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organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 70| Part 8| August 2014| Page o850
doi:10.1107/S1600536814015256

2-[(4,6-Di­amino­pyrimidin-2-yl)sulfan­yl]-N-(2-methyl­phen­yl)acetamide

S. Subasri,a Timiri Ajay Kumar,b Barji Nayan Sinha,b Venkatesh Jayaprakashb and Devadasan Velmurugana*

aCentre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India, and bDepartment of pharmaceutical Sciences, Birla Institute of Technology, Mesra, Ranchi, India
*Correspondence e-mail: shirai2011@gmail.com

Edited by H. Stoeckli-Evans, University of Neuchâtel, Switzerland (Received 12 June 2014; accepted 29 June 2014; online 5 July 2014)

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 mol­ecule 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, mol­ecules are linked via pairs of N—H⋯N hydrogen bonds, forming inversion dimers with an R22(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).

Keywords: crystal structure.

CCDC reference: 1010947

Related literature

For the synthesis of the title compound, see: Xu et al. (2010[Xu, L. B., Sun, W., Liu, H. Y., Wang, L. L., Xiao, J. H., Yang, X. H. & Li, S. (2010). Chin. Chem. Lett. 21, 1318-1321.]). For the biological activity of pyrimidine derivatives, see: Hocková et al. (2003[Hocková, D., Holý, A., Masojídková, M., Andrei, G., Snoeck, R., De Clercq, E. & Balzarini, J. (2003). J. Med. Chem. 46, 5064-5073.], 2004[Hocková, D., Holý, A. N., Masojídková, M., Andrei, G., Snoeck, R., De Clercq, E. & Balzarini, J. (2004). Bioorg. Med. Chem. 12, 3197-3202.]); Perales et al. (2011[Perales, J. B., Freeman, J., Bacchi, C. J., Bowling, T., Don, R., Gaukel, E., Mercer, L., et al. (2011). Bioorg. Med. Chem. Lett. 21, 2816-2819.]); Xu et al. (2010[Xu, L. B., Sun, W., Liu, H. Y., Wang, L. L., Xiao, J. H., Yang, X. H. & Li, S. (2010). Chin. Chem. Lett. 21, 1318-1321.]).

[Scheme 1]

Experimental

Crystal data

  • C13H15N5OS

  • Mr = 289.36

  • Monoclinic, P 21 /c

  • 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[Bruker (2008). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.687, Tmax = 0.746

  • 12825 measured reflections

  • 3417 independent reflections

  • 2654 reflections with I > 2σ(I)

  • Rint = 0.025
Refinement

  • R[F2 > 2σ(F2)] = 0.039

  • wR(F2) = 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

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) -x+1, -y, -z+2; (ii) [x, -y+{\script{1\over 2}}, z+{\script{1\over 2}}].

Data collection: APEX2 (Bruker, 2008[Bruker (2008). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2008[Bruker (2008). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012[Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849-854.]); software used to prepare material for publication: SHELXL97 and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information

CCDC reference: 1010947

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536814015256/su2743sup1.cif

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

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

checkCIF report


Comment top

Diaminopyrimidines are an important class of six membered heterocyclic compounds with many applications. For example, some derivatives are been reported to have anticancer activity, selectively inhibiting c-Fms kinase of M-CSF-dependent myeloid leukemia cells (Xu et al., 2010). Some 2,4-diamino-pyrimidine derivatives have been shown to have anti-retro viral activity (Hocková et al., 2003,2004), and anti-trypanosoma brucei activity (Perales et al., 2011). In search for antiviral agents the title compound was designed and synthesized for targeting NS2B-NS3 protease. We report herein on its synthesis and crystal structure.

In the title compound, Fig. 1, the pyrimidine ring (N1/N2/C1-C4) makes a dihedral angle of 54.73 (9)° with the benzene ring (C7-C12). The molecule adopts an extended conformation which is evident from torsion angle C5—C6—N5—C7 = 178.42 (15) °. The amine group, atom N3, deviates from the pyrimidine ring by -0.0672 (15) Å, while atom N4 atom deviates from the same ring by 0.0824 (18) Å. The methyl carbon atom C13 deviates from the benzene ring to which it is attached by 0.0204 (22) Å.

In the crystal, molecules are linked by pairs of N—H···N hydrogen bonds forming inversion dimers and enclosing R22(8) ring motifs (Table 1 and Fig. 2). The dimers are linked via trifurcated N—H···O and C—H···O hydrogen bonds involving atom O1 as an acceptor (Table 1 and Fig. 2) forming forming sheets parallel to (100).

Related literature top

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 top

The title compound was synthesized according to the reported procedure (Xu et al., 2010). To a solution of 4,6-diamino-pyrimidine-2-thiol (0.5 g; 3.52 mmol) in 25 ml of ethanol was added potassium hydroxide(0.2g; 3.52 mmol) and the mixture was refluxed for 30 mins. Then 3.52 mmol of 2-chloro-N-phenylacetamide was added and the mixture refluxed for 1-4 h. At the end of the reaction, monitored by TLC, ethanol was evaporated in vacuo and cold water was added. The precipitate formed was filtered and dried to give the title compound as a crystalline powder (Yield of 88-96%). Block-like colourless crystals were obtained by slow evaporation of a solution in methanol at room temperature.

Refinement top

The NH and C-bound H atoms were placed in idealized positions and refined using a riding model: N-H = 0.86 Å, C-H = 0.93, 0.97 and 0.96 Å for CH, CH2 and CH3 H atoms, respectively, with Uiso(H) = 1.5Ueq(C-methyl) and = 1.2Ueq(N,C) for other H atoms.

Computing details top

Data collection: APEX2 (Bruker, 2008); cell refinement: SAINT (Bruker, 2008); data reduction: SAINT (Bruker, 2008); 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 (Sheldrick, 2008) and PLATON (Spek, 2009).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title molecule, with atom labelling. Displacement ellipsoids are drawn at the 30% probability level.
[Figure 2] Fig. 2. The crystal packing of the title compound, viewed along the b axis. The hydrogen bonds are shown as dashed lines (see Table 1 for details; the C and N-bound H-atoms not involved in hydrogen bonding have been omitted for clarity).
2-[(4,6-Diaminopyrimidin-2-yl)sulfanyl]-N-(2-methylphenyl)acetamide top
Crystal data top
C13H15N5OSZ = 4
Mr = 289.36F(000) = 608
Monoclinic, P21/cDx = 1.355 Mg m−3
Hall symbol: -P 2ybcMo Kα radiation, λ = 0.71073 Å
a = 22.782 (5) ŵ = 0.23 mm−1
b = 7.144 (5) ÅT = 293 K
c = 8.857 (5) ÅBlock, colourless
β = 100.189 (5)°0.30 × 0.25 × 0.20 mm
V = 1418.8 (13) Å3
Data collection top
Bruker SMART APEXII area-detector
diffractometer		3417 independent reflections
Radiation source: fine-focus sealed tube2654 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.025
ω and ϕ scansθmax = 28.4°, θmin = 1.8°
Absorption correction: multi-scan
(SADABS; Bruker, 2008)		h = −30→30
Tmin = 0.687, Tmax = 0.746k = −9→8
12825 measured reflectionsl = −11→11
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.039Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.128H-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 parametersΔρmax = 0.25 e Å−3
0 restraintsΔρmin = −0.23 e Å−3
Crystal data top
C13H15N5OSV = 1418.8 (13) Å3
Mr = 289.36Z = 4
Monoclinic, P21/cMo Kα radiation
a = 22.782 (5) ŵ = 0.23 mm−1
b = 7.144 (5) ÅT = 293 K
c = 8.857 (5) Å0.30 × 0.25 × 0.20 mm
β = 100.189 (5)°
Data collection top
Bruker SMART APEXII area-detector
diffractometer		3417 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2008)		2654 reflections with I > 2σ(I)
Tmin = 0.687, Tmax = 0.746Rint = 0.025
12825 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0390 restraints
wR(F2) = 0.128H-atom parameters constrained
S = 1.02Δρmax = 0.25 e Å−3
3417 reflectionsΔρmin = −0.23 e Å−3
182 parameters
Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
C10.44402 (7)−0.1657 (2)1.14271 (18)0.0541 (4)
C20.40616 (8)−0.2557 (2)1.22577 (18)0.0565 (4)
H20.4169−0.36871.27510.068*
C30.35231 (7)−0.1729 (2)1.23308 (15)0.0479 (4)
C40.37612 (6)0.06758 (19)1.08993 (15)0.0428 (3)
C50.29403 (7)0.3577 (2)1.06689 (17)0.0498 (4)
H5A0.29100.29071.16040.060*
H5B0.29580.49051.09020.060*
C60.23955 (7)0.3184 (2)0.94817 (15)0.0450 (3)
C70.15591 (7)0.0929 (3)0.88301 (19)0.0600 (4)
C80.12155 (9)0.1991 (4)0.7684 (3)0.0836 (7)
H80.13350.31920.74710.100*
C90.06952 (10)0.1246 (5)0.6865 (3)0.1038 (9)
H90.04670.19450.60890.125*
C100.05148 (10)−0.0489 (5)0.7182 (3)0.1083 (9)
H100.0161−0.09740.66360.130*
C110.08558 (10)−0.1541 (4)0.8317 (3)0.0879 (7)
H110.0727−0.27340.85240.105*
C120.13842 (7)−0.0871 (3)0.9157 (2)0.0623 (5)
C130.17501 (10)−0.2061 (3)1.0374 (2)0.0705 (5)
H13A0.1746−0.15201.13640.106*
H13B0.2153−0.21221.01960.106*
H13C0.1585−0.33001.03390.106*
N10.42970 (6)0.00314 (17)1.07572 (14)0.0492 (3)
N20.33525 (5)−0.01003 (16)1.15794 (12)0.0447 (3)
N30.31124 (7)−0.2447 (2)1.31032 (16)0.0624 (4)
H3A0.2779−0.18771.30880.075*
H3B0.3185−0.34741.36090.075*
N40.49728 (8)−0.2346 (3)1.1248 (2)0.0820 (5)
H4A0.5195−0.17231.07380.098*
H4B0.5091−0.34101.16430.098*
N50.20923 (6)0.1643 (2)0.97155 (15)0.0572 (4)
H50.22400.09951.05110.069*
O10.22618 (6)0.42293 (18)0.83847 (13)0.0687 (4)
S10.361751 (18)0.28855 (6)1.00258 (5)0.05785 (16)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0596 (9)0.0472 (9)0.0498 (8)0.0097 (7)−0.0054 (7)0.0037 (7)
C20.0738 (11)0.0425 (8)0.0486 (8)0.0117 (8)−0.0017 (7)0.0092 (6)
C30.0688 (10)0.0384 (7)0.0326 (6)0.0011 (7)−0.0014 (6)−0.0002 (5)
C40.0536 (8)0.0356 (7)0.0345 (6)0.0012 (6)−0.0054 (5)−0.0015 (5)
C50.0628 (9)0.0354 (7)0.0490 (8)0.0060 (7)0.0039 (6)−0.0007 (6)
C60.0508 (8)0.0444 (8)0.0414 (7)0.0090 (6)0.0124 (6)0.0012 (6)
C70.0461 (8)0.0792 (12)0.0535 (9)−0.0016 (8)0.0058 (7)0.0023 (8)
C80.0543 (11)0.1116 (18)0.0796 (13)−0.0008 (11)−0.0025 (9)0.0239 (12)
C90.0571 (12)0.160 (3)0.0862 (15)−0.0027 (16)−0.0096 (10)0.0175 (17)
C100.0581 (13)0.165 (3)0.0938 (17)−0.0216 (16)−0.0090 (11)−0.0151 (18)
C110.0645 (12)0.1092 (18)0.0881 (14)−0.0245 (12)0.0087 (11)−0.0199 (14)
C120.0539 (9)0.0765 (13)0.0579 (9)−0.0093 (9)0.0139 (7)−0.0114 (8)
C130.0777 (13)0.0576 (11)0.0757 (12)−0.0109 (9)0.0124 (10)−0.0059 (9)
N10.0530 (7)0.0419 (7)0.0487 (7)0.0059 (6)−0.0023 (5)0.0030 (5)
N20.0585 (7)0.0362 (6)0.0365 (6)0.0039 (5)0.0002 (5)0.0000 (5)
N30.0830 (11)0.0503 (8)0.0549 (8)0.0077 (7)0.0146 (7)0.0147 (6)
N40.0690 (11)0.0739 (11)0.1029 (14)0.0298 (9)0.0151 (9)0.0318 (10)
N50.0551 (8)0.0603 (8)0.0521 (7)−0.0044 (6)−0.0020 (6)0.0133 (6)
O10.0780 (8)0.0694 (8)0.0540 (7)−0.0050 (6)−0.0013 (6)0.0188 (6)
S10.0529 (3)0.0455 (3)0.0740 (3)0.00657 (17)0.00824 (19)0.02046 (18)
Geometric parameters (Å, º) top
C1—N41.345 (2)C7—N51.419 (2)
C1—N11.358 (2)C8—C91.382 (3)
C1—C21.387 (3)C8—H80.9300
C2—C31.374 (2)C9—C101.351 (4)
C2—H20.9300C9—H90.9300
C3—N31.354 (2)C10—C111.379 (4)
C3—N21.3625 (19)C10—H100.9300
C4—N21.317 (2)C11—C121.384 (3)
C4—N11.3312 (19)C11—H110.9300
C4—S11.7630 (17)C12—C131.504 (3)
C5—C61.505 (2)C13—H13A0.9600
C5—S11.8054 (17)C13—H13B0.9600
C5—H5A0.9700C13—H13C0.9600
C5—H5B0.9700N3—H3A0.8600
C6—O11.2207 (18)N3—H3B0.8600
C6—N51.335 (2)N4—H4A0.8600
C7—C81.392 (3)N4—H4B0.8600
C7—C121.392 (3)N5—H50.8600
N4—C1—N1115.18 (16)C8—C9—H9119.7
N4—C1—C2123.50 (16)C9—C10—C11119.9 (2)
N1—C1—C2121.30 (15)C9—C10—H10120.0
C3—C2—C1118.03 (15)C11—C10—H10120.0
C3—C2—H2121.0C10—C11—C12121.9 (3)
C1—C2—H2121.0C10—C11—H11119.1
N3—C3—N2114.04 (15)C12—C11—H11119.1
N3—C3—C2124.29 (14)C11—C12—C7117.5 (2)
N2—C3—C2121.65 (15)C11—C12—C13120.6 (2)
N2—C4—N1129.18 (13)C7—C12—C13121.89 (16)
N2—C4—S1119.08 (11)C12—C13—H13A109.5
N1—C4—S1111.74 (11)C12—C13—H13B109.5
C6—C5—S1111.95 (10)H13A—C13—H13B109.5
C6—C5—H5A109.2C12—C13—H13C109.5
S1—C5—H5A109.2H13A—C13—H13C109.5
C6—C5—H5B109.2H13B—C13—H13C109.5
S1—C5—H5B109.2C4—N1—C1114.78 (14)
H5A—C5—H5B107.9C4—N2—C3114.77 (13)
O1—C6—N5124.40 (15)C3—N3—H3A120.0
O1—C6—C5120.05 (14)C3—N3—H3B120.0
N5—C6—C5115.54 (13)H3A—N3—H3B120.0
C8—C7—C12120.68 (18)C1—N4—H4A120.0
C8—C7—N5121.56 (19)C1—N4—H4B120.0
C12—C7—N5117.76 (15)H4A—N4—H4B120.0
C9—C8—C7119.5 (2)C6—N5—C7128.79 (14)
C9—C8—H8120.2C6—N5—H5115.6
C7—C8—H8120.2C7—N5—H5115.6
C10—C9—C8120.6 (2)C4—S1—C5102.08 (8)
C10—C9—H9119.7
N4—C1—C2—C3−178.67 (16)N5—C7—C12—C13−1.6 (3)
N1—C1—C2—C32.8 (2)N2—C4—N1—C1−0.8 (2)
C1—C2—C3—N3−179.76 (15)S1—C4—N1—C1179.04 (11)
C1—C2—C3—N21.9 (2)N4—C1—N1—C4177.99 (14)
S1—C5—C6—O1−78.22 (17)C2—C1—N1—C4−3.3 (2)
S1—C5—C6—N5100.79 (14)N1—C4—N2—C35.1 (2)
C12—C7—C8—C90.1 (3)S1—C4—N2—C3−174.73 (9)
N5—C7—C8—C9−179.1 (2)N3—C3—N2—C4176.08 (12)
C7—C8—C9—C100.9 (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—C120.0 (4)C5—C6—N5—C7178.42 (15)
C10—C11—C12—C70.9 (3)C8—C7—N5—C6−11.7 (3)
C10—C11—C12—C13−179.2 (2)C12—C7—N5—C6169.09 (16)
C8—C7—C12—C11−0.9 (3)N2—C4—S1—C59.30 (12)
N5—C7—C12—C11178.33 (17)N1—C4—S1—C5−170.54 (10)
C8—C7—C12—C13179.20 (19)C6—C5—S1—C4−98.07 (12)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N4—H4A···N1i0.862.263.115 (2)175
N3—H3A···O1ii0.862.273.045 (2)150
N5—H5···O1ii0.862.543.264 (3)142
C13—H13A···O1ii0.962.553.385 (3)145
Symmetry codes: (i) −x+1, −y, −z+2; (ii) x, −y+1/2, z+1/2.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N4—H4A···N1i0.862.263.115 (2)175
N3—H3A···O1ii0.862.273.045 (2)150
N5—H5···O1ii0.862.543.264 (3)142
C13—H13A···O1ii0.962.553.385 (3)145
Symmetry codes: (i) −x+1, −y, −z+2; (ii) x, −y+1/2, z+1/2.
 

Acknowledgements

The authors thank the TBI X-ray facility, CAS in Crystallography and Biophysics, University of Madras, India, for the data collection. SS and DV thank the UGC (SAP–CAS) for the departmental facilities. SS also thanks UGC for the award of meritorious fellowship.

References

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ISSN: 2056-9890
Volume 70| Part 8| August 2014| Page o850
doi:10.1107/S1600536814015256
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