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Natural bond orbital analysis in the ONETEP code: Applications to large protein systems.
MedLine Citation:
PMID:  23065758     Owner:  NLM     Status:  Publisher    
Abstract/OtherAbstract:
First principles electronic structure calculations are typically performed in terms of molecular orbitals (or bands), providing a straightforward theoretical avenue for approximations of increasing sophistication, but do not usually provide any qualitative chemical information about the system. We can derive such information via post-processing using natural bond orbital (NBO) analysis, which produces a chemical picture of bonding in terms of localized Lewis-type bond and lone pair orbitals that we can use to understand molecular structure and interactions. We present NBO analysis of large-scale calculations with the ONETEP linear-scaling density functional theory package, which we have interfaced with the NBO 5 analysis program. In ONETEP calculations involving thousands of atoms, one is typically interested in particular regions of a nanosystem whilst accounting for long-range electronic effects from the entire system. We show that by transforming the Non-orthogonal Generalized Wannier Functions of ONETEP to natural atomic orbitals, NBO analysis can be performed within a localized region in such a way that ensures the results are identical to an analysis on the full system. We demonstrate the capabilities of this approach by performing illustrative studies of large proteins-namely, investigating changes in charge transfer between the heme group of myoglobin and its ligands with increasing system size and between a protein and its explicit solvent, estimating the contribution of electronic delocalization to the stabilization of hydrogen bonds in the binding pocket of a drug-receptor complex, and observing, in situ, the n → π* hyperconjugative interactions between carbonyl groups that stabilize protein backbones. © 2012 Wiley Periodicals, Inc.
Authors:
Louis P Lee; Daniel J Cole; Mike C Payne; Chris-Kriton Skylaris
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Publication Detail:
Type:  JOURNAL ARTICLE     Date:  2012-10-15
Journal Detail:
Title:  Journal of computational chemistry     Volume:  -     ISSN:  1096-987X     ISO Abbreviation:  J Comput Chem     Publication Date:  2012 Oct 
Date Detail:
Created Date:  2012-10-15     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  9878362     Medline TA:  J Comput Chem     Country:  -    
Other Details:
Languages:  ENG     Pagination:  -     Citation Subset:  -    
Copyright Information:
Copyright © 2012 Wiley Periodicals, Inc.
Affiliation:
TCM Group, Cavendish Laboratory, 19 JJ Thomson Ave, Cambridge CB3 0HE, United Kingdom. lpl24@cam.ac.uk.
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