Semi-empirical and linear-scaling DFT methods to characterize duplex DNA and G-quadruplexes in the presence of interacting small molecules

descriptionPublicationkeyboard_double_arrow_right Article , Preprint 01 Jan 2022Embargo end date: 01 Jan 2022 United Kingdom English Publisher:Royal Society of Chemistry (RSC)Journal:Physical Chemistry Chemical Physics, volume 24, pages 11,510-11,519 (issn: 1463-9076, eissn: 1463-9084,

Copyright policy )Funded by:FCT | BioISI, FCT | INSILNANOBIOSOL, FCT | BioISI

Authors: Ortiz de Luzuriaga, Iker; Elleuchi, Sawssen; Jarraya, Khaled; Artacho, Emilio; López, Xabier; Gil, Adrià;

doi: 10.1039/d2cp00214k , 10.48550/arxiv.2201.07157 , 10.17863/cam.123249

pmid: 35362496

arXiv: 2201.07157

handle: 10261/303697

Semi-empirical and linear-scaling DFT methods to characterize duplex DNA and G-quadruplexes in the presence of interacting small molecules

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Abstract

SIESTA LS-DFT method at LMKLL/DZDP level and PM6-DH2 semi-empirical method are suitable to obtain correct geometries for DNA structures interacting with small molecules. However, only the SIESTA method reproduces the interaction energies when comparing to DLPNO-CCSD(T) and data bases.

Country

United Kingdom

Related Organizations

Instituto de Síntesis Química y Catálisis Homogénea
Spain
University of Cambridge
United Kingdom
University of Sfax
Tunisia
Ikerbasque
Spain
University of Lisbon
Portugal

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Keywords

Chemical Physics (physics.chem-ph), FOS: Physical sciences, Hydrogen Bonding, DNA, Computational Physics (physics.comp-ph), Ligands, G-Quadruplexes, Physics - Chemical Physics, Quantum Theory, Physics - Computational Physics

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