supplementary materials


HTML versionpdf versioncif file3d viewstructure factorssupplementary materialsCIF check reportsimilar papers buy article online

hk2356 scheme

Acta Cryst. (2007). E63, m2962-m2963    [ doi:10.1107/S1600536807055225 ]

Aqua(5-nitro-1H-benzimidazole)(oxydiacetato)copper(II)

W.-J. Zhang, Y.-T. Li and Z.-Y. Wu

Abstract top

In the molecule of the title compound, [Cu(C4H4O5)(C7H5N3O2)(H2O)], the CuII atom is coordinated by one tridentate oxydiacetate (ODA) dianion, one monodentate nitrobenzimidazole (NBZIM) molecule and one H2O molecule, in a distorted square-based pyramidal geometry. In the crystal structure, O-H...O, N-H...O and C-H...O hydrogen bonds link the molecules, forming a three-dimensional network. [pi]-[pi] Stacking interactions between parallel NBZIM rings consolidate the supramolecular structure [the shortest interplanar distances are 3.360 (3) and 3.269 (3) Å].

Comment top

Benzimidazole transition metal complexes are of great interest of relevance to metalloproteins such as haemoglobin, haemocyanin and blue-copper proteins (Vigato et al., 1990; Bouwman et al., 1990). They are also used as mimics of the self-assembling process (Ruttimann et al., 1992). These potential and versatile applications are stimulating researchers to synthesize new complexes containing benzimidazoles with potential chemical and biological properties. We report herein the crystal structure of the title compound, (I), a CuII complex with oxydiacetate (ODA) and nitrobenzimidazole (NBZIM).

In the molecule of (I) (Fig. 1), the CuII atom is coordinated by one (ODA) dianion, one NBZIM molecule and one H2O molecule, in a distorted square base pyramidal coordination geometry (Table 1). The O1, O3 and O4 donor atoms from the tridentate ODA ligand and N1 atom of NBZIM define the square base, whereas the apical position is occupied by O8 oxygen atom of water. N1, O1, O3 and O4 are similarly displaced from the mean plane of such base [deviations from 0.0600 (9) to 0.0796 (12) Å]. The CuII atom displaces 0.1334 (11) Å from the plane towards O8 oxygen atom.

Different from another similar complex [Cu(BZIM)(ODA)(H2O)]n (BZIM = benzimidazole) (Cao et al., 2004), the ODA ion in (I) behaves as a tridentate ligand and the chelating CuII atom is in a meridional coordination mode. It forms two five-membered chelating rings; A (Cu1/O1/O3/C1/C2) and B (Cu1/O3/O4/C3/C4) around the CuII atom. Ring A is nearly planar, [the maximum deviation being 0.008 (2) Å (for atom C2)], whereas ring B has an envelope conformation with atom Cu1 displaced by 0.266(%) Å from the plane of the other ring atoms. The NBZIM molecule coordinates to the CuII atom in a monodentate fashion. The nitro group is co-planar with the benzimidazole ring [the maximum atomic deviation is 0.514 (4) Å (for atom O7)].

In the crystal structure, O—H···O, N—H···O and C—H···O hydrogen bonds (Table 2, Fig. 2) link the molecules to form a three-dimensional network. A supramolecular structure is consolidated by two types of strong π-π stacking interactions between neighboring parallel NBZIM ring systems [symmetry codes: 1 − x, 1 − y, −z and −x, 1 − y, −z.]. The shortest interplanar distances are 3.360 (3) Å and 3.269 (3) Å, respectively.

Related literature top

For general background, see: Vigato et al. (1990); Bouwman et al. (1990); Ruttimann et al. (1992). For related structures, see: Cao et al. (2004).

Experimental top

For the preparation of the title compound, oxydiacetic acid (27 mg, 0.2 mmol) and sodium carbonate (21 mg, 0.2 mmol) were dissolved in water (5 ml). A methanol solution containing copper dichloride dihydrate (34 mg, 0.2 mmol) was then slowly added with continuous stirring. After 30 min, 5 ml me thanol solution of nitrobenzimidazole (33 mg, 0.2 mmol) was added dropwise to the reaction solution. The mixture was refluxed for 5 h and then slowly filtered. Blue single crystals of the title compound were obtained from the filtrate after 7 d. Analysis calculated for C11H11CuN3O8: C 35.07, H 2.94, N 11.15%; found: C 35.10, H 3.00, N 11.21%.

Refinement top

H atoms (for H2O) were located in difference syntheses and constrained to ride on their parent atom [O—H = 0.7950, 0.7851 Å and Uiso(H) = 1.95Ueq(O)]. The remaining H atoms were positioned geometrically, with N—H = 0.86 Å (for NH) and C—H = 0.93 and 0.97 Å, for aromatic and methylene H atoms and constrained to ride on their parent atoms, with Uiso(H) = 1.2Ueq(C,N).

Computing details top

Data collection: SMART (Bruker, 2002); cell refinement: SAINT (Bruker, 2002); data reduction: SAINT (Bruker, 2002); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997) and CAMERON (Watkin et al., 1993); software used to prepare material for publication: WinGX (Farrugia, 1999).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title molecule, with the atom-numbering scheme. Displacement ellipsoids are drawn at the 50% probability level
[Figure 2] Fig. 2. A packing diagram of (I). Hydrogen bonds are shown as dashed lines. H atoms not involved in hydrogen bonding were omitted for clarity [symmetry codes: (i) −x, 1 − y, 1 − z; (ii) 1 + x, y, z; (iii) 1 − x, 2 − y, −z; (iv) 1 − x, 1 − y, −z].
Aqua(6-nitro-1H-benzimidazole)(oxydiacetato)copper(II) top
Crystal data top
[Cu(C4H4O5)(C7H5N3O2)(H2O)]Z = 2
Mr = 376.77F000 = 382
Triclinic, P1Dx = 1.804 Mg m−3
Hall symbol: -P 1Mo Kα radiation
λ = 0.71073 Å
a = 6.961 (3) ÅCell parameters from 1984 reflections
b = 9.190 (4) Åθ = 2.4–27.9º
c = 11.691 (5) ŵ = 1.62 mm−1
α = 68.694 (5)ºT = 298 (2) K
β = 87.316 (5)ºBlock, green
γ = 84.623 (5)º0.48 × 0.31 × 0.27 mm
V = 693.6 (5) Å3
Data collection top
Bruker CCD area-detector
diffractometer		2470 independent reflections
Radiation source: fine-focus sealed tube2007 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.015
T = 298(2) Kθmax = 25.2º
φ and ω scansθmin = 1.9º
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)		h = −8→8
Tmin = 0.510, Tmax = 0.668k = −5→11
3708 measured reflectionsl = −13→14
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.031H-atom parameters constrained
wR(F2) = 0.082  w = 1/[σ2(Fo2) + (0.0392P)2 + 0.3047P]
where P = (Fo2 + 2Fc2)/3
S = 1.06(Δ/σ)max = 0.001
2470 reflectionsΔρmax = 0.52 e Å−3
208 parametersΔρmin = −0.35 e Å−3
Primary atom site location: structure-invariant direct methodsExtinction correction: none
Crystal data top
[Cu(C4H4O5)(C7H5N3O2)(H2O)]γ = 84.623 (5)º
Mr = 376.77V = 693.6 (5) Å3
Triclinic, P1Z = 2
a = 6.961 (3) ÅMo Kα
b = 9.190 (4) ŵ = 1.62 mm−1
c = 11.691 (5) ÅT = 298 (2) K
α = 68.694 (5)º0.48 × 0.31 × 0.27 mm
β = 87.316 (5)º
Data collection top
Bruker CCD area-detector
diffractometer		2470 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)		2007 reflections with I > 2σ(I)
Tmin = 0.510, Tmax = 0.668Rint = 0.015
3708 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.031208 parameters
wR(F2) = 0.082H-atom parameters constrained
S = 1.06Δρmax = 0.52 e Å−3
2470 reflectionsΔρmin = −0.35 e Å−3
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 > 2sigma(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
Cu10.24432 (5)0.75145 (4)0.25300 (3)0.03187 (13)
O10.4483 (3)0.8870 (2)0.24224 (16)0.0340 (5)
O20.5871 (3)1.0114 (3)0.34360 (18)0.0491 (6)
O30.2009 (3)0.7724 (3)0.41289 (19)0.0483 (6)
O4−0.0046 (3)0.6608 (3)0.29471 (18)0.0417 (5)
O5−0.2437 (3)0.6150 (3)0.43260 (18)0.0455 (5)
O60.1047 (4)0.1687 (3)0.2491 (2)0.0640 (7)
O70.1297 (4)0.1101 (3)0.0858 (3)0.0603 (7)
O80.4380 (3)0.5216 (2)0.34517 (17)0.0410 (5)
H1W0.38240.47300.40610.080*
H2W0.53090.55110.36240.080*
N10.2740 (3)0.7418 (3)0.08959 (19)0.0281 (5)
N20.3290 (3)0.8066 (3)−0.1096 (2)0.0337 (5)
N30.1424 (4)0.2014 (3)0.1398 (3)0.0449 (7)
C10.4652 (4)0.9264 (3)0.3348 (2)0.0333 (6)
C20.3239 (4)0.8678 (3)0.4418 (2)0.0360 (7)
H2A0.39320.80770.51660.043*
H2B0.24910.95560.45410.043*
C30.0111 (4)0.7501 (4)0.4616 (3)0.0388 (7)
H3A−0.05850.85020.45200.047*
H3B0.01500.68610.54830.047*
C4−0.0883 (4)0.6686 (3)0.3913 (2)0.0331 (6)
H20.35540.8634−0.18420.040*
C50.3159 (4)0.8532 (3)−0.0143 (2)0.0325 (6)
H50.33450.9547−0.02040.039*
C60.2930 (4)0.6519 (3)−0.0676 (2)0.0294 (6)
C70.2858 (4)0.5453 (4)−0.1271 (3)0.0367 (7)
H70.31150.5737−0.21080.044*
C80.2395 (4)0.3980 (4)−0.0573 (3)0.0381 (7)
H80.23320.3234−0.09320.046*
C90.2015 (4)0.3589 (3)0.0685 (3)0.0330 (6)
C100.2107 (4)0.4606 (3)0.1305 (2)0.0308 (6)
H100.18730.43050.21450.037*
C110.2573 (4)0.6106 (3)0.0590 (2)0.0258 (6)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cu10.0323 (2)0.0444 (2)0.0285 (2)−0.01726 (15)0.00659 (13)−0.02199 (16)
O10.0370 (11)0.0443 (12)0.0268 (10)−0.0188 (9)0.0052 (8)−0.0170 (9)
O20.0606 (14)0.0634 (15)0.0330 (11)−0.0393 (12)0.0052 (10)−0.0213 (10)
O30.0463 (13)0.0768 (16)0.0457 (12)−0.0397 (12)0.0233 (10)−0.0450 (12)
O40.0381 (11)0.0596 (14)0.0377 (11)−0.0229 (10)0.0080 (9)−0.0265 (10)
O50.0327 (11)0.0621 (14)0.0394 (12)−0.0206 (10)0.0063 (9)−0.0123 (11)
O60.0870 (19)0.0435 (14)0.0569 (16)−0.0176 (13)−0.0015 (14)−0.0094 (12)
O70.0625 (16)0.0414 (13)0.0909 (19)−0.0059 (12)−0.0105 (14)−0.0387 (13)
O80.0429 (12)0.0513 (13)0.0311 (10)−0.0126 (10)0.0020 (9)−0.0158 (10)
N10.0294 (12)0.0343 (13)0.0265 (12)−0.0094 (10)0.0021 (9)−0.0165 (10)
N20.0324 (13)0.0458 (15)0.0251 (12)−0.0138 (11)0.0050 (10)−0.0136 (11)
N30.0357 (15)0.0383 (15)0.0616 (19)0.0005 (12)−0.0113 (13)−0.0186 (14)
C10.0404 (16)0.0359 (16)0.0271 (14)−0.0137 (13)0.0002 (12)−0.0132 (12)
C20.0459 (17)0.0421 (17)0.0285 (14)−0.0191 (14)0.0028 (12)−0.0195 (13)
C30.0329 (16)0.0543 (19)0.0356 (16)−0.0120 (14)0.0113 (12)−0.0232 (14)
C40.0283 (15)0.0394 (17)0.0304 (15)−0.0086 (13)0.0003 (12)−0.0097 (13)
C50.0321 (15)0.0350 (16)0.0352 (16)−0.0119 (12)0.0016 (12)−0.0163 (13)
C60.0191 (13)0.0436 (17)0.0314 (14)−0.0059 (12)0.0020 (10)−0.0200 (13)
C70.0294 (15)0.056 (2)0.0343 (15)−0.0065 (14)0.0026 (12)−0.0275 (15)
C80.0271 (15)0.0507 (19)0.0514 (18)0.0000 (13)−0.0055 (13)−0.0364 (16)
C90.0219 (14)0.0319 (15)0.0496 (17)−0.0035 (11)−0.0052 (12)−0.0193 (13)
C100.0266 (14)0.0375 (16)0.0305 (14)−0.0045 (12)−0.0017 (11)−0.0142 (12)
C110.0204 (13)0.0341 (15)0.0281 (13)−0.0054 (11)−0.0023 (10)−0.0162 (12)
Geometric parameters (Å, °) top
Cu1—O11.9450 (19)N2—C51.328 (3)
Cu1—N11.945 (2)N2—C61.369 (4)
Cu1—O31.955 (2)N2—H20.8600
Cu1—O41.957 (2)C5—H50.9300
Cu1—O82.321 (2)C6—C71.397 (4)
O1—C11.274 (3)C6—C111.405 (4)
O2—C11.237 (3)C7—C81.363 (4)
C1—C21.522 (4)C7—H70.9300
C2—O31.414 (3)C8—C91.400 (4)
C2—H2A0.9700C8—H80.9300
C2—H2B0.9700C9—C101.383 (4)
O3—C31.417 (3)C9—N31.470 (4)
C3—C41.520 (4)C10—C111.388 (4)
C3—H3A0.9700C10—H100.9300
C3—H3B0.9700N3—O61.223 (4)
C4—O51.234 (3)N3—O71.231 (3)
C4—O41.269 (3)O8—H2W0.7851
N1—C51.314 (3)O8—H1W0.7950
N1—C111.392 (3)
O1—Cu1—N198.39 (8)C5—N1—C11105.1 (2)
O1—Cu1—O382.00 (8)C5—N1—Cu1128.69 (19)
N1—Cu1—O3176.16 (9)C11—N1—Cu1126.17 (17)
O1—Cu1—O4159.71 (9)C5—N2—C6107.7 (2)
N1—Cu1—O497.48 (8)C5—N2—H2126.2
O3—Cu1—O481.33 (8)C6—N2—H2126.2
O1—Cu1—O894.16 (9)N1—C5—N2113.4 (2)
N1—Cu1—O894.12 (8)N1—C5—H5123.3
O3—Cu1—O889.66 (9)N2—C5—H5123.3
O4—Cu1—O897.21 (9)N2—C6—C7132.3 (3)
C1—O1—Cu1116.08 (17)N2—C6—C11105.5 (2)
O2—C1—O1124.6 (3)C7—C6—C11122.2 (3)
O2—C1—C2117.2 (2)C8—C7—C6117.2 (3)
O1—C1—C2118.1 (2)C8—C7—H7121.4
O3—C2—C1107.5 (2)C6—C7—H7121.4
O3—C2—H2A110.2C7—C8—C9120.0 (3)
C1—C2—H2A110.2C7—C8—H8120.0
O3—C2—H2B110.2C9—C8—H8120.0
C1—C2—H2B110.2C10—C9—C8124.2 (3)
H2A—C2—H2B108.5C10—C9—N3117.2 (3)
C2—O3—C3122.8 (2)C8—C9—N3118.6 (3)
C2—O3—Cu1116.24 (16)C9—C10—C11115.6 (2)
C3—O3—Cu1115.29 (17)C9—C10—H10122.2
O3—C3—C4107.4 (2)C11—C10—H10122.2
O3—C3—H3A110.2C10—C11—N1131.0 (2)
C4—C3—H3A110.2C10—C11—C6120.7 (2)
O3—C3—H3B110.2N1—C11—C6108.3 (2)
C4—C3—H3B110.2O6—N3—O7123.3 (3)
H3A—C3—H3B108.5O6—N3—C9118.5 (3)
O5—C4—O4125.1 (3)O7—N3—C9118.2 (3)
O5—C4—C3117.6 (2)Cu1—O8—H2W103.3
O4—C4—C3117.3 (2)Cu1—O8—H1W106.2
C4—O4—Cu1116.29 (18)H2W—O8—H1W109.6
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
O8—H1W···O5i0.792.002.788 (3)170
O8—H2W···O5ii0.792.032.810 (3)172
N2—H2···O2iii0.861.852.708 (3)179
C7—H7···O8iv0.932.593.322 (3)135
Symmetry codes: (i) −x, −y+1, −z+1; (ii) x+1, y, z; (iii) −x+1, −y+2, −z; (iv) −x+1, −y+1, −z.
Selected geometric parameters (Å, °) top
Cu1—O11.9450 (19)Cu1—O41.957 (2)
Cu1—N11.945 (2)Cu1—O82.321 (2)
Cu1—O31.955 (2)
O1—Cu1—N198.39 (8)O3—Cu1—O481.33 (8)
O1—Cu1—O382.00 (8)O1—Cu1—O894.16 (9)
N1—Cu1—O3176.16 (9)N1—Cu1—O894.12 (8)
O1—Cu1—O4159.71 (9)O3—Cu1—O889.66 (9)
N1—Cu1—O497.48 (8)O4—Cu1—O897.21 (9)
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
O8—H1W···O5i0.792.002.788 (3)170
O8—H2W···O5ii0.792.032.810 (3)172
N2—H2···O2iii0.861.852.708 (3)179
C7—H7···O8iv0.932.593.322 (3)135
Symmetry codes: (i) −x, −y+1, −z+1; (ii) x+1, y, z; (iii) −x+1, −y+2, −z; (iv) −x+1, −y+1, −z.
Acknowledgements top

This project was supported by the National Natural Science Foundation of China (grant No. 30672515) and the Natural Science Foundation of Qingdao City (grant No.06–2–2–11-jch).

references
References top

Bouwman, E., Driessed, W. L. & Reedijk, J. (1990). Coord. Chem. Rev. 104, 143–172.

Bruker (2002). SAINT and SMART. Bruker AXS Inc., Madison, Wisconsin, USA.

Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565–?.

Farrugia, L. J. (1999). J. Appl. Cryst. 32, 837–838.

Cao, L., Li, N. & Xu, D.-J. (2004). Acta Cryst. E60, m1066–m1067.

Ruttimann, S., Pigust, C., Bernardinelli, G. & Bocquet, B. (1992). J. Am. Chem. Soc. 114, 4230–4237.

Sheldrick, G. M. (1997). SHELXS97 and SHELXL97. University of Göttingen, Germany.

Sheldrick, G. M. (2003). SADABS. Version 2.10. University of Göttingen, Germany.

Vigato, P. A., Tamburini, S. & Fenton, D. E. (1990). Coord. Chem. Rev. 106, 25–170.

Watkin, D. M., Pearce, L. & Prout, C. K. (1993). CAMERON. Chemical Crystallography Laboratory, University of Oxford, England.