Many nucleos(t)ides exist in solution as a mixture of 'north' (C2'-exo/C3'-endo) and 'south' (C2'-endo/C3'-exo) conformers.  Rigorous identification of the N/S conformations and their relative populations is often performed by providing the program PSEUROT with 1H-1H coupling constant data (3J) obtained from high-resolution 1H NMR spectra.  PSUEROT then attempts to 'build' a pair of N/S conformers that best replicate in experimental J's.  The user must specify, from a limited selection within PSEUROT, the 'A' and 'B' parameters that allow PSEUROT to perform this building properly.  This is a major limitation of the program, as A and B parameters for novel furanose rings not in the PSEUROT database must be derived from either from a large body of crystal structures or from high-level quantum mechanical structures.  This talk will describe our recent success at deriving the A and B parameters for a variety of novel nucleosides using molecular mechanics (Amber) calculations.

Conformational analysis of nucleosides: A systematic update of PSEUROT using quantum mechanical- and molecular mechanics-derived parameters

244th National Meeting (2012)

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