The University of Southampton
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CHEM6144 Chemistry through the Computational Microscope

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

Module Aims

At the end of this module you will have an understanding of: • Force field simulation methods as applied to chemical and biological systems. • Theory and application of quantum chemistry methods to compute properties of molecules, biomolecules and materials. • How to set up a classical molecular dynamics simulation using widely available software. • How to set up a quantum chemistry calculation using widely available software. • How to extract chemical information from the outputs of computational chemistry calculations.

Learning Outcomes

Learning Outcomes

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

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 such as Density Functional Theory (DFT)

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.

TypeHours
Revision20
Wider reading or practice60
Preparation for scheduled sessions40
Lecture24
Practical classes and workshops6
Total study time150

Resources & Reading list

Andrew Leach. Molecular Modelling: Principles and Applications. 

Frank Jensen (2006). Introduction to computational chemistry. 

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

Assessment

Summative

MethodPercentage contribution
Exam 50%
Written assignment 50%

Referral

MethodPercentage contribution
Exam 50%
Written assignment 50%

Linked modules

Part 4 Option 4985; 4998; 4999; 5016; 5017; 5018; 5246; 5866 Pre-requisites: CHEM2013 Atomic And Molecular Interactions 2016-17, CHEM2012 Change And Equilibrium 2016-17

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