Updates to Protex for Simulating Proton Transfers in an Ionic Liquid.

ABSTRACT: The Python-based program Protex was initially developed for simulating proton transfers in a pure protic ionic liquid via polarizable molecular dynamics simulations. This method employs a single topology approach wherein deprotonated species retain a dummy atom, which is transformed into a real hydrogen atom during the protonation process. In this work, we extended Protex to include more intricate systems and to facilitate the simulation of the Grotthuss mechanism to enhance alignment with the empirical findings. The handling of proton transfer events within Protex was further refined for increased flexibility. In the original model, each deprotonated molecule contained a single dummy atom connected to the hydrogen acceptor atom. This model posed limitations for molecules with multiple ato

SUBMITTER: Godeny M 

PROVIDER: S-EPMC11017242 | biostudies-literature | 2024 Apr

REPOSITORIES: biostudies-literature