|
|
Quantum mechanical study of the electron hoping processes of conjugated systems.
Tichý, Ondřej ; Burda, Jaroslav (advisor) ; Pittner, Jiří (referee)
In this thesis the electron hopping of selected heterocyclic compounds and selected carotenoids was studied using QM/MM simulations of excited states dynamics. Tully electron hopping and semiempirical methods OMx in combination with MRCI method was used in the simulations. Calculations were performed using Newton-X, MNDO99, MNDO2020 and Gromacs. The lifetimes of the excited states were estimated based on the simulations. The results showed that used methods correctly describes the time evolution of excited states of heterocyclic compounds. In case of carotenoids only deexcitation from first excited state was described correctly.
|
|
|
Quantum mechanical study of the electron hoping processes of conjugated systems.
Vavrečka, Adam ; Burda, Jaroslav (advisor) ; Šebesta, Filip (referee)
Mean lifetimes of the two lowest singlet excited states of linear conjugated polyenes from ethene to docosaundecaene were explored. The semiempirical OM2/MNDO me- thod using MRCISD computational level was used to perform molecular and electronic dynamics of these molecules in n-hexane. In each step the time-dependent Schrödinger equation was solved and the transitions between states were carried out by the Tully's fewest switches algorithm. Mean lifetimes were determined by fitting the time dependent probabilities of the excited states according to the exponential decay law. The lifetimes of the S2 state are very short: from hexatriene's 7 fs to octatetraene's 51 fs. As for the S1 state lifetime, ethene has the shortest one, 89 fs, in contrast to octatetraene, whose S1 state lifetime is 1275 fs. The lifetimes are significantly shorter in comparison with the previous gas-phase study. 1
|
|
| |
|
|
MD simulations of complexes between nucleic acids and RNase H
Bartek, Tomáš ; Barvík, Ivan (advisor) ; Burda, Jaroslav (referee)
The aim of this diploma thesis was to study interactions between human Rase H enzyme and a natural and modified substrate using molecular dynamics simulations (altogether 9 MD runs ere produced). Conformational preferences of internucleotide linkages (undergoing contacts with the RNase H enzyme) were studied using several versions of the AMBER force field. Either one or two copies of RNase H were included into the simulated system. As the most important DNA-binding residues were recognized Trp93 and Ser101 in the first DNA binding site and Thr49 and Arg47 in the second DNA binding site. Further, the AMBER force field was re-parameterized slightly using ab initio calculations to produce force constants for the modified phosphonate internucleotide linkage. Biologically active version of the modified internucleotide linkage C3-O3-P-C-O5-C5 was able to bind Arg47 using two hydrogen bonds within the 10 ns MD run (even more effciently than in the case of MD runs with natural internucleotide linkages). On the other hand, the biologically inactive C3-O3-C-P-O5-C5 internucleotide linkage lose contacts with Arg47 quickly.
|
|
| |
|
|
Accurate Quantum Mechanical Calculations on Noncovalent Interactions: Rationalization of X-ray Crystal Geometries by Quantum Chemistry Tools
Hostaš, Jiří ; Hobza, Pavel (advisor) ; Burda, Jaroslav (referee) ; Jurečka, Petr (referee)
There is a need for reliable rules of thumb for various applications in the area of biochemistry, supramolecular chemistry and material sciences. Simultaneously, the amount of information, which we can gather from X-ray crystal geometries about the nature of recognition processes, is limited. Deeper insight into the noncovalent interactions playing the most important role is needed in order to revise these universal rules governing any recognition process. In this thesis, systematic development and study of the accuracy of the computational chemistry methods followed by their applications in protein DNA and host guest systems, are presented. The non-empirical quantum mechanical tools (DFT-D, MP2.5, CCSD(T) etc. methods) were utilized in several projects. We found and confirmed unique low lying interaction energies distinct from the rest of the distributions in several amino acid−base pairs opening a way toward universal rules governing the selective binding of any DNA sequence. Further, the predictions and examination of changes of Gibbs energies (ΔG) and its subcomponents have been made in several cases and carefully compared with experiments. We determined that the choline (Ch+) guest is bound 2.8 kcal/mol stronger (calculated ΔG) than acetylcholine (ACh+) to self-assembled triple helicate rigid...
|
|
|
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.
|
|
| |
|
| |
|
| |
guest ::
RSS feed.