Molecular Modelling in Biotechnology

Adatok

A Tantárgybejelentőben megadott hivatalos adatok az alábbi tanévre: 2024-2025

Tematika

Students will get deeper insights into the mechanisms of drug interactions at molecular level applying fundamental molecular modelling methods. Further answering the scientific questions students will get skills to perform high quality figures and schemes of molecules and molecular interactions to present their results and presentation content in lectures, diploma works or thesises. In this course the basic examination methods of theoretical chemistry will be discussed by the practical point of view in the frame of following subtopics: Methods of molecular modelling. Description of the forcefield, semiempirical, ab initio and density functional methods, advantages and disadvantages. Discovering the balance between the model ant the calculation methods. The algorithm of the choice of appropriate model and calculation method. Short description of the basic rules and mathematical background of theoretical chemistry. calculation of the electronic structure of atoms and molecules. Calculation the equilibrium conformations of molecules, the role of the entropy in the interactions of bioactive molecules and its calculation. Description of the correlation between the reactivity and the temperature. Examples at molecular level. Considering the molecular environment: explicit and implicit methods. Interesting examples and applications in biotechnology.

Előadások

• 1. Experimental results raise the necessity of quantum-chemical description of the structure of materials. Quantitization and related quantities (energy, momentum, spin). Simple mathematical descriptions. - Kunsági-Máté Sándor
• 2. Axiomatic description of the quantum theory. Atomic unit system. Overview on the exact and approximative solutions of the time - independent Schrödinger equation. - Kunsági-Máté Sándor
• 3. Approximative solutions: the molecular mechanics methods. - Kunsági-Máté Sándor
• 4. Semi - empirical methods, advantages and disadvantages. - Kunsági-Máté Sándor
• 5. Conformation analysis, energy minimization algorithms. - Kunsági-Máté Sándor
• 6. Electronic structure of molecules. The chemical bonds, tipes of bonds. The structure of molecules, stereochemistry. - Kunsági-Máté Sándor
• 7. Modelling in comparison with the experiments, calculation of the enthalpy, entropy and their appropriate experimental values. - Kunsági-Máté Sándor
• 8. Calculation of the static potential energy surfaces of chemical reactions. Methods to determine the transition states associated to the chemical reactions. Activation energy and activation free enthalpy. - Kunsági-Máté Sándor
• 9. Modelling the elementary chemical reactions. Calculation of molecular dynamics. Determination of the rection rate using direct trajectory method. - Kunsági-Máté Sándor
• 10. Molecular capsules and drug design - Kunsági-Máté Sándor
• 11. Role of the molecular symmetry, point groups and the symmetry of molecular vibrations. - Kunsági-Máté Sándor
• 12. Interactions of the primycin, ergosterol and oleic acid as plasma membrane unit. - Kunsági-Máté Sándor
• 13. Modelling the interactions of bioactive molecules with molecular containers in accordance with molecular packing of drugs. - Kunsági-Máté Sándor
• 14. Quantum - chemical background of the rules in atomic and molecular spectroscopy. Rules of Raman and Infrared transitions and their relationship with the molecular symmetry. - Kunsági-Máté Sándor
• 15. Effective calculation methods to consider the molecular environment: Onsager-model, Polarizable Continuum Model - Kunsági-Máté Sándor
• 16. Methods for consideration of the solvents: the Onsager-model, and the Polarizable Continuum Model, PCM. Explicit consideration of the solvent molecules. The TIP3P model. - Kunsági-Máté Sándor
• 17. Examples: modelling the systems possessing high symmetry and infinite volume. Crystals and polymers. - Kunsági-Máté Sándor
• 18. Examples: conformation analysis, bong length, bond angle and dihedral angles. The bipyridile and thionine molecules. Calixarenes and stereoisomers. Importance of hydrogen bonds in the stability of molecular geometries. - Kunsági-Máté Sándor
• 19. Calculation of the host - guest interactions, calculations of interactions of calixarenes with neutral molecules based on pi-pi interactions. - Kunsági-Máté Sándor
• 20. Investigations of the conformation changes of proteins by fluorescence and calorimetric methods. - Kunsági-Máté Sándor
• 21. Ab initio calculations of electronic interactions in inclusion complexes of calix- and thiacalix[n]arenes and block s cations - Kunsági-Máté Sándor
• 22. Calix[n]arene-based drug carriers: A DFT study of their electronic interactions with a chemotherapeutic agent used against leukemia - Kunsági-Máté Sándor
• 23. Coordination of Methanol Clusters to Benzene. Modelling the microsolvation. - Kunsági-Máté Sándor
• 24. Cluster formation in protic molecular environment. Conclusion on drug design. - Kunsági-Máté Sándor

Gyakorlatok

Szemináriumok

A tananyag elsajátításához szükséges segédanyagok

Kötelező irodalom

P.W. Atkins: Physical Chemistry

Saját oktatási anyag

Slides and notes of all lectures are available electronically. All topics discussed will be associated with papers published recently. Those papers together with the related doctoral dissertations in English will also be offered to support the teaching.

Jegyzet

Slides and Summaries of lectures are available electronically

Ajánlott irodalom

Jensen_F.-Introduction_to_Computational_Chemistry_(2007)

Scientific papers, list will be given during the lectures

A félév elfogadásának feltételei

Presentation about topics selected.

Félévközi ellenőrzések

Summary and presentation about a selected topic and test.

Távolmaradás pótlásának lehetőségei

There is no possibility to make up for a missed lecture

Vizsgakérdések

Methods of molecular modelling. Description of the forcefield, semiempirical, ab initio and density functional methods, avantages and disadvantages. The balance between the model ant the calculation methods. The algorithm of the choice of appropriate model and calculation method.Short description of the basic rules and mathematical background of theoretical chemistry. calculation of the electronic structure of atoms and molecules. Calculation the equilibrium conformations of molecules, the role of the entropy in the interactions of bioactive molecules and its calculation. Description of the correlation between the reactivity and the temperature. Examples at moecular level. Considering the molecular environment: explicit and implicit methods. Interesting examples and applications in pharmacy.

Vizsgáztatók

Gyakorlatok, szemináriumok oktatói