Development of a polarizable intermolecular potential function (PIPF) for liquid amides and alkanes

Area of Science:

• Computational Chemistry
• Molecular Dynamics
• Biophysics

Background:

• Accurate molecular simulations require precise force fields.
• Polarization effects are crucial for understanding liquid properties, especially in amides.
• Existing force fields may not fully capture these polarization phenomena.

Purpose of the Study:

• To develop and validate a polarizable intermolecular potential function (PIPF) for liquid alkanes and amides.
• To integrate this PIPF with the CHARMM22 force field (PIPF-CHARMM).
• To assess its performance in molecular dynamics simulations and for protein backbone modeling.

Main Methods:

• Development of a polarizable intermolecular potential function using the Thole interacting dipole (TID) model.
• Molecular dynamics simulations of liquid alkanes and amides.
• Comparison of computed properties (heat of vaporization, liquid density, dipole moment) with experimental data.
• Evaluation of protein backbone potential energy surfaces (amide bond rotation, Ramachandran plots) against ab initio calculations.

Main Results:

• The PIPF-CHARMM potential accurately describes structural and thermodynamic properties of liquid alkanes and amides, with computed values within 1.4% of experimental data.
• Significant increase in molecular dipole moments (1.5–1.8 D) observed for amides due to polarization.
• Polarization energies contribute substantially (6–24%) to total intermolecular interaction energy.
• Promising agreement with ab initio and CHARMM22 results for protein backbone representations.

Conclusions:

• The developed PIPF-CHARMM potential offers an adequate description of liquid alkanes and amides.
• Polarization is a key factor in the behavior of liquid amides.
• The PIPF-CHARMM shows potential as a foundation for a comprehensive polarizable protein force field.