title: Self-consistent field convergence for proteins: a comparison of full and localized-molecular-orbital schemes.
abstract: Proteins in the gas phase present an extreme (and unrealistic) challenge for self-consistent-field iteration schemes because their ionized groups are very strong electron donors or acceptors, depending on their formal charge. This means that gas-phase proteins have a very small band gap but that their frontier orbitals are localized compared to "normal" conjugated semiconductors. The frontier orbitals are thus likely to be separated in space so that they are close to, but not quite, orthogonal during the SCF iterations. We report full SCF calculations using the massively parallel EMPIRE code and linear scaling localized-molecular-orbital (LMO) calculations using Mopac2009. The LMO procedure can lead to artificially over-polarized wavefunctions in gas-phase proteins. The full SCF iteration procedure can be very slow to converge because many cycles are needed to overcome the over-polarization by inductive charge shifts. Example molecules have been constructed to demonstrate this behavior. The two approaches give identical results if solvent effects are included.
authors.affiliation: Computer-Chemie-Centrum and Interdisciplinary Center for Molecular Materials, Department Chemie und Pharmazie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nägelsbachstrasse 25, 91052, Erlangen, Germany.
authors.forename: Christian R
authors.initials: CR
authors.lastname: Wick
authors.forename: Matthias
authors.initials: M
authors.lastname: Hennemann
authors.forename: James J P
authors.initials: JJ
authors.lastname: Stewart
authors.forename: Timothy
authors.initials: T
authors.lastname: Clark
mesh_terms: D003198:Computer Simulation; D006801:Humans; D008958:Models, Molecular; D015394:Molecular Structure; D057105:Nuclear Receptor Subfamily 4, Group A, Member 1 / Q000737:chemistry; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D012984:Software
chemical_list: C539821:NR4A1 protein, human; D057105:Nuclear Receptor Subfamily 4, Group A, Member 1; D011506:Proteins