Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807055225/hk2356sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536807055225/hk2356Isup2.hkl |
CCDC reference: 672626
Key indicators
- Single-crystal X-ray study
- T = 298 K
- Mean (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
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%.
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).
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).
[Cu(C4H4O5)(C7H5N3O2)(H2O)] | Z = 2 |
Mr = 376.77 | F(000) = 382 |
Triclinic, P1 | Dx = 1.804 Mg m−3 |
Hall symbol: -P 1 | Mo Kα radiation, λ = 0.71073 Å |
a = 6.961 (3) Å | Cell parameters from 1984 reflections |
b = 9.190 (4) Å | θ = 2.4–27.9° |
c = 11.691 (5) Å | µ = 1.62 mm−1 |
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 |
Bruker CCD area-detector diffractometer | 2470 independent reflections |
Radiation source: fine-focus sealed tube | 2007 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.015 |
ϕ and ω scans | θmax = 25.2°, θmin = 1.9° |
Absorption correction: multi-scan (SADABS; Sheldrick, 2003) | h = −8→8 |
Tmin = 0.510, Tmax = 0.668 | k = −5→11 |
3708 measured reflections | l = −13→14 |
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)] = 0.031 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.082 | H-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 parameters | Δρmax = 0.52 e Å−3 |
0 restraints | Δρmin = −0.35 e Å−3 |
[Cu(C4H4O5)(C7H5N3O2)(H2O)] | γ = 84.623 (5)° |
Mr = 376.77 | V = 693.6 (5) Å3 |
Triclinic, P1 | Z = 2 |
a = 6.961 (3) Å | Mo Kα radiation |
b = 9.190 (4) Å | µ = 1.62 mm−1 |
c = 11.691 (5) Å | T = 298 K |
α = 68.694 (5)° | 0.48 × 0.31 × 0.27 mm |
β = 87.316 (5)° |
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 = 0.668 | Rint = 0.015 |
3708 measured reflections |
R[F2 > 2σ(F2)] = 0.031 | 0 restraints |
wR(F2) = 0.082 | H-atom parameters constrained |
S = 1.06 | Δρmax = 0.52 e Å−3 |
2470 reflections | Δρmin = −0.35 e Å−3 |
208 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 | ||
Cu1 | 0.24432 (5) | 0.75145 (4) | 0.25300 (3) | 0.03187 (13) | |
O1 | 0.4483 (3) | 0.8870 (2) | 0.24224 (16) | 0.0340 (5) | |
O2 | 0.5871 (3) | 1.0114 (3) | 0.34360 (18) | 0.0491 (6) | |
O3 | 0.2009 (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) | |
O6 | 0.1047 (4) | 0.1687 (3) | 0.2491 (2) | 0.0640 (7) | |
O7 | 0.1297 (4) | 0.1101 (3) | 0.0858 (3) | 0.0603 (7) | |
O8 | 0.4380 (3) | 0.5216 (2) | 0.34517 (17) | 0.0410 (5) | |
H1W | 0.3824 | 0.4730 | 0.4061 | 0.080* | |
H2W | 0.5309 | 0.5511 | 0.3624 | 0.080* | |
N1 | 0.2740 (3) | 0.7418 (3) | 0.08959 (19) | 0.0281 (5) | |
N2 | 0.3290 (3) | 0.8066 (3) | −0.1096 (2) | 0.0337 (5) | |
N3 | 0.1424 (4) | 0.2014 (3) | 0.1398 (3) | 0.0449 (7) | |
C1 | 0.4652 (4) | 0.9264 (3) | 0.3348 (2) | 0.0333 (6) | |
C2 | 0.3239 (4) | 0.8678 (3) | 0.4418 (2) | 0.0360 (7) | |
H2A | 0.3932 | 0.8077 | 0.5166 | 0.043* | |
H2B | 0.2491 | 0.9556 | 0.4541 | 0.043* | |
C3 | 0.0111 (4) | 0.7501 (4) | 0.4616 (3) | 0.0388 (7) | |
H3A | −0.0585 | 0.8502 | 0.4520 | 0.047* | |
H3B | 0.0150 | 0.6861 | 0.5483 | 0.047* | |
C4 | −0.0883 (4) | 0.6686 (3) | 0.3913 (2) | 0.0331 (6) | |
H2 | 0.3554 | 0.8634 | −0.1842 | 0.040* | |
C5 | 0.3159 (4) | 0.8532 (3) | −0.0143 (2) | 0.0325 (6) | |
H5 | 0.3345 | 0.9547 | −0.0204 | 0.039* | |
C6 | 0.2930 (4) | 0.6519 (3) | −0.0676 (2) | 0.0294 (6) | |
C7 | 0.2858 (4) | 0.5453 (4) | −0.1271 (3) | 0.0367 (7) | |
H7 | 0.3115 | 0.5737 | −0.2108 | 0.044* | |
C8 | 0.2395 (4) | 0.3980 (4) | −0.0573 (3) | 0.0381 (7) | |
H8 | 0.2332 | 0.3234 | −0.0932 | 0.046* | |
C9 | 0.2015 (4) | 0.3589 (3) | 0.0685 (3) | 0.0330 (6) | |
C10 | 0.2107 (4) | 0.4606 (3) | 0.1305 (2) | 0.0308 (6) | |
H10 | 0.1873 | 0.4305 | 0.2145 | 0.037* | |
C11 | 0.2573 (4) | 0.6106 (3) | 0.0590 (2) | 0.0258 (6) |
U11 | U22 | U33 | U12 | U13 | U23 | |
Cu1 | 0.0323 (2) | 0.0444 (2) | 0.0285 (2) | −0.01726 (15) | 0.00659 (13) | −0.02199 (16) |
O1 | 0.0370 (11) | 0.0443 (12) | 0.0268 (10) | −0.0188 (9) | 0.0052 (8) | −0.0170 (9) |
O2 | 0.0606 (14) | 0.0634 (15) | 0.0330 (11) | −0.0393 (12) | 0.0052 (10) | −0.0213 (10) |
O3 | 0.0463 (13) | 0.0768 (16) | 0.0457 (12) | −0.0397 (12) | 0.0233 (10) | −0.0450 (12) |
O4 | 0.0381 (11) | 0.0596 (14) | 0.0377 (11) | −0.0229 (10) | 0.0080 (9) | −0.0265 (10) |
O5 | 0.0327 (11) | 0.0621 (14) | 0.0394 (12) | −0.0206 (10) | 0.0063 (9) | −0.0123 (11) |
O6 | 0.0870 (19) | 0.0435 (14) | 0.0569 (16) | −0.0176 (13) | −0.0015 (14) | −0.0094 (12) |
O7 | 0.0625 (16) | 0.0414 (13) | 0.0909 (19) | −0.0059 (12) | −0.0105 (14) | −0.0387 (13) |
O8 | 0.0429 (12) | 0.0513 (13) | 0.0311 (10) | −0.0126 (10) | 0.0020 (9) | −0.0158 (10) |
N1 | 0.0294 (12) | 0.0343 (13) | 0.0265 (12) | −0.0094 (10) | 0.0021 (9) | −0.0165 (10) |
N2 | 0.0324 (13) | 0.0458 (15) | 0.0251 (12) | −0.0138 (11) | 0.0050 (10) | −0.0136 (11) |
N3 | 0.0357 (15) | 0.0383 (15) | 0.0616 (19) | 0.0005 (12) | −0.0113 (13) | −0.0186 (14) |
C1 | 0.0404 (16) | 0.0359 (16) | 0.0271 (14) | −0.0137 (13) | 0.0002 (12) | −0.0132 (12) |
C2 | 0.0459 (17) | 0.0421 (17) | 0.0285 (14) | −0.0191 (14) | 0.0028 (12) | −0.0195 (13) |
C3 | 0.0329 (16) | 0.0543 (19) | 0.0356 (16) | −0.0120 (14) | 0.0113 (12) | −0.0232 (14) |
C4 | 0.0283 (15) | 0.0394 (17) | 0.0304 (15) | −0.0086 (13) | 0.0003 (12) | −0.0097 (13) |
C5 | 0.0321 (15) | 0.0350 (16) | 0.0352 (16) | −0.0119 (12) | 0.0016 (12) | −0.0163 (13) |
C6 | 0.0191 (13) | 0.0436 (17) | 0.0314 (14) | −0.0059 (12) | 0.0020 (10) | −0.0200 (13) |
C7 | 0.0294 (15) | 0.056 (2) | 0.0343 (15) | −0.0065 (14) | 0.0026 (12) | −0.0275 (15) |
C8 | 0.0271 (15) | 0.0507 (19) | 0.0514 (18) | 0.0000 (13) | −0.0055 (13) | −0.0364 (16) |
C9 | 0.0219 (14) | 0.0319 (15) | 0.0496 (17) | −0.0035 (11) | −0.0052 (12) | −0.0193 (13) |
C10 | 0.0266 (14) | 0.0375 (16) | 0.0305 (14) | −0.0045 (12) | −0.0017 (11) | −0.0142 (12) |
C11 | 0.0204 (13) | 0.0341 (15) | 0.0281 (13) | −0.0054 (11) | −0.0023 (10) | −0.0162 (12) |
Cu1—O1 | 1.9450 (19) | N2—C5 | 1.328 (3) |
Cu1—N1 | 1.945 (2) | N2—C6 | 1.369 (4) |
Cu1—O3 | 1.955 (2) | N2—H2 | 0.8600 |
Cu1—O4 | 1.957 (2) | C5—H5 | 0.9300 |
Cu1—O8 | 2.321 (2) | C6—C7 | 1.397 (4) |
O1—C1 | 1.274 (3) | C6—C11 | 1.405 (4) |
O2—C1 | 1.237 (3) | C7—C8 | 1.363 (4) |
C1—C2 | 1.522 (4) | C7—H7 | 0.9300 |
C2—O3 | 1.414 (3) | C8—C9 | 1.400 (4) |
C2—H2A | 0.9700 | C8—H8 | 0.9300 |
C2—H2B | 0.9700 | C9—C10 | 1.383 (4) |
O3—C3 | 1.417 (3) | C9—N3 | 1.470 (4) |
C3—C4 | 1.520 (4) | C10—C11 | 1.388 (4) |
C3—H3A | 0.9700 | C10—H10 | 0.9300 |
C3—H3B | 0.9700 | N3—O6 | 1.223 (4) |
C4—O5 | 1.234 (3) | N3—O7 | 1.231 (3) |
C4—O4 | 1.269 (3) | O8—H2W | 0.7851 |
N1—C5 | 1.314 (3) | O8—H1W | 0.7950 |
N1—C11 | 1.392 (3) | ||
O1—Cu1—N1 | 98.39 (8) | C5—N1—C11 | 105.1 (2) |
O1—Cu1—O3 | 82.00 (8) | C5—N1—Cu1 | 128.69 (19) |
N1—Cu1—O3 | 176.16 (9) | C11—N1—Cu1 | 126.17 (17) |
O1—Cu1—O4 | 159.71 (9) | C5—N2—C6 | 107.7 (2) |
N1—Cu1—O4 | 97.48 (8) | C5—N2—H2 | 126.2 |
O3—Cu1—O4 | 81.33 (8) | C6—N2—H2 | 126.2 |
O1—Cu1—O8 | 94.16 (9) | N1—C5—N2 | 113.4 (2) |
N1—Cu1—O8 | 94.12 (8) | N1—C5—H5 | 123.3 |
O3—Cu1—O8 | 89.66 (9) | N2—C5—H5 | 123.3 |
O4—Cu1—O8 | 97.21 (9) | N2—C6—C7 | 132.3 (3) |
C1—O1—Cu1 | 116.08 (17) | N2—C6—C11 | 105.5 (2) |
O2—C1—O1 | 124.6 (3) | C7—C6—C11 | 122.2 (3) |
O2—C1—C2 | 117.2 (2) | C8—C7—C6 | 117.2 (3) |
O1—C1—C2 | 118.1 (2) | C8—C7—H7 | 121.4 |
O3—C2—C1 | 107.5 (2) | C6—C7—H7 | 121.4 |
O3—C2—H2A | 110.2 | C7—C8—C9 | 120.0 (3) |
C1—C2—H2A | 110.2 | C7—C8—H8 | 120.0 |
O3—C2—H2B | 110.2 | C9—C8—H8 | 120.0 |
C1—C2—H2B | 110.2 | C10—C9—C8 | 124.2 (3) |
H2A—C2—H2B | 108.5 | C10—C9—N3 | 117.2 (3) |
C2—O3—C3 | 122.8 (2) | C8—C9—N3 | 118.6 (3) |
C2—O3—Cu1 | 116.24 (16) | C9—C10—C11 | 115.6 (2) |
C3—O3—Cu1 | 115.29 (17) | C9—C10—H10 | 122.2 |
O3—C3—C4 | 107.4 (2) | C11—C10—H10 | 122.2 |
O3—C3—H3A | 110.2 | C10—C11—N1 | 131.0 (2) |
C4—C3—H3A | 110.2 | C10—C11—C6 | 120.7 (2) |
O3—C3—H3B | 110.2 | N1—C11—C6 | 108.3 (2) |
C4—C3—H3B | 110.2 | O6—N3—O7 | 123.3 (3) |
H3A—C3—H3B | 108.5 | O6—N3—C9 | 118.5 (3) |
O5—C4—O4 | 125.1 (3) | O7—N3—C9 | 118.2 (3) |
O5—C4—C3 | 117.6 (2) | Cu1—O8—H2W | 103.3 |
O4—C4—C3 | 117.3 (2) | Cu1—O8—H1W | 106.2 |
C4—O4—Cu1 | 116.29 (18) | H2W—O8—H1W | 109.6 |
D—H···A | D—H | H···A | D···A | D—H···A |
O8—H1W···O5i | 0.79 | 2.00 | 2.788 (3) | 170 |
O8—H2W···O5ii | 0.79 | 2.03 | 2.810 (3) | 172 |
N2—H2···O2iii | 0.86 | 1.85 | 2.708 (3) | 179 |
C7—H7···O8iv | 0.93 | 2.59 | 3.322 (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)] |
Mr | 376.77 |
Crystal system, space group | Triclinic, 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) |
V (Å3) | 693.6 (5) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 1.62 |
Crystal size (mm) | 0.48 × 0.31 × 0.27 |
Data collection | |
Diffractometer | Bruker CCD area-detector diffractometer |
Absorption correction | Multi-scan (SADABS; Sheldrick, 2003) |
Tmin, Tmax | 0.510, 0.668 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 3708, 2470, 2007 |
Rint | 0.015 |
(sin θ/λ)max (Å−1) | 0.600 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.031, 0.082, 1.06 |
No. of reflections | 2470 |
No. of parameters | 208 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 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).
Cu1—O1 | 1.9450 (19) | Cu1—O4 | 1.957 (2) |
Cu1—N1 | 1.945 (2) | Cu1—O8 | 2.321 (2) |
Cu1—O3 | 1.955 (2) | ||
O1—Cu1—N1 | 98.39 (8) | O3—Cu1—O4 | 81.33 (8) |
O1—Cu1—O3 | 82.00 (8) | O1—Cu1—O8 | 94.16 (9) |
N1—Cu1—O3 | 176.16 (9) | N1—Cu1—O8 | 94.12 (8) |
O1—Cu1—O4 | 159.71 (9) | O3—Cu1—O8 | 89.66 (9) |
N1—Cu1—O4 | 97.48 (8) | O4—Cu1—O8 | 97.21 (9) |
D—H···A | D—H | H···A | D···A | D—H···A |
O8—H1W···O5i | 0.79 | 2.00 | 2.788 (3) | 169.7 |
O8—H2W···O5ii | 0.79 | 2.03 | 2.810 (3) | 171.6 |
N2—H2···O2iii | 0.86 | 1.85 | 2.708 (3) | 178.9 |
C7—H7···O8iv | 0.93 | 2.59 | 3.322 (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. |
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.