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

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 73| Part 2| February 2017| Pages 306-309
https://doi.org/10.1107/S2056989017001293

Crystal structures of 2-[(4,6-di­amino­pyrimidin-2-yl)sulfan­yl]-N-(naphthalen-1-yl)acetamide and 2-[(4,6-di­amino­pyrimidin-2-yl)sulfan­yl]-N-(4-fluoro­phen­yl)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 11 January 2017; accepted 25 January 2017; online 31 January 2017)

The title compounds, C16H15N5OS, (I), and C12H12FN5OS, (II), are [(di­amino­pyrimidine)­sulfan­yl]acetamide derivatives. In (I), the pyrimidine ring is inclined to the naphthalene ring system by 55.5 (1)°, while in (II), the pyrimidine ring is inclined to the benzene ring by 58.93 (8)°. In (II), there is an intra­molecular N—H⋯N hydrogen bond and a short C—H⋯O contact. In the crystals of (I) and (II), mol­ecules are linked by pairs of N—H⋯N hydrogen bonds, forming inversion dimers with R22(8) ring motifs. In the crystal of (I), the dimers are linked by bifurcated N—H⋯(O,O) and C—H⋯O hydrogen bonds, forming layers parallel to (100). In the crystal of (II), the dimers are linked by N—H⋯O hydrogen bonds, also forming layers parallel to (100). The layers are linked by C—H⋯F hydrogen bonds, forming a three-dimensional architecture.

CCDC references: 1529608; 1529607

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1. Chemical context

As a result of the innate ability of bacteria to develop resistance to available anti­biotics, there is a critical need to develop new agents to treat more strains that are resilient. Several classes of di­amino­pyrimidines have been reported as new therapeutic agents. Derivatives of di­amino­pyrimidines also exhibit anti-cancer activity (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.]), immune suppressant activity (Blumenkopf et al., 2002[Blumenkopf, T., Mueller, E. & Roskamp, E. (2002). Google Patents.]), hair-growth-stimulant properties, 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.]). They are also used as potential 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 anti-viral agents (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.]). In this connection, the title 4,6-di­amino­pyrimidine-based analogues have been synthesized as potential anti­viral agents against dengue for targeting NS2B/NS3 protease.

2. Structural commentary

The mol­ecular structure of compound (I)[link] is shown in Fig. 1[link]. The pyrimidine ring is twisted with respect to the thio­acetamide unit with the N1—C11—C12—S1 torsion angle being 140.88 (18)°. The pyrimidine ring (C13–C16/N2/N3) makes a dihedral angle of 55.5 (1)° with the naphthalene ring system (C1–C10). The amine nitro­gen atoms, N4 and N5, deviate by 0.0235 and 0.0291 Å, respectively, from the plane of the pyrimidine ring.

[Scheme 1]
[Figure 1]
Figure 1
The mol­ecular structure of compound (I)[link], showing the atom labelling and displacement ellipsoids drawn at the 50% probability level.

The mol­ecular structure of compound (II)[link] is shown in Fig. 2[link]. Here, the pyrimidine ring is twisted with respect to the thio­acetamide unit with the N1—C7—C8—S1 torsion angle being −82.44 (14)°. The pyrimidine ring (C9–C12/N2/N3) makes a dihedral angle of 58.93 (8)° with the benzene ring (C1–C6). The amine nitro­gen atoms, N4 and N5, deviate by 0.0247 and 0.0564 Å, respectively, from the pyrimidine ring. In compound (II)[link], there is an intra­molecular N—H⋯N hydrogen bond and a short C—H⋯O inter­action present (Table 2[link] and Fig. 2[link]).

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

D—H⋯A D—H H⋯A D⋯A D—H⋯A
N1—H1⋯N3 0.86 2.25 2.990 (2) 145
C3—H3⋯O1 0.93 2.31 2.903 (2) 121
N5—H5A⋯N2i 0.86 2.29 3.139 (2) 169
N4—H4A⋯O1ii 0.86 2.23 2.9852 (18) 146
C2—H2⋯F1iii 0.93 2.48 3.404 (3) 172
Symmetry codes: (i) -x, -y, -z+1; (ii) [x, -y+{\script{1\over 2}}, z+{\script{1\over 2}}]; (iii) [-x+1, y+{\script{1\over 2}}, -z+{\script{1\over 2}}].
[Figure 2]
Figure 2
The mol­ecular structure of compound (II)[link], showing the atom labelling and displacement ellipsoids drawn at the 50% probability level.

3. Supra­molecular features

In the crystal of compound (I)[link], mol­ecules are linked by pairs of N5—H5A⋯N3i hydrogen bonds, forming inversion dimers with an [R_{2}^{2}](8) ring motif (Table 1[link] and Fig. 3[link]). The dimers are linked by bifurcated N—H⋯(O,O) and C—H⋯O hydrogen bonds, forming layers parallel to the bc plane (Table 1[link] and Fig. 3[link]).

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

D—H⋯A D—H H⋯A D⋯A D—H⋯A
N5—H5A⋯N3i 0.86 2.27 3.110 (4) 167
N1—H1A⋯O1ii 0.86 2.05 2.890 (3) 165
N4—H4B⋯O1iii 0.86 2.36 2.964 (3) 127
C12—H12A⋯O1ii 0.97 2.58 3.408 (3) 143
Symmetry codes: (i) -x+1, -y, -z+1; (ii) [x, -y+{\script{1\over 2}}, z+{\script{1\over 2}}]; (iii) [x, -y-{\script{1\over 2}}, z+{\script{1\over 2}}].
[Figure 3]
Figure 3
A view along the b axis, of the crystal packing of compound (I)[link]. Hydrogen bonds are shown as dashed lines (see Table 1[link]). For clarity, only the NH and NH2 hydrogens and the C-bound H atoms involved in hydrogen bonding have been included.

In the crystal of compound (II)[link], inversion dimers, with an [R_{2}^{2}](8), ring motif, are also formed via pairs of N5—H5A⋯N2i hydrogen bonds (Table 2[link] and Fig. 4[link]). This time the dimers are linked by N—H⋯O hydrogen bonds and also form layers parallel to the bc plane (Table 2[link] and Fig. 4[link]). The layers are linked by C—H⋯F hydrogen bonds, forming a three-dimensional architecture (Table 2[link] and Fig. 4[link]).

[Figure 4]
Figure 4
The crystal packing of compound (II)[link] viewed along the b axis. Hydrogen bonds are shown as dashed lines (see Table 2[link]). For clarity, only the NH and NH2 hydrogens and the C-bound H atoms involved in hydrogen bonding have been included.

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-(pyrimidin-2-yl)-N-phenyl­acetamide yielded only five hits. They include two 4,6-di­methyl­pyrimidine analogues viz. 2-(4,6-di­methyl­pyrimidin-2-ylsulfan­yl)-N-phenyl acetamide (DIWXAJ; Gao et al., 2008[Gao, L.-X., Fang, G.-J., Feng, J.-G., Liang, D. & Wang, W. (2008). Acta Cryst. E64, o760.]) and N-(2-chloro­phen­yl)-2-(4,6-di­methyl­pyrimidin-2-ylsulfan­yl)acetamide (QOTQEW; Li et al., 2009[Li, Q., Wang, W., Wang, H., Gao, Y. & Qiu, H. (2009). Acta Cryst. E65, o959.]), and three 4,6-di­amino­pyrimidine compounds viz. 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.]), 2-[(4,6-di­amino­pyrimidin-2-yl)sulfan­yl]-N-(3-nitro­phen­yl)acetamide (Subasri et al., 2014[Subasri, S., Kumar, T. A., Sinha, B. N., Jayaprakash, V. & Velmurugan, D. (2014). Acta Cryst. E70, o850.]) and 2-[(4,6-di­amino­pyrimidin-2-yl)sulfan­yl]-N-(2-chloro­phen­yl)acetamide (Subasri et al., 2014[Subasri, S., Kumar, T. A., Sinha, B. N., Jayaprakash, V. & Velmurugan, D. (2014). Acta Cryst. E70, o850.]).

5. Synthesis and crystallization

Compound (I)[link]: To a solution of 4,6-di­amino-pyrimidine-2-thiol (0.5 g, 3.52 mmol) in 25 ml of ethanol, potassium hydroxide (0.2 g, 3.52 mmol) was added and the mixture refluxed for 30 min. Then 3.52 mmol of 2-chloro-N-(naphthalen-1-yl)acetamide was added and the mixture refluxed for 2.5 h. On completion of the reaction (monitored by TLC), the ethanol was evaporated in vacuo and cold water was added. The precipitate that formed was filtered and dried to give compound (I)[link] as a crystalline powder (yield 92%).

Compound (II)[link]: To a solution of 4,6-di­amino-pyrimidine-2-thiol (0.5 g, 3.52 mmol) in 25 ml of ethanol, potassium hydroxide (0.2 g, 3.52 mmol) was added and the mixture refluxed for 30 min. Then 3.52 mmol of 2-chloro-N-(4-fluoro­phen­yl)acetamide was added and the mixture refluxed for 4 h. On completion of the reaction (monitored by TLC), 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 88%).

Colourless block-like crystals were obtained by slow evaporation of a solution in CH3OH for compound (I)[link] and C4H8O2 for compound (II)[link].

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 as riding: C—H = 0.93–0.97 Å, N—H = 0.86 Å with Uiso(H) = 1.2Ueq(N,C).

Table 3
Experimental details

  (I) (II)
Crystal data
Chemical formula C16H15N5OS C12H12FN5OS
Mr 325.39 293.33
Crystal system, space group Monoclinic, P21/c Monoclinic, P21/c
Temperature (K) 293 293
a, b, c (Å) 25.1895 (16), 6.9411 (4), 8.9697 (6) 21.7358 (7), 7.3726 (3), 8.4487 (3)
β (°) 90.943 (4) 93.092 (1)
V (Å3) 1568.08 (17) 1351.93 (9)
Z 4 4
Radiation type Mo Kα Mo Kα
μ (mm−1) 0.22 0.25
Crystal size (mm) 0.30 × 0.25 × 0.20 0.31 × 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). 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 0.752, 0.831 0.652, 0.753
No. of measured, independent and observed [I > 2σ(I)] reflections 14522, 3849, 2095 12316, 3312, 2829
Rint 0.063 0.025
(sin θ/λ)max (Å−1) 0.669 0.667
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.052, 0.153, 0.98 0.037, 0.109, 1.05
No. of reflections 3849 3312
No. of parameters 208 181
H-atom treatment H-atom parameters constrained H-atom parameters constrained
Δρmax, Δρmin (e Å−3) 0.38, −0.23 0.22, −0.22
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: 1529608; 1529607

Crystal structure: contains datablocks global, I, II. DOI: https://doi.org/10.1107/S2056989017001293/su5347sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989017001293/su5347Isup2.hkl

Structure factors: contains datablock II. DOI: https://doi.org/10.1107/S2056989017001293/su5347IIsup3.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2056989017001293/su5347Isup4.cml

Supporting information file. DOI: https://doi.org/10.1107/S2056989017001293/su5347IIsup5.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) for (I); SHELXL2016/4 (Sheldrick, 2015) and PLATON (Spek, 2009) for (II).

(I) 2-[(4,6-Diaminopyrimidin-2-yl)sulfanyl]-N-(naphthalen-1-yl)acetamide top
Crystal data top
C16H15N5OSF(000) = 680
Mr = 325.39Dx = 1.378 Mg m−3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
a = 25.1895 (16) ÅCell parameters from 3849 reflections
b = 6.9411 (4) Åθ = 1.6–28.4°
c = 8.9697 (6) ŵ = 0.22 mm−1
β = 90.943 (4)°T = 293 K
V = 1568.08 (17) Å3Block, colourless
Z = 40.30 × 0.25 × 0.20 mm
Data collection top
Bruker SMART APEXII area-detector
diffractometer		2095 reflections with I > 2σ(I)
ω and φ scansRint = 0.063
Absorption correction: multi-scan
(SADABS; Bruker, 2008)		θmax = 28.4°, θmin = 1.6°
Tmin = 0.752, Tmax = 0.831h = −33→33
14522 measured reflectionsk = −7→9
3849 independent reflectionsl = −11→12
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)] = 0.052Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.153H-atom parameters constrained
S = 0.98 w = 1/[σ2(Fo2) + (0.0671P)2 + 0.3358P]
where P = (Fo2 + 2Fc2)/3
3849 reflections(Δ/σ)max = 0.001
208 parametersΔρmax = 0.38 e Å−3
0 restraintsΔρmin = −0.23 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
N50.49526 (12)−0.2169 (5)0.6491 (4)0.1242 (15)
H5A0.517831−0.1513830.5991310.149*
H5B0.505205−0.3197720.6951980.149*
C10.15258 (14)−0.2816 (4)0.5842 (3)0.0706 (9)
H10.156295−0.4012050.5388760.085*
C20.10801 (13)−0.2407 (5)0.6613 (3)0.0696 (9)
H20.081326−0.3328200.6673150.084*
C30.10145 (10)−0.0625 (4)0.7317 (3)0.0562 (7)
C40.05553 (12)−0.0167 (6)0.8124 (3)0.0725 (9)
H40.028614−0.1077490.8194830.087*
C50.04960 (12)0.1557 (6)0.8794 (3)0.0740 (9)
H50.0190650.1816970.9327780.089*
C60.08929 (11)0.2952 (5)0.8688 (3)0.0634 (8)
H60.0850360.4138960.9153020.076*
C70.13418 (10)0.2591 (4)0.7911 (3)0.0501 (6)
H70.1601000.3540180.7842840.060*
C80.14195 (9)0.0796 (4)0.7205 (2)0.0452 (6)
C90.18804 (10)0.0334 (4)0.6386 (2)0.0432 (6)
C100.19288 (11)−0.1441 (4)0.5729 (3)0.0576 (7)
H100.223334−0.1733790.5202150.069*
C110.26297 (9)0.1951 (3)0.5182 (2)0.0413 (6)
C120.30711 (10)0.3383 (4)0.5478 (3)0.0483 (6)
H12A0.3107000.3575110.6545690.058*
H12B0.2971110.4608710.5035920.058*
C130.38351 (10)0.0615 (3)0.5853 (2)0.0422 (6)
C140.44443 (12)−0.1587 (5)0.6552 (3)0.0688 (8)
C150.40599 (12)−0.2535 (4)0.7352 (3)0.0668 (8)
H150.414154−0.3643390.7891690.080*
C160.35572 (11)−0.1801 (4)0.7331 (3)0.0481 (6)
N10.22916 (8)0.1726 (3)0.6311 (2)0.0438 (5)
H1A0.2327510.2496340.7056630.053*
N20.34334 (7)−0.0183 (3)0.6559 (2)0.0427 (5)
N30.43337 (8)0.0052 (3)0.5783 (2)0.0540 (6)
N40.31453 (10)−0.2587 (3)0.8082 (2)0.0607 (6)
H4A0.283743−0.2052320.8039600.073*
H4B0.319286−0.3617820.8598410.073*
O10.25760 (7)0.1132 (3)0.39688 (16)0.0502 (5)
S10.37019 (3)0.26816 (10)0.47685 (8)0.0554 (2)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N50.0625 (18)0.132 (3)0.179 (3)0.0403 (19)0.033 (2)0.099 (3)
C10.092 (2)0.0530 (19)0.0668 (19)−0.0148 (18)0.0000 (17)−0.0022 (14)
C20.077 (2)0.064 (2)0.0671 (19)−0.0257 (17)−0.0050 (16)0.0057 (15)
C30.0522 (17)0.065 (2)0.0511 (14)−0.0107 (14)0.0013 (12)0.0105 (13)
C40.0508 (18)0.102 (3)0.0654 (18)−0.0192 (18)0.0071 (14)0.0168 (18)
C50.0437 (17)0.113 (3)0.0657 (18)0.0019 (19)0.0160 (13)0.008 (2)
C60.0519 (17)0.082 (2)0.0570 (16)0.0086 (16)0.0112 (13)−0.0039 (15)
C70.0420 (14)0.0617 (18)0.0467 (14)0.0001 (13)0.0078 (11)−0.0006 (12)
C80.0440 (14)0.0538 (16)0.0380 (12)−0.0021 (12)0.0010 (10)0.0044 (11)
C90.0475 (14)0.0455 (15)0.0370 (11)−0.0025 (12)0.0051 (10)0.0015 (10)
C100.0686 (19)0.0518 (17)0.0526 (15)−0.0014 (15)0.0095 (13)−0.0034 (13)
C110.0460 (14)0.0401 (14)0.0383 (12)0.0119 (11)0.0109 (10)0.0039 (10)
C120.0532 (16)0.0384 (14)0.0538 (14)0.0032 (12)0.0137 (12)0.0049 (11)
C130.0452 (14)0.0398 (14)0.0417 (12)−0.0040 (12)0.0053 (10)0.0008 (10)
C140.0571 (19)0.070 (2)0.080 (2)0.0153 (16)0.0118 (15)0.0257 (17)
C150.069 (2)0.0556 (19)0.0763 (19)0.0123 (16)0.0136 (16)0.0266 (15)
C160.0615 (17)0.0387 (15)0.0444 (13)−0.0024 (13)0.0094 (12)0.0017 (11)
N10.0465 (12)0.0458 (12)0.0395 (10)−0.0020 (10)0.0129 (8)−0.0056 (9)
N20.0477 (12)0.0369 (12)0.0437 (10)−0.0037 (9)0.0069 (9)0.0039 (9)
N30.0437 (13)0.0538 (14)0.0646 (13)0.0023 (11)0.0074 (10)0.0137 (11)
N40.0713 (16)0.0460 (14)0.0656 (14)−0.0062 (12)0.0217 (12)0.0134 (11)
O10.0575 (11)0.0562 (11)0.0373 (9)0.0086 (9)0.0110 (7)−0.0004 (8)
S10.0494 (4)0.0524 (5)0.0651 (4)0.0038 (3)0.0200 (3)0.0208 (3)
Geometric parameters (Å, º) top
N5—C141.345 (4)C9—N11.419 (3)
N5—H5A0.8600C10—H100.9300
N5—H5B0.8600C11—O11.234 (3)
C1—C21.358 (4)C11—N11.343 (3)
C1—C101.398 (4)C11—C121.512 (4)
C1—H10.9300C12—S11.789 (2)
C2—C31.400 (4)C12—H12A0.9700
C2—H20.9300C12—H12B0.9700
C3—C41.411 (4)C13—N31.318 (3)
C3—C81.424 (4)C13—N21.324 (3)
C4—C51.349 (5)C13—S11.762 (2)
C4—H40.9300C14—N31.357 (3)
C5—C61.396 (4)C14—C151.382 (4)
C5—H50.9300C15—C161.365 (4)
C6—C71.362 (3)C15—H150.9300
C6—H60.9300C16—N21.353 (3)
C7—C81.413 (3)C16—N41.360 (3)
C7—H70.9300N1—H1A0.8600
C8—C91.421 (3)N4—H4A0.8600
C9—C101.372 (3)N4—H4B0.8600
C14—N5—H5A120.0C1—C10—H10119.6
C14—N5—H5B120.0O1—C11—N1123.4 (2)
H5A—N5—H5B120.0O1—C11—C12121.8 (2)
C2—C1—C10120.1 (3)N1—C11—C12114.7 (2)
C2—C1—H1119.9C11—C12—S1114.45 (17)
C10—C1—H1119.9C11—C12—H12A108.6
C1—C2—C3121.3 (3)S1—C12—H12A108.6
C1—C2—H2119.4C11—C12—H12B108.6
C3—C2—H2119.4S1—C12—H12B108.6
C2—C3—C4122.3 (3)H12A—C12—H12B107.6
C2—C3—C8119.4 (3)N3—C13—N2129.4 (2)
C4—C3—C8118.3 (3)N3—C13—S1112.83 (17)
C5—C4—C3121.8 (3)N2—C13—S1117.67 (18)
C5—C4—H4119.1N5—C14—N3114.8 (3)
C3—C4—H4119.1N5—C14—C15123.6 (3)
C4—C5—C6120.0 (3)N3—C14—C15121.6 (3)
C4—C5—H5120.0C16—C15—C14118.2 (3)
C6—C5—H5120.0C16—C15—H15120.9
C7—C6—C5120.6 (3)C14—C15—H15120.9
C7—C6—H6119.7N2—C16—N4114.5 (2)
C5—C6—H6119.7N2—C16—C15121.5 (2)
C6—C7—C8120.9 (3)N4—C16—C15123.9 (2)
C6—C7—H7119.5C11—N1—C9126.0 (2)
C8—C7—H7119.5C11—N1—H1A117.0
C7—C8—C9123.4 (2)C9—N1—H1A117.0
C7—C8—C3118.4 (2)C13—N2—C16114.9 (2)
C9—C8—C3118.2 (2)C13—N3—C14114.3 (2)
C10—C9—N1121.4 (2)C16—N4—H4A120.0
C10—C9—C8120.2 (2)C16—N4—H4B120.0
N1—C9—C8118.3 (2)H4A—N4—H4B120.0
C9—C10—C1120.8 (3)C13—S1—C12100.80 (11)
C9—C10—H10119.6
C10—C1—C2—C3−0.5 (5)O1—C11—C12—S1−42.3 (3)
C1—C2—C3—C4180.0 (3)N1—C11—C12—S1140.88 (18)
C1—C2—C3—C81.0 (4)N5—C14—C15—C16179.9 (3)
C2—C3—C4—C5−179.8 (3)N3—C14—C15—C161.3 (5)
C8—C3—C4—C5−0.8 (4)C14—C15—C16—N2−0.4 (4)
C3—C4—C5—C60.7 (5)C14—C15—C16—N4−179.3 (3)
C4—C5—C6—C70.0 (5)O1—C11—N1—C910.4 (4)
C5—C6—C7—C8−0.6 (4)C12—C11—N1—C9−172.8 (2)
C6—C7—C8—C9−179.7 (2)C10—C9—N1—C1131.7 (4)
C6—C7—C8—C30.5 (4)C8—C9—N1—C11−150.3 (2)
C2—C3—C8—C7179.3 (2)N3—C13—N2—C160.8 (4)
C4—C3—C8—C70.2 (4)S1—C13—N2—C16177.84 (17)
C2—C3—C8—C9−0.6 (4)N4—C16—N2—C13178.5 (2)
C4—C3—C8—C9−179.7 (2)C15—C16—N2—C13−0.5 (3)
C7—C8—C9—C10−180.0 (2)N2—C13—N3—C140.0 (4)
C3—C8—C9—C10−0.1 (3)S1—C13—N3—C14−177.2 (2)
C7—C8—C9—N12.1 (3)N5—C14—N3—C13−179.8 (3)
C3—C8—C9—N1−178.1 (2)C15—C14—N3—C13−1.1 (4)
N1—C9—C10—C1178.4 (2)N3—C13—S1—C12−165.84 (19)
C8—C9—C10—C10.6 (4)N2—C13—S1—C1216.6 (2)
C2—C1—C10—C9−0.2 (4)C11—C12—S1—C13−64.63 (19)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N5—H5A···N3i0.862.273.110 (4)167
N1—H1A···O1ii0.862.052.890 (3)165
N4—H4B···O1iii0.862.362.964 (3)127
C12—H12A···O1ii0.972.583.408 (3)143
Symmetry codes: (i) −x+1, −y, −z+1; (ii) x, −y+1/2, z+1/2; (iii) x, −y−1/2, z+1/2.
(II) 2-[(4,6-Diaminopyrimidin-2-yl)sulfanyl]-N-(4-fluorophenyl)acetamide top
Crystal data top
C12H12FN5OSF(000) = 608
Mr = 293.33Dx = 1.441 Mg m−3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
a = 21.7358 (7) ÅCell parameters from 3312 reflections
b = 7.3726 (3) Åθ = 1.9–28.3°
c = 8.4487 (3) ŵ = 0.25 mm−1
β = 93.092 (1)°T = 293 K
V = 1351.93 (9) Å3Block, colourless
Z = 40.31 × 0.25 × 0.20 mm
Data collection top
Bruker SMART APEXII area-detector
diffractometer		2829 reflections with I > 2σ(I)
ω and φ scansRint = 0.025
Absorption correction: multi-scan
(SADABS; Bruker, 2008)		θmax = 28.3°, θmin = 1.9°
Tmin = 0.652, Tmax = 0.753h = −28→28
12316 measured reflectionsk = −5→9
3312 independent reflectionsl = −7→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)] = 0.037Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.109H-atom parameters constrained
S = 1.05 w = 1/[σ2(Fo2) + (0.055P)2 + 0.3099P]
where P = (Fo2 + 2Fc2)/3
3312 reflections(Δ/σ)max = 0.001
181 parametersΔρmax = 0.22 e Å−3
0 restraintsΔρmin = −0.22 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
C10.43036 (9)−0.1374 (4)0.4152 (3)0.0777 (6)
C20.42379 (9)0.0399 (4)0.3738 (3)0.0824 (6)
H20.4503580.0924660.3042720.099*
C30.37714 (8)0.1422 (3)0.4359 (2)0.0658 (4)
H30.3720020.2635680.4083770.079*
C40.33831 (6)0.0600 (2)0.53966 (17)0.0480 (3)
C50.34659 (8)−0.1211 (2)0.5791 (2)0.0605 (4)
H50.320667−0.1756660.6491090.073*
C60.39282 (10)−0.2211 (3)0.5158 (3)0.0746 (5)
H60.398185−0.3429570.5412730.089*
C70.26854 (6)0.32063 (19)0.58470 (16)0.0432 (3)
C80.21206 (7)0.36589 (19)0.67409 (17)0.0482 (3)
H8A0.2102500.4961990.6889630.058*
H8B0.2161050.3102160.7781520.058*
C90.13013 (6)0.07360 (17)0.65615 (14)0.0378 (3)
C100.06207 (7)−0.1564 (2)0.67975 (18)0.0501 (3)
C110.10494 (7)−0.2466 (2)0.77884 (18)0.0505 (3)
H110.095821−0.3580650.8235020.061*
C120.16170 (7)−0.16497 (18)0.80890 (15)0.0415 (3)
F10.47632 (7)−0.2347 (3)0.3527 (2)0.1187 (6)
N10.28896 (5)0.15094 (17)0.60807 (15)0.0480 (3)
H10.2691930.0879890.6743510.058*
N20.07407 (5)0.00964 (16)0.61864 (14)0.0452 (3)
N30.17559 (5)−0.00336 (14)0.74173 (12)0.0390 (2)
N40.20765 (7)−0.23810 (17)0.90067 (16)0.0546 (3)
H4A0.242409−0.1827650.9129260.066*
H4B0.202291−0.3402280.9471360.066*
N50.00588 (8)−0.2236 (2)0.6394 (2)0.0815 (5)
H5A−0.019470−0.1620800.5790470.098*
H5B−0.004701−0.3281490.6740680.098*
O10.29125 (5)0.43187 (15)0.49776 (14)0.0597 (3)
S10.14082 (2)0.29101 (5)0.57535 (5)0.05097 (13)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0526 (10)0.0988 (16)0.0819 (13)0.0139 (10)0.0035 (9)−0.0235 (12)
C20.0581 (11)0.1083 (18)0.0830 (13)−0.0068 (11)0.0248 (10)−0.0037 (13)
C30.0548 (9)0.0710 (11)0.0728 (11)−0.0055 (8)0.0142 (8)0.0061 (9)
C40.0429 (7)0.0532 (8)0.0478 (7)−0.0038 (6)−0.0002 (6)−0.0007 (6)
C50.0577 (9)0.0563 (10)0.0677 (10)0.0023 (7)0.0049 (7)0.0015 (8)
C60.0682 (11)0.0665 (12)0.0885 (14)0.0138 (9)−0.0011 (10)−0.0103 (10)
C70.0453 (7)0.0420 (7)0.0418 (6)−0.0102 (5)−0.0029 (5)0.0014 (5)
C80.0597 (8)0.0347 (7)0.0508 (7)−0.0064 (6)0.0081 (6)−0.0023 (6)
C90.0447 (6)0.0333 (6)0.0366 (6)0.0004 (5)0.0123 (5)−0.0009 (5)
C100.0498 (8)0.0469 (8)0.0543 (8)−0.0080 (6)0.0102 (6)0.0061 (6)
C110.0604 (9)0.0395 (7)0.0521 (8)−0.0086 (6)0.0088 (7)0.0089 (6)
C120.0551 (7)0.0340 (6)0.0361 (6)0.0012 (5)0.0082 (5)−0.0014 (5)
F10.0774 (9)0.1484 (14)0.1323 (13)0.0357 (9)0.0230 (8)−0.0415 (11)
N10.0499 (6)0.0442 (6)0.0508 (6)−0.0030 (5)0.0106 (5)0.0070 (5)
N20.0442 (6)0.0422 (6)0.0499 (6)−0.0029 (5)0.0079 (5)0.0056 (5)
N30.0467 (6)0.0320 (5)0.0390 (5)−0.0001 (4)0.0081 (4)0.0003 (4)
N40.0677 (8)0.0397 (6)0.0557 (7)−0.0015 (6)−0.0045 (6)0.0089 (5)
N50.0586 (9)0.0747 (11)0.1098 (14)−0.0267 (8)−0.0091 (8)0.0363 (10)
O10.0564 (6)0.0514 (6)0.0719 (7)−0.0071 (5)0.0085 (5)0.0188 (5)
S10.0472 (2)0.0404 (2)0.0655 (2)−0.00120 (14)0.00437 (16)0.01690 (16)
Geometric parameters (Å, º) top
C1—C61.358 (3)C8—H8B0.9700
C1—C21.359 (3)C9—N31.3207 (17)
C1—F11.359 (2)C9—N21.3288 (17)
C2—C31.389 (3)C9—S11.7625 (13)
C2—H20.9300C10—N51.345 (2)
C3—C41.388 (2)C10—N21.3594 (18)
C3—H30.9300C10—C111.388 (2)
C4—C51.386 (2)C11—C121.384 (2)
C4—N11.4144 (19)C11—H110.9300
C5—C61.378 (3)C12—N41.3438 (19)
C5—H50.9300C12—N31.3606 (17)
C6—H60.9300N1—H10.8600
C7—O11.2227 (16)N4—H4A0.8600
C7—N11.3386 (19)N4—H4B0.8600
C7—C81.513 (2)N5—H5A0.8600
C8—S11.8054 (15)N5—H5B0.8600
C8—H8A0.9700
C6—C1—C2122.69 (18)H8A—C8—H8B107.7
C6—C1—F1118.8 (2)N3—C9—N2128.87 (12)
C2—C1—F1118.5 (2)N3—C9—S1119.50 (10)
C1—C2—C3119.57 (19)N2—C9—S1111.64 (10)
C1—C2—H2120.2N5—C10—N2115.21 (15)
C3—C2—H2120.2N5—C10—C11123.17 (14)
C4—C3—C2118.9 (2)N2—C10—C11121.61 (14)
C4—C3—H3120.6C12—C11—C10117.71 (13)
C2—C3—H3120.6C12—C11—H11121.1
C5—C4—C3119.78 (16)C10—C11—H11121.1
C5—C4—N1116.72 (14)N4—C12—N3114.66 (13)
C3—C4—N1123.49 (16)N4—C12—C11123.98 (13)
C6—C5—C4120.67 (18)N3—C12—C11121.34 (13)
C6—C5—H5119.7C7—N1—C4129.45 (13)
C4—C5—H5119.7C7—N1—H1115.3
C1—C6—C5118.4 (2)C4—N1—H1115.3
C1—C6—H6120.8C9—N2—C10114.92 (12)
C5—C6—H6120.8C9—N3—C12115.35 (11)
O1—C7—N1125.03 (14)C12—N4—H4A120.0
O1—C7—C8121.11 (13)C12—N4—H4B120.0
N1—C7—C8113.84 (12)H4A—N4—H4B120.0
C7—C8—S1113.63 (10)C10—N5—H5A120.0
C7—C8—H8A108.8C10—N5—H5B120.0
S1—C8—H8A108.8H5A—N5—H5B120.0
C7—C8—H8B108.8C9—S1—C8103.11 (7)
S1—C8—H8B108.8
C6—C1—C2—C30.2 (3)O1—C7—N1—C4−1.5 (2)
F1—C1—C2—C3179.92 (18)C8—C7—N1—C4177.03 (13)
C1—C2—C3—C40.2 (3)C5—C4—N1—C7−176.10 (15)
C2—C3—C4—C5−0.1 (3)C3—C4—N1—C73.0 (2)
C2—C3—C4—N1−179.19 (16)N3—C9—N2—C101.3 (2)
C3—C4—C5—C6−0.3 (3)S1—C9—N2—C10−178.73 (10)
N1—C4—C5—C6178.83 (15)N5—C10—N2—C9−178.64 (15)
C2—C1—C6—C5−0.6 (3)C11—C10—N2—C92.5 (2)
F1—C1—C6—C5179.66 (18)N2—C9—N3—C12−4.68 (19)
C4—C5—C6—C10.7 (3)S1—C9—N3—C12175.34 (9)
O1—C7—C8—S196.18 (14)N4—C12—N3—C9−177.50 (12)
N1—C7—C8—S1−82.44 (14)C11—C12—N3—C94.35 (18)
N5—C10—C11—C12178.71 (16)N3—C9—S1—C8−11.34 (11)
N2—C10—C11—C12−2.5 (2)N2—C9—S1—C8168.68 (10)
C10—C11—C12—N4−179.08 (14)C7—C8—S1—C991.88 (11)
C10—C11—C12—N3−1.1 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···N30.862.252.990 (2)145
C3—H3···O10.932.312.903 (2)121
N5—H5A···N2i0.862.293.139 (2)169
N4—H4A···O1ii0.862.232.9852 (18)146
C2—H2···F1iii0.932.483.404 (3)172
Symmetry codes: (i) −x, −y, −z+1; (ii) x, −y+1/2, z+1/2; (iii) −x+1, 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 a meritorious fellowship.

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Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 73| Part 2| February 2017| Pages 306-309
https://doi.org/10.1107/S2056989017001293
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