Acta Cryst. (2009). E65, o2994 [ doi:10.1107/S1600536809045140 ]
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.
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.
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)
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).
![[Figure 1]](./bt5117fig1thm.gif)
| Fig. 1. The crystal structure diagram of the title compound duly labeled with 50% probability level of drawn thermal ellipsoids. |
![[Figure 2]](./bt5117fig2thm.gif)
| 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. |
| C12H10N4S | F(000) = 504 |
| Mr = 242.30 | Dx = 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 |
| Bruker Kappa APEXII CCD diffractometer | 2941 independent reflections |
| Radiation source: fine-focus sealed tube | 2102 reflections with I > 2σ(I) |
| graphite | Rint = 0.032 |
| φ and ω scans | θmax = 28.3°, θmin = 2.3° |
| Absorption correction: multi-scan (SADABS; Bruker, 2007) | h = −7→6 |
| Tmin = 0.930, Tmax = 0.978 | k = −12→12 |
| 7941 measured reflections | l = −28→29 |
| 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(Fo2) + (0.0419P)2] where P = (Fo2 + 2Fc2)/3 |
| S = 0.98 | (Δ/σ)max < 0.001 |
| 2941 reflections | Δρmax = 0.17 e Å−3 |
| 157 parameters | Δρmin = −0.16 e Å−3 |
| 0 restraints | Absolute structure: Flack (1983), 1207 Friedel pairs |
| Primary atom site location: structure-invariant direct methods | Flack parameter: −0.09 (8) |
| C12H10N4S | V = 1185.79 (11) Å3 |
| Mr = 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 |
| 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 = 0.978 | Rint = 0.032 |
| 7941 measured reflections | θmax = 28.3° |
| R[F2 > 2σ(F2)] = 0.040 | H atoms treated by a mixture of independent and constrained refinement |
| wR(F2) = 0.088 | Δρmax = 0.17 e Å−3 |
| S = 0.98 | Δρmin = −0.16 e Å−3 |
| 2941 reflections | Absolute structure: Flack (1983), 1207 Friedel pairs |
| 157 parameters | Flack parameter: −0.09 (8) |
| 0 restraints |
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. |
| x | y | z | Uiso*/Ueq | ||
| 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* |
| 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) |
| 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) |
| 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 codes: (i) −x+2, y−1/2, −z+1/2. |
| 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 codes: (i) −x+2, y−1/2, −z+1/2. |
IF acknowledges the Higher Education Commission, Pakistan for providing funding for this research.
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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.