diplomsko delo
Jure Kovač (Author), Matija Tomšič (Mentor)

Abstract

Za raziskovanje termodinamskih, strukturnih in dinamičnih lastnosti modelnih tekočih sistemov se v kemiji pogosto uporablja računalniške simulacije molekulske dinamike. Model konkretnega raziskovalnega sistema pripravimo s pomočjo t.i. »polja sil«. Polje sil je matematični izraz za potencialno energijo modelnega sistema v odvisnosti od položajev delcev sistema (atomi ali psevdo-atomi) s pripadajočimi parametri. Polja sil se med seboj lahko razlikujejo, ker so bila razvita za uporabo na različnih sistemih, ker so bila parametrizirana na različne načine in ker različno podrobno opišejo realni sistem. V diplomskem delu smo na primeru modelnega heksan-1-ola ob uporabi različnih polj sil (AMBER, CHARMM, OPLS, TraPPE in GROMOS) izvedli simulacije molekulske dinamike s programskim paketom GROMACS. Iz rezultatov simulacij smo izračunali različne radialne in prostorske porazdelitvene funkcije, razdaljo od-konca-do-konca, gostoto, difuzijski koeficient in izparilno entalpijo. Iz radialnih porazdelitvenih funkcij je razvidno, da imajo modeli heksan-1-ola z različnimi polji sil različne strukturne lastnosti tekoče faze, pri čemer kažeta united-atom modela (TraPPE in GROMOS) večjo tendenco po tvorbi vodikovih vezi, kot all-atom modeli (AMBER, CHARMM in OPLS). Iz medmolekulskih prostorskih porazdelitvenih funkcij smo ugotovili, da je povezovanje z vodikovimi vezmi v united-atom modelih nekoliko bolj usmerjeno, kot je pri all-atom modelih. Izračunana gostota modelnih sistemov se dobro ujema z eksperimentalno vrednostjo gostote, z izjemo modela s poljem sil AMBER. Najboljše ujemanje izračunanega difuzijskega koeficienta modelnega heksan-1 ola z eksperimentalno vrednostjo je bilo doseženo z modeloma OPLS in GROMOS. Izračunana izparilna entalpija modelov s polji sil TraPPE in OPLS se dobro ujema z eksperimentalno vrednostjo, medtem ko pri ostalih modelih ne dobimo dobrega ujemanja. Iz intramolekulskih prostorskih porazdelitvenih funkcij in porazdelitve razdalj od konca do-konca molekule je razvidno, da so modelne molekule heksan-1-ola s poljem sil GROMOS najbolj fleksibilne, tiste s poljem sil TraPPE, pa najbolj toge.

Keywords

računalniške simulacije;polje sil;heksan-1-ol;termodinamski ansambli;diplomska dela;

Data

Language: Slovenian
Year of publishing:
Typology: 2.11 - Undergraduate Thesis
Organization: UL FKKT - Faculty of Chemistry and Chemical Technology
Publisher: [J. Kovač]
UDC: 544.272(043.2)
COBISS: 122152963 Link will open in a new window
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Other data

Secondary language: English
Secondary title: Influence of different force fields on the properties of model liquids
Secondary abstract: Molecular dynamics simulations are commonly used in chemistry to study the thermodynamic, structural, and dynamic properties of model liquid systems. A force field is a mathematical expression for the potential energy of the model system as a function of the positions of the particles of the system (atoms or pseudo-atoms), including the parameters therein. Force fields differ from each other because they are developed for different model systems, are parameterized differently, and describe the real system in a different level of detail. In this work, we performed molecular dynamics simulations of a model of hexan-1-ol using different force fields (AMBER, CHARMM, OPLS, TraPPE, and GROMOS) with the simulation software package GROMACS. Various radial and spatial distribution functions, density, diffusion coefficient, end-to-end distance and enthalpy of vaporization were calculated from the simulation results. The radial distribution functions show that the different hexan-1-ol models have different structural properties of the liquid phase. The united-atom models (TraPPE and GROMOS) show a greater tendency to form hydrogen bonds than the all-atom models (OPLS, AMBER, and CHARMM). The calculated density of all model systems agrees well with the experimental value, except for the model AMBER. The best agreement of the calculated diffusion coefficient with the experimental value was obtained with the OPLS and GROMOS models. The calculated enthalpy of vaporization of the TraPPE and OPLS models agrees well with the experimental value, while the other models do not give such agreement. From the intramolecular spatial distributions and the distribution of the end to-end molecular distance, we can conclude that the model molecules are most flexible in the GROMOS model and most rigid in the TRAPPE model.
Secondary keywords: computer simulations;molecular dynamics;force field;fluid;hexane-1-ol;Tekočine;Molekularna dinamika;Univerzitetna in visokošolska dela;
Type (COBISS): Bachelor thesis/paper
Study programme: 1000373
Embargo end date (OpenAIRE): 1970-01-01
Thesis comment: Univ. v Ljubljani, Fak. za kemijo in kemijsko tehnologijo, UNI Kemija
Pages: 36 str.
ID: 16317293