Subject: Molecular Modeling

Scientific Area:



64 Hours

Number of ECTS:




Overall objectives:

1 - 1 - To acquire the needed knowledge and competencies to tackle and solve molecular modeling problems using computational tools.
2 - To get acquainted will available approaches to design and optimize the 3D structure of small molecules.
3 - To explain the basic algorithms used in software applications of the chemistry and biochemistry areas.
4 - To use the most convenient molecular modeling techniques to describe and predict equilibrium and dynamic properties of molecular, macromolecular and biological systems.
5 - Capacity to identify the best approaches to describe and analyze molecular, macromolecular and biological systems given their dimensions and the type of properties under study.
6 - Capacity to employ software in the study and analysis of 3D structure of small molecules.


1 - INTRODUCTION TO COMPUTATIONAL CHEMISTRY: Historical perspective, hardware, software and intervention areas.
2 - MOLECULAR MECHANICS: Motion equations, force fields, basic algorithms and applications.
3 - QUANTUM MECHANICS: Molecular orbital theory, semi-empirical TOM Implementation, Hartree-Fock method and excited electronic states.
4 - MODELING OF MOLECULES: Free energy calculations, solvation and chemical reactions.
5 - LIGAND DESIGN: Computational representation of molecules, molecular docking, similarity based methods and combinatorial chemistry.


P.W. Atkins , Physical Chemistry , Oxford University Press
Frank Jensen , 1999 , Introduction to Computational Chemistry , John Wiley & Sons
Warren J. Hehre , 2003 , A Guide to Molecular Mechanics and Quantum Chemical Calculations , Wavefunction Inc.
Andrew R. Leach , 2001 , Molecular modelling: Principles and Applications , Prentice Hall
David C. Young , 2001 , Computational Chemistry: A Practical Guide for Applying Techniques to Real-World Problems , John Wiley & Sons
M. P. Allen & D. J. Tildesley , 1991 , Computer simulation of Liquids , Clarendon Press

Assesssment methods and criteria:

Classification Type: Quantitativa (0-20)

Evaluation Methodology:
This course includes 32 hours of theoretical classes and 32 hours of theoretical-practical (TP) classes. The analytical method will be used in the theoretical classes and analytical and synthetic methods in the TP classes. We will have oral presentations in the theoretical classes, occasionally with support materials (physical models of molecules). In the TP classes we will have directed tasks, problem solving and case studies. The evaluation of this course encompasses: Mini-project (30%) - to assess knowledge and understanding of the course topics. Additionally, it allows the assessment of written expression, the capacity to describe, resume, and relate different topics of the course, as well as the skill to do autonomous work towards a specific objective. Two TP exams (35% each) - to assess the understanding of the course topics and the skills in using the software applications.