Computational Modelling Group

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.

Centre for Doctoral Training in Next Generation Computational Modelling

Hans Fangohr, Ian Hawke, Peter Horak (Investigators), Susanne Ufermann Fangohr, Thorsten Wittemeier, Kieran Selvon, Alvaro Perez-Diaz, David Lusher, Ashley Setter, Emanuele Zappia, Hossam Ragheb, Ryan Pepper, Stephen Gow, Jan Kamenik, Paul Chambers, Robert Entwistle, Rory Brown, Joshua Greenhalgh, James Harrison, Jonathon Waters, Ioannis Begleris, Craig Rafter

The £10million Centre for Doctoral Training was launched in November 2013 and is jointly funded by EPSRC, the University of Southampton, and its partners.

The NGCM brings together world-class simulation modelling research activities from across the University of Southampton and hosts a 4-year doctoral training programme that is the first of its kind in the UK.

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.

Dipole moment and theoretical spectroscopy: a computational approach

Chris-Kriton Skylaris (Investigator), Valerio Vitale

The present project represents a first step towards the implementation of a new technique to calculate the whole vibrational spectra of molecules in a formally exact way, which fully takes into account anharmonicity and conformational transitions, at a finite temperature, both in gas phase and in solution in a single ab initio molecular dynamics simulation.

First Principles Simulation of Glycine Adsorption to Amorphous Silica

Chris-Kriton Skylaris (Investigator), Benjamin Lowe

Understanding the molecular interactions between silica and biomolecules is an important in the fields of Bionanotechnology, Biomimetic Material Science and Prebiotic Chemistry. DFT calculations were performed based on a literature study to better understand the interaction between silica and glycine.

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.

Large-Scale Quantum Chemistry Simulations of Organic Photovoltaics

Chris-Kriton Skylaris (Investigator), Gabriele Boschetto

The aim of this project is to use first principles quantum mechanical calculations to provide a detailed atomic-level understanding of OPV materials and models of bulk heterojunctions on a far larger scale than possible before by using the ONETEP program for linear-scaling first principles quantum mechanical calculations.

The hydrogen abstraction phase of the CYP-cyclohexene reaction, using large-scale DFT

Chris-Kriton Skylaris (Investigator), Chris Pittock, Karl Wilkinson

Studying the hydrogen-abstraction reaction between cyclohexene and the active site of cytochrome P450. This starts a series of reactions that eventually oxidise the small molecule to become either an epoxide or an alcohol.

Understanding the finer detail of this reaction can assist towards a model that will predict the breakdown of drugs in the human body.

Vibrational spectroscopy from ab initio molecular dynamics

Hans Fangohr, Chris-Kriton Skylaris (Investigators), Valerio Vitale

In this project I used the Fourier transform of the time correlation function (FTTCF) formalism, that allows to compute the vibrational spectra of molecules both in gas and condensed phase, at finite temperature, in a single ab initio molecular dynamics simulation.