Molecular simulations describing structure-properties relationship and including molecular mechanics and molecular dynamics. Various branches of molecular simulations can be applied in physics, chemistry and material design. Crystal structures are visualized in Materials Studio modelling environment.

Molecular mechanics: molecular systems and crystal energy description on the base of empirical force fields. Bond energy in harmonic approximation. Inharmonic potential. Angles bond, torsion, inversion terms. Nonbond interactions: van der Walls, Coulomb, Hydrogen bond. Ewald summation.

Modeling strategy: Building of initial models, suitable energy approximation, choice of empirical force field, minimization strategy. The role of experiments in creation of modeling strategy and results verification. Infrared spectroscopy, X-ray diffraction as complementary methods in the complex structure analysis. The molecular simulation results interpretation. Practical examples of molecular modeling are applied on various structures and bond geometries.

Molecular dynamics: Deterministic molecular dynamics, Newton equation integration, stochastic methods (Monte Carlo) in molecular dynamics, statistic ensembles, temperature and pressure control, dynamics strategies.

Study of dynamic processes: sorption, diffusion, absorption, intercalation, phase transition.

Lecture is based on knowledge of solid physics. The aim is to show new trends in structure analysis and describe properties in design of new perspective materials.

Theoretical basis of molecular simulations with empirical potentials i.e. molecular mechanics and molecular dynamics is presented. Practical exercises are done in the Cerius2 and Material Studio modelling environment.