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Acta Crystallogr Sect E Struct Rep Online. 2010 August 1; 66(Pt 8): m980.
Published online 2010 July 21. doi:  10.1107/S1600536810028503
PMCID: PMC3007343

Dibenzoatobis[3-(pyrrol-1-ylmeth­yl)pyridine]­zinc(II)

Abstract

In the title compound, [Zn(C7H5O2)2(C10H10N2)2], the ZnII ion, located on a twofold axis, is coordinated by two N atoms from two 3-(pyrrol-1-ylmeth­yl)pyridine ligands and two O atoms from two benzoate ligands in a distorted tetra­hedral geometry. The pyridine and the pyrrole rings are nearly perpendicular to each other, making a dihedral angle of 84.83 (7)°.

Related literature

For examples of inter­actions between transition metal ions and biologically active mol­ecules, see: Daniele et al. (2008 [triangle]); Parkin (2004 [triangle]); Tshuva & Lippard (2004 [triangle]). For related structures, see: Lee et al. (2008 [triangle]); Park et al. (2008 [triangle]); Shin et al.(2009 [triangle]); Yu et al. (2008 [triangle], 2009 [triangle], 2010 [triangle]). For a description of the Cambridge Structural Database, see: Allen (2002 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-66-0m980-scheme1.jpg

Experimental

Crystal data

  • [Zn(C7H5O2)2(C10H10N2)2]
  • M r = 623.99
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-0m980-efi1.jpg
  • a = 14.4347 (14) Å
  • b = 9.4399 (9) Å
  • c = 11.1959 (11) Å
  • β = 102.896 (2)°
  • V = 1487.1 (2) Å3
  • Z = 2
  • Mo Kα radiation
  • μ = 0.87 mm−1
  • T = 170 K
  • 0.15 × 0.10 × 0.03 mm

Data collection

  • Bruker SMART CCD diffractometer
  • 8090 measured reflections
  • 2904 independent reflections
  • 2204 reflections with I > 2σ(I)
  • R int = 0.065

Refinement

  • R[F 2 > 2σ(F 2)] = 0.034
  • wR(F 2) = 0.071
  • S = 0.91
  • 2904 reflections
  • 195 parameters
  • H-atom parameters constrained
  • Δρmax = 0.52 e Å−3
  • Δρmin = −0.51 e Å−3

Data collection: SMART (Bruker, 1997 [triangle]); cell refinement: SAINT (Bruker, 1997 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: ORTEPIII (Burnett & Johnson, 1996 [triangle]) and ORTEP-3 for Windows (Farrugia, 1997 [triangle]); software used to prepare material for publication: SHELXTL (Sheldrick, 2008 [triangle]).

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536810028503/dn2587sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810028503/dn2587Isup2.hkl

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

Acknowledgments

Financial support from Korea Ministry Environment "ET-Human resource development Project" and the Cooperative Research Program for Agricultural Science & Technology Development (20070301–036-019–02) is gratefully acknowledged.

supplementary crystallographic information

Comment

The interaction of transition metal ions with biologically active molecules such as amino acids, proteins, sugars, nucleotides etc, is of great importance in the study of biological systems (Daniele, et al., 2008; Parkin, 2004; Tshuva & Lippard, 2004). As possible models for studying such interaction, the chemistry of transition metal ions with fulvic acids and humic acids has been intensively examined. Our group have reported a variety of structures of copper(II) and zinc(II) benzoates with quinoxaline, 6-methylquinoline, 3-methylquinoline, trans-1-(2-pyridyl)-2-(4-pyridyl)ethylene, and di-2-pyridyl ketone (Lee, et al., 2008; Yu, et al., 2008;Park, et al., 2008; Shin, et al.,2009;Yu, et al., 2009; Yu et al.,2010) in order to study the interaction of the transition metal ions with various acids. In this work, we have employed zinc(II) benzoate as a building block and 3-(pyrrol-1-ylmethyl)pyridine as a ligand.

In the title compound, the ZnII ion is located on a two fold axis and is coordinated by two nitrogen atoms from two symmetry related 3-(pyrrol-1-ylmethyl)pyridine ligands and two oxygen atoms from two symmetry related benzoate ligands to form a distorted tetrahedral geometry (Fig. 1). Zn—N and Zn—O bond distances are in agreement with reported bond distances in the Cambridge Structural Database (Allen, 2002). The pyridine and the pyrrol rings are nearly perpendicular to each other making a dihedral angle of 84.83 (7)°.

Experimental

30.4 mg (0.1 mmol) of Zn(NO3)2.6H2O and 28.0 mg (0.2 mmol) of C6H5COONH4 were dissolved in 4 ml H2O and carefully layered by 4 ml acetone solution of 3-(pyrrol-1-ylmethyl)pyridine (31.8 mg, 0.2 mmol). Suitable crystals of the title compound for X-ray analysis were obtained in a few weeks.

Refinement

H atoms were placed in calculated positions and treated as riding with C—H distances of 0.95 Å (pyridine and pyrrolidine) and 0.99 Å (methylene) and with Uiso(H)= 1.2Ueq(C).

Figures

Fig. 1.
The structure of the title compound showing the atom-labeling scheme. Displacement ellipsoids are shown at the 30% probability level. H atoms are represented as samll spheres of arbitrary radii. [Symmetry code: (i) 1-x, y, 3/2-z].

Crystal data

[Zn(C7H5O2)2(C10H10N2)2]F(000) = 648
Mr = 623.99Dx = 1.394 Mg m3
Monoclinic, P2/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ycCell parameters from 2361 reflections
a = 14.4347 (14) Åθ = 2.6–24.6°
b = 9.4399 (9) ŵ = 0.87 mm1
c = 11.1959 (11) ÅT = 170 K
β = 102.896 (2)°Plate, colorless
V = 1487.1 (2) Å30.15 × 0.10 × 0.03 mm
Z = 2

Data collection

Bruker SMART CCD diffractometer2204 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.065
graphiteθmax = 26.0°, θmin = 2.2°
[var phi] and ω scansh = −9→17
8090 measured reflectionsk = −11→11
2904 independent reflectionsl = −13→13

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.034Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.071H-atom parameters constrained
S = 0.91w = 1/[σ2(Fo2) + (0.0248P)2] where P = (Fo2 + 2Fc2)/3
2904 reflections(Δ/σ)max < 0.001
195 parametersΔρmax = 0.52 e Å3
0 restraintsΔρmin = −0.51 e Å3

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*/Ueq
Zn10.50000.58373 (4)0.75000.02372 (12)
O110.39278 (9)0.51333 (15)0.63040 (12)0.0289 (4)
O120.36133 (10)0.38352 (16)0.78176 (13)0.0376 (4)
C110.33872 (14)0.4306 (2)0.67596 (19)0.0259 (5)
C120.24503 (14)0.3958 (2)0.59353 (18)0.0241 (5)
C130.22904 (14)0.4186 (2)0.46787 (18)0.0294 (5)
H130.27940.45110.43300.035*
C140.14056 (16)0.3944 (2)0.3935 (2)0.0364 (6)
H140.13030.40940.30760.044*
C150.06679 (16)0.3482 (2)0.4441 (2)0.0395 (6)
H150.00560.33300.39300.047*
C160.08190 (16)0.3240 (3)0.5688 (2)0.0387 (6)
H160.03110.29240.60340.046*
C170.17063 (15)0.3458 (2)0.6428 (2)0.0310 (5)
H170.18130.32660.72810.037*
N210.45103 (11)0.72476 (17)0.86239 (14)0.0238 (4)
N220.22689 (12)1.08801 (19)0.91482 (16)0.0316 (4)
C210.48598 (14)0.7216 (2)0.98335 (18)0.0258 (5)
H210.53240.65231.01620.031*
C220.45709 (15)0.8149 (2)1.06183 (19)0.0325 (5)
H220.48240.80881.14760.039*
C230.39112 (15)0.9174 (2)1.01497 (19)0.0328 (5)
H230.37080.98291.06820.039*
C240.35458 (14)0.9243 (2)0.88950 (19)0.0283 (5)
C250.38588 (14)0.8249 (2)0.81762 (18)0.0258 (5)
H250.36020.82700.73180.031*
C260.28375 (16)1.0365 (2)0.8315 (2)0.0380 (6)
H26A0.31841.11710.80530.046*
H26B0.24100.99660.75760.046*
C270.24005 (15)1.2131 (2)0.9763 (2)0.0337 (5)
H270.28431.28470.96750.040*
C280.17895 (16)1.2179 (3)1.0527 (2)0.0389 (6)
H280.17251.29321.10650.047*
C290.12722 (16)1.0912 (3)1.0374 (2)0.0443 (6)
H290.07901.06491.07860.053*
C300.15875 (16)1.0129 (3)0.9527 (2)0.0429 (6)
H300.13680.92120.92480.051*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Zn10.0232 (2)0.0247 (2)0.0228 (2)0.0000.00434 (14)0.000
O110.0247 (8)0.0311 (9)0.0300 (8)−0.0069 (7)0.0045 (7)−0.0004 (7)
O120.0319 (9)0.0500 (11)0.0286 (9)−0.0016 (7)0.0017 (7)0.0079 (7)
C110.0262 (12)0.0236 (12)0.0279 (12)0.0047 (10)0.0060 (9)−0.0044 (10)
C120.0244 (11)0.0186 (11)0.0291 (12)0.0026 (9)0.0053 (9)−0.0004 (9)
C130.0300 (12)0.0264 (12)0.0319 (12)−0.0026 (10)0.0073 (10)−0.0006 (10)
C140.0398 (14)0.0333 (14)0.0307 (13)−0.0035 (11)−0.0039 (11)0.0008 (10)
C150.0244 (13)0.0347 (14)0.0524 (16)−0.0013 (11)−0.0066 (11)−0.0031 (12)
C160.0274 (13)0.0373 (14)0.0528 (16)−0.0030 (11)0.0121 (12)−0.0014 (12)
C170.0303 (13)0.0293 (12)0.0337 (13)0.0007 (10)0.0078 (10)0.0015 (10)
N210.0230 (10)0.0257 (10)0.0228 (9)−0.0016 (7)0.0054 (7)0.0014 (8)
N220.0309 (10)0.0248 (10)0.0403 (11)0.0040 (9)0.0104 (8)0.0000 (9)
C210.0243 (12)0.0289 (12)0.0240 (12)0.0007 (9)0.0051 (9)0.0047 (10)
C220.0374 (14)0.0400 (14)0.0196 (11)−0.0015 (11)0.0052 (10)0.0004 (10)
C230.0416 (14)0.0297 (12)0.0290 (12)0.0012 (11)0.0121 (10)−0.0053 (11)
C240.0312 (12)0.0252 (12)0.0296 (12)0.0010 (10)0.0094 (10)0.0008 (10)
C250.0266 (12)0.0290 (12)0.0209 (11)0.0006 (10)0.0038 (9)0.0017 (10)
C260.0456 (15)0.0331 (14)0.0367 (14)0.0114 (11)0.0122 (12)0.0002 (11)
C270.0319 (13)0.0268 (13)0.0417 (14)0.0008 (10)0.0070 (11)−0.0017 (11)
C280.0350 (15)0.0418 (15)0.0410 (14)0.0066 (11)0.0107 (12)−0.0063 (12)
C290.0298 (13)0.0471 (16)0.0604 (17)0.0038 (12)0.0197 (12)0.0083 (14)
C300.0353 (15)0.0275 (14)0.0649 (18)−0.0029 (11)0.0093 (13)−0.0004 (12)

Geometric parameters (Å, °)

Zn1—O11i1.9248 (13)N22—C271.359 (3)
Zn1—O111.9248 (13)N22—C261.457 (3)
Zn1—N21i2.0621 (16)C21—C221.373 (3)
Zn1—N212.0621 (16)C21—H210.9500
O11—C111.287 (2)C22—C231.377 (3)
O12—C111.239 (2)C22—H220.9500
C11—C121.494 (3)C23—C241.387 (3)
C12—C131.391 (3)C23—H230.9500
C12—C171.395 (3)C24—C251.376 (3)
C13—C141.379 (3)C24—C261.514 (3)
C13—H130.9500C25—H250.9500
C14—C151.383 (3)C26—H26A0.9900
C14—H140.9500C26—H26B0.9900
C15—C161.384 (3)C27—C281.359 (3)
C15—H150.9500C27—H270.9500
C16—C171.377 (3)C28—C291.400 (3)
C16—H160.9500C28—H280.9500
C17—H170.9500C29—C301.359 (3)
N21—C211.336 (2)C29—H290.9500
N21—C251.349 (2)C30—H300.9500
N22—C301.355 (3)
O11i—Zn1—O11139.60 (9)N21—C21—C22122.29 (19)
O11i—Zn1—N21i108.40 (6)N21—C21—H21118.9
O11—Zn1—N21i97.49 (6)C22—C21—H21118.9
O11i—Zn1—N2197.48 (6)C21—C22—C23119.3 (2)
O11—Zn1—N21108.39 (6)C21—C22—H22120.3
N21i—Zn1—N2199.58 (9)C23—C22—H22120.3
C11—O11—Zn1113.47 (13)C22—C23—C24119.6 (2)
O12—C11—O11122.87 (19)C22—C23—H23120.2
O12—C11—C12121.42 (19)C24—C23—H23120.2
O11—C11—C12115.70 (18)C25—C24—C23117.37 (19)
C13—C12—C17118.95 (19)C25—C24—C26120.30 (18)
C13—C12—C11120.95 (18)C23—C24—C26122.32 (19)
C17—C12—C11120.04 (18)N21—C25—C24123.58 (18)
C14—C13—C12120.5 (2)N21—C25—H25118.2
C14—C13—H13119.8C24—C25—H25118.2
C12—C13—H13119.8N22—C26—C24112.46 (17)
C13—C14—C15119.9 (2)N22—C26—H26A109.1
C13—C14—H14120.0C24—C26—H26A109.1
C15—C14—H14120.0N22—C26—H26B109.1
C14—C15—C16120.2 (2)C24—C26—H26B109.1
C14—C15—H15119.9H26A—C26—H26B107.8
C16—C15—H15119.9N22—C27—C28108.1 (2)
C17—C16—C15119.9 (2)N22—C27—H27125.9
C17—C16—H16120.0C28—C27—H27125.9
C15—C16—H16120.0C27—C28—C29107.3 (2)
C16—C17—C12120.5 (2)C27—C28—H28126.3
C16—C17—H17119.8C29—C28—H28126.3
C12—C17—H17119.8C30—C29—C28107.3 (2)
C21—N21—C25117.83 (17)C30—C29—H29126.3
C21—N21—Zn1120.05 (14)C28—C29—H29126.3
C25—N21—Zn1122.09 (13)N22—C30—C29108.3 (2)
C30—N22—C27108.97 (18)N22—C30—H30125.9
C30—N22—C26125.30 (19)C29—C30—H30125.9
C27—N22—C26125.43 (19)
O11i—Zn1—O11—C1156.95 (13)N21i—Zn1—N21—C2556.41 (14)
N21i—Zn1—O11—C11−172.84 (13)C25—N21—C21—C220.7 (3)
N21—Zn1—O11—C11−70.10 (14)Zn1—N21—C21—C22178.71 (15)
Zn1—O11—C11—O12−10.7 (3)N21—C21—C22—C23−1.2 (3)
Zn1—O11—C11—C12168.33 (12)C21—C22—C23—C240.3 (3)
O12—C11—C12—C13−164.0 (2)C22—C23—C24—C251.0 (3)
O11—C11—C12—C1317.0 (3)C22—C23—C24—C26−178.4 (2)
O12—C11—C12—C1718.9 (3)C21—N21—C25—C240.8 (3)
O11—C11—C12—C17−160.13 (18)Zn1—N21—C25—C24−177.24 (15)
C17—C12—C13—C141.1 (3)C23—C24—C25—N21−1.6 (3)
C11—C12—C13—C14−176.02 (19)C26—C24—C25—N21177.83 (19)
C12—C13—C14—C150.5 (3)C30—N22—C26—C24−70.4 (3)
C13—C14—C15—C16−1.1 (3)C27—N22—C26—C24102.6 (2)
C14—C15—C16—C17−0.1 (4)C25—C24—C26—N22153.59 (19)
C15—C16—C17—C121.8 (3)C23—C24—C26—N22−27.0 (3)
C13—C12—C17—C16−2.3 (3)C30—N22—C27—C28−0.7 (3)
C11—C12—C17—C16174.9 (2)C26—N22—C27—C28−174.69 (19)
O11i—Zn1—N21—C21−11.37 (15)N22—C27—C28—C290.2 (3)
O11—Zn1—N21—C21137.18 (14)C27—C28—C29—C300.3 (3)
N21i—Zn1—N21—C21−121.55 (16)C27—N22—C30—C290.9 (3)
O11i—Zn1—N21—C25166.58 (15)C26—N22—C30—C29174.90 (19)
O11—Zn1—N21—C25−44.86 (16)C28—C29—C30—N22−0.8 (3)

Symmetry codes: (i) −x+1, y, −z+3/2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: DN2587).

References

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