Ethyl 2-{[4-(pyridin-4-yl)pyrimidin-2-yl]sulfan­yl}acetate

Wang, C.-H.

doi:10.1107/S1600536811004272

organic compounds

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ISSN: 2056-9890

Volume 67| Part 3| March 2011| Page o690

doi:10.1107/S1600536811004272

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Ethyl 2-{[4-(pyridin-4-yl)pyrimidin-2-yl]sulfanyl}acetate

Chuan-Hu Wang ^a ^*

^aDepartment of Applied Chemistry and Environmental Engineering, Bengbu College, Bengbu, 233030, People's Republic of China
^*Correspondence e-mail: wangchuanhu2003@yahoo.com.cn

(Received 31 January 2011; accepted 4 February 2011; online 23 February 2011)

In the title molecule, C₁₃H₁₃N₃O₂S, the pyridine and pyrimidine rings form a dihedral angle of 3.8 (1)°. The crystal packing exhibits weak intermolecular C—H⋯O hydrogen bonds.

Related literature

For details of the synthesis and general background to the rational design and assembly of coordination polymers with thioethers, see: Dong et al. (2008 , 2009 ). For the crystal structures of coordination complexes with related ligands, see: Du et al. (2004 ); Zhu et al. (2009 ).

Experimental

Crystal data

C₁₃H₁₃N₃O₂S
M_r = 275.33
Triclinic, $[P \overline 1]$
a = 8.6579 (8) Å
b = 9.7394 (9) Å
c = 9.9188 (8) Å
α = 62.661 (6)°
β = 71.416 (5)°
γ = 65.024 (6)°
V = 665.35 (10) Å³
Z = 2
Mo Kα radiation
μ = 0.25 mm⁻¹
T = 291 K
0.32 × 0.24 × 0.18 mm

Data collection

Bruker SMART CCD area-detector diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2000 ) T_min = 0.917, T_max = 0.966
11760 measured reflections
3021 independent reflections
2387 reflections with I > 2σ(I)
R_int = 0.032

Refinement

R[F² > 2σ(F²)] = 0.038
wR(F²) = 0.115
S = 1.04
3021 reflections
173 parameters
H-atom parameters constrained
Δρ_max = 0.24 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
C3—H3⋯O1ⁱ	0.93	2.52	3.383 (2)	154
C7—H7⋯O1ⁱⁱ	0.93	2.61	3.373 (2)	140
Symmetry codes: (i) -x+1, -y, -z+2; (ii) x, y, z+1.

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/S1600536811004272/cv5047sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536811004272/cv5047Isup2.hkl

checkCIF report

Comment top

Remarkable attention has been paid to the rational design and assembly of new coordination polymers with thioethers (Dong et al., 2008; 2009; Du et al., 2004; Zhu et al., 2009). Herewith we report the synthesis and crystal structure of the title compound (I)- a new derivative of 4-(4-pyridinyl)pyrimidine-2-thiol.

In (I) (Fig. 1), the pyridine and pyrimidine rings form a dihedral angle of 3.8 (1)°. The crystal packing exhibits weak intermolecular C—H···O hydrogen bonds (Table 1).

Related literature top

For details of the synthesis and general background to the rational design and assembly of coordination polymers with thioethers, see: Dong et al. (2008, 2009). 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 similar procedure reported in the literature (Dong et al., 2008; 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 dry ethanol (100 ml), ethyl 2-bromoacetate (3.34 g, 20 mmol) in CCl₄ (30 ml) was added. The mixture was stirred and refluxed for 8 h. After cooling, precipitates were filtered, washed by water and ethanol, and dried in vacuum. Single crystals suitable for X-ray diffraction were grown from 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 and the atomic numbering.

Ethyl 2-{[4-(pyridin-4-yl)pyrimidin-2-yl]sulfanyl}acetate top

Crystal data top

C₁₃H₁₃N₃O₂S	Z = 2
M_r = 275.33	F(000) = 288.0
Triclinic, P1	D_x = 1.374 Mg m⁻³
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 8.6579 (8) Å	Cell parameters from 3021 reflections
b = 9.7394 (9) Å	θ = 2.3–27.5°
c = 9.9188 (8) Å	µ = 0.25 mm⁻¹
α = 62.661 (6)°	T = 291 K
β = 71.416 (5)°	Block, colorless
γ = 65.024 (6)°	0.32 × 0.24 × 0.18 mm
V = 665.35 (10) Å³

Data collection top

Bruker SMART CCD area-detector diffractometer	3021 independent reflections
Radiation source: fine-focus sealed tube	2387 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.032
ϕ and ω scans	θ_max = 27.5°, θ_min = 2.3°
Absorption correction: multi-scan (SADABS; Bruker, 2000)	h = −11→10
T_min = 0.917, T_max = 0.966	k = −12→12
11760 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)] = 0.038	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.115	H-atom parameters constrained
S = 1.04	w = 1/[σ²(F_o²) + (0.0658P)² + 0.067P] where P = (F_o² + 2F_c²)/3
3021 reflections	(Δ/σ)_max < 0.001
173 parameters	Δρ_max = 0.24 e Å⁻³
0 restraints	Δρ_min = −0.20 e Å⁻³

Crystal data top

C₁₃H₁₃N₃O₂S	γ = 65.024 (6)°
M_r = 275.33	V = 665.35 (10) Å³
Triclinic, P1	Z = 2
a = 8.6579 (8) Å	Mo Kα radiation
b = 9.7394 (9) Å	µ = 0.25 mm⁻¹
c = 9.9188 (8) Å	T = 291 K
α = 62.661 (6)°	0.32 × 0.24 × 0.18 mm
β = 71.416 (5)°

Data collection top

Bruker SMART CCD area-detector diffractometer	3021 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2000)	2387 reflections with I > 2σ(I)
T_min = 0.917, T_max = 0.966	R_int = 0.032
11760 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.038	0 restraints
wR(F²) = 0.115	H-atom parameters constrained
S = 1.04	Δρ_max = 0.24 e Å⁻³
3021 reflections	Δρ_min = −0.20 e Å⁻³
173 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	0.21141 (18)	0.00339 (18)	0.89933 (17)	0.0411 (3)
C2	0.3174 (2)	−0.21822 (19)	1.10105 (19)	0.0496 (4)
H2	0.3517	−0.3308	1.1555	0.060*
C3	0.3336 (2)	−0.12042 (18)	1.15846 (18)	0.0459 (4)
H3	0.3793	−0.1652	1.2484	0.055*
C4	0.27871 (17)	0.04721 (17)	1.07653 (16)	0.0376 (3)
C5	0.28647 (18)	0.16653 (17)	1.12645 (16)	0.0388 (3)
C6	0.3582 (2)	0.1176 (2)	1.25464 (18)	0.0478 (4)
H6	0.4018	0.0070	1.3141	0.057*
C7	0.3641 (2)	0.2347 (2)	1.2930 (2)	0.0568 (4)
H7	0.4126	0.1991	1.3794	0.068*
C8	0.2241 (2)	0.3332 (2)	1.04370 (19)	0.0525 (4)
H8	0.1740	0.3725	0.9573	0.063*
C9	0.2372 (3)	0.4407 (2)	1.0913 (2)	0.0660 (5)
H9	0.1960	0.5521	1.0335	0.079*
C10	0.0836 (2)	0.2913 (2)	0.6641 (2)	0.0515 (4)
H10A	0.0315	0.3439	0.5718	0.062*
H10B	−0.0042	0.3227	0.7439	0.062*
C11	0.2273 (2)	0.35667 (18)	0.63290 (16)	0.0422 (3)
C12	0.2788 (2)	0.5879 (2)	0.6083 (2)	0.0620 (5)
H12A	0.3426	0.6012	0.5056	0.074*
H12B	0.3603	0.5258	0.6805	0.074*
C13	0.1774 (3)	0.7498 (3)	0.6187 (3)	0.0927 (8)
H13A	0.1014	0.8124	0.5432	0.139*
H13B	0.2542	0.8066	0.6002	0.139*
H13C	0.1108	0.7354	0.7193	0.139*
N1	0.3051 (2)	0.39441 (19)	1.21466 (18)	0.0644 (4)
N2	0.21695 (15)	0.11055 (14)	0.94434 (14)	0.0392 (3)
N3	0.25523 (17)	−0.15909 (16)	0.97173 (16)	0.0482 (3)
O1	0.37818 (15)	0.29263 (14)	0.59842 (13)	0.0516 (3)
O2	0.15904 (14)	0.50272 (13)	0.64426 (13)	0.0512 (3)
S1	0.14603 (6)	0.07492 (5)	0.72151 (5)	0.05259 (16)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0408 (8)	0.0366 (8)	0.0520 (8)	−0.0153 (6)	−0.0068 (6)	−0.0197 (6)
C2	0.0542 (9)	0.0320 (8)	0.0601 (10)	−0.0176 (7)	−0.0095 (7)	−0.0119 (7)
C3	0.0514 (9)	0.0366 (8)	0.0489 (8)	−0.0168 (7)	−0.0111 (7)	−0.0113 (7)
C4	0.0365 (7)	0.0348 (7)	0.0428 (7)	−0.0142 (6)	−0.0023 (6)	−0.0159 (6)
C5	0.0402 (8)	0.0373 (8)	0.0415 (7)	−0.0142 (6)	−0.0015 (6)	−0.0188 (6)
C6	0.0573 (9)	0.0410 (8)	0.0463 (8)	−0.0143 (7)	−0.0124 (7)	−0.0162 (7)
C7	0.0713 (11)	0.0575 (11)	0.0533 (9)	−0.0186 (9)	−0.0167 (8)	−0.0282 (8)
C8	0.0712 (11)	0.0398 (9)	0.0521 (9)	−0.0135 (8)	−0.0201 (8)	−0.0192 (7)
C9	0.1000 (15)	0.0390 (9)	0.0678 (11)	−0.0152 (9)	−0.0285 (10)	−0.0238 (8)
C10	0.0549 (9)	0.0403 (8)	0.0677 (10)	−0.0094 (7)	−0.0271 (8)	−0.0213 (8)
C11	0.0533 (9)	0.0353 (8)	0.0405 (7)	−0.0108 (7)	−0.0175 (6)	−0.0130 (6)
C12	0.0637 (11)	0.0517 (10)	0.0791 (12)	−0.0294 (9)	−0.0024 (9)	−0.0277 (9)
C13	0.0989 (17)	0.0653 (14)	0.133 (2)	−0.0416 (13)	0.0127 (15)	−0.0589 (15)
N1	0.0889 (11)	0.0530 (9)	0.0664 (9)	−0.0200 (8)	−0.0205 (8)	−0.0321 (8)
N2	0.0434 (7)	0.0334 (6)	0.0460 (7)	−0.0143 (5)	−0.0076 (5)	−0.0172 (5)
N3	0.0534 (8)	0.0346 (7)	0.0629 (8)	−0.0176 (6)	−0.0102 (6)	−0.0199 (6)
O1	0.0513 (7)	0.0473 (7)	0.0572 (7)	−0.0104 (5)	−0.0108 (5)	−0.0241 (5)
O2	0.0521 (6)	0.0386 (6)	0.0680 (7)	−0.0148 (5)	−0.0100 (5)	−0.0237 (5)
S1	0.0670 (3)	0.0416 (2)	0.0651 (3)	−0.0161 (2)	−0.0253 (2)	−0.0246 (2)

Geometric parameters (Å, º) top

C1—N2	1.3323 (17)	C8—H8	0.9300
C1—N3	1.3367 (19)	C9—N1	1.332 (2)
C1—S1	1.7582 (16)	C9—H9	0.9300
C2—N3	1.329 (2)	C10—C11	1.514 (2)
C2—C3	1.383 (2)	C10—S1	1.7858 (16)
C2—H2	0.9300	C10—H10A	0.9700
C3—C4	1.387 (2)	C10—H10B	0.9700
C3—H3	0.9300	C11—O1	1.1984 (18)
C4—N2	1.3456 (18)	C11—O2	1.3342 (17)
C4—C5	1.4886 (19)	C12—O2	1.4529 (19)
C5—C8	1.385 (2)	C12—C13	1.479 (3)
C5—C6	1.388 (2)	C12—H12A	0.9700
C6—C7	1.381 (2)	C12—H12B	0.9700
C6—H6	0.9300	C13—H13A	0.9600
C7—N1	1.325 (2)	C13—H13B	0.9600
C7—H7	0.9300	C13—H13C	0.9600
C8—C9	1.385 (2)

N2—C1—N3	127.86 (14)	C11—C10—S1	115.61 (11)
N2—C1—S1	118.93 (11)	C11—C10—H10A	108.4
N3—C1—S1	113.18 (10)	S1—C10—H10A	108.4
N3—C2—C3	123.15 (14)	C11—C10—H10B	108.4
N3—C2—H2	118.4	S1—C10—H10B	108.4
C3—C2—H2	118.4	H10A—C10—H10B	107.4
C2—C3—C4	117.32 (15)	O1—C11—O2	124.33 (14)
C2—C3—H3	121.3	O1—C11—C10	126.61 (14)
C4—C3—H3	121.3	O2—C11—C10	109.02 (13)
N2—C4—C3	120.88 (13)	O2—C12—C13	107.85 (15)
N2—C4—C5	116.22 (12)	O2—C12—H12A	110.1
C3—C4—C5	122.90 (13)	C13—C12—H12A	110.1
C8—C5—C6	116.98 (13)	O2—C12—H12B	110.1
C8—C5—C4	120.72 (13)	C13—C12—H12B	110.1
C6—C5—C4	122.29 (13)	H12A—C12—H12B	108.5
C7—C6—C5	119.32 (15)	C12—C13—H13A	109.5
C7—C6—H6	120.3	C12—C13—H13B	109.5
C5—C6—H6	120.3	H13A—C13—H13B	109.5
N1—C7—C6	124.28 (16)	C12—C13—H13C	109.5
N1—C7—H7	117.9	H13A—C13—H13C	109.5
C6—C7—H7	117.9	H13B—C13—H13C	109.5
C9—C8—C5	119.20 (15)	C7—N1—C9	116.14 (14)
C9—C8—H8	120.4	C1—N2—C4	116.09 (12)
C5—C8—H8	120.4	C2—N3—C1	114.65 (12)
N1—C9—C8	124.07 (17)	C11—O2—C12	116.28 (12)
N1—C9—H9	118.0	C1—S1—C10	101.64 (7)
C8—C9—H9	118.0

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C3—H3···O1ⁱ	0.93	2.52	3.383 (2)	154
C7—H7···O1ⁱⁱ	0.93	2.61	3.373 (2)	140

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

Experimental details

Crystal data
Chemical formula	C₁₃H₁₃N₃O₂S
M_r	275.33
Crystal system, space group	Triclinic, P1
Temperature (K)	291
a, b, c (Å)	8.6579 (8), 9.7394 (9), 9.9188 (8)
α, β, γ (°)	62.661 (6), 71.416 (5), 65.024 (6)
V (Å³)	665.35 (10)
Z	2
Radiation type	Mo Kα
µ (mm⁻¹)	0.25
Crystal size (mm)	0.32 × 0.24 × 0.18

Data collection
Diffractometer	Bruker SMART CCD area-detector diffractometer
Absorption correction	Multi-scan (SADABS; Bruker, 2000)
T_min, T_max	0.917, 0.966
No. of measured, independent and observed [I > 2σ(I)] reflections	11760, 3021, 2387
R_int	0.032
(sin θ/λ)_max (Å⁻¹)	0.649

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.038, 0.115, 1.04
No. of reflections	3021
No. of parameters	173
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.24, −0.20

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
C3—H3···O1ⁱ	0.93	2.52	3.383 (2)	154
C7—H7···O1ⁱⁱ	0.93	2.61	3.373 (2)	140

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

Acknowledgements

The author is indebted to the National Natural Science Foundation of China (grant No. 20871039) for financial support.

References

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