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metal-organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 68| Part 6| June 2012| Page m767
doi:10.1107/S1600536812020910

Bis(2-amino­methyl-1H-benzimidazole-κ2N2,N3)bis­­(nitrato-κO)copper(II)

Jing Zhao,a,b Heng Zhang,c Xueliang Zhaic and Guoyi Zhua*

aChangchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China, bGraduate University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China, and cInstrumental Analysis Center, Hebei Normal University, Shijiazhuang 050024, People's Republic of China
*Correspondence e-mail: zhuguoyi@ciac.jl.cn

(Received 6 May 2012; accepted 8 May 2012; online 16 May 2012)

In the title compound, [Cu(NO3)2(C8H9N3)2], the CuII atom, lying on an inversion center, has a distorted octa­hedral coordination environment defined by four N atoms from two chelating 2-amino­methyl-1H-benzimidazole ligands and two O atoms from two monodentate nitrate anions. In the crystal, N—H⋯O hydrogen bonds link the complex mol­ecules into a three-dimensional network. An intra­molecular N—H⋯O hydrogen bond is also observed.

Related literature

For the synthesis of the 2-(2-amino­meth­yl)benzimidazole ligand, see: Pascaly et al. (2001[Pascaly, M., Duda, M., Schweppe, F., Zurlinden, K., Müller, F. K. & Krebs, B. (2001). J. Chem. Soc. Dalton Trans. pp. 828-837.]). For the structures and properties of transition metal complexes with 2-(2-amino­meth­yl)benzimidazole ligands, see: Gable et al. (1996[Gable, R. W., Hartshorn, R. M., Mcfadyen, W. D. & Nunno, L. (1996). Aust. J. Chem. 49, 625-632.]); Gómez-Segura et al. (2006[Gómez-Segura, J., Prieto, M. J., Font-Bardia, M., Solans, X. & Moreno, V. (2006). Inorg. Chem. 45, 10031-10033.]); He et al. (2003[He, Y., Kou, H.-Z., Wang, R.-J. & Li, Y.-D. (2003). Transition Met. Chem. 28, 464-467.]); Jiang et al. (2004[Jiang, Y.-B., Kou, H.-Z., Gao, F. & Wang, R.-J. (2004). Acta Cryst. C60, m261-m262.]).

[Scheme 1]

Experimental

Crystal data

  • [Cu(NO3)2(C8H9N3)2]

  • Mr = 481.93

  • Trigonal, [R \overline 3]

  • a = 24.6913 (8) Å

  • c = 7.9620 (5) Å

  • V = 4203.8 (4) Å3

  • Z = 9

  • Mo Kα radiation

  • μ = 1.23 mm−1

  • T = 184 K

  • 0.34 × 0.21 × 0.11 mm
Data collection

  • Bruker APEXII CCD diffractometer

  • Absorption correction: multi-scan (SADABS; Sheldrick, 1996[Sheldrick, G. M. (1996). SADABS. University of Göttingen, Germany.]) Tmin = 0.681, Tmax = 0.877

  • 7196 measured reflections

  • 1833 independent reflections

  • 1764 reflections with I > 2σ(I)

  • Rint = 0.015
Refinement

  • R[F2 > 2σ(F2)] = 0.023

  • wR(F2) = 0.063

  • S = 1.04

  • 1833 reflections

  • 142 parameters

  • H-atom parameters constrained

  • Δρmax = 0.52 e Å−3

  • Δρmin = −0.23 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A D⋯A D—H⋯A
N3—H3A⋯O1i 0.92 2.42 3.266 (2) 153
N3—H3A⋯O3i 0.92 2.37 3.0521 (17) 131
N3—H3B⋯O1ii 0.92 2.33 3.1036 (19) 142
N2—H2⋯O3iii 0.88 2.50 3.0276 (18) 119
N2—H2⋯O3iv 0.88 2.40 3.0823 (18) 134
N2—H2⋯O2iii 0.88 2.20 2.8901 (17) 135
Symmetry codes: (i) [-y+{\script{4\over 3}}, x-y-{\script{1\over 3}}, z-{\script{1\over 3}}]; (ii) [-x+{\script{5\over 3}}, -y+{\script{1\over 3}}, -z+{\script{1\over 3}}]; (iii) [-x+y+{\script{5\over 3}}, -x+{\script{4\over 3}}, z-{\script{2\over 3}}]; (iv) x, y, z-1.

Data collection: APEX2 (Bruker, 2007[Bruker (2007). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2007[Bruker (2007). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXTL.

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536812020910/hy2548sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536812020910/hy2548Isup2.hkl

checkCIF report


Comment top

Benzimidazole is of considerable interest as a ligand for transition metal ions. Some of their polyfunctional derivatives have been proved to possess extensive biological activities (Gómez-Segura et al., 2006). Therefore, substituted benzimidazoles have attracted interest of various research groups, especially the substitution at 1, 2 and 5 positions of the benzimidazole ring is very important for their coordination behavior. The 2-(2-aminomethyl)-1H-benzimidazole (AMBI) ligand is a suitable model system for compounds of this sort, which is a bidentate ligand and can chelate a 3d metal ion through two nitrogen atoms of the pendant aminomethyl group and the imidazole ring (Gable et al., 1996; He et al., 2003; Jiang et al., 2004). Moreover, AMBI possesses a larger conjugated π-system and a nitrogen electron-donor of the secondary amine group, which has an important effect on the structures and functions of the complexes. On the other hand, metalloproteins that contain Cu are widespread. Characterization of model Cu complexes that mimic Cu proteins has led to a better understanding of the chemistry of Cu in biological systems. A new copper(II) complex with AMBI, which is reported in this paper, may be of interest with respect to both of the above-mentioned areas.

In the title compound, as shown in Fig. 1, two bidentate AMBI ligands are coordinated to the CuII atom via two N atoms and two nitrate anions are coordinated to the CuII atom via one O atom. The coordination geometry around the CuII atom, which lies on an inversion center, is distorted octahedral, with a bite angle of 83.84 (5)° for two bidentate ligands. The other cis bond angles at the CuII atom fall in the range of 80.71 (5)–99.29 (5)° and the trans bond angles are 180°, suggesting a significant deviation from a perfect octahedral coordination. The Cu—N bond lengths are 1.9839 (12) and 2.0244 (12) Å, with an average of 2.0042 (12) Å. The Cu—O bond length is 2.5870 (12) Å. Extensive N—H···O hydrogen bonds in the crystal, as shown in Fig. 2 and Table 1, link the complex molecules into a three-dimensional network.

Related literature top

For the synthesis of the 2-(2-aminomethyl)benzimidazole ligand, see: Pascaly et al. (2001). For the structures and properties of transition metal complexes with 2-(2-aminomethyl)benzimidazole ligands, see: Gable et al. (1996); Gómez-Segura et al. (2006); He et al. (2003); Jiang et al. (2004).

Experimental top

The title compound was prepared by adding a methanol-water solution (4:1 v/v, 5 ml) of Cu(NO3)2.3H2O (0.1 mmol) to a methanol solution (5 ml) of 2-(2-aminomethyl)benzimidazole (0.2 mmol) (Pascaly et al., 2001). The blue mixture was stirred at room temperature for 4 h and then filtered. Purple crystals suitable for X-ray diffraction were obtained by slow evaporation of the solvent after several days. Analysis, calculated for C16H18CuN8O6: C 39.88, H 3.76, N 23.25%; found: C 39.92, H 3.75, N 23.30%.

Refinement top

H atoms bonded to C and N atoms were positioned geometrically and refined as riding atoms, with C—H = 0.95 (aromatic), 0.99 (CH2) and N—H = 0.88 (NH), 0.92 (NH2) Å and with Uiso(H) = 1.2Ueq(C,N).

Computing details top

Data collection: APEX2 (Bruker, 2007); cell refinement: SAINT (Bruker, 2007); data reduction: SAINT (Bruker, 2007); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. Molecular structure of the title complex, with displacement ellipsoids drawn at the 30% probability level. [Symmetry code: (A) -x+5/3, -y+1/3, -z+1/3.]
[Figure 2] Fig. 2. The packing diagram viewed along the c axis.
Bis(2-aminomethyl-1H-benzimidazole- κ2N2,N3)bis(nitrato-κO)copper(II) top
Crystal data top
[Cu(NO3)2(C8H9N3)2]Dx = 1.713 Mg m−3
Mr = 481.93Mo Kα radiation, λ = 0.71073 Å
Trigonal, R3Cell parameters from 5478 reflections
Hall symbol: -R 3θ = 2.7–26.0°
a = 24.6913 (8) ŵ = 1.23 mm−1
c = 7.9620 (5) ÅT = 184 K
V = 4203.8 (4) Å3Block, purple
Z = 90.34 × 0.21 × 0.11 mm
F(000) = 2223
Data collection top
Bruker APEXII CCD
diffractometer		1833 independent reflections
Radiation source: fine-focus sealed tube1764 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.015
ϕ and ω scansθmax = 26.0°, θmin = 1.7°
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)		h = −27→30
Tmin = 0.681, Tmax = 0.877k = −25→30
7196 measured reflectionsl = −9→8
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)] = 0.023Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.063H-atom parameters constrained
S = 1.04 w = 1/[σ2(Fo2) + (0.0358P)2 + 6.4022P]
where P = (Fo2 + 2Fc2)/3
1833 reflections(Δ/σ)max = 0.001
142 parametersΔρmax = 0.52 e Å−3
0 restraintsΔρmin = −0.23 e Å−3
Crystal data top
[Cu(NO3)2(C8H9N3)2]Z = 9
Mr = 481.93Mo Kα radiation
Trigonal, R3µ = 1.23 mm−1
a = 24.6913 (8) ÅT = 184 K
c = 7.9620 (5) Å0.34 × 0.21 × 0.11 mm
V = 4203.8 (4) Å3
Data collection top
Bruker APEXII CCD
diffractometer		1833 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)		1764 reflections with I > 2σ(I)
Tmin = 0.681, Tmax = 0.877Rint = 0.015
7196 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0230 restraints
wR(F2) = 0.063H-atom parameters constrained
S = 1.04Δρmax = 0.52 e Å−3
1833 reflectionsΔρmin = −0.23 e Å−3
142 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
Cu10.83330.16670.16670.01942 (10)
O10.85026 (6)0.28108 (7)0.46236 (18)0.0427 (3)
O20.89291 (6)0.22280 (5)0.43740 (16)0.0339 (3)
O30.94763 (5)0.31844 (5)0.52565 (15)0.0321 (3)
N10.84262 (6)0.24335 (6)0.05919 (15)0.0205 (3)
N20.89615 (6)0.31981 (6)−0.12266 (16)0.0241 (3)
H20.92350.3420−0.20090.029*
N30.90693 (6)0.18332 (6)0.01943 (15)0.0222 (3)
H3A0.94170.19580.08560.027*
H3B0.89860.1469−0.03390.027*
N40.89671 (6)0.27418 (6)0.47583 (16)0.0249 (3)
C10.92024 (7)0.23207 (7)−0.10792 (19)0.0237 (3)
H1A0.90530.2126−0.21960.028*
H1B0.96580.2615−0.11490.028*
C20.88719 (7)0.26609 (7)−0.05640 (18)0.0207 (3)
C30.82031 (7)0.28550 (7)0.06771 (18)0.0212 (3)
C40.77224 (8)0.28515 (8)0.1601 (2)0.0283 (3)
H40.74790.25240.23670.034*
C50.76134 (8)0.33433 (8)0.1360 (2)0.0326 (4)
H50.72840.33480.19670.039*
C60.79714 (9)0.38357 (8)0.0253 (2)0.0349 (4)
H60.78860.41690.01400.042*
C70.84461 (8)0.38431 (8)−0.0675 (2)0.0319 (4)
H70.86930.4176−0.14260.038*
C80.85467 (7)0.33414 (7)−0.04615 (18)0.0232 (3)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cu10.01800 (15)0.01646 (14)0.02290 (16)0.00795 (10)0.00401 (9)0.00463 (9)
O10.0359 (7)0.0535 (8)0.0510 (8)0.0317 (7)−0.0132 (6)−0.0165 (6)
O20.0334 (6)0.0253 (6)0.0454 (7)0.0165 (5)−0.0137 (5)−0.0077 (5)
O30.0276 (6)0.0252 (6)0.0372 (7)0.0086 (5)−0.0043 (5)−0.0033 (5)
N10.0208 (6)0.0184 (6)0.0215 (6)0.0092 (5)0.0021 (5)0.0019 (5)
N20.0250 (7)0.0214 (6)0.0236 (6)0.0100 (5)0.0049 (5)0.0066 (5)
N30.0199 (6)0.0210 (6)0.0245 (6)0.0094 (5)0.0017 (5)0.0024 (5)
N40.0272 (7)0.0284 (7)0.0207 (6)0.0151 (6)−0.0016 (5)0.0002 (5)
C10.0240 (7)0.0245 (7)0.0220 (7)0.0117 (6)0.0050 (6)0.0037 (6)
C20.0200 (7)0.0194 (7)0.0188 (7)0.0069 (6)−0.0004 (5)0.0010 (5)
C30.0223 (7)0.0182 (7)0.0221 (7)0.0094 (6)−0.0032 (6)−0.0008 (5)
C40.0279 (8)0.0276 (8)0.0308 (8)0.0150 (7)0.0040 (6)0.0037 (6)
C50.0332 (9)0.0338 (9)0.0376 (9)0.0218 (8)0.0015 (7)−0.0005 (7)
C60.0407 (10)0.0280 (8)0.0437 (10)0.0229 (8)−0.0037 (8)0.0016 (7)
C70.0354 (9)0.0239 (8)0.0362 (9)0.0148 (7)−0.0002 (7)0.0071 (7)
C80.0222 (7)0.0200 (7)0.0241 (7)0.0081 (6)−0.0031 (6)0.0007 (6)
Geometric parameters (Å, º) top
Cu1—N11.9839 (12)C1—C21.492 (2)
Cu1—N32.0244 (12)C1—H1A0.9900
Cu1—O22.5870 (12)C1—H1B0.9900
O1—N41.2454 (18)C3—C41.393 (2)
O2—N41.2621 (17)C3—C81.402 (2)
O3—N41.2483 (17)C4—C51.382 (2)
N1—C21.3250 (19)C4—H40.9500
N1—C31.4016 (19)C5—C61.401 (3)
N2—C21.3390 (19)C5—H50.9500
N2—C81.381 (2)C6—C71.378 (3)
N2—H20.8800C6—H60.9500
N3—C11.4798 (19)C7—C81.390 (2)
N3—H3A0.9200C7—H70.9500
N3—H3B0.9200
N1—Cu1—N1i179.999 (1)N3—C1—H1A110.1
N1—Cu1—N383.84 (5)C2—C1—H1A110.1
N1i—Cu1—N396.16 (5)N3—C1—H1B110.1
N1—Cu1—N3i96.16 (5)C2—C1—H1B110.1
N1i—Cu1—N3i83.84 (5)H1A—C1—H1B108.4
N3—Cu1—N3i180.00 (5)N1—C2—N2112.60 (13)
N1—Cu1—O294.86 (4)N1—C2—C1121.64 (13)
N1i—Cu1—O285.14 (4)N2—C2—C1125.70 (13)
N3—Cu1—O299.29 (5)C4—C3—N1132.16 (14)
N3i—Cu1—O280.71 (5)C4—C3—C8119.72 (14)
N4—O2—Cu1118.50 (9)N1—C3—C8108.09 (13)
C2—N1—C3105.70 (12)C5—C4—C3117.45 (15)
C2—N1—Cu1112.29 (10)C5—C4—H4121.3
C3—N1—Cu1141.90 (10)C3—C4—H4121.3
C2—N2—C8107.67 (12)C4—C5—C6122.28 (16)
C2—N2—H2126.2C4—C5—H5118.9
C8—N2—H2126.2C6—C5—H5118.9
C1—N3—Cu1111.94 (9)C7—C6—C5120.84 (15)
C1—N3—H3A109.2C7—C6—H6119.6
Cu1—N3—H3A109.2C5—C6—H6119.6
C1—N3—H3B109.2C6—C7—C8116.89 (15)
Cu1—N3—H3B109.2C6—C7—H7121.6
H3A—N3—H3B107.9C8—C7—H7121.6
O1—N4—O3120.07 (13)N2—C8—C7131.30 (15)
O1—N4—O2120.38 (14)N2—C8—C3105.93 (13)
O3—N4—O2119.55 (13)C7—C8—C3122.77 (15)
N3—C1—C2107.95 (12)
Symmetry code: (i) −x+5/3, −y+1/3, −z+1/3.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H3A···O1ii0.922.423.266 (2)153
N3—H3A···O3ii0.922.373.0521 (17)131
N3—H3B···O1i0.922.333.1036 (19)142
N2—H2···O3iii0.882.503.0276 (18)119
N2—H2···O3iv0.882.403.0823 (18)134
N2—H2···O2iii0.882.202.8901 (17)135
Symmetry codes: (i) −x+5/3, −y+1/3, −z+1/3; (ii) −y+4/3, x−y−1/3, z−1/3; (iii) −x+y+5/3, −x+4/3, z−2/3; (iv) x, y, z−1.

Experimental details

Crystal data
Chemical formula[Cu(NO3)2(C8H9N3)2]
Mr481.93
Crystal system, space groupTrigonal, R3
Temperature (K)184
a, c (Å)24.6913 (8), 7.9620 (5)
V (Å3)4203.8 (4)
Z9
Radiation typeMo Kα
µ (mm−1)1.23
Crystal size (mm)0.34 × 0.21 × 0.11
Data collection
DiffractometerBruker APEXII CCD
diffractometer
Absorption correctionMulti-scan
(SADABS; Sheldrick, 1996)
Tmin, Tmax0.681, 0.877
No. of measured, independent and
observed [I > 2σ(I)] reflections		7196, 1833, 1764
Rint0.015
(sin θ/λ)max (Å−1)0.617
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.023, 0.063, 1.04
No. of reflections1833
No. of parameters142
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å−3)0.52, −0.23

Computer programs: APEX2 (Bruker, 2007), SAINT (Bruker, 2007), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H3A···O1i0.922.423.266 (2)153
N3—H3A···O3i0.922.373.0521 (17)131
N3—H3B···O1ii0.922.333.1036 (19)142
N2—H2···O3iii0.882.503.0276 (18)119
N2—H2···O3iv0.882.403.0823 (18)134
N2—H2···O2iii0.882.202.8901 (17)135
Symmetry codes: (i) −y+4/3, x−y−1/3, z−1/3; (ii) −x+5/3, −y+1/3, −z+1/3; (iii) −x+y+5/3, −x+4/3, z−2/3; (iv) x, y, z−1.
 

Acknowledgements

This work was supported by the Youth Foundation of Hebei Normal University (No. L2006Q20).

References

First citationBruker (2007). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
 First citationGable, R. W., Hartshorn, R. M., Mcfadyen, W. D. & Nunno, L. (1996). Aust. J. Chem. 49, 625–632.  CAS Google Scholar
 First citationGómez-Segura, J., Prieto, M. J., Font-Bardia, M., Solans, X. & Moreno, V. (2006). Inorg. Chem. 45, 10031–10033.  Web of Science PubMed Google Scholar
 First citationHe, Y., Kou, H.-Z., Wang, R.-J. & Li, Y.-D. (2003). Transition Met. Chem. 28, 464–467.  Web of Science CSD CrossRef CAS Google Scholar
 First citationJiang, Y.-B., Kou, H.-Z., Gao, F. & Wang, R.-J. (2004). Acta Cryst. C60, m261–m262.  Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
 First citationPascaly, M., Duda, M., Schweppe, F., Zurlinden, K., Müller, F. K. & Krebs, B. (2001). J. Chem. Soc. Dalton Trans. pp. 828–837.  Web of Science CSD CrossRef Google Scholar
 First citationSheldrick, G. M. (1996). SADABS. University of Göttingen, Germany.  Google Scholar
 First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar

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Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 68| Part 6| June 2012| Page m767
doi:10.1107/S1600536812020910
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