Module code: CHE2032

Module Overview

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

Module provider


Module Leader

HOWLIN BJ Dr (Chemistry)

Number of Credits: 15

ECTS Credits: 7.5

Framework: FHEQ Level 5

JACs code: I100

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

Module Availability

Semester 2

Prerequisites / Co-requisites


Module content

Indicative content includes:

Introduction to molecular modelling and computational chemistry.

Simple theory of molecular mechanics and molecular orbital calculations. Energy expressions and minimisation techniques.

Small Molecule Modelling.

Practical applications using MOE and GAUSSIAN on PCs with GAUSSVIEW.

Conformations in molecules and conformational analysis.

Using GAUSSIAN to predict and animate IR and NMR spectra of simple molecules

Protein Modelling and Databases

Introduction to protein three-dimensional structure covering amino acids, codes for amino acids, sequence analysis, primary, secondary, tertiary and quaternary structure.

The Protein Database for protein X-ray structures and using the Web Browser.

Protein structure prediction, use of artificial intelligence (the EMBL Predict-Protein programme) and other internet resources.

The use of MOE for visualising structures.

Introduction to chemoinformatics, what it is, what it can do.

3D-2D reduction- the SMILES string

Introduction to the use of MOE databases

Designing QSAR equations using MOE

Practical exercise on Nicotinic inhibitors using MOE

Designing new drugs using QSAR

Does it exist? Validating results

Lipinski’s rule of Five




Assessment pattern

Assessment type Unit of assessment Weighting
Coursework COURSEWORK 100

Alternative Assessment

N/A - Retake Coursework

Assessment Strategy

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

Practical skills in computer modelling

Thus, the summative assessment for this module consists of:

Coursework on protein modelling, 50% (meets learning outcomes 1,2)
Coursework on QSAR, 50% (meets learning outcomes 3 and 4)


Formative assessment

Hands on guidance to the coursework will be given



Individual and in class feedback will be given on the progress in modelling

Module aims

  • To introduce students to the techniques of molecular modelling applied to both small molecules and proteins and the use of a range of databases in these studies.
  • To examine simple quantum mechanical calculations.
  • To gain practical experience in homology modelling of proteins.
  • To introduce the concepts behind chemoinformatics.
  • To describe the representation of structural and chemical data.
  • To introduce the use of 2-dimensional reduction, for specifying chemical structures.
  • To study the use of databases to store and retrieve structural and chemical data.

Learning outcomes

Attributes Developed
1 Be familiar with the wide range of modelling techniques as a precursor to applying these to the Industrial Research Year and beyond   K
2 Have an in-depth appreciation of how to carry out practical projects requiring teamwork and initiative to use the most advanced methods to store and retrieve 3-dimensional data in a database and to display it in a variety of ways. CPT
3 Critically understand the science behind how to reduce a 3-dimensional structure to a 2-D format. KC
4 Have an in-depth understanding of how to carry out QSAR analysis on pharmaceutical compounds. KPT

Attributes Developed

C - Cognitive/analytical

K - Subject knowledge

T - Transferable skills

P - Professional/Practical skills

Overall student workload

Independent Study Hours: 117

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 (33 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


Programmes this module appears in

Programme Semester Classification Qualifying conditions
Chemistry MChem 2 Optional A weighted aggregate mark of 40% is required to pass the module
Chemistry with Forensic Investigation MChem 2 Optional A weighted aggregate mark of 40% is required to pass the module
Chemistry BSc (Hons) 2 Optional A weighted aggregate mark of 40% is required to pass the module
Chemistry with Forensic Investigation BSc (Hons) 2 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 2018/9 academic year.