organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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6-Benzyl­sulfanyl-9H-purine

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[Lepage, G. A., Junga, J. G. & Bowman, B. (1964). Cancer Res. 24, 835-840.]); Mitsuya & Border (1986[Mitsuya, H. & Border, S. (1986). Proc. Natl. Acad. Sci. USA, 83 1911-1915.]); Ragazzi et al. (1989[Ragazzi, E., Froldi, G., Santi-Sonein, E., Borea, P. A. & Fassina, G. (1989). Pharmacol Res. 21,707-717.]).

[Scheme 1]

Experimental

Crystal data
  • C12H10N4S

  • Mr = 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[Bruker (2007). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.930, Tmax = 0.978

  • 7941 measured reflections

  • 2941 independent reflections

  • 2102 reflections with I > 2σ(I)

  • Rint = 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

  • Δρmax = 0.17 e Å−3

  • Δρmin = −0.17 e Å−3

  • Absolute structure: Flack (1983[Flack, H. D. (1983). Acta Cryst. A39, 876-881.]), 1207 Friedel pairs

  • Flack parameter: −0.09 (8)

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA 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[Bruker (2007). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2007[Bruker (2007). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997[Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565.]) and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]); software used to prepare material for publication: WinGX (Farrugia, 1999[Farrugia, L. J. (1999). J. Appl. Cryst. 32, 837-838.]) and PLATON.

Supporting information


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.

Refinement top

The H-atoms bonded to C were refined geometrically and treated as riding atoms with Caromatic—H = 0.93Å and Cmethylene—H = 0.97Å and Uiso(H) = 1.2Ueq(C). The N–H atom was refined at calculated position with N–H=0.894 (19) Uiso(H) = 1.2Ueq (parent N-atom)

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
[Figure 1] Fig. 1. The crystal structure diagram of the title compound duly labeled with 50% probability level of drawn thermal ellipsoids.
[Figure 2] 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
C12H10N4SF(000) = 504
Mr = 242.30Dx = 1.357 Mg m3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 2230 reflections
a = 5.5717 (3) Åθ = 2.3–24.8°
b = 9.4733 (4) ŵ = 0.26 mm1
c = 22.4656 (14) ÅT = 296 K
V = 1185.79 (11) Å3Needle, red
Z = 40.29 × 0.12 × 0.09 mm
Data collection top
Bruker Kappa APEXII CCD
diffractometer
2941 independent reflections
Radiation source: fine-focus sealed tube2102 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.032
ϕ and ω scansθmax = 28.3°, θmin = 2.3°
Absorption correction: multi-scan
(SADABS; Bruker, 2007)
h = 76
Tmin = 0.930, Tmax = 0.978k = 1212
7941 measured reflectionsl = 2829
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.040H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.088 w = 1/[σ2(Fo2) + (0.0419P)2]
where P = (Fo2 + 2Fc2)/3
S = 0.98(Δ/σ)max < 0.001
2941 reflectionsΔρmax = 0.17 e Å3
157 parametersΔρmin = 0.17 e Å3
0 restraintsAbsolute structure: Flack (1983), 1207 Friedel pairs
Primary atom site location: structure-invariant direct methodsAbsolute structure parameter: 0.09 (8)
Crystal data top
C12H10N4SV = 1185.79 (11) Å3
Mr = 242.30Z = 4
Orthorhombic, P212121Mo Kα radiation
a = 5.5717 (3) ŵ = 0.26 mm1
b = 9.4733 (4) ÅT = 296 K
c = 22.4656 (14) Å0.29 × 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)
Tmin = 0.930, Tmax = 0.978Rint = 0.032
7941 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.040H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.088Δρmax = 0.17 e Å3
S = 0.98Δρmin = 0.17 e Å3
2941 reflectionsAbsolute structure: Flack (1983), 1207 Friedel pairs
157 parametersAbsolute 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
xyzUiso*/Ueq
S10.47086 (11)0.20744 (5)0.15044 (2)0.05534 (18)
N10.3943 (4)0.07206 (16)0.13660 (7)0.0553 (5)
N20.6348 (4)0.25776 (16)0.18001 (8)0.0577 (5)
N30.9619 (4)0.16476 (15)0.23955 (8)0.0519 (5)
H3N1.020 (4)0.2456 (19)0.2541 (8)0.062*
N40.8929 (3)0.06585 (15)0.22833 (7)0.0488 (4)
C10.7639 (4)0.15403 (16)0.20432 (9)0.0454 (5)
C20.7219 (4)0.01004 (17)0.19749 (8)0.0432 (5)
C30.5298 (4)0.02806 (17)0.16181 (8)0.0447 (5)
C40.4558 (4)0.2074 (2)0.14777 (10)0.0618 (6)
H40.35780.27500.13020.074*
C51.0294 (4)0.03046 (17)0.25248 (10)0.0530 (5)
H51.16080.00900.27640.064*
C60.2345 (4)0.2002 (2)0.09542 (10)0.0662 (6)
H6A0.27630.13280.06460.079*
H6B0.08620.16940.11400.079*
C70.2003 (4)0.3442 (2)0.06836 (9)0.0500 (5)
C80.3547 (5)0.3944 (2)0.02616 (10)0.0646 (6)
H80.48830.34090.01580.077*
C90.3174 (5)0.5222 (2)0.00144 (11)0.0741 (8)
H90.42280.55320.03070.089*
C100.1270 (6)0.6027 (2)0.01415 (12)0.0708 (7)
H100.10110.68890.00460.085*
C110.0261 (5)0.5576 (3)0.05709 (12)0.0780 (7)
H110.15500.61390.06840.094*
C120.0092 (5)0.4280 (3)0.08406 (10)0.0690 (6)
H120.09760.39720.11310.083*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.0640 (4)0.0405 (3)0.0616 (3)0.0021 (3)0.0128 (3)0.0078 (2)
N10.0659 (12)0.0470 (9)0.0530 (11)0.0109 (9)0.0074 (9)0.0019 (8)
N20.0708 (12)0.0373 (8)0.0650 (12)0.0098 (9)0.0048 (11)0.0040 (8)
N30.0602 (12)0.0309 (7)0.0647 (11)0.0005 (8)0.0058 (10)0.0064 (7)
N40.0571 (11)0.0330 (7)0.0562 (11)0.0034 (8)0.0085 (9)0.0020 (7)
C10.0582 (14)0.0303 (9)0.0478 (11)0.0028 (9)0.0053 (10)0.0011 (8)
C20.0525 (13)0.0308 (9)0.0464 (11)0.0040 (9)0.0029 (9)0.0022 (8)
C30.0526 (12)0.0386 (9)0.0431 (11)0.0025 (9)0.0044 (10)0.0049 (8)
C40.0758 (16)0.0467 (11)0.0627 (13)0.0193 (12)0.0046 (14)0.0087 (11)
C50.0587 (14)0.0378 (9)0.0625 (13)0.0042 (10)0.0083 (12)0.0024 (9)
C60.0704 (15)0.0566 (12)0.0715 (15)0.0128 (12)0.0217 (12)0.0201 (11)
C70.0496 (13)0.0480 (11)0.0525 (13)0.0036 (10)0.0095 (10)0.0048 (10)
C80.0681 (16)0.0550 (12)0.0705 (15)0.0111 (11)0.0186 (13)0.0048 (12)
C90.094 (2)0.0577 (13)0.0710 (17)0.0028 (15)0.0181 (15)0.0168 (12)
C100.0819 (19)0.0491 (12)0.0814 (18)0.0038 (13)0.0133 (16)0.0103 (13)
C110.0651 (17)0.0740 (15)0.0948 (19)0.0241 (15)0.0010 (17)0.0048 (14)
C120.0568 (15)0.0833 (15)0.0668 (15)0.0018 (15)0.0091 (13)0.0148 (12)
Geometric parameters (Å, º) top
S1—C31.7495 (17)C6—C71.506 (3)
S1—C61.808 (2)C6—H6A0.9700
N1—C31.338 (2)C6—H6B0.9700
N1—C41.350 (3)C7—C81.366 (3)
N2—C41.322 (3)C7—C121.374 (3)
N2—C11.334 (2)C8—C91.376 (3)
N3—C51.358 (2)C8—H80.9300
N3—C11.362 (3)C9—C101.352 (4)
N3—H3N0.894 (19)C9—H90.9300
N4—C51.306 (2)C10—C111.357 (4)
N4—C21.380 (2)C10—H100.9300
C1—C21.392 (2)C11—C121.383 (3)
C2—C31.385 (3)C11—H110.9300
C4—H40.9300C12—H120.9300
C5—H50.9300
C3—S1—C6101.51 (10)C7—C6—H6A109.8
C3—N1—C4116.80 (18)S1—C6—H6A109.8
C4—N2—C1111.39 (16)C7—C6—H6B109.8
C5—N3—C1106.18 (16)S1—C6—H6B109.8
C5—N3—H3N128.6 (13)H6A—C6—H6B108.2
C1—N3—H3N124.8 (14)C8—C7—C12117.73 (19)
C5—N4—C2104.28 (15)C8—C7—C6121.1 (2)
N2—C1—N3128.28 (17)C12—C7—C6121.2 (2)
N2—C1—C2125.9 (2)C7—C8—C9121.6 (2)
N3—C1—C2105.86 (16)C7—C8—H8119.2
N4—C2—C3133.49 (16)C9—C8—H8119.2
N4—C2—C1109.82 (18)C10—C9—C8119.9 (2)
C3—C2—C1116.67 (18)C10—C9—H9120.1
N1—C3—C2119.75 (16)C8—C9—H9120.1
N1—C3—S1121.40 (16)C9—C10—C11120.0 (2)
C2—C3—S1118.85 (14)C9—C10—H10120.0
N2—C4—N1129.52 (19)C11—C10—H10120.0
N2—C4—H4115.2C10—C11—C12120.1 (2)
N1—C4—H4115.2C10—C11—H11120.0
N4—C5—N3113.9 (2)C12—C11—H11120.0
N4—C5—H5123.1C7—C12—C11120.7 (2)
N3—C5—H5123.1C7—C12—H12119.7
C7—C6—S1109.51 (15)C11—C12—H12119.7
C4—N2—C1—N3179.25 (19)C6—S1—C3—C2173.43 (16)
C4—N2—C1—C20.2 (3)C1—N2—C4—N11.0 (3)
C5—N3—C1—N2179.4 (2)C3—N1—C4—N20.8 (3)
C5—N3—C1—C20.2 (2)C2—N4—C5—N30.4 (2)
C5—N4—C2—C3178.5 (2)C1—N3—C5—N40.4 (2)
C5—N4—C2—C10.2 (2)C3—S1—C6—C7165.98 (17)
N2—C1—C2—N4179.20 (19)S1—C6—C7—C877.9 (2)
N3—C1—C2—N40.0 (2)S1—C6—C7—C12103.9 (2)
N2—C1—C2—C30.6 (3)C12—C7—C8—C92.2 (4)
N3—C1—C2—C3178.62 (17)C6—C7—C8—C9176.1 (2)
C4—N1—C3—C20.2 (3)C7—C8—C9—C101.6 (4)
C4—N1—C3—S1179.49 (15)C8—C9—C10—C110.3 (4)
N4—C2—C3—N1179.0 (2)C9—C10—C11—C121.4 (4)
C1—C2—C3—N10.8 (3)C8—C7—C12—C111.0 (4)
N4—C2—C3—S10.7 (3)C6—C7—C12—C11177.3 (2)
C1—C2—C3—S1178.90 (15)C10—C11—C12—C70.8 (4)
C6—S1—C3—N16.23 (19)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H3N···N4i0.894 (19)1.892 (19)2.773 (2)167.9 (18)
Symmetry code: (i) x+2, y1/2, z+1/2.

Experimental details

Crystal data
Chemical formulaC12H10N4S
Mr242.30
Crystal system, space groupOrthorhombic, P212121
Temperature (K)296
a, b, c (Å)5.5717 (3), 9.4733 (4), 22.4656 (14)
V3)1185.79 (11)
Z4
Radiation typeMo Kα
µ (mm1)0.26
Crystal size (mm)0.29 × 0.12 × 0.09
Data collection
DiffractometerBruker Kappa APEXII CCD
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2007)
Tmin, Tmax0.930, 0.978
No. of measured, independent and
observed [I > 2σ(I)] reflections
7941, 2941, 2102
Rint0.032
(sin θ/λ)max1)0.666
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.040, 0.088, 0.98
No. of reflections2941
No. of parameters157
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.17, 0.17
Absolute structureFlack (1983), 1207 Friedel pairs
Absolute structure parameter0.09 (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···AD—HH···AD···AD—H···A
N3—H3N···N4i0.894 (19)1.892 (19)2.773 (2)167.9 (18)
Symmetry code: (i) x+2, y1/2, z+1/2.
 

Acknowledgements

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

References

First citationBruker (2007). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
First citationFarrugia, L. J. (1997). J. Appl. Cryst. 30, 565.  CrossRef IUCr Journals Google Scholar
First citationFarrugia, L. J. (1999). J. Appl. Cryst. 32, 837–838.  CrossRef CAS IUCr Journals Google Scholar
First citationFlack, H. D. (1983). Acta Cryst. A39, 876–881.  CrossRef CAS Web of Science IUCr Journals Google Scholar
First citationLepage, G. A., Junga, J. G. & Bowman, B. (1964). Cancer Res. 24, 835–840.  PubMed CAS Web of Science Google Scholar
First citationMitsuya, H. & Border, S. (1986). Proc. Natl. Acad. Sci. USA, 83 1911–1915.  Google Scholar
First citationRagazzi, E., Froldi, G., Santi-Sonein, E., Borea, P. A. & Fassina, G. (1989). Pharmacol Res. 21,707–717.  CrossRef CAS PubMed Web of Science Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationSpek, A. L. (2009). Acta Cryst. D65, 148–155.  Web of Science CrossRef CAS IUCr Journals Google Scholar

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ISSN: 2056-9890
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