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Dynamic Processes in Porous Nanomaterials: Adsorption and Diffusion
Trachta, Michal ; Bludský, Ota (advisor) ; Heard, Christopher James (referee) ; Čičmanec, Pavel (referee)
Dynamical processes in porous nanomaterials (adsorption, diffusion, separation) play a significant role in many industrial applications. Modeling of these applications theoretically provides atomistic details of adsorption and diffusion phenomena - information that is often difficult to obtain using contemporary experimental methods. Theory may thus provide a deeper insight into these processes, e.g., explaining the mechanisms and assisting in the search for new materials suited for a specific application through material screening. In this work, the dynamical processes in porous materials were investigated by means of force field and ab initio modeling. On a set of relevant simulation data, two particular problems related to the modeling of such processes are thoroughly addressed: (i) the sensitivity of the results to material geometry, and (ii) the accuracy of the potential energy surface description. Regarding the structure description, the reliability of theoretically-predicted structures is still limited, despite the significant increase in computational power and algorithm development. The drawbacks of individual methods are identified; even state-of-the-art density functional theory approaches suffer from inaccuracies, e.g., due to an imbalance between the semi-local (GGA) functional and...
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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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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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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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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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Potential energy surface of the HeNO+complex
Vranková, Veronika ; Soldán, Pavel (advisor) ; Bludský, Ota (referee)
V tejto práci sme sa zaoberali konštrukciou plochy potenciálnej energie molekulárneho komplexu HeNO + z poskytnutých ab initio dát. Ako prvé sme odvodili kvali- tatívne korektný výraz pre interakčný Hamiltonián komplexu HeNO + pre ve©ké intermolekulárne vzdialenosti. Rozhodli sme sa pracova' v multipólovej aprox- imácii, ktorú je možné použi' práve pri ve©kých intermolekulárnych vzdialenos- tiach. Pre multipólový rozvoj sme použili formuláciu kartézskych tenzorov. Takýto interakčný Hamiltonián bol následne použitý ako porucha systému v poruchovej teórii intermolekulárnych síl, z ktorej sme odvodlili výraz pre elektro- statickú, indukčnú a disperznú energiu. Tento záver bol potrebný pre konštruk- ciu korektného reprodukčného jadra pre 1D RKHS interpoláčnú a extrapolačnú procedúru, ktorú sme skombinovali s Gaussovou-Legendrovou kvadratúrou. Napísali sme program v jazyku Fortran90, ktorý prislúcha našim teoretickým výsledkom a ktorého výstupom sú hodnoty interakčného potenciálu na vopred zvolených súradniciach. Taktiež sme určili globálne minimum a sedlové body plochy po- tenciálnej energie HeNO + komplexu. 1
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Theoretical investigation of microporous materials for adsorption and catalysis
Položij, Miroslav ; Nachtigall, Petr (advisor) ; Bludský, Ota (referee) ; Cwiklik, Lukasz (referee)
Theoretical investigation of microporous materials for adsorption and catalysis Microporous materials are defined by a presence of pores with diameter smaller than 2 nm. They comprise a large variety of materials from amorphous materials to very well defined crystalline materials like zeolites or metal organic frameworks. Microporous materials are industrially very important group of materials used for adsorption, gas capture, molecular sieving, or heterogeneous catalysis. Zeolites are by far the most important group of microporous materials due to their use as catalysts for the petroleum cracking. One of the main limitations of the zeolite use in catalysis is their limited pore size. This obstacle can be solved by use of hierarchical zeolites with a secondary mesopore network which allows overcoming the diffusion problems. The aims of this study can be divided into two parts. In the first part, the structures of two-dimensional and hierarchical zeolites were investigated theoretically to identify the structure of new materials and to obtain reliable models to study the hierarchical zeolites. In the second part, the catalytic properties of several microporous materials were modelled to explain their experimental activity. The results of this thesis were used to identify the structure of a large...
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