Separation of chiral nanotubes with an opposite handedness by chiral oligopeptide adsorption: A molecular dynamics study

Adsorption Affinities of Small Volatile Organic Molecules on Graphene Surfaces for Novel Nanofiller Design: A DFT Study

The adsorption of organic molecules on graphene surfaces is a crucial process in many different research areas. Nano-sized carbon allotropes, such as graphene and carbon nanotubes, have shown promise as fillers due to their exceptional properties, including their large surface area, thermal and electrical conductivity, and potential for weight reduction. Surface modification methods, such as the "pyrrole methodology", have been explored to tailor the properties of carbon allotropes. In this theoretical work, an ab initio study based on Density Functional Theory is performed to investigate the adsorption process of small volatile organic molecules (such as pyrrole derivatives) on graphene surface. The effects of substituents, and different molecular species are examined to determine the influence of the aromatic ring or the substituent of pyrrole's aromatic ring on the adsorption energy. The number of atoms and presence of π electrons significantly influence the corresponding adsorption energy. Interestingly, pyrroles and cyclopentadienes are 10 kJ mol-1 more stable than the corresponding unsaturated ones. Pyrrole oxidized derivatives display more favorable supramolecular interactions with graphene surface. Intermolecular interactions affect the first step of the adsorption process and are important to better understand possible surface modifications for carbon allotropes and to design novel nanofillers in polymer composites.

Adsorption and Self-Aggregation of Chiral [5]-Aza[6]helicenes on DNA Architecture: A Molecular Dynamics Study

Helicenes are an extremely interesting class of conjugated molecules without asymmetric carbon atoms but with intrinsic chirality. These molecules can interact with double-stranded chiral B-DNA architecture, modifying after their adsorption the hydrophilicity exposed by DNA to the biological environment. They also form ordered structures due to self-aggregation processes with possible different light emissions. Following initial studies based on molecular mechanics (MM) and molecular dynamics (MD) simulations regarding the adsorption and self-aggregation process of 5-aza[5]helicenes on double-stranded B-DNA, this theoretical work investigates the interaction between (M)- and (P)-5-aza[6]helicenes with double-helix DNA. Initially, the interaction of the pure single enantiomer with DNA is studied. Possible preferential absorption in minor or major grooves can occur. Afterward, the interaction of enantiopure compounds (M)- and (P)-5-aza[6]helicenes, potentially occurring in a racemic mixture at different concentrations, was investigated, taking into consideration both competitive adsorption on DNA and the possible helicenes' self-aggregation process. The structural selectivity of DNA binding and the role of helicene concentration in adsorption and the self-aggregation process are interesting. In addition, the ability to form ordered structures on DNA that follow its chiral architecture, thanks to favorable van der Waals intermolecular interactions, is curious.

α-Helical Antimicrobial Peptide Encapsulation and Release from Boron Nitride Nanotubes: A Computational Study

Introduction

Antimicrobial peptides are potential therapeutics as anti-bacteria, anti-viruses, anti-fungi, or anticancers. However, they suffer from a short half-life and drug resistance which limit their long-term clinical usage.

Methods

Herein, we captured the encapsulation of antimicrobial peptide HA-FD-13 into boron nitride nanotube (BNNT) (20,20) and its release due to subsequent insertion of BNNT (14,14) with molecular dynamics simulation.

Results

The peptide-BNNT (20,20) van der Waals (vdW) interaction energy decreased to −270 kcal·mol⁻¹ at the end of the simulation (15 ns). However, during the period of 0.2–1.8 ns, when half of the peptide was inside the nanotube, the encapsulation was paused due to an energy barrier in the vicinity of BNNT and subsequently the external intervention, such that the self-adjustment of the peptide allowed full insertion. The free energy of the encapsulation process was −200.12 kcal·mol⁻¹, suggesting that the insertion procedure occurred spontaneously.

Discussion

Once the BNNT (14,14) entered into the BNNT (20,20), the peptide was completely released after 83.8 ps. This revealed that the vdW interaction between the BNNT (14,14) and BNNT (20,20) was stronger than between BNNT (20,20) and the peptide; therefore, the BNNT (14,14) could act as a piston pushing the peptide outside the BNNT (20,20). Moreover, the sudden drop in the vdW energy between nanotubes to the value of the −1300 Kcal·mol⁻¹ confirmed the self-insertion of the BNNT (14,14) into the BNNT (20,20) and correspondingly the release of the peptide.

Surface Chemistry, Crystal Structure, Size and Topography Role in the Albumin Adsorption Process on TiO2 Anatase Crystallographic Faces and Its 3D-Nanocrystal: A Molecular Dynamics Study

TiO2 is widely used in biomaterial implants. The topography, chemical and structural properties of titania surfaces are an important aspect to study. The size of TiO2 nanoparticles synthetized by sol–gel method can influence the responses in the biological environment, and by using appropriate heat treatments different contents of different polymorphs can be formed. Protein adsorption is a crucial step for the biological responses, involving, in particular, albumin, the most abundant blood protein. In this theoretical work, using molecular mechanics and molecular dynamics methods, the adsorption process of an albumin subdomain is reported both onto specific different crystallographic faces of TiO2 anatase and also on its ideal three-dimensional nanosized crystal, using the simulation protocol proposed in my previous theoretical studies about the adsorption process on hydrophobic ordered graphene-like or hydrophilic amorphous polymeric surfaces. The different surface chemistry of anatase crystalline faces and the nanocrystal topography influence the adsorption process, in particular the interaction strength and protein fragment conformation, then its biological activity. This theoretical study can be a useful tool to better understand how the surface chemistry, crystal structure, size and topography play a key role in protein adsorption process onto anatase surface so widely used as biomaterial.

Adsorption of Chiral [5]-Aza[5]helicenes on DNA Can Modify Its Hydrophilicity and Affect Its Chiral Architecture: A Molecular Dynamics Study

Helicenes are interesting chiral molecules without asymmetric carbon atoms but with intrinsic chirality. Functionalized 5-Aza[5]helicenes can form non-covalent complexes with anticancer drugs and therefore be potential carriers. The paper highlights the different structural selectivity for DNA binding for two enantiopure compounds and the influence of concentration on their adsorption and self-aggregation process. In this theoretical study based on atomistic molecular dynamics simulations the interaction between (M)- and (P)-5-Aza[5]helicenes with double helix B-DNA is investigated. At first the interaction of single pure enantiomer with DNA is studied, in order to find the preferred site of interaction at the major or minor groove. Afterwards, the interaction of the enantiomers at different concentrations was investigated considering both competitive adsorption on DNA and possible helicenes self-aggregation. Therefore, racemic mixtures were studied. The helicenes studied are able to bind DNA modulating or locally modifying its hydrophilic surface into hydrophobic after adsorption of the first helicene layer partially covering the negative charge of DNA at high concentration. The (P)-enantiomer shows a preferential binding affinity of DNA helical structure even during competitive adsorption in the racemic mixtures. These DNA/helicenes non-covalent complexes exhibit a more hydrophobic exposed surface and after self-aggregation a partially hidden DNA chiral architecture to the biological environment.

Enantioseparation processes and mechanisms in functionalized graphene membranes: Facilitated or retarded transport?

Up to date, functionalized graphene-based membranes have exhibited a promising potential in the enantioseparation. However, since precisely controlling the interlayer distance of two-dimensional materials is a great challenge in practical experiments, the transport mechanism of chiral guests in such membranes, together with various critical parameters that play a controlling role in the transport behaviors of the preferentially binding enantiomer in narrow channels, remains to be explored. The molecular dynamics (MD) simulation, especially using the steered MD (SMD) method, might be an alternative way to investigate the enantioseparation processes and mechanisms of layered membranes with different interlayer distances. In this work, D-alanine modified graphene sheets with different interlayer distances were built as membrane models, whereas D- and L-phenylalanine were selected as chiral probes. The effect of the interlayer distance and the applied external force on the enantioseparation performance was examined. Results show that such two parameters exert a significant influence on the enantioseparation performance: (a) Increasing the interlayer distance would result in a conversion from the retarded to the facilitated mechanism at a proper external force (medium); (b) both the large and small driving forces would only lead to the appearance of the retarded transport for the preferential enantiomer, unlike the moderate force; (c) the interaction energy of L-phenylalanine with D-isomer selector decreases with the rising interlayer distances studied in this work, regardless of what the external force is. Our findings can provide guidance on the practical applications in the membrane-based chiral separation.

Osteogenic activity of titanium surfaces with hierarchical micro-/nano-structures obtained by hydrofluoric acid treatment

An easier method for constructing the hierarchical micro-/nano-structures on the surface of dental implants in the clinic is needed. In this study, three different titanium surfaces with microscale grooves (width 0.5–1, 1–1.5, and 1.5–2 μm) and nanoscale nanoparticles (diameter 20–30, 30–50, and 50–100 nm, respectively) were obtained by treatment with different concentrations of hydrofluoric acid (HF) and at different etching times (1%, 3 min; 0.5%, 12 min; and 1.5%, 12 min, respectively; denoted as groups HF1, HF2, and HF3). The biological response to the three different titanium surfaces was evaluated by in vitro human bone marrow-derived mesenchymal stem cell (hBMMSC) experiments and in vivo animal experiments. The results showed that cell adhesion, proliferation, alkaline phosphatase activity, and mineralization of hBMMSCs were increased in the HF3 group. After the different surface implants were inserted into the distal femurs of 40 rats, the bone–implant contact in groups HF1, HF2, and HF3 was 33.17%±2.2%, 33.82%±3.42%, and 41.04%±3.08%, respectively. Moreover, the maximal pullout force in groups HF1, HF2, and HF3 was 57.92±2.88, 57.83±4.09, and 67.44±6.14 N, respectively. The results showed that group HF3 with large micron grooves (1.5–2.0 μm) and large nanoparticles (50–100 nm) showed the best bio-functionality for the hBMMSC response and osseointegration in animal experiments compared with other groups.

The Reciprocal Principle of Selectand-Selector-Systems in Supramolecular Chromatography †

In selective chromatography and electromigration methods, supramolecular recognition of selectands and selectors is due to the fast and reversible formation of association complexes governed by thermodynamics. Whereas the selectand molecules to be separated are always present in the mobile phase, the selector employed for the separation of the selectands is either part of the stationary phase or is added to the mobile phase. By the reciprocal principle, the roles of selector and selectand can be reversed. In this contribution in honor of Professor Stig Allenmark, the evolution of the reciprocal principle in chromatography is reviewed and its advantages and limitations are outlined. Various reciprocal scenarios, including library approaches, are discussed in efforts to optimize selectivity in separation science.