Computational Tools for Handling Molecular Clusters: Configurational Sampling, Storage, Analysis, and Machine Learning.

Computational modeling of atmospheric molecular clusters requires a comprehensive understanding of their complex configurational spaces, interaction patterns, stabilities against fragmentation, and even dynamic behaviors. To address these needs, we introduce the Jammy Key framework, a collection of automated scripts that facilitate and streamline molecular cluster modeling workflows. Jammy Key handles file manipulations between varieties of integrated third-party programs.

Further cautionary tales on thermostatting in molecular dynamics: Energy equipartitioning and non-equilibrium processes in gas-phase simulations.

Molecular dynamics (MD) simulations of gas-phase chemical reactions are typically carried out on a small number of molecules near thermal equilibrium by means of various thermostatting algorithms. Correct equipartitioning of kinetic energy among translations, rotations, and vibrations of the simulated reactants is critical for many processes occurring in the gas phase. As thermalizing collisions are infrequent in gas-phase simulations, the thermostat has to efficiently reach equipartitioning in the system during equilibration and maintain it throughout the actual simulation.

Atmospheric Sulfuric Acid-Multi-Base New Particle Formation Revealed through Quantum Chemistry Enhanced by Machine Learning.

The formation of molecular clusters and secondary aerosols in the atmosphere has a significant impact on the climate. Studies typically focus on the new particle formation (NPF) of sulfuric acid (SA) with a single base molecule (e.g.

Ion-Molecule Rate Constants for Reactions of Sulfuric Acid with Acetate and Nitrate Ions.

Atmospheric nucleation from precursor gases is a significant source of cloud condensation nuclei in the troposphere and thus can affect the Earth's radiative balance. Sulfuric acid, ammonia, and amines have been identified as key nucleation precursors in the atmosphere. Studies have also shown that atmospheric ions can react with sulfuric acid to form stable clusters in a process referred to as ion-induced nucleation (IIN).

Separation of isomers using a differential mobility analyser (DMA): Comparison of experimental vs modelled ion mobility.

Mass spectrometry is uniquely suited to identify and quantify environmentally relevant molecules and molecular clusters. Mass spectrometry alone is, however, not able to distinguish between isomers. In this study, we demonstrate the use of both an experimental set-up using a differential mobility analyser, and computational ion mobility calculations for identification of isomers.