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Acta Crystallogr Sect E Struct Rep Online. 2008 January 1; 64(Pt 1): m182.
Published online 2007 December 12. doi:  10.1107/S160053680706610X
PMCID: PMC2915116

Bis[2-(2-amino­ethyl)-1H-benzimidazole-κ2 N 2,N 3]zinc(II) bis­(perchlorate)

Abstract

In the title compound, [Zn(C9H11N3)2](ClO4)2, the ZnII atom resides on a crystallographic twofold axis and is coordinated by two benzimidazole N [Zn(...)N = 1.993 (4) Å] and two amine N atoms [Zn(...)N = 2.036 (4) Å] in a distorted tetra­hedral geometry. The crystal packing is dominated by N—H(...)O inter­actions involving the perchlorate anions and π–π stacking inter­actions with an inter­planar separation of 3.42 Å. A weak C—H(...)O inter­action is also present.

Related literature

For related literature, see: Cescon & Day (1961 [triangle]); Maurva et al. (2006 [triangle]); Qiu & Tong (2005 [triangle]); Vallee & Auld (1990 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-64-0m182-scheme1.jpg

Experimental

Crystal data

  • [Zn(C9H11N3)2](ClO4)2
  • M r = 586.69
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-64-0m182-efi1.jpg
  • a = 11.150 (3) Å
  • b = 15.343 (4) Å
  • c = 14.156 (4) Å
  • β = 93.322 (4)°
  • V = 2417.7 (12) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 1.29 mm−1
  • T = 293 (2) K
  • 0.30 × 0.20 × 0.20 mm

Data collection

  • Bruker SMART CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Sheldrick, 1996 [triangle]) T min = 0.698, T max = 0.782
  • 5777 measured reflections
  • 2131 independent reflections
  • 1880 reflections with I > 2σ(I)
  • R int = 0.023

Refinement

  • R[F 2 > 2σ(F 2)] = 0.066
  • wR(F 2) = 0.184
  • S = 1.10
  • 2131 reflections
  • 172 parameters
  • 15 restraints
  • H-atom parameters constrained
  • Δρmax = 0.81 e Å−3
  • Δρmin = −0.47 e Å−3

Data collection: SMART (Bruker, 2000 [triangle]); cell refinement: SAINT (Bruker, 2000 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997 [triangle]); molecular graphics: SHELXTL (Bruker, 2000 [triangle]); software used to prepare material for publication: SHELXTL.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S160053680706610X/gg2058sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S160053680706610X/gg2058Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

The authors are grateful to the National Natural Science Foundation of China for financial support (grant No. 30470408).

supplementary crystallographic information

Comment

Benzimidazole is of considerable interest as a ligand for transition metal ions. The complexes of transition metal salts with benzimidazole derivatives have been extensively studied as models of some important biological molecules (Maurva et al., 2006). Incorporation of a benzimidazole moiety into alpha-amino acid molecules appeared to be of interest since the benzimidazole group has known biological activity, and its attachment to a carrier group such as an amino acid can facilitate this activity (Cescon & Day, 1961). Zinc complexes may be found in numerous biological systems. They function not only as catalytic centres in enzymes, but also as structural elements supporting three-dimensional protein structures (Vallee & Auld, 1990). In the present paper, we report the synthesis and crystal structure of a new zinc(II) benzimidazole complex, the title compound.

In (I), the Zn(II) ion exhibits a distorted tetrahedral geometry. The coordination sphere of the Zn(II) ion is comprised with two benzimidazole N atoms and two amine N atoms. The Zn—N bond distances (Table 1) are different from those reported in the literature. The Zn—N1 bond distance of 1.993 (4) Å is smaller than that reported in the literature (Qiu & Tong, 2005). The N1—Zn—N3 and N1—Zn—N3A (symmetry code: A -x + 2,y,-z + 1/2) bond angles are 97.02 (16)° and 118.10 (17) °, respectively, indicating a distortion of the tetrahedral coordination.

The ellipsoid plot of the molecule is shown in Fig. 1. The crystal structure of (I) is composed of Bis(1H-2-aminoethylbenzimidazole)zinc(II) cations and perchlorate anions. As illustrated in Fig. 2, intramolecular N—H···O hydrogen bonds and π···π stacking interactions between the benzene ring and imidazole ring [Cg1···Cg2(1/2 - x,1/2 - y,1 - z) = 3.7296 Å; Cg1 is the centroid of atoms N1,C1,C6,N2,C7, Cg2 is the centroid of atoms C1—C6] play key roles in stabilizing the crystal packing. The detailed hydrogen bonds information are listed in Table 2.

Experimental

All chemicals were of reagent grade and commercially available from the Beijing Chemical Reagents Company of China, and were used without further purification.

The title compound was prepared by adding a methanol solution (5 ml) of Zn(ClO4)2.6H2O (0.5 mmol) to a methanol solution (10 ml) of 2-aminoethybenzimidazole dihydrochloride (0.5 mmol) (Cescon & Day, 1961) neutralized by potassium carbonate. The mixture was stirred for about four hours and then filtered. Afterwards, the filtrate was slowly evaporated at room temperature to yield colorless crystals of (I) suitable for X-ray analysis. Elemental analyses of the title compound found: C 36.86%, H 3.75%, N 14.33%, and the components of the compound are calculated as C 36.85%, H 3.79%, N 14.30%.

Refinement

Disorder is present in the perchlorate anion and aminoethyl bridge and was modelled successfully. H atoms were placed in calculated positions and included in the refinement in the riding-model approximation, with C—H distances in the range 0.93–0.97 Å, N—H distances in the range 0.86–0.90 Å and Uiso(H) = 1.2Ueq of the carrier atom.

Figures

Fig. 1.
The structure of the title compound with 30% displacement ellipsoids. H atoms have been omitted for clarity.
Fig. 2.
The packing diagram of (I) with N—H···O hydrogen bonds shown as dashed lines.

Crystal data

[Zn(C9H11N3)2](ClO4)2F000 = 1200
Mr = 586.69Dx = 1.612 Mg m3
Monoclinic, C2/cMo Kα radiation λ = 0.71073 Å
Hall symbol: -C 2ycCell parameters from 1957 reflections
a = 11.150 (3) Åθ = 2.3–23.9º
b = 15.343 (4) ŵ = 1.29 mm1
c = 14.156 (4) ÅT = 293 (2) K
β = 93.322 (4)ºBlock, colorless
V = 2417.7 (12) Å30.30 × 0.20 × 0.20 mm
Z = 4

Data collection

Bruker SMART CCD area-detector diffractometer2131 independent reflections
Radiation source: fine-focus sealed tube1880 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.023
T = 293(2) Kθmax = 25.0º
[var phi] and ω scansθmin = 2.3º
Absorption correction: multi-scan(SADABS; Sheldrick, 1996)h = −13→13
Tmin = 0.698, Tmax = 0.782k = −18→18
5777 measured reflectionsl = −10→16

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.066H-atom parameters constrained
wR(F2) = 0.184  w = 1/[σ2(Fo2) + (0.1191P)2 + 1.6906P] where P = (Fo2 + 2Fc2)/3
S = 1.10(Δ/σ)max < 0.001
2131 reflectionsΔρmax = 0.81 e Å3
172 parametersΔρmin = −0.47 e Å3
15 restraintsExtinction correction: none
Primary atom site location: structure-invariant direct methods

Special details

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)

xyzUiso*/UeqOcc. (<1)
Zn11.00000.13946 (4)0.25000.0506 (3)
N10.8741 (3)0.2124 (2)0.1829 (3)0.0534 (9)
N20.6929 (3)0.2674 (3)0.1500 (3)0.0655 (11)
H2A0.61650.27450.15040.079*
C10.8843 (4)0.2811 (3)0.1191 (3)0.0538 (11)
C20.9833 (5)0.3136 (4)0.0754 (4)0.0712 (14)
H21.05950.29000.08720.085*
C30.9638 (6)0.3819 (4)0.0142 (5)0.0805 (16)
H31.02870.4055−0.01550.097*
C40.8497 (6)0.4174 (4)−0.0050 (4)0.0776 (16)
H40.84130.4643−0.04640.093*
C50.7494 (6)0.3855 (3)0.0351 (4)0.0686 (14)
H50.67320.40830.02110.082*
C60.7700 (4)0.3157 (3)0.0990 (3)0.0549 (11)
C70.7577 (4)0.2068 (3)0.1993 (4)0.0624 (12)
C80.7035 (6)0.1424 (4)0.2624 (5)0.0905 (17)
H8A0.62980.16750.28370.109*0.594 (12)
H8B0.68120.09160.22470.109*0.594 (12)
H8A'0.68760.17280.32050.109*0.406 (12)
H8B'0.62610.12640.23270.109*0.406 (12)
Cl10.37395 (13)0.37873 (10)0.10975 (10)0.0736 (4)
O10.4321 (5)0.2999 (4)0.1393 (6)0.141 (2)
N30.8879 (4)0.0694 (3)0.3295 (3)0.0673 (11)
H3A0.87250.01790.30080.081*0.594 (12)
H3B0.92560.05840.38610.081*0.594 (12)
H3A'0.91790.01520.33720.081*0.406 (12)
H3B'0.88690.09400.38710.081*0.406 (12)
O20.4361 (8)0.4352 (7)0.0603 (7)0.214 (5)
O30.2643 (9)0.3764 (10)0.130 (2)0.235 (14)0.594 (12)
C90.7735 (7)0.1132 (8)0.3445 (6)0.0905 (17)0.594 (12)
H9A0.72430.07350.37900.109*0.594 (12)
H9B0.79040.16330.38490.109*0.594 (12)
O3'0.2863 (12)0.3531 (10)0.0330 (13)0.118 (6)0.406 (12)
C9'0.7639 (7)0.0630 (5)0.2892 (9)0.061 (4)0.406 (12)
H9A'0.76420.02600.23370.073*0.406 (12)
H9B'0.71670.03350.33500.073*0.406 (12)
O40.364 (2)0.4319 (9)0.1837 (10)0.337 (9)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Zn10.0418 (4)0.0565 (5)0.0526 (5)0.000−0.0053 (3)0.000
N10.0406 (19)0.056 (2)0.063 (2)0.0001 (15)−0.0033 (16)0.0050 (17)
N20.0411 (19)0.069 (2)0.086 (3)0.0064 (18)0.0020 (19)0.003 (2)
C10.050 (2)0.051 (2)0.060 (3)−0.0044 (18)−0.009 (2)−0.004 (2)
C20.057 (3)0.076 (3)0.080 (4)−0.005 (2)−0.002 (3)0.015 (3)
C30.076 (4)0.074 (3)0.092 (4)−0.009 (3)0.005 (3)0.026 (3)
C40.094 (4)0.062 (3)0.075 (4)0.001 (3)−0.010 (3)0.012 (3)
C50.077 (4)0.053 (2)0.074 (3)0.008 (2)−0.019 (3)−0.003 (2)
C60.054 (3)0.047 (2)0.062 (3)0.0038 (19)−0.009 (2)−0.009 (2)
C70.044 (2)0.063 (3)0.080 (3)0.001 (2)−0.001 (2)0.012 (2)
C80.061 (3)0.099 (3)0.113 (4)0.001 (2)0.019 (3)0.030 (3)
Cl10.0667 (9)0.0818 (9)0.0722 (9)0.0043 (6)0.0054 (7)0.0076 (7)
O10.095 (4)0.146 (5)0.182 (6)0.024 (4)0.007 (4)0.039 (4)
N30.064 (2)0.073 (3)0.065 (2)−0.004 (2)0.005 (2)0.014 (2)
O20.172 (7)0.230 (9)0.236 (9)−0.102 (7)−0.023 (7)0.106 (8)
O30.056 (6)0.149 (11)0.51 (4)0.036 (6)0.073 (12)0.136 (18)
C90.061 (3)0.099 (3)0.113 (4)0.001 (2)0.019 (3)0.030 (3)
O3'0.048 (7)0.149 (13)0.152 (14)0.004 (6)−0.036 (7)−0.047 (10)
C9'0.055 (7)0.056 (7)0.072 (8)−0.012 (5)0.009 (6)0.012 (6)
O40.57 (3)0.241 (13)0.207 (10)−0.006 (16)0.084 (15)−0.121 (10)

Geometric parameters (Å, °)

Zn1—N1i1.993 (4)C8—H8A0.9700
Zn1—N11.993 (4)C8—H8B0.9700
Zn1—N3i2.036 (4)C8—H8A'0.9700
Zn1—N32.036 (4)C8—H8B'0.9700
N1—C71.335 (6)C3—H30.9300
N1—C11.397 (6)Cl1—O31.273 (10)
C5—C41.373 (9)Cl1—O21.333 (7)
C5—C61.412 (7)Cl1—O41.336 (10)
C5—H50.9300Cl1—O11.423 (6)
C1—C21.389 (7)Cl1—O3'1.472 (12)
C1—C61.394 (6)N3—C9'1.468 (8)
C7—N21.347 (6)N3—C91.468 (8)
C7—C81.484 (7)N3—H3A0.9000
C6—N21.372 (6)N3—H3B0.9000
N2—H2A0.8600N3—H3A'0.9000
C2—C31.369 (8)N3—H3B'0.9000
C2—H20.9300C9—H9A0.9700
C4—C31.396 (8)C9—H9B0.9700
C4—H40.9300C9'—H9A'0.9700
C8—C9'1.433 (7)C9'—H9B'0.9700
C8—C91.433 (7)
N1i—Zn1—N1111.6 (2)H8A—C8—H8B'59.1
N1i—Zn1—N3i97.02 (16)H8B—C8—H8B'50.4
N1—Zn1—N3i118.10 (17)H8A'—C8—H8B'106.7
N1i—Zn1—N3118.10 (17)C2—C3—C4122.1 (5)
N1—Zn1—N397.02 (16)C2—C3—H3119.0
N3i—Zn1—N3116.3 (3)C4—C3—H3119.0
C7—N1—C1106.1 (4)O3—Cl1—O2132.2 (7)
C7—N1—Zn1123.1 (3)O3—Cl1—O473.4 (14)
C1—N1—Zn1130.6 (3)O2—Cl1—O494.9 (10)
C4—C5—C6115.4 (5)O3—Cl1—O1109.7 (6)
C4—C5—H5122.3O2—Cl1—O1117.7 (6)
C6—C5—H5122.3O4—Cl1—O1110.3 (9)
C2—C1—C6120.9 (4)O3—Cl1—O3'63.5 (13)
C2—C1—N1130.9 (4)O2—Cl1—O3'97.4 (9)
C6—C1—N1108.2 (4)O4—Cl1—O3'131.1 (11)
N1—C7—N2111.3 (4)O1—Cl1—O3'105.2 (7)
N1—C7—C8125.6 (4)C9'—N3—Zn1114.5 (5)
N2—C7—C8123.1 (4)C9—N3—Zn1113.9 (5)
N2—C6—C1106.2 (4)C9'—N3—H3A67.4
N2—C6—C5131.6 (5)C9—N3—H3A108.8
C1—C6—C5122.2 (5)Zn1—N3—H3A108.8
C7—N2—C6108.2 (4)C9'—N3—H3B135.6
C7—N2—H2A125.9C9—N3—H3B108.8
C6—N2—H2A125.9Zn1—N3—H3B108.8
C3—C2—C1117.1 (5)H3A—N3—H3B107.7
C3—C2—H2121.5C9'—N3—H3A'108.6
C1—C2—H2121.5C9—N3—H3A'136.4
C5—C4—C3122.4 (5)Zn1—N3—H3A'108.6
C5—C4—H4118.8H3A—N3—H3A'45.8
C3—C4—H4118.8H3B—N3—H3A'64.4
C9'—C8—C945.1 (7)C9'—N3—H3B'108.6
C9'—C8—C7121.6 (6)C9—N3—H3B'67.7
C9—C8—C7118.3 (6)Zn1—N3—H3B'108.6
C9'—C8—H8A130.4H3A—N3—H3B'139.9
C9—C8—H8A107.7H3B—N3—H3B'45.6
C7—C8—H8A107.7H3A'—N3—H3B'107.6
C9'—C8—H8B64.1C8—C9—N3117.6 (6)
C9—C8—H8B107.7C8—C9—H9A107.9
C7—C8—H8B107.7N3—C9—H9A107.9
H8A—C8—H8B107.1C8—C9—H9B107.9
C9'—C8—H8A'106.9N3—C9—H9B107.9
C9—C8—H8A'65.3H9A—C9—H9B107.2
C7—C8—H8A'106.9C8—C9'—N3117.6 (6)
H8A—C8—H8A'49.3C8—C9'—H9A'107.9
H8B—C8—H8A'143.1N3—C9'—H9A'107.9
C9'—C8—H8B'106.9C8—C9'—H9B'107.9
C9—C8—H8B'134.5N3—C9'—H9B'107.9
C7—C8—H8B'106.9H9A'—C9'—H9B'107.2

Symmetry codes: (i) −x+2, y, −z+1/2.

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N2—H2A···O10.862.092.946 (6)174
N3—H3A···O4ii0.902.122.953 (15)154
C8—H8A···O1iii0.972.423.210 (9)138

Symmetry codes: (ii) x+1/2, y−1/2, z; (iii) −x+1, y, −z+1/2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: GG2058).

References

  • Bruker (2000). SMART (Version 5.0), SAINT (Version 6.02) and SHELXTL (Version 6.1). Bruker AXS Inc., Madison, Wisconsin, USA.
  • Cescon, L. A. & Day, A. R. (1961). J. Org. Chem.27, 581–586.
  • Maurva, M. R., Kumar, A., Ebel, M. & Rehder, D. (2006). Inorg. Chem.45, 5924–5937. [PubMed]
  • Qiu, X.-H. & Tong, X.-L. (2005). Acta Cryst. E61, m2302–m2304.
  • Sheldrick, G. M. (1990). Acta Cryst. A46, 467–473.
  • Sheldrick, G. M. (1996). SADABS University of Göttingen, Germany.
  • Sheldrick, G. M. (1997). SHELXL97 and SHELXS97 University of Göttingen, Germany.
  • Vallee, B. L. & Auld, D. S. (1990). Biochemistry, 29, 5647–5659. [PubMed]

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