Document Detail


Semi-empirical molecular orbital methods including dispersion corrections for the accurate prediction of the full range of intermolecular interactions in biomolecules.
MedLine Citation:
PMID:  17492099     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Semi-empirical calculations including an empirical dispersive correction are used to calculate intermolecular interaction energies and structures for a large database containing 156 biologically relevant molecules (hydrogen-bonded DNA base pairs, interstrand base pairs, stacked base pairs and amino acid base pairs) for which MP2 and CCSD(T) complete basis set (CBS) limit estimates of the interaction energies are available. The dispersion corrected semi-empirical methods are parameterised against a small training set of 22 complexes having a range of biologically important non-covalent interactions. For the full molecule set (156 complexes), compared to the high-level ab initio database, the mean unsigned errors of the interaction energies at the corrected semi-empirical level are 1.1 (AM1-D) and 1.2 (PM3-D) kcal mol(-1), being a significant improvement over existing AM1 and PM3 methods (8.6 and 8.2 kcal mol(-1)). Importantly, the new semi-empirical methods are capable of describing the diverse range of biological interactions, most notably stacking interactions, which are poorly described by both current AM1 and PM3 methods and by many DFT functionals. The new methods require no more computer time than existing semi-empirical methods and therefore represent an important advance in the study of important biological interactions.
Authors:
Jonathan P McNamara; Ian H Hillier
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Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't     Date:  2007-03-22
Journal Detail:
Title:  Physical chemistry chemical physics : PCCP     Volume:  9     ISSN:  1463-9076     ISO Abbreviation:  Phys Chem Chem Phys     Publication Date:  2007 May 
Date Detail:
Created Date:  2007-05-11     Completed Date:  2007-10-04     Revised Date:  2008-11-21    
Medline Journal Info:
Nlm Unique ID:  100888160     Medline TA:  Phys Chem Chem Phys     Country:  England    
Other Details:
Languages:  eng     Pagination:  2362-70     Citation Subset:  IM    
Affiliation:
School of Chemistry, University of Manchester, Oxford Road, Manchester, UK.
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MeSH Terms
Descriptor/Qualifier:
Base Pairing*
Energy Transfer
Hydrogen Bonding
Hydrophobicity
Models, Chemical*
Models, Molecular
Molecular Conformation
Nucleic Acids / chemistry*
Nucleotides / chemistry*
Proteins / chemistry*
Quantum Theory
Static Electricity
Thermodynamics
Chemical
Reg. No./Substance:
0/Nucleic Acids; 0/Nucleotides; 0/Proteins

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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