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Course, academic year 2023/2024
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Computer Simulations of Chemical Reactions and Enzyme Catalysis - MC260P87
Title: Počítačové modelování chemických reakcí a enzymové katalýzy
Czech title: Počítačové modelování chemických reakcí a enzymové katalýzy
Guaranteed by: Department of Physical and Macromolecular Chemistry (31-260)
Faculty: Faculty of Science
Actual: from 2014
Semester: winter
E-Credits: 3
Examination process: winter s.:
Hours per week, examination: winter s.:2/0, Ex [HT]
Capacity: unlimited
Min. number of students: unlimited
4EU+: no
Virtual mobility / capacity: no
State of the course: taught
Language: Czech
Note: enabled for web enrollment
Guarantor: prof. Mgr. Lubomír Rulíšek, DSc.
Is incompatible with: MC260P131
Annotation -
Computer modeling of chemical and biochemical processes, such as organic and bioinorganic reactions, including enzymatic reactions, is an integral part of our understanding of these processes at atomic or even electron level. The aim of this course is to get acquainted with modern methods of theoretical and computational chemistry. Emphasis is placed on combined methods of quantum mechanics and molecular mechanics (QM / MM), practical use of statistical mechanics including the theory of transition state and its relation to chemical reactivity and selectivity, explanation of the principles of modern solvation methods, use of molecular dynamics for statistical sampling of phase space, comparison of calculated data with experimental data and critical evaluation of the suitability of individual methods for solving practical problems. Last but not least, the course also deals with the redox processes in bioanorganic systems and the methods of their theoretical description. Lectures are held - after an agreement - in English.
Last update: Rulíšek Lubomír, prof. Mgr., DSc. (26.06.2019)
Literature - Czech

F. Jensen: Introduction to Computational Chemistry, Wiley, 1999.

Christopher J. Cramer: Essentials of Computational Chemistry: Theories and Models, Wiley, 2004.

A.R. Leach: Molecular Modelling: Principles and Applications

Robert A. Copeland: ENZYMES: A Practical Introduction to Structure, Mechanism, and Data Analysis

W. Thiel, H. M. Senn: QM/MM Methods for Biological Systems. Top Curr Chem (2007) 268: 173–290

A. Warshel: Computer Modeling of Chemical Reactions in Enzymes and Solutions, Wiley, 1997.

Last update: Rulíšek Lubomír, prof. Mgr., DSc. (19.04.2018)
Requirements to the exam -

The exam takes the form of homework assignments at the end of the course and a short oral interview. A student is required to have a deeper understanding of the subject, that is to understand basic principles of enzyme catalysis and chemical reactivity, without the need for detailed knowledge of all equations and their derivation.

Last update: Rulíšek Lubomír, prof. Mgr., DSc. (26.06.2019)
Syllabus -

1/ Quantum Mechanics: Key Concepts, Methods, and Machinery

2/ Molecular Mechanics: Key Concepts, Methods, and Machinery

3/ Solvation Methods: Polarized Continuum Methods (PCM, COSMO, COSMO-RS), Explicit Solvation

4/ QM/MM Methods and Energy Minimization: Background, Theory, Applications, and Examples

5/ Statistical Thermodynamics: Essential Concepts (Partition Functions, Boltzmann Population, Entropy, Enthalpy, Free Energy)

6/ Free Energy Perturbation (Thermodynamic Integration) and PMF Methods: Concept, Theory, Applications

7/ Transition State Theory: Eyring Equation (Theory, Applicability and Limitations, Kinetic Isotope Effects, Tunneling Correction), More Advanced Theories (Variational Transition State Theory)

8/ Concepts in (Bio)Catalysis: Kinetic/thermodynamic correlations (BEP principle, Westheimer Effect); Marcus Theory for Electron Transfer and Beyond, adiabatic versus non-adiabatic reaction dynamics; Applications

9/ Modelling Chemical Reactions in Solution vs. Enzymes: Theory and Applications (Reaction Mechanisms: Search for Transition States, Search for Rate-Determining Step in Multistep Reactions), Metals in Solution vs Enzymes (Entantic States, Electronic Structure Contributions to Reactivity), Reaction Selectivity - Case Studies (eg. C-H bond Activation, hydroxylation vs. halogenation vs. desaturation).

Last update: Rulíšek Lubomír, prof. Mgr., DSc. (26.06.2019)
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