Creating metastable clusters and assemblies and characterizing their intermolecular interactions

With support from the Macromolecular, Supramolecular and Nanochemistry program in the Division of Chemistry, Dr. S. Alex Kandel of the University of Notre Dame is exploring how molecules self-assemble as clusters and as monolayers on surfaces.

A combined experimental and theoretical approach is devised where experiments probe self-assembly of molecules and the data obtained is used to tune the theoretical calculations to ultimately obtain realistic models for how molecules self-assemble and provide insight on the role of intermolecular interactions in the process. A special focus of the project is on amino acids, which are the basic building blocks of proteins, because it is the interactions between amino acids is what determine the structure and thus the function of these essential biological molecules.

While the interactions of individual amino acids are simple, extended amino acid systems such as proteins rapidly become challenging with increasing size. The project seeks to improve theoretical models of amino acids, advancing our understanding of these fundamental molecules, while at the same time improving computer simulations of a wide range of biological processes.

In the course of conducting the project, graduate, undergraduate and high-school students will be trained in advanced scientific research methods. Instrument development for this project places an emphasis on rapid prototyping and three-dimensional printing, in order to make reproduction of scientific tools inexpensive and simple, and thus accessible even for those in the community without access to extensive scientific infrastructure, including undergraduate institutions and high schools.

Plans and instructions for assembly for all instruments will be published freely online. Also a publicly available website containing the entire scientific output of the laboratory has been organized using a browsable and searchable database.

The research activities of this project explore molecular self-assembly into clusters and monolayers on surfaces. The emphasis is on non-equilibrium self-assembly, where multiple metastable structures form as the result of kinetic controls. This is in contrast to typical self-assembly experiments, which generally seek to prepare the system in a single, thermodynamically stable state.

The goal is to use the multiple metastable structures produced to draw inferences about a larger region of the intermolecular potential energy surface than is ordinarily probed by experiments. Because of this, the research affords the possibility of refining and improving polarizable force fields to be used in large-scale simulations of strongly interacting molecules.

On the experimental side, clusters and monolayers on surfaces will be studied in ultra-high-vacuum and at low temperature using scanning tunneling microscopy. As a complementary technique, electrospray ionization mass spectrometry will be employed to study gas-phase cluster ions, as past results have shown that there is often coincidence between preferential formation of a particular cluster size in the gas phase and the observation of that cluster size on the surface.

Experiments will probe self-assembly of amino acids and related molecules, and will proceed hand-in-hand with theoretical calculations in an effort to obtain a better model of intermolecular interactions in these systems. Ab initio calculations will initially be used to obtain parameters for molecules of interest for the AMOEBA force field, and comparison of experimentally observed structures to those arising from simulations should allow parameters to be adjusted to better capture the effect of intermolecular interactions.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.