The observed differences among periodic DFT, QM/MM and MM simulations, nevertheless, suggest that explicitly including electronic polarization and potentially charge transfer in the MM model can be important to the quantitative accuracy.
The strategy of integrating multiple computational methods to cross-validate each other for complex interfaces is applicable to many problems that involve both inorganic/metallic and organic/biomolecular components, such as functionalized nanoparticles.
The dissertation, of up to 10,000 words, and worth 30 credits, is to be on a topic chosen by the candidate (with advice from his or her supervisor), and written under supervision. Dissertation topics must have be approved by the prospective supervisor.
(Please note that this is your responsibility to arrange, and therefore you should be pro-active in seeking guidance from an appropriate member of staff.) The topic and supervisor’s name must be given to the Chair of the Postgraduate Assessment Sub-Board by filling in the GDip Dissertation proposal form, and returning it to the Department office, by Monday 11 March 2019.
First, various QM approaches for calculating noncovalent interaction energies are compared in over 1,200 gas-phase dimers.
In particular, we study semiempirical PMx methods, density functional theory (DFT) approaches, and symmetry-adapted perturbation theory (SAPT).Download the Dissertation proposal form (doc) Your hard copies need not be bound, but please make sure that they are securely fastened together using either a staple or a loose cover folder.If you are not in London by the date of submission, you are welcome to submit your hard copies by post.For the Grb2 SH2 domain, the thermodynamics of ligand preorganization are studied by computing relative binding enthalpies for flexible and constrained ligands.We are well equipped with a Heidelberg Suprasetter Computer-to-Plate (CTP) system.This protocol involves using a correlated (CCSD(T)) method to first calibrate Density Functional Theory (DFT) as the QM approach, which is then used in QM/MM simulations to compute relevant free energy quantities at the solid/water interface using a mean-field approximation of Yang that decouples QM and MM thermal fluctuations; gas-phase QM/MM and periodic DFT calculations are used to determine the proper QM size in the QM/MM simulations.Finally, the QM/MM free energy results are compared with those obtained from MM simulations to directly calibrate the force field model for the solid/water interface.Lastly, binding interactions are examined between heteroallene-containing guests and cucurbituril host systems using quantum calculations and in Grb2 SH2 complexes using molecular dynamics simulations.For the host-guest systems, the heteroallenes are shown to exhibit attractive interactions with the carbonyl oxygens of the host, and these interactions are found to be primarily electrostatic and dispersive in nature.The topic and supervisor’s name must be given to the Chair of the MA Committee using the MA Dissertation proposal form, which must be returned to the Department office by Monday 11 March 2019.The supervisor of your MA dissertation will give detailed advice on the project.