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Updated: Aug 5, 2026
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Free Radicals in Chemical Biology: from Chemical Behavior to Biomarker Development
Published on: April 15, 2013
Reaction coordinates of biomolecular isomerization
P G Bolhuis1, C Dellago, D Chandler
1Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom.
Summary
Transition path sampling reveals that describing alanine dipeptide isomerization requires more than just phi and psi angles. Solvent effects in aqueous solution are more specific than simple friction models suggest.
Area of Science:
- Computational chemistry
- Molecular dynamics simulations
- Biophysics
Background:
- Understanding molecular isomerization is crucial for chemical and biological processes.
- Traditional models often simplify reaction coordinates, potentially missing key dynamics.
- Alanine dipeptide serves as a fundamental model system for studying conformational changes.
Purpose of the Study:
- To investigate the essential degrees of freedom for alanine dipeptide isomerization using transition path sampling.
- To compare the dynamics in vacuum versus aqueous solution.
- To evaluate the adequacy of current reaction coordinate definitions and solvent models.
Main Methods:
- Application of transition path sampling to molecular dynamics simulations.
- Analysis of dihedral angles (phi, psi) and other relevant degrees of freedom.
- Modeling of alanine dipeptide in both vacuum and aqueous environments.
Main Results:
- Isomerization of alanine dipeptide necessitates more degrees of freedom beyond phi and psi.
- An additional dihedral angle was identified as significant in vacuum simulations.
- Solvent variables play a specific and critical role in solution, exceeding typical friction model capabilities.
Conclusions:
- The reaction coordinate for alanine dipeptide isomerization is complex and multi-dimensional.
- Solvent interactions are highly specific and crucial for accurate molecular dynamics modeling.
- Findings have implications for simulating larger biomolecules and understanding their conformational dynamics.
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