Module code: CHE3053

Module provider


Module Leader

HOWLIN BJ Dr (Chemistry)

Number of Credits


ECT Credits



FHEQ Level 6

JACs code


Module cap (Maximum number of students)


Module Availability

Semester 1

Overall student workload

Assessment pattern

Assessment type Unit of assessment Weighting
School-timetabled exam/test PRACTICAL IN CLASS TEST 50%
Examination EXAMINATION - 1 HOUR 30 MINUTES 50%

Alternative Assessment


Prerequisites / Co-requisites


Module overview

To provide practical experience in modern computer graphics and modelling techniques for the chemical industry and research.

Module aims

To discuss the theory and practice of modelling as applied to pharmaceuticals and proteins.

To provide the background necessary for students to comprehend and criticise the results of simulation on the above systems.

To give students the opportunity to carry out and comment on the results of a simulation

To cover a range of selected topics in molecular orbital calculations appropriate to research.

To cover a range of selected topics in chemometrics appropriate to research.

Learning outcomes

Attributes Developed
Confidently carry out and comment on the results of a protein modelling simulation.
Comprehend and analyse the results of simulation of a QSAR.
Systematically understand the process of molecular modelling.
Have the ability to apply appropriate chemometric techniques to solve multivariate and complex data analysis and modelling problems.
Have a deep understanding of modern molecular orbital methods.

Attributes Developed

C - Cognitive/analytical

K - Subject knowledge

T - Transferable skills

P - Professional/Practical skills

Module content

Indicative content includes:


Introduction to bioinformatics

Internet resources for bioinformatics

Examining protein structure

Using MOE for molecular modelling of proteins

Protein-ligand docking in pharmaceutical drug design

Examples of protein modelling using pharmaceutical examples e.g. GPCRs and plant proteins

Further analysis of protein structure using molecular dynamics

Point mutation and mutational analysis

Introduction to Chemometrics

Basic statistical concepts

Introduction to Multivariate Data Analysis

Principal Component Analysis

Multivariant Regression: MLR, PCR and PLS

Examples of applications to current research

Introduction to quantum chemical calculations: Schrödinger equation, Born-Oppenheimer approximation, Hartree-Fock method

Wave functions, basis sets

Closed shell and open shell systems, self-consistent field

Optimisation techniques, gradients, Hessian matrix

Post-Hartree-Fock concepts: many-body perturbation theory, configuration interaction. QM/MM methods, density functional theory

Use of ab initio program package GAUSSIAN. Structure of input and output files

Interpretation of the results of ab initio calculations: geometries and energies

Interpretation of the results of ab initio calculations: molecular properties

Interpretation of the results of ab initio calculations: molecular orbitals


Methods of Teaching / Learning

The learning and teaching strategy is designed to:

Give the student both practical and theoretical knowledge of modern molecular modelling


The learning and teaching methods include:

A Hands on workshop approach will be taken to the computational modelling in the computing laboratory (30 hours).

Assessment Strategy

The assessment strategy is designed to provide students with the opportunity to demonstrate

Practical skills in Molecular Modelling and knowledge of the underlying theory.


Thus, the summative assessment for this module consists of:

Practical in class test, 1 hour, 50% (meets learning outcomes 1,2,4)

Formal examination, 1.5 hours, 50% (meets learning outcomes 3 and 5)


Formative assessment

A 'mock' practical exam will be held and the results discussed



Individual and in class feedback will be given on the in class mock test

Reading list


Please note that the information detailed within this record is accurate at the time of publishing and may be subject to change. This record contains information for the most up to date version of the programme / module for the 2017/8 academic year.