Crystal and molecular structure of (−)-(5S)-5-hydroxy-5,6-dihydrothymidine

Abstract

CIoH16N206 is monoclinic, space group P21, with a = 5-534 (2), b = 12.023 (3), c = 9-242 (3) A, ]/= 97.91 (3) °. The structure was refined to an R of 0.070 for 1138 significant reflexions. The pyrimidine ring displays a twisted half-chair conformation with C(5) and C(6) displaced by 0.286 and 0.362 A on opposite sides of the plane. The conformation about the glycosyl linkage is anti with :¢ = 68-7 °.

Principles of Nucleic Acid Structure

“…In general, C2,-endo allows more conformational freedom for torsion angles X and yas indicated by population of x(syn) and y(-sc) ranges, which are either largely suppressed (x) or not existent (y) in Ca,-endo (N) pucker. Five data points around P -90° (04 ,-endo) have been omitted: for the derivative displayed in Figure 4-10, P = 91.3°, 'Tm = 45.8°; for deoxyguanosine 5'-phosphate, P = 83.3°, 'Tm = 40.8° (300); for dihydrothymidine, P = 84.3°, Tm = 31.6° (397); for 5-hydroxy-5, 6-dihydrothymidine, P = 95.7°, Tm = 37.6° (398); and for 1-I3-D-arabinofuranosylthymine, P = 105.5", Tm = 41.4° (399). On the other side of the pseudorotation cycle (P -270°, 04,-exo), no data points are found.…”

“…This kind of stacking specificity even overrides hydrogen-bonding effects. In the series deoxyadenosine monohydrate (492), adenosine 5'-phosphate (493), adenosine: 5-bromouridine (494), deoxyguanosine: 5-bromodeoxyuridine (398), the purine bases all stack in the pattern described in Figure 6-8a although crystal space groups, cell dimensions, molecular packing, and hydrogen-bonding schemes differ from each other. Similarly, the stacking specificity is pronounced in halogenated bases.…”

A conformational study of the adducts of 2′-deoxythymidine and 2,2,6,6-tetramethyl-1,4-piperidone-N-oxyl by 1H and 13C nuclear magnetic resonance

“…Evidence points to a distorted half-chair conformation for 5,6-saturated pyrimidines in which C5 and C6 lie on opposite sides of the mean plane defined by Nl--C2-N3--C4 (7,(17)(18)(19). Of the molecules considered here, crystallographic data are available only for 5HS, which shows a half-chair with the 5-hydroxyl and 5-methyl groups in pseudo-axial and pseudo-equatorial positions, respectively (7).…”

Radiation-induced binding of 2,2,6,6-tetramethyl-1,4-piperidone-N-oxyl to thymidine in oxygen-free aqueous solutions. Isolation and characterization of the adducts

“…In the same way, the two 5 s diastereoisomers 2 and 4 have been prepared from the (5s)-diastereoisomer of 5-hydroxy-5,6-dihydrothymidine (10) (39). The cis and trans configuration of the two nucleosides of each pair of 5R and 5 s diastereoisomers could be deduced by considering the y-effect of the C(6) TAN substituent on the 13C nmr chemical shift value of the pyrimidine methyl group.…”