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Acta Crystallogr Sect E Struct Rep Online. 2009 June 1; 65(Pt 6): m658–m659.
Published online 2009 May 20. doi:  10.1107/S1600536809017772
PMCID: PMC2969578

A neutral cubane with a ZnII 4O4 core: tetra­benzoato­tetra­kis(μ3-hydroxydi-2-pyridylmethano­lato)tetra­zinc(II)–acetone–methanol (1/2/1)

Abstract

In the title compound, [Zn4(C11H9N2O2)4(C7H5O2)4]·2(CH3)2CO·CH3OH, the tetra­nuclear mol­ecule lies on a fourfold inversion axis. ZnII ions and μ3-O atoms in the cubane core occupy alternating vertices, forming two inter­penetrating tetra­hedra. Each ZnII ion is further coordinated by two N atoms from two different (py)2C(OH)O ligands (py is pyrid­yl) and one O atom from a monodentate benzoate ligand, forming a distorted octa­hedral environment. The (py)2C(OH)O ligand acts in an η1313 manner, forming two five-membered ZnNCCO chelating rings with two different ZnII atoms sharing a common C—O bond, and an alkoxide-type bond to a third ZnII ion. There are four symmetry-related intra­molecular O—H(...)O hydrogen bonds between the two types of ligands. In the asymmetric unit, there is a half-occupancy acetone solvent mol­ecule and a half-occupancy methanol solvent molecule that lies on a twofold rotation axis.

Related literature

For background to transition metal ions as the major cationic contributors to the inorganic composition of natural water and biological fluids, see: Daniele et al. (2008 [triangle]); For related crystal structures, see: Lee et al. (2008 [triangle]); Park et al. (2008 [triangle]); Yu et al. (2008 [triangle]); Stoumpos et al. (2008 [triangle]); Papaefstathiou & Perlepes (2002 [triangle]); Papatriantafyllopoulou et al. (2007 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-0m658-scheme1.jpg

Experimental

Crystal data

  • [Zn4(C11H9N2O2)4(C7H5O2)4]·2C3H6O·CH4O
  • M r = 6795.70
  • Tetragonal, An external file that holds a picture, illustration, etc.
Object name is e-65-0m658-efi1.jpg
  • a = 14.3201 (4) Å
  • c = 37.730 (2) Å
  • V = 7737.1 (5) Å3
  • Z = 1
  • Mo Kα radiation
  • μ = 1.30 mm−1
  • T = 170 K
  • 0.10 × 0.08 × 0.05 mm

Data collection

  • Bruker SMART CCD diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 1997 [triangle]) T min = 0.883, T max = 0.937
  • 22787 measured reflections
  • 4628 independent reflections
  • 4279 reflections with I > 2σ(I)
  • R int = 0.029

Refinement

  • R[F 2 > 2σ(F 2)] = 0.034
  • wR(F 2) = 0.110
  • S = 1.09
  • 4628 reflections
  • 245 parameters
  • 5 restraints
  • H-atom parameters constrained
  • Δρmax = 1.37 e Å−3
  • Δρmin = −0.42 e Å−3
  • Absolute structure: Flack (1983 [triangle]), 2045 Friedel pairs
  • Flack parameter: 0.002 (13)

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: SHELXTL (Sheldrick, 2008 [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/S1600536809017772/lh2815sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809017772/lh2815Isup2.hkl

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

Acknowledgments

Financial support from the Korea Ministry of the 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

Transition metal ions have, recently, received attention as the major cationic contributors to the inorganic composition of natural water and biological fluids (Daniele, et al., 2008). While the main interest is focused on the interaction of transition metal ions with biologically active molecules such as amino acids, proteins, sugars and nucleotides, the study on the interaction of the transition metal ions with fulvic acids and humic acids, mainly found in soil, is in incipient stages. As models to examine the interaction, therefore, we have previously used copper(II) benzoate as a building block and reported the structures of copper(II) benzoates with quinoxaline, 6-methylquinoline, and 3-methylquinoline (Lee, et al., 2008; Yu, et al., 2008; Park, et al., 2008). In this work, we have employed zinc(II) benzoate as a building block and di-2-pyridyl ketone as a ligand. We report herein the structure of the product of zinc(II) benzoate with di-2-pyridyl ketone.

The crystal structure contains tetranuclear [Zn4(O2CPh)4{(py)2C(OH)O}4] molecules (Fig. 1), similar to the corresponding Mn4 cubane compound (Stoumpos, et al., 2008). The tetramolecular molecule lies on a fourfold inversion center and hence the asymmetric unit contains a quarter of a molecule. ZnII ions and µ3-O atoms in the cubane [ZnII43-OR)4]4+ core occupy alternate vertices. Thus, the molecule consists of two interpenetrating tetrahedra: one contains four µ3-O atoms originating from the (py)2C(OH)O ligands, and the other contains four ZnII atoms. Each ZnII center is coordinated by two N atoms from two different (py)2C(OH)O ligands and one O atom from a monodentate PhCO2- ligand to form a distorted octahedral geometry. The (py)2C(OH)O ligands acts as η1313 to form two five-membered ZnNCCO chelating rings with two different ZnII ions sharing a common C—O edge and an alkoxide-type bond to a third ZnII ion. This ligation mode is common for the hydrated di-2-pyridyl ketone, (py)2C(OH)O- (Papaefstathiou & Perlepes, 2002; Papatriantafyllopoulou,et al., 2007). There are intramolecular hydrogen bonds interactions between the protonated O atom of the (py)2C(OH)O ligand and the uncoordinated O atom of the monodentate PhCO2 group.

Experimental

38.0 mg (0.125 mmol) of Zn(NO3)2.6H2O and 35.5 mg (0.25 mmol) of C6H5COONH4 were dissolved in 4 ml water and carefully layered by 4 ml solution of a mixture of acetone, methanol and ethanol (2/2/2) of di-2-pyridyl ketone ligand (46.1 mg, 0.25 mmol). Crystals of the title compound suitable for X-ray analysis were obtained in a few weeks.

Refinement

H atoms were placed in calculated positions with C—H distances of 0.93–0.98 Å and O—H = 0.82 Å. They were included in the refinement in a riding-motion approximation with Uiso(H) = 1.2Ueq(C) or 1.5Ueq(Cmethyl and O).

Figures

Fig. 1.
Partially labeled molecular structure of the title complex. Displacement ellipsoids areshown at the 30% probability level. The green dotted lines represent hydrogen bonds. Solvent molecules are not shown.

Crystal data

[Zn4(C11H9N2O2)4(C7H5O2)4]·2C3H6O·CH4ODx = 1.458 Mg m3
Mr = 6795.70Mo Kα radiation, λ = 0.71073 Å
Tetragonal, I42dCell parameters from 8208 reflections
Hall symbol: I -4 2bwθ = 2.8–27.0°
a = 14.3201 (4) ŵ = 1.30 mm1
c = 37.730 (2) ÅT = 170 K
V = 7737.1 (5) Å3Polyhedron, colorless
Z = 10.10 × 0.08 × 0.05 mm
F(000) = 3496

Data collection

Bruker SMART CCD diffractometer4628 independent reflections
Radiation source: fine-focus sealed tube4279 reflections with I > 2σ(I)
graphiteRint = 0.029
[var phi] and ω scansθmax = 28.3°, θmin = 1.5°
Absorption correction: multi-scan (SADABS; Bruker, 1997)h = −18→18
Tmin = 0.883, Tmax = 0.937k = −9→18
22787 measured reflectionsl = −48→48

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.034H-atom parameters constrained
wR(F2) = 0.110w = 1/[σ2(Fo2) + (0.0787P)2 + 0.4409P] where P = (Fo2 + 2Fc2)/3
S = 1.09(Δ/σ)max = 0.001
4628 reflectionsΔρmax = 1.37 e Å3
245 parametersΔρmin = −0.42 e Å3
5 restraintsAbsolute structure: Flack (1983), 2045 Friedel pairs
Primary atom site location: structure-invariant direct methodsFlack parameter: 0.002 (13)

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)
Zn10.61621 (2)0.51226 (2)0.470190 (8)0.01677 (10)
O10.50301 (15)0.59983 (13)0.47540 (5)0.0177 (4)
O20.53176 (14)0.75354 (15)0.45808 (6)0.0237 (5)
H2O0.59080.74290.45750.036*
O30.73924 (15)0.58089 (15)0.47172 (6)0.0257 (4)
O40.71640 (16)0.73233 (17)0.46138 (9)0.0390 (6)
N10.58789 (18)0.55925 (18)0.41603 (6)0.0197 (5)
N20.67260 (17)0.38313 (19)0.45377 (6)0.0204 (5)
C10.6300 (2)0.5287 (2)0.38641 (8)0.0262 (6)
H10.67120.47680.38810.031*
C20.6162 (3)0.5691 (3)0.35381 (9)0.0366 (8)
H20.64650.54550.33330.044*
C30.5566 (3)0.6455 (3)0.35178 (10)0.0404 (10)
H30.54480.67480.32960.049*
C40.5141 (3)0.6789 (3)0.38253 (8)0.0331 (8)
H40.47410.73180.38180.040*
C50.5320 (2)0.6328 (2)0.41431 (8)0.0210 (6)
C60.4901 (2)0.6676 (2)0.44992 (7)0.0187 (5)
C70.6154 (2)0.3128 (2)0.44535 (7)0.0192 (5)
C80.6484 (2)0.2278 (2)0.43286 (9)0.0256 (6)
H80.60640.17830.42770.031*
C90.7445 (3)0.2165 (2)0.42796 (10)0.0325 (8)
H90.76850.16040.41810.039*
C100.8032 (2)0.2871 (3)0.43751 (10)0.0330 (8)
H100.86890.27970.43530.040*
C110.7658 (2)0.3707 (2)0.45060 (9)0.0280 (7)
H110.80690.41970.45740.034*
C120.7640 (2)0.6651 (2)0.47105 (9)0.0227 (6)
C130.8626 (2)0.6836 (2)0.48381 (8)0.0237 (6)
C140.9023 (2)0.7726 (2)0.48046 (11)0.0341 (8)
H140.86760.82180.46990.041*
C150.9924 (3)0.7888 (3)0.49264 (12)0.0461 (10)
H151.01960.84890.49000.055*
C161.0423 (3)0.7181 (3)0.50846 (13)0.0474 (11)
H161.10390.72950.51680.057*
C171.0032 (3)0.6313 (3)0.51216 (11)0.0398 (8)
H171.03740.58290.52340.048*
C180.9141 (2)0.6138 (3)0.49960 (9)0.0306 (7)
H180.88820.55300.50190.037*
O1S0.9292 (16)1.1086 (15)0.3972 (6)0.218 (6)*0.50
C1S0.9466 (13)1.0280 (17)0.3923 (6)0.218 (6)*0.50
C2S0.965 (2)0.972 (2)0.4275 (8)0.218 (6)*0.50
H2S11.02590.98860.43720.328*0.50
H2S20.96340.90450.42240.328*0.50
H2S30.91600.98650.44480.328*0.50
C3S0.9503 (19)0.975 (2)0.3559 (7)0.218 (6)*0.50
H3S10.89560.93400.35370.328*0.50
H3S21.00730.93700.35470.328*0.50
H3S30.95041.02010.33640.328*0.50
O2S0.75001.0096 (11)0.37500.110 (5)*0.50
H2S0.71971.02920.35740.164*0.25
C21S0.75000.9049 (11)0.37500.139 (10)*0.50
H21A0.79990.88210.35950.208*0.25
H21B0.68960.88210.36640.208*0.25
H21C0.76050.88210.39920.208*0.25

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Zn10.01658 (17)0.01739 (17)0.01634 (15)0.00064 (12)0.00086 (12)0.00068 (12)
O10.0189 (9)0.0175 (9)0.0167 (9)0.0029 (8)0.0001 (8)0.0034 (7)
O20.0206 (10)0.0193 (10)0.0311 (11)−0.0009 (9)0.0009 (8)−0.0005 (9)
O30.0216 (11)0.0258 (11)0.0296 (11)−0.0035 (9)0.0013 (9)−0.0002 (10)
O40.0214 (11)0.0262 (13)0.0693 (19)−0.0015 (9)−0.0062 (11)0.0019 (12)
N10.0201 (12)0.0213 (12)0.0176 (11)0.0003 (9)0.0009 (9)0.0007 (9)
N20.0182 (12)0.0232 (12)0.0199 (11)0.0025 (11)0.0015 (9)0.0025 (10)
C10.0244 (15)0.0299 (16)0.0244 (14)0.0035 (13)0.0059 (12)0.0000 (12)
C20.044 (2)0.044 (2)0.0218 (15)0.0112 (18)0.0101 (15)0.0016 (14)
C30.050 (2)0.048 (2)0.0227 (16)0.0158 (19)0.0113 (16)0.0114 (15)
C40.0378 (19)0.0376 (18)0.0238 (15)0.0120 (16)0.0058 (14)0.0085 (13)
C50.0206 (14)0.0214 (14)0.0211 (14)0.0008 (12)0.0015 (10)0.0043 (11)
C60.0199 (14)0.0168 (13)0.0194 (12)0.0026 (12)0.0006 (11)0.0040 (10)
C70.0206 (14)0.0207 (13)0.0163 (12)0.0010 (12)0.0005 (11)0.0006 (10)
C80.0267 (15)0.0255 (16)0.0245 (15)0.0056 (13)−0.0002 (12)−0.0017 (12)
C90.0317 (18)0.0298 (17)0.0361 (18)0.0124 (15)0.0060 (15)−0.0024 (14)
C100.0231 (16)0.0371 (19)0.0388 (19)0.0086 (14)0.0068 (14)0.0018 (15)
C110.0214 (15)0.0312 (17)0.0315 (17)−0.0005 (13)0.0033 (12)0.0037 (14)
C120.0192 (14)0.0267 (15)0.0221 (14)−0.0017 (11)0.0049 (12)−0.0030 (13)
C130.0204 (15)0.0263 (16)0.0246 (14)−0.0009 (12)0.0040 (12)−0.0069 (12)
C140.0275 (18)0.0260 (17)0.049 (2)−0.0028 (14)0.0040 (14)−0.0056 (14)
C150.0283 (18)0.0291 (18)0.081 (3)−0.0061 (16)−0.001 (2)−0.0103 (19)
C160.0218 (17)0.048 (2)0.072 (3)−0.0035 (16)−0.0083 (18)−0.020 (2)
C170.0292 (17)0.038 (2)0.052 (2)0.0050 (16)−0.0075 (17)−0.0062 (17)
C180.0270 (16)0.0290 (16)0.0357 (17)−0.0039 (14)−0.0012 (13)−0.0028 (14)

Geometric parameters (Å, °)

Zn1—O32.018 (2)C9—C101.365 (5)
Zn1—O12.059 (2)C9—H90.9500
Zn1—O1i2.0776 (19)C10—C111.401 (5)
Zn1—N22.111 (3)C10—H100.9500
Zn1—N12.189 (2)C11—H110.9500
Zn1—O1ii2.351 (2)C12—C131.515 (4)
O1—C61.378 (3)C13—C181.378 (5)
O1—Zn1iii2.0777 (19)C13—C141.401 (5)
O1—Zn1ii2.352 (2)C14—C151.389 (5)
O2—C61.402 (4)C14—H140.9500
O2—H2O0.8587C15—C161.376 (6)
O3—C121.257 (4)C15—H150.9500
O4—C121.235 (4)C16—C171.371 (6)
N1—C51.325 (4)C16—H160.9500
N1—C11.343 (4)C17—C181.384 (5)
N2—C71.336 (4)C17—H170.9500
N2—C111.352 (4)C18—H180.9500
C1—C21.374 (5)O1S—C1S1.195 (10)
C1—H10.9500C1S—C2S1.57 (2)
C2—C31.391 (5)C1S—C3S1.57 (2)
C2—H20.9500C2S—H2S10.9800
C3—C41.394 (5)C2S—H2S20.9800
C3—H30.9500C2S—H2S30.9800
C4—C51.392 (4)C3S—H3S10.9800
C4—H40.9500C3S—H3S20.9800
C5—C61.553 (4)C3S—H3S30.9800
C6—C7ii1.546 (4)O2S—C21S1.499 (2)
C7—C81.388 (4)O2S—H2S0.8400
C7—C6ii1.546 (4)C21S—H21A0.98000
C8—C91.398 (5)C21S—H21B0.98000
C8—H80.9500C21S—H21C0.98000
O3—Zn1—O1112.83 (9)C7—C8—H8120.6
O3—Zn1—O1i96.98 (9)C9—C8—H8120.6
O1—Zn1—O1i83.16 (8)C10—C9—C8119.1 (3)
O3—Zn1—N295.80 (9)C10—C9—H9120.5
O1—Zn1—N2149.64 (9)C8—C9—H9120.5
O1i—Zn1—N2103.94 (9)C9—C10—C11119.4 (3)
O3—Zn1—N192.22 (9)C9—C10—H10120.3
O1—Zn1—N175.88 (9)C11—C10—H10120.3
O1i—Zn1—N1159.01 (9)N2—C11—C10121.4 (3)
N2—Zn1—N193.79 (10)N2—C11—H11119.3
O3—Zn1—O1ii164.53 (8)C10—C11—H11119.3
O1—Zn1—O1ii80.57 (8)O4—C12—O3126.7 (3)
O1i—Zn1—O1ii76.33 (8)O4—C12—C13118.1 (3)
N2—Zn1—O1ii72.80 (8)O3—C12—C13115.2 (3)
N1—Zn1—O1ii98.82 (8)C18—C13—C14118.8 (3)
C6—O1—Zn1117.87 (17)C18—C13—C12120.6 (3)
C6—O1—Zn1iii126.55 (17)C14—C13—C12120.6 (3)
Zn1—O1—Zn1iii104.24 (9)C15—C14—C13119.9 (4)
C6—O1—Zn1ii108.97 (17)C15—C14—H14120.0
Zn1—O1—Zn1ii98.51 (8)C13—C14—H14120.1
Zn1iii—O1—Zn1ii94.78 (7)C16—C15—C14120.2 (4)
C6—O2—H2O104.9C16—C15—H15119.9
C12—O3—Zn1135.5 (2)C14—C15—H15119.9
C5—N1—C1119.3 (3)C17—C16—C15119.9 (4)
C5—N1—Zn1113.71 (19)C17—C16—H16120.0
C1—N1—Zn1126.4 (2)C15—C16—H16120.0
C7—N2—C11119.1 (3)C16—C17—C18120.5 (4)
C7—N2—Zn1119.66 (19)C16—C17—H17119.8
C11—N2—Zn1121.3 (2)C18—C17—H17119.8
N1—C1—C2122.9 (3)C13—C18—C17120.6 (4)
N1—C1—H1118.6C13—C18—H18119.7
C2—C1—H1118.5C17—C18—H18119.7
C1—C2—C3118.0 (3)O1S—C1S—C2S114 (2)
C1—C2—H2121.0O1S—C1S—C3S128 (2)
C3—C2—H2121.0C2S—C1S—C3S119 (2)
C2—C3—C4119.4 (3)C1S—C2S—H2S1109.5
C2—C3—H3120.3C1S—C2S—H2S2109.4
C4—C3—H3120.3H2S1—C2S—H2S2109.5
C5—C4—C3118.3 (3)C1S—C2S—H2S3109.5
C5—C4—H4120.9H2S1—C2S—H2S3109.5
C3—C4—H4120.9H2S2—C2S—H2S3109.5
N1—C5—C4122.0 (3)C1S—C3S—H3S1109.5
N1—C5—C6116.5 (2)C1S—C3S—H3S2109.4
C4—C5—C6121.4 (3)H3S1—C3S—H3S2109.5
O1—C6—O2114.1 (2)C1S—C3S—H3S3109.5
O1—C6—C7ii109.6 (2)H3S1—C3S—H3S3109.5
O2—C6—C7ii106.3 (2)H3S2—C3S—H3S3109.5
O1—C6—C5109.0 (2)C21S—O2S—H2S109.5
O2—C6—C5107.9 (2)O2S—C21S—H21A109.00
C7ii—C6—C5109.8 (2)O2S—C21S—H21B109.00
N2—C7—C8122.1 (3)H21A—C21S—H21B110.00
N2—C7—C6ii115.9 (2)O2S—C21S—H21C109.00
C8—C7—C6ii122.0 (3)H21A—C21S—H21C109.00
C7—C8—C9118.8 (3)H21B—C21S—H21C109.00

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

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
O2—H2O···O40.861.812.664 (3)172

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: LH2815).

References

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