ECTS credits ECTS credits: 5
ECTS Hours Rules/Memories Student's work ECTS: 85 Hours of tutorials: 5 Expository Class: 15 Interactive Classroom: 20 Total: 125
Use languages Spanish, Galician, English
Type: Ordinary subject Master’s Degree RD 1393/2007 - 822/2021
Departments: Chemical Physics, External department linked to the degrees
Areas: Chemical Physics, Área externa M.U en Química Teórica y Modelización Computacional (3ª ed)...
Center Faculty of Chemistry
Call: Annual
Teaching: Sin Docencia (Ofertada)
Enrolment: No Matriculable (Sólo Alumnado Repetidor)
Chemical Reaction Dynamics is the area of science that links the macroscopic measurements performed in the reaction kinetics studies with the individual molecular collisions that are behind any chemical process. The goal of the present course is to provide to the students an overview of this branch of the Chemical Physics. Special emphasis will be put on the following aspects of the subject:
- Relationship between microscopic and macroscopic observables.
- Features, properties and limitations of the theoretical methods most commonly employed in Reaction Dynamics.
- Reaction mechanisms at a molecular level.
- Experimental techniques.
o Molecular reaction dynamics: Introductory concepts of molecular reaction dynamics. Types of molecular collisions. Scattering angle. Reaction rate and cross-section. Excitation function. Opacity function. Differential cross-section. Theoretical methods in collision dynamics: quantum and quasi-classical trajectory (QCT) methods. Experimental observables. Mechanism of reactive collisions. Potential energy surfaces. Examples: Cl + HI, F + H2. Hands-on session.
o Reaction rate theories: Introduction to chemical kinetics. Reaction rate, rate constant, reaction order and differential rate equations. Conventional transition state theory (TST): statistical and thermodynamic formulations, calculation of partition functions. Variational transition state theory (VTST). Tunneling corrections. Hands-on session: VTST calculations for H + CH3CH2OH -> H2 + CH3CHOH.
o Automated methods for predicting reaction mechanisms. Simulation of coupled chemical reactions by Kinetic Monte Carlo. Hands-on session: Unimolecular decomposition of formic acid.
o Molecular Dynamics: The classical equations of motion. Numerical integration algorithms. Periodic boundary conditions. Types of ensembles. Thermostats and barostats. Force fields: types and their computational cost. Examples. Hands-on session.
o Theoretical study of the mechanism and kinetics of enzyme reactions: Review of quantum mechanics/molecular mechanics (QM/MM) approach. QM/MM potential energy surfaces. QM/MM molecular dynamics: umbrella sampling method. EA-VTST/MT: rate constant calculation in enzyme reactions. Examples: HCV NS3/NS4A protease reactions. Hands-on session.
o Calculating kinetic coefficients of chemical reactions using quantum dynamics: Rate constants from flux correlation functions. Thermal flux eigenstates: physical interpretation. Multiconfigurational time-dependent Hartree method (MCTDH). Benchmark polyatomic calculations. Examples: H +CH4, N + N2.
o Wave-packet quantum dynamics: overview and applications to chemical reactions. Introduction to reaction dynamics. Quantum scattering. Propagators. Observables. S-matrix. Wave-packet. Representations. Hamiltonian. Real wave-packet method. Examples: He + HeH+, Ne + H2+ and H + OH. Hands-on session.
1.- “Molecular Reaction Dynamics”, Raphael D. Levine, Cambridge University Press, 2005.
2.- “Tutorials in Molecular Reaction Dynamics”, Mark Brouard and Claire Vallance, Royal Society of Chemistry, 2011.
3.- “Chemical kinetics”, Keith J. Laidler, Harper&Row, 1987.
4.- “Theory of Chemical Reaction Dynamics”, Michael Baer (Ed.), Vol IV, CRC Press,1985.
5.- “Molecular collision theory”, M. S. Child, Academic Press, Inc., New York, 1974.
6.- “Understanding molecular simulation”, D. Frenkel and B. Smit, Academic Press, 2002.
7.- "Chemical kinetics", K.J. Laidler, HarperRow, 1987.
8.-“Introduction to QM/MM simulations”, Gerrit Groenhof in “Methods in Molecular Biology” (Clifton, N.J.) 924, 2013, pg. 43-66.
These learning objectives contribute to provide the following skills for the students:
BASIC AND GENERAL SKILLS
o Students possess and understand knowledge that provides a basis or opportunity to be original in the development and/or application of ideas, often in a research context.
o Students know how to apply the acquired knowledge and their problem solving capacity in new or little known environments within broader (or multidisciplinary) contexts related to their area of study.
o Students know how to communicate their conclusions and the knowledge and reasons that support them to specialized and non-specialized audiences in a clear and unambiguous way.
o Students possess the learning skills that allow them to continue studying in a way that will be self-directed or autonomous.
o Students are able to foster, in academic and professional contexts, technological and scientific progress within a society based on knowledge and respect for: a) fundamental rights and equal opportunities between men and women, b) The principles of equal opportunities and universal accessibility for persons with disabilities, and c) the values of a culture of peace and democratic values.
o Students develop a critical thinking and reasoning and know how to communicate them in an egalitarian and non-sexist way both in oral and written form, in their own language and in a foreign language.
CROSS-COMPREHENSIVE SKILLS
o Students are able to adapt their selves to different cultural environments by demonstrating that they are able to respond to change with flexibility.
o Students have the ability of analyze and synthesize in such a way that they can understand, interpret and evaluate the relevant information by assuming with responsibility their own learning or, in the future, the identification of professional exits and employment fields.
SPECIFIC SKILLS
o Students demonstrate their knowledge and understanding of the facts applying concepts, principles and theories related to the Theoretical Chemistry and Computational Modeling.
o Students have the ability to handle the main sources of scientific information related to Theoretical Chemistry and Computational Modeling. They are able to search for relevant information in web pages of structural data, physical chemical experimental data, databases of molecular calculations, databases of scientific bibliography and scientific works.
o Students are able to relate macroscopic observations carried out within the field of Chemical Kinetics with individual collisions taking place at the molecular level.
Lecture: The Professor will deliver face-to-face, or, online video lectures about the theoretical contents of the course during two-hour sessions. The presentations will be based on the different materials available at the Moodle platform.
Network teaching: All the tools available at the Moodle website (https://posgrado.uam.es) will be used (uploading of teaching materials, utilization of work team strategies, wiki, blogs, e-mail, etc.).
Tutoring sessions: The professor can organize either individual or group tutoring sessions about particular topics and questions raised by students.
Online Seminars: After the lecturing period, online seminars between the Professor and the students will be arranged at the virtual classroom in order to teach some subjects and also to discuss the results being obtained, the potential problems and difficulties in using the various methodologies as well as to supervise the preparation of the required reports.
Lecture classes in the computing lab: Teaching will be done in a computer lab, Two hours lectures will include an introduction, a theory to introduce the basic concepts and practical work. Student will learn through practicing. During the practical sessions the student will develop his own programs.
First opportunity:
The knowledge acquired by the student will be assessed throughout the course, trying to ensure that the student advances regularly and constantly through the course.
The final grade will be based on the exercises, assignments and discussion that will be carried out during the course. There will also be an exam at the end. The final mark will be calculated as follows:
Completion of required work: 80%
Final exam: 20%
Second opportunity:
The final mark will be calculated as follows:
Final exam: 50%
Completion of required work: 50%
Contact hours:
Theoretical lessons in classroom / virtual classroom ............................. 35 hours
Independent study hours:
self-study or group study ...............................................................50 hours
Elaboration of a memory based on the exercises proposed in class…………………40 hours
TOTAL (5 ECTS * 25 hours/ECTS)......................................................125 hours
The general recommendation for all the subjects of the master.
Marta Castiñeira Reis
- Department
- Chemical Physics
- Area
- Chemical Physics
- marta.castineira.reis [at] usc.es
- Category
- Xunta Post-doctoral Contract