Putting chemistry in shape

18^th September 2018, 13:00 Ashton Lecture Theater
Dr. Senja Dominique Barthel
Laboratory of molecular simulation
EPFL

Abstract

Many properties in chemistry are related to shapes. These shapes can be found in the bond-network of a molecule, the shapes of electronic densities, the pore shapes of nanoporous materials, the shapes of configuration landscapes whose minimal energy paths give catalytic pathways, etc. The understanding of shape plays an important role in the molecular design of materials. Chemist often have a good intuition on how to think about shape and its impact, but often lack the language and tools to translate and quantify their intuition.

In this talk, I exemplify the wide range of research where the chemical intuition is translated into mathematical concepts that lead to computable quantities:
We will see how graph algorithms can be used to distinguish and classify materials as different as crystalline extended framework materials and surfaces formed from carbons that mimic triply periodic minimal surfaces.
I will present successes, challenges, and ideas on how to capture different aspects of the pore shapes of nanoporous materials. Persistent homology is used for their overall comparison, and volume computation gives an example of established basic descriptors that are still under computational development. A flood-fill style algorithm describes aspects of the diffusion of gasses through the pores. This algorithm works on scalar fields and can be equally applied to analyse bond types encoded in electron densities.