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

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2-Amino-9-[(1S,3R,4S)-4-hydr­­oxy-3-hy­droxy­methyl-2-methyl­ene­cyclo­pent­yl]-1,9-di­hydro-6H-purin-6-one monohydrate

aDepartment of Pharmacy, Shandong Medical College, Jinan 250002, People's Republic of China, and bState Key Laboratory of Solid Lubrication, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 73000, People's Republic of China
*Correspondence e-mail: liuzhilu2009@yahoo.com.cn

(Received 4 August 2009; accepted 19 August 2009; online 26 August 2009)

In the crystal of the title compound, C12H15N5O3·H2O, the component species are linked by N—H⋯N, N—H⋯O, O—H⋯N and O—H⋯O hydrogen bonds, forming a three-dimesnional network.

Related literature

For background, see: Czarnik (2008[Czarnik, A. W. (2008). J. Comb. Chem. 10, 1-2.]).

[Scheme 1]

Experimental

Crystal data
  • C12H15N5O3·H2O

  • Mr = 295.31

  • Orthorhombic, C 2221

  • a = 6.9986 (10) Å

  • b = 11.6229 (10) Å

  • c = 33.932 (3) Å

  • V = 2760.1 (5) Å3

  • Z = 8

  • Mo Kα radiation

  • μ = 0.11 mm−1

  • T = 273 K

  • 0.12 × 0.10 × 0.08 mm

Data collection
  • Bruker APEXII CCD diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2004[Bruker (2004). APEX2, SAINT-Plus and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.987, Tmax = 0.991

  • 6725 measured reflections

  • 1377 independent reflections

  • 1270 reflections with I > 2σ(I)

  • Rint = 0.030

Refinement
  • R[F2 > 2σ(F2)] = 0.030

  • wR(F2) = 0.079

  • S = 1.00

  • 1377 reflections

  • 204 parameters

  • 4 restraints

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

  • Δρmax = 0.16 e Å−3

  • Δρmin = −0.18 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
O1—H1⋯N4i 0.82 2.04 2.857 (2) 172
O2—H2A⋯O1Wii 0.82 1.83 2.639 (3) 169
N3—H3B⋯O3iii 0.86 2.24 3.039 (3) 154
N5—H5C⋯N2iii 0.97 (3) 1.86 (3) 2.829 (3) 177 (3)
O1W—H2W⋯O1iv 0.819 (19) 2.113 (10) 2.900 (3) 161 (3)
O1W—H1W⋯O2v 0.821 (12) 2.000 (16) 2.783 (3) 159 (4)
Symmetry codes: (i) [x-{\script{1\over 2}}, y-{\script{1\over 2}}, z]; (ii) x+1, y, z; (iii) [-x+{\script{3\over 2}}, y+{\script{1\over 2}}, -z+{\script{3\over 2}}]; (iv) x, -y, -z+1; (v) [x-{\script{1\over 2}}, -y+{\script{1\over 2}}, -z+1].

Data collection: APEX2 (Bruker, 2004[Bruker (2004). APEX2, SAINT-Plus and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT-Plus (Bruker, 2004[Bruker (2004). APEX2, SAINT-Plus and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT-Plus; 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: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXTL.

Supporting information


Comment top

The research of anti-hepatitis B virus (anti-HBV) drug has long been one of the serious diseases threatening human's health, and thus searching for effective medicines to cure such illness has led to significant interest over the past decades (Czarnik, 2008). In this article, we report the crystal structural characterization of 2-Amino-1,9-dihydro-9-[(1S,3R,4S)-4-hydroxy-3- (hydroxymethyl)-2-methylenecyclopentyl]-6H-purin-6-one.

As shown in figure 1, the asymmetrical unit contains one 2-Amino-1,9-dihydro-9-[(1S,3R,4S)-4-hydroxy-3-(hydroxymethyl)-2 -methylenecyclopentyl]-6H-purin-6-one and one water molecule. In addition, it is noteworthy that the multipoint hydrogen-bonding links also exist between the hydrogen atoms including N3—H3B···O3, 3.039 (3) Å; O1—H1···N4, 2.861 (2) Å; O2—H2A···O1W, 2.634 (2) Å; O1W—H2W···O1, 2.899 (3) Å; O1W—H1W···O2, 2.786 (3) Å; this may make a contribution to stabilizing the chain structure, shown in figure 2.

Related literature top

For background, see: Czarnik (2008).

Experimental top

The reaction was performed in a 25-ml Teflon-lined stainless steel vessel. The powder of 2-amino-1,9-dihydro-9-[(1S,3R,4S)-4-hydroxy-3-(hydroxymethyl)-2 -methylenecyclopentyl]-6H-purin-6-one (1 mmol) in 5 ml water and 5 ml etanol was heated to 443 K and kept at this temperature for one day. Upon cooling, colourless blocks of (I) were recovered. Anal. Calc. for C12H17N5O4: C 48.76, H 5.08, N 23.70%; Found: 48.68, H 5.05, N 23.66%.

Refinement top

Anomalous dispersion was negligible and Friedel pairs were merged before refinement.

All hydrogen atoms bound to carbon were refined using a riding model with C—H = 0.93 (aryl), 0.97 (methylene) or 0.96 Å (methyl), and with Uiso(H) = 1.2Ueq(C) (aryl, methylene) or 1.5Ueq(C) (methyl). The water H atoms were refined with restraints of O—H = 0.82 (1)Å and H···H = 1.38 (1)Å.

Computing details top

Data collection: APEX2 (Bruker, 2004); cell refinement: SAINT-Plus (Bruker, 2004); data reduction: SAINT-Plus (Bruker, 2004); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. A view of (I) with displacement ellipsoids drawn at the 30% probability level.
[Figure 2] Fig. 2. A view of (I) packing strcuture.
2-Amino-9-[(1S,3R,4S)-4-hydroxy-3-hydroxymethyl- 2-methylenecyclopentyl]-1,9-dihydro-6H-purin-6-one monohydrate top
Crystal data top
C12H15N5O3·H2OF(000) = 1248
Mr = 295.31Dx = 1.421 Mg m3
Orthorhombic, C2221Mo Kα radiation, λ = 0.71073 Å
Hall symbol: C 2c 2Cell parameters from 1377 reflections
a = 6.9986 (10) Åθ = 3.4–25.0°
b = 11.6229 (10) ŵ = 0.11 mm1
c = 33.932 (3) ÅT = 273 K
V = 2760.1 (5) Å3Block, colorless
Z = 80.12 × 0.10 × 0.08 mm
Data collection top
Bruker APEXII CCD
diffractometer
1377 independent reflections
Radiation source: fine-focus sealed tube1270 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.030
ϕ and ω scansθmax = 25.0°, θmin = 3.4°
Absorption correction: multi-scan
(SADABS; Bruker, 2004)
h = 88
Tmin = 0.987, Tmax = 0.991k = 1113
6725 measured reflectionsl = 3340
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)] = 0.030Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.079H atoms treated by a mixture of independent and constrained refinement
S = 1.00 w = 1/[σ2(Fo2) + (0.055P)2 + 0.4836P]
where P = (Fo2 + 2Fc2)/3
1377 reflections(Δ/σ)max = 0.001
204 parametersΔρmax = 0.16 e Å3
4 restraintsΔρmin = 0.18 e Å3
Crystal data top
C12H15N5O3·H2OV = 2760.1 (5) Å3
Mr = 295.31Z = 8
Orthorhombic, C2221Mo Kα radiation
a = 6.9986 (10) ŵ = 0.11 mm1
b = 11.6229 (10) ÅT = 273 K
c = 33.932 (3) Å0.12 × 0.10 × 0.08 mm
Data collection top
Bruker APEXII CCD
diffractometer
1377 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2004)
1270 reflections with I > 2σ(I)
Tmin = 0.987, Tmax = 0.991Rint = 0.030
6725 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0304 restraints
wR(F2) = 0.079H atoms treated by a mixture of independent and constrained refinement
S = 1.00Δρmax = 0.16 e Å3
1377 reflectionsΔρmin = 0.18 e Å3
204 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
C10.5675 (3)0.0420 (2)0.57539 (7)0.0345 (5)
H1A0.59600.10420.55730.041*
H1B0.62670.05970.60050.041*
C20.6493 (3)0.0717 (2)0.55918 (6)0.0297 (5)
H20.58380.09300.53470.036*
C30.6333 (3)0.16870 (18)0.58921 (6)0.0269 (5)
C40.8242 (3)0.18411 (18)0.60945 (6)0.0267 (5)
H40.88000.25620.59990.032*
C50.9461 (3)0.0841 (2)0.59303 (7)0.0314 (5)
H5A1.07960.10600.59110.038*
H5B0.93550.01640.60960.038*
C60.8611 (3)0.0616 (2)0.55207 (6)0.0306 (5)
H60.89610.01460.54200.037*
C70.7957 (4)0.10135 (19)0.67986 (7)0.0364 (6)
H70.79950.02420.67270.044*
C80.8003 (3)0.29145 (18)0.67510 (6)0.0293 (5)
C90.7746 (4)0.25703 (19)0.71395 (7)0.0338 (5)
C100.7892 (3)0.48170 (19)0.68899 (6)0.0327 (5)
C110.7511 (4)0.34291 (19)0.74423 (7)0.0353 (5)
C120.4843 (4)0.2341 (2)0.59666 (9)0.0445 (6)
H12A0.49350.29310.61510.053*
H12B0.36970.22150.58350.053*
N10.8142 (3)0.19086 (16)0.65304 (5)0.0310 (4)
N20.7723 (3)0.13654 (16)0.71662 (6)0.0395 (5)
N30.7949 (3)0.59520 (16)0.67918 (6)0.0424 (5)
H3A0.81060.61530.65500.051*
H3B0.78290.64680.69720.051*
N40.8083 (3)0.40206 (16)0.66034 (5)0.0331 (5)
N50.7614 (3)0.45538 (16)0.72814 (5)0.0362 (5)
O10.3698 (2)0.03239 (15)0.58020 (5)0.0387 (4)
H10.34050.05250.60260.058*
O20.9107 (3)0.15191 (15)0.52463 (5)0.0422 (5)
H2A1.02330.14550.51830.063*
O30.7248 (3)0.32814 (15)0.78032 (5)0.0499 (5)
O1W0.2565 (3)0.13435 (18)0.49421 (6)0.0500 (5)
H2W0.274 (5)0.0919 (17)0.4753 (5)0.069 (12)*
H1W0.274 (7)0.2029 (6)0.4897 (8)0.102 (16)*
H5C0.754 (5)0.518 (2)0.7470 (8)0.080 (10)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0340 (12)0.0315 (13)0.0380 (13)0.0029 (10)0.0012 (10)0.0008 (11)
C20.0331 (12)0.0313 (12)0.0246 (10)0.0001 (10)0.0015 (9)0.0007 (9)
C30.0304 (11)0.0236 (11)0.0269 (10)0.0008 (9)0.0050 (9)0.0052 (9)
C40.0325 (11)0.0223 (11)0.0252 (10)0.0022 (9)0.0036 (8)0.0009 (9)
C50.0267 (11)0.0321 (12)0.0355 (12)0.0022 (10)0.0017 (9)0.0033 (10)
C60.0371 (12)0.0267 (11)0.0282 (11)0.0004 (10)0.0072 (9)0.0033 (9)
C70.0539 (15)0.0242 (11)0.0312 (12)0.0028 (11)0.0004 (11)0.0012 (9)
C80.0357 (12)0.0269 (11)0.0255 (11)0.0007 (10)0.0004 (9)0.0028 (9)
C90.0461 (13)0.0291 (11)0.0260 (11)0.0006 (11)0.0023 (11)0.0004 (9)
C100.0390 (13)0.0317 (12)0.0272 (11)0.0021 (11)0.0011 (10)0.0027 (9)
C110.0455 (13)0.0346 (11)0.0258 (12)0.0019 (12)0.0012 (10)0.0007 (9)
C120.0395 (14)0.0359 (14)0.0580 (17)0.0044 (12)0.0021 (12)0.0019 (12)
N10.0416 (11)0.0256 (9)0.0260 (9)0.0015 (9)0.0005 (8)0.0019 (8)
N20.0594 (13)0.0299 (10)0.0292 (10)0.0009 (10)0.0029 (10)0.0047 (8)
N30.0707 (15)0.0281 (10)0.0284 (10)0.0006 (11)0.0061 (10)0.0004 (8)
N40.0477 (12)0.0273 (10)0.0243 (9)0.0005 (9)0.0033 (9)0.0017 (8)
N50.0544 (12)0.0298 (10)0.0242 (9)0.0007 (10)0.0036 (9)0.0041 (8)
O10.0332 (9)0.0438 (10)0.0389 (9)0.0070 (8)0.0015 (7)0.0058 (8)
O20.0431 (10)0.0434 (10)0.0401 (9)0.0010 (8)0.0184 (8)0.0074 (8)
O30.0824 (14)0.0433 (10)0.0239 (8)0.0004 (10)0.0077 (8)0.0016 (7)
O1W0.0490 (11)0.0500 (12)0.0512 (12)0.0011 (11)0.0141 (9)0.0074 (10)
Geometric parameters (Å, º) top
C1—O11.398 (3)C8—N41.381 (3)
C1—C21.542 (3)C8—C91.389 (3)
C1—H1A0.9700C8—N11.392 (3)
C1—H1B0.9700C9—N21.403 (3)
C2—C61.506 (3)C9—C111.442 (3)
C2—C31.524 (3)C10—N41.349 (3)
C2—H20.9800C10—N31.361 (3)
C3—C121.316 (3)C10—N51.377 (3)
C3—C41.513 (3)C11—O31.250 (3)
C4—N11.483 (2)C11—N51.418 (3)
C4—C51.546 (3)C12—H12A0.9300
C4—H40.9800C12—H12B0.9300
C5—C61.534 (3)N3—H3A0.8600
C5—H5A0.9700N3—H3B0.8600
C5—H5B0.9700N5—H5C0.97 (3)
C6—O21.445 (3)O1—H10.8200
C6—H60.9800O2—H2A0.8200
C7—N21.323 (3)O1W—H2W0.819 (19)
C7—N11.388 (3)O1W—H1W0.821 (12)
C7—H70.9300
O1—C1—C2109.91 (19)N2—C7—N1113.4 (2)
O1—C1—H1A109.7N2—C7—H7123.3
C2—C1—H1A109.7N1—C7—H7123.3
O1—C1—H1B109.7N4—C8—C9128.1 (2)
C2—C1—H1B109.7N4—C8—N1125.74 (19)
H1A—C1—H1B108.2C9—C8—N1106.11 (19)
C6—C2—C3103.73 (19)C8—C9—N2110.5 (2)
C6—C2—C1110.8 (2)C8—C9—C11119.4 (2)
C3—C2—C1111.62 (18)N2—C9—C11130.0 (2)
C6—C2—H2110.2N4—C10—N3119.1 (2)
C3—C2—H2110.2N4—C10—N5123.8 (2)
C1—C2—H2110.2N3—C10—N5117.10 (19)
C12—C3—C4123.0 (2)O3—C11—N5120.7 (2)
C12—C3—C2127.9 (2)O3—C11—C9128.3 (2)
C4—C3—C2109.04 (18)N5—C11—C9110.97 (18)
N1—C4—C3114.69 (17)C3—C12—H12A120.0
N1—C4—C5115.16 (18)C3—C12—H12B120.0
C3—C4—C5103.58 (17)H12A—C12—H12B120.0
N1—C4—H4107.7C7—N1—C8105.70 (17)
C3—C4—H4107.7C7—N1—C4128.21 (18)
C5—C4—H4107.7C8—N1—C4125.75 (18)
C6—C5—C4103.91 (17)C7—N2—C9104.25 (19)
C6—C5—H5A111.0C10—N3—H3A120.0
C4—C5—H5A111.0C10—N3—H3B120.0
C6—C5—H5B111.0H3A—N3—H3B120.0
C4—C5—H5B111.0C10—N4—C8111.93 (18)
H5A—C5—H5B109.0C10—N5—C11125.68 (18)
O2—C6—C2106.42 (19)C10—N5—H5C118 (2)
O2—C6—C5111.52 (19)C11—N5—H5C116 (2)
C2—C6—C5102.89 (18)C1—O1—H1109.5
O2—C6—H6111.8C6—O2—H2A109.5
C2—C6—H6111.8H2W—O1W—H1W115 (2)
C5—C6—H6111.8
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1···N4i0.822.042.857 (2)172
O2—H2A···O1Wii0.821.832.639 (3)169
N3—H3B···O3iii0.862.243.039 (3)154
N5—H5C···N2iii0.97 (3)1.86 (3)2.829 (3)177 (3)
O1W—H2W···O1iv0.82 (2)2.11 (1)2.900 (3)161 (3)
O1W—H1W···O2v0.82 (1)2.00 (2)2.783 (3)159 (4)
Symmetry codes: (i) x1/2, y1/2, z; (ii) x+1, y, z; (iii) x+3/2, y+1/2, z+3/2; (iv) x, y, z+1; (v) x1/2, y+1/2, z+1.

Experimental details

Crystal data
Chemical formulaC12H15N5O3·H2O
Mr295.31
Crystal system, space groupOrthorhombic, C2221
Temperature (K)273
a, b, c (Å)6.9986 (10), 11.6229 (10), 33.932 (3)
V3)2760.1 (5)
Z8
Radiation typeMo Kα
µ (mm1)0.11
Crystal size (mm)0.12 × 0.10 × 0.08
Data collection
DiffractometerBruker APEXII CCD
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2004)
Tmin, Tmax0.987, 0.991
No. of measured, independent and
observed [I > 2σ(I)] reflections
6725, 1377, 1270
Rint0.030
(sin θ/λ)max1)0.595
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.030, 0.079, 1.00
No. of reflections1377
No. of parameters204
No. of restraints4
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.16, 0.18

Computer programs: APEX2 (Bruker, 2004), SAINT-Plus (Bruker, 2004), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1···N4i0.822.042.857 (2)172
O2—H2A···O1Wii0.821.832.639 (3)169
N3—H3B···O3iii0.862.243.039 (3)154
N5—H5C···N2iii0.97 (3)1.86 (3)2.829 (3)177 (3)
O1W—H2W···O1iv0.819 (19)2.113 (10)2.900 (3)161 (3)
O1W—H1W···O2v0.821 (12)2.000 (16)2.783 (3)159 (4)
Symmetry codes: (i) x1/2, y1/2, z; (ii) x+1, y, z; (iii) x+3/2, y+1/2, z+3/2; (iv) x, y, z+1; (v) x1/2, y+1/2, z+1.
 

Acknowledgements

This work was supported by the Chinese Academy of Sciences (`Hundred Talents Program') and the Ministry of Science and Technology of China (project of `973' plan, No. 2007CB607606).

References

First citationBruker (2004). APEX2, SAINT-Plus and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
First citationCzarnik, A. W. (2008). J. Comb. Chem. 10, 1–2.  Web of Science CrossRef CAS Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar

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