Molecular Simulations in Chemical Physics - NBCM055
Title in English: Molekulární simulace v chemické fyzice
Guaranteed by: Department of Chemical Physics and Optics (32-KCHFO)
Faculty: Faculty of Mathematics and Physics
Actual: from 2017 to 2019
Semester: both
E-Credits: 5
Hours per week, examination: 2/1 C+Ex [hours/week]
Capacity: unlimited
Min. number of students: unlimited
State of the course: taught
Language: Czech
Teaching methods: full-time
Note: you can enroll for the course in winter and in summer semester
Guarantor: RNDr. Petr Kovář, Ph.D.
doc. RNDr. Miroslav Pospíšil, Ph.D.
Classification: Physics > Biophysics and Chemical Physics
Opinion survey results   Examination dates   Schedule   Noticeboard   
Annotation -
Last update: prof. RNDr. Marek Procházka, Ph.D. (29.01.2019)
Empirical force fields. Molecular mechanics. Anharmonicity of crystal potentials and symmetry of bonds. Thermal motion of atoms - molecular dynamics. Prediction of structures and properties using combined modelling and experimental data.
Aim of the course -
Last update: POSPISIL/MFF.CUNI.CZ (05.04.2008)

Lectures give information about knowledge in the design of new materials with desirable properties by molecular modeling methods.

Course completion requirements -
Last update: doc. RNDr. Miroslav Pospíšil, Ph.D. (09.10.2017)

The gain of the credit is a prerequisite for the examination.

The credit is bound to the credit computational task, it is assumed that there will be correction deadlines for the credit test and the exam.

Literature - Czech
Last update: POSPISIL/MFF.CUNI.CZ (04.04.2008)

P. Comba, T.W. Hambley: Molecular Modeling of Inorganic Compouds, VCH, 1995, Weinheim.

W. Gans, A. Amann, J. C. A. Boeyens: Fundamental Principles of Molecular Modeling, Plenum Press, 1996, New York.

M. A. C. Nascimento ed.: The Chemistry of the XXI Century - Molecular Modeling, World Scientific Publishing, 1994, Singapore.

C.R.A. Catlow, A.M. Stoneham and Sir J. M. Thomas eds.: New methods for modelling processes within solids and at their surfaces, Oxford science publications, 1993, Cambridge

Vassilios Galiatsatos ed.: Molecular simulation methods for predicting polymer properties, Wiley, 2005, New Jersey.

Teaching methods -
Last update: doc. RNDr. Miroslav Pospíšil, Ph.D. (09.10.2017)

Lecture (2 hours) and practical seminar (1 hour)

Requirements to the exam -
Last update: doc. RNDr. Miroslav Pospíšil, Ph.D. (11.10.2017)

The exam consists of written preparation and oral part. Written preparation precedes the oral part. The student receives three questions, each question is evaluated by a mark, and the resulting mark is the average mark of the marks on the individual questions. If one of the questions is rated as unsatisfactory it means failure to complete the test. Failure to pass the exam means that three questions will be asked again at the next term of exam.

Requirements at the oral part of the exam correspond to the syllabus of the subject in the scope that was presented at the lecture.

Syllabus -
Last update: doc. RNDr. Miroslav Pospíšil, Ph.D. (28.01.2019)

The role of molecular simulations to understand structure relationships and substance properties. Areas of practical use of molecular simulations in physics, chemistry and material research. Visualization of crystal structures using the Materials Studio software, examples of structure relationships and properties on selected examples. Demonstration of the structure-type relationship, their symmetry and the shape of the diffractograms. Molecular Mechanics: Describing energy of molecular systems and crystals using empirical force fields. Binding energy in harmonic and anharmonic approximation. Angle couplings, deformation of coupling angles, torsion members. Non-bond interactions, van der Waals - vdW potential types, hydrogen bonding, electrostatic interactions, charge calculation methods.

Modeling strategies: modeling and parameterization of models, compiling the expression for energy - finding a suitable approximation. Basic types of force fields for molecular simulations. Selection of force fields. Optimization strategy based on experimental data. The key role of experimental data in modeling and verification of modeling results. Rtg. diffraction, chemical analysis, TEM, thermogravimetry and vibrational spectroscopy as complementary methods of complex structural analysis for the interpretation of molecular-mechanical simulations. Practical examples of molecular-mechanical simulations in studying structures and bonds. Possibilities of using molecular dynamics for the study of dynamic processes in materials - sorption, diffusion, phase transitions.