LIFE SCIENCES

Nanometer-size clusters of gold, stabilized at the surface by organic ligand molecules, form a class of very interesting novel nanomaterials that can be employed in a wide range of studies in molecular biology, inorganic chemistry, surface science and materials science with a wide range of potential applications in site-specific bioconjugate labelling and sensing, drug delivery and medical therapy, functionalisation of metal surfaces for sensing, molecular recognition and molecular electronics, and noble metal nanoparticle catalysis. Refinements of the synthesis methods in the last ten years by several groups have enabled controlled synthesis of a few particularly stable clusters in 1 - 3 nm range, and a few have by now been determined up to molecular precision. Recent applications have used such clusters for site-specific labeling of enteroviruses for TEM imaging (Ref. 1). Still, very little is known about their interactions, at the molecular level, with biomolecules and biological nanoparticles in water.

This project, run by a team of scientists of the University of Jyväskylä in Finland, aimed at studying the structure, surface chemistry and functionalization strategies of gold nanoclusters in water, having from a few tens to a few hundreds of gold atoms, and their interactions with enteroviruses. All the computations were intimately linked to interpret experimental results by collaborators of the scientific team. During the project, a novel discovery of a water-soluble 68-atom gold cluster was made, and the atomic structure of its metal core was solved for the first time by electron microscopy and interpreted by the team’s density functional theory (DFT) calculations (Ref. 2.). These DFT calculations also revealed the important role of the interface between the organic surface, counterions and water molecules in defining the hydrodynamic properties of Au102 and Au144 nanoclusters (Ref. 3).

Towards the end of the project, full hydrated virus models of the enterovirus EV1 were built and tested in large-scale GROMACS molecular dynamics simulations involving in total of 5 million atoms, and mechanistic binding of a gold cluster Au102 to the virus capsid was studied (see the figure).

This project was made possible through the Partnership for Advanced Computing in Europe (PRACE). HPC system Hermit of the High Performance Computing Center Stuttgart (HLRS) served as computing platform for this project.