Graph-based Automated Macro-Molecule Assembly

J Chem Inf Model. 2022 Aug 22;62(16):3714-3723. doi: 10.1021/acs.jcim.2c00609. Epub 2022 Aug 8.

Abstract

We present a general molecular framework assembly algorithm that takes a largely arbitrary molecular fragment database and a user-supplied target template graph as input. Automatic assembly of molecular fragments from the database, following a prescribed, user-supplied set of connection rules, then turns the template graph into an actual, chemically reasonable molecular framework. Assembly capabilities of our algorithm are tested by producing several abstract, closed-loop shapes. To indicate a few of many possible application areas we demonstrate a host-guest complex and a road toward catalysis. Postassembly substituent exchange can be used to produce electric fields of desired values at desired points inside the framework or at its surface as a stepping stone toward rationally designed, artificial heterogeneous catalysts.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Databases, Factual