Module Details

The information contained in this module specification was correct at the time of publication but may be subject to change, either during the session because of unforeseen circumstances, or following review of the module at the end of the session. Queries about the module should be directed to the member of staff with responsibility for the module.
Title MOLECULAR MODELLING
Code CHEM473
Coordinator Dr N Berry
Chemistry
Ngberry@liverpool.ac.uk
Year CATS Level Semester CATS Value
Session 2016-17 Level 7 FHEQ First Semester 7.5

Pre-requisites before taking this module (or general academic requirements):

BSc (Hons) in Chemistry. 

Aims

To introduce students to molecular modelling techniques in chemistry.


Learning Outcomes

By the end of this module students will have:

  • Be able to predict the ground state energy and structure of isolated molecules (for relatively simple systems).
  • Be able to estimate equilibrium constants, rate constants and calculate transition states for simple reactions.
  • Be able to rationalise some aspects of reactivity (charge density, frontier orbitals).
  • Have some understanding of intermolecular forces and complexes (pharmacological example)

Teaching and Learning Strategies

Lecture -

Laboratory Work -


Syllabus

Students will be introduced to many of the skills necessary to perform basic molecular modelling calculations.

Computational Chemistry (Ab initio, semi-empirical, molecular mechincs), Molecular Simulation, Molecular Graphics - Definitions, Applications

Ab initio - Born-Oppenheimer approximation, Orbital approximation, Linear combination of atomic orbitals, Self consistent field, Variational principle and Hartree-Fock, Basis sets, Solving approximate Schrodinger equation, Limitations of Hartree-Fock calculations, Accuracy and utility of calculations

Semi-emipirical - Assumptions, Formulation, Inclusion of experimental data in model, Advantages and disadvantages of the method, Application using frontier molecular orbitals (orbital control versus charge control)

Solvation models - Importance in chemistry, Diffic ulty in modelling, Explicit and implicit models

Geometry optimisation - Potential energy surface, Energy minima (local and global), Transition state

Electron correlation - DFT theory includes some electron correlation, Assumptions, Advantages and disadvantages of DFT

Molecular mechanics - Assumptions, Formulation, Inclusion of experimental data in model, Advantages and disadvantages of the method

Conformational searching - Systematic and Monte-Carlo methods, Boltzmann distribution

Non-covalent forces - Electrostatic, Hydrogen bonding, pi-pi stacking, Dispersion, Hydrophobic, Cooperativity, Hunter-Sanders model of pi-pi stacking, Biological example


Recommended Texts

Reading lists are managed at readinglists.liverpool.ac.uk. Click here to access the reading lists for this module.
Explanation of Reading List:

Teaching Schedule

  Lectures Seminars Tutorials Lab Practicals Fieldwork Placement Other TOTAL
Study Hours 5

    5

    10
Timetable (if known)              
Private Study 65
TOTAL HOURS 75

Assessment

EXAM Duration Timing
(Semester)
% of
final
mark
Resit/resubmission
opportunity
Penalty for late
submission
Notes
             
CONTINUOUS Duration Timing
(Semester)
% of
final
mark
Resit/resubmission
opportunity
Penalty for late
submission
Notes
Coursework  5x6 hour assignments  Semester 1  100  Yes  Standard UoL penalty applies  Assessment 1 Notes (applying to all assessments) Five Computer modelling Exercises. This work is not marked anonymously. August resit for PGT students if applicable.