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A molecular dynamics method for calculating molecular volume changes appropriate for biomolecular simulation.

Russell DeVane1, Christina Ridley, Randy W Larsen

  • 1Department of Chemistry, University of South Florida, Tampa, Florida 33620-5250, USA.

Biophysical Journal
|October 29, 2003
PubMed
Summary

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This study introduces a molecular dynamics method to measure molecular volume changes in solution, complementing experimental photothermal techniques. The simulation accurately captures thermodynamic volume changes, aiding biophysical research.

Area of Science:

  • Biophysics
  • Computational Chemistry
  • Physical Chemistry

Background:

  • Photothermal methods measure molecular volume changes on nanosecond timescales, crucial for studying transient species in solution.
  • A microscopic understanding of condensed-phase volume changes is needed to complement experimental data.

Purpose of the Study:

  • To develop and demonstrate a molecular dynamics (MD) method that mimics experimental measurements of molecular volume changes.
  • To provide microscopic resolution to thermodynamic measurements of solvated molecules.

Main Methods:

  • Isothermal-isobaric (NPT) molecular dynamics simulations were performed on solutions.
  • The volume of the system was calculated with and without a specific solute molecule to determine the solute's thermodynamic volume.

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  • Simulations were conducted on neat water, aqueous methane (charged and neutral), and an aqueous beta-sheet peptide.

    • Main Results:

    • The developed MD method successfully mimics experimental measurements of molecular volume changes.
    • Simulations lasting a few nanoseconds can discern volume changes of approximately 1.0 ml/mole.
    • The computational precision is comparable to empirical measurements.

    Conclusions:

    • The MD technique provides a synergistic approach with experimental methods for studying solvated molecules.
    • This method offers microscopic insights into thermodynamic volume changes, advancing biophysical investigations.