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Computational Study of the Interactions of Transition Metal Complexes with Biomolecules Using Quantum Chemical Methods.
Šebesta, Filip ; Burda, Jaroslav (advisor) ; Sochorová Vokáčová, Zuzana (referee)
It has been proven that platinum complexes are active in anticancer treatment as well as several other transition metals. There is an effort in recent medicine to replace cisplatin complexes by drugs with smaller side effects. This work focuses on the reaction of 5'-dGMP (2'-deoxyguanosine- 5'˗monophosphate) with a platinum complex PtIV (dach)Cl4 (dach=diaminocyclohexane) forming PtIV (dach)Cl3(N7-cGMP) complex. The explored reaction can be divided into two (independent) steps: cyclization of phosphate and substitution reaction where a new complex with coordinate- covalent bond between platinum atom and nitrogen N7 of guanine is formed releasing chloride particle. Here I studied geometry parameters which are important in the above mentioned reaction. The reaction course is observed from the thermodynamic point of view. The structures were optimized at the DFT level with B3LYP functional in basis set 6-31G* and PCM/UA0 solvation model. The energy parameters and electron density distribution were computed at the B3LYP/6˗311++G(2df,2pd) level in the D˗PCM/sUAKS solvation model.
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Theoretical characterization of reaction center of photosystem
Vokáčová, Zuzana
Spectral properties of reaction center of photosystem II (RC PS II) and some chosen pigment molecules were studied by methods of quantum chemistry. Absorption spectra of six monomer unit of RC PS II were computed with semiempirical method and on the DFT level. Spectra of monomers obtained by the semiepirical ZINDO method are red shifted and spectra obtained by TDDFT are blue shifted from measured spectrum of chlorophyll a. The shift is a result of applied method. Next, electron transitions of chosen part of chlorophyll-pheophytin complex of RC PS II were obtained by semiempirical method. A goal was to describe differences, which follows from enlarging size of the reaction complex. A difference in the spectra correlates with various groups of pigments, which belong to active and inactive branches. Red shift of spectral lines was found only for the central dimer in comparison with electron transitions of chlorophyll a. Spectra of selected pigment molecules (chlorophylls, bacteriochlorophylls, carotenoids, phycobilins) were calculated on the DFT level and a good agreement with experimental data was achieved. An expected spectral-lines dependence on molecular structures was obtained. The relationship of some substituents, the length of unsaturated chains of chromofor and some modification of structure was searched.
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Studium termodynamických a kinetických parametrů interakcí oligomerních modelů DNK s organokovovými komplexy aktivními v protirakovinné léčbě stanovených metodami kvantové chemie a kombinovanými QM/MM metodami
Matunová, Petra ; Burda, Jaroslav (advisor) ; Sochorová Vokáčová, Zuzana (referee)
It has been proven that platinum and ruthenium complexes are active in anti- cancer treatment. Nowadays, the common chemotherapeutica have a lot of side effects, therefore, drugs with fewer negative impacts are intensively searched for. The first part of the thesis focuses on the study of cis-[Pt(NH3)2Cl2] (cisplatin, DDP) and four platinum potential anticancer agents PtCl2(diaminocyclohexane), PtCl2(NH3)(cyclohexylamine) (JM118), cis-[PtCl2(NH3)(piperidine)] and trans-[PtCl2(NH3)(thiazole)]. Thermodynamic and kinetic parameters of reac- tions of these complexes in semi-hydrated and fully-hydrated form with guanine were studied using QM methods. The reaction with guanine is the key process ini- tiating the anticancer activity. Analyses of electron density were performed at the B3LYP/6-311++G(2df,2pd) level of theory in IEF-PCM model. The second part of the thesis studies the reaction of the so-called 'piano stool' Ru(II) transition metal complex, [Ru(II)(η6 -p-cymene(nalidixic acid)(H2O)]2+ , first with guanine using QM methods and second with ds-DNA model using QM/MM methods. The reaction site, which is described by QM method, is two consecutive guanines and the Ru(II) complex. Analyses of thermodynamic and kinetic parameters, and electron density were performed at the B97D/6-31G* level of theory. All the...
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Computational Study of the Properties and Reactivity of Bioinroganic Transition Metal Complexes
Baxová, Katarína ; Burda, Jaroslav (advisor) ; Sochorová Vokáčová, Zuzana (referee)
This work is focused on the reactions of diaqua-tetrakis(μ-acetylato)dirhodium(II,II) with guanine, that shows anti-cancer activities. Guanine can bond to the complex either by oxygen O6 or by nitrogen N7. We studied three possible versions of the system - one that is protonated on guanine, one protonated on the paddle-wheel and a neutral one. For all 6 reactions transition structures were found. For reactants, tranzition states and products we computed the values of electron density in the critical points of bonds, partial atom charges and the interaction energies of the system, guanine and water on the b3lyp/aug-cc- pvdz level. Pseudobasis and pseudopotentials were employed in the case of rhodium atom. For all the reactions thermodynamical properties were computed. Powered by TCPDF (www.tcpdf.org)
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Computational Study of the Interactions of Transition Metal Complexes with Biomolecules Using Quantum Chemical Methods.
Šebesta, Filip ; Burda, Jaroslav (advisor) ; Sochorová Vokáčová, Zuzana (referee)
It has been proven that platinum complexes are active in anticancer treatment as well as several other transition metals. There is an effort in recent medicine to replace cisplatin complexes by drugs with smaller side effects. This work focuses on the reaction of 5'-dGMP (2'-deoxyguanosine- 5'˗monophosphate) with a platinum complex PtIV (dach)Cl4 (dach=diaminocyclohexane) forming PtIV (dach)Cl3(N7-cGMP) complex. The explored reaction can be divided into two (independent) steps: cyclization of phosphate and substitution reaction where a new complex with coordinate- covalent bond between platinum atom and nitrogen N7 of guanine is formed releasing chloride particle. Here I studied geometry parameters which are important in the above mentioned reaction. The reaction course is observed from the thermodynamic point of view. The structures were optimized at the DFT level with B3LYP functional in basis set 6-31G* and PCM/UA0 solvation model. The energy parameters and electron density distribution were computed at the B3LYP/6˗311++G(2df,2pd) level in the D˗PCM/sUAKS solvation model.
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Theoretical characterization of reaction center of photosystem
Vokáčová, Zuzana
Spectral properties of reaction center of photosystem II (RC PS II) and some chosen pigment molecules were studied by methods of quantum chemistry. Absorption spectra of six monomer unit of RC PS II were computed with semiempirical method and on the DFT level. Spectra of monomers obtained by the semiepirical ZINDO method are red shifted and spectra obtained by TDDFT are blue shifted from measured spectrum of chlorophyll a. The shift is a result of applied method. Next, electron transitions of chosen part of chlorophyll-pheophytin complex of RC PS II were obtained by semiempirical method. A goal was to describe differences, which follows from enlarging size of the reaction complex. A difference in the spectra correlates with various groups of pigments, which belong to active and inactive branches. Red shift of spectral lines was found only for the central dimer in comparison with electron transitions of chlorophyll a. Spectra of selected pigment molecules (chlorophylls, bacteriochlorophylls, carotenoids, phycobilins) were calculated on the DFT level and a good agreement with experimental data was achieved. An expected spectral-lines dependence on molecular structures was obtained. The relationship of some substituents, the length of unsaturated chains of chromofor and some modification of structure was searched.
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