
Acta Cryst. (2008). E64, o715 [ doi:10.1107/S1600536808006727 ]
The crystal structure of the title compound, C30H38N2O5Si, has been investigated to establish the relative stereochemistry at the spiro ring junction and the two anomeric centres. Each of the O atoms in the tetrahydropyran rings adopts an axial position on the neighbouring ring. This bis-diaxial conformation is adopted, thus gaining maximum stablization from the anomeric effect. The silyl-protected hydroxymethyl and uracil substituents adopt equatorial positions on their associated tetrahydropyran rings, thereby minimizing unfavourable steric interactions. The dimeric (2'R*,6'R*,8'R*)- and (2'S*,6'S*,8'S*)-uridine units are connected to each other across crystallographic inversion centres via intermolecular N-H
O hydrogen bonds.
To a suspension of uracil (6.95 mg, 61.9 µmol) in hexamethyldisilazane (0.5 ml) under an atmosphere of argon was added ammonium sulfate (2 crystals) and the mixture was heated to reflux until the white solid dissolved. After 3 h, the mixture was concentrated in vacuo to a thick yellow oil. 8-(tert-Butyldiphenylsilyloxymethyl)-2-acetoxy-1,7-dioxaspiro[5.5] undecane (18.8 mg, 38.9 µmol) in CH2Cl2 (1.0 ml) was transferred to the yellow oil via cannula. Freshly prepared TMSOTf solution (95.4 µL, 66.8 µmol, 0.70 mol L-1 in CH2Cl2) was added dropwise. After 3 h, saturated NaHCO3 solution (2 ml) and CH2Cl2 (2 ml) were added and the mixture was stirred for 15 min. The aqueous phase was extracted with CH2Cl2 (3 x 4 ml). The combined organic extracts were dried over MgSO4 and concentrated in vacuo. Purification by flash chromatography using hexane–EtOAc (19:1 to 7:3) as eluent yielded the title compound (7.50 mg, 36%) as a pale-yellow powder. Recrystallization from hexane–CH2Cl2 afforded pale yellow needles.
HRMS (FAB): found MH+, 535.2633, C30H39N2O5Si requires 535.2628.
νmax (film)/cm-1: 3376 (N–H), 2919 (C–H), 1689 (C=O), 1668 (C=O), 1456, 1377, 1267 (C–O), 1103 (C–O), 982, 699.
δH (300 MHz; CDCl3): 1.07 (9 H, s, OSiPh2tBu), 1.31–1.38 (1 H, m, H9'A), 1.41–1.51 (3 H, m, H3'A, H5'A and H11'A), 1.56–1.76 (5 H, m, H4'A, H5'B, H9'B, H10'A and H11'B), 1.80–1.94 (2 H, m, H3'B and H10'B), 2.07–2.16 (1 H, m, H4'B), 3.63 (1 H, dd, JAB 10.4 and JH1''A,8' 4.5, H1''A), 3.72 (1 H, dd, JAB 10.4 and JH1''B,8' 5.3, H1''B), 3.82–3.89 (1 H, m, H8'), 5.73 (1 H, d, J5,6 8.2, H5), 5.94 (1 H, dd, J2'ax,3'ax 11.1 and J2'ax,3'eq 2.5, H2'ax), 7.33–7.42 (6 H, m, Ph), 7.46 (1 H, d, J6,5 8.2, H6), 7.70–7.76 (4 H, m, Ph), 8.17 (1 H, br s, NH).
δC (75 MHz; CDCl3): 17.9 (CH2, C4'), 18.0 (CH2, C10'), 19.3 (C, OSiPh2tBu), 26.5 (CH2, C9'), 26.8 (CH3, OSiPh2tBu), 30.3 (CH2, C3'), 34.7 (CH2, C5'), 34.8 (CH2, C11'), 67.0 (CH2, C1''), 70.7 (CH, C8'), 76.8 (CH, C2'), 99.1 (C, C6'), 102.1 (CH, C5), 127.6 (CH, Ph), 129.5 (CH, Ph), 129.5 (CH, Ph), 133.8 (C, Ph), 135.7 (CH, Ph), 135.7 (CH, Ph), 140.3 (CH, C6), 149.7 (C, C2), 162.8 (C, C4).
m/z (FAB): 535 (MH+, 3%), 477 (M – tBu, 11), 457 (M – Ph, 3), 423 (C26H35O3Si, 19), 239 (SiPh2tBu, 8), 199 (35), 197 (35), 135 (100), 105 (32), 91 (73).
H atoms were placed in calculated positions and were refined using a riding model (C—H = 0.93 or 0.97 Å), with U iso(H) = 1.2 or 1.5 times Ueq(C).
Data collection: SMART (Siemens, 1995); cell refinement: SAINT (Siemens, 1995); data reduction: SAINT (Siemens, 1995); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEPIII (Burnett & Johnson, 1996) and Mercury (Macrae et al., 2006); software used to prepare material for publication: SHELXTL (Sheldrick, 2008) and publCIF (Westrip, 2008).
| C30H38N2O5Si | Dx = 1.289 Mg m−3 |
| Mr = 534.71 | Melting point: 482.4(9) K |
| Monoclinic, P21/n | Mo Kα radiation λ = 0.71073 Å |
| a = 14.7960 (2) Å | Cell parameters from 5612 reflections |
| b = 12.5092 (2) Å | θ = 1.8–26.4º |
| c = 15.0935 (1) Å | µ = 0.13 mm−1 |
| β = 99.420 (1)º | T = 293 (2) K |
| V = 2755.93 (6) Å3 | Needle, pale yellow |
| Z = 4 | 0.32 × 0.26 × 0.12 mm |
| F000 = 1144 |
| Siemens SMART CCD diffractometer | 5612 independent reflections |
| Radiation source: fine-focus sealed tube | 4327 reflections with I > 2σ(I) |
| Monochromator: graphite | Rint = 0.044 |
| T = 293(2) K | θmax = 26.4º |
| area–detector ω scans | θmin = 1.8º |
| Absorption correction: multi-scan (SADABS; Sheldrick, 1996) | h = −14→18 |
| Tmin = 0.960, Tmax = 0.985 | k = −15→12 |
| 15898 measured reflections | l = −18→18 |
| 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)] = 0.052 | H-atom parameters constrained |
| wR(F2) = 0.111 | w = 1/[σ2(Fo2) + (0.0251P)2 + 2.8069P] where P = (Fo2 + 2Fc2)/3 |
| S = 1.09 | (Δ/σ)max = 0.001 |
| 5612 reflections | Δρmax = 0.30 e Å−3 |
| 343 parameters | Δρmin = −0.34 e Å−3 |
| Primary atom site location: structure-invariant direct methods | Extinction correction: none |
| C30H38N2O5Si | V = 2755.93 (6) Å3 |
| Mr = 534.71 | Z = 4 |
| Monoclinic, P21/n | Mo Kα |
| a = 14.7960 (2) Å | µ = 0.13 mm−1 |
| b = 12.5092 (2) Å | T = 293 (2) K |
| c = 15.0935 (1) Å | 0.32 × 0.26 × 0.12 mm |
| β = 99.420 (1)º |
| Siemens SMART CCD diffractometer | 5612 independent reflections |
| Absorption correction: multi-scan (SADABS; Sheldrick, 1996) | 4327 reflections with I > 2σ(I) |
| Tmin = 0.960, Tmax = 0.985 | Rint = 0.044 |
| 15898 measured reflections |
| R[F2 > 2σ(F2)] = 0.052 | 343 parameters |
| wR(F2) = 0.111 | H-atom parameters constrained |
| S = 1.09 | Δρmax = 0.30 e Å−3 |
| 5612 reflections | Δρmin = −0.34 e Å−3 |
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 > 2σ(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 | ||
| Si | 0.55794 (4) | 0.75101 (5) | 0.10014 (4) | 0.01617 (14) | |
| O1' | 0.36047 (10) | 1.12404 (11) | 0.28260 (9) | 0.0173 (3) | |
| O1'' | 0.56790 (11) | 0.86029 (11) | 0.16209 (10) | 0.0199 (3) | |
| O2 | 0.19564 (11) | 0.89649 (12) | 0.17326 (11) | 0.0253 (4) | |
| O4 | 0.00327 (12) | 1.13783 (12) | 0.01545 (10) | 0.0267 (4) | |
| N1 | 0.21693 (12) | 1.07393 (14) | 0.21025 (12) | 0.0179 (4) | |
| N3 | 0.10473 (13) | 1.02092 (14) | 0.09140 (12) | 0.0205 (4) | |
| H3A | 0.0807 | 0.9715 | 0.0555 | 0.025* | |
| C1'' | 0.53531 (16) | 0.87555 (17) | 0.24520 (14) | 0.0208 (5) | |
| H1''A | 0.5834 | 0.8591 | 0.2951 | 0.025* | |
| H1''B | 0.4837 | 0.8287 | 0.2484 | 0.025* | |
| C2 | 0.17425 (15) | 0.98991 (17) | 0.15908 (14) | 0.0188 (5) | |
| C2' | 0.28987 (15) | 1.04722 (17) | 0.28551 (14) | 0.0180 (4) | |
| H2'A | 0.3136 | 0.9758 | 0.2758 | 0.022* | |
| C3' | 0.25589 (15) | 1.04928 (18) | 0.37497 (14) | 0.0204 (5) | |
| H3'A | 0.2081 | 0.9962 | 0.3752 | 0.025* | |
| H3'B | 0.2304 | 1.1190 | 0.3844 | 0.025* | |
| C4' | 0.33596 (15) | 1.02537 (18) | 0.44990 (14) | 0.0197 (5) | |
| H4'A | 0.3162 | 1.0321 | 0.5079 | 0.024* | |
| H4'B | 0.3572 | 0.9528 | 0.4440 | 0.024* | |
| C4 | 0.06939 (16) | 1.12308 (18) | 0.07495 (14) | 0.0208 (5) | |
| C5 | 0.11736 (15) | 1.20464 (18) | 0.13209 (14) | 0.0204 (5) | |
| H5A | 0.0996 | 1.2758 | 0.1242 | 0.025* | |
| C5' | 0.41357 (15) | 1.10398 (17) | 0.44375 (14) | 0.0195 (5) | |
| H5'A | 0.3947 | 1.1752 | 0.4585 | 0.023* | |
| H5'B | 0.4667 | 1.0844 | 0.4873 | 0.023* | |
| C6' | 0.43971 (15) | 1.10504 (16) | 0.35013 (14) | 0.0174 (4) | |
| C6 | 0.18739 (15) | 1.17817 (17) | 0.19652 (14) | 0.0199 (5) | |
| H6A | 0.2169 | 1.2317 | 0.2331 | 0.024* | |
| O7' | 0.47639 (10) | 1.00155 (11) | 0.33619 (9) | 0.0176 (3) | |
| C7 | 0.57397 (15) | 0.63171 (16) | 0.17660 (13) | 0.0172 (4) | |
| C8 | 0.50484 (15) | 0.55495 (17) | 0.17660 (14) | 0.0189 (5) | |
| H8A | 0.4524 | 0.5591 | 0.1334 | 0.023* | |
| C8' | 0.50635 (15) | 0.99104 (17) | 0.24987 (14) | 0.0185 (5) | |
| H8'A | 0.4542 | 1.0045 | 0.2021 | 0.022* | |
| C9' | 0.58166 (15) | 1.07096 (17) | 0.24148 (15) | 0.0216 (5) | |
| H9'A | 0.6008 | 1.0634 | 0.1833 | 0.026* | |
| H9'B | 0.6343 | 1.0573 | 0.2875 | 0.026* | |
| C9 | 0.51259 (16) | 0.47299 (17) | 0.23927 (14) | 0.0210 (5) | |
| H9A | 0.4657 | 0.4231 | 0.2374 | 0.025* | |
| C10 | 0.58946 (16) | 0.46522 (18) | 0.30429 (15) | 0.0225 (5) | |
| H10A | 0.5940 | 0.4110 | 0.3470 | 0.027* | |
| C10' | 0.54654 (16) | 1.18395 (17) | 0.25179 (14) | 0.0212 (5) | |
| H10'A | 0.4993 | 1.2008 | 0.2012 | 0.025* | |
| H10'B | 0.5963 | 1.2346 | 0.2523 | 0.025* | |
| C11' | 0.50739 (15) | 1.19351 (17) | 0.33940 (14) | 0.0193 (5) | |
| H11'A | 0.5573 | 1.1913 | 0.3898 | 0.023* | |
| H11'B | 0.4770 | 1.2621 | 0.3406 | 0.023* | |
| C11 | 0.66025 (17) | 0.53891 (19) | 0.30570 (15) | 0.0253 (5) | |
| H11A | 0.7128 | 0.5331 | 0.3486 | 0.030* | |
| C12 | 0.65222 (16) | 0.62106 (18) | 0.24300 (15) | 0.0233 (5) | |
| H12A | 0.6997 | 0.6702 | 0.2449 | 0.028* | |
| C13 | 0.44029 (15) | 0.74260 (17) | 0.03190 (13) | 0.0186 (4) | |
| C14 | 0.41471 (16) | 0.66001 (18) | −0.03071 (14) | 0.0231 (5) | |
| H14A | 0.4575 | 0.6079 | −0.0386 | 0.028* | |
| C15 | 0.32729 (17) | 0.65419 (19) | −0.08109 (15) | 0.0265 (5) | |
| H15A | 0.3123 | 0.5998 | −0.1229 | 0.032* | |
| C16 | 0.26269 (17) | 0.7308 (2) | −0.06812 (15) | 0.0286 (6) | |
| H16A | 0.2040 | 0.7274 | −0.1014 | 0.034* | |
| C17 | 0.28483 (16) | 0.8121 (2) | −0.00618 (16) | 0.0277 (5) | |
| H17A | 0.2409 | 0.8623 | 0.0030 | 0.033* | |
| C18 | 0.37312 (16) | 0.81829 (18) | 0.04222 (15) | 0.0232 (5) | |
| H18A | 0.3880 | 0.8742 | 0.0826 | 0.028* | |
| C19 | 0.63144 (17) | 0.87945 (18) | −0.02047 (15) | 0.0259 (5) | |
| H19A | 0.6769 | 0.8915 | −0.0580 | 0.039* | |
| H19B | 0.6350 | 0.9350 | 0.0238 | 0.039* | |
| H19C | 0.5717 | 0.8798 | −0.0566 | 0.039* | |
| C20 | 0.74439 (16) | 0.7706 (2) | 0.08381 (16) | 0.0269 (5) | |
| H20A | 0.7896 | 0.7806 | 0.0456 | 0.040* | |
| H20B | 0.7549 | 0.7037 | 0.1149 | 0.040* | |
| H20C | 0.7486 | 0.8278 | 0.1267 | 0.040* | |
| C22 | 0.64860 (15) | 0.77039 (17) | 0.02668 (14) | 0.0189 (5) | |
| C23 | 0.64515 (17) | 0.68136 (18) | −0.04386 (15) | 0.0257 (5) | |
| H23A | 0.6922 | 0.6932 | −0.0797 | 0.039* | |
| H23B | 0.5863 | 0.6818 | −0.0818 | 0.039* | |
| H23C | 0.6548 | 0.6134 | −0.0142 | 0.039* |
| U11 | U22 | U33 | U12 | U13 | U23 | |
| Si | 0.0173 (3) | 0.0145 (3) | 0.0176 (3) | −0.0002 (2) | 0.0056 (2) | −0.0012 (2) |
| O1' | 0.0150 (8) | 0.0180 (8) | 0.0192 (7) | −0.0014 (6) | 0.0034 (6) | 0.0004 (6) |
| O1'' | 0.0240 (9) | 0.0181 (8) | 0.0197 (7) | −0.0022 (6) | 0.0095 (7) | −0.0046 (6) |
| O2 | 0.0260 (9) | 0.0176 (8) | 0.0308 (9) | 0.0007 (7) | 0.0003 (7) | −0.0006 (7) |
| O4 | 0.0294 (9) | 0.0247 (9) | 0.0235 (8) | 0.0001 (7) | −0.0029 (7) | 0.0028 (7) |
| O7' | 0.0206 (8) | 0.0159 (7) | 0.0179 (7) | 0.0016 (6) | 0.0075 (6) | −0.0022 (6) |
| N1 | 0.0160 (9) | 0.0184 (9) | 0.0194 (9) | 0.0006 (7) | 0.0028 (7) | −0.0002 (7) |
| N3 | 0.0227 (10) | 0.0192 (9) | 0.0193 (9) | −0.0011 (8) | 0.0027 (8) | −0.0020 (8) |
| C1'' | 0.0256 (12) | 0.0199 (11) | 0.0183 (10) | 0.0031 (9) | 0.0076 (9) | −0.0003 (9) |
| C2 | 0.0177 (11) | 0.0215 (11) | 0.0185 (10) | −0.0007 (9) | 0.0066 (9) | −0.0003 (9) |
| C2' | 0.0186 (11) | 0.0159 (10) | 0.0198 (10) | 0.0005 (9) | 0.0038 (9) | 0.0011 (8) |
| C3' | 0.0187 (11) | 0.0202 (11) | 0.0237 (11) | −0.0013 (9) | 0.0076 (9) | 0.0020 (9) |
| C4' | 0.0206 (12) | 0.0216 (11) | 0.0181 (10) | 0.0015 (9) | 0.0069 (9) | 0.0004 (9) |
| C4 | 0.0217 (12) | 0.0226 (12) | 0.0190 (11) | −0.0001 (9) | 0.0062 (9) | 0.0052 (9) |
| C5 | 0.0223 (12) | 0.0174 (11) | 0.0226 (11) | 0.0021 (9) | 0.0068 (9) | 0.0039 (9) |
| C5' | 0.0217 (12) | 0.0193 (11) | 0.0185 (10) | 0.0024 (9) | 0.0058 (9) | −0.0021 (9) |
| C6' | 0.0172 (11) | 0.0162 (10) | 0.0187 (10) | 0.0017 (9) | 0.0031 (9) | −0.0016 (8) |
| C6 | 0.0208 (12) | 0.0169 (11) | 0.0231 (11) | −0.0017 (9) | 0.0070 (9) | 0.0006 (9) |
| C7 | 0.0197 (11) | 0.0166 (10) | 0.0166 (10) | 0.0010 (9) | 0.0068 (9) | −0.0025 (8) |
| C8 | 0.0159 (11) | 0.0200 (11) | 0.0213 (11) | 0.0006 (9) | 0.0049 (9) | −0.0013 (9) |
| C8' | 0.0223 (12) | 0.0183 (11) | 0.0161 (10) | 0.0016 (9) | 0.0062 (9) | −0.0016 (8) |
| C9' | 0.0205 (12) | 0.0216 (11) | 0.0243 (11) | −0.0017 (9) | 0.0084 (10) | −0.0028 (9) |
| C9 | 0.0207 (12) | 0.0185 (11) | 0.0255 (11) | −0.0028 (9) | 0.0086 (10) | −0.0009 (9) |
| C10 | 0.0297 (13) | 0.0174 (11) | 0.0212 (11) | 0.0009 (10) | 0.0068 (10) | 0.0024 (9) |
| C10' | 0.0224 (12) | 0.0192 (11) | 0.0226 (11) | −0.0058 (9) | 0.0057 (9) | −0.0012 (9) |
| C11' | 0.0188 (11) | 0.0176 (11) | 0.0220 (11) | −0.0016 (9) | 0.0047 (9) | −0.0021 (9) |
| C11 | 0.0246 (13) | 0.0271 (12) | 0.0228 (11) | −0.0010 (10) | −0.0006 (10) | 0.0015 (10) |
| C12 | 0.0248 (13) | 0.0211 (11) | 0.0243 (11) | −0.0040 (10) | 0.0048 (10) | −0.0010 (9) |
| C13 | 0.0197 (11) | 0.0191 (11) | 0.0176 (10) | −0.0015 (9) | 0.0046 (9) | 0.0028 (9) |
| C14 | 0.0244 (13) | 0.0227 (12) | 0.0235 (11) | −0.0017 (10) | 0.0073 (10) | −0.0022 (9) |
| C15 | 0.0304 (14) | 0.0299 (13) | 0.0188 (11) | −0.0105 (11) | 0.0032 (10) | −0.0003 (10) |
| C16 | 0.0213 (12) | 0.0390 (15) | 0.0237 (11) | −0.0044 (11) | −0.0017 (10) | 0.0105 (11) |
| C17 | 0.0215 (13) | 0.0299 (13) | 0.0311 (13) | 0.0053 (10) | 0.0030 (10) | 0.0044 (11) |
| C18 | 0.0259 (13) | 0.0207 (11) | 0.0235 (11) | 0.0020 (10) | 0.0052 (10) | 0.0021 (9) |
| C19 | 0.0322 (14) | 0.0227 (12) | 0.0254 (12) | −0.0005 (10) | 0.0122 (10) | 0.0013 (10) |
| C20 | 0.0210 (12) | 0.0334 (14) | 0.0275 (12) | −0.0019 (10) | 0.0077 (10) | 0.0027 (10) |
| C22 | 0.0186 (11) | 0.0192 (11) | 0.0203 (10) | −0.0003 (9) | 0.0074 (9) | −0.0001 (9) |
| C23 | 0.0292 (14) | 0.0229 (12) | 0.0282 (12) | 0.0009 (10) | 0.0139 (11) | −0.0030 (10) |
| Si—O1'' | 1.6491 (15) | C8'—C9' | 1.518 (3) |
| Si—C13 | 1.875 (2) | C8'—H8'A | 0.9800 |
| Si—C7 | 1.878 (2) | C9'—C10' | 1.523 (3) |
| Si—C22 | 1.891 (2) | C9'—H9'A | 0.9700 |
| O1'—C2' | 1.425 (2) | C9'—H9'B | 0.9700 |
| O1'—C6' | 1.442 (3) | C9—C10 | 1.379 (3) |
| O1''—C1'' | 1.428 (2) | C9—H9A | 0.9300 |
| O2—C2 | 1.220 (3) | C10—C11 | 1.393 (3) |
| O4—C4 | 1.229 (3) | C10—H10A | 0.9300 |
| O7'—C6' | 1.433 (2) | C10'—C11' | 1.533 (3) |
| O7'—C8' | 1.449 (2) | C10'—H10'A | 0.9700 |
| N1—C6 | 1.380 (3) | C10'—H10'B | 0.9700 |
| N1—C2 | 1.393 (3) | C11'—H11'A | 0.9700 |
| N1—C2' | 1.472 (3) | C11'—H11'B | 0.9700 |
| N3—C2 | 1.381 (3) | C11—C12 | 1.389 (3) |
| N3—C4 | 1.388 (3) | C11—H11A | 0.9300 |
| N3—H3A | 0.8600 | C12—H12A | 0.9300 |
| C1''—C8' | 1.512 (3) | C13—C18 | 1.400 (3) |
| C1''—H1''A | 0.9700 | C13—C14 | 1.409 (3) |
| C1''—H1''B | 0.9700 | C14—C15 | 1.391 (3) |
| C2'—C3' | 1.516 (3) | C14—H14A | 0.9300 |
| C2'—H2'A | 0.9800 | C15—C16 | 1.390 (3) |
| C3'—C4' | 1.528 (3) | C15—H15A | 0.9300 |
| C3'—H3'A | 0.9700 | C16—C17 | 1.384 (3) |
| C3'—H3'B | 0.9700 | C16—H16A | 0.9300 |
| C4'—C5' | 1.526 (3) | C17—C18 | 1.391 (3) |
| C4'—H4'A | 0.9700 | C17—H17A | 0.9300 |
| C4'—H4'B | 0.9700 | C18—H18A | 0.9300 |
| C4—C5 | 1.445 (3) | C19—C22 | 1.540 (3) |
| C5—C6 | 1.341 (3) | C19—H19A | 0.9600 |
| C5—H5A | 0.9300 | C19—H19B | 0.9600 |
| C5'—C6' | 1.525 (3) | C19—H19C | 0.9600 |
| C5'—H5'A | 0.9700 | C20—C22 | 1.534 (3) |
| C5'—H5'B | 0.9700 | C20—H20A | 0.9600 |
| C6'—C11' | 1.519 (3) | C20—H20B | 0.9600 |
| C6—H6A | 0.9300 | C20—H20C | 0.9600 |
| C7—C8 | 1.403 (3) | C22—C23 | 1.536 (3) |
| C7—C12 | 1.408 (3) | C23—H23A | 0.9600 |
| C8—C9 | 1.387 (3) | C23—H23B | 0.9600 |
| C8—H8A | 0.9300 | C23—H23C | 0.9600 |
| O1''—Si—C13 | 110.29 (9) | C9'—C8'—H8'A | 109.0 |
| O1''—Si—C7 | 108.65 (8) | C8'—C9'—C10' | 109.60 (18) |
| C13—Si—C7 | 107.79 (10) | C8'—C9'—H9'A | 109.8 |
| O1''—Si—C22 | 102.72 (9) | C10'—C9'—H9'A | 109.8 |
| C13—Si—C22 | 111.66 (9) | C8'—C9'—H9'B | 109.8 |
| C7—Si—C22 | 115.59 (10) | C10'—C9'—H9'B | 109.8 |
| C2'—O1'—C6' | 112.48 (15) | H9'A—C9'—H9'B | 108.2 |
| C1''—O1''—Si | 126.65 (13) | C10—C9—C8 | 120.3 (2) |
| C6'—O7'—C8' | 113.14 (15) | C10—C9—H9A | 119.9 |
| C6—N1—C2 | 121.73 (18) | C8—C9—H9A | 119.9 |
| C6—N1—C2' | 120.30 (17) | C9—C10—C11 | 119.7 (2) |
| C2—N1—C2' | 117.74 (17) | C9—C10—H10A | 120.2 |
| C2—N3—C4 | 127.16 (19) | C11—C10—H10A | 120.2 |
| C2—N3—H3A | 116.4 | C9'—C10'—C11' | 110.13 (18) |
| C4—N3—H3A | 116.4 | C9'—C10'—H10'A | 109.6 |
| O1''—C1''—C8' | 107.92 (17) | C11'—C10'—H10'A | 109.6 |
| O1''—C1''—H1''A | 110.1 | C9'—C10'—H10'B | 109.6 |
| C8'—C1''—H1''A | 110.1 | C11'—C10'—H10'B | 109.6 |
| O1''—C1''—H1''B | 110.1 | H10'A—C10'—H10'B | 108.1 |
| C8'—C1''—H1''B | 110.1 | C6'—C11'—C10' | 112.58 (17) |
| H1''A—C1''—H1''B | 108.4 | C6'—C11'—H11'A | 109.1 |
| O2—C2—N3 | 122.6 (2) | C10'—C11'—H11'A | 109.1 |
| O2—C2—N1 | 123.0 (2) | C6'—C11'—H11'B | 109.1 |
| N3—C2—N1 | 114.42 (19) | C10'—C11'—H11'B | 109.1 |
| O1'—C2'—N1 | 105.77 (16) | H11'A—C11'—H11'B | 107.8 |
| O1'—C2'—C3' | 111.57 (17) | C12—C11—C10 | 119.9 (2) |
| N1—C2'—C3' | 112.05 (17) | C12—C11—H11A | 120.0 |
| O1'—C2'—H2'A | 109.1 | C10—C11—H11A | 120.0 |
| N1—C2'—H2'A | 109.1 | C11—C12—C7 | 121.6 (2) |
| C3'—C2'—H2'A | 109.1 | C11—C12—H12A | 119.2 |
| C2'—C3'—C4' | 109.02 (18) | C7—C12—H12A | 119.2 |
| C2'—C3'—H3'A | 109.9 | C18—C13—C14 | 116.9 (2) |
| C4'—C3'—H3'A | 109.9 | C18—C13—Si | 120.88 (17) |
| C2'—C3'—H3'B | 109.9 | C14—C13—Si | 122.19 (17) |
| C4'—C3'—H3'B | 109.9 | C15—C14—C13 | 121.9 (2) |
| H3'A—C3'—H3'B | 108.3 | C15—C14—H14A | 119.0 |
| C5'—C4'—C3' | 109.21 (17) | C13—C14—H14A | 119.0 |
| C5'—C4'—H4'A | 109.8 | C16—C15—C14 | 119.1 (2) |
| C3'—C4'—H4'A | 109.8 | C16—C15—H15A | 120.5 |
| C5'—C4'—H4'B | 109.8 | C14—C15—H15A | 120.5 |
| C3'—C4'—H4'B | 109.8 | C17—C16—C15 | 120.7 (2) |
| H4'A—C4'—H4'B | 108.3 | C17—C16—H16A | 119.7 |
| O4—C4—N3 | 120.0 (2) | C15—C16—H16A | 119.7 |
| O4—C4—C5 | 125.8 (2) | C16—C17—C18 | 119.6 (2) |
| N3—C4—C5 | 114.18 (19) | C16—C17—H17A | 120.2 |
| C6—C5—C4 | 120.3 (2) | C18—C17—H17A | 120.2 |
| C6—C5—H5A | 119.9 | C17—C18—C13 | 121.8 (2) |
| C4—C5—H5A | 119.9 | C17—C18—H18A | 119.1 |
| C6'—C5'—C4' | 111.68 (17) | C13—C18—H18A | 119.1 |
| C6'—C5'—H5'A | 109.3 | C22—C19—H19A | 109.5 |
| C4'—C5'—H5'A | 109.3 | C22—C19—H19B | 109.5 |
| C6'—C5'—H5'B | 109.3 | H19A—C19—H19B | 109.5 |
| C4'—C5'—H5'B | 109.3 | C22—C19—H19C | 109.5 |
| H5'A—C5'—H5'B | 107.9 | H19A—C19—H19C | 109.5 |
| O7'—C6'—O1' | 109.20 (16) | H19B—C19—H19C | 109.5 |
| O7'—C6'—C11' | 111.75 (17) | C22—C20—H20A | 109.5 |
| O1'—C6'—C11' | 106.17 (16) | C22—C20—H20B | 109.5 |
| O7'—C6'—C5' | 106.73 (16) | H20A—C20—H20B | 109.5 |
| O1'—C6'—C5' | 110.88 (17) | C22—C20—H20C | 109.5 |
| C11'—C6'—C5' | 112.14 (17) | H20A—C20—H20C | 109.5 |
| C5—C6—N1 | 122.0 (2) | H20B—C20—H20C | 109.5 |
| C5—C6—H6A | 119.0 | C20—C22—C23 | 108.30 (19) |
| N1—C6—H6A | 119.0 | C20—C22—C19 | 108.97 (19) |
| C8—C7—C12 | 116.7 (2) | C23—C22—C19 | 109.75 (18) |
| C8—C7—Si | 121.68 (17) | C20—C22—Si | 110.46 (14) |
| C12—C7—Si | 121.27 (16) | C23—C22—Si | 111.55 (15) |
| C9—C8—C7 | 121.8 (2) | C19—C22—Si | 107.78 (15) |
| C9—C8—H8A | 119.1 | C22—C23—H23A | 109.5 |
| C7—C8—H8A | 119.1 | C22—C23—H23B | 109.5 |
| O7'—C8'—C1'' | 105.03 (16) | H23A—C23—H23B | 109.5 |
| O7'—C8'—C9' | 110.61 (17) | C22—C23—H23C | 109.5 |
| C1''—C8'—C9' | 114.08 (19) | H23A—C23—H23C | 109.5 |
| O7'—C8'—H8'A | 109.0 | H23B—C23—H23C | 109.5 |
| C1''—C8'—H8'A | 109.0 |
| D—H···A | D—H | H···A | D···A | D—H···A |
| N3—H3A···O4i | 0.86 | 2.03 | 2.873 (2) | 166 |
| Symmetry codes: (i) −x, −y+2, −z. |
| D—H···A | D—H | H···A | D···A | D—H···A |
| N3—H3A···O4i | 0.86 | 2.03 | 2.873 (2) | 166 |
| Symmetry codes: (i) −x, −y+2, −z. |
The authors thank the New Zealand Tertiary Education Commission for the award of a Top Achiever Doctoral Scholarship (KWC).
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The title uridine was prepared as a part of study to elaborate 6,6-spiroacetal scaffolds to incorporate a nucleobase at the anomeric position, thus generating a collection of novel hybrid structures. Similar syntheses of 6,6-spiroacetal based molecules in the presence of a Lewis acid and persilylated nucleophile have been reported by Mead & Zemribo (1996) and Brimble et al. (1998, 2004).
Figure 1 depicts the structure and atom numbering of the title uridine. The spiroacetal ring system adopts a conformation in which each of the O atoms (O1' and O7') adjacent to the C6' spirocentre adopts an axial position on the neighbouring ring, thus gaining maximum stabilization from the anomeric effect. The silyl-protected hydroxymethyl and uracil substituents adopt equatorial positions on their associated tetrahydropyran rings in order to minimized unfavourable steric interactions.
Figure 2 depicts molecular packing of racemic uridine units. The dimeric (2'R*,6'R*,8'R*) and (2'S*,6'S*,8'S*)-uridine units are connected to each other by the crystallographic inversion centres via intermolecular N3–H3A···O4 hydrogen bonds (Table 1).