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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. π–π Stacking inter­actions between parallel NBZIM rings consolidate the supra­molecular structure [the shortest interplanar distances are 3.360 (3) and 3.269 (3) Å].

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807055225/hk2356sup1.cif
Contains datablocks global, I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536807055225/hk2356Isup2.hkl
Contains datablock I

CCDC reference: 672626

Key indicators

  • Single-crystal X-ray study
  • T = 298 K
  • Mean [sigma](C-C) = 0.004 Å
  • R factor = 0.031
  • wR factor = 0.082
  • Data-to-parameter ratio = 11.9

checkCIF/PLATON results

No syntax errors found



Alert level C PLAT062_ALERT_4_C Rescale T(min) & T(max) by ..................... 0.96 PLAT154_ALERT_1_C The su's on the Cell Angles are Equal (x 10000) 500 Deg.
Alert level G PLAT794_ALERT_5_G Check Predicted Bond Valency for Cu1 (2) 2.20
0 ALERT level A = In general: serious problem 0 ALERT level B = Potentially serious problem 2 ALERT level C = Check and explain 1 ALERT level G = General alerts; check 1 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 0 ALERT type 2 Indicator that the structure model may be wrong or deficient 0 ALERT type 3 Indicator that the structure quality may be low 1 ALERT type 4 Improvement, methodology, query or suggestion 1 ALERT type 5 Informative message, check

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 = 376.77F(000) = 382
Triclinic, P1Dx = 1.804 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 6.961 (3) ÅCell parameters from 1984 reflections
b = 9.190 (4) Åθ = 2.4–27.9°
c = 11.691 (5) ŵ = 1.62 mm1
α = 68.694 (5)°T = 298 K
β = 87.316 (5)°Block, green
γ = 84.623 (5)°0.48 × 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)
Graphite monochromatorRint = 0.015
ϕ and ω scansθmax = 25.2°, θmin = 1.9°
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
h = 88
Tmin = 0.510, Tmax = 0.668k = 511
3708 measured reflectionsl = 1314
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)] = 0.031Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.082H-atom parameters constrained
S = 1.06 w = 1/[σ2(Fo2) + (0.0392P)2 + 0.3047P]
where P = (Fo2 + 2Fc2)/3
2470 reflections(Δ/σ)max = 0.001
208 parametersΔρmax = 0.52 e Å3
0 restraintsΔρmin = 0.35 e Å3
Crystal data top
[Cu(C4H4O5)(C7H5N3O2)(H2O)]γ = 84.623 (5)°
Mr = 376.77V = 693.6 (5) Å3
Triclinic, P1Z = 2
a = 6.961 (3) ÅMo Kα radiation
b = 9.190 (4) ŵ = 1.62 mm1
c = 11.691 (5) ÅT = 298 K
α = 68.694 (5)°0.48 × 0.31 × 0.27 mm
β = 87.316 (5)°
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)] = 0.0310 restraints
wR(F2) = 0.082H-atom parameters constrained
S = 1.06Δρmax = 0.52 e Å3
2470 reflectionsΔρmin = 0.35 e Å3
208 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
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)
O40.0046 (3)0.6608 (3)0.29471 (18)0.0417 (5)
O50.2437 (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)
H3A0.05850.85020.45200.047*
H3B0.01500.68610.54830.047*
C40.0883 (4)0.6686 (3)0.3913 (2)0.0331 (6)
H20.35540.86340.18420.040*
C50.3159 (4)0.8532 (3)0.0143 (2)0.0325 (6)
H50.33450.95470.02040.039*
C60.2930 (4)0.6519 (3)0.0676 (2)0.0294 (6)
C70.2858 (4)0.5453 (4)0.1271 (3)0.0367 (7)
H70.31150.57370.21080.044*
C80.2395 (4)0.3980 (4)0.0573 (3)0.0381 (7)
H80.23320.32340.09320.046*
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, º) 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, º) 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.

Experimental details

Crystal data
Chemical formula[Cu(C4H4O5)(C7H5N3O2)(H2O)]
Mr376.77
Crystal system, space groupTriclinic, P1
Temperature (K)298
a, b, c (Å)6.961 (3), 9.190 (4), 11.691 (5)
α, β, γ (°)68.694 (5), 87.316 (5), 84.623 (5)
V3)693.6 (5)
Z2
Radiation typeMo Kα
µ (mm1)1.62
Crystal size (mm)0.48 × 0.31 × 0.27
Data collection
DiffractometerBruker CCD area-detector
diffractometer
Absorption correctionMulti-scan
(SADABS; Sheldrick, 2003)
Tmin, Tmax0.510, 0.668
No. of measured, independent and
observed [I > 2σ(I)] reflections
3708, 2470, 2007
Rint0.015
(sin θ/λ)max1)0.600
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.031, 0.082, 1.06
No. of reflections2470
No. of parameters208
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.52, 0.35

Computer programs: SMART (Bruker, 2002), SAINT (Bruker, 2002), SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), ORTEP-3 for Windows (Farrugia, 1997) and CAMERON (Watkin et al., 1993), WinGX (Farrugia, 1999).

Selected geometric parameters (Å, º) 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, º) top
D—H···AD—HH···AD···AD—H···A
O8—H1W···O5i0.792.002.788 (3)169.7
O8—H2W···O5ii0.792.032.810 (3)171.6
N2—H2···O2iii0.861.852.708 (3)178.9
C7—H7···O8iv0.932.593.322 (3)135.4
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.
 

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