Abstract
A detailed study of energy differences between the highest occupied and lowest unoccupied molecular orbitals (HOMO–LUMO gaps) in protein systems and water clusters is presented. Recent work questioning the applicability of Kohn–Sham density-functional theory to proteins and large water clusters (Rudberg 2012 J. Phys.: Condens. Matter 24 072202) has demonstrated vanishing HOMO–LUMO gaps for these systems, which is generally attributed to the treatment of exchange in the functional used. The present work shows that the vanishing gap is, in fact, an electrostatic artefact of the method used to prepare the system. Practical solutions for ensuring the gap is maintained when the system size is increased are demonstrated. This work has important implications for the use of large-scale density-functional theory in biomolecular systems, particularly in the simulation of photoemission, optical absorption and electronic transport, all of which depend critically on differences between energies of molecular orbitals.
Highlights
Density-functional theory (DFT) [1, 2] simulations are becoming increasingly widespread for simulating biological systems at the level of individual atoms and electrons
We suggest a number of practical measures for preparing large systems that do not lead to a vanishing HOMO–LUMO gap and open the way for continued investigations of biomolecular systems with Kohn–Sham DFT
We have demonstrated that water clusters extracted from the equilibrated bulk display large multipole moments, as measured both by molecular mechanics (MM) and quantum mechanics (QM)
Summary
Density-functional theory (DFT) [1, 2] simulations are becoming increasingly widespread for simulating biological systems at the level of individual atoms and electrons. It has been shown that recovery of a sizeable gap and robust self-consistent convergence of the electronic energy levels is possible by including electrostatically embedded point charges to represent water molecules around an inner cluster treated with quantum mechanics (QM) [19, 27] or by simulating the system in a dielectric medium [23]. These results point to the possibility that the vanishing gap is a surface effect and not an inherent difficulty with pure Kohn–Sham DFT.
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