Elastic displacements and step interactions on metallic surfaces: GIXD and ab initio study of Au(332)

International audienceWe have studied the energetics, relaxation and interactions of steps on the Au(332) vicinal surface, using a combination of grazing incidence X-ray diffraction (GIXD), anisotropic linear elasticity (ALE) theory, and ab initio density functional theory (DFT). We find that the initial force distribution on a bulk-truncated surface, as well as the resulting pattern of atomic relaxations, can be reproduced excellently by a buried dipole elastic model. The close agreement obtained between experimental and calculated X-ray diffraction profiles allows us to precisely determine the value of the elastic dipole density at the steps. We also use these results to obtain an experimental estimate of the surface stress on an unreconstructed Au(111) facet, 2.3+/-0.4 Nm-1, and the value of the step-step elastic interaction energy: 950 +/- 150 meV.Å

A Novel Conserved Isoform of the Ubiquitin Ligase UFD2a/UBE4B Is Expressed Exclusively in Mature Striated Muscle Cells

Yeast Ufd2p was the first identified E4 multiubiquitin chain assembly factor. Its vertebrate homologues later referred to as UFD2a, UBE4B or E4B were also shown to have E3 ubiquitin ligase activity. UFD2a function in the brain has been well established in vivo, and in vitro studies have shown that its activity is essential for proper condensation and segregation of chromosomes during mitosis. Here we show that 2 alternative splice forms of UFD2a, UFD2a-7 and -7/7a, are expressed sequentially during myoblast differentiation of C2C12 cell cultures and during cardiotoxin-induced regeneration of skeletal muscle in mice. UFD2a-7 contains an alternate exon 7, and UFD2a-7/7a, the larger of the 2 isoforms, contains an additional novel exon 7a. Analysis of protein or mRNA expression in mice and zebrafish revealed that a similar pattern of isoform switching occurs during developmental myogenesis of cardiac and skeletal muscle. In vertebrates (humans, rodents, zebrafish), UFD2a-7/7a is expressed only in mature striated muscle. This unique tissue specificity is further validated by the conserved presence of 2 muscle-specific splicing regulatory motifs located in the 3′ introns of exons 7 and 7a. UFD2a interacts with VCP/p97, an AAA-type ATPase implicated in processes whose functions appear to be regulated, in part, through their interaction with one or more of 15 previously identified cofactors. UFD2a-7/7a did not interact with VCP/p97 in yeast 2-hybrid experiments, which may allow the ATPase to bind cofactors that facilitate its muscle-specific functions. We conclude that the regulated expression of these UFD2a isoforms most likely imparts divergent functions that are important for myogenisis

Support work function as a descriptor and predictor for the charge and morphology of deposited Au nanoparticles

We show, using density functional theory calculations, that the charge, magnetic moment, and morphology of deposited Au nanoclusters can be tuned widely by doping the oxide support with aliovalent cations and anions. As model systems, we have considered Aun (n = 1, 2, or 20) deposited on doped MgO and MgO/Mo supports. The supports have been substitutionally doped with varying concentrations θ of F, Al, N, Na, or Li. At θ = 2.78%, by varying the dopant species, we are able to tune the charge of the Au monomer between −0.84e and +0.21e, the Au dimer between −0.87e and −0.16e, and, most interestingly, Au20 between −3.97e and +0.49e. These ranges can be further extended by varying θ. These changes in charge are correlated with changes in adsorption and/or cluster geometry and magnetic moment. We find that the work function Φ of the bare support is a good predictor and descriptor of both the geometry and charge of the deposited Au cluster; it can, therefore, be used to quickly estimate which dopant species and concentration can result in a desired cluster morphology and charge state. This is of interest as these parameters are known to significantly impact cluster reactivity, with positively or negatively charged clusters being preferred as catalysts for different chemical reactions. It is particularly noteworthy that the Na-doped and Li-doped supports succeed in making Au20 positively charged, given the high electronegativity of Au.peerReviewe

Dynamics of weak interactions in the ligand layer of meta-mercaptobenzoic acid protected gold nanoclusters Au68(m-MBA)32 and Au144(m-MBA)40

Atomically precise metal nanoclusters, stabilized and functionalized by organic ligands, are emerging nanomaterials with potential applications in plasmonics, nano-electronics, bio-imaging, nanocatalysis, and as therapeutic agents or drug carriers in nanomedicine. The ligand layer has an important role in modifying the physico-chemical properties of the clusters and in defining the interactions between the clusters and the environment. While this role is well recognized from a great deal of experimental studies, there is very little theoretical information on dynamical processes within the layer itself. Here, we have performed extensive molecular dynamics simulations, with forces calculated from the density functional theory, to investigate thermal stability and dynamics of the ligand layer of the meta-mercaptobenzoic acid (m-MBA) protected Au68 and Au144 nanoclusters, which are the first two gold nanoclusters structurally solved to atomic precision by electron microscopy [Azubel et al., Science, 2014, 345, 909 and ACS Nano, 2017, 11, 11866]. We visualize and analyze dynamics of three distinct non-covalent interactions, viz., ligand–ligand hydrogen bonding, metal–ligand O[double bond, length as m-dash]C–OH⋯Au interaction, and metal–ligand Ph(π)⋯Au interaction. We discuss their relevance for defining, at the same time, the dynamic stability and reactivity of the cluster. These interactions promote the possibility of ligand addition reactions for bio-functionalization or allow the protected cluster to act as a catalyst where active sites are dynamically accessible inside the ligand layer.peerReviewe

Selective Acrolein Hydrogenation over Ligand-Protected Gold Clusters : A Venus Flytrap Mechanism

The catalytic partial hydrogenation of α,β-unsaturated aldehydes is an ideal reaction to understand the selectivity between two different functional groups Here the two functional groups are C═C and C═O, and the hydrogenation of C═O is preferentially desired due to the importance of the issuing products, unsaturated alcohols, in fine-chemical industries. Using density functional theory calculations, we investigate the catalytic competency toward this reaction of a Au nanocluster in the presence of protecting ligands that offer higher stability and the possibility for the uniform distribution of size-selected clusters in the catalytic system. meta-Mercaptobenzoic-acid-protected-protected Au clusters exhibit special (bidentate) ligand–metal interactions: two weak interactions, O═C–OH···Au and Ph(π)···Au, in addition to the strong S–Au covalent bonds. We find that Ph(π)···Au interactions break (or open) to expose unprotected, low-coordinated Au sites on the cluster, which have a high propensity for trapping incoming reactant molecules. We study the partial hydrogenation of acrolein at these sites and find that the unsaturated alcohol, 1-propenol, is selectively favored over possible products. The opening of the π···Au interaction and the trapping of reactant molecules at Au sites are similar to a Venus flytrap mechanism where the flowers in the plant exhibit motion to actively trap its prey.peerReviewe

Computational Criteria for Hydrogen Evolution Activity on Ligand-protected Au25-based Nanoclusters

The hydrogen evolution reaction (HER) is a critical reaction in addressing climate change, however, it requires catalysts to be generated on an industrial scale. Nanomaterials offer several advantages over conventional HER catalysts, notably the possibility of atomic precision in tailoring the intrinsic activity. Ligand-protected metal clusters, such as the thiolate-protected MAu24SR18 (M = Au, Cu, Pd), are of particular interest as not only are they electrocatalytically active towards HER, but the charge state and composition can be precisely tuned. Here, we present a comprehensive computational study examining how the charge state and dopants affect the catalytic activity of [MAu24}SCH3)18}]^q towards the Volmer step of the HER. According to the Sabatier principle, H adsorption energy should be nearly thermoneutral for an ideal catalyst. Our results show that adsorption energies alone are an insufficient criterion to identify a promising catalytic material; kinetic barriers and experimentally relevant redox potentials should also be considered. Notably, this work explains the relative activity of MAu24SR18 (M = Au, Cu, Pd) clusters reported by Kumar et al., (Nanoscale 2020, 12, 9969). Our results validate a more thorough computational approach that includes charge and potential to understand and screen electrocatalytically active nanoclusters

Computational Criteria for Hydrogen Evolution Activity on Ligand-Protected Au25-Based Nanoclusters

The hydrogen evolution reaction (HER) is a critical reaction in addressing climate change; however, it requires catalysts to be generated on an industrial scale. Nanomaterials offer several advantages over conventional HER catalysts, including the possibility of atomic precision in tailoring the intrinsic activity. Ligand-protected metal clusters, such as the thiolate-protected MAu24(SR)18 (where M is Au, Cu, Pd), are of particular interest as not only are they electrocatalytically active toward HER, but the charge state and composition can be precisely tuned. Here, we present a comprehensive computational study examining how the charge state and dopants affect the catalytic activity of [MAu24(SCH3)18]q toward the Volmer step of the HER. Assuming an adsorbed hydrogen atom to be the key intermediate, then, according to the Sabatier principle, the H adsorption energy should be nearly thermoneutral for an ideal HER catalyst. Our results show that adsorption energies alone are an insufficient criterion to identify a promising catalytic material; experimentally relevant redox potentials, the corresponding catalyst’s charge states, and the kinetic barriers should also be considered. Notably, this work explains the relative activity of MAu24(SR)18 (M = Au, Cu, Pd) clusters reported by Kumar et al. (Nanoscale 2020, 12, 9969). Our results validate a more thorough computational approach that includes charge and redox potential to understand and screen electrocatalytically active nanoclusters.peerReviewe

Addressing Dynamics at Catalytic Heterogeneous Interfaces with DFT-MD : Anomalous Temperature Distributions from Commonly Used Thermostats

Density functional theory-based molecular dynamics (DFT-MD) has been widely used for studying the chemistry of heterogeneous interfacial systems under operational conditions. We report frequently overlooked errors in thermostated or constant-temperature DFT-MD simulations applied to study (electro)catalytic chemistry. Our results demonstrate that commonly used thermostats such as Nose−Hoover, Berendsen, and simple velocity rescaling methods fail to provide are liable temperature description for systems considered. Instead, nonconstant temperatures and large temperature gradients within the different parts of the system are observed. The errors are not a “feature” of any particular code but a represent in several ab initio molecular dynamics implementations. This uneven temperature distribution, due to inadequate thermostatting, is well-known in the classical MD community, where it is ascribed to the failure in kinetic energy equipartition among different degrees of freedom in heterogeneous systems (Harvey et al. J. Comput. Chem. 1998, 726−740) and termed the flying ice cube effect. We provide tantamount evidence that interfacial systems are susceptible to substantial flying ice cube effects and demonstrate that the traditional Nose−Hoover and Berendsen thermostats should be applied with care when simulating, for example, catalytic properties or structures of solvated interfaces and supported clusters. We conclude that the flying ice cube effect in these systems can be conveniently avoided using Langevin dynamics.peerReviewe

Binding Behavior of Carbonmonoxide to Gold Atoms on Ag(001)

The adsorption behavior of single CO molecules at 4 K bound to Au adatoms on a Ag(001) metal surface is studied with scanning tunneling microscopy (STM) and inelastic electron tunneling spectroscopy (IETS). In contrast to earlier observations two different binding configurations are observed—one on top of a Au adatom and the other one adsorbed laterally to Au on Ag(001). Moreover, IETS reveals different low-energy vibrational energies for the two binding sites as compared to the one for a single CO molecule bound to Ag(001). Density functional theory (DFT) calculations of the adsorption energies, the diffusion barriers, and the vibrational frequencies of the CO molecule on the different binding sites rationalize the experimental findings.peerReviewe