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 that more degrees of freedom than the traditional dihedral angles, φ and ψ, are necessary to describe the reaction coordinates for isomerization of this molecule. In vacuum, an additional dihedral angle is identified as significant. In solution, solvent variables are shown to play a significant role, and this role appears to be more specific than can be captured by friction models. Implications for larger molecules are discussed.