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Acta Crystallogr Sect E Struct Rep Online. 2009 March 1; 65(Pt 3): o652.
Published online 2009 February 28. doi:  10.1107/S1600536809006400
PMCID: PMC2968606

2-(Pyrimidin-2-ylsulfan­yl)acetic acid

Abstract

The mol­ecule of the title compound, C6H6N2O2S, lies on a crystallographic mirror plane with the methyl­ene H atoms related by mirror symmetry. In the crystal packing, mol­ecules are linked into layers by inter­molecular O—H(...)N and C—H(...)O hydrogen bonds.

Related literature

For the coordination chemistry of thio­ether ligands, see: Li & Bu (2008 [triangle]); Bu et al. (2003 [triangle]); Chen et al. (2003 [triangle]); Demadis & Coucouvanis (1995 [triangle]); Peng et al. (2006 [triangle]). For bond-length data, see: Allen et al. (1987 [triangle]).

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Object name is e-65-0o652-scheme1.jpg

Experimental

Crystal data

  • C6H6N2O2S
  • M r = 170.19
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-65-0o652-efi1.jpg
  • a = 14.660 (6) Å
  • b = 6.579 (2) Å
  • c = 7.664 (3) Å
  • V = 739.2 (5) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.38 mm−1
  • T = 153 K
  • 0.22 × 0.20 × 0.07 mm

Data collection

  • Bruker P4 diffractometer
  • Absorption correction: multi-scan (SADABS; Sheldrick, 1996 [triangle]) T min = 0.920, T max = 0.974
  • 5392 measured reflections
  • 911 independent reflections
  • 828 reflections with I > 2σ(I)
  • R int = 0.024

Refinement

  • R[F 2 > 2σ(F 2)] = 0.032
  • wR(F 2) = 0.086
  • S = 1.07
  • 911 reflections
  • 70 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.22 e Å−3
  • Δρmin = −0.20 e Å−3

Data collection: SMART (Siemens, 1996 [triangle]); cell refinement: SAINT (Siemens, 1994 [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/S1600536809006400/rz2292sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809006400/rz2292Isup2.hkl

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

Acknowledgments

We gratefully acknowledge the financial support of the National Natural Science Foundation of China.

supplementary crystallographic information

Comment

Great efforts have been focused on the rational design and synthesis of metal-organic coordination architectures by using flexible bridging ligands due to their flexibility and conformational freedoms, which offer the possibility for the construction of unprecedented frameworks (Li & Bu, 2008). Recently, flexible thioethers have been well established ligands in coordination and metallosupramolecular chemistry because of their rich structural information (Bu et al., 2003; Chen et al., 2003; Demadis & Coucouvanis, 1995; Peng et al., 2006). In the process of preparing metal-organic coordination architectures, single-crystals of the title compound were obtained unexpectedly.

The molecular structure and the atom-numbering scheme of the title compound are shown in Fig. 1. The molecule lies on a mirror plane, with the methylene H atoms related by mirror symmetry. All bond lengths (Allen et al., 1987) and angles show normal value. In the crystal packing, molecules are linked into layers perpendicular to the b axis by intermolecular O—H···N and C—H···O hydrogen bonds (Table 1).

Experimental

A mixture of Co(Ac)2.6H2O (0.142 g, 0.50 mmol), (2-Pyrimidylthio)acetic acid (0.035 g, 0.20 mmol) and sodium azide (0.032 g, 0.50 mmol) in H2O (10 ml) was stirred for 1 h, then filtered, and the filtrate was kept at room temperature. Single crystals of the title compound were obtained by slow evaporation of the solvent after a few days.

Refinement

Hydrogen atoms bound to C atoms were positioned geometrically with C—H = 0.93-0.97 Å, and constrained to ride on their parent atoms, with Uiso(H) = 1.2Ueq(C). The H atom bound to O was freely refined.

Figures

Fig. 1.
The molecular structure of the title compound, with the atom-numbering scheme. Displacement ellipsoids are drawn at the 50% probability level.

Crystal data

C6H6N2O2SF(000) = 352
Mr = 170.19Dx = 1.529 Mg m3
Orthorhombic, PnmaMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2nCell parameters from 2019 reflections
a = 14.660 (6) Åθ = 4.3–27.5°
b = 6.579 (2) ŵ = 0.38 mm1
c = 7.664 (3) ÅT = 153 K
V = 739.2 (5) Å3Prism, colorless
Z = 40.22 × 0.20 × 0.07 mm

Data collection

Bruker P4 diffractometer911 independent reflections
Radiation source: fine-focus sealed tube828 reflections with I > 2σ(I)
graphiteRint = 0.024
ω scansθmax = 27.5°, θmin = 4.3°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)h = −18→18
Tmin = 0.920, Tmax = 0.974k = −8→7
5392 measured reflectionsl = −9→9

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)] = 0.032Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.086H atoms treated by a mixture of independent and constrained refinement
S = 1.07w = 1/[σ2(Fo2) + (0.0435P)2 + 0.2357P] where P = (Fo2 + 2Fc2)/3
911 reflections(Δ/σ)max < 0.001
70 parametersΔρmax = 0.22 e Å3
0 restraintsΔρmin = −0.20 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*/UeqOcc. (<1)
S10.36018 (3)0.25000.16539 (6)0.0429 (2)
O20.09853 (9)0.25000.24621 (18)0.0421 (4)
H10.067 (2)0.25000.345 (4)0.088 (10)*
O10.21943 (9)0.25000.42130 (18)0.0516 (4)
N20.50091 (10)0.2500−0.0392 (2)0.0373 (4)
C20.24089 (12)0.25000.1111 (3)0.0415 (5)
H2A0.22620.36960.04260.050*0.50
H2B0.22620.13040.04260.050*0.50
C30.40934 (12)0.2500−0.0428 (2)0.0334 (4)
C40.54355 (13)0.2500−0.1933 (3)0.0408 (5)
H40.60700.2500−0.19600.049*
C10.18678 (12)0.25000.2774 (2)0.0349 (4)
N10.35745 (10)0.2500−0.1845 (2)0.0395 (4)
C60.40261 (14)0.2500−0.3361 (2)0.0437 (5)
H60.36900.2500−0.43900.052*
C50.49614 (14)0.2500−0.3477 (3)0.0446 (5)
H50.52590.2500−0.45490.054*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
S10.0244 (3)0.0774 (4)0.0270 (3)0.000−0.00018 (16)0.000
O20.0221 (6)0.0738 (10)0.0304 (7)0.000−0.0008 (5)0.000
O10.0293 (7)0.0959 (12)0.0298 (7)0.000−0.0031 (5)0.000
N20.0246 (7)0.0571 (10)0.0304 (8)0.0000.0002 (6)0.000
C20.0251 (8)0.0698 (14)0.0298 (9)0.000−0.0004 (7)0.000
C30.0262 (8)0.0448 (10)0.0292 (8)0.000−0.0004 (7)0.000
C40.0284 (9)0.0549 (12)0.0391 (10)0.0000.0054 (7)0.000
C10.0254 (8)0.0481 (11)0.0311 (9)0.000−0.0012 (7)0.000
N10.0293 (8)0.0593 (11)0.0299 (8)0.000−0.0015 (6)0.000
C60.0403 (11)0.0632 (13)0.0277 (9)0.000−0.0041 (8)0.000
C50.0416 (10)0.0624 (14)0.0299 (9)0.0000.0075 (8)0.000

Geometric parameters (Å, °)

S1—C31.7507 (19)C2—H2B0.9700
S1—C21.7976 (19)C3—N11.326 (2)
O2—C11.316 (2)C4—C51.372 (3)
O2—H10.89 (3)C4—H40.9300
O1—C11.202 (2)N1—C61.337 (2)
N2—C41.336 (2)C6—C51.374 (3)
N2—C31.343 (2)C6—H60.9300
C2—C11.501 (3)C5—H50.9300
C2—H2A0.9700
C3—S1—C2100.92 (9)N2—C4—H4119.2
C1—O2—H1111 (2)C5—C4—H4119.2
C4—N2—C3116.72 (16)O1—C1—O2123.91 (17)
C1—C2—S1108.51 (13)O1—C1—C2124.65 (16)
C1—C2—H2A110.0O2—C1—C2111.44 (16)
S1—C2—H2A110.0C3—N1—C6115.33 (17)
C1—C2—H2B110.0N1—C6—C5123.38 (18)
S1—C2—H2B110.0N1—C6—H6118.3
H2A—C2—H2B108.4C5—C6—H6118.3
N1—C3—N2126.17 (17)C4—C5—C6116.72 (18)
N1—C3—S1120.70 (14)C4—C5—H5121.6
N2—C3—S1113.13 (13)C6—C5—H5121.6
N2—C4—C5121.68 (18)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
O2—H1···N2i0.89 (3)1.78 (3)2.663 (2)178 (3)
C6—H6···O1ii0.932.443.266 (3)148
C5—H5···O2iii0.932.473.403 (3)178

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: RZ2292).

References

  • Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1–19.
  • Bu, X.-H., Xie, Y.-B., Li, J.-R. & Zhang, R.-H. (2003). Inorg. Chem.42, 7422–7430. [PubMed]
  • Chen, C.-L., Su, C.-Y., Cai, Y.-P., Zhang, H.-X., Xu, A.-W., Kang, B.-S. & zur Loye, H.-C. (2003). Inorg. Chem.42, 3738–3750. [PubMed]
  • Demadis, K. D. & Coucouvanis, D. (1995). Inorg. Chem.34, 3658–3666.
  • Li, J.-R. & Bu, X.-H. (2008). Eur. J. Inorg. Chem. pp. 27–40.
  • Peng, R., Li, D., Wu, T., Zhou, X.-P. & Ng, S. W. (2006). Inorg. Chem.45, 4035–4046. [PubMed]
  • Sheldrick, G. M. (1996). SADABS University of Göttingen, Germany.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Siemens (1994). SAINT Siemens Analytical X-ray Instruments Inc., Madison, Wisconsin, USA.
  • Siemens (1996). SMART Siemens Analytical X-ray Instruments Inc., Madison, Wisconsin, USA.

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