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Combined QM/MM decsription of interaction of Ru(II) 'piano-stool' organometallic complexes with oligomer models of DNA
Zábojníková, Tereza ; Burda, Jaroslav (advisor) ; Sychrovský, Vladimír (referee)
This work is focused on 4 organometalic drugs with "piano-stool" Ru(II) structure: these complexes are: nalidixic acid, thio-nalidixic acid, ofloxacin and cinoxacin. Thermodynamic parameters of three type of reactions with water were analyzed for each of these four complexes. All complexes were examined in both protonated and deprotonated state, since all of these complexes are acids and they behave differently in acidic and neutral enviroment. Optimalization was performed using DFT method B3PW91 in basis 6-31+G*. Energies were calculated in basis 6-311++G(2df,2pd) using DFT method B3LYP and NPA analysis was performed for finding partial charges on atoms.
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Noncovalent Interactions in the Gas Phase and Aqueous Solution: Theoretical Study
Zendlová, Lucie ; Hobza, Pavel (advisor) ; Burda, Jaroslav (referee) ; Vondrášek, Jiří (referee) ; Jurečka, Petr (referee)
EAPUr rr|lclltal \ alLlť5' 5 Conclusions :, , . In the ia) part of present work we c intera cti on b etween u d"',il ". . . thy;';; il:'::: :íJTj.:lÍ' lI jl.#.ffiJ,lil itt8:"é'siia small number or*u.",7nJ organió solvent ňr"."i", (CH3.H, solvents yů[T"i^f.completely different interactions between the bases and the b"''" p.'"{ ;' "idilnn il#} il-t ÍT:!fl,-. i: : " o:] Y" .'h:.-S,t.* tu,", ot tt," moleóule Iuórc 'u'r' u property, and the'. .'l,'..,ťff,.'*lt'Lť':.lill:ilF.S'T!,l;situated above or belolthe !Á; ;;i. ;';;lě'"o ri," olašó ň"l"-.\,," ,, unique y"J::fiffii:x::. ."n'o*ison with otr,!. .otu"nt,, uň.'r,"í'ř;;.". are the In the ib) part_of present work based on the MD, SCC_DDFTB_D and ;"",'.Y|Tť'.#1.:."ffi i"T."lrJ'".r""u.'".XincorporateJ."-oŇTduplexwe i) Replacing nucleic acid base by modified nucleobase X leads.*:'] ,o Structural changes of the centrď -uuš"-pui. Gtu.tarrangement of central modified base pairs). ónli with ttresma'lest modified nucleobase p 'r'" Á.iJ.;;*;;.í' (A-P, P-T) stay planar. In the case 'of.B-T, Á-il.;';6 in specificorientation, one of the modified nuú"JÁ""x"*íto.""a outfrom DNA duplex. ii) Incre, .,""olr'iT"i1iTi1fi" or modified nucleobase X increases rhe iii) The highest s.ďectivity among- all base ana|ogue studied wasfound for modified nu"l"obus" O In the secono pu* of...
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Interaction of Metal Cations in Bioorganic Environment. Computational Study Using Quantum Mechanics and Molecular MechanicsTools.
Futera, Zdeněk ; Burda, Jaroslav (advisor) ; Bouř, Petr (referee) ; Clark, Tim (referee)
Interactions of Metal Cations in Bioorganic Environment Computational Study Using Quantum Mechanics and Molecular Mechanics Tools Zdeněk Futera Biologically relevant interactions of piano-stool ruthenium(II) complexes with ds-DNA are studied by QM/MM computational technique. The whole re- action mechanism is divided into three phases - hydration of [RuII (η6 - benzene)(en)Cl]+ , consequent binding DNA and final intra-strand cross-link formation between two adjacent guanines. Free energy profiles of all reactions are explored by QM/MM MD umbrella sampling approach where the Ru(II) complex is described by DFT. For that purpose, special QM/MM software was developed to couple Gaussian and Amber programs. Calculated free energy barriers of Ru(II) hydration as well as DNA binding process are in good agreement with experimentally determined rate constants. Reaction pathway for cross-link formation was predicted that is feasible from both thermodynamical and kinetical point of view.
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The Study of hydration models on platinum complexes important in anticancer cure
Bradáč, Ondřej ; Burda, Jaroslav (advisor) ; Záliš, Stanislav (referee)
In this work, there are studied some biologically important platinum complexes, cisplatin analogues, with central platinum atom in state Pt(II), or Pt(IV). I concentrated on the hydration processes of the examined complexes. Thermodynamical and kinetical aspects of reactions were studied and NPA charge analyses were carried out, too. All computations were performed on DFT level with B3LYP functional. All reactions were considered in vacuum. Supermolecular approach was used for energy calculations.
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Quantum mechanical study of the electron hopingp rocesses of heterocyclic molecules.Simulation of absorption and emission spectra.
Tichý, Ondřej ; Burda, Jaroslav (advisor) ; Profant, Václav (referee)
This thesis is about computing lifetimes of excited states of molecules by using semiempirical methods in simulations of molecular dynamics. Pyrimidine nucleobases and three aza- derivatives were chosen as reference molecules. Simulations of molecular dynamics by program MNDO99 were performed with these molecules and static spectra were computed by programs Gaussian and Orca. All the examined molecules have femtosecond lifetimes of second excited states, pyrimidine nucleobases have also short lifetimes of first excited states in hundreds of femtoseconds. The computed first excited states of aza-derivatives have lifetimes in tens or hundreds of picoseconds and suggest that the higher stability of the states is related to the smaller number of amino groups attached to the ring.
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Quantum mechanical study of transition metal hydrides; comparison of vibrational analysis with experimental data.
Smítalová, Kateřina ; Burda, Jaroslav (advisor) ; Pospíšil, Miroslav (referee)
This thesis compares the results of four theoretical methods to calculate the molecular orbitals against the experimental data. The calculations were carried out in five basis sets, differing mainly in size, upon the set of reference molecules - diatomic hydrides of transition metals. The values, compared to the experiment, include interatomic distance, dissociation energy, anharmonicity and selected vibrational data. Calculations ignoring the theory of relativity provided unusable results. Coupled cluster method was confirmed as the most accurate one and the accuracy of the basis sets was corresponding with their sizes. Results of one of the smaller-sized basis sets were significantly improved with the addition of several polarizing orbitals. Keeping the calculation times significantly shorter, its accuracy was similar to the largest of the used basis sets.
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