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Development and applications of molecular dynamics for molecular spectroscopy
Kessler, Jiří ; Bouř, Petr (advisor) ; Bludský, Ota (referee) ; Setnička, Vladimír (referee)
This Thesis deals with simulations of chiroptical spectra using a combination of molecular dynamics and quantum chemistry. Molecular dynamics was used to explore conformational behaviour of studied systems (proteins), quantum chemistry for calculation of spectral prop- erties. The Quantum chemical methods are limited to relatively small systems. We overcome this problem mostly by a fragmentation of studied systems, when smaller, computationally feasible, fragments are created and used for the quantum chemical calculations. Calculated properties were then transferred to the big molecule. Vibrational Optical Activity (VOA) spectra of poly-L-glutamic acid fibrils (PLGA), insulin prefibrillar form and native globular proteins were studied. The simulated spectra provided satisfactory agreement with the experiment and were used for its interpretation. Experimental Vibrational Circular Dichroism (VCD) spectra of poly-L-glutamic acid fibrils were only qualitatively reproduced by the simulation. We could reproduce the major amide I band and a smaller negative band associated with the side chain carboxyl group. Our simulation procedure was then extended to a set of globular proteins and their Raman Optical Activity (ROA) spectra. Here we achieved an exceptional precision. For example, we were able to reproduce...
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Lattice energies of molecular solids
Hofierka, Jaroslav ; Klimeš, Jiří (advisor) ; Bludský, Ota (referee)
Molecular solids are important materials with many applications in various fields of science and industry. They are often characterized by a rich phase diagram and the ability to adopt multiple crystal structures (polymorphism). To describe small energy differences between various phases or polymorphs, accurate quantum mechanical methods are needed. In this thesis, lattice energies of methane, methanol, ammonia, and carbon dioxide are calculated using two different approaches, namely, the fragment approach and the periodic boundary conditions (PBC) approach. These two schemes have different requirements in terms of compute cost and human time needed to obtain precise results. In the fragment scheme, the Hartree-Fock, MP2, and CCSD(T) quantum mechanical methods are employed. In the PBC scheme, the Hartree- Fock and MP2 lattice energies are calculated. For all four systems, which differ in the nature of prevalent intermolecular interactions, a very good agreement in the range of 0.1 - 0.6 kJ/mol was found between both approaches at the MP2 level.
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Computational investigation of adsorption of saturated and unsaturated hydrocarbons in CPO-27 Metal-Organic Framework
Smetanová, Tereza ; Nachtigall, Petr (advisor) ; Bludský, Ota (referee)
Title: Computational investigation of adsorption of saturated and unsaturated hydrocarbons in CPO-27 Metal-Organic Framework Abstract: The adsorption of hydrocarbons on coordinatively unsaturated sites (cus) in CPO-27 Metal-Organic Framework (MOF) was investigated computationally. Different levels of density functional theory (DFT), including vdW-DF2, PBE, DFT-D2 functionals, were used and their performance was compared to a reference method DFT/CC and available experimental data. The adsorption properties of Cu and Mg containing CPO-27 for ethane, ethylene, propane and propylene separations were investigated and discussed. Keywords: adsorption, metal-organic frameworks, density functional theory, coordinatively unsaturated sites, open metal sites
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Modeling of bio-inorganic interfaces
Trachta, Michal ; Bludský, Ota (advisor) ; Nachtigall, Petr (referee)
Dynamic atomistic description of bio-inorganic interfaces represents a challenging problem for contemporary computational chemistry. A detailed analysis of processes occurring on the interface between biomolecule and inorganic material can help our understanding of various processes, ranging from chromatography and protein separation to protein immobilization techniques and their effect on enzyme activity or protein conformational stability. High complexity of bio- inorganic interfaces prevents detailed investigation using accurate, but computationally demanding ab initio methods. Since reliable empirical potentials are not available for these systems, the aim of this work is to develop force fields based on ab initio data as well as a general methodology for parameterization of such force fields. Our potential fitting procedure was carried out in an automated fashion based on molecular dynamics simulation. The resulting potentials were applied for investigation of inorganic material's influence on polypeptide conformations.
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Studium biologicky relevantních systémů v elektronicky excitovaných stavech
Zámečníková, Martina ; Soldán, Pavel (advisor) ; Bludský, Ota (referee) ; Nachtigallová, Dana (referee)
Very short lifetimes of excited states of isolated bases in nucleic acids, on the picosec- ond order, are believed to contribute to photostability of the genetic code. When embedded in DNA this behavior becomes more complex, mainly due to their inter- actions via stacking and hydrogen bonding. The DNA photophysiscs is not fully understood yet. It depends e.g. on the conformation and the character of excited states. The studies on smaller systems can help to improve the understanding of these phenomena. The aim of this work was to examine the dynamics of the excited states of the n → π∗ character of the complex of N-methylformamide dimer and two waters. The study was performed using non-adiabatic dynamics simulations with on-the-fly Surface Hopping algorithm based on the potential energy surfaces and non-adiabatic couplings obtained with multi-reference approach. The results show that after the vertical excitation into delocalized S2 state the system relaxes into S1 state within several tens femtoseconds. For majority of the population, the charac- ter of the state then oscillates between localized and delocalized during the whole course of the dynamics. Comparison with calculations with the waters removed in- dicates that the delocalization is caused by waters serving as a bridge between the two chromophores. 1
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Modelování ADOR syntézy nových zeolitů
Trachta, Michal ; Bludský, Ota (advisor) ; Nachtigall, Petr (referee)
Zeolites are materials with a large variety of applications in industry. They are able to catalyze many types of reactions and can be used as molecular sieves or adsorbents. Tailored design of zeolites is an important goal for chemists as the full control over zeolite porosity and composition can lead to optimal materials for industrial purposes. Recently, a new strategy for the zeolite synthesis was proposed and successfully applied for several systems. This strategy, called ADOR, can lead to synthesis of many new materials with a defined structure and porosity. The synthesis of new zeolites from lamellar precursors, which is in the heart of the ADOR process, may become widely used technique in the near future. In this work we focus on hypothetical products of the ADOR process and address the relationship between their structure and feasibility of their synthesis. Keywords: ADOR process, hypothetical zeolites, in silico investigation
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Theoretical Investigation of Metal Oraganic Frameworks
Hezinová, Markéta ; Nachtigall, Petr (advisor) ; Bludský, Ota (referee)
Metal-Organic Frameworks (MOFs) with coordinatively unsaturated sites (cus's) have shown very good adsorption properties for Sulphur-containing aromatic compounds. One of the promising applications of MOFs currently under investigation is their use in the separation of sulphur-containing compounds from various hydrocarbons. A theoretical investigation of thiophene, dibenzothiophene (DBT) and toluene adsorption on CPO-27(X) and CuBTC MOFs, and NaY zeolite (Si/Al ratio 2.7:1) is presented. The reliability of the method was tested on the small cluster models mimicking the coordinatively unsaturated sites in CPO-27 MOF with respect to the CCSD(T/CBS benchmark calculations. The results of periodic DFT calculations employing vdW-DF2 functional accounting for the dispersion interactions obtained herein were used for the interpretation of experimental results obtained by experimental co-workers. At low coverages, the interaction energies calculated for thiophene adsorbed on CPO- 27(X), where X is Cu, Zn, Mg, Co, and Ni, are increasing in order Zn2+ < Cu2+ < Mg2+ < Co2+ < Ni2+ , which is in good agreement with the experimental data. The adsorption in CPO-27(X) is driven mainly by two factors: (i) an electrostatic interaction between X2+ cus site of CPO- 27(X) and Sulphur atom on thiophene , and (ii)...
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Nonlocal correlation in density functional theory
Hermann, Jan ; Bludský, Ota (advisor) ; Fišer, Jiří (referee)
e van der Waals (vdW) interactions, or dispersion forces, are crucial in many chem- ical, physical and biological processes and received much attention from developers of density functional theory (DFT) methods. e most popular non-empirical DFT method for treating vdW interactions is the vdW density functional by Dion et al. (vdW-DF). Despite its success, vdW-DF is not accurate enough for many chemical applications. Here, we investigate two possible ways how to improve its accuracy. First, we reoptimize the only weakly speci ed parameter of vdW-DF for several semi-local functionals. On the S benchmark database set, we nd that revPBE is the best performer, decreasing the error from . % to . %. Second, a system-speci c but very accurate (∼ . kcal/mol) DFT correction scheme is proposed for precise calcula- tions of adsorbent−adsorbate interactions by combining vdW-DF and the empirical DFT/CC correction scheme. e new approach is applied to small molecules (CH , CO , H , H O, N ) interacting with a quartz surface and a lamella of UTL zeolite. e very high accuracy of the new scheme and its relatively easy use and numerical stability compared to the earlier DFT/CC scheme o er a straightforward solution for obtaining reliable predictions of adsorption energies.
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Assessment of dispersion corrected density functional methods.
Hermann, Jan ; Bludský, Ota (advisor) ; Nachtigallová, Dana (referee)
The problem of dispersion interaction in the DFT is reviewed, followed by a systematic study of the behaviour, in particular the transferability, of the LAP method. Dispersion is a kind of van der Waals forces, dominant in important molecular systems such as biomolecules or adsorption systems. The DFT is an ever increasingly used method for modelling chemical sys- tems. However, dispersion is rendered rather poorly in the DFT. We give an illustration of the problem and present some known correction methods. One of them is the local atomic potential (LAP) approach which we develop further from its original formulation, and this enables us to exactly match the benchmark interaction curves. We apply this development on systems consisting of benzene and a noble gas. We construct the LAPs for noble gas atoms and for carbon. It is shown that the LAP approach is poorly transfer- able based on our calculations. The investigation reported in this bachelor's thesis represents the rst attempt for an detailed study of the behaviour of the LAP method.
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A novel approach for description of non-covalent intermolecular interactions
Rubeš, Miroslav ; Bludský, Ota (advisor) ; Fišer, Jiří (referee) ; Jurečka, Petr (referee)
Charles University in Prague Faculty of Science Department of Modeling of Chemical Properties of Bio- and Nanostructures A novel approach for description of non-covalent intermolecular interactions Dissertation Thesis Abstract Mgr. Miroslav Rubeš Supervisor: RNDr. Ota Bludský, CSc. Institute of Organic Chemistry and Biochemistry AS CR Center for Biomolecules and Complex Molecular Systems Prague 2010 Introduction Non-covalent interactions play a major role in many important physical, chemical, and biological processes that include, for instance, inter-molecular interactions between biomolecules, adsorption and separation, self-assembly in supra-molecular chemistry, and catalytic activity. To gain a deeper understanding of such processes at the atomistic level it is often necessary to investigate these systems theoretically. Due to the complex character of relevant systems, realistic models include hundreds of atoms and, thus, the computational investigation must rely on rather approximate methods. An accurate description of these systems still represents a major challenge for theoretical chemists. Methods based on density functionals (density functional theory, DFT) are currently among the most popular approaches for computational treatment of large systems. Unfortunately, the non-covalent interactions...
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