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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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Bacterial biofilm formation
Sochorová, Zuzana ; Weiser, Jaroslav (advisor) ; Zikánová, Blanka (referee)
Biofilms are formed by microorganisms living together in a hydrated extracellular matrix. Formation of such clusters of bacteria brings many benefits. The increased resistance to antibiotics is the main one. Creating a biofilm is analogous to the development of multicellular organisms. Biofilm cells communicate with each other with signaling molecules. Signaling molecules make the biofilm more compact structure. Extracellular matrix, in which bacteria live, maintains biofilm structure, affects cell adhesion and protects cells against environmental influences. Bacteria also interact with the environment through the extracellular matrix. The matrix is composed of various biopolymers and proteins. Biofilms are a common cause of infections associated with implants. There are several ways to prevent bacteria in biofilm to antibiotics. These include a slow diffusion of substances, a slow growth or an adaptation to stress. The formation of persistent cells that are tolerant to the antibiotics is the cause of their survival as well as a new population may arise from them. The surface proteins are important elements for the formation of biofilms, they facilitate adhesion and subsequent establishment of biofilm. A protein Bap was the first identified protein. Later its homologues were found, such as BapA,...
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Spacecraft observations of waves in low-latitude magnetospheric plasma
Sochorová, Zuzana ; Santolík, Ondřej (advisor) ; Chum, Jaroslav (referee) ; Tichý, Milan (referee)
Title: Spacecraft observations of waves in low-latitude magnetospheric plasma Author: Zuzana Sochorová Department: Department of Surface and Plasma Science Supervisor: prof. Ondřej Santolík, Department of Surface and Plasma Science, Institute of Atmospheric Physics AS CR Abstract: The present doctoral thesis is based on the analysis of the electromagne- tic equatorial noise (EN) emissions. These waves propagate in the vicinity of the geomagnetic equator at frequencies between the local proton cyclotron frequency and the lower hybrid frequency. We used data obtained by the 4 Cluster spacecraft during the period from January 2001 to December 2010. The analysis is based on the data from the STAFF-SA instrument. We have developed 3 selection criteria for the visual identification and we have compiled a database of more than 2000 events. We demonstrate than EN occurs in almost entire analyzed range of the McIlwain's parameter from about L ∼ 1 to L ∼ 10. EN mostly occurs between L = 3 and L = 5.5. Analysis of occurrence rates as a function of magnetic local time shows strong variations outside of the plasmasphere (with an increase in the afternoon sector), while the occurrence rate inside the plasmasphere is almost independent. We have also analyzed the inner structure of EN. We use data from the WBD instrument...
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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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Frequencies of attenuation in the power spectra observed by the DEMETER spacecraft
Záhlava, Jan ; Němec, František (advisor) ; Sochorová, Zuzana (referee)
Předmětem bakalářské práce je analýza zvláštních efekt· pozorovaných ve frekvenčně-časových spektrogramech změřených družicí DEMETER v pásmu velmi nízkých frekvencí. Jedná se o periodické utlumení frekvenční závislosti elektrické intenzity, které se spojitě mění v čase. Při detailním zkoumání se ukazuje, že jsou tyto útlumové události tvořeny z hvizd· pocházejících z bleskových emisí. Porovnání závislosti doby trvání útlumových událostí na geomagnetické délce s délkovou závislostí četnosti výskytu blesk· ukazuje, že jsou útlumové události posunuty oproti blesk·m přibližně o 30◦ západním směrem. Podařilo se nám vysvětlit tento posun a vytvořit jednoduchý model možného formování útlumových událostí založený na módové teorii šíření vln ve vlnovodu. 1
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Magnetospheric line radiation observed by the DEMETER spacecraft
Bezděková, Barbora ; Němec, František (advisor) ; Sochorová, Zuzana (referee)
Frequency-time spectrograms of electromagnetic waves observed in the Earth's inner magnetosphere in the frequency range 1-8 kHz sometimes contain nearly horizontal and almost parallel intense lines. Such events were observed both by ground-based instruments and satellites, and they are called Magnetospheric Line Radiation (MLR). We systematically analyze 1230 MLR events identified in the data of the DEMETER spacecraft (2004-2010, altitude of about 700 km). We focus on a possible connection between the event occurrence and solar wind parameters. Long analyzed data interval allows us to evaluate a possible influence of the solar cycle and season of the year. We show that there is a statistically significant correlation between MLR events and solar wind parameters, and that the events are observed more often during the winter months and preferably during the solar maximum. The events occur less frequently at geomagnetic longitudes of South Atlantic Anomaly (SAA). We analyze spectra of energetic electrons precipitating in this region at the times of MLR events, which are supposed to be related to the wave generation. Powered by TCPDF (www.tcpdf.org)
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Monitoring of Mycobacterium smegmatis floating biofilm development - morphological and proteome analysis
Sochorová, Zuzana ; Weiser, Jaroslav (advisor) ; Zikánová, Blanka (referee)
Microorganisms grow in planktonic form, but more often they adhere to a number of surfaces and create three-dimensional structures called biofilms. Floating biofilms, which are formed at the water-air interface, are one of the life strategies, which the bacteria can take. Non-pathogenic Mycobacterium smegmatis was used as a laboratory model for the study of this kind of biofilm. The understanding of mechanisms of their formation of this species may be applicable to the pathogenic species of the genus Mycobacterium, study of which in the laboratory brings a number of disadvantages. This diploma thesis focuses on the morphological and proteome analysis of the M. smegmatis floating biofilm. Using a stereo microscope and scanning electron microscopy was observed that bacteria clump and create the "nucleation centres" at the beginning of the biofilm development. This centers grow to the surroundings and connect afterwards. In the later stages of the development the centers fuse in compact layer, which then grows into the compact and multilayer biofilm. The key method in this study was two-dimensional electrophoresis of proteins. The proteome analysis of floating biofilm was performed with this method. The preparation of protein samples and the method for protein concentration measurement was optimized....
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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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