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A three-layer ONIOM model for the outside binding of cationic porphyrins and nucleotide pair DNA.
MedLine Citation:
PMID:  23053008     Owner:  NLM     Status:  Publisher    
Abstract/OtherAbstract:
In this work we investigated the outside binding mode between a cationic porphyrin and a nucleotide pair of DNA, adenine-thymine and guanine-cytosine, in a supramolecular assembly. We used two structural models (semi-extended, extended) that differ in the size of porphyrin, two kinds of theoretical methods: a three layer ONIOM (B3LYP/6-31G(d)/PM3/UFF), and DFT B3LYP/6-31G(d,p), and three cationic porphyrins. ONIOM method was first tested on the semi-extended model that was calculated in four environments: gas phase, solution phase using an explicit solvent model (H(2)O), in the presence of a sodium cation (Na(+)) and in both (H(2)O + Na(+)). From interaction energy results, we found that the affinity of the cationic substituent by the adenine nucleotide is favored upon the thymine nucleotide. The extended model that considers the whole porphyrin was applied in the gas phase to the four nucleotides. All the cationic porphyrins showed affinity by the nucleotides in the order adenine > guanine > thymine > cytosine. The interaction energy values for outside binding showed a strong porphyrin-nucleotide interaction (≈-90 kcal mol(-1)), that slightly varies between the nucleotides suggesting that this kind of cationic porphyrin has a little selectivity for some of them. We also found that the effect of the nature of the cationic substituent (chain length) in the porphyrin on the outside binding is small (≈2-13 kcal mol(-1)). Coherence between the results showed that ONIOM is a useful tool to get a reasonable molecular geometry to be used as a starting point in calculations of density functional theory.
Authors:
Gloria I Cárdenas-Jirón; Luis Cortez-Santibañez
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Publication Detail:
Type:  JOURNAL ARTICLE     Date:  2012-10-11
Journal Detail:
Title:  Journal of molecular modeling     Volume:  -     ISSN:  0948-5023     ISO Abbreviation:  J Mol Model     Publication Date:  2012 Oct 
Date Detail:
Created Date:  2012-10-11     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  9806569     Medline TA:  J Mol Model     Country:  -    
Other Details:
Languages:  ENG     Pagination:  -     Citation Subset:  -    
Affiliation:
Theoretical Chemistry Laboratory, Faculty of Chemistry and Biology, University of Santiago de Chile (USACH), Casilla 40, Correo 33, Santiago, Chile, gloria.cardenas@usach.cl.
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