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

Choudhury, M.; Viswanathan, V.; Timiri, A.K.; Sinha, B.N.; Jayaprakash, V.; Velmurugan, D.

doi:10.1107/S2414314618006004

organic compounds

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ISSN: 2414-3146

Volume 3| Part 4| April 2018| x180600

https://doi.org/10.1107/S2414314618006004

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

Manisha Choudhury,^a Vijayan Viswanathan,^a Ajay Kumar Timiri,^b Barij Nayan Sinha,^b Venkatesan Jayaprakash ^b 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 Science and Technology, Birla Institute of Technology, Mesta, Ranchi 835215, Jharkhand, India
^*Correspondence e-mail: shirai2011@gmail.com

Edited by H. Ishida, Okayama University, Japan (Received 5 March 2018; accepted 18 April 2018; online 24 April 2018)

In the title compound, C₁₃H₁₅N₅O₂S, the acetamide N—C(=O)—C plane makes dihedral angles of 30.51 (11) and 51.93 (11)°, respectively, with the benzene ring and the pyrimidine ring. The dihedral angle between the benzene and pyrimidine rings is 43.40 (6)°. There is an intramolecular N—H⋯N hydrogen bond with an S(7) ring motif. In the crystal, molecules are linked by pairs of intermolecular N—H⋯N hydrogen bonds, forming inversion dimers with an R₂²(8) ring motif. The molecules are further linked by intermolecular N—H⋯O hydrogen bonds, forming a C(9) chain along [100]. Intermolecular C—H⋯π and N—H⋯π interactions are also observed.

Keywords: crystal structure; 2; 4-diaminopyrimidine derivative.

CCDC reference: 1838329

Structure description

2,4-Diaminopyrimidine derivatives are reported to be potent antimalarial and anti-filarial agents because of their inhibition of dihydrofolate reductase (DHFR) (Neekhara et al., 2006 ; Sharma et al., 2013 ). Furthermore, they have also exhibited anti-retroviral activity (Hocková et al., 2004 ), antibacterial (Kandeel et al., 1994 ) and potential anti-microbial properties (Holla et al., 2006 ). As part of our own studies in this area, we report herein the synthesis and crystal structure of the title compound.

The title molecule has an intramolecular N—H⋯N hydrogen bond with an S(7) ring motif (Table 1 and Fig. 1). The methyl group (C1) is oriented syn-periplanar to atom C7 [C7—C2—O2—C1 = 5.7 (3)°] and anti-periplanar to atom C3 [C3—C2—O2—C1 = −174.8 (2)°]. The pyrimidine ring makes a dihedral angle of 43.40 (6)° with the benzene ring. The acetamide N5/C8/O1/C9 plane makes dihedral angles of 30.51 (11) and 51.93 (11)°, respectively, with the benzene and pyrimidine rings. The bond lengths C10—S1 [1.7664 (17) Å] and C9—S1 [1.808 (2) Å] are comparable with the values reported in the literature (1.751 and 1.813 Å, respectively; Allen et al., 1987 ).

Table 1
Hydrogen-bond geometry (Å, °)

Cg1 and Cg2 are the centroids of the N3/C10/N4/C11–C13 and C2–C7 rings, respectively.

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1D⋯N4ⁱ	0.91 (2)	2.17 (2)	3.048 (2)	164.2 (2)
N2—H2B⋯O1ⁱⁱ	0.87 (2)	2.08 (2)	2.922 (2)	163.1 (2)
N5—H5⋯N3	0.84 (2)	2.06 (2)	2.863 (2)	160.3 (2)
N2—H2A⋯Cg1ⁱⁱⁱ	0.91 (2)	2.62 (1)	3.533 (2)	156.7 (2)
C4—H4⋯Cg2^iv	0.93	2.76	3.623 (2)	134
Symmetry codes: (i) -x, -y+1, -z; (ii) $[x-{\script{1\over 2}}, y, -z+{\script{1\over 2}}]$ ; (iii) $[-x, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (iv) $[-x+{\script{1\over 2}}, y-{\script{1\over 2}}, z]$ .

Figure 1
The molecular structure of the title compound, showing the atom labelling and displacement ellipsoids drawn at the 50% probability level. The N—H⋯N hydrogen bond is shown as thin dashed line.

In the crystal, the molecules are linked into inversion dimers with an R₂²(8) ring motif by pairs of N—H⋯N hydrogen bonds (Table 1, Fig. 2). Adjacent molecules are further linked via N—H⋯O hydrogen bonds, forming a C(9) chain along [100]. The crystal packing also features C—H⋯π and N—H⋯π interactions (Table 1 and Fig. 3).

Figure 2
A packing diagram of the title compound, showing the N—H⋯N and N—H⋯O hydrogen bonds (dashed lines). Hydrogen atoms not involved in the hydrogen bonds have been omitted for clarity. [Symmetry codes: (i) −x, −y + 1, −z; (ii) x − $[{1\over 2}]$ , y, −z + $[{1\over 2}]$ .]

Figure 3
A packing diagram of the title compound, showing the C—H⋯π and N—H⋯π interactions (dashed lines). Hydrogen atoms not involved in these interactions have been omitted for clarity. [Symmetry codes: (iii) −x, y − $[{1\over 2}]$ , −z + $[{1\over 2}]$ ; (vi) −x + $[{1\over 2}]$ , y − $[{1\over 2}]$ , z.]

Synthesis and crystallization

To a solution of 4,6-diamino-pyrimidine-2-thiol (0.5 g, 3.52 mmol) in 25 ml of ethanol was added (0.2g, 3.52 mmol) potassium hydroxide and the mixture was refluxed for about 30 min. An equimolar quantity of 2-chloro-N-(4-methoxyphenyl)acetamide (3.52 mmol) was then added and reflux was continued for 4 h. Evaporation of the organic layer in a vacuum provided the title compound. After purification, single crystals were obtained from an ethanol solution by slow evaporation of the solvent.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2.

Table 2
Experimental details

Crystal data
Chemical formula	C₁₃H₁₅N₅O₂S
M_r	305.36
Crystal system, space group	Orthorhombic, Pbca
Temperature (K)	293
a, b, c (Å)	18.2763 (6), 7.5909 (2), 20.0571 (6)
V (Å³)	2782.59 (14)
Z	8
Radiation type	Mo Kα
μ (mm⁻¹)	0.25
Crystal size (mm)	0.30 × 0.25 × 0.20

Data collection
Diffractometer	Bruker SMART APEXII area-detector diffractometer
Absorption correction	Multi-scan (SADABS; Bruker, 2008 )
T_min, T_max	0.753, 0.823
No. of measured, independent and observed [I > 2σ(I)] reflections	14130, 3471, 2119
R_int	0.043
(sin θ/λ)_max (Å⁻¹)	0.668

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.042, 0.110, 1.02
No. of reflections	3471
No. of parameters	211
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.25, −0.27
Computer programs: APEX2 and SAINT (Bruker, 2008), SHELXS97 (Sheldrick, 2008 ), SHELXL2016 (Sheldrick, 2015 ), ORTEP-3 for Windows (Farrugia, 2012 ) and PLATON (Spek, 2015 ).

Structural data

CCDC reference: 1838329

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S2414314618006004/is4027sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314618006004/is4027Isup3.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2414314618006004/is4027Isup3.cml

checkCIF report

Computing details top

Data collection: APEX2 (Bruker, 2008); cell refinement: APEX2 (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: SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2015).

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

Crystal data top

C₁₃H₁₅N₅O₂S	D_x = 1.458 Mg m⁻³
M_r = 305.36	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, Pbca	Cell parameters from 3471 reflections
a = 18.2763 (6) Å	θ = 2.0–28.3°
b = 7.5909 (2) Å	µ = 0.25 mm⁻¹
c = 20.0571 (6) Å	T = 293 K
V = 2782.59 (14) Å³	Block, yellow
Z = 8	0.30 × 0.25 × 0.20 mm
F(000) = 1280

Data collection top

Bruker SMART APEXII area-detector diffractometer	2119 reflections with I > 2σ(I)
ω and φ scans	R_int = 0.043
Absorption correction: multi-scan (SADABS; Bruker, 2008)	θ_max = 28.3°, θ_min = 2.0°
T_min = 0.753, T_max = 0.823	h = −24→15
14130 measured reflections	k = −10→8
3471 independent reflections	l = −13→26

Refinement top

Refinement on F²	0 restraints
Least-squares matrix: full	Hydrogen site location: mixed
R[F² > 2σ(F²)] = 0.042	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.110	w = 1/[σ²(F_o²) + (0.0494P)² + 0.2859P] where P = (F_o² + 2F_c²)/3
S = 1.02	(Δ/σ)_max < 0.001
3471 reflections	Δρ_max = 0.25 e Å⁻³
211 parameters	Δρ_min = −0.27 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.

Refinement. The C-bound H atoms were placed in calculated positions with C—H = 0.93–0.97 Å and refined as riding with U_iso(H) = 1.5U_eq(C) for methyl group or U_iso(H) = 1.2U_eq(C) for other groups. The N-bound H atoms were located in a difference Fourier map and refined freely.

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

	x	y	z	U_iso*/U_eq
H1D	−0.0645 (12)	0.581 (3)	0.0150 (12)	0.064 (7)*
H1E	−0.1267 (12)	0.591 (3)	0.0632 (11)	0.052 (7)*
H2A	−0.0275 (12)	0.190 (3)	0.2877 (11)	0.048 (7)*
H2B	−0.1027 (12)	0.269 (3)	0.2704 (10)	0.045 (6)*
H5	0.1243 (11)	0.295 (3)	0.2612 (9)	0.042 (6)*
C1	0.11212 (15)	0.6519 (4)	0.56365 (12)	0.0726 (8)
H1A	0.1009	0.7542	0.5375	0.109*
H1B	0.1226	0.6868	0.6086	0.109*
H1C	0.0710	0.5731	0.5634	0.109*
C2	0.16810 (11)	0.5039 (3)	0.47250 (9)	0.0387 (5)
C3	0.22722 (11)	0.4076 (3)	0.44951 (9)	0.0399 (5)
H3	0.2665	0.3864	0.4778	0.048*
C4	0.22885 (10)	0.3426 (3)	0.38539 (9)	0.0375 (5)
H4	0.2690	0.2781	0.3707	0.045*
C5	0.17026 (10)	0.3739 (3)	0.34272 (9)	0.0337 (5)
C6	0.11077 (10)	0.4671 (3)	0.36636 (10)	0.0404 (5)
H6	0.0710	0.4867	0.3383	0.049*
C7	0.10898 (11)	0.5321 (3)	0.43086 (10)	0.0425 (5)
H7	0.0684	0.5942	0.4460	0.051*
C8	0.22034 (10)	0.2696 (3)	0.23446 (9)	0.0363 (5)
C9	0.19429 (11)	0.1899 (3)	0.16929 (9)	0.0406 (5)
H9A	0.1574	0.1017	0.1791	0.049*
H9B	0.2352	0.1303	0.1482	0.049*
C10	0.06326 (9)	0.3615 (3)	0.13367 (9)	0.0299 (4)
C11	−0.04605 (9)	0.4777 (3)	0.10243 (9)	0.0325 (4)
C12	−0.07491 (10)	0.4288 (3)	0.16389 (9)	0.0349 (5)
H12	−0.1223	0.4598	0.1760	0.042*
C13	−0.03109 (10)	0.3332 (3)	0.20616 (9)	0.0325 (5)
N1	−0.08541 (11)	0.5584 (3)	0.05502 (9)	0.0468 (5)
N2	−0.05566 (11)	0.2679 (3)	0.26481 (8)	0.0457 (5)
N3	0.04068 (8)	0.3016 (2)	0.19228 (7)	0.0335 (4)
N4	0.02461 (8)	0.4414 (2)	0.08647 (7)	0.0339 (4)
N5	0.16624 (9)	0.3033 (2)	0.27763 (8)	0.0366 (4)
O1	0.28525 (7)	0.2957 (2)	0.24536 (7)	0.0565 (5)
O2	0.17327 (8)	0.5664 (2)	0.53655 (7)	0.0524 (4)
S1	0.15638 (2)	0.34642 (8)	0.11078 (2)	0.03976 (17)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.091 (2)	0.083 (2)	0.0438 (14)	0.0218 (17)	0.0071 (13)	−0.0136 (14)
C2	0.0467 (11)	0.0393 (13)	0.0301 (10)	−0.0042 (10)	0.0000 (9)	0.0051 (9)
C3	0.0375 (11)	0.0489 (14)	0.0331 (10)	−0.0014 (10)	−0.0062 (8)	0.0058 (10)
C4	0.0302 (9)	0.0455 (13)	0.0368 (10)	0.0031 (9)	0.0001 (8)	0.0029 (10)
C5	0.0320 (10)	0.0369 (12)	0.0322 (10)	−0.0021 (9)	−0.0023 (8)	0.0037 (9)
C6	0.0361 (10)	0.0487 (14)	0.0365 (10)	0.0056 (10)	−0.0048 (8)	0.0044 (10)
C7	0.0446 (11)	0.0403 (13)	0.0425 (11)	0.0078 (10)	0.0043 (9)	0.0003 (10)
C8	0.0305 (10)	0.0429 (13)	0.0356 (10)	0.0038 (10)	−0.0027 (8)	0.0036 (9)
C9	0.0361 (10)	0.0468 (14)	0.0390 (11)	0.0108 (10)	−0.0029 (9)	−0.0053 (10)
C10	0.0272 (9)	0.0354 (12)	0.0270 (9)	−0.0013 (8)	−0.0012 (7)	−0.0045 (8)
C11	0.0310 (9)	0.0356 (12)	0.0309 (9)	0.0021 (8)	−0.0030 (8)	−0.0060 (9)
C12	0.0268 (9)	0.0479 (14)	0.0300 (10)	0.0044 (9)	0.0009 (7)	−0.0046 (9)
C13	0.0305 (9)	0.0394 (13)	0.0278 (9)	−0.0027 (9)	0.0014 (7)	−0.0060 (9)
N1	0.0378 (10)	0.0685 (15)	0.0341 (10)	0.0194 (10)	0.0001 (8)	0.0072 (10)
N2	0.0324 (10)	0.0698 (15)	0.0349 (10)	−0.0007 (10)	0.0029 (8)	0.0128 (10)
N3	0.0267 (8)	0.0445 (11)	0.0292 (8)	−0.0003 (8)	−0.0001 (6)	0.0015 (7)
N4	0.0293 (8)	0.0437 (11)	0.0286 (8)	0.0028 (8)	0.0006 (6)	0.0013 (8)
N5	0.0261 (8)	0.0518 (12)	0.0319 (8)	−0.0013 (8)	−0.0032 (7)	−0.0015 (8)
O1	0.0273 (7)	0.0955 (13)	0.0466 (8)	−0.0007 (8)	−0.0033 (6)	−0.0068 (9)
O2	0.0659 (10)	0.0570 (11)	0.0343 (7)	0.0039 (9)	−0.0024 (7)	−0.0048 (7)
S1	0.0274 (2)	0.0607 (4)	0.0311 (3)	0.0034 (2)	0.00268 (19)	0.0036 (2)

Geometric parameters (Å, º) top

C1—O2	1.402 (3)	C9—S1	1.808 (2)
C1—H1A	0.9600	C9—H9A	0.9700
C1—H1B	0.9600	C9—H9B	0.9700
C1—H1C	0.9600	C10—N3	1.326 (2)
C2—O2	1.373 (2)	C10—N4	1.328 (2)
C2—C7	1.382 (3)	C10—S1	1.7664 (17)
C2—C3	1.384 (3)	C11—N1	1.341 (2)
C3—C4	1.378 (3)	C11—N4	1.359 (2)
C3—H3	0.9300	C11—C12	1.391 (2)
C4—C5	1.391 (2)	C12—C13	1.373 (3)
C4—H4	0.9300	C12—H12	0.9300
C5—C6	1.381 (3)	C13—N2	1.353 (2)
C5—N5	1.413 (2)	C13—N3	1.362 (2)
C6—C7	1.385 (3)	N1—H1D	0.91 (2)
C6—H6	0.9300	N1—H1E	0.81 (2)
C7—H7	0.9300	N2—H2A	0.91 (2)
C8—O1	1.222 (2)	N2—H2B	0.87 (2)
C8—N5	1.339 (2)	N5—H5	0.84 (2)
C8—C9	1.517 (3)

O2—C1—H1A	109.5	S1—C9—H9A	108.6
O2—C1—H1B	109.5	C8—C9—H9B	108.6
H1A—C1—H1B	109.5	S1—C9—H9B	108.6
O2—C1—H1C	109.5	H9A—C9—H9B	107.6
H1A—C1—H1C	109.5	N3—C10—N4	128.54 (16)
H1B—C1—H1C	109.5	N3—C10—S1	120.52 (13)
O2—C2—C7	124.45 (19)	N4—C10—S1	110.91 (13)
O2—C2—C3	116.15 (17)	N1—C11—N4	115.81 (17)
C7—C2—C3	119.40 (18)	N1—C11—C12	123.17 (17)
C4—C3—C2	121.13 (18)	N4—C11—C12	121.00 (16)
C4—C3—H3	119.4	C13—C12—C11	117.83 (17)
C2—C3—H3	119.4	C13—C12—H12	121.1
C3—C4—C5	119.78 (18)	C11—C12—H12	121.1
C3—C4—H4	120.1	N2—C13—N3	115.64 (17)
C5—C4—H4	120.1	N2—C13—C12	122.45 (17)
C6—C5—C4	118.82 (18)	N3—C13—C12	121.89 (16)
C6—C5—N5	118.06 (16)	C11—N1—H1D	119.2 (15)
C4—C5—N5	122.95 (18)	C11—N1—H1E	119.7 (16)
C5—C6—C7	121.46 (18)	H1D—N1—H1E	121 (2)
C5—C6—H6	119.3	C13—N2—H2A	119.3 (14)
C7—C6—H6	119.3	C13—N2—H2B	116.0 (14)
C2—C7—C6	119.38 (19)	H2A—N2—H2B	120 (2)
C2—C7—H7	120.3	C10—N3—C13	114.85 (15)
C6—C7—H7	120.3	C10—N4—C11	115.47 (15)
O1—C8—N5	124.76 (19)	C8—N5—C5	129.15 (17)
O1—C8—C9	121.55 (17)	C8—N5—H5	114.1 (13)
N5—C8—C9	113.67 (16)	C5—N5—H5	116.1 (14)
C8—C9—S1	114.65 (15)	C2—O2—C1	117.90 (17)
C8—C9—H9A	108.6	C10—S1—C9	104.07 (9)

O2—C2—C3—C4	−178.18 (19)	S1—C10—N3—C13	175.11 (14)
C7—C2—C3—C4	1.4 (3)	N2—C13—N3—C10	177.94 (18)
C2—C3—C4—C5	0.0 (3)	C12—C13—N3—C10	−3.5 (3)
C3—C4—C5—C6	−1.3 (3)	N3—C10—N4—C11	5.3 (3)
C3—C4—C5—N5	−176.38 (19)	S1—C10—N4—C11	−172.79 (14)
C4—C5—C6—C7	1.1 (3)	N1—C11—N4—C10	179.97 (18)
N5—C5—C6—C7	176.5 (2)	C12—C11—N4—C10	−1.5 (3)
O2—C2—C7—C6	178.01 (19)	O1—C8—N5—C5	0.2 (4)
C3—C2—C7—C6	−1.5 (3)	C9—C8—N5—C5	178.83 (19)
C5—C6—C7—C2	0.3 (3)	C6—C5—N5—C8	152.0 (2)
O1—C8—C9—S1	−102.2 (2)	C4—C5—N5—C8	−32.9 (3)
N5—C8—C9—S1	79.2 (2)	C7—C2—O2—C1	5.7 (3)
N1—C11—C12—C13	174.4 (2)	C3—C2—O2—C1	−174.8 (2)
N4—C11—C12—C13	−4.0 (3)	N3—C10—S1—C9	15.55 (19)
C11—C12—C13—N2	−174.90 (19)	N4—C10—S1—C9	−166.19 (14)
C11—C12—C13—N3	6.7 (3)	C8—C9—S1—C10	−86.82 (15)
N4—C10—N3—C13	−2.8 (3)

Hydrogen-bond geometry (Å, º) top

Cg1 and Cg2 are the centroids of the N3/C10/N4/C11–C13 and C2–C7 rings, respectively.

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1D···N4ⁱ	0.91 (2)	2.17 (2)	3.048 (2)	164.2 (2)
N2—H2B···O1ⁱⁱ	0.87 (2)	2.08 (2)	2.922 (2)	163.1 (2)
N5—H5···N3	0.84 (2)	2.06 (2)	2.863 (2)	160.3 (2)
N2—H2A···Cg1ⁱⁱⁱ	0.91 (2)	2.62 (1)	3.533 (2)	156.7 (2)
C4—H4···Cg2^iv	0.93	2.76	3.623 (2)	134

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

Acknowledgements

The authors the thank TBI X-ray facility, CAS in Crystallography and Biophysics, University of Madras, India, for data collection.

Funding information

MC thanks the CSIR, Government of India, for an SRF fellowship.

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