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Hoffmann, R. A wiki for the life sciences where authorship matters. Nature Genetics (2008)

Intramolecular hydrogen bonding and molecular conformations of nucleosides. N (6)-dimethyl-2',3'-isopropylidene adenosine.

The physical properties of an adenosine derivative, N(6)-dimethyl-2',3'-O-isopropylidene adenosine, Derivative 1, which is capable of intramolecular hydrogen bond formation between base-ring and sugar exocyclic hydroxymethyl group, have been studied in solution by infrared, circular dichroic and nuclear magnetic resonance spectroscopy. Analysis of the 220 MHZ 1H NMR spectrum of Derivative 1 in C2HCl2 solution indicated an overwhelming preference for the gg conformation for rotation about the C(4')--C5') bond and a predominant conformation for rotation about the C(5')--O(5') bond in which OH(5') projects towards the base ring. The purine base ring was shown to be in a predominant syn conformation with respect to the sugar ring by 100 MHZ 1H nuclear Overhauser experiments, by analysis of 3J(13C,H1') magnitudes observed in proton-coupled 13C NMR experiments and by CD measurements. Combination of each conformation feature of Derivative 1 in non-polar solvents is consistent with the overall molecular conformation observed in the solid state in which intramolecular hydrogenbonding exists between purine N(3) and the sugar CH2OH group; the presence of a strong intramolecular hydrogen bond was observed by infrared spectroscopy. The sugar ring conformations of 2',3'-O-isopropylidene ribonucleosides were analysed in terms of the pseudorotational properties of the ring; the N and S conformations tend toward to C(2')-exo and C(3')-'exo conformations, respectively, compared to normal ribonucleosides (C(3')-endo and C(2')-endo, respectively). The presence of the hydrogen bond in the derivative is sufficient to promote the S-type conformations (approx. 80%--90%) compared to cases where such a strong hydrogen bond is unlikely to be present approx. 40--50%).[1]


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