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Crystal structures of 2-[(4,6-di­amino­pyrimidin-2-yl)sulfan­yl]-N-(2,4-di­methyl­phen­yl)acetamide and 2-[(4,6-di­amino­pyrimidin-2-yl)sulfan­yl]-N-(3-meth­­oxy­phen­yl)acetamide

aCentre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India, and bDepartment of Pharmaceutical Science and Technology, Birla Institute of Technology, Mesta, Ranchi 835 215, Jharkhand, India
*Correspondence e-mail: shirai2011@gmail.com

Edited by H. Stoeckli-Evans, University of Neuchâtel, Switzerland (Received 23 May 2017; accepted 1 June 2017; online 13 June 2017)

In the title compounds, C14H17N5OS (I) and C13H15N5O2S (II), the dihedral angle between the pyrimidine and benzene rings is 58.64 (8)° in (I) and 78.33 (9)° in (II). In both compounds, there is an intra­molecular C—H⋯O hydrogen bond, and in (II) there is also an intra­molecular N—H⋯N hydrogen bond present. In the crystals of both compounds, a pair of N—H⋯N hydrogen bonds links the individual mol­ecules to form inversion dimers with R22(8) ring motifs. In (I), the dimers are linked by N—H⋯O and C—H⋯O hydrogen bonds, enclosing R21(14), R21(11) and R21(7) ring motifs, forming layers parallel to the (100) plane. There is also an N—H⋯π inter­action present within the layer. In (II), the inversion dimers are linked by N—H⋯O hydrogen bonds enclosing an R44(18) ring motif. The presence of N—H⋯O and C—H⋯O hydrogen bonds generate an R21(6) ring motif. The combination of these various hydrogen bonds results in the formation of layers parallel to the (1-11) plane.

1. Chemical context

Di­amino­pyrimidine derivatives have been proved to be an important class of compounds because of their therapeutic and pharmacological properties. One such important property is its inhibition potency against cancer targets. As a result of the limited capacity of drugs that can cure or at least prolong the survival of cancer patients, there is always an strong requirement for new chemotherapeutics. It has been reported that di­amino­pyrimidines show inhibition against cyclin-dependent kinases (cdks), thus arresting cell proliferation in cancer cells (Mesguiche et al., 2003[Mesguiche, V., Parsons, R. J., Arris, C. E., Bentley, J., Boyle, F. T., Curtin, N. J., Davies, T. G., Endicott, J. A., Gibson, A. E., Golding, B. T., Griffin, R. J., Jewsbury, P., Johnson, L. N., Newell, D. R., Noble, M. E. M., Wang, L. Z. & Hardcastle, I. R. (2003). Bioorg. Med. Chem. Lett. 13, 217-222.]). 2,4-Di­amino­pyrimidine derivatives have also shown effective suppression of anaplastic lymphoma kinase (ALK), one of the receptor tyrosine kinases that is involved in a variety of tumours (Achary et al., 2017[Achary, R., Mathi, G. R., Lee, D. H., Yun, C. S., Lee, C. O., Kim, H. R., Park, C. H., Kim, P. & Hwang, J. Y. (2017). Bioorg. Med. Chem. Lett. 27, 2185-2191.]). 2,4-Di­amino­pyrimidine derivatives have also been reported to exhibit potent inhibitory activity against influenza viruses (Kimura et al., 2006[Kimura, H., Katoh, T., Kajimoto, T., Node, M., Hisaki, M., Sugimoto, Y., Majima, T., Uehara, Y. & Yamori, T. (2006). Anticancer Res. 26, 91-97.]) and have anti-retroviral activity (Hocková et al., 2004[Hocková, D., Holý, A. N., Masojídková, M., Andrei, G., Snoeck, R., De Clercq, E. & Balzarini, J. (2004). Bioorg. Med. Chem. 12, 3197-3202.]), anti-bacterial (Kandeel et al., 1994[Kandeel, M., El-Meligie, S., Omar, R., Roshdy, S. & Youssef, K. (1994). J. Pharm. Sci. 3, 197-205.]) and potential anti-microbial properties (Holla et al., 2006[Holla, B. S., Mahalinga, M., Karthikeyan, M. S., Akberali, P. M. & Shetty, N. S. (2006). Bioorg. Med. Chem. 14, 2040-2047.]). Several di­amino­pyrimidine derivatives have shown good activity, efficiency against the malarial parasite Plasmodium falciparum K1 strain (Phuangsawai et al., 2016[Phuangsawai, O., Beswick, P., Ratanabunyong, S., Tabtimmai, L., Suphakun, P., Obounchoey, P., Srisook, P., Horata, N., Chuckowree, I., Hannongbua, S., Ward, S. E., Choowongkomon, K. & Gleeson, M. P. (2016). Eur. J. Med. Chem. 124, 896-905.]; Chiang et al., 2009[Chiang, A. N., Valderramos, J. C., Balachandran, R., Chovatiya, R. J., Mead, B. P., Schneider, C., Bell, S. L., Klein, M. G., Huryn, D. M., Chen, X. S., Day, B. W., Fidock, D. A., Wipf, P. & Brodsky, J. L. (2009). Bioorg. Med. Chem. 17, 1527-1533.]). Inter­estingly, they also act as calcium channel blocking agents (Manjula et al., 2004[Manjula, A., Rao, V. & Neelakantan, P. (2004). Synth. Commun. 34, 2665-2671.]; Singh et al., 2009[Singh, K., Arora, D., Poremsky, E., Lowery, J. & Moreland, R. S. (2009). Eur. J. Med. Chem. 44, 1997-2001.]). As part of our own studies in this area, we report herein on the syntheses and crystal structure analyses of the title compounds, 2-[(4,6-di­amino­pyrimidin-2-yl)sulfan­yl]-N-(2,4-di­methyl­phen­yl)acet­amide (I)[link] and [2-((4,6-di­amino­pyrimidin-2-yl)sulfan­yl]-N-(3-meth­oxy­phen­yl)acetamide (II)[link].

[Scheme 1]

2. Structural commentary

The mol­ecular structures of compounds (I)[link] and (II)[link] are shown in Figs. 1[link] and 2[link], respectively. Compound (I)[link] crystallizes in the monoclinic space group P21/c and compound (II)[link] in the triclinic space group P[\overline{1}]. In compounds (I)[link] and (II)[link], the di­amino­pyrimidine and benzene rings are inclined to one another by 58.64 (8) and 78.33 (9)°, respectively. The torsion angle C4—S1—C5—C6 = 98.12 (11) ° in compound (I)[link] and −80.14 (14) ° in compound (II)[link], torsion angles S1—C5—C6—N5 = −101.92 (14) ° in compound (I)[link] and 82.23 (16) ° in compound (II)[link], and C5—C6—N5—C7 = 178.66 (15)° in compound (I)[link] and −172.71 (14) ° in compound (II)[link]. The bond lengths C4—S1 = 1.7650 (14) Å and C5—S1 = 1.8053 (16) Å in compound (I)[link], and C4—S1 = 1.7721 (17) Å and C5—S1 = 1.8126 (18) Å in compound (II)[link], are comparable with the values reported for a similar structure, 2-[(4,6-di­amino­pyrimidin-2-yl)sulfan­yl]-N-(2-methyl­phen­yl)acetamide, viz. 1.763 and 1.805 Å, respectively (Subasri et al., 2014[Subasri, S., Kumar, T. A., Sinha, B. N., Jayaprakash, V. & Velmurugan, D. (2014). Acta Cryst. E70, o850.]). In compound (I)[link], atoms C13 and C14 deviate from the benzene ring by 0.010 (3) and 0.012 (3) Å, respectively. Atoms N1 and N2 deviate from the mean plane of the pyrimidine ring by −0.0819 (18) and 0.0636 (14) Å, respectively, in compound (I)[link], and by 0.0360 (3) and 0.0273 (3) Å, respectively, in compound (II)[link]. In both compounds, an intra­molecular hydrogen bond, C8—H8⋯O1, forms an S(6) ring motif, and in compound (II)[link] there is also an intra­molecular N—H⋯N hydrogen bond present that forms an S(7) ring motif (see Tables 1[link] and 2[link]).

Table 1
Hydrogen-bond geometry (Å, °) for (I)[link]

Cg1 is the centroid of the N3/N4/C1–C4 ring.

D—H⋯A D—H H⋯A DA D—H⋯A
C8—H8⋯O1 0.93 2.30 2.8752 (1) 120
N1—H1A⋯N3i 0.86 2.26 3.1187 (1) 175
N2—H2A⋯O1ii 0.86 2.32 3.1032 (1) 152
N5—H5⋯O1ii 0.86 2.51 3.2640 (1) 146
C13—H13C⋯O1ii 0.96 2.56 3.3880 (1) 144
N2—H2BCg1iii 0.86 2.88 3.4851 (1) 130
Symmetry codes: (i) -x, -y+2, -z+2; (ii) [x, -y+{\script{3\over 2}}, z-{\script{1\over 2}}]; (iii) [x, -y+{\script{3\over 2}}, z-{\script{3\over 2}}].

Table 2
Hydrogen-bond geometry (Å, °) for (II)[link]

D—H⋯A D—H H⋯A DA D—H⋯A
N5—H5⋯N4 0.86 2.15 2.861 (3) 140
C8—H8⋯O1 0.93 2.34 2.911 (3) 120
N1—H1A⋯N3i 0.86 2.21 3.035 (3) 162
N1—H1B⋯O1ii 0.86 2.08 2.891 (3) 157
N2—H2B⋯O2iii 0.86 2.55 3.210 (3) 135
C2—H2⋯O2iii 0.93 2.59 3.272 (3) 130
Symmetry codes: (i) -x+1, -y+1, -z+1; (ii) x+1, y+1, z; (iii) -x+1, -y+2, -z+2.
[Figure 1]
Figure 1
The mol­ecular structure of (I)[link], showing the atom labelling and displacement ellipsoids drawn at 50% probability level. The C—H⋯O contact is shown as a dashed line (see Table 1[link]).
[Figure 2]
Figure 2
The mol­ecular structure of (II)[link], showing the atom labelling and displacement ellipsoids drawn at 50% probability level. The N—H⋯N and C—H⋯O contacts are shown as dashed lines (see Table 2[link]).

3. Supra­molecular features

The hydrogen-bonding geometry of compounds (I)[link] and (II)[link] are given in Tables 1[link] and 2[link], respectively. In compound (I)[link], atom O1 is a triple acceptor of hydrogen bonds. The N5—H5⋯O1ii hydrogen bonds form a chain running along the c-axis direction. The N2—H2A⋯O1ii and C13—H13C⋯O1ii hydrogen bonds generate an R21(14) ring motif, and the N2—H2A⋯O1ii and N5—H5⋯O1ii hydrogen bonds form an R21(11) ring motif, and N5—H5⋯O1ii and C13—H13⋯O1ii hydrogen bonds generate an R21(7) ring motif (Table 1[link] and Fig. 3[link]). There is also a N2—H2Bπ inter­action present within the layer (Table 1[link] and Fig. 4[link]), with the separation distance between the donor and acceptor, Cg1, being 3.4851 (1) Å. The N1—H1A⋯N3i hydrogen bond generates an inversion dimer with an R22(8) ring motif (Table 1[link] and Fig. 5[link]). As a result of the hydrogen bonding, layers parallel to the bc plane are formed.

[Figure 3]
Figure 3
The crystal packing of (I)[link], viewed along the b axis, C—H⋯O and N—H⋯O hydrogen bonds generate R21(14), R21(11) and R21(7) ring motifs. In this and subsequent figures, the hydrogen bonds are shown as dashed lines and H atoms not involved in hydrogen bonding have been omitted for clarity.
[Figure 4]
Figure 4
A partial view of the crystal packing of (I)[link], viewed approximately along the c axis, showing the N—H⋯π inter­actions.
[Figure 5]
Figure 5
A view along the b axis of the crystal packing of (I)[link], showing the N—H⋯N hydrogen bonds that generate an R22(8) ring motif.

In compound (II)[link], atom O2 is a double acceptor of hydrogen bonds. The N2—H2B⋯O2iii hydrogen bond forms an R22(26) ring motif and hydrogen bond C2—H2⋯O2iii generates an R22(26) ring motif (Table 2[link] and Fig. 6[link]). These two inter­molecular hydrogen bonds generate an R21(6) ring motif, which is shown in Fig. 6[link]. Mol­ecules are linked by a pair of N1—H1A⋯N3i hydrogen bonds, forming an inversion dimer with an R22(8) ring motif, and hydrogen bonds N1—H1B⋯O1ii and N1—H1A⋯N3i generate an R44(18) ring motif (Table 2[link] and Fig. 7[link]). The combination of these various hydrogen bonds results in the formation of layers parallel to (1[\overline{1}]1).

[Figure 6]
Figure 6
The crystal packing of (II)[link], viewed along the a axis, C—H⋯O and N—H⋯O hydrogen bonds generate two R22(26) ring motifs and one R21(6) ring motif.
[Figure 7]
Figure 7
A partial view along the a axis of the crystal packing of (II)[link]. The N—H⋯N hydrogen bonds generate an R22(8) ring motif and N—H⋯O and N—H⋯N hydrogen bonds an R44(18) ring motif.

4. Database survey

A search of the Cambridge Structure Database (Version 5.37, update May 2016; Groom et al., 2016[Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171-179.]) for 2-[(pyrimidine-2-yl)sulfan­yl]-N-phenyl­acetamide yielded seven hits. Three of these involve (4,6-di­amino­pyrmidin-2-yl) groups. They include the 2-methyl­phenyl analogue, 2-[(4,6-di­amino­pyrimidin-2-yl)sulfan­yl]-N-(2-methyl­phen­yl)acetamide (GOKWIO; Subasri et al., 2014[Subasri, S., Kumar, T. A., Sinha, B. N., Jayaprakash, V. & Velmurugan, D. (2014). Acta Cryst. E70, o850.]), the 2-chloro­phenyl analogue, N-(2-chloro­phen­yl)-2-[(4,6-di­amino­pyrimidin-2-yl) sulfan­yl]acetamide (ARARUI; Subasri et al., 2016[Subasri, S., Timiri, A. K., Barji, N. S., Jayaprakash, V., Vijayan, V. & Velmurugan, D. (2016). Acta Cryst. E72, 1171-1175.]) and the 3-nitro­phenyl analogue, 2-[(4,6-di­amino­pyrimidin-2-yl)sulfan­yl]-N-(3-nitro­phen­yl)acetamide (ARAROC; Subasri et al., 2016[Subasri, S., Timiri, A. K., Barji, N. S., Jayaprakash, V., Vijayan, V. & Velmurugan, D. (2016). Acta Cryst. E72, 1171-1175.]). Here the pyrimidine and benzene rings are inclined to one another by 54.73, 67.11 and 56.19°, respectively, compared to 58.64 (8) ° in compound (I)[link], and 78.33 (9) ° in compound (II)[link].

5. Synthesis and crystallization

Compound (I): To a solution of 4,6-di­amino-pyrimidine-2-thiol (0.5 g, 3.52 mmol) in 25 ml of ethanol in a round-bottom flask, potassium hydroxide (0.2 g, 3.52 mmol) was added and the mixture was refluxed for 30 min. 2,4-Di­methyl­phenyl acetamide (3.52 mmol) was added and the mixture was refluxed for 3 h. At the end of the reaction (observed by TLC), the ethanol was evaporated under vacuum and cold water was added. The precipitate formed was filtered and dried to give compound (I)[link] as a crystalline powder (yield 67%). After purification, the compound was recrystallized from ethanol solution by slow evaporation of the solvent.

Compound (II): To a solution of 4,6-di­amino-pyrimidine-2-thiol (0.5 g, 3.52 mmol) in 25 ml of ethanol in a round-bottom flask was added potassium hydroxide (0.2 g, 3.52 mmol) and the mixture was refluxed for 30 min. 3-Meth­oxy­phenyl acetamide (3.52 mmol) was added and the mixture was refluxed for 3 h. At the end of the reaction (observed by TLC), the ethanol was evaporated under vacuum and cold water was added, and the precipitate formed was filtered and dried to give compound (II)[link] as a shiny powder (yield 73%). After purification, the compound was recrystallized from ethanol solution by slow evaporation of the solvent.

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 3[link]. For both compounds the hydrogen atoms were placed in calculated positions and refined using the riding model: C—H = 0.93–0.97 Å and N—H = 0.86 Å, with Uiso(H) = 1.5Ueq(C-meth­yl) and 1.2Ueq(N,C) for other H atoms.

Table 3
Experimental details

  (I) (II)
Crystal data
Chemical formula C14H17N5OS C13H15N5O2S
Mr 303.38 305.36
Crystal system, space group Monoclinic, P21/c Triclinic, P[\overline{1}]
Temperature (K) 293 293
a, b, c (Å) 23.7716 (6), 7.0073 (2), 9.0909 (2) 8.014 (5), 8.724 (5), 12.068 (5)
α, β, γ (°) 90, 90.086 (2), 90 106.561 (5), 97.888 (5), 110.461 (5)
V3) 1514.31 (7) 730.9 (7)
Z 4 2
Radiation type Mo Kα Mo Kα
μ (mm−1) 0.22 0.23
Crystal size (mm) 0.24 × 0.18 × 0.12 0.30 × 0.25 × 0.20
 
Data collection
Diffractometer Bruker SMART APEXII area-detector Bruker SMART APEXII area-detector
Absorption correction Multi-scan (SADABS; Bruker, 2008[Bruker (2008). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Multi-scan (SADABS; Bruker, 2008[Bruker (2008). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.])
Tmin, Tmax 0.785, 0.854 0.785, 0.843
No. of measured, independent and observed [I > 2σ(I)] reflections 13879, 3705, 2750 10789, 2991, 2616
Rint 0.022 0.026
(sin θ/λ)max−1) 0.666 0.627
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.040, 0.119, 1.06 0.037, 0.110, 0.81
No. of reflections 3705 2991
No. of parameters 192 191
H-atom treatment H-atom parameters constrained H-atom parameters constrained
Δρmax, Δρmin (e Å−3) 0.22, −0.24 0.17, −0.27
Computer programs: APEX2 and SAINT (Bruker, 2008[Bruker (2008). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]), SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]), SHELXL2016 (Sheldrick, 2015[Sheldrick, G. M. (2015). Acta Cryst. C71, 3-8.]), ORTEP-3 for Windows (Farrugia, 2012[Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849-854.]) and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information


Computing details top

For both compounds, 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: SHELXL2016 (Sheldrick, 2015); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012); software used to prepare material for publication: SHELXL2016 (Sheldrick, 2015) and PLATON (Spek, 2009).

(I) 2-[(4,6-Diaminopyrimidin-2-yl)sulfanyl]-N-(2,4-dimethylphenyl)acetamide top
Crystal data top
C14H17N5OSF(000) = 640
Mr = 303.38Dx = 1.331 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
a = 23.7716 (6) ÅCell parameters from 3705 reflections
b = 7.0073 (2) Åθ = 1.7–28.3°
c = 9.0909 (2) ŵ = 0.22 mm1
β = 90.086 (2)°T = 293 K
V = 1514.31 (7) Å3Block, yellow
Z = 40.24 × 0.18 × 0.12 mm
Data collection top
Bruker SMART APEXII area-detector
diffractometer
2750 reflections with I > 2σ(I)
ω and φ scansRint = 0.022
Absorption correction: multi-scan
(SADABS; Bruker, 2008)
θmax = 28.3°, θmin = 1.7°
Tmin = 0.785, Tmax = 0.854h = 3131
13879 measured reflectionsk = 89
3705 independent reflectionsl = 1211
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)] = 0.040Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.119H-atom parameters constrained
S = 1.06 w = 1/[σ2(Fo2) + (0.0584P)2 + 0.2187P]
where P = (Fo2 + 2Fc2)/3
3705 reflections(Δ/σ)max < 0.001
192 parametersΔρmax = 0.22 e Å3
0 restraintsΔρmin = 0.24 e Å3
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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
S10.13091 (2)0.71159 (6)0.94117 (5)0.05991 (16)
N40.15430 (5)1.00969 (16)0.76929 (12)0.0459 (3)
N30.06610 (5)0.99914 (17)0.89584 (13)0.0492 (3)
C40.11650 (6)0.9332 (2)0.85688 (15)0.0434 (3)
O10.25886 (5)0.58619 (18)1.04523 (13)0.0688 (4)
C60.24589 (6)0.6857 (2)0.94031 (15)0.0464 (3)
N20.17546 (7)1.2451 (2)0.60612 (15)0.0646 (4)
H2A0.2068331.1868780.5920340.078*
H2B0.1681821.3486690.5590120.078*
N50.27421 (5)0.84155 (19)0.89770 (15)0.0563 (3)
H50.2610740.8989410.8214150.068*
C10.13761 (7)1.1740 (2)0.70222 (15)0.0492 (4)
C30.05202 (7)1.1694 (2)0.83485 (18)0.0547 (4)
C20.08687 (8)1.2589 (2)0.73351 (18)0.0577 (4)
H20.0762401.3723760.6883290.069*
C130.30123 (8)1.2195 (2)0.8120 (2)0.0647 (5)
H13A0.3144361.3487410.8061180.097*
H13B0.2628231.2188070.8445370.097*
H13C0.3036241.1608940.7167850.097*
C50.19468 (6)0.6392 (2)0.84913 (17)0.0503 (4)
H5A0.1934610.5029200.8306920.060*
H5B0.1972590.7038240.7550230.060*
C120.33675 (7)1.1105 (3)0.91894 (17)0.0562 (4)
C70.32294 (7)0.9247 (3)0.96134 (18)0.0565 (4)
N10.00214 (7)1.2404 (2)0.8769 (2)0.0826 (5)
H1A0.0183581.1783440.9383850.099*
H1B0.0093231.3478100.8423660.099*
C110.38453 (8)1.1920 (3)0.9800 (2)0.0705 (5)
H110.3941291.3155350.9524170.085*
C80.35657 (8)0.8271 (3)1.0617 (2)0.0766 (6)
H80.3475270.7032401.0896680.092*
C100.41862 (8)1.0979 (4)1.0800 (2)0.0808 (6)
C90.40379 (8)0.9168 (4)1.1195 (3)0.0893 (7)
H90.4259690.8514701.1871780.107*
C140.47024 (9)1.1953 (5)1.1442 (3)0.1146 (10)
H14A0.4751441.1561411.2445770.172*
H14B0.4653421.3311801.1402490.172*
H14C0.5028471.1600631.0882240.172*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.0529 (3)0.0458 (2)0.0810 (3)0.00850 (17)0.00160 (19)0.01998 (19)
N40.0599 (8)0.0368 (6)0.0410 (6)0.0054 (5)0.0075 (5)0.0003 (5)
N30.0506 (7)0.0421 (7)0.0548 (7)0.0071 (5)0.0109 (5)0.0004 (5)
C40.0536 (8)0.0356 (7)0.0410 (7)0.0034 (6)0.0147 (6)0.0033 (5)
O10.0774 (8)0.0705 (8)0.0585 (7)0.0070 (6)0.0125 (6)0.0206 (6)
C60.0516 (8)0.0440 (8)0.0435 (7)0.0096 (6)0.0034 (6)0.0017 (6)
N20.0844 (11)0.0560 (8)0.0535 (8)0.0111 (7)0.0005 (7)0.0154 (6)
N50.0545 (8)0.0549 (8)0.0594 (8)0.0026 (6)0.0117 (6)0.0135 (6)
C10.0680 (10)0.0419 (8)0.0376 (7)0.0041 (7)0.0122 (6)0.0001 (6)
C30.0606 (10)0.0471 (9)0.0565 (9)0.0121 (7)0.0149 (7)0.0009 (7)
C20.0735 (11)0.0445 (8)0.0549 (9)0.0145 (7)0.0132 (8)0.0076 (7)
C130.0729 (12)0.0532 (10)0.0679 (11)0.0045 (8)0.0029 (9)0.0017 (8)
C50.0584 (9)0.0348 (7)0.0577 (9)0.0078 (6)0.0064 (7)0.0034 (6)
C120.0504 (9)0.0651 (11)0.0530 (9)0.0023 (7)0.0089 (7)0.0082 (7)
C70.0469 (8)0.0662 (11)0.0564 (9)0.0006 (7)0.0009 (7)0.0014 (8)
N10.0686 (10)0.0731 (11)0.1062 (13)0.0325 (8)0.0045 (9)0.0260 (9)
C110.0574 (10)0.0841 (14)0.0700 (11)0.0136 (9)0.0119 (9)0.0166 (10)
C80.0549 (11)0.0888 (15)0.0860 (13)0.0017 (10)0.0144 (9)0.0159 (11)
C100.0484 (10)0.1182 (19)0.0758 (13)0.0087 (11)0.0010 (9)0.0205 (12)
C90.0524 (11)0.127 (2)0.0887 (15)0.0051 (12)0.0168 (10)0.0071 (14)
C140.0601 (13)0.167 (3)0.117 (2)0.0246 (15)0.0090 (12)0.0338 (19)
Geometric parameters (Å, º) top
S1—C41.7650 (14)C13—H13B0.9600
S1—C51.8053 (16)C13—H13C0.9600
N4—C41.3157 (19)C5—H5A0.9700
N4—C11.3616 (18)C5—H5B0.9700
N3—C41.3325 (19)C12—C111.386 (2)
N3—C31.3577 (19)C12—C71.397 (3)
O1—C61.2209 (17)C7—C81.391 (2)
C6—N51.340 (2)N1—H1A0.8600
C6—C51.507 (2)N1—H1B0.8600
N2—C11.350 (2)C11—C101.384 (3)
N2—H2A0.8600C11—H110.9300
N2—H2B0.8600C8—C91.389 (3)
N5—C71.419 (2)C8—H80.9300
N5—H50.8600C10—C91.365 (3)
C1—C21.375 (2)C10—C141.520 (3)
C3—N11.342 (2)C9—H90.9300
C3—C21.389 (2)C14—H14A0.9600
C2—H20.9300C14—H14B0.9600
C13—C121.496 (2)C14—H14C0.9600
C13—H13A0.9600
C4—S1—C5102.04 (7)S1—C5—H5A109.4
C4—N4—C1114.62 (13)C6—C5—H5B109.4
C4—N3—C3114.68 (14)S1—C5—H5B109.4
N4—C4—N3129.41 (13)H5A—C5—H5B108.0
N4—C4—S1119.27 (11)C11—C12—C7117.76 (17)
N3—C4—S1111.33 (11)C11—C12—C13120.75 (17)
O1—C6—N5124.39 (14)C7—C12—C13121.48 (15)
O1—C6—C5120.58 (14)C8—C7—C12120.26 (16)
N5—C6—C5115.02 (13)C8—C7—N5122.22 (17)
C1—N2—H2A120.0C12—C7—N5117.53 (14)
C1—N2—H2B120.0C3—N1—H1A120.0
H2A—N2—H2B120.0C3—N1—H1B120.0
C6—N5—C7128.82 (13)H1A—N1—H1B120.0
C6—N5—H5115.6C10—C11—C12123.1 (2)
C7—N5—H5115.6C10—C11—H11118.5
N2—C1—N4114.07 (14)C12—C11—H11118.5
N2—C1—C2124.03 (14)C9—C8—C7119.3 (2)
N4—C1—C2121.90 (15)C9—C8—H8120.4
N1—C3—N3115.25 (16)C7—C8—H8120.4
N1—C3—C2123.37 (15)C9—C10—C11117.66 (18)
N3—C3—C2121.35 (15)C9—C10—C14121.7 (2)
C1—C2—C3117.79 (14)C11—C10—C14120.7 (2)
C1—C2—H2121.1C10—C9—C8122.0 (2)
C3—C2—H2121.1C10—C9—H9119.0
C12—C13—H13A109.5C8—C9—H9119.0
C12—C13—H13B109.5C10—C14—H14A109.5
H13A—C13—H13B109.5C10—C14—H14B109.5
C12—C13—H13C109.5H14A—C14—H14B109.5
H13A—C13—H13C109.5C10—C14—H14C109.5
H13B—C13—H13C109.5H14A—C14—H14C109.5
C6—C5—S1111.24 (10)H14B—C14—H14C109.5
C6—C5—H5A109.4
C1—N4—C4—N34.6 (2)N5—C6—C5—S1101.92 (14)
C1—N4—C4—S1175.79 (10)C4—S1—C5—C698.12 (11)
C3—N3—C4—N40.5 (2)C11—C12—C7—C80.0 (3)
C3—N3—C4—S1179.87 (10)C13—C12—C7—C8179.62 (17)
C5—S1—C4—N48.96 (12)C11—C12—C7—N5179.55 (15)
C5—S1—C4—N3171.36 (10)C13—C12—C7—N50.8 (2)
O1—C6—N5—C70.7 (3)C6—N5—C7—C815.4 (3)
C5—C6—N5—C7178.66 (15)C6—N5—C7—C12165.04 (15)
C4—N4—C1—N2176.34 (12)C7—C12—C11—C100.1 (3)
C4—N4—C1—C24.7 (2)C13—C12—C11—C10179.58 (17)
C4—N3—C3—N1177.94 (14)C12—C7—C8—C90.3 (3)
C4—N3—C3—C23.6 (2)N5—C7—C8—C9179.83 (18)
N2—C1—C2—C3179.97 (15)C12—C11—C10—C90.2 (3)
N4—C1—C2—C31.2 (2)C12—C11—C10—C14179.48 (19)
N1—C3—C2—C1178.45 (16)C11—C10—C9—C80.5 (3)
N3—C3—C2—C13.2 (2)C14—C10—C9—C8179.8 (2)
O1—C6—C5—S177.43 (16)C7—C8—C9—C100.6 (4)
Hydrogen-bond geometry (Å, º) top
Cg1 is the centroid of the N3/N4/C1–C4 ring.
D—H···AD—HH···AD···AD—H···A
C8—H8···O10.932.302.8752 (1)120
N1—H1A···N3i0.862.263.1187 (1)175
N2—H2A···O1ii0.862.323.1032 (1)152
N5—H5···O1ii0.862.513.2640 (1)146
C13—H13C···O1ii0.962.563.3880 (1)144
N2—H2B···Cg1iii0.862.883.4851 (1)130
Symmetry codes: (i) x, y+2, z+2; (ii) x, y+3/2, z1/2; (iii) x, y+3/2, z3/2.
(II) 2-[(4,6-Diaminopyrimidin-2-yl)sulfanyl]-N-(3-methoxyphenyl)acetamide top
Crystal data top
C13H15N5O2SZ = 2
Mr = 305.36F(000) = 320
Triclinic, P1Dx = 1.388 Mg m3
a = 8.014 (5) ÅMo Kα radiation, λ = 0.71073 Å
b = 8.724 (5) ÅCell parameters from 2991 reflections
c = 12.068 (5) Åθ = 1.8–26.5°
α = 106.561 (5)°µ = 0.23 mm1
β = 97.888 (5)°T = 293 K
γ = 110.461 (5)°Block, yellow
V = 730.9 (7) Å30.30 × 0.25 × 0.20 mm
Data collection top
Bruker SMART APEXII area-detector
diffractometer
2616 reflections with I > 2σ(I)
ω and φ scansRint = 0.026
Absorption correction: multi-scan
(SADABS; Bruker, 2008)
θmax = 26.5°, θmin = 1.8°
Tmin = 0.785, Tmax = 0.843h = 109
10789 measured reflectionsk = 1010
2991 independent reflectionsl = 1515
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)] = 0.037Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.110H-atom parameters constrained
S = 0.81 w = 1/[σ2(Fo2) + (0.082P)2 + 0.3261P]
where P = (Fo2 + 2Fc2)/3
2991 reflections(Δ/σ)max = 0.001
191 parametersΔρmax = 0.17 e Å3
0 restraintsΔρmin = 0.27 e Å3
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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
C10.2721 (2)0.7765 (2)0.75950 (14)0.0415 (4)
C20.4285 (2)0.8303 (2)0.72068 (14)0.0416 (4)
H20.5178680.9447350.7556170.050*
C30.4481 (2)0.70658 (19)0.62691 (13)0.0371 (3)
C40.1714 (2)0.50538 (19)0.61966 (13)0.0345 (3)
C50.1544 (2)0.2625 (2)0.63675 (15)0.0478 (4)
H5A0.1759560.3683790.6617750.057*
H5B0.2712830.1658030.5896400.057*
C60.0831 (2)0.2295 (2)0.74625 (15)0.0451 (4)
C70.1429 (2)0.3944 (2)0.94683 (13)0.0388 (3)
C80.1195 (3)0.2573 (2)0.98958 (17)0.0524 (4)
H80.0297650.1451190.9454100.063*
C90.2324 (3)0.2922 (3)1.09848 (19)0.0610 (5)
H90.2172770.2013941.1272990.073*
C100.3670 (3)0.4566 (2)1.16652 (17)0.0519 (4)
H100.4412290.4765961.2399840.062*
C110.3892 (2)0.5915 (2)1.12302 (14)0.0414 (4)
C120.2776 (2)0.5599 (2)1.01376 (14)0.0397 (3)
H120.2932600.6509000.9850610.048*
C130.6424 (3)0.7978 (3)1.29014 (18)0.0632 (5)
H13A0.5767350.7809291.3495430.095*
H13B0.7312480.9171311.3175830.095*
H13C0.7046990.7207801.2768370.095*
N40.13965 (18)0.61019 (17)0.70978 (11)0.0396 (3)
N30.31604 (17)0.54040 (16)0.57426 (11)0.0368 (3)
N20.2417 (3)0.8847 (2)0.85299 (15)0.0634 (5)
H2A0.1438700.8460000.8765130.076*
H2B0.3202630.9918120.8885340.076*
N10.5973 (2)0.74522 (19)0.58440 (14)0.0527 (4)
H1A0.6060000.6663650.5264650.063*
H1B0.6844960.8489020.6150320.063*
N50.03559 (19)0.37602 (17)0.83726 (12)0.0425 (3)
H50.0477860.4726280.8270870.051*
O10.1275 (2)0.08145 (17)0.74876 (13)0.0675 (4)
O20.51589 (19)0.76002 (16)1.18149 (11)0.0584 (4)
S10.00691 (5)0.28602 (5)0.54469 (3)0.04131 (14)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0530 (9)0.0339 (8)0.0391 (8)0.0203 (7)0.0146 (7)0.0113 (6)
C20.0476 (9)0.0276 (7)0.0427 (8)0.0118 (6)0.0105 (7)0.0081 (6)
C30.0413 (8)0.0308 (7)0.0357 (7)0.0122 (6)0.0090 (6)0.0106 (6)
C40.0364 (7)0.0323 (7)0.0323 (7)0.0130 (6)0.0046 (6)0.0113 (6)
C50.0302 (7)0.0491 (10)0.0466 (9)0.0049 (7)0.0058 (6)0.0087 (7)
C60.0359 (8)0.0407 (9)0.0453 (9)0.0031 (7)0.0145 (7)0.0103 (7)
C70.0421 (8)0.0363 (8)0.0376 (8)0.0151 (6)0.0163 (6)0.0115 (6)
C80.0598 (10)0.0365 (9)0.0551 (10)0.0112 (8)0.0152 (8)0.0187 (8)
C90.0724 (13)0.0485 (10)0.0673 (12)0.0203 (9)0.0154 (10)0.0348 (9)
C100.0593 (10)0.0522 (10)0.0500 (10)0.0255 (9)0.0104 (8)0.0248 (8)
C110.0459 (8)0.0374 (8)0.0417 (8)0.0201 (7)0.0111 (7)0.0119 (7)
C120.0472 (8)0.0330 (8)0.0397 (8)0.0163 (7)0.0127 (7)0.0139 (6)
C130.0604 (11)0.0612 (12)0.0535 (11)0.0200 (10)0.0085 (9)0.0171 (9)
N40.0433 (7)0.0355 (7)0.0396 (7)0.0161 (6)0.0133 (5)0.0117 (5)
N30.0382 (6)0.0315 (6)0.0349 (6)0.0108 (5)0.0090 (5)0.0082 (5)
N20.0777 (11)0.0396 (8)0.0652 (10)0.0191 (8)0.0375 (9)0.0052 (7)
N10.0504 (8)0.0339 (7)0.0568 (9)0.0046 (6)0.0241 (7)0.0037 (6)
N50.0473 (7)0.0336 (7)0.0391 (7)0.0098 (6)0.0117 (6)0.0108 (5)
O10.0721 (9)0.0383 (7)0.0593 (8)0.0068 (6)0.0068 (7)0.0129 (6)
O20.0670 (8)0.0390 (7)0.0513 (7)0.0153 (6)0.0123 (6)0.0118 (5)
S10.0384 (2)0.0372 (2)0.0341 (2)0.00654 (16)0.00462 (15)0.00617 (16)
Geometric parameters (Å, º) top
C1—N41.358 (2)C8—C91.375 (3)
C1—C21.374 (2)C8—H80.9300
C1—N21.361 (2)C9—C101.378 (3)
C2—C31.393 (2)C9—H90.9300
C2—H20.9300C10—C111.387 (3)
C3—N11.339 (2)C10—H100.9300
C3—N31.357 (2)C11—O21.363 (2)
C4—N41.325 (2)C11—C121.383 (2)
C4—N31.327 (2)C12—H120.9300
C4—S11.7721 (17)C13—O21.418 (2)
C5—C61.510 (3)C13—H13A0.9600
C5—S11.8126 (18)C13—H13B0.9600
C5—H5A0.9700C13—H13C0.9600
C5—H5B0.9700N2—H2A0.8600
C6—O11.224 (2)N2—H2B0.8600
C6—N51.345 (2)N1—H1A0.8600
C7—C121.381 (2)N1—H1B0.8600
C7—C81.397 (2)N5—H50.8600
C7—N51.409 (2)
N4—C1—C2122.38 (14)C8—C9—H9118.7
N4—C1—N2115.28 (15)C9—C10—C11118.53 (17)
C2—C1—N2122.31 (16)C9—C10—H10120.7
C1—C2—C3117.36 (14)C11—C10—H10120.7
C1—C2—H2121.3O2—C11—C12115.38 (14)
C3—C2—H2121.3O2—C11—C10124.50 (15)
N1—C3—N3116.77 (14)C12—C11—C10120.12 (16)
N1—C3—C2121.86 (14)C7—C12—C11120.61 (15)
N3—C3—C2121.37 (14)C7—C12—H12119.7
N4—C4—N3128.70 (14)C11—C12—H12119.7
N4—C4—S1119.42 (12)O2—C13—H13A109.5
N3—C4—S1111.88 (11)O2—C13—H13B109.5
C6—C5—S1111.79 (12)H13A—C13—H13B109.5
C6—C5—H5A109.3O2—C13—H13C109.5
S1—C5—H5A109.3H13A—C13—H13C109.5
C6—C5—H5B109.3H13B—C13—H13C109.5
S1—C5—H5B109.3C4—N4—C1114.83 (14)
H5A—C5—H5B107.9C4—N3—C3115.33 (13)
O1—C6—N5124.17 (17)C1—N2—H2A120.0
O1—C6—C5122.10 (15)C1—N2—H2B120.0
N5—C6—C5113.70 (15)H2A—N2—H2B120.0
C12—C7—C8119.78 (15)C3—N1—H1A120.0
C12—C7—N5116.25 (14)C3—N1—H1B120.0
C8—C7—N5123.97 (15)H1A—N1—H1B120.0
C9—C8—C7118.46 (17)C6—N5—C7129.44 (15)
C9—C8—H8120.8C6—N5—H5115.3
C7—C8—H8120.8C7—N5—H5115.3
C10—C9—C8122.51 (17)C11—O2—C13117.88 (14)
C10—C9—H9118.7C4—S1—C5103.05 (8)
N4—C1—C2—C30.1 (2)S1—C4—N4—C1178.68 (11)
N2—C1—C2—C3177.81 (16)C2—C1—N4—C41.3 (2)
C1—C2—C3—N1178.60 (15)N2—C1—N4—C4179.36 (14)
C1—C2—C3—N31.3 (2)N4—C4—N3—C30.6 (2)
S1—C5—C6—O195.98 (18)S1—C4—N3—C3179.78 (10)
S1—C5—C6—N582.23 (16)N1—C3—N3—C4178.93 (14)
C12—C7—C8—C90.2 (3)C2—C3—N3—C41.0 (2)
N5—C7—C8—C9179.56 (17)O1—C6—N5—C75.5 (3)
C7—C8—C9—C100.0 (3)C5—C6—N5—C7172.71 (14)
C8—C9—C10—C110.1 (3)C12—C7—N5—C6168.50 (15)
C9—C10—C11—O2179.53 (18)C8—C7—N5—C611.7 (3)
C9—C10—C11—C120.1 (3)C12—C11—O2—C13175.89 (16)
C8—C7—C12—C110.2 (2)C10—C11—O2—C134.7 (3)
N5—C7—C12—C11179.57 (14)N4—C4—S1—C58.27 (14)
O2—C11—C12—C7179.39 (14)N3—C4—S1—C5171.36 (11)
C10—C11—C12—C70.1 (2)C6—C5—S1—C480.14 (14)
N3—C4—N4—C11.8 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N5—H5···N40.862.152.861 (3)140
C8—H8···O10.932.342.911 (3)120
N1—H1A···N3i0.862.213.035 (3)162
N1—H1B···O1ii0.862.082.891 (3)157
N2—H2B···O2iii0.862.553.210 (3)135
C2—H2···O2iii0.932.593.272 (3)130
Symmetry codes: (i) x+1, y+1, z+1; (ii) x+1, y+1, z; (iii) x+1, y+2, z+2.
 

Acknowledgements

MC thanks CSIR, Government of India, for the SRF fellowship and MC, VV and DV thank TBI X-ray facility, CAS in Crystallography and Biophysics, University of Madras, India, for data collection.

References

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