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.
Aims and Objectives
Learning Outcomes
Learning Outcomes
Having successfully completed this module you will be able to:
- To be able to use molecular dynamics simulations to solve chemical problems
- To be able to use quantum chemistry calculations to solve chemical problems
Disciplinary Specific Learning Outcomes
Having successfully completed this module you will be able to:
- To instil a critical awareness of advances at the forefront of the chemical science discipline
Transferable and Generic Skills
Having successfully completed this module you will be able to:
- The ability to adapt and apply methodology to the solution of unfamiliar problems
- To develop in students the ability to adapt and apply methodology to the solution of unfamiliar types of problems
Subject Specific Intellectual and Research Skills
Having successfully completed this module you will be able to:
- To prepare students effectively for professional employment or doctoral studies in the chemical sciences
Subject Specific Practical Skills
Having successfully completed this module you will be able to:
- To extend students' comprehension of key chemical concepts and so provide them with an in-depth understanding of specialised areas of chemistry
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).
Learning and Teaching
Teaching and learning methods
Teaching methods: Lectures, workshops, directed reading, Blackboard
online support.
Learning methods: Independent study, student motivated peer group
study, student driven tutor support.
| Type | Hours |
|---|---|
| Practical classes and workshops | 6 |
| Preparation for scheduled sessions | 40 |
| Lecture | 24 |
| Wider reading or practice | 60 |
| Revision | 20 |
| Total study time | 150 |
Assessment
Assessment strategy
Exam (1 hours): 50%
Written assignments: 50%
Summative
This is how we’ll formally assess what you have learned in this module.
| Method | Percentage contribution |
|---|---|
| Assignment | 25% |
| Assignment | 25% |
| Examination | 50% |