C8863 Free Energy Calculations

Faculty of Science
Spring 2023
Extent and Intensity
2/0. 2 credit(s) (plus 1 credit for an exam). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
Teacher(s)
RNDr. Petr Kulhánek, Ph.D. (lecturer)
Guaranteed by
RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research - Faculty of Science
Supplier department: National Centre for Biomolecular Research - Faculty of Science
Timetable
Mon 9:00–10:50 C04/118
Prerequisites
Basic level of general, physical and computational chemistry.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
there are 20 fields of study the course is directly associated with, display
Course objectives
The course is oriented to obtaining basic knowledge about the free energy calculations employing computational chemistry methods. Students will get an overview of available methods, their advantages and drawbacks. Obtained knowledge should be enough for independent solution of real problems from chemistry, supermolecular chemistry and biochemistry.
Learning outcomes
Student will be able to:
- choose a suitable method for calculating free energy;
- determine the composition of the reaction mixture in equilibrium;
- design appropriate thermodynamic cycles;
- describe chemical transformations by potential of mean force;
Syllabus
  • 1. Free Energy and its Relation to Thermochemistry and Kinetics. Experimental Methods of its Measurement. Statistical Physics and Free Energy.
  • 2. Overview of Computational Chemistry. Monte-Carlo versus Molecular Dynamics. Potential Energy Calculations (ab initio, molecular mechanics). Difference between Potential (PES) and Free (FES) Energy Surfaces.
  • 3. Overview of Methods of Free Energy Calculations: End-point Methods, Alchemical Transformations, Potential of Mean Force Methods, Special Methods.
  • 4. End-point Methods. Free Energy from Local Extrema on PES. MM/XXSA (XX=PB,GB,LR). Solvation Free Energy Calculations. Entropy Contribution Calculations.
  • 5. Alchemical Transformations. Free Energy Perturbations (FEP). Thermodynamical Integration (TI). Problems with Atom Anihilation and Creation. Staging versus Sampling.
  • 6. Potential of Mean Force Methods (PMF). Sampling Problem. Adaptive Biasing Force Method. Blue Moon Method. Umbrella Sampling. Metadynamics. Steered Dynamics. Multiple Walkers Approach.
  • 7. Special Methods. Sampling Improving. Replica-Exchange Molecular Dynamics, etc.
Literature
  • Free energy calculations : theory and applications in chemistry a biology. Edited by Christophe Chipot - Andrew Pohorille. Berlin: Springer, 2007. xviii, 517. ISBN 9783540384472. info
  • CRAMER, Christopher J. Essentials of computational chemistry : theories and models. 2nd ed. Chichester: John Wiley & Sons, 2004. xx, 596. ISBN 0470091819. info
  • LEACH, Andrew R. Molecular modelling : principles and applications. 2nd ed. Harlow: Prentice Hall, 2001. xxiii, 744. ISBN 0582382106. info
Teaching methods
presentation, class discussion
Assessment methods
The course ends with a written test, which is optionally followed by an oral examination. The test will have 50 questions, multiple choises, correct answer plus one point, incorrect answer minus a quarter point. Duration one hour. Classification: F < 30 points; 30 <= E < 35 points; 35 <= D < 40 points; 40 <= C < 45; 45 <= A a B. Mark can be improved by one level (and unlimited worse) by oral examination.
Language of instruction
Czech
Follow-Up Courses
Further Comments
The course is taught annually.
The course is also listed under the following terms Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019, Spring 2020, Spring 2022.
  • Enrolment Statistics (recent)
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