7—C2—N2—Cu2−171.1 (2)
C3—C2—C7—C6−1.6 (5)O2W—Cu2—N2—C147.3 (2)
N2—C2—C7—C6178.3 (3)O1W—Cu2—N2—C1139.6 (2)
C3—C2—C7—N1178.7 (3)O5W—Cu2—N2—C1−129.5 (2)
N2—C2—C7—N1−1.3 (3)O3W—Cu2—N2—C1−41.8 (2)
C3—C4—C8—O267.2 (4)O2W—Cu2—N2—C2−141.6 (3)
C5—C4—C8—O2−116.9 (3)O1W—Cu2—N2—C2−49.4 (3)
C3—C4—C8—O1−109.2 (3)O5W—Cu2—N2—C241.6 (3)
C5—C4—C8—O166.7 (4)O3W—Cu2—N2—C2129.2 (3)
C6—C5—C9—O436.1 (4)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
O10W—H10A···O1Wi0.80 (3)2.09 (3)2.855 (3)160 (4)
O10W—H10B···O3ii0.81 (3)2.05 (3)2.802 (3)155 (4)
O9W—H9B···O4iii0.81 (3)1.94 (3)2.739 (3)174 (4)
O7W—H7B···O6W0.83 (3)1.95 (3)2.758 (4)166 (4)
O7W—H7A···O30.81 (3)1.94 (3)2.735 (3)165 (4)
O6W—H6C···O20.79 (3)2.03 (3)2.773 (3)156 (5)
O6W—H6B···O1iv0.84 (3)1.96 (3)2.772 (4)162 (5)
O5W—H5A···O2v0.78 (2)1.84 (3)2.611 (3)170 (4)
O5W—H5B···O10W0.80 (2)2.01 (3)2.793 (3)169 (4)
O4W—H4A···O10Wvi0.81 (3)1.96 (3)2.760 (3)168 (5)
O4W—H4B···O7Wii0.79 (3)1.97 (3)2.723 (4)160 (5)
O3W—H3C···O9Wi0.78 (2)2.05 (3)2.820 (3)172 (4)
O3W—H3B···O3ii0.81 (2)2.00 (3)2.800 (3)170 (4)
O2W—H2A···O4vii0.82 (3)1.93 (3)2.709 (3)160 (4)
O2W—H2B···O9W0.80 (3)1.94 (3)2.735 (3)172 (4)
O1W—H1D···O1v0.78 (2)1.85 (3)2.621 (3)170 (4)
N1—H1A···O7Wiii0.861.972.805 (3)163

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: KJ2082).

References

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