Molecular reaction dynamics has become an integral part of modern chemistry and is set to become a cornerstone for much of the natural sciences. 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 to reactions on 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 with 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 present school is open to European master and PhD students and postdocs with interest to understand chemical reactions at molecular level and to apply the theoretical and computational chemistry to this matter. First-year students of the Erasmus+ Master European in Theoretical Chemistry and Molecular Modelling will attend to this school as a part of their mandatory subjects although second-year students of this Master but from the rest of Europe it is expected that can attend too.
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 explained.
There will be 7 theoretical lectures distributed in 10 sessions (2h/session, 20h) and 7 practical sessions (2h/session, 16h) in the computer laboratory, corresponding to the concepts previously explained in the theoretical lectures. The following 7 lectures are planned:
1. Molecular reaction dynamics (Theo-1: 2 sessions; Susana Gómez):
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: quasi-classical trajectory (QCT) methods. Experimental observables. Reaction mechanisms. Potential energy surfaces.
2. Reaction rate theories (Theo-2; 2 sessions; Ramón Sayós):
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, and application to gas-surface processes. Variational transition state theory (VTST). Several tunneling corrections. Examples. Available software.
3. Kinetic Monte Carlo simulations (Theo-3; 1 session; Ramón Sayós):
The master equation. Lattice-gas models. Kinetic Monte Carlo (kMC) algorithms.
Advantages and shortcomings of kMC method. Examples. Available software.
4. Molecular Dynamics (Theo-4; 1 session; Xavier Giménez):
The classical equations of motion. Integration algorithm. Canonical Ensembles. Algorithms for practical use. Force Fields and their computational cast. Examples.
5. Theoretical study of the mechanism and kinetics of enzyme reactions (Theo-5; 1 session; Rodrigo Martínez):
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.
6. Calculating kinetic coefficients of chemical reactions using quantum dynamics (Theo-6; 1 session; Fermin Huarte):
Rate constants from flux correlation functions. Thermal flux eigenstates: physical interpretation. Multiconfigurational time-dependent Hartree method (MCTDH). Benchmark polyatomic calculations. Examples.
7. Wave-packet quantum dynamics: overview and applications to chemical reactions (Theo-7; 1 session; Pablo Gamallo):
Introduction to reaction dynamics. Quantum scattering. Propagators. Observables. S-matrix. Wave-packet. Representations. Hamiltonian. Real wave-packet method. Examples.