Studium interakcí organické hmoty a jejích složek pomocí molekulární dynamiky.

Bc. Hana BARVÍKOVÁ

Diplomová práce

Study of interactions of organic matter and its components via molecular dynamics.

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.

Klíčová slova

molekulární dynamika, počítačové simulace, GROMACS, modelování interakcí, organické molekuly, minerální povrchy, křemen, povrchová hustota náboje, silové pole, adsorpce, termodynamika, interakční energie, potenciál střední síly, PMF

Jazyk práce: čeština

Datum vytvoření / odevzdání či podání práce: 25. 4. 2014

Zveřejnit od: 25. 4. 2014

Obhajoba závěrečné práce

• Vedoucí: doc. RNDr. Milan Předota, Ph.D.

JIHOČESKÁ UNIVERZITA V ČESKÝCH BUDĚJOVICÍCH

Přírodovědecká fakulta

Magisterský studijní program / obor:
Biofyzika / Biofyzika