Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270101021904/jz1488sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S0108270101021904/jz1488Isup2.hkl |
CCDC reference: 182993
The title compound was synthesized independently in two laboratories at the time when compound (II) was not synthetically available (Reese & Whitall, 1976; Kasai et al., 1976). The procedure of Reese & Whittall (1976) was used in the rpesent case and the compound obtained was recrystallized from acetonitrile.
All H atoms were found in a difference electron-density map and were placed at calculated positions (C—H = 0.95–1.00 Å), with isotropic displacement parameters taken from the adjacent atom multiplied by 1.2 (1.5 for methyl), except for the hydroxyl and water H atoms, which were freely refined. In the absence of suitable anomalous scatterers for Mo Kα radiation, the determination of the absolute configuration was not possible from the X-ray data. The absolute configuration was assigned to agree with the known chirality of the ribofuranose moiety and the Friedel diffraction data were merged accordingly.
Data collection: KappaCCD Reference Manual (Nonius, 1998); cell refinement: DENZO and SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO and SCALEPACK; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEPII (Johnson, 1971), PLATON (Spek, 1998) and ORTEP-3 (Farugia, 1999); software used to prepare material for publication: SHELXL97.
C13H13N5O4·H2O | F(000) = 672 |
Mr = 321.30 | Dx = 1.574 Mg m−3 Dm = 1.56 (5) Mg m−3 Dm measured by flotation in ? |
Orthorhombic, P212121 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2ac 2ab | Cell parameters from 2371 reflections |
a = 4.9211 (1) Å | θ = 3–25° |
b = 13.3792 (2) Å | µ = 0.12 mm−1 |
c = 20.5881 (4) Å | T = 200 K |
V = 1355.53 (4) Å3 | Plate, colourless |
Z = 4 | 0.33 × 0.28 × 0.22 mm |
Nonius KappaCCD diffractometer | 2157 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.014 |
Graphite monochromator | θmax = 30.5°, θmin = 1.8° |
Detector resolution: 0.055 pixels mm-1 | h = −6→6 |
ω scans | k = −18→18 |
3821 measured reflections | l = −29→29 |
2331 independent reflections |
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)] = 0.034 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.080 | Calculated w = 1/[σ2(Fo2) + (0.0374P)2 + 0.3423P] where P = (Fo2 + 2Fc2)/3 |
S = 1.04 | (Δ/σ)max = 0.001 |
2331 reflections | Δρmax = 0.23 e Å−3 |
226 parameters | Δρmin = −0.19 e Å−3 |
0 restraints | Extinction correction: SHELXL97, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.019 (3) |
C13H13N5O4·H2O | V = 1355.53 (4) Å3 |
Mr = 321.30 | Z = 4 |
Orthorhombic, P212121 | Mo Kα radiation |
a = 4.9211 (1) Å | µ = 0.12 mm−1 |
b = 13.3792 (2) Å | T = 200 K |
c = 20.5881 (4) Å | 0.33 × 0.28 × 0.22 mm |
Nonius KappaCCD diffractometer | 2157 reflections with I > 2σ(I) |
3821 measured reflections | Rint = 0.014 |
2331 independent reflections |
R[F2 > 2σ(F2)] = 0.034 | 0 restraints |
wR(F2) = 0.080 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.04 | Δρmax = 0.23 e Å−3 |
2331 reflections | Δρmin = −0.19 e Å−3 |
226 parameters |
Experimental. KappaCCD diffractometer. 136 frames in 4 sets of ω scans. Rotation/frame=2°. Crystal-detector distance=33 mm. Measuring time=120 s/°. |
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' | 0.8558 (4) | −0.08979 (11) | 0.67753 (7) | 0.0228 (3) | |
H1 | 0.9843 | −0.0792 | 0.7145 | 0.027* | |
C2' | 0.7025 (4) | −0.18850 (11) | 0.68628 (8) | 0.0248 (3) | |
H2 | 0.5432 | −0.1812 | 0.7161 | 0.030* | |
O2 | 0.8908 (3) | −0.25914 (9) | 0.70947 (6) | 0.0310 (3) | |
H20 | 0.814 (6) | −0.2972 (19) | 0.7430 (11) | 0.060 (8)* | |
C3' | 0.6135 (4) | −0.21009 (11) | 0.61550 (8) | 0.0234 (3) | |
H3 | 0.4288 | −0.1814 | 0.6075 | 0.028* | |
O3 | 0.6184 (3) | −0.31213 (8) | 0.59728 (7) | 0.0331 (3) | |
H30 | 0.477 (6) | −0.3372 (19) | 0.6136 (11) | 0.049 (7)* | |
C4' | 0.8263 (3) | −0.15407 (11) | 0.57456 (7) | 0.0215 (3) | |
H4 | 0.9384 | −0.2044 | 0.5506 | 0.026* | |
O4' | 1.0010 (2) | −0.10089 (8) | 0.61926 (5) | 0.0230 (2) | |
C5' | 0.7094 (3) | −0.08146 (11) | 0.52599 (7) | 0.0219 (3) | |
H5A | 0.8606 | −0.0478 | 0.5030 | 0.026* | |
H5B | 0.6032 | −0.1192 | 0.4933 | 0.026* | |
N1 | 0.3945 (3) | 0.11696 (10) | 0.70705 (6) | 0.0262 (3) | |
C2 | 0.5864 (4) | 0.05412 (12) | 0.72294 (7) | 0.0258 (4) | |
H2A | 0.6597 | 0.0490 | 0.7655 | 0.031* | |
N3 | 0.6718 (3) | −0.00408 (9) | 0.67144 (6) | 0.0211 (3) | |
C3A | 0.5232 (3) | 0.02707 (10) | 0.61891 (7) | 0.0180 (3) | |
N4 | 0.5331 (3) | −0.00497 (9) | 0.55554 (6) | 0.0188 (3) | |
C4A | 0.3643 (3) | 0.04601 (10) | 0.51372 (7) | 0.0197 (3) | |
N5 | 0.3514 (3) | 0.03438 (9) | 0.45054 (6) | 0.0231 (3) | |
C6 | 0.1468 (4) | 0.09967 (11) | 0.43060 (8) | 0.0256 (3) | |
C10 | 0.0780 (5) | 0.10951 (14) | 0.36026 (8) | 0.0355 (4) | |
H10A | −0.1055 | 0.1371 | 0.3558 | 0.053* | |
H10B | 0.0856 | 0.0436 | 0.3396 | 0.053* | |
H10C | 0.2088 | 0.1543 | 0.3392 | 0.053* | |
C7 | 0.0384 (4) | 0.14886 (12) | 0.48193 (8) | 0.0269 (3) | |
H7A | −0.1051 | 0.1964 | 0.4810 | 0.032* | |
N8 | 0.1811 (3) | 0.11534 (9) | 0.53658 (6) | 0.0218 (3) | |
C9 | 0.1567 (4) | 0.14967 (11) | 0.60122 (8) | 0.0242 (3) | |
O1 | −0.0127 (3) | 0.21207 (10) | 0.61578 (6) | 0.0399 (3) | |
C9A | 0.3520 (4) | 0.10114 (10) | 0.64129 (7) | 0.0212 (3) | |
O1W | 0.6553 (3) | −0.09176 (10) | 0.36276 (6) | 0.0297 (3) | |
H1W | 0.562 (6) | −0.0516 (18) | 0.3904 (12) | 0.054 (7)* | |
H2W | 0.536 (6) | −0.1379 (19) | 0.3479 (12) | 0.055 (7)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
C1' | 0.0227 (7) | 0.0237 (7) | 0.0220 (6) | 0.0030 (7) | −0.0012 (7) | 0.0030 (6) |
C2' | 0.0251 (8) | 0.0206 (7) | 0.0287 (7) | 0.0040 (7) | 0.0065 (7) | 0.0065 (6) |
O2 | 0.0376 (7) | 0.0276 (6) | 0.0276 (5) | 0.0104 (6) | 0.0054 (6) | 0.0108 (5) |
C3' | 0.0197 (7) | 0.0168 (6) | 0.0337 (7) | 0.0001 (6) | 0.0035 (7) | 0.0026 (6) |
O3 | 0.0334 (7) | 0.0178 (5) | 0.0480 (7) | −0.0025 (6) | 0.0027 (7) | −0.0017 (5) |
C4' | 0.0189 (7) | 0.0195 (6) | 0.0260 (7) | 0.0018 (6) | 0.0022 (6) | −0.0010 (6) |
O4' | 0.0176 (5) | 0.0267 (5) | 0.0246 (5) | −0.0011 (5) | 0.0010 (5) | 0.0023 (4) |
C5' | 0.0243 (8) | 0.0213 (7) | 0.0201 (6) | 0.0031 (6) | 0.0027 (6) | −0.0011 (5) |
N1 | 0.0369 (8) | 0.0213 (6) | 0.0203 (6) | 0.0005 (6) | 0.0016 (6) | −0.0033 (5) |
C2 | 0.0364 (10) | 0.0231 (7) | 0.0179 (6) | −0.0014 (7) | 0.0001 (7) | −0.0019 (6) |
N3 | 0.0261 (7) | 0.0185 (5) | 0.0186 (5) | 0.0010 (6) | −0.0016 (6) | −0.0004 (4) |
C3A | 0.0209 (7) | 0.0153 (6) | 0.0178 (6) | −0.0014 (6) | −0.0003 (6) | 0.0006 (5) |
N4 | 0.0218 (6) | 0.0178 (5) | 0.0170 (5) | 0.0026 (6) | −0.0003 (5) | −0.0012 (4) |
C4A | 0.0207 (7) | 0.0167 (6) | 0.0216 (6) | −0.0018 (6) | −0.0005 (6) | 0.0014 (5) |
N5 | 0.0263 (7) | 0.0219 (6) | 0.0210 (6) | −0.0029 (6) | −0.0028 (6) | 0.0012 (5) |
C6 | 0.0278 (8) | 0.0225 (7) | 0.0266 (7) | −0.0059 (7) | −0.0076 (7) | 0.0043 (6) |
C10 | 0.0462 (11) | 0.0324 (8) | 0.0278 (8) | −0.0078 (9) | −0.0143 (8) | 0.0053 (7) |
C7 | 0.0268 (8) | 0.0226 (7) | 0.0314 (8) | −0.0005 (7) | −0.0076 (7) | 0.0080 (6) |
N8 | 0.0244 (7) | 0.0173 (5) | 0.0237 (6) | 0.0017 (6) | −0.0016 (6) | 0.0012 (5) |
C9 | 0.0262 (8) | 0.0186 (6) | 0.0278 (7) | 0.0023 (7) | 0.0030 (7) | −0.0005 (6) |
O1 | 0.0442 (8) | 0.0357 (6) | 0.0399 (7) | 0.0203 (7) | 0.0019 (7) | −0.0039 (6) |
C9A | 0.0248 (7) | 0.0176 (6) | 0.0213 (6) | 0.0002 (7) | 0.0015 (6) | −0.0014 (5) |
O1W | 0.0280 (6) | 0.0333 (6) | 0.0278 (6) | −0.0056 (6) | 0.0051 (6) | −0.0056 (5) |
C1'—O4' | 1.4043 (19) | C2—H2A | 0.9500 |
C1'—N3 | 1.467 (2) | N3—C3A | 1.3706 (19) |
C1'—C2' | 1.532 (2) | C3A—N4 | 1.3742 (18) |
C1'—H1 | 1.0000 | C3A—C9A | 1.380 (2) |
C2'—O2 | 1.4071 (19) | N4—C4A | 1.3771 (19) |
C2'—C3' | 1.549 (2) | C4A—N5 | 1.3117 (18) |
C2'—H2 | 1.0000 | C4A—N8 | 1.377 (2) |
O2—H20 | 0.94 (3) | N5—C6 | 1.395 (2) |
C3'—O3 | 1.4161 (18) | C6—C7 | 1.355 (2) |
C3'—C4' | 1.539 (2) | C6—C10 | 1.493 (2) |
C3'—H3 | 1.0000 | C10—H10A | 0.9800 |
O3—H30 | 0.84 (3) | C10—H10B | 0.9800 |
C4'—O4' | 1.4463 (19) | C10—H10C | 0.9800 |
C4'—C5' | 1.508 (2) | C7—N8 | 1.400 (2) |
C4'—H4 | 1.0000 | C7—H7A | 0.9500 |
C5'—N4 | 1.4731 (19) | N8—C9 | 1.4128 (19) |
C5'—H5A | 0.9900 | C9—O1 | 1.217 (2) |
C5'—H5B | 0.9900 | C9—C9A | 1.423 (2) |
N1—C2 | 1.306 (2) | O1W—H1W | 0.91 (3) |
N1—C9A | 1.3862 (18) | O1W—H2W | 0.91 (3) |
C2—N3 | 1.3808 (19) | ||
O4'—C1'—N3 | 108.90 (11) | N3—C2—H2A | 123.5 |
O4'—C1'—C2' | 105.06 (12) | C3A—N3—C2 | 105.79 (13) |
N3—C1'—C2' | 112.34 (14) | C3A—N3—C1' | 129.39 (12) |
O4'—C1'—H1 | 110.1 | C2—N3—C1' | 124.28 (12) |
N3—C1'—H1 | 110.1 | N3—C3A—N4 | 129.45 (14) |
C2'—C1'—H1 | 110.1 | N3—C3A—C9A | 106.30 (12) |
O2—C2'—C1' | 107.13 (14) | N4—C3A—C9A | 124.25 (14) |
O2—C2'—C3' | 112.35 (12) | C3A—N4—C4A | 114.68 (12) |
C1'—C2'—C3' | 100.92 (12) | C3A—N4—C5' | 129.03 (13) |
O2—C2'—H2 | 111.9 | C4A—N4—C5' | 116.18 (12) |
C1'—C2'—H2 | 111.9 | N5—C4A—N8 | 112.78 (14) |
C3'—C2'—H2 | 111.9 | N5—C4A—N4 | 126.19 (14) |
C2'—O2—H20 | 110.4 (17) | N8—C4A—N4 | 121.01 (12) |
O3—C3'—C4' | 108.23 (13) | C4A—N5—C6 | 104.63 (14) |
O3—C3'—C2' | 115.09 (13) | C7—C6—N5 | 111.04 (14) |
C4'—C3'—C2' | 103.41 (13) | C7—C6—C10 | 128.65 (17) |
O3—C3'—H3 | 109.9 | N5—C6—C10 | 120.30 (15) |
C4'—C3'—H3 | 109.9 | C6—C10—H10A | 109.5 |
C2'—C3'—H3 | 109.9 | C6—C10—H10B | 109.5 |
C3'—O3—H30 | 105.3 (18) | H10A—C10—H10B | 109.5 |
O4'—C4'—C5' | 109.37 (12) | C6—C10—H10C | 109.5 |
O4'—C4'—C3' | 107.20 (12) | H10A—C10—H10C | 109.5 |
C5'—C4'—C3' | 114.65 (14) | H10B—C10—H10C | 109.5 |
O4'—C4'—H4 | 108.5 | C6—C7—N8 | 105.89 (14) |
C5'—C4'—H4 | 108.5 | C6—C7—H7A | 127.1 |
C3'—C4'—H4 | 108.5 | N8—C7—H7A | 127.1 |
C1'—O4'—C4' | 107.05 (12) | C4A—N8—C7 | 105.64 (13) |
N4—C5'—C4' | 113.47 (12) | C4A—N8—C9 | 126.64 (13) |
N4—C5'—H5A | 108.9 | C7—N8—C9 | 127.60 (14) |
C4'—C5'—H5A | 108.9 | O1—C9—N8 | 120.87 (15) |
N4—C5'—H5B | 108.9 | O1—C9—C9A | 129.24 (15) |
C4'—C5'—H5B | 108.9 | N8—C9—C9A | 109.89 (13) |
H5A—C5'—H5B | 107.7 | C3A—C9A—N1 | 110.10 (14) |
C2—N1—C9A | 104.80 (13) | C3A—C9A—C9 | 123.12 (13) |
N1—C2—N3 | 113.00 (13) | N1—C9A—C9 | 126.75 (14) |
N1—C2—H2A | 123.5 | H1W—O1W—H2W | 107 (2) |
O4'—C1'—C2'—O2 | 77.94 (15) | C4'—C5'—N4—C4A | −163.17 (14) |
N3—C1'—C2'—O2 | −163.82 (12) | C3A—N4—C4A—N5 | 174.80 (15) |
O4'—C1'—C2'—C3' | −39.75 (15) | C5'—N4—C4A—N5 | −1.8 (2) |
N3—C1'—C2'—C3' | 78.49 (14) | C3A—N4—C4A—N8 | −6.9 (2) |
O2—C2'—C3'—O3 | 29.3 (2) | C5'—N4—C4A—N8 | 176.57 (14) |
C1'—C2'—C3'—O3 | 143.13 (14) | N8—C4A—N5—C6 | −0.22 (18) |
O2—C2'—C3'—C4' | −88.50 (15) | N4—C4A—N5—C6 | 178.22 (15) |
C1'—C2'—C3'—C4' | 25.31 (15) | C4A—N5—C6—C7 | −0.51 (19) |
O3—C3'—C4'—O4' | −126.53 (13) | C4A—N5—C6—C10 | 178.24 (16) |
C2'—C3'—C4'—O4' | −4.01 (15) | N5—C6—C7—N8 | 1.00 (19) |
O3—C3'—C4'—C5' | 111.86 (15) | C10—C6—C7—N8 | −177.62 (17) |
C2'—C3'—C4'—C5' | −125.62 (13) | N5—C4A—N8—C7 | 0.83 (18) |
N3—C1'—O4'—C4' | −81.63 (14) | N4—C4A—N8—C7 | −177.71 (14) |
C2'—C1'—O4'—C4' | 38.91 (15) | N5—C4A—N8—C9 | −175.40 (15) |
C5'—C4'—O4'—C1' | 103.27 (14) | N4—C4A—N8—C9 | 6.1 (2) |
C3'—C4'—O4'—C1' | −21.60 (15) | C6—C7—N8—C4A | −1.07 (18) |
O4'—C4'—C5'—N4 | −63.47 (17) | C6—C7—N8—C9 | 175.10 (16) |
C3'—C4'—C5'—N4 | 56.94 (18) | C4A—N8—C9—O1 | 179.47 (16) |
C9A—N1—C2—N3 | −0.93 (19) | C7—N8—C9—O1 | 4.1 (3) |
N1—C2—N3—C3A | 1.29 (19) | C4A—N8—C9—C9A | −0.4 (2) |
N1—C2—N3—C1' | −170.97 (14) | C7—N8—C9—C9A | −175.78 (15) |
O4'—C1'—N3—C3A | 38.0 (2) | N3—C3A—C9A—N1 | 0.56 (18) |
C2'—C1'—N3—C3A | −77.95 (19) | N4—C3A—C9A—N1 | −179.05 (14) |
O4'—C1'—N3—C2 | −151.65 (15) | N3—C3A—C9A—C9 | −177.46 (15) |
C2'—C1'—N3—C2 | 92.40 (18) | N4—C3A—C9A—C9 | 2.9 (2) |
C2—N3—C3A—N4 | 178.52 (16) | C2—N1—C9A—C3A | 0.21 (19) |
C1'—N3—C3A—N4 | −9.8 (3) | C2—N1—C9A—C9 | 178.14 (16) |
C2—N3—C3A—C9A | −1.06 (17) | O1—C9—C9A—C3A | 176.22 (17) |
C1'—N3—C3A—C9A | 170.66 (15) | N8—C9—C9A—C3A | −4.0 (2) |
N3—C3A—N4—C4A | −176.77 (15) | O1—C9—C9A—N1 | −1.5 (3) |
C9A—C3A—N4—C4A | 2.7 (2) | N8—C9—C9A—N1 | 178.37 (15) |
N3—C3A—N4—C5' | −0.8 (3) | O4'—C1'—N3—C2 | −151.65 (15) |
C9A—C3A—N4—C5' | 178.76 (15) | O4'—C1'—N3—C3A | 38.0 (2) |
C4'—C5'—N4—C3A | 20.9 (2) |
Experimental details
Crystal data | |
Chemical formula | C13H13N5O4·H2O |
Mr | 321.30 |
Crystal system, space group | Orthorhombic, P212121 |
Temperature (K) | 200 |
a, b, c (Å) | 4.9211 (1), 13.3792 (2), 20.5881 (4) |
V (Å3) | 1355.53 (4) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.12 |
Crystal size (mm) | 0.33 × 0.28 × 0.22 |
Data collection | |
Diffractometer | Nonius KappaCCD diffractometer |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 3821, 2331, 2157 |
Rint | 0.014 |
(sin θ/λ)max (Å−1) | 0.714 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.034, 0.080, 1.04 |
No. of reflections | 2331 |
No. of parameters | 226 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.23, −0.19 |
Computer programs: KappaCCD Reference Manual (Nonius, 1998), DENZO and SCALEPACK (Otwinowski & Minor, 1997), DENZO and SCALEPACK, SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), ORTEPII (Johnson, 1971), PLATON (Spek, 1998) and ORTEP-3 (Farugia, 1999), SHELXL97.
C1'—O4' | 1.4043 (19) | N3—C3A | 1.3706 (19) |
C1'—N3 | 1.467 (2) | C3A—N4 | 1.3742 (18) |
C1'—C2' | 1.532 (2) | C3A—C9A | 1.380 (2) |
C2'—O2 | 1.4071 (19) | N4—C4A | 1.3771 (19) |
C2'—C3' | 1.549 (2) | C4A—N5 | 1.3117 (18) |
C3'—O3 | 1.4161 (18) | C4A—N8 | 1.377 (2) |
C3'—C4' | 1.539 (2) | N5—C6 | 1.395 (2) |
C4'—O4' | 1.4463 (19) | C6—C7 | 1.355 (2) |
C4'—C5' | 1.508 (2) | C6—C10 | 1.493 (2) |
C5'—N4 | 1.4731 (19) | C7—N8 | 1.400 (2) |
N1—C2 | 1.306 (2) | N8—C9 | 1.4128 (19) |
N1—C9A | 1.3862 (18) | C9—O1 | 1.217 (2) |
C2—N3 | 1.3808 (19) | C9—C9A | 1.423 (2) |
O4'—C1'—C2'—O2 | 77.94 (15) | O3—C3'—C4'—C5' | 111.86 (15) |
N3—C1'—C2'—O2 | −163.82 (12) | C2'—C3'—C4'—C5' | −125.62 (13) |
O4'—C1'—C2'—C3' | −39.75 (15) | N3—C1'—O4'—C4' | −81.63 (14) |
N3—C1'—C2'—C3' | 78.49 (14) | C2'—C1'—O4'—C4' | 38.91 (15) |
O2—C2'—C3'—O3 | 29.3 (2) | C5'—C4'—O4'—C1' | 103.27 (14) |
C1'—C2'—C3'—O3 | 143.13 (14) | C3'—C4'—O4'—C1' | −21.60 (15) |
O2—C2'—C3'—C4' | −88.50 (15) | O4'—C4'—C5'—N4 | −63.47 (17) |
C1'—C2'—C3'—C4' | 25.31 (15) | C3'—C4'—C5'—N4 | 56.94 (18) |
O3—C3'—C4'—O4' | −126.53 (13) | O4'—C1'—N3—C3A | 38.0 (2) |
C2'—C3'—C4'—O4' | −4.01 (15) | O4'—C1'—N3—C2 | −151.65 (15) |
Intramolecularly cyclized nucleosides and nucleotides have been the focus of much attention as useful models for studies of the stereochemistry of nucleic acids (Mizuno, 1986; Maruyama et al., 1988; Yoshimura et al., 1992, and referneces therein). Wye (Y or Yt base), (I), is the base of the nucleoside wyosine (Yt), (II). Recently, the structures of wyosine, wybutosine and β-hydroxywybutosine, as a rare nucleoside isolated from yeast tRNAsPhe, have been unambiguously assigned by chemical means (Itaya & Kanai, 1999). Since the highly fluorescent and structurally unique wye can be selectively excized from the oligonucleotide of its anticodon region (Eisinger et al., 1971), it is a specific example where just one nucleoside can be split off at its N-glycosidic bond. The structure of aglycon wye has also been determined crystallographically (Nygjerd et al., 1975)
A common feature of wye nucleosides is their unusual susceptibility to acidic hydrolysis (Itaya et al., 1980). However, 4,5'-cyclowyosine, (III), possesses a hydrolytic stability comparable to that of guanosine; the same is true for 3,5'-cycloguanosine. The large reactivity difference between (II) and (III) may be attributed to the fixation of torsion angles in the sugar moiety and consequently to the anticipated planarity of the imidazo[1,2-a]purine ring. In contrast, in the anti orientation, he extended form of the molecule is more susceptible to solvation by water molecules (Seela & Bussmann, 1985).
A pre-check using the Cambridge Structural Database (Release 5.2.1, April 2001; Allen & Kennard, 1993) gave no results on structural work on nucleosides with wye (I) as the aglycon moiety. Therefore, to the best of our knowledge, this paper provides the first accurate structural parameters for 4,5'-cyclowyosine (3,4-dihydro-6-methyl-3-β-D-ribofuranosyl-4,5'-cyclo-9H- imidazo[1,2-a]purin-9-one hydrate), (III), and confirms the prediction by Reese & Whittall (1976) and Seela & Bussmann (1985) based on the chemical evidence. However, the molecule crystallizes with one water molecule in the asymmetric unit (Fig. 1 and Table 1).
The orientation of the heterocyclic base wye relative to the sugar moiety is syn, as determined by the torsion angle about the N-glycosidic bond (Sundaralingam, 1975). The appropriate torsion angles O4'—C1'—N3—C2 and O4'—C1'—N3—C3a in this study are -151.7 (2) and 38.0 (2)°, respectively. The ribofuranose moiety exhibits a β-D configuration with the envelope C1'-endo pucker. The conformation about the C4'—C5' bond [torsion angle O4'—C4'—C5'—N4 - 63.5 (2)°] is in the gauche range. The Cremer–Pople (Cremer & Pople, 1975) puckering parameters q2 and ϕ2 are 0.380 (2) Å and 223.2 (3)° (Spek, 1998; Farrugia, 2000). The bond lengths and angles are normal and in agreement with the values reported for the related compounds. The bond lengths of the aglycon moiety (wye) [C3a—C9a 1.380 (2), C6—C7 1.355 (2), N1—C2 1.306 (2) and C4a—N5 1.312 (2) Å] suggest some double-bond character. The dihedral angles between the planes defined by atoms N1/C2/N3/C3a/C9a (plane A), C3a/N4/C4a/N8/C9 (plane B) and C4a/N5/C6/C7/N8 (plane C) are A/B 2.1 (1)° and B/C 3.9 (1)°. The overall geometry of the wye entity is very similar to that found in the structure of the Yt base (Nygjerd et al., 1975). The bond distances in both structures were checked by a one-parameter significance test t0 (Cruickshank & Robertson, 1953). For bond lengths, the mean value was 0.8, which implies that the distances are not significantly different in both structures. Only the distances N1—C2 and C2—N3 differ, because a wye moiety is linked to the sugar part and there is no H atom attached to N1.
The OH groups of the ribofuranose part, the N atoms of the wye entity and a water molecule are involved in a system of hydrogen bonds (Table 1) of the O—H···O and O—H···N types. One water H atom forms a nearly linear hydrogen bond to the N5 atom of the wye unit, whilst the second water H atom is linked to the O2 atom of a neighbouring molecule. The hydroxyl H atoms attached to atoms O2 and O3 are connected to atom N1 and the water molecule, respectively. There are also three weak C—H···O interactions. The molecules are stacked in a columnar arrangement parallel to the short a axis (4.921 Å), as is shown in Fig. 2.