Computational Modelling Group

Molecular Mechanics

Molecular Mechanics (also known as Newtonian Mechanics) is one of the simplest methods of calculating the total energy of a molecular system, by combining the attractive energy of electrostatic and non-polar interactions, with the repulsive energy of steric geometry. Its speed of calculation makes it both a good candidate for multi-scale simulations, biomolecular dynamics and as a precursor to more advanced calculations, such as Quantum Mechanical methods.

Image taken from http://www.chem.ucla.edu/c125/NIH/MolMechanics.htm

For queries about this topic, contact Chris Pittock.

View the calendar of events relating to this topic.

Projects

Ab initio simulations of chemical reactions on platinum nanoparticles

Chris-Kriton Skylaris (Investigator), Álvaro Ruiz-Serrano, Peter Cherry

•Use first principles calculations to study the relationship between shape and size of nanoparticle and the oxygen adsorption energy.

• Investigate the effect of high oxygen coverage on the catalytic activity of the nanoparticles.

Can we calculate the pKa of new drugs, based on their structure alone?

Chris-Kriton Skylaris (Investigator), Chris Pittock, Jacek Dziedzic

The pKa of an active compound in a pharmaceutical drug affects how it is absorbed and distributed around the human body. While there are various computational methods to predict pKa using only molecular structure data, these tend to be specialised to only one class of drug - we aim to generate a more generalised prediction method using quantum mechanics.

Computational chemistry study on the interaction mechanism of imidazolium based ionic liquid lubricants with metal surface

Ugur Mart (Investigator)

We propose a fundamental research to investigate the interaction mechanism of ionic liquids (ILs) with metal surfaces, molecular structure and organization on the surface along with chemical reactions using computational chemistry methods at molecular level.

Electrostatic embedded energy calculations of proteins, using the ONETEP DFT code

Chris-Kriton Skylaris (Investigator), Stephen Fox, Chris Pittock

Calculating the energy of a biomolecule in solvent, using quantum mechanics (QM) is possible, but extremely challenging, even with linear-scaling QM methods like ONETEP. Using electrostatic embedding, a novel twist on the existing QM/MM method is used to calculate the binding energy of a small ligand to a solvated protein, increasing the accuracy and realism of our general project work.

Hybrid quantum and classical free energy methods in computational drug optimisation

Jonathan Essex, Chris-Kriton Skylaris (Investigators), Christopher Cave-Ayland

This work is based around the application of thermodynamics and quantum mechanics to the field of computational drug design and optimisation. Through the application of these theories the calculation of the physical properties of drug-like molecules is possible and hence some predictive power for their pharmaceutical activity in vivo can be obtained.

Investigation into the Interfacial Physics of Field Effect Biosensors

Nicolas Green, Chris-Kriton Skylaris (Investigators), Benjamin Lowe

This interdisciplinary research aims to improve understanding of Field Effect Transistor Biosensors (Bio-FETs) and to work towards a multiscale model which can be used to better understand and predict device response.

The application and critical assessment of protein-ligand binding affinities

Jonathan Essex (Investigator), Ioannis Haldoupis

A method that can accurately predict the binding affinity of small molecules to a protein target would be imperative to pharmaceutical development due to the time and resources that could be saved. A head-to-head comparison of such methodology, ranging from approximate methods to more rigorous methods, is performed in order to assess their accuracy and utility across a range of targets.

THE NORM MATE TRANSPORTER FROM N. GONORRHEAE: INSIGHTS INTO DRUG & ION BINDING FROM ATOMISTIC MOLECULAR DYNAMICS SIMULATIONS

Syma Khalid (Investigator), Daniel Holdbrook, Thomas Piggot, Yuk Leung

The multidrug and toxic compound extrusion (MATE) transporters extrude a wide variety of substrates out of both mammalian and bacterial cells via the electrochemical gradient of protons and cations across the membrane. Multiple atomistic simulation are performed on a MATE transporter, NorM from Neisseria gonorrheae (NorM_NG) and NorM from Vibrio cholera (NorM_VC). These simulations have allowed us to identify the nature of the drug-protein/ion-protein interactions, and secondly determine how these interactions contribute to the conformational rearrangements of the protein.

Water Molecules in Protein Binding Sites

Jonathan Essex (Investigator), Michael Bodnarchuk

Water molecules are commonplace in protein binding sites, although the true location of them can often be hard to predict from crystallographic methods. We are developing tools which enable the location and affinity of water molecules to be found.

People

Jonathan Essex
Professor, Chemistry (FNES)
Graeme Day
Reader, Chemistry (FNES)
Nicolas Green
Reader, Electronics and Computer Science (FPAS)
Denis Kramer
Lecturer, Engineering Sciences (FEE)
Chris-Kriton Skylaris
Lecturer, Chemistry (FNES)
Syma Khalid
Principal Research Fellow, Chemistry (FNES)
Jacek Dziedzic
Research Fellow, Chemistry (FNES)
Ugur Mart
Research Fellow, Engineering Sciences (FEE)
Michael Bodnarchuk
Postgraduate Research Student, Chemistry (FNES)
Christopher Cave-Ayland
Postgraduate Research Student, Electronics and Computer Science (FPAS)
Peter Cherry
Postgraduate Research Student, Chemistry (FNES)
Caroline Duignan
Postgraduate Research Student, Biological Sciences (FNES)
Joseph Egan
Postgraduate Research Student, Mathematics (FSHS)
Stephen Fox
Postgraduate Research Student, Chemistry (FNES)
Ric Gillams
Postgraduate Research Student, Chemistry (FNES)
Ioannis Haldoupis
Postgraduate Research Student, Chemistry (FNES)
Yuk Leung
Postgraduate Research Student, Chemistry (FNES)
Benjamin Lowe
Postgraduate Research Student, Electronics and Computer Science (FPAS)
Can Pervane
Postgraduate Research Student, Electronics and Computer Science (FPAS)
Lyuboslav Petrov
Postgraduate Research Student, Electronics and Computer Science (FPAS)
Maximillian Phipps
Postgraduate Research Student, Chemistry (FNES)
Chris Pittock
Postgraduate Research Student, Chemistry (FNES)
Álvaro Ruiz-Serrano
Postgraduate Research Student, Chemistry (FNES)
Daniel Holdbrook
None, None
Thomas Piggot
None, None