Iron-sulfur peptides mimicking ferredoxin for an efficient electron transfer to hydrogenase.

In the green alga Chlamydomonas reinhardtii, hydrogenase HydA1 converts protons and electrons to H2 at the H-cluster, which includes a [4Fe-4S] cluster linked to a [2Fe] cluster. The yield of H2 is limited by the electron transfer to HydA1, mediated by the iron-sulfur unit of a photosynthetic electron transfer ferredoxin (PetF). In this study, I have investigated by molecular dynamics and the hybrid quantum mechanics/molecular mechanics method two canonical iron-sulfur peptides (PM1 and FBM) that hold potential as PetF replacements. Using a docking approach, I predict that the distance between the two iron-sulfur clusters in FBM/HydA1 is shorter than in PM1/HydA1, ensuring a greater electron transfer rate. This finding is in line with the reported higher H2 production rates for FBM/HydA1. I also show that the redox potential of these peptides, and therefore their electron transfer properties, can be changed by single-residue mutations in the secondary coordination sphere of their cluster. In particular, I have designed a PM1 variant that disrupts the hydrogen-bonding network between water and the cluster, shifting the redox potential negatively compared to PM1. These results will guide experiments aimed at replacing PetF with peptides that can unlock the biotechnological potential of the alga.

Electrocatalytic OER behavior of the Bi-Fe-O system: an understanding from the perspective of the presence of oxygen vacancies.

This study aims to understand and correlate the role of the nature and relative concentration of oxygen vacancies with the trend observed in the OER with the Bi-Fe-O system. To understand this, we first investigated the system of oxides using X-ray photoelectron spectroscopy (XPS) and electron paramagnetic resonance (EPR), which revealed the presence of oxygen vacancies in the system. Density functional theory (DFT) was employed to investigate the relative concentration of these vacancies by calculating their formation energies. Positron annihilation lifetime spectroscopy (PALS) was carried out to understand the nature of these oxygen vacancies. We observed that the presence of a higher concentration of monovacancies created due to the absence of oxygen from the structure of Bi2Fe4O9 was mainly responsible for the high performance of the oxide towards the OER compared to that of the other oxides viz-BiFeO3 and Bi25FeO40 of the Bi-Fe-O system.

Anomalous Viscosity of a Racemate: A Simple Experiment Demonstrating Chirally Induced Spin Selectivity.

It has been known for over a century that racemic solutions of hydrogen-bonded compounds are less viscous than their component enantiomers, but this fact has so far remained unexplained. Here we confirm it using enantiomers of lactic acid and compare it to molecular dynamics (MD) simulations of lactic acid viscosity. The effect is absent in classical MD. We suggest that the anomalous viscosity of racemates may be due to a recently discovered magnetic intermolecular force due to spin-dependent charge reorganization.

Residues surrounding the active centre of carbon monoxide dehydrogenase are key in converting [Formula: see text] to CO.

The enzyme carbon monoxide dehydrogenase is capable of efficiently converting [Formula: see text] to CO and, therefore, can enable an affordable [Formula: see text] recycling strategy. The reduction of [Formula: see text] occurs at a peculiar nickel-iron-sulfur cluster, following a mechanism that remains little understood. In this study, we have used ab initio molecular dynamics simulations to explore the free energy landscape of the reaction. We predict the existence of a COOH ligand that strongly interacts with the surrounding protein residues and favours a mechanism where a [Formula: see text] molecule is eliminated before CO. We have taken advantages of the insights offered by our simulations to revisit the catalytic mechanism and the role of the residues surrounding the active centre in particular, thus assisting in the design of inorganic catalysts that mimic the enzyme.

The mechanism underlying the functionalisation of cobalt nanoparticles by carboxylic acids: a first-principles computational study.

The promise of biocompatible magnetic nanoparticles with high magnetic saturation in the implementation as drug carriers and hyperthermia agents has generated significant interest in functionalised cobalt nanoparticles. Carboxylic acid coatings on metallic nanoparticles have been shown as an attractive option owing to their respectable stability and biocompatibility. However, only limited information is available on the molecular mechanism leading to the formation of such protective coatings. In this study, ab initio molecular dynamics simulations have been used to unravel the functionalisation mechanism starting from a neutral cobalt cluster and valeric acid molecules. Three stages were detected in the coating process: (i) rapid initial adsorption of acid molecules, (ii) simultaneous adsorption of new molecules and dissociation of those already interacting with the cluster, and, finally, (iii) grouping of dissociated hydrogen atoms and subsequent desorption of acid molecules. The fate of the hydrogen atoms was probed through a combination of static and dynamic ab initio modelling approaches, which predicted H2 generation with favourable energetics. A better understanding of the functionalisation and interaction mechanisms will aid the rational design of biocompatible cobalt nanoparticles for various applications.

Binding modes of carboxylic acids on cobalt nanoparticles.

Owing to their high saturation magnetisation, cobalt nanoparticles hold significant potential for the hyperthermia treatment of tumours. Covalent binding of carboxylic acids to the nanoparticles can induce biocompatibility, whilst also preventing the formation of surface oxides which reduce the magnetic properties of cobalt. Understanding the origin of the acid-metal interaction is key, yet probably the most experimentally challenging step, for the rational design of such entities. In this density functional theory study, we use static calculations to establish that a 57-atom Co cluster is the smallest model able to reproduce the adsorption behaviour of carboxylic acids, and ab initio metadynamics to obtain the structure and the free energy landscape for its interaction with valeric acid. Our simulations show that a bridging bidentate binding mode has a stronger affinity compared to monodentate binding, with energetically high transition barriers between the two. A chelate interaction mode of two carboxyl oxygen atoms can be formed as an intermediate. These results clarify the organic-inorganic interactions in the cobalt-acid system, providing a basis for the rational design of biocompatible metallic nanoparticles.

Mixing thermodynamics and electronic structure of the Pt1-x Ni x (0 ≤ x ≤ 1) bimetallic alloy.

The development of affordable bifunctional platinum alloys as electrode materials for the oxygen reduction reaction (ORR) and oxygen evolution reaction (OER) remains one of the biggest challenges for the transition towards renewable energy sources. Yet, there is very little information on the optimal ratio between platinum and the transition metal used in the alloy and its impact on the electronic properties. Here, we have employed spin-polarised density functional simulations with long-range dispersion corrections [DFT-D3-(BJ)], to investigate the thermodynamics of mixing, as well as the electronic and magnetic properties of the Pt1-x Ni x solid solution. The Ni incorporation is an exothermic process and the alloy composition Pt0.5Ni0.5 is the most thermodynamically stable. The Pt0.5Ni0.5 solid solution is highly ordered as it is composed mainly of two symmetrically inequivalent configurations of homogeneously distributed atoms. We have obtained the atomic projections of the electronic density of states and band structure, showing that the Pt0.5Ni0.5 alloy has metallic character. The suitable electronic properties of the thermodynamically stable Pt0.5Ni0.5 solid solution shows promise as a sustainable catalyst for future regenerative fuel cells.

Thermal Properties and Segregation Behavior of Pt Nanowires Modified with Au, Ag, and Pd Atoms: A Classical Molecular Dynamics Study.

Platinum nanowires (NWs) have been reported to be catalytically active toward the oxygen reduction reaction (ORR). The edge modification of Pt NWs with metals M (M = Au, Ag, or Pd) may have a positive impact on the overall ORR activity by facilitating diffusion of adsorbed oxygen, Oads, and hydroxyl groups, OHads, between the {001} and {111} terraces. In the present study, we have employed classical molecular dynamics simulations to investigate the segregation behavior of Au, Ag, and Pd decorating the edges of Pt NWs. We observe that, under vacuum conditions, Pd prefers to diffuse toward the core rather than stay on the NW surface. Ag and Au atoms are mobile at temperatures as low as 900 K; they remain on the surface but do not appear to be preferentially more stable at edge sites. To effect segregation of Au and Ag atoms toward the edge, we propose annealing in the presence of different reactive gas environments. Overall, our study suggests potential experimental steps required for the synthesis of Pt nanowires and nanoparticles with improved Oads and OHads interfacet diffusion rates and consequently an improved ORR activity.

A highly reactive precursor in the iron sulfide system.

Iron sulfur (Fe-S) phases have been implicated in the emergence of life on early Earth due to their catalytic role in the synthesis of prebiotic molecules. Similarly, Fe-S phases are currently of high interest in the development of green catalysts and energy storage. Here we report the synthesis and structure of a nanoparticulate phase (FeSnano) that is a necessary solid-phase precursor to the conventionally assumed initial precipitate in the iron sulfide system, mackinawite. The structure of FeSnano contains tetrahedral iron, which is compensated by monosulfide and polysulfide sulfur species. These together dramatically affect the stability and enhance the reactivity of FeSnano.

Calcium Phosphate Deposition on Planar and Stepped (101) Surfaces of Anatase TiO2: Introducing an Interatomic Potential for the TiO2/Ca-PO4/Water Interface.

Titanium is commonly employed in orthopaedic and dental surgery, owing to its good mechanical properties. The titanium metal is usually passivated by a thin layer of its oxide, and in order to promote its integration with the biological tissue, it is covered by a bioactive material such as calcium phosphate (CaP). Here, we have investigated the deposition of calcium and phosphate species on the anatase phase of titanium dioxide (TiO2) using interatomic potential-based molecular dynamics simulations. We have combined different force fields developed for CaP, TiO2, and water, benchmarking the results against density functional theory calculations. On the basis of our study, we consider that the new parameters can be used successfully to study the nucleation of CaP on realistic anatase and rutile TiO2 nanoparticles, including surface defects.

CO2 interaction with violarite (FeNi2S4) surfaces: a dispersion-corrected DFT study.

The unbridled emissions of gases derived from the use of fossil fuels have led to an excessive concentration of carbon dioxide (CO2) in the atmosphere with concomitant problems to the environment. It is therefore imperative that new cost-effective catalysts are developed to mitigate the resulting harmful effects through the activation and conversion of CO2 molecules. In this paper, we have used calculations based on the density functional theory (DFT), including two semi-empirical approaches for the long-range dispersion interactions (-D2 and -D3), to explore the interaction of CO2 with the surfaces of spinel-structured violarite (FeNi2S4). This ternary sulfide contains iron ions in the highest possible oxidation state, while the nickel atoms are in the mixed 2+/3+ valence state. We found that CO2 interaction with violarite is only moderate due to the repulsion between the oxygen lone pairs and the electronic clouds of the sulfur surface atoms. This suggests that the CO2 activation is not dictated by the presence of nickel, as compared to the pure iron-isomorph greigite (Fe3S4). These results differ from findings in (Ni,Fe) ferredoxin enzymes, where the Ni/Fe ratio influences the redox potential, which suggests that the periodic crystal structure of violarite may hinder its redox capability.

Structure and dynamics of water at the mackinawite (001) surface.

We present a molecular dynamics investigation of the properties of water at the interface with the mackinawite (001) surface. We find water in the first layer to be characterised by structural properties which are reminiscent of hydrophobic substrates, with the bulk behaviour being recovered beyond the second layer. In addition, we show that the mineral surface reduces the mobility of interfacial water compared to the bulk. Finally, we discuss the important differences introduced by simulating water under conditions of high temperature and pressure, a scenario relevant to geochemistry.

Aqueous Fe2S2 cluster: structure, magnetic coupling, and hydration behaviour from Hubbard U density functional theory.

We present a DFT + U investigation of the all-ferrous Fe2S2 cluster in aqueous solution. We determine the value of U by tuning the geometry of the cluster in the gas-phase to that obtained by the highly accurate CCSD(T) method. When the optimised value of U is employed for the aqueous Fe2S2 cluster (Fe2S2(aq)), the resulting geometry agrees well with the X-ray diffraction structure, while the magnetic coupling is in line with the estimate from Mössbauer data. Molecular dynamics trajectories predict Fe2S2(aq) to be stable in water, regardless of the introduction of U. However, significant differences arise in the geometry, hydration, and exchange constant of the solvated clusters.

Protonated Carboxyl Anchor for Stable Adsorption of Ru N749 Dye (Black Dye) on a TiO2 Anatase (101) Surface.

We have investigated the adsorption stability of ruthenium N749 dye [black dye (BD)], a highly efficient dye for dye-sensitized solar cells (DSCs), through protonated and deprotonated carboxyl group anchors on a TiO2 anatase (101) surface by using first-principles calculations. Geometry optimizations of the surface system with a supercell and the UV-visible spectrum calculation of the optimized dye structure were carried out. Among the configurations with one and two anchors, the BD adsorption anchored with one protonated carboxyl group was found to be the most stable, in contrast to most previous reports. Hydrogen bonding between the proton retained in BD and the surface oxygen is responsible for the stability of the protonated anchor. We confirmed that the calculated UV-visible spectrum of the most stable dye structure shows the best consistency with the experimental data. It is also demonstrated that the electronic density of states largely depends on the proton position. This novel aspect of adsorption via a protonated carboxyl anchor gives a new perspective for interfacial electronic processes of DSCs.