prikaz prve stranice dokumenta Simulacije molekulske dinamike kompleksa odabranih homociklopeptida s kloridnim, bromidnim i jodidnim anionima
Embargo period 2025-12-11
master's thesis
Simulacije molekulske dinamike kompleksa odabranih homociklopeptida s kloridnim, bromidnim i jodidnim anionima
Zagreb: University of Zagreb, Faculty of Science, 2023. urn:nbn:hr:217:404445
Petranović, Ivan
University of Zagreb
Faculty of Science
Department of Chemistry

Institutional repository: Repository of the Faculty of Science

Cite this document

Petranović, I. (2023). Simulacije molekulske dinamike kompleksa odabranih homociklopeptida s kloridnim, bromidnim i jodidnim anionima (Master's thesis). Zagreb: University of Zagreb, Faculty of Science. Retrieved from https://urn.nsk.hr/urn:nbn:hr:217:404445

Petranović, Ivan. "Simulacije molekulske dinamike kompleksa odabranih homociklopeptida s kloridnim, bromidnim i jodidnim anionima." Master's thesis, University of Zagreb, Faculty of Science, 2023. https://urn.nsk.hr/urn:nbn:hr:217:404445

Petranović, Ivan. "Simulacije molekulske dinamike kompleksa odabranih homociklopeptida s kloridnim, bromidnim i jodidnim anionima." Master's thesis, University of Zagreb, Faculty of Science, 2023. https://urn.nsk.hr/urn:nbn:hr:217:404445

Petranović, I. (2023). 'Simulacije molekulske dinamike kompleksa odabranih homociklopeptida s kloridnim, bromidnim i jodidnim anionima', Master's thesis, University of Zagreb, Faculty of Science, accessed 22 November 2024, https://urn.nsk.hr/urn:nbn:hr:217:404445

Petranović I. Simulacije molekulske dinamike kompleksa odabranih homociklopeptida s kloridnim, bromidnim i jodidnim anionima [Master's thesis]. Zagreb: University of Zagreb, Faculty of Science; 2023 [cited 2024 November 22] Available at: https://urn.nsk.hr/urn:nbn:hr:217:404445

I. Petranović, "Simulacije molekulske dinamike kompleksa odabranih homociklopeptida s kloridnim, bromidnim i jodidnim anionima", Master's thesis, University of Zagreb, Faculty of Science, Zagreb, 2023. Available at: https://urn.nsk.hr/urn:nbn:hr:217:404445

Metadata
TitleSimulacije molekulske dinamike kompleksa odabranih homociklopeptida s kloridnim, bromidnim i jodidnim anionima
Title (english)Molecular dynamics simulations of selected homocyclopeptides with chloride, bromide and iodide anions
AuthorIvan Petranović
MentorGordan Horvat (mentor)
Committee memberGordan Horvat (predsjednik povjerenstva)
Committee memberIvan Kodrin (član povjerenstva)
Committee memberAleksandra Maršavelski (član povjerenstva)
Committee memberTomica Hrenar (član povjerenstva)
GranterUniversity of Zagreb
Faculty of Science
(Department of Chemistry)
Zagreb
Defense date and country2023-12-11, 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
Keywords (english)
Languagecroatian
URN:NBNurn:nbn:hr:217:404445
ProjectNumber: 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 programmeTitle: 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 resourceText
File originBorn digital
Access conditionsEmbargoed access
Embargo expiration date: 2025-12-11
Terms of useLicence In copyright icon
Created on2024-01-10 13:28:09