2-[(4-Chloro­benz­yl)sulfan­yl]-4-(2-methyl­prop­yl)-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/S1600536812025810

. 2012 Jun 13;68(Pt 7):o2055–o2056. doi: 10.1107/S1600536812025810

2-[(4-Chlorobenzyl)sulfanyl]-4-(2-methylpropyl)-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: PMC3393322 PMID: 22807879

Abstract

In the title compound, C₂₂H₂₀ClN₃S₂, the S-bound benzene rings are inclined [dihedral angles = 78.13 (10) and 36.70 (9)°] with respect to the pyrimidine ring. The methylpropyl group occupies a position normal to the pyrimidine ring [N—C—C—C torsion angle = 92.3 (2)°]. In the crystal, supramolecular layers are formed in the bc plane, being consolidated by C—H⋯π and π—π interactions, the latter between the pyrimidine and S-bound benzene rings [inter-centroid distance = 3.7683 (12) Å].

Related literature

For the chemotherapeutic activity of pyrimidine derivatives, see: Al-Abdullah et al. (2011 ▶); Brunelle et al. (2007 ▶); Ding et al. (2006 ▶); Al-Safarjalani et al. (2005 ▶). For a related pyrimidine structure, see: El-Emam et al. (2011 ▶).

Experimental

Crystal data

C₂₂H₂₀ClN₃S₂
M _r = 425.98
Monoclinic,
a = 13.7771 (2) Å
b = 8.4961 (1) Å
c = 18.5878 (2) Å
β = 97.559 (1)°
V = 2156.82 (5) Å³
Z = 4
Cu Kα radiation
μ = 3.47 mm⁻¹
T = 294 K
0.35 × 0.30 × 0.25 mm

Data collection

Agilent SuperNova Dual diffractometer with Atlas detector
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2012 ▶) T _min = 0.611, T _max = 1.000
15819 measured reflections
4512 independent reflections
4113 reflections with I > 2σ(I)
R _int = 0.018

Refinement

R[F ² > 2σ(F ²)] = 0.041
wR(F ²) = 0.117
S = 1.04
4512 reflections
254 parameters
H-atom parameters constrained
Δρ_max = 0.41 e Å⁻³
Δρ_min = −0.46 e Å⁻³

Data collection: CrysAlis PRO (Agilent, 2012 ▶); 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 for Windows (Farrugia, 1997 ▶) and DIAMOND (Brandenburg, 2006 ▶); software used to prepare material for publication: publCIF (Westrip, 2010 ▶).

Supplementary Material

Crystal structure: contains datablock(s) general, I. DOI: 10.1107/S1600536812025810/pv2554sup1.cif

e-68-o2055-sup1.cif^{(21.8KB, cif)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536812025810/pv2554Isup2.hkl

e-68-o2055-Isup2.hkl^{(216.6KB, hkl)}

Supplementary material file. DOI: 10.1107/S1600536812025810/pv2554Isup3.cml

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

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

Cg1 is the centroid of the C17–C22 ring.

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C6—H6⋯Cg1ⁱ	0.98	2.92	3.789 (2)	148

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Symmetry code: (i) Inline graphic .

Acknowledgments

The financial support of the Deanship of Scientific Research and the Research Center of the College of Pharmacy, King Saud University, is greatly appreciated. We also thank the Ministry of Higher Education (Malaysia) for funding structural studies through the High-Impact Research scheme (UM.C/HIR/MOHE/SC/12).

supplementary crystallographic information

Comment

The chemotherapeutic efficacy of pyrimidine derivatives is related to their ability to inhibit vital enzymes responsible for DNA biosynthesis. Thus, several non-nucleoside pyrimidine derivatives exhibit anti-cancer (Al-Safarjalani et al., 2005), anti-viral (Brunelle et al., 2007; Ding et al., 2006) and anti-bacterial activities (Al-Abdullah et al., 2011). In continuation of our interest in the chemical, pharmacological and structural properties of pyrimidine derivatives (El-Emam et al., 2011), we synthesized the title compound as a potential chemotherapeutic agent.

With respect to the pyrimidine ring in the title molecule (Fig. 1), the S1- and S2-bound benzene rings form dihedral angles of 78.13 (10) and 36.70 (9)°, respectively, indicating orthogonal and splayed orientations, respectively; the dihedral angle between the benzene rings = 69.72 (11)°. The methylpropyl group occupies a position normal to the pyrimidine ring with the N2—C4—C5—C6 torsion angle being 92.3 (2)°.

In the crystal packing, supramolecular layers, consolidated by C—H···π, Table 1, and π—π interactions between the pyrimidine and the S1-bound benzene rings [ring centroid(N1,N2,C1–C4)···centroid(C10–C15) distance = 3.7683 (12) Å, angle of inclination = 5.52 (10)° for symmetry operation: 1 - x, -1/2 + y, 3/2 - z], are formed in the bc plane, Fig. 2.

Experimental

To a solution of 2-(4-chlorobenzylsulfanyl)-6-chloro-4-(2-methylpropyl)pyrimidine-5-carbonitrile (705 mg, 2 mmol) in dry pyridine (3 ml), thiophenol (220 mg, 2 mmol) was added and the mixture was heated under reflux for 6 h. On cooling, the solvent was distilled off in vacuo and water (5 ml) was added to the residue. The separated precipitate was filtered, washed with cold water, dried and crystallized from ethanol to yield 724 mg (85%) of the title compound as colourless crystals. M.pt: 394–396 K. Crystals for the X-ray analysis were obtained by slow evaporation of a solution of the title compound in CHCl₃:EtOH (1:1, 5 ml) held at room temperature.