Search for dissertations about: "empirical valence bond method"

Showing result 1 - 5 of 8 swedish dissertations containing the words empirical valence bond method.

  1. 1. Calculations of Reaction Mechanisms and Entropic Effects in Enzyme Catalysis

    University dissertation from Uppsala : Acta Universitatis Upsaliensis

    Author : Masoud Kazemi; Uppsala universitet.; Uppsala universitet.; [2017]
    Keywords : NATURVETENSKAP; NATURAL SCIENCES; NATURVETENSKAP; NATURAL SCIENCES; Enzyme catalysis; Entropy; Cytidine deamination; Ribosome; Peptidyl-tRNA hydrolysis; Peptide bond formation; Empirical valence bond method; Density functional theory; Biology with specialization in Structural Biology; Biologi med inriktning mot strukturbiologi; Biokemi; Biochemistry; Biology with specialization in Molecular Biotechnology; Biologi med inriktning mot molekylär bioteknik;

    Abstract : Ground state destabilization is a hypothesis to explain enzyme catalysis. The most popular interpretation of it is the entropic effect, which states that enzymes accelerate biochemical reactions by bringing the reactants to a favorable position and orientation and the entropy cost of this is compensated by enthalpy of binding. READ MORE

  2. 2. Computational modelling of enzyme selectivity

    University dissertation from Uppsala : Acta Universitatis Upsaliensis

    Author : Paul Bauer; Uppsala universitet.; Uppsala universitet.; Uppsala universitet.; [2017]
    Keywords : NATURVETENSKAP; NATURAL SCIENCES; enantiomer; epoxide hydrolase; chiral catalysis; empirical valence bond approach; method development; Biokemi; Biochemistry;

    Abstract : Enantioselective reactions are one of the ways to produce pure chiral compounds. Understanding the basis of this selectivity makes it possible to guide enzyme design towards more efficient catalysts. READ MORE

  3. 3. Ligand binding and enzyme catalysis studied by molecular dynamics simulations

    University dissertation from Uppsala : Acta Universitatis Upsaliensis

    Author : Tomas Hansson; Uppsala universitet.; [1998]
    Keywords : NATURVETENSKAP; NATURAL SCIENCES; Molecular biology; molecular dynamics simulation; free energy; linear response; drug design; empirical valence bond; HIV protease; protein tyrosine phosphatase; Molekylärbiologi; NATURAL SCIENCES Biology Cell and molecular biology Molecular biology; NATURVETENSKAP Biologi Cell- och molekylärbiologi Molekylärbiologi; molekylärbiologi; Molecular Biology;

    Abstract : Molecular dynamics simulations and free energy calculations can be applied to biomolecular systems to predict ligand binding affinities. Combined with hybrid quantum-classical potential energy surfaces, such computations can also be used to probe enzymatic catalysis mechanisms. READ MORE

  4. 4. Molecular Simulation of Enzyme Catalysis and Inhibition

    University dissertation from Uppsala : Acta Universitatis Upsaliensis

    Author : Sinisa Bjelic; Uppsala universitet.; [2007]
    Keywords : Theoretical chemistry; enzyme catalysis; enzyme inhibition; computer simulations; molecular dynamics; empirical valence bond method; structure-based inhibitor design; Teoretisk kemi;

    Abstract : The reaction mechanisms for the hemoglobin degrading enzymes in the Plasmodium falciparum malaria parasite, plasmepsin II (Plm II) and histo-aspartic protease (HAP), have been analyzed by molecular simulations. The reaction free energy profiles, calculated by the empirical valence bond (EVB) method in combination with molecular dynamics (MD) and free energy perturbation (FEP) simulations are in good agreement with experimental data. READ MORE

  5. 5. Single-photon multiple ionisation of atoms and molecules investigated by coincidence spectroscopy Site-specific effects in acetaldehyde and carbon dioxide

    University dissertation from Uppsala : Acta Universitatis Upsaliensis

    Author : Sergey Zagorodskikh; Uppsala universitet.; [2016]
    Keywords : NATURVETENSKAP; NATURAL SCIENCES; acetaldehyde; carbon dioxide; xenon; electron correlation; double ionisation; triple ionisation; core-valence ionisation; site-specific Auger decay; multiple Auger decay; branching ratios; site-specific photodissociation; molecular rearrangement; time-of-flight multi-electron-ion coincidence spectroscopy; synchrotron radiation; Physics with spec. in Atomic; Molecular and Condensed Matter Physics; Fysik med inriktning mot atom- molekyl- och kondenserande materiens fysik;

    Abstract : In this thesis, multiple ionisation processes of free atoms and molecules upon single photon absorption are studied by means of a versatile multi-electron-ion coincidence spectroscopy method based on a magnetic bottle, primarily in combination with synchrotron radiation. The latter offered the possibility to access not only valence but also core levels, revealing processes, which promote the target systems into different charge states. READ MORE