organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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2-(Pyrimidin-2-ylsulfan­yl)acetic acid

aHefei National Laboratory for Physical Sciences at the Microscale and Department of Materials Science & Engineering, University of Science and Technology of China, Hefei 230026, People's Republic of China
*Correspondence e-mail: cqw@ustc.edu.cn

(Received 24 January 2009; accepted 21 February 2009; online 28 February 2009)

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[Li, J.-R. & Bu, X.-H. (2008). Eur. J. Inorg. Chem. pp. 27-40.]); Bu et al. (2003[Bu, X.-H., Xie, Y.-B., Li, J.-R. & Zhang, R.-H. (2003). Inorg. Chem. 42, 7422-7430.]); Chen et al. (2003[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.]); Demadis & Coucouvanis (1995[Demadis, K. D. & Coucouvanis, D. (1995). Inorg. Chem. 34, 3658-3666.]); Peng et al. (2006[Peng, R., Li, D., Wu, T., Zhou, X.-P. & Ng, S. W. (2006). Inorg. Chem. 45, 4035-4046.]). For bond-length data, see: Allen et al. (1987[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.]).

[Scheme 1]

Experimental

Crystal data
  • C6H6N2O2S

  • Mr = 170.19

  • Orthorhombic, P n m a

  • 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[Sheldrick, G. M. (1996). SADABS. University of Göttingen, Germany.]) Tmin = 0.920, Tmax = 0.974

  • 5392 measured reflections

  • 911 independent reflections

  • 828 reflections with I > 2σ(I)

  • Rint = 0.024

Refinement
  • R[F2 > 2σ(F2)] = 0.032

  • wR(F2) = 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

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
O2—H1⋯N2i 0.89 (3) 1.78 (3) 2.663 (2) 178 (3)
C6—H6⋯O1ii 0.93 2.44 3.266 (3) 148
C5—H5⋯O2iii 0.93 2.47 3.403 (3) 178
Symmetry codes: (i) [x-{\script{1\over 2}}, y, -z+{\script{1\over 2}}]; (ii) x, y, z-1; (iii) [x+{\script{1\over 2}}, -y+{\script{1\over 2}}, -z-{\script{1\over 2}}].

Data collection: SMART (Siemens, 1996[Siemens (1996). SMART. Siemens Analytical X-ray Instruments Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Siemens, 1994[Siemens (1994). SAINT. Siemens Analytical X-ray Instruments Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXTL.

Supporting information


Comment top

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).

Related literature top

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

Experimental top

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 top

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.

Computing details top

Data collection: SMART (Siemens, 1996); cell refinement: SAINT (Siemens, 1994); data reduction: SAINT (Siemens, 1994); 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. The molecular structure of the title compound, with the atom-numbering scheme. Displacement ellipsoids are drawn at the 50% probability level.
2-(Pyrimidin-2-ylsulfanyl)acetic acid top
Crystal data top
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 top
Bruker P4
diffractometer
911 independent reflections
Radiation source: fine-focus sealed tube828 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.024
ω scansθmax = 27.5°, θmin = 4.3°
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)
h = 1818
Tmin = 0.920, Tmax = 0.974k = 87
5392 measured reflectionsl = 99
Refinement top
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 = 1.07 w = 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
Crystal data top
C6H6N2O2SV = 739.2 (5) Å3
Mr = 170.19Z = 4
Orthorhombic, PnmaMo Kα radiation
a = 14.660 (6) ŵ = 0.38 mm1
b = 6.579 (2) ÅT = 153 K
c = 7.664 (3) Å0.22 × 0.20 × 0.07 mm
Data collection top
Bruker P4
diffractometer
911 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)
828 reflections with I > 2σ(I)
Tmin = 0.920, Tmax = 0.974Rint = 0.024
5392 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0320 restraints
wR(F2) = 0.086H atoms treated by a mixture of independent and constrained refinement
S = 1.07Δρmax = 0.22 e Å3
911 reflectionsΔρmin = 0.20 e Å3
70 parameters
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)
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)0.25000.0392 (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)0.25000.0428 (2)0.0334 (4)
C40.54355 (13)0.25000.1933 (3)0.0408 (5)
H40.60700.25000.19600.049*
C10.18678 (12)0.25000.2774 (2)0.0349 (4)
N10.35745 (10)0.25000.1845 (2)0.0395 (4)
C60.40261 (14)0.25000.3361 (2)0.0437 (5)
H60.36900.25000.43900.052*
C50.49614 (14)0.25000.3477 (3)0.0446 (5)
H50.52590.25000.45490.054*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.0244 (3)0.0774 (4)0.0270 (3)0.0000.00018 (16)0.000
O20.0221 (6)0.0738 (10)0.0304 (7)0.0000.0008 (5)0.000
O10.0293 (7)0.0959 (12)0.0298 (7)0.0000.0031 (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)0.0000.0004 (7)0.000
C30.0262 (8)0.0448 (10)0.0292 (8)0.0000.0004 (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)0.0000.0012 (7)0.000
N10.0293 (8)0.0593 (11)0.0299 (8)0.0000.0015 (6)0.000
C60.0403 (11)0.0632 (13)0.0277 (9)0.0000.0041 (8)0.000
C50.0416 (10)0.0624 (14)0.0299 (9)0.0000.0075 (8)0.000
Geometric parameters (Å, º) top
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, º) top
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) x1/2, y, z+1/2; (ii) x, y, z1; (iii) x+1/2, y+1/2, z1/2.

Experimental details

Crystal data
Chemical formulaC6H6N2O2S
Mr170.19
Crystal system, space groupOrthorhombic, Pnma
Temperature (K)153
a, b, c (Å)14.660 (6), 6.579 (2), 7.664 (3)
V3)739.2 (5)
Z4
Radiation typeMo Kα
µ (mm1)0.38
Crystal size (mm)0.22 × 0.20 × 0.07
Data collection
DiffractometerBruker P4
diffractometer
Absorption correctionMulti-scan
(SADABS; Sheldrick, 1996)
Tmin, Tmax0.920, 0.974
No. of measured, independent and
observed [I > 2σ(I)] reflections
5392, 911, 828
Rint0.024
(sin θ/λ)max1)0.649
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.032, 0.086, 1.07
No. of reflections911
No. of parameters70
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.22, 0.20

Computer programs: SMART (Siemens, 1996), SAINT (Siemens, 1994), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top
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) x1/2, y, z+1/2; (ii) x, y, z1; (iii) x+1/2, y+1/2, z1/2.
 

Acknowledgements

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

References

First citationAllen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1–19.  CrossRef Web of Science Google Scholar
First citationBu, X.-H., Xie, Y.-B., Li, J.-R. & Zhang, R.-H. (2003). Inorg. Chem. 42, 7422–7430.  Web of Science CSD CrossRef PubMed CAS Google Scholar
First citationChen, 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.  Web of Science CSD CrossRef PubMed CAS Google Scholar
First citationDemadis, K. D. & Coucouvanis, D. (1995). Inorg. Chem. 34, 3658–3666.  CSD CrossRef CAS Web of Science Google Scholar
First citationLi, J.-R. & Bu, X.-H. (2008). Eur. J. Inorg. Chem. pp. 27–40.  Web of Science CrossRef Google Scholar
First citationPeng, R., Li, D., Wu, T., Zhou, X.-P. & Ng, S. W. (2006). Inorg. Chem. 45, 4035–4046.  Web of Science CSD CrossRef PubMed CAS Google Scholar
First citationSheldrick, G. M. (1996). SADABS. University of Göttingen, Germany.  Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationSiemens (1994). SAINT. Siemens Analytical X-ray Instruments Inc., Madison, Wisconsin, USA.  Google Scholar
First citationSiemens (1996). SMART. Siemens Analytical X-ray Instruments Inc., Madison, Wisconsin, USA.  Google Scholar

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