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Acta Cryst. (2009). E65, m661    [ doi:10.1107/S160053680901808X ]

Bis[2-(pyrrolidin-2-yl)-1H-benzimidazole-[kappa]2N2,N3]copper(II) dinitrate dihydrate

J. Dai

Abstract top

In the title compound, [Cu(C11H13N3)2](NO3)2·2H2O, synthesized by hydrothermal reaction of Cu(NO3)2 and racemic 2-(pyrrolidin-2-yl)-1H-1,3-benzimidazole, the CuII atom lies on an inversion centre. The distorted octahedral CuII environment contains two planar trans-related N,N-chelating 2-(pyrrolidin-2-yl)-1H-1,3-benzimidazole ligands in the equatorial plane and two monodentate nitrate anions, which are in weak interaction with the Cu atom, in the axial positions. The two benzimidazole ligands have opposite configurations (R/S and S/R) and compound is a meso complex. In the crystal, N-H...O and O-H...O hydrogen bonds generate an infinite three-dimensional network. One methylene group of the pyrrolidine ring is disordered over two position with a 0.56 (3):0.44 (3) occupancy.

Comment top

Amino acid derivatives have found wide range of applications in material science, such as ferroelectric, fluorescence and dielectric behaviors. And there has been an increased interest in the preparation of amino acid coordination compound (Aminabhavi et al., 1986; Dai & Fu 2008a; Fu & Ye 2007; Dai & Fu 2008b; Fu, et al. 2007). We report here the crystal structure of the title compound, [Nitrate-[2-(pyrrolidin-2-yl)-1H-benzimidazole] Copper(II)] dihydrate.

In the title compound, the CuII atom lies on an inversion centre. The distorted octahedral CuII environment contains two planar trans-related N,N-chelating 2-(pyrrolidin-2-yl)-1H-1,3-benzimidazole ligands in the equatorial plane and two monodentate nitrate anion ligands which are in weak interaction with the Cu atom in the axial position. The two benzimidazole ligands have opposite configuration R,S and S,R and the complex is meso(Fig. 1).

In the crystal structure, molecules are linked into a three-dimension network by N—H···O and O—H···O hydrogen bonds.(Fig.2, Table 1).

Related literature top

For physical properties such as the ferroelectric and dielectric behavior of metal-organic coordination compounds, see: Fu et al. (2007). For the synthesis, see: Aminabhavi et al. (1986). For related structures, see: Dai & Fu (2008a,b); Fu & Ye (2007).

Experimental top

The racemic ligand 2-(pyrrolidin-2-yl)-1H-benzo[d]imidazole was synthesized by reaction of S-pyrrolidine-2-carboxylic acid and benzene-1,2-diamine according to the procedure described in the literature(Aminabhavi, et al.(1986)). A mixture of 2-(pyrrolidin-2-yl)-1H-benzo[d]imidazole (0.1 mmol) and Cu(NO3)2 (0.1 mmol) and water (1 ml) sealed in a glass tube were maintained at 70 °C. Crystals suitable for X-ray analysis were obtained after 5 days.

Refinement top

All H atoms attached to C and N atoms were fixed geometrically and treated as riding with C—H = 0.93 Å (aromatic), 0.97 Å (methylene) or 0.98 Å (methine) and N—H = 0.91 Å (N3), 0.86 Å (N2) with Uiso(H) = 1.2Ueq(C,N). H atoms of water molecule located in difference Fouriermaps and in the last stage of refinement they were treated as riding on the O atom with Uiso(H) = 1.5Ueq(O).

One of the pyrrolidine rings is disordered with the C10 atom statistically distributed over two positions. These disorders were treated using the tools (SAME and PART) available in SHELXL97 (Sheldrick, 2008).

Computing details top

Data collection: CrystalClear (Rigaku, 2005); cell refinement: CrystalClear (Rigaku, 2005); data reduction: CrystalClear (Rigaku, 2005); 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. A view of the title compound with the atomic numbering scheme. Displacement ellipsoids were drawn at the 30% probability level. H atoms have been omitted. The weak interaction of CuII with nitrate is shown.
[Figure 2] Fig. 2. The crystal packing of the title compound viewed along the a axis and all hydrogen atoms not involved in hydrogen bonding (dashed lines) were omitted for clarity.
Bis[2-(pyrrolidin-2-yl)-1H-benzimidazole- κ2N2,N3]copper(II) dinitrate dihydrate top
Crystal data top
[Cu(C11H13N3)2](NO3)2·2H2OZ = 1
Mr = 598.08F000 = 311
Triclinic, P1Dx = 1.554 Mg m−3
Hall symbol: -P 1Mo Kα radiation
λ = 0.71073 Å
a = 8.2790 (17) ÅCell parameters from 2913 reflections
b = 8.4446 (17) Åθ = 3.4–27.5º
c = 9.759 (2) ŵ = 0.92 mm−1
α = 100.37 (3)ºT = 298 K
β = 107.15 (3)ºBlock, blue
γ = 91.37 (3)º0.35 × 0.30 × 0.15 mm
V = 639.1 (2) Å3
Data collection top
Rigaku Mercury2
diffractometer		2914 independent reflections
Radiation source: fine-focus sealed tube2566 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.027
Detector resolution: 13.6612 pixels mm-1θmax = 27.5º
T = 298 Kθmin = 3.4º
CCD profile fitting scansh = −10→10
Absorption correction: multi-scan
(CrystalClear; Rigaku, 2005)		k = −10→10
Tmin = 0.732, Tmax = 0.871l = −12→12
6713 measured reflections
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)] = 0.043H-atom parameters constrained
wR(F2) = 0.101  w = 1/[σ2(Fo2) + (0.0352P)2 + 0.444P]
where P = (Fo2 + 2Fc2)/3
S = 1.11(Δ/σ)max < 0.001
2914 reflectionsΔρmax = 0.33 e Å−3
188 parametersΔρmin = −0.31 e Å−3
6 restraintsExtinction correction: none
Primary atom site location: structure-invariant direct methods
Crystal data top
[Cu(C11H13N3)2](NO3)2·2H2Oγ = 91.37 (3)º
Mr = 598.08V = 639.1 (2) Å3
Triclinic, P1Z = 1
a = 8.2790 (17) ÅMo Kα
b = 8.4446 (17) ŵ = 0.92 mm−1
c = 9.759 (2) ÅT = 298 K
α = 100.37 (3)º0.35 × 0.30 × 0.15 mm
β = 107.15 (3)º
Data collection top
Rigaku Mercury2
diffractometer		2914 independent reflections
Absorption correction: multi-scan
(CrystalClear; Rigaku, 2005)		2566 reflections with I > 2σ(I)
Tmin = 0.732, Tmax = 0.871Rint = 0.027
6713 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0436 restraints
wR(F2) = 0.101H-atom parameters constrained
S = 1.11Δρmax = 0.33 e Å−3
2914 reflectionsΔρmin = −0.31 e Å−3
188 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*/UeqOcc. (<1)
Cu11.00000.50000.50000.03289 (14)
O10.8537 (3)0.0645 (3)0.4119 (3)0.0643 (6)
O20.6487 (3)0.0360 (3)0.2118 (3)0.0745 (7)
O30.7605 (3)0.2727 (3)0.3222 (3)0.0647 (6)
N10.9102 (2)0.4814 (2)0.6652 (2)0.0329 (4)
N20.7676 (3)0.5950 (3)0.8117 (2)0.0406 (5)
H2B0.71150.66470.85020.049*
N30.8509 (3)0.6877 (2)0.4834 (2)0.0345 (4)
H3B0.91030.77010.46630.041*
N40.7551 (3)0.1246 (3)0.3161 (2)0.0425 (5)
C10.8109 (3)0.4496 (3)0.8525 (3)0.0383 (6)
C20.7753 (4)0.3760 (4)0.9580 (3)0.0507 (7)
H2A0.71510.42561.01840.061*
C30.8337 (4)0.2263 (4)0.9686 (3)0.0552 (8)
H3A0.81150.17211.03690.066*
C40.9250 (4)0.1551 (4)0.8794 (3)0.0564 (8)
H4A0.96430.05450.89090.068*
C50.9603 (4)0.2272 (3)0.7737 (3)0.0467 (6)
H5A1.02080.17690.71390.056*
C60.9014 (3)0.3778 (3)0.7609 (2)0.0348 (5)
C70.8291 (3)0.6078 (3)0.7009 (3)0.0338 (5)
C80.8131 (3)0.7461 (3)0.6234 (3)0.0380 (6)
H8A0.89660.83500.68300.046*
C90.6378 (4)0.8083 (5)0.5821 (4)0.0658 (9)
H9A0.57890.79400.65200.079*
H9B0.64460.92160.57640.079*
C110.6832 (4)0.6571 (4)0.3660 (3)0.0542 (8)
H11A0.68110.71920.29110.065*
H11B0.66100.54350.32090.065*
O1W0.5901 (3)0.7856 (3)0.9583 (3)0.0757 (7)
H1WA0.50450.83170.89680.113*
H1WB0.61690.84511.05960.113*
C100.5552 (12)0.709 (2)0.4410 (13)0.066 (3)0.56 (3)
H10A0.47360.76980.38220.079*0.56 (3)
H10B0.49480.61510.45240.079*0.56 (3)
C10'0.5655 (18)0.773 (2)0.4195 (16)0.055 (3)0.44 (3)
H10C0.56420.87110.38090.066*0.44 (3)
H10D0.45070.72260.38960.066*0.44 (3)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cu10.0347 (2)0.0409 (3)0.0285 (2)0.01231 (17)0.01597 (17)0.00874 (17)
O10.0575 (13)0.0570 (13)0.0686 (14)0.0016 (10)−0.0016 (11)0.0231 (11)
O20.0782 (16)0.0615 (14)0.0594 (14)0.0032 (12)−0.0028 (13)−0.0098 (11)
O30.0681 (15)0.0449 (12)0.0709 (15)0.0090 (10)0.0053 (12)0.0119 (11)
N10.0356 (10)0.0360 (10)0.0300 (10)0.0063 (8)0.0148 (8)0.0052 (8)
N20.0427 (12)0.0473 (12)0.0368 (11)0.0108 (10)0.0227 (10)0.0027 (9)
N30.0368 (11)0.0351 (10)0.0355 (11)0.0066 (8)0.0161 (9)0.0077 (8)
N40.0372 (12)0.0490 (13)0.0411 (12)0.0057 (10)0.0151 (10)0.0025 (10)
C10.0386 (13)0.0454 (14)0.0311 (12)−0.0013 (11)0.0142 (10)0.0025 (10)
C20.0549 (17)0.0651 (19)0.0374 (14)−0.0001 (14)0.0250 (13)0.0056 (13)
C30.075 (2)0.0581 (18)0.0381 (15)−0.0063 (16)0.0241 (14)0.0133 (13)
C40.085 (2)0.0457 (16)0.0441 (16)0.0056 (15)0.0246 (16)0.0150 (13)
C50.0660 (18)0.0421 (15)0.0378 (14)0.0090 (13)0.0244 (13)0.0076 (11)
C60.0401 (13)0.0387 (13)0.0257 (11)0.0003 (10)0.0127 (10)0.0024 (10)
C70.0313 (12)0.0393 (13)0.0306 (12)0.0026 (10)0.0120 (10)0.0016 (10)
C80.0420 (14)0.0362 (13)0.0383 (13)0.0094 (11)0.0177 (11)0.0033 (10)
C90.064 (2)0.081 (2)0.071 (2)0.0437 (18)0.0356 (18)0.0315 (19)
C110.0545 (18)0.0480 (16)0.0471 (16)0.0155 (13)−0.0014 (14)0.0035 (13)
O1W0.0743 (16)0.0971 (18)0.0527 (13)0.0449 (14)0.0207 (12)0.0000 (12)
C100.036 (3)0.071 (7)0.086 (5)0.000 (4)0.003 (3)0.032 (5)
C10'0.041 (5)0.049 (7)0.071 (6)0.018 (5)0.012 (4)0.009 (5)
Geometric parameters (Å, °) top
Cu1—N1i1.9922 (19)C4—C51.384 (4)
Cu1—N11.9922 (19)C4—H4A0.9300
Cu1—N32.032 (2)C5—C61.386 (4)
Cu1—N3i2.032 (2)C5—H5A0.9300
O1—N41.241 (3)C7—C81.490 (3)
O2—N41.240 (3)C8—C91.520 (4)
O3—N41.241 (3)C8—H8A0.9800
N1—C71.324 (3)C9—C101.438 (13)
N1—C61.405 (3)C9—C10'1.492 (15)
N2—C71.343 (3)C9—H9A0.9700
N2—C11.382 (3)C9—H9B0.9700
N2—H2B0.8600C11—C101.488 (12)
N3—C81.491 (3)C11—C10'1.529 (11)
N3—C111.499 (3)C11—H11A0.9700
N3—H3B0.9100C11—H11B0.9700
C1—C21.391 (4)O1W—H1WA0.9281
C1—C61.397 (3)O1W—H1WB0.9827
C2—C31.375 (4)C10—H10A0.9700
C2—H2A0.9300C10—H10B0.9700
C3—C41.383 (4)C10'—H10C0.9700
C3—H3A0.9300C10'—H10D0.9700
N1i—Cu1—N1180.000 (1)N1—C7—C8121.5 (2)
N1i—Cu1—N397.34 (8)N2—C7—C8126.0 (2)
N1—Cu1—N382.66 (8)C7—C8—N3106.82 (19)
N1i—Cu1—N3i82.66 (8)C7—C8—C9115.3 (2)
N1—Cu1—N3i97.34 (8)N3—C8—C9106.4 (2)
N3—Cu1—N3i180.00 (12)C7—C8—H8A109.4
C7—N1—C6105.71 (19)N3—C8—H8A109.4
C7—N1—Cu1112.43 (16)C9—C8—H8A109.4
C6—N1—Cu1141.85 (16)C10—C9—C8102.8 (6)
C7—N2—C1107.5 (2)C10'—C9—C8108.6 (5)
C7—N2—H2B126.2C10—C9—H9A111.2
C1—N2—H2B126.2C10'—C9—H9A126.7
C8—N3—C11106.2 (2)C8—C9—H9A111.2
C8—N3—Cu1110.88 (15)C10—C9—H9B111.2
C11—N3—Cu1116.78 (16)C10'—C9—H9B87.2
C8—N3—H3B107.5C8—C9—H9B111.2
C11—N3—H3B107.5H9A—C9—H9B109.1
Cu1—N3—H3B107.5C10—C11—N3105.4 (5)
O2—N4—O3118.9 (2)N3—C11—C10'106.2 (5)
O2—N4—O1119.9 (2)C10—C11—H11A110.7
O3—N4—O1121.2 (2)N3—C11—H11A110.7
N2—C1—C2131.1 (2)C10'—C11—H11A88.8
N2—C1—C6106.1 (2)C10—C11—H11B110.7
C2—C1—C6122.8 (3)N3—C11—H11B110.7
C3—C2—C1116.6 (3)C10'—C11—H11B129.2
C3—C2—H2A121.7H11A—C11—H11B108.8
C1—C2—H2A121.7H1WA—O1W—H1WB110.4
C2—C3—C4121.0 (3)C9—C10—C11109.9 (6)
C2—C3—H3A119.5C9—C10—H10A109.7
C4—C3—H3A119.5C11—C10—H10A109.7
C3—C4—C5122.7 (3)C9—C10—H10B109.7
C3—C4—H4A118.7C11—C10—H10B109.7
C5—C4—H4A118.7H10A—C10—H10B108.2
C4—C5—C6117.1 (3)C9—C10'—C11104.9 (8)
C4—C5—H5A121.5C9—C10'—H10C110.8
C6—C5—H5A121.5C11—C10'—H10C110.8
C5—C6—C1119.8 (2)C9—C10'—H10D110.8
C5—C6—N1132.0 (2)C11—C10'—H10D110.8
C1—C6—N1108.1 (2)H10C—C10'—H10D108.8
N1—C7—N2112.5 (2)
N3—Cu1—N1—C7−11.34 (17)Cu1—N1—C7—C8−0.8 (3)
N3i—Cu1—N1—C7168.66 (17)C1—N2—C7—N1−0.1 (3)
N3—Cu1—N1—C6168.4 (3)C1—N2—C7—C8−179.6 (2)
N3i—Cu1—N1—C6−11.6 (3)N1—C7—C8—N317.5 (3)
N1i—Cu1—N3—C8−159.18 (16)N2—C7—C8—N3−163.0 (2)
N1—Cu1—N3—C820.82 (16)N1—C7—C8—C9135.5 (3)
N1i—Cu1—N3—C1179.0 (2)N2—C7—C8—C9−45.1 (4)
N1—Cu1—N3—C11−101.0 (2)C11—N3—C8—C7102.9 (2)
C7—N2—C1—C2−178.2 (3)Cu1—N3—C8—C7−24.9 (2)
C7—N2—C1—C60.3 (3)C11—N3—C8—C9−20.7 (3)
N2—C1—C2—C3178.1 (3)Cu1—N3—C8—C9−148.6 (2)
C6—C1—C2—C3−0.2 (4)C7—C8—C9—C10−88.1 (7)
C1—C2—C3—C40.8 (5)N3—C8—C9—C1030.0 (7)
C2—C3—C4—C5−1.2 (5)C7—C8—C9—C10'−112.9 (9)
C3—C4—C5—C60.7 (5)N3—C8—C9—C10'5.3 (10)
C4—C5—C6—C1−0.1 (4)C8—N3—C11—C103.6 (8)
C4—C5—C6—N1−178.1 (3)Cu1—N3—C11—C10127.8 (7)
N2—C1—C6—C5−178.9 (2)C8—N3—C11—C10'28.3 (10)
C2—C1—C6—C5−0.2 (4)Cu1—N3—C11—C10'152.6 (9)
N2—C1—C6—N1−0.4 (3)C10'—C9—C10—C1178.5 (18)
C2—C1—C6—N1178.3 (2)C8—C9—C10—C11−28.4 (12)
C7—N1—C6—C5178.6 (3)N3—C11—C10—C916.2 (12)
Cu1—N1—C6—C5−1.1 (5)C10'—C11—C10—C9−79 (2)
C7—N1—C6—C10.4 (3)C10—C9—C10'—C11−68.1 (16)
Cu1—N1—C6—C1−179.4 (2)C8—C9—C10'—C1111.8 (14)
C6—N1—C7—N2−0.2 (3)C10—C11—C10'—C967 (2)
Cu1—N1—C7—N2179.63 (16)N3—C11—C10'—C9−24.6 (14)
C6—N1—C7—C8179.4 (2)
Symmetry codes: (i) −x+2, −y+1, −z+1.
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
N3—H3B···O1i0.912.252.986 (3)137
O1W—H1WA···O2ii0.931.922.836 (4)169
O1W—H1WB···O2iii0.981.942.861 (3)155
N2—H2B···O1W0.861.862.706 (3)168
Symmetry codes: (i) −x+2, −y+1, −z+1; (ii) −x+1, −y+1, −z+1; (iii) x, y+1, z+1.
Table 1
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
N3—H3B···O1i0.912.252.986 (3)137
O1W—H1WA···O2ii0.931.922.836 (4)169
O1W—H1WB···O2iii0.981.942.861 (3)155
N2—H2B···O1W0.861.862.706 (3)168
Symmetry codes: (i) −x+2, −y+1, −z+1; (ii) −x+1, −y+1, −z+1; (iii) x, y+1, z+1.
Acknowledgements top

This work was supported by a Start-up Grant from Southeast University to Professor Ren-Gen Xiong.

references
References top

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Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122.