Chemistry through the Computational Microscope

Learning Outcomes

Learning Outcomes

Having successfully completed this module you will be able to:

• Problems of an unfamiliar nature are tackled with appropriate methodology and taking into account the possible absence of complete data.
• To prepare students effectively for professional employment or doctoral studies in the chemical sciences;
• To instil a critical awareness of advances at the forefront of the chemical science discipline
• Knowledge base extends to a systematic understanding and critical awareness of topics which are informed by the forefront of the discipline
• To develop in students the ability to adapt and apply methodology to the solution of unfamiliar types of problems
• The ability to adapt and apply methodology to the solution of unfamiliar problems
• To extend students' comprehension of key chemical concepts and so provide them with an in-depth understanding of specialised areas of chemistry;

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 such as Density Functional Theory (DFT)

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.

Resources & Reading list

Textbooks

Attila Szabo and Neil S. Ostlund. Modern Quantum Chemistry: Introduction to Advanced Electronic Structure Theory. Dover.

Frank Jensen (2006). Introduction to computational chemistry. Wiley.

Andrew Leach. Molecular Modelling: Principles and Applications.

Summative

This is how we’ll formally assess what you have learned in this module.

Referral

This is how we’ll assess you if you don’t meet the criteria to pass this module.