Computational Tool for Determining Local Dielectric Constants in Heterogeneous Nanoscale Systems from Molecular Dynamics Trajectories.

Abstract

In this work, we describe a computational tool designed to determine the local dielectric constants (ε) of charge-neutral heterogeneous systems by analyzing dipole moment fluctuations from molecular dynamics (MD) trajectories. Unlike conventional methods, our tool can calculate dielectric constants for dynamically evolving selections of molecules within a defined region of space, rather than for fixed sets of molecules. We validated our approach by computing the dielectric constants of TIP3P water nanospheres, achieving results consistent with literature values for bulk water. We then applied our tool to more complex systems, the water slabs around solvated phospholipid bilayers, where we observed a lower dielectric constant of water near the bilayer headgroups (ε = 20-50) compared to nanospheres of bulk water (ε = 58-62) with the same number of molecules. Our tool also enabled us to compute the dielectric constants of water in more heterogeneous systems, where water surrounding asymmetrically distributed phospholipids on single-walled carbon nanotubes also exhibited lower dielectric constants than in bulk water nanospheres. Addition of positively charged peptides that bind to phospholipid-nanotube conjugates further lowered the dielectric constants of water in the immediate vicinity of these conjugates. Moreover, we estimated dielectric constants for lipids in symmetric bilayers, where values are well-documented, and for asymmetric phospholipid-wrapped nanotube systems, which were previously unexplored, and found that dielectric constants of phospholipids depend on their arrangement in the assembled aggregate. The results align with the literature for bilayers and provide new insights for phospholipid-nanotube systems. The ability of our tool to provide local dielectric constants for both well-studied and novel systems advances our understanding of molecular environments and interactions.