research communications\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 73| Part 4| April 2017| Pages 467-471
https://doi.org/10.1107/S2056989017003243

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

CROSSMARK_Color_square_no_text.svg
S. Subasri,a Timiri Ajay Kumar,b Barij Nayan Sinha,b Venkatesan Jayaprakash,b Vijayan Viswanathana 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 & Technology, Birla Institute of Technology, Mesra, Ranchi 835 215, Jharkhand, India
*Correspondence e-mail: shirai2011@gmail.com

Edited by H. Stoeckli-Evans, University of Neuchâtel, Switzerland (Received 26 January 2017; accepted 27 February 2017; online 3 March 2017)

The title compounds, C12H12ClN5OS, (I), and C12H12ClN5OS, (II), are 2-[(di­amino­pyrimidin-2-yl)sulfan­yl]acetamides. Compound (II), crystallizes with two independent mol­ecules (A and B) in the asymmetric unit. In each of the mol­ecules, in both (I) and (II), an intra­molecular N—H⋯N hydrogen bond forms an S(7) ring motif. The pyrimidine ring is inclined to the benzene ring by 42.25 (14)° in (I), and by 59.70 (16) and 62.18 (15)° in mol­ecules A and B, respectively, of compound (II). In the crystal of (I), mol­ecules are linked by pairs of N—H⋯N hydrogen bonds, forming inversion dimers with an R22(8) ring motif. The dimers are linked via bifurcated N—H⋯O and C—H⋯O hydrogen bonds, forming corrugated layers parallel to the ac plane. In the crystal of (II), the A mol­ecules are linked through N—H⋯O and N—H⋯Cl hydrogen bonds, forming layers parallel to (100). The B mol­ecules are also linked by N—H⋯O and N—H⋯Cl hydrogen bonds, also forming layers parallel to (100). The parallel layers of A and B mol­ecules are linked via N—H⋯N hydrogen bonds, forming a three-dimensional structure.

CCDC references: 1534990; 1534989

Similar articles

1. Chemical context

Di­amino­pyrimidine derivatives are reported to be therapeutic agents towards anti-cancer activity, selectively inhibiting c-Fms kinase of M-CSF-dependent myeloid leukemia cells (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.]). They have also shown anti­bacterial activity (Kandeel et al., 1994[Kandeel, M., El-Meligie, S., Omar, R., Roshdy, S. & Youssef, K. (1994). J. Pharm. Sci. 3, 197-205.]), are potential anti­microbial (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.]) and anti-AIDS agents (Nogueras et al., 1993[Nogueras, M., Sánchez, A., Melguizo, M., Quijano, M. L. & Melgarejo, M. (1993). Bioorg. Med. Chem. Lett. 3, 601-606.]) and anti­viral agents (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., Masoj\?ídková, M., Andrei, G., Snoeck, R., De Clercq, E. & Balzarini, J. (2004). Bioorg. Med. Chem. 12, 3197-3202.]) and have shown promise as immunosuppressants (Blumenkopf et al., 2002[Blumenkopf, T. A., Mueller, E. E. & Roskamp, E. J. (2002). Google Patents. WO2001040215 A1. PCT/IB2000/001628.]). In this connection, the title 2-[(4,6-di­amino­pyrimidin-2-yl)sulfan­yl] based analogues have been synthesized as anti­viral agents against NS2B/NS3 Dengue protease. We report herein on the syntheses and crystal structures of the title compounds, (I)[link] and (II)[link].

2. Structural commentary

The mol­ecular structures of compounds (I)[link] and (II)[link] are shown in Figs. 1[link] and 2[link], respectively. Compound (II)[link] crystallizes with two independent mol­ecules (A and B) in the asymmetric unit, which have similar conformations (Fig. 3[link]). The mol­ecules of both compounds are folded with the pyrimidine ring being inclined to the benzene ring by 42.25 (14)° in (I)[link], and by 59.70 (16) and 62.18 (15)° in mol­ecules A and B, respectively, of compound (II)[link]. In compound (I)[link], the N1—C7—C8—S1 torsion angle is 77.2 (3)°, while in mol­ecule A of compound (II)[link], N5—C6—C5—S1 is 85.2 (3)°, and in mol­ecule B N10—C18—C17—S2 is 68.4 (3)°.

[Scheme 1]
[Figure 1]
Figure 1
The mol­ecular structure of compound (I)[link], with the atom labelling. Displacement ellipsoids are drawn at the 30% probability level. The intra­molecular N—H⋯N hydrogen bond is shown as a dashed lines (see Table 1[link]).
[Figure 2]
Figure 2
The mol­ecular structure of the two independent mol­ecules (A and B) of compound (II)[link], with the atom labelling. Displacement ellipsoids are drawn at the 30% probability level. The intra­molecular N—H⋯N hydrogen bonds are shown as dashed lines (see Table 2[link]).
[Figure 3]
Figure 3
An AutoMolFit (PLATON; Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]) view of mol­ecule B (red) on mol­ecule A (back) of (II)[link].

In compound (I)[link], the intra­molecular N1—H1A⋯N2 hydrogen bond (Table 1[link]) generates an S(7) ring motif, as shown in Fig. 1[link]. Amine atoms N4 and N5 attached to the pyrimidine ring deviate by 0.018 (3) and 0.060 (3) Å, respectively. The chlorine atom Cl1 attached to the benzene ring deviates by 0.058 (1) Å.

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

D—H⋯A D—H H⋯A D⋯A D—H⋯A
N1—H1A⋯N2 0.86 2.06 2.856 (3) 154
N5—H5A⋯N3i 0.86 2.16 2.990 (3) 162
N4—H4B⋯O1ii 0.86 2.22 2.969 (3) 146
C11—H11⋯O1ii 0.93 2.45 3.144 (3) 132
Symmetry codes: (i) -x, -y, -z+1; (ii) [x-{\script{1\over 2}}, y, -z+{\script{1\over 2}}].

In compound (II)[link], intra­molecular N5—H5⋯N4 and N10—H10⋯N9 hydrogen bonds (Table 2[link] and Fig. 2[link]) in mol­ecules A and B, respectively, also generate S(7) ring motifs. In mol­ecule A, the amine group atoms N1 and N2 attached to the pyrim­idine ring deviate by 0.006 (3) and 0.004 (3) Å, respectively. The chlorine atom Cl1 attached to the benzene ring deviates by 0.013 (1) Å. In mol­ecule B, the amine group atoms N6 and N7 attached to the pyrimidine ring deviate by −0.003 (3) and 0.050 (3) Å, respectively. Atom Cl2 attached to the benzene ring deviates by 0.074 (1) Å.

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

D—H⋯A D—H H⋯A D⋯A D—H⋯A
N5—H5⋯N4 0.86 2.25 2.962 (3) 140
N10—H10A⋯N9 0.86 2.02 2.826 (3) 157
N1—H1B⋯O1i 0.86 2.19 2.931 (4) 145
N2—H2B⋯Cl1i 0.86 2.76 3.405 (3) 133
N6—H6A⋯O2ii 0.86 2.51 3.340 (4) 162
N6—H6B⋯Cl2iii 0.86 2.70 3.556 (3) 176
N7—H7B⋯O2iii 0.86 2.24 3.002 (4) 148
N1—H1A⋯N8iv 0.86 2.21 3.070 (4) 174
N7—H7A⋯N3v 0.86 2.19 3.046 (4) 178
Symmetry codes: (i) [x, -y+{\script{3\over 2}}, z+{\script{1\over 2}}]; (ii) -x+2, -y+1, -z; (iii) [x, -y+{\script{3\over 2}}, z-{\script{1\over 2}}]; (iv) [x-1, -y+{\script{3\over 2}}, z+{\script{1\over 2}}]; (v) [x+1, -y+{\script{3\over 2}}, z-{\script{1\over 2}}].

3. Supra­molecular features

In the crystal of (I)[link], mol­ecules are linked by pairs of N—H⋯N hydrogen bonds, forming inversion dimers with an R22(8) ring motif (Table 1[link] and Fig. 4[link]). The dimers are linked by via bifurcated N—H⋯O and C—H⋯O hydrogen bonds, forming corrugated layers parallel to the ac plane (Table 1[link] and Fig. 5[link]).

[Figure 4]
Figure 4
The crystal packing of compound (I)[link] viewed along the b axis. H atoms not involved in hydrogen bonding (see Table 1[link]), have been excluded for clarity.
[Figure 5]
Figure 5
The crystal packing of compound (I)[link] viewed along the a axis. H atoms not involved in hydrogen bonding (see Table 1[link]), have been excluded for clarity.

In the crystal of (II)[link], the A mol­ecules are linked through N—H⋯O and N—H⋯Cl hydrogen bonds, forming layers parallel to (100). Likewise the B mol­ecules are also linked by N—H⋯O and N—H⋯Cl hydrogen bonds, forming layers parallel to (100). The parallel layers of A and layers of B mol­ecules are linked via N—H⋯N hydrogen bonds, forming a three-dimensional structure (Table 2[link] and Fig. 6[link]).

[Figure 6]
Figure 6
The crystal packing of compound (II)[link] viewed along the b axis (colour code: A mol­ecules black, B mol­ecules red). H atoms not involved in hydrogen bonding (see Table 2[link]), have been excluded for clarity.

4. Database survey

A search of the Cambridge Structural 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 five hits. Three of these involve (4,6-di­amino­pyrmidin-2-yl) groups. They include 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.]). Here the pyrimidine and benzene rings are inclined to one another by 67.84 (6)°, compared to 42.25 (14)° in (I)[link], and 59.70 (16) and 62.18 (15)° in mol­ecules A and B, respectively, of compound (II)[link]. As in the title compounds, there is also an intra­molecular N—H⋯N hydrogen bond present, stabilizing the folded conformation of the mol­ecule.

5. Synthesis and crystallization

Compound (I)[link]:

To a solution of 4,6-di­amino-pyrimidine-2-sulfanyl (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 min, after which 3.52 mmol of 2-chloro-N-(4-chloro­phen­yl)acetamide derivative was added and refluxed for 4 h. At the end of the reaction (monitored by TLC), the ethanol was evaporated in vacuo and cold water was added; the precipitate formed was filtered and dried to give compound (I)[link] as a crystalline powder (yield 97%). Colourless block-like crystals were obtained from a solution in methanol and ethyl acetate (1:1) by slow evaporation of the solvents at room temperature.

Compound (II)[link]:

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 min. Then 3.52 mmol of 2-chloro-N-(3-chloro­phen­yl)acetamide was added and refluxed for 3 h. At the end of the reaction (monitored by TLC), the ethanol was evaporated in vacuo and cold water was added and the precipitate formed was filtered and dried to give compound (II)[link] as a crystalline powder (yield 92%). Colourless block-like crystals were obtained from a solution in methanol and ethyl acetate (2:1) by slow evaporation of the solvents at room temperature.

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 3[link]. For both (I)[link] and (II)[link], hydrogen atoms were placed in calculated positions and refined as riding: C—H = 0.93–0.97 Å and N—H = 0.86 Å, with Uiso(H) = 1.2Ueq(N,C).

Table 3
Experimental details

  (I) (II)
Crystal data
Chemical formula C12H12ClN5OS C12H12ClN5OS
Mr 309.78 309.78
Crystal system, space group Orthorhombic, Pbca Monoclinic, P21/c
Temperature (K) 293 293
a, b, c (Å) 18.2743 (12), 7.4835 (5), 19.8021 (12) 18.220 (2), 8.1180 (12), 19.628 (2)
α, β, γ (°) 90, 90, 90 90, 108.761 (8), 90
V (Å3) 2708.1 (3) 2748.9 (6)
Z 8 8
Radiation type Mo Kα Mo Kα
μ (mm−1) 0.44 0.43
Crystal size (mm) 0.28 × 0.25 × 0.18 0.31 × 0.22 × 0.16
 
Data collection
Diffractometer Bruker SMART APEXII area-detector Bruker SMART APEXII area-detector
Absorption correction Multi-scan (SADABS; Bruker, 2008[Bruker (2008). SMART, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Multi-scan (SADABS; Bruker, 2008[Bruker (2008). SMART, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.])
Tmin, Tmax 0.741, 0.863 0.742, 0.892
No. of measured, independent and observed [I > 2σ(I)] reflections 22685, 3372, 2007 25810, 6858, 3462
Rint 0.060 0.075
(sin θ/λ)max (Å−1) 0.669 0.668
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.050, 0.161, 1.08 0.050, 0.155, 0.96
No. of reflections 3372 6858
No. of parameters 181 361
H-atom treatment H-atom parameters constrained H-atom parameters constrained
Δρmax, Δρmin (e Å−3) 0.42, −0.69 0.42, −0.42
Computer programs: APEX2 and SAINT (Bruker, 2008[Bruker (2008). SMART, 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.]) and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information

CCDC references: 1534990; 1534989

Crystal structure: contains datablocks global, I, II. DOI: https://doi.org/10.1107/S2056989017003243/su5348sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989017003243/su5348Isup4.hkl

Structure factors: contains datablock II. DOI: https://doi.org/10.1107/S2056989017003243/su5348IIsup3.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2056989017003243/su5348Isup4.cml

Supporting information file. DOI: https://doi.org/10.1107/S2056989017003243/su5348IIsup5.cml

checkCIF report


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: PLATON (Spek, 2009); software used to prepare material for publication: SHELXL2016 (Sheldrick, 2015) and PLATON (Spek, 2009).

(I) N-(4-Chlorophenyl)-2-[(4,6-diaminopyrimidin-2-yl)sulfanyl]acetamide top
Crystal data top
C12H12ClN5OSDx = 1.520 Mg m−3
Mr = 309.78Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, PbcaCell parameters from 3372 reflections
a = 18.2743 (12) Åθ = 2.1–28.4°
b = 7.4835 (5) ŵ = 0.44 mm−1
c = 19.8021 (12) ÅT = 293 K
V = 2708.1 (3) Å3Block, colourless
Z = 80.28 × 0.25 × 0.18 mm
F(000) = 1280
Data collection top
Bruker SMART APEXII area-detector
diffractometer		2007 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.060
ω and φ scansθmax = 28.4°, θmin = 2.1°
Absorption correction: multi-scan
(SADABS; Bruker, 2008)		h = −23→24
Tmin = 0.741, Tmax = 0.863k = −9→9
22685 measured reflectionsl = −26→26
3372 independent reflections
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)] = 0.050Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.161H-atom parameters constrained
S = 1.08 w = 1/[σ2(Fo2) + (0.0795P)2 + 0.3384P]
where P = (Fo2 + 2Fc2)/3
3372 reflections(Δ/σ)max < 0.001
181 parametersΔρmax = 0.42 e Å−3
0 restraintsΔρmin = −0.69 e Å−3
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
C10.21682 (15)0.1105 (4)0.10059 (13)0.0467 (7)
H10.2596550.1659740.1148730.056*
C20.21206 (16)0.0419 (4)0.03543 (13)0.0524 (7)
H20.2515060.0520140.0060020.063*
C30.14875 (17)−0.0409 (4)0.01479 (13)0.0523 (7)
C40.08942 (17)−0.0537 (4)0.05714 (15)0.0563 (8)
H40.046632−0.1085500.0424050.068*
C50.09364 (15)0.0152 (4)0.12158 (14)0.0505 (7)
H50.0533550.0074910.1501220.061*
C60.15764 (13)0.0963 (4)0.14435 (12)0.0411 (6)
C70.21262 (13)0.2114 (4)0.25020 (12)0.0417 (6)
C80.18937 (14)0.2955 (4)0.31653 (13)0.0466 (7)
H8A0.1516150.3833610.3074010.056*
H8B0.2309530.3582630.3356290.056*
C90.06049 (13)0.1256 (4)0.36033 (12)0.0370 (6)
C10−0.04825 (13)0.0187 (4)0.39846 (12)0.0388 (6)
C11−0.07960 (13)0.0629 (4)0.33698 (12)0.0423 (6)
H11−0.1279890.0337070.3275030.051*
C12−0.03712 (13)0.1511 (4)0.29042 (12)0.0384 (6)
N10.15680 (11)0.1680 (3)0.20979 (10)0.0439 (6)
H1A0.1139960.1868300.2263800.053*
N20.03568 (10)0.1801 (3)0.30081 (10)0.0393 (5)
N30.02360 (10)0.0518 (3)0.41104 (10)0.0396 (5)
N4−0.06459 (12)0.2133 (4)0.23153 (10)0.0513 (6)
H4A−0.0364710.2673170.2033300.062*
H4B−0.1101880.1987520.2222760.062*
N5−0.08599 (12)−0.0543 (4)0.44936 (11)0.0533 (7)
H5A−0.064552−0.0771790.4870410.064*
H5B−0.131697−0.0783370.4443960.064*
O10.27697 (10)0.1893 (4)0.23652 (10)0.0662 (7)
S10.15519 (3)0.13935 (11)0.37853 (3)0.0458 (2)
CL10.14411 (6)−0.13289 (15)−0.06572 (4)0.0831 (4)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0401 (14)0.061 (2)0.0392 (13)0.0034 (13)0.0018 (11)0.0079 (13)
C20.0559 (17)0.060 (2)0.0414 (14)0.0041 (15)0.0078 (13)0.0057 (14)
C30.076 (2)0.0448 (17)0.0356 (13)−0.0015 (15)0.0010 (13)0.0034 (12)
C40.0668 (19)0.054 (2)0.0478 (15)−0.0159 (15)−0.0061 (14)0.0062 (15)
C50.0508 (16)0.056 (2)0.0446 (15)−0.0121 (14)0.0037 (12)0.0070 (14)
C60.0404 (14)0.0481 (17)0.0349 (12)0.0039 (12)0.0025 (10)0.0061 (12)
C70.0361 (13)0.0500 (17)0.0390 (13)0.0010 (12)0.0049 (11)0.0045 (12)
C80.0396 (14)0.0560 (18)0.0441 (14)−0.0070 (12)0.0021 (11)−0.0017 (13)
C90.0320 (12)0.0451 (16)0.0338 (11)0.0015 (11)0.0008 (9)−0.0041 (11)
C100.0361 (13)0.0442 (16)0.0362 (12)−0.0026 (11)0.0054 (10)−0.0040 (11)
C110.0329 (13)0.0544 (18)0.0396 (13)−0.0040 (11)−0.0016 (11)−0.0011 (12)
C120.0347 (13)0.0466 (17)0.0339 (12)0.0035 (11)−0.0013 (10)−0.0046 (11)
N10.0330 (11)0.0617 (16)0.0370 (11)0.0029 (10)0.0041 (9)0.0006 (10)
N20.0307 (10)0.0526 (14)0.0344 (10)0.0011 (9)0.0008 (9)0.0016 (10)
N30.0328 (11)0.0517 (15)0.0344 (10)−0.0028 (9)0.0001 (8)0.0007 (10)
N40.0372 (12)0.0783 (19)0.0385 (11)−0.0016 (12)−0.0058 (10)0.0095 (12)
N50.0426 (13)0.0767 (19)0.0405 (11)−0.0161 (12)−0.0008 (10)0.0088 (12)
O10.0304 (10)0.114 (2)0.0538 (12)0.0020 (11)0.0062 (8)−0.0101 (12)
S10.0312 (3)0.0698 (5)0.0363 (3)−0.0015 (3)−0.0016 (3)0.0060 (3)
CL10.1216 (9)0.0854 (7)0.0422 (4)−0.0171 (6)0.0013 (4)−0.0090 (4)
Geometric parameters (Å, º) top
C1—C61.390 (3)C8—H8B0.9700
C1—C21.391 (4)C9—N21.327 (3)
C1—H10.9300C9—N31.329 (3)
C2—C31.375 (4)C9—S11.771 (2)
C2—H20.9300C10—N51.338 (3)
C3—C41.374 (4)C10—N31.359 (3)
C3—CL11.739 (3)C10—C111.386 (3)
C4—C51.378 (4)C11—C121.374 (4)
C4—H40.9300C11—H110.9300
C5—C61.393 (4)C12—N41.352 (3)
C5—H50.9300C12—N21.364 (3)
C6—N11.403 (3)N1—H1A0.8600
C7—O11.218 (3)N4—H4A0.8600
C7—N11.337 (3)N4—H4B0.8600
C7—C81.517 (4)N5—H5A0.8600
C8—S11.807 (3)N5—H5B0.8600
C8—H8A0.9700
C6—C1—C2120.1 (3)H8A—C8—H8B107.6
C6—C1—H1120.0N2—C9—N3128.7 (2)
C2—C1—H1120.0N2—C9—S1119.79 (18)
C3—C2—C1119.7 (3)N3—C9—S1111.47 (17)
C3—C2—H2120.2N5—C10—N3115.8 (2)
C1—C2—H2120.2N5—C10—C11123.1 (2)
C4—C3—C2120.9 (3)N3—C10—C11121.1 (2)
C4—C3—CL1119.6 (2)C12—C11—C10118.1 (2)
C2—C3—CL1119.5 (2)C12—C11—H11121.0
C3—C4—C5119.7 (3)C10—C11—H11121.0
C3—C4—H4120.2N4—C12—N2116.0 (2)
C5—C4—H4120.2N4—C12—C11122.3 (2)
C4—C5—C6120.7 (3)N2—C12—C11121.7 (2)
C4—C5—H5119.7C7—N1—C6129.6 (2)
C6—C5—H5119.7C7—N1—H1A115.2
C1—C6—C5119.0 (2)C6—N1—H1A115.2
C1—C6—N1123.7 (2)C9—N2—C12114.7 (2)
C5—C6—N1117.2 (2)C9—N3—C10115.3 (2)
O1—C7—N1124.8 (3)C12—N4—H4A120.0
O1—C7—C8121.3 (2)C12—N4—H4B120.0
N1—C7—C8113.9 (2)H4A—N4—H4B120.0
C7—C8—S1114.6 (2)C10—N5—H5A120.0
C7—C8—H8A108.6C10—N5—H5B120.0
S1—C8—H8A108.6H5A—N5—H5B120.0
C7—C8—H8B108.6C9—S1—C8103.73 (12)
S1—C8—H8B108.6
C6—C1—C2—C3−0.4 (4)O1—C7—N1—C6−2.5 (5)
C1—C2—C3—C41.4 (5)C8—C7—N1—C6176.8 (3)
C1—C2—C3—CL1−177.9 (2)C1—C6—N1—C7−22.2 (5)
C2—C3—C4—C5−0.9 (5)C5—C6—N1—C7161.4 (3)
CL1—C3—C4—C5178.4 (2)N3—C9—N2—C12−2.0 (4)
C3—C4—C5—C6−0.5 (5)S1—C9—N2—C12175.36 (19)
C2—C1—C6—C5−1.0 (4)N4—C12—N2—C9176.9 (2)
C2—C1—C6—N1−177.3 (3)C11—C12—N2—C9−3.5 (4)
C4—C5—C6—C11.5 (4)N2—C9—N3—C104.2 (4)
C4—C5—C6—N1178.1 (3)S1—C9—N3—C10−173.28 (19)
O1—C7—C8—S1−103.4 (3)N5—C10—N3—C9−179.5 (2)
N1—C7—C8—S177.2 (3)C11—C10—N3—C9−1.0 (4)
N5—C10—C11—C12174.5 (3)N2—C9—S1—C817.9 (2)
N3—C10—C11—C12−3.8 (4)N3—C9—S1—C8−164.3 (2)
C10—C11—C12—N4−174.2 (3)C7—C8—S1—C9−88.3 (2)
C10—C11—C12—N26.3 (4)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1A···N20.862.062.856 (3)154
N5—H5A···N3i0.862.162.990 (3)162
N4—H4B···O1ii0.862.222.969 (3)146
C11—H11···O1ii0.932.453.144 (3)132
Symmetry codes: (i) −x, −y, −z+1; (ii) x−1/2, y, −z+1/2.
(II) N-(3-Chlorophenyl)-2-[(4,6-diaminopyrimidin-2-yl)sulfanyl]acetamide top
Crystal data top
C12H12ClN5OSF(000) = 1280
Mr = 309.78Dx = 1.497 Mg m−3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
a = 18.220 (2) ÅCell parameters from 6858 reflections
b = 8.1180 (12) Åθ = 1.2–28.4°
c = 19.628 (2) ŵ = 0.43 mm−1
β = 108.761 (8)°T = 293 K
V = 2748.9 (6) Å3Block, colourless
Z = 80.31 × 0.22 × 0.16 mm
Data collection top
Bruker SMART APEXII area-detector
diffractometer		3462 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.075
ω and φ scansθmax = 28.4°, θmin = 1.2°
Absorption correction: multi-scan
(SADABS; Bruker, 2008)		h = −24→24
Tmin = 0.742, Tmax = 0.892k = −10→10
25810 measured reflectionsl = −26→26
6858 independent reflections
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)] = 0.050Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.155H-atom parameters constrained
S = 0.96 w = 1/[σ2(Fo2) + (0.0646P)2 + 0.6656P]
where P = (Fo2 + 2Fc2)/3
6858 reflections(Δ/σ)max = 0.001
361 parametersΔρmax = 0.42 e Å−3
0 restraintsΔρmin = −0.42 e Å−3
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
C10.43039 (17)0.6518 (4)0.39062 (15)0.0438 (7)
C20.50489 (17)0.5880 (4)0.41809 (15)0.0461 (8)
H20.5335240.5999680.4664720.055*
C30.53498 (16)0.5069 (4)0.37174 (15)0.0424 (7)
C40.42495 (16)0.5606 (4)0.27980 (15)0.0400 (7)
C50.42189 (17)0.4300 (4)0.14672 (16)0.0485 (8)
H5A0.4480330.3451470.1806680.058*
H5B0.3859490.3759400.1052420.058*
C60.48119 (18)0.5233 (4)0.12307 (16)0.0473 (8)
C70.61562 (17)0.6320 (4)0.17094 (16)0.0476 (8)
C80.67034 (19)0.6788 (5)0.23523 (18)0.0592 (9)
H80.6634190.6506190.2786890.071*
C90.7347 (2)0.7666 (5)0.2351 (2)0.0737 (11)
H90.7704440.8003650.2783670.088*
C100.7465 (2)0.8045 (5)0.1718 (2)0.0663 (10)
H100.7903230.8630550.1716670.080*
C110.69326 (19)0.7553 (4)0.10864 (18)0.0554 (9)
C120.62693 (19)0.6684 (4)0.10619 (18)0.0538 (8)
H120.5913680.6357820.0626200.065*
C131.07720 (18)0.5427 (4)−0.18594 (16)0.0518 (8)
C141.11114 (17)0.6066 (4)−0.23360 (16)0.0545 (9)
H141.0851280.607744−0.2828670.065*
C151.18621 (18)0.6699 (4)−0.20499 (16)0.0504 (8)
C161.18492 (16)0.6063 (4)−0.09333 (15)0.0422 (7)
C171.17491 (16)0.5113 (4)0.04034 (15)0.0474 (8)
H17A1.1522190.4187320.0095040.057*
H17B1.2075280.4670640.0859400.057*
C181.11047 (17)0.6094 (4)0.05351 (16)0.0457 (7)
C190.98833 (16)0.7549 (4)−0.01350 (15)0.0428 (7)
C200.93861 (17)0.7880 (4)−0.08218 (16)0.0488 (8)
H200.9484650.742561−0.1218650.059*
C210.87475 (18)0.8876 (4)−0.09216 (17)0.0554 (9)
H210.8418090.907855−0.1385520.066*
C220.85896 (18)0.9577 (4)−0.03444 (17)0.0533 (8)
H220.8159211.024970−0.0410840.064*
C230.90908 (17)0.9246 (4)0.03344 (16)0.0477 (8)
C240.97354 (17)0.8249 (4)0.04526 (16)0.0460 (8)
H241.0063640.8050750.0917430.055*
N10.39450 (15)0.7294 (4)0.43183 (13)0.0584 (8)
H1A0.3479480.7652560.4128960.070*
H1B0.4181590.7429200.4770510.070*
N20.60725 (15)0.4414 (4)0.39269 (13)0.0573 (7)
H2A0.6249040.3963670.3614540.069*
H2B0.6354440.4448160.4372080.069*
N30.38865 (13)0.6359 (3)0.31978 (12)0.0436 (6)
N40.49560 (13)0.4945 (3)0.30007 (12)0.0412 (6)
N50.55000 (14)0.5449 (3)0.17471 (13)0.0501 (7)
H50.5545870.4995130.2154680.060*
N61.00456 (16)0.4803 (4)−0.20701 (15)0.0811 (11)
H6A0.9847420.445292−0.1754290.097*
H6B0.9781470.475742−0.2520090.097*
N71.22370 (15)0.7369 (4)−0.24649 (14)0.0698 (9)
H7A1.2697920.775136−0.2273750.084*
H7B1.2017390.741880−0.2923270.084*
N81.22428 (13)0.6664 (3)−0.13364 (12)0.0461 (6)
N91.11350 (14)0.5443 (3)−0.11441 (12)0.0479 (6)
N101.05376 (13)0.6562 (3)−0.00640 (12)0.0448 (6)
H10A1.0582360.620508−0.0461270.054*
O10.46540 (13)0.5750 (4)0.06196 (11)0.0714 (7)
O21.11150 (13)0.6397 (3)0.11485 (11)0.0643 (7)
S10.36824 (4)0.56020 (11)0.18798 (4)0.0463 (2)
S21.23535 (4)0.62488 (11)−0.00038 (4)0.0492 (2)
CL10.70803 (5)0.80248 (14)0.02776 (5)0.0738 (3)
CL20.89352 (5)1.01784 (12)0.10723 (5)0.0649 (3)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0507 (17)0.045 (2)0.0406 (16)−0.0074 (15)0.0221 (14)−0.0013 (14)
C20.0525 (17)0.053 (2)0.0330 (15)−0.0094 (16)0.0143 (13)−0.0020 (15)
C30.0464 (16)0.0413 (19)0.0398 (16)−0.0036 (14)0.0143 (13)0.0040 (14)
C40.0466 (16)0.0371 (18)0.0393 (15)−0.0063 (14)0.0178 (13)−0.0023 (13)
C50.0539 (17)0.052 (2)0.0403 (16)−0.0006 (16)0.0166 (14)−0.0116 (15)
C60.0552 (18)0.055 (2)0.0380 (16)0.0100 (16)0.0232 (15)0.0024 (15)
C70.0521 (17)0.046 (2)0.0499 (18)0.0132 (16)0.0232 (15)0.0032 (16)
C80.061 (2)0.069 (3)0.0482 (19)0.0039 (19)0.0180 (17)0.0030 (18)
C90.066 (2)0.089 (3)0.062 (2)−0.001 (2)0.0159 (19)−0.002 (2)
C100.054 (2)0.073 (3)0.069 (2)−0.0075 (19)0.0165 (19)−0.003 (2)
C110.059 (2)0.056 (2)0.058 (2)0.0111 (18)0.0301 (17)0.0080 (18)
C120.0582 (19)0.055 (2)0.0527 (19)0.0064 (17)0.0240 (16)0.0013 (17)
C130.0544 (18)0.059 (2)0.0405 (17)−0.0068 (17)0.0129 (15)−0.0037 (16)
C140.0539 (18)0.075 (3)0.0339 (16)−0.0053 (18)0.0128 (14)−0.0001 (16)
C150.0532 (18)0.059 (2)0.0424 (17)0.0088 (16)0.0201 (15)0.0042 (16)
C160.0478 (16)0.0424 (19)0.0394 (15)0.0039 (15)0.0182 (13)0.0018 (14)
C170.0470 (16)0.055 (2)0.0384 (16)−0.0037 (15)0.0117 (13)0.0106 (15)
C180.0487 (17)0.050 (2)0.0405 (17)−0.0135 (15)0.0176 (14)−0.0007 (15)
C190.0411 (15)0.0448 (19)0.0436 (17)−0.0150 (14)0.0151 (13)−0.0049 (15)
C200.0448 (17)0.060 (2)0.0409 (17)−0.0111 (16)0.0123 (14)0.0017 (16)
C210.0499 (18)0.064 (2)0.0470 (18)−0.0147 (17)0.0079 (15)0.0024 (17)
C220.0452 (17)0.053 (2)0.060 (2)−0.0072 (16)0.0147 (16)0.0037 (17)
C230.0510 (17)0.050 (2)0.0471 (18)−0.0123 (16)0.0227 (15)−0.0012 (15)
C240.0470 (17)0.050 (2)0.0417 (17)−0.0109 (15)0.0149 (14)0.0024 (15)
N10.0530 (15)0.086 (2)0.0404 (14)0.0043 (15)0.0203 (12)−0.0148 (14)
N20.0543 (15)0.071 (2)0.0427 (15)0.0115 (15)0.0108 (12)0.0000 (14)
N30.0461 (13)0.0513 (17)0.0367 (13)−0.0030 (12)0.0180 (11)−0.0083 (12)
N40.0487 (14)0.0416 (15)0.0345 (13)0.0011 (12)0.0153 (11)−0.0003 (11)
N50.0552 (15)0.0582 (19)0.0387 (14)0.0041 (14)0.0178 (12)0.0082 (13)
N60.0650 (18)0.131 (3)0.0406 (16)−0.044 (2)0.0086 (14)−0.0034 (18)
N70.0558 (16)0.114 (3)0.0421 (15)−0.0083 (17)0.0198 (13)0.0182 (16)
N80.0448 (13)0.0557 (18)0.0399 (14)0.0009 (12)0.0167 (11)0.0077 (12)
N90.0468 (14)0.0583 (18)0.0372 (14)−0.0109 (13)0.0115 (11)−0.0003 (13)
N100.0414 (13)0.0570 (18)0.0359 (13)−0.0045 (12)0.0126 (11)−0.0002 (12)
O10.0594 (14)0.113 (2)0.0437 (13)0.0075 (14)0.0188 (11)0.0222 (14)
O20.0714 (15)0.0839 (18)0.0362 (12)0.0075 (14)0.0152 (11)−0.0032 (12)
S10.0464 (4)0.0585 (6)0.0351 (4)0.0021 (4)0.0146 (3)−0.0024 (4)
S20.0415 (4)0.0653 (6)0.0391 (4)−0.0092 (4)0.0107 (3)0.0047 (4)
CL10.0698 (6)0.0948 (8)0.0647 (6)−0.0090 (5)0.0327 (5)0.0072 (5)
CL20.0665 (5)0.0756 (7)0.0602 (5)0.0000 (5)0.0308 (4)−0.0049 (5)
Geometric parameters (Å, º) top
C1—N11.348 (4)C15—N71.336 (4)
C1—N31.360 (3)C15—N81.348 (4)
C1—C21.389 (4)C16—N81.320 (3)
C2—C31.372 (4)C16—N91.331 (4)
C2—H20.9300C16—S21.766 (3)
C3—N21.355 (4)C17—C181.508 (4)
C3—N41.362 (3)C17—S21.808 (3)
C4—N31.327 (3)C17—H17A0.9700
C4—N41.332 (4)C17—H17B0.9700
C4—S11.766 (3)C18—O21.223 (3)
C5—C61.510 (4)C18—N101.346 (4)
C5—S11.800 (3)C19—C241.388 (4)
C5—H5A0.9700C19—C201.387 (4)
C5—H5B0.9700C19—N101.405 (4)
C6—O11.215 (3)C20—C211.378 (4)
C6—N51.346 (4)C20—H200.9300
C7—C121.383 (4)C21—C221.378 (4)
C7—C81.386 (4)C21—H210.9300
C7—N51.411 (4)C22—C231.378 (4)
C8—C91.374 (5)C22—H220.9300
C8—H80.9300C23—C241.383 (4)
C9—C101.361 (5)C23—CL21.736 (3)
C9—H90.9300C24—H240.9300
C10—C111.366 (5)N1—H1A0.8600
C10—H100.9300N1—H1B0.8600
C11—C121.387 (4)N2—H2A0.8600
C11—CL11.736 (3)N2—H2B0.8600
C12—H120.9300N5—H50.8600
C13—N91.346 (4)N6—H6A0.8600
C13—N61.352 (4)N6—H6B0.8600
C13—C141.378 (4)N7—H7A0.8600
C14—C151.398 (4)N7—H7B0.8600
C14—H140.9300N10—H10A0.8600
N1—C1—N3116.0 (3)C18—C17—S2115.1 (2)
N1—C1—C2122.9 (3)C18—C17—H17A108.5
N3—C1—C2121.1 (3)S2—C17—H17A108.5
C3—C2—C1118.1 (3)C18—C17—H17B108.5
C3—C2—H2121.0S2—C17—H17B108.5
C1—C2—H2121.0H17A—C17—H17B107.5
N2—C3—N4115.0 (3)O2—C18—N10124.6 (3)
N2—C3—C2122.9 (3)O2—C18—C17120.6 (3)
N4—C3—C2122.0 (3)N10—C18—C17114.9 (2)
N3—C4—N4128.8 (3)C24—C19—C20119.2 (3)
N3—C4—S1111.4 (2)C24—C19—N10122.4 (3)
N4—C4—S1119.8 (2)C20—C19—N10118.3 (3)
C6—C5—S1112.9 (2)C21—C20—C19120.6 (3)
C6—C5—H5A109.0C21—C20—H20119.7
S1—C5—H5A109.0C19—C20—H20119.7
C6—C5—H5B109.0C22—C21—C20121.0 (3)
S1—C5—H5B109.0C22—C21—H21119.5
H5A—C5—H5B107.8C20—C21—H21119.5
O1—C6—N5124.5 (3)C23—C22—C21117.8 (3)
O1—C6—C5120.8 (3)C23—C22—H22121.1
N5—C6—C5114.8 (3)C21—C22—H22121.1
C12—C7—C8120.1 (3)C22—C23—C24122.6 (3)
C12—C7—N5122.3 (3)C22—C23—CL2119.1 (3)
C8—C7—N5117.6 (3)C24—C23—CL2118.2 (2)
C9—C8—C7120.3 (3)C23—C24—C19118.8 (3)
C9—C8—H8119.8C23—C24—H24120.6
C7—C8—H8119.8C19—C24—H24120.6
C10—C9—C8120.3 (4)C1—N1—H1A120.0
C10—C9—H9119.8C1—N1—H1B120.0
C8—C9—H9119.8H1A—N1—H1B120.0
C9—C10—C11119.2 (3)C3—N2—H2A120.0
C9—C10—H10120.4C3—N2—H2B120.0
C11—C10—H10120.4H2A—N2—H2B120.0
C10—C11—C12122.5 (3)C4—N3—C1115.3 (2)
C10—C11—CL1119.5 (3)C4—N4—C3114.6 (2)
C12—C11—CL1118.0 (3)C6—N5—C7128.7 (3)
C7—C12—C11117.5 (3)C6—N5—H5115.6
C7—C12—H12121.2C7—N5—H5115.6
C11—C12—H12121.2C13—N6—H6A120.0
N9—C13—N6115.3 (3)C13—N6—H6B120.0
N9—C13—C14121.8 (3)H6A—N6—H6B120.0
N6—C13—C14122.8 (3)C15—N7—H7A120.0
C13—C14—C15117.4 (3)C15—N7—H7B120.0
C13—C14—H14121.3H7A—N7—H7B120.0
C15—C14—H14121.3C16—N8—C15115.7 (3)
N7—C15—N8116.7 (3)C16—N9—C13115.5 (2)
N7—C15—C14122.0 (3)C18—N10—C19129.5 (3)
N8—C15—C14121.3 (3)C18—N10—H10A115.3
N8—C16—N9128.2 (3)C19—N10—H10A115.3
N8—C16—S2112.7 (2)C4—S1—C5103.66 (14)
N9—C16—S2119.0 (2)C16—S2—C17102.99 (14)
N1—C1—C2—C3178.0 (3)N10—C19—C24—C23178.0 (3)
N3—C1—C2—C3−0.6 (4)N4—C4—N3—C12.2 (5)
C1—C2—C3—N2179.3 (3)S1—C4—N3—C1−175.7 (2)
C1—C2—C3—N43.1 (4)N1—C1—N3—C4179.5 (3)
S1—C5—C6—O1−93.7 (3)C2—C1—N3—C4−1.9 (4)
S1—C5—C6—N585.2 (3)N3—C4—N4—C30.1 (4)
C12—C7—C8—C92.3 (5)S1—C4—N4—C3177.8 (2)
N5—C7—C8—C9−178.8 (3)N2—C3—N4—C4−179.4 (3)
C7—C8—C9—C10−1.9 (6)C2—C3—N4—C4−2.9 (4)
C8—C9—C10—C110.6 (6)O1—C6—N5—C72.0 (5)
C9—C10—C11—C120.3 (6)C5—C6—N5—C7−176.9 (3)
C9—C10—C11—CL1−179.8 (3)C12—C7—N5—C6−20.0 (5)
C8—C7—C12—C11−1.4 (5)C8—C7—N5—C6161.1 (3)
N5—C7—C12—C11179.7 (3)N9—C16—N8—C152.3 (5)
C10—C11—C12—C70.1 (5)S2—C16—N8—C15−174.2 (2)
CL1—C11—C12—C7−179.8 (2)N7—C15—N8—C16177.1 (3)
N9—C13—C14—C151.8 (5)C14—C15—N8—C16−2.7 (5)
N6—C13—C14—C15179.0 (3)N8—C16—N9—C130.1 (5)
C13—C14—C15—N7−178.9 (3)S2—C16—N9—C13176.4 (2)
C13—C14—C15—N80.8 (5)N6—C13—N9—C16−179.7 (3)
S2—C17—C18—O2−112.5 (3)C14—C13—N9—C16−2.2 (5)
S2—C17—C18—N1068.4 (3)O2—C18—N10—C194.6 (5)
C24—C19—C20—C21−0.7 (4)C17—C18—N10—C19−176.3 (3)
N10—C19—C20—C21−178.3 (3)C24—C19—N10—C181.4 (5)
C19—C20—C21—C220.5 (5)C20—C19—N10—C18178.8 (3)
C20—C21—C22—C23−0.1 (5)N3—C4—S1—C5−172.4 (2)
C21—C22—C23—C24−0.1 (5)N4—C4—S1—C59.5 (3)
C21—C22—C23—CL2177.2 (2)C6—C5—S1—C4−88.7 (2)
C22—C23—C24—C19−0.1 (4)N8—C16—S2—C17−172.9 (2)
CL2—C23—C24—C19−177.5 (2)N9—C16—S2—C1710.3 (3)
C20—C19—C24—C230.6 (4)C18—C17—S2—C16−86.9 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N5—H5···N40.862.252.962 (3)140
N10—H10A···N90.862.022.826 (3)157
N1—H1B···O1i0.862.192.931 (4)145
N2—H2B···Cl1i0.862.763.405 (3)133
N6—H6A···O2ii0.862.513.340 (4)162
N6—H6B···Cl2iii0.862.703.556 (3)176
N7—H7B···O2iii0.862.243.002 (4)148
N1—H1A···N8iv0.862.213.070 (4)174
N7—H7A···N3v0.862.193.046 (4)178
Symmetry codes: (i) x, −y+3/2, z+1/2; (ii) −x+2, −y+1, −z; (iii) x, −y+3/2, z−1/2; (iv) x−1, −y+3/2, z+1/2; (v) x+1, −y+3/2, 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 a meritorious fellowship.

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ISSN: 2056-9890
Volume 73| Part 4| April 2017| Pages 467-471
https://doi.org/10.1107/S2056989017003243
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