Reaction coordinates of biomolecular isomerization

Transition path sampling has been applied to the molecular dynamics of the alanine dipeptide in vacuum and in aqueous solution. The analysis shows tha t more degrees of freedom than the traditional dihedral angles, phi and psi , are necessary to describe the reaction coordinates for isomerization of t his molecule. In vacuum, an additional dihedral angle is identified as sign ificant. In solution, solvent variables are shown to play a significant rol e, and this role appears to be more specific than can be captured by fricti on models. Implications for larger molecules are discussed.