Structural and Electronic Rearrangements in Fe2S2, Fe3S4, and Fe4S4 Atomic Clusters under the Attack of NO, CO, and O2

Producción CientíficaWe report results, based on density functional theory–generalized gradient approximation calculations, that shed light on how NO, CO, and O2 interact with Fe2S2, Fe3S4, and Fe4S4 clusters and how they modify their structural and electronic properties. The interest in these small iron sulfide clusters comes from the fact that they are at the protein cores and that elucidating fundamental aspects of their interaction with those light molecules which are known to modify their functionality may help in understanding complex behaviors in biological systems. CO and NO are found to bind molecularly, leading to moderate relaxations in the clusters, but nevertheless to changes in the spin-polarized electronic structure and related properties. In contrast, dissociative chemisorption of O2 is much more stable than molecular adsorption, giving rise to significant structural distortions, particularly in Fe4S4 that splits into two Fe2S2 subclusters. As a consequence, oxygen tends to strongly reduce the spin polarization in Fe and to weaken the Fe–Fe interaction inducing antiparallel couplings that, in the case of Fe4S4, clearly arise from indirect Fe–Fe exchange coupling mediated by O. The three molecules (particularly CO) enhance the stability of the iron–sulfur clusters. This increase is noticeably more pronounced for Fe2S2 than for the other iron–sulfur clusters of different compositions, a result that correlates with the fact that in recent experiments of CO reaction with FemSm (m = 1–4), the Fe2S2CO product results as a prominent one.Junta de Castilla y León (Ref. project VA124G18)Ministerio de Economía, Industria y Competitividad (Project PGC2018-093745-B-I00) and FEDE

Reflectivity Anisotropy Spectra of Cu- and Ag- (110) surfaces from {\it ab initio} theory

We are able to disentagle the effects of the intraband and interband parts of the bulk dielectric function on the bare dielectric anisotropy of the surface. We show how the position, sign and amplitude of the structures observed in such spectra depend on the above quantities. The lineshape of all the calculated structures agree very well with the ones observed experimentally for samples treated by suitable surface cleaning. In particular, we reproduce the observed single peak structure of Ag at high energy, found to represent a state of the clean surface different from the one giving the originally observed double peak structure. This results is not reproduced by the 'local field' model.Comment: 4 pages, 3 figures. submitted to Phys. Rev. Let

Magnetism of small V clusters embedded in a Cu fcc matrix: an ab initio study

We present extensive first principles density functional theory (DFT) calculations dedicated to analyze the magnetic and electronic properties of small V$_{n}$ clusters (n=1,2,3,4,5,6) embedded in a Cu fcc matrix. We consider different cluster structures such as: i) a single V impurity, ii) several V$_{2}$ dimers having different interatomic distance and varying local atomic environment, iii) V$_{3}$ and iv) V$_{4}$ clusters for which we assume compact as well as 2- and 1-dimensional atomic configurations and finally, in the case of the v) V$_{5}$ and vi) V$_{6}$ structures we consider a square pyramid and a square bipyramid together with linear arrays, respectively. In all cases, the V atoms are embedded as substitutional impurities in the Cu network. In general, and as in the free standing case, we have found that the V clusters tend to form compact atomic arrays within the cooper matrix. Our calculated non spin-polarized density of states at the V sites shows a complex peaked structure around the Fermi level that strongly changes as a function of both the interatomic distance and local atomic environment, a result that anticipates a non trivial magnetic behavior. In fact, our DFT calculations reveal, in each one of our clusters systems, the existence of different magnetic solutions (ferromagnetic, ferrimagnetic, and antiferromagnetic) with very small energy differences among them, a result that could lead to the existence of complex finite-temperature magnetic properties. Finally, we compare our results with recent experimental measurements.Comment: 7 pages and 4 figure

Band-width control in a perovskite-type 3d^1 correlated metal Ca_1-xSr_xVO_3. II. Optical spectroscopy investigation

Optical conductivity spectra of single crystals of Ca_1-xSr_xVO_3 have been studied to elucidate how the electronic behavior depends on the strength of the electron correlation without changing the nominal number of electrons per vanadium atom. The effective mass deduced by the analysis of the Drude-like contribution do not show critical enhancement, even though the system is close to the Mott transition. Besides the Drude-like contribution, two anomalous features were observed in the optical conductivity spectra of the intraband transition within the 3d band. These features can be assigned to transitions involving the incoherent and coherent bands near the Fermi level. The large spectral weight redistribution in this system, however, does not involve a large mass enhancement.Comment: 12 pages in a Phys. Rev. B camera-ready format with 16 EPS figures embedded. LaTeX 2.09 source file using "camera.sty" and "prbplug.sty" provided by N. Shirakawa. For OzTeX (Macintosh), use "ozfig.sty" instead of "psfig.sty". "ozfig.sty" can be also obtained by e-mail request to N. Shirakawa: . Submitted to Phys. Rev. B. See "Part I (by Inoue et al.)" at cond-mat/980107

Orbital Physics in the Perovskite Ti Oxides

In the perovskite Ti oxide RTiO3 (R=rare-earth ions), the Ti t2g orbitals and spins in the 3d^1 state couple each other through the strong electron correlations, resulting in a rich variety of orbital-spin phases. The origin and nature of orbital-spin states of these Mott insulators have been intensively studied. In this article, we review the studies on orbital physics in the perovskite titanates. We focus on the following three topics: (1) the origin and nature of the ferromagnetism as well as the orbital ordering in the compounds with relatively small R ions such as GdTiO3 and YTiO3, (2) the origin of the G-type antiferromagnetism and the orbital state in LaTiO3, and (3) the orbital-spin structures in other AFM(G) compounds with relatively large R ions (R=Ce, Pr, Nd and Sm). On the basis of these discussions, we discuss the whole phase diagram together with mechanisms of the magnetic phase transition. We also show that the Ti t2g degeneracy is inherently lifted in the titanates, which allows the single-band descriptions of the ground-state and low-energy electronic structures as a good starting point. Our analyses indicate that these compounds offer touchstone materials described by the single-band Hubbard model on the cubic lattice. From this insight, we also reanalyze the hole-doped titanates. Experimentally revealed filling-dependent and bandwidth-dependent properties and the critical behavior of the metal-insulator transitions are discussed in the light of theories based on the single-band Hubbard models.Comment: Review article, 26 pages, to appear in New Journal of Physic

Cation-swapped homogeneous nanoparticles in perovskite oxides for high power density

Exsolution has been intensively studied in the fields of energy conversion and storage as a method for the preparation of catalytically active and durable metal nanoparticles. Under typical conditions, however, only a limited number of nanoparticles can be exsolved from the host oxides. Herein, we report the preparation of catalytic nanoparticles by selective exsolution through topotactic ion exchange, where deposited Fe guest cations can be exchanged with Co host cations in PrBaMn1.7Co0.3O5+delta. Interestingly, this phenomenon spontaneously yields the host PrBaMn1.7Fe0.3O5+delta, liberating all the Co cations from the host owing to the favorable incorporation energy of Fe into the lattice of the parent host (Delta E-incorporation = -0.41 eV) and the cation exchange energy (Delta E-exchange = -0.34 eV). Remarkably, the increase in the number of exsolved nanoparticles leads to their improved catalytic activity as a solid oxide fuel cell electrode and in the dry reforming of methane

The interaction between the proliferating macroalga Asparagopsis taxiformis and the coral Astroides calycularis induces changes in microbiome and metabolomic fingerprints

Mediterranean Sea ecosystems are considered as hotspots of biological introductions, exposed to possible negative effects of non-indigenous species. In such temperate marine ecosystems, macroalgae may be dominant, with a great percentage of their diversity represented by introduced species. Their interaction with temperate indigenous benthic organisms have been poorly investigated. To provide new insights, we performed an experimental study on the interaction between the introduced proliferative red alga Asparagopsis taxiformis and the indigenous Mediterranean coral Astroides calycularis. The biological response measurements included meta-barcoding of the associated microbial communities and metabolomic fingerprinting of both species. Significant changes were detected among both associated microbial communities, the interspecific differences decreasing with stronger host interaction. No short term effects of the macroalga on the coral health, neither on its polyp activity or its metabolism, were detected. In contrast, the contact interaction with the coral induced a change in the macroalgal metabolomic fingerprint with a significant increase of its bioactivity against the marine bacteria Aliivibrio fischeri. This induction was related to the expression of bioactive metabolites located on the macroalgal surface, a phenomenon which might represent an immediate defensive response of the macroalga or an allelopathic offense against coral.ERA-NET Biome project "SEAPROLIF"; CNRS; Provence Alpes Cote d'Azur Region; TOTAL Fundation; Fundacao para a Ciencia e a Tecnologia (FCT) [Netbiome/0002/2011]; FCT fellowships [SFRH/BPD/63703/2009, SFRH/BPD/107878/2015]info:eu-repo/semantics/publishedVersio

Computational models in plant-pathogen interactions: the case of Phytophthora infestans

<p>Abstract</p> <p>Background</p> <p><it>Phytophthora infestans </it>is a devastating oomycete pathogen of potato production worldwide. This review explores the use of computational models for studying the molecular interactions between <it>P. infestans </it>and one of its hosts, <it>Solanum tuberosum</it>.</p> <p>Modeling and conclusion</p> <p>Deterministic logistics models have been widely used to study pathogenicity mechanisms since the early 1950s, and have focused on processes at higher biological resolution levels. In recent years, owing to the availability of high throughput biological data and computational resources, interest in stochastic modeling of plant-pathogen interactions has grown. Stochastic models better reflect the behavior of biological systems. Most modern approaches to plant pathology modeling require molecular kinetics information. Unfortunately, this information is not available for many plant pathogens, including <it>P. infestans</it>. Boolean formalism has compensated for the lack of kinetics; this is especially the case where comparative genomics, protein-protein interactions and differential gene expression are the most common data resources.</p

Analyses of genome architecture and gene expression reveal novel candidate virulence factors in the secretome of Phytophthora infestans

<p>Abstract</p> <p>Background</p> <p><it>Phytophthora infestans </it>is the most devastating pathogen of potato and a model organism for the oomycetes. It exhibits high evolutionary potential and rapidly adapts to host plants. The <it>P. infestans </it>genome experienced a repeat-driven expansion relative to the genomes of <it>Phytophthora sojae </it>and <it>Phytophthora ramorum </it>and shows a discontinuous distribution of gene density. Effector genes, such as members of the RXLR and Crinkler (CRN) families, localize to expanded, repeat-rich and gene-sparse regions of the genome. This distinct genomic environment is thought to contribute to genome plasticity and host adaptation.</p> <p>Results</p> <p>We used <it>in silico </it>approaches to predict and describe the repertoire of <it>P. infestans </it>secreted proteins (the secretome). We defined the "plastic secretome" as a subset of the genome that (i) encodes predicted secreted proteins, (ii) is excluded from genome segments orthologous to the <it>P. sojae </it>and <it>P. ramorum </it>genomes and (iii) is encoded by genes residing in gene sparse regions of <it>P. infestans </it>genome. Although including only ~3% <it>of P. infestans </it>genes, the plastic secretome contains ~62% of known effector genes and shows >2 fold enrichment in genes induced <it>in planta</it>. We highlight 19 plastic secretome genes induced <it>in planta </it>but distinct from previously described effectors. This list includes a trypsin-like serine protease, secreted oxidoreductases, small cysteine-rich proteins and repeat containing proteins that we propose to be novel candidate virulence factors.</p> <p>Conclusions</p> <p>This work revealed a remarkably diverse plastic secretome. It illustrates the value of combining genome architecture with comparative genomics to identify novel candidate virulence factors from pathogen genomes.</p