Monoclinic polymorph of 2-(pyrimidin-2-ylsulfan­yl)acetic acid

Ramos Silva, M.; Pereira Silva, P.S.; Yuste, C.; Paixão, J.A.

doi:10.1107/S1600536811000651

organic compounds

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ISSN: 2056-9890

Volume 67| Part 2| February 2011| Page o340

doi:10.1107/S1600536811000651

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Monoclinic polymorph of 2-(pyrimidin-2-ylsulfanyl)acetic acid

Manuela Ramos Silva,^a ^* Pedro S. Pereira Silva,^a Consuelo Yuste ^a and José A. Paixão ^a

^aCEMDRX, Physics Department, University of Coimbra, P-3004-516 Coimbra, Portugal
^*Correspondence e-mail: manuela@pollux.fis.uc.pt

(Received 29 December 2010; accepted 5 January 2011; online 12 January 2011)

The title compound, C₆H₆N₂O₂S, is a new polymorphic form of 2-(pyrimidin-2-ylsulfanyl)acetic acid. Unlike the previous orthorhombic polymorph [Pan & Chen (2009 ) Acta Cryst. E65, o652], the molecules are not planar: the aromatic ring makes an angle of 80.67 (17)° with the carboxyl plane. In the crystal, molecules are linked by O—H⋯N hydrogen bonds into chains along [ $[\overline{1}]$ 02].

Related literature

For the previously reported orthorhombic polymorph, see: Pan & Chen (2009).

Experimental

Crystal data

C₆H₆N₂O₂S
M_r = 170.19
Monoclinic, P 2₁ /c
a = 8.2617 (3) Å
b = 10.3028 (4) Å
c = 9.9289 (3) Å
β = 119.845 (2)°
V = 733.05 (4) Å³
Z = 4
Mo Kα radiation
μ = 0.39 mm⁻¹
T = 293 K
0.40 × 0.23 × 0.20 mm

Data collection

Bruker APEX CCD area-detector diffractometer
Absorption correction: multi-scan (SADABS; Sheldrick, 2000 ) T_min = 0.891, T_max = 0.999
14257 measured reflections
1688 independent reflections
1532 reflections with I > 2σ(I)
R_int = 0.027

Refinement

R[F² > 2σ(F²)] = 0.054
wR(F²) = 0.133
S = 1.17
1688 reflections
100 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.31 e Å⁻³
Δρ_min = −0.18 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O2—H2⋯N2ⁱ	0.74	1.97	2.700 (3)	166
Symmetry code: (i) $[x-1, -y+{\script{3\over 2}}, z-{\script{1\over 2}}]$ .

Data collection: SMART (Bruker, 2003 ); cell refinement: SAINT (Bruker, 2003); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEPII (Johnson, 1976 ); software used to prepare material for publication: SHELXL97.

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536811000651/bt5454sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536811000651/bt5454Isup2.hkl

checkCIF report

Comment top

In an attempt to synthesize low dimensional compounds with transition metal elements, crystals of a new monoclinic phase of the title compound (Fig. 1) were obtained. In the previously reported orthorhombic phase the molecules are planar and pack in layers, joined by a O—H···N intermolecular bond (Pan & Chen, 2009). In the new monoclinic phase the molecules are not planar, the C3—S1—C2—C1 torsion angle is 77.84 (18)°. There is a similar strong hydrogen bond (Table 1) as in the orthorhombic phase, but in the title compound this intermolecular bond groups the molecules in chains, that run along the [-102] direction.

Related literature top

For the previously reported polymorph, see: Pan & Chen (2009).

Experimental top

0.2 mmol of 2-(Pyrimidin-2-ylsulfanyl)acetic acid (98%) and 0.2 mmol of CuCl₂.2H₂O (99.0%)were dissolved in 20 ml of water plus 20 ml of ethanol. The solution was slightly warmed and left to evaporate for a few weeks. After that time, small yellowish single crystals were obtained.

Computing details top

Data collection: SMART (Bruker, 2003); cell refinement: SAINT (Bruker, 2003); data reduction: SAINT (Bruker, 2003); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEPII (Johnson, 1976); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Figures top

	Fig. 1. ORTEPII (Johnson, 1976) plot of the title compound. Displacement ellipsoids are drawn at the 50% level.
	Fig. 2. Packing of the molecules in the unit cell showing the H-bonds as dashed lines.

2-(pyrimidin-2-ylsulfanyl)acetic acid top

Crystal data top

C₆H₆N₂O₂S	F(000) = 352
M_r = 170.19	D_x = 1.542 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
a = 8.2617 (3) Å	Cell parameters from 6019 reflections
b = 10.3028 (4) Å	θ = 2.8–27.2°
c = 9.9289 (3) Å	µ = 0.39 mm⁻¹
β = 119.845 (2)°	T = 293 K
V = 733.05 (4) Å³	Prism, yellow
Z = 4	0.40 × 0.23 × 0.20 mm

Data collection top

Bruker APEX CCD area-detector diffractometer	1688 independent reflections
Radiation source: fine-focus sealed tube	1532 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.027
ϕ and ω scans	θ_max = 27.6°, θ_min = 2.8°
Absorption correction: multi-scan (SADABS; Sheldrick, 2000)	h = −10→10
T_min = 0.891, T_max = 0.999	k = −13→13
14257 measured reflections	l = −12→12

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)] = 0.054	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.133	H atoms treated by a mixture of independent and constrained refinement
S = 1.17	w = 1/[σ²(F_o²) + (0.0619P)² + 0.3572P] where P = (F_o² + 2F_c²)/3
1688 reflections	(Δ/σ)_max < 0.001
100 parameters	Δρ_max = 0.31 e Å⁻³
0 restraints	Δρ_min = −0.18 e Å⁻³

Crystal data top

C₆H₆N₂O₂S	V = 733.05 (4) Å³
M_r = 170.19	Z = 4
Monoclinic, P2₁/c	Mo Kα radiation
a = 8.2617 (3) Å	µ = 0.39 mm⁻¹
b = 10.3028 (4) Å	T = 293 K
c = 9.9289 (3) Å	0.40 × 0.23 × 0.20 mm
β = 119.845 (2)°

Data collection top

Bruker APEX CCD area-detector diffractometer	1688 independent reflections
Absorption correction: multi-scan (SADABS; Sheldrick, 2000)	1532 reflections with I > 2σ(I)
T_min = 0.891, T_max = 0.999	R_int = 0.027
14257 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.054	0 restraints
wR(F²) = 0.133	H atoms treated by a mixture of independent and constrained refinement
S = 1.17	Δρ_max = 0.31 e Å⁻³
1688 reflections	Δρ_min = −0.18 e Å⁻³
100 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
S1	0.79236 (8)	0.78200 (6)	0.43768 (7)	0.0451 (2)
O2	0.2618 (3)	0.7405 (2)	0.1323 (3)	0.0642 (6)
H2	0.2106	0.7051	0.0572	0.096*
O1	0.5054 (3)	0.63141 (18)	0.1564 (2)	0.0544 (5)
C1	0.4398 (3)	0.7107 (2)	0.2002 (3)	0.0383 (5)
C2	0.5444 (3)	0.7939 (2)	0.3434 (3)	0.0411 (5)
H2A	0.5048	0.7701	0.4171	0.049*
H2B	0.5094	0.8838	0.3146	0.049*
C3	0.8442 (3)	0.8782 (2)	0.3184 (2)	0.0358 (5)
N1	0.7074 (2)	0.92846 (19)	0.1883 (2)	0.0407 (4)
C6	0.7635 (4)	1.0039 (2)	0.1100 (3)	0.0495 (6)
H6	0.6732	1.0425	0.0185	0.059*
C5	0.9468 (4)	1.0271 (3)	0.1575 (3)	0.0544 (7)
H5	0.9820	1.0810	0.1013	0.065*
C4	1.0766 (4)	0.9677 (3)	0.2916 (3)	0.0536 (7)
H4	1.2028	0.9803	0.3261	0.064*
N2	1.0268 (3)	0.8926 (2)	0.3736 (2)	0.0459 (5)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.0382 (3)	0.0520 (4)	0.0360 (3)	−0.0017 (2)	0.0116 (2)	0.0089 (2)
O2	0.0394 (10)	0.0662 (13)	0.0664 (13)	0.0044 (8)	0.0108 (9)	−0.0106 (10)
O1	0.0514 (10)	0.0554 (11)	0.0595 (11)	−0.0035 (8)	0.0299 (9)	−0.0133 (9)
C1	0.0362 (11)	0.0383 (12)	0.0411 (12)	−0.0037 (8)	0.0197 (9)	0.0045 (9)
C2	0.0398 (12)	0.0454 (13)	0.0418 (12)	−0.0021 (9)	0.0233 (10)	−0.0007 (10)
C3	0.0341 (10)	0.0336 (11)	0.0360 (11)	0.0000 (8)	0.0147 (9)	−0.0030 (8)
N1	0.0371 (9)	0.0426 (11)	0.0396 (10)	0.0039 (8)	0.0169 (8)	0.0058 (8)
C6	0.0604 (15)	0.0433 (14)	0.0478 (13)	0.0062 (11)	0.0291 (12)	0.0072 (11)
C5	0.0705 (17)	0.0440 (14)	0.0667 (17)	−0.0068 (12)	0.0477 (15)	−0.0022 (12)
C4	0.0437 (13)	0.0522 (15)	0.0729 (18)	−0.0101 (11)	0.0350 (13)	−0.0138 (13)
N2	0.0325 (9)	0.0479 (12)	0.0511 (12)	−0.0016 (8)	0.0161 (9)	−0.0032 (9)

Geometric parameters (Å, º) top

S1—C3	1.753 (2)	C3—N2	1.333 (3)
S1—C2	1.783 (2)	N1—C6	1.335 (3)
O2—C1	1.313 (3)	C6—C5	1.365 (4)
O2—H2	0.7449	C6—H6	0.9300
O1—C1	1.177 (3)	C5—C4	1.370 (4)
C1—C2	1.510 (3)	C5—H5	0.9300
C2—H2A	0.9700	C4—N2	1.328 (3)
C2—H2B	0.9700	C4—H4	0.9300
C3—N1	1.327 (3)

C3—S1—C2	102.08 (10)	N2—C3—S1	113.08 (16)
C1—O2—H2	109.4	C3—N1—C6	114.8 (2)
O1—C1—O2	125.2 (2)	N1—C6—C5	123.2 (2)
O1—C1—C2	126.1 (2)	N1—C6—H6	118.4
O2—C1—C2	108.7 (2)	C5—C6—H6	118.4
C1—C2—S1	115.15 (16)	C6—C5—C4	117.1 (2)
C1—C2—H2A	108.5	C6—C5—H5	121.5
S1—C2—H2A	108.5	C4—C5—H5	121.5
C1—C2—H2B	108.5	N2—C4—C5	121.6 (2)
S1—C2—H2B	108.5	N2—C4—H4	119.2
H2A—C2—H2B	107.5	C5—C4—H4	119.2
N1—C3—N2	126.8 (2)	C4—N2—C3	116.5 (2)
N1—C3—S1	120.15 (16)

O1—C1—C2—S1	8.2 (3)	C3—N1—C6—C5	0.8 (4)
O2—C1—C2—S1	−172.38 (16)	N1—C6—C5—C4	0.8 (4)
C3—S1—C2—C1	77.84 (18)	C6—C5—C4—N2	−1.2 (4)
C2—S1—C3—N1	−4.9 (2)	C5—C4—N2—C3	0.0 (4)
C2—S1—C3—N2	174.94 (16)	N1—C3—N2—C4	1.8 (4)
N2—C3—N1—C6	−2.2 (3)	S1—C3—N2—C4	−177.99 (18)
S1—C3—N1—C6	177.60 (17)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O2—H2···N2ⁱ	0.74	1.97	2.700 (3)	166

Symmetry code: (i) x−1, −y+3/2, z−1/2.

Experimental details

Crystal data
Chemical formula	C₆H₆N₂O₂S
M_r	170.19
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	293
a, b, c (Å)	8.2617 (3), 10.3028 (4), 9.9289 (3)
β (°)	119.845 (2)
V (Å³)	733.05 (4)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.39
Crystal size (mm)	0.40 × 0.23 × 0.20

Data collection
Diffractometer	Bruker APEX CCD area-detector diffractometer
Absorption correction	Multi-scan (SADABS; Sheldrick, 2000)
T_min, T_max	0.891, 0.999
No. of measured, independent and observed [I > 2σ(I)] reflections	14257, 1688, 1532
R_int	0.027
(sin θ/λ)_max (Å⁻¹)	0.652

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.054, 0.133, 1.17
No. of reflections	1688
No. of parameters	100
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.31, −0.18

Computer programs: SMART (Bruker, 2003), SAINT (Bruker, 2003), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEPII (Johnson, 1976).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O2—H2···N2ⁱ	0.74	1.97	2.700 (3)	166

Symmetry code: (i) x−1, −y+3/2, z−1/2.

Acknowledgements

This work was supported by Fundo Europeu de Desenvolvimento Regional-QREN-COMPETE through project PTDC/FIS/102284/2008-Fundação para a Ciência e a Tecnologia (FCT).

References

Bruker (2003). SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Johnson, C. K. (1976). ORTEPII. Report ORNL-5138. Oak Ridge National Laboratory, Tennessee, USA. Google Scholar
Pan, J. X. & Chen, Q. W. (2009). Acta Cryst. E65, o652. Web of Science CSD CrossRef IUCr Journals Google Scholar
Sheldrick, G. M. (2000). SADABS. University of Göttingen, Germany. Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar