The University of Southampton
Courses

CHEM6144 Chemical Modelling

Module Overview

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.

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. Integrators: Verlet, velocity Verlet, leapfrog Verlet 5. Practicalities of setting up an MD simulation, including equilibration protocols 6. Analysis methods 7. Enhanced sampling methods, e.g. metadynamics and parallel tempering. 8. Free energy calculation methods such a umbrella sampling and thermodynamic integration 9. Brief introduction into coarse-grain models, scope, limitations. 10. Water models, atomistic and coarse grained. 11. Monte Carlo Theory, scope and limitations. Examples of applications For quantum chemistry calculations, we will cover: 1. Quantum mechanical operators, The Schrödinger equation, Expectation values of quantum mechanical operators, bra-ket notation 2. Full Hamiltonian operators for molecules 3. The Born-Oppenheimer approximation, Molecular Orbitals, antisymmetry and spin, many-electron wavefunctions 4. Energy of a Slater determinant, energies of different electronic configurations. 5. The Hartree-Fock equations, the self-consistent field procedure, exchange energy, 6. functions, matrix form of the Hartree-Fock equations. 7. Gaussian basis sets 8. Examples of molecular properties from Hartree-Fock calculations. Atomic charges, dipole moments and other observables. 9. Potential energy surfaces, geometry optimisation, ab initio and classical molecular dynamics 10. Normal models and IR spectra calculation 11. Electronic correlation. DFT and other methods beyond Hartree-Fock

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

Resources & Reading list

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

Andrew Leach. Molecular Modelling: Principles and Applications. 

Frank Jensen (2006). Introduction to computational chemistry. 

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

To study this module, you will need to have studied the following module(s):

CodeModule
CHEM2012Change and Equilibrium
CHEM2013Atomic and Molecular Interactions
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