Learning Outcomes:
On completion of the module, students will be able to:
Part (I): Aspects of classical simulation
1) Describe the physical principles underlying molecular simulations.
2) Relate molecular structure to thermodynamic and dynamic properties using ensemble averages from simulation data.
3) Analyse and interpret molecular dynamics trajectories using standard structural and dynamical observables, including assessment of sampling, convergence, and uncertainty.
4) Evaluate the strengths and limitations of simulation-based approaches, as well as the use of experimental and machine-learning-derived structures.
Part (II): Aspects of classical and quantum simulations
1) Describe the concept of a geometry optimization/energy minimization using a molecular mechanics approach.
2) Describe the concept of a geometry optimization/energy minimization within electronic structure calculations, i.e. within a quantum mechanical framework.
3) Understand the use of the Born-Oppenheimer approximation in the estimation of the molecular potential energy curve.
4) Understand the basic principles of Principal Component Analysis (PCA).
5) Practice using PCA to analyze a complex data set.
6) Describe the electronic structure of polyatomic systems in the Hückel approximation; understand the concept of basis sets and the mathematical representation of these functions.
7) Understand how Density Functional Theory (DFT) can be applied to investigate the electronic structure of small molecules.
Part (III): Advanced Kinetics
1) Describe reaction mechanisms.
2) Describe reaction mechanism of polymerization.
3) Describe molecular motion in gases using the kinetic model of gases.
4) Provide a quantitative explanation for rates of bimolecular elementary reactions using the collision theory.
5) Understand how the RRK model predicts the steric factor and rate constant of unimolecular reactions.
6) Describe the factors that affect the rates of diffusion-controlled reactions in solution and understand how the material balance equation takes account of diffusion, convection, reaction.
7) Understand how the concepts of statistical thermodynamics can be applied to the calculation of rate constants using the Eyring equation of the transition state theory.
Indicative Module Content:
This module is an introduction to advanced physical chemistry subjects. This includes the following subjects:
A. Advanced Kinetics
1) Reaction mechanisms. 2) Example of reaction mechanism - polymerization. 3) Molecular motion in gases using the kinetic model of gases. 4) Quantitative explanation for rates of bimolecular elementary reactions using the collision theory. 5) The RRK model predicts the steric factor and rate constant of unimolecular reactions. 6) Factors that affect the rates of diffusion-controlled reactions in solution and understand how the material balance equation takes account of diffusion, convection, reaction. 7) Apply statistical thermodynamics to the calculation of rate constants using the Eyring equation of the transition state theory.
B. Models of Bonding
1) Describe the property of electron spin. 2) Describe the structure of many-electron atoms in terms of the orbital approximation. 3) Describe the Pauli principle and its implications for Hund’s rules and for the nature of singlet and triplet states. 4) Understand the use of the Born-Oppenheimer approximation in the estimation of the molecular potential energy curve. 5) Describe the electronic structure of homonuclear diatomic molecules in terms of bonds and π bonds using the valence bond theory. 6) Describe the electronic structure of polyatomic molecules in terms of promotion and hybridization using the valence bond theory. 7) Describe the electronic structure of diatomic molecules in terms of the linear combination of atomic orbitals using the molecular orbital theory. 8) Understand the emergence of bonding orbitals, anti-bonding orbitals, orbitals, and π orbitals in the context of the molecular orbital theory. 9) Understand the role of polar bonds, electronegativity, and the variation principle in describing the electronic structure of selected heteronuclear diatomic molecules. 10) Describe the electronic structure of polyatomic systems in the Hückel approximation
C. Magnetic Resonance
1) Understand the physical basis for the unusual information content and appearance of NMR spectra and the causes of low sensitivity. 2) Understand the link between dynamics and relaxation mechanisms in NMR and how these affect the spectra and provide information about dynamic molecular processes. 3) Understand the advantages of pulsed techniques and Fourier analysis in manipulating and presenting the spectral information. 4) Describe the applications of these principles through case studies in multiple-pulse NMR and MR imaging.