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Acta Crystallogr Sect E Struct Rep Online. 2009 September 1; 65(Pt 9): o2232.
Published online 2009 August 26. doi:  10.1107/S1600536809032966
PMCID: PMC2969881

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

Abstract

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 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-o2232-scheme1.jpg

Experimental

Crystal data

  • C12H15N5O3·H2O
  • M r = 295.31
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-65-o2232-efi1.jpg
  • 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 [triangle]) T min = 0.987, T max = 0.991
  • 6725 measured reflections
  • 1377 independent reflections
  • 1270 reflections with I > 2σ(I)
  • R int = 0.030

Refinement

  • R[F 2 > 2σ(F 2)] = 0.030
  • wR(F 2) = 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

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

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809032966/hb5032sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809032966/hb5032Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

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).

supplementary crystallographic information

Comment

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.

Experimental

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

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.

Figures

Fig. 1.
A view of (I) with displacement ellipsoids drawn at the 30% probability level.
Fig. 2.
A view of (I) packing strcuture.

Crystal data

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

Bruker APEXII CCD diffractometer1377 independent reflections
Radiation source: fine-focus sealed tube1270 reflections with I > 2σ(I)
graphiteRint = 0.030
[var phi] and ω scansθmax = 25.0°, θmin = 3.4°
Absorption correction: multi-scan (SADABS; Bruker, 2004)h = −8→8
Tmin = 0.987, Tmax = 0.991k = −11→13
6725 measured reflectionsl = −33→40

Refinement

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 = 1.00w = 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 = −0.17 e Å3

Special details

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)

xyzUiso*/Ueq
C10.5675 (3)−0.0420 (2)0.57539 (7)0.0345 (5)
H1A0.5960−0.10420.55730.041*
H1B0.6267−0.05970.60050.041*
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)
H60.8961−0.01460.54200.037*
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)
H10.3405−0.05250.60260.058*
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)

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, °)

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, °)

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) x−1/2, y−1/2, z; (ii) x+1, y, z; (iii) −x+3/2, y+1/2, −z+3/2; (iv) x, −y, −z+1; (v) x−1/2, −y+1/2, −z+1.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: HB5032).

References

  • Bruker (2004). APEX2, SAINT-Plus and SADABS Bruker AXS Inc., Madison, Wisconsin, USA.
  • Czarnik, A. W. (2008). J. Comb. Chem.10, 1–2.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]

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