PROGRAMMING AND MOLECULE VISUALIZATION
Knowledge of the basic operation of a computer in a Windows or Linux or Mac environment.
The exam will be a practical computer test. The practical test will consist of a computer exercise on one of the topics and / or applications made during the lessons. The student's ability to perform the exercise correctly will be positively evaluated.
The student will learn the basics necessary to address the problems relating to the application of computer / computational / graphical methods to inherently chemical problems. The course consists of two strongly integrated and interdependent modules. As a result of the strong integration of the two modules, the exam is unique. In particular, the training objectives of the two modules are: MODULE A • To provide the basic concepts of the MATLAB programming language • Introduce the student to the use of programs for visualizing molecules in 3D MODULE B • Apply the basic notions of MATLAB programming in the writing of simple programs for data analysis and function visualization (in 2 and 3 dimensions). • Application of molecular graphics programs to chemical problems EXPECTED LEARNING RESULTS At the end of the course, the student will be able to: • Carry out the implementation of simple calculation algorithms with MATLAB • Graphically represent molecular systems in 3D. • Visualize molecular orbitals • Carry out a conformational analysis
MODULE A: • The MATLAB programming environment • Working with the MATLAB user interface • Variables and commands • Data management • Data interpolation and extrapolation • Graphical representation of data • Automate scripted commands • Working with tabular data • Adapt models to empirical data • Introduction to the use of molecular visualization and manipulation programs (AVOGADRO and VMD) • Preparation of a molecular model MODULE B: • Creation, use and analysis of data tables in the MATLAB environment • Graphical representation of atomic and molecular wave functions using MATLAB • Visualization and conformational analysis of molecules with AVOGADRO and VMD • Use of web resources for molecular graphics and for visualization of the electronic structure of molecular systems in 3 dimensions.