Empirical Nanotube Model for Biological Applications

Abstract

An empirical model is developed to capture the electrostatics of finite-length single-walled armchair carbon nanotubes for biological applications. Atomic partial charges are determined to match the electrostatic potential field computed at the B3LYP/6-31G* level of density functional theory, and a tight-binding Hamiltonian is selected which permits one to reproduce the dielectric properties in good agreement with density functional theory results. The new description is applied to study movement of a water molecule through a finite-length nanotube channel in order to demonstrate the method's feasibility. We find that atomic partial charges on the tube edges dominate the interaction between the nanotube and the entering water molecule, while the polarization of the nanotube lowers the electrostatic energy of the water molecule significantly inside the tube.

The role of molecular modeling in bionanotechnology

“…The structure of a 12-section SWNT is shown in figure 1 a, b. Our calculations [24] suggest that the atomic partial charges at the tube edges are an order of magnitude larger than those in the middle of the tube, and each hydrogen atom loses 0.13 -0.14 electrons to carbon atoms, as a hydrogen atom has a lower electronegativity than a carbon atom. The charge transfer creates an appreciable dipole moment at the tube edges, which can interact with the solutes and affect their transport behavior through the SWNT.…”

“…For long tube segments, where first principle calculations are too costly, empirical expressions of partial charges are suggested [24]. When compared to the results from the computationally expensive first principle method, a good agreement is found for key properties including energy gaps and dielectric constants [24] in the suggested model despite its extreme computational simplicity.…”

“…In the following, the suitability of the polarizable SWNT model, demonstrated through studies [23,24,27] of these two types of interactions, is reviewed.…”

“…In figure 1 c, we present the potential energy between a water molecule and a 12-section SWNT segment [24]. The oxygen atom of a water molecule is moved along the tube axis z, and the hydrogen atoms are symmetrically placed giving the water molecule a fixed orientation.…”

What makes a good graphene-binding peptide? Adsorption of amino acids and peptides at aqueous graphene interfaces

“…neglecting polarisation effects. While this approximation can be understood from a practical point of view, a number of recent studies have shown that polarisation can influence the behaviour of the the graphitic-aqueous interfaces [45][46][47][48] as well as the interaction of biomolecules with such substrates, especially in the case of charged species. [49][50][51] One of the major challenges in incorporating polarisation effects into the FF is the increased computational cost.…”