Si/Al and metal loading effects on the templated synthesis of Ni nanowires in CAN and MOR zeolite frameworks

Zeolites with 1D pore channels, such as cancrinite (CAN) and mordenite (MOR), have the potential to be used as templates in the synthesis of subnanometre metal nanowires. Previous studies show a strong correlation between the location of Al atoms in zeolites and the positioning of the metal atoms inside the zeolite framework. Thus, Metropolis Monte Carlo simulations were used here to study the behaviour of Ni atoms within the CAN- and MOR-type zeolites at different Si/Al ratios and Ni loadings. It was found for both zeolite frameworks that a lower Si/Al ratio favoured energetically the positioning of Ni atoms in the 1D pore channels and that higher loadings of Ni promote the formation of 1D Ni structures. These results suggest that it is possible to use zeolites with the CAN and MOR frameworks and low Si/Al ratio as effective templates for the synthesis of metal nanowires.     

Formation of one-dimensional Pt structures in VET-type zeolites: a combined force field and first principles study

The viability of forming stable one-dimensional Pt structures inside the pores of VET-type zeolites is evaluated in this study by using molecular simulations. The resulting nanostructures were optimised and analysed as formed both inside and outside the zeolite. The results show that, theoretically, it is possible to obtain thermally stable ultrathin nanowires in VET zeolites with a low Si/Al ratio using high temperatures during formation. The results also show that the structures obtained with the pcff force field for the ultrathin nanowires are qualitatively similar to those obtained after geometric optimisation with DFT.     

Modeling of Platinum Clusters in H-Mordenite

The size, location and structure of Pt clusters in H-mordenite have been investigated by molecular mechanics energy minimization and molecular dynamics simulation techniques using the Catalysis software of Molecular Simulations (MSI). Lattice energy minimizations are performed to study the effects of the specific framework aluminum positions on the location and stability of monoatomic Pt sites in H-mordenite. The lattice energies relative to the siliceous platinum-aluminosilicate structure reveal that the stability of a single Pt atom in H-mordenite is remarkably influenced by the specific location of the Al atoms in the lattice. At the studied Si/Al ratio of two Al ions per unit cell, a stabilization of the H-mordenite lattice upon Pt deposition is obtained. Moreover, lattice energy calculations on Pt/aluminosilicate mordenites of different metal contents per unit cell have been performed. An optimum size for the aggregate confined to the 12-ring main channel that is almost independent of the Pt content per mordenite unit cell has been found. The structural features of the resulting clusters at the end of molecular dynamics simulations on Pt/alumina-mordenites reflect a strong metal-zeolite interaction. The present results are consistent with a previous molecular dynamics simulation study on the structure of platinum deposited on SiO₂ surfaces.     

A comparative study of the adsorption of water and methanol in zeolite BEA: a molecular simulation study

Grand canonical Monte Carlo simulations were carried out to study the equilibrium adsorption concentration of methanol and water in all-silica BEA zeolite and HBEA zeolites with different Si/Al ratios over a wide range of temperatures and loadings. These zeolites have oval-shaped channels with one side longer than the other. Water sorption into the hydrophobic BEA zeolite had a sharp transition with its sorption going from zero to near full capacity over a very small pressure range. Methanol sorption was much more gradual with respect to pressure. With the addition of hydrophilic sites for the HBEA zeolites by decreasing the Si/Al ratio, adsorption at lower pressures increased significantly for water and methanol. At higher loadings, water and methanol adsorption were found to behave in fundamentally different ways. Water structures in the zeolite channels formed hydrogen-bonded chains while maximising contact with the surfaces on the longer edges of the zeolite channels. Methanol molecules, in contrast, formed very few hydrogen bonds between themselves, with their hydroxyl groups primarily binding with surface of the shorter edge of the zeolite channels and their methyl groups located near the middle of the zeolite channels. The addition of hydrophilic groups in the HBEA zeolites strongly influenced positions of the methanol hydroxyl groups at high loadings, but did not have a significant effect on water structure.     

Molecular dynamics study of core–shell structure from carbon nanotube and platinum nanowire

The interaction between the carbon nanotubes (CNTs) and platinum (Pt) nanowires (NWs) was investigated using forced field-based molecular dynamics (MD) simulations. Our results display that the Pt NW can induce the self-assembly of the CNTs to form a shell-core structure, this is because of the van der Waals interaction and the offset face-to-face π–π stacking interaction. The diameter of the CNT plays a major role in the formation of shell–core structure. Furthermore, the position of the CNT on the Pt NW also affects the formation of shell–core configuration, whereas the cross section of the NWs has a negligible effect on the fabrication process. Moreover, the interaction between multi-wall carbon nanotube and Pt nanowires was also discussed in detail, it is worth noting that the formation conformation of the CNT is also much more stable.     

Towards Engineering Nanoporous Platinum Thin Films for Highly Efficient Catalytic Applications

Porous metals attract significant interest for use in diverse electrochemical catalytic applications. However the fabrication of scalable and controlled porous metal structures on the nanoscale, particularly with highly catalytic pure Pt, still remains a significant challenge. We demonstrate highly engineered nanoporous Pt thin films by the dealloying of a Pt‐Si binary alloy system with a predetermined alloy composition. Controlled pore dimensions and nanostructures are obtained by tailoring the Pt‐Si alloy composition followed by selective Si etching. As a result, isotropic open nanopores are formed in continuous Pt ligaments and the porosity becomes larger on increasing the Si/Pt atomic ratio, which leads to the formation of a higher surface area and active catalytic sites. The formed nanoporous Pt film shows a 32‐times‐higher catalytic activity than Pt/C catalysts, with a high current density and low charge‐transfer resistance during methanol electro‐oxidation. The results reported here open up possibilities to develop high‐performance and reliable catalytic electrodes in energy and environmental applications.     

A molecular dynamics simulation of hexagonal solid platinum nanowires

Experimental evidence of the existence of multi-wall platinum (Pt) nanowires (NWs) has been reported. In this paper, we investigated structural formation of Pt NWs using the classical molecular dynamics (MD) simulation method. The simulations began from initial configurations with random distributions of atomic positions. The initial configuration was minimised by the steepest descent method, and assigned a temperature of 601?K with a random distribution of atomic velocities. Then simulated annealing was applied such that the temperature of the system was reduced gradually to 1?K and a stable NW structure was obtained. Types of hexagonal solid Pt NWs featuring different structures than those of previously reported NWs were found. Details of structural characteristics and mechanical properties of these Pt NWs are presented.     

Molecular dynamics investigation of membrane-bound bundles of the channel-forming transmembrane domain of viral protein U from the human immunodeficiency virus HIV-1

Molecular dynamics (MD) simulations have been carried out on bundles of the channel-forming transmembrane (TM) domain of the viral protein U (VPU(1-27) and VPU(6-27)) from the human immunodeficiency virus (HIV-1). Simulations of hexameric and pentameric bundles of VPU(6-27) in an octane/water membrane mimetic system suggested that the pentamer is the preferred oligomer. Accordingly, an unconstrained pentameric helix bundle of VPU(1-27) was then placed in a hydrated palmitoyl-oleyl-3-n-glycero-phosphatidylethanolamine (POPE) lipid bilayer and its structural properties calculated from a 3-ns MD run. Some water molecules, initially inside the channel lumen, were expelled halfway through the simulation and the bundle adopted a conical structure reminiscent of previous MD results obtained for VPU(6-27) in an octane/water system. The pore constriction generated may correspond to a closed state of the channel and underlies the relocation of the W residue toward the pore lumen. The relative positions of the helices with respect to the bilayer and their interactions with the lipids are discussed. The observed structure is stabilized via specific interactions between the VPU helices and the carbonyl oxygen atoms of the lipid molecules, particularly at the Q and S residues.     

Removal of free fatty acid in waste frying oil by esterification with methanol on zeolite catalysts

The removal of free fatty acid (FFA) in waste frying oil by esterification with methanol was conducted using various zeolite catalysts. The ZSM-5 (MFI), mordenite (MOR), faujasite (FAU), beta (BEA) zeolites, and silicalite were employed with different Si/Al molar ratio in the reaction. The effects of acidic properties and pore structure of the zeolite catalysts were discussed relating to the conversion of the FFA. The MFI zeolite induced an improvement of the removal efficiency of FFA by cracking to the FFA in its pore structure due to its narrow pore mouth. The catalytic activity for FFA removal was lowered with decreasing of acid strength of the zeolites. The strong acid sites of zeolites induced the high conversion of FFA comparatively. The acid strength and pore structure of acidic zeolites affected the catalytic activity in FFA removal.     

Silicon reduces aluminum accumulation and mitigates toxic effects in cowpea plants

Aluminum (Al) is the third most abundant metal in the Earth’s surface, and Al toxicity promotes several negative effects in plant metabolism. Silicon (Si) is the second most common mineral in soil and is considered a beneficial element for plants, improving their tolerance to biotic and abiotic stresses. The aim of this study is to determine whether Si can reduce the accumulation of Al, explain the possible contribution of Si in mitigating Al toxicity, and indicate the better Si dose–response for cowpea plants. The experiment had a factorial design with two levels of aluminum (0 and 10 mM Al) and three levels of silicon (0, 1.25 and 2.50 mM Si). The utilization of Si in plants exposed to Al toxicity contributed to significant reductions in the Al contents of all tissues, corresponding to reductions of 51, 29 and 41% in roots, stems and leaves, respectively, upon treatment with 2.50 mM Si + 10 mM Al compared to the control treatment (0 mM Si + 10 mM Al). Al toxicity promoted decreases in Φ_PSII, q_P and ETR, whereas 2.50 mM Si induced increases of 54, 185 and 29%, respectively. Plants exposed to Al had lower values of P _N, WUE and P _N/C _i, whereas Si application at a concentration of 2.50 mM yielded improvements of 53, 32 and 67%, respectively. Al exposure increased SOD, CAT, APX and POX activities, whereas treatment with 2.50 mM Si + 10 mM Al produced significant variations of 72, 97, 48 and 32%, respectively, compared to 0 mM Si + 10 mM Al. Our results proved that Si reduced the Al contents in all tissues. Si also improved the photochemical efficiency of PSII, gas exchange, pigments and antioxidant enzymes, contributing to a reduction in the accumulation of oxidative compounds. These benefits corroborate the multiple roles exercised by Si in metabolism and reveal that Si immobilizes the Al in roots and reduce the accumulation of this metal in other organs, mitigating the damage caused by Al in cowpea plants. In relation to dose–response, plants exposed to 1.25 mM Si without Al presented better results in terms of growth, whereas the toxic effects of plants exposed to Al were mitigated with 2.50 mM Si.     

Dynamics and energetics of water permeation through the aquaporin channel

Structural properties of water inside bovine aquaporin-1 are investigated by molecular simulation. The calculations, which are based on the recently determined X-ray structure at 2.2 A resolution (Sui et al., Nature 2001;414:872-878), are carried out on one monomeric subunit immersed in a water-n-octane-water bilayer. Molecular dynamics (MD) simulations suggest that His182, a fully conserved residue in the channel pore, is protonated in the delta position. Furthermore, they reveal a highly ordered water structure in the channel, induced by the electrostatic properties of the protein. Multiple-steering MD simulations are used to calculate the free-energy of water diffusion. To the best of our knowledge, this represents the first free-energy calculation based on the new, high-resolution structure of the pore. The calculated barrier is 2.5 kcal/mol, and it is associated to water permeation through the Asn-Pro-Ala (NPA) region of the pore, where water molecules are only hydrogen-bonded with themselves. These findings are fully consistent with those based on the previous MD studies on the human protein (de Groot and Grubmüller, Science 2001;294:2353-2357).     

Molecular dynamics simulations of the Cx26 hemichannel: evaluation of structural models with Brownian dynamics

The recently published crystal structure of the Cx26 gap junction channel provides a unique opportunity for elucidation of the structure of the conductive connexin pore and the molecular determinants of its ion permeation properties (conductance, current-voltage [I-V] relations, and charge selectivity). However, the crystal structure was incomplete, most notably lacking the coordinates of the N-terminal methionine residue, which resides within the pore, and also lacking two cytosolic domains. To allow computational studies for comparison with the known channel properties, we completed the structure. Grand canonical Monte Carlo Brownian dynamics (GCMC/BD) simulations of the completed and the published Cx26 hemichannel crystal structure indicate that the pore is too narrow to permit significant ion flux. The GCMC/BD simulations predict marked inward current rectification and almost perfect anion selectivity, both inconsistent with known channel properties. The completed structure was refined by all-atom molecular dynamics (MD) simulations (220 ns total) in an explicit solvent and POPC membrane system. These MD simulations produced an equilibrated structure with a larger minimal pore diameter, which decreased the height of the permeation barrier formed by the N terminus. GCMC/BD simulations of the MD-equilibrated structure yielded more appropriate single-channel conductance and less anion/cation selectivity. However, the simulations much more closely matched experimentally determined I-V relations when the charge effects of specific co- and posttranslational modifications of Cx26 previously identified by mass spectrometry were incorporated. We conclude that the average equilibrated structure obtained after MD simulations more closely represents the open Cx26 hemichannel structure than does the crystal structure, and that co- and posttranslational modifications of Cx26 hemichannels are likely to play an important physiological role by defining the conductance and ion selectivity of Cx26 channels. Furthermore, the simulations and data suggest that experimentally observed heterogeneity in Cx26 I-V relations can be accounted for by variation in co- and posttranslational modifications.     

Mineral colloids mediate organic carbon accumulation in a temperate forest Spodosol: depth-wise changes in pore water chemistry

Mobile submicron mineral phases within soil pore waters are presumed to play a major role in the transport and availability of organic carbon (OC) in subsurface horizons. This work reports on the composition of the?<?0.45 µm and 0.45–1.2 µm size fractions of extracted soil pore waters from horizons of a well-drained-Spodosol-soil to reveal conditions favorable for carbon mobility and accumulation. These operationally defined quantities are abbreviated SF-S (size fraction small) and SF-L (size fraction large) to identify the?<?0.45 µm and the 0.45–1.2 µm size fraction filtrates, respectively. It is found that in the SF-S fraction, OC mass concentrations are more than 30–50 times higher than metal (M?=?Fe?+?Al) mass concentrations in all Spodosol horizons, with metal-to-carbon (M/C) atomic ratios of 0.15–0.03. Chemical equilibrium modeling calculations estimate?>?95% of the total Fe and Al in SF-S are complexed with OC in all Spodosol horizons. In contrast with the SF-S, the SF-L had much greater OC concentrations and even lower M/C (<?0.01), except in the Bh horizon (M/C?=?0.05). In Bh, major accumulation of organic matter occurred above the lesser-accumulating Bhs, the latter having higher pH, but much lower OC in all forms (soil, colloidal). Infrared spectroscopy indicates the SF-L fraction of soil pore waters contains both organic and inorganic constituents, including amorphous silica, the second-most abundant component after OC. Mineral-organic associations such as mineral crystallites embedded in OC are observed in the SF-L fraction by transmission electron microscopy (TEM). Transmission electron microscopy also reveal carbon-rich amorphous structures containing traces of Fe, Al and Si, and small (~?100 nm) spherical amorphous SiO₂ particles. These observations provide support for the main mechanism of OC accumulation in Spodosols being the downward movement of colloids (organic, OC-sorbed mineral and organo-mineral), followed by colloid immobilization due to a combination of increases in pH and M/C ratio. The occurrence of these three types of colloidal structures in pore waters seems to depend on the pH and the relative supply of OC and Fe?+?Al to pore waters. Similar colloidal structures might also contribute to the transport and availability of OC in subsurface horizons of soils that range in the accumulation of organic and organo-metallic compounds, that is, in the expression of spodic properties.     

Characterization of a Novel Water Pocket Inside the Human Cx26 Hemichannel Structure

Connexins (Cxs) are a family of vertebrate proteins constituents of gap junction channels (GJCs) that connect the cytoplasm of adjacent cells by the end-to-end docking of two Cx hemichannels. The intercellular transfer through GJCs occurs by passive diffusion allowing the exchange of water, ions, and small molecules. Despite the broad interest to understand, at the molecular level, the functional state of Cx-based channels, there are still many unanswered questions regarding structure-function relationships, perm-selectivity, and gating mechanisms. In particular, the ordering, structure, and dynamics of water inside Cx GJCs and hemichannels remains largely unexplored. In this work, we describe the identification and characterization of a believed novel water pocket—termed the IC pocket—located in-between the four transmembrane helices of each human Cx26 (hCx26) monomer at the intracellular (IC) side. Using molecular dynamics (MD) simulations to characterize hCx26 internal water structure and dynamics, six IC pockets were identified per hemichannel. A detailed characterization of the dynamics and ordering of water including conformational variability of residues forming the IC pockets, together with multiple sequence alignments, allowed us to propose a functional role for this cavity. An in vitro assessment of tracer uptake suggests that the IC pocket residue Arg-143 plays an essential role on the modulation of the hCx26 hemichannel permeability.     

Characterization of a Novel Water Pocket Inside the Human Cx26 Hemichannel Structure

Connexins (Cxs) are a family of vertebrate proteins constituents of gap junction channels (GJCs) that connect the cytoplasm of adjacent cells by the end-to-end docking of two Cx hemichannels. The intercellular transfer through GJCs occurs by passive diffusion allowing the exchange of water, ions, and small molecules. Despite the broad interest to understand, at the molecular level, the functional state of Cx-based channels, there are still many unanswered questions regarding structure-function relationships, perm-selectivity, and gating mechanisms. In particular, the ordering, structure, and dynamics of water inside Cx GJCs and hemichannels remains largely unexplored. In this work, we describe the identification and characterization of a believed novel water pocket—termed the IC pocket—located in-between the four transmembrane helices of each human Cx26 (hCx26) monomer at the intracellular (IC) side. Using molecular dynamics (MD) simulations to characterize hCx26 internal water structure and dynamics, six IC pockets were identified per hemichannel. A detailed characterization of the dynamics and ordering of water including conformational variability of residues forming the IC pockets, together with multiple sequence alignments, allowed us to propose a functional role for this cavity. An in vitro assessment of tracer uptake suggests that the IC pocket residue Arg-143 plays an essential role on the modulation of the hCx26 hemichannel permeability.     

Asymmetric effects of litter removal and litter addition on the structure and function of soil microbial communities in a managed pine forest

Aims

The effect of different MeJA doses applied prior to or simultaneously with toxic Al on biochemical and physiological properties of Vaccinium corymbosum cultivars with contrasting Al resistance was studied.

Methods

Legacy (Al-resistant) and Bluegold (Al-sensitive) plants were treated with and without toxic Al under controlled conditions: a) without Al and MeJA, b) 100 μM Al, c) 100 μM Al + 5 μM MeJA, d) 100 μM Al + 10 μM MeJA and e) 100 μM Al + 50 μM MeJA. MeJA was applied to leaves 24 h prior to or simultaneously with Al in nutrient solution. After 48 h, Al-concentration, lipid peroxidation (LP), H₂O₂, antioxidant activity, total phenols, total flavonoids, phenolic compounds and superoxide dismutase activity (SOD) of plant organs were analyzed.

Results

Al-concentrations increased with Al-treatment in both cultivars, being Al, LP and H₂O₂ concentrations reduced with low simultaneous MeJA application. Higher MeJA doses induced more oxidative damage than the lowest. Legacy increased mainly non-enzymatic compounds, whereas Bluegold increased SOD activity to counteract Al³⁺.

Conclusions

Low MeJA doses applied simultaneously with Al³⁺ increased Al-resistance in Legacy by increasing phenolic compounds, while Bluegold reduced oxidative damage through increment of SOD activity, suggesting a diminution of its Al-sensitivity. Higher MeJA doses could be potentially toxic. Studies are needed to determine the molecular mechanisms involved in the protective MeJA effect against Al-toxicity.

     

Theoretical and computational models of biological ion channels

The goal of this review is to establish a broad and rigorous theoretical framework to describe ion permeation through biological channels. This framework is developed in the context of atomic models on the basis of the statistical mechanical projection-operator formalism of Mori and Zwanzig. The review is divided into two main parts. The first part introduces the fundamental concepts needed to construct a hierarchy of dynamical models at different level of approximation. In particular, the potential of mean force (PMF) as a configuration-dependent free energy is introduced, and its significance concerning equilibrium and non-equilibrium phenomena is discussed. In addition, fundamental aspects of membrane electrostatics, with a particular emphasis on the influence of the transmembrane potential, as well as important computational techniques for extracting essential information from all-atom molecular dynamics (MD) simulations are described and discussed. The first part of the review provides a theoretical formalism to 'translate' the information from the atomic structure into the familiar language of phenomenological models of ion permeation. The second part is aimed at reviewing and contrasting results obtained in recent computational studies of three very different channels: the gramicidin A (gA) channel, which is a narrow one-ion pore (at moderate concentration), the KcsA channel from Streptomyces lividans, which is a narrow multi-ion pore, and the outer membrane matrix porin F (OmpF) from Escherichia coli, which is a trimer of three beta-barrel subunits each forming wide aqueous multi-ion pores. Comparison with experiments demonstrates that current computational models are approaching semi-quantitative accuracy and are able to provide significant insight into the microscopic mechanisms of ion conduction and selectivity. We conclude that all-atom MD with explicit water molecules can represent important structural features of complex biological channels accurately, including such features as the location of ion-binding sites along the permeation pathway. We finally discuss the broader issue of the validity of ion permeation models and an outlook to the future.     

Thermal and pressure-induced martensitic phase transformations in a Ni–Al alloy modelled by Sutton–Chen embedded atom method

The Ni–Al alloys which exhibit the thermoelastic martensitic phase transformations in the composition range from 60 to 65 atomic percentage (at.%) of Ni are widely used in the high technology applications. In this study, both thermal and pressure-induced phase transformations in Ni-37.5 at.%Al alloy model were investigated by a molecular dynamics (MD) method. Physical interactions between atoms in the alloy system were modelled using the Sutton–Chen version of the embedded atom method based on many-body interactions. The potential parameters for cross interactions between Ni and Al atoms were estimated by optimising the results obtained from the MD simulations, taking into account the experimental data including the crystal lattice properties of the model alloy in high temperature phase.     

Water and deuterium oxide permeability through aquaporin 1: MD predictions and experimental verification

Determining the mechanisms of flux through protein channels requires a combination of structural data, permeability measurement, and molecular dynamics (MD) simulations. To further clarify the mechanism of flux through aquaporin 1 (AQP1), osmotic p(f) (cm(3)/s/pore) and diffusion p(d) (cm(3)/s/pore) permeability coefficients per pore of H(2)O and D(2)O in AQP1 were calculated using MD simulations. We then compared the simulation results with experimental measurements of the osmotic AQP1 permeabilities of H(2)O and D(2)O. In this manner we evaluated the ability of MD simulations to predict actual flux results. For the MD simulations, the force field parameters of the D(2)O model were reparameterized from the TIP3P water model to reproduce the experimentally observed difference in the bulk self diffusion constants of H(2)O vs. D(2)O. Two MD systems (one for each solvent) were constructed, each containing explicit palmitoyl-oleoyl-phosphatidyl-ethanolamine (POPE) phospholipid molecules, solvent, and AQP1. It was found that the calculated value of p(f) for D(2)O is approximately 15% smaller than for H(2)O. Bovine AQP1 was reconstituted into palmitoyl-oleoyl-phosphatidylcholine (POPC) liposomes, and it was found that the measured macroscopic osmotic permeability coefficient P(f) (cm/s) of D(2)O is approximately 21% lower than for H(2)O. The combined computational and experimental results suggest that deuterium oxide permeability through AQP1 is similar to that of water. The slightly lower observed osmotic permeability of D(2)O compared to H(2)O in AQP1 is most likely due to the lower self diffusion constant of D(2)O.