metal-organic compounds
Tetraaquabis{2-[4-(4-pyridyl)pyrimidin-2-ylsulfanyl]acetato}zinc
aSchool of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, People's Republic of China
*Correspondence e-mail: zhuhaibin@seu.edu.cn
In the title compound, [Zn(C11H8N3O2S)2(H2O)4], the ZnII ion lies on an inversion centre and is coordinated by four water molecules and two N atoms from two 2-[4-(4-pyridyl)pyrimidin-2-ylsulfanyl]acetate (L) ligands in a distorted octahedral geometry. In L, the pyridine and pyrimidine rings are twisted at an angle of 11.2 (1)°. The coordinated water molecules and the acetate groups are involved in the formation of a three-dimensional hydrogen-bonded network, which consolidates the crystal packing.
Experimental
Crystal data
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Refinement
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Data collection: APEX2 (Bruker, 2007); cell SAINT-Plus (Bruker, 2007); data reduction: SAINT-Plus; 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.
Supporting information
10.1107/S160053681102993X/cv5136sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: 10.1107/S160053681102993X/cv5136Isup2.hkl
The mixture of Zn(NO3)2 (0.1 mmol), L (0.2 mmol) and NaOH (0.2 mmol) in 10 ml of H2O was stirred for 30 min at room temperature. After filtration, the mother liquid was stood for three weeks to give yellow crystals suitable for X-ray diffraction analysis.
C-bound H atoms were positioned geometrically (C—H = 0.93 Å) and allowed to ride on their parent atoms, with Uiso(H) = 1.2 Ueq(C). The positions of the water H atoms were found from a difference Fourier map and refined with restraint O—H = 0.82 (2) Å using a riding model, with Uiso(H) = 1.2 Ueq(O).
Data collection: APEX2 (Bruker, 2007); cell
SAINT-Plus (Bruker, 2007); data reduction: SAINT-Plus (Bruker, 2007); 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).[Zn(C11H8N3O2S)2(H2O)4] | F(000) = 1296 |
Mr = 630.00 | Dx = 1.714 Mg m−3 |
Orthorhombic, Pbca | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ac 2ab | Cell parameters from 2465 reflections |
a = 7.199 (7) Å | θ = 2.3–25.5° |
b = 11.792 (11) Å | µ = 1.24 mm−1 |
c = 28.77 (3) Å | T = 298 K |
V = 2442 (4) Å3 | Block, yellow |
Z = 4 | 0.20 × 0.20 × 0.15 mm |
Bruker APEXII CCD area-detector diffractometer | 2465 independent reflections |
Radiation source: fine-focus sealed tube | 1836 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.051 |
ϕ and ω scans | θmax = 27.1°, θmin = 1.4° |
Absorption correction: multi-scan (SADABS; Bruker, 2001) | h = −8→9 |
Tmin = 0.780, Tmax = 0.830 | k = −14→14 |
16776 measured reflections | l = −34→32 |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.033 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.086 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.02 | w = 1/[σ2(Fo2) + (0.0432P)2 + 0.3573P] where P = (Fo2 + 2Fc2)/3 |
2465 reflections | (Δ/σ)max < 0.001 |
190 parameters | Δρmax = 0.23 e Å−3 |
4 restraints | Δρmin = −0.45 e Å−3 |
[Zn(C11H8N3O2S)2(H2O)4] | V = 2442 (4) Å3 |
Mr = 630.00 | Z = 4 |
Orthorhombic, Pbca | Mo Kα radiation |
a = 7.199 (7) Å | µ = 1.24 mm−1 |
b = 11.792 (11) Å | T = 298 K |
c = 28.77 (3) Å | 0.20 × 0.20 × 0.15 mm |
Bruker APEXII CCD area-detector diffractometer | 2465 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2001) | 1836 reflections with I > 2σ(I) |
Tmin = 0.780, Tmax = 0.830 | Rint = 0.051 |
16776 measured reflections |
R[F2 > 2σ(F2)] = 0.033 | 4 restraints |
wR(F2) = 0.086 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.02 | Δρmax = 0.23 e Å−3 |
2465 reflections | Δρmin = −0.45 e Å−3 |
190 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
Zn1 | 0.0000 | 0.5000 | 0.5000 | 0.02474 (14) | |
S1 | 0.01224 (8) | 0.60147 (5) | 0.17445 (2) | 0.02955 (17) | |
N2 | 0.1353 (3) | 0.80094 (16) | 0.20795 (6) | 0.0297 (5) | |
N1 | 0.0402 (3) | 0.65524 (16) | 0.26077 (6) | 0.0264 (5) | |
O4 | 0.2360 (2) | 0.41441 (14) | 0.47861 (5) | 0.0314 (4) | |
H4WB | 0.307 (3) | 0.396 (2) | 0.4993 (7) | 0.038* | |
H4WA | 0.302 (3) | 0.450 (2) | 0.4603 (7) | 0.038* | |
C1 | 0.0700 (3) | 0.6981 (2) | 0.21845 (8) | 0.0256 (5) | |
C10 | 0.0382 (3) | 0.6859 (2) | 0.12255 (8) | 0.0283 (5) | |
H10A | −0.0412 | 0.7522 | 0.1244 | 0.034* | |
H10B | 0.1658 | 0.7114 | 0.1198 | 0.034* | |
O1 | −0.0740 (3) | 0.51902 (14) | 0.08678 (6) | 0.0396 (5) | |
C5 | 0.0435 (3) | 0.67551 (18) | 0.34366 (8) | 0.0236 (5) | |
C4 | 0.0801 (3) | 0.72292 (19) | 0.29679 (7) | 0.0241 (5) | |
C11 | −0.0136 (3) | 0.6163 (2) | 0.08050 (8) | 0.0269 (5) | |
N3 | −0.0130 (2) | 0.58138 (16) | 0.43217 (6) | 0.0255 (4) | |
O2 | 0.0038 (2) | 0.66402 (14) | 0.04128 (6) | 0.0339 (4) | |
O3 | −0.1746 (3) | 0.36656 (14) | 0.47517 (6) | 0.0342 (4) | |
H3WB | −0.118 (3) | 0.3056 (17) | 0.4696 (9) | 0.041* | |
H3WA | −0.269 (3) | 0.355 (2) | 0.4908 (8) | 0.041* | |
C7 | 0.0205 (3) | 0.6920 (2) | 0.42625 (8) | 0.0287 (6) | |
H7A | 0.0259 | 0.7377 | 0.4525 | 0.034* | |
C3 | 0.1516 (3) | 0.83095 (19) | 0.28983 (8) | 0.0295 (5) | |
H3B | 0.1814 | 0.8781 | 0.3147 | 0.035* | |
C9 | 0.0026 (3) | 0.5610 (2) | 0.34959 (8) | 0.0301 (6) | |
H9A | −0.0059 | 0.5135 | 0.3239 | 0.036* | |
C8 | −0.0249 (3) | 0.5184 (2) | 0.39326 (8) | 0.0309 (6) | |
H8A | −0.0534 | 0.4418 | 0.3962 | 0.037* | |
C2 | 0.1763 (4) | 0.86515 (19) | 0.24447 (8) | 0.0311 (6) | |
H2B | 0.2245 | 0.9372 | 0.2391 | 0.037* | |
C6 | 0.0476 (3) | 0.7421 (2) | 0.38362 (8) | 0.0294 (5) | |
H6A | 0.0685 | 0.8197 | 0.3815 | 0.035* |
U11 | U22 | U33 | U12 | U13 | U23 | |
Zn1 | 0.0297 (2) | 0.0257 (2) | 0.0188 (2) | 0.00061 (16) | 0.00071 (16) | −0.00053 (15) |
S1 | 0.0392 (4) | 0.0303 (3) | 0.0191 (3) | −0.0049 (3) | −0.0001 (3) | 0.0019 (2) |
N2 | 0.0318 (11) | 0.0314 (11) | 0.0259 (10) | −0.0026 (9) | −0.0017 (9) | 0.0039 (9) |
N1 | 0.0317 (12) | 0.0287 (11) | 0.0187 (10) | 0.0006 (8) | −0.0007 (8) | 0.0016 (8) |
O4 | 0.0326 (10) | 0.0363 (10) | 0.0255 (9) | 0.0049 (8) | 0.0041 (8) | 0.0036 (8) |
C1 | 0.0233 (12) | 0.0312 (13) | 0.0222 (12) | 0.0020 (10) | −0.0017 (9) | −0.0006 (10) |
C10 | 0.0328 (14) | 0.0304 (13) | 0.0216 (12) | −0.0034 (10) | 0.0017 (10) | 0.0032 (10) |
O1 | 0.0562 (12) | 0.0353 (10) | 0.0274 (10) | −0.0098 (9) | −0.0089 (9) | 0.0006 (8) |
C5 | 0.0238 (12) | 0.0261 (12) | 0.0210 (12) | 0.0020 (9) | −0.0029 (9) | 0.0013 (10) |
C4 | 0.0218 (12) | 0.0287 (12) | 0.0217 (12) | 0.0019 (10) | −0.0018 (10) | 0.0008 (10) |
C11 | 0.0275 (13) | 0.0307 (13) | 0.0226 (12) | 0.0033 (10) | 0.0000 (10) | 0.0015 (10) |
N3 | 0.0291 (11) | 0.0275 (11) | 0.0200 (10) | 0.0010 (8) | −0.0004 (8) | −0.0019 (8) |
O2 | 0.0474 (11) | 0.0340 (10) | 0.0203 (9) | 0.0031 (8) | 0.0014 (7) | 0.0017 (7) |
O3 | 0.0373 (11) | 0.0329 (10) | 0.0325 (10) | −0.0045 (8) | −0.0010 (8) | −0.0016 (8) |
C7 | 0.0347 (14) | 0.0288 (13) | 0.0225 (12) | 0.0031 (10) | −0.0018 (10) | −0.0062 (10) |
C3 | 0.0339 (14) | 0.0271 (13) | 0.0276 (13) | −0.0002 (10) | −0.0047 (11) | −0.0022 (10) |
C9 | 0.0393 (15) | 0.0289 (13) | 0.0220 (12) | −0.0023 (11) | −0.0014 (10) | −0.0066 (10) |
C8 | 0.0436 (16) | 0.0257 (12) | 0.0233 (13) | −0.0046 (11) | −0.0005 (11) | −0.0001 (10) |
C2 | 0.0328 (14) | 0.0267 (13) | 0.0339 (14) | −0.0042 (11) | −0.0028 (11) | 0.0045 (11) |
C6 | 0.0358 (14) | 0.0247 (12) | 0.0277 (13) | 0.0001 (10) | −0.0036 (11) | −0.0015 (10) |
Zn1—O4 | 2.070 (2) | C5—C9 | 1.393 (3) |
Zn1—O4i | 2.070 (2) | C5—C6 | 1.392 (3) |
Zn1—O3i | 2.137 (2) | C5—C4 | 1.483 (3) |
Zn1—O3 | 2.137 (2) | C4—C3 | 1.388 (3) |
Zn1—N3i | 2.176 (2) | C11—O2 | 1.267 (3) |
Zn1—N3 | 2.176 (2) | N3—C7 | 1.337 (3) |
S1—C1 | 1.753 (3) | N3—C8 | 1.346 (3) |
S1—C10 | 1.804 (3) | O3—H3WB | 0.843 (16) |
N2—C2 | 1.328 (3) | O3—H3WA | 0.822 (17) |
N2—C1 | 1.335 (3) | C7—C6 | 1.375 (3) |
N1—C1 | 1.336 (3) | C7—H7A | 0.9300 |
N1—C4 | 1.339 (3) | C3—C2 | 1.377 (3) |
O4—H4WB | 0.810 (16) | C3—H3B | 0.9300 |
O4—H4WA | 0.821 (16) | C9—C8 | 1.367 (4) |
C10—C11 | 1.508 (3) | C9—H9A | 0.9300 |
C10—H10A | 0.9700 | C8—H8A | 0.9300 |
C10—H10B | 0.9700 | C2—H2B | 0.9300 |
O1—C11 | 1.240 (3) | C6—H6A | 0.9300 |
O4—Zn1—O4i | 180.00 (8) | C6—C5—C4 | 122.3 (2) |
O4—Zn1—O3i | 88.60 (9) | N1—C4—C3 | 121.0 (2) |
O4i—Zn1—O3i | 91.40 (9) | N1—C4—C5 | 116.1 (2) |
O4—Zn1—O3 | 91.40 (9) | C3—C4—C5 | 122.9 (2) |
O4i—Zn1—O3 | 88.60 (9) | O1—C11—O2 | 125.1 (2) |
O3i—Zn1—O3 | 180.0 | O1—C11—C10 | 118.2 (2) |
O4—Zn1—N3i | 90.94 (7) | O2—C11—C10 | 116.6 (2) |
O4i—Zn1—N3i | 89.06 (7) | C7—N3—C8 | 116.3 (2) |
O3i—Zn1—N3i | 89.99 (8) | C7—N3—Zn1 | 122.44 (15) |
O3—Zn1—N3i | 90.01 (8) | C8—N3—Zn1 | 120.33 (17) |
O4—Zn1—N3 | 89.06 (7) | Zn1—O3—H3WB | 113.9 (19) |
O4i—Zn1—N3 | 90.94 (7) | Zn1—O3—H3WA | 114.9 (19) |
O3i—Zn1—N3 | 90.01 (8) | H3WB—O3—H3WA | 111 (3) |
O3—Zn1—N3 | 89.99 (8) | N3—C7—C6 | 123.9 (2) |
N3i—Zn1—N3 | 180.0 | N3—C7—H7A | 118.0 |
C1—S1—C10 | 102.37 (13) | C6—C7—H7A | 118.0 |
C2—N2—C1 | 114.66 (19) | C2—C3—C4 | 116.9 (2) |
C1—N1—C4 | 116.4 (2) | C2—C3—H3B | 121.5 |
Zn1—O4—H4WB | 115.2 (19) | C4—C3—H3B | 121.5 |
Zn1—O4—H4WA | 114.8 (18) | C8—C9—C5 | 119.9 (2) |
H4WB—O4—H4WA | 104 (3) | C8—C9—H9A | 120.0 |
N2—C1—N1 | 127.3 (2) | C5—C9—H9A | 120.0 |
N2—C1—S1 | 120.71 (17) | N3—C8—C9 | 123.5 (2) |
N1—C1—S1 | 111.96 (18) | N3—C8—H8A | 118.2 |
C11—C10—S1 | 109.75 (17) | C9—C8—H8A | 118.2 |
C11—C10—H10A | 109.7 | N2—C2—C3 | 123.6 (2) |
S1—C10—H10A | 109.7 | N2—C2—H2B | 118.2 |
C11—C10—H10B | 109.7 | C3—C2—H2B | 118.2 |
S1—C10—H10B | 109.7 | C7—C6—C5 | 119.4 (2) |
H10A—C10—H10B | 108.2 | C7—C6—H6A | 120.3 |
C9—C5—C6 | 116.8 (2) | C5—C6—H6A | 120.3 |
C9—C5—C4 | 121.0 (2) |
Symmetry code: (i) −x, −y+1, −z+1. |
D—H···A | D—H | H···A | D···A | D—H···A |
O4—H4WB···O2ii | 0.81 (2) | 1.96 (2) | 2.759 (3) | 170 (3) |
O4—H4WA···O1iii | 0.82 (2) | 1.82 (2) | 2.632 (3) | 172 (2) |
O3—H3WB···O2iv | 0.84 (2) | 1.89 (2) | 2.728 (3) | 176 (3) |
O3—H3WA···O2v | 0.82 (2) | 2.24 (2) | 3.060 (3) | 172 (3) |
Symmetry codes: (ii) −x+1/2, −y+1, z+1/2; (iii) x+1/2, y, −z+1/2; (iv) −x, y−1/2, −z+1/2; (v) −x−1/2, −y+1, z+1/2. |
Experimental details
Crystal data | |
Chemical formula | [Zn(C11H8N3O2S)2(H2O)4] |
Mr | 630.00 |
Crystal system, space group | Orthorhombic, Pbca |
Temperature (K) | 298 |
a, b, c (Å) | 7.199 (7), 11.792 (11), 28.77 (3) |
V (Å3) | 2442 (4) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 1.24 |
Crystal size (mm) | 0.20 × 0.20 × 0.15 |
Data collection | |
Diffractometer | Bruker APEXII CCD area-detector diffractometer |
Absorption correction | Multi-scan (SADABS; Bruker, 2001) |
Tmin, Tmax | 0.780, 0.830 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 16776, 2465, 1836 |
Rint | 0.051 |
(sin θ/λ)max (Å−1) | 0.641 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.033, 0.086, 1.02 |
No. of reflections | 2465 |
No. of parameters | 190 |
No. of restraints | 4 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.23, −0.45 |
Computer programs: APEX2 (Bruker, 2007), SAINT-Plus (Bruker, 2007), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).
D—H···A | D—H | H···A | D···A | D—H···A |
O4—H4WB···O2i | 0.810 (16) | 1.957 (17) | 2.759 (3) | 170 (3) |
O4—H4WA···O1ii | 0.821 (16) | 1.818 (16) | 2.632 (3) | 172 (2) |
O3—H3WB···O2iii | 0.843 (16) | 1.886 (17) | 2.728 (3) | 176 (3) |
O3—H3WA···O2iv | 0.822 (17) | 2.243 (17) | 3.060 (3) | 172 (3) |
Symmetry codes: (i) −x+1/2, −y+1, z+1/2; (ii) x+1/2, y, −z+1/2; (iii) −x, y−1/2, −z+1/2; (iv) −x−1/2, −y+1, z+1/2. |
Acknowledgements
The authors acknowledge the Teaching and Research Programme for Excellent Young Teachers of Southeast University (grant No. 3207041202).
References
Bruker (2001). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Bruker (2007). APEX2 and SAINT-Plus. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Zhu, H.-B., Xu, G. & Sun, Y.-Y. (2009). Acta Cryst. E65, m1126. Web of Science CSD CrossRef IUCr Journals Google Scholar
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In our previous work, we have reported the crystal structure of mononuclear Mn(II) complex with the ligand of 2-(4-(pyridine-3-yl)pyrimidin-2-ylthio)acetic acid (Zhu et al., 2009). Herein, we present a Zn(II) complex with the ligand of 2-(4-(pyridine-4-yl)pyrimidin-2-ylthio)acetic acid.
Similar to the reported Mn(II) coordination compound (Zhu et al., 2009), the Zn(II) center in the title compound also adopts an octahedral coordination geometry defined by four water O atoms in equatorial positions and two N atoms in apical positions (Fig. 1). The Zn—O bond lengths vary from 2.070 (2) to 2.137 (2)Å, and the Zn—N bond length is 2.176 (2) Å. Intermolecular O—H···O hydrogen bonds (Table 1) consolidate the crystal packing.