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

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Projects

Ab initio simulations of chemical reactions on platinum nanoparticles

Chris-Kriton Skylaris (Investigator), Alvaro 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.

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.

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.