6-Benzyl­sulfanyl-9H-purine

Fatima, I.; Munawar, M.A.; Khan, M.A.; Nadeem, S.; Amjad, R.

doi:10.1107/S1600536809045140

organic compounds

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ISSN: 2056-9890

Volume 65| Part 12| December 2009| Page o2994

doi:10.1107/S1600536809045140

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6-Benzylsulfanyl-9H-purine

Ismat Fatima,^a Munawar Ali Munawar,^a ^* Misbahul Ain Khan,^a Sohail Nadeem ^a and Rana Amjad ^a

^aInstitute of Chemistry, University of the Punjab, New Campus, Lahore, Pakistan
^*Correspondence e-mail: munawaralimunawar@yahoo.com

(Received 26 October 2009; accepted 28 October 2009; online 4 November 2009)

The phenyl ring of the title compound, C₁₂H₁₀N₄S, a purine derivative, is oriented at a dihedral angle of 76.65 (6)° with respect to the purine ring system. An intermolecular N—H⋯N hydrogen bonds stabilizes the crystal structure.

Related literature

For the biological activity of purine derivatives, see: Lepage et al. (1964 ); Mitsuya & Border (1986 ); Ragazzi et al. (1989 ).

Experimental

Crystal data

C₁₂H₁₀N₄S
M_r = 242.30
Orthorhombic, P 2₁ 2₁ 2₁
a = 5.5717 (3) Å
b = 9.4733 (4) Å
c = 22.4656 (14) Å
V = 1185.79 (11) Å³
Z = 4
Mo Kα radiation
μ = 0.26 mm⁻¹
T = 296 K
0.29 × 0.12 × 0.09 mm

Data collection

Bruker Kappa APEXII CCD diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2007 ) T_min = 0.930, T_max = 0.978
7941 measured reflections
2941 independent reflections
2102 reflections with I > 2σ(I)
R_int = 0.032

Refinement

R[F² > 2σ(F²)] = 0.040
wR(F²) = 0.088
S = 0.98
2941 reflections
157 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.17 e Å⁻³
Δρ_min = −0.17 e Å⁻³
Absolute structure: Flack (1983 ), 1207 Friedel pairs
Flack parameter: −0.09 (8)

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N3—H3N⋯N4ⁱ	0.894 (19)	1.892 (19)	2.773 (2)	167.9 (18)
Symmetry code: (i) $[-x+2, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]$ .

Data collection: APEX2 (Bruker, 2007); cell refinement: SAINT (Bruker, 2007); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997 ) and PLATON (Spek, 2009 ); software used to prepare material for publication: WinGX (Farrugia, 1999 ) and PLATON.

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536809045140/bt5117sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536809045140/bt5117Isup2.hkl

checkCIF report

Comment top

The synthesis of purine derivatives has received considerable attention on account of their biological activity especially as antitumor (Lepage et al., 1964), anti HTVL (Mitsuya & Border, 1986) and anti asthmatic (Ragazzi et al., 1989) agents. During our search to find new synthetic antithyroid agents, certain purine derivatives were prepared. 6-(benzylthio)-7H-purine was synthesized during such an effort. The compound is now under study for possible antithyroid activity.

The phenyl ring is oriented at adihedral angle of 76.65 (6) ° with respect to purine ring system. An intermolecular N–H···N hydrogen bonds stabilizes the crystal structure.

Related literature top

For the biological activity of purine derivatives, see: Lepage et al. (1964); Mitsuya & Border (1986); Ragazzi et al. (1989).

Experimental top

To a solution of 6-mercaptopurine (0.171 g) 1 mmol in 2 N NaOH (10 ml), benzyl bromide 1 mmol (0.171 g) was added and stirred at room temperature for 30 minutes. The pH of the mixture was adjusted at 5 with glacial acetic acid and the precipitates were collected, washed with water and diethyl ether. The crystals suitable for X-ray diffraction were grown in dichloromethane by slow evaporation at room temperature.

Computing details top

Data collection: APEX2 (Bruker, 2007); cell refinement: SAINT (Bruker, 2007); data reduction: SAINT (Bruker, 2007); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997) and PLATON (Spek, 2009); software used to prepare material for publication: WinGX (Farrugia, 1999) and PLATON (Spek, 2009).

Figures top

	Fig. 1. The crystal structure diagram of the title compound duly labeled with 50% probability level of drawn thermal ellipsoids.
	Fig. 2. Unit cell diagram showing the intermolecular hydrogen bonding using dashed lines. The hydrogen atoms not involved in hydrogen bonding have been omitted for clarity.

6-Benzylsulfanyl-9H-purine top

Crystal data top

C₁₂H₁₀N₄S	F(000) = 504
M_r = 242.30	D_x = 1.357 Mg m⁻³
Orthorhombic, P2₁2₁2₁	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2ab	Cell parameters from 2230 reflections
a = 5.5717 (3) Å	θ = 2.3–24.8°
b = 9.4733 (4) Å	µ = 0.26 mm⁻¹
c = 22.4656 (14) Å	T = 296 K
V = 1185.79 (11) Å³	Needle, red
Z = 4	0.29 × 0.12 × 0.09 mm

Data collection top

Bruker Kappa APEXII CCD diffractometer	2941 independent reflections
Radiation source: fine-focus sealed tube	2102 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.032
ϕ and ω scans	θ_max = 28.3°, θ_min = 2.3°
Absorption correction: multi-scan (SADABS; Bruker, 2007)	h = −7→6
T_min = 0.930, T_max = 0.978	k = −12→12
7941 measured reflections	l = −28→29

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.040	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.088	w = 1/[σ²(F_o²) + (0.0419P)²] where P = (F_o² + 2F_c²)/3
S = 0.98	(Δ/σ)_max < 0.001
2941 reflections	Δρ_max = 0.17 e Å⁻³
157 parameters	Δρ_min = −0.17 e Å⁻³
0 restraints	Absolute structure: Flack (1983), 1207 Friedel pairs
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: −0.09 (8)

Crystal data top

C₁₂H₁₀N₄S	V = 1185.79 (11) Å³
M_r = 242.30	Z = 4
Orthorhombic, P2₁2₁2₁	Mo Kα radiation
a = 5.5717 (3) Å	µ = 0.26 mm⁻¹
b = 9.4733 (4) Å	T = 296 K
c = 22.4656 (14) Å	0.29 × 0.12 × 0.09 mm

Data collection top

Bruker Kappa APEXII CCD diffractometer	2941 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2007)	2102 reflections with I > 2σ(I)
T_min = 0.930, T_max = 0.978	R_int = 0.032
7941 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.040	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.088	Δρ_max = 0.17 e Å⁻³
S = 0.98	Δρ_min = −0.17 e Å⁻³
2941 reflections	Absolute structure: Flack (1983), 1207 Friedel pairs
157 parameters	Absolute structure parameter: −0.09 (8)
0 restraints

Special details top

Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'s involving l.s. planes.

Refinement. Refinement of F² against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The threshold expression of F² > 2σ(F²) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F² are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

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

	x	y	z	U_iso*/U_eq
S1	0.47086 (11)	0.20744 (5)	0.15044 (2)	0.05534 (18)
N1	0.3943 (4)	−0.07206 (16)	0.13660 (7)	0.0553 (5)
N2	0.6348 (4)	−0.25776 (16)	0.18001 (8)	0.0577 (5)
N3	0.9619 (4)	−0.16476 (15)	0.23955 (8)	0.0519 (5)
H3N	1.020 (4)	−0.2456 (19)	0.2541 (8)	0.062*
N4	0.8929 (3)	0.06585 (15)	0.22833 (7)	0.0488 (4)
C1	0.7639 (4)	−0.15403 (16)	0.20432 (9)	0.0454 (5)
C2	0.7219 (4)	−0.01004 (17)	0.19749 (8)	0.0432 (5)
C3	0.5298 (4)	0.02806 (17)	0.16181 (8)	0.0447 (5)
C4	0.4558 (4)	−0.2074 (2)	0.14777 (10)	0.0618 (6)
H4	0.3578	−0.2750	0.1302	0.074*
C5	1.0294 (4)	−0.03046 (17)	0.25248 (10)	0.0530 (5)
H5	1.1608	−0.0090	0.2764	0.064*
C6	0.2345 (4)	0.2002 (2)	0.09542 (10)	0.0662 (6)
H6A	0.2763	0.1328	0.0646	0.079*
H6B	0.0862	0.1694	0.1140	0.079*
C7	0.2003 (4)	0.3442 (2)	0.06836 (9)	0.0500 (5)
C8	0.3547 (5)	0.3944 (2)	0.02616 (10)	0.0646 (6)
H8	0.4883	0.3409	0.0158	0.077*
C9	0.3174 (5)	0.5222 (2)	−0.00144 (11)	0.0741 (8)
H9	0.4228	0.5532	−0.0307	0.089*
C10	0.1270 (6)	0.6027 (2)	0.01415 (12)	0.0708 (7)
H10	0.1011	0.6889	−0.0046	0.085*
C11	−0.0261 (5)	0.5576 (3)	0.05709 (12)	0.0780 (7)
H11	−0.1550	0.6139	0.0684	0.094*
C12	0.0092 (5)	0.4280 (3)	0.08406 (10)	0.0690 (6)
H12	−0.0976	0.3972	0.1131	0.083*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.0640 (4)	0.0405 (3)	0.0616 (3)	−0.0021 (3)	−0.0128 (3)	0.0078 (2)
N1	0.0659 (12)	0.0470 (9)	0.0530 (11)	−0.0109 (9)	−0.0074 (9)	0.0019 (8)
N2	0.0708 (12)	0.0373 (8)	0.0650 (12)	−0.0098 (9)	−0.0048 (11)	−0.0040 (8)
N3	0.0602 (12)	0.0309 (7)	0.0647 (11)	0.0005 (8)	−0.0058 (10)	0.0064 (7)
N4	0.0571 (11)	0.0330 (7)	0.0562 (11)	−0.0034 (8)	−0.0085 (9)	0.0020 (7)
C1	0.0582 (14)	0.0303 (9)	0.0478 (11)	−0.0028 (9)	0.0053 (10)	0.0011 (8)
C2	0.0525 (13)	0.0308 (9)	0.0464 (11)	−0.0040 (9)	0.0029 (9)	0.0022 (8)
C3	0.0526 (12)	0.0386 (9)	0.0431 (11)	−0.0025 (9)	0.0044 (10)	0.0049 (8)
C4	0.0758 (16)	0.0467 (11)	0.0627 (13)	−0.0193 (12)	−0.0046 (14)	−0.0087 (11)
C5	0.0587 (14)	0.0378 (9)	0.0625 (13)	−0.0042 (10)	−0.0083 (12)	0.0024 (9)
C6	0.0704 (15)	0.0566 (12)	0.0715 (15)	−0.0128 (12)	−0.0217 (12)	0.0201 (11)
C7	0.0496 (13)	0.0480 (11)	0.0525 (13)	−0.0036 (10)	−0.0095 (10)	0.0048 (10)
C8	0.0681 (16)	0.0550 (12)	0.0705 (15)	0.0111 (11)	0.0186 (13)	0.0048 (12)
C9	0.094 (2)	0.0577 (13)	0.0710 (17)	−0.0028 (15)	0.0181 (15)	0.0168 (12)
C10	0.0819 (19)	0.0491 (12)	0.0814 (18)	0.0038 (13)	−0.0133 (16)	0.0103 (13)
C11	0.0651 (17)	0.0740 (15)	0.0948 (19)	0.0241 (15)	0.0010 (17)	−0.0048 (14)
C12	0.0568 (15)	0.0833 (15)	0.0668 (15)	−0.0018 (15)	0.0091 (13)	0.0148 (12)

Geometric parameters (Å, º) top

S1—C3	1.7495 (17)	C6—C7	1.506 (3)
S1—C6	1.808 (2)	C6—H6A	0.9700
N1—C3	1.338 (2)	C6—H6B	0.9700
N1—C4	1.350 (3)	C7—C8	1.366 (3)
N2—C4	1.322 (3)	C7—C12	1.374 (3)
N2—C1	1.334 (2)	C8—C9	1.376 (3)
N3—C5	1.358 (2)	C8—H8	0.9300
N3—C1	1.362 (3)	C9—C10	1.352 (4)
N3—H3N	0.894 (19)	C9—H9	0.9300
N4—C5	1.306 (2)	C10—C11	1.357 (4)
N4—C2	1.380 (2)	C10—H10	0.9300
C1—C2	1.392 (2)	C11—C12	1.383 (3)
C2—C3	1.385 (3)	C11—H11	0.9300
C4—H4	0.9300	C12—H12	0.9300
C5—H5	0.9300

C3—S1—C6	101.51 (10)	C7—C6—H6A	109.8
C3—N1—C4	116.80 (18)	S1—C6—H6A	109.8
C4—N2—C1	111.39 (16)	C7—C6—H6B	109.8
C5—N3—C1	106.18 (16)	S1—C6—H6B	109.8
C5—N3—H3N	128.6 (13)	H6A—C6—H6B	108.2
C1—N3—H3N	124.8 (14)	C8—C7—C12	117.73 (19)
C5—N4—C2	104.28 (15)	C8—C7—C6	121.1 (2)
N2—C1—N3	128.28 (17)	C12—C7—C6	121.2 (2)
N2—C1—C2	125.9 (2)	C7—C8—C9	121.6 (2)
N3—C1—C2	105.86 (16)	C7—C8—H8	119.2
N4—C2—C3	133.49 (16)	C9—C8—H8	119.2
N4—C2—C1	109.82 (18)	C10—C9—C8	119.9 (2)
C3—C2—C1	116.67 (18)	C10—C9—H9	120.1
N1—C3—C2	119.75 (16)	C8—C9—H9	120.1
N1—C3—S1	121.40 (16)	C9—C10—C11	120.0 (2)
C2—C3—S1	118.85 (14)	C9—C10—H10	120.0
N2—C4—N1	129.52 (19)	C11—C10—H10	120.0
N2—C4—H4	115.2	C10—C11—C12	120.1 (2)
N1—C4—H4	115.2	C10—C11—H11	120.0
N4—C5—N3	113.9 (2)	C12—C11—H11	120.0
N4—C5—H5	123.1	C7—C12—C11	120.7 (2)
N3—C5—H5	123.1	C7—C12—H12	119.7
C7—C6—S1	109.51 (15)	C11—C12—H12	119.7

C4—N2—C1—N3	−179.25 (19)	C6—S1—C3—C2	173.43 (16)
C4—N2—C1—C2	−0.2 (3)	C1—N2—C4—N1	1.0 (3)
C5—N3—C1—N2	179.4 (2)	C3—N1—C4—N2	−0.8 (3)
C5—N3—C1—C2	0.2 (2)	C2—N4—C5—N3	0.4 (2)
C5—N4—C2—C3	−178.5 (2)	C1—N3—C5—N4	−0.4 (2)
C5—N4—C2—C1	−0.2 (2)	C3—S1—C6—C7	−165.98 (17)
N2—C1—C2—N4	−179.20 (19)	S1—C6—C7—C8	77.9 (2)
N3—C1—C2—N4	0.0 (2)	S1—C6—C7—C12	−103.9 (2)
N2—C1—C2—C3	−0.6 (3)	C12—C7—C8—C9	−2.2 (4)
N3—C1—C2—C3	178.62 (17)	C6—C7—C8—C9	176.1 (2)
C4—N1—C3—C2	−0.2 (3)	C7—C8—C9—C10	1.6 (4)
C4—N1—C3—S1	179.49 (15)	C8—C9—C10—C11	0.3 (4)
N4—C2—C3—N1	179.0 (2)	C9—C10—C11—C12	−1.4 (4)
C1—C2—C3—N1	0.8 (3)	C8—C7—C12—C11	1.0 (4)
N4—C2—C3—S1	−0.7 (3)	C6—C7—C12—C11	−177.3 (2)
C1—C2—C3—S1	−178.90 (15)	C10—C11—C12—C7	0.8 (4)
C6—S1—C3—N1	−6.23 (19)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3N···N4ⁱ	0.894 (19)	1.892 (19)	2.773 (2)	167.9 (18)

Symmetry code: (i) −x+2, y−1/2, −z+1/2.

Experimental details

Crystal data
Chemical formula	C₁₂H₁₀N₄S
M_r	242.30
Crystal system, space group	Orthorhombic, P2₁2₁2₁
Temperature (K)	296
a, b, c (Å)	5.5717 (3), 9.4733 (4), 22.4656 (14)
V (Å³)	1185.79 (11)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.26
Crystal size (mm)	0.29 × 0.12 × 0.09

Data collection
Diffractometer	Bruker Kappa APEXII CCD diffractometer
Absorption correction	Multi-scan (SADABS; Bruker, 2007)
T_min, T_max	0.930, 0.978
No. of measured, independent and observed [I > 2σ(I)] reflections	7941, 2941, 2102
R_int	0.032
(sin θ/λ)_max (Å⁻¹)	0.666

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.040, 0.088, 0.98
No. of reflections	2941
No. of parameters	157
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.17, −0.17
Absolute structure	Flack (1983), 1207 Friedel pairs
Absolute structure parameter	−0.09 (8)

Computer programs: APEX2 (Bruker, 2007), SAINT (Bruker, 2007), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 for Windows (Farrugia, 1997) and PLATON (Spek, 2009), WinGX (Farrugia, 1999) and PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3N···N4ⁱ	0.894 (19)	1.892 (19)	2.773 (2)	167.9 (18)

Symmetry code: (i) −x+2, y−1/2, −z+1/2.

Acknowledgements

IF acknowledges the Higher Education Commission, Pakistan for providing funding for this research.

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