Original title: Studium interakcí organické hmoty a jejích složek pomocí molekulární dynamiky
Translated title: Study of interactions of organic matter and its components via molecular dynamics
Authors: BARVÍKOVÁ, Hana
Document type: Master’s theses
Year: 2014
Language: cze
Abstract: Humic acids and humates are principal components of humic substances major organic constituents of soil, peat, coal and water around the world. I was involved in research into molecular dynamics simulations of interactions of quartz surfaces with aqueous solutions of ions and small organic molecules representing basic building blocks of larger biomolecules and functional groups of organic matter. We studied interactions of molecules with surfaces for a set of surface charge densities corresponding to the experimentally or environmentally relevant ranges of pH values employing molecular mechanics, molecular dynamics and ab initio techniques. Simulated quartz surfaces covered the range of surface charge densities 0.00, -0.03, -0.06 and -0.12 C-m-2, approximately corresponding to pH values 4.5, 7.5, 9.5 and 11. As model molecules, benzoic acid, phenol, o-salicylic acid and their conjugated bases were chosen. My task was to prepare topologies and parametric models of selected organic matter basic building blocks organic molecules. I focused on studying interactions of these molecules in an aqueous environment with mineral surface quartz. The aim was to process simulation results and analyse conformations of the adsorption complexes and their thermodynamic properties such as interaction energies, free energies and adsorption geometries.
Keywords: adsoption; computer simulations; force field; GROMACS; interaction energy; mineral surfaces; modelling interactions; molecular dynamics; organic molecules; PMF; potential of mean force; quartz; surface charge density; termodynamics; adsorpce; GROMACS; interakční energie; křemen; minerální povrchy; modelování interakcí; molekulární dynamika; organické molekuly; PMF; potenciál střední síly; povrchová hustota náboje; počítačové simulace; silové pole; termodynamika
Citation: BARVÍKOVÁ, Hana. Studium interakcí organické hmoty a jejích složek pomocí molekulární dynamiky. České Budějovice, 2014. diplomová práce (Mgr.). JIHOČESKÁ UNIVERZITA V ČESKÝCH BUDĚJOVICÍCH. Přírodovědecká fakulta

Institution: University of South Bohemia in České Budějovice (web)
Document availability information: Fulltext is available in the Digital Repository of University of South Bohemia.
Original record: http://www.jcu.cz/vskp/30962

Permalink: http://www.nusl.cz/ntk/nusl-173115


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Universities and colleges > Public universities > University of South Bohemia in České Budějovice
Academic theses (ETDs) > Master’s theses