Encapsulation of a Chloroform Molecule in a Peptide Nanotube

Fainida Rahmat,Ngamta Thamwattana

doi:10.4236/abb.2014.59088

Abstract

We determine the encapsulation of a chloroform molecule into a D,L-Ala cyclopeptide nanotube by investigating the interaction energy between the two molecular structures. We employ the Lennard-Jones potential and a continuum approach which assumes that the atoms are evenly distributed over the molecules providing average atomic densities. Our result demonstrates that the encapsulation depends on the size of the molecule and the internal diameter of the peptide nantube. In particular, the on-axis chloroform molecule is only accepted into a peptide nanotube whose internal radius is greater than 5 ?. If located near the edge of the nanotube, then it is unlikely that the chloroform molecule will enter the nanotube. This is due to the energy valley that the molecule will need to overcome to move past the edge into the open end of the nanotube.

Highlights

Peptide nanotubes have promising applications in many fields, such as chemical, biological, medical and material sciences [1]
This paper investigates two scenarios of a chloroform molecule interacting with a peptide nanotube by employing the Lennard-Jones potential and a continuum approach
We find that an on-axis chloroform molecule is accepted into a peptide nanotube of inner radii 5 Å or 6.5 Å, and is rejected from a tube of inner radius 4.25 Å

Summary

Introduction

Peptide nanotubes have promising applications in many fields, such as chemical, biological, medical and material sciences [1]. We employ the Lennard-Jones potential and the continuum approach to derive an analytical expression for the interaction energy between a chloroform molecule and a peptide nanotube. This model can be used to determine the condition under which the chloroform molecule will be encapsulated into a peptide nanotube. By minimizing the interaction energy we can predict its preferred location inside the nanotube We note that this model can be adopted to study other spherical molecular structures interacting with peptide nanotubes.

Modelling Approach

Interaction between an on-Axis Chloroform Molecule and a Peptide Nanotube

Interaction for a Chloroform Molecule near the Edge of a Peptide Nanotube

Numerical Results

Summary