Presenter 1: Yonghong Zeng (PhD Student, School of Chemical Engineering)

Title: Fundamental Study of Adsorption of Strongly Associating Fluids on Graphite Surface using Monte Carlo Simulation

Abstract: Adsorption of associating fluids such as water, methanol and ammonia on graphite surface has been a subject of many experimental studies because of the practical interest in gas separation and purification process.  Experimental observations suggest that despite of the dominance of the basal plane graphene surfaces on the faces of the polyhedral crystal of graphitized thermal carbon black, it possesses strong adsorption sites, which could be either ultrafine pores (due to the overlapping of solid-fluid potentials exerted by opposite surfaces) or functional groups grafted at the edges of the graphene layers (exerting very strong electrostatic interactions with adsorbates bearing partial charges). To gain a fundamental understanding of the nature of these strong sites and their discrimination, we use two analysis tools: (1) Henry constant obtained by Monte Carlo integration to determine the relative strength of basal plane and strong sites in the limit of zero loading; (2) Monte Carlo simulation to obtain the isotherm and isosteric heat so that we can gauge the effects of loading on the interactions.

Presenter 2: Katarzyna Koziara (PhD Student, School of Chemistry and Molecular Biosciences)

Title: Validation and development of force field parameters for drug and drug-like molecules and their applications in structure-based drug design

Abstract: Computational approaches are widely used to help discover and develop new drugs, in particular, to understand how these molecules interact with their biomolecular targets. There are well-optimized and validated force field parameters available to describe interactions of common biomolecules, however these are not designed to represent heteromolecularligands such as drug molecules. Errors in parameters can lead to the failure of computational drug design efforts. With over 25% of all the structures in the Protein Data Bank (PDB) containing ligands and over a million ligand molecules of potential interest in drug design in other databases, ligand validation and parameterisation represents a significant scientific challenge. As a response to the high demand for interaction parameters for ligands, a web accessible Automated force field Topology Builder (ATB; and Repository that generates parameters that can be used in X-ray refinement, structure-based drug design and study of biomolecule:ligand complexes was developed. In this work, molecular dynamics simulations were used to calculate the thermodynamic properties for the validation and refinement of the ATB force field parameters. The fully automated validation protocol of the ATB parameters for small organic molecules based on thermodynamic and structural information was developed and incorporated into the ATB methodology. A novel method to refine parameters in classical force fields in an automated manner that can be extended to parameterisation of all atom types is also presented. Protein:ligand X-ray crystal structures were also studied via molecular dynamics simulations in conjunction with the ATB force field parameters to identify binding modes of the ligands.