Molecular insights into chromatography: Automated workflows for the virtual design of methacrylate-based chromatography resins

Computational chemistry provides invaluable insights into the behaviors and properties of various materials at the molecular level. This capability is of particular interest in chromatography where adsorbents engage with target molecules through intricate interactions. However, the broad integration of molecular simulations into the field of chromatography has been notably limited, despite significant achievements in previous studies. One potential reason is the requirement for considerable expertise to effectively configure these simulations, presenting a significant barrier to entry. In this context, workflow management systems (WMSs) provide a viable solution by allowing experts to automate complex simulation tasks, making them accessible to the wider research community without necessitating in-depth knowledge of the simulation process. This manuscript outlines the creation and application of two automated workflows designed to generate comprehensive all-atom models of methacrylate-based chromatography resin surfaces and to rapidly calculate binding free energies with peptides as target molecules. These innovations represent a significant advancement in the field by streamlining the simulation process, enhancing predictive accuracy, and making complex molecular modeling more accessible to researchers across disciplines. By publishing these workflows, we aim to catalyze molecular modeling in the field of chromatography by encouraging scientists to utilize and build upon our work.