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Acta Cryst. (2009). E65, m658-m659    [ doi:10.1107/S1600536809017772 ]

A neutral cubane with a ZnII4O4 core: tetrabenzoatotetrakis([mu]3-hydroxydi-2-pyridylmethanolato)tetrazinc(II)-acetone-methanol (1/2/1)

D. H. Shin, S.-H. Han, P.-G. Kim, C. Kim and Y. Kim

Abstract top

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 [mu]3-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 [eta]1:[eta]3:[eta]1:[mu]3 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.

Comment top

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 [ZnII4(µ3-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 η1:η3:η1:µ3 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.

Related literature top

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); For related crystal structures, see: Lee et al. (2008); Park et al. (2008); Yu et al. (2008); Stoumpos et al. (2008); Papaefstathiou & Perlepes (2002); Papatriantafyllopoulou et al., (2007).

Experimental top

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 top

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).

Computing details top

Data collection: SMART (Bruker, 1997); cell refinement: SAINT (Bruker, 1997); data reduction: SAINT (Bruker, 1997); 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. 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.
Tetrabenzoatotetrakis(µ3-hydroxydi-2-pyridylmethanolato)tetrazinc(II)– acetone–methanol (1/2/1) top
Crystal data top
[Zn4(C11H9N2O2)4(C7H5O2)4]·2C3H6O·CH4ODx = 1.458 Mg m−3
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 mm−1
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 top
Bruker SMART CCD
diffractometer		4628 independent reflections
Radiation source: fine-focus sealed tube4279 reflections with I > 2σ(I)
graphiteRint = 0.029
φ 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 top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.034H-atom parameters constrained
wR(F2) = 0.110 w = 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 Å−3
245 parametersΔρmin = −0.42 e Å−3
5 restraintsAbsolute structure: Flack (1983), 2045 Friedel pairs
Primary atom site location: structure-invariant direct methodsFlack parameter: 0.002 (13)
Crystal data top
[Zn4(C11H9N2O2)4(C7H5O2)4]·2C3H6O·CH4OZ = 1
Mr = 6795.70Mo Kα radiation
Tetragonal, I42dµ = 1.30 mm−1
a = 14.3201 (4) ÅT = 170 K
c = 37.730 (2) Å0.10 × 0.08 × 0.05 mm
V = 7737.1 (5) Å3
Data collection top
Bruker SMART CCD
diffractometer		4628 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 1997)		4279 reflections with I > 2σ(I)
Tmin = 0.883, Tmax = 0.937Rint = 0.029
22787 measured reflectionsθmax = 28.3°
Refinement top
R[F2 > 2σ(F2)] = 0.034H-atom parameters constrained
wR(F2) = 0.110Δρmax = 1.37 e Å−3
S = 1.09Δρmin = −0.42 e Å−3
4628 reflectionsAbsolute structure: Flack (1983), 2045 Friedel pairs
245 parametersFlack parameter: 0.002 (13)
5 restraints
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)
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) top
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, °) top
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, °) top
D—H···AD—HH···AD···AD—H···A
O2—H2O···O40.861.812.664 (3)172
Table 1
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
O2—H2O···O40.861.812.664 (3)172
Acknowledgements top

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.

references
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