Jedan od najvažnijih dijelova gorivne ćelije s polimernom membranom (PEMFC) je membranski elektrodni sklop (MEA). Međutim, trajnost PEMFC-a uvelike se smanjuje odjeljivanjem membrane od elektrodnih ...slojeva potaknutog nejednakim naprezanjima zbog nekonzistentnog širenja pod utjecajem topline i vlage. U ovome je radu prikazan molekulski model membrane i elektrodnih slojeva načinjen na temelju literaturnih podataka i s pomoću komercijalnog softvera radi pronalaženja stabilne strukture membranskog elektrodnog sklopa. Kao materijal membrane vodljive za protone razmatran je ionomer Nafion, a kao materijal elektroda kompozit Nafiona s platinom na grafenu. Ponašanje koeficijenta toplinskog rastezanja i koeficijenta rastezanja pod utjecajem vlage istraženo je molekulskom dinamikom. Strukturna stabilnost modela troslojnog sklopa MEA (anoda/membrana/katoda) proučena je uz djelovanje različitih vanjskih tlakova i računajući vezne energije između slojeva te između grafena i platine. Rezultati pokazuju da su pri vrlo visokim tlakovima molekule u unutrašnjosti previše zbijene pa se čestice platine odvajaju od nosača, dok s niskim tlakovima slabe veze između slojeva.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
A systematic study of the non-radiative deactivation mechanisms of the three photoexcited N-acetylphenylalanylamide conformers was conducted in order to disclose the experimentally observed ...conformational dependent lifetime of phenyl vibrationless 1* excited state. The all-atom trajectory surface hopping non-adiabatic molecular dynamics simulations, based on linear response time dependent density functional theory, were utilized for blind screening of relaxation pathways and revealed a number of excitation transfer mechanisms from 1* to the 1n* excited states localized on each of the two amide groups. Possible pathways were further refined by obtaining conical intersection barrier energies from corresponding reaction paths constructed at the coupled cluster (CC2) level of theory. Finally, from semiclassical consideration of conical intersection accessibility with only the nuclear zero point vibrational energy and from the increased rigidity of the second amide group towards distorsion upon its methylation, it was concluded that the classically accessible part of conical intersection seam for population transfer to the 1n* state of the second amide group is the largest for the conformer with the shortest 1* state lifetime.
A systematic study of the non-radiative deactivation mechanisms of the three photoexcited N-acetylphenylalanylamide conformers was conducted in order to disclose the experimentally observed conformational dependent lifetime of phenyl vibrationless 1* excited state. The all-atom trajectory surface hopping non-adiabatic molecular dynamics simulations, based on linear response time dependent density functional theory, were utilized for blind screening of relaxation pathways and revealed a number of excitation transfer mechanisms from 1* to the 1n* excited states localized on each of the two amide groups. Possible pathways were further refined by obtaining conical intersection barrier energies from corresponding reaction paths constructed at the coupled cluster (CC2) level of theory. Finally, from semiclassical consideration of conical intersection accessibility with only the nuclear zero point vibrational energy and from the increased rigidity of the second amide group towards distorsion upon its methylation, it was concluded that the classically accessible part of conical intersection seam for population transfer to the 1n* state of the second amide group is the largest for the conformer with the shortest 1* state lifetime.
Provedeno je sustavno istraživanje neradijativnih deaktivacijskih mehanizama odgovornih za eksperimentalno opaženu konformacijsku ovisnost vremena života vibracijski osnovnog pobuđenog fenilnog 1* elektronskog stanja u tri konformera N-acetilfenilalanilamida. Simulacije metodom neadijabatske molekulske dinamike, s preskokom među plohama elektronske potencijalne energije dobivenih vremenski ovisnom teorijom funkcionala gustoće, ukazale su na nekoliko mehanizama prijenosa ekscitacije iz 1* u 1n* stanja locirana na pojedinim amidnim grupama. Pronađeni mehanizmi potom su utočnjeni pripadajućim vrijednostima energijama barijera koničnih presjecišta dobivenih ih reakcijskih puteva izračunatim na razini teorije spregnutih grozdova (CC2). Konačno, iz poluklasičnog razmatranja dostupnosti koničnog presjecišta samo na temelju nuklearne vibracijske energije nulte točke te iz povećanja rigidnosti druge peptidne skupine naspram njene deformacije usljed metilacije, određeno je kako klasično dostupan dio šava koničnog presjecišta za prijenos populacije u 1n* stanje druge peptidne skupine je najveći u konformeru s najkraćim vremenom života pobuđenog 1* stanja.
Sažetak Dipeptidil-peptidaza III (DPP III) je o cinku ovisna egzopeptidaza koja katalizira reakciju hidrolize peptidne veze odcjepljujući dipeptid s N-kraja svojih supstrata. U okviru ove doktorske ...disertacije detaljno je istražena struktura i dinamika ljudske DPP III i njenih kompleksa primjenom računalnih pristupa različitih stupnjeva složenosti. Modeliranje je bilo temeljeno na trodimenzionalnim strukturama enzima određenim rentgenskom strukturnom analizom. Molekulsko-dinamičke (MD) simulacije slobodnog (bez vezanog liganda) enzima otkrile su veliku fleksibilnost proteina, a simulacije kompleksa DPP III sa sintetskim i peptidnim supstratima pridonijele su razumijevanju široke supstratne specifičnosti ovoga enzima, te u kombinaciji s računom slobodne energije omogućile određivanje najvjerojatnijeg i kemijski aktivnog načina vezanja supstrata. Aktivna konformacija enzima dodatno je potvrđena primjenom različitih MD metoda i hibridnim kvantno-mehaničkim molekulskomehaničkim (QM/MM) računima različitih načina koordinacije cinka. Mehanizam reakcije hidrolize određen je na modelnom sustavu sastavljenom od supstrata, aminokiselinskih ostataka koji neposredno sudjeluju u procesu katalize i ostataka koji koordiniraju ion cinka.
The dipeptidyl-peptidase III (DPP III) is a zinc-exopeptidase that hydrolyzes dipeptide from the N-terminus of its substrates. In this thesis a structure and dynamics of ligand-free enzyme and its complexes is investigated in detail by multi scale computational approaches. Modeling study was based on the three-dimensional enzymes structures obtained by X-ray diffraction analysis. Molecular dynamics (MD) simulations of the ligand-free enzyme revealed large flexibility of the protein, while the simulations of DPP III in the complexes with synthetic and peptide substrates enabled understanding of its broad substrate specificity, and, in combination with the free energy calculations, helped in determination of the most probable and chemically active ligand binding mode. The active enzyme conformation was confirmed by different MD approaches as well as by the hybrid quantum mechanicsmolecular mechanics (QM/MM) calculation of the different zinc ion coordinations. The reaction mechanism was determined using the model system consisting of substrate, amino acids participating in catalysis and the residues that coordinate the zinc ion.
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