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We report results from full atomistic molecular dynamics simulations on the properties of biomimetic nanopores. This latter result was obtained through the direct insertion of an α-hemolysin protein inside a hydrophobic solid-state nanopore. Upon translocation of different DNA strands, we demonstrate here that the theoretical system presents the same discrimination properties as the experimental one obtained previously. This opens an interesting way to promote the stability of a specific protein inside a solid nanopore to develop further biomimetic applications for DNA or protein sequencing.

The behavior of confined anticancer carboplatin (CPT) molecules in a single (10, 10) boron nitride nanotube (BNNT) was studied by means of molecular dynamics simulations. Our study revealed a very large storage capacity of BNNT. Analysis of the energy profiles depending on the number of confined molecules, and on their spatial organization allowed us to quantify the ability of BNNT to vectorize CPT. Indeed, BNNT despite its small radius presented a large inner volume that favored stable encapsulation of multiple active anticancer molecules. Moreover, in our molecular dynamics simulations, the empty BNNT and the BNNT filled with CPT diffused spontaneously to the cell membrane and were able to passively enter inside lipid bilayers by a lipid-assisted mechanism. This property has been used to deliver naturally anticancer drugs to cellular targets. Using this enhanced drug delivery system, we have provided a definitive solution to the problem of drug release and have thus opened up a new way of targeting cancer cells. Indeed, regardless of the mode of action of the platinum complex towards the cell, the delivery of the drug on site should limit the side effects of the drug. [ABSTRACT FROM AUTHOR]

Detection of a single macromolecule based on the use of artificial nanopores is an attractive and promising field of research. In this work, we report a device based on a 5 nm single nanopore with a high length/diameter ratio, tailored by the track etching and atomic layer deposition techniques. The translocation of neutral polyethylene glycol (PEG) and charged polyethylene glycol-carboxylate (PEG-carboxylate) molecules of low molar masses (200 and 600 g mol−1) through this nanodevice was studied. It was shown that charged PEG-carboxylate molecules, which permeate through the pore, promote an unusual blockade of ionic current whereas the neutral PEG molecules do not show such behaviour. The molecular dynamics simulation shows that both neutral and charged PEGs permeate through the nanopore close to its inner surface. The main difference between the two macromolecules is the existence of a structured shell of cations around the charged PEG, which is likely to cause the observed unusual current blockade. [ABSTRACT FROM AUTHOR]

A water molecule is the foundation of life and is the primary compound in every living system. While many of its properties are understood in a bulk solvent, its behavior in a small hydrophobic nanopore still raises fundamental questions. For instance, a wetting/dewetting transition in a hydrophobic solid-state or a polymer nanopore occurs stochastically and can only be prevented by external physical stimuli. Controlling these transitions would be a primary requirement to improve many applications. Some biological channels, such as gramicidin A (gA) proteins, show a high rate of water and ion diffusion in their central subnanochannel while their external surface is highly hydrophobic. The diameter of this channel is significantly smaller than the inner size of the lowest artificial nanopore in which water drying occurs (i.e. 1.4 nm). In this paper, we propose an innovative idea to generate nanopore wetting as a result of which the application of an external field is no longer required. In a nanopore, the drying or wetting of the inner walls occurs randomly (in experiments and in simulations). However, we have shown how the confinement of gA, in a dried hydrophobic nanopore, rapidly generates a stable wetting of the latter. We believe that this simple idea, based on biomimetism, could represent a real breakthrough that could help to improve and develop new nanoscale applications.

Anticancer drug transport is now becoming an important scientific challenge since it would allow localizing the drug release near the tumor cell, avoiding secondary medical effects. We present theoretical results, based on density functional theory and molecular dynamics simulations, which demonstrate the stability of functionalized single (10,10) boron nitride nanotubes (BNNTs) filled with anticancer molecule such as carboplatin (CPT). For this functionalized system we determine the dependence of the adsorption energy on the molecule displacement near the inner BNNTs surface, together with their local morphological and electrical changes and compare the values to the adsorption energy obtained on the outer surface. Quantum simulations show that the most stable physisorption state is located inside the nanotube, with no net charge transfer. This demonstrates that chemotherapeutic encapsulation is the most favorable way to transport drug molecules. The solvent effect and dispersion repulsion contributions are then taken into account using molecular dynamics simulations. Our results confirm that carboplatin therapeutic agents are not affected when they are adsorbed inside BNNTs by the surrounding water molecules.

Full DFT-D2 calculations were carried out to study the interactions between single wall (10,10) boron nitride nanotubes (BNNTs) and different molecules, such as azomethine (C2H5N) and an anticancer agent (Pt(IV) complex) linked to an amino-derivative chain. The geometry of the (10,10) BNNT-azomethine and the BNNT-amino derivative system was optimised by considering different molecular configurations on the inner and outer surfaces of the nanotube. Simulation results showed that the most stable physisorption state for both molecules was located inside the nanotube in a parallel configuration. We showed also that the molecular chemisorption was possible only when the azomethine was present above two adjacent B and N atoms of a hexagon. The attachment of an azomethine plus a subsequent drug did not perturb the cycloaddition process. Moreover, all theoretical results showed that the therapeutic agent complex was not affected when it was attached onto BNNTs.

Hydrogen and halogen bonds have been associated for the growth of 2D compact supramolecular networks on a silicon surface. These interactions have been elucidated in a complete monolayer of a 4,4''-dibromo-p-terphenyl (DBT) molecule on a Si(111)-B surface by combining scanning tunneling microscopy (STM) and density functional theory (DFT) calculations.

Biological ion channels present unique ionic properties. They can be highly permeable to ions, while selecting only one type of ions, without external energy supply. An important research field has been developed to transfer these properties to solid state nanoporous membranes in order to develop artificial biomimetic nanofilters. One of the promising ways to develop biomimetic structures is based on the direct insertion of the gramicidin A, i.e. an ionic channel, inside a nanopore. Experiments have recently proved the feasibility of such a hybrid membrane with very interesting results regarding the ionic selectivity. Here, we propose to interpret these experiments using theoretical molecular dynamic simulations which allow us to analyze more profoundly the structures of the proteins confined inside the nanopore and the relation between their conformation and the observed ionic properties.

Four-dimensional (4D) printing, combining three-dimensional (3D) printing with time-dependent stimuli-responsive shape transformation, eliminates the limitations of the conventional 3D printing technique for the fabrication of complex hollow constructs. However, existing 4D printing techniques have limitations in terms of the shapes that can be created using a single shape-changing object. In this paper, we report an advanced 4D fabrication approach for vascular junctions, particularly T-junctions, using the 4D printing technique based on coordinated sequential folding of two or more specially designed shape-changing elements. In our approach, the T-junction is split into two components, and each component is 4D printed using different synthesized shape memory polyurethanes and their nanohybrids, which have been synthesized with varying hard segment contents and by incorporating different weight percentages of photo-responsive copper sulfide-polyvinyl pyrrolidone nanoparticles. The formation of a T-junction is demonstrated by assigning different shape memory behaviors to each component of the T-junction. A cell culture study with human umbilical vein endothelial cells reveals that the cells proliferate over time, and almost 90% of cells remain viable on day 7. Finally, the formation of the T-junction in the presence of near-infrared light has been demonstrated after seeding the endothelial cells on the programmed flat surface of the two components and fluorescence microscopy at day 3 and 7 reveals that the cells adhered well and continue to proliferate over time. Hence, the proposed alternative approach has huge potential and can be used to fabricate vascular junctions in the future. [ABSTRACT FROM AUTHOR]

Multiple intermolecular interactions offer a high degree of controllability of on-surface molecular assemblies. Here, two kinds of molecular networks were formed by depositing 11,11,12,12-tetrabromo-1,4,5,8-tetraaza-9,10-anthraquinodimethane derivatives with two different alkyl groups in length (C4 and C8) on clean Ag(111) surfaces under ultrahigh vacuum. The detailed structures of each network before and after the cleavage of the C–Br bonds were investigated with high-resolution scanning tunneling microscopy at low temperature. We found that the diffusion of the Br atoms by high-temperature annealing plays a role in the formation of Br-mediated self-assembly. While dissociated Br atoms interacted with alkyl groups by hydrogen bonding through C–H⋯Br contacts in both systems, the different strengths of the van der Waals interactions between the alkyl groups resulted in the formation of different structures. [ABSTRACT FROM AUTHOR]

The fabrication of well-organised molecular assemblies on surfaces is fundamental for the creation of functional molecular systems applicable to nanoelectronic and molecular devices. In this study, we investigated the effect of substitution positions of alkyl chains on the formation of halogen-bonded molecular networks. For this purpose, building blocks with different head groups (i.e., pyridine (Py) or tetrafluoro-iodobenzene (FI)) were substituted with hexadecyloxy chains at either the 3,4- or the 3,5-positions. The two-dimensional assembly of each compound as a single-component system was studied using scanning tunnelling microscopy (STM) at the highly oriented pyrolytic graphite (HOPG)/1-phenyloctane interface. All compounds displayed linear structures in which the alkyl chains were aligned along one of the HOPG axes. In the exceptional case of FI bearing hexadecyloxy chains at the 3,5-positions (denoted as FI-3,5), hexagonal arrays were tentatively formed owing to the triangular molecular arrangement induced by halogen bonding. A bicomponent blend of Py-3,4/FI-3,5 (1 : 1 molar ratio) enabled the formation of a honeycomb structure, whereas that of Py-3,5/FI-3,4 (1 : 1 molar ratio) produced a rectangular assembly that was periodically arranged in a zig-zag fashion. Finally, based on the observed blend ratio dependence, the formation of these different two-dimensional structures by variation in the substitution positions of the alkyl chains was discussed in terms of molecule–molecule and molecule–substrate interactions. [ABSTRACT FROM AUTHOR]

The adsorption of phthalocyanine (H2Pc) on the 6H-SiC(0001)-(3 × 3) surface is investigated using X-ray photoelectron spectroscopy (XPS), near edge X-ray absorption fine structure spectroscopy (NEXAFS), and density functional theory (DFT) calculations. Spectral features are tracked from the submonolayer to the multilayer growth regime, observing a significant modification of spectroscopic signals at low coverage with respect to the multilayer films, where molecules are weakly interacting. Molecules stay nearly flat on the surface at the mono and submonolayers. Previously proposed adsorption models, where the molecule binds by two N atoms to corresponding Si adatoms, do not reproduce the experimental spectra at the submonolayer coverage. We find instead that another adsorption model where the molecule replaces the two central H atoms by a Si adatom, effectively forming Si-phthalocyanine (SiPc), is both energetically more stable and yields in combination a better agreement between the experimental and simulated spectra. This suggests that the 6H-SiC(0001)-(3 × 3) surface may be a candidate substrate for the on-surface synthesis of SiPc molecules. [ABSTRACT FROM AUTHOR]

Age-related macular degeneration (AMD) is the third major cause of blindness in people aged above 60 years. It causes dysfunction of the retinal pigment epithelium (RPE) and leads to an irreversible loss of central vision. The present clinical treatment options are more palliative in controlling the progression of the disease and do not functionally restore the degenerated RPE monolayer and photoreceptors. Currently, the clinical transplantation of RPE cells has shown poor engraftment potential due to the absence of an intact Bruch's membrane in AMD patients, thereby the vision is unable to be restored completely. Although tissue engineering strategies target the development of Bruch's membrane-mimetic substrates, the challenge still lies in the development of an ultrathin, biologically and mechanically equivalent membrane to restore visual acuity. Further, existing limitations such as cellular aggregation, surgical complications including retinal tissue damage, tissue rejection, disease transmission, inferior mechanical strength, and the loss of vision over time demand the search for an ideal strategy to restore the functional RPE. Hence, this review aims to provide insights into various approaches, from conventional cell therapy to 3D bioprinting, and their unmet challenges in treating AMD by outlining the pathophysiology of AMD and the host tissue response with respect to injury, treatment and preclinical animal models. [ABSTRACT FROM AUTHOR]

Gas hydrates have received considerable attention due to their important role in flow assurance for the oil and gas industry, their extensive natural occurrence on Earth and extraterrestrial planets, and their significant applications in sustainable technologies including but not limited to gas and energy storage, gas separation, and water desalination. Given not only their inherent structural flexibility depending on the type of guest gas molecules and formation conditions, but also the synthetic effects of a wide range of chemical additives on their properties, these variabilities could be exploited to optimise the role of gas hydrates. This includes increasing their industrial applications, understanding and utilising their role in Nature, identifying potential methods for safely extracting natural gases stored in naturally occurring hydrates within the Earth, and for developing green technologies. This review summarizes the different properties of gas hydrates as well as their formation and dissociation kinetics and then reviews the fast-growing literature reporting their role and applications in the aforementioned fields, mainly concentrating on advances during the last decade. Challenges, limitations, and future perspectives of each field are briefly discussed. The overall objective of this review is to provide readers with an extensive overview of gas hydrates that we hope will stimulate further work on this riveting field. [ABSTRACT FROM AUTHOR]

Hexagonal arrays were fabricated via intermolecular halogen bonding between two linear molecular building blocks in a bicomponent blend. The substitution position of the pyridine N atom involved in the halogen bond plays an important role in the formation of the hexagonal structures. [ABSTRACT FROM AUTHOR]

Covering: up to the end of 2017 C–C bond formations are frequently the key steps in cofactor and natural product biosynthesis. Historically, C–C bond formations were thought to proceed by two electron mechanisms, represented by Claisen condensation in fatty acids and polyketide biosynthesis. These types of mechanisms require activated substrates to create a nucleophile and an electrophile. More recently, increasing number of C–C bond formations catalyzed by radical SAM enzymes are being identified. These free radical mediated reactions can proceed between almost any sp3 and sp2 carbon centers, allowing introduction of C–C bonds at unconventional positions in metabolites. Therefore, free radical mediated C–C bond formations are frequently found in the construction of structurally unique and complex metabolites. This review discusses our current understanding of the functions and mechanisms of C–C bond forming radical SAM enzymes and highlights their important roles in the biosynthesis of structurally complex, naturally occurring organic molecules. Mechanistic consideration of C–C bond formation by radical SAM enzymes identifies the significance of three key mechanistic factors: radical initiation, acceptor substrate activation and radical quenching. Understanding the functions and mechanisms of these characteristic enzymes will be important not only in promoting our understanding of radical SAM enzymes, but also for understanding natural product and cofactor biosynthesis. [ABSTRACT FROM AUTHOR]

The co-deposition of 1,4-di(4′,4′′-pyridyl)benzene and 1,4-di(4′,4′′-bromophenyl)benzene on Si(111)–B surface leads to the formation of a highly regular self-assembly. The formation of this network has been investigated by STM and has been elucidated in the light of sergeants & soldiers principle due to halogen bonding on a silicon surface. [ABSTRACT FROM AUTHOR]

We selectively engineer three two-dimensional self-assembled hybrid PTCDI–NaCl nanoarchitectures, i.e. a flower-structure, a mesh-structure and a chain-structure on Au(111). Scanning tunneling microscopy reveals that NaCl-dimers selectively interact with molecular N–H groups. The PTCDI…NaCl-dimer binding appears to be highly directional. Hybrid molecular-ionic self-assembly is a promising alternative to metal-coordinated and multicomponent organic nanostructures to engineer novel nanoarchitectures on surfaces. [ABSTRACT FROM AUTHOR]

The table of contents for the June 3, 2014 issue of the journal "Chemical Communications" is presented.