Given the recent and ongoing increases in computational resources for simulating large biomolecules, and the variety of complex environments researchers wish to study these systems in, it is worth examining how conventional molecular mechanics algorithms could be improved upon by including interactions that are historically neglected. Specifically, force fields that are based on fixed charges only implicitly incorporate polarization energies through their parameterization and other included forces, and struggle to quantitatively describe the extent to which other <i>ab initio</i> interactions are at play. As such, we will present our approach to augmenting AMBER based force fields for nucleic acids with the ability to explicitly account for electron polarization. Within our model, the traditionally fixed charges are replaced with fluctuating charge densities that can adjust to a molecule's geometry and environment. With the aid of density functional theory calculations of small oligonucleotides, we examine how the balance of frozen electrostatics, polarization, and charge transfer can be used to improve the description of hydrogen bonding in nucleic acid simulations.

Simulations in charge of their own electrostatics: Augmenting a nucleic acid force field with fluctuating charge densities

ACS Spring 2022

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