Self-consistent field convergence for proteins: a comparison of full and localized-molecular-orbital schemes
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.
KeywordsLinear scaling LMO-SCF NDDO Proteins Self-consistent field
- 1.Clark T, Stewart JJP (2011) MNDO-like semiempirical molecular orbital theory and its application to large systems. In: Reimers JJ (ed) Computational methods for large systems, chap 8. Wiley, Chichester,Google Scholar
- 7.Hennemann M, Clark T (2013) EMPIRE. Universität Erlangen-Nürnberg and Cepos InSilico Ltd (http://www.ceposinsilico.de/products/empire.htm). Accessed 19 Jan 2014
- 8.Stewart JJP (2008) MOPAC2009. Stewart Computational Chemistry, Colorado Springs, CO, USA. http://OpenMOPAC.net. Accessed 19 Jan 2014
- 11.Min JR, Schuetz A, Loppnau P, Weigelt J, Sundstrom M, Arrowsmith CH, Edwards AM, Bochkarev A, Plotnikov AN (2014) Human NR4A1 ligand-binding domain. http://www.pdb.org/pdb/explore/explore.do?structureId=2QW4. Accessed 19 Jan 2014
- 12.Case DA, Darden TA, Cheatham III TE, Simmerling CL, Wang J, Duke RE, Luo R, Walker RC, Zhang W, Merz KM, Roberts B, Hayik S, Roitberg A, Seabra G, Swails J, Goetz AW, Kolossváry I, Wong KF, Paesani F, Vanicek J, Wolf RM, Liu J, Wu X, Brozell SR, Steinbrecher T, Gohlke H, Cai Q, Ye X, Wang J, Hsieh M-J, Cui G, Roe DR, Mathews DH, Seetin MG, Salomon-Ferrer R, Sagui C, Babin V, Luchko T, Gusarov S, Kovalenko A, Kollman PA (2012) AMBER 12. University of California, San Francisco. http://ambermd.org/. Accessed 19 Jan 2014