2-Benzyl-sulfanyl-4-[(4-methyl-phen-yl)sulfan-yl]-6-pentyl-pyrimidine-5-carbonitrile.

In the title compound, C(24)H(25)N(3)S(2), the S-bound benzene rings have orthogonal [dihedral angle = 85.31 (9)°] and splayed [67.92 (11)°] orientations with respect to the pyrimidine ring; the dihedral angle between the benzene rings is 48.18 (12)°. The pentyl group has an extended all-trans conformation and lies to one side of the pyrimidine ring [the N(py)-C(py)-C(p)-C(p) torsion angle = -85.7 (2)°; py = pyrimidine and p = pent-yl].

Related literature

For the chemotherapeutic activity of pyrimidine derivatives see: Ghoshal & Jacob (1997 ▶); De Corte (2005 ▶); Al-Omar et al. (2010 ▶); Al-Abdullah et al. (2011 ▶); Al-Turkistani et al. (2011 ▶). For a related pyrimidine structure, see: El-Emam et al. (2012 ▶).

Experimental

Crystal data

C24H25N3S2

M = 419.59

Monoclinic,

a = 9.9178 (2) Å

b = 8.2235 (2) Å

c = 28.4388 (8) Å

β = 96.115 (2)°

V = 2306.24 (10) Å3

Z = 4

Cu Kα radiation

μ = 2.19 mm−1

T = 294 K

0.40 × 0.20 × 0.10 mm

Data collection

Agilent SuperNova Dual diffractometer with Atlas detector

Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2012 ▶) T min = 0.689, T max = 1.000

9523 measured reflections

4746 independent reflections

3720 reflections with I > 2σ(I)

R int = 0.017

Refinement

R[F 2 > 2σ(F 2)] = 0.044

wR(F 2) = 0.138

S = 1.03

4746 reflections

264 parameters

H-atom parameters constrained

Δρmax = 0.18 e Å−3

Δρmin = −0.24 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 ▶).

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536812025275/zl2483sup1.cif

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536812025275/zl2483Isup2.hkl

Supplementary material file. DOI: 10.1107/S1600536812025275/zl2483Isup3.cml

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

C24H25N3S2	F(000) = 888
Mr = 419.59	Dx = 1.208 Mg m−3
Monoclinic, P21/c	Cu Kα radiation, λ = 1.54184 Å
Hall symbol: -P 2ybc	Cell parameters from 3374 reflections
a = 9.9178 (2) Å	θ = 4.6–76.5°
b = 8.2235 (2) Å	µ = 2.19 mm−1
c = 28.4388 (8) Å	T = 294 K
β = 96.115 (2)°	Prism, colourless
V = 2306.24 (10) Å3	0.40 × 0.20 × 0.10 mm
Z = 4

Agilent SuperNova Dual diffractometer with Atlas detector	4746 independent reflections
Radiation source: SuperNova (Cu) X-ray Source	3720 reflections with I > 2σ(I)
Mirror monochromator	Rint = 0.017
Detector resolution: 10.4041 pixels mm-1	θmax = 76.7°, θmin = 5.6°
ω scan	h = −12→10
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2012)	k = −10→10
Tmin = 0.689, Tmax = 1.000	l = −35→29
9523 measured reflections

Refinement on F2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.044	H-atom parameters constrained
wR(F2) = 0.138	w = 1/[σ2(Fo2) + (0.0721P)2 + 0.1537P] where P = (Fo2 + 2Fc2)/3
S = 1.03	(Δ/σ)max = 0.001
4746 reflections	Δρmax = 0.18 e Å−3
264 parameters	Δρmin = −0.24 e Å−3
0 restraints	Extinction correction: SHELXL, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.0040 (4)

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.

	x	y	z	Uiso*/Ueq
S1	0.78263 (6)	0.31009 (7)	0.67270 (2)	0.0889 (2)
S2	0.60772 (5)	0.79595 (6)	0.773134 (19)	0.08036 (18)
N1	0.68705 (13)	0.56138 (17)	0.71826 (5)	0.0665 (3)
N2	0.58228 (15)	0.79774 (19)	0.68118 (6)	0.0764 (4)
N3	0.6892 (3)	0.4609 (4)	0.55333 (8)	0.1323 (9)
C1	0.70156 (16)	0.4995 (2)	0.67609 (7)	0.0696 (4)
C2	0.62755 (16)	0.7066 (2)	0.71888 (7)	0.0678 (4)
C3	0.59644 (18)	0.7347 (3)	0.63894 (8)	0.0775 (5)
C4	0.65498 (17)	0.5814 (3)	0.63450 (7)	0.0745 (5)
C5	0.6733 (2)	0.5142 (3)	0.58931 (8)	0.0940 (6)
C6	0.84843 (18)	0.2845 (2)	0.73261 (7)	0.0729 (5)
C7	0.97186 (19)	0.3532 (3)	0.74887 (8)	0.0858 (6)
H7	1.0217	0.4096	0.7283	0.103*
C8	1.0201 (2)	0.3376 (3)	0.79569 (9)	0.0886 (6)
H8	1.1030	0.3847	0.8064	0.106*
C9	0.9493 (2)	0.2538 (3)	0.82738 (8)	0.0825 (5)
C10	0.8272 (2)	0.1824 (3)	0.80980 (8)	0.0846 (6)
H10	0.7786	0.1229	0.8301	0.102*
C11	0.77708 (18)	0.1978 (2)	0.76337 (8)	0.0787 (5)
H11	0.6948	0.1497	0.7525	0.094*
C12	1.0013 (3)	0.2400 (4)	0.87868 (10)	0.1206 (9)
H12A	1.0233	0.1287	0.8861	0.181*
H12B	0.9329	0.2767	0.8977	0.181*
H12C	1.0811	0.3059	0.8851	0.181*
C13	0.6781 (3)	0.6417 (3)	0.81484 (8)	0.0932 (6)
H13A	0.6102	0.5595	0.8189	0.112*
H13B	0.7550	0.5892	0.8028	0.112*
C14	0.7221 (2)	0.7210 (2)	0.86107 (7)	0.0781 (5)
C15	0.8585 (3)	0.7470 (4)	0.87499 (10)	0.1021 (7)
H15	0.9228	0.7152	0.8553	0.123*
C16	0.8998 (3)	0.8197 (4)	0.91789 (13)	0.1233 (10)
H16	0.9918	0.8365	0.9267	0.148*
C17	0.8086 (4)	0.8667 (4)	0.94725 (11)	0.1249 (10)
H17	0.8378	0.9148	0.9761	0.150*
C18	0.6744 (4)	0.8435 (3)	0.93449 (10)	0.1126 (8)
H18	0.6112	0.8762	0.9545	0.135*
C19	0.6317 (2)	0.7711 (3)	0.89167 (9)	0.0911 (6)
H19	0.5394	0.7557	0.8833	0.109*
C20	0.5482 (2)	0.8344 (3)	0.59621 (8)	0.0928 (6)
H20A	0.5996	0.8045	0.5704	0.111*
H20B	0.5653	0.9484	0.6033	0.111*
C21	0.3988 (2)	0.8112 (3)	0.58083 (8)	0.0843 (5)
H21A	0.3462	0.8583	0.6043	0.101*
H21B	0.3785	0.6959	0.5787	0.101*
C22	0.3585 (2)	0.8912 (3)	0.53285 (7)	0.0885 (6)
H22A	0.3891	1.0033	0.5342	0.106*
H22B	0.4049	0.8360	0.5091	0.106*
C23	0.2100 (2)	0.8882 (4)	0.51799 (9)	0.1024 (7)
H23A	0.1632	0.9429	0.5417	0.123*
H23B	0.1792	0.7762	0.5162	0.123*
C24	0.1729 (3)	0.9695 (4)	0.47047 (8)	0.1191 (9)
H24A	0.0762	0.9674	0.4629	0.179*
H24B	0.2151	0.9124	0.4465	0.179*
H24C	0.2038	1.0802	0.4719	0.179*

	U11	U22	U33	U12	U13	U23
S1	0.0998 (4)	0.0797 (3)	0.0874 (4)	0.0206 (3)	0.0105 (3)	−0.0054 (3)
S2	0.0877 (3)	0.0652 (3)	0.0881 (3)	0.0125 (2)	0.0093 (2)	0.0008 (2)
N1	0.0611 (7)	0.0595 (7)	0.0790 (9)	0.0001 (6)	0.0086 (6)	0.0046 (7)
N2	0.0701 (8)	0.0691 (9)	0.0894 (11)	0.0054 (7)	0.0059 (7)	0.0147 (8)
N3	0.160 (2)	0.153 (2)	0.0858 (13)	0.0146 (18)	0.0225 (14)	−0.0026 (15)
C1	0.0595 (8)	0.0677 (9)	0.0822 (11)	−0.0005 (7)	0.0107 (8)	0.0044 (9)
C2	0.0556 (8)	0.0622 (9)	0.0855 (11)	−0.0011 (7)	0.0069 (7)	0.0079 (8)
C3	0.0629 (9)	0.0820 (12)	0.0871 (13)	−0.0012 (9)	0.0061 (8)	0.0159 (10)
C4	0.0656 (9)	0.0816 (11)	0.0763 (11)	−0.0025 (8)	0.0076 (8)	0.0072 (9)
C5	0.0948 (14)	0.1054 (17)	0.0820 (13)	0.0045 (12)	0.0112 (11)	0.0084 (13)
C6	0.0685 (9)	0.0600 (9)	0.0909 (12)	0.0119 (8)	0.0116 (8)	0.0009 (9)
C7	0.0723 (11)	0.0789 (12)	0.1077 (16)	−0.0043 (9)	0.0165 (11)	0.0062 (11)
C8	0.0663 (10)	0.0827 (12)	0.1157 (17)	−0.0002 (9)	0.0046 (10)	−0.0039 (12)
C9	0.0767 (11)	0.0776 (11)	0.0935 (14)	0.0201 (10)	0.0096 (10)	−0.0055 (10)
C10	0.0753 (11)	0.0795 (12)	0.1015 (15)	0.0072 (9)	0.0207 (10)	0.0103 (11)
C11	0.0645 (9)	0.0689 (10)	0.1023 (15)	0.0031 (8)	0.0074 (9)	0.0035 (10)
C12	0.1118 (19)	0.148 (3)	0.0993 (18)	0.0205 (18)	−0.0022 (14)	−0.0077 (18)
C13	0.1218 (17)	0.0681 (11)	0.0882 (14)	0.0101 (11)	0.0048 (12)	0.0053 (10)
C14	0.0911 (12)	0.0633 (10)	0.0812 (12)	0.0077 (9)	0.0148 (10)	0.0089 (9)
C15	0.0923 (14)	0.1062 (17)	0.1091 (18)	0.0028 (13)	0.0160 (13)	0.0138 (15)
C16	0.114 (2)	0.117 (2)	0.132 (3)	−0.0128 (17)	−0.0209 (19)	0.0136 (19)
C17	0.173 (3)	0.0932 (18)	0.102 (2)	−0.002 (2)	−0.014 (2)	0.0037 (15)
C18	0.160 (3)	0.0864 (15)	0.0962 (17)	0.0159 (17)	0.0345 (17)	−0.0002 (13)
C19	0.0950 (14)	0.0792 (12)	0.1008 (16)	0.0110 (11)	0.0191 (12)	0.0042 (12)
C20	0.0897 (13)	0.0930 (14)	0.0945 (15)	0.0018 (11)	0.0043 (11)	0.0267 (12)
C21	0.0856 (12)	0.0820 (12)	0.0841 (13)	0.0078 (10)	0.0038 (10)	0.0106 (10)
C22	0.0912 (13)	0.0908 (14)	0.0825 (13)	0.0047 (11)	0.0050 (10)	0.0070 (11)
C23	0.0898 (13)	0.1191 (19)	0.0964 (15)	0.0044 (13)	0.0022 (11)	0.0204 (14)
C24	0.1070 (16)	0.148 (2)	0.0972 (17)	−0.0055 (17)	−0.0142 (13)	0.0290 (17)

S1—C1	1.7601 (19)	C13—H13A	0.9700
S1—C6	1.771 (2)	C13—H13B	0.9700
S2—C2	1.739 (2)	C14—C19	1.377 (3)
S2—C13	1.824 (2)	C14—C15	1.385 (3)
N1—C1	1.325 (2)	C15—C16	1.381 (4)
N1—C2	1.333 (2)	C15—H15	0.9300
N2—C3	1.329 (3)	C16—C17	1.352 (5)
N2—C2	1.345 (2)	C16—H16	0.9300
N3—C5	1.140 (3)	C17—C18	1.355 (4)
C1—C4	1.396 (3)	C17—H17	0.9300
C3—C4	1.399 (3)	C18—C19	1.381 (4)
C3—C20	1.501 (3)	C18—H18	0.9300
C4—C5	1.428 (3)	C19—H19	0.9300
C6—C7	1.383 (3)	C20—C21	1.511 (3)
C6—C11	1.381 (3)	C20—H20A	0.9700
C7—C8	1.372 (3)	C20—H20B	0.9700
C7—H7	0.9300	C21—C22	1.529 (3)
C8—C9	1.384 (3)	C21—H21A	0.9700
C8—H8	0.9300	C21—H21B	0.9700
C9—C10	1.390 (3)	C22—C23	1.489 (3)
C9—C12	1.499 (3)	C22—H22A	0.9700
C10—C11	1.366 (3)	C22—H22B	0.9700
C10—H10	0.9300	C23—C24	1.518 (3)
C11—H11	0.9300	C23—H23A	0.9700
C12—H12A	0.9600	C23—H23B	0.9700
C12—H12B	0.9600	C24—H24A	0.9600
C12—H12C	0.9600	C24—H24B	0.9600
C13—C14	1.491 (3)	C24—H24C	0.9600
C1—S1—C6	100.16 (9)	C19—C14—C13	122.7 (2)
C2—S2—C13	102.22 (9)	C15—C14—C13	120.3 (2)
C1—N1—C2	116.55 (16)	C16—C15—C14	120.5 (3)
C3—N2—C2	116.38 (17)	C16—C15—H15	119.7
N1—C1—C4	121.56 (17)	C14—C15—H15	119.7
N1—C1—S1	118.93 (13)	C17—C16—C15	121.0 (3)
C4—C1—S1	119.50 (15)	C17—C16—H16	119.5
N1—C2—N2	126.81 (19)	C15—C16—H16	119.5
N1—C2—S2	118.82 (14)	C16—C17—C18	119.8 (3)
N2—C2—S2	114.34 (14)	C16—C17—H17	120.1
N2—C3—C4	121.19 (18)	C18—C17—H17	120.1
N2—C3—C20	117.6 (2)	C17—C18—C19	119.8 (3)
C4—C3—C20	121.2 (2)	C17—C18—H18	120.1
C1—C4—C3	117.46 (18)	C19—C18—H18	120.1
C1—C4—C5	120.89 (19)	C14—C19—C18	121.8 (3)
C3—C4—C5	121.57 (19)	C14—C19—H19	119.1
N3—C5—C4	179.3 (3)	C18—C19—H19	119.1
C7—C6—C11	119.6 (2)	C3—C20—C21	112.55 (18)
C7—C6—S1	119.71 (16)	C3—C20—H20A	109.1
C11—C6—S1	120.65 (16)	C21—C20—H20A	109.1
C8—C7—C6	119.4 (2)	C3—C20—H20B	109.1
C8—C7—H7	120.3	C21—C20—H20B	109.1
C6—C7—H7	120.3	H20A—C20—H20B	107.8
C7—C8—C9	122.0 (2)	C20—C21—C22	111.03 (18)
C7—C8—H8	119.0	C20—C21—H21A	109.4
C9—C8—H8	119.0	C22—C21—H21A	109.4
C8—C9—C10	117.3 (2)	C20—C21—H21B	109.4
C8—C9—C12	121.7 (2)	C22—C21—H21B	109.4
C10—C9—C12	121.0 (2)	H21A—C21—H21B	108.0
C11—C10—C9	121.5 (2)	C23—C22—C21	113.75 (19)
C11—C10—H10	119.3	C23—C22—H22A	108.8
C9—C10—H10	119.3	C21—C22—H22A	108.8
C10—C11—C6	120.11 (19)	C23—C22—H22B	108.8
C10—C11—H11	119.9	C21—C22—H22B	108.8
C6—C11—H11	119.9	H22A—C22—H22B	107.7
C9—C12—H12A	109.5	C22—C23—C24	112.6 (2)
C9—C12—H12B	109.5	C22—C23—H23A	109.1
H12A—C12—H12B	109.5	C24—C23—H23A	109.1
C9—C12—H12C	109.5	C22—C23—H23B	109.1
H12A—C12—H12C	109.5	C24—C23—H23B	109.1
H12B—C12—H12C	109.5	H23A—C23—H23B	107.8
C14—C13—S2	108.96 (14)	C23—C24—H24A	109.5
C14—C13—H13A	109.9	C23—C24—H24B	109.5
S2—C13—H13A	109.9	H24A—C24—H24B	109.5
C14—C13—H13B	109.9	C23—C24—H24C	109.5
S2—C13—H13B	109.9	H24A—C24—H24C	109.5
H13A—C13—H13B	108.3	H24B—C24—H24C	109.5
C19—C14—C15	117.1 (2)
C2—N1—C1—C4	−0.9 (2)	C6—C7—C8—C9	0.4 (3)
C2—N1—C1—S1	178.62 (12)	C7—C8—C9—C10	1.2 (3)
C6—S1—C1—N1	−10.82 (15)	C7—C8—C9—C12	−178.7 (2)
C6—S1—C1—C4	168.75 (14)	C8—C9—C10—C11	−1.7 (3)
C1—N1—C2—N2	−0.9 (3)	C12—C9—C10—C11	178.3 (2)
C1—N1—C2—S2	−179.06 (12)	C9—C10—C11—C6	0.6 (3)
C3—N2—C2—N1	1.2 (3)	C7—C6—C11—C10	1.1 (3)
C3—N2—C2—S2	179.48 (13)	S1—C6—C11—C10	−178.29 (15)
C13—S2—C2—N1	−1.69 (16)	C2—S2—C13—C14	156.66 (16)
C13—S2—C2—N2	179.92 (14)	S2—C13—C14—C19	75.3 (2)
C2—N2—C3—C4	0.2 (3)	S2—C13—C14—C15	−104.8 (2)
C2—N2—C3—C20	−179.37 (16)	C19—C14—C15—C16	0.2 (4)
N1—C1—C4—C3	2.2 (3)	C13—C14—C15—C16	−179.7 (2)
S1—C1—C4—C3	−177.32 (13)	C14—C15—C16—C17	0.1 (5)
N1—C1—C4—C5	179.03 (17)	C15—C16—C17—C18	−0.4 (5)
S1—C1—C4—C5	−0.5 (2)	C16—C17—C18—C19	0.4 (4)
N2—C3—C4—C1	−1.9 (3)	C15—C14—C19—C18	−0.2 (3)
C20—C3—C4—C1	177.73 (17)	C13—C14—C19—C18	179.6 (2)
N2—C3—C4—C5	−178.63 (18)	C17—C18—C19—C14	0.0 (4)
C20—C3—C4—C5	1.0 (3)	N2—C3—C20—C21	−85.7 (2)
C1—S1—C6—C7	−85.01 (17)	C4—C3—C20—C21	94.7 (2)
C1—S1—C6—C11	94.37 (16)	C3—C20—C21—C22	−170.5 (2)
C11—C6—C7—C8	−1.6 (3)	C20—C21—C22—C23	−173.8 (2)
S1—C6—C7—C8	177.82 (16)	C21—C22—C23—C24	179.6 (2)