Gold/titania catalysts are widely used for key reactions, notably including the selective oxidation of alcohols in the liquid phase. Our large‐scale ab initio simulations disclose that the ...liquid‐phase reaction mechanism is distinctly different from that in the gas phase because of active participation of water molecules. While concerted charge transfers related to O2 splitting and ion of both protonic and hydridic hydrogens are enforced under dry conditions, stepwise charge transfer is preferred in the condensed phase. Dissociation of reactive water molecules and subsequent Grotthuss migration of protonic defects, H+(aq), allows for such a decoupling of the oxidation process, both in time and space. It is expected that these observations are paradigmatic for heterogeneous catalysis in aqueous phases.
Just add water: Solvent may dramatically affect heterogeneously catalyzed processes. Advanced ab initio simulations reveal the effect of water on methanol oxidation over titania‐supported gold nanoparticles. The reaction mechanism in the liquid phase versus the gas phase is distinctly different because water molecules actively participate in oxidation and alter all charge‐transfer steps in the reaction.
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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.
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.
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•PBE and LDA agree in predicting the thermal conductivity of III-V semiconductors.•PBE predicts a smaller acoustic-optical phonon gap than LDA.•This leads to softer force constants ...but increases the number of scattering events.•BAs is a limit case due to its extremely large acoustic-optical gap.
In this contribution we assess the performance of two different exchange-correlation functionals in the first-principles prediction of the lattice thermal conductivity of bulk semiconductors, namely the local density approximation (LDA) and the Perdew-Burke-Ernzerhof implementation of the generalized gradient approximation (GGA). Both functionals are shown to give results in good agreement with experimental measurements. Such a consistency between the two functionals may seem a bit surprising, as the LDA is known to overbind and the GGA to soften the interatomic bonds. Such features ought to greatly affect the value of the system interatomic force constants (IFCs) which are necessary for the first-principles prediction of the lattice thermal conductivity. We choose AlAs and BAs to represent III-V semiconductors in the zincblende structure.
We show that, in the case of AlAs, the errors introduced by the approximate exchange-correlation functionals tend to cancel themselves. In the case of LDA, the overbinding generates larger absolute third-order IFCs, which tend to increase the three-phonon scattering rates. On the other hand, larger absolute second-order IFCs lead to a larger acoustic-optical phonon band gap which in turns decrease the available phase space for three-phonon scattering, compensating the increase in the scattering rates due to stiffer IFCs. As AlAs is a typical III-V semiconductor in the zincblende structure, we expect these findings to hold for general compounds of the same family. On the other hand, BAs can be considered a special instance thereof: due to the large gap between acoustic and optical phonons, the available scattering volume for three-phonon processes is already very limited in both LDA and PBE. In this case we find that the LDA increase in scattering rates due to stiffer bonds is partially compensated by an increase in phonon group velocities.