The maximum number of absences allowed is 25% of the total number of planned classes, as determined by the existing rule in this Faculty. Physical sciences > Chemistry > Computational chemistry They are followed by a short period of discussion with the audience, and each group will evaluate them using a five grade scale. Those presentations will take place in the last class of the semester and will have a maximum duration of 15 minutes. Although all the groups have to perform the three practical works, one of them will be attributed randomly to each group for final oral presentation. The teacher will moderate discussions between the working groups and, whenever necessary for the development of projects, he will give a brief explanation or demonstration in the laboratory.
Avogadro molecular modeling program series#
Learning takes place according to a PBL (problem-based learning) paradigm in which students are confronted with a series of problems over the implementation of three projects whose resolution requires the knowledge of the underlying theoretical foundations. Classes are held in a dedicated room equipped with 20 computers Dual / intel on Linux environment and connected to the Internet a projector and a blackboard are also available. Each classroom has a maximum of 20 students which are organized in working groups of two elements. Modern techniques of molecular modeling are discussed in this course. Fernandes Cinquentenário da Simulação Computacional em Mecânica Estatística, Bol. Jensen Introduction to Computational Chemistry, John Wiley & Sons, 1999į. Leach Molecular Modelling-Principles and Applications, Prentice Hall, 2001į. Cramer Essentials of Computational Chemistry: Theories and Models, John Wiley & Sons Ltd, 2002Ī. Hinchliffe Alan Molecular Modelling for beginners, Wiley, 2008Ĭ. Using programs for visualization and manipulation of molecular models, GaussView and Molden. Using the Gaussian03 program package and the GROMACS molecular dynamics program. This course is structured into three modules that correspond to three distinct computing works, including: I-Quantum calculation of molecular properties (Hartree-Fock) II-Modeling a chemical reaction of the SN2 type (Hartree-Fock) III-Study of solvated system (Molecular Dynamics method) Theory behind the calculation methods used (quantum and classical methods, respectively, Hartree-Fock and Molecular Dynamics). Apply MD simulations to study the hydration of monoatomic ions. R un and interpret the results of molecular dynamics(MD) simulations using the program Gromacs. Apply HF calculations to study the geometric stability of molecules, and the mechanism of a simple chemical reaction. R un and interpret the results of Hartree-Fock(HF) quantum calculations using the Gaussian09 program. Distinguish classical and quantum modeling methods, concerning their applicability, data type of input and output. On successful completion of this course the student will be able to: Familiarity with computer programs for calculation, visualization and manipulation of molecular models in Linux operating system. Application of theoretical models to predict and interpret physical and chemical properties of simple molecular systems.
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