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

Subasri, S.; Timiri, A.K.; Barji, N.S.; Jayaprakash, V.; Vijayan, V.; Velmurugan, D.

doi:10.1107/S2056989016011658

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ISSN: 2056-9890

Volume 72| Part 8| August 2016| Pages 1171-1175

https://doi.org/10.1107/S2056989016011658

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

S. Subasri,^a Ajay Kumar Timiri,^b Nayan Sinha Barji,^b Venkatesan Jayaprakash,^b Viswanathan Vijayan ^a and Devadasan Velmurugan ^a ^*

^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 1 July 2016; accepted 18 July 2016; online 22 July 2016)

The title compounds, C₁₂H₁₂N₆O₃S·H₂O, (I), and C₁₂H₁₂ClN₅OS, (II), are 2-[(4,6-diaminopyrimidin-2-yl)sulfanyl]acetamides. Compound (I) crystallized as a monohydrate. In both compounds, the molecules have a folded conformation, with the pyrimidine ring being inclined to the benzene ring by 56.18 (6)° in (I) and by 67.84 (6)° in (II). In both molecules, there is an intramolecular N—H⋯N hydrogen bond stabilizing the folded conformation. In (I), there is also a C—H⋯O intramolecular short contact, and in (II) an intramolecular N—H⋯Cl hydrogen bond is present. In the crystal of (I), molecules are linked by a series of N—H⋯O, O—H⋯O and O—H⋯N hydrogen bonds, forming undulating sheets parallel to the (100). The sheets are linked via an N—H⋯O_water hydrogen bond, forming a three-dimensional network. In the crystal of (II), molecules are linked by a series of N—H⋯O, N—H⋯N and C—H⋯O hydrogen bonds, forming slabs parallel to (001).

Keywords: crystal structure; acetamides; intramolecular N—H⋯O and N—H⋯Cl hydrogen bonds; network; framework.

CCDC references: 1494258; 1494257

1. Chemical context

Recent studies have shown that diamino substituted pyrimidines are active inhibitors of human dihydrofolate reductase (hDHFR) and also possess inhibitory potency against tyrosine kinase (Gangjee et al., 2006 ). 2,4-diamino pyrimidine derivatives have anti-retro viral activity (Hocková et al., 2004 ) and also anti-trypanosoma brucei activity (Perales et al., 2011 ). A series of 2,4-diaminopyrimidines have as also been prepared to study their immuno-suppressant activity (Blumenkopf et al., 2003 ). Pyrimidines are also potent antiviral agents and a series of N-benzyl-2-(4,6-diaminopyrimidin-2-ylsulfanyl)acetamides have been designed to fight Dengue Virus Protease (Timiri et al., 2016 ). A series 5-substituted benzyl-2,4-diamino pyrimidine derivatives have also been synthesized as c-Fms kinase inhibitors (Xu et al., 2010 ). As part of our studies in this area, we now describe the syntheses and crystal structures of the title compounds.

2. Structural commentary

The molecular structures of compounds (I) and (II) are illustrated in Figs. 1 and 2, respectively. In compound (I), the pyrimidine ring makes a dihedral angle of 56.18 (6)° with the benzene ring (C7–C12). The nitro group is inclined by 16.3 (3)° to the benzene ring to which it is attached. The amine nitrogen atoms, N1 and N2, are displaced from the pyrimidine ring by 0.028 (2) and 0.026 (2) Å, respectively.

Figure 1
The molecular structure of compound (I)

, with atom labelling. Displacement ellipsoids are drawn at the 50% probability level. Intramolecular hydrogen bonds are shown as dashed lines (see Table 1

Figure 2
The molecular structure of compound (II)

, with atom labelling. Displacement ellipsoids are drawn at the 50% probability level. Intramolecular hydrogen bonds are shown as dashed lines (see Table 2

In compound (II), the pyrimidine ring makes a dihedral angle of 67.84 (6)° with the chlorobenzene ring (C7–C12). The amine nitrogen atoms, N1 and N2, are displaced from the pyrimidine ring by 0.009 (2) and 0.030 (2) Å, respectively. The chlorine atom, Cl1, attached to the benzene ring deviates by 0.053 (1) Å from the ring plane.

In both the compounds, the folded conformation is reinforced by an intramolecular N—H⋯O hydrogen bond [Fig. 1, Table 1 for (I) and Fig. 2, Table 2 for (II)]. In (I) there is an intramolecular C—H⋯O contact (Table 1 and Fig. 1) and in (II) an intramolecular N—H⋯Cl hydrogen bond is also present (Table 2 and Fig. 2).

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

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N5—H5⋯N4	0.86 (3)	2.05 (3)	2.832 (3)	151 (3)
C12—H12⋯O1	0.93	2.35	2.911 (3)	118
N1—H1A⋯O1Wⁱ	0.83 (3)	2.16 (3)	2.979 (3)	170 (2)
N1—H1B⋯O2ⁱⁱ	0.84 (3)	2.29 (3)	3.082 (3)	159 (3)
N2—H2A⋯O3ⁱⁱⁱ	0.80 (3)	2.58 (3)	3.255 (3)	143 (3)
N2—H2B⋯O1ⁱⁱ	0.83 (3)	2.09 (3)	2.904 (3)	170 (3)
O1W—H1WA⋯N3^iv	0.86	2.09	2.919 (3)	162
O1W—H1WB⋯O3^v	0.90	2.64	3.294 (3)	130
Symmetry codes: (i) x-1, y, z; (ii) $[-x+{\script{1\over 2}}, y+{\script{1\over 2}}, z+{\script{1\over 2}}]$ ; (iii) x, y, z+1; (iv) $[-x+1, -y+1, z-{\script{1\over 2}}]$ ; (v) $[-x+1, -y+1, z+{\script{1\over 2}}]$ .

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

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N5—H5⋯N4	0.85 (2)	2.12 (2)	2.898 (2)	152 (2)
N2—H2A⋯Cl1	0.81 (3)	2.81 (2)	3.493 (2)	143 (2)
N1—H1A⋯N3ⁱ	0.85 (2)	2.21 (2)	3.058 (2)	174 (2)
N1—H1B⋯O1ⁱⁱ	0.83 (2)	2.21 (2)	2.992 (2)	157 (2)
N2—H2A⋯O1ⁱⁱⁱ	0.81 (3)	2.56 (2)	3.095 (2)	124 (2)
C2—H2⋯O1ⁱⁱ	0.93	2.64	3.353 (2)	134
Symmetry codes: (i) -x, -y, -z+1; (ii) x-1, y-1, z; (iii) x-1, y, z.

3. Supramolecular features

In the crystal of compound (I), molecules are linked by a series of N—H⋯O, O—H⋯O and O—H⋯N hydrogen bonds, forming undulating sheets parallel to the bc plane (Table 1 and Fig. 3). The sheets are linked via an N—H⋯O_water hydrogen bond, forming a three-dimensional network (Table 1 and Fig. 3). Through pairs of N—H⋯O hydrogen bonds, R₂²(15) and R₄⁴(29) ring motifs are generated (Table 1 and Fig. 4).

Figure 3
The crystal packing of compound (I)

, viewed along the b axis. Hydrogen bonds are shown as dashed lines (see Table 1

). C-bound H atoms have been excluded for clarity.

Figure 4
A view of the hydrogen-bonded ring motifs in the crystal of compound (I)

. Details of the hydrogen bonding are given in Table 1

In the crystal of compound (II), molecules are linked by a series of N—H⋯O, N—H⋯N and C—H⋯O hydrogen bonds, forming slabs parallel to the ab plane (Table 2 and Fig. 5). Through pairs of N—H⋯N hydrogen bonds, R²₂₍8) ring motifs are generated, and through further pairs of N—H⋯N and N—H⋯O hydrogen bonds R₄⁴(18) ring motifs are also formed (Table 2 and Fig. 6).

Figure 5
The crystal packing of compound (II)

, viewed along the a axis. Hydrogen bonds are shown as dashed lines (see Table 2

)·C-bound H atoms have been excluded for clarity.

Figure 6
A view of the hydrogen-bonded ring motifs in the crystal of compound (II)

. Details of the hydrogen bonding are given in Table 2

4. Database survey

A search of the Cambridge Structural Database (Version 5.37, update May 2016; Groom et al., 2016 ) for 2-(pyrimidin-2-ylsulfanyl)-N-phenylacetamides yielded only three hits. There are two 4,6-dimethylpyrimidine analogues viz. 2-(4,6-dimethylpyrimidin-2-ylsulfanyl)-N-phenylacetamide (DIWXAJ; Gao et al., 2008 ) and N-(2-chlorophenyl)-2-(4,6-dimethylpyrimidin-2-ylsulfanyl)acetamide QOTQEW; Li et al., 2009 ), but only one 4,6-diaminopyrimidine compound viz. 2-[(4,6-diaminopyrimidin-2-yl)sulfanyl]-N-(2-methylphenyl)acetamide (GOKWIO; Subasri et al., 2014 ). In the 4,6-dimethylpyrimidine analogues, DIWXAJ and QOTQEW, the pyrimidine ring is inclined to the benzene ring by 88.86 (15) and 79.60 (8)°, respectively. In the 4,6-diaminopyrimidine compound, GOKWIO, the two rings are inclined to one another by 54.73 (9)°. This last value is similar to that observed in the compound (I), viz. 56.18 (6)°.

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 half an hour and to it 3.52 mmol of 3-nitro phenylacetamide was added and refluxed for 4 h. At the end of the reaction (observed by TLC), ethanol was evaporated under vacuum and cold water was added and the precipitate filtered and dried to give compound (I) as a crystalline powder (yield 88–96%). After purification, the compound was recrystallized from ethyl acetate 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 potassium hydroxide (0.2 g; 3.52 mmol) was added and refluxed for half an hour and to it 3.52 mmol of 2-chloro-phenylacetamide was added and the mixture was refluxed for 3 h. At the end of the reaction (observed by TLC), ethanol was evaporated under vacuum and cold water was added, and the precipitate was filtered and dried to give compound (II) as a crystalline powder (yield 88–96%). 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. For both compounds, the NH₂ and NH H atoms, and the water H atoms for (I), were located in difference Fourier maps. The N-bound H atoms were freely refined, while the water H atoms were initially freely refined and in the final cycles of refinement as riding atoms. The C-bound H atoms were placed in calculated positions and refined as riding: C—H = 0.93–0.97 Å with U_iso(H) = 1.2U_eq(C).

Table 3
Experimental details

	(I)	(II)
Crystal data
Chemical formula	C₁₂H₁₂N₆O₃S·H₂O	C₁₂H₁₂ClN₅OS
M_r	338.35	309.78
Crystal system, space group	Orthorhombic, Pna2₁	Triclinic, P $[\overline{1}]$
Temperature (K)	293	293
a, b, c (Å)	7.2326 (1), 14.3442 (2), 14.0940 (3)	7.2528 (2), 7.6249 (3), 13.0649 (4)
α, β, γ (°)	90, 90, 90	91.410 (2), 105.924 (2), 94.647 (2)
V (Å³)	1462.19 (4)	691.68 (4)
Z	4	2
Radiation type	Mo Kα	Mo Kα
μ (mm⁻¹)	0.25	0.43
Crystal size (mm)	0.30 × 0.25 × 0.20	0.30 × 0.20 × 0.15

Data collection
Diffractometer	Bruker SMART APEXII area-detector	Bruker SMART APEXII area-detector
Absorption correction	Multi-scan (SADABS; Bruker, 2008 )	Multi-scan (SADABS; Bruker, 2008)
T_min, T_max	0.785, 0.845	0.785, 0.845
No. of measured, independent and observed [I > 2σ(I)] reflections	7912, 3265, 3034	10154, 2822, 2519
R_int	0.021	0.022
(sin θ/λ)_max (Å⁻¹)	0.667	0.626

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.027, 0.069, 1.04	0.035, 0.099, 1.04
No. of reflections	3265	2822
No. of parameters	229	201
No. of restraints	1	0
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.16, −0.17	0.50, −0.50
Absolute structure	Flack x determined using 1217 quotients [(I⁺)−(I⁻)]/[(I⁺)+(I⁻)] (Parsons et al., 2013 )	–
Absolute structure parameter	0.07 (3)	–
Computer programs: APEX2 (Bruker, 2008), SAINT (Bruker, 2008), SHELXS97 (Sheldrick, 2008 ), Mercury (Macrae et al., 2008 ) and PLATON (Spek, 2009 ), SHELXL2014 (Sheldrick, 2015 ) and PLATON (Spek, 2009).

Supporting information

CCDC references: 1494258; 1494257

Crystal structure: contains datablocks global, I, II. DOI: https://doi.org/10.1107/S2056989016011658/su5311sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989016011658/su5311Isup2.hkl

Structure factors: contains datablock II. DOI: https://doi.org/10.1107/S2056989016011658/su5311IIsup3.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2056989016011658/su5311Isup4.cml

Supporting information file. DOI: https://doi.org/10.1107/S2056989016011658/su5311IIsup5.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: SHELXL2014 (Sheldrick, 2015); molecular graphics: Mercury (Macrae et al., 2008) and PLATON (Spek, 2009); software used to prepare material for publication: SHELXL2014 (Sheldrick, 2015) and PLATON (Spek, 2009).

(I) 2-[(4,6-Diaminopyrimidin-2-yl)sulfanyl]-N-(3-nitrophenyl)acetamide monohydrate top

Crystal data top

C₁₂H₁₂N₆O₃S·H₂O	D_x = 1.537 Mg m⁻³
M_r = 338.35	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, Pna2₁	Cell parameters from 3265 reflections
a = 7.2326 (1) Å	θ = 2.0–28.3°
b = 14.3442 (2) Å	µ = 0.25 mm⁻¹
c = 14.0940 (3) Å	T = 293 K
V = 1462.19 (4) Å³	Block, colourless
Z = 4	0.30 × 0.25 × 0.20 mm
F(000) = 704

Data collection top

Bruker SMART APEXII area-detector diffractometer	3034 reflections with I > 2σ(I)
ω and φ scans	R_int = 0.021
Absorption correction: multi-scan (SADABS; Bruker, 2008)	θ_max = 28.3°, θ_min = 2.0°
T_min = 0.785, T_max = 0.845	h = −5→9
7912 measured reflections	k = −18→19
3265 independent reflections	l = −15→18

Refinement top

Refinement on F²	Hydrogen site location: mixed
Least-squares matrix: full	H atoms treated by a mixture of independent and constrained refinement
R[F² > 2σ(F²)] = 0.027	w = 1/[σ²(F_o²) + (0.0396P)² + 0.1263P] where P = (F_o² + 2F_c²)/3
wR(F²) = 0.069	(Δ/σ)_max = 0.001
S = 1.04	Δρ_max = 0.16 e Å⁻³
3265 reflections	Δρ_min = −0.17 e Å⁻³
229 parameters	Extinction correction: SHELXL, Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
1 restraint	Extinction coefficient: 0.0039 (10)
Primary atom site location: structure-invariant direct methods	Absolute structure: Flack x determined using 1217 quotients [(I⁺)-(I^-)]/[(I⁺)+(I^-)] (Parsons et al., 2013)
Secondary atom site location: difference Fourier map	Absolute structure parameter: 0.07 (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

	x	y	z	U_iso*/U_eq
S1	0.12955 (8)	0.37215 (3)	0.66439 (4)	0.03810 (14)
O1	0.2112 (3)	0.32497 (11)	0.42274 (13)	0.0555 (5)
O2	0.4515 (3)	0.40381 (12)	0.13791 (14)	0.0570 (5)
O3	0.4586 (3)	0.53670 (14)	0.06709 (14)	0.0602 (5)
N1	−0.0426 (3)	0.69929 (14)	0.58998 (15)	0.0483 (5)
H1A	−0.112 (3)	0.6759 (19)	0.550 (2)	0.039 (7)*
H1B	−0.049 (4)	0.7564 (18)	0.601 (2)	0.048 (7)*
N2	0.2912 (3)	0.62828 (15)	0.87403 (16)	0.0473 (5)
H2A	0.343 (4)	0.587 (2)	0.902 (2)	0.052 (9)*
H2B	0.303 (4)	0.683 (2)	0.891 (2)	0.058 (8)*
N3	0.2016 (2)	0.51355 (12)	0.77054 (12)	0.0346 (4)
N4	0.0368 (2)	0.54948 (11)	0.62840 (12)	0.0327 (4)
N5	0.1324 (3)	0.47612 (12)	0.44843 (13)	0.0361 (4)
H5	0.081 (4)	0.5115 (19)	0.490 (2)	0.050 (7)*
N6	0.4308 (3)	0.48792 (13)	0.13678 (13)	0.0404 (4)
C1	0.0378 (3)	0.64158 (12)	0.65303 (16)	0.0351 (4)
C2	0.1209 (3)	0.67214 (15)	0.73550 (15)	0.0386 (5)
H2	0.1206	0.7349	0.7522	0.046*
C3	0.2048 (3)	0.60567 (14)	0.79264 (17)	0.0359 (4)
C4	0.1191 (3)	0.49297 (13)	0.68900 (14)	0.0318 (4)
C5	0.0093 (3)	0.36034 (14)	0.55277 (16)	0.0369 (5)
H5A	−0.0345	0.2967	0.5466	0.044*
H5B	−0.0979	0.4010	0.5532	0.044*
C6	0.1278 (3)	0.38380 (14)	0.46763 (15)	0.0350 (4)
C7	0.2255 (3)	0.52300 (13)	0.37571 (15)	0.0327 (4)
C8	0.2440 (4)	0.61934 (14)	0.38488 (18)	0.0418 (5)
H8	0.2021	0.6488	0.4396	0.050*
C9	0.3239 (4)	0.67138 (15)	0.31366 (19)	0.0471 (6)
H9	0.3368	0.7355	0.3211	0.057*
C10	0.3850 (3)	0.62925 (15)	0.23135 (18)	0.0418 (5)
H10	0.4364	0.6640	0.1823	0.050*
C11	0.3670 (3)	0.53390 (15)	0.22449 (15)	0.0339 (4)
C12	0.2907 (3)	0.47907 (13)	0.29473 (15)	0.0331 (4)
H12	0.2832	0.4147	0.2880	0.040*
O1W	0.7494 (3)	0.61566 (15)	0.42859 (15)	0.0615 (5)
H1WA	0.7637	0.5885	0.3748	0.092*
H1WB	0.6377	0.6003	0.4521	0.092*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.0581 (3)	0.0259 (2)	0.0302 (2)	−0.00098 (19)	−0.0040 (2)	0.0025 (2)
O1	0.0851 (13)	0.0319 (8)	0.0494 (11)	0.0075 (8)	0.0205 (9)	−0.0010 (7)
O2	0.0763 (12)	0.0476 (9)	0.0470 (11)	0.0082 (9)	0.0072 (9)	−0.0122 (8)
O3	0.0765 (12)	0.0711 (12)	0.0328 (9)	−0.0071 (10)	0.0107 (9)	0.0022 (9)
N1	0.0692 (15)	0.0309 (9)	0.0448 (12)	0.0072 (9)	−0.0120 (11)	−0.0024 (8)
N2	0.0644 (14)	0.0385 (11)	0.0390 (12)	−0.0024 (10)	−0.0091 (10)	−0.0079 (9)
N3	0.0424 (9)	0.0331 (8)	0.0283 (9)	−0.0021 (7)	0.0003 (7)	−0.0017 (7)
N4	0.0427 (9)	0.0278 (7)	0.0278 (8)	−0.0008 (7)	0.0018 (7)	−0.0007 (6)
N5	0.0507 (11)	0.0288 (8)	0.0287 (9)	0.0018 (7)	0.0073 (8)	−0.0020 (7)
N6	0.0394 (9)	0.0484 (10)	0.0336 (10)	−0.0015 (8)	−0.0007 (8)	−0.0030 (8)
C1	0.0408 (10)	0.0297 (8)	0.0349 (11)	0.0008 (7)	0.0066 (9)	−0.0008 (8)
C2	0.0517 (13)	0.0281 (9)	0.0360 (11)	−0.0036 (9)	0.0036 (10)	−0.0058 (8)
C3	0.0396 (10)	0.0362 (9)	0.0320 (11)	−0.0049 (9)	0.0062 (8)	−0.0038 (8)
C4	0.0378 (10)	0.0285 (9)	0.0290 (11)	−0.0033 (8)	0.0059 (8)	−0.0007 (7)
C5	0.0467 (11)	0.0319 (10)	0.0322 (11)	−0.0077 (8)	−0.0008 (9)	−0.0009 (8)
C6	0.0446 (12)	0.0303 (9)	0.0302 (11)	−0.0013 (8)	−0.0024 (9)	−0.0007 (7)
C7	0.0395 (11)	0.0295 (9)	0.0292 (10)	−0.0005 (8)	−0.0003 (8)	0.0008 (8)
C8	0.0561 (13)	0.0317 (10)	0.0376 (12)	0.0005 (9)	0.0074 (10)	−0.0035 (9)
C9	0.0664 (15)	0.0280 (9)	0.0469 (13)	−0.0015 (10)	0.0084 (12)	0.0025 (9)
C10	0.0500 (13)	0.0350 (11)	0.0404 (13)	−0.0008 (9)	0.0078 (11)	0.0076 (9)
C11	0.0360 (10)	0.0369 (10)	0.0288 (10)	0.0026 (9)	−0.0001 (8)	−0.0002 (8)
C12	0.0380 (10)	0.0301 (8)	0.0311 (10)	−0.0006 (8)	−0.0011 (8)	−0.0003 (8)
O1W	0.0706 (12)	0.0695 (12)	0.0444 (11)	−0.0050 (9)	−0.0003 (10)	−0.0118 (9)

Geometric parameters (Å, º) top

S1—C4	1.769 (2)	C1—C2	1.380 (3)
S1—C5	1.805 (2)	C2—C3	1.388 (3)
O1—C6	1.215 (3)	C2—H2	0.9300
O2—N6	1.216 (2)	C5—C6	1.512 (3)
O3—N6	1.223 (3)	C5—H5A	0.9700
N1—C1	1.347 (3)	C5—H5B	0.9700
N1—H1A	0.83 (3)	C7—C12	1.386 (3)
N1—H1B	0.84 (3)	C7—C8	1.394 (3)
N2—C3	1.346 (3)	C8—C9	1.378 (3)
N2—H2A	0.80 (3)	C8—H8	0.9300
N2—H2B	0.83 (3)	C9—C10	1.381 (3)
N3—C4	1.328 (3)	C9—H9	0.9300
N3—C3	1.358 (3)	C10—C11	1.377 (3)
N4—C4	1.319 (3)	C10—H10	0.9300
N4—C1	1.366 (2)	C11—C12	1.380 (3)
N5—C6	1.352 (3)	C12—H12	0.9300
N5—C7	1.398 (3)	O1W—H1WA	0.8582
N5—H5	0.86 (3)	O1W—H1WB	0.9004
N6—C11	1.475 (3)

C4—S1—C5	104.01 (9)	C6—C5—H5A	108.9
C1—N1—H1A	117.8 (18)	S1—C5—H5A	108.9
C1—N1—H1B	120 (2)	C6—C5—H5B	108.9
H1A—N1—H1B	120 (3)	S1—C5—H5B	108.9
C3—N2—H2A	117 (2)	H5A—C5—H5B	107.7
C3—N2—H2B	121 (2)	O1—C6—N5	124.3 (2)
H2A—N2—H2B	121 (3)	O1—C6—C5	122.68 (19)
C4—N3—C3	114.97 (18)	N5—C6—C5	113.01 (18)
C4—N4—C1	115.30 (18)	C12—C7—C8	119.6 (2)
C6—N5—C7	129.02 (18)	C12—C7—N5	123.27 (17)
C6—N5—H5	115.5 (19)	C8—C7—N5	117.05 (19)
C7—N5—H5	115.1 (19)	C9—C8—C7	120.6 (2)
O2—N6—O3	123.9 (2)	C9—C8—H8	119.7
O2—N6—C11	118.11 (18)	C7—C8—H8	119.7
O3—N6—C11	117.96 (18)	C8—C9—C10	120.6 (2)
N1—C1—N4	115.1 (2)	C8—C9—H9	119.7
N1—C1—C2	123.28 (19)	C10—C9—H9	119.7
N4—C1—C2	121.57 (19)	C11—C10—C9	117.6 (2)
C1—C2—C3	117.44 (19)	C11—C10—H10	121.2
C1—C2—H2	121.3	C9—C10—H10	121.2
C3—C2—H2	121.3	C10—C11—C12	123.6 (2)
N2—C3—N3	116.0 (2)	C10—C11—N6	118.26 (19)
N2—C3—C2	122.1 (2)	C12—C11—N6	118.14 (18)
N3—C3—C2	121.9 (2)	C11—C12—C7	117.89 (17)
N4—C4—N3	128.79 (18)	C11—C12—H12	121.1
N4—C4—S1	119.62 (15)	C7—C12—H12	121.1
N3—C4—S1	111.59 (15)	H1WA—O1W—H1WB	108.8
C6—C5—S1	113.43 (15)

C4—N4—C1—N1	178.57 (19)	S1—C5—C6—N5	−84.2 (2)
C4—N4—C1—C2	0.5 (3)	C6—N5—C7—C12	18.1 (3)
N1—C1—C2—C3	−177.6 (2)	C6—N5—C7—C8	−164.9 (2)
N4—C1—C2—C3	0.3 (3)	C12—C7—C8—C9	1.0 (4)
C4—N3—C3—N2	−178.7 (2)	N5—C7—C8—C9	−176.0 (2)
C4—N3—C3—C2	2.5 (3)	C7—C8—C9—C10	0.8 (4)
C1—C2—C3—N2	179.3 (2)	C8—C9—C10—C11	−1.5 (4)
C1—C2—C3—N3	−1.9 (3)	C9—C10—C11—C12	0.5 (3)
C1—N4—C4—N3	0.3 (3)	C9—C10—C11—N6	179.7 (2)
C1—N4—C4—S1	−179.23 (14)	O2—N6—C11—C10	164.8 (2)
C3—N3—C4—N4	−1.7 (3)	O3—N6—C11—C10	−15.6 (3)
C3—N3—C4—S1	177.82 (16)	O2—N6—C11—C12	−15.9 (3)
C5—S1—C4—N4	−0.85 (19)	O3—N6—C11—C12	163.6 (2)
C5—S1—C4—N3	179.56 (14)	C10—C11—C12—C7	1.3 (3)
C4—S1—C5—C6	81.31 (16)	N6—C11—C12—C7	−177.94 (17)
C7—N5—C6—O1	1.4 (4)	C8—C7—C12—C11	−2.0 (3)
C7—N5—C6—C5	−179.6 (2)	N5—C7—C12—C11	174.86 (19)
S1—C5—C6—O1	94.8 (2)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N5—H5···N4	0.86 (3)	2.05 (3)	2.832 (3)	151 (3)
C12—H12···O1	0.93	2.35	2.911 (3)	118
N1—H1A···O1Wⁱ	0.83 (3)	2.16 (3)	2.979 (3)	170 (2)
N1—H1B···O2ⁱⁱ	0.84 (3)	2.29 (3)	3.082 (3)	159 (3)
N2—H2A···O3ⁱⁱⁱ	0.80 (3)	2.58 (3)	3.255 (3)	143 (3)
N2—H2B···O1ⁱⁱ	0.83 (3)	2.09 (3)	2.904 (3)	170 (3)
O1W—H1WA···N3^iv	0.86	2.09	2.919 (3)	162
O1W—H1WB···O3^v	0.90	2.64	3.294 (3)	130

Symmetry codes: (i) x−1, y, z; (ii) −x+1/2, y+1/2, z+1/2; (iii) x, y, z+1; (iv) −x+1, −y+1, z−1/2; (v) −x+1, −y+1, z+1/2.

(II) N-(2-Chlorophenyl)-2-[(4,6-diaminopyrimidin-2-yl)sulfanyl]acetamide top

Crystal data top

C₁₂H₁₂ClN₅OS	Z = 2
M_r = 309.78	F(000) = 320
Triclinic, P1	D_x = 1.487 Mg m⁻³
a = 7.2528 (2) Å	Mo Kα radiation, λ = 0.71073 Å
b = 7.6249 (3) Å	Cell parameters from 2822 reflections
c = 13.0649 (4) Å	θ = 1.6–26.4°
α = 91.410 (2)°	µ = 0.43 mm⁻¹
β = 105.924 (2)°	T = 293 K
γ = 94.647 (2)°	Block, colourless
V = 691.68 (4) Å³	0.30 × 0.20 × 0.15 mm

Data collection top

Bruker SMART APEXII area-detector diffractometer	2519 reflections with I > 2σ(I)
ω and φ scans	R_int = 0.022
Absorption correction: multi-scan (SADABS; Bruker, 2008)	θ_max = 26.4°, θ_min = 1.6°
T_min = 0.785, T_max = 0.845	h = −9→8
10154 measured reflections	k = −9→9
2822 independent reflections	l = −16→16

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.035	Hydrogen site location: mixed
wR(F²) = 0.099	H atoms treated by a mixture of independent and constrained refinement
S = 1.04	w = 1/[σ²(F_o²) + (0.0515P)² + 0.2692P] where P = (F_o² + 2F_c²)/3
2822 reflections	(Δ/σ)_max < 0.001
201 parameters	Δρ_max = 0.50 e Å⁻³
0 restraints	Δρ_min = −0.50 e Å⁻³

Special details top

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
Cl1	−0.32045 (7)	0.83502 (8)	0.11080 (5)	0.06488 (18)
S1	0.22688 (6)	0.44103 (6)	0.41282 (3)	0.04714 (15)
O1	0.35760 (17)	0.81194 (17)	0.26781 (10)	0.0503 (3)
N1	−0.2505 (3)	−0.0531 (2)	0.40354 (14)	0.0541 (4)
H1A	−0.163 (3)	−0.091 (3)	0.4537 (18)	0.051 (6)*
H1B	−0.361 (3)	−0.101 (3)	0.3829 (18)	0.058 (6)*
N2	−0.4671 (2)	0.4665 (2)	0.23211 (16)	0.0576 (5)
H2A	−0.437 (3)	0.572 (3)	0.2321 (18)	0.062 (7)*
H2B	−0.584 (4)	0.428 (3)	0.2221 (19)	0.070 (7)*
N3	−0.03937 (19)	0.19020 (19)	0.40540 (10)	0.0396 (3)
N4	−0.14840 (18)	0.44884 (18)	0.31711 (10)	0.0371 (3)
N5	0.0527 (2)	0.6847 (2)	0.20471 (11)	0.0416 (3)
H5	−0.040 (3)	0.631 (3)	0.2233 (15)	0.045 (5)*
C1	−0.2221 (2)	0.1113 (2)	0.37325 (12)	0.0383 (3)
C2	−0.3723 (2)	0.1992 (2)	0.31353 (13)	0.0403 (4)
H2	−0.4970	0.1447	0.2910	0.048*
C3	−0.3310 (2)	0.3694 (2)	0.28860 (13)	0.0378 (3)
C4	−0.0176 (2)	0.3525 (2)	0.37342 (11)	0.0353 (3)
C5	0.2110 (3)	0.6742 (2)	0.39173 (13)	0.0453 (4)
H5A	0.0924	0.7068	0.4045	0.054*
H5B	0.3169	0.7396	0.4442	0.054*
C6	0.2155 (2)	0.7302 (2)	0.28193 (12)	0.0359 (3)
C7	0.0187 (2)	0.7245 (2)	0.09613 (12)	0.0375 (3)
C8	−0.1521 (2)	0.7917 (2)	0.04306 (14)	0.0428 (4)
C9	−0.1897 (3)	0.8314 (3)	−0.06301 (15)	0.0545 (5)
H9	−0.3048	0.8763	−0.0976	0.065*
C10	−0.0557 (4)	0.8039 (3)	−0.11667 (15)	0.0603 (6)
H10	−0.0795	0.8312	−0.1879	0.072*
C11	0.1148 (3)	0.7360 (3)	−0.06546 (15)	0.0556 (5)
H11	0.2048	0.7168	−0.1024	0.067*
C12	0.1516 (3)	0.6965 (2)	0.04065 (14)	0.0454 (4)
H12	0.2665	0.6508	0.0748	0.055*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cl1	0.0473 (3)	0.0730 (4)	0.0803 (4)	0.0106 (2)	0.0244 (2)	0.0255 (3)
S1	0.0309 (2)	0.0609 (3)	0.0435 (2)	−0.00578 (18)	0.00128 (17)	0.0193 (2)
O1	0.0404 (6)	0.0548 (7)	0.0492 (7)	−0.0158 (5)	0.0072 (5)	0.0071 (6)
N1	0.0440 (9)	0.0474 (9)	0.0579 (10)	−0.0079 (7)	−0.0061 (8)	0.0187 (7)
N2	0.0319 (8)	0.0501 (10)	0.0858 (13)	0.0021 (7)	0.0066 (8)	0.0271 (9)
N3	0.0339 (7)	0.0466 (8)	0.0349 (7)	−0.0005 (6)	0.0043 (5)	0.0105 (6)
N4	0.0318 (6)	0.0431 (7)	0.0360 (7)	−0.0010 (5)	0.0094 (5)	0.0082 (5)
N5	0.0339 (7)	0.0515 (8)	0.0360 (7)	−0.0097 (6)	0.0072 (6)	0.0099 (6)
C1	0.0388 (8)	0.0418 (8)	0.0307 (7)	−0.0015 (7)	0.0052 (6)	0.0049 (6)
C2	0.0314 (8)	0.0458 (9)	0.0390 (8)	−0.0034 (6)	0.0037 (6)	0.0068 (7)
C3	0.0322 (8)	0.0447 (9)	0.0364 (8)	0.0017 (6)	0.0097 (6)	0.0070 (6)
C4	0.0315 (7)	0.0469 (9)	0.0262 (7)	−0.0018 (6)	0.0073 (6)	0.0049 (6)
C5	0.0447 (9)	0.0511 (10)	0.0343 (8)	−0.0120 (7)	0.0062 (7)	−0.0025 (7)
C6	0.0355 (8)	0.0324 (7)	0.0376 (8)	−0.0031 (6)	0.0082 (6)	0.0013 (6)
C7	0.0398 (8)	0.0337 (8)	0.0350 (8)	−0.0089 (6)	0.0069 (6)	0.0043 (6)
C8	0.0405 (9)	0.0384 (8)	0.0446 (9)	−0.0071 (7)	0.0061 (7)	0.0053 (7)
C9	0.0582 (11)	0.0472 (10)	0.0447 (10)	−0.0083 (8)	−0.0049 (8)	0.0103 (8)
C10	0.0873 (15)	0.0526 (11)	0.0325 (9)	−0.0121 (10)	0.0073 (9)	0.0031 (8)
C11	0.0761 (14)	0.0496 (10)	0.0447 (10)	−0.0064 (9)	0.0269 (10)	−0.0024 (8)
C12	0.0486 (10)	0.0421 (9)	0.0456 (9)	−0.0015 (7)	0.0145 (8)	0.0029 (7)

Geometric parameters (Å, º) top

Cl1—C8	1.7397 (19)	C1—C2	1.386 (2)
S1—C4	1.7753 (15)	C2—C3	1.375 (2)
S1—C5	1.8135 (19)	C2—H2	0.9300
O1—C6	1.2207 (19)	C5—C6	1.515 (2)
N1—C1	1.340 (2)	C5—H5A	0.9700
N1—H1A	0.85 (2)	C5—H5B	0.9700
N1—H1B	0.83 (2)	C7—C12	1.382 (2)
N2—C3	1.346 (2)	C7—C8	1.388 (2)
N2—H2A	0.81 (3)	C8—C9	1.383 (3)
N2—H2B	0.85 (3)	C9—C10	1.371 (3)
N3—C4	1.327 (2)	C9—H9	0.9300
N3—C1	1.359 (2)	C10—C11	1.382 (3)
N4—C4	1.318 (2)	C10—H10	0.9300
N4—C3	1.360 (2)	C11—C12	1.384 (3)
N5—C6	1.340 (2)	C11—H11	0.9300
N5—C7	1.417 (2)	C12—H12	0.9300
N5—H5	0.85 (2)

C4—S1—C5	103.22 (8)	S1—C5—H5A	108.5
C1—N1—H1A	118.4 (15)	C6—C5—H5B	108.5
C1—N1—H1B	116.7 (16)	S1—C5—H5B	108.5
H1A—N1—H1B	123 (2)	H5A—C5—H5B	107.5
C3—N2—H2A	116.6 (17)	O1—C6—N5	124.20 (15)
C3—N2—H2B	118.0 (17)	O1—C6—C5	121.24 (15)
H2A—N2—H2B	120 (2)	N5—C6—C5	114.56 (14)
C4—N3—C1	115.11 (13)	C12—C7—C8	118.68 (15)
C4—N4—C3	114.72 (13)	C12—C7—N5	121.45 (15)
C6—N5—C7	125.63 (14)	C8—C7—N5	119.87 (15)
C6—N5—H5	116.8 (13)	C9—C8—C7	121.22 (18)
C7—N5—H5	117.5 (13)	C9—C8—Cl1	118.54 (15)
N1—C1—N3	117.08 (15)	C7—C8—Cl1	120.20 (13)
N1—C1—C2	121.83 (15)	C10—C9—C8	119.36 (19)
N3—C1—C2	121.08 (14)	C10—C9—H9	120.3
C3—C2—C1	117.94 (14)	C8—C9—H9	120.3
C3—C2—H2	121.0	C9—C10—C11	120.31 (17)
C1—C2—H2	121.0	C9—C10—H10	119.8
N2—C3—N4	115.59 (15)	C11—C10—H10	119.8
N2—C3—C2	122.48 (15)	C10—C11—C12	120.09 (19)
N4—C3—C2	121.90 (15)	C10—C11—H11	120.0
N4—C4—N3	129.18 (14)	C12—C11—H11	120.0
N4—C4—S1	118.71 (12)	C7—C12—C11	120.34 (18)
N3—C4—S1	112.10 (11)	C7—C12—H12	119.8
C6—C5—S1	115.29 (12)	C11—C12—H12	119.8
C6—C5—H5A	108.5

C4—N3—C1—N1	179.80 (16)	C7—N5—C6—C5	178.60 (16)
C4—N3—C1—C2	−1.4 (2)	S1—C5—C6—O1	−106.66 (16)
N1—C1—C2—C3	178.13 (17)	S1—C5—C6—N5	74.10 (18)
N3—C1—C2—C3	−0.6 (3)	C6—N5—C7—C12	47.4 (2)
C4—N4—C3—N2	179.24 (16)	C6—N5—C7—C8	−133.27 (18)
C4—N4—C3—C2	−2.5 (2)	C12—C7—C8—C9	−0.5 (2)
C1—C2—C3—N2	−179.19 (18)	N5—C7—C8—C9	−179.80 (15)
C1—C2—C3—N4	2.7 (3)	C12—C7—C8—Cl1	−178.14 (12)
C3—N4—C4—N3	0.3 (2)	N5—C7—C8—Cl1	2.5 (2)
C3—N4—C4—S1	178.72 (11)	C7—C8—C9—C10	0.0 (3)
C1—N3—C4—N4	1.7 (2)	Cl1—C8—C9—C10	177.71 (14)
C1—N3—C4—S1	−176.86 (11)	C8—C9—C10—C11	0.5 (3)
C5—S1—C4—N4	15.56 (15)	C9—C10—C11—C12	−0.5 (3)
C5—S1—C4—N3	−165.73 (12)	C8—C7—C12—C11	0.5 (2)
C4—S1—C5—C6	−89.86 (13)	N5—C7—C12—C11	179.79 (15)
C7—N5—C6—O1	−0.6 (3)	C10—C11—C12—C7	0.0 (3)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N5—H5···N4	0.85 (2)	2.12 (2)	2.898 (2)	152 (2)
N2—H2A···Cl1	0.81 (3)	2.81 (2)	3.493 (2)	143 (2)
N1—H1A···N3ⁱ	0.85 (2)	2.21 (2)	3.058 (2)	174 (2)
N1—H1B···O1ⁱⁱ	0.83 (2)	2.21 (2)	2.992 (2)	157 (2)
N2—H2A···O1ⁱⁱⁱ	0.81 (3)	2.56 (2)	3.095 (2)	124 (2)
C2—H2···O1ⁱⁱ	0.93	2.64	3.353 (2)	134

Symmetry codes: (i) −x, −y, −z+1; (ii) x−1, y−1, z; (iii) x−1, y, z.

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 the UGC for the award of a meritorious fellowship.

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CRYSTALLOGRAPHIC
COMMUNICATIONS

ISSN: 2056-9890

Volume 72| Part 8| August 2016| Pages 1171-1175

https://doi.org/10.1107/S2056989016011658

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

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

1. Chemical context

2. Structural commentary

3. Supra­molecular features

4. Database survey

5. Synthesis and crystallization

6. Refinement

Supporting information

Acknowledgements

References

research communications

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

3. Supramolecular features