2-Benzyl­sulfanyl-4-pentyl-6-(phenyl­sulfan­yl)pyrimidine-5-carbonitrile

Ali A El-Emam; Omar A Al-Deeb; Abdulghafoor A Al-Turkistani; Seik Weng Ng; Edward R T Tiekink

doi:10.1107/S1600536811044746

. 2011 Oct 29;67(Pt 11):o3126. doi: 10.1107/S1600536811044746

2-Benzylsulfanyl-4-pentyl-6-(phenylsulfanyl)pyrimidine-5-carbonitrile

Ali A El-Emam ^a,^‡, Omar A Al-Deeb ^a, Abdulghafoor A Al-Turkistani ^a, Seik Weng Ng ^b,^c, Edward R T Tiekink ^b,^*

PMCID: PMC3247510 PMID: 22220128

Abstract

In the title pyrimidine derivative, C₂₃H₂₃N₃S₂, the phenylsulfanyl and benzylsulfanyl benzene rings are orientated away from the carbonitrile group and are twisted out of the plane of the central ring with dihedral angles of 77.66 (6) and 64.73 (5)°, respectively. The n-pentyl group has an extended trans conformation. In the crystal, supramolecular layers in the ab plane are sustained by C—H⋯π and π–π interactions [pyrimidine–phenylsulfanyl centroid–centroid distance = 3.8087 (7) Å].

Related literature

For the chemotherapeutic activity of pyrimidine derivatives, see: Al-Safarjalani et al. (2005 ▶); Pauwels (2004 ▶); Hawser et al. (2006 ▶), Al-Omar et al. (2010 ▶); Al-Abdullah et al. (2011 ▶). For a related pyrimidine structure, see: Nasir et al. (2010 ▶).

Experimental

Crystal data

C₂₃H₂₃N₃S₂
M _r = 405.56
Monoclinic,
a = 9.0093 (1) Å
b = 8.2137 (1) Å
c = 28.6398 (3) Å
β = 98.427 (1)°
V = 2096.45 (4) Å³
Z = 4
Cu Kα radiation
μ = 2.39 mm⁻¹
T = 100 K
0.25 × 0.25 × 0.15 mm

Data collection

Agilent SuperNova Dual diffractometer with an Atlas detector
Absorption correction: multi-scan (CrysAlis PRO: Agilent, 2010 ▶) T _min = 0.586, T _max = 0.715
8836 measured reflections
4307 independent reflections
4029 reflections with I > 2σ(I)
R _int = 0.017

Refinement

R[F ² > 2σ(F ²)] = 0.030
wR(F ²) = 0.084
S = 1.02
4307 reflections
253 parameters
H-atom parameters constrained
Δρ_max = 0.26 e Å⁻³
Δρ_min = −0.26 e Å⁻³

Data collection: CrysAlis PRO (Agilent, 2010 ▶); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: ORTEP-3 (Farrugia, 1997 ▶) and DIAMOND (Brandenburg, 2006 ▶); software used to prepare material for publication: publCIF (Westrip, 2010 ▶).

Supplementary Material

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536811044746/hg5126sup1.cif

e-67-o3126-sup1.cif^{(20.2KB, cif)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536811044746/hg5126Isup2.hkl

e-67-o3126-Isup2.hkl^{(211.1KB, hkl)}

Supplementary material file. DOI: 10.1107/S1600536811044746/hg5126Isup3.cml

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Table 1. Hydrogen-bond geometry (Å, °).

Cg1 is the centroid of the C6–C11 ring.

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C21—H21b⋯Cg1ⁱ	0.99	3.00	3.8443 (14)	148

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Symmetry code: (i) Inline graphic .

Acknowledgments

We thank the Deanship of Scientific Research and the Research Center of the College of Pharmacy, King Saud University, and the University of Malaya for supporting this study.

supplementary crystallographic information

Comment

The chemotherapeutic efficacy of pyrimidine derivatives is related to their ability to inhibit vital enzymes responsible for DNA biosynthesis. A large array of pyrimidine non-nucleoside derivatives possess various chemotherapeutic properties. These properties include anti-cancer (Al-Safarjalani et al., 2005), anti-viral (Pauwels, 2004), anti-bacterial (Hawser et al., 2006; Al-Abdullah et al., 2011). In continuation to our interest in the chemical and pharmacological properties of pyrimidine-5-carbonitrile derivatives (Al-Omar et al., 2010; Al-Abdullah et al., 2011), we synthesized the title compound, (I), as a potential chemotherapeutic agent, and as part of on-going structural studies of pyrimidine derivatives (Nasir et al., 2010), the crystal structure determination is reported herein.

The molecule of (I), Fig. 1, is a tetra-substituted pyrimidine derivative. With reference to the pyrimidine ring, the S-benzene and benzyl-benzene rings are each twisted out of the plane as indicated in the respective dihedral angles of 77.66 (6) and 64.73 (5)°. The dihedral angle between the benzene rings is 51.74 (6)°, indicating a non-parallel orientation, and they are directed to the same side of the molecule, i.e. away from the carbonitrile group. The n-pentyl group has an extended trans-conformation: the range of torsion angles = 174.92 (10) to -179.41 (12)°.

Weak C—H···π, Table 1, and π–π interactions feature in the crystal packing. The π–π interactions occur between the pyrimidine and S-benzene ring with the separation between the ring centroids being 3.8087 (7) Å [angle between rings = 14.45 (6)° for symmetry operation 3/2 - x, 1/2 + y, 1/2 - z]. The C—H···π interaction involves a methylene-H atom interacting with the benzyl-benzene ring. The interactions lead to supramolecular layers that inter-digitate along the c axis. Globally, the crystal structure comprises alternating pyrimidine-rich and aromatic regions stacking along the c direction.

Experimental

To a solution of 2-(benzylthio)-4-chloro-6-(n-pentyl)pyrimidine-5-carbonitrile (665 mg, 2.0 mmol) in dry pyridine (3 ml) was added thiophenol (220 mg, 2.0 mmol). The mixture was heated for 6 h. On cooling, the solvent was distilled off in vacuo, and water (5 ml) was added to the residue. The precipitate was filtered, washed with cold water, dried and crystallized from ethanol to yield 625 mg (77%) of the title compound as colourless crystals, M.pt. 373–375 K. ¹H NMR (DMSO-d₆): δ 0.86 (t, 3H, CH₃, J = 7.0 Hz), 1.30–1.33 (m, 4H, CH₂CH₂CH₃), 1.66–1.69 (m, 2H, CH₂—CH₂CH₂CH₃), 2.77 (t, 2H, CH₂—CH₂CH₂CH₂CH₃, J = 7.0 Hz), 3.99 (s, 2H, CH₂S), 6.99–7.0 (m, 2H, Ar—H), 7.15–7.22 (m, 3H, Ar—H), 7.50–7.52 (m, 3H, Ar—H), 7.66–7.68 (m, 2H, Ar—H). ¹³C NMR: 13.70 (CH₃), 21.72 (CH₂CH₃), 26.93 (CH₂CH₂CH₃), 30.62 (CH₂CH₂CH₂CH₃), 33.97 (CH₂CH₂CH₂CH₂CH₃), 35.64 (CH₂S), 98.94 (pym. ring), 114.22 (CN), 125.17, 127.12, 128.30, 128.63, 129.56, 130.47, 135.81, 137.0 (Ar—C), 171.98, 172.71, 172.85 (pym. ring).