Automated and Efficient Generation of General Molecular Aggregate Structures

Abstract

Modeling intermolecular interactions of complex non-covalent structures is important in many areas of chemistry. To facilitate the generation of reasonable dimer, oligomer, and general aggregate geometries, we introduce an automated computational interaction site screening (aISS) workflow. This easy-to-use tool combines a genetic algorithm employing the intermolecular force-field xTB-IFF for initial search steps with the general force-field GFN-FF and the semi-empirical GFN2-xTB method for geometry optimizations. Compared with the alternative CREST program, aISS yields similar results but with computer time savings of 1-3 orders of magnitude. This allows for the treatment of systems with thousands of atoms composed of elements up to radon, e.g., metal-organic complexes, or even polyhedra and zeolite cut-outs which were not accessible before. Moreover, aISS can identify reactive sites and provides options like site-directed (user-guided) screening.

Rotational spectroscopy of hydrogen-bonded binary trifluoro-propanol conformers: conformational diversity, preference and abundances in a jet expansion

“…For the conformational search of the TFP dimer, we utilized CREST, an efficient scheme which combines semiempirical tight-binding (TB) 32 quantum chemistry methods with a meta-dynamics driven search algorithm 21,22 for fast conformational search. A few binary conformations were created using chemical intuition and served as the initial geometry input for CREST.…”

“…In the current study, we applied jet-cooled CP-FTMW spectroscopy and a recently developed conformational searching tool, CREST, 21,22 to explore the rich conformational landscape of the 3,3,3-trifluoropropanol (TFP) dimer. The monomeric TFP conformers have been investigated with a static gas sample using microwave spectroscopy 23 and with a jet expansion using CP-FTMW 24 and Raman spectroscopy 25 where two TFP conformers were observed.…”

Revisiting HomochiralversusHeterochiral Interactions through a Long Detective Story of a Useful Azobis-Nitrile and Puzzling Racemate

“…The most stable conformer was optimized with the GFN-FF force field in water (ALPB). Then, that structure was used for building the molecular clusters by employing the automated interaction site screening (aISS) submodule of the xTB program package . The screening is based on the rigid intermolecular force field xTB-IFF followed by final optimization at the GFN-FF force field in water (ALPB).…”

Möbius boron-nitride nanobelts interacting with heavy metal nanoclusters

“…First, we optimized the structures of each individual system (two nanobelts and four nanoclusters for each metal). Then, using the automated Interaction Site Screening (aISS) [39],…”