| Parametrization of an empirical correction term to density functional theory for an accurate description of pi-stacking interactions in nucleic acids. | |
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MedLine Citation:
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PMID: 17949028 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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We present an accurate parametrization of density functional theory augmented with an empirical correction term to describe properly pi-stacking interactions in nucleic acids. The approach is based on the popular Perdew-Burke-Ernzerhof (PBE), Becke-Perdew (BP), and hybrid Becke-Lee-Yang-Parr (B3LYP) density functionals augmented by a classical London C(6)R(-6) dispersion term. The novelty of our implementation lies in the accurate tuning of the empirical parameters, included in the [formula: see text] damping function, to reproduce high-level post Hartree-Fock calculations. In particular, we present sets of parameters and the needed code to correct the PBE, BP, and B3LYP results from the Turbomole and ADF packages in connection with basis sets of double and triple zeta quality. The developed approach is validated by comparison with the JSCH-2005 benchmark and with best quality stacking energies reported in the literature for the stacking of H-bonded nucleic acids base pairs. |
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Authors:
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Jean-Marie Ducéré; Luigi Cavallo |
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Publication Detail:
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Type: Journal Article; Research Support, Non-U.S. Gov't Date: 2007-10-19 |
Journal Detail:
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Title: The journal of physical chemistry. B Volume: 111 ISSN: 1520-6106 ISO Abbreviation: J Phys Chem B Publication Date: 2007 Nov |
Date Detail:
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Created Date: 2007-11-08 Completed Date: 2007-12-06 Revised Date: - |
Medline Journal Info:
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Nlm Unique ID: 101157530 Medline TA: J Phys Chem B Country: United States |
Other Details:
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Languages: eng Pagination: 13124-34 Citation Subset: IM |
Affiliation:
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Dipartimento di Chimica, Università di Salerno, Via ponte don Melillo, Fisciano (SA), I-84084, Italy. |
Export Citation:
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APA/MLA Format Download EndNote Download BibTex |
| MeSH Terms | |
Descriptor/Qualifier:
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Computer Simulation DNA / chemistry* Dimerization Models, Chemical* Models, Molecular RNA / chemistry* Solvents Thermodynamics |
| Chemical | |
Reg. No./Substance:
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0/Solvents; 63231-63-0/RNA; 9007-49-2/DNA |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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