2-(Pyrimidin-2-ylsulfan­yl)acetic acid

Pan, J.X.; Chen, Q.W.

doi:10.1107/S1600536809006400

organic compounds

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ISSN: 2056-9890

Volume 65| Part 3| March 2009| Page o652

doi:10.1107/S1600536809006400

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2-(Pyrimidin-2-ylsulfanyl)acetic acid

Jian Xin Pan ^a and Qian Wang Chen ^a ^*

^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 ); 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

Crystal data

C₆H₆N₂O₂S
M_r = 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 ) 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[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
Δρ_max = 0.22 e Å⁻³
Δρ_min = −0.20 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	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 ); cell refinement: SAINT (Siemens, 1994 ); data reduction: SAINT; 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

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536809006400/rz2292sup1.cif

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

checkCIF report

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.

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

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

C₆H₆N₂O₂S	F(000) = 352
M_r = 170.19	D_x = 1.529 Mg m⁻³
Orthorhombic, Pnma	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2n	Cell parameters from 2019 reflections
a = 14.660 (6) Å	θ = 4.3–27.5°
b = 6.579 (2) Å	µ = 0.38 mm⁻¹
c = 7.664 (3) Å	T = 153 K
V = 739.2 (5) Å³	Prism, colorless
Z = 4	0.22 × 0.20 × 0.07 mm

Data collection top

Bruker P4 diffractometer	911 independent reflections
Radiation source: fine-focus sealed tube	828 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.024
ω scans	θ_max = 27.5°, θ_min = 4.3°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	h = −18→18
T_min = 0.920, T_max = 0.974	k = −8→7
5392 measured reflections	l = −9→9

Refinement top

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)] = 0.032	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.086	H atoms treated by a mixture of independent and constrained refinement
S = 1.07	w = 1/[σ²(F_o²) + (0.0435P)² + 0.2357P] where P = (F_o² + 2F_c²)/3
911 reflections	(Δ/σ)_max < 0.001
70 parameters	Δρ_max = 0.22 e Å⁻³
0 restraints	Δρ_min = −0.20 e Å⁻³

Crystal data top

C₆H₆N₂O₂S	V = 739.2 (5) Å³
M_r = 170.19	Z = 4
Orthorhombic, Pnma	Mo Kα radiation
a = 14.660 (6) Å	µ = 0.38 mm⁻¹
b = 6.579 (2) Å	T = 153 K
c = 7.664 (3) Å	0.22 × 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)
T_min = 0.920, T_max = 0.974	R_int = 0.024
5392 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.032	0 restraints
wR(F²) = 0.086	H atoms treated by a mixture of independent and constrained refinement
S = 1.07	Δρ_max = 0.22 e Å⁻³
911 reflections	Δρ_min = −0.20 e Å⁻³
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

	x	y	z	U_iso*/U_eq	Occ. (<1)
S1	0.36018 (3)	0.2500	0.16539 (6)	0.0429 (2)
O2	0.09853 (9)	0.2500	0.24621 (18)	0.0421 (4)
H1	0.067 (2)	0.2500	0.345 (4)	0.088 (10)*
O1	0.21943 (9)	0.2500	0.42130 (18)	0.0516 (4)
N2	0.50091 (10)	0.2500	−0.0392 (2)	0.0373 (4)
C2	0.24089 (12)	0.2500	0.1111 (3)	0.0415 (5)
H2A	0.2262	0.3696	0.0426	0.050*	0.50
H2B	0.2262	0.1304	0.0426	0.050*	0.50
C3	0.40934 (12)	0.2500	−0.0428 (2)	0.0334 (4)
C4	0.54355 (13)	0.2500	−0.1933 (3)	0.0408 (5)
H4	0.6070	0.2500	−0.1960	0.049*
C1	0.18678 (12)	0.2500	0.2774 (2)	0.0349 (4)
N1	0.35745 (10)	0.2500	−0.1845 (2)	0.0395 (4)
C6	0.40261 (14)	0.2500	−0.3361 (2)	0.0437 (5)
H6	0.3690	0.2500	−0.4390	0.052*
C5	0.49614 (14)	0.2500	−0.3477 (3)	0.0446 (5)
H5	0.5259	0.2500	−0.4549	0.054*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.0244 (3)	0.0774 (4)	0.0270 (3)	0.000	−0.00018 (16)	0.000
O2	0.0221 (6)	0.0738 (10)	0.0304 (7)	0.000	−0.0008 (5)	0.000
O1	0.0293 (7)	0.0959 (12)	0.0298 (7)	0.000	−0.0031 (5)	0.000
N2	0.0246 (7)	0.0571 (10)	0.0304 (8)	0.000	0.0002 (6)	0.000
C2	0.0251 (8)	0.0698 (14)	0.0298 (9)	0.000	−0.0004 (7)	0.000
C3	0.0262 (8)	0.0448 (10)	0.0292 (8)	0.000	−0.0004 (7)	0.000
C4	0.0284 (9)	0.0549 (12)	0.0391 (10)	0.000	0.0054 (7)	0.000
C1	0.0254 (8)	0.0481 (11)	0.0311 (9)	0.000	−0.0012 (7)	0.000
N1	0.0293 (8)	0.0593 (11)	0.0299 (8)	0.000	−0.0015 (6)	0.000
C6	0.0403 (11)	0.0632 (13)	0.0277 (9)	0.000	−0.0041 (8)	0.000
C5	0.0416 (10)	0.0624 (14)	0.0299 (9)	0.000	0.0075 (8)	0.000

Geometric parameters (Å, º) top

S1—C3	1.7507 (19)	C2—H2B	0.9700
S1—C2	1.7976 (19)	C3—N1	1.326 (2)
O2—C1	1.316 (2)	C4—C5	1.372 (3)
O2—H1	0.89 (3)	C4—H4	0.9300
O1—C1	1.202 (2)	N1—C6	1.337 (2)
N2—C4	1.336 (2)	C6—C5	1.374 (3)
N2—C3	1.343 (2)	C6—H6	0.9300
C2—C1	1.501 (3)	C5—H5	0.9300
C2—H2A	0.9700

C3—S1—C2	100.92 (9)	N2—C4—H4	119.2
C1—O2—H1	111 (2)	C5—C4—H4	119.2
C4—N2—C3	116.72 (16)	O1—C1—O2	123.91 (17)
C1—C2—S1	108.51 (13)	O1—C1—C2	124.65 (16)
C1—C2—H2A	110.0	O2—C1—C2	111.44 (16)
S1—C2—H2A	110.0	C3—N1—C6	115.33 (17)
C1—C2—H2B	110.0	N1—C6—C5	123.38 (18)
S1—C2—H2B	110.0	N1—C6—H6	118.3
H2A—C2—H2B	108.4	C5—C6—H6	118.3
N1—C3—N2	126.17 (17)	C4—C5—C6	116.72 (18)
N1—C3—S1	120.70 (14)	C4—C5—H5	121.6
N2—C3—S1	113.13 (13)	C6—C5—H5	121.6
N2—C4—C5	121.68 (18)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	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−1/2, y, −z+1/2; (ii) x, y, z−1; (iii) x+1/2, −y+1/2, −z−1/2.

Experimental details

Crystal data
Chemical formula	C₆H₆N₂O₂S
M_r	170.19
Crystal system, space group	Orthorhombic, Pnma
Temperature (K)	153
a, b, c (Å)	14.660 (6), 6.579 (2), 7.664 (3)
V (Å³)	739.2 (5)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.38
Crystal size (mm)	0.22 × 0.20 × 0.07

Data collection
Diffractometer	Bruker P4 diffractometer
Absorption correction	Multi-scan (SADABS; Sheldrick, 1996)
T_min, T_max	0.920, 0.974
No. of measured, independent and observed [I > 2σ(I)] reflections	5392, 911, 828
R_int	0.024
(sin θ/λ)_max (Å⁻¹)	0.649

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.032, 0.086, 1.07
No. of reflections	911
No. of parameters	70
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	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···A	D—H	H···A	D···A	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−1/2, y, −z+1/2; (ii) x, y, z−1; (iii) x+1/2, −y+1/2, −z−1/2.

Acknowledgements

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

References

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