Simulacije molekulske dinamike kompleksa odabranih homociklopeptida s kloridnim, bromidnim i jodidnim anionima

master's thesis

• Title (english): Molecular dynamics simulations of selected homocyclopeptides with chloride, bromide and iodide anions
• Author: Ivan Petranović
• Mentor: Gordan Horvat (mentor)
• Committee member: Gordan Horvat (predsjednik povjerenstva)
• Committee member: Ivan Kodrin (član povjerenstva)
• Committee member: Aleksandra Maršavelski (član povjerenstva)
• Committee member: Tomica Hrenar (član povjerenstva)
• Granter: University of Zagreb; Faculty of Science; (Department of Chemistry); Zagreb
• Defense date and country: 2023-12-11, Croatia
• Scientific / art field, discipline and subdiscipline: NATURAL SCIENCES; Chemistry

Abstract

Ciklopeptidi su makrociklički spojevi sa izraženim ion-receptorskim svojstvima. Okosnica
takvih molekula je zbog cikličke strukture sterički ograničena u odnosu na linearne peptide.
Pogodni su za dizajn anionskih receptora strukturiranog veznog mjesta u kojem se anion
koordinira atomima vodika amidnih skupina okosnice peptida. Pritom najčešće nastaju
kompleksi stehiometrije 1:1 (receptor:anion), gdje uslijed uređenosti strukture veznog mjesta
postoji mogućnost specifičnog vezanja pojedinih aniona. U ovom je radu razvijena
metodologija istraživanja termodinamičke stabilnosti anionskih kompleksa ciklopeptida
korištenjem simulacija molekulske dinamike uz alkemijske transformacije iona i bočnih
ogranaka ciklopeptida. Izračunate su standardne Gibbsove energije za supstitucije aniona,
disocijacije anionskih kompleksa te mutacije bočnih ogranaka u dva otapala, acetonitrilu i
metanolu. U simulacijama su korištena dva popularna polja sila (OPLS-AA i CHARMM36). U
slučaju kompleksa čija je termodinamička stabilnost eksperimentalno određena, računalni
rezultati uspoređeni s literaturnim vrijednostima.

Abstract (english)

Cyclopeptides are macrocyclic compounds with prominent ion-receptive properties. Cyclic
structure sterically restricts the backbone of such compounds compared to their linear
counterparts. The well structured anion binding site of cyclopeptides makes them a suitable
target for anion receptor design. The formed anion complexes usually have 1:1 stoichiometry
but the structure of the binding site occasionally allows for binding of additional anions. This
thesis develops a methodology for the study of thermodynamic stability of cyclopeptide-anion
complexes using molecular dynamics in conjuction with alchemical transformations of ions and
cyclopeptide side chains in acetonitrile and methanol. Standard Gibbs energies for anion
substitution, complex dissociation and side chain mutations are calculated using two popular
force fields (OPLS-AA and CHARMM36). These results are compared with the experimentally
obtained values where data is available.

• Keywords: alkemijske transformacije; anioni; kompleksi; ciklopeptidi; molekulska dinamika
• Keywords (english): alchemical transformations; anions; complexes; cyclopeptides; molecular dynamics
• Language: croatian
• URN:NBN: urn:nbn:hr:217:404445
• Project: Number: IP-2019-04-9560; Title: Koordinacijske reakcije makrocikličkih liganada u otopini; Title: Coordination Reactions of Macrocyclic Ligands in Solution; Acronym: MacroSol; Leader: Vladislav Tomišić; Jurisdiction: Croatia; Funder: HRZZ; Funding stream: IP
• Study programme: Title: Graduate university studies in chemistry; specializations in: Graduate university studies in chemistry; Course: Graduate university studies in chemistry; Study programme type: university; Study level: graduate; Academic / professional title: sveučilišni/a magistar/magistra kemije (sveučilišni/a magistar/magistra kemije)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Embargoed access; Embargo expiration date: 2025-12-11
• Created on: 2024-01-10 13:28:09