Classical Molecular Dynamics with Mobile Protons.

Area of Science:

• Computational chemistry
• Biophysics
• Physical chemistry

Background:

• Classical molecular dynamics simulations cannot simulate chemical bond formation or breakage.
• Studying proton transfer, a fundamental chemical reaction, is thus challenging with standard methods.
• Existing methods for classical proton transfer are complex and not widely adopted.

Purpose of the Study:

• To develop an efficient and accurate computational method for simulating proton transfer in molecular systems.
• To overcome the limitations of classical molecular dynamics in handling chemical reactions.
• To enable routine study of proton transfer processes in biological and material systems.

Main Methods:

• Combined molecular dynamics with periodic stochastic proton hops.
• Introduced a non-Boltzmann acceptance criterion for computational efficiency.
• Adjusted parameters heuristically to maintain thermodynamic equilibria and proton transfer rates.
• Implemented the algorithm in the CHARMM program.

Main Results:

• Tested on proton diffusion in water and carbon nanotubes, and proton conductance in the gramicidin A channel.
• Successfully reproduced enhanced proton diffusivity in carbon nanotubes.
• Provided a reasonable estimation of proton conductance in the gramicidin A channel.
• Proposed parameters for hydronium, Asp, Glu, and His residues.

Conclusions:

• The proposed method offers an efficient and effective way to simulate proton transfer in classical molecular dynamics.
• This approach overcomes significant limitations of standard simulations for chemical reactions.
• The model shows promise for studying proton transport in biological channels and nanomaterials.