Module code: CHE3053

Module Overview

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

Module provider


Module Leader

HOWLIN Brendan (Chemistry)

Number of Credits: 15

ECTS Credits: 7.5

Framework: FHEQ Level 6

Module cap (Maximum number of students): N/A

Overall student workload

Workshop Hours: 30

Independent Learning Hours: 120

Module Availability

Semester 1

Prerequisites / Co-requisites


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, DFT 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


Assessment pattern

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

Alternative Assessment


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

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.
  • To introduce students to advanced techniques of molecular modelling applied to both small molecules and proteins, and the use of a range of databases in these studies.

Learning outcomes

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

Attributes Developed

C - Cognitive/analytical

K - Subject knowledge

T - Transferable skills

P - Professional/Practical skills

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).

Indicated Lecture Hours (which may also include seminars, tutorials, workshops and other contact time) are approximate and may include in-class tests where one or more of these are an assessment on the module. In-class tests are scheduled/organised separately to taught content and will be published on to student personal timetables, where they apply to taken modules, as soon as they are finalised by central administration. This will usually be after the initial publication of the teaching timetable for the relevant semester.

Reading list
Upon accessing the reading list, please search for the module using the module code: CHE3053

Programmes this module appears in

Programme Semester Classification Qualifying conditions
Chemistry BSc (Hons) 1 Optional A weighted aggregate mark of 40% is required to pass the module
Chemistry with Forensic Investigation BSc (Hons) 1 Optional A weighted aggregate mark of 40% is required to pass the module
Medicinal Chemistry BSc (Hons) 1 Optional A weighted aggregate mark of 40% is required to pass the module

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 2019/0 academic year.