Modelling the Structure and Interactions of Bioactive Molecules

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 pharmacy.

Előadások

• 1. 1 lecture 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. 1 lecture 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
• 3. 2 lecture 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
• 4. 2 lecture 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
• 5. 3 lecture Approximative solutions: the molecular mechanics methods. - Kunsági-Máté Sándor
• 6. 3 lecture Approximative solutions: the molecular mechanics methods. - Kunsági-Máté Sándor
• 7. 4 lecture Semi - empirical methods, advantages and disadvantages. - Kunsági-Máté Sándor
• 9. 5 lecture Conformation analysis, energy minimization algorithms. - Kunsági-Máté Sándor
• 11. 6 lecture Electronic structure of molecules. The chemical bonds, tipes of bonds. The structure of molecules, stereochemistry. - Kunsági-Máté Sándor
• 13. 7 lecture Modelling in comparison with the experiments, calculation of the enthalpy, entropy and their appropriate experimental values. - Kunsági-Máté Sándor
• 15. 8 lecture Molecular symmetry, point groups and the symmetry of molecular vibrations. - Kunsági-Máté Sándor
• 17. 9 lecture Interactions of the primycin, ergosterol and oleic acid as plasma membrane unit. - Kunsági-Máté Sándor
• 19. 10 lecture Modelling the interactions of bioactive molecules with molecular containers in accordance with molecular packing of drugs. - Kunsági-Máté Sándor
• 21. 11 lecture 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
• 23. 12 lecture Effective calculation methods to consider the molecular environment: Onsager-model, Polarizable Continuum Model - Kunsági-Máté Sándor
• 25. 13 lecture Examples: simple chemical reactions, calculation of the stability weak molecular complexes, conformation analysis. - Kunsági-Máté Sándor
• 27. 14 lecture Examples: modelling the systems possessing high symmetry and infinite volume. Crystals and polymers. - Kunsági-Máté Sándor

Gyakorlatok

• 4. 4 practice : Geometry optimization and conformation analysis. Energy minimization algorythm mostly used in geometry optimization practice. - Kunsági-Máté Sándor
• 5. 5 practice: 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
• 6. 6 practice Molecular dynamics methods, Monte-Carlo method and the Langevin model. The implicite consideration of the molecular environment. - Kunsági-Máté Sándor
• 7. 7 practice Modelling the elementary chemical reactions. Calculation of molecular dynamics. Determination of the rection rate using direct trajectory method. - Kunsági-Máté Sándor
• 8. 8 practice 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
• 9. 9 practice Calculation of molecular parameters have significant importance in the practice. The QSAR and the molecular similarity - analysis. - Kunsági-Máté Sándor
• 10. 10 practice 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
• 11. 11 practice Examples: interactions of molecules. Calculation of the host - guest interactions, calculations of interactions of calixarenes with neutral molecules based on pi-pi interactions. - Kunsági-Máté Sándor
• 12. 12 practice Examples : elementary dissociation reactions: dissociation of asymmetric olefines. Effect of melecular environment on the reaction rate. - Kunsági-Máté Sándor
• 13. 13 practice Examples: Interaction of Primycin and oleic acid. Calculation of the interaction energy in system possessing large numbers of electrons. - Kunsági-Máté Sándor
• 14. 14 practice E+xamples: dynamic processes: modelling the crystal growth. - Kunsági-Máté Sándor

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 preparation about a selected topic.

Félévközi ellenőrzések

Summary and presentation about a topics selected, test in the second half of the semester.

Távolmaradás pótlásának lehetőségei

Upto 15% is allowed, electronical material is available

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

• Kunsági-Máté Sándor