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

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216208%3A11310%2F13%3A10191787" target="_blank" >RIV/00216208:11310/13:10191787 - isvavai.cz</a>
Alternative codes found
RIV/61388963:_____/13:00394209 RIV/61989592:15310/13:33148130 RIV/60461373:22330/13:43896533
Result on the web
<a href="http://dx.doi.org/10.1021/jp400198h" target="_blank" >http://dx.doi.org/10.1021/jp400198h</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1021/jp400198h" target="_blank" >10.1021/jp400198h</a>

Result language
angličtina
Original language name
On the Association of the Base Pairs on the Silica Surface Based on Free Energy Biased Molecular Dynamics Simulation and Quantum Mechanical Calculations
Original language 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 (W
Czech name
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Czech description
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Type
J<sub>x</sub> - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)
CEP classification
CF - Physical chemistry and theoretical chemistry
OECD FORD branch
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Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year
2013
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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