Energetics and J-coupling constants for Ala, Gly, and Val peptides demonstrated using ABEEM polarizable force field in vacuo and an aqueous solution

The development of an atom-bond electronegativity equalisation method at the sigma pi-level (ABEEM) polarisable force field (PFF) for peptides is presented. ABEEM PFF utilises a fluctuating charge model to explicitly describe the polarisation effects in an extensive environment. The partial charge of any individual site changes in response to changes in its surroundings. The peptide parameters are derived from ab initio methods in vacuum using a consistent and automatic protocol. By including explicit sigma- and pi-bond sites and lone pair sites, the anisotropy around an atom has been characterised. The fluctuating charge at each site ensures the distinction between the intrinsic behaviour observed among the various conformations of peptides, as corroborated by the agreement between quantum mechanics (QM) and ABEEM PFF concerning the calculated energy order, charge distribution, locations of minima, and potential energy surface (PES) in vacuo. The energy barriers in the PES have been clearly described using ABEEM PFF, in which a good charge distribution plays a vital role. Molecular dynamic simulations have been performed for short peptides in explicit ABEEM 7P-water boxes to examine their conformational properties in solution. The J-coupling constants obtained using ABEEM PFF are consistent with the experimental nuclear magnetic resonance (NMR) spectra and the influence of the chain length and temperature also investigated. The results demonstrate that the ABEEM PFF method is capable of locating conformations and describing the energetics of peptides with high accuracy and efficiency both in vacuo and an aqueous solution.

Automated summary

This article presents the development of an atom-bond electronegativity equalisation method at the sigma pi-level (ABEEM) polarisable force field (PFF) for peptides. The ABEEM PFF utilises a fluctuating charge model to explicitly describe the polarisation effects in an extensive environment. Molecular dynamic simulations have been performed to examine the conformational properties of peptides in solution. Results show that the ABEEM PFF method is capable of accurately locating conformations and describing the energetics of peptides both in vacuo and aqueous solution.