Federico Zipoli

Simulation of electrocatalytic hydrogen production by a bioinspired catalyst anchored to a pyrite electrode.

The possibility of using the active site, the [FeFe](H) cluster, of the bacterial di-iron hydrogenases as a catalyst for hydrogen production from water by electro- or photocatalysis is of current scientific and technological interest. We present here a theoretical study of hydrogen production by a modified [FeFe](H) cluster stably linked to a pyrite electrode immersed in acidified water. We employed state-of-the-art electronic-structure and first-principles molecular-dynamics methods. We found that a stable sulfur link of the cluster to the surface analogous to that linking the cluster to its enzyme environment cannot be made. However, we have discovered a modification of the cluster which does form a stable, tridentate link to the surface. The pyrite electrode readily produces hydrogen from acidified water when functionalized with the modified cluster, which remains stable throughout the hydrogen production cycle.

Oxidation State Changes and Electron Flow in Enzymatic Catalysis and Electrocatalysis through Wannier‐Function Analysis

In catalysis by metalloenzymes and in electrocatalysis by clusters related in structure and composition to the active components of such enzymes transition-metal atoms can play a central role in the catalyzed redox reactions. Changes to their oxidation states (OSs) are critical for understanding the reactions. The OS is a local property and we introduce a new, generally useful local method for determining OSs, their changes, and the associated bonding changes and electron flow. The method is based on computing optimally localized orbitals (OLOs). With this method, we analyze two cases, superoxide reductase (SOR) and a proposed hydrogen-producing model electrocatalyst [FeS(2)]/[FeFe](P), a modification of the active site of the diiron hydrogenase enzymes. Both utilize an under-coordinated Fe site where a one-electron reduction (for SOR) or a two-electron reduction (for [FeFe](P)) of the substrate occurs. We obtain the oxidation states of the Fe atoms and of their critical ligands, the changes of the bonds to those ligands, and the electron flow during the catalytic cycle, thereby demonstrating that OLOs constitute a powerful interpretive tool for unraveling reaction mechanisms by first-principles computations.

Multilevel Ultrafast Flexible Nanoscale Nonvolatile Hybrid Graphene Oxide–Titanium Oxide Memories

Graphene oxide (GO) resistive memories offer the promise of low-cost environmentally sustainable fabrication, high mechanical flexibility and high optical transparency, making them ideally suited to future flexible and transparent electronics applications. However, the dimensional and temporal scalability of GO memories, i.e., how small they can be made and how fast they can be switched, is an area that has received scant attention. Moreover, a plethora of GO resistive switching characteristics and mechanisms has been reported in the literature, sometimes leading to a confusing and conflicting picture. Consequently, the potential for graphene oxide to deliver high-performance memories operating on nanometer length and nanosecond time scales is currently unknown. Here we address such shortcomings, presenting not only the smallest (50 nm), fastest (sub-5 ns), thinnest (8 nm) GO-based memory devices produced to date, but also demonstrate that our approach provides easily accessible multilevel (4-level, 2-bit per cell) storage capabilities along with excellent endurance and retention performance-all on both rigid and flexible substrates. Via comprehensive experimental characterizations backed-up by detailed atomistic simulations, we also show that the resistive switching mechanism in our Pt/GO/Ti/Pt devices is driven by redox reactions in the interfacial region between the top (Ti) electrode and the GO layer.

Theoretical Design by First Principles Molecular Dynamics of a Bioinspired Electrode-Catalyst System for Electrocatalytic Hydrogen Production from Acidified Water.

Bacterial di-iron hydrogenases produce hydrogen efficiently from water. Accordingly, we have studied by first-principles molecular-dynamics simulations (FPMD) electrocatalytic hydrogen production from acidified water by their common active site, the [FeFe]H cluster, extracted from the enzyme and linked directly to the (100) surface of a pyrite electrode. We found that the cluster could not be attached stably to the surface via a thiol link analogous to that which attaches it to the rest of the enzyme, despite the similarity of the (100) pyrite surface to the Fe4S4 cubane to which it is linked in the enzyme. We report here a systematic sequence of modifications of the structure and composition of the cluster devised to maintain the structural stability of the pyrite/cluster complex in water throughout its hydrogen production cycle, an example of the molecular design of a complex system by FPMD.

Mechanism of H2 production by the [FeFe]H subcluster of di-iron hydrogenases: implications for abiotic catalysts.

To explore the possibility that the active center of the di-iron hydrogenases, the [FeFe] H subcluster, can serve by itself as an efficient hydrogen-producing catalyst, we perform comprehensive calculations of the catalytic properties of the subcluster in vacuo using first principles density functional theory. For completeness, we examine all nine possible geometrical isomers of the Fe(II)Fe(I) active-ready state and report in detail on the relevant ones that lead to the production of H 2. These calculations, carried out at the generalized gradient approximation level, indicate that the most efficient catalytic site in the isolated [FeFe] H subcluster is the Fe d center distal (d) to the [4Fe-4S] H cluster; the other iron center site, the proximal Fe p, also considered in this study, has much higher energy barriers. The pathways with the most favorable kinetics (lowest energy barrier to reaction) proceed along configurations with a CO ligand in a bridging position. The most favorable of these CO-bridging pathways start from isomers where the distal CN (-) ligand is in up position, the vacancy V in down position, and the remaining distal CO is either cis or trans with respect to the proximal CO. These isomers, not observed in the available enzyme X-ray structures, are only marginally less stable than the most stable nonbridging Fe d-CO-terminal isomer. Our calculations indicate that this CO-bridging CN-up isomer has a small barrier to production of H 2 that is compatible with the observed rate for the enzyme. These results suggest that catalysis of H 2 production could proceed on this stereochemically modified [FeFe] H subcluster alone, thus offering a promising target for functional bioinspired catalyst design.

Inherent stochasticity in phase-change memory devices

A two terminal nanoscale device showing inherent stochastic behavior can be a key enabler for a wide range of applications such as stochastic computing, machine learning and neuromorphic engineering. In this article we investigate the inherent stochasticity associated with two key attributes of phase-change memory devices, namely, threshold switching and memory switching. The physical origin of this stochasticity is traced to the differences in the atomic configurations of the amorphous phase created via the melt-quench process after each RESET operation, which is validated by simulation and experimental results. We also present experimental results for one specific application namely, a true random number generator.

Hydrogen production by the naked active site of the di-iron hydrogenases in water.

We explored the reactivity of the active center of the [FeFe]-hydrogenases detached from the enzyme and immersed in acidified water by first-principles Car-Parrinello molecular-dynamics simulations. We focused on the identification of the structures that are stable and metastable in acidified water and on their activity for hydrogen production. Our calculations revealed that the naked active center could be an efficient catalyst provided that electrons are transferred to the cluster. We found that both bridging and terminal isomers are present at equilibrium and that the bridging configuration is essential for efficient hydrogen production. The formation of the hydrogen molecule occurs via sequential protonations of the distal iron and of the N-atom of the S-CH(2)-NH-CH(2)-S chelating group. H(2) desorption does not involve a significant energy barrier, making the process very efficient at room temperature. We established that the bottleneck in the reaction is the direct proton transfer from water to the vacant site of the distal iron. Moreover, we found that even if the terminal isomer is present at the equilibrium, its strong local hydrophobicity prevents poisoning of the cluster.

Carbon-Based Resistive Memories

Carbon-based nonvolatile resistive memories are an emerging technology. Switching endurance remains a challenge in carbon memories based on tetrahedral amorphous carbon (ta-C). One way to counter this is by oxygenation to increase the repeatability of reversible switching. Here, we overview the current status of carbon memories. We then present a comparative study of oxygen-free and oxygenated carbon-based memory devices, combining experiments and molecular dynamics (MD) simulations.

Reactive potential for the study of phase-change materials: GeTe

We developed a classical potential to model phase-change materials based on the binary chalcogenide alloy of GeTe that are currently exploited for memory applications. Our potential is based on the recently proposed extension of the Tersoff potential plus additional terms to better reproduce the structure of the amorphous and the crystalline phases of GeTe. The parameters defining the potential reported in this work were fitted to reproduce the energies and forces of a database of reference structures obtained via density-functional theory molecular-dynamics simulations. This paper reports on the method used to construct the potential and on its validation against first-principles calculations either available in literature or part of this work. We found that the structural properties of amorphous GeTe were well reproduced. The advantage of the current implementation toward more flexible neural network-based methods is that most of the parameters can be reconnected to physical properties. Moreover, the relatively small number of parameters results in a simple implementation and facilitates the introductions of further interactions among additional species.

Multiscale Quantum Simulation of Resistance Switching in Amorphous Carbon

Abstract Ab initio calculations on the basis of quantum molecular dynamics CPMD (Car-Parrinello Molecular Dynamics) code are used to simulate the resistance-change in amorphous carbon. These simulations show that the resistance change is related to changes in the atomic structures of conducting dots due to thermal effects. Different scenarios of the temperature growth and possible annealing procedures are considered. The energy gap between two structural stages and the density of states at different temperatures are determined. The electronic density is used to identify conductive pathways through the system. A multiscale model of resistance switching based on the reduced Ehrenfest molecular dynamics is suggested. This computational model combines long-time-scale CPMD calculations of thermodynamic equilibrium states with the short-time-scale calculations of transitions to a new configurations using excited states of the electronic system. The simulations were performed on the IBM Blue Gene/P supercomputer at Moscow State University.