2-[(4,6-Di-amino-pyrimidin-2-yl)sulfan-yl]-N-(2-methyl-phen-yl)acetamide.

In the title compound, C13H15NOS, the plane of the pyrimidine ring makes a dihedral angle of 54.73 (9)° with that of the o-tolyl ring. The mol-ecule adopts an extended conformation, which is evident from the C-C(=O)-N-Car (ar = aromatic) torsion angle of 178.42 (15)°. In the crystal, mol-ecules are linked via pairs of N-H⋯N hydrogen bonds, forming inversion dimers with an R (2) 2(8) ring motif. The dimers are linked by N-H⋯O and C-H⋯O hydrogen bonds, with the O atom accepting three such interactions, forming sheets parallel to (100).

Related literature

For the synthesis of the title compound, see: Xu et al. (2010 ▶). For the biological activity of pyrimidine derivatives, see: Hocková et al. (2003 ▶, 2004 ▶); Perales et al. (2011 ▶); Xu et al. (2010 ▶).

Experimental

Crystal data

C13H15N5OS

M = 289.36

Monoclinic,

a = 22.782 (5) Å

b = 7.144 (5) Å

c = 8.857 (5) Å

β = 100.189 (5)°

V = 1418.8 (13) Å3

Z = 4

Mo Kα radiation

μ = 0.23 mm−1

T = 293 K

0.30 × 0.25 × 0.20 mm

Data collection

Bruker SMART APEXII area-detector diffractometer

Absorption correction: multi-scan (SADABS; Bruker, 2008 ▶) T min = 0.687, T max = 0.746

12825 measured reflections

3417 independent reflections

2654 reflections with I > 2σ(I)

R int = 0.025

Refinement

R[F 2 > 2σ(F 2)] = 0.039

wR(F 2) = 0.128

S = 1.02

3417 reflections

182 parameters

H-atom parameters constrained

Δρmax = 0.25 e Å−3

Δρmin = −0.23 e Å−3

Data collection: APEX2 (Bruker, 2008 ▶); cell refinement: SAINT (Bruker, 2008 ▶); data reduction: SAINT; 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, 2012 ▶); software used to prepare material for publication: SHELXL97 and PLATON (Spek, 2009 ▶).

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536814015256/su2743sup1.cif

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536814015256/su2743Isup2.hkl

Click here for additional data file.

Supporting information file. DOI: 10.1107/S1600536814015256/su2743Isup3.cml

CCDC reference: 1010947

Additional supporting information: crystallographic information; 3D view; checkCIF report

C13H15N5OS	Z = 4
Mr = 289.36	F(000) = 608
Monoclinic, P21/c	Dx = 1.355 Mg m−3
Hall symbol: -P 2ybc	Mo Kα radiation, λ = 0.71073 Å
a = 22.782 (5) Å	µ = 0.23 mm−1
b = 7.144 (5) Å	T = 293 K
c = 8.857 (5) Å	Block, colourless
β = 100.189 (5)°	0.30 × 0.25 × 0.20 mm
V = 1418.8 (13) Å3

Bruker SMART APEXII area-detector diffractometer	3417 independent reflections
Radiation source: fine-focus sealed tube	2654 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.025
ω and φ scans	θmax = 28.4°, θmin = 1.8°
Absorption correction: multi-scan (SADABS; Bruker, 2008)	h = −30→30
Tmin = 0.687, Tmax = 0.746	k = −9→8
12825 measured reflections	l = −11→11

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)] = 0.039	Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.128	H-atom parameters constrained
S = 1.02	w = 1/[σ2(Fo2) + (0.0743P)2 + 0.1678P] where P = (Fo2 + 2Fc2)/3
3417 reflections	(Δ/σ)max = 0.001
182 parameters	Δρmax = 0.25 e Å−3
0 restraints	Δρmin = −0.23 e Å−3

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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 > 2sigma(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
C1	0.44402 (7)	−0.1657 (2)	1.14271 (18)	0.0541 (4)
C2	0.40616 (8)	−0.2557 (2)	1.22577 (18)	0.0565 (4)
H2	0.4169	−0.3687	1.2751	0.068*
C3	0.35231 (7)	−0.1729 (2)	1.23308 (15)	0.0479 (4)
C4	0.37612 (6)	0.06758 (19)	1.08993 (15)	0.0428 (3)
C5	0.29403 (7)	0.3577 (2)	1.06689 (17)	0.0498 (4)
H5A	0.2910	0.2907	1.1604	0.060*
H5B	0.2958	0.4905	1.0902	0.060*
C6	0.23955 (7)	0.3184 (2)	0.94817 (15)	0.0450 (3)
C7	0.15591 (7)	0.0929 (3)	0.88301 (19)	0.0600 (4)
C8	0.12155 (9)	0.1991 (4)	0.7684 (3)	0.0836 (7)
H8	0.1335	0.3192	0.7471	0.100*
C9	0.06952 (10)	0.1246 (5)	0.6865 (3)	0.1038 (9)
H9	0.0467	0.1945	0.6089	0.125*
C10	0.05148 (10)	−0.0489 (5)	0.7182 (3)	0.1083 (9)
H10	0.0161	−0.0974	0.6636	0.130*
C11	0.08558 (10)	−0.1541 (4)	0.8317 (3)	0.0879 (7)
H11	0.0727	−0.2734	0.8524	0.105*
C12	0.13842 (7)	−0.0871 (3)	0.9157 (2)	0.0623 (5)
C13	0.17501 (10)	−0.2061 (3)	1.0374 (2)	0.0705 (5)
H13A	0.1746	−0.1520	1.1364	0.106*
H13B	0.2153	−0.2122	1.0196	0.106*
H13C	0.1585	−0.3300	1.0339	0.106*
N1	0.42970 (6)	0.00314 (17)	1.07572 (14)	0.0492 (3)
N2	0.33525 (5)	−0.01003 (16)	1.15794 (12)	0.0447 (3)
N3	0.31124 (7)	−0.2447 (2)	1.31032 (16)	0.0624 (4)
H3A	0.2779	−0.1877	1.3088	0.075*
H3B	0.3185	−0.3474	1.3609	0.075*
N4	0.49728 (8)	−0.2346 (3)	1.1248 (2)	0.0820 (5)
H4A	0.5195	−0.1723	1.0738	0.098*
H4B	0.5091	−0.3410	1.1643	0.098*
N5	0.20923 (6)	0.1643 (2)	0.97155 (15)	0.0572 (4)
H5	0.2240	0.0995	1.0511	0.069*
O1	0.22618 (6)	0.42293 (18)	0.83847 (13)	0.0687 (4)
S1	0.361751 (18)	0.28855 (6)	1.00258 (5)	0.05785 (16)

	U11	U22	U33	U12	U13	U23
C1	0.0596 (9)	0.0472 (9)	0.0498 (8)	0.0097 (7)	−0.0054 (7)	0.0037 (7)
C2	0.0738 (11)	0.0425 (8)	0.0486 (8)	0.0117 (8)	−0.0017 (7)	0.0092 (6)
C3	0.0688 (10)	0.0384 (7)	0.0326 (6)	0.0011 (7)	−0.0014 (6)	−0.0002 (5)
C4	0.0536 (8)	0.0356 (7)	0.0345 (6)	0.0012 (6)	−0.0054 (5)	−0.0015 (5)
C5	0.0628 (9)	0.0354 (7)	0.0490 (8)	0.0060 (7)	0.0039 (6)	−0.0007 (6)
C6	0.0508 (8)	0.0444 (8)	0.0414 (7)	0.0090 (6)	0.0124 (6)	0.0012 (6)
C7	0.0461 (8)	0.0792 (12)	0.0535 (9)	−0.0016 (8)	0.0058 (7)	0.0023 (8)
C8	0.0543 (11)	0.1116 (18)	0.0796 (13)	−0.0008 (11)	−0.0025 (9)	0.0239 (12)
C9	0.0571 (12)	0.160 (3)	0.0862 (15)	−0.0027 (16)	−0.0096 (10)	0.0175 (17)
C10	0.0581 (13)	0.165 (3)	0.0938 (17)	−0.0216 (16)	−0.0090 (11)	−0.0151 (18)
C11	0.0645 (12)	0.1092 (18)	0.0881 (14)	−0.0245 (12)	0.0087 (11)	−0.0199 (14)
C12	0.0539 (9)	0.0765 (13)	0.0579 (9)	−0.0093 (9)	0.0139 (7)	−0.0114 (8)
C13	0.0777 (13)	0.0576 (11)	0.0757 (12)	−0.0109 (9)	0.0124 (10)	−0.0059 (9)
N1	0.0530 (7)	0.0419 (7)	0.0487 (7)	0.0059 (6)	−0.0023 (5)	0.0030 (5)
N2	0.0585 (7)	0.0362 (6)	0.0365 (6)	0.0039 (5)	0.0002 (5)	0.0000 (5)
N3	0.0830 (11)	0.0503 (8)	0.0549 (8)	0.0077 (7)	0.0146 (7)	0.0147 (6)
N4	0.0690 (11)	0.0739 (11)	0.1029 (14)	0.0298 (9)	0.0151 (9)	0.0318 (10)
N5	0.0551 (8)	0.0603 (8)	0.0521 (7)	−0.0044 (6)	−0.0020 (6)	0.0133 (6)
O1	0.0780 (8)	0.0694 (8)	0.0540 (7)	−0.0050 (6)	−0.0013 (6)	0.0188 (6)
S1	0.0529 (3)	0.0455 (3)	0.0740 (3)	0.00657 (17)	0.00824 (19)	0.02046 (18)

C1—N4	1.345 (2)	C7—N5	1.419 (2)
C1—N1	1.358 (2)	C8—C9	1.382 (3)
C1—C2	1.387 (3)	C8—H8	0.9300
C2—C3	1.374 (2)	C9—C10	1.351 (4)
C2—H2	0.9300	C9—H9	0.9300
C3—N3	1.354 (2)	C10—C11	1.379 (4)
C3—N2	1.3625 (19)	C10—H10	0.9300
C4—N2	1.317 (2)	C11—C12	1.384 (3)
C4—N1	1.3312 (19)	C11—H11	0.9300
C4—S1	1.7630 (17)	C12—C13	1.504 (3)
C5—C6	1.505 (2)	C13—H13A	0.9600
C5—S1	1.8054 (17)	C13—H13B	0.9600
C5—H5A	0.9700	C13—H13C	0.9600
C5—H5B	0.9700	N3—H3A	0.8600
C6—O1	1.2207 (18)	N3—H3B	0.8600
C6—N5	1.335 (2)	N4—H4A	0.8600
C7—C8	1.392 (3)	N4—H4B	0.8600
C7—C12	1.392 (3)	N5—H5	0.8600
N4—C1—N1	115.18 (16)	C8—C9—H9	119.7
N4—C1—C2	123.50 (16)	C9—C10—C11	119.9 (2)
N1—C1—C2	121.30 (15)	C9—C10—H10	120.0
C3—C2—C1	118.03 (15)	C11—C10—H10	120.0
C3—C2—H2	121.0	C10—C11—C12	121.9 (3)
C1—C2—H2	121.0	C10—C11—H11	119.1
N3—C3—N2	114.04 (15)	C12—C11—H11	119.1
N3—C3—C2	124.29 (14)	C11—C12—C7	117.5 (2)
N2—C3—C2	121.65 (15)	C11—C12—C13	120.6 (2)
N2—C4—N1	129.18 (13)	C7—C12—C13	121.89 (16)
N2—C4—S1	119.08 (11)	C12—C13—H13A	109.5
N1—C4—S1	111.74 (11)	C12—C13—H13B	109.5
C6—C5—S1	111.95 (10)	H13A—C13—H13B	109.5
C6—C5—H5A	109.2	C12—C13—H13C	109.5
S1—C5—H5A	109.2	H13A—C13—H13C	109.5
C6—C5—H5B	109.2	H13B—C13—H13C	109.5
S1—C5—H5B	109.2	C4—N1—C1	114.78 (14)
H5A—C5—H5B	107.9	C4—N2—C3	114.77 (13)
O1—C6—N5	124.40 (15)	C3—N3—H3A	120.0
O1—C6—C5	120.05 (14)	C3—N3—H3B	120.0
N5—C6—C5	115.54 (13)	H3A—N3—H3B	120.0
C8—C7—C12	120.68 (18)	C1—N4—H4A	120.0
C8—C7—N5	121.56 (19)	C1—N4—H4B	120.0
C12—C7—N5	117.76 (15)	H4A—N4—H4B	120.0
C9—C8—C7	119.5 (2)	C6—N5—C7	128.79 (14)
C9—C8—H8	120.2	C6—N5—H5	115.6
C7—C8—H8	120.2	C7—N5—H5	115.6
C10—C9—C8	120.6 (2)	C4—S1—C5	102.08 (8)
C10—C9—H9	119.7
N4—C1—C2—C3	−178.67 (16)	N5—C7—C12—C13	−1.6 (3)
N1—C1—C2—C3	2.8 (2)	N2—C4—N1—C1	−0.8 (2)
C1—C2—C3—N3	−179.76 (15)	S1—C4—N1—C1	179.04 (11)
C1—C2—C3—N2	1.9 (2)	N4—C1—N1—C4	177.99 (14)
S1—C5—C6—O1	−78.22 (17)	C2—C1—N1—C4	−3.3 (2)
S1—C5—C6—N5	100.79 (14)	N1—C4—N2—C3	5.1 (2)
C12—C7—C8—C9	0.1 (3)	S1—C4—N2—C3	−174.73 (9)
N5—C7—C8—C9	−179.1 (2)	N3—C3—N2—C4	176.08 (12)
C7—C8—C9—C10	0.9 (4)	C2—C3—N2—C4	−5.39 (19)
C8—C9—C10—C11	−0.9 (5)	O1—C6—N5—C7	−2.6 (3)
C9—C10—C11—C12	0.0 (4)	C5—C6—N5—C7	178.42 (15)
C10—C11—C12—C7	0.9 (3)	C8—C7—N5—C6	−11.7 (3)
C10—C11—C12—C13	−179.2 (2)	C12—C7—N5—C6	169.09 (16)
C8—C7—C12—C11	−0.9 (3)	N2—C4—S1—C5	9.30 (12)
N5—C7—C12—C11	178.33 (17)	N1—C4—S1—C5	−170.54 (10)
C8—C7—C12—C13	179.20 (19)	C6—C5—S1—C4	−98.07 (12)

D—H···A	D—H	H···A	D···A	D—H···A
N4—H4A···N1i	0.86	2.26	3.115 (2)	175
N3—H3A···O1ii	0.86	2.27	3.045 (2)	150
N5—H5···O1ii	0.86	2.54	3.264 (3)	142
C13—H13A···O1ii	0.96	2.55	3.385 (3)	145

Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N4—H4A⋯N1i	0.86	2.26	3.115 (2)	175
N3—H3A⋯O1ii	0.86	2.27	3.045 (2)	150
N5—H5⋯O1ii	0.86	2.54	3.264 (3)	142
C13—H13A⋯O1ii	0.96	2.55	3.385 (3)	145

Symmetry codes: (i) ; (ii) .