2-{[4-(Pyridin-2-yl)pyrimidin-2-yl]sulfan­yl}acetic acid

Wang, L.; Dong, H.-Z.

doi:10.1107/S1600536811039791

organic compounds

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ISSN: 2056-9890

Volume 67| Part 11| November 2011| Page o2916

doi:10.1107/S1600536811039791

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2-{[4-(Pyridin-2-yl)pyrimidin-2-yl]sulfanyl}acetic acid

Lin Wang ^a and Hua-Ze Dong ^a ^*

^aDeparment of Chemistry and Chemical Engineering, Hefei Normal University, Hefei 230061, People's Republic of China
^*Correspondence e-mail: dapdong@163.com

(Received 17 August 2011; accepted 28 September 2011; online 12 October 2011)

In the title molecule, C₁₁H₉N₃O₂S, the pyridine and pyrimidine rings are almost parallel [dihedral angle = 6.7 (1)°]. In the crystal, adjacent molecules are joined by O—H⋯N and C—H⋯O hydrogen bonds, leading to the formation of a sheet parallel to (10 $[\overline{2}]$ ).

Related literature

For details of the synthesis and general background, see: Dong et al. (2009 ); Wang (2011 ). For the crystal structures of coordination complexes with related ligands, see: Du et al. (2004 ); Zhu et al. (2009 ).

Experimental

Crystal data

C₁₁H₉N₃O₂S
M_r = 247.28
Monoclinic, P 2₁ /c
a = 6.5722 (2) Å
b = 22.4650 (8) Å
c = 7.4314 (2) Å
β = 93.237 (2)°
V = 1095.45 (6) Å³
Z = 4
Mo Kα radiation
μ = 0.29 mm⁻¹
T = 291 K
0.28 × 0.20 × 0.18 mm

Data collection

Bruker SMART CCD area-detector diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2000 ) T_min = 0.920, T_max = 0.950
10868 measured reflections
2524 independent reflections
2116 reflections with I > 2σ(I)
R_int = 0.022

Refinement

R[F² > 2σ(F²)] = 0.035
wR(F²) = 0.096
S = 1.05
2524 reflections
155 parameters
H-atom parameters constrained
Δρ_max = 0.21 e Å⁻³
Δρ_min = −0.24 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O2—H2⋯N2ⁱ	0.82	1.87	2.694 (2)	178
C2—H2A⋯O1ⁱⁱ	0.93	2.58	3.230 (2)	127
C8—H8⋯O2ⁱⁱⁱ	0.93	2.48	3.392 (2)	165
C9—H9⋯O1^iv	0.93	2.45	3.296 (2)	151
Symmetry codes: (i) $[x+1, -y+{\script{1\over 2}}, z+{\script{1\over 2}}]$ ; (ii) $[x-1, -y+{\script{1\over 2}}, z-{\script{1\over 2}}]$ ; (iii) -x+1, -y+1, -z+1; (iv) $[-x, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]$ .

Data collection: SMART (Bruker, 2000); cell refinement: SAINT (Bruker, 2000); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 ); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536811039791/kj2186sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536811039791/kj2186Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536811039791/kj2186Isup3.cml

checkCIF report

Comment top

The rational dsign and assembly of new coordination polymers with with thioethers derived from 4-pyridinyl pyrimidine-2-thiol have received considerable attention in recent years (Dong et al., 2009; Du et al., 2004; Wang, 2011; Zhu et al., 2009). Here we report the crystal structure of a newly synthesized compound derived from 4-(4-pyridinyl)pyrimidine-2-thiol.

The molecular structure of title compound is shown in Fig. 1 together with the atom-numbering scheme. The pyridine and pyrimidine rings are almost parallel with a dihedral angle of 6.7 (1)°. Molecules are linked by O-H···N hydrogen bonds into a chain running in direction [2 0 1]. C-H···O interactions join these chains into a two-dimensional network with base vectors [2 0 1] and [0 1 0] (equivalent to a sheet parallel to the (1 0 -2) lattice planes). Geometrical details are given in Table 1; a plot is given in Fig. 2.

Related literature top

For details of the synthesis and general background, see: Dong et al. (2009); Wang (2011). For the crystal structures of coordination complexes with related ligands, see: Du et al. (2004); Zhu et al. (2009).

Experimental top

All solvents and chemicals were of analytical grade and were used without further purification. The title compound was prepared by a similar procedure as reported in the literature (Dong et al., 2009). To a solution of 4-(4-pyridinyl)pyrimidine-2-thiol (3.78 g, 20 mmol) and sodium hydroxide (0.80 g, 20 mmol) in water (30 ml), 2-bromoacetic acid (2.78 g, 20 mmol) in water (30 ml) was added. The mixture was stirred at room temperature for 4 h. Dilute hydrochloric acid was added to the reacted solution until the pH was about 4. Precipitates were filtered, washed by water and ethanol, and dried in vacuum. Single crystals suitable for X-ray diffraction were grown from a methanol solution by slow evaporation in air at room temperature.

Computing details top

Data collection: SMART (Bruker, 2000); cell refinement: SAINT (Bruker, 2000); data reduction: SAINT (Bruker, 2000); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top

	Fig. 1. The structure of the title compound, showing 30% probability displacement ellipsoids.
	Fig. 2. Perspective view of the crystal packing. Hydrogen bonding interactions are indicated with dashed lines.

2-{[4-(Pyridin-2-yl)pyrimidin-2-yl]sulfanyl}acetic acid top

Crystal data top

C₁₁H₉N₃O₂S	F(000) = 512.0
M_r = 247.28	D_x = 1.499 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 2524 reflections
a = 6.5722 (2) Å	θ = 1.8–27.5°
b = 22.4650 (8) Å	µ = 0.29 mm⁻¹
c = 7.4314 (2) Å	T = 291 K
β = 93.237 (2)°	Block, pale yellow
V = 1095.45 (6) Å³	0.28 × 0.20 × 0.18 mm
Z = 4

Data collection top

Bruker SMART CCD area-detector diffractometer	2524 independent reflections
Radiation source: fine-focus sealed tube	2116 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.022
ϕ and ω scans	θ_max = 27.5°, θ_min = 1.8°
Absorption correction: multi-scan (SADABS; Bruker, 2000)	h = −8→8
T_min = 0.920, T_max = 0.950	k = −24→29
10868 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)] = 0.035	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.096	H-atom parameters constrained
S = 1.05	w = 1/[σ²(F_o²) + (0.0449P)² + 0.289P] where P = (F_o² + 2F_c²)/3
2524 reflections	(Δ/σ)_max = 0.001
155 parameters	Δρ_max = 0.21 e Å⁻³
0 restraints	Δρ_min = −0.24 e Å⁻³

Crystal data top

C₁₁H₉N₃O₂S	V = 1095.45 (6) Å³
M_r = 247.28	Z = 4
Monoclinic, P2₁/c	Mo Kα radiation
a = 6.5722 (2) Å	µ = 0.29 mm⁻¹
b = 22.4650 (8) Å	T = 291 K
c = 7.4314 (2) Å	0.28 × 0.20 × 0.18 mm
β = 93.237 (2)°

Data collection top

Bruker SMART CCD area-detector diffractometer	2524 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2000)	2116 reflections with I > 2σ(I)
T_min = 0.920, T_max = 0.950	R_int = 0.022
10868 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.035	0 restraints
wR(F²) = 0.096	H-atom parameters constrained
S = 1.05	Δρ_max = 0.21 e Å⁻³
2524 reflections	Δρ_min = −0.24 e Å⁻³
155 parameters

Special details top

Experimental. The structure was solved by direct methods (Bruker, 2000) and successive difference Fourier syntheses.

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
C1	−0.0901 (2)	0.34978 (6)	0.26132 (19)	0.0342 (3)
C2	−0.3668 (2)	0.39680 (7)	0.1300 (2)	0.0412 (4)
H2A	−0.4973	0.3959	0.0747	0.049*
C3	−0.2718 (2)	0.45062 (7)	0.1562 (2)	0.0391 (3)
H3	−0.3370	0.4860	0.1229	0.047*
C4	−0.0745 (2)	0.45042 (6)	0.23433 (19)	0.0327 (3)
C5	0.0431 (2)	0.50633 (6)	0.25998 (19)	0.0333 (3)
C6	0.2462 (2)	0.50591 (7)	0.3208 (2)	0.0427 (4)
H6	0.3120	0.4702	0.3493	0.051*
C7	0.3493 (3)	0.55934 (8)	0.3385 (2)	0.0511 (4)
H7	0.4862	0.5602	0.3778	0.061*
C8	0.2464 (3)	0.61115 (7)	0.2972 (2)	0.0493 (4)
H8	0.3113	0.6478	0.3096	0.059*
C9	0.0444 (3)	0.60757 (7)	0.2367 (3)	0.0490 (4)
H9	−0.0242	0.6428	0.2078	0.059*
C10	0.2527 (2)	0.30146 (7)	0.4321 (2)	0.0380 (3)
H10A	0.3269	0.3242	0.3463	0.046*
H10B	0.2369	0.3259	0.5380	0.046*
C11	0.3674 (2)	0.24555 (7)	0.4832 (2)	0.0365 (3)
N1	0.01710 (17)	0.39939 (5)	0.28821 (16)	0.0340 (3)
N2	−0.27844 (18)	0.34541 (6)	0.18112 (18)	0.0391 (3)
N3	−0.0580 (2)	0.55666 (6)	0.21748 (19)	0.0432 (3)
O1	0.30963 (19)	0.19622 (5)	0.4458 (2)	0.0623 (4)
O2	0.53762 (17)	0.25707 (5)	0.57657 (19)	0.0544 (3)
H2	0.5945	0.2257	0.6057	0.082*
S1	0.00702 (6)	0.280700 (17)	0.33349 (6)	0.04496 (15)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0331 (7)	0.0315 (7)	0.0371 (8)	−0.0008 (6)	−0.0044 (6)	0.0020 (6)
C2	0.0329 (7)	0.0395 (8)	0.0500 (9)	0.0000 (6)	−0.0100 (6)	0.0044 (7)
C3	0.0357 (7)	0.0329 (8)	0.0477 (9)	0.0046 (6)	−0.0053 (6)	0.0035 (6)
C4	0.0344 (7)	0.0297 (7)	0.0338 (7)	0.0004 (5)	0.0004 (6)	0.0001 (5)
C5	0.0373 (7)	0.0279 (7)	0.0345 (7)	0.0011 (6)	−0.0004 (6)	−0.0005 (6)
C6	0.0425 (8)	0.0330 (8)	0.0512 (9)	−0.0010 (6)	−0.0106 (7)	0.0027 (7)
C7	0.0470 (9)	0.0454 (10)	0.0591 (11)	−0.0091 (7)	−0.0137 (8)	−0.0012 (8)
C8	0.0612 (10)	0.0321 (8)	0.0543 (10)	−0.0104 (7)	0.0000 (8)	−0.0057 (7)
C9	0.0564 (10)	0.0281 (8)	0.0628 (11)	0.0042 (7)	0.0045 (8)	−0.0008 (7)
C10	0.0340 (7)	0.0297 (8)	0.0491 (9)	0.0002 (6)	−0.0078 (6)	0.0004 (6)
C11	0.0324 (7)	0.0313 (8)	0.0452 (8)	0.0003 (6)	−0.0041 (6)	−0.0005 (6)
N1	0.0328 (6)	0.0284 (6)	0.0399 (7)	−0.0004 (5)	−0.0052 (5)	0.0024 (5)
N2	0.0347 (6)	0.0331 (7)	0.0482 (7)	−0.0028 (5)	−0.0096 (5)	0.0040 (5)
N3	0.0418 (7)	0.0286 (7)	0.0587 (8)	0.0041 (5)	0.0000 (6)	0.0007 (6)
O1	0.0526 (7)	0.0291 (6)	0.1011 (11)	−0.0001 (5)	−0.0329 (7)	−0.0024 (6)
O2	0.0424 (6)	0.0322 (6)	0.0852 (9)	0.0028 (5)	−0.0269 (6)	−0.0038 (6)
S1	0.0384 (2)	0.0272 (2)	0.0670 (3)	−0.00354 (15)	−0.01691 (18)	0.00762 (17)

Geometric parameters (Å, º) top

C1—N1	1.3276 (18)	C7—C8	1.372 (2)
C1—N2	1.3466 (18)	C7—H7	0.9300
C1—S1	1.7507 (15)	C8—C9	1.380 (2)
C2—N2	1.3377 (19)	C8—H8	0.9300
C2—C3	1.369 (2)	C9—N3	1.331 (2)
C2—H2A	0.9300	C9—H9	0.9300
C3—C4	1.3909 (19)	C10—C11	1.503 (2)
C3—H3	0.9300	C10—S1	1.7964 (14)
C4—N1	1.3453 (17)	C10—H10A	0.9700
C4—C5	1.4815 (19)	C10—H10B	0.9700
C5—N3	1.3401 (18)	C11—O1	1.1991 (18)
C5—C6	1.385 (2)	C11—O2	1.3085 (17)
C6—C7	1.381 (2)	O2—H2	0.8200
C6—H6	0.9300

N1—C1—N2	126.48 (13)	C7—C8—C9	118.45 (15)
N1—C1—S1	121.11 (10)	C7—C8—H8	120.8
N2—C1—S1	112.41 (10)	C9—C8—H8	120.8
N2—C2—C3	122.31 (13)	N3—C9—C8	123.84 (15)
N2—C2—H2A	118.8	N3—C9—H9	118.1
C3—C2—H2A	118.8	C8—C9—H9	118.1
C2—C3—C4	117.60 (13)	C11—C10—S1	108.22 (10)
C2—C3—H3	121.2	C11—C10—H10A	110.1
C4—C3—H3	121.2	S1—C10—H10A	110.1
N1—C4—C3	121.20 (13)	C11—C10—H10B	110.1
N1—C4—C5	117.57 (12)	S1—C10—H10B	110.1
C3—C4—C5	121.23 (13)	H10A—C10—H10B	108.4
N3—C5—C6	122.60 (14)	O1—C11—O2	123.76 (14)
N3—C5—C4	115.89 (12)	O1—C11—C10	124.47 (13)
C6—C5—C4	121.49 (13)	O2—C11—C10	111.76 (12)
C7—C6—C5	118.94 (15)	C1—N1—C4	116.48 (12)
C7—C6—H6	120.5	C2—N2—C1	115.86 (12)
C5—C6—H6	120.5	C9—N3—C5	117.29 (14)
C8—C7—C6	118.87 (15)	C11—O2—H2	109.5
C8—C7—H7	120.6	C1—S1—C10	101.46 (7)
C6—C7—H7	120.6

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O2—H2···N2ⁱ	0.82	1.87	2.694 (2)	178
C2—H2A···O1ⁱⁱ	0.93	2.58	3.230 (2)	127
C8—H8···O2ⁱⁱⁱ	0.93	2.48	3.392 (2)	165
C9—H9···O1^iv	0.93	2.45	3.296 (2)	151

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

Experimental details

Crystal data
Chemical formula	C₁₁H₉N₃O₂S
M_r	247.28
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	291
a, b, c (Å)	6.5722 (2), 22.4650 (8), 7.4314 (2)
β (°)	93.237 (2)
V (Å³)	1095.45 (6)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.29
Crystal size (mm)	0.28 × 0.20 × 0.18

Data collection
Diffractometer	Bruker SMART CCD area-detector diffractometer
Absorption correction	Multi-scan (SADABS; Bruker, 2000)
T_min, T_max	0.920, 0.950
No. of measured, independent and observed [I > 2σ(I)] reflections	10868, 2524, 2116
R_int	0.022
(sin θ/λ)_max (Å⁻¹)	0.651

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.035, 0.096, 1.05
No. of reflections	2524
No. of parameters	155
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.21, −0.24

Computer programs: SMART (Bruker, 2000), SAINT (Bruker, 2000), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O2—H2···N2ⁱ	0.82	1.87	2.694 (2)	178
C2—H2A···O1ⁱⁱ	0.93	2.58	3.230 (2)	127
C8—H8···O2ⁱⁱⁱ	0.93	2.48	3.392 (2)	165
C9—H9···O1^iv	0.93	2.45	3.296 (2)	151

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

Acknowledgements

This work was supported by the National Science Foundation of China (No. 20871039), the Program for Excellent Young Talents in Universities of Anhui Province (2011SQRL128) and the Science Foundation of Hefei Normal University(2010kj01zd).

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