Simulation Modeling of Biomolecules
A.Y. 2020/2021
Learning objectives
The course presents some techniques based on the qualitative theory of molecular orbitals useful in the study of the electronic structure, the molecular geometry and the reactivity of transition metal complexes. The laboratory experiences will guide the student in the calculation of the molecular orbitals of some organometallic species.
Expected learning outcomes
The student will be able to qualitatively describe the electronic structure of transition metal complexes and to use this information to rationalize or predict their geometry and reactivity.
Lesson period: Second semester
Assessment methods: Esame
Assessment result: voto verbalizzato in trentesimi
Single course
This course cannot be attended as a single course. Please check our list of single courses to find the ones available for enrolment.
Course syllabus and organization
Single session
Responsible
Lesson period
Second semester
The lessons will be held on MS Teams according to the timetable. The registrations will be made available on Ariel. The exams will be performed on MS Teams.
Course syllabus
Basic concepts:
- Basic molecular modeling. Force fields.
- Statistical mechanics review.
- Molecular dynamics.
- Monte Carlo method.
- The sampling problem. Enhanced sampling methods. Parallel tempering.
- Free energy calculation. Thermodynamic perturbation and integration.
- Umbrella sampling. Jarzynski equality based methods.
- Simplified approaches to calculate binding free energies (MM/GBSA, MM/PBSA).
- Analysis of data from molecular simulations. Essential Dynamics. Communication propensity.
Applications:
-Force fields for special systems: Alogens and Metals
- Force field-based conformational analysis.
- Molecular docking.
- Protein-protein interactions: how to model them?
- Design of modulators of protein-protein interactions.
- The problem of protein folding. Folding inhibitors drugs.
-Antifreeze proteins modeling.
- Basic molecular modeling. Force fields.
- Statistical mechanics review.
- Molecular dynamics.
- Monte Carlo method.
- The sampling problem. Enhanced sampling methods. Parallel tempering.
- Free energy calculation. Thermodynamic perturbation and integration.
- Umbrella sampling. Jarzynski equality based methods.
- Simplified approaches to calculate binding free energies (MM/GBSA, MM/PBSA).
- Analysis of data from molecular simulations. Essential Dynamics. Communication propensity.
Applications:
-Force fields for special systems: Alogens and Metals
- Force field-based conformational analysis.
- Molecular docking.
- Protein-protein interactions: how to model them?
- Design of modulators of protein-protein interactions.
- The problem of protein folding. Folding inhibitors drugs.
-Antifreeze proteins modeling.
Prerequisites for admission
Basic knowledge of math, physics, physical and organic chemistry
Teaching methods
Frontal lessons assisted by the use of slides (See section on the Emergency didactic).
Teaching Resources
- M.P. Allen, D.J. Tildesley, Computer simulation of liquids.
- A. R. Leach, Molecular Modelling - Principles and Applications, Longman
-Selected papers on specific subjects suggested during the lesseons
- A. R. Leach, Molecular Modelling - Principles and Applications, Longman
-Selected papers on specific subjects suggested during the lesseons
Assessment methods and Criteria
Oral exam. The exam will consist of a discussion which aims to verify the preparation of the student on the course contents. The examination will typically include a few questions concerning both basic simulation methods and their applications to the study of biomolecules.
CHIM/02 - PHYSICAL CHEMISTRY - University credits: 6
Lessons: 48 hours
Professor:
Pieraccini Stefano
Professor(s)
Reception:
On appointment
Teacher's Office (Dipartimento di Chimica - Ground Floor -B Section) or on MS Teams