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

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890

9-Benzyl-6-benzyl­sulfanyl-9H-purin-2-amine

aPharmaceutical Design and Simulation (PhDs) Laboratory, School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia, bMalaysian Institute of Pharmaceuticals and Nutraceuticals, Ministry of Science Technology and Inovation, 11700 Halaman Bukit Gambir, Pulau Pinang, Malaysia, and cX-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia
*Correspondence e-mail: arazaki@usm.my

(Received 19 December 2013; accepted 28 January 2014; online 12 February 2014)

In the title compound, C19H17N5S, the dihedral angles between the purine ring system (r.m.s. deviation = 0.009 Å) and the S-bound and methyl­ene-bound phenyl rings are 74.67 (8) and 71.28 (7)°, respectively. In the crystal, inversion dimers linked by pairs of N—H⋯N hydrogen bonds generate R22(8) loops. C—H⋯N inter­actions link the dimers into (100) sheets.

Related literature

For background to the biological activity of thio­purine derivatives, see: Hadda et al. (2009[Hadda, V., Pandey, B. D., Gupta, R. & Goel, A. (2009). JPGM, 55, 139-140.]); Nguyen et al. (2009[Nguyen, T., Vacek, P. M., O'Neill, P., Colletti, R. B. & Finette, B. A. (2009). Cancer Res. 69, 7004-7012.]). For further synthetic details, see: Banh et al. (2011[Banh, T. N., Kode, N. R. & Phadtare, S. (2011). Lett. Drug. Des. Discov. 8, 709-716.]); Salvatore et al. (2002[Salvatore, R. N., Nagle, A. S. & Jung, K. W. (2002). J. Org. Chem. 67, 674-683.], 2005[Salvatore, R. N., Smith, R. A., Nischwitz, A. K. & Gavin, T. (2005). Tetrahedron Lett. 46, 8931-8935.]).

[Scheme 1]

Experimental

Crystal data
  • C19H17N5S

  • Mr = 347.44

  • Monoclinic, P 21 /c

  • a = 16.7346 (7) Å

  • b = 5.5511 (3) Å

  • c = 20.4817 (10) Å

  • β = 121.325 (3)°

  • V = 1625.31 (14) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.21 mm−1

  • T = 100 K

  • 0.69 × 0.19 × 0.14 mm

Data collection
  • Bruker SMART APEXII CCD diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2009)[Bruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.] Tmin = 0.868, Tmax = 0.972

  • 16728 measured reflections

  • 4956 independent reflections

  • 3416 reflections with I > 2σ(I)

  • Rint = 0.048

Refinement
  • R[F2 > 2σ(F2)] = 0.050

  • wR(F2) = 0.137

  • S = 1.06

  • 4956 reflections

  • 234 parameters

  • H atoms treated by a mixture of independent and constrained refinement

  • Δρmax = 0.33 e Å−3

  • Δρmin = −0.58 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N5—H1N5⋯N3i 0.91 (3) 2.14 (3) 3.040 (3) 173 (2)
C7—H7B⋯N3ii 0.99 2.57 3.548 (2) 172
C8—H8A⋯N2iii 0.95 2.39 3.274 (2) 155
Symmetry codes: (i) -x+1, -y+1, -z; (ii) -x+1, -y+2, -z; (iii) [-x+1, y+{\script{1\over 2}}, -z+{\script{1\over 2}}].

Data collection: APEX2 (Bruker, 2009)[Bruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]; cell refinement: SAINT (Bruker, 2009)[Bruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]; data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information


Introduction top

Thio­purine and its analogues possess a broad pharmacological activity for example as a cytotoxic agent (Nguyen et al., 2009) and in the treatment of lupus nephritis (Hadda et al., 2009). As part of our studies in this area, we report the synthesis and structure of the title compound.

Experimental top

The method to synthesize the title compound was modified from a few papers (Banh et al., 2011; Salvatore et al., 2002; Salvatore et al., 2005). 2-amino-9H-purine-6-thiol (0.598 mmol) was mixed with cesium carbonate (0.598 mmol) in 3.5 ml of di­methyl­formamide and then stirred vigorously for 15 minutes. Another mixture containing benzyl bromide (1.315 mmol), tetra­butyl­ammonium iodide (0.598 mmol) in 3.5 ml of DMF was added to the first mixture and the stirring was continued at room temperature for six hours. The reaction progress was monitored by TLC using n-hexane:ethyl acetate (0.5:3.5) as a solvent. After the product being formed, the reaction mixture was diluted with 70 mL of water and then extracted using 3 × 70 ml of ethyl acetate. The organic phase was collected, washed with 3× 70 ml of water and then dried over anhydrous magnesium sulfate. This organic phase was then evaporated in vacuo and the crude product was re-crystallized from a hot methanol to afford the title compound as colourless blocks.

Refinement top

N bound H atoms were located from difference Fourier maps and freely refined. The remaining H atoms were positioned geometrically and refined using a riding model with with C–H = 0.95–0.99 Å and Uiso(H) = 1.2Ueq(C).

Results and discussion top

The purin ring is almost planar with the maximum deviation of 0.014 (2)Å at atom C11. It makes a dihedral angle of 71.28 and 74.67 (8)° with the two benzene rings, C1—C6 and C14—C19, respectively and these two benzene rings make a dihedral angle of 76.04)10)° with each other (Fig. 1).

In the crytsal structure, two dimers involving N5—H1N5···N3i and C7—H7B···N3ii are observed. These two dimers formed stacked molecules down the b-axis. Inter­molecular inter­actions of C8—H8A···N2iii further expand the molecules into infinite layers parallel to the bc-plane (Fig. 2).

Related literature top

For background to the biological activity of thiopurine derivatives, see: Hadda et al. (2009); Nguyen et al. (2009). For further synthetic details, see: Banh et al. (2011); Salvatore et al. (2002, 2005).

Computing details top

Data collection: APEX2 (Bruker, 2009); cell refinement: SAINT (Bruker, 2009); data reduction: SAINT (Bruker, 2009); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).

Figures top
[Figure 1] Fig. 1. The asymmetric unit of the title compound, showing 50% probability displacement ellipsoids.
[Figure 2] Fig. 2. The crystal packing of (I). Dashed lines indicate hydrogen bonds. H atoms not involved in the hydrogen bond interactions have been omitted for clarity.
9-Benzyl-6-benzylsulfanyl-9H-purin-2-amine top
Crystal data top
C19H17N5SF(000) = 728
Mr = 347.44Dx = 1.420 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 3425 reflections
a = 16.7346 (7) Åθ = 2.3–30.0°
b = 5.5511 (3) ŵ = 0.21 mm1
c = 20.4817 (10) ÅT = 100 K
β = 121.325 (3)°Block, colourless
V = 1625.31 (14) Å30.69 × 0.19 × 0.14 mm
Z = 4
Data collection top
Bruker SMART APEXII CCD
diffractometer
4956 independent reflections
Radiation source: fine-focus sealed tube3416 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.048
φ and ω scansθmax = 30.6°, θmin = 2.0°
Absorption correction: multi-scan
(SADABS; Bruker, 2009)
h = 2323
Tmin = 0.868, Tmax = 0.972k = 77
16728 measured reflectionsl = 2529
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.050Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.137H atoms treated by a mixture of independent and constrained refinement
S = 1.06 w = 1/[σ2(Fo2) + (0.0602P)2 + 0.4349P]
where P = (Fo2 + 2Fc2)/3
4956 reflections(Δ/σ)max < 0.001
234 parametersΔρmax = 0.33 e Å3
0 restraintsΔρmin = 0.58 e Å3
Crystal data top
C19H17N5SV = 1625.31 (14) Å3
Mr = 347.44Z = 4
Monoclinic, P21/cMo Kα radiation
a = 16.7346 (7) ŵ = 0.21 mm1
b = 5.5511 (3) ÅT = 100 K
c = 20.4817 (10) Å0.69 × 0.19 × 0.14 mm
β = 121.325 (3)°
Data collection top
Bruker SMART APEXII CCD
diffractometer
4956 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2009)
3416 reflections with I > 2σ(I)
Tmin = 0.868, Tmax = 0.972Rint = 0.048
16728 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0500 restraints
wR(F2) = 0.137H atoms treated by a mixture of independent and constrained refinement
S = 1.06Δρmax = 0.33 e Å3
4956 reflectionsΔρmin = 0.58 e Å3
234 parameters
Special details top

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'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 > σ(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
S10.24764 (3)0.72454 (8)0.12637 (3)0.01824 (13)
N10.52964 (10)1.0733 (3)0.14394 (8)0.0147 (3)
N20.42255 (10)1.0996 (3)0.17932 (8)0.0169 (3)
N30.47003 (10)0.7208 (3)0.06126 (8)0.0148 (3)
N40.32973 (10)0.5624 (3)0.05291 (8)0.0151 (3)
N50.39014 (11)0.3896 (3)0.01293 (9)0.0183 (3)
C10.70179 (12)0.7950 (3)0.20967 (10)0.0170 (4)
H1A0.66190.77240.22930.020*
C20.77591 (13)0.6376 (3)0.23027 (10)0.0200 (4)
H2A0.78650.50800.26420.024*
C30.83454 (13)0.6682 (4)0.20170 (10)0.0211 (4)
H3A0.88380.55700.21470.025*
C40.82082 (13)0.8621 (3)0.15408 (10)0.0210 (4)
H4A0.86170.88630.13550.025*
C50.74731 (12)1.0206 (3)0.13374 (10)0.0190 (4)
H5A0.73851.15380.10160.023*
C60.68604 (12)0.9858 (3)0.16023 (9)0.0154 (3)
C70.60378 (12)1.1554 (3)0.13203 (10)0.0176 (4)
H7A0.62711.31240.15810.021*
H7B0.57671.18260.07670.021*
C80.49754 (13)1.1938 (3)0.18504 (10)0.0165 (4)
H8A0.52741.33300.21490.020*
C90.46824 (11)0.8869 (3)0.10795 (9)0.0133 (3)
C100.39805 (12)0.5647 (3)0.03571 (9)0.0144 (3)
C110.33280 (12)0.7292 (3)0.10083 (9)0.0138 (3)
C120.40253 (12)0.9046 (3)0.13023 (9)0.0141 (3)
C130.19169 (13)0.4383 (3)0.08654 (10)0.0186 (4)
H13A0.24090.32150.09500.022*
H13B0.16360.38060.11600.022*
C140.11669 (12)0.4322 (3)0.00268 (10)0.0166 (4)
C150.10259 (13)0.6128 (3)0.04927 (10)0.0198 (4)
H15A0.14210.75040.03270.024*
C160.03108 (13)0.5934 (3)0.12532 (11)0.0221 (4)
H16A0.02190.71900.16010.027*
C170.02712 (13)0.3932 (3)0.15127 (11)0.0217 (4)
H17A0.07610.38120.20330.026*
C180.01235 (13)0.2113 (3)0.09980 (11)0.0217 (4)
H18A0.05120.07260.11680.026*
C190.05850 (13)0.2296 (3)0.02383 (11)0.0196 (4)
H19A0.06770.10320.01070.023*
H1N50.4310 (15)0.370 (4)0.0289 (12)0.030 (6)*
H2N50.3390 (15)0.304 (4)0.0358 (12)0.024 (6)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.0183 (2)0.0203 (2)0.0209 (2)0.00120 (18)0.0136 (2)0.00239 (18)
N10.0136 (7)0.0158 (7)0.0139 (7)0.0025 (6)0.0066 (6)0.0020 (6)
N20.0205 (8)0.0153 (7)0.0157 (7)0.0009 (6)0.0100 (6)0.0001 (6)
N30.0160 (7)0.0152 (7)0.0150 (7)0.0017 (6)0.0095 (6)0.0013 (6)
N40.0148 (7)0.0163 (7)0.0158 (7)0.0013 (6)0.0090 (6)0.0001 (6)
N50.0161 (8)0.0203 (8)0.0209 (8)0.0053 (7)0.0113 (7)0.0083 (6)
C10.0161 (9)0.0189 (9)0.0148 (8)0.0039 (7)0.0072 (7)0.0020 (7)
C20.0188 (9)0.0186 (9)0.0177 (9)0.0028 (7)0.0061 (7)0.0005 (7)
C30.0174 (9)0.0218 (9)0.0200 (9)0.0004 (7)0.0067 (8)0.0035 (7)
C40.0183 (9)0.0238 (10)0.0231 (9)0.0039 (8)0.0121 (8)0.0046 (8)
C50.0203 (9)0.0188 (9)0.0176 (8)0.0052 (7)0.0097 (8)0.0025 (7)
C60.0151 (9)0.0153 (8)0.0140 (8)0.0039 (7)0.0062 (7)0.0047 (6)
C70.0180 (9)0.0156 (8)0.0214 (9)0.0016 (7)0.0117 (8)0.0005 (7)
C80.0214 (9)0.0140 (8)0.0140 (8)0.0004 (7)0.0092 (7)0.0013 (6)
C90.0140 (8)0.0134 (8)0.0107 (7)0.0003 (6)0.0051 (6)0.0004 (6)
C100.0148 (8)0.0141 (8)0.0142 (8)0.0004 (7)0.0074 (7)0.0006 (6)
C110.0134 (8)0.0149 (8)0.0129 (8)0.0017 (6)0.0066 (7)0.0026 (6)
C120.0165 (8)0.0131 (8)0.0139 (8)0.0007 (7)0.0088 (7)0.0002 (6)
C130.0196 (9)0.0171 (9)0.0222 (9)0.0022 (7)0.0129 (8)0.0012 (7)
C140.0133 (8)0.0187 (9)0.0196 (8)0.0001 (7)0.0099 (7)0.0001 (7)
C150.0189 (9)0.0178 (9)0.0241 (9)0.0003 (7)0.0122 (8)0.0008 (7)
C160.0227 (10)0.0212 (9)0.0225 (9)0.0048 (8)0.0118 (8)0.0056 (8)
C170.0168 (9)0.0252 (10)0.0194 (9)0.0033 (8)0.0068 (7)0.0007 (8)
C180.0180 (9)0.0203 (9)0.0268 (10)0.0015 (7)0.0117 (8)0.0013 (8)
C190.0184 (9)0.0187 (9)0.0235 (9)0.0003 (7)0.0122 (8)0.0017 (7)
Geometric parameters (Å, º) top
S1—C111.7551 (17)C5—C61.400 (2)
S1—C131.8091 (18)C5—H5A0.9500
N1—C91.372 (2)C6—C71.513 (2)
N1—C81.384 (2)C7—H7A0.9900
N1—C71.456 (2)C7—H7B0.9900
N2—C81.307 (2)C8—H8A0.9500
N2—C121.395 (2)C9—C121.396 (2)
N3—C91.340 (2)C11—C121.393 (2)
N3—C101.349 (2)C13—C141.512 (2)
N4—C111.331 (2)C13—H13A0.9900
N4—C101.360 (2)C13—H13B0.9900
N5—C101.348 (2)C14—C151.390 (2)
N5—H1N50.90 (2)C14—C191.399 (2)
N5—H2N50.87 (2)C15—C161.390 (3)
C1—C21.392 (2)C15—H15A0.9500
C1—C61.392 (2)C16—C171.388 (3)
C1—H1A0.9500C16—H16A0.9500
C2—C31.390 (3)C17—C181.386 (3)
C2—H2A0.9500C17—H17A0.9500
C3—C41.389 (3)C18—C191.385 (3)
C3—H3A0.9500C18—H18A0.9500
C4—C51.388 (3)C19—H19A0.9500
C4—H4A0.9500
C11—S1—C13100.87 (8)N3—C9—N1127.88 (15)
C9—N1—C8105.78 (14)N3—C9—C12126.53 (15)
C9—N1—C7127.68 (14)N1—C9—C12105.59 (14)
C8—N1—C7125.79 (14)N5—C10—N3118.33 (15)
C8—N2—C12103.57 (14)N5—C10—N4114.32 (15)
C9—N3—C10111.85 (14)N3—C10—N4127.34 (15)
C11—N4—C10117.98 (14)N4—C11—C12120.50 (15)
C10—N5—H1N5123.6 (14)N4—C11—S1118.92 (13)
C10—N5—H2N5118.7 (14)C12—C11—S1120.58 (13)
H1N5—N5—H2N5117.1 (19)C11—C12—N2133.42 (15)
C2—C1—C6120.00 (16)C11—C12—C9115.76 (15)
C2—C1—H1A120.0N2—C12—C9110.81 (15)
C6—C1—H1A120.0C14—C13—S1117.49 (13)
C3—C2—C1120.58 (17)C14—C13—H13A107.9
C3—C2—H2A119.7S1—C13—H13A107.9
C1—C2—H2A119.7C14—C13—H13B107.9
C4—C3—C2119.68 (18)S1—C13—H13B107.9
C4—C3—H3A120.2H13A—C13—H13B107.2
C2—C3—H3A120.2C15—C14—C19118.40 (17)
C5—C4—C3119.92 (17)C15—C14—C13124.32 (16)
C5—C4—H4A120.0C19—C14—C13117.28 (16)
C3—C4—H4A120.0C16—C15—C14120.45 (17)
C4—C5—C6120.63 (17)C16—C15—H15A119.8
C4—C5—H5A119.7C14—C15—H15A119.8
C6—C5—H5A119.7C17—C16—C15120.97 (17)
C1—C6—C5119.13 (16)C17—C16—H16A119.5
C1—C6—C7122.79 (15)C15—C16—H16A119.5
C5—C6—C7118.07 (15)C18—C17—C16118.67 (17)
N1—C7—C6115.28 (14)C18—C17—H17A120.7
N1—C7—H7A108.5C16—C17—H17A120.7
C6—C7—H7A108.5C19—C18—C17120.73 (18)
N1—C7—H7B108.5C19—C18—H18A119.6
C6—C7—H7B108.5C17—C18—H18A119.6
H7A—C7—H7B107.5C18—C19—C14120.75 (17)
N2—C8—N1114.24 (15)C18—C19—H19A119.6
N2—C8—H8A122.9C14—C19—H19A119.6
N1—C8—H8A122.9
C6—C1—C2—C30.2 (3)C10—N4—C11—C122.0 (2)
C1—C2—C3—C42.1 (3)C10—N4—C11—S1178.00 (12)
C2—C3—C4—C51.6 (3)C13—S1—C11—N49.65 (15)
C3—C4—C5—C60.6 (3)C13—S1—C11—C12170.34 (14)
C2—C1—C6—C52.0 (2)N4—C11—C12—N2178.87 (17)
C2—C1—C6—C7176.53 (16)S1—C11—C12—N21.1 (3)
C4—C5—C6—C12.4 (2)N4—C11—C12—C91.9 (2)
C4—C5—C6—C7176.18 (16)S1—C11—C12—C9178.12 (12)
C9—N1—C7—C669.9 (2)C8—N2—C12—C11179.67 (19)
C8—N1—C7—C6121.46 (18)C8—N2—C12—C90.37 (18)
C1—C6—C7—N114.7 (2)N3—C9—C12—C110.5 (3)
C5—C6—C7—N1163.78 (15)N1—C9—C12—C11179.30 (14)
C12—N2—C8—N10.76 (19)N3—C9—C12—N2179.94 (15)
C9—N1—C8—N20.87 (19)N1—C9—C12—N20.13 (18)
C7—N1—C8—N2171.58 (15)C11—S1—C13—C1483.26 (14)
C10—N3—C9—N1179.61 (16)S1—C13—C14—C1515.4 (2)
C10—N3—C9—C120.6 (2)S1—C13—C14—C19165.09 (13)
C8—N1—C9—N3179.63 (17)C19—C14—C15—C161.2 (3)
C7—N1—C9—N39.2 (3)C13—C14—C15—C16179.25 (16)
C8—N1—C9—C120.55 (17)C14—C15—C16—C170.6 (3)
C7—N1—C9—C12171.03 (16)C15—C16—C17—C180.3 (3)
C9—N3—C10—N5178.94 (15)C16—C17—C18—C190.6 (3)
C9—N3—C10—N40.5 (2)C17—C18—C19—C140.0 (3)
C11—N4—C10—N5179.75 (15)C15—C14—C19—C180.9 (3)
C11—N4—C10—N30.8 (3)C13—C14—C19—C18179.50 (16)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N5—H1N5···N3i0.91 (3)2.14 (3)3.040 (3)173 (2)
C7—H7B···N3ii0.992.573.548 (2)172
C8—H8A···N2iii0.952.393.274 (2)155
Symmetry codes: (i) x+1, y+1, z; (ii) x+1, y+2, z; (iii) x+1, y+1/2, z+1/2.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N5—H1N5···N3i0.91 (3)2.14 (3)3.040 (3)173 (2)
C7—H7B···N3ii0.992.573.548 (2)172
C8—H8A···N2iii0.952.393.274 (2)155
Symmetry codes: (i) x+1, y+1, z; (ii) x+1, y+2, z; (iii) x+1, y+1/2, z+1/2.
 

Footnotes

Additional correspondence author, e-mail: habibahw@usm.my.

§Thomson Reuters ResearcherID: A-5599-2009.

Acknowledgements

MH and HAW acknowledge the Malaysian Ministry of Science, Technology and Innovations (MOSTI) for funding the synthetic chemistry work under 304/PFARMASI/650600/I121. MH thanks Universiti Sains Malaysia for the award of a postgraduate fellowship

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