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•Potential-induced surface reconstruction on Au(111).•Zig-zag and straight structures of reconstructed Au(111) surface.•Potential-induced reconstruction kinetics on Au(111).•Ab initio ...simulations of zig-zag and straight rows of reconstructed surface.
We report in this communication, through in situ STM images correlated with time, and ab initio simulations of binding energies, how potential-induced surface reconstruction is formed on Au(111) single crystal in 0.1 M H2SO4. It was found that while the electrode potential after lifting the reconstructed surface is switched back to a more negative value than the potential of zero charge, the formation process of the reconstructed surface goes through two consecutive routes. In the more kinetically favorable step, and within a few minutes, the reconstructed surface follows three different lattice directions with a high proportion of semi zig-zag structures. However, by maintaining the negative applied potential, the surface reconstruction rearranges to a straighter reconstructed pattern in the second step, which is more energetically favorable.
The adsorption performance of hydrogen molecules over the transition metals (TM = Os, Ru, and Fe)-embedded graphitic carbon nitride (gCN) and also the binding energy of these TM elements over the gCN ...are investigated using DFT computations. The obtained results showthat the interaction energy between Os-embedded gCN and H2 molecule (with Eads of −2.452 eV) is superior than those of the other reported adsorbents. Based on these results, it is inferred that the maximum storage number of H2 molecules adsorbed over the TM–embedded gCN are 6 hydrogen molecules. The results reveal that with adsorption of H2 molecules over the gCN, conduction band and valence band energy levels have crossed each other close to the Fermi level EF, thus the semi-conductive behavior of these systems is converted to a conductive state. Finally, it is concluded that the Os–modified gCN is suitable for storaging of H2 molecules.
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•Adsorption of H2 molecules over Os-, Ru-, and Fe-embedded gCN were studied.•The Os-embedded gCN displayed the strongest adsorption energy for H2 molecules.•The Os-embedded gCN demonstrated magnetic moment of 0.77 μB.•The band gap energy of gCN was remarkably decreased by H2 adsorption.
Quantum computers can in principle solve certain problems exponentially more quickly than their classical counterparts. We have not yet reached the advent of useful quantum computation, but when we ...do, it will affect nearly all scientific disciplines. In this review, we examine how current quantum algorithms could revolutionize computational biology and bioinformatics. There are potential benefits across the entire field, from the ability to process vast amounts of information and run machine learning algorithms far more efficiently, to algorithms for quantum simulation that are poised to improve computational calculations in drug discovery, to quantum algorithms for optimization that may advance fields from protein structure prediction to network analysis. However, these exciting prospects are susceptible to “hype,” and it is also important to recognize the caveats and challenges in this new technology. Our aim is to introduce the promise and limitations of emerging quantum computing technologies in the areas of computational molecular biology and bioinformatics.
This article is categorized under:
Structure and Mechanism > Computational Biochemistry and Biophysics
Data Science > Computer Algorithms and Programming
Electronic Structure Theory > Ab Initio Electronic Structure Methods
Quantum computers promise faster algorithms that can affect molecular biology and bioinformatics – for example, in data analysis, electronic structure simulations and protein modeling.
The atomic-scale response of inhomogeneous fluids at interfaces and surrounding solute particles plays a critical role in governing chemical, electrochemical, and biological processes. Classical ...molecular dynamics simulations have been applied extensively to simulate the response of fluids to inhomogeneities directly, but are limited by the accuracy of the underlying interatomic potentials. Here, we use neural network potentials (NNPs) trained to ab initio simulations to accurately predict the inhomogeneous responses of two distinct fluids: liquid water and molten NaCl. Although NNPs can be readily trained to model complex bulk systems across a range of state points, we show that to appropriately model a fluid's response at an interface, relevant inhomogeneous configurations must be included in the training data. In order to sufficiently sample appropriate configurations of such inhomogeneous fluids, we develop protocols based on molecular dynamics simulations in the presence of external potentials. We demonstrate that NNPs trained on inhomogeneous fluid configurations can more accurately predict several key properties of fluids-including the density response, surface tension and size-dependent cavitation free energies-for liquid water and molten NaCl, compared to both empirical interatomic potentials and NNPs that are not trained on such inhomogeneous configurations. This work therefore provides a first demonstration and framework to extract the response of inhomogeneous fluids from first principles for classical density-functional treatment of fluids free from empirical potentials.
We study the effect of nitrogen content on functional properties, thermal stability and oxidation resistance of hard and optically transparent amorphous Hf-Y-Si-B-C-N coatings prepared by pulsed ...magnetron sputtering. Ab-initio simulations are performed to link the experimentally obtained properties with the atomic and electronic structures of the fabricated materials. It is shown that the content of N in the material, varied from subsaturation 46 at.% to saturation 51 at.%, is of significant importance for the optimization of thermal stability and tuning the refractive index and extinction coefficient. We identify an optimum N2 content in the plasma and in turn N content in the coatings which outperform the previously introduced high-temperature material Hf6Y2Si29B12C2N45. The results constitute a progress in the efforts to combine multiple functional properties with exceptional (above 1300 °C) thermal stability and oxidation resistance.
A typical binary amorphous telluride GeTe2 is investigated from first‐principles molecular dynamics simulations. After a comparison with chemical analogs from neutron or X‐ray diffraction ...experiments, such as GeO2 or GeSe2, the structure of this material is studied by examining real and reciprocal space properties. It is found that the base geometrical motifs of the germanium atom can be either in tetrahedral or in defected coordinations involving pyramidal units. A review of previous results for other compositions reveals that such binary Ge tellurides contain soft tetrahedra, at variance with lighter chalcogenides, such as GeS and GeSe, and are characterized by an increased angular bending motion (typically 20°) as compared with, e.g., GeS (5°). In addition, for amorphous Ge‐rich materials, GeTe2 and GeTe, a secondary tetrahedral geometry appears, related to the presence of GeGe bonds, having a larger mean angle of about 125°. These typical features not only relate to characteristics observed from scattering experiments but may also be a crucial feature for the understanding of the phase‐change phenomena.
First‐principles molecular dynamics simulations of amorphous GeTe2 reveal that the base geometrical motifs of the germanium atom can be either in defected coordinations involving pyramidal units or in tetrahedral geometry. The latter appears, furthermore, to be soft with increased bending motions and two possible angles.
Single enantiomers of mandelic acid (1), 3-phenyllactic acid (2), and 3-(4-hydroxyphenyl)lactic acid (3) are the subject of many fields of investigation, spanning from the pharmaceutical synthesis to ...that of biocompatible and biodegradable polymers, while passing from the interest towards their antimicrobial activity to their role as biomarkers of particular pathological conditions or occupational exposures to specific xenobiotics. All above mentioned issues justify the need for accurate analytical methods enabling the correct determination of the individual enantiomers. So far, all the developed liquid chromatography (LC) methods were not or hardly compatible with mass spectrometry (MS) detection. In this paper, a commercially available Cinchona-alkaloid derivative zwitterionic chiral stationary phase that is, the CHIRALPAK® ZWIX(−) was successfully used to optimize the enantioresolution of compounds 1–3 under polar-ionic (PI) conditions with a mobile phase consisting of an acetonitrile/methanol 95/5 (v/v) mixture with 80 mM formic acid. With the optimized conditions, enantioseparation and enantioresolution values up to 1.46 and 4.41, respectively, were obtained. In order to assess the applicability of the optimized enantioselective chromatography conditions in real-life scenarios and on MS-based systems, a proof-of-concept application was efficiently carried out by analysing dry urine spot samples spiked with 1 by means of a LC-MS system. The (S)<(R) enantiomer elution order (EEO) was established for compounds 1 and 2 by analysing a pure enantiomeric standard of known configuration. This was not possible for 3 because not commercially available. For this compound, the same EEO was identified applying a procedure based on ab initio time-dependent density-functional theory simulations coupled to electronic circular dichroism analyses. Moreover, a molecular dynamics simulation unveiled the role of the phenolic OH in compound 3 in the retention mechanism.
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•ZWIX(−) allows the enantioresolution of the three aromatic α-hydroxy acids.•The optimized polar-ionic conditions are fully compatible with MS detectors.•The developed LC method can be used to study biological matrices with MS detectors.•Combining in silico simulations and ECD analyses is useful to derive the EEO.•The retention mechanism can be explained with molecular dynamic simulations.
High entropy alloys (HEAs) in the hexagonal close-packed (hcp) phase usually show poor mechanical properties. We demonstrate here, by use of ab initio simulations and detailed experimental ...investigations, that the mechanical properties can be improved by optimizing the microstructure. In particular we design a dual-phase HEA consisting of a body-centered cubic (bcc) matrix and hcp laths, with nanoprecipitates of the ω phase in the Sc-Ti-Zr-Hf-Re system, by controlling the Re content. This dedicated microstructure reveals, already in the as-cast state, high compressive strength and good ductility of 1910 MPa and 8%, respectively. Our study lifts the hcp-based HEAs onto a competitive, technological level.
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•Ab initio calculations demonstrate the stabilization of the bcc and the ω phases when adding Re to the Sc-Ti-Zr-Hf system,•Detailed experimental observations including TEM analysis confirm the stabilization and reveal ω nanoparticles,•A mechanically superior dual-phase bcc+hcp microstructure strengthened by ω nanoparticles is designed
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