title: Electrostatic embedding in large-scale first principles quantum mechanical calculations on biomolecules.
abstract: Biomolecular simulations with atomistic detail are often required to describe interactions with chemical accuracy for applications such as the calculation of free energies of binding or chemical reactions in enzymes. Force fields are typically used for this task but these rely on extensive parameterisation which in cases can lead to limited accuracy and transferability, for example for ligands with unusual functional groups. These limitations can be overcome with first principles calculations with methods such as density functional theory (DFT) but at a much higher computational cost. The use of electrostatic embedding can significantly reduce this cost by representing a portion of the simulated system in terms of highly localised charge distributions. These classical charge distributions are electrostatically coupled with the quantum system and represent the effect of the environment in which the quantum system is embedded. In this paper we describe and evaluate such an embedding scheme in which the polarisation of the electronic density by the embedding charges occurs self-consistently during the calculation of the density. We have implemented this scheme in a linear-scaling DFT program as our aim is to treat with DFT entire biomolecules (such as proteins) and large portions of the solvent. We test this approach in the calculation of interaction energies of ligands with biomolecules and solvent and investigate under what conditions these can be obtained with the same level of accuracy as when the entire system is described by DFT, for a variety of neutral and charged species.
authors.affiliation: School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom.
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: Fox
authors.forename: Chris
authors.initials: C
authors.lastname: Pittock
authors.forename: Thomas
authors.initials: T
authors.lastname: Fox
authors.forename: Christofer S
authors.initials: CS
authors.lastname: Tautermann
authors.forename: Noj
authors.initials: N
authors.lastname: Malcolm
authors.forename: Chris-Kriton
authors.initials: CK
authors.lastname: Skylaris
mesh_terms: D001224:Aspartic Acid / Q000737:chemistry; D017122:Bacteriophage T4 / Q000201:enzymology; D008024:Ligands; D056004:Molecular Dynamics Simulation; D009113:Muramidase / Q000737:chemistry / Q000378:metabolism; D011487:Protein Conformation; D011789:Quantum Theory; D012997:Solvents / Q000737:chemistry; D055672:Static Electricity; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
chemical_list: D008024:Ligands; D012997:Solvents; D014867:Water; D001224:Aspartic Acid; D009113:Muramidase