Toward Automated Tools for Characterization of Molecular Porosity

Abstract

The emerging advanced porous materials, e.g. extended framework materials and porous molecular materials, offer an unprecedented level of control of their structure and function. The enormous possibilities for tuning these materials by changing their building blocks mean that, in principle, optimally performing materials for a variety of applications can be systematically designed. However, the process of finding a set of optimal structures for a given application requires computational high-throughput tools to analyze and sieve through many candidate materials. In particular, in the case of porous molecular materials, the analysis and selection of a molecule is one of the key aspects as the structure of the molecule determines the structure of the resulting material, and very often the porosity of the molecule significantly contributes to the porous properties of the resulting material. In this work, we introduce definitions and algorithms to characterize porosity at the molecular level, along with a software implementation of these algorithms. We demonstrate applications of the software tool in the discovery and characterization of porous molecules among ca. 94 million molecules currently enlisted in the PubChem database.

Unlocking the computational design of metal–organic cages

“…The volume and shape of the pore is inherently linked to a MOCs host–guest properties. There are multiple examples of software available for analysing single-molecule pores, such as: pyWindow, 139 MoliPor, 140 and VOIDOO. 141 Rizzuto et al show an example of the use of VOIDOO to calculate pore volumes and help rationalise the entropic self-sorting outcome in heteroleptic MOCs.…”

“… 141 Rizzuto et al show an example of the use of VOIDOO to calculate pore volumes and help rationalise the entropic self-sorting outcome in heteroleptic MOCs. 142 We have developed pyWindow, which uses a spherical probe for cavity measures and, like MoliPor, 140 includes a sampling algorithm for detecting windows. 139 Geometrical analyses of the cage and pore structure are cheap and insightful heuristics for structure–property relationships.…”

$n$-gon centers and central lines

“…Also, in Computational Chemistry central lines could be useful in problems concerning porosity. In this kind of problems, the target is to find trajectories to put an atom inside a "cage" (a molecule whose vertices are other atoms) in order to change the properties of the material (see [7]).…”