About: On the Association of the Base Pairs on the Silica Surface Based on Free Energy Biased Molecular Dynamics Simulation and Quantum Mechanical Calculations

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About: On the Association of the Base Pairs on the Silica Surface Based on Free Energy Biased Molecular Dynamics Simulation and Quantum Mechanical Calculations Goto Sponge NotDistinct Permalink

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
rdfs:seeAlso	http://dx.doi.org/10.1021/jp400198h
Description	The adsorption of the DNA bases and base pairs on the hydrophobic silica surface has been investigated by ab initio quantum mechanical (QM) methods (DFT-D) and molecular mechanics (MM) and also by biased molecular dynamics (MD) simulations (metadynamics). The structures of all the clusters (surface with single-bases and base pairs) predicted by means of the force field are compared with the results of direct QM calculations. The MM interaction energies for all clusters agreed well with the QM ones, which justifies the use of MM methods in the evaluation of accurate adsorption free energies. Rigid rotor-harmonic oscillator-ideal gas (RR-HO-IG) calculations based on QM and MM entropies as well as biased metadynamics (MTD) simulations based on MM demonstrated that mA-mT (Adenine-Thymine) and mG-mC (Guanine-Cytosine) base pairs are adsorbed on a fully solvated silica surface in different H-bonded forms. Both QM and MM techniques convincingly demonstrated that adsorptions of any H-bonded (Watson-Crick (WC), non-WC, and Hoogsteen) structures on the surface are stronger than that of any pi-pi stacked structures. The adsorption of the DNA bases and base pairs on the hydrophobic silica surface has been investigated by ab initio quantum mechanical (QM) methods (DFT-D) and molecular mechanics (MM) and also by biased molecular dynamics (MD) simulations (metadynamics). The structures of all the clusters (surface with single-bases and base pairs) predicted by means of the force field are compared with the results of direct QM calculations. The MM interaction energies for all clusters agreed well with the QM ones, which justifies the use of MM methods in the evaluation of accurate adsorption free energies. Rigid rotor-harmonic oscillator-ideal gas (RR-HO-IG) calculations based on QM and MM entropies as well as biased metadynamics (MTD) simulations based on MM demonstrated that mA-mT (Adenine-Thymine) and mG-mC (Guanine-Cytosine) base pairs are adsorbed on a fully solvated silica surface in different H-bonded forms. Both QM and MM techniques convincingly demonstrated that adsorptions of any H-bonded (Watson-Crick (WC), non-WC, and Hoogsteen) structures on the surface are stronger than that of any pi-pi stacked structures. (en)
Title	On the Association of the Base Pairs on the Silica Surface Based on Free Energy Biased Molecular Dynamics Simulation and Quantum Mechanical Calculations On the Association of the Base Pairs on the Silica Surface Based on Free Energy Biased Molecular Dynamics Simulation and Quantum Mechanical Calculations (en)
skos:prefLabel	On the Association of the Base Pairs on the Silica Surface Based on Free Energy Biased Molecular Dynamics Simulation and Quantum Mechanical Calculations On the Association of the Base Pairs on the Silica Surface Based on Free Energy Biased Molecular Dynamics Simulation and Quantum Mechanical Calculations (en)
skos:notation	RIV/00216208:11310/13:10191787!RIV14-GA0-11310___
http://linked.open...avai/predkladatel	Přírodovědecká fakulta
http://linked.open...avai/riv/aktivita	I P Z
http://linked.open...avai/riv/aktivity	I, P(ED2.1.00/03.0058), P(GBP208/12/G016), Z(MSM6046137305)
http://linked.open...iv/cisloPeriodika	21
http://linked.open...vai/riv/dodaniDat	2014
http://linked.open...aciTvurceVysledku	Haldar, Susanta
http://linked.open.../riv/druhVysledku	J - Článek v odborném periodiku
http://linked.open...iv/duvernostUdaju	S - Úplné a pravdivé údaje nepodléhající ochraně podle zvláštních právních předpisů
http://linked.open...titaPredkladatele	Univerzita Karlova v Praze / Přírodovědecká fakulta
http://linked.open...dnocenehoVysledku	93840
http://linked.open...ai/riv/idVysledku	RIV/00216208:11310/13:10191787
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	atomic charges; stacked structures; ab-initio; force-field; center-dot-thymine; isolated snall peptides (en)
http://linked.open.../riv/klicoveSlovo	atomic charges ab-initio force-field center-dot-thymine isolated snall peptides stacked structures
http://linked.open...odStatuVydavatele	NL - Nizozemsko
http://linked.open...ontrolniKodProRIV	[3D6FFE5C71D0]
http://linked.open...i/riv/nazevZdroje	Journal of Physical Chemistry C
http://linked.open...in/vavai/riv/obor	CF
http://linked.open...ichTvurcuVysledku	1 (xsd:int)
http://linked.open...cetTvurcuVysledku	3 (xsd:int)
http://linked.open...vavai/riv/projekt	Controlling structure and function of biomolecules at the molecular scale: theory meets experiment Regional Centre of Advanced Technologies and Materials
http://linked.open...UplatneniVysledku	2013
http://linked.open...v/svazekPeriodika	117
http://linked.open...iv/tvurceVysledku	Hobza, Pavel Spiwok, Vojtěch Haldar, Susanta
http://linked.open...ain/vavai/riv/wos	000319896700022
http://linked.open...n/vavai/riv/zamer	Teoretické základy potravinářských a biochemických technologií
issn	1932-7447
number of pages	10 (xsd:int)
http://bibframe.org/vocab/doi	10.1021/jp400198h
http://localhost/t...ganizacniJednotka	11310

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