6-(2-Methyl-prop-yl)-4-oxo-2-sulfanyl-idene-1,2,3,4-tetra-hydro-pyrimidine-5-carbonitrile.

The title thio-uracil derivative, C(9)H(11)N(3)OS, exists in the thione form. The six atoms comprising the ring are almost coplanar [r.m.s. deviation = 0.015 Å] and the 2-methyl-propyl group lies approximately perpendicular to this plane [the N-C-C-C torsion angle is 72.88 (14)°]. Linear supra-molecular chains along [001] sustained by N-H⋯O and N-H⋯S hydrogen bonding feature in the crystal packing.

Related literature

For the biological activity of uracil and pyrimidine derivatives see: Ding et al. (2006 ▶); Hawser et al., (2006 ▶); Brunelle et al. (2007 ▶); Al-Safarjalani et al. (2005 ▶); Al-Omar et al. (2010 ▶); Al-Abdullah et al. (2011 ▶); Al-Turkistani et al. (2011 ▶). For related uracil structures, see: Tiekink (1989 ▶); Nasir et al. (2010 ▶); El-Emam et al. (2011 ▶).

Experimental

Crystal data

C9H11N3OS

M = 209.27

Monoclinic,

a = 25.8985 (6) Å

b = 7.0479 (2) Å

c = 11.1811 (2) Å

β = 98.527 (2)°

V = 2018.33 (8) Å3

Z = 8

Cu Kα radiation

μ = 2.62 mm−1

T = 100 K

0.35 × 0.20 × 0.03 mm

Data collection

Agilent SuperNova Dual diffractometer with Atlas detector

Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2011 ▶) T min = 0.461, T max = 0.926

6870 measured reflections

2102 independent reflections

1989 reflections with I > 2σ(I)

R int = 0.024

Refinement

R[F 2 > 2σ(F 2)] = 0.030

wR(F 2) = 0.086

S = 1.03

2102 reflections

135 parameters

2 restraints

H atoms treated by a mixture of independent and constrained refinement

Δρmax = 0.27 e Å−3

Δρmin = −0.28 e Å−3

Data collection: CrysAlis PRO (Agilent, 2011 ▶); 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 ▶).

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536812005119/hg5174sup1.cif

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536812005119/hg5174Isup2.hkl

Supplementary material file. DOI: 10.1107/S1600536812005119/hg5174Isup3.cml

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

C9H11N3OS	F(000) = 880
Mr = 209.27	Dx = 1.377 Mg m−3
Monoclinic, C2/c	Cu Kα radiation, λ = 1.54184 Å
Hall symbol: -C 2yc	Cell parameters from 4317 reflections
a = 25.8985 (6) Å	θ = 4.0–76.1°
b = 7.0479 (2) Å	µ = 2.62 mm−1
c = 11.1811 (2) Å	T = 100 K
β = 98.527 (2)°	Needle, colourless
V = 2018.33 (8) Å3	0.35 × 0.20 × 0.03 mm
Z = 8

Agilent SuperNova Dual diffractometer with Atlas detector	2102 independent reflections
Radiation source: SuperNova (Cu) X-ray Source	1989 reflections with I > 2σ(I)
Mirror monochromator	Rint = 0.024
Detector resolution: 10.4041 pixels mm-1	θmax = 76.3°, θmin = 6.5°
ω scans	h = −31→32
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2011)	k = −8→8
Tmin = 0.461, Tmax = 0.926	l = −14→10
6870 measured reflections

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)] = 0.030	Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.086	H atoms treated by a mixture of independent and constrained refinement
S = 1.03	w = 1/[σ2(Fo2) + (0.0528P)2 + 1.3984P] where P = (Fo2 + 2Fc2)/3
2102 reflections	(Δ/σ)max = 0.002
135 parameters	Δρmax = 0.27 e Å−3
2 restraints	Δρmin = −0.28 e Å−3

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	0.550100 (11)	0.21184 (4)	0.42164 (3)	0.01651 (12)
O1	0.43446 (3)	0.31829 (14)	0.72665 (8)	0.0189 (2)
N1	0.44705 (4)	0.25643 (16)	0.37760 (9)	0.0154 (2)
N2	0.48422 (4)	0.27666 (15)	0.57730 (9)	0.0143 (2)
N3	0.30186 (4)	0.37646 (18)	0.58639 (10)	0.0225 (3)
C1	0.49111 (5)	0.24972 (18)	0.46022 (11)	0.0144 (2)
C2	0.43658 (5)	0.30269 (17)	0.61833 (11)	0.0146 (3)
C3	0.39202 (5)	0.31030 (17)	0.52342 (11)	0.0150 (3)
C4	0.39788 (5)	0.28817 (16)	0.40487 (11)	0.0151 (3)
C5	0.34180 (5)	0.34614 (19)	0.55782 (10)	0.0166 (3)
C6	0.35440 (5)	0.29348 (18)	0.30154 (11)	0.0165 (3)
H6A	0.3644	0.3779	0.2381	0.020*
H6B	0.3232	0.3490	0.3297	0.020*
C7	0.33981 (5)	0.09633 (18)	0.24532 (10)	0.0160 (3)
H7	0.3698	0.0480	0.2073	0.019*
C8	0.29278 (5)	0.1211 (2)	0.14684 (12)	0.0246 (3)
H8A	0.3012	0.2133	0.0870	0.037*
H8B	0.2629	0.1670	0.1831	0.037*
H8C	0.2840	−0.0010	0.1071	0.037*
C9	0.32809 (5)	−0.0459 (2)	0.34028 (12)	0.0221 (3)
H9A	0.3589	−0.0599	0.4022	0.033*
H9B	0.3193	−0.1689	0.3017	0.033*
H9C	0.2986	−0.0004	0.3780	0.033*
H1N	0.4514 (7)	0.243 (3)	0.3021 (9)	0.026 (4)*
H2N	0.5113 (5)	0.275 (3)	0.6341 (13)	0.023 (4)*

	U11	U22	U33	U12	U13	U23
S1	0.01253 (17)	0.02143 (19)	0.01565 (18)	0.00095 (10)	0.00231 (11)	0.00078 (10)
O1	0.0159 (4)	0.0270 (5)	0.0136 (4)	0.0004 (4)	0.0013 (3)	−0.0010 (3)
N1	0.0141 (5)	0.0193 (5)	0.0125 (5)	−0.0002 (4)	0.0014 (4)	−0.0001 (4)
N2	0.0112 (5)	0.0176 (5)	0.0134 (5)	0.0001 (4)	−0.0003 (4)	−0.0001 (4)
N3	0.0173 (5)	0.0264 (6)	0.0232 (5)	0.0018 (5)	0.0018 (4)	−0.0033 (5)
C1	0.0153 (6)	0.0121 (5)	0.0155 (6)	−0.0014 (4)	0.0009 (4)	0.0007 (4)
C2	0.0137 (6)	0.0130 (6)	0.0168 (6)	−0.0004 (4)	0.0016 (5)	0.0000 (4)
C3	0.0128 (6)	0.0149 (6)	0.0167 (6)	−0.0003 (4)	0.0006 (4)	−0.0003 (4)
C4	0.0139 (6)	0.0122 (6)	0.0186 (6)	−0.0003 (4)	0.0009 (5)	0.0006 (4)
C5	0.0165 (6)	0.0168 (6)	0.0152 (5)	0.0002 (5)	−0.0014 (4)	−0.0016 (4)
C6	0.0150 (6)	0.0183 (7)	0.0152 (6)	0.0013 (4)	−0.0012 (5)	−0.0003 (4)
C7	0.0122 (5)	0.0193 (6)	0.0162 (5)	0.0005 (4)	0.0011 (4)	−0.0028 (5)
C8	0.0230 (7)	0.0251 (7)	0.0224 (6)	0.0030 (5)	−0.0075 (5)	−0.0055 (5)
C9	0.0201 (6)	0.0233 (7)	0.0224 (6)	−0.0050 (5)	0.0014 (5)	0.0004 (5)

S1—C1	1.6693 (13)	C6—C7	1.5486 (17)
O1—C2	1.2254 (15)	C6—H6A	0.9900
N1—C1	1.3583 (16)	C6—H6B	0.9900
N1—C4	1.3711 (16)	C7—C9	1.5232 (18)
N1—H1N	0.873 (9)	C7—C8	1.5261 (16)
N2—C1	1.3605 (16)	C7—H7	1.0000
N2—C2	1.3909 (16)	C8—H8A	0.9800
N2—H2N	0.874 (9)	C8—H8B	0.9800
N3—C5	1.1470 (17)	C8—H8C	0.9800
C2—C3	1.4482 (17)	C9—H9A	0.9800
C3—C4	1.3653 (18)	C9—H9B	0.9800
C3—C5	1.4323 (17)	C9—H9C	0.9800
C4—C6	1.4895 (17)
C1—N1—C4	124.66 (11)	C4—C6—H6B	108.8
C1—N1—H1N	116.1 (12)	C7—C6—H6B	108.8
C4—N1—H1N	119.2 (12)	H6A—C6—H6B	107.7
C1—N2—C2	125.81 (10)	C9—C7—C8	110.98 (10)
C1—N2—H2N	119.4 (12)	C9—C7—C6	111.67 (10)
C2—N2—H2N	114.7 (12)	C8—C7—C6	108.10 (10)
N1—C1—N2	115.64 (11)	C9—C7—H7	108.7
N1—C1—S1	122.58 (9)	C8—C7—H7	108.7
N2—C1—S1	121.77 (9)	C6—C7—H7	108.7
O1—C2—N2	120.65 (11)	C7—C8—H8A	109.5
O1—C2—C3	124.98 (11)	C7—C8—H8B	109.5
N2—C2—C3	114.37 (10)	H8A—C8—H8B	109.5
C4—C3—C5	121.13 (11)	C7—C8—H8C	109.5
C4—C3—C2	121.06 (11)	H8A—C8—H8C	109.5
C5—C3—C2	117.79 (11)	H8B—C8—H8C	109.5
N1—C4—C3	118.37 (11)	C7—C9—H9A	109.5
N1—C4—C6	116.87 (11)	C7—C9—H9B	109.5
C3—C4—C6	124.75 (12)	H9A—C9—H9B	109.5
N3—C5—C3	179.16 (14)	C7—C9—H9C	109.5
C4—C6—C7	113.78 (10)	H9A—C9—H9C	109.5
C4—C6—H6A	108.8	H9B—C9—H9C	109.5
C7—C6—H6A	108.8
C4—N1—C1—N2	0.16 (19)	C1—N1—C4—C3	−1.67 (19)
C4—N1—C1—S1	−179.61 (10)	C1—N1—C4—C6	179.07 (12)
C2—N2—C1—N1	2.54 (19)	C5—C3—C4—N1	179.23 (11)
C2—N2—C1—S1	−177.70 (9)	C2—C3—C4—N1	0.68 (18)
C1—N2—C2—O1	177.06 (12)	C5—C3—C4—C6	−1.58 (19)
C1—N2—C2—C3	−3.35 (18)	C2—C3—C4—C6	179.87 (11)
O1—C2—C3—C4	−178.83 (12)	N1—C4—C6—C7	72.88 (14)
N2—C2—C3—C4	1.60 (17)	C3—C4—C6—C7	−106.32 (14)
O1—C2—C3—C5	2.58 (19)	C4—C6—C7—C9	53.98 (14)
N2—C2—C3—C5	−176.99 (11)	C4—C6—C7—C8	176.33 (11)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1N···S1i	0.87 (1)	2.51 (1)	3.3723 (11)	172 (2)
N2—H2N···O1ii	0.87 (1)	1.96 (1)	2.8210 (14)	168 (2)

Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1N⋯S1i	0.87 (1)	2.51 (1)	3.3723 (11)	172 (2)
N2—H2N⋯O1ii	0.87 (1)	1.96 (1)	2.8210 (14)	168 (2)

Symmetry codes: (i) ; (ii) .