Modeling the stucture and reactivity of organic compounds using a new cluster-continuum solvation method

doctoral thesis

• Title: Modeliranje strukture i reaktivnosti organskih molekula novom klaster-kontinuum metodom solvatacije
• Author: Igor Rončević
• Mentor: Zlatko Mihalić (mentor)
• Committee member: Branimir Bertoša (predsjednik povjerenstva)
• Committee member: Zlatko Mihalić (član povjerenstva)
• Committee member: Zoran Glasovac (član povjerenstva)
• Granter: University of Zagreb; Faculty of Science; (Department of Chemistry); Zagreb
• Defense date and country: 2015-06-30, Croatia
• Scientific / art field, discipline and subdiscipline: NATURAL SCIENCES; Chemistry
• Universal decimal classification (UDC): 54; NATURAL SCIENCES; Chemistry. Crystallography. Mineralogy

Abstract

U ovoj disertaciji predstavljena je i primijenjena nova klaster-kontinuum metoda za opis solvatacije. U odnosu na postojeće, ova metoda uvodi novi pristup generiranju klastera na način da se solutu dodaju najvažnije molekule otapala. Pristup se temelji na konceptu solvatacijskih sfera funkcionalnih skupina. Radijusi solvatacijskih sfera dobivaju se analizom radijalnih funkcija raspodjele molekula otapala oko funkcionalnih skupina soluta, što omogućuje eliminaciju molekula otapala koje nisu potrebne za točan opis solvatacije. Nakon toga, daljnja analiza vrši se usporedbom interakcijskih energija preostalih molekula otapala. Predstavljena metoda omogućuje jednostavno, efikasno i nepristrano dobivanje geometrija s određenim brojem molekula otapala. Testiranje metode provedeno je na dva modelna sustava u vodi. Analizom dobivenih geometrija identificirani su obrasci vezanja nabijenih i neutralnih vrsta s molekulama vode, dok su dobivene energije, utežene Boltzmannovom raspodjelom, dale vrijednosti termodinamičkih veličina u odstupanju od 1 kcal/mol od eksperimentalnih. Nakon toga, metoda je iskorištena za istraživanje mogućih reakcijskih mehanizama hidrolize acetil-klorida.

Abstract (english)

In this dissertation, a new cluster-continuum solvation modeling method is presented and applied. The most important feature of this method is a novel approach for the generation of clusters, in which only important solvent molecules are added to the solute. This approach is based on the concept of functional group solvation spheres. Solvation sphere radii are defined by analyzing radial distribution functions of solvent molecules around solute functional groups, which enables the elimination of molecules unperturbed by the solute. Also, the presented method implements a procedure for simple, effective and unbiased generation of geometries with a selected number of solvent molecules. This is achieved by sorting the solvent molecules according to their interaction energy. The method was tested on two model systems, using water as the solvent. The patterns of solvent-solute bonding for neutral and charged molecules were identified by analysis of obtained geometries, while the calculated Boltzmann weighted Gibbs energies gave values of thermodynamic quantities with an average deviation of 1 kcal/mol when compared to experimental data. After that, the method was used for the investigation of acetyl-chloride hydrolysis reaction mechanisms.

• Keywords: fragmentacijske metode (EFP); klaster-kontinuum metoda; ravnoteža u otapalu; reakcijski mehanizam; solvatacija; solvatacijske sfere; teorija funkcionala gustoće
• Keywords (english): cluster-continuum; density functional theory (DFT); equilibrium in solution; fragmentation methods (EFP); reaction mechanism; solvation; solvation spheres
• Language: croatian
• URN:NBN: urn:nbn:hr:217:272091
• Study programme: Title: Kemija; Study programme type: sveučilišni; Study level: poslijediplomski doktorski; Academic / professional title: doktor/doktorica znanosti, područje prirodnih znanosti, polje kemija (doktor/doktorica znanosti, područje prirodnih znanosti, polje kemija)
• Type of resource: Text
• Extent: 160 str. ; 30 cm
• File origin: Born digital
• Access conditions: Open access
• Created on: 2017-02-10 12:15:17