Courses / Modules / CHEM3051 Chemistry through the Computational Microscope

Chemistry through the Computational Microscope

CATS points

ECTS points

7.5

Level

Level 6

Module lead

Chris-Kriton Skylaris

Academic year

2027-28

Module overview

This module builds on the student’s core understanding of the structure of atoms and molecules to predict their behaviour using state-of-the art computational chemistry methods. This will involve learning how quantum chemistry methods can be used to study atoms and molecules and how classical mechanics methods can be used to simulate molecules and biomolecules. These two methodologies are related and we will explore their respective and mutual applications. Emphasis will be placed upon learning how to use these methods for real-life applications.

Syllabus

For force field based simulations, we will cover: 1. Molecular mechanics force fields (functional forms and parameterisation) 2. Energy minimisation techniques (steepest descents and conjugate gradients) 3. Molecular dynamics- theory, scope and limitations. 4. Pros and cons of different Integrators for molecular dynamics. 5. Practicalities of setting up an MD simulation, including equilibration protocols 6. Extracting the relevant chemical information from your simulations. 7. Enhanced sampling methods, e.g. metadynamics and parallel tempering. 8. Free energy calculations used in drug design. 9. Brief introduction into coarse-grain models, scope, limitations. 10. Can we simulate water? 11. Introduction to Monte Carlo Theory, scope and limitations. Examples of applications For quantum chemistry calculations, we will cover: 1. Revisiting the Schrödinger equation: can we achieve chemical accuracy? 2. Hamiltonian operators for molecules 3. The Born-Oppenheimer approximation, a new look at Molecular Orbitals, many-electron wavefunctions 4. Energies of different electronic configurations. 5. The Hartree-Fock equations, the self-consistent field procedure, exchange energy, 6. Practical details of calculations: Basis functions, matrix form of the Hartree-Fock equations. 7. Gaussian basis sets 8. How to set up and perform a Hartree-Fock calculation with available software 9. How to compute molecular properties from your Hartree-Fock calculations. 10. Making your molecules move: geometry optimisation, ab initio molecular dynamics. 11. Connection with spectroscopy: visualising molecular vibrations and computing IR spectra 12. Electronic correlation. Introduction to more sophisticated methods, in particular Density Functional Theory (DFT) and its variants (exchange-correlation functionals).

Chemistry through the Computational Microscope

Module overview

Aims and Objectives

Learning Outcomes

Syllabus

Learning and Teaching

Teaching and learning methods

Assessment

Assessment strategy