organic compounds
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
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.
Experimental
Crystal data
|
Refinement
|
Data collection: APEX2 (Bruker, 2004); cell SAINT-Plus (Bruker, 2004); data reduction: SAINT-Plus; 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.
Supporting information
10.1107/S1600536809032966/hb5032sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536809032966/hb5032Isup2.hkl
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%.
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.
Data collection: APEX2 (Bruker, 2004); cell
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).Fig. 1. A view of (I) with displacement ellipsoids drawn at the 30% probability level. | |
Fig. 2. A view of (I) packing strcuture. |
C12H15N5O3·H2O | F(000) = 1248 |
Mr = 295.31 | Dx = 1.421 Mg m−3 |
Orthorhombic, C2221 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: C 2c 2 | Cell parameters from 1377 reflections |
a = 6.9986 (10) Å | θ = 3.4–25.0° |
b = 11.6229 (10) Å | µ = 0.11 mm−1 |
c = 33.932 (3) Å | T = 273 K |
V = 2760.1 (5) Å3 | Block, colorless |
Z = 8 | 0.12 × 0.10 × 0.08 mm |
Bruker APEXII CCD diffractometer | 1377 independent reflections |
Radiation source: fine-focus sealed tube | 1270 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.030 |
ϕ and ω scans | θmax = 25.0°, θmin = 3.4° |
Absorption correction: multi-scan (SADABS; Bruker, 2004) | h = −8→8 |
Tmin = 0.987, Tmax = 0.991 | k = −11→13 |
6725 measured reflections | l = −33→40 |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.030 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.079 | H 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 parameters | Δρmax = 0.16 e Å−3 |
4 restraints | Δρmin = −0.18 e Å−3 |
C12H15N5O3·H2O | V = 2760.1 (5) Å3 |
Mr = 295.31 | Z = 8 |
Orthorhombic, C2221 | Mo Kα radiation |
a = 6.9986 (10) Å | µ = 0.11 mm−1 |
b = 11.6229 (10) Å | T = 273 K |
c = 33.932 (3) Å | 0.12 × 0.10 × 0.08 mm |
Bruker APEXII CCD diffractometer | 1377 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2004) | 1270 reflections with I > 2σ(I) |
Tmin = 0.987, Tmax = 0.991 | Rint = 0.030 |
6725 measured reflections |
R[F2 > 2σ(F2)] = 0.030 | 4 restraints |
wR(F2) = 0.079 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.00 | Δρmax = 0.16 e Å−3 |
1377 reflections | Δρmin = −0.18 e Å−3 |
204 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
C1 | 0.5675 (3) | −0.0420 (2) | 0.57539 (7) | 0.0345 (5) | |
H1A | 0.5960 | −0.1042 | 0.5573 | 0.041* | |
H1B | 0.6267 | −0.0597 | 0.6005 | 0.041* | |
C2 | 0.6493 (3) | 0.0717 (2) | 0.55918 (6) | 0.0297 (5) | |
H2 | 0.5838 | 0.0930 | 0.5347 | 0.036* | |
C3 | 0.6333 (3) | 0.16870 (18) | 0.58921 (6) | 0.0269 (5) | |
C4 | 0.8242 (3) | 0.18411 (18) | 0.60945 (6) | 0.0267 (5) | |
H4 | 0.8800 | 0.2562 | 0.5999 | 0.032* | |
C5 | 0.9461 (3) | 0.0841 (2) | 0.59303 (7) | 0.0314 (5) | |
H5A | 1.0796 | 0.1060 | 0.5911 | 0.038* | |
H5B | 0.9355 | 0.0164 | 0.6096 | 0.038* | |
C6 | 0.8611 (3) | 0.0616 (2) | 0.55207 (6) | 0.0306 (5) | |
H6 | 0.8961 | −0.0146 | 0.5420 | 0.037* | |
C7 | 0.7957 (4) | 0.10135 (19) | 0.67986 (7) | 0.0364 (6) | |
H7 | 0.7995 | 0.0242 | 0.6727 | 0.044* | |
C8 | 0.8003 (3) | 0.29145 (18) | 0.67510 (6) | 0.0293 (5) | |
C9 | 0.7746 (4) | 0.25703 (19) | 0.71395 (7) | 0.0338 (5) | |
C10 | 0.7892 (3) | 0.48170 (19) | 0.68899 (6) | 0.0327 (5) | |
C11 | 0.7511 (4) | 0.34291 (19) | 0.74423 (7) | 0.0353 (5) | |
C12 | 0.4843 (4) | 0.2341 (2) | 0.59666 (9) | 0.0445 (6) | |
H12A | 0.4935 | 0.2931 | 0.6151 | 0.053* | |
H12B | 0.3697 | 0.2215 | 0.5835 | 0.053* | |
N1 | 0.8142 (3) | 0.19086 (16) | 0.65304 (5) | 0.0310 (4) | |
N2 | 0.7723 (3) | 0.13654 (16) | 0.71662 (6) | 0.0395 (5) | |
N3 | 0.7949 (3) | 0.59520 (16) | 0.67918 (6) | 0.0424 (5) | |
H3A | 0.8106 | 0.6153 | 0.6550 | 0.051* | |
H3B | 0.7829 | 0.6468 | 0.6972 | 0.051* | |
N4 | 0.8083 (3) | 0.40206 (16) | 0.66034 (5) | 0.0331 (5) | |
N5 | 0.7614 (3) | 0.45538 (16) | 0.72814 (5) | 0.0362 (5) | |
O1 | 0.3698 (2) | −0.03239 (15) | 0.58020 (5) | 0.0387 (4) | |
H1 | 0.3405 | −0.0525 | 0.6026 | 0.058* | |
O2 | 0.9107 (3) | 0.15191 (15) | 0.52463 (5) | 0.0422 (5) | |
H2A | 1.0233 | 0.1455 | 0.5183 | 0.063* | |
O3 | 0.7248 (3) | 0.32814 (15) | 0.78032 (5) | 0.0499 (5) | |
O1W | 0.2565 (3) | 0.13435 (18) | 0.49421 (6) | 0.0500 (5) | |
H2W | 0.274 (5) | 0.0919 (17) | 0.4753 (5) | 0.069 (12)* | |
H1W | 0.274 (7) | 0.2029 (6) | 0.4897 (8) | 0.102 (16)* | |
H5C | 0.754 (5) | 0.518 (2) | 0.7470 (8) | 0.080 (10)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
C1 | 0.0340 (12) | 0.0315 (13) | 0.0380 (13) | −0.0029 (10) | −0.0012 (10) | −0.0008 (11) |
C2 | 0.0331 (12) | 0.0313 (12) | 0.0246 (10) | −0.0001 (10) | −0.0015 (9) | 0.0007 (9) |
C3 | 0.0304 (11) | 0.0236 (11) | 0.0269 (10) | 0.0008 (9) | 0.0050 (9) | 0.0052 (9) |
C4 | 0.0325 (11) | 0.0223 (11) | 0.0252 (10) | −0.0022 (9) | 0.0036 (8) | −0.0009 (9) |
C5 | 0.0267 (11) | 0.0321 (12) | 0.0355 (12) | 0.0022 (10) | 0.0017 (9) | −0.0033 (10) |
C6 | 0.0371 (12) | 0.0267 (11) | 0.0282 (11) | 0.0004 (10) | 0.0072 (9) | −0.0033 (9) |
C7 | 0.0539 (15) | 0.0242 (11) | 0.0312 (12) | 0.0028 (11) | 0.0004 (11) | 0.0012 (9) |
C8 | 0.0357 (12) | 0.0269 (11) | 0.0255 (11) | −0.0007 (10) | 0.0004 (9) | −0.0028 (9) |
C9 | 0.0461 (13) | 0.0291 (11) | 0.0260 (11) | −0.0006 (11) | 0.0023 (11) | 0.0004 (9) |
C10 | 0.0390 (13) | 0.0317 (12) | 0.0272 (11) | −0.0021 (11) | 0.0011 (10) | −0.0027 (9) |
C11 | 0.0455 (13) | 0.0346 (11) | 0.0258 (12) | −0.0019 (12) | 0.0012 (10) | 0.0007 (9) |
C12 | 0.0395 (14) | 0.0359 (14) | 0.0580 (17) | 0.0044 (12) | 0.0021 (12) | −0.0019 (12) |
N1 | 0.0416 (11) | 0.0256 (9) | 0.0260 (9) | −0.0015 (9) | 0.0005 (8) | −0.0019 (8) |
N2 | 0.0594 (13) | 0.0299 (10) | 0.0292 (10) | −0.0009 (10) | 0.0029 (10) | 0.0047 (8) |
N3 | 0.0707 (15) | 0.0281 (10) | 0.0284 (10) | −0.0006 (11) | 0.0061 (10) | −0.0004 (8) |
N4 | 0.0477 (12) | 0.0273 (10) | 0.0243 (9) | −0.0005 (9) | 0.0033 (9) | −0.0017 (8) |
N5 | 0.0544 (12) | 0.0298 (10) | 0.0242 (9) | −0.0007 (10) | 0.0036 (9) | −0.0041 (8) |
O1 | 0.0332 (9) | 0.0438 (10) | 0.0389 (9) | −0.0070 (8) | 0.0015 (7) | 0.0058 (8) |
O2 | 0.0431 (10) | 0.0434 (10) | 0.0401 (9) | 0.0010 (8) | 0.0184 (8) | 0.0074 (8) |
O3 | 0.0824 (14) | 0.0433 (10) | 0.0239 (8) | −0.0004 (10) | 0.0077 (8) | 0.0016 (7) |
O1W | 0.0490 (11) | 0.0500 (12) | 0.0512 (12) | 0.0011 (11) | 0.0141 (9) | 0.0074 (10) |
C1—O1 | 1.398 (3) | C8—N4 | 1.381 (3) |
C1—C2 | 1.542 (3) | C8—C9 | 1.389 (3) |
C1—H1A | 0.9700 | C8—N1 | 1.392 (3) |
C1—H1B | 0.9700 | C9—N2 | 1.403 (3) |
C2—C6 | 1.506 (3) | C9—C11 | 1.442 (3) |
C2—C3 | 1.524 (3) | C10—N4 | 1.349 (3) |
C2—H2 | 0.9800 | C10—N3 | 1.361 (3) |
C3—C12 | 1.316 (3) | C10—N5 | 1.377 (3) |
C3—C4 | 1.513 (3) | C11—O3 | 1.250 (3) |
C4—N1 | 1.483 (2) | C11—N5 | 1.418 (3) |
C4—C5 | 1.546 (3) | C12—H12A | 0.9300 |
C4—H4 | 0.9800 | C12—H12B | 0.9300 |
C5—C6 | 1.534 (3) | N3—H3A | 0.8600 |
C5—H5A | 0.9700 | N3—H3B | 0.8600 |
C5—H5B | 0.9700 | N5—H5C | 0.97 (3) |
C6—O2 | 1.445 (3) | O1—H1 | 0.8200 |
C6—H6 | 0.9800 | O2—H2A | 0.8200 |
C7—N2 | 1.323 (3) | O1W—H2W | 0.819 (19) |
C7—N1 | 1.388 (3) | O1W—H1W | 0.821 (12) |
C7—H7 | 0.9300 | ||
O1—C1—C2 | 109.91 (19) | N2—C7—N1 | 113.4 (2) |
O1—C1—H1A | 109.7 | N2—C7—H7 | 123.3 |
C2—C1—H1A | 109.7 | N1—C7—H7 | 123.3 |
O1—C1—H1B | 109.7 | N4—C8—C9 | 128.1 (2) |
C2—C1—H1B | 109.7 | N4—C8—N1 | 125.74 (19) |
H1A—C1—H1B | 108.2 | C9—C8—N1 | 106.11 (19) |
C6—C2—C3 | 103.73 (19) | C8—C9—N2 | 110.5 (2) |
C6—C2—C1 | 110.8 (2) | C8—C9—C11 | 119.4 (2) |
C3—C2—C1 | 111.62 (18) | N2—C9—C11 | 130.0 (2) |
C6—C2—H2 | 110.2 | N4—C10—N3 | 119.1 (2) |
C3—C2—H2 | 110.2 | N4—C10—N5 | 123.8 (2) |
C1—C2—H2 | 110.2 | N3—C10—N5 | 117.10 (19) |
C12—C3—C4 | 123.0 (2) | O3—C11—N5 | 120.7 (2) |
C12—C3—C2 | 127.9 (2) | O3—C11—C9 | 128.3 (2) |
C4—C3—C2 | 109.04 (18) | N5—C11—C9 | 110.97 (18) |
N1—C4—C3 | 114.69 (17) | C3—C12—H12A | 120.0 |
N1—C4—C5 | 115.16 (18) | C3—C12—H12B | 120.0 |
C3—C4—C5 | 103.58 (17) | H12A—C12—H12B | 120.0 |
N1—C4—H4 | 107.7 | C7—N1—C8 | 105.70 (17) |
C3—C4—H4 | 107.7 | C7—N1—C4 | 128.21 (18) |
C5—C4—H4 | 107.7 | C8—N1—C4 | 125.75 (18) |
C6—C5—C4 | 103.91 (17) | C7—N2—C9 | 104.25 (19) |
C6—C5—H5A | 111.0 | C10—N3—H3A | 120.0 |
C4—C5—H5A | 111.0 | C10—N3—H3B | 120.0 |
C6—C5—H5B | 111.0 | H3A—N3—H3B | 120.0 |
C4—C5—H5B | 111.0 | C10—N4—C8 | 111.93 (18) |
H5A—C5—H5B | 109.0 | C10—N5—C11 | 125.68 (18) |
O2—C6—C2 | 106.42 (19) | C10—N5—H5C | 118 (2) |
O2—C6—C5 | 111.52 (19) | C11—N5—H5C | 116 (2) |
C2—C6—C5 | 102.89 (18) | C1—O1—H1 | 109.5 |
O2—C6—H6 | 111.8 | C6—O2—H2A | 109.5 |
C2—C6—H6 | 111.8 | H2W—O1W—H1W | 115 (2) |
C5—C6—H6 | 111.8 |
D—H···A | D—H | H···A | D···A | 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 | 0.82 (2) | 2.11 (1) | 2.900 (3) | 161 (3) |
O1W—H1W···O2v | 0.82 (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. |
Experimental details
Crystal data | |
Chemical formula | C12H15N5O3·H2O |
Mr | 295.31 |
Crystal system, space group | Orthorhombic, C2221 |
Temperature (K) | 273 |
a, b, c (Å) | 6.9986 (10), 11.6229 (10), 33.932 (3) |
V (Å3) | 2760.1 (5) |
Z | 8 |
Radiation type | Mo Kα |
µ (mm−1) | 0.11 |
Crystal size (mm) | 0.12 × 0.10 × 0.08 |
Data collection | |
Diffractometer | Bruker APEXII CCD diffractometer |
Absorption correction | Multi-scan (SADABS; Bruker, 2004) |
Tmin, Tmax | 0.987, 0.991 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 6725, 1377, 1270 |
Rint | 0.030 |
(sin θ/λ)max (Å−1) | 0.595 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.030, 0.079, 1.00 |
No. of reflections | 1377 |
No. of parameters | 204 |
No. of restraints | 4 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.16, −0.18 |
Computer programs: APEX2 (Bruker, 2004), SAINT-Plus (Bruker, 2004), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).
D—H···A | D—H | H···A | D···A | 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−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. |
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
Bruker (2004). APEX2, SAINT-Plus and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Czarnik, A. W. (2008). J. Comb. Chem. 10, 1–2. Web of Science CrossRef CAS Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
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.