1,4-Bis(pyrimidin-2-yl­sulfanyl)­butane

Akbar, M.; Quereshi, F.A.; Nasir, W.; Adnan, A.; Ng, S.W.

doi:10.1107/S1600536810041103

organic compounds

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ISSN: 2056-9890

Volume 66| Part 11| November 2010| Page o2849

https://doi.org/10.1107/S1600536810041103

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1,4-Bis(pyrimidin-2-ylsulfanyl)butane

Muhammad Akbar,^a Fahim Ashraf Quereshi,^a Waqar Nasir,^a Ahmad Adnan ^a and Seik Weng Ng ^b ^*

^aDepartment of Chemistry, Government College University, 54000 Lahore, Pakistan, and ^bDepartment of Chemistry, University of Malaya, 50603 Kuala Lumpur, Malaysia
^*Correspondence e-mail: seikweng@um.edu.my

(Received 7 October 2010; accepted 12 October 2010; online 20 October 2010)

The –SCH₂CH₂CH₂CH₂S– portion of the title compound, C₁₂H₁₄N₂S₂, adopts an extended zigzag conformation. The angles at the tetrahedral carbon atoms are marginally increased [113.63 (12)° and 111.38 (17)° for S—C—C and C—C—C respectively] from the idealized tetrahedral angle. The molecule lies on an inversion center located at the mid-point of the butyl chain. In the crystal, there is a π–π stacking interaction between inversion-related pyrimidine rings with mean interplanar spacing of 3.494 (2) Å.

Related literature

For the structure of a silver perchlorate adduct of the title compound see: Wang & Zheng (2007 ).

Experimental

Crystal data

C₁₂H₁₄N₄S₂
M_r = 278.39
Triclinic, $[P \overline 1]$
a = 5.5025 (1) Å
b = 7.6617 (1) Å
c = 8.3598 (2) Å
α = 86.915 (1)°
β = 87.253 (1)°
γ = 75.853 (1)°
V = 341.03 (1) Å³
Z = 1
Mo Kα radiation
μ = 0.38 mm⁻¹
T = 293 K
0.35 × 0.20 × 0.10 mm

Data collection

Bruker Kappa APEXII diffractometer
Absorption correction: multi-scan (SADABS; Sheldrick, 1996 ) T_min = 0.849, T_max = 1.000
5571 measured reflections
1524 independent reflections
1384 reflections with I > 2σ(I)
R_int = 0.025

Refinement

R[F² > 2σ(F²)] = 0.036
wR(F²) = 0.115
S = 1.05
1524 reflections
82 parameters
H-atom parameters constrained
Δρ_max = 0.23 e Å⁻³
Δρ_min = −0.23 e Å⁻³

Data collection: APEX2 (Bruker, 2009 ); cell refinement: SAINT (Bruker, 2009); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: X-SEED (Barbour, 2001 ); software used to prepare material for publication: publCIF (Westrip, 2010 ).

Supporting information

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S1600536810041103/pk2276sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536810041103/pk2276Isup2.hkl

checkCIF report

Comment top

The bis(arylthio)alkane ligands are excellent 'flexible' ligands for binding to silver(I) compounds. The title ligand (Scheme I) has been used in the synthesis of a silver perchlorate adduct; the ligand binds through its nitrogen donor sites (Wang & Zheng, 2007). The ligand itself exists as a centrosymmetric compound (Fig. 1) with an inversion center located at the mid-point of the butyl chain. The –SCH₂CH₂CH₂CH₂S– portion of the molecule of C₁₂H₁₄N₂S₂ adopts an extended zigzag conformation, and the angles at the tetrahedral C atoms are marginally increased from the idealized 109.5 ° (113.62 (12)° and 111.38 (17)° for S—C—C and C—C—C respectively).

Related literature top

For the structure of a silver perchlorate adduct, see: Wang & Zheng (2007).

Experimental top

To the ethanol mixture (50 ml) of 2-mercaptopyrimidine (2 g, 17.8 mmol) and sodium bicarbonate (1.8 g, 21.4 mmol) was added 1,4-dichlorobutane (1.13 g, 8.92 mmol). The mixture was heated for 6 h and the progress of the reaction was monitored by TLC (chloroform: ethyl acetate 9:1). The mixture was filtered and the solvent was allowed to evaporate. The colorless crystals that were isolated were collected and washed with hexane; yield 82%.

Structure description top

For the structure of a silver perchlorate adduct, see: Wang & Zheng (2007).

Computing details top

Data collection: APEX2 (Bruker, 2009); cell refinement: SAINT (Bruker, 2009); data reduction: SAINT (Bruker, 2009); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: X-SEED (Barbour, 2001); software used to prepare material for publication: publCIF (Westrip, 2010).

Figures top

Fig. 1. Thermal ellipsoid plot (Barbour, 2001) of C₁₂H₁₄N₂S₂ at the 50% probability level; hydrogen atoms are drawn as spheres of arbitrary radius. The molecule lies about a center-of-inversion.

1,4-Bis(pyrimidin-2-ylsulfanyl)butane top

Crystal data top

C₁₂H₁₄N₄S₂	Z = 1
M_r = 278.39	F(000) = 146
Triclinic, P1	D_x = 1.356 Mg m⁻³
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 5.5025 (1) Å	Cell parameters from 3569 reflections
b = 7.6617 (1) Å	θ = 2.4–28.3°
c = 8.3598 (2) Å	µ = 0.38 mm⁻¹
α = 86.915 (1)°	T = 293 K
β = 87.253 (1)°	Prism, pale yellow
γ = 75.853 (1)°	0.35 × 0.20 × 0.10 mm
V = 341.03 (1) Å³

Data collection top

Bruker Kappa APEXII diffractometer	1524 independent reflections
Radiation source: fine-focus sealed tube	1384 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.025
Detector resolution: 0 pixels mm^-1	θ_max = 27.5°, θ_min = 2.7°
φ and ω scans	h = −7→7
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	k = −9→9
T_min = 0.849, T_max = 1.000	l = −10→10
5571 measured reflections

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)] = 0.036	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.115	H-atom parameters constrained
S = 1.05	w = 1/[σ²(F_o²) + (0.0684P)² + 0.0791P] where P = (F_o² + 2F_c²)/3
1524 reflections	(Δ/σ)_max = 0.001
82 parameters	Δρ_max = 0.23 e Å⁻³
0 restraints	Δρ_min = −0.23 e Å⁻³

Crystal data top

C₁₂H₁₄N₄S₂	γ = 75.853 (1)°
M_r = 278.39	V = 341.03 (1) Å³
Triclinic, P1	Z = 1
a = 5.5025 (1) Å	Mo Kα radiation
b = 7.6617 (1) Å	µ = 0.38 mm⁻¹
c = 8.3598 (2) Å	T = 293 K
α = 86.915 (1)°	0.35 × 0.20 × 0.10 mm
β = 87.253 (1)°

Data collection top

Bruker Kappa APEXII diffractometer	1524 independent reflections
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	1384 reflections with I > 2σ(I)
T_min = 0.849, T_max = 1.000	R_int = 0.025
5571 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.036	0 restraints
wR(F²) = 0.115	H-atom parameters constrained
S = 1.05	Δρ_max = 0.23 e Å⁻³
1524 reflections	Δρ_min = −0.23 e Å⁻³
82 parameters

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
S1	0.00757 (8)	0.83807 (5)	0.36197 (5)	0.0497 (2)
N1	0.2131 (3)	0.68013 (19)	0.09155 (18)	0.0464 (3)
N2	−0.2078 (3)	0.8589 (2)	0.09199 (19)	0.0505 (4)
C1	0.3698 (3)	0.5370 (2)	0.46719 (19)	0.0437 (4)
H1A	0.3522	0.4713	0.3742	0.052*
H1B	0.2444	0.5191	0.5479	0.052*
C2	0.3247 (3)	0.7362 (2)	0.4204 (2)	0.0469 (4)
H2A	0.4395	0.7516	0.3321	0.056*
H2B	0.3622	0.7989	0.5103	0.056*
C3	0.0099 (3)	0.78350 (19)	0.16033 (19)	0.0396 (3)
C4	0.1936 (3)	0.6518 (3)	−0.0632 (2)	0.0533 (4)
H4	0.3305	0.5800	−0.1171	0.064*
C5	−0.0195 (4)	0.7241 (3)	−0.1458 (2)	0.0541 (4)
H5	−0.0289	0.7042	−0.2539	0.065*
C6	−0.2187 (3)	0.8274 (3)	−0.0615 (2)	0.0539 (4)
H6	−0.3667	0.8770	−0.1140	0.065*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.0475 (3)	0.0499 (3)	0.0434 (3)	0.00536 (19)	−0.00486 (18)	−0.00421 (18)
N1	0.0412 (7)	0.0462 (7)	0.0472 (8)	−0.0017 (6)	−0.0016 (6)	−0.0023 (6)
N2	0.0391 (7)	0.0549 (8)	0.0517 (9)	0.0004 (6)	−0.0063 (6)	−0.0012 (6)
C1	0.0419 (8)	0.0443 (8)	0.0420 (8)	−0.0037 (6)	−0.0078 (7)	−0.0004 (6)
C2	0.0467 (8)	0.0440 (8)	0.0470 (9)	−0.0035 (7)	−0.0116 (7)	−0.0020 (7)
C3	0.0384 (7)	0.0352 (7)	0.0428 (8)	−0.0048 (6)	−0.0032 (6)	0.0013 (6)
C4	0.0500 (10)	0.0566 (10)	0.0485 (10)	−0.0038 (8)	0.0045 (7)	−0.0067 (8)
C5	0.0603 (11)	0.0596 (10)	0.0419 (9)	−0.0130 (8)	−0.0047 (8)	−0.0021 (7)
C6	0.0474 (9)	0.0605 (10)	0.0514 (10)	−0.0075 (8)	−0.0134 (8)	0.0033 (8)

Geometric parameters (Å, º) top

S1—C3	1.7571 (17)	C1—H1B	0.9700
S1—C2	1.8076 (16)	C2—H2A	0.9700
N1—C3	1.328 (2)	C2—H2B	0.9700
N1—C4	1.337 (2)	C4—C5	1.370 (3)
N2—C6	1.325 (2)	C4—H4	0.9300
N2—C3	1.337 (2)	C5—C6	1.374 (3)
C1—C2	1.517 (2)	C5—H5	0.9300
C1—C1ⁱ	1.524 (3)	C6—H6	0.9300
C1—H1A	0.9700

C3—S1—C2	103.41 (8)	H2A—C2—H2B	107.7
C3—N1—C4	115.09 (14)	N1—C3—N2	127.07 (15)
C6—N2—C3	115.78 (15)	N1—C3—S1	120.73 (12)
C2—C1—C1ⁱ	111.38 (17)	N2—C3—S1	112.20 (12)
C2—C1—H1A	109.4	N1—C4—C5	122.81 (16)
C1ⁱ—C1—H1A	109.4	N1—C4—H4	118.6
C2—C1—H1B	109.4	C5—C4—H4	118.6
C1ⁱ—C1—H1B	109.4	C4—C5—C6	116.83 (17)
H1A—C1—H1B	108.0	C4—C5—H5	121.6
C1—C2—S1	113.63 (12)	C6—C5—H5	121.6
C1—C2—H2A	108.8	N2—C6—C5	122.41 (16)
S1—C2—H2A	108.8	N2—C6—H6	118.8
C1—C2—H2B	108.8	C5—C6—H6	118.8
S1—C2—H2B	108.8

C1ⁱ—C1—C2—S1	−173.69 (15)	C2—S1—C3—N1	3.47 (15)
C3—S1—C2—C1	−82.52 (14)	C2—S1—C3—N2	−175.76 (12)
C4—N1—C3—N2	0.6 (3)	C3—N1—C4—C5	0.2 (3)
C4—N1—C3—S1	−178.46 (12)	N1—C4—C5—C6	−0.8 (3)
C6—N2—C3—N1	−0.7 (3)	C3—N2—C6—C5	−0.1 (3)
C6—N2—C3—S1	178.47 (13)	C4—C5—C6—N2	0.8 (3)

Symmetry code: (i) −x+1, −y+1, −z+1.

Experimental details

Crystal data
Chemical formula	C₁₂H₁₄N₄S₂
M_r	278.39
Crystal system, space group	Triclinic, P1
Temperature (K)	293
a, b, c (Å)	5.5025 (1), 7.6617 (1), 8.3598 (2)
α, β, γ (°)	86.915 (1), 87.253 (1), 75.853 (1)
V (Å³)	341.03 (1)
Z	1
Radiation type	Mo Kα
µ (mm⁻¹)	0.38
Crystal size (mm)	0.35 × 0.20 × 0.10

Data collection
Diffractometer	Bruker Kappa APEXII diffractometer
Absorption correction	Multi-scan (SADABS; Sheldrick, 1996)
T_min, T_max	0.849, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections	5571, 1524, 1384
R_int	0.025
(sin θ/λ)_max (Å⁻¹)	0.650

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.036, 0.115, 1.05
No. of reflections	1524
No. of parameters	82
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.23, −0.23

Computer programs: APEX2 (Bruker, 2009), SAINT (Bruker, 2009), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), X-SEED (Barbour, 2001), publCIF (Westrip, 2010).

Acknowledgements

We thank the Higher Education Commission of Pakistan, GC University and the University of Malaya for supporting this study.

References

Barbour, L. J. (2001). J. Supramol. Chem. 1, 189–191. CrossRef CAS Google Scholar
Bruker (2009). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Sheldrick, G. M. (1996). 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
Wang, S.-L. & Zheng, Y. (2007). Acta Cryst. E63, m2528. Web of Science CSD CrossRef IUCr Journals Google Scholar
Westrip, S. P. (2010). J. Appl. Cryst. 43, 920–925. Web of Science CrossRef CAS IUCr Journals Google Scholar