Modelling peptide nanotubes for artificial ion channels

Exploring carbon catenoids and their applications for encapsulation of carbon nanostructures

Carbon nanostructures of various shapes are among materials that have been extensively studied due to their unique chemical and physical properties. In this paper, we propose a new geometry of carbon nanostructures known as molecular carbon catenoid to compare with theoretical catenoid found from minimising the Willmore energy functional. Since applications of this structure include electron and molecular transport, this paper mathematically models the energetic behaviour of an atom and a spherical molecule entering a catenoid using the Lennard-Jones potential and a continuum approach. The suction energy is also obtained to determine the size of catenoid suitable for encapsulation of various structures. Results shown for theoretical catenoid using continuum modelling approach are found to be in good agreement with numerical simulations for molecular carbon catenoid.

Hydrogen-Bond-Driven Peptide Nanotube Formation: A DFT Study

DFT calculations were carried out to examine geometries and binding energies of H-bond-driven peptide nanotubes. A bolaamphiphile molecule, consisting of two N-α amido glycylglycine head groups linked by either one CH2 group or seven CH2 groups, is used as a building block for nanotube self-assembly. In addition to hydrogen bonds between adjacent carboxy or amide groups, nanotube formation is also driven by weak C-H· · ·O hydrogen bonds between a methylene group and the carboxy OH group, and between a methylene group and an amide O=C group. The intratubular O-H· · ·O=C hydrogen bonds account for approximately a third of the binding energies. Binding energies calculated with the wB97XD/DGDZVP method show that the hydrocarbon chains play a stabilizing role in nanotube self-assembly. The shortest nanotube has the length of a single monomer and a diameter than increases with the number of monomers. Lengthening of the tubular structure occurs through intertubular O-H· · ·O=C hydrogen bonds. The average intertubular O-H· · ·O=C hydrogen bond binding energy is estimated to change with the size of the nanotubes, decreasing slightly towards some plateau value near 15 kcal/mol according to the wB97XD/DGDZVP method.

Modeling Ultrafast Transport of Water Clusters in Carbon Nanotubes

Carbon nanotubes can be used as ultrafast liquid transporters for water purification and drug delivery applications. In this study, we mathematically model the interaction between water clusters and carbon nanotubes using a continuum approach with the Lennard-Jones potential. Since the structure of water clusters depends on the confining material, this paper models the cluster as a cylindrical column of water molecules located inside a carbon nanotube. By assuming the system of two concentric cylinders, we derive analytical expressions for the interaction energy and force, which are used to determine the mechanics and physical parameters that optimize water transport in the nanotubes. Additionally, we adopt Verlet algorithm to investigate the ultrahigh-speed dynamics of water clusters inside carbon nanotubes. For a given carbon nanotube, we find that the cluster's length and the surface's wettability are important factors in controlling the dynamics of water transport. Our findings here demonstrate the possibility of using carbon nanotubes as effective nanopumps in water purification and nanomedical devices.

Modeling Interactions between Graphene and Heterogeneous Molecules

The Lennard–Jones potential and a continuum approach can be used to successfully model interactions between various regular shaped molecules and nanostructures. For single atomic species molecules, the interaction can be approximated by assuming a uniform distribution of atoms over surfaces or volumes, which gives rise to a constant atomic density either over or throughout the molecule. However, for heterogeneous molecules, which comprise more than one type of atoms, the situation is more complicated. Thus far, two extended modeling approaches have been considered for heterogeneous molecules, namely a multi-surface semi-continuous model and a fully continuous model with average smearing of atomic contribution. In this paper, we propose yet another modeling approach using a single continuous surface, but replacing the atomic density and attractive and repulsive constants in the Lennard–Jones potential with functions, which depend on the heterogeneity across the molecules, and the new model is applied to study the adsorption of coronene onto a graphene sheet. Comparison of results is made between the new model and two other existing approaches as well as molecular dynamics simulations performed using the LAMMPS molecular dynamics simulator. We find that the new approach is superior to the other continuum models and provides excellent agreement with molecular dynamics simulations.

Interacting Ru(bpy) 3 2 + Dye Molecules and TiO2 Semiconductor in Dye-Sensitized Solar Cells

Solar energy is an alternative source of energy that can be used to replace fossil fuels. Various types of solar cells have been developed to harvest this seemingly endless supply of energy, leading to the construction of solar cell devices, such as dye-sensitized solar cells. An important factor that affects energy conversion efficiency of dye-sensitized solar cells is the distribution of dye molecules within the porous semiconductor (TiO 2 ). In this paper, we formulate a continuum model for the interaction between the dye molecule Tris(2,2 ′ -bipyridyl)ruthenium(II) (Ru(bpy) 3 2 + ) and titanium dioxide (TiO 2 ) semiconductor. We obtain the equilibrium position at the minimum energy position between the dye molecules and between the dye and TiO 2 nanoporous structure. Our main outcome is an analytical expression for the energy of the two molecules as a function of their sizes. We also show that the interaction energy obtained using the continuum model is in close agreement with molecular dynamics simulations.

Characterization of New Cyclic D,L-α-Alternate Amino Acid Peptides by Capillary Electrophoresis Coupled to Electrospray Ionization Mass Spectrometry

The self-assembly of peptide nanotubes (PNTs) depends on the structure and chemistry of cyclic peptide (CP) monomers, impacting on their properties, which makes the choice of their monomers and their characterization a high challenge. For this purpose, we developed for the first time a capillary electrophoresis coupled to electrospray ionization mass spectrometry (CE-ESI-MS) methodology and characterized a set of eight original CP sequences of 8, 10, and 12 D,L-α-alternate amino acids with a controlled internal diameter (from 7 to 13 Å) and various properties (diameter, global surface charge, hydrophobicity). This new CE-ESI-MS methodology allows verifying the structure, the purity, as well as the stability (when stored during several months) of interesting potential precursors for PNTs that could be employed as nanoplatforms in diagnostics or pseudo sieving tools for separation purposes.

Design, synthesis, and characterization of new cyclic d,l-α-alternate amino acid peptides by capillary electrophoresis coupled to electrospray ionization mass spectrometry

The self-assembly of peptide nanotubes (PNTs) depends on the structure and chemistry of cyclic peptide (CP) monomers, having an impact on their properties, making the choice of their monomers and their characterization a great challenge. We synthesized for the first time a new set of eight original CP sequences of 8, 10, and 12 d,l-α-alternate amino acids with a controlled internal diameter from 7 to 13 Å. They present various properties (e.g., diameter, global surface charge, hydrophobicity) that can open the way to new applications. Their structure and purity were determined thanks to a capillary electrophoresis coupled to electrospray ionization mass spectrometry (CE-ESI-MS) methodology developed for the first time for this purpose. The CPs were successfully separated in a basic hydro-organic background electrolyte (BGE, pH 8.0, H2O/EtOH 50:50, v/v) and analyzed in MS positive mode. The effect of CP structure on electrophoretic mobility was studied, and the mass spectra were deeply analyzed. This methodology allowed verifying their purity and the absence of linear peptide precursors as well as their stability when stored over several months. Therefore, we have developed a new CE-ESI-MS methodology for the structure and purity control of interesting potential precursors for PNTs that could be employed as nanoplatforms in diagnostics or as pseudo sieving tools for separative purposes.

Transport behavior of a single Ca(2+), K(+), and Na(+) in a water-filled transmembrane cyclic peptide nanotube

Molecular dynamics simulations have been performed to investigate the transport properties of a single Ca(2+), K(+), and Na(+) in a water-filled transmembrane cyclic peptide nanotube (CPNT). Two transmembrane CPNTs, i.e., 8×(WL)n=4,5/POPE (with uniform lengths but various radii), were applied to clarify the dependence of ionic transport properties on the channel radius. A huge energy barrier keeps Ca(2+) out of the octa-CPNT, while Na(+) and K(+) can be trapped in two CPNTs. The dominant electrostatic interaction of a cation with water molecules leads to a high distribution of channel water around the cation and D-defects in the first and last gaps, and significantly reduces the axial diffusion of channel water. Water-bridged interactions were mostly found between the artificially introduced Ca(2+) and the framework of the octa-CPNT, and direct coordinations with the tube wall mostly occur for K(+) in the octa-CPNT. A cation may drift rapidly or behave lazily in a CPNT. K(+) behaves most actively and can visit the whole deca-CPNT quickly. The first solvation shells of Ca(2+) and Na(+) are basically saturated in two CPNTs, while the hydration of K(+) is incomplete in the octa-CPNT. The solvation structure of Ca(2+) in the octa-CPNT is most stable, while that of K(+) in the deca-CPNT is most labile. Increasing the channel radius induces numerous interchange attempts between the first-shell water molecules of a cation and the ones in the outer region, especially for the K(+) system.

High length-diameter ratio nanotubes self-assembled from a facial cyclopeptide

A six-residue facial cyclopeptide was designed with the following sequence: c-[D-Leu-L-Lys-D-Ala-L-Lys-D-Leu-L-Gln] (CP). Extensive hydrogen bonding between the cyclopeptide backbones mainly regulated CP to self-assemble into single-walled nanotubes. Simultaneously, the hydrophobic interaction among facial hydrophobic side chains of CP was introduced to stabilize the hydrogen bonding, resulting in the formation of the thick-walled nanotubes with high length–diameter ratios.

Biological applications of peptides nanotubes: an overview

Recently, self-assemblies of peptide nanotubes (PNTs) have appeared as one of the most interesting nanostructures to be explored in the field of nanotechnology. These smart assemblies can have diverse applications, such as in the design of nanoreactors, sensors, electronics, and stimulus-responsive materials. Recent publications indicate that PNT synthesis and production are under extensive study. However, a more detailed safety and nanotoxicology evaluation of these materials is still necessary. This is of paramount importance since interesting and novel biomedical applications based on the use of PNTs, including the development of smart nanodevices and drug delivery systems, are under way. To this end, the aim of this mini-review is to discuss the recent biomedical applications of PNTs and, it hopes, to be a source of inspiration for researchers in different areas of expertise related to nanotechnology.