Abstract:

The advance of computer simulations to understand the behavior of material started in the '60, in recent years due to the computer power increase, simulations can predict the properties of materials with a great accuracy and speed.

Molecular Dynamics simulation is a technique for computing the equilibrium and transport properties of a traditional many-body system; the nuclear motion of the constituent particles obeys the law of classical mechanics. These simulations are very similar to real experiments.

During our courses at the Faculty of Chemistry of UNAM (National University of Mexico), the use of computer programs to model chemical events is increasing every year. Students simulate several experiments in order to understand the basic variables involved.

When a real experiment is performed a sample of the material to be studied has to be prepared. This sample is connected to a measuring instrument (thermometer, manometer, calorimeter ...) and the property of interest is measured during a certain period of time. These measurements are subject to statist noise, the longer the data are obtained the more accurate the measurements are. In Molecular Dynamics simulation, the same approach is followed, with he advantage that, (if the model is properly established) the data can be obtained with more accuracy, speed and more variables can be involved.

The use of Molecular Modeling programs allows the simulation of dynamic visualization of chemical entities in order to understand this behavior. Students improve their learning skills when they can simulate several variables and understand the basics of molecular behavior.

The use of 3D tools allows a better perception of the models and molecular structures.

This work was partially supported by a grant from Dirección General de Asuntos del Personal Académico (DGAPA) Universidad Nacional Autónoma de México PE205313

Keywords:

Chemical reactions, Animation, Molecular Modeling, Reaction Mechanism, 3D visualization.