School on Kinetics and Dynamics of Chemical Reactions
Molecular reaction dynamics is the study of elementary processes and the means of probing them, understanding them, and controlling them. It can be applied to reactions in solution and onto surfaces, exploring the elementary steps in catalysis. Nowadays, chemistry requires a molecular level understanding of the reactivity. Moreover, chemical kinetics in an old discipline (born in 1850) that deals with the rates of chemical reaction and how these rates depend on factors such as concentration and temperature. Although it in principle presents a macroscopic point of view, this can be directly related to the molecular point of view. Thus, kinetic or dynamic Monte Carlo simulations allow us to bridge the gap of many orders of magnitude in length and time scales between the processes on the molecular scale and the macroscopic kinetics.
The school is open to European master and PhD students and postdocs with interest in understanding reactivity at molecular level and to apply the computational chemistry to this matter. First-year students of the Erasmus+ Master European in Theoretical Chemistry and Molecular Modeling will attend to this school as a part of their mandatory subjects although it will be also open to post-doc students.
The school will cover the principal aspects of the kinetics and dynamics of chemical reactions, centred mainly in the theoretical and computational approaches, although some experimental techniques will also be explained.
There will be 8 theoretical lectures distributed in 9 sessions (2h/session, 18h) and 7 practical exercises distributed in 9 sessions (2h/session, 18h) in the computer laboratory, corresponding to the concepts previously explained in the theoretical lectures. The following 8 lectures are planned:
1. Molecular reaction dynamics (Theo-1: 2 sessions; Dra. Susana Gómez, University of Salamanca): 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,..
2. Reaction rate theories (Theo-2; 1 session; Dr. Saulo Vázquez, University of Santiago de Compostela):Introduction to chemical kinetics: reaction rate, rate constant, reaction order, temperature effects, catalysis and differential rate equations. Collision theory. Conventional transition state theory (TST): statistical and thermodynamic formulations, calculation of partition functions. Variational transition state theory (VTST). Several tunnelling corrections. Available software.
3. Automatic methods for reaction mechanisms prediction (Theo-3; 1 session; Dr. Saulo Vázquez, University of Santiago de Compostela): Kinetic Monte Carlo simulation of coupled chemical reactions.
4. Kinetic Monte Carlo simulations (Theo-4; 1 session; Dr. Pablo Gamallo, University of Barcelona): The master equation. Lattice-gas models. Kinetic Monte Carlo (kMC) algorithms. Advantages and shortcomings of kMC method. Available software. Examples: catalytic oxidation of CO at RuO2(110) and water gas sfhit
reaction on Cu(111).
5. Molecular Dynamics (Theo-5; 1 session; Dr. Xavier Giménez, University of Barcelona): 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.
6. Theoretical study of the mechanism and kinetics of enzyme reactions (Theo-6; 1 session; Dr. Rodrigo Martínez, University of La Rioja): 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.
7. Calculating kinetic coefficients of chemical reactions using quantum dynamics (Theo-7; 1 session; Dr. Fermin Huarte, University of Barcelona): 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,...
8. Wave-packet quantum dynamics: overview and applications to chemical reactions (Theo-8; 1 session; Dr. Pablo Gamallo, University of Barcelona): 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.
Pablo Gamallo (Universitat de Barcelona & Institut de Química Teòrica i Computacional) - Organiser
Susana Gómez Carrasco (University of Salamanca) - Organiser
Saulo Vazquez (Universidad de Santiago de Compostela) - Organiser