Empirical Valence-Bond Models Based on Polarizable Force Fields for Infrared Spectroscopy

This chapter describes an accurate computational framework for modeling the Infrared (IR) spectra of biomolecules undergoing proton transfer in the gas phase. It presents the experimental motivation behind the development of the framework, which focuses on the aspartate molecule, and proceeds by showing the limitations of standard quantum mechanical (QM) approaches, as well as the simulations with non-reactive force fields, for reproducing IR spectra. The chapter relies on the accuracy of the atomic multipole optimized energetics for biomolecular simulation (AMOEBA) force field to describe the main part of the proton motion. It discusses the implementation of a two-state empirical valence-bond (EVB) model for the computation of IR spectra, in particular for systems containing a signature of proton motion in flexible molecules. This model uses the AMOEBA polarizable force field to describe the potential energy of the diabatic states and a simple form of the coupling potential.