Carbon nanotubes (CNTs) facilitate microscopic arrangement of water molecules into wires resulting in increased permeability and proton transport. In addition, given their hydrophobicity, CNTs are expected to partition into lipid bilayers forming membrane channels providing efficient proton conduction pathways across the membrane. In this study, we investigate systems of increasing complexity (isolated CNT, CNT-membrane) to assess the effects of the environment on the proton transport mechanism. Our hypothesis are that i) CNT polarization must be important in the charge transport process and ii) lipid bilayer electrostatic potential might influence the thermodynamics of proton transport. For this purpose, we implemented in NAMD a multi-level hybrid Quantum Mechanics / Molecular Mechanics (QM/MM) method, allowing for different QM levels of theory in the same simulation. In this work, species involved in proton hopping were treated at Density Functional Theory (DFT) level, while polarization effects were included by electrostatic embedding of a semi-empirical QM region.<br/><br/>Molecular dynamics simulations were performed to analyze the relevant species involved in proton transport. Free energy profiles were obtained using umbrella sampling for a collective variable tracking the position of the excess charge in the nanotube. Results show that the inclusion of polarization effects in the CNT at semi-empirical level, greatly reduces the energy profile barriers and changes the local minima landscape obtained with the CNT treated at molecular mechanics level, supporting our initial hypothesis. Preliminary results of a CNT:POPC membrane system indicate the proton transport free energy bottleneck occurs at the edges of the nanotube, during the insertion of the excess charge into the CNT, suggesting lipids' charged head groups might play an important role. We expect to test our hypothesis using membranes with different lipid composition and functionalized CNTs.<br/><br/>NAMD, a molecular dynamics code, recently implemented QM/MM through direct communication with popular QM codes. We present a new feature that provides flexibility over QM levels, allowing for the study of larger systems with high accuracy.

Proton transport through carbon nanotubes: Multi-level quantum mechanics/molecular mechanics simulations with NAMD

2019 Fall National Meeting

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