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Sample records for heme electronic structure

  1. Heme isomers substantially affect heme's electronic structure and function

    DEFF Research Database (Denmark)

    Kepp, Kasper Planeta

    2017-01-01

    Inspection of heme protein structures in the protein data bank reveals four isomers of heme characterized by different relative orientations of the vinyl side chains; remarkably, all these have been reported in multiple protein structures. Density functional theory computations explain this as du...

  2. Structural Characterization of Heme Environmental Mutants of CgHmuT that Shuttles Heme Molecules to Heme Transporters

    Directory of Open Access Journals (Sweden)

    Norifumi Muraki

    2016-05-01

    Full Text Available Corynebacteria contain a heme uptake system encoded in hmuTUV genes, in which HmuT protein acts as a heme binding protein to transport heme to the cognate transporter HmuUV. The crystal structure of HmuT from Corynebacterium glutamicum (CgHmuT reveals that heme is accommodated in the central cleft with His141 and Tyr240 as the axial ligands and that Tyr240 forms a hydrogen bond with Arg242. In this work, the crystal structures of H141A, Y240A, and R242A mutants were determined to understand the role of these residues for the heme binding of CgHmuT. Overall and heme environmental structures of these mutants were similar to those of the wild type, suggesting that there is little conformational change in the heme-binding cleft during heme transport reaction with binding and the dissociation of heme. A loss of one axial ligand or the hydrogen bonding interaction with Tyr240 resulted in an increase in the redox potential of the heme for CgHmuT to be reduced by dithionite, though the wild type was not reduced under physiological conditions. These results suggest that the heme environmental structure stabilizes the ferric heme binding in CgHmuT, which will be responsible for efficient heme uptake under aerobic conditions where Corynebacteria grow.

  3. Mini Heme-Proteins: Designability of Structure and Diversity of Functions.

    Science.gov (United States)

    Rai, Jagdish

    2017-08-30

    Natural heme proteins may have heme bound to poly-peptide chain as a cofactor via noncovalent forces or heme as a prosthetic group may be covalently bound to the proteins. Nature has used porphyrins in diverse functions like electron transfer, oxidation, reduction, ligand binding, photosynthesis, signaling, etc. by modulating its properties through diverse protein matrices. Synthetic chemists have tried to utilize these molecules in equally diverse industrial and medical applications due to their versatile electro-chemical and optical properties. The heme iron has catalytic activity which can be modulated and enhanced for specific applications by protein matrix around it. Heme proteins can be designed into novel enzymes for sterio specific catalysis ranging from oxidation to reduction. These designed heme-proteins can have applications in industrial catalysis and biosensing. A peptide folds around heme easily due to hydrophobic effect of the large aromatic ring of heme. The directional property of co-ordinate bonding between peptide and metal ion in heme further specifies the structure. Therefore heme proteins can be easily designed for targeted structure and catalytic activity. The central aromatic chemical entity in heme viz. porphyrin is a very ancient molecule. Its presence in the prebiotic soup and in all forms of life suggests that it has played a vital role in the origin and progressive evolution of living organisms. Porphyrin macrocycles are highly conjugated systems composed of four modified pyrrole subunits interconnected at their α -carbon atoms via methine (=CH-) bridges. Initial minimalist models of hemoproteins focused on effect of heme-ligand co-ordinate bonding on chemical reactivity, spectroscopy, electrochemistry and magnetic properties of heme. The great sensitivity of these spectroscopic features of heme to its surrounding makes them extremely useful in structural elucidation of designed heme-peptide complexes. Therefore heme proteins are

  4. HemeBIND: a novel method for heme binding residue prediction by combining structural and sequence information

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    Hu Jianjun

    2011-05-01

    Full Text Available Abstract Background Accurate prediction of binding residues involved in the interactions between proteins and small ligands is one of the major challenges in structural bioinformatics. Heme is an essential and commonly used ligand that plays critical roles in electron transfer, catalysis, signal transduction and gene expression. Although much effort has been devoted to the development of various generic algorithms for ligand binding site prediction over the last decade, no algorithm has been specifically designed to complement experimental techniques for identification of heme binding residues. Consequently, an urgent need is to develop a computational method for recognizing these important residues. Results Here we introduced an efficient algorithm HemeBIND for predicting heme binding residues by integrating structural and sequence information. We systematically investigated the characteristics of binding interfaces based on a non-redundant dataset of heme-protein complexes. It was found that several sequence and structural attributes such as evolutionary conservation, solvent accessibility, depth and protrusion clearly illustrate the differences between heme binding and non-binding residues. These features can then be separately used or combined to build the structure-based classifiers using support vector machine (SVM. The results showed that the information contained in these features is largely complementary and their combination achieved the best performance. To further improve the performance, an attempt has been made to develop a post-processing procedure to reduce the number of false positives. In addition, we built a sequence-based classifier based on SVM and sequence profile as an alternative when only sequence information can be used. Finally, we employed a voting method to combine the outputs of structure-based and sequence-based classifiers, which demonstrated remarkably better performance than the individual classifier alone

  5. Heme and erythropoieis: more than a structural role

    OpenAIRE

    Chiabrando, Deborah; Mercurio, Sonia; Tolosano, Emanuela

    2014-01-01

    Erythropoiesis is the biological process that consumes the highest amount of body iron for heme synthesis. Heme synthesis in erythroid cells is finely coordinated with that of alpha (α) and beta (β)-globin, resulting in the production of hemoglobin, a tetramer of 2α- and 2β-globin chains, and heme as the prosthetic group. Heme is not only the structural component of hemoglobin, but it plays multiple regulatory roles during the differentiation of erythroid precursors since it controls its own ...

  6. The DFT-DVM theoretical study of the differences of quadrupole splitting and the iron electronic structure for the rough heme models for {alpha}- and {beta}-subunits in deoxyhemoglobin and for deoxymyoglobin

    Energy Technology Data Exchange (ETDEWEB)

    Yuryeva, E. I. [Institute of Solid State Chemistry of the Ural Branch of the Russian Academy of Sciences (Russian Federation); Oshtrakh, M. I., E-mail: oshtrakh@mail.utnet.ru [Ural State Technical University-UPI, Faculty of Physical Techniques and Devices for Quality Control (Russian Federation)

    2008-01-15

    Quantum chemical calculations of the iron electron structure and {sup 57}Fe quadrupole splitting were made by density functional theory and X{alpha} discrete variation method for the rough heme models for {alpha}- and {beta}-subunits in deoxyhemoglobin and for deoxymyoglobin accounting stereochemical differences of the active sites in native proteins. The calculations revealed differences of quadrupole splitting temperature dependences for three models indicating sensitivity of quadrupole splitting and Fe(II) electronic structure to small variations of iron stereochemistry.

  7. Nuclear resonance vibrational spectroscopy applied to [Fe(OEP)(NO)]: the vibrational assignments of five-coordinate ferrous heme-nitrosyls and implications for electronic structure.

    Science.gov (United States)

    Lehnert, Nicolai; Galinato, Mary Grace I; Paulat, Florian; Richter-Addo, George B; Sturhahn, Wolfgang; Xu, Nan; Zhao, Jiyong

    2010-05-03

    -O bonds are 2.83-2.94 (based on the DFT functional applied) and about 12.15 mdyn/A, respectively. The electronic structures of 5C ferrous heme-nitrosyls in different model complexes are then analyzed, and variations in their properties based on different porphyrin substituents are explained. Finally, the shortcomings of different DFT functionals in describing the axial FeNO subunit in heme-nitrosyls are elucidated.

  8. Heme and erythropoieis: more than a structural role.

    Science.gov (United States)

    Chiabrando, Deborah; Mercurio, Sonia; Tolosano, Emanuela

    2014-06-01

    Erythropoiesis is the biological process that consumes the highest amount of body iron for heme synthesis. Heme synthesis in erythroid cells is finely coordinated with that of alpha (α) and beta (β)-globin, resulting in the production of hemoglobin, a tetramer of 2α- and 2β-globin chains, and heme as the prosthetic group. Heme is not only the structural component of hemoglobin, but it plays multiple regulatory roles during the differentiation of erythroid precursors since it controls its own synthesis and regulates the expression of several erythroid-specific genes. Heme is synthesized in developing erythroid progenitors by the stage of proerythroblast, through a series of eight enzymatic reactions divided between mitochondria and cytosol. Defects of heme synthesis in the erythroid lineage result in sideroblastic anemias, characterized by microcytic anemia associated to mitochondrial iron overload, or in erythropoietic porphyrias, characterized by porphyrin deposition in erythroid cells. Here, we focus on the heme biosynthetic pathway and on human erythroid disorders due to defective heme synthesis. The regulatory role of heme during erythroid differentiation is discussed as well as the heme-mediated regulatory mechanisms that allow the orchestration of the adaptive cell response to heme deficiency. Copyright© Ferrata Storti Foundation.

  9. Multi-heme Cytochromes in Shewanella oneidensis MR-1: Structures, functions and opportunities

    Energy Technology Data Exchange (ETDEWEB)

    Breuer, Marian; Rosso, Kevin M.; Blumberger, Jochen; Butt, Julea N.

    2014-11-05

    Multi-heme cytochromes are employed by a range of microorganisms to transport electrons over distances of up to tens of nanometers. Perhaps the most spectacular utilization of these proteins is in the reduction of extracellular solid substrates, including electrodes and insoluble mineral oxides of Fe(III) and Mn(III/IV), by species of Shewanella and Geobacter. However, multi-heme cytochromes are found in numerous and phylogenetically diverse prokaryotes where they participate in electron transfer and redox catalysis that contributes to biogeochemical cycling of N, S and Fe on the global scale. These properties of multi-heme cytochromes have attracted much interest and contributed to advances in bioenergy applications and bioremediation of contaminated soils. Looking forward there are opportunities to engage multi-heme cytochromes for biological photovoltaic cells, microbial electrosynthesis and developing bespoke molecular devices. As a consequence it is timely to review our present understanding of these proteins and we do this here with a focus on the multitude of functionally diverse multi-heme cytochromes in Shewanella oneidensis MR-1. We draw on findings from experimental and computational approaches which ideally complement each other in the study of these systems: computational methods can interpret experimentally determined properties in terms of molecular structure to cast light on the relation between structure and function. We show how this synergy has contributed to our understanding of multi-heme cytochromes and can be expected to continue to do so for greater insight into natural processes and their informed exploitation in biotechnologies.

  10. Protein Machineries Involved in the Attachment of Heme to Cytochrome c: Protein Structures and Molecular Mechanisms

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    Carlo Travaglini-Allocatelli

    2013-01-01

    Full Text Available Cytochromes c (Cyt c are ubiquitous heme-containing proteins, mainly involved in electron transfer processes, whose structure and functions have been and still are intensely studied. Surprisingly, our understanding of the molecular mechanism whereby the heme group is covalently attached to the apoprotein (apoCyt in the cell is still largely unknown. This posttranslational process, known as Cyt c biogenesis or Cyt c maturation, ensures the stereospecific formation of the thioether bonds between the heme vinyl groups and the cysteine thiols of the apoCyt heme binding motif. To accomplish this task, prokaryotic and eukaryotic cells have evolved distinctive protein machineries composed of different proteins. In this review, the structural and functional properties of the main maturation apparatuses found in gram-negative and gram-positive bacteria and in the mitochondria of eukaryotic cells will be presented, dissecting the Cyt c maturation process into three functional steps: (i heme translocation and delivery, (ii apoCyt thioreductive pathway, and (iii apoCyt chaperoning and heme ligation. Moreover, current hypotheses and open questions about the molecular mechanisms of each of the three steps will be discussed, with special attention to System I, the maturation apparatus found in gram-negative bacteria.

  11. Comparative analysis of the heme iron electronic structure and stereochemistry in tetrameric rabbit hemoglobin and monomeric soybean leghemoglobin a using Mössbauer spectroscopy with a high velocity resolution

    Science.gov (United States)

    Alenkina, I. V.; Kumar, A.; Berkovsky, A. L.; Oshtrakh, M. I.

    2018-02-01

    A comparative study of tetrameric rabbit hemoglobin and monomeric soybean leghemoglobin a in the oxy- and deoxy-forms was carried out using 57Fe Mössbauer spectroscopy with a high velocity resolution in order to analyze the heme iron electronic structure and stereochemistry in relation to the Mössbauer hyperfine parameters. The Mössbauer spectra of tetrameric rabbit hemoglobin in both forms were fitted using two quadrupole doublets related to the 57Fe in ɑ- and β-subunits. In contrast, the Mössbauer spectra of monomeric soybean leghemoglobin a were fitted using: (i) two quadrupole doublets for the oxy-form related to two conformational states of the distal His E7 imidazole ring and different hydrogen bonding of oxygen molecule in the oxy-form and (ii) using three quadrupole doublets for deoxy-form related to three conformational states of the proximal His F8 imidazole ring. Small variations of Mössbauer hyperfine parameters related to small differences in the heme iron electronic structure and stereochemistry in tetrameric rabbit hemoglobin and monomeric soybean leghemoglobin a are discussed.

  12. Electrochemistry and electron paramagnetic resonance spectroscopy of cytochrome c and its heme-disrupted analogs.

    Science.gov (United States)

    Novak, David; Mojovic, Milos; Pavicevic, Aleksandra; Zatloukalova, Martina; Hernychova, Lenka; Bartosik, Martin; Vacek, Jan

    2018-02-01

    Cytochrome c (cyt c) is one of the most studied conjugated proteins due to its electron-transfer properties and ability to regulate the processes involved in homeostasis or apoptosis. Here we report an electrochemical strategy for investigating the electroactivity of cyt c and its analogs with a disrupted heme moiety, i.e. apocytochrome c (acyt c) and porphyrin cytochrome c (pcyt c). The electrochemical data are supplemented with low-temperature and spin-probe electron paramagnetic resonance (EPR) spectroscopy. The main contribution of this report is a complex evaluation of cyt c reduction and oxidation at the level of surface-localized amino acid residues and the heme moiety in a single electrochemical scan. The electrochemical pattern of cyt c is substantially different to both analogs acyt c and pcyt c, which could be applicable in further studies on the redox properties and structural stability of cytochromes and other hemeproteins. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. Unique structure and stability of HmuY, a novel heme-binding protein of Porphyromonas gingivalis.

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    Halina Wójtowicz

    2009-05-01

    Full Text Available Infection, survival, and proliferation of pathogenic bacteria in humans depend on their capacity to impair host responses and acquire nutrients in a hostile environment. Among such nutrients is heme, a co-factor for oxygen storage, electron transport, photosynthesis, and redox biochemistry, which is indispensable for life. Porphyromonas gingivalis is the major human bacterial pathogen responsible for severe periodontitis. It recruits heme through HmuY, which sequesters heme from host carriers and delivers it to its cognate outer-membrane transporter, the TonB-dependent receptor HmuR. Here we report that heme binding does not significantly affect the secondary structure of HmuY. The crystal structure of heme-bound HmuY reveals a new all-beta fold mimicking a right hand. The thumb and fingers pinch heme iron through two apical histidine residues, giving rise to highly symmetric octahedral iron co-ordination. The tetrameric quaternary arrangement of the protein found in the crystal structure is consistent with experiments in solution. It shows that thumbs and fingertips, and, by extension, the bound heme groups, are shielded from competing heme-binding proteins from the host. This may also facilitate heme transport to HmuR for internalization. HmuY, both in its apo- and in its heme-bound forms, is resistant to proteolytic digestion by trypsin and the major secreted proteases of P. gingivalis, gingipains K and R. It is also stable against thermal and chemical denaturation. In conclusion, these studies reveal novel molecular properties of HmuY that are consistent with its role as a putative virulence factor during bacterial infection.

  14. Electronic Structure of the Ferryl Intermediate in the α-Ketoglutarate Dependent Non-Heme Iron Halogenase SyrB2: Contributions to H Atom Abstraction Reactivity

    Czech Academy of Sciences Publication Activity Database

    Srnec, Martin; Wong, S. D.; Matthews, M. L.; Krebs, C.; Bollinger, J. M.; Solomon, E. I.

    2016-01-01

    Roč. 138, č. 15 (2016), s. 5110-5122 ISSN 0002-7863 R&D Projects: GA ČR(CZ) GJ15-10279Y Institutional support: RVO:61388955 Keywords : Ferryl intermediate * syringomycin halogenase * electronic structure Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 13.858, year: 2016

  15. Heme and menaquinone induced electron transport in lactic acid bacteria

    OpenAIRE

    Brooijmans, Rob; Smit, Bart; Santos, Filipe; van Riel, Jan; de Vos, Willem M; Hugenholtz, Jeroen

    2009-01-01

    Abstract Background For some lactic acid bacteria higher biomass production as a result of aerobic respiration has been reported upon supplementation with heme and menaquinone. In this report, we have studied a large number of species among lactic acid bacteria for the existence of this trait. Results Heme- (and menaquinone) stimulated aerobic growth was observed for several species and genera of lactic acid bacteria. These include Lactobacillus plantarum, Lactobacillus rhamnosus, Lactobacill...

  16. Tyrosine oxidation in heme oxygenase: examination of long-range proton-coupled electron transfer.

    Science.gov (United States)

    Smirnov, Valeriy V; Roth, Justine P

    2014-10-01

    Heme oxygenase is responsible for the degradation of a histidine-ligated ferric protoporphyrin IX (Por) to biliverdin, CO, and the free ferrous ion. Described here are studies of tyrosyl radical formation reactions that occur after oxidizing Fe(III)(Por) to Fe(IV)=O(Por(·+)) in human heme oxygenase isoform-1 (hHO-1) and the structurally homologous protein from Corynebacterium diphtheriae (cdHO). Site-directed mutagenesis on hHO-1 probes the reduction of Fe(IV)=O(Por(·+)) by tyrosine residues within 11 Å of the prosthetic group. In hHO-1, Y58· is implicated as the most likely site of oxidation, based on the pH and pD dependent kinetics. The absence of solvent deuterium isotope effects in basic solutions of hHO-1 and cdHO contrasts with the behavior of these proteins in the acidic solution, suggesting that long-range proton-coupled electron transfer predominates over electron transfer.

  17. Heme and menaquinone induced electron transport in lactic acid bacteria

    NARCIS (Netherlands)

    Brooijmans, R.J.W.; Smit, B.; Santos, dos F.; Riel, van J.; Vos, de W.M.; Hugenholtz, J.

    2009-01-01

    ABSTRACT: BACKGROUND: For some lactic acid bacteria higher biomass production as a result of aerobic respiration has been reported upon supplementation with heme and menaquinone. In this report, we have studied a large number of species among lactic acid bacteria for the existence of this trait.

  18. Structures of the multicomponent Rieske non-heme iron toluene 2, 3-dioxygenase enzyme system

    Energy Technology Data Exchange (ETDEWEB)

    Friemann, Rosmarie [Department of Molecular Biology, Swedish University of Agricultural Sciences, Box 590, 751 24 Uppsala (Sweden); Lee, Kyoung [Department of Microbiology, Changwon National University, Changwon, Kyoungnam 641-773 (Korea, Republic of); Department of Microbiology, The University of Iowa, Iowa City, Iowa 52242 (United States); Brown, Eric N. [Department of Biochemistry, The University of Iowa, Iowa City, Iowa 52242 (United States); Gibson, David T. [Department of Microbiology, The University of Iowa, Iowa City, Iowa 52242 (United States); Eklund, Hans [Department of Molecular Biology, Swedish University of Agricultural Sciences, Box 590, 751 24 Uppsala (Sweden); Ramaswamy, S., E-mail: s-ramaswamy@uiowa.edu [Department of Biochemistry, The University of Iowa, Iowa City, Iowa 52242 (United States); Department of Molecular Biology, Swedish University of Agricultural Sciences, Box 590, 751 24 Uppsala (Sweden)

    2009-01-01

    The crystal structures of the three-component toluene 2, 3-dioxygenase system provide a model for electron transfer among bacterial Rieske non-heme iron dioxygenases. Bacterial Rieske non-heme iron oxygenases catalyze the initial hydroxylation of aromatic hydrocarbon substrates. The structures of all three components of one such system, the toluene 2, 3-dioxygenase system, have now been determined. This system consists of a reductase, a ferredoxin and a terminal dioxygenase. The dioxygenase, which was cocrystallized with toluene, is a heterohexamer containing a catalytic and a structural subunit. The catalytic subunit contains a Rieske [2Fe–2S] cluster and mononuclear iron at the active site. This iron is not strongly bound and is easily removed during enzyme purification. The structures of the enzyme with and without mononuclear iron demonstrate that part of the structure is flexible in the absence of iron. The orientation of the toluene substrate in the active site is consistent with the regiospecificity of oxygen incorporation seen in the product formed. The ferredoxin is Rieske type and contains a [2Fe–2S] cluster close to the protein surface. The reductase belongs to the glutathione reductase family of flavoenzymes and consists of three domains: an FAD-binding domain, an NADH-binding domain and a C-terminal domain. A model for electron transfer from NADH via FAD in the reductase and the ferredoxin to the terminal active-site mononuclear iron of the dioxygenase is proposed.

  19. Heme and menaquinone induced electron transport in lactic acid bacteria

    Directory of Open Access Journals (Sweden)

    Santos Filipe

    2009-05-01

    Full Text Available Abstract Background For some lactic acid bacteria higher biomass production as a result of aerobic respiration has been reported upon supplementation with heme and menaquinone. In this report, we have studied a large number of species among lactic acid bacteria for the existence of this trait. Results Heme- (and menaquinone stimulated aerobic growth was observed for several species and genera of lactic acid bacteria. These include Lactobacillus plantarum, Lactobacillus rhamnosus, Lactobacilllus brevis, Lactobacillus paralimentarius, Streptococcus entericus and Lactococcus garviae. The increased biomass production without further acidification, which are respiration associated traits, are suitable for high-throughput screening as demonstrated by the screening of 8000 Lactococcus lactis insertion mutants. Respiration-negative insertion-mutants were found with noxA, bd-type cytochrome and menaquinol biosynthesis gene-disruptions. Phenotypic screening and in silico genome analysis suggest that respiration can be considered characteristic for certain species. Conclusion We propose that the cyd-genes were present in the common ancestor of lactic acid bacteria, and that multiple gene-loss events best explains the observed distribution of these genes among the species.

  20. Heme and menaquinone induced electron transport in lactic acid bacteria.

    Science.gov (United States)

    Brooijmans, Rob; Smit, Bart; Santos, Filipe; van Riel, Jan; de Vos, Willem M; Hugenholtz, Jeroen

    2009-05-29

    For some lactic acid bacteria higher biomass production as a result of aerobic respiration has been reported upon supplementation with heme and menaquinone. In this report, we have studied a large number of species among lactic acid bacteria for the existence of this trait. Heme- (and menaquinone) stimulated aerobic growth was observed for several species and genera of lactic acid bacteria. These include Lactobacillus plantarum, Lactobacillus rhamnosus, Lactobacilllus brevis, Lactobacillus paralimentarius, Streptococcus entericus and Lactococcus garviae. The increased biomass production without further acidification, which are respiration associated traits, are suitable for high-throughput screening as demonstrated by the screening of 8000 Lactococcus lactis insertion mutants. Respiration-negative insertion-mutants were found with noxA, bd-type cytochrome and menaquinol biosynthesis gene-disruptions. Phenotypic screening and in silico genome analysis suggest that respiration can be considered characteristic for certain species. We propose that the cyd-genes were present in the common ancestor of lactic acid bacteria, and that multiple gene-loss events best explains the observed distribution of these genes among the species.

  1. Modeling and computations of the intramolecular electron transfer process in the two-heme protein cytochrome em>c>4

    DEFF Research Database (Denmark)

    Natzmutdinov, Renat R.; Bronshtein, Michael D.; Zinkicheva, Tamara T.

    2012-01-01

    force were determined using dielectric continuum models. We then calculated the electronic transmission coefficient of the intramolecular ET rate using perturbation theory combined with the electronic wave functions determined by the DFT calculations for different heme group orientations and Fe...

  2. Electron transfer among the CuA-, heme b- and a3-centers of Thermus thermophilus cytochrome ba3

    DEFF Research Database (Denmark)

    Farver, Ole; Chen, Ying; Fee, James A

    2006-01-01

    The 1-methyl-nicotinamide radical (MNA(*)), produced by pulse radiolysis has previously been shown to reduce the Cu(A)-site of cytochromes aa(3), a process followed by intramolecular electron transfer (ET) to the heme a but not to the heme a(3) [Farver, O., Grell, E., Ludwig, B., Michel, H. and P...

  3. Solution 1H NMR investigation of the active site molecular and electronic structures of substrate-bound, cyanide-inhibited HmuO, a bacterial heme oxygenase from Corynebacterium diphtheriae.

    Science.gov (United States)

    Li, Yiming; Syvitski, Ray T; Chu, Grace C; Ikeda-Saito, Masao; Mar, Gerd N La

    2003-02-28

    The molecular structure and dynamic properties of the active site environment of HmuO, a heme oxygenase (HO) from the pathogenic bacterium Corynebacterium diphtheriae, have been investigated by (1)H NMR spectroscopy using the human HO (hHO) complex as a homology model. It is demonstrated that not only the spatial contacts among residues and between residues and heme, but the magnetic axes that can be related to the direction and magnitude of the steric tilt of the FeCN unit are strongly conserved in the two HO complexes. The results indicate that very similar contributions of steric blockage of several meso positions and steric tilt of the attacking ligand are operative. A distal H-bond network that involves numerous very strong H-bonds and immobilized water molecules is identified in HmuO that is analogous to that previously identified in hHO (Li, Y., Syvitski, R. T., Auclair, K., Wilks, A., Ortiz de Montellano, P. R., and La Mar, G. N. (2002) J. Biol. Chem. 277, 33018-33031). The NMR results are completely consistent with the very recent crystal structure of the HmuO.substrate complex. The H-bond network/ordered water molecules are proposed to orient the distal water molecule near the catalytically key Asp(136) (Asp(140) in hHO) that stabilizes the hydroperoxy intermediate. The dynamic stability of this H-bond network in HmuO is significantly greater than in hHO and may account for the slower catalytic rate in bacterial HO compared with mammalian HO.

  4. Tuning of Hemes b Equilibrium Redox Potential Is Not Required for Cross-Membrane Electron Transfer.

    Science.gov (United States)

    Pintscher, Sebastian; Kuleta, Patryk; Cieluch, Ewelina; Borek, Arkadiusz; Sarewicz, Marcin; Osyczka, Artur

    2016-03-25

    In biological energy conversion, cross-membrane electron transfer often involves an assembly of two hemesb The hemes display a large difference in redox midpoint potentials (ΔEm_b), which in several proteins is assumed to facilitate cross-membrane electron transfer and overcome a barrier of membrane potential. Here we challenge this assumption reporting on hemebligand mutants of cytochromebc1in which, for the first time in transmembrane cytochrome, one natural histidine has been replaced by lysine without loss of the native low spin type of heme iron. With these mutants we show that ΔEm_b can be markedly increased, and the redox potential of one of the hemes can stay above the level of quinone pool, or ΔEm_b can be markedly decreased to the point that two hemes are almost isopotential, yet the enzyme retains catalytically competent electron transfer between quinone binding sites and remains functionalin vivo This reveals that cytochromebc1can accommodate large changes in ΔEm_b without hampering catalysis, as long as these changes do not impose overly endergonic steps on downhill electron transfer from substrate to product. We propose that hemesbin this cytochrome and in other membranous cytochromesbact as electronic connectors for the catalytic sites with no fine tuning in ΔEm_b required for efficient cross-membrane electron transfer. We link this concept with a natural flexibility in occurrence of several thermodynamic configurations of the direction of electron flow and the direction of the gradient of potential in relation to the vector of the electric membrane potential. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  5. Heme Sensor Proteins*

    Science.gov (United States)

    Girvan, Hazel M.; Munro, Andrew W.

    2013-01-01

    Heme is a prosthetic group best known for roles in oxygen transport, oxidative catalysis, and respiratory electron transport. Recent years have seen the roles of heme extended to sensors of gases such as O2 and NO and cell redox state, and as mediators of cellular responses to changes in intracellular levels of these gases. The importance of heme is further evident from identification of proteins that bind heme reversibly, using it as a signal, e.g. to regulate gene expression in circadian rhythm pathways and control heme synthesis itself. In this minireview, we explore the current knowledge of the diverse roles of heme sensor proteins. PMID:23539616

  6. Structural characterization of human heme oxygenase-1 in complex with azole-based inhibitors.

    Science.gov (United States)

    Rahman, Mona N; Vlahakis, Jason Z; Roman, Gheorghe; Vukomanovic, Dragic; Szarek, Walter A; Nakatsu, Kanji; Jia, Zongchao

    2010-03-01

    The development of inhibitors specific for heme oxygenases (HO) aims to provide powerful tools in understanding the HO system. Based on the lead structure (2S, 4S)-2-[2-(4-chlorophenyl)ethyl]-2-[(1H-imidazol-1-yl)methyl]-4-[((4-aminophenyl)thio)methyl]-1,3-dioxolane (azalanstat, QC-1) we have synthesized structural modifications to develop novel and selective HO inhibitors. The structural study of human HO-1 (hHO-1) in complex with a select group of the inhibitors was initiated using X-ray crystallographic techniques. Comparison of the structures of four such compounds each in complex with hHO-1 revealed a common binding mode, despite having different structural fragments. The compounds bind to the distal side of heme through an azole "anchor" which coordinates with the heme iron. An expansion of the distal pocket, mainly due to distal helix flexibility, allows accommodation of the compounds without displacing heme or the critical Asp140 residue. Rather, binding displaces a catalytically critical water molecule and disrupts an ordered hydrogen-bond network involving Asp140. The presence of a triazole "anchor" may provide further stability via a hydrogen bond with the protein. A hydrophobic pocket acts to stabilize the region occupied by the phenyl or adamantanyl moieties of these compounds. Further, a secondary hydrophobic pocket is formed via "induced fit" to accommodate bulky substituents at the 4-position of the dioxolane ring. Copyright 2009 Elsevier Inc. All rights reserved.

  7. Single or functionalized fullerenes interacting with heme group

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    Costa, Wallison Chaves; Diniz, Eduardo Moraes, E-mail: eduardo.diniz@ufma.br [Departamento de Física, Universidade Federal do Maranhão, Avenida dos Portugueses, 1966, CEP 65080-805, São Luís - MA (Brazil)

    2014-09-15

    The heme group is responsible for iron transportation through the bloodstream, where iron participates in redox reactions, electron transfer, gases detection etc. The efficiency of such processes can be reduced if the whole heme molecule or even the iron is somehow altered from its original oxidation state, which can be caused by interactions with nanoparticles as fullerenes. To verify how such particles alter the geometry and electronic structure of heme molecule, here we report first principles calculations based on density functional theory of heme group interacting with single C{sub 60} fullerene or with C{sub 60} functionalized with small functional groups (−CH{sub 3}, −COOH, −NH{sub 2}, −OH). The calculations shown that the system heme + nanoparticle has a different spin state in comparison with heme group if the fullerene is functionalized. Also a functional group can provide a stronger binding between nanoparticle and heme molecule or inhibit the chemical bonding in comparison with single fullerene results. In addition heme molecule loses electrons to the nanoparticles and some systems exhibited a geometry distortion in heme group, depending on the binding energy. Furthermore, one find that such nanoparticles induce a formation of spin up states in heme group. Moreover, there exist modifications in density of states near the Fermi energy. Although of such changes in heme electronic structure and geometry, the iron atom remains in the heme group with the same oxidation state, so that processes that involve the iron might not be affected, only those that depend on the whole heme molecule.

  8. Structure prediction and activity analysis of human heme oxygenase-1 and its mutant.

    Science.gov (United States)

    Xia, Zhen-Wei; Zhou, Wen-Pu; Cui, Wen-Jun; Zhang, Xue-Hong; Shen, Qing-Xiang; Li, Yun-Zhu; Yu, Shan-Chang

    2004-08-15

    To predict wild human heme oxygenase-1 (whHO-1) and hHO-1 His25Ala mutant (delta hHO-1) structures, to clone and express them and analyze their activities. Swiss-PdbViewer and Antheprot 5.0 were used for the prediction of structure diversity and physical-chemical changes between wild and mutant hHO-1. hHO-1 His25Ala mutant cDNA was constructed by site-directed mutagenesis in two plasmids of E. coli DH5alpha. Expression products were purified by ammonium sulphate precipitation and Q-Sepharose Fast Flow column chromatography, and their activities were measured. rHO-1 had the structure of a helical fold with the heme sandwiched between heme-heme oxygenase-1 helices. Bond angle, dihedral angle and chemical bond in the active pocket changed after Ala25 was replaced by His25, but Ala25 was still contacting the surface and the electrostatic potential of the active pocket was negative. The mutated enzyme kept binding activity to heme. Two vectors pBHO-1 and pBHO-1(M) were constructed and expressed. Ammonium sulphate precipitation and column chromatography yielded 3.6-fold and 30-fold higher purities of whHO-1, respectively. The activity of delta hHO-1 was reduced 91.21% after mutation compared with whHO-1. Proximal His25 ligand is crucial for normal hHO-1 catalytic activity. delta hHO-1 is deactivated by mutation but keeps the same binding site as whHO-1. delta hHO-1 might be a potential inhibitor of whHO-1 for preventing neonatal hyperbilirubinemia.

  9. Temperature dependence of Q-band electron paramagnetic resonance spectra of nitrosyl heme proteins

    Energy Technology Data Exchange (ETDEWEB)

    Flores, Marco; Wajnberg, Eliane; Bemski, George

    1997-11-01

    The Q-band (35 GHz) electron paramagnetic resonance (EPR) spectra of nitrosyl hemoglobin (Hb N O) and nitrosyl myoglobin (Mb NO) were studied as a function of temperature between 19 K and 200 K. The spectra of both heme proteins show classes of variations as a function of temperature. The first one has previously been associated with the existence of two paramagnetic species, one with rhombic and the other with axial symmetry. The second one manifests itself in changes in the g-factors and linewidths of each species. These changes are correlated with the conformational substates model and associate the variations of g-values with changes in the angle of the N(his)-Fe-N (NO) bond in the rhombic species and with changes in the distance between Fe and N of the proximal (F8) histidine in the axial species. (author) 24 refs., 6 figs.

  10. Heme: From quantum spin crossover to oxygen manager of life

    DEFF Research Database (Denmark)

    Kepp, Kasper Planeta

    2016-01-01

    The review discusses how the electronic structure of heme explains its central importance to oxygen-based life on Earth. Emphasis is on the chemical bonding of heme, its spin crossover, reversible O2 binding, and O-O bond activation, put in relation to its physiological functions. The review disc...

  11. Gas-phase spectroscopy of ferric heme-NO complexes

    DEFF Research Database (Denmark)

    Wyer, J.A.; Jørgensen, Anders; Pedersen, Bjarke

    2013-01-01

    and significantly blue-shifted compared to ferric heme nitrosyl proteins (maxima between 408 and 422 nm). This is in stark contrast to the Q-band absorption where the protein microenvironment is nearly innocent in perturbing the electronic structure of the porphyrin macrocycle. Photodissociation is primarily...... maxima of heme and its complexes with amino acids and NO. Not so innocent: Weakly bound complexes between ferric heme and NO were synthesised in the gas phase, and their absorption measured from photodissociation yields. Opposite absorption trends in the Soret-band are seen upon NO addition to heme ions...

  12. Heme Synthesis and Acquisition in Bacterial Pathogens

    OpenAIRE

    Choby, Jacob E.; Skaar, Eric P.

    2016-01-01

    Bacterial pathogens require the iron-containing cofactor heme to cause disease. Heme is essential to the function of hemoproteins, which are involved in energy generation by the electron transport chain, detoxification of host immune effectors, and other processes. During infection, bacterial pathogens must synthesize heme or acquire heme from the host; however, host heme is sequestered in high-affinity hemoproteins. Pathogens have evolved elaborate strategies to acquire heme from host source...

  13. Structural and Functional Models of Non-Heme Iron Enzymes : A Study of the 2-His-1-Carboxylate Facial Triad Structural Motif

    NARCIS (Netherlands)

    Bruijnincx, P.C.A.

    2007-01-01

    The structural and functional modeling of a specific group of non-heme iron enzymes by the synthesis of small synthetic analogues is the topic of this thesis. The group of non-heme iron enzymes with the 2-His-1-carboxylate facial triad has recently been established as a common platform for the

  14. Electrochemistry and biosensing reactivity of heme proteins adsorbed on the structure-tailored mesoporous Nb2O5 matrix

    International Nuclear Information System (INIS)

    Xu Xin; Tian Bozhi; Zhang Song; Kong Jilie; Zhao Dongyuan; Liu Baohong

    2004-01-01

    The highly ordered mesoporous niobium oxides fabricated by self-adjusted synthesis have been used as immobilization matrices of heme proteins including Cytochrome c (Cyt C) and horseradish peroxidase (HRP) for their large surface areas, narrow pore size distributions and good biocompatibility. The assembling process was investigated by cyclic voltammetry, amperometry and potential step chronoamperometry in details. Niobium oxide matrices with different structural features were templated with the surfactants and the selectivity of these hosts to specific protein characteristics was determined. It was observed that proteins could be readily assembled onto the mesoporous films with detectable retention of bioactivity. The Nb 2 O 5 matrix with a tailored pore size and counterpoised surface charge to that of hemes allowed for a maximum adsorption capacity of biomolecules. The adsorbed redox molecules exhibited direct electrochemical behavior and gave a pair of well-defined quasi-reversible cyclic voltammetric peaks, indicating that the mesoporous niobium oxide matrix could effectively promote the direct electron transfer between the protein redox site adsorbed and the electrode surface. The midpoint redox potentials of adsorbed Cyt-c and HRP were 14 and -122 mV versus SCE, respectively. Furthermore, the immobilized HRP onto Nb 2 O 5 derived electrode presented good bioactivity and thus was fabricated as an amperometric biosensor for the response of hydrogen peroxide in the range from 0.1 μM to 0.1 mM

  15. NirN Protein from Pseudomonas aeruginosa is a Novel Electron-bifurcating Dehydrogenase Catalyzing the Last Step of Heme d1 Biosynthesis*

    Science.gov (United States)

    Adamczack, Julia; Hoffmann, Martin; Papke, Ulrich; Haufschildt, Kristin; Nicke, Tristan; Bröring, Martin; Sezer, Murat; Weimar, Rebecca; Kuhlmann, Uwe; Hildebrandt, Peter; Layer, Gunhild

    2014-01-01

    Heme d1 plays an important role in denitrification as the essential cofactor of the cytochrome cd1 nitrite reductase NirS. At present, the biosynthesis of heme d1 is only partially understood. The last step of heme d1 biosynthesis requires a so far unknown enzyme that catalyzes the introduction of a double bond into one of the propionate side chains of the tetrapyrrole yielding the corresponding acrylate side chain. In this study, we show that a Pseudomonas aeruginosa PAO1 strain lacking the NirN protein does not produce heme d1. Instead, the NirS purified from this strain contains the heme d1 precursor dihydro-heme d1 lacking the acrylic double bond, as indicated by UV-visible absorption spectroscopy and resonance Raman spectroscopy. Furthermore, the dihydro-heme d1 was extracted from purified NirS and characterized by UV-visible absorption spectroscopy and finally identified by high-resolution electrospray ionization mass spectrometry. Moreover, we show that purified NirN from P. aeruginosa binds the dihydro-heme d1 and catalyzes the introduction of the acrylic double bond in vitro. Strikingly, NirN uses an electron bifurcation mechanism for the two-electron oxidation reaction, during which one electron ends up on its heme c cofactor and the second electron reduces the substrate/product from the ferric to the ferrous state. On the basis of our results, we propose novel roles for the proteins NirN and NirF during the biosynthesis of heme d1. PMID:25204657

  16. Structure of the Mitochondrial Aminolevulinic Acid Synthase, a Key Heme Biosynthetic Enzyme.

    Science.gov (United States)

    Brown, Breann L; Kardon, Julia R; Sauer, Robert T; Baker, Tania A

    2018-04-03

    5-Aminolevulinic acid synthase (ALAS) catalyzes the first step in heme biosynthesis. We present the crystal structure of a eukaryotic ALAS from Saccharomyces cerevisiae. In this homodimeric structure, one ALAS subunit contains covalently bound cofactor, pyridoxal 5'-phosphate (PLP), whereas the second is PLP free. Comparison between the subunits reveals PLP-coupled reordering of the active site and of additional regions to achieve the active conformation of the enzyme. The eukaryotic C-terminal extension, a region altered in multiple human disease alleles, wraps around the dimer and contacts active-site-proximal residues. Mutational analysis demonstrates that this C-terminal region that engages the active site is important for ALAS activity. Our discovery of structural elements that change conformation upon PLP binding and of direct contact between the C-terminal extension and the active site thus provides a structural basis for investigation of disruptions in the first step of heme biosynthesis and resulting human disorders. Copyright © 2018 Elsevier Ltd. All rights reserved.

  17. Influence of heme environment structure on dioxygen affinity for the dual function Amphitrite ornata hemoglobin/dehaloperoxidase. Insights into the evolutional structure-function adaptations

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Shengfang; Sono, Masanori; Wang, Chunxue; Du, Jing; Lebioda, Lukasz; Dawson, John H. [SC

    2014-05-15

    Sea worm, Amphitrite ornata, has evolved its globin (an O2 carrier) also to serves as a dehaloperoxidase (DHP) to detoxify haloaromatic pollutants generated by competing species. A previous mutagenesis study by our groups on both DHP and sperm whale myoglobin (SW Mb) revealed some structural factors that influence the dehaloperoxidase activities (significantly lower for Mb) of both proteins. Using an isocyanide/O2 partition constant measurement method in this study, we have examined the effects of these structural factors on the O2 equilibrium constants (KO2) of DHP, SW Mb, and their mutants. A clear trend of decreasing O2 affinity and increasing catalytic activity along with the increase in the distal His Nεheme iron distance is observed. An H93K/T95H Mb double mutant mimicking the DHP proximal His positioning exhibited markedly enhanced O2 affinity, confirming the essential effect of proximal His rotation on the globin function of DHP. For DHP, the L100F, T56G and M86E variants showed the effects of distal volume, distal His flexibility and proximal electronic push, respectively, on the O2 affinity. This study provides insights into how DHP has evolved its heme environment to gain significantly enhanced peroxidase capability without compromising its primary function as an O2 carrier.

  18. Heme Synthesis and Acquisition in Bacterial Pathogens.

    Science.gov (United States)

    Choby, Jacob E; Skaar, Eric P

    2016-08-28

    Bacterial pathogens require the iron-containing cofactor heme to cause disease. Heme is essential to the function of hemoproteins, which are involved in energy generation by the electron transport chain, detoxification of host immune effectors, and other processes. During infection, bacterial pathogens must synthesize heme or acquire heme from the host; however, host heme is sequestered in high-affinity hemoproteins. Pathogens have evolved elaborate strategies to acquire heme from host sources, particularly hemoglobin, and both heme acquisition and synthesis are important for pathogenesis. Paradoxically, excess heme is toxic to bacteria and pathogens must rely on heme detoxification strategies. Heme is a key nutrient in the struggle for survival between host and pathogen, and its study has offered significant insight into the molecular mechanisms of bacterial pathogenesis. Copyright © 2016 Elsevier Ltd. All rights reserved.

  19. Heterogeneous electron transfer of a two-centered heme protein: redox and electrocatalytic properties of surface-immobilized cytochrome C(4).

    Science.gov (United States)

    Monari, Stefano; Battistuzzi, Gianantonio; Borsari, Marco; Di Rocco, Giulia; Martini, Laura; Ranieri, Antonio; Sola, Marco

    2009-10-15

    The recombinant diheme cytochrome c(4) from the psycrophilic bacterium Pseudoalteromonas haloplanktis TAC 125 and its Met64Ala and Met164Ala variants, which feature a hydroxide ion axially bound to the heme iron at the N- and C-terminal domains, respectively, were found to exchange electrons efficiently with a gold electrode coated with a SAM of 11-mercapto-1-undecanoic acid. The mutation-induced removal of the redox equivalence of the two heme groups and changes in the net charge of the protein lobes yield two-centered protein systems with unprecedented properties in the electrode-immobilized state. The heterogeneous and intraheme electron transfer processes were characterized for these species in which the high- and low-potential heme groups are swapped over in the bilobal protein framework and experience a constrained (M64A) and unconstrained (M164A) orientation toward the electrode. The reduction thermodynamics for the native and mutated hemes were measured for the first time for a diheme cytochrome c. In the diffusing regime, they reproduce closely those for the corresponding centers in single-heme class-I cytochromes c, despite the low sequence identity. Larger differences are observed in the thermodynamics of the immobilized species and in the heterogeneous electron transfer rate constants. T-dependent kinetic measurements show that the proteins are positioned approximately 7 A from the HOOC-terminated SAM-coated electrode. Protein-electrode orientation and efficient intraheme ET enable the His,OH(-)-ligated heme A of the immobilized Met64Ala variant to carry out the reductive electrocatalysis of molecular oxygen. This system therefore constitutes a novel two-centered heme-based biocatalytic interface to be exploited for "third-generation" amperometric biosensing.

  20. Visualizing changes in electron distribution in coupled chains of cytochrome bc(1) by modifying barrier for electron transfer between the FeS cluster and heme c(1).

    Science.gov (United States)

    Cieluch, Ewelina; Pietryga, Krzysztof; Sarewicz, Marcin; Osyczka, Artur

    2010-02-01

    Cytochrome c(1) of Rhodobacter (Rba.) species provides a series of mutants which change barriers for electron transfer through the cofactor chains of cytochrome bc(1) by modifying heme c(1) redox midpoint potential. Analysis of post-flash electron distribution in such systems can provide useful information about the contribution of individual reactions to the overall electron flow. In Rba. capsulatus, the non-functional low-potential forms of cytochrome c(1) which are devoid of the disulfide bond naturally present in this protein revert spontaneously by introducing a second-site suppression (mutation A181T) that brings the potential of heme c(1) back to the functionally high levels, yet maintains it some 100 mV lower from the native value. Here we report that the disulfide and the mutation A181T can coexist in one protein but the mutation exerts a dominant effect on the redox properties of heme c(1) and the potential remains at the same lower value as in the disulfide-free form. This establishes effective means to modify a barrier for electron transfer between the FeS cluster and heme c(1) without breaking disulfide. A comparison of the flash-induced electron transfers in native and mutated cytochrome bc(1) revealed significant differences in the post-flash equilibrium distribution of electrons only when the connection of the chains with the quinone pool was interrupted at the level of either of the catalytic sites by the use of specific inhibitors, antimycin or myxothiazol. In the non-inhibited system no such differences were observed. We explain the results using a kinetic model in which a shift in the equilibrium of one reaction influences the equilibrium of all remaining reactions in the cofactor chains. It follows a rather simple description in which the direction of electron flow through the coupled chains of cytochrome bc(1) exclusively depends on the rates of all reversible partial reactions, including the Q/QH2 exchange rate to/from the catalytic sites

  1. Comparison of the crystal structure and function to wild-type and His25Ala mutant human heme oxygenase-1.

    Science.gov (United States)

    Zhou, Wen-Pu; Zhong, Wen-Wei; Zhang, Xue-Hong; Ding, Jian-Ping; Zhang, Zi-Li; Xia, Zhen-Wei

    2009-03-01

    Human heme oxygenase-1 (hHO-1) is a rate-limiting enzyme in heme metabolism. It regulates serum bilirubin level. Site-directed mutagenesis studies indicate that the proximal residue histidine 25 (His25) plays a key role in hHO-1 activity. A highly purified hHO-1 His25Ala mutant was generated and crystallized with a new expression system. The crystal structure of the mutant was determined by X-ray diffraction technology and molecular replacement at the resolution of 2.8 A, and the model of hHO-1 His25Ala mutant was refined. The final crystallographic and free R factors were 0.245 and 0.283, respectively. The standard bond length deviation was 0.007 A, and the standard bond angle deviation was 1.3 degrees . The mutation of His25 to Ala led to an empty pocket underneath the ferric ion in the heme, leading to loss of binding iron ligand. Although this did not cause an overall structural change, the enzymatic activity of the mutant hHO-1 was reduced by 90%. By supplementing imidazole, the HO-1 activity was restored approximately 90% to its normal level. These data suggest that Ala25 remains unchanged in the structure compared to His25, but the important catalytic function of hHO-1 is lost. Thus, it appears that His25 is a crucial residue for proper hHO-1 catalysis.

  2. Gold nanoparticle assisted assembly of a heme protein for enhancement of long-range interfacial electron transfer

    DEFF Research Database (Denmark)

    Jensen, Palle Skovhus; Chi, Qijin; Grumsen, Flemming Bjerg

    2007-01-01

    and characterization of water-soluble gold nanoparticles (AuNPs) with core diameter 3-4 nm and their application for the enhancement of long-range interfacial ET of a heme protein. Gold nanoparticles were electrostatically conjugated with cyt c to form nanoparticle-protein hybrid ET systems with well...... and the protein molecule. When the nanoparticle-protein conjugates are assembled on Au(111) surfaces, long-range interfacial ET across a physical distance of over 50 A via the nanoparticle becomes feasible. Moreover, significant enhancement of the interfacial ET rate by more than an order of magnitude compared...... with that of cyt c in the absence of AuNPs is observed. AuNPs appear to serve as excellent ET relays, most likely by facilitating the electronic coupling between the protein redox center and the electrode surface....

  3. Control of intracellular heme levels: Heme transporters and Heme oxygenases

    Science.gov (United States)

    Khan, Anwar A.; Quigley, John G.

    2011-01-01

    Heme serves as a co-factor in proteins involved in fundamental biological processes including oxidative metabolism, oxygen storage and transport, signal transduction and drug metabolism. In addition, heme is important for systemic iron homeostasis in mammals. Heme has important regulatory roles in cell biology, yet excessive levels of intracellular heme are toxic; thus, mechanisms have evolved to control the acquisition, synthesis, catabolism and expulsion of cellular heme. Recently, a number of transporters of heme and heme synthesis intermediates have been described. Here we review aspects of heme metabolism and discuss our current understanding of heme transporters, with emphasis on the function of the cell-surface heme exporter, FLVCR. Knockdown of Flvcr in mice leads to both defective erythropoiesis and disturbed systemic iron homeostasis, underscoring the critical role of heme transporters in mammalian physiology. PMID:21238504

  4. Solution NMR characterization of magnetic/electronic properties of azide and cyanide-inhibited substrate complexes of human heme oxygenase: implications for steric ligand tilt.

    Science.gov (United States)

    Peng, Dungeng; Ogura, Hiroshi; Ma, Li-Hua; Evans, John P; de Montellano, Paul R Ortiz; La Mar, Gerd N

    2013-04-01

    Solution 2D (1)H NMR was carried out on the azide-ligated substrate complex of human heme oxygenase, hHO, to provide information on the active site molecular structure, chromophore electronic/magnetic properties, and the distal H-bond network linked to the exogenous ligand by catalytically relevant oriented water molecules. While 2D NMR exhibited very similar patterns of two-dimensional nuclear Overhauser spectroscopy cross peaks of residues with substrate and among residues as the previously characterized cyanide complex, significant, broadly distributed chemical shift differences were observed for both labile and non-labile protons. The anisotropy and orientation of the paramagnetic susceptibility tensor, χ, were determined for both the azide and cyanide complexes. The most significant difference observed is the tilt of the major magnetic axes from the heme normal, which is only half as large for the azide than cyanide ligand, with each ligand tilted toward the catalytically cleaved α-meso position. The difference in chemical shifts is quantitatively correlated with differences in dipolar shifts in the respective complexes for all but the distal helix. The necessity of considering dipolar shifts, and hence determination of the orientation/anisotropy of χ, in comparing chemical shifts involving paramagnetic complexes, is emphasized. The analysis shows that the H-bond network cannot detect significant differences in H-bond acceptor properties of cyanide versus azide ligands. Lastly, significant retardation of distal helix labile proton exchange upon replacing cyanide with azide indicates that the dynamic stability of the distal helix is increased upon decreasing the steric interaction of the ligand with the distal helix. Copyright © 2013. Published by Elsevier Inc.

  5. Coordination and redox state-dependent structural changes of the heme-based oxygen sensor AfGcHK associated with intraprotein signal transduction.

    Science.gov (United States)

    Stranava, Martin; Man, Petr; Skálová, Tereza; Kolenko, Petr; Blaha, Jan; Fojtikova, Veronika; Martínek, Václav; Dohnálek, Jan; Lengalova, Alzbeta; Rosůlek, Michal; Shimizu, Toru; Martínková, Markéta

    2017-12-22

    The heme-based oxygen sensor histidine kinase Af GcHK is part of a two-component signal transduction system in bacteria. O 2 binding to the Fe(II) heme complex of its N-terminal globin domain strongly stimulates autophosphorylation at His 183 in its C-terminal kinase domain. The 6-coordinate heme Fe(III)-OH - and -CN - complexes of Af GcHK are also active, but the 5-coordinate heme Fe(II) complex and the heme-free apo-form are inactive. Here, we determined the crystal structures of the isolated dimeric globin domains of the active Fe(III)-CN - and inactive 5-coordinate Fe(II) forms, revealing striking structural differences on the heme-proximal side of the globin domain. Using hydrogen/deuterium exchange coupled with mass spectrometry to characterize the conformations of the active and inactive forms of full-length Af GcHK in solution, we investigated the intramolecular signal transduction mechanisms. Major differences between the active and inactive forms were observed on the heme-proximal side (helix H5), at the dimerization interface (helices H6 and H7 and loop L7) of the globin domain and in the ATP-binding site (helices H9 and H11) of the kinase domain. Moreover, separation of the sensor and kinase domains, which deactivates catalysis, increased the solvent exposure of the globin domain-dimerization interface (helix H6) as well as the flexibility and solvent exposure of helix H11. Together, these results suggest that structural changes at the heme-proximal side, the globin domain-dimerization interface, and the ATP-binding site are important in the signal transduction mechanism of Af GcHK. We conclude that Af GcHK functions as an ensemble of molecules sampling at least two conformational states. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  6. Out of plane distortions of the heme b of Escherichia coli succinate dehydrogenase.

    Directory of Open Access Journals (Sweden)

    Quang M Tran

    Full Text Available The role of the heme b in Escherichia coli succinate dehydrogenase is highly ambiguous and its role in catalysis is questionable. To examine whether heme reduction is an essential step of the catalytic mechanism, we generated a series of site-directed mutations around the heme binding pocket, creating a library of variants with a stepwise decrease in the midpoint potential of the heme from the wild-type value of +20 mV down to -80 mV. This difference in midpoint potential is enough to alter the reactivity of the heme towards succinate and thus its redox state under turnover conditions. Our results show both the steady state succinate oxidase and fumarate reductase catalytic activity of the enzyme are not a function of the redox potential of the heme. As well, lower heme potential did not cause an increase in the rate of superoxide production both in vitro and in vivo. The electron paramagnetic resonance (EPR spectrum of the heme in the wild-type enzyme is a combination of two distinct signals. We link EPR spectra to structure, showing that one of the signals likely arises from an out-of-plane distortion of the heme, a saddled conformation, while the second signal originates from a more planar orientation of the porphyrin ring.

  7. Catalytic enhancement of the heme-based oxygen-sensing phosphodiesterase EcDOS by hydrogen sulfide is caused by changes in heme coordination structure

    Czech Academy of Sciences Publication Activity Database

    Yang, F.; Fojtíková, V.; Man, Petr; Stráňava, M.; Martínková, M.; Du, Y.; Huang, D.; Shimizu, T.

    2015-01-01

    Roč. 28, č. 4 (2015), s. 637-652 ISSN 0966-0844 Grant - others:OPPC(XE) CZ.2.16/3.1.00/24023 Institutional support: RVO:61388971 Keywords : Heme * O-2 sensor * Phosphodiesterase Subject RIV: CE - Biochemistry Impact factor: 2.134, year: 2015

  8. Control of intracellular heme levels: Heme transporters and heme oxygenases

    OpenAIRE

    Khan, Anwar A.; Quigley, John G.

    2011-01-01

    Heme serves as a co-factor in proteins involved in fundamental biological processes including oxidative metabolism, oxygen storage and transport, signal transduction and drug metabolism. In addition, heme is important for systemic iron homeostasis in mammals. Heme has important regulatory roles in cell biology, yet excessive levels of intracellular heme are toxic; thus, mechanisms have evolved to control the acquisition, synthesis, catabolism and expulsion of cellular heme. Recently, a number...

  9. Electron Transport in a Dioxygenase-Ferredoxin Complex: Long Range Charge Coupling between the Rieske and Non-Heme Iron Center.

    Directory of Open Access Journals (Sweden)

    Wayne K Dawson

    Full Text Available Dioxygenase (dOx utilizes stereospecific oxidation on aromatic molecules; consequently, dOx has potential applications in bioremediation and stereospecific oxidation synthesis. The reactive components of dOx comprise a Rieske structure Cys2[2Fe-2S]His2 and a non-heme reactive oxygen center (ROC. Between the Rieske structure and the ROC, a universally conserved Asp residue appears to bridge the two structures forming a Rieske-Asp-ROC triad, where the Asp is known to be essential for electron transfer processes. The Rieske and ROC share hydrogen bonds with Asp through their His ligands; suggesting an ideal network for electron transfer via the carboxyl side chain of Asp. Associated with the dOx is an itinerant charge carrying protein Ferredoxin (Fdx. Depending on the specific cognate, Fdx may also possess either the Rieske structure or a related structure known as 4-Cys-[2Fe-2S] (4-Cys. In this study, we extensively explore, at different levels of theory, the behavior of the individual components (Rieske and ROC and their interaction together via the Asp using a variety of density function methods, basis sets, and a method known as Generalized Ionic Fragment Approach (GIFA that permits setting up spin configurations manually. We also report results on the 4-Cys structure for comparison. The individual optimized structures are compared with observed spectroscopic data from the Rieske, 4-Cys and ROC structures (where information is available. The separate pieces are then combined together into a large Rieske-Asp-ROC (donor/bridge/acceptor complex to estimate the overall coupling between individual components, based on changes to the partial charges. The results suggest that the partial charges are significantly altered when Asp bridges the Rieske and the ROC; hence, long range coupling through hydrogen bonding effects via the intercalated Asp bridge can drastically affect the partial charge distributions compared to the individual isolated

  10. Heme transport and erythropoiesis

    Science.gov (United States)

    Yuan, Xiaojing; Fleming, Mark D.; Hamza, Iqbal

    2013-01-01

    In humans, systemic heme homeostasis is achieved via coordinated regulation of heme synthesis, transport and degradation. Although the heme biosynthesis and degradation pathways have been well characterized, the pathways for heme trafficking and incorporation into hemoproteins remains poorly understood. In the past few years, researchers have exploited genetic, cellular and biochemical tools, to identify heme transporters and, in the process, reveal unexpected functions for this elusive group of proteins. However, given the complexity of heme trafficking pathways, current knowledge of heme transporters is fragmented and sometimes contradictory. This review seeks to focus on recent studies on heme transporters with specific emphasis on their functions during erythropoiesis. PMID:23415705

  11. Electron transfer patterns of the di-heme protein cytochrome c(4) from Pseudomonas stutzeri

    DEFF Research Database (Denmark)

    Raffalt, Anders Christer; Schmidt, L.; Christensen, Hans Erik Mølager

    2009-01-01

    protein structural mobility in the overall two-ET process. We suggest that conformational protein mobility blocks intramolecular interheme ET in bulk homogeneous solution but triggers opening of this gated ET channel in the electrochemical environment or in the membrane environment of natural respiratory...

  12. Electronic structure of silicene

    International Nuclear Information System (INIS)

    Voon, L. C. Lew Yan

    2015-01-01

    In this topical review, we discuss the electronic structure of free-standing silicene by comparing results obtained using different theoretical methods. Silicene is a single atomic layer of silicon similar to graphene. The interest in silicene is the same as for graphene, in being two-dimensional and possessing a Dirac cone. One advantage of silicene is due to its compatibility with current silicon electronics. Both empirical and first-principles techniques have been used to study the electronic properties of silicene. We will provide a brief overview of the parameter space for first-principles calculations. However, since the theory is standard, no extensive discussion will be included. Instead, we will emphasize what empirical methods can provide to such investigations and the current state of these theories. Finally, we will review the properties computed using both types of theories for free-standing silicene, with emphasis on areas where we have contributed. Comparisons to graphene is provided throughout. (topical review)

  13. Electronic band structure

    International Nuclear Information System (INIS)

    Grosso, G.

    1986-01-01

    The aim of this chapter is to present, in detail, some theoretical methods used to calculate electronic band structures in crystals. The basic strategies employed to attack the problem of electronic-structure calculations are presented. Successive sections present the basic formulations of the tight-binding, orthogonalized-plane-wave, Green'sfunction, and pseudopotential methods with a discussion of their application to perfect solids. Exemplifications in the case of a few selected problems provide further insight by the author into the physical aspects of the different methods and are a guide to the use of their mathematical techniques. A discussion is offered of completely a priori Hartree-Fock calculations and attempts to extend them. Special aspects of the different methods are also discussed in light of recently published related work

  14. Binding of Pseudomonas aeruginosa Apo-Bacterioferritin Associated Ferredoxin to Bacterioferritin B Promotes Heme Mediation of Electron Delivery and Mobilization of Core Mineral Iron†

    Science.gov (United States)

    Weeratunga, Saroja K.; Gee, Casey E.; Lovell, Scott; Zeng, Yuhong; Woodin, Carrie L.; Rivera, Mario

    2009-01-01

    The bfrB gene from Pseudomonas aeruginosa was cloned and expressed in E. coli. The resultant protein (BfrB), which assembles into a 445.3 kDa complex0020from 24 identical subunits, binds 12 molecules of heme axially coordinated by two Met residues. BfrB, isolated with 5–10 iron atoms per protein molecule, was reconstituted with ferrous ions to prepare samples with a core mineral containing 600 ± 40 ferric ions per BfrB molecule and approximately one phosphate molecule per iron atom. In the presence of sodium dithionite or in the presence of P. aeruginosa ferredoxin NADP reductase (FPR) and NADPH the heme in BfrB remains oxidized and the core iron mineral is mobilized sluggishly. In stark contrast, addition of NADPH to a solution containing BfrB, FPR and the apo-form of P. aeruginosa bacterioferritin associated ferredoxin (apo-Bfd) results in rapid reduction of the heme in BfrB and in the efficient mobilization of the core iron mineral. Results from additional experimentation indicate that Bfd must bind to BfrB to promote heme mediation of electrons from the surface to the core to support the efficient mobilization of ferrous ions from BfrB. In this context, the thus far mysterious role of heme in bacterioferritins has been brought to the front by reconstituting BfrB with its physiological partner, apo-Bfd. These findings are discussed in the context of a model for the utilization of stored iron in which the significant upregulation of the bfd gene under low-iron conditions [Ochsner, U.A., Wilderman, P.J., Vasil, A.I., and Vasil, M.L. (2002) Mol. Microbiol. 45, 1277–1287] ensures sufficient concentrations of apo-Bfd to bind BfrB and unlock the iron stored in its core. Although these findings are in contrast to previous speculations suggesting redox mediation of electron transfer by holo-Bfd, the ability of apo-Bfd to promote iron mobilization is an economical strategy used by the cell because it obviates the need to further deplete cellular iron levels to

  15. The electronic structures of solids

    CERN Document Server

    Coles, B R

    2013-01-01

    The Electronic Structures of Solids aims to provide students of solid state physics with the essential concepts they will need in considering properties of solids that depend on their electronic structures and idea of the electronic character of particular materials and groups of materials. The book first discusses the electronic structure of atoms, including hydrogen atom and many-electron atom. The text also underscores bonding between atoms and electrons in metals. Discussions focus on bonding energies and structures in the solid elements, eigenstates of free-electron gas, and electrical co

  16. Human heme oxygenase oxidation of 5- and 15-phenylhemes.

    Science.gov (United States)

    Wang, Jinling; Niemevz, Fernando; Lad, Latesh; Huang, Liusheng; Alvarez, Diego E; Buldain, Graciela; Poulos, Thomas L; de Montellano, Paul R Ortiz

    2004-10-08

    Human heme oxygenase-1 (hHO-1) catalyzes the O2-dependent oxidation of heme to biliverdin, CO, and free iron. Previous work indicated that electrophilic addition of the terminal oxygen of the ferric hydroperoxo complex to the alpha-meso-carbon gives 5-hydroxyheme. Earlier efforts to block this reaction with a 5-methyl substituent failed, as the reaction still gave biliverdin IXalpha. Surprisingly, a 15-methyl substituent caused exclusive cleavage at the gamma-meso-rather than at the normal, unsubstituted alpha-meso-carbon. No CO was formed in these reactions, but the fragment cleaved from the porphyrin eluded identification. We report here that hHO-1 cleaves 5-phenylheme to biliverdin IXalpha and oxidizes 15-phenylheme at the alpha-meso position to give 10-phenylbiliverdin IXalpha. The fragment extruded in the oxidation of 5-phenylheme is benzoic acid, one oxygen of which comes from O2 and the other from water. The 2.29- and 2.11-A crystal structures of the hHO-1 complexes with 1- and 15-phenylheme, respectively, show clear electron density for both the 5- and 15-phenyl rings in both molecules of the asymmetric unit. The overall structure of 15-phenylheme-hHO-1 is similar to that of heme-hHO-1 except for small changes in distal residues 141-150 and in the proximal Lys18 and Lys22. In the 5-phenylheme-hHO-1 structure, the phenyl-substituted heme occupies the same position as heme in the heme-HO-1 complex but the 5-phenyl substituent disrupts the rigid hydrophobic wall of residues Met34, Phe214, and residues 26-42 near the alpha-meso carbon. The results provide independent support for an electrophilic oxidation mechanism and support a role for stereochemical control of the reaction regiospecificity.

  17. Structure of the C-terminal heme-binding domain of THAP domain containing protein 4 from Homo sapiens

    Energy Technology Data Exchange (ETDEWEB)

    Bianchetti, Christopher M.; Bingman, Craig A.; Phillips, Jr., George N. (UW)

    2012-03-15

    functionally characterized. On the basis of prior work, we predicted that cTHAP4 is composed of a heme-binding nitrobindin domain, making THAP4 the only human THAP protein predicted to bind a cofactor. Nitrobindin, a recently characterized protein from Arabidopsis thaliana, is structurally similar and exhibits nitric oxide (NO)-binding properties that resemble the heme-binding nitrophorins. Nitrophorins use a heme moiety to store, transport, and release NO in a pH-specific manner. Although the exact function of nitrobindin is not fully known, the similarities between the well-characterized nitrophorins imply a role in NO transport, sensing, or metabolism. To better elucidate the possible function of THAP4, we solved the hemebound structure of cTHAP4 to a resolution of 1.79 {angstrom}.

  18. Structure-Function Relationships in the Gas-Sensing Heme-Dependent Transcription Factors RcoM and DNR

    Science.gov (United States)

    Bowman, Hannah E.

    Transition metals play an important role in many biological processes, however, they are also toxic at high concentrations. Therefore, the uptake and efflux of these metals must be tightly regulated by the cell. Bacteria have evolved a variety of pathways and regulatory systems to monitor the presence and concentration of metals in the cellular environment. A key component of those systems are transcription factors that either "sense metals" or use "metal sensors". The first class of these proteins have metals as their allosteric effector ligand. The second class of these proteins utilize transition metal containing cofactors to sense other environmental cues through the specific chemistry afforded by the cofactor. Chapter 1 reviews the current literature regarding both types of transcription factors. The focus of this work has been on two heme-containing, gas-sensing transcription factors found in bacteria, RcoM (regulator of CO metabolism) and DNR (dissimilative nitrate respiration regulator). RcoM is a CO-dependent protein found in Burkholderia xenovorans and sits upstream of the cox operon for oxidative CO metabolism. RcoM senses the presence of CO, as well as changes in redox potential, through a ligand switch process at its heme cofactor. Chapter 2 details spectroscopic characterization of several methionine mutants to identify the Fe(II) ligand trans to His 74. That study concludes that Met104 acts as the CO-replacable ligand. Met105, while not the ligand, does play an important role in reversibility of the ligand switch process. RcoM has a unique tertiary structure that combines a sensory domain and a DNA-binding domain normally found in two-component systems. Chapter 3 provides evidence that RcoM adopts a dimeric state. Further biophysical and structural characterization gives further insight into how the two domains are organized and the implications for the DNA-binding mechanism. DNR is a NO-sensing transcription factor from Pseudomonas aeruginosa and

  19. Mechanism governing heme synthesis reveals a GATA factor/heme circuit that controls differentiation.

    Science.gov (United States)

    Tanimura, Nobuyuki; Miller, Eli; Igarashi, Kazuhiko; Yang, David; Burstyn, Judith N; Dewey, Colin N; Bresnick, Emery H

    2016-02-01

    Metal ion-containing macromolecules have fundamental roles in essentially all biological processes throughout the evolutionary tree. For example, iron-containing heme is a cofactor in enzyme catalysis and electron transfer and an essential hemoglobin constituent. To meet the intense demand for hemoglobin assembly in red blood cells, the cell type-specific factor GATA-1 activates transcription of Alas2, encoding the rate-limiting enzyme in heme biosynthesis, 5-aminolevulinic acid synthase-2 (ALAS-2). Using genetic editing to unravel mechanisms governing heme biosynthesis, we discovered a GATA factor- and heme-dependent circuit that establishes the erythroid cell transcriptome. CRISPR/Cas9-mediated ablation of two Alas2 intronic cis elements strongly reduces GATA-1-induced Alas2 transcription, heme biosynthesis, and surprisingly, GATA-1 regulation of other vital constituents of the erythroid cell transcriptome. Bypassing ALAS-2 function in Alas2 cis element-mutant cells by providing its catalytic product 5-aminolevulinic acid rescues heme biosynthesis and the GATA-1-dependent genetic network. Heme amplifies GATA-1 function by downregulating the heme-sensing transcriptional repressor Bach1 and via a Bach1-insensitive mechanism. Through this dual mechanism, heme and a master regulator collaborate to orchestrate a cell type-specific transcriptional program that promotes cellular differentiation. © 2015 The Authors.

  20. Characterization of Human and Yeast Mitochondrial Glycine Carriers with Implications for Heme Biosynthesis and Anemia.

    Science.gov (United States)

    Lunetti, Paola; Damiano, Fabrizio; De Benedetto, Giuseppe; Siculella, Luisa; Pennetta, Antonio; Muto, Luigina; Paradies, Eleonora; Marobbio, Carlo Marya Thomas; Dolce, Vincenza; Capobianco, Loredana

    2016-09-16

    Heme is an essential molecule in many biological processes, such as transport and storage of oxygen and electron transfer as well as a structural component of hemoproteins. Defects of heme biosynthesis in developing erythroblasts have profound medical implications, as represented by sideroblastic anemia. The synthesis of heme requires the uptake of glycine into the mitochondrial matrix where glycine is condensed with succinyl coenzyme A to yield δ-aminolevulinic acid. Herein we describe the biochemical and molecular characterization of yeast Hem25p and human SLC25A38, providing evidence that they are mitochondrial carriers for glycine. In particular, the hem25Δ mutant manifests a defect in the biosynthesis of δ-aminolevulinic acid and displays reduced levels of downstream heme and mitochondrial cytochromes. The observed defects are rescued by complementation with yeast HEM25 or human SLC25A38 genes. Our results identify new proteins in the heme biosynthetic pathway and demonstrate that Hem25p and its human orthologue SLC25A38 are the main mitochondrial glycine transporters required for heme synthesis, providing definitive evidence of their previously proposed glycine transport function. Furthermore, our work may suggest new therapeutic approaches for the treatment of congenital sideroblastic anemia. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  1. Challenging Density Functional Theory Calculations with Hemes and Porphyrins

    Science.gov (United States)

    de Visser, Sam P.; Stillman, Martin J.

    2016-01-01

    In this paper we review recent advances in computational chemistry and specifically focus on the chemical description of heme proteins and synthetic porphyrins that act as both mimics of natural processes and technological uses. These are challenging biochemical systems involved in electron transfer as well as biocatalysis processes. In recent years computational tools have improved considerably and now can reproduce experimental spectroscopic and reactivity studies within a reasonable error margin (several kcal·mol−1). This paper gives recent examples from our groups, where we investigated heme and synthetic metal-porphyrin systems. The four case studies highlight how computational modelling can correctly reproduce experimental product distributions, predicted reactivity trends and guide interpretation of electronic structures of complex systems. The case studies focus on the calculations of a variety of spectroscopic features of porphyrins and show how computational modelling gives important insight that explains the experimental spectra and can lead to the design of porphyrins with tuned properties. PMID:27070578

  2. Challenging Density Functional Theory Calculations with Hemes and Porphyrins

    Directory of Open Access Journals (Sweden)

    Sam P. de Visser

    2016-04-01

    Full Text Available In this paper we review recent advances in computational chemistry and specifically focus on the chemical description of heme proteins and synthetic porphyrins that act as both mimics of natural processes and technological uses. These are challenging biochemical systems involved in electron transfer as well as biocatalysis processes. In recent years computational tools have improved considerably and now can reproduce experimental spectroscopic and reactivity studies within a reasonable error margin (several kcal·mol−1. This paper gives recent examples from our groups, where we investigated heme and synthetic metal-porphyrin systems. The four case studies highlight how computational modelling can correctly reproduce experimental product distributions, predicted reactivity trends and guide interpretation of electronic structures of complex systems. The case studies focus on the calculations of a variety of spectroscopic features of porphyrins and show how computational modelling gives important insight that explains the experimental spectra and can lead to the design of porphyrins with tuned properties.

  3. Transmutation of a heme protein.

    Science.gov (United States)

    Barker, P D; Ferrer, J C; Mylrajan, M; Loehr, T M; Feng, R; Konishi, Y; Funk, W D; MacGillivray, R T; Mauk, A G

    1993-01-01

    Residue Asn57 of bovine liver cytochrome b5 has been replaced with a cysteine residue, and the resulting variant has been isolated from recombinant Escherichia coli as a mixture of four major species: A, BI, BII, and C. A combination of electronic spectroscopy, 1H NMR spectroscopy, resonance Raman spectroscopy, electrospray mass spectrometry, and direct electrochemistry has been used to characterize these four major cytochrome derivatives. The red form A (E(m) = -19 mV) is found to possess a heme group bound covalently through a thioether linkage involving Cys57 and the alpha carbon of the heme 4-vinyl group. Form BI has a covalently bound heme group coupled through a thioether linkage involving the beta carbon of the heme 4-vinyl group. Form BII is similar to BI except that the sulfur involved in the thioether linkage is oxidized to a sulfoxide. The green form C (E(m) = 175 mV) possesses a noncovalently bound prosthetic group with spectroscopic properties characteristic of a chlorin. A mechanism is proposed for the generation of these derivatives, and the implications of these observations for the biosynthesis of cytochrome c and naturally occurring chlorin prosthetic groups are discussed. PMID:8341666

  4. Electronic structure of superlattices

    International Nuclear Information System (INIS)

    Altarelli, M.

    1987-01-01

    Calculations of electronic states in semiconductor superlattices are briefly reviewed, with emphasis on the envelope-function method and on comparison with experiments. The energy levels in presence of external magnetic fields are discussed and compared to magneto-optical experiments. (author) [pt

  5. Electronic structure of alloys

    International Nuclear Information System (INIS)

    Ehrenreich, H.; Schwartz, L.M.

    1976-01-01

    The description of electronic properties of binary substitutional alloys within the single particle approximation is reviewed. Emphasis is placed on a didactic exposition of the equilibrium properties of the transport and magnetic properties of such alloys. Topics covered include: multiple scattering theory; the single band alloy; formal extensions of the theory; the alloy potential; realistic model state densities; the s-d model; and the muffin tin model. 43 figures, 3 tables, 151 references

  6. Characterization of Heme Proteins Involved in Microbial Exoelectric Activity and Small Molecule-Sensing

    KAUST Repository

    Vogler, Malvina M.

    2018-01-01

    Heme proteins, also termed cytochromes, are a widespread class of metalloproteins containing an Fe-protoporphyrin IX cofactor. They perform numerous functions in nature such as oxygen-transport by hemoglobin, monooxygenation reactions catalyzed by Cytochrome P-450, and electron transfer reactions during photosynthesis. The differences between proteincofactor binding characteristics and the cofactor environment greatly influence the extensive range of functions. In this dissertation, proteins from the Mtr pathway of Shewanella oneidensis are characterized. These c-type cytochromes contain multiple heme cofactors per protein molecule that covalently attach to the protein amino acid sequence and are involved in electron transfer to extracellular metal oxides during anaerobic conditions. Successful recombinant expression of pathway components MtrC and MtrA is achieved in Escherichia coli. Heme-dependent gel staining and UV/Vis spectroscopy show characteristic c-type cytochrome characteristics. Mass spectrometry confirms that the correct extensive post-translational modifications were performed and the ten heme groups were incorporated per protein of MtrC and MtrA and the correct lipid-anchor was attached to extracellular MtrC. Raman spectroscopy measurements of MtrA provide intriguing structural information and highlight the strong influence of the heme cofactors within the protein structure. Next, an Arabidopsis thaliana protein is analyzed. It was previously identified via a motif search of the plant genome, based on conserved residues in the H4 NOX pocket. Here, the incorporation of a heme b cofactor is confirmed. UV/Vis spectroscopy under anaerobic conditions demonstrates reversible binding of nitric oxide to the heme iron and depicts the previously published characteristic absorption maxima for other H-NOX proteins.

  7. Electronics for Piezoelectric Smart Structures

    Science.gov (United States)

    Warkentin, D. J.; Tani, J.

    1997-01-01

    This paper briefly presents work addressing some of the basic considerations for the electronic components used in smart structures incorporating piezoelectric elements. After general remarks on the application of piezoelectric elements to the problem of structural vibration control, three main topics are described. Work to date on the development of techniques for embedding electronic components within structural parts is presented, followed by a description of the power flow and dissipation requirements of those components. Finally current work on the development of electronic circuits for use in an 'active wall' for acoustic noise is introduced.

  8. The Structure of the Complex between Yeast Frataxin and Ferrochelatase: CHARACTERIZATION AND PRE-STEADY STATE REACTION OF FERROUS IRON DELIVERY AND HEME SYNTHESIS.

    Science.gov (United States)

    Söderberg, Christopher; Gillam, Mallory E; Ahlgren, Eva-Christina; Hunter, Gregory A; Gakh, Oleksandr; Isaya, Grazia; Ferreira, Gloria C; Al-Karadaghi, Salam

    2016-05-27

    Frataxin is a mitochondrial iron-binding protein involved in iron storage, detoxification, and delivery for iron sulfur-cluster assembly and heme biosynthesis. The ability of frataxin from different organisms to populate multiple oligomeric states in the presence of metal ions, e.g. Fe(2+) and Co(2+), led to the suggestion that different oligomers contribute to the functions of frataxin. Here we report on the complex between yeast frataxin and ferrochelatase, the terminal enzyme of heme biosynthesis. Protein-protein docking and cross-linking in combination with mass spectroscopic analysis and single-particle reconstruction from negatively stained electron microscopic images were used to verify the Yfh1-ferrochelatase interactions. The model of the complex indicates that at the 2:1 Fe(2+)-to-protein ratio, when Yfh1 populates a trimeric state, there are two interaction interfaces between frataxin and the ferrochelatase dimer. Each interaction site involves one ferrochelatase monomer and one frataxin trimer, with conserved polar and charged amino acids of the two proteins positioned at hydrogen-bonding distances from each other. One of the subunits of the Yfh1 trimer interacts extensively with one subunit of the ferrochelatase dimer, contributing to the stability of the complex, whereas another trimer subunit is positioned for Fe(2+) delivery. Single-turnover stopped-flow kinetics experiments demonstrate that increased rates of heme production result from monomers, dimers, and trimers, indicating that these forms are most efficient in delivering Fe(2+) to ferrochelatase and sustaining porphyrin metalation. Furthermore, they support the proposal that frataxin-mediated delivery of this potentially toxic substrate overcomes formation of reactive oxygen species. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  9. Structure-Activity Relationships of 1,2-Disubstituted Benzimidazoles: Selective Inhibition of Heme Oxygenase-2 Activity.

    Science.gov (United States)

    Kong, Xianqi; Vukomanovic, Dragic; Nakatsu, Kanji; Szarek, Walter A

    2015-08-01

    Devising ways to up- or down-regulate heme oxygenase activity is attracting much interest as a strategy for the treatment of a variety of disorders. With a view of obtaining compounds that exhibit high potency and selectivity as inhibitors of the heme oxygenase-2 (HO-2) isozyme (constitutive) relative to the heme oxygenase-1 (HO-1) isozyme (inducible), several 1,2-disubstituted 1H-benzimidazoles were designed and synthesized. Specifically, analogues were synthesized in which the C2 substituent was the following: (1H-imidazol-1-yl)methyl, (N-morpholinyl)methyl, cyclopentylmethyl, cyclohexylmethyl, or (norborn-2-yl)methyl. Compounds with the cyclic system in the C2 substituent being a carbocyclic ring, especially cyclohexyl or norborn-2-yl, and the N1 substituent being a ring-substituted benzyl group, especially 4-chlorobenzyl or 4-bromobenzyl, best exhibited the target criteria of high potency and selectivity toward inhibition of HO-2. The new candidates should be useful pharmacological tools and may have therapeutic applications. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Electronic structure of silicon superlattices

    International Nuclear Information System (INIS)

    Krishnamurthy, S.; Moriarty, J.A.

    1984-01-01

    Utilizing a new complex-band-structure technique, the electronic structure of model Si-Si/sub 1-x/Ge/sub x/ and MOS superlattices has been obtained over a wide range of layer thickness d (11 less than or equal to d less than or equal to 110 A). For d greater than or equal to 44 A, it is found that these systems exhibit a direct fundamental band gap. Further calculations of band-edge effective masses and impurity scattering rates suggest the possibility of a band-structure-driven enhancement in electron mobility over bulk silicon

  11. An ethane-bridged porphyrin dimer as a model of di-heme proteins: inorganic and bioinorganic perspectives and consequences of heme-heme interactions.

    Science.gov (United States)

    Sil, Debangsu; Rath, Sankar Prasad

    2015-10-07

    Interaction between heme centers has been cleverly implemented by Nature in order to regulate different properties of multiheme cytochromes, thereby allowing them to perform a wide variety of functions. Our broad interest lies in unmasking the roles played by heme-heme interactions in modulating different properties viz., metal spin state, redox potential etc., of the individual heme centers using an ethane-bridged porphyrin dimer as a synthetic model of dihemes. The large differences in the structure and properties of the diheme complexes, as compared to the monoheme analogs, provide unequivocal evidence of the role played by heme-heme interactions in the dihemes. This Perspective provides a brief account of our recent efforts to explore these interesting aspects and the subsequent outcomes.

  12. Moessbauer spectroscopic study of polymer-bound heme complexes

    International Nuclear Information System (INIS)

    Tsuchida, Eishun; Nishide, Hiroyuki; Yokoyama, Hiroyuki; Inoue, Hidenari; Shirai, Tsuneo.

    1984-01-01

    Moessbauer spectra were measured on the heme complexes of poly(1-vinyl- and 1-vinyl-2-methylimidazole)(PVI and PMI) and heme derivatives with covalently bound imidazoleligand (IH) and 2-methylimidazole-ligand (MIH) embedded in poly(1-vinyl-2-pyrrolidone) film. Quadrupole splitting (ΔE sub(Q)) for the carbon monoxide adduct of PMI-heme indicated large electronic field gradient at the iron nucleus, probably due to steric hindrance of the polymer chain, and this behavior agreed with its low affinity with carbon monoxide. PMI-heme formed an oxygen adduct and its isomer shift and ΔE sub(Q) values were obtained. (author)

  13. Electronic structure and correlation effects in actinides

    International Nuclear Information System (INIS)

    Albers, R.C.

    1998-01-01

    This report consists of the vugraphs given at a conference on electronic structure. Topics discussed are electronic structure, f-bonding, crystal structure, and crystal structure stability of the actinides and how they are inter-related

  14. Ballistic transport and electronic structure

    NARCIS (Netherlands)

    Schep, Kees M.; Kelly, Paul J.; Bauer, Gerrit E.W.

    1998-01-01

    The role of the electronic structure in determining the transport properties of ballistic point contacts is studied. The conductance in the ballistic regime is related to simple geometrical projections of the Fermi surface. The essential physics is first clarified for simple models. For real

  15. The Electronic Structure of Calcium

    DEFF Research Database (Denmark)

    Jan, J.-P.; Skriver, Hans Lomholt

    1981-01-01

    The electronic structure of calcium under pressure is re-examined by means of self-consistent energy band calculations based on the local density approximation and using the linear muffin-tin orbitals (LMTO) method with corrections to the atomic sphere approximation included. At zero pressure...

  16. Electronic structure of metal clusters

    International Nuclear Information System (INIS)

    Wertheim, G.K.

    1989-01-01

    Photoemission spectra of valence electrons in metal clusters, together with threshold ionization potential measurements, provide a coherent picture of the development of the electronic structure from the isolated atom to the large metallic cluster. An insulator-metal transition occurs at an intermediate cluster size, which serves to define the boundary between small and large clusters. Although the outer electrons may be delocalized over the entire cluster, a small cluster remains insulating until the density of states near the Fermi level exceeds 1/kT. In large clusters, with increasing cluster size, the band structure approaches that of the bulk metal. However, the bands remain significantly narrowed even in a 1000-atom cluster, giving an indication of the importance of long-range order. The core-electron binding-energy shifts of supported metal clusters depend on changes in the band structure in the initial state, as well as on various final-state effects, including changes in core hole screening and the coulomb energy of the final-state charge. For cluster supported on amorphous carbon, this macroscopic coulomb shift is often dominant, as evidenced by the parallel shifts of the core-electron binding energy and the Fermi edge. Auger data confirm that final-state effects dominate in cluster of Sn and some other metals. Surface atom core-level shifts provide a valuable guide to the contributions of initial-state changes in band structure to cluster core-electron binding energy shifts, especially for Au and Pt. The available data indicate that the shift observed in supported, metallic clusters arise largely from the charge left on the cluster by photoemission. As the metal-insulator transition is approached from above, metallic screening is suppressed and the shift is determined by the local environment. (orig.)

  17. Heme in pathophysiology: a matter of scavenging, metabolism and trafficking across cell membranes

    OpenAIRE

    Chiabrando, Deborah; Vinchi, Francesca; Fiorito, Veronica; Mercurio, Sonia; Tolosano, Emanuela

    2014-01-01

    Heme (iron-protoporphyrin IX) is an essential co-factor involved in multiple biological processes: oxygen transport and storage, electron transfer, drug and steroid metabolism, signal transduction, and micro RNA processing. However, excess free-heme is highly toxic due to its ability to promote oxidative stress and lipid peroxidation, thus leading to membrane injury and, ultimately, apoptosis. Thus, heme metabolism needs to be finely regulated. Intracellular heme amount is controlled at multi...

  18. Heme Gazing: Illuminating Eukaryotic Heme Trafficking, Dynamics, and Signaling with Fluorescent Heme Sensors.

    Science.gov (United States)

    Hanna, David A; Martinez-Guzman, Osiris; Reddi, Amit R

    2017-04-04

    Heme (iron protoporphyrin IX) is an essential protein prosthetic group and signaling molecule required for most life on Earth. All heme-dependent processes require the dynamic and rapid mobilization of heme from sites of synthesis or uptake to hemoproteins present in virtually every subcellular compartment. The cytotoxicity and hydrophobicity of heme necessitate that heme mobilization be carefully controlled to mitigate the deleterious effects of this essential toxin. Indeed, a number of disorders, including certain cancers, cardiovascular diseases, and aging and age-related neurodegenerative diseases, are tied to defects in heme homeostasis. However, the molecules and mechanisms that mediate heme transport and trafficking, and the dynamics of these processes, are poorly understood. This is in large part due to the lack of physical tools for probing cellular heme. Herein, we discuss the recent development of fluorescent probes that can monitor and image kinetically labile heme with respect to its mobilization and role in signaling. In particular, we will highlight how heme gazing with these tools can uncover new heme trafficking factors upon being integrated with genetic screens and illuminate the concentration, subcellular distribution, and dynamics of labile heme in various physiological contexts. Altogether, the monitoring of labile heme, along with recent biochemical and cell biological studies demonstrating the reversible regulation of certain cellular processes by heme, is challenging us to reconceptualize heme from being a static cofactor buried in protein active sites to a dynamic and mobile signaling molecule.

  19. Mutations in the FMN domain modulate MCD spectra of the heme site in the oxygenase domain of inducible nitric oxide synthase.

    Science.gov (United States)

    Sempombe, Joseph; Elmore, Bradley O; Sun, Xi; Dupont, Andrea; Ghosh, Dipak K; Guillemette, J Guy; Kirk, Martin L; Feng, Changjian

    2009-05-27

    The nitric oxide synthase (NOS) output state for NO production is a complex of the flavin mononucleotide (FMN)-binding domain and the heme domain, and thereby it facilitates the interdomain electron transfer from the FMN to the catalytic heme site. Emerging evidence suggests that interdomain FMN-heme interactions are important in the formation of the output state because they guide the docking of the FMN domain to the heme domain. In this study, notable effects of mutations in the adjacent FMN domain on the heme structure in a human iNOS bidomain oxygenase/FMN construct have been observed by using low-temperature magnetic circular dichroism (MCD) spectroscopy. The comparative MCD study of wild-type and mutant proteins clearly indicates that a properly docked FMN domain contributes to the observed L-Arg perturbation of the heme MCD spectrum in the wild-type protein and that the conserved surface residues in the FMN domain (E546 and E603) play key roles in facilitating a productive alignment of the FMN and heme domains in iNOS.

  20. Stability enhancement of cytochrome c through heme deprotonation and mutations.

    Science.gov (United States)

    Sonoyama, Takafumi; Hasegawa, Jun; Uchiyama, Susumu; Nakamura, Shota; Kobayashi, Yuji; Sambongi, Yoshihiro

    2009-01-01

    The chemical denaturation of Pseudomonas aeruginosa cytochrome c(551) variants was examined at pH 5.0 and 3.6. All variants were stabilized at both pHs compared with the wild-type. Remarkably, the variants carrying the F34Y and/or E43Y mutations were more stabilized than those having the F7A/V13M or V78I ones at pH 5.0 compared with at pH 3.6 by ~3.0-4.6 kJ/mol. Structural analyses predicted that the side chains of introduced Tyr-34 and Tyr-43 become hydrogen donors for the hydrogen bond formation with heme 17-propionate at pH 5.0, but less efficiently at pH 3.6, because the propionate is deprotonated at the higher pH. Our results provide an insight into a stabilization strategy for heme proteins involving variation of the heme electronic state and introduction of appropriate mutations.

  1. Heme Recognition By a Staphylococcus Aureus IsdE

    Energy Technology Data Exchange (ETDEWEB)

    Grigg, J.C.; Vermeiren, C.L.; Heinrichs, D.E.; Murphy, M.E.P.

    2009-06-03

    Staphylococcus aureus is a Gram-positive bacterial pathogen and a leading cause of hospital acquired infections. Because the free iron concentration in the human body is too low to support growth, S. aureus must acquire iron from host sources. Heme iron is the most prevalent iron reservoir in the human body and a predominant source of iron for S. aureus. The iron-regulated surface determinant (Isd) system removes heme from host heme proteins and transfers it to IsdE, the cognate substrate-binding lipoprotein of an ATP-binding cassette transporter, for import and subsequent degradation. Herein, we report the crystal structure of the soluble portion of the IsdE lipoprotein in complex with heme. The structure reveals a bi-lobed topology formed by an N- and C-terminal domain bridged by a single {alpha}-helix. The structure places IsdE as a member of the helical backbone metal receptor superfamily. A six-coordinate heme molecule is bound in the groove established at the domain interface, and the heme iron is coordinated in a novel fashion for heme transporters by Met{sup 78} and His{sup 229}. Both heme propionate groups are secured by H-bonds to IsdE main chain and side chain groups. Of these residues, His{sup 299} is essential for IsdE-mediated heme uptake by S. aureus when growth on heme as a sole iron source is measured. Multiple sequence alignments of homologues from several other Gram-positive bacteria, including the human pathogens pyogenes, Bacillus anthracis, and Listeria monocytogenes, suggest that these other systems function equivalently to S. aureus IsdE with respect to heme binding and transport.

  2. Electronic structure of lanthanide scandates

    Science.gov (United States)

    Mizzi, Christopher A.; Koirala, Pratik; Marks, Laurence D.

    2018-02-01

    X-ray photoelectron spectroscopy, ultraviolet photoelectron spectroscopy, and density functional theory calculations were used to study the electronic structure of three lanthanide scandates: GdSc O3,TbSc O3 , and DySc O3 . X-ray photoelectron spectra simulated from first-principles calculations using a combination of on-site hybrid and GGA +U methods were found to be in good agreement with experimental x-ray photoelectron spectra. The hybrid method was used to model the ground state electronic structure and the GGA +U method accounted for the shift of valence state energies due to photoelectron emission via a Slater-Janak transition state approach. From these results, the lanthanide scandate valence bands were determined to be composed of Ln 4 f ,O 2 p , and Sc 3 d states, in agreement with previous work. However, contrary to previous work the minority Ln 4 f states were found to be located closer to, and in some cases at, the valence band maximum. This suggests that minority Ln 4 f electrons may play a larger role in lanthanide scandate properties than previously thought.

  3. Study on models of O2 binding to heme using density functional theory

    Directory of Open Access Journals (Sweden)

    Hovorun D. M.

    2009-08-01

    Full Text Available Aim. To study a mechanism of molecular oxygen binding to heme three models of geometry structure of the complex are considered: the axis of O2 molecule is situated perpendicularly to the porphin macrocycle, parallel, and angularly. Methods. The Fe(II porphin complexes with dioxygen are calculated by the quantum-chemical method of density functional theory with the UB3LYP/6-311G approximation. Results. The optimized geometry and electron structures as well as the absorption IR spectra of the complexes in the high-spin (septet state are described. Conclusions. It is shown that the main mechanism of spin-orbit coupling during the O2 binding to heme is connected with peculiarity of the O2 molecule electronic structure.

  4. Electron scattering and nuclear structure

    International Nuclear Information System (INIS)

    Frois, B.

    1987-01-01

    The search for the appropriate degrees of freedom to describe nuclei is the central focus of nuclear physics today. Therefore the authors explore in this review their current understanding of nuclear structure as defined by electromagnetic data. The precision of the electromagnetic probe allows us to define accurately the limits of present theoretical descriptions. The authors review here a broad range of subjects that have been addressed by recent experiments, from the study of meson exchange currents and single-particle distributions to collective excitations in heavy nuclei. However, they do not discuss elastic magnetic scattering, inelastic excitation of discrete states, or single-nucleon knockout reactions since these reactions were recently reviewed. The principal aim of this review is to offer a fresh perspective on nuclear structure, based on the new generation of electron scattering data presented here and in the above-mentioned articles

  5. Synthesis of 5-hydroxyectoine from ectoine: crystal structure of the non-heme iron(II and 2-oxoglutarate-dependent dioxygenase EctD.

    Directory of Open Access Journals (Sweden)

    Klaus Reuter

    2010-05-01

    Full Text Available As a response to high osmolality, many microorganisms synthesize various types of compatible solutes. These organic osmolytes aid in offsetting the detrimental effects of low water activity on cell physiology. One of these compatible solutes is ectoine. A sub-group of the ectoine producer's enzymatically convert this tetrahydropyrimidine into a hydroxylated derivative, 5-hydroxyectoine. This compound also functions as an effective osmostress protectant and compatible solute but it possesses properties that differ in several aspects from those of ectoine. The enzyme responsible for ectoine hydroxylation (EctD is a member of the non-heme iron(II-containing and 2-oxoglutarate-dependent dioxygenases (EC 1.14.11. These enzymes couple the decarboxylation of 2-oxoglutarate with the formation of a high-energy ferryl-oxo intermediate to catalyze the oxidation of the bound organic substrate. We report here the crystal structure of the ectoine hydroxylase EctD from the moderate halophile Virgibacillus salexigens in complex with Fe(3+ at a resolution of 1.85 A. Like other non-heme iron(II and 2-oxoglutarate dependent dioxygenases, the core of the EctD structure consists of a double-stranded beta-helix forming the main portion of the active-site of the enzyme. The positioning of the iron ligand in the active-site of EctD is mediated by an evolutionarily conserved 2-His-1-carboxylate iron-binding motif. The side chains of the three residues forming this iron-binding site protrude into a deep cavity in the EctD structure that also harbours the 2-oxoglutarate co-substrate-binding site. Database searches revealed a widespread occurrence of EctD-type proteins in members of the Bacteria but only in a single representative of the Archaea, the marine crenarchaeon Nitrosopumilus maritimus. The EctD crystal structure reported here can serve as a template to guide further biochemical and structural studies of this biotechnologically interesting enzyme family.

  6. Electronic structure of spin systems

    Energy Technology Data Exchange (ETDEWEB)

    Saha-Dasgupta, Tanusri

    2016-04-15

    Highlights: • We review the theoretical modeling of quantum spin systems. • We apply the Nth order muffin-tin orbital electronic structure method. • The method shows the importance of chemistry in the modeling. • CuTe{sub 2}O{sub 5} showed a 2-dimensional coupled spin dimer behavior. • Ti substituted Zn{sub 2}VO(PO{sub 4}){sub 2} showed spin gap behavior. - Abstract: Low-dimensional quantum spin systems, characterized by their unconventional magnetic properties, have attracted much attention. Synthesis of materials appropriate to various classes within these systems has made this field very attractive and a site of many activities. The experimental results like susceptibility data are fitted with the theoretical model to derive the underlying spin Hamiltonian. However, often such a fitting procedure which requires correct guess of the assumed spin Hamiltonian leads to ambiguity in deciding the representative model. In this review article, we will describe how electronic structure calculation within the framework of Nth order muffin-tin orbital (NMTO) based Wannier function technique can be utilized to identify the underlying spin model for a large number of such compounds. We will show examples from compounds belonging to vanadates and cuprates.

  7. Covalent heme attachment to the protein in human heme oxygenase-1 with selenocysteine replacing the His25 proximal iron ligand.

    Science.gov (United States)

    Jiang, Yongying; Trnka, Michael J; Medzihradszky, Katalin F; Ouellet, Hugues; Wang, Yongqiang; Ortiz de Montellano, Paul R

    2009-03-01

    To characterize heme oxygenase with a selenocysteine (SeCys) as the proximal iron ligand, we have expressed truncated human heme oxygenase-1 (hHO-1) His25Cys, in which Cys-25 is the only cysteine, in the Escherichia coli cysteine auxotroph strain BL21(DE3)cys. Selenocysteine incorporation into the protein was demonstrated by both intact protein mass measurement and mass spectrometric identification of the selenocysteine-containing tryptic peptide. One selenocysteine was incorporated into approximately 95% of the expressed protein. Formation of an adduct with Ellman's reagent (DTNB) indicated that the selenocysteine in the expressed protein was in the reduced state. The heme-His25SeCys hHO-1 complex could be prepared by either (a) supplementing the overexpression medium with heme, or (b) reconstituting the purified apoprotein with heme. Under reducing conditions in the presence of imidazole, a covalent bond is formed by addition of the selenocysteine residue to one of the heme vinyl groups. No covalent bond is formed when the heme is replaced by mesoheme, in which the vinyls are replaced by ethyl groups. These results, together with our earlier demonstration that external selenolate ligands can transfer an electron to the iron [Y. Jiang, P.R. Ortiz de Montellano, Inorg. Chem. 47 (2008) 3480-3482 ], indicate that a selenyl radical is formed in the hHO-1 His25SeCys mutant that adds to a heme vinyl group.

  8. Electronic structure of semiconductor interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Herman, F

    1983-02-01

    The study of semiconductor interfaces is one of the most active and exciting areas of current semiconductor research. Because interfaces play a vital role in modern semiconductor technology (integrated circuits, heterojunction lasers, solar cells, infrared detectors, etc.), there is a strong incentive to understand interface properties at a fundamental level and advance existing technology thereby. At the same time, technological advances such as molecular beam epitaxy have paved the way for the fabrication of semiconductor heterojunctions and superlattices of novel design which exhibit unusual electronic, optical, and magnetic properties and offer unique opportunities for fundamental scientific research. A general perspective on this subject is offered treating such topics as the atomic and electronic structure of semiconductor surfaces and interfaces; oxidation and oxide layers; semiconductor heterojunctions and superlattices; rectifying metal-semiconductor contacts; and interface reactions. Recent progress is emphasized and some future directions are indicated. In addition, the role that large-scale scientific computation has played in furthering our theoretical understanding of semiconductor surfaces and interfaces is discussed. Finally, the nature of theoretical models, and the role they play in describing the physical world is considered.

  9. Electronic structure of semiconductor interfaces

    International Nuclear Information System (INIS)

    Herman, F.

    1983-01-01

    The study of semiconductor interfaces is one of the most active and exciting areas of current semiconductor research. Because interfaces play a vital role in modern semiconductor technology (integrated circuits, heterojunction lasers, solar cells, infrared detectors, etc.), there is a strong incentive to understand interface properties at a fundamental level and advance existing technology thereby. At the same time, technological advances such as molecular beam epitaxy have paved the way for the fabrication of semiconductor heterojunctions and superlattices of novel design which exhibit unusual electronic, optical, and magnetic properties and offer unique opportunities for fundamental scientific research. A general perspective on this subject is offered treating such topics as the atomic and electronic structure of semiconductor surfaces and interfaces; oxidation and oxide layers; semiconductor heterojunctions and superlattices; rectifying metal-semiconductor contacts; and interface reactions. Recent progress is emphasized and some future directions are indicated. In addition, the role that large-scale scientific computation has played in furthering our theoretical understanding of semiconductor surfaces and interfaces is discussed. Finally, the nature of theoretical models, and the role they play in describing the physical world is considered. (Author) [pt

  10. Wiring of heme enzymes by methylene-blue labeled dendrimers

    DEFF Research Database (Denmark)

    Álvarez-Martos, Isabel; Shahdost-fard, Faezeh; Ferapontova, Elena

    2017-01-01

    Redox-modified branched 3D dendrimeric nanostructures may be considered as perspective wires for electrical connection between redox enzymes and electrodes. Here, we studied electron transfer (ET) reactions and bioelectrocatalysis of heme-containing horseradish peroxidase (HRP) and heme- and moli......Redox-modified branched 3D dendrimeric nanostructures may be considered as perspective wires for electrical connection between redox enzymes and electrodes. Here, we studied electron transfer (ET) reactions and bioelectrocatalysis of heme-containing horseradish peroxidase (HRP) and heme......- and molibdopterin-containing sulfite oxidase (SOx), wired to gold by the methylene blue (MB)-labeled polyamidoamine (PAMAM) dendrimers. The enzymes’ electrochemical transformation and bioelectrocatalytic function could be followed at both unlabeled and MB-labeled dendrimer-modified electrodes with the formal redox......, optimization of bioelectrocatalysis of complex intermembrane and, possibly, membrane enzymes....

  11. Energy transfer at the active sites of heme proteins

    International Nuclear Information System (INIS)

    Dlott, D.D.; Hill, J.R.

    1995-01-01

    Experiments using a picosecond pump-probe apparatus at the Picosecond Free-electron Laser Center at Stanford University, were performed to investigate the relaxation of carbon monoxide bound to the active sites of heme proteins. The significance of these experiments is two-fold: (1) they provide detailed information about molecular dynamics occurring at the active sites of proteins; and (2) they provide insight into the nature of vibrational relaxation processes in condensed matter. Molecular engineering is used to construct various molecular systems which are studied with the FEL. We have studied native proteins, mainly myoglobin obtained from different species, mutant proteins produced by genetic engineering using recombinant DNA techniques, and a variety of model systems which mimic the structures of the active sites of native proteins, which are produced using molecular synthesis. Use of these different systems permits us to investigate how specific molecular structural changes affect dynamical processes occurring at the active sites. This research provides insight into the problems of how different species needs are fulfilled by heme proteins which have greatly different functionality, which is induced by rather small structural changes

  12. Mimicking heme enzymes in the solid state: metal-organic materials with selectively encapsulated heme.

    Science.gov (United States)

    Larsen, Randy W; Wojtas, Lukasz; Perman, Jason; Musselman, Ronald L; Zaworotko, Michael J; Vetromile, Carissa M

    2011-07-13

    To carry out essential life processes, nature has had to evolve heme enzymes capable of synthesizing and manipulating complex molecules. These proteins perform a plethora of chemical reactions utilizing a single iron porphyrin active site embedded within an evolutionarily designed protein pocket. We herein report the first class of metal-organic materials (MOMs) that mimic heme enzymes in terms of both structure and reactivity. The MOMzyme-1 class is based upon a prototypal MOM, HKUST-1, into which catalytically active metalloporphyrins are selectively encapsulated in a "ship-in-a-bottle" fashion within one of the three nanoscale cages that exist in HKUST-1. MOMs offer unparalleled levels of permanent porosity and their modular nature affords enormous diversity of structures and properties. The MOMzyme-1 class could therefore represent a new paradigm for heme biomimetic catalysis since it combines the activity of a homogeneous catalyst with the stability and recyclability of heterogeneous catalytic systems within a single material.

  13. X-ray absorption spectroscopic studies of mononuclear non-heme iron enzymes

    Energy Technology Data Exchange (ETDEWEB)

    Westre, Tami E. [Stanford Univ., CA (United States)

    1996-01-01

    Fe-K-edge X-ray absorption spectroscopy (XAS) has been used to investigate the electronic and geometric structure of the iron active site in non-heme iron enzymes. A new theoretical extended X-ray absorption fine structure (EXAFS) analysis approach, called GNXAS, has been tested on data for iron model complexes to evaluate the utility and reliability of this new technique, especially with respect to the effects of multiple-scattering. In addition, a detailed analysis of the 1s→3d pre-edge feature has been developed as a tool for investigating the oxidation state, spin state, and geometry of iron sites. Edge and EXAFS analyses have then been applied to the study of non-heme iron enzyme active sites.

  14. Genome-based analysis of heme biosynthesis and uptake in prokaryotic systems.

    Science.gov (United States)

    Cavallaro, Gabriele; Decaria, Leonardo; Rosato, Antonio

    2008-11-01

    Heme is the prosthetic group of many proteins that carry out a variety of key biological functions. In addition, for many pathogenic organisms, heme (acquired from the host) may constitute a very important source of iron. Organisms can meet their heme demands by taking it up from external sources, by producing the cofactor through a dedicated biosynthetic pathway, or both. Here we analyzed the distribution of proteins specifically involved in the processes of heme biosynthesis and heme uptake in 474 prokaryotic organisms. These data allowed us to identify which organisms are capable of performing none, one, or both processes, based on the similarity to known systems. Some specific instances where one or more proteins along the pathways had unusual modifications were singled out. For two key protein domains involved in heme uptake, we could build a series of structural models, which suggested possible alternative modes of heme binding. Future directions for experimental work are given.

  15. One ring to rule them all: trafficking of heme and heme synthesis intermediates in the metazoans.

    Science.gov (United States)

    Hamza, Iqbal; Dailey, Harry A

    2012-09-01

    The appearance of heme, an organic ring surrounding an iron atom, in evolution forever changed the efficiency with which organisms were able to generate energy, utilize gasses and catalyze numerous reactions. Because of this, heme has become a near ubiquitous compound among living organisms. In this review we have attempted to assess the current state of heme synthesis and trafficking with a goal of identifying crucial missing information, and propose hypotheses related to trafficking that may generate discussion and research. The possibilities of spatially organized supramolecular enzyme complexes and organelle structures that facilitate efficient heme synthesis and subsequent trafficking are discussed and evaluated. Recently identified players in heme transport and trafficking are reviewed and placed in an organismal context. Additionally, older, well established data are reexamined in light of more recent studies on cellular organization and data available from newer model organisms. This article is part of a Special Issue entitled: Cell Biology of Metals. Copyright © 2012 Elsevier B.V. All rights reserved.

  16. Electronic structure of human hemoglobin: ultrasoft X-ray emission study

    International Nuclear Information System (INIS)

    Soldatov, A.V.; Kravtsova, A.N.; Fedorovich, E.N.; Kurmaev, E.Z.; Moewes, A.

    2004-01-01

    Full text: The iron L 2,3 and carbon, nitrogen and oxygen Kα X-ray emission spectra (XES) of human hemoglobin have been recorded at the soft X-ray spectroscopy endstation on Undulator Beam line 8.0 at Advanced Light Source (ALS) located at the Lawrence Berkeley National Laboratory. The theoretical calculations of Fe L 3 -XES have been performed using ab initio code FEFF8.2. The calculations have been carried out for the structure of hemoglobin presented in PDB (entry 3HHB) as well as for the molecule with symmetrical heme plane. It was found that the Fe L 3 emission spectrum calculated for the ideal molecule agrees slightly better with the experiment as compared with those calculated for the real molecule. Thus, one can use the structure of the ideal molecule for theoretical Fe L 3 -XES simulations. The theoretical analysis has shown that the fist peak of experimental Fe L 3 - emission spectrum is enhanced by the nearest nitrogen atoms lying in heme plane around the central iron atom. The theoretical C K- and N K-XES spectra of hemoglobin have been calculated. A good agreement between theoretical and experimental spectra has been obtained. The distribution of the partial electronic densities of states in the valence and conduction bands of hemoglobin has been determined

  17. Improved Method for the Incorporation of Heme Cofactors into Recombinant Proteins Using Escherichia coli Nissle 1917.

    Science.gov (United States)

    Fiege, Kerstin; Querebillo, Christine Joy; Hildebrandt, Peter; Frankenberg-Dinkel, Nicole

    2018-05-15

    Recombinant production of heme proteins in Escherichia coli is often limited by the availability of heme in the host. Therefore, several methods, including the reconstitution of heme proteins after production but prior to purification or the HPEX system, conferring the ability to take up external heme have been developed and used in the past. Here we describe the use of the apathogenic E. coli strain Nissle 1917 (EcN) as a suitable host for the recombinant production of heme proteins. EcN has an advantage over commonly used lab strains in that it is able to take up heme from the environment through the heme receptor ChuA. Expression of several heme proteins from different prokaryotic sources led to high yield and quantitative incorporation of the cofactor when heme was supplied in the growth medium. Comparative UV-vis and resonance Raman measurements revealed that the method employed has significant influence on heme coordination with the EcN system representing the most native situation. Therefore, the use of EcN as a host for recombinant heme protein production represents an inexpensive and straightforward method to facilitate further investigations of structure and function.

  18. Electronic structure studies of fullerites and fullerides

    International Nuclear Information System (INIS)

    Merkel, M.; Sohmen, E.; Masaki, A.; Romberg, H.; Alexander, M.; Knupfer, M.; Golden, M.S.; Adelmann, P.; Renker, B.; Fink, J.

    1993-01-01

    The electronic structure of fullerites and fullerides has been investigated by high-resolution photoemission and by high-energy electron energy-loss spectroscopy in transmission. Information on the occupied Π and σ bands, on the unoccupied Π * and σ * bands, and on the joint density of states has been obtained. In particular, we report on the changes of the electronic structure of fullerides as a function of dopant concentration. (orig.)

  19. Solvated electron structure in glassy matrices

    International Nuclear Information System (INIS)

    Kevan, L.

    1981-01-01

    Current knowledge of the detailed geometrical structure of solvated electrons in aqueous and organic media is summarized. The geometry of solvated electrons in glassy methanol, ethanol, and 2-methyltetrahydrofuran is discussed. Advanced electron magnetic resonance methods and development of new methods of analysis of electron spin echo modulation patterns, second moment line shapes, and forbidden photon spin-flip transitions for paramagnetic species in these disordered systems are discussed. 66 references are cited

  20. Electronic structure and tautomerism of thioamides

    Energy Technology Data Exchange (ETDEWEB)

    Novak, Igor, E-mail: inovak@csu.edu.au [Charles Sturt University, POB 883, Orange, NSW 2800 (Australia); Klasinc, Leo, E-mail: klasinc@irb.hr [Physical Chemistry Department, Ruđer Bošković Institute, HR-10002 Zagreb (Croatia); McGlynn, Sean P., E-mail: sean.mcglynn@chemgate.chem.lsu.edu [Louisiana State University, Baton Rouge, LA 70803 (United States)

    2016-05-15

    Highlights: • Electronic structure of thioamide group and its relation to Lewis basicity. • Tautomerism of the (thio)amide groups. • Substituent effects on the electronic structure of (thio)amide group. - Abstract: The electronic structures of several thioamides have been studied by UV photoelectron spectroscopy (UPS). The relative stabilities of keto–enol tautomers have been determined using high-level ab initio calculations and the results were used in the analysis of UPS spectra. The main features of electronic structure and tautomerism of thioamide derivatives are discussed. The predominant tautomers in the gas phase are of keto–(thio)keto form. The addition of cyclohexanone moiety to the thioamide group enhances the Lewis base character of the sulfur atom. The addition of phenyl group to the (thio)amide group significantly affects its electronic structure.

  1. X-ray absorption spectroscopy of soybean lipoxygenase-1 : Influence of lipid hydroperoxide activation and lyophilization on the structure of the non-heme iron active site

    NARCIS (Netherlands)

    Vliegenthart, J.F.G.; Heijdt, L.M. van der; Feiters, M.C.; Navaratnam, S.; Nolting, H.-F.; Hermes, C.; Veldink, G.A.

    1992-01-01

    X-ray absorption spectra at the Fe K-edge of the non-heme iron site in Fe(II) as well as Fe(III) soybean lipoxygenase-1, in frozen solution or lyophilized, are presented; the latter spectra were obtained by incubation of the Fe(II) enzyme with its product hydroperoxide. An edge shift of about 23 eV

  2. Electron scattering and nuclear structure

    International Nuclear Information System (INIS)

    Wolynec, E.

    1985-01-01

    A review of the historical development and the theory necessary to the interpretation of the experimental results is made. Some measurement techniques, experimental results and the technique of analysis of these data are presented. Future perspectives, due to the appearence of continous electron current accelerators, in this field of study are discussed. (L.C.) [pt

  3. Electron gun controlled smart structure

    Science.gov (United States)

    Martin, Jeffrey W.; Main, John Alan; Redmond, James M.; Henson, Tammy D.; Watson, Robert D.

    2001-01-01

    Disclosed is a method and system for actively controlling the shape of a sheet of electroactive material; the system comprising: one or more electrodes attached to the frontside of the electroactive sheet; a charged particle generator, disposed so as to direct a beam of charged particles (e.g. electrons) onto the electrode; a conductive substrate attached to the backside of the sheet; and a power supply electrically connected to the conductive substrate; whereby the sheet changes its shape in response to an electric field created across the sheet by an accumulation of electric charge within the electrode(s), relative to a potential applied to the conductive substrate. Use of multiple electrodes distributed across on the frontside ensures a uniform distribution of the charge with a single point of e-beam incidence, thereby greatly simplifying the beam scanning algorithm and raster control electronics, and reducing the problems associated with "blooming". By placing a distribution of electrodes over the front surface of a piezoelectric film (or other electroactive material), this arrangement enables improved control over the distribution of surface electric charges (e.g. electrons) by creating uniform (and possibly different) charge distributions within each individual electrode. Removal or deposition of net electric charge can be affected by controlling the secondary electron yield through manipulation of the backside electric potential with the power supply. The system can be used for actively controlling the shape of space-based deployable optics, such as adaptive mirrors and inflatable antennae.

  4. Heme degrading protein HemS is involved in oxidative stress response of Bartonella henselae.

    Directory of Open Access Journals (Sweden)

    MaFeng Liu

    Full Text Available Bartonellae are hemotropic bacteria, agents of emerging zoonoses. These bacteria are heme auxotroph Alphaproteobacteria which must import heme for supporting their growth, as they cannot synthesize it. Therefore, Bartonella genome encodes for a complete heme uptake system allowing the transportation of this compound across the outer membrane, the periplasm and the inner membranes. Heme has been proposed to be used as an iron source for Bartonella since these bacteria do not synthesize a complete system required for iron Fe³⁺ uptake. Similarly to other bacteria which use heme as an iron source, Bartonellae must transport this compound into the cytoplasm and degrade it to allow the release of iron from the tetrapyrrole ring. For Bartonella, the gene cluster devoted to the synthesis of the complete heme uptake system also contains a gene encoding for a polypeptide that shares homologies with heme trafficking or degrading enzymes. Using complementation of an E. coli mutant strain impaired in heme degradation, we demonstrated that HemS from Bartonella henselae expressed in E. coli allows the release of iron from heme. Purified HemS from B. henselae binds heme and can degrade it in the presence of a suitable electron donor, ascorbate or NADPH-cytochrome P450 reductase. Knocking down the expression of HemS in B. henselae reduces its ability to face H₂O₂ induced oxidative stress.

  5. Increased heme synthesis in yeast induces a metabolic switch from fermentation to respiration even under conditions of glucose repression.

    Science.gov (United States)

    Zhang, Tiantian; Bu, Pengli; Zeng, Joey; Vancura, Ales

    2017-10-13

    Regulation of mitochondrial biogenesis and respiration is a complex process that involves several signaling pathways and transcription factors as well as communication between the nuclear and mitochondrial genomes. Under aerobic conditions, the budding yeast Saccharomyces cerevisiae metabolizes glucose predominantly by glycolysis and fermentation. We have recently shown that altered chromatin structure in yeast induces respiration by a mechanism that requires transport and metabolism of pyruvate in mitochondria. However, how pyruvate controls the transcriptional responses underlying the metabolic switch from fermentation to respiration is unknown. Here, we report that this pyruvate effect involves heme. We found that heme induces transcription of HAP4 , the transcriptional activation subunit of the Hap2/3/4/5p complex, required for growth on nonfermentable carbon sources, in a Hap1p- and Hap2/3/4/5p-dependent manner. Increasing cellular heme levels by inactivating ROX1 , which encodes a repressor of many hypoxic genes, or by overexpressing HEM3 or HEM12 induced respiration and elevated ATP levels. Increased heme synthesis, even under conditions of glucose repression, activated Hap1p and the Hap2/3/4/5p complex and induced transcription of HAP4 and genes required for the tricarboxylic acid (TCA) cycle, electron transport chain, and oxidative phosphorylation, leading to a switch from fermentation to respiration. Conversely, inhibiting metabolic flux into the TCA cycle reduced cellular heme levels and HAP4 transcription. Together, our results indicate that the glucose-mediated repression of respiration in budding yeast is at least partly due to the low cellular heme level. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  6. Introduction of a covalent histidine-heme linkage in a hemoglobin: a promising tool for heme protein engineering.

    Science.gov (United States)

    Rice, Selena L; Preimesberger, Matthew R; Johnson, Eric A; Lecomte, Juliette T J

    2014-12-01

    The hemoglobins of the cyanobacteria Synechococcus and Synechocystis (GlbNs) are capable of spontaneous and irreversible attachment of the b heme to the protein matrix. The reaction, which saturates the heme 2-vinyl by addition of a histidine residue, is reproduced in vitro by preparing the recombinant apoprotein, adding ferric heme, and reducing the iron to the ferrous state. Spontaneous covalent attachment of the heme is potentially useful for protein engineering purposes. Thus, to explore whether the histidine-heme linkage can serve in such applications, we attempted to introduce it in a test protein. We selected as our target the heme domain of Chlamydomonas eugametos LI637 (CtrHb), a eukaryotic globin that exhibits less than 50% sequence identity with the cyanobacterial GlbNs. We chose two positions, 75 in the FG corner and 111 in the H helix, to situate a histidine near a vinyl group. We characterized the proteins with gel electrophoresis, absorbance spectroscopy, and NMR analysis. Both T111H and L75H CtrHbs reacted upon reduction of the ferric starting material containing cyanide as the distal ligand to the iron. With L75H CtrHb, nearly complete (>90%) crosslinking was observed to the 4-vinyl as expected from the X-ray structure of wild-type CtrHb. Reaction of T111H CtrHb also occurred at the 4-vinyl, in a 60% yield indicating a preference for the flipped heme orientation in the starting material. The work suggests that the His-heme modification will be applicable to the design of proteins with a non-dissociable heme group. Copyright © 2014 Elsevier Inc. All rights reserved.

  7. Heme orientational disorder in human adult hemoglobin reconstituted with a ring fluorinated heme and its functional consequences

    International Nuclear Information System (INIS)

    Nagao, Satoshi; Hirai, Yueki; Kawano, Shin; Imai, Kiyohiro; Suzuki, Akihiro; Yamamoto, Yasuhiko

    2007-01-01

    A ring fluorinated heme, 13,17-bis(2-carboxylatoethyl)-3,8-diethyl-2-fluoro-7,12, 18-trimethyl-porphyrin-atoiron(III), has been incorporated into human adult hemoglobin (Hb A). The heme orientational disorder in the individual subunits of the protein has been readily characterized using 19 F NMR and the O 2 binding properties of the protein have been evaluated through the oxygen equilibrium analysis. The equilibrated orientations of hemes in α- and β- subunits of the reconstituted protein were found to be almost completely opposite to each other, and hence were largely different from those of the native and the previously reported reconstituted proteins [T. Jue, G.N. La Mar, Heme orientational heterogeneity in deuterohemin-reconstituted horse and human hemoglobin characterized by proton nuclear magnetic resonance spectroscopy, Biochem. Biophys. Res. Commun. 119 (1984) 640-645]. Despite the large difference in the degree of the heme orientational disorder in the subunits of the proteins, the O 2 affinity and the cooperativity of the protein reconstituted with 2-MF were similar to those of the proteins reconstituted with a series of hemes chemically modified at the heme 3- and 8-positions [K. Kawabe, K. Imaizumi, Z. Yoshida, K. Imai, I. Tyuma, Studies on reconstituted myoglobins and hemoglobins II. Role of the heme side chains in the oxygenation of hemoglobin, J. Biochem. 92 (1982) 1713-1722], whose O 2 affinity and cooperativity were higher and lower, respectively, relative to those of native protein. These results indicated that the heme orientational disorder could exert little effect, if any, on the O 2 affinity properties of Hb A. This finding provides new insights into structure-function relationship of Hb A

  8. STRUCTURAL STABILITY AND ELECTRONIC STRUCTURE OF ...

    African Journals Online (AJOL)

    2012-12-31

    Dec 31, 2012 ... may be applications at high temperature strength and corrosion ... B2 structure, like that found in cesium-chloride (CsCl) and chemical formula RM, where R denotes a rare - earth element and M denotes a late transition metal ...

  9. The Effect of Distal Interactions on O2-Binding to Heme

    DEFF Research Database (Denmark)

    Kepp, Kasper Planeta; Dasmeh, Pouria

    2013-01-01

    This paper reports DFT-computed electronic ground states, Mössbauer isomer shifts, O-O and Fe-O vibration frequencies, and thermodynamics of O2-binding of heme models representing different distal (position E7) interactions, strictly validated against experimental data. Based on the results...... hydrogen bonds can further reduce isomer shifts up to 0.07 mm/s. The O-O stretch vibration, the O-O distance, and the isomer shift possess substantial heuristic value in interpreting electronic structure, whereas other properties are less effective, based on computed correlation coefficients. Shorter Fe...

  10. Electronic structure of metallic glasses

    International Nuclear Information System (INIS)

    Oelhafen, P.; Lapka, R.; Gubler, U.; Krieg, J.; DasGupta, A.; Guentherodt, H.J.; Mizoguchi, T.; Hague, C.; Kuebler, J.; Nagel, S.R.

    1981-01-01

    This paper is organized in six sections and deals with (1) the glassy transition metal alloys, their d-band structure, the d-band shifts on alloying and their relation to the alloy heat of formation (ΔH) and the glass forming ability, (2) the glass to crystal phase transition viewed by valence band spectroscopy, (3) band structure calculations, (4) metallic glasses prepared by laser glazing, (5) glassy normal metal alloys, and (6) glassy hydrides

  11. Electronic structure and tautomerism of aryl ketones

    International Nuclear Information System (INIS)

    Novak, Igor; Klasinc, Leo; Šket, Boris; McGlynn, S.P.

    2015-01-01

    Graphical abstract: Photoelectron spectroscopy, tautomerism. - Highlights: • UV photoelectron spectroscopy of aryl ketones. • The relative stability of tautomers and their electronic structures. • The factors influencing tautomerism. - Abstract: The electronic structures of several aryl ketones (AK) and their α-halo derivatives have been studied by UV photoelectron spectroscopy (UPS). The relative stabilities of keto–enol tautomers have been determined using high-level ab initio calculations and the results were used in the analysis of UPS spectra. The main features of electronic structure and tautomerism of the AK derivatives are discussed

  12. Phenomenology of the electron structure function

    International Nuclear Information System (INIS)

    Slominski, W.; Szwed, J.

    2001-01-01

    The advantages of introducing the electron structure function (ESF) in electron induced processes are demonstrated. Contrary to the photon structure function it is directly measured in such processes. At present energies, a simultaneous analysis of both the electron and the photon structure functions gives an important test of the experimentally applied methods. Estimates of the ESF at LEP momenta are given. At very high momenta contributions from W and Z bosons together with γ-Z interference can be observed. Predictions for the next generation of experiments are given. (orig.)

  13. Electronic structure and tautomerism of aryl ketones

    Energy Technology Data Exchange (ETDEWEB)

    Novak, Igor, E-mail: inovak@csu.edu.au [Charles Sturt University, POB 883, Orange, NSW 2800 (Australia); Klasinc, Leo, E-mail: klasinc@irb.hr [Physical Chemistry Department, Ruđer Bošković Institute, HR-10002 Zagreb (Croatia); Šket, Boris, E-mail: Boris.Sket@fkkt.uni-lj.si [Faculty of Chemistry and Chemical Technology, University of Ljubljana, SI-1000 (Slovenia); McGlynn, S.P., E-mail: sean.mcglynn@chemgate.chem.lsu.edu [Louisiana State University, Baton Rouge, LA 70803 (United States)

    2015-07-15

    Graphical abstract: Photoelectron spectroscopy, tautomerism. - Highlights: • UV photoelectron spectroscopy of aryl ketones. • The relative stability of tautomers and their electronic structures. • The factors influencing tautomerism. - Abstract: The electronic structures of several aryl ketones (AK) and their α-halo derivatives have been studied by UV photoelectron spectroscopy (UPS). The relative stabilities of keto–enol tautomers have been determined using high-level ab initio calculations and the results were used in the analysis of UPS spectra. The main features of electronic structure and tautomerism of the AK derivatives are discussed.

  14. Isocyanides inhibit human heme oxygenases at the verdoheme stage.

    Science.gov (United States)

    Evans, John P; Kandel, Sylvie; Ortiz de Montellano, Paul R

    2009-09-22

    Heme oxygenases (HO) catalyze the oxidative cleavage of heme to generate biliverdin, CO, and free iron. In humans, heme oxygenase-1 (hHO-1) is overexpressed in tumor tissues, where it helps to protect cancer cells from anticancer agents, while HOs in fungal pathogens, such as Candida albicans, function as the primary means of iron acquisition. Thus, HO can be considered a potential therapeutic target for certain diseases. In this study, we have examined the equilibrium binding of three isocyanides, isopropyl, n-butyl, and benzyl, to the two major human HO isoforms (hHO-1 and hHO-2), Candida albicans HO (CaHmx1), and human cytochrome P450 CYP3A4 using electronic absorption spectroscopy. Isocyanides coordinate to both ferric and ferrous HO-bound heme, with tighter binding by the more hydrophobic isocyanides and 200-300-fold tighter binding to the ferrous form. Benzyl isocyanide was the strongest ligand to ferrous heme in all the enzymes. Because the dissociation constants (KD) of the ligands for ferrous heme-hHO-1 were below the limit of accuracy for equilibrium titrations, stopped-flow kinetic experiments were used to measure the binding parameters of the isocyanides to ferrous hHO-1. Steady-state activity assays showed that benzyl isocyanide was the most potent uncompetitive inhibitor with respect to heme with a KI = 0.15 microM for hHO-1. Importantly, single turnover assays revealed that the reaction was completely stopped by coordination of the isocyanide to the verdoheme intermediate rather than to the ferric heme complex. Much tighter binding of the inhibitor to the verdoheme intermediate differentiates it from inhibition of, for example, CYP3A4 and offers a possible route to more selective inhibitor design.

  15. Isocyanides Inhibit Human Heme Oxygenases at the Verdoheme Stage†

    Science.gov (United States)

    Evans, John P.; Kandel, Sylvie; Ortiz de Montellano, Paul R.

    2010-01-01

    Heme oxygenases (HO) catalyze the oxidative cleavage of heme to generate biliverdin, CO, and free iron. In humans, heme oxygenase-1 (hHO-1) is overexpressed in tumor tissues, where it helps to protect cancer cells from anticancer agents, while HOs in fungal pathogens, such as Candida albicans, function as the primary means of iron acquisition. Thus, HO can be considered a potential therapeutic target for certain diseases. In this study, we have examined the equilibrium binding of three isocyanides; isopropyl, n-butyl, and benzyl, to the two major human HO isoforms (hHO-1 and hHO-2), Candida albicans HO (CaHmx1), and human cytochrome P450 CYP3A4 using electronic absorption spectroscopy. Isocyanides coordinate to both ferric and ferrous HO-bound heme, with tighter binding by the more hydrophobic isocyanides, and 200-300-fold tighter binding to the ferrous form. Benzyl isocyanide was the strongest ligand to ferrous heme in all the enzymes. Because the dissociation constants (KD) of the ligands for ferrous heme-hHO-1 were below the limit of accuracy for equilibrium titrations, stopped-flow kinetic experiments were used to measure the binding parameters of the isocyanides to ferrous hHO-1. Steady-state activity assays showed that benzyl isocyanide was the most potent uncompetitive inhibitor with respect to heme with a KI = 0.15 μM for hHO-1. Importantly, single turnover assays revealed that the reaction was completely stopped by coordination of the isocyanide to the verdoheme intermediate rather than to the ferric heme complex. Much tighter binding of the inhibitor to the verdoheme intermediate differentiates it from inhibition of, for example, CYP3A4 and offers a possible route to more selective inhibitor design. PMID:19694439

  16. Conformational control of cofactors in nature: The effect of methoxy group orientation on the electronic structure of ubisemiquinone

    Science.gov (United States)

    De Almeida, Wagner B.; O'Malley, Patrick J.

    2018-03-01

    Ubiquinone is the key electron and proton transfer agent in biology. Its mechanism involves the formation of its intermediate one-electron reduced form, the ubisemiquinone radical. This is formed in a protein-bound form which permits the semiquinone to vary its electronic and redox properties. This can be achieved by hydrogen bonding acceptance by one or both oxygen atoms or as we now propose by restricted orientations for the methoxy groups of the headgroup. We show how the orientation of the two methoxy groups of the quinone headgroup affects the electronic structure of the semiquinone form and demonstrate a large dependence of the ubisemiquinone spin density distribution on the orientation each methoxy group takes with respect to the headgroup ring plane. This is shown to significantly modify associated hyperfine couplings which in turn needs to be accounted for in interpreting experimental values in vivo. The study uncovers the key potential role the methoxy group orientation can play in controlling the electronic structure and spin density of ubisemiquinone and provides an electronic-level insight into the variation in electron affinity and redox potential of ubiquinone as a function of the methoxy orientation. Taken together with the already known influence of cofactor conformation on heme and chlorophyll electronic structure, it reveals a more widespread role for cofactor conformational control of electronic structure and associated electron transfer in biology.

  17. Synthetic heme/copper assemblies: toward an understanding of cytochrome c oxidase interactions with dioxygen and nitrogen oxides.

    Science.gov (United States)

    Hematian, Shabnam; Garcia-Bosch, Isaac; Karlin, Kenneth D

    2015-08-18

    Our long-time niche in synthetic biological inorganic chemistry has been to design ligands and generate coordination complexes of copper or iron ions or both, those reacting with dioxygen (O2) or nitrogen oxides (e.g., nitric oxide (NO(g)) and nitrite (NO2(-))) or both. As inspiration for this work, we turn to mitochondrial cytochrome c oxidase, which is responsible for dioxygen consumption and is also the predominant target for NO(g) and nitrite within mitochondria. In this Account, we highlight recent advances in studying synthetic heme/Cu complexes in two respects. First, there is the design, synthesis, and characterization of new O2 adducts whose further study will add insights into O2 reductive cleavage chemistry. Second, we describe how related heme/Cu constructs reduce nitrite ion to NO(g) or the reverse, oxidize NO(g) to nitrite. The reactions of nitrogen oxides occur as part of CcO's function, which is intimately tied to cellular O2 balance. We had first discovered that reduced heme/Cu compounds react with O2 giving μ-oxo heme-Fe(III)-O-Cu(II)(L) products; their properties are discussed. The O-atom is derived from dioxygen, and interrogations of these systems led to the construction and characterization of three distinctive classes of heme-peroxo complexes, two high-spin and one low-spin species. Recent investigations include a new approach to the synthesis of low-spin heme-peroxo-Cu complexes, employing a "naked" synthon, where the copper ligand denticity and geometric types can be varied. The result is a collection of such complexes; spectroscopic and structural features (by DFT calculations) are described. Some of these compounds are reactive toward reductants/protons effecting subsequent O-O cleavage. This points to how subtle improvements in ligand environment lead to a desired local structure and resulting optimized reactivity, as known to occur at enzyme active sites. The other sector of research is focused on heme/Cu assemblies mediating the redox

  18. The heme-heme oxygenase system: a molecular switch in wound healing.

    NARCIS (Netherlands)

    Wagener, F.A.D.T.G.; Beurden, H.E. van; Hoff, J.W. Von den; Adema, G.J.; Figdor, C.G.

    2003-01-01

    When cells are injured they release their contents, resulting in a local accumulation of free heme proteins and heme. Here, we investigated the involvement of heme and its degrading enzyme heme oxygenase (HO) in the inflammatory process during wound healing. We observed that heme directly

  19. Epitaxial graphene electronic structure and transport

    International Nuclear Information System (INIS)

    De Heer, Walt A; Berger, Claire; Wu Xiaosong; Sprinkle, Mike; Hu Yike; Ruan Ming; First, Phillip N; Stroscio, Joseph A; Haddon, Robert; Piot, Benjamin; Faugeras, Clement; Potemski, Marek; Moon, Jeong-Sun

    2010-01-01

    Since its inception in 2001, the science and technology of epitaxial graphene on hexagonal silicon carbide has matured into a major international effort and is poised to become the first carbon electronics platform. A historical perspective is presented and the unique electronic properties of single and multilayered epitaxial graphenes on electronics grade silicon carbide are reviewed. Early results on transport and the field effect in Si-face grown graphene monolayers provided proof-of-principle demonstrations. Besides monolayer epitaxial graphene, attention is given to C-face grown multilayer graphene, which consists of electronically decoupled graphene sheets. Production, structure and electronic structure are reviewed. The electronic properties, interrogated using a wide variety of surface, electrical and optical probes, are discussed. An overview is given of recent developments of several device prototypes including resistance standards based on epitaxial graphene quantum Hall devices and new ultrahigh frequency analogue epitaxial graphene amplifiers.

  20. Instructional Approach to Molecular Electronic Structure Theory

    Science.gov (United States)

    Dykstra, Clifford E.; Schaefer, Henry F.

    1977-01-01

    Describes a graduate quantum mechanics projects in which students write a computer program that performs ab initio calculations on the electronic structure of a simple molecule. Theoretical potential energy curves are produced. (MLH)

  1. Heme metabolism in stress regulation and protein production: from Cinderella to a key player

    DEFF Research Database (Denmark)

    Martinez Ruiz, José Luis; Petranovic, D.; Nielsen, Jens

    2016-01-01

    Heme biosynthesis is a highly conserved pathway which is present in all kingdoms, from Archaea to higher organisms such as plants and mammals. The heme molecule acts as a prosthetic group for different proteins and enzymes involved in energy metabolism and reactions involved in electron transfer....

  2. Characterization of SiaA, a streptococcal heme-binding protein associated with a heme ABC transport system.

    Science.gov (United States)

    Sook, Brian R; Block, Darci R; Sumithran, Suganya; Montañez, Griselle E; Rodgers, Kenton R; Dawson, John H; Eichenbaum, Zehava; Dixon, Dabney W

    2008-02-26

    Many pathogenic bacteria require heme and obtain it from their environment. Heme transverses the cytoplasmic membrane via an ATP binding cassette (ABC) pathway. Although a number of heme ABC transport systems have been described in pathogenic bacteria, there is as yet little biophysical characterization of the proteins in these systems. The sia (hts) gene cluster encodes a heme ABC transporter in the Gram positive Streptococcus pyogenes. The lipoprotein-anchored heme binding protein (HBP) of this transporter is SiaA (HtsA). In the current study, resonance Raman (rR), magnetic circular dichroism (MCD), and nuclear magnetic resonance (NMR) spectroscopies were used to determine the coordination state and spin state of both the ferric and ferrous forms of this protein. Identifiers from these techniques suggest that the heme is six-coordinate and low-spin in both oxidation states of the protein, with methionine and histidine as axial ligands. SiaA has a pKa of 9.7 +/- 0.1, attributed to deprotonation of the axial histidine. Guanidinium titration studies show that the ferric state is less stable than the ferrous state, with DeltaG(H2O) values for the oxidized and reduced proteins of 7.3 +/- 0.8 and 16.0 +/- 3.6 kcal mol-1, respectively. The reductive and oxidative midpoint potentials determined via spectroelectrochemistry are 83 +/- 3 and 64 +/- 3 mV, respectively; the irreversibility of heme reduction suggests that redox cycling of the heme is coupled to a kinetically sluggish change in structure or conformation. The biophysical characterization described herein will significantly advance our understanding of structure-function relationships in HBP.

  3. Heme-based sensors in biological systems.

    Science.gov (United States)

    Rodgers, K R

    1999-04-01

    The past several years have been witness to a staggering rate of advancement in the understanding of how organisms respond to changes in the availability of diatomic molecules that are toxic and/or crucial to survival. Heme-based sensors presently constitute the majority of the proteins known to sense NO, O2 and CO and to initiate the chemistry required to adapt to changes in their availabilities. Knowledge of the three characterized members of this class, soluble guanylate cyclase, FixL and CooA, has grown substantially during the past year. The major advances have resulted from a broad range of approaches to elucidation of both function and mechanism. They include growth in the understanding of the interplay between the heme and protein in soluble guanylate cyclase, as well as alternate means for its stimulation. Insight into the O2-induced structural changes in FixL has been supplied by the single crystal structure of the heme domain of Bradyrhizobium japonicum. Finally, the ligation environment and ligand interchange that facilitates CO sensing by CooA has been established by spectroscopic and mutagenesis techniques.

  4. Electron conductance in curved quantum structures

    DEFF Research Database (Denmark)

    Willatzen, Morten; Gravesen, Jens

    2010-01-01

    is computationally fast and provides direct (geometrical) parameter insight as regards the determination of the electron transmission coefficient. We present, as a case study, calculations of the electron conductivity of a helically shaped quantum-wire structure and discuss the influence of the quantum......A differential-geometry analysis is employed to investigate the transmission of electrons through a curved quantum-wire structure. Although the problem is a three-dimensional spatial problem, the Schrodinger equation can be separated into three general coordinates. Hence, the proposed method...

  5. Overview of nuclear structure with electrons

    International Nuclear Information System (INIS)

    Geesaman, D. F.

    1999-01-01

    Following a broad summary of the author's view of nuclear structure in 1974, he will discuss the key elements they have learned in the past 25 years from the research at the M.I.T. Bates Linear Accelerator center and its sister electron accelerator laboratories. Electron scattering has provided the essential measurements for most of the progress. The future is bright for nuclear structure research as their ability to realistically calculate nuclear structure observables has dramatically advanced and they are increasingly able to incorporate an understanding of quantum chromodynamics into their picture of the nucleus

  6. Cyanide does more to inhibit heme enzymes, than merely serving as an active-site ligand

    Energy Technology Data Exchange (ETDEWEB)

    Parashar, Abhinav [Center for Biomedical Research, VIT University, Vellore, Tamil Nadu, 632014 India (India); Venkatachalam, Avanthika [REDOx Lab, PSG Institute of Advanced Studies, Avinashi Road, Peelamedu, Coimbatore, Tamil Nadu, 641004 (India); Gideon, Daniel Andrew [Center for Biomedical Research, VIT University, Vellore, Tamil Nadu, 632014 India (India); Manoj, Kelath Murali, E-mail: satyamjayatu@yahoo.com [REDOx Lab, PSG Institute of Advanced Studies, Avinashi Road, Peelamedu, Coimbatore, Tamil Nadu, 641004 (India)

    2014-12-12

    Highlights: • Cyanide (CN) is a well-studied toxic principle, known to inhibit heme-enzymes. • Inhibition is supposed to result from CN binding at the active site as a ligand. • Diverse heme enzymes’ CN inhibition profiles challenge prevailing mechanism. • Poor binding efficiency of CN at low enzyme concentrations and ligand pressures. • CN-based diffusible radicals cause ‘non-productive electron transfers’ (inhibition). - Abstract: The toxicity of cyanide is hitherto attributed to its ability to bind to heme proteins’ active site and thereby inhibit their activity. It is shown herein that the long-held interpretation is inadequate to explain several observations in heme-enzyme reaction systems. Generation of cyanide-based diffusible radicals in heme-enzyme reaction milieu could shunt electron transfers (by non-active site processes), and thus be detrimental to the efficiency of oxidative outcomes.

  7. Dietary Heme Induces Gut Dysbiosis, Aggravates Colitis, and Potentiates the Development of Adenomas in Mice

    Directory of Open Access Journals (Sweden)

    Marco Constante

    2017-09-01

    Full Text Available Dietary heme can be used by colonic bacteria equipped with heme-uptake systems as a growth factor and thereby impact on the microbial community structure. The impact of heme on the gut microbiota composition may be particularly pertinent in chronic inflammation such as in inflammatory bowel disease (IBD, where a strong association with gut dysbiosis has been consistently reported. In this study we investigated the influence of dietary heme on the gut microbiota and inferred metagenomic composition, and on chemically induced colitis and colitis-associated adenoma development in mice. Using 16S rRNA gene sequencing, we found that mice fed a diet supplemented with heme significantly altered their microbiota composition, characterized by a decrease in α-diversity, a reduction of Firmicutes and an increase of Proteobacteria, particularly Enterobacteriaceae. These changes were similar to shifts seen in dextran sodium sulfate (DSS-treated mice to induce colitis. In addition, dietary heme, but not systemically delivered heme, contributed to the exacerbation of DSS-induced colitis and facilitated adenoma formation in the azoxymethane/DSS colorectal cancer (CRC mouse model. Using inferred metagenomics, we found that the microbiota alterations elicited by dietary heme resulted in non-beneficial functional shifts, which were also characteristic of DSS-induced colitis. Furthermore, a reduction in fecal butyrate levels was found in mice fed the heme supplemented diet compared to mice fed the control diet. Iron metabolism genes known to contribute to heme release from red blood cells, heme uptake, and heme exporter proteins, were significantly enriched, indicating a shift toward favoring the growth of bacteria able to uptake heme and protect against its toxicity. In conclusion, our data suggest that luminal heme, originating from dietary components or gastrointestinal bleeding in IBD and, to lesser extent in CRC, directly contributes to microbiota dysbiosis

  8. Direct electrochemistry and electrocatalysis of heme proteins immobilised in carbon-coated nickel magnetic nanoparticle-chitosan-dimethylformamide composite films in room-temperature ionic liquids.

    Science.gov (United States)

    Wang, Ting; Wang, Lu; Tu, Jiaojiao; Xiong, Huayu; Wang, Shengfu

    2013-12-01

    The direct electrochemistry and electrocatalysis of heme proteins entrapped in carbon-coated nickel magnetic nanoparticle-chitosan-dimethylformamide (CNN-CS-DMF) composite films were investigated in the hydrophilic ionic liquid [bmim][BF4]. The surface morphologies of a representative set of films were characterised via scanning electron microscopy. The proteins immobilised in the composite films were shown to retain their native secondary structure using UV-vis spectroscopy. The electrochemical performance of the heme proteins-CNN-CS-DMF films was evaluated via cyclic voltammetry and chronoamperometry. A pair of stable and well-defined redox peaks was observed for the heme protein films at formal potentials of -0.151 V (HRP), -0.167 V (Hb), -0.155 V (Mb) and -0.193 V (Cyt c) in [bmim][BF4]. Moreover, several electrochemical parameters of the heme proteins were calculated by nonlinear regression analysis of the square-wave voltammetry. The addition of CNN significantly enhanced not only the electron transfer of the heme proteins but also their electrocatalytic activity toward the reduction of H2O2. Low apparent Michaelis-Menten constants were obtained for the heme protein-CNN-CS-DMF films, demonstrating that the biosensors have a high affinity for H2O2. In addition, the resulting electrodes displayed a low detection limit and improved sensitivity for detecting H2O2, which indicates that the biocomposite film can serve as a platform for constructing new non-aqueous biosensors for real detection. Copyright © 2013 Elsevier B.V. All rights reserved.

  9. Heme Mobilization in Animals: A Metallolipid's Journey.

    Science.gov (United States)

    Reddi, Amit R; Hamza, Iqbal

    2016-06-21

    Heme is universally recognized as an essential and ubiquitous prosthetic group that enables proteins to carry out a diverse array of functions. All heme-dependent processes, from protein hemylation to heme signaling, require the dynamic and rapid mobilization of heme to hemoproteins present in virtually every subcellular compartment. The cytotoxicity and hydrophobicity of heme necessitates that heme mobilization is carefully controlled at the cellular and systemic level. However, the molecules and mechanisms that mediate heme homeostasis are poorly understood. In this Account, we provide a heuristic paradigm with which to conceptualize heme trafficking and highlight the most recent developments in the mechanisms underlying heme trafficking. As an iron-containing tetrapyrrole, heme exhibits properties of both transition metals and lipids. Accordingly, we propose its transport and trafficking will reflect principles gleaned from the trafficking of both metals and lipids. Using this conceptual framework, we follow the flow of heme from the final step of heme synthesis in the mitochondria to hemoproteins present in various subcellular organelles. Further, given that many cells and animals that cannot make heme can assimilate it intact from nutritional sources, we propose that intercellular heme trafficking pathways must exist. This necessitates that heme be able to be imported and exported from cells, escorted between cells and organs, and regulated at the organismal level via a coordinated systemic process. In this Account, we highlight recently discovered heme transport and trafficking factors and provide the biochemical foundation for the cell and systems biology of heme. Altogether, we seek to reconceptualize heme from an exchange inert cofactor buried in hemoprotein active sites to an exchange labile and mobile metallonutrient.

  10. Electronic Structure of Eu6C60

    Institute of Scientific and Technical Information of China (English)

    WANG Xiao-Xiong; LI Hong-Nian; XU Ya-Bo; WANG Peng; ZHANG Wen-Hua; XU Fa-Qiang

    2009-01-01

    We study the valence band of Eu-intercalated C60 by synchrotron radiation photoelectron spectroscopy to un-derstand the ferromagnetism (FM) and the giant magnetoresistance (GMR) of Eu6C60. The results reveal the semiconducting property and the remarkable 5d6s-π hybridization. Eu-C60 bonding has both ionic and covalent contributions. No more than half the 5d6s electrons transfer from Eu to the LUMO derived band of C60, and the LUMO+1 derived band is not filled. The remaining valence electrons of Eu, together with some π (LUMO, HOMO and HOMO-1) electrons, constitute the covalent bond. The electronic structure implies that the magnetic coupling in Eu6C60 should be through the intra-atomic f-sd exchange and the medium of the π electrons. The possibility of the GMR being tunnelling magnetoresistance is ruled out.

  11. Atomic and electronic structures of novel silicon surface structures

    Energy Technology Data Exchange (ETDEWEB)

    Terry, J.H. Jr.

    1997-03-01

    The modification of silicon surfaces is presently of great interest to the semiconductor device community. Three distinct areas are the subject of inquiry: first, modification of the silicon electronic structure; second, passivation of the silicon surface; and third, functionalization of the silicon surface. It is believed that surface modification of these types will lead to useful electronic devices by pairing these modified surfaces with traditional silicon device technology. Therefore, silicon wafers with modified electronic structure (light-emitting porous silicon), passivated surfaces (H-Si(111), Cl-Si(111), Alkyl-Si(111)), and functionalized surfaces (Alkyl-Si(111)) have been studied in order to determine the fundamental properties of surface geometry and electronic structure using synchrotron radiation-based techniques.

  12. Structural changes induced by electron irradiation

    International Nuclear Information System (INIS)

    Koike, J.; Pedraza, D.F.

    1993-01-01

    Highly oriented pyrolytic graphite was irradiated at room temperature with 300 kV electrons. Transmission electron microscopy and electron energy loss spectroscopy were employed to study the structural changes produced by irradiation. The occurrence of a continuous ring intensity in the selected area diffraction (SAD) pattern obtained on a specimen irradiated with the electron beam parallel to the c-crystallographic axis indicated that microstructural changes had occurred. However, from the SAD pattern obtained for the specimens tilted relative to the irradiation direction, it was found that up to a fluence of 1.1x10 27 e/m 2 graphite remained crystalline. An SAD pattern of a specimen irradiated with the electron beam perpendicular to the c-axis confirmed the persistence of crystalline order. High resolution electron microscopy showed that ordering along the c-axis direction remained. A density reduction of 8.9% due to irradiation was determined from the plasmon frequency shift. A qualitative model is proposed to explain these observations. A new determination of the threshold displacement energy, Ed, of carbon atoms in graphite was done by examining the appearance of a continuous ring in the SAD pattern at various electron energies. A value of 30 eV was obtained whether the incident electron beam was parallel or perpendicular to the c-axis, demonstrating that Ed is independent of the displacement direction

  13. Structural stability and electronic structure of YCu ductile ...

    African Journals Online (AJOL)

    We investigate the structural, elastic and electronic properties of cubic YCu intermetallic compound. Which crystallize in the CsCl- B2 type structure, the investigated using the first principle full potential linearized augmented plane wave method (FP-LAPW) within density functional Theory (DFT). We used generalized ...

  14. Peroxide Activation for Electrophilic Reactivity by the Binuclear Non-heme Iron Enzyme AurF

    International Nuclear Information System (INIS)

    Park, Kiyoung; Li, Ning; Kwak, Yeonju; Srnec, Martin

    2017-01-01

    Binuclear non-heme iron enzymes activate O 2 for diverse chemistries that include oxygenation of organic substrates and hydrogen atom abstraction. This process often involves the formation of peroxo-bridged biferric intermediates, only some of which can perform electrophilic reactions. To elucidate the geometric and electronic structural requirements to activate peroxo reactivity, the active peroxo intermediate in 4-aminobenzoate N-oxygenase (AurF) has been characterized spectroscopically and computationally. A magnetic circular dichroism study of reduced AurF shows that its electronic and geometric structures are poised to react rapidly with O 2 . Nuclear resonance vibrational spectroscopic definition of the peroxo intermediate formed in this reaction shows that the active intermediate has a protonated peroxo bridge. Density functional theory computations on the structure established here show that the protonation activates peroxide for electrophilic/single-electron-transfer reactivity. As a result, this activation of peroxide by protonation is likely also relevant to the reactive peroxo intermediates in other binuclear non-heme iron enzymes.

  15. Explaining the atypical reaction profiles of heme enzymes with a novel mechanistic hypothesis and kinetic treatment.

    Directory of Open Access Journals (Sweden)

    Kelath Murali Manoj

    Full Text Available Many heme enzymes show remarkable versatility and atypical kinetics. The fungal extracellular enzyme chloroperoxidase (CPO characterizes a variety of one and two electron redox reactions in the presence of hydroperoxides. A structural counterpart, found in mammalian microsomal cytochrome P450 (CYP, uses molecular oxygen plus NADPH for the oxidative metabolism (predominantly hydroxylation of substrate in conjunction with a redox partner enzyme, cytochrome P450 reductase. In this study, we employ the two above-mentioned heme-thiolate proteins to probe the reaction kinetics and mechanism of heme enzymes. Hitherto, a substrate inhibition model based upon non-productive binding of substrate (two-site model was used to account for the inhibition of reaction at higher substrate concentrations for the CYP reaction systems. Herein, the observation of substrate inhibition is shown for both peroxide and final substrate in CPO catalyzed peroxidations. Further, analogy is drawn in the "steady state kinetics" of CPO and CYP reaction systems. New experimental observations and analyses indicate that a scheme of competing reactions (involving primary product with enzyme or other reaction components/intermediates is relevant in such complex reaction mixtures. The presence of non-selective reactive intermediate(s affords alternate reaction routes at various substrate/product concentrations, thereby leading to a lowered detectable concentration of "the product of interest" in the reaction milieu. Occam's razor favors the new hypothesis. With the new hypothesis as foundation, a new biphasic treatment to analyze the kinetics is put forth. We also introduce a key concept of "substrate concentration at maximum observed rate". The new treatment affords a more acceptable fit for observable experimental kinetic data of heme redox enzymes.

  16. Electron acoustic nonlinear structures in planetary magnetospheres

    Science.gov (United States)

    Shah, K. H.; Qureshi, M. N. S.; Masood, W.; Shah, H. A.

    2018-04-01

    In this paper, we have studied linear and nonlinear propagation of electron acoustic waves (EAWs) comprising cold and hot populations in which the ions form the neutralizing background. The hot electrons have been assumed to follow the generalized ( r , q ) distribution which has the advantage that it mimics most of the distribution functions observed in space plasmas. Interestingly, it has been found that unlike Maxwellian and kappa distributions, the electron acoustic waves admit not only rarefactive structures but also allow the formation of compressive solitary structures for generalized ( r , q ) distribution. It has been found that the flatness parameter r , tail parameter q , and the nonlinear propagation velocity u affect the propagation characteristics of nonlinear EAWs. Using the plasmas parameters, typically found in Saturn's magnetosphere and the Earth's auroral region, where two populations of electrons and electron acoustic solitary waves (EASWs) have been observed, we have given an estimate of the scale lengths over which these nonlinear waves are expected to form and how the size of these structures would vary with the change in the shape of the distribution function and with the change of the plasma parameters.

  17. Structure of conduction electrons on polysilanes

    Energy Technology Data Exchange (ETDEWEB)

    Ichikawa, Tsuneki [Hokkaido Univ., Sapporo (Japan); Kumagai, Jun

    1998-10-01

    The orbital structures of conduction electrons on permethylated oligosilane, Si{sub 2n}(CH{sub 3}){sub 2n+2}(n = 2 - 8), and poly(cyclohexylmethylsilane) have been determined by the electron spin-echo envelope modulation signals of the radical anions of these silanes in a deuterated rigid matrix at 77 K. The conduction electron on permethylated oligosilane is delocalized over the entire main chain, whereas that on poly(cyclohexylmethylsilane) is localized on a part of the main chain composed of about six Si atoms. Quantum-chemical calculations suggest that Anderson localization due to fluctuation of {sigma} conjugation by conformational disorder of the main chain is responsible for the localization of both the conduction electron and the hole. (author)

  18. Electronic structure of MgB2

    Indian Academy of Sciences (India)

    Abstract. Results of ab initio electronic structure calculations on the compound MgB2 using the. FPLAPW method employing GGA for the exchange-correlation energy are presented. Total energy minimization enables us to estimate the equilibrium volume, c/a ratio and the bulk modulus, all of which are in excellent ...

  19. Electronic structure of Fe-based superconductors

    Indian Academy of Sciences (India)

    Abstract. Fe-based superconductors have drawn much attention during the last decade due to the presence of superconductivity in materials containing the magnetic element, Fe, and the coexistence of superconductivity and magnetism. Extensive study of the electronic structure of these systems suggested the dominant ...

  20. Electronic structure of Fe-based superconductors

    Indian Academy of Sciences (India)

    2015-05-29

    May 29, 2015 ... Fe-based superconductors have drawn much attention during the last decade due to the presence of superconductivity in materials containing the magnetic element, Fe, and the coexistence of superconductivity and magnetism. Extensive study of the electronic structure of these systems suggested the ...

  1. Electronic structure of MgB 2

    Indian Academy of Sciences (India)

    Results of ab initio electronic structure calculations on the compound MgB2 using the FPLAPW method employing GGA for the exchange-correlation energy are presented. Total energy minimization enables us to estimate the equilibrium volume, / ratio and the bulk modulus, all of which are in excellent agreement with ...

  2. The electronic structure of antiferromagnetic chromium

    DEFF Research Database (Denmark)

    Skriver, Hans Lomholt

    1981-01-01

    The author has used the local spin density formalism to perform self-consistent calculations of the electronic structure of chromium in the non-magnetic and commensurate antiferromagnetic phases, as a function of the lattice parameter. A change of a few per cent in the atomic radius brings...

  3. Electronic structure calculations of calcium silicate hydrates

    International Nuclear Information System (INIS)

    Sterne, P.A.; Meike, A.

    1995-11-01

    Many phases in the calcium-silicate-hydrate system can develop in cement exposed over long periods of time to temperatures above 25 C. As a consequence, chemical reactions involving these phases can affect the relative humidity and water chemistry of a radioactive waste repository that contains significant amounts of cement. In order to predict and simulate these chemical reactions, the authors are developing an internally consistent database of crystalline Ca-Si-hydrate structures. The results of first principles electronic structure calculations on two such phases, wollastonite (CaSiO 3 ) and xonotlite (Ca 6 Si 6 O 17 (OH) 2 ), are reported here. The calculated ground state properties are in very good agreement with experiment, providing equilibrium lattice parameters within about 1--1.4% of the experimentally reported values. The roles of the different types of oxygen atoms, which are fundamental to understanding the energetics of crystalline Ca-Si-hydrates are briefly discussed in terms of their electronic state densities. The good agreement with experiment for the lattice parameters and the consistency of the electronic density of states features for the two structures demonstrate the applicability of these electronic structure methods in calculating the fundamental properties of these phases

  4. Electronic structure and electron dynamics at Si(100)

    Energy Technology Data Exchange (ETDEWEB)

    Weinelt, M. [Universitaet Erlangen-Nuernberg, Lehrstuhl fuer Festkoerperphysik, Erlangen (Germany); Max-Born-Institut, Berlin (Germany); Kutschera, M.; Schmidt, R.; Orth, C.; Fauster, T. [Universitaet Erlangen-Nuernberg, Lehrstuhl fuer Festkoerperphysik, Erlangen (Germany); Rohlfing, M. [International University Bremen, School of Engineering and Science, P.O. Box 750 561, Bremen (Germany)

    2005-02-01

    The electronic structure and electron dynamics at a Si(100) surface is studied by two-photon photoemission (2PPE). At 90 K the occupied D{sub up} dangling-bond state is located 150{+-}50 meV below the valence-band maximum (VBM) at the center of the surface Brillouin zone anti {gamma} and exhibits an effective hole mass of (0.5{+-}0.15)m{sub e}. The unoccupied D{sub down} band has a local minimum at anti {gamma} at 650{+-}50 meV above the VBM and shows strong dispersion along the dimer rows of the c(4 x 2) reconstructed surface. At 300 K the D{sub down} position shifts comparable to the Si conduction-band minimum by 40 meV to lower energies but the dispersion of the dangling-bond states is independent of temperature. The surface band bending for p-doped silicon is less than 30 meV, while acceptor-type defects cause significant and preparation-dependent band bending on n-doped samples. 2PPE spectra of Si(100) are dominated by interband transitions between the occupied and unoccupied surface states and emission out of transiently and permanently charged surface defects. Including electron-hole interaction in many-body calculations of the quasi-particle band structure leads us to assign a dangling-bond split-off state to a quasi-one-dimensional surface exciton with a binding energy of 130 meV. Electrons resonantly excited to the unoccupied D{sub down} dangling-bond band with an excess energy of about 350 meV need 1.5{+-}0.2 ps to scatter via phonon emission to the band bottom at anti {gamma} and relax within 5 ps with an excited hole in the occupied surface band to form an exciton living for nanoseconds. (orig.)

  5. Diamond surface: atomic and electronic structure

    International Nuclear Information System (INIS)

    Pate, B.B.

    1984-01-01

    Experimental studies of the diamond surface (with primary emphasis on the (111) surface) are presented. Aspects of the diamond surface which are addressed include (1) the electronic structure, (2) the atomic structure, and (3) the effect of termination of the lattice by foreign atoms. Limited studies of graphite are discussed for comparison with the diamond results. Experimental results from valence band and core level photoemission spectroscopy (PES), Auger electron spectroscopy (AES), low energy electron diffraction (LEED), and carbon 1s near edge x-ray absorption fine structure (NEXAFS) spectroscopy (both the total electron yield (TEY) and Auger electron yield (AEY) techniques) are used to study and characterize both the clean and hydrogenated surface. In addition, the interaction of hydrogen with the diamond surface is examined using results from vibrational high resolution low energy electron loss spectroscopy (in collaboration with Waclawski, Pierce, Swanson, and Celotta at the National Bureau of Standards) and photon stimulated ion desorption (PSID) yield at photon energies near the carbon k-edge (hv greater than or equal to 280 eV). Both EELS and PSID verify that the mechanically polished 1 x 1 surface is hydrogen terminated and also that the reconstructed surface is hydrogen free. The (111) 2 x 2/2 x 1 reconstructed surface is obtained from the hydrogenated (111) 1 x 1:H surface by annealing to approx. = 1000 0 C. We observe occupied intrinsic surface states and a surface chemical shift (0.95 +- 0.1 eV) to lower binding energy of the carbon 1s level on the hydrogen-free reconstructed surface. Atomic hydrogen is found to be reactive with the reconstructed surface, while molecular hydrogen is relatively inert. Exposure of the reconstructed surface to atomic hydrogen results in chemisorption of hydrogen and removal of the intrinsic surface state emission in and near the band gap region

  6. Electronic structure and electron momentum density in TiSi

    Energy Technology Data Exchange (ETDEWEB)

    Ghaleb, A.M. [Department of Physics, College of Science, University of Kirkuk, Kirkuk (Iraq); Mohammad, F.M. [Department of Physics, College of Science, University of Tikreet, Tikreet (Iraq); Sahariya, Jagrati [Department of Physics, University College of Science, M.L. Sukhadia University, Udaipur 313001, Rajasthan (India); Sharma, Mukesh [Physics Division, Forensic Science Laboratory, Jaipur, Rajasthan (India); Ahuja, B.L., E-mail: blahuja@yahoo.com [Department of Physics, University College of Science, M.L. Sukhadia University, Udaipur 313001, Rajasthan (India)

    2013-03-01

    We report the electron momentum density in titanium monosilicide using {sup 241}Am Compton spectrometer. Experimental Compton profile has been compared with the theoretical profiles computed using linear combination of atomic orbitals (LCAO). The energy bands, density of states and Fermi surface structures of TiSi are reported using the LCAO and the full potential linearized augmented plane wave methods. Theoretical anisotropies in directional Compton profiles are interpreted in terms of energy bands. To confirm the conducting behavior, we also report the real space analysis of experimental Compton profile of TiSi.

  7. Stanniocalcin 1 binds hemin through a partially conserved heme regulatory motif

    International Nuclear Information System (INIS)

    Westberg, Johan A.; Jiang, Ji; Andersson, Leif C.

    2011-01-01

    Highlights: → Stanniocalcin 1 (STC1) binds heme through novel heme binding motif. → Central iron atom of heme and cysteine-114 of STC1 are essential for binding. → STC1 binds Fe 2+ and Fe 3+ heme. → STC1 peptide prevents oxidative decay of heme. -- Abstract: Hemin (iron protoporphyrin IX) is a necessary component of many proteins, functioning either as a cofactor or an intracellular messenger. Hemoproteins have diverse functions, such as transportation of gases, gas detection, chemical catalysis and electron transfer. Stanniocalcin 1 (STC1) is a protein involved in respiratory responses of the cell but whose mechanism of action is still undetermined. We examined the ability of STC1 to bind hemin in both its reduced and oxidized states and located Cys 114 as the axial ligand of the central iron atom of hemin. The amino acid sequence differs from the established (Cys-Pro) heme regulatory motif (HRM) and therefore presents a novel heme binding motif (Cys-Ser). A STC1 peptide containing the heme binding sequence was able to inhibit both spontaneous and H 2 O 2 induced decay of hemin. Binding of hemin does not affect the mitochondrial localization of STC1.

  8. Stanniocalcin 1 binds hemin through a partially conserved heme regulatory motif

    Energy Technology Data Exchange (ETDEWEB)

    Westberg, Johan A., E-mail: johan.westberg@helsinki.fi [Department of Pathology, Haartman Institute, University of Helsinki and HUSLAB, P.O. Box 21, Haartmaninkatu 3, FI-00014 Helsinki (Finland); Jiang, Ji, E-mail: ji.jiang@helsinki.fi [Department of Pathology, Haartman Institute, University of Helsinki and HUSLAB, P.O. Box 21, Haartmaninkatu 3, FI-00014 Helsinki (Finland); Andersson, Leif C., E-mail: leif.andersson@helsinki.fi [Department of Pathology, Haartman Institute, University of Helsinki and HUSLAB, P.O. Box 21, Haartmaninkatu 3, FI-00014 Helsinki (Finland)

    2011-06-03

    Highlights: {yields} Stanniocalcin 1 (STC1) binds heme through novel heme binding motif. {yields} Central iron atom of heme and cysteine-114 of STC1 are essential for binding. {yields} STC1 binds Fe{sup 2+} and Fe{sup 3+} heme. {yields} STC1 peptide prevents oxidative decay of heme. -- Abstract: Hemin (iron protoporphyrin IX) is a necessary component of many proteins, functioning either as a cofactor or an intracellular messenger. Hemoproteins have diverse functions, such as transportation of gases, gas detection, chemical catalysis and electron transfer. Stanniocalcin 1 (STC1) is a protein involved in respiratory responses of the cell but whose mechanism of action is still undetermined. We examined the ability of STC1 to bind hemin in both its reduced and oxidized states and located Cys{sup 114} as the axial ligand of the central iron atom of hemin. The amino acid sequence differs from the established (Cys-Pro) heme regulatory motif (HRM) and therefore presents a novel heme binding motif (Cys-Ser). A STC1 peptide containing the heme binding sequence was able to inhibit both spontaneous and H{sub 2}O{sub 2} induced decay of hemin. Binding of hemin does not affect the mitochondrial localization of STC1.

  9. Hemoglobin and heme scavenger receptors

    DEFF Research Database (Denmark)

    Nielsen, Marianne Jensby; Møller, Holger Jon; Moestrup, Søren Kragh

    2010-01-01

    Heme, the functional group of hemoglobin, myoglobin, and other hemoproteins, is a highly toxic substance when it appears in the extracellular milieu. To circumvent potential harmful effects of heme from hemoproteins released during physiological or pathological cell damage (such as hemolysis...... and rhabdomyolysis), specific high capacity scavenging systems have evolved in the mammalian organism. Two major systems, which essentially function in a similar way by means of a circulating latent plasma carrier protein that upon ligand binding is recognized by a receptor, are represented by a) the hemoglobin...

  10. A dual component heme biosensor that integrates heme transport and synthesis in bacteria.

    Science.gov (United States)

    Nobles, Christopher L; Clark, Justin R; Green, Sabrina I; Maresso, Anthony W

    2015-11-01

    Bacterial pathogens acquire host iron to power cellular processes and replication. Heme, an iron-containing cofactor bound to hemoglobin, is scavenged by bacterial proteins to attain iron. Methods to measure intracellular heme are laborious, involve complex chemistry, or require radioactivity. Such drawbacks limit the study of the mechanistic steps of heme transport and breakdown. Hypothesizing heme homeostasis could be measured with fluorescent methods, we coupled the conversion of heme to biliverdin IXα (a product of heme catabolism) by heme oxygenase 1 (HO1) with the production of near-infrared light upon binding this verdin by infrared fluorescent protein (IFP1.4). The resultant heme sensor, IFP-HO1, was fluorescent in pathogenic E. coli exposed to heme but not in the absence of the heme transporter ChuA and membrane coupling protein TonB, thereby validating their long-standing proposed role in heme uptake. Fluorescence was abolished in a strain lacking hemE, the central gene in the heme biosynthetic pathway, but stimulated by iron, signifying the sensor reports on intracellular heme production. Finally, an invasive strain of E. coli harboring the sensor was fluorescent during an active infection. This work will allow researchers to expand the molecular toolbox used to study heme and iron acquisition in culture and during infection. Copyright © 2015 Elsevier B.V. All rights reserved.

  11. 3D Printed structural electronics: embedding and connecting electronic components into freeform electronic devices

    NARCIS (Netherlands)

    Maalderink, H.H.H.; Bruning, F.B.J.; Schipper, M.M.R. de; Werff, J.J.J. van der; Germs, W.W.C.; Remmers, J.J.C.; Meinders, E.R.

    2018-01-01

    The need for personalised and smart products drives the development of structural electronics with mass-customisation capability. A number of challenges need to be overcome in order to address the potential of complete free form manufacturing of electronic devices. One key challenge is the

  12. 3D Printed structural electronics : embedding and connecting electronic components into freeform electronic devices

    NARCIS (Netherlands)

    Maalderink, H.H.; Bruning, F.B.J.; de Schipper, M.R.; van der Werff, J.J.; Germs, W.C.; Remmers, J.J.C.; Meinders, E.R.

    2018-01-01

    The need for personalised and smart products drives the development of structural electronics with mass-customisation capability. A number of challenges need to be overcome in order to address the potential of complete free form manufacturing of electronic devices. One key challenge is the

  13. Electronic structure of super heavy atoms revisited

    International Nuclear Information System (INIS)

    Gitman, D M; Levin, A D; Tyutin, I V; Voronov, B L

    2013-01-01

    The electronic structure of an atom with Z ⩽ Z c = 137 can be described by the Dirac equation with the Coulomb field of a point charge Ze. It was believed that the Dirac equation with Z > Z c poses difficulties because the formula for the lower energy level of the Dirac Hamiltonian formally gives imaginary eigenvalues. But a strict mathematical consideration shows that difficulties with the electronic spectrum for Z > Z c do not arise if the Dirac Hamiltonian is correctly defined as a self-adjoint operator. In this paper, we briefly summarize the main physical results of that consideration in a form suitable for physicists with some additional new details and numerical calculations of the electronic spectra. (comment)

  14. Electronic Structure of Strongly Correlated Materials

    CERN Document Server

    Anisimov, Vladimir

    2010-01-01

    Electronic structure and physical properties of strongly correlated materials containing elements with partially filled 3d, 4d, 4f and 5f electronic shells is analyzed by Dynamical Mean-Field Theory (DMFT). DMFT is the most universal and effective tool used for the theoretical investigation of electronic states with strong correlation effects. In the present book the basics of the method are given and its application to various material classes is shown. The book is aimed at a broad readership: theoretical physicists and experimentalists studying strongly correlated systems. It also serves as a handbook for students and all those who want to be acquainted with fast developing filed of condensed matter physics.

  15. Electronic band structures of binary skutterudites

    International Nuclear Information System (INIS)

    Khan, Banaras; Aliabad, H.A. Rahnamaye; Saifullah; Jalali-Asadabadi, S.; Khan, Imad; Ahmad, Iftikhar

    2015-01-01

    The electronic properties of complex binary skutterudites, MX 3 (M = Co, Rh, Ir; X = P, As, Sb) are explored, using various density functional theory (DFT) based theoretical approaches including Green's Function (GW) as well as regular and non-regular Tran Blaha modified Becke Jhonson (TB-mBJ) methods. The wide range of calculated bandgap values for each compound of this skutterudites family confirm that they are theoretically as challenging as their experimental studies. The computationally expensive GW method, which is generally assume to be efficient in the reproduction of the experimental bandgaps, is also not very successful in the calculation of bandgaps. In this article, the issue of the theoretical bandgaps of these compounds is resolved by reproducing the accurate experimental bandgaps, using the recently developed non-regular TB-mBJ approach, based on DFT. The effectiveness of this technique is due to the fact that a large volume of the binary skutterudite crystal is empty and hence quite large proportion of electrons lie outside of the atomic spheres, where unlike LDA and GGA which are poor in the treatment of these electrons, this technique properly treats these electrons and hence reproduces the clear electronic picture of these compounds. - Highlights: • Theoretical and experimental electronic band structures of binary skutterudites are reviewed. • The literature reveals that none of the existing theoretical results are consistent with the experiments. • GW, regular and non-regular TB-mBJ methods are used to reproduce the correct results. • The GW and regular TB-mBJ results are better than the available results in literature. • However, non-regular TB-mBJ reproduces the correct experimental band structures

  16. Electronic band structures of binary skutterudites

    Energy Technology Data Exchange (ETDEWEB)

    Khan, Banaras [Center for Computational Materials Science, University of Malakand, Chakdara (Pakistan); Department of Physics, University of Malakand, Chakdara (Pakistan); Aliabad, H.A. Rahnamaye [Department of Physics, Hakim Sabzevari University, Sabzevar (Iran, Islamic Republic of); Saifullah [Center for Computational Materials Science, University of Malakand, Chakdara (Pakistan); Department of Physics, University of Malakand, Chakdara (Pakistan); Jalali-Asadabadi, S. [Department of Physics, Faculty of Science, University of Isfahan (UI), 81744 Isfahan (Iran, Islamic Republic of); Khan, Imad [Center for Computational Materials Science, University of Malakand, Chakdara (Pakistan); Department of Physics, University of Malakand, Chakdara (Pakistan); Ahmad, Iftikhar, E-mail: ahma5532@gmail.com [Center for Computational Materials Science, University of Malakand, Chakdara (Pakistan); Department of Physics, University of Malakand, Chakdara (Pakistan)

    2015-10-25

    The electronic properties of complex binary skutterudites, MX{sub 3} (M = Co, Rh, Ir; X = P, As, Sb) are explored, using various density functional theory (DFT) based theoretical approaches including Green's Function (GW) as well as regular and non-regular Tran Blaha modified Becke Jhonson (TB-mBJ) methods. The wide range of calculated bandgap values for each compound of this skutterudites family confirm that they are theoretically as challenging as their experimental studies. The computationally expensive GW method, which is generally assume to be efficient in the reproduction of the experimental bandgaps, is also not very successful in the calculation of bandgaps. In this article, the issue of the theoretical bandgaps of these compounds is resolved by reproducing the accurate experimental bandgaps, using the recently developed non-regular TB-mBJ approach, based on DFT. The effectiveness of this technique is due to the fact that a large volume of the binary skutterudite crystal is empty and hence quite large proportion of electrons lie outside of the atomic spheres, where unlike LDA and GGA which are poor in the treatment of these electrons, this technique properly treats these electrons and hence reproduces the clear electronic picture of these compounds. - Highlights: • Theoretical and experimental electronic band structures of binary skutterudites are reviewed. • The literature reveals that none of the existing theoretical results are consistent with the experiments. • GW, regular and non-regular TB-mBJ methods are used to reproduce the correct results. • The GW and regular TB-mBJ results are better than the available results in literature. • However, non-regular TB-mBJ reproduces the correct experimental band structures.

  17. Electronic structure of Pu carbides: photoelectron spectroscopy

    Czech Academy of Sciences Publication Activity Database

    Gouder, T.; Havela, L.; Shick, Alexander; Huber, F.

    2008-01-01

    Roč. 403, č. 5-9 (2008), s. 852-853 ISSN 0921-4526 R&D Projects: GA AV ČR(CZ) IAA100100530 Grant - others:EU(XE) RITA -CT-2006-026176 Institutional research plan: CEZ:AV0Z10100520 Keywords : photoemission * electronic structure * plutonium Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 0.822, year: 2008

  18. Structural and electronic properties of thallium compounds

    International Nuclear Information System (INIS)

    Paliwal, Neetu; Srivastava, Vipul

    2016-01-01

    The tight binding linear muffin-tin-orbital (TB-LMTO) method within the local density approximation (LDA has been used to calculate structural and electronic properties of thallium pnictides TlX (X=Sb, Bi) at high pressure. As a function of volume, the total energy is evaluated. Apart from this, the lattice parameter (a_0), bulk modulus (B_0), band structure (BS) and density of states (DOS) are calculated. From energy band diagram we observed metallic behaviour in TlSb and TlBi compounds. The values of equilibrium lattice constants and bulk modulus are agreed well with the available data.

  19. Structural and electronic properties of thallium compounds

    Energy Technology Data Exchange (ETDEWEB)

    Paliwal, Neetu, E-mail: neetumanish@gmail.com [Department of Physics, AISECT University Bhopal, 464993 (India); Srivastava, Vipul [Department of Engineering Physics, NRI Institute of Research & Technology, Raisen Road, Bhopal, 462021 (India)

    2016-05-06

    The tight binding linear muffin-tin-orbital (TB-LMTO) method within the local density approximation (LDA has been used to calculate structural and electronic properties of thallium pnictides TlX (X=Sb, Bi) at high pressure. As a function of volume, the total energy is evaluated. Apart from this, the lattice parameter (a{sub 0}), bulk modulus (B{sub 0}), band structure (BS) and density of states (DOS) are calculated. From energy band diagram we observed metallic behaviour in TlSb and TlBi compounds. The values of equilibrium lattice constants and bulk modulus are agreed well with the available data.

  20. Structural dynamics of electronic and photonic systems

    CERN Document Server

    Suhir, Ephraim; Steinberg, David S

    2011-01-01

    The proposed book will offer comprehensive and versatile methodologies and recommendations on how to determine dynamic characteristics of typical micro- and opto-electronic structural elements (printed circuit boards, solder joints, heavy devices, etc.) and how to design a viable and reliable structure that would be able to withstand high-level dynamic loading. Particular attention will be given to portable devices and systems designed for operation in harsh environments (such as automotive, aerospace, military, etc.)  In-depth discussion from a mechanical engineer's viewpoint will be conducte

  1. Ironing out the Details: Exploring the Role of Iron and Heme in Blood-Sucking Arthropods

    Science.gov (United States)

    Whiten, Shavonn R.; Eggleston, Heather; Adelman, Zach N.

    2018-01-01

    Heme and iron are essential molecules for many physiological processes and yet have the ability to cause oxidative damage such as lipid peroxidation, protein degradation, and ultimately cell death if not controlled. Blood-sucking arthropods have evolved diverse methods to protect themselves against iron/heme-related damage, as the act of bloodfeeding itself is high risk, high reward process. Protective mechanisms in medically important arthropods include the midgut peritrophic matrix in mosquitoes, heme aggregation into the crystalline structure hemozoin in kissing bugs and hemosomes in ticks. Once heme and iron pass these protective mechanisms they are presumed to enter the midgut epithelial cells via membrane-bound transporters, though relatively few iron or heme transporters have been identified in bloodsucking arthropods. Upon iron entry into midgut epithelial cells, ferritin serves as the universal storage protein and transport for dietary iron in many organisms including arthropods. In addition to its role as a nutrient, heme is also an important signaling molecule in the midgut epithelial cells for many physiological processes including vitellogenesis. This review article will summarize recent advancements in heme/iron uptake, detoxification and exportation in bloodfeeding arthropods. While initial strides have been made at ironing out the role of dietary iron and heme in arthropods, much still remains to be discovered as these molecules may serve as novel targets for the control of many arthropod pests. PMID:29387018

  2. Correlated electronic structure of CeN

    Energy Technology Data Exchange (ETDEWEB)

    Panda, S.K., E-mail: swarup.panda@physics.uu.se [Department of Physics and Astronomy, Uppsala University, P.O. Box 516, SE-751 20 Uppsala (Sweden); Di Marco, I. [Department of Physics and Astronomy, Uppsala University, P.O. Box 516, SE-751 20 Uppsala (Sweden); Delin, A. [Department of Physics and Astronomy, Uppsala University, P.O. Box 516, SE-751 20 Uppsala (Sweden); KTH Royal Institute of Technology, School of Information and Communication Technology, Department of Materials and Nano Physics, Electrum 229, SE-164 40 Kista (Sweden); KTH Royal Institute of Technology, Swedish e-Science Research Center (SeRC), SE-100 44 Stockholm (Sweden); Eriksson, O., E-mail: olle.eriksson@physics.uu.se [Department of Physics and Astronomy, Uppsala University, P.O. Box 516, SE-751 20 Uppsala (Sweden)

    2016-04-15

    Highlights: • The electronic structure of CeN is studied within the GGA+DMFT approach using SPTF and Hubbard I approximation. • 4f spectral functions from SPTF and Hubbard I are coupled to explain the various spectroscopic manifestations of CeN. • The calculated XPS and BIS spectra show good agreement with the corresponding experimental spectra. • The contribution of the various l-states and the importance of cross-sections for the photoemission process are analyzed. - Abstract: We have studied in detail the electronic structure of CeN including spin orbit coupling (SOC) and electron–electron interaction, within the dynamical mean-field theory combined with density-functional theory in generalized gradient approximation (GGA+DMFT). The effective impurity problem has been solved through the spin-polarized T-matrix fluctuation-exchange (SPTF) solver and the Hubbard I approximation (HIA). The calculated l-projected atomic partial densities of states and the converged potential were used to obtain the X-ray-photoemission-spectra (XPS) and Bremstrahlung Isochromat spectra (BIS). Following the spirit of Gunnarsson–Schonhammer model, we have coupled the SPTF and HIA 4f spectral functions to explain the various spectroscopic manifestations of CeN. Our computed spectra in such a coupled scheme explain the experimental data remarkably well, establishing the validity of our theoretical model in analyzing the electronic structure of CeN. The contribution of the various l-states in the total spectra and the importance of cross sections are also analyzed in detail.

  3. Electronic structure theory of the superheavy elements

    Energy Technology Data Exchange (ETDEWEB)

    Eliav, Ephraim, E-mail: ephraim@tau.ac.il [School of Chemistry, Tel Aviv University, 6997801 Tel Aviv (Israel); Fritzsche, Stephan, E-mail: s.fritzsche@gsi.de [Helmholtz-Institut Jena, Fröbelstieg 3, D-07743 Jena (Germany); Theoretisch-Physikalisches Institut, Friedrich-Schiller-Universität Jena, D-07743 Jena (Germany); Kaldor, Uzi, E-mail: kaldor@tau.ac.il [School of Chemistry, Tel Aviv University, 6997801 Tel Aviv (Israel)

    2015-12-15

    High-accuracy calculations of atomic properties of the superheavy elements (SHE) up to element 122 are reviewed. The properties discussed include ionization potentials, electron affinities and excitation energies, which are associated with the spectroscopic and chemical behavior of these elements, and are therefore of considerable interest. Accurate predictions of these quantities require high-order inclusion of relativity and electron correlation, as well as large, converged basis sets. The Dirac–Coulomb–Breit Hamiltonian, which includes all terms up to second order in the fine-structure constant α, serves as the framework for the treatment; higher-order Lamb shift terms are considered in some selected cases. Electron correlation is treated by either the multiconfiguration self-consistent-field approach or by Fock-space coupled cluster theory. The latter is enhanced by the intermediate Hamiltonian scheme, allowing the use of larger model (P) spaces. The quality of the calculations is assessed by applying the same methods to lighter homologs of the SHEs and comparing with available experimental information. Very good agreement is obtained, within a few hundredths of an eV, and similar accuracy is expected for the SHEs. Many of the properties predicted for the SHEs differ significantly from what may be expected by straightforward extrapolation of lighter homologs, demonstrating that the structure and chemistry of SHEs are strongly affected by relativity. The major scientific challenge of the calculations is to find the electronic structure and basic atomic properties of the SHE and assign its proper place in the periodic table. Significant recent developments include joint experimental–computational studies of the excitation spectrum of Fm and the ionization energy of Lr, with excellent agreement of experiment and theory, auguring well for the future of research in the field.

  4. Synthesis and Evaluation of Amyloid β Derived and Amyloid β Independent Enhancers of the Peroxidase-like Activity of Heme.

    Science.gov (United States)

    Wißbrock, Amelie; Kühl, Toni; Silbermann, Katja; Becker, Albert J; Ohlenschläger, Oliver; Imhof, Diana

    2017-01-12

    Labile heme has been suggested to have an impact in several severe diseases. In the context of Alzheimer's disease (AD), however, decreased levels of free heme have been reported. Therefore, we were looking for an assay system that can be used for heme concentration determination. From a biochemical point of view the peroxidase activity of the Aβ-heme complex seemed quite attractive to pursue this goal. As a consequence, a peptide that is able to increase the readout even in the case of a low heme concentration is favorable. The examination of Aβ- and non-Aβ-derived peptides in complex with heme revealed that the peroxidase-like activity significantly depends on the peptide sequence and length. A 23mer His-based peptide derived from human fatty acyl-CoA reductase 1 in complex with heme exhibited a significantly higher peroxidase activity than Aβ(40)-heme. Structural modeling of both complexes demonstrated that heme binding via a histidine can be supported by hydrogen bond interactions of a basic residue near the propionate carboxyl function of protoporphyrin IX. Furthermore, the interplay of Aβ-heme and the lipoprotein LDL as a potential physiological effector of Aβ was examined.

  5. Visualization of the role of host heme on the virulence of the heme auxotroph Streptococcus agalactiae.

    Science.gov (United States)

    Joubert, Laetitia; Dagieu, Jean-Baptiste; Fernandez, Annabelle; Derré-Bobillot, Aurélie; Borezée-Durant, Elise; Fleurot, Isabelle; Gruss, Alexandra; Lechardeur, Delphine

    2017-01-16

    Heme is essential for several cellular key functions but is also toxic. Whereas most bacterial pathogens utilize heme as a metabolic cofactor and iron source, the impact of host heme during bacterial infection remains elusive. The opportunist pathogen Streptococcus agalactiae does not synthesize heme but still uses it to activate a respiration metabolism. Concomitantly, heme toxicity is mainly controlled by the HrtBA efflux transporter. Here we investigate how S. agalactiae manages heme toxicity versus benefits in the living host. Using bioluminescent bacteria and heme-responsive reporters for in vivo imaging, we show that the capacity of S. agalactiae to overcome heme toxicity is required for successful infection, particularly in blood-rich organs. Host heme is simultaneously required, as visualized by a generalized infection defect of a respiration-negative mutant. In S. agalactiae, HrtBA expression responds to an intracellular heme signal via activation of the two-component system HssRS. A hssRS promoter-driven intracellular luminescent heme sensor was designed to identify host compartments that supply S. agalactiae with heme. S. agalactiae acquires heme in heart, kidneys, and liver, but not in the brain. We conclude that S. agalactiae response to heme is organ-dependent, and its efflux may be particularly relevant in late stages of infection.

  6. Spectral-Product Methods for Electronic Structure Calculations (Preprint)

    National Research Council Canada - National Science Library

    Langhoff, P. W; Mills, J. E; Boatz, J. A

    2006-01-01

    .... The spectral-product approach to molecular electronic structure avoids the repeated evaluations of the one- and two-electron integrals required in construction of polyatomic Hamiltonian matrices...

  7. Spectral-Product Methods for Electronic Structure Calculations (Postprint)

    National Research Council Canada - National Science Library

    Langhoff, P. W; Hinde, R. J; Mills, J. D; Boatz, J. A

    2007-01-01

    .... The spectral-product approach to molecular electronic structure avoids the repeated evaluations of the one- and two-electron integrals required in construction of polyatomic Hamiltonian matrices...

  8. Electronic structure and superconductivity of europium

    International Nuclear Information System (INIS)

    Nixon, Lane W.; Papaconstantopoulos, D.A.

    2010-01-01

    We have calculated the electronic structure of Eu for the bcc, hcp, and fcc crystal structures for volumes near equilibrium up to a calculated 90 GPa pressure using the augmented-plane-wave method in the local-density approximation. The frozen-core approximation was used with a semi-empirical shift of the f-states energies in the radial Schroedinger equation to move the occupied 4f valence states below the Γ 1 energy and into the core. This shift of the highly localized f-states yields the correct europium phase ordering with lattice parameters and bulk moduli in good agreement with experimental data. The calculated superconductivity properties under pressure for the bcc and hcp structures are also found to agree with and follow a T c trend similar to recent measurement by Debessai et al.

  9. Electromagnetic Radiation of Electrons in Periodic Structures

    CERN Document Server

    Potylitsyn, Alexander Petrovich

    2011-01-01

    Periodic magnetic structures (undulators) are widely used in accelerators to generate monochromatic undulator radiation (UR) in the range from far infrared to the hard X-ray region. Another periodic crystalline structure is used to produce quasimonochromatic polarized photon beams via the coherent bremsstrahlung mechanism (CBS). Due to such characteristics as monochromaticity, polarization and adjustability, these types of radiation is of large interest for applied and basic research of accelerator-emitted radiation. The book provides a detailed overview of the fundamental principles behind electromagnetic radiation emitted from accelerated charged particles (e.g. UR, CBS, radiation of fast electrons in Laser flash fields) as well as a unified description of relatively new radiation mechanisms which attracted great interest in recent years. This are the so-called polarization radiation excited by the Coulomb field of incident particles in periodic structures, parametric X-rays, resonant transition radiation a...

  10. Boson structure functions from inelastic electron scattering

    International Nuclear Information System (INIS)

    De Jager, C.W.

    1986-01-01

    The even /sup 104-110/Pd isotopes and /sup 196/Pt have been investigated at NIKHEF-K by high-resolution inelastic electron scattering. A new IBA-2 calculation has been performed for the Pd isotopes, in which the ratio of the proton and neutron coupling constants is taken from pion scattering. One set of boson structure functions sufficed for the description of the first and second E2-excitations in all Pd isotopes. The data showed no sensitivity for different structure functions for proton and neutron bosons. A preliminary analysis of a number of negative parity states (3/sup -/,5/sup -/ and 7/sup -/), observed in /sup 196/Pt, was performed through the introduction of an f-boson. The first E4-excitation in the palladium isotopes can be reasonably described with a β-structure function, but all other E4-excitations require the introduction of g-boson admixtures

  11. Photoelectron spectroscopy bulk and surface electronic structures

    CERN Document Server

    Suga, Shigemasa

    2014-01-01

    Photoelectron spectroscopy is now becoming more and more required to investigate electronic structures of various solid materials in the bulk, on surfaces as well as at buried interfaces. The energy resolution was much improved in the last decade down to 1 meV in the low photon energy region. Now this technique is available from a few eV up to 10 keV by use of lasers, electron cyclotron resonance lamps in addition to synchrotron radiation and X-ray tubes. High resolution angle resolved photoelectron spectroscopy (ARPES) is now widely applied to band mapping of materials. It attracts a wide attention from both fundamental science and material engineering. Studies of the dynamics of excited states are feasible by time of flight spectroscopy with fully utilizing the pulse structures of synchrotron radiation as well as lasers including the free electron lasers (FEL). Spin resolved studies also made dramatic progress by using higher efficiency spin detectors and two dimensional spin detectors. Polarization depend...

  12. Electronic Structures of LNA Phosphorothioate Oligonucleotides

    Directory of Open Access Journals (Sweden)

    Henrik G. Bohr

    2017-09-01

    Full Text Available Important oligonucleotides in anti-sense research have been investigated in silico and experimentally. This involves quantum mechanical (QM calculations and chromatography experiments on locked nucleic acid (LNA phosphorothioate (PS oligonucleotides. iso-potential electrostatic surfaces are essential in this study and have been calculated from the wave functions derived from the QM calculations that provide binding information and other properties of these molecules. The QM calculations give details of the electronic structures in terms of e.g., energy and bonding, which make them distinguish or differentiate between the individual PS diastereoisomers determined by the position of sulfur atoms. Rules are derived from the electronic calculations of these molecules and include the effects of the phosphorothioate chirality and formation of electrostatic potential surfaces. Physical and electrochemical descriptors of the PS oligonucleotides are compared to the experiments in which chiral states on these molecules can be distinguished. The calculations demonstrate that electronic structure, electrostatic potential, and topology are highly sensitive to single PS configuration changes and can give a lead to understanding the activity of the molecules. Keywords: LNA phosphorothioate, DNA/LNA oligonucleotide, diastereoisomers, Hartree-Fock calculations, iso-potential surface, anion chromatograms

  13. Tyrosine B10 triggers a heme propionate hydrogen bonding network loop with glutamine E7 moiety

    International Nuclear Information System (INIS)

    Ramos-Santana, Brenda J.; López-Garriga, Juan

    2012-01-01

    Highlights: ► H-bonding network loop by PheB10Tyr mutation is proposed. ► The propionate group H-bonding network restricted the flexibility of the heme. ► The hydrogen bonding interaction modulates the electron density of the iron. ► Propionate H-bonding network loop explains the heme-ligand stabilization. -- Abstract: Propionates, as peripheral groups of the heme active center in hemeproteins have been described to contribute in the modulation of heme reactivity and ligand selection. These electronic characteristics prompted the question of whether the presence of hydrogen bonding networks between propionates and distal amino acids present in the heme ligand moiety can modulate physiological relevant events, like ligand binding association and dissociation activities. Here, the role of these networks was evaluated by NMR spectroscopy using the hemoglobin I PheB10Tyr mutant from Lucina pectinata as model for TyrB10 and GlnE7 hemeproteins. 1 H-NMR results for the rHbICN PheB10Tyr derivative showed chemical shifts of TyrB10 OHη at 31.00 ppm, GlnE7 N ε1 H/N ε2 H at 10.66 ppm/−3.27 ppm, and PheE11 C δ H at 11.75 ppm, indicating the presence of a crowded, collapsed, and constrained distal pocket. Strong dipolar contacts and inter-residues crosspeaks between GlnE7/6-propionate group, GlnE7/TyrB10 and TyrB10/CN suggest that this hydrogen bonding network loop between GlnE7, TyrB10, 6-propionate group, and the heme ligand contribute significantly to the modulation of the heme iron electron density as well as the ligand stabilization mechanism. Therefore, the network loop presented here support the fact that the electron withdrawing character of the hydrogen bonding is controlled by the interaction of the propionates and the nearby electronic environments contributing to the modulation of the heme electron density state. Thus, we hypothesize that in hemeproteins with similar electrostatic environment the flexibility of the heme-6-propionate promotes a hydrogen

  14. Extraordinary electronic properties in uncommon structure types

    Science.gov (United States)

    Ali, Mazhar Nawaz

    In this thesis I present the results of explorations into several uncommon structure types. In Chapter 1 I go through the underlying idea of how we search for new compounds with exotic properties in solid state chemistry. The ideas of exploring uncommon structure types, building up from the simple to the complex, using chemical intuition and thinking by analogy are discussed. Also, the history and basic concepts of superconductivity, Dirac semimetals, and magnetoresistance are briefly reviewed. In chapter 2, the 1s-InTaS2 structural family is introduced along with the discovery of a new member of the family, Ag0:79VS2; the synthesis, structure, and physical properties of two different polymorphs of the material are detailed. Also in this chapter, we report the observation of superconductivity in another 1s structure, PbTaSe2. This material is especially interesting due to it being very heavy (resulting in very strong spin orbit coulping (SOC)), layered, and noncentrosymmetric. Electronic structure calculations reveal the presence of a bulk 3D Dirac cone (very similar to graphene) that is gapped by SOC originating from the hexagonal Pb layer. In Chapter 3 we show the re-investigation of the crystal structure of the 3D Dirac semimetal, Cd3As2. It is found to be centrosymmetric, rather than noncentrosymmetric, and as such all bands are spin degenerate and there is a 4-fold degenerate bulk Dirac point at the Fermi level, making Cd3As2 a 3D electronic analog to graphene. Also, for the first time, scanning tunneling microscopy experiments identify a 2x2 surface reconstruction in what we identify as the (112) cleavage plane of single crystals; needle crystals grow with a [110] long axis direction. Lastly, in chapter 4 we report the discovery of "titanic" (sadly dubbed ⪉rge, nonsaturating" by Nature editors and given the acronym XMR) magnetoresistance (MR) in the non-magnetic, noncentrosymmetric, layered transition metal dichalcogenide WTe2; over 13 million% at 0.53 K in

  15. Projected quasiparticle theory for molecular electronic structure

    Science.gov (United States)

    Scuseria, Gustavo E.; Jiménez-Hoyos, Carlos A.; Henderson, Thomas M.; Samanta, Kousik; Ellis, Jason K.

    2011-09-01

    We derive and implement symmetry-projected Hartree-Fock-Bogoliubov (HFB) equations and apply them to the molecular electronic structure problem. All symmetries (particle number, spin, spatial, and complex conjugation) are deliberately broken and restored in a self-consistent variation-after-projection approach. We show that the resulting method yields a comprehensive black-box treatment of static correlations with effective one-electron (mean-field) computational cost. The ensuing wave function is of multireference character and permeates the entire Hilbert space of the problem. The energy expression is different from regular HFB theory but remains a functional of an independent quasiparticle density matrix. All reduced density matrices are expressible as an integration of transition density matrices over a gauge grid. We present several proof-of-principle examples demonstrating the compelling power of projected quasiparticle theory for quantum chemistry.

  16. Studies in the electronic structure of matter

    International Nuclear Information System (INIS)

    Swarts, C.A.

    1979-01-01

    The results of various theories for the angular distribution of electrons photoemitted from the outermost p-shell of rare gas atoms are compared. The theories compared are the local density theories of Slater (X/sub α/) and of Hohenberg, Kohn and Sham, the pseudopotential method, Hartree-Fock theory as evaluated by Kennedy and Manson, and Amusia's random phase approximation with exchange (RPAE). Extended Huekel theory is applied to GaAs, GaP, and to the nitrogen isoelectronic trap in GaAs and GaP. The computer perfect crystal band structures are found to be in reasonable agreement with those computed with empirical pseudopotentials. Nitrogen impurity levels in GaAs and GaP are calculated using a cluster model. By means of model calculations for an independent electron metal, exact lineshapes are obtained for the photon absorption, emission and photoemission spectra of deep core states. 97 references

  17. Studies in the electronic structure of matter

    International Nuclear Information System (INIS)

    Miller, D.L.

    1979-01-01

    KLL Auger transition rates for helium are computed using simple atomic orbital wavefunctions which take into account the difference in average electron--electron repulsion of initial and final states. The results are consistent with transition rates computed by other authors using a variety of many-electron techniques. It is suggested that wavefunctions determined in the manner described provide a useful representation of the autoionizing state within the first Bohr radius. A method for extracting atomic pseudopotentials from photoelectron angular distributions is described and applied photoionization of the outermost p shells of Ar, Kr, and Xe and to the 4d shell of Xe. The pseudopotentials obtained reproduce the data, and also predict accurate cross sections and phase shifts for photoelectron energies up to 100 eV. It is suggested that the pseudopotentials aptly mimic the effects of intrashell electron--electron correlations in the photoionization process. The extended Hueckel theory is applied to the nitrogen trap in GaAs and GaP. Perfect crystal band structures are computed and are shown to be in reasonable agreement with those computed with empirical pseudopotentials. Nitrogen impurity levels in GaAs and GaP are computed using an extended Hueckel cluster model. In each case the model predicts two states within the band gap, in contrast to experiment which detects one impurity state in GaP and none in GaAs. It is suggested that the choice of cluster used unrealistically concentrates states near the conduction band edge on the central atom

  18. Studies in the electronic structure of matter

    International Nuclear Information System (INIS)

    Miller, D.L.

    1979-01-01

    KLL Auger transition rates for helium are computed using simple atomic orbital wavefunctions which take into account the difference in average electron-electron repulsion of initial and final states. The results are consistent with transition rates computed by other authors using a variety of many-electron techniques. It is suggested that wavefunctions determined in the manner described provide a useful representation of the autoionizing state within the first Bohr radius. A method for extracting atomic psuedopotentials from photoelectron angular distributions is described and applied photoionization of the outermost p shells of Ar, Kr, and Xe and to the 4d shell of Xe. The pseudopotentials obtained reproduce the data, and also predict accurate cross sections and phase shifts for photoelectron energies up to 100 eV. It is suggested that the pseudopotentials aptly mimic the effects of intrashell electron-electron correlations in the photoionization process. The extended Hueckel theory is applied to the nitrogen trap in GaAs and GaP. Perfect crystal band structures are computed and are shown to be in reasonable agreement with those computed with empirical psuedopotentials. Nitrogen impurity levles in GaAs and GaP are computed using an extended Hueckel cluster model. In each case the model predicts two states within the band gap, in contrast to experiment which detects one impurity state in GaP and none in GaAs. It is suggested that the choice of cluster used unrealistically concentrates states near the conduction band edge on the central atom

  19. Electronic structure of defects in semiconductor heterojunctions

    International Nuclear Information System (INIS)

    Haussy, Bernard; Ganghoffer, Jean Francois

    2002-01-01

    Full text.heterojunctions and semiconductors and superlattices are well known and well used by people interested in optoelectronics communications. Components based on the use of heterojunctions are interesting for confinement of light and increase of quantum efficiency. An heterojunction is the contact zone between two different semiconductors, for example GaAs and Ga 1-x Al x As. Superlattices are a succession of heterojunctions (up to 10 or 20). These systems have been the subjects of many experiments ao analyse the contact between semiconductors. They also have been theoretically studied by different types of approach. The main result of those studies is the prediciton of band discontinuities. Defects in heterojunctions are real traps for charge carriers; they can affect the efficiency of the component decreasing the currents and the fluxes in it. the knowledge of their electronic structure is important, a great density of defects deeply modifies the electronic structure of the whole material creating real new bands of energy in the band structure of the component. in the first part of this work, we will describe the heterostructure and the defect in terms of quantum wells and discrete levels. This approach allows us to show the role of the width of the quantum well describing the structure but induces specific behaviours due to the one dimensional modelling. Then a perturbative treatment is proposed using the Green's functions formalism. We build atomic chains with different types of atoms featuring the heterostructure and the defect. Densities of states of a structure with a defect and levels associated to the defect are obtained. Results are comparable with the free electrons work, but the modelling do not induce problems due to a one dimensional approach. To extend our modelling, a three dimensions approach, based on a cavity model, is investigated. The influence of the defect, - of hydrogenoid type - introduced in the structure, is described by a cavity

  20. Atomic Reference Data for Electronic Structure Calculations

    CERN Document Server

    Kotochigova, S; Shirley, E L

    We have generated data for atomic electronic structure calculations, to provide a standard reference for results of specified accuracy under commonly used approximations. Results are presented here for total energies and orbital energy eigenvalues for all atoms from H to U, at microHartree accuracy in the total energy, as computed in the local-density approximation (LDA) the local-spin-density approximation (LSD); the relativistic local-density approximation (RLDA); and scalar-relativistic local-density approximation (ScRLDA).

  1. The electronic structure of impurities in semiconductors

    CERN Multimedia

    Nylandsted larsen, A; Svane, A

    2002-01-01

    The electronic structure of isolated substitutional or interstitial impurities in group IV, IV-IV, and III-V compound semiconductors will be studied. Mössbauer spectroscopy will be used to investigate the incorporation of the implanted isotopes on the proper lattice sites. The data can be directly compared to theoretical calculations using the LMTO scheme. Deep level transient spectroscopy will be used to identify the band gap levels introduced by metallic impurities, mainly in Si~and~Si$ _{x}$Ge$_{1-x}$. \\\\ \\\\

  2. Unoccupied surface electronic structure of Gd(0001)

    International Nuclear Information System (INIS)

    Li, D.; Dowben, P.A.; Ortega, J.E.; Himpsel, F.J.

    1994-01-01

    The unoccupied surface electronic structure of Gd(0001) was investigated with high-resolution inverse-photoemission spectroscopy. An empty surface state near E F is observed at bar Γ. Two other surface-sensitive features are also revealed at 1.2 and 3.1 eV above the Fermi level. Hydrogen adsorption on Gd surfaces was used to distinguish the surface-sensitive features from the bulk features. The unoccupied bulk-band critical points are determined to be Γ 3 + at 1.9 eV and A 1 at 0.8 eV

  3. Cobalamins uncovered by modern electronic structure calculations

    DEFF Research Database (Denmark)

    Kepp, Kasper Planeta; Ryde, Ulf

    2009-01-01

    electronic-structure calculations, in particular density functional methods, the understanding of the molecular mechanism of cobalamins has changed dramatically, going from a dominating view of trans-steric strain effects to a much more complex view involving an arsenal of catalytic strategies. Among...... these are cis-steric distortions, electrostatic stabilization of radical products, the realization that nucleotide units can serve as polar handles, and the careful design of the active sites, with polar residues in the radical enzymes and non-polar residues in the transferases. Together, these strategies...

  4. Electronic golden structure of the periodic chart

    Energy Technology Data Exchange (ETDEWEB)

    Malinowski, Leonard J. [Interdisciplinary Research Club, Monroeville, PA (United States)], E-mail: LJMalinowski@gmail.com

    2009-11-15

    The golden ratio has been studied since the ancient Greeks due to its inherent symmetry and aesthetic beauty, especially in the five Platonic Solids. The golden mean is now established as a pillar of El Naschie's E infinity where it achieves the physical manifestation of 0.618 034 MeV. The largest atomic electron orbital total energies average to the golden mean energy. This paper examines the golden ratio in order to expand upon a century old attempt to produce a relatively static, visual, geometric model of atomic structure.

  5. Electronic golden structure of the periodic chart

    International Nuclear Information System (INIS)

    Malinowski, Leonard J.

    2009-01-01

    The golden ratio has been studied since the ancient Greeks due to its inherent symmetry and aesthetic beauty, especially in the five Platonic Solids. The golden mean is now established as a pillar of El Naschie's E infinity where it achieves the physical manifestation of 0.618 034 MeV. The largest atomic electron orbital total energies average to the golden mean energy. This paper examines the golden ratio in order to expand upon a century old attempt to produce a relatively static, visual, geometric model of atomic structure.

  6. Electronic structure of A15 compounds

    International Nuclear Information System (INIS)

    Pickett, W.E.

    1980-01-01

    For the past twenty-five years compounds with the A15 crystal structure have dominated the class of high temperature superconductors. The crystal structure of an A15 compound A 3 B is cubic (space group O/sub h/ 3 ). However, the site symmetry (D/sub 2d/) of the A atoms is much lower than cubic, an unusual occurrence in cubic binary compounds. Variations on this theme have supplied the basis of many theoretical models of the anomalous temperature (T) dependence of normal state properties and the low temperature cubic reversible tetragonal structural transformations which accompany high values of T/sub c/ in A15 compounds. In this paper results of self-consistent pseudopotential band structure calculations are used to assess some important aspects of the unique and unusual behavior in A15 compounds: (1) the role of the B atom in determining the overall electronic structure will be shown to be important; (2) the effect of the low site symmetry of the A atom on the charge density and potential will be assessed; and (3) the bonding will be shown to be metallic-covalent with no significant A-B charge transfer

  7. Electronic structure of point defects in semiconductors

    International Nuclear Information System (INIS)

    Bruneval, Fabien

    2014-01-01

    This 'Habilitation a diriger des Recherches' memoir presents most of my scientific activities during the past 7 years, in the field of electronic structure calculations of defects in solids. Point defects (vacancies, interstitials, impurities) in functional materials are a key parameter to determine if these materials will actually fill the role they have been assigned or not. Indeed, the presence of defects cannot be avoided when the temperature is increased or when the material is subjected to external stresses, such as irradiation in the nuclear reactors and in artificial satellites with solar radiations. However, in many cases, defects are introduced in the materials on purpose to tune the electronic transport, optical or even magnetic properties. This procedure is called the doping of semiconductors, which is the foundation technique for transistors, diodes, or photovoltaic cells. However, doping is not always straightforward and unexpected features may occur, such as doping asymmetry or Fermi level pinning, which can only be explained by complex phenomena involving different types of defects or complexes of defects. In this context, the calculations of electronic structure ab initio is an ideal tool to complement the experimental observations, to gain the understanding of phenomena at the atomic level, and even to predict the properties of defects. The power of the ab initio calculations comes from their ability to describe any system of electrons and nuclei without any specific adjustment. But although there is a strong need for numerical simulations in this field, the ab initio calculations for defects are still under development as of today. The work presented in this memoir summarizes my contributions to methodological developments on this subject. These developments have followed two main tracks. The first topic is the better understanding of the unavoidable finite size effects. Indeed, defects in semiconductors or insulators are generally present in

  8. Electronic structure of hcp transition metals

    DEFF Research Database (Denmark)

    Jepsen, O.; Andersen, O. Krogh; Mackintosh, A. R.

    1975-01-01

    Using the linear muffin-tin-orbital method described in the previous paper, we have calculated the electronic structures of the hcp transition metals, Zr, Hf, Ru, and Os. We show how the band structures of these metals may be synthesized from the sp and d bands, and illustrate the effects...... of hybridization, relativistic band shifts, and spin-orbit coupling by the example of Os. By making use of parameters derived from the muffin-tin potential, we discuss trends in the positions and widths of the energy bands, especially the d bands, as a function of the location in the periodic table. The densities...... of states of the four metals are presented, and the calculated heat capacities compared with experiment. The Fermi surfaces of both Ru and Os are found to be in excellent quantitative agreement with de Haas-van Alphen measurements, indicating that the calculated d-band position is misplaced by less than 10...

  9. Experimental Benchmarking of Pu Electronic Structure

    International Nuclear Information System (INIS)

    Tobin, J.G.; Moore, K.T.; Chung, B.W.; Wall, M.A.; Schwartz, A.J.; Ebbinghaus, B.B.; Butterfield, M.T.; Teslich, N.E. Jr.; Bliss, R.A.; Morton, S.A.; Yu, S.W.; Komesu, T.; Waddill, G.D.; van der Laan, G.; Kutepov, A.L.

    2008-01-01

    The standard method to determine the band structure of a condensed phase material is to (1) obtain a single crystal with a well defined surface and (2) map the bands with angle resolved photoelectron spectroscopy (occupied or valence bands) and inverse photoelectron spectroscopy (unoccupied or conduction bands). Unfortunately, in the case of Pu, the single crystals of Pu are either nonexistent, very small and/or having poorly defined surfaces. Furthermore, effects such as electron correlation and a large spin-orbit splitting in the 5f states have further complicated the situation. Thus, we have embarked upon the utilization of unorthodox electron spectroscopies, to circumvent the problems caused by the absence of large single crystals of Pu with well-defined surfaces. Our approach includes the techniques of resonant photoelectron spectroscopy, x-ray absorption spectroscopy, electron energy loss spectroscopy, Fano Effect measurements, and Bremstrahlung Isochromat Spectroscopy, including the utilization of micro-focused beams to probe single-crystallite regions of polycrystalline Pu samples.

  10. Deep learning and the electronic structure problem

    Science.gov (United States)

    Mills, Kyle; Spanner, Michael; Tamblyn, Isaac

    In the past decade, the fields of artificial intelligence and computer vision have progressed remarkably. Supported by the enthusiasm of large tech companies, as well as significant hardware advances and the utilization of graphical processing units to accelerate computations, deep neural networks (DNN) are gaining momentum as a robust choice for many diverse machine learning applications. We have demonstrated the ability of a DNN to solve a quantum mechanical eigenvalue equation directly, without the need to compute a wavefunction, and without knowledge of the underlying physics. We have trained a convolutional neural network to predict the total energy of an electron in a confining, 2-dimensional electrostatic potential. We numerically solved the one-electron Schrödinger equation for millions of electrostatic potentials, and used this as training data for our neural network. Four classes of potentials were assessed: the canonical cases of the harmonic oscillator and infinite well, and two types of randomly generated potentials for which no analytic solution is known. We compare the performance of the neural network and consider how these results could lead to future advances in electronic structure theory.

  11. Structure and navigation for electronic publishing

    Science.gov (United States)

    Tillinghast, John; Beretta, Giordano B.

    1998-01-01

    The sudden explosion of the World Wide Web as a new publication medium has given a dramatic boost to the electronic publishing industry, which previously was a limited market centered around CD-ROMs and on-line databases. While the phenomenon has parallels to the advent of the tabloid press in the middle of last century, the electronic nature of the medium brings with it the typical characteristic of 4th wave media, namely the acceleration in its propagation speed and the volume of information. Consequently, e-publications are even flatter than print media; Shakespeare's Romeo and Juliet share the same computer screen with a home-made plagiarized copy of Deep Throat. The most touted tool for locating useful information on the World Wide Web is the search engine. However, due to the medium's flatness, sought information is drowned in a sea of useless information. A better solution is to build tools that allow authors to structure information so that it can easily be navigated. We experimented with the use of ontologies as a tool to formulate structures for information about a specific topic, so that related concepts are placed in adjacent locations and can easily be navigated using simple and ergonomic user models. We describe our effort in building a World Wide Web based photo album that is shared among a small network of people.

  12. Electronic structure and superconductivity of fcc Cr

    International Nuclear Information System (INIS)

    Xu, J.; Freeman, A.J.; Jarlborg, T.; Brodsky, M.B.

    1984-01-01

    Results of self-consistent electronic structure calculations are reported for metastable fcc Cr metal. Unlike the case of bcc Cr which has E/sub F/ at a minimum in the density of states (DOS), the DOS at E/sub F/ in fcc Cr is at a peak making this one of the higher-DOS metals with the fcc structure (e.g., comparable with that of Ni and Pt). A calculated Stoner factor of 0.82 indicates that ferromagnetic ordering is not expected. Calculations of the electron-phonon coupling parameter lambda and superconducting transition temperature T/sub c/ were made using the rigid-ion approximation and strong-coupling theory with various estimates of the (unknown) phonon contribution. We conclude that T/sub c/'sroughly-equal2.5 K are reasonable, although they are substantially smaller than the T/sub c/roughly-equal10 K derived from measurements on Au-Cr-Au sandwiches

  13. Identification of residues in the heme domain of soluble guanylyl cyclase that are important for basal and stimulated catalytic activity.

    Directory of Open Access Journals (Sweden)

    Padmamalini Baskaran

    Full Text Available Nitric oxide signals through activation of soluble guanylyl cyclase (sGC, a heme-containing heterodimer. NO binds to the heme domain located in the N-terminal part of the β subunit of sGC resulting in increased production of cGMP in the catalytic domain located at the C-terminal part of sGC. Little is known about the mechanism by which the NO signaling is propagated from the receptor domain (heme domain to the effector domain (catalytic domain, in particular events subsequent to the breakage of the bond between the heme iron and Histidine 105 (H105 of the β subunit. Our modeling of the heme-binding domain as well as previous homologous heme domain structures in different states point to two regions that could be critical for propagation of the NO activation signal. Structure-based mutational analysis of these regions revealed that residues T110 and R116 in the αF helix-β1 strand, and residues I41 and R40 in the αB-αC loop mediate propagation of activation between the heme domain and the catalytic domain. Biochemical analysis of these heme mutants allows refinement of the map of the residues that are critical for heme stability and propagation of the NO/YC-1 activation signal in sGC.

  14. A Heme-Sensing Mechanism in the Translational Regulation of Mitochondrial Cytochrome c Oxidase Biogenesis

    Science.gov (United States)

    Soto, Iliana C.; Fontanesi, Flavia; Myers, Richard S.; Hamel, Patrice; Barrientos, Antoni

    2012-01-01

    Heme plays fundamental roles as cofactor and signaling molecule in multiple pathways devoted to oxygen sensing and utilization in aerobic organisms. For cellular respiration, heme serves as a prosthetic group in electron transfer proteins and redox enzymes. Here we report that in the yeast Saccharomyces cerevisiae a heme-sensing mechanism translationally controls the biogenesis of cytochrome c oxidase (COX), the terminal mitochondrial respiratory chain enzyme. We show that Mss51, a COX1 mRNA-specific translational activator and Cox1 chaperone, which coordinates Cox1 synthesis in mitoribosomes with its assembly in COX, is a heme-binding protein. Mss51 contains two heme regulatory motifs or Cys-Pro-X domains located in its N-terminus. Using a combination of in vitro and in vivo approaches, we have demonstrated that these motifs are important for heme binding and efficient performance of Mss51 functions. We conclude that heme sensing by Mss51 regulates COX biogenesis and aerobic energy production. PMID:23217259

  15. Electronic structure of Ca, Sr, and Ba under pressure.

    Science.gov (United States)

    Animalu, A. O. E.; Heine, V.; Vasvari, B.

    1967-01-01

    Electronic band structure calculations phase of Ca, Sr and Ba over wide range of atomic volumes under pressure electronic band structure calculations for fcc phase of Ca, Sr and Ba over wide range of atomic volumes under pressure electronic band structure calculations for fcc phase of Ca, Sr and Ba over wide range of atomic volumes under pressure

  16. Investigation of the hyperfine properties of deoxy hemoglobin based on its electronic structure obtained by Hartree-Fock-Roothan procedure

    Energy Technology Data Exchange (ETDEWEB)

    Lata, K. Ramani [State University of New York at Albany, Department of Physics (United States); Sahoo, N. [University of Texas M.D. Anderson Cancer Center, Department of Radiation Physics (United States); Dubey, Archana [University of Central Florida, Department of Physics (United States); Scheicher, R. H. [Uppsala University, Condensed Matter Theory Group, Department of Physics and Materials Science (Sweden); Badu, S. R.; Pink, R. H.; Mahato, Dip N. [State University of New York at Albany, Department of Physics (United States); Schulte, A. F.; Saha, H. P. [University of Central Florida, Department of Physics (United States); Maharjan, N. B. [State University of New York at Albany, Department of Physics (United States); Chow, Lee [University of Central Florida, Department of Physics (United States); Das, T. P., E-mail: tpd56@albany.edu [State University of New York at Albany, Department of Physics (United States)

    2008-01-15

    The electronic structure of the heme unit of deoxyhemoglobin including the proximal imidazole has been studied using the first-principles Hartree-Fock procedure. Our results for the {sup 57m}Fe isomer shift and asymmetry parameter are in very good agreement with the values obtained from Moessbauer spectroscopy measurements. The {sup 57m}Fe nuclear quadrupole coupling constant is smaller than the experimental result and possible ways to improve the agreement in the future are discussed. Improved analysis of the Moessbauer data, removing some approximations made for deriving the magnetic hyperfine tensor for the {sup 57m}Fe nucleus, is suggested to allow quantitative comparison with our results in the future.

  17. Structure and Heme-Independent Peroxidase Activity of a Fully-Coordinated Mononuclear Mn(II) Complex with a Schiff-Base Tripodal Ligand Containing Three Imidazole Groups

    Energy Technology Data Exchange (ETDEWEB)

    Sarkar, Shuranjan; Lee, Hong In [Kyungpook National University, Daegu (Korea, Republic of); Moon, Do Hyun [Pohang Accelerator Laboratory, Pohang (Korea, Republic of); Lah, Myoung Soo [Ulsan National Institute of Science and Technology, Ulsan (Korea, Republic of)

    2010-11-15

    New complex [Mn(II)H{sub 1.5}L]{sub 2}[Mn(II)H{sub 3}L]{sub 2}(ClO{sub 4}){sub 5}·3H{sub 2}O, where H{sub 3}L is tris{2-(4-imidazolyl)methyliminoethyl} amine (imtren), has been prepared by reacting manganese(II) perchlorate hexahydrate with the imtren ligand in methanol. X-ray crystallographic study revealed that the imtren ligand hexadentately binds to Mn(II) ion through the three Schiff-base imine N atoms and three imidazole N atoms with a distorted octahedral geometry, and the apical tertiary amine N atom of the ligand pseudo-coordinates to Mn(II), forming overall a pseudo-seven coordination environment. The hydrogen-bonds between imidazole and imidazolate of [Mn(II)H{sub 1.5}L]{sup 0.5+} complex ions are extended to build a 2D puckered network with trigonal voids. [Mn(II)H{sub 3}L]{sup 2+} complex ions constitutes another extended 2D puckered layer without hydrogen bonds. Two layers are wedged each other to constitute overall stack of the crystal. Peroxidase activity of complex 1 was examined by observing the oxidation of 2,2'-azinobis(3-ethylbenzothiazoline)- 6-sulfonic acid (ABTS) with hydrogen peroxide in the presence of complex 1. Generation of ABTS{sup +·} was observed by UV-vis and EPR spectroscopies, indicating that the complex 1, a fully-coordinated mononuclear Mn(II) complex with nitrogen-only ligand, has a heme-independent peroxidase activity.

  18. Electronic structure of MnSi : The role of electron-electron interactions

    NARCIS (Netherlands)

    Carbone, F; Zangrando, M; Brinkman, A; Nicolaou, A; Bondino, F; Magnano, E; Nugroho, A. A.; Parmigiani, F; Jarlborg, T; van der Marel, D

    We present an experimental study of the electronic structure of MnSi. Using x-ray absorption spectroscopy (XAS), x-ray photoemission, and x-ray fluorescence, we provide experimental evidence that MnSi has a mixed valence ground state. We show that self-consistent local density approximation

  19. Electronic structure of MnSi: The role of electron-electron interactions

    NARCIS (Netherlands)

    Carbone, F.; Zangrando, M.; Brinkman, Alexander; Nicolaou, A.; Bondino, F.; Magnano, E.; Nugroho, A.A.; Parmigiani, F.; Jarlborg, Th.; van der Marel, D.

    2006-01-01

    We present an experimental study of the electronic structure of MnSi. Using x-ray absorption spectroscopy (XAS), x-ray photoemission, and x-ray fluorescence, we provide experimental evidence that MnSi has a mixed valence ground state. We show that self-consistent local density approximation

  20. Fingerprint-based structure retrieval using electron density.

    Science.gov (United States)

    Yin, Shuangye; Dokholyan, Nikolay V

    2011-03-01

    We present a computational approach that can quickly search a large protein structural database to identify structures that fit a given electron density, such as determined by cryo-electron microscopy. We use geometric invariants (fingerprints) constructed using 3D Zernike moments to describe the electron density, and reduce the problem of fitting of the structure to the electron density to simple fingerprint comparison. Using this approach, we are able to screen the entire Protein Data Bank and identify structures that fit two experimental electron densities determined by cryo-electron microscopy. Copyright © 2010 Wiley-Liss, Inc.

  1. Heme Oxygenase-1 and breast cancer resistance protein protect against heme-induced toxicity

    NARCIS (Netherlands)

    Wagener, Frank A D T G; Dankers, Anita C A; van Summeren, Frank; Scharstuhl, Alwin; van den Heuvel, Jeroen J M W; Koenderink, Jan B; Pennings, Sebastiaan W C; Russel, Frans G M; Masereeuw, R.

    2013-01-01

    Heme is the functional group of diverse hemoproteins and crucial for many cellular processes. However, heme is increasingly recognized as a culprit for a wide variety of pathologies, including sepsis, malaria, and kidney failure. Excess of free heme can be detrimental to tissues by mediating

  2. Electromagnetic radiation of electrons in periodic structures

    International Nuclear Information System (INIS)

    Potylitsyn, Alexander Petrovich

    2011-01-01

    Periodic magnetic structures (undulators) are widely used in accelerators to generate monochromatic undulator radiation (UR) in the range from far infrared to the hard X-ray region. Another periodic crystalline structure is used to produce quasimonochromatic polarized photon beams via the coherent bremsstrahlung mechanism (CBS). Due to such characteristics as monochromaticity, polarization and adjustability, these types of radiation is of large interest for applied and basic research of accelerator-emitted radiation. The book provides a detailed overview of the fundamental principles behind electromagnetic radiation emitted from accelerated charged particles (e.g. UR, CBS, radiation of fast electrons in Laser flash fields) as well as a unified description of relatively new radiation mechanisms which attracted great interest in recent years. This are the so-called polarization radiation excited by the Coulomb field of incident particles in periodic structures, parametric X-rays, resonant transition radiation and the Smith-Purcell effect. Characteristics of such radiation sources and perspectives of their usage are discussed. The recent experimental results as well as their interpretation are presented. (orig.)

  3. Analysis of the electronic structure of human hemoglobin from soft X-ray emission

    International Nuclear Information System (INIS)

    Soldatov, A.V.; Kravtsova, A.N.; Fedorovich, E.N.; Ankudinov, A.; Moewes, A.; Kurmaev, E.Z.

    2005-01-01

    We present X-ray emission spectra (XES) of human hemoglobin excited near the iron L 2,3 threshold and the nitrogen and carbon K-edges. The experiment is compared with our calculations of the corresponding spectra and gives good agreement. We find that the Fe L 3 emission is affected by the nearest nitrogen atoms located in the heme plane around the central iron atom. The distribution of the partial electronic densities of states of hemoglobin is determined

  4. Heme and HO-1 inhibition of HCV, HBV, and HIV

    Directory of Open Access Journals (Sweden)

    Warren N Schmidt

    2012-10-01

    Full Text Available Hepatitis C virus, human immunodeficiency virus, and hepatitis B virus are chronic viral infections that cause considerable morbidity and mortality throughout the world. In the decades following the identification and sequencing of these viruses, in vitro experiments demonstrated that heme oxygenase-1, its oxidative products, and related compounds of the heme oxygenase system are virucidal for all three viruses. The purpose of this review is to critically evaluate and summarize the seminal studies that described and characterized this remarkable behavior. It will also discuss more recent work that discovered the antiviral mechanisms and target sites of these unique antiviral agents. In spite of the fact that these viruses are diverse pathogens with quite profound differences in structure and life cycle, it is significant that heme and related compounds show striking similarity for viral target sites across all three species. Collectively, these findings strongly indicate that we should move forward and develop heme and related tetrapyrroles into versatile antiviral agents that could be used therapeutically in patients with single or multiple viral infections.

  5. Electron Liquids in Semiconductor Quantum Structures

    International Nuclear Information System (INIS)

    Pinczuk, Aron

    2009-01-01

    The groups led by Stormer and Pinczuk have focused this project on goals that seek the elucidation of novel many-particle effects that emerge in two-dimensional electron systems (2DES) as the result from fundamental quantum interactions. This experimental research is conducted under extreme conditions of temperature and magnetic field. From the materials point of view, the ultra-high mobility systems in GaAs/AlGaAs quantum structures continue to be at the forefront of this research. The newcomer materials are based on graphene, a single atomic layer of graphite. The graphene research is attracting enormous attention from many communities involved in condensed matter research. The investigated many-particle phenomena include the integer and fractional quantum Hall effect, composite fermions, and Dirac fermions, and a diverse group of electron solid and liquid crystal phases. The Stormer group performed magneto-transport experiments and far-infrared spectroscopy, while the Pinczuk group explores manifestations of such phases in optical spectra.

  6. Electrons and photons in periodic structures

    DEFF Research Database (Denmark)

    Pedersen, Jesper Goor

    . In particular, the modulation leads to the emergence of band gaps, which are accompanied by a strongly modified density of states near and within the band gap. The main focus is on two applications of such modified densities of states. Firstly, the intentional introduction of defects in an otherwise perfectly...... periodic modulation of an electron gas leads to the emergence of localized defect states with energies within the band gap, where no propagating modes exist. Secondly, the divergence of the photonic density of states near a photonic band gap leads to strongly modified light-matter interactions, which has...... of the density of states near the band gap edge. Using a perturbative approach, we demonstrate certain limits of the attainable slow down factors due to broadening of electromagnetic modes. We discuss the effect of damping due to a finite conductivity as well as structural disorder, and provide a common...

  7. Electronic structure of single crystal C60

    International Nuclear Information System (INIS)

    Wu, J.; Shen, Z.X.; Dessau, D.S.; Cao, R.; Marshall, D.S.; Pianetta, P.; Lindau, I.; Yang, X.; Terry, J.; King, D.M.; Wells, B.O.; Elloway, D.; Wendt, H.R.; Brown, C.A.; Hunziker, H.; Vries, M.S. de

    1992-01-01

    We report angle-resolved photoemission data from single crystals of C 60 cleaved in UHV. Unlike the other forms of pure carbon, the valence band spectrum of C 60 consists of many sharp features that can be essentially accounted for by the quantum chemical calculations describing individual molecules. This suggests that the electronic structure of solid C 60 is mainly determined by the bonding interactions within the individual molecules. We also observe remarkable intensity modulations of the photoemission features as a function of photon energy, suggesting strong final state effects. Finally, we address the issue of the band width of the HOMO state of C 60 . We assert that the width of the photoemission peak of C 60 does not reflect the intrinsic band width because it is broadened by the non 0-0 transitions via the Franck-Condon principle. Our view point provides a possible reconciliation between these photoemission data and those measured by other techniques. (orig.)

  8. Multilevel domain decomposition for electronic structure calculations

    International Nuclear Information System (INIS)

    Barrault, M.; Cances, E.; Hager, W.W.; Le Bris, C.

    2007-01-01

    We introduce a new multilevel domain decomposition method (MDD) for electronic structure calculations within semi-empirical and density functional theory (DFT) frameworks. This method iterates between local fine solvers and global coarse solvers, in the spirit of domain decomposition methods. Using this approach, calculations have been successfully performed on several linear polymer chains containing up to 40,000 atoms and 200,000 atomic orbitals. Both the computational cost and the memory requirement scale linearly with the number of atoms. Additional speed-up can easily be obtained by parallelization. We show that this domain decomposition method outperforms the density matrix minimization (DMM) method for poor initial guesses. Our method provides an efficient preconditioner for DMM and other linear scaling methods, variational in nature, such as the orbital minimization (OM) procedure

  9. Considerations on the mechanism of action of artemisinin antimalarials: part 1--the 'carbon radical' and 'heme' hypotheses.

    Science.gov (United States)

    Haynes, Richard K; Cheu, Kwan-Wing; N'Da, David; Coghi, Paolo; Monti, Diego

    2013-08-01

    - reactions employing catalytic reagents under aqueous or semi-aqueous conditions - to those conducted under highly reducing and eminently artificial conditions, usually in the solvent dimethyl sulfoxide (DMSO) that both forms well characterized complexes with heme-Fe(2+) and actually assists in driving single electron transfer processes. It is noted that alkylated products tend to form in high yields under the last conditions, and this aspect is readily explained. Irrespective of product yields obtained under various conditions, an overarching correlation between facility of the reaction of the peroxide with heme and their antimalarial activities does not exist. The is underscored by the reproducible outcomes of reactions conducted under biomimetic conditions indicating adducts cannot form in physiologically meaningful concentrations and that heme is a recalcitrant reaction partner to artemisinins in general. Again, as in the case of the C-radical hypothesis, structure-activity data from a wide variety of artemisinins and synthetic peroxides is difficult to reconcile with the heme hypothesis. This applies in particular to dimeric and trimeric artemisinin derivatives where the ascribing of biological activity to reactions of the derived radicals or to the vastly encumbered artemisinin-heme adducts is physically unrealistic. Finally, the facile metabolism and induction of metabolism of the current clinically used artemisinins by members of the CYP superfamily - heme proteins that require an intimate interaction of the heme with the artemisinin for metabolism to occur - is incompatible with the oft-cited proclivity of the peroxide to associate via complex formation with heme as a prelude to its 'activation' as an antimalarial agent within the malaria parasite. (ABSTRACT TRUNCATED)

  10. A role for heme in Alzheimer's disease: Heme binds amyloid β and has altered metabolism

    OpenAIRE

    Atamna, Hani; Frey, William H.

    2004-01-01

    Heme is a common factor linking several metabolic perturbations in Alzheimer's disease (AD), including iron metabolism, mitochondrial complex IV, heme oxygenase, and bilirubin. Therefore, we determined whether heme metabolism was altered in temporal lobes obtained at autopsy from AD patients and age-matched nondemented subjects. AD brain demonstrated 2.5-fold more heme-b (P < 0.01) and 26% less heme-a (P = 0.16) compared with controls, resulting in a highly significant 2.9-fold decrease in he...

  11. Electronic structure of semiconductor quantum films

    International Nuclear Information System (INIS)

    Zhang, S.B.; Yeh, C.; Zunger, A.

    1993-01-01

    The electronic structure of thin (≤30 A) free-standing ideal films of Si(001), Si(110), and GaAs(110) is calculated using a plane-wave pseudopotential description. Unlike the expectation based on the simple effective-mass model, we find the following. (i) The band gaps of (001) quantum films exhibit even-odd oscillation as a function of the number N of monolayers. (ii) In addition to sine-type envelope functions which vanish at the film boundaries, some states have cosine envelope functions with extrema at boundaries. (iii) Even-layer Si(001) films exhibit at the valence-band maximum a state whose energy does not vary with the film thickness. Such zero confinement states have constant envelope throughout the film. (iv) Optical transitions in films exhibit boundary-imposed selection rules. Furthermore, oscillator strengths for pseudodirect transitions in the vicinity of forbidden direct transitions can be enhanced by several orders of magnitude. These findings, obtained in direct supercell calculations, can be explained in terms of a truncated crystal (TC) analysis. In this approach the film's wave functions are expanded in terms of pairs of bulk wave functions exhibiting a destructive interference at the boundaries. This maps the eigenvalue spectra of a film onto the bulk band structure evaluated at special k points which satisfy the boundary conditions. We find that the TC representation reproduces accurately the above-mentioned results of direct diagonalization of the film's Hamiltonian. This provides a simple alternative to the effective-mass model and relates the properties of quantum structures to those of the bulk material

  12. Studies in the electronic structure of matter

    International Nuclear Information System (INIS)

    Swarts, C.A.

    1979-01-01

    Chapter I: Here the results of various theories for the angular distribution of electrons photoemitted from the outermost p-shell of rare gas atoms are compared. The theories compared are (I) the local density theories of Slater (X/sub α/) and of Hohenberg, Kohn and Sham, (II) the pseudopotential method, (III) Hartree-Fock theory as evaluated by Kennedy and Manson, and (IV) Amusia's Random Phase Approximation with Exchange (RPAE). It is shown that the local density theories, although simple, generally fail to produce reliable cross section; the more complicated Hartree-Fock method is no more reliable; the a priori RPAE method is most reliable, but tedious; and the phenomenological pseudopotential method offers a good combination of reliability and simplicity. The muffin-tin approximation, widely used in molecular and condensed matter physics, is examined and found to be adequate. Chapter II: Extended Hueckel theory is applied to GaAs, GaP and to the nitrogen isoelectronic trap in GaAs and GaP. The computed perfect crystal band structures are found to be in reasonable agreement with those computed with empirical pseudopotentials. Nitrogen impurity levels in GaAs and GaP are calculated using a cluster model. Chapter III: By means of model calculations for an independent electron metal, we obtain exact lineshapes for the photon absorption, emission and photoemission spectra of deep core states. We find in each case an X-ray edge anomaly as pedicted by Nozieres and De Dominicis. Sumrules are used as a general check on the calculations and to explain the deviations of the exact theory from the exciton theory away from threshold

  13. Nonlinearity in structural and electronic materials

    International Nuclear Information System (INIS)

    Bishop, A.R.; Beardmore, K.M.; Ben-Naim, E.

    1997-01-01

    This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The project strengthens a nonlinear technology base relevant to a variety of problems arising in condensed matter and materials science, and applies this technology to those problems. In this way the controlled synthesis of, and experiments on, novel electronic and structural materials provide an important focus for nonlinear science, while nonlinear techniques help advance the understanding of the scientific principles underlying the control of microstructure and dynamics in complex materials. This research is primarily focused on four topics: (1) materials microstructure: growth and evolution, and porous media; (2) textures in elastic/martensitic materials; (3) electro- and photo-active polymers; and (4) ultrafast photophysics in complex electronic materials. Accomplishments included the following: organization of a ''Nonlinear Materials'' seminar series and international conferences including ''Fracture, Friction and Deformation,'' ''Nonequilibrium Phase Transitions,'' and ''Landscape Paradigms in Physics and Biology''; invited talks at international conference on ''Synthetic Metals,'' ''Quantum Phase Transitions,'' ''1996 CECAM Euroconference,'' and the 1995 Fall Meeting of the Materials Research Society; large-scale simulations and microscopic modeling of nonlinear coherent energy storage at crack tips and sliding interfaces; large-scale simulation and microscopic elasticity theory for precursor microstructure and dynamics at solid-solid diffusionless phase transformations; large-scale simulation of self-assembling organic thin films on inorganic substrates; analysis and simulation of smoothing of rough atomic surfaces; and modeling and analysis of flux pattern formation in equilibrium and nonequilibrium Josephson junction arrays and layered superconductors

  14. Mechanisms of heme utilization by Francisella tularensis.

    Directory of Open Access Journals (Sweden)

    Helena Lindgren

    Full Text Available Francisella tularensis is a highly virulent facultative intracellular pathogen causing the severe disease tularemia in mammals. As for other bacteria, iron is essential for its growth but very few mechanisms for iron acquisition have been identified. Here, we analyzed if and how F. tularensis can utilize heme, a major source of iron in vivo. This is by no means obvious since the bacterium lacks components of traditional heme-uptake systems. We show that SCHU S4, the prototypic strain of subspecies tularensis, grew in vitro with heme as the sole iron source. By screening a SCHU S4 transposon insertion library, 16 genes were identified as important to efficiently utilize heme, two of which were required to avoid heme toxicity. None of the identified genes appeared to encode components of a potential heme-uptake apparatus. Analysis of SCHU S4 deletion mutants revealed that each of the components FeoB, the siderophore system, and FupA, contributed to the heme-dependent growth. In the case of the former two systems, iron acquisition was impaired, whereas the absence of FupA did not affect iron uptake but led to abnormally high binding of iron to macromolecules. Overall, the present study demonstrates that heme supports growth of F. tularensis and that the requirements for the utilization are highly complex and to some extent novel.

  15. Identification of the Mitochondrial Heme Metabolism Complex.

    Science.gov (United States)

    Medlock, Amy E; Shiferaw, Mesafint T; Marcero, Jason R; Vashisht, Ajay A; Wohlschlegel, James A; Phillips, John D; Dailey, Harry A

    2015-01-01

    Heme is an essential cofactor for most organisms and all metazoans. While the individual enzymes involved in synthesis and utilization of heme are fairly well known, less is known about the intracellular trafficking of porphyrins and heme, or regulation of heme biosynthesis via protein complexes. To better understand this process we have undertaken a study of macromolecular assemblies associated with heme synthesis. Herein we have utilized mass spectrometry with coimmunoprecipitation of tagged enzymes of the heme biosynthetic pathway in a developing erythroid cell culture model to identify putative protein partners. The validity of these data obtained in the tagged protein system is confirmed by normal porphyrin/heme production by the engineered cells. Data obtained are consistent with the presence of a mitochondrial heme metabolism complex which minimally consists of ferrochelatase, protoporphyrinogen oxidase and aminolevulinic acid synthase-2. Additional proteins involved in iron and intermediary metabolism as well as mitochondrial transporters were identified as potential partners in this complex. The data are consistent with the known location of protein components and support a model of transient protein-protein interactions within a dynamic protein complex.

  16. Ligand exchange reactions of the heme group in hemoglobin and myoglobin as studied by pulse radiolysis

    International Nuclear Information System (INIS)

    Raap, I.A.

    1978-01-01

    In this thesis, the kinetic aspects of the ligand exchange reactions of hemoglobin are studied using the pulse radiolysis technique, in particular, the reactions of hydrated electrons with methemoglobin. A hitherto unobserved transient state of the heme group is observed which appears immediately after the rapid reduction process. The absorption spectrum of this new species has the characteristics of a ferrous low-spin state and can therefore be ascribed to the formation of a hemochrome non-equilibrium state. The subsequent relaxation of this intermediate structure into a deoxy-conformation is dependent on the amount of proton activity in the solution and on the presence of organic and inorganic phosphate anions. The final absorption spectrum of the heme group is shown to correspond to a ferrous high-spin state in the relaxed quaternary conformation. This is in agreement with the kinetics observen the binding of carbon monoxide and oxygen to partially reduced methemoglobin. At reduction degrees of methemoglobin as well as of valncy 8ybrids where there is an important contribution from species with two reduced subunits, the binding of carbon monoxide to hemoglobin occurs with on-rate constants characteristic for the tensed quaternary conformation. It is argued that this conformational change of hemoglobin (the R-to-T transition) takes place very rapidly, which suggests the participation of an activated relaxed conformation. In addition, it is found that there is a distinct heterogeneity in the binding of oxygen to partially reduced methemoglobin even at low degrees of reduction

  17. Graph-based linear scaling electronic structure theory

    Energy Technology Data Exchange (ETDEWEB)

    Niklasson, Anders M. N., E-mail: amn@lanl.gov; Negre, Christian F. A.; Cawkwell, Marc J.; Swart, Pieter J.; Germann, Timothy C.; Bock, Nicolas [Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Mniszewski, Susan M.; Mohd-Yusof, Jamal; Wall, Michael E.; Djidjev, Hristo [Computer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Rubensson, Emanuel H. [Division of Scientific Computing, Department of Information Technology, Uppsala University, Box 337, SE-751 05 Uppsala (Sweden)

    2016-06-21

    We show how graph theory can be combined with quantum theory to calculate the electronic structure of large complex systems. The graph formalism is general and applicable to a broad range of electronic structure methods and materials, including challenging systems such as biomolecules. The methodology combines well-controlled accuracy, low computational cost, and natural low-communication parallelism. This combination addresses substantial shortcomings of linear scaling electronic structure theory, in particular with respect to quantum-based molecular dynamics simulations.

  18. Prebiotics increase heme iron bioavailability and do not affect non-heme iron bioavailability in humans.

    Science.gov (United States)

    Weinborn, Valerie; Valenzuela, Carolina; Olivares, Manuel; Arredondo, Miguel; Weill, Ricardo; Pizarro, Fernando

    2017-05-24

    The aim of this study was to establish the effect of a prebiotic mix on heme and non-heme iron (Fe) bioavailability in humans. To this purpose, twenty-four healthy women were randomized into one of two study groups. One group ate one yogurt per day for 12 days with a prebiotic mix (prebiotic group) and the other group received the same yogurt but without the prebiotic mix (control group). Before and after the intake period, the subjects participated in Fe absorption studies. These studies used 55 Fe and 59 Fe radioactive isotopes as markers of heme Fe and non-heme Fe, respectively, and Fe absorption was measured by the incorporation of radioactive Fe into erythrocytes. The results showed that there were no significant differences in heme and non-heme Fe bioavailability in the control group. Heme Fe bioavailability of the prebiotic group increased significantly by 56% post-prebiotic intake. There were no significant differences in non-heme Fe bioavailability in this group. We concluded that daily consumption of a prebiotic mix increases heme Fe bioavailability and does not affect non-heme iron bioavailability.

  19. Electronic structure and chemical properties of superheavy elements

    Energy Technology Data Exchange (ETDEWEB)

    Pershina, V [Gesellschaft fuer Schwerionenforschung (GSI), Helmholtzzentrum fuer Schwerionenforschung Gmbh (Germany)

    2009-12-31

    Relativistic electronic structure calculations of superheavy elements (Z>=104) are analyzed. Preference is given to those related to experimental research. The role of relativistic effects is discussed.

  20. Heme oxygenase-1: a metabolic nike.

    Science.gov (United States)

    Wegiel, Barbara; Nemeth, Zsuzsanna; Correa-Costa, Matheus; Bulmer, Andrew C; Otterbein, Leo E

    2014-04-10

    Heme degradation, which was described more than 30 years ago, is still very actively explored with many novel discoveries on its role in various disease models every year. The heme oxygenases (HO) are metabolic enzymes that utilize NADPH and oxygen to break apart the heme moiety liberating biliverdin (BV), carbon monoxide (CO), and iron. Heme that is derived from hemoproteins can be toxic to the cells and if not removed immediately, it causes cell apoptosis and local inflammation. Elimination of heme from the milieu enables generation of three products that influences numerous metabolic changes in the cell. CO has profound effects on mitochondria and cellular respiration and other hemoproteins to which it can bind and affect their function, while BV and bilirubin (BR), the substrate and product of BV, reductase, respectively, are potent antioxidants. Sequestration of iron into ferritin and its recycling in the tissues is a part of the homeodynamic processes that control oxidation-reduction in cellular metabolism. Further, heme is an important component of a number of metabolic enzymes, and, therefore, HO-1 plays an important role in the modulation of cellular bioenergetics. In this review, we describe the cross-talk between heme oxygenase-1 (HO-1) and its products with other metabolic pathways. HO-1, which we have labeled Nike, the goddess who personified victory, dictates triumph over pathophysiologic conditions, including diabetes, ischemia, and cancer.

  1. Electronic structure of shandite Co3Sn2S2

    Science.gov (United States)

    Dedkov, Y. S.; Holder, M.; Molodtsov, S. L.; Rosner, H.

    2008-03-01

    The electronic structure of shandite Co3Sn2S2 was determined by photoelectron spectroscopy and compared with ab initio band structure calculations. Presented results give evidence that this compound has half-metallic ferromagnetic properties.

  2. A rapid, simple method for obtaining radiochemically pure hepatic heme

    International Nuclear Information System (INIS)

    Bonkowski, H.L.; Bement, W.J.; Erny, R.

    1978-01-01

    Radioactively-labelled heme has usually been isolated from liver to which unlabelled carrier has been added by long, laborious techniques involving organic solvent extraction followed by crystallization. A simpler, rapid method is devised for obtaining radiochemically-pure heme synthesized in vivo in rat liver from delta-amino[4- 14 C]levulinate. This method, in which the heme is extracted into ethyl acetate/glacial acetic acid and in which porphyrins are removed from the heme-containing organic phase with HCl washes, does not require addition of carrier heme. The new method gives better heme recoveries than and heme specific activities identical to, those obtained using the crystallization method. In this new method heme must be synthesized from delta-amino[4- 14 C]levulinate; it is not satisfactory to use [2- 14 C]glycine substrate because non-heme counts are isolated in the heme fraction. (Auth.)

  3. Heme environment in HmuY, the heme-binding protein of Porphyromonas gingivalis

    International Nuclear Information System (INIS)

    Wojtowicz, Halina; Wojaczynski, Jacek; Olczak, Mariusz; Kroliczewski, Jaroslaw; Latos-Grazynski, Lechoslaw; Olczak, Teresa

    2009-01-01

    Porphyromonas gingivalis, a Gram-negative anaerobic bacterium implicated in the development and progression of chronic periodontitis, acquires heme for growth by a novel mechanism composed of HmuY and HmuR proteins. The aim of this study was to characterize the nature of heme binding to HmuY. The protein was expressed, purified and detailed investigations using UV-vis absorption, CD, MCD, and 1 H NMR spectroscopy were carried out. Ferric heme bound to HmuY may be reduced by sodium dithionite and re-oxidized by potassium ferricyanide. Heme complexed to HmuY, with a midpoint potential of 136 mV, is in a low-spin Fe(III) hexa-coordinate environment. Analysis of heme binding to several single and double HmuY mutants with the methionine, histidine, cysteine, or tyrosine residues replaced by an alanine residue identified histidines 134 and 166 as potential heme ligands.

  4. Heme environment in HmuY, the heme-binding protein of Porphyromonas gingivalis

    Energy Technology Data Exchange (ETDEWEB)

    Wojtowicz, Halina [Laboratory of Biochemistry, Faculty of Biotechnology, University of Wroclaw, Tamka 2, 50-137 Wroclaw (Poland); Wojaczynski, Jacek [Department of Chemistry, University of Wroclaw, 50-383 Wroclaw (Poland); Olczak, Mariusz [Laboratory of Biochemistry, Faculty of Biotechnology, University of Wroclaw, Tamka 2, 50-137 Wroclaw (Poland); Kroliczewski, Jaroslaw [Laboratory of Biophysics, Faculty of Biotechnology, University of Wroclaw, 50-148 Wroclaw (Poland); Latos-Grazynski, Lechoslaw [Department of Chemistry, University of Wroclaw, 50-383 Wroclaw (Poland); Olczak, Teresa [Laboratory of Biochemistry, Faculty of Biotechnology, University of Wroclaw, Tamka 2, 50-137 Wroclaw (Poland)

    2009-05-29

    Porphyromonas gingivalis, a Gram-negative anaerobic bacterium implicated in the development and progression of chronic periodontitis, acquires heme for growth by a novel mechanism composed of HmuY and HmuR proteins. The aim of this study was to characterize the nature of heme binding to HmuY. The protein was expressed, purified and detailed investigations using UV-vis absorption, CD, MCD, and {sup 1}H NMR spectroscopy were carried out. Ferric heme bound to HmuY may be reduced by sodium dithionite and re-oxidized by potassium ferricyanide. Heme complexed to HmuY, with a midpoint potential of 136 mV, is in a low-spin Fe(III) hexa-coordinate environment. Analysis of heme binding to several single and double HmuY mutants with the methionine, histidine, cysteine, or tyrosine residues replaced by an alanine residue identified histidines 134 and 166 as potential heme ligands.

  5. Analysis of the electrochemistry of hemes with Ems spanning 800 mV

    Science.gov (United States)

    Zheng, Zhong; Gunner, M. R.

    2009-01-01

    The free energy of heme reduction in different proteins is found to vary over more than 18 kcal/mol. It is a challenge to determine how proteins manage to achieve this enormous range of Ems with a single type of redox cofactor. Proteins containing 141 unique hemes of a-, b-, and c-type, with bis-His, His-Met, and aquo-His ligation were calculated using Multi-Conformation Continuum Electrostatics (MCCE). The experimental Ems range over 800 mV from −350 mV in cytochrome c3 to 450 mV in cytochrome c peroxidase (vs. SHE). The quantitative analysis of the factors that modulate heme electrochemistry includes the interactions of the heme with its ligands, the solvent, the protein backbone, and sidechains. MCCE calculated Ems are in good agreement with measured values. Using no free parameters the slope of the line comparing calculated and experimental Ems is 0.73 (R2 = 0.90), showing the method accounts for 73% of the observed Em range. Adding a +160 mV correction to the His-Met c-type hemes yields a slope of 0.97 (R2 = 0.93). With the correction 65% of the hemes have an absolute error smaller than 60 mV and 92% are within 120 mV. The overview of heme proteins with known structures and Ems shows both the lowest and highest potential hemes are c-type, whereas the b-type hemes are found in the middle Em range. In solution, bis-His ligation lowers the Em by ≈205 mV relative to hemes with His-Met ligands. The bis-His, aquo-His, and His-Met ligated b-type hemes all cluster about Ems which are ≈200 mV more positive in protein than in water. In contrast, the low potential bis-His c-type hemes are shifted little from in solution, whereas the high potential His-Met c-type hemes are raised by ≈300 mV from solution. The analysis shows that no single type of interaction can be identified as the most important in setting heme electrochemistry in proteins. For example, the loss of solvation (reaction field) energy, which raises the Em, has been suggested to be a major factor in

  6. Electronic conductance of quantum wire with serial periodic potential structures

    International Nuclear Information System (INIS)

    Fayad, Hisham M.; Shabat, Mohammed M.; Abdus Salam International Centre for Theoretical Physics, Trieste

    2000-08-01

    A theory based on the total transfer matrix is presented to investigate the electronic conductance in a quantum wire with serial periodic potentials. We apply the formalism in computation of the electronic conductance in a wire with different physical parameters of the wire structure. The numerical results could be used in designing some future quantum electronic devices. (author)

  7. Insights on Heme Synthesis in the Malaria Parasite.

    Science.gov (United States)

    Nagaraj, Viswanathan A; Padmanaban, Govindarajan

    2017-08-01

    The malaria parasite has a functional heme-biosynthetic pathway, although it can access host hemoglobin-heme. The heme pathway is dispensable for blood stages, but essential in the mosquito stages which do not acquire hemoglobin-heme. We propose that the blood stage parasites maintain a dynamic heme pool through multiple back-up mechanisms. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. Structure of liquid alkali metals as electron-ion plasmas

    International Nuclear Information System (INIS)

    Chaturvedi, D.K.; Senatore, G.; Tosi, M.P.

    1980-08-01

    The static structure factor of liquid alkali metals near freezing, and its dependence on temperature and pressure, are evaluated in an electron-ion plasma model from an accurate theoretical determination of the structure factor of the one-component classical plasma and electron-screening theory. Very good agreement is obtained with the available experimental data. (author)

  9. In vitro Activation of heme oxygenase-2 by menadione and its analogs.

    Science.gov (United States)

    Vukomanovic, Dragic; Rahman, Mona N; Bilokin, Yaroslav; Golub, Andriy G; Brien, James F; Szarek, Walter A; Jia, Zongchao; Nakatsu, Kanji

    2014-02-18

    Previously, we reported that menadione activated rat, native heme oxygenase-2 (HO-2) and human recombinant heme oxygenase-2 selectively; it did not activate spleen, microsomal heme oxygenase-1. The purpose of this study was to explore some structure-activity relationships of this activation and the idea that redox properties may be an important aspect of menadione efficacy. Heme oxygenase activity was determined in vitro using rat spleen and brain microsomes as the sources of heme oxygenase-1 and -2, respectively, as well as recombinant, human heme oxygenase-2. Menadione analogs with bulky aliphatic groups at position-3, namely vitamins K1 and K2, were not able to activate HO-2. In contrast, several compounds with similar bulky but less lipophilic moieties at position-2 (and -3) were able to activate HO-2 many fold; these compounds included polar, rigid, furan-containing naphthoquinones, furan-benzoxazine naphthoquinones, 2-(aminophenylphenyl)-3-piperidin-1-yl naphthoquinones. To explore the idea that redox properties might be involved in menadione efficacy, we tested analogs such as 1,4-dimethoxy-2-methylnaphthalene, pentafluoromenadione, monohalogenated naphthoquinones, α-tetralone and 1,4-naphthoquinone. All of these compounds were inactive except for 1,4-naphthoquinone. Menadione activated full-length recombinant human heme oxygenase-2 (FL-hHO-2) as effectively as rat brain enzyme, but it did not activate rat spleen heme oxygenase. These observations are consistent with the idea that naphthoquinones such as menadione bind to a receptor in HO-2 and activate the enzyme through a mechanism that may involve redox properties.

  10. Electronic structure of Mo and W investigated with positron annihilation

    Energy Technology Data Exchange (ETDEWEB)

    Dutschke, Markus [Theoretical Physics III, Center for Electronic Correlations and Magnetism, Institute of Physics, University of Augsburg (Germany); Sekania, Michael [Theoretical Physics III, Center for Electronic Correlations and Magnetism, Institute of Physics, University of Augsburg (Germany); Andronikashvili Institute of Physics, Tbilisi (Georgia); Benea, Diana [Faculty of Physics, Babes-Bolyai University, Cluj-Napoca (Romania); Department of Chemistry, Ludwig Maximilian University of Munich (Germany); Ceeh, Hubert; Weber, Joseph A.; Hugenschmidt, Christoph [FRM II, Technische Universitaet Muenchen, Garching (Germany); Chioncel, Liviu [Theoretical Physics III, Center for Electronic Correlations and Magnetism, Institute of Physics, University of Augsburg (Germany); Augsburg Center for Innovative Technologies, University of Augsburg (Germany)

    2016-07-01

    We perform electronic structure calculations to analyze the momentum distribution of the transition metals molybdenum and tungsten. We study the influence of positron-electron and the electron-electron interactions on the shape of the two-dimensional angular correlation of positron annihilation radiation (2D-ACAR) spectra. Our analysis is performed within the framework of the combined Density Functional (DFT) and Dynamical Mean-Field Theory (DMFT). Computed spectra are compared with recent experimental investigations.

  11. Electronic structures of elements according to ionization energies.

    Science.gov (United States)

    Zadeh, Dariush H

    2017-11-28

    The electronic structures of elements in the periodic table were analyzed using available experimental ionization energies. Two new parameters were defined to carry out the study. The first parameter-apparent nuclear charge (ANC)-quantified the overall charge of the nucleus and inner electrons observed by an outer electron during the ionization process. This parameter was utilized to define a second parameter, which presented the shielding ability of an electron against the nuclear charge. This second parameter-electron shielding effect (ESE)-provided an insight into the electronic structure of atoms. This article avoids any sort of approximation, interpolation or extrapolation. First experimental ionization energies were used to obtain the two aforementioned parameters. The second parameter (ESE) was then graphed against the electron number of each element, and was used to read the corresponding electronic structure. The ESE showed spikes/peaks at the end of each electronic shell, providing insight into when an electronic shell closes and a new one starts. The electronic structures of elements in the periodic table were mapped using this methodology. These graphs did not show complete agreement with the previously known "Aufbau" filling rule. A new filling rule was suggested based on the present observations. Finally, a new way to organize elements in the periodic table is suggested. Two earlier topics of effective nuclear charge, and shielding factor were also briefly discussed and compared numerically to demonstrate the capability of the new approach.

  12. Correct Brillouin zone and electronic structure of BiPd

    Science.gov (United States)

    Yaresko, Alexander; Schnyder, Andreas P.; Benia, Hadj M.; Yim, Chi-Ming; Levy, Giorgio; Damascelli, Andrea; Ast, Christian R.; Peets, Darren C.; Wahl, Peter

    2018-02-01

    A promising route to the realization of Majorana fermions is in noncentrosymmetric superconductors, in which spin-orbit coupling lifts the spin degeneracy of both bulk and surface bands. A detailed assessment of the electronic structure is critical to evaluate their suitability for this through establishing the topological properties of the electronic structure. This requires correct identification of the time-reversal-invariant momenta. One such material is BiPd, a recently rediscovered noncentrosymmetric superconductor which can be grown in large, high-quality single crystals and has been studied by several groups using angular resolved photoemission to establish its surface electronic structure. Many of the published electronic structure studies on this material are based on a reciprocal unit cell which is not the actual Brillouin zone of the material. We show here the consequences of this for the electronic structures and show how the inferred topological nature of the material is affected.

  13. Electronic structure of hybrid interfaces for polymer-based electronics

    International Nuclear Information System (INIS)

    Fahlman, M; Crispin, A; Crispin, X; Henze, S K M; Jong, M P de; Osikowicz, W; Tengstedt, C; Salaneck, W R

    2007-01-01

    The fundamentals of the energy level alignment at anode and cathode electrodes in organic electronics are described. We focus on two different models that treat weakly interacting organic/metal (and organic/organic) interfaces: the induced density of interfacial states model and the so-called integer charge transfer model. The two models are compared and evaluated, mainly using photoelectron spectroscopy data of the energy level alignment of conjugated polymers and molecules at various organic/metal and organic/organic interfaces. We show that two different alignment regimes are generally observed: (i) vacuum level alignment, which corresponds to the lack of vacuum level offsets (Schottky-Mott limit) and hence the lack of charge transfer across the interface, and (ii) Fermi level pinning where the resulting work function of an organic/metal and organic/organic bilayer is independent of the substrate work function and an interface dipole is formed due to charge transfer across the interface. We argue that the experimental results are best described by the integer charge transfer model which predicts the vacuum level alignment when the substrate work function is above the positive charge transfer level and below the negative charge transfer level of the conjugated material. The model further predicts Fermi level pinning to the positive (negative) charge transfer level when the substrate work function is below (above) the positive (negative) charge transfer level. The nature of the integer charge transfer levels depend on the materials system: for conjugated large molecules and polymers, the integer charge transfer states are polarons or bipolarons; for small molecules' highest occupied and lowest unoccupied molecular orbitals and for crystalline systems, the relevant levels are the valence and conduction band edges. Finally, limits and further improvements to the integer charge transfer model are discussed as well as the impact on device design. (topical review)

  14. The electronic structure of core states under extreme compressions

    International Nuclear Information System (INIS)

    Straub, G.K.

    1992-01-01

    At normal density and for modest compressions, the electronic structure of a metal can be accurately described by treating the conduction electrons and their interactions with the usual methods of band theory. The core electrons remain essentially the same as for an isolated free atom and do not participate in the bonding forces responsible for creating a condensed phase. As the density increases, the core electrons begin to ''see'' one another as the overlap of the tails of wave functions can no longer be neglected. The electronic structure of the core electrons is responsible for an effective repulsive interaction that eventually becomes free-electron-like at very high compressions. The electronic structure of the interacting core electrons may be treated in a simple manner using the Atomic Surface Method (ASM). The ASM is a first-principles treatment of the electronic structure involving a rigorous integration of the Schroedinger equation within the atomic-sphere approximation. Solid phase wave functions are constructed from isolated atom wave functions and the band width W l and the center of gravity of the band C l are obtained from simple formulas. The ASM can also utilize analytic forms of the atomic wave functions and thus provide direct functional dependence of various aspects of the electronic structure. Of particular use in understanding the behavior of the core electrons, the ASM provides the ability to analytically determine the density dependence of the band widths and positions. The process whereby core states interact with one another is best viewed as the formation of narrow electron bands formed from atomic states. As the core-core overlap increases, the bands increase in width and mean energy. In Sec.3 this picture is further developed and from the ASM one obtains the analytic dependence on density of the relative motion of the different bands. Also in Sec. 3 is a discussion of the transition to free electron bands

  15. Structure and function of cytochrome c2 in electron transfer complexes with the photosynthetic reaction center of Rhodobacter sphaeroides: optical linear dichroism and EPR.

    Science.gov (United States)

    Drepper, F; Mathis, P

    1997-02-11

    The photosynthetic reaction center (RC) and its secondary electron donor the water-soluble cytochrome (cyt) c2 from the purple bacterium Rhodobacter sphaeroides have been used in cross-linked and non-cross-linked complexes, oriented in compressed gels or partially dried multilayers, to study the respective orientation of the primary donor P (BChl dimer) and of cyt c2. Three methods were used: (i) Polarized optical absorption spectra at 295 and 10 K were measured and the linear dichroism of the two individual transitions (Qx, Qy), which are nearly degenerate within the alpha-band of reduced cyt c2, was determined. Attribution of the polarization directions to the molecular axes within the heme plane yielded the average cyt orientation in the complexes. (ii) Time-resolved flash absorption measurements using polarized light allowed determination of the orientation of cyt c2 in complexes which differ in their kinetics of electron transfer. (iii) EPR spectroscopy of ferricyt c2 in cross-linked RC-cyt c2 complexes was used to determine the angle between the heme and the membrane plane. The results suggest the following structural properties for the docking of cyt c2 to the RC: (i) In cross-linked complexes, the two cytochromes displaying half-lives of 0.7 and 60 micros for electron transfer to P+ are similarly oriented (difference plane is parallel to the symmetry axis of the RC (0 degrees +/- 10 degrees). Moreover, the Qy transition, which is assumed to be polarized within the ring III-ring I direction of the heme plane, makes an angle of 56 degrees +/- 1 degree with the symmetry axis. (iii) The dichroism spectrum for the fast phase (0.7 micros) for the non-cross-linked cyt c2-RC complex suggests an orientation similar to that of cross-linked cyt c2, but the heme plane is tilted about 20 degrees closer to the membrane. An alternative model is that two or more bound states of cyt c2 with heme plane tilt angles between 0 degrees and 30 degrees allow the fast electron

  16. Orbital Models and Electronic Structure Theory

    DEFF Research Database (Denmark)

    Linderberg, Jan

    2012-01-01

    This tribute to the work by Carl Johan Ballhausen focuses on the emergence of quantitative means for the study of the electronic properties of complexes and molecules. Development, refinement and application of the orbital picture elucidated electric and magnetic features of ranges of molecules...

  17. Crystal structure from one-electron theory

    DEFF Research Database (Denmark)

    Skriver, H. L.

    1985-01-01

    The authors have studied the crystal structure of all the 3d, 4d, and 5d transition metals at zero pressure and temperature by means of the linear muffin-tin orbital method and Andersen's force theorem. They find that, although the structural energy differences seem to be overestimated by the the......The authors have studied the crystal structure of all the 3d, 4d, and 5d transition metals at zero pressure and temperature by means of the linear muffin-tin orbital method and Andersen's force theorem. They find that, although the structural energy differences seem to be overestimated...

  18. Structural characterization of the heme-based oxygen sensor, AfGcHK, its interactions with the cognate response regulator, and their combined mechanism of action in a bacterial two-component signaling system

    Czech Academy of Sciences Publication Activity Database

    Stráňava, M.; Martínek, V.; Man, Petr; Fojtíková, V.; Kavan, Daniel; Vaněk, O.; Shimizu, T.; Martínková, M.

    2016-01-01

    Roč. 84, č. 10 (2016), s. 1375-1389 ISSN 1097-0134 R&D Projects: GA MŠk(CZ) ED1.1.00/02.0109 Institutional support: RVO:61388971 Keywords : heme-based oxygen sensor * histidine kinase * two-component signal transduction system Subject RIV: CE - Biochemistry

  19. Nitric oxide heme interactions in nitrophorin from Cimex lectularius

    Energy Technology Data Exchange (ETDEWEB)

    Christmann, R.; Auerbach, H., E-mail: auerbach@physik.uni-kl.de [University of Kaiserslautern, Department of Physics (Germany); Berry, R. E.; Walker, F. A. [The University of Arizona, Department of Chemistry and Biochemistry (United States); Schünemann, V. [University of Kaiserslautern, Department of Physics (Germany)

    2016-12-15

    The nitrophorin from the bedbug Cimex lectularius (cNP) is a nitric oxide (NO) carrying protein. Like the nitrophorins (rNPs) from the kissing bug Rhodnius prolixus, cNP forms a stable heme Fe(III)-NO complex, where the NO can be stored reversibly for a long period of time. In both cases, the NPs are found in the salivary glands of blood-sucking bugs. The insects use the nitrophorins to transport the NO to the victim’s tissues, resulting in vasodilation and reduced blood coagulation. However, the structure of cNP is significantly different to those of the rNPs from Rhodnius prolixus. Furthermore, the cNP can bind a second NO molecule to the proximal heme cysteine when present at higher concentrations. High field Mössbauer spectroscopy on {sup 57}Fe enriched cNP complexed with NO shows reduction of the heme iron and formation of a ferrous nitric oxide (Fe(II)-NO) complex. Density functional theory calculations reproduce the experimental Mössbauer parameters and confirm this observation.

  20. Complex band structure and electronic transmission eigenchannels

    DEFF Research Database (Denmark)

    Jensen, Anders; Strange, Mikkel; Smidstrup, Soren

    2017-01-01

    and complex band structure, in this case individual eigenchannel transmissions and different complex bands. We present calculations of decay constants for the two most conductive states as determined by complex band structure and standard DFT Landauer transport calculations for one semi-conductor and two...

  1. Syntheses and electronic structures of decamethylmetallocenes

    International Nuclear Information System (INIS)

    Robbins, J.L.

    1981-04-01

    The synthesis of decamethylmanganocene [(eta-C 5 (CH 3 ) 5 ) 2 Mn or (Me 5 Cp) 2 Mn)] is described. Magnetic susceptibility and electron paramagnetic resonance (EPR) studies show that (Me 5 Cp) 2 Mn is a low-spin, 17-electron compound with an orbitally degenerate, 2 E/sub 2g/ [e/sub 2g/ 3 a/sub 1g/ 2 ] ground state. An x-ray crystallographic study of (Me 5 Cp) 2 Mn shows that it is a monomeric, D/sub 5d/ decamethylmetallocene with metal to ring carbon distances that are about 0.3 A shorter than those determined for high-spin manganocenes. The syntheses of new (Me 5 Cp) 2 M (M = Mg,V,Cr,Co, and Ni) and [(Me 5 Cp) 2 M]PF 6 (M = Cr,Co, and Ni) compounds are described. In addition, a preparative route to a novel, dicationic decamethylmetallocene, [(Me 5 Cp) 2 Ni](PF 6 ) 2 is reported. Infrared, nuclear magnetic resonance, magnetic susceptibility, and/or x-ray crystallographic studies indicate that all the above compounds are D/sub 5d/ or D/sub 5h/ decamethylmetallocenes with low-spin electronic configurations. Cyclic voltammetry studies verify the reversibility and the one-electron nature of the (Me 5 Cp) 2 M → [(Me 5 Cp) 2 M] + (M = Cr,Mn,Fe,Co,Ni), [(Me 5 Cp) 2 Mn] - → (Me 5 Cp) 2 Mn and [(Me 5 Cp) 2 Ni] + → [Me 5 Cp) 2 Ni] 2+ redox reactions. These studies reveal that the neutral decamethylmetallocenes are much more easily oxidized than their metallocene counterparts. This result attests to the electron-donating properties of the ten substituent methyl groups. Proton and carbon-13 NMR data are reported for the diamagnetic Mg(II), Mn(I), Fe(II), Co(III), and Ni(IV) decamethylmetallocenes and for [(Me 5 Cp) 2 V(CO) 2 ] + . The uv-visible absorption spectra of the 15-, 18- and 20- electron decamethylmetallocenes are also reported

  2. Syntheses and electronic structures of decamethylmetallocenes

    Energy Technology Data Exchange (ETDEWEB)

    Robbins, J.L.

    1981-04-01

    The synthesis of decamethylmanganocene ((eta-C/sub 5/(CH/sub 3/)/sub 5/)/sub 2/Mn or (Me/sub 5/Cp)/sub 2/Mn)) is described. Magnetic susceptibility and electron paramagnetic resonance (EPR) studies show that (Me/sub 5/Cp)/sub 2/Mn is a low-spin, 17-electron compound with an orbitally degenerate, /sup 2/E/sub 2g/ (e/sub 2g//sup 3/ a/sub 1g//sup 2/) ground state. An x-ray crystallographic study of (Me/sub 5/Cp)/sub 2/Mn shows that it is a monomeric, D/sub 5d/ decamethylmetallocene with metal to ring carbon distances that are about 0.3 A shorter than those determined for high-spin manganocenes. The syntheses of new (Me/sub 5/Cp)/sub 2/M (M = Mg,V,Cr,Co, and Ni) and ((Me/sub 5/Cp)/sub 2/M)PF/sub 6/ (M = Cr,Co, and Ni) compounds are described. In addition, a preparative route to a novel, dicationic decamethylmetallocene, ((Me/sub 5/Cp)/sub 2/Ni)(PF/sub 6/)/sub 2/ is reported. Infrared, nuclear magnetic resonance, magnetic susceptibility, and/or x-ray crystallographic studies indicate that all the above compounds are D/sub 5d/ or D/sub 5h/ decamethylmetallocenes with low-spin electronic configurations. Cyclic voltammetry studies verify the reversibility and the one-electron nature of the (Me/sub 5/Cp)/sub 2/M ..-->.. ((Me/sub 5/Cp)/sub 2/M)/sup +/ (M = Cr,Mn,Fe,Co,Ni), ((Me/sub 5/Cp)/sub 2/Mn)/sup -/ ..-->.. (Me/sub 5/Cp)/sub 2/Mn and ((Me/sub 5/Cp)/sub 2/Ni)/sup +/ ..-->.. (Me/sub 5/Cp)/sub 2/Ni)/sup 2 +/ redox reactions. These studies reveal that the neutral decamethylmetallocenes are much more easily oxidized than their metallocene counterparts. This result attests to the electron-donating properties of the ten substituent methyl groups. Proton and carbon-13 NMR data are reported for the diamagnetic Mg(II), Mn(I), Fe(II), Co(III), and Ni(IV) decamethylmetallocenes and for ((Me/sub 5/Cp)/sub 2/V(CO)/sub 2/)/sup +/. The uv-visible absorption spectra of the 15-, 18- and 20- electron decamethylmetallocenes are also reported.

  3. Pulse Radiolysis Studies of Temperature Dependent Electron Transfers among Redox Centers in ba(3)-Cytochrome c Oxidase from Thermus thermophilus

    DEFF Research Database (Denmark)

    Farver, Ole; Wherland, Scot; Antholine, William E

    2010-01-01

    The functioning of cytochrome c oxidases involves orchestration of long-range electron transfer (ET) events among the four redox active metal centers. We report the temperature dependence of electron transfer from the Cu(A)(r) site to the low-spin heme-(a)b(o) site, i.e., Cu(A)(r) + heme-a(b)(o) ......The functioning of cytochrome c oxidases involves orchestration of long-range electron transfer (ET) events among the four redox active metal centers. We report the temperature dependence of electron transfer from the Cu(A)(r) site to the low-spin heme-(a)b(o) site, i.e., Cu(A)(r) + heme...... in cytochrome ba(3) had no effect on the rate of this reaction whereas the II-Met160Leu Cu(A)-mutation was slower by an amount corresponding to a decreased driving force of ∼0.06 eV. The structures support the presence of a common, electron-conducting "wire" between Cu(A) and heme-a(b). The transfer...

  4. Electronic structure and optical properties of solid C60

    International Nuclear Information System (INIS)

    Mattesini, M.; Ahuja, R.; Sa, L.; Hugosson, H.W.; Johansson, B.; Eriksson, O.

    2009-01-01

    The electronic structure and the optical properties of face-centered-cubic C 60 have been investigated by using an all-electron full-potential method. Our ab initio results show that the imaginary dielectric function for high-energy values looks very similar to that of graphite, revealing close electronic structure similarities between the two systems. We have also identified the origin of different peaks in the dielectric function of fullerene by means of the calculated electronic density of states. The computed optical spectrum compares fairly well with the available experimental data for the Vis-UV absorption spectrum of solid C 60 .

  5. Measurement of Heme Synthesis Levels in Mammalian Cells.

    Science.gov (United States)

    Hooda, Jagmohan; Alam, Maksudul; Zhang, Li

    2015-07-09

    Heme serves as the prosthetic group for a wide variety of proteins known as hemoproteins, such as hemoglobin, myoglobin and cytochromes. It is involved in various molecular and cellular processes such as gene transcription, translation, cell differentiation and cell proliferation. The biosynthesis levels of heme vary across different tissues and cell types and is altered in diseased conditions such as anemia, neuropathy and cancer. This technique uses [4-(14)C] 5-aminolevulinic acid ([(14)C] 5-ALA), one of the early precursors in the heme biosynthesis pathway to measure the levels of heme synthesis in mammalian cells. This assay involves incubation of cells with [(14)C] 5-ALA followed by extraction of heme and measurement of the radioactivity incorporated into heme. This procedure is accurate and quick. This method measures the relative levels of heme biosynthesis rather than the total heme content. To demonstrate the use of this technique the levels of heme biosynthesis were measured in several mammalian cell lines.

  6. Electronic structure of fractionally nuclear charged atoms

    International Nuclear Information System (INIS)

    Pavao, Antonio C.; Bastos, Cristiano C.; Ferreira, Joacy V.

    2008-01-01

    Different properties of quark chemistry are studied by performing accurate ab initio Hartree- Fock calculations on fractionally nuclear charged atoms. Ground and first excited states of sodium atoms with quarks attached to the nucleus are obtained using CI calculations. It is suggested that the sodium 2 P -> 2 S electronic transition can be used as a guide in searching for unconfined quarks. Also, the variation of the binding electronic energy with nuclear charge in the isoelectronic series of fractionally nuclear charged atoms A ±2/3 and A ±1/3 (A = H, Li, Na, P and Ca) is analyzed. The present calculations suggest that unconfined colored particles have large appetite for heavy nuclei and that quark-antiquark pairs could be stabilized in presence of the atomic matter. (author)

  7. Tailoring electronic structure of polyazomethines thin films

    OpenAIRE

    J. Weszka; B. Hajduk; M. Domański; M. Chwastek; J. Jurusik; B. Jarząbek; H. Bednarski; P. Jarka

    2010-01-01

    Purpose: The aim of this work is to show how electronic properties of polyazomethine thin films deposited by chemical vapor deposition method (CVD) can be tailored by manipulating technological parameters of pristine films preparation as well as modifying them while the as-prepared films put into iodine atmosphere.Design/methodology/approach: The recent achievements in the field of designing and preparation methods to be used while preparing polymer photovoltaic solar cells or optoelectronic ...

  8. Electronic structure and formation energy of a vacancy in aluminum

    International Nuclear Information System (INIS)

    Chakraborty, B.; Siegel, R.W.

    1981-11-01

    The electronic structure of a vacancy in Al was calculated self-consistently using norm-conserving ionic pseudopotentials obtained from ab initio atomic calculations. A 27-atom-site supercell containing 1 vacancy and 26 atoms was used to simulate the environment of the vacancy. A vacancy formation energy of 1.5 eV was also calculated (cf. the experimental value of 0.66 eV). The effects of the supercell and the nature of the ionic potential on the resulting electronic structure and formation energy are discussed. Results for the electronic structure of a divacancy are also presented. 3 figures

  9. One-Electron Theory of Metals. Cohesive and Structural Properties

    DEFF Research Database (Denmark)

    Skriver, Hans Lomholt

    The work described in the report r.nd the 16 accompanying publications is based upon a one-electron theory obtained within the local approximation to density-functional theory, and deals with the ground state of metals as obtained from selfconsistent electronic-structure calculations performed...... by means of the Linear Muffin-Tin Orbital (LMTO) method. It has been the goal of the work to establish how well this one-electron approach describes physical properties such as the crystal structures of the transition metals, the structural phase transitions in the alkali, alkaline earth, and rare earth...

  10. Heme biosynthesis and its regulation : Toward understanding and improvement of heme biosynthesis in filamentous fungi.

    NARCIS (Netherlands)

    S. de Weert; P.J. Punt; Christien Lokman; C.A. van den Hondel; A.C. Franken; A.F. Ram

    2011-01-01

    Heme biosynthesis in fungal host strains has acquired considerable interest in relation to the production of secreted heme-containing peroxidases. Class II peroxidase enzymes have been suggested as eco-friendly replacements of polluting chemical processes in industry. These peroxidases are naturally

  11. Heme biosynthesis and its regulation: Towards understanding and improvement of heme biosynthesis in filamentous fungi

    NARCIS (Netherlands)

    Franken, A.C.W.; Lokman, B.C.; Ram, A.F.J.; Punt, P.J.; Hondel, C.A.M.J.J. van den; Weert, S. de

    2011-01-01

    Heme biosynthesis in fungal host strains has acquired considerable interest in relation to the production of secreted heme-containing peroxidases. Class II peroxidase enzymes have been suggested as eco-friendly replacements of polluting chemical processes in industry. These peroxidases are naturally

  12. Structure and electron-ion correlation in liquid Mg

    Energy Technology Data Exchange (ETDEWEB)

    Tahara, Shuta [Graduate School of Sciences, Kyushu University, 4-2-1 Ropponmatsu Chuo-ku, Fukuoka 810-8560 (Japan); Fujii, Hiroyuki [Graduate School of Sciences, Kyushu University, 4-2-1 Ropponmatsu Chuo-ku, Fukuoka 810-8560 (Japan); Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto Sayo-cho, Sayo-gun, Hyogo 679-5198 (Japan); Yokota, Yukinobu [Graduate School of Sciences, Kyushu University, 4-2-1 Ropponmatsu Chuo-ku, Fukuoka 810-8560 (Japan); Kawakita, Yukinobu [Department of Physics, Faculty of Sciences, Kyushu University, 4-2-1 Ropponmatsu Chuo-ku, Fukuoka 810-8560 (Japan); Kohara, Shinji [Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto Sayo-cho, Sayo-gun, Hyogo 679-5198 (Japan); Takeda, Shin' ichi [Department of Physics, Faculty of Sciences, Kyushu University, 4-2-1 Ropponmatsu Chuo-ku, Fukuoka 810-8560 (Japan)]. E-mail: takeda@rc.kyushu-u.ac.jp

    2006-11-15

    For liquid Mg at 700 deg. C, structure factors were obtained from both neutron and X-ray diffraction measurements. The bond angle and coordination number distributions were derived from the reverse Monte Carlo analysis. By a combination of both structure factors, charge density function and electron-ion partial structure factor were deduced.

  13. Structural and electronic parameters of ferroelectric KWOF

    Science.gov (United States)

    Atuchin, V. V.; Gavrilova, T. A.; Kesler, V. G.; Molokeev, M. S.; Aleksandrov, K. S.

    2010-11-01

    The low-temperature ferroelectric G2 polymorph of K 3WO 3F 3 oxyfluoride is formed by chemical synthesis. The electronic parameters of G2-K 3WO 3F 3 have been measured by X-ray photoelectron spectroscopy under excitation with Al Kα radiation (1486.6 eV). Detailed spectra have been recorded for all element core levels and Auger lines. The chemical bonding effects in the WO 3F 3 and WO 6 octahedrons are considered by using the binding energy difference ΔBE(O-W)=BE(O 1s)-BE(W 4f).

  14. Nodal Structure of the Electronic Wigner Function

    DEFF Research Database (Denmark)

    Schmider, Hartmut; Dahl, Jens Peder

    1996-01-01

    On the example of several atomic and small molecular systems, the regular behavior of nodal patterns in the electronic one-particle reduced Wigner function is demonstrated. An expression found earlier relates the nodal pattern solely to the dot-product of the position and the momentum vector......, if both arguments are large. An argument analogous to the ``bond-oscillatory principle'' for momentum densities links the nuclear framework in a molecule to an additional oscillatory term in momenta parallel to bonds. It is shown that these are visible in the Wigner function in terms of characteristic...

  15. Electronic structure of the light actinides

    International Nuclear Information System (INIS)

    Dunlap, B.D.

    1976-01-01

    In the last few years, considerable advances have been made in our understanding of the properties of the light actinides. Although these are 5f transition elements formally equivalent to the lanthanide (4f) elements, these materials show a much more varied behavior due to the larger spatial extent and ionizability of the 5f electrons. A review is given of some areas of current interest, especially where hyperfine measurements have played an active role. These include studies of a variety of magnetic phenomena, systematics of isomer shift measurements, and studies of paramagnetic relaxation

  16. Electron beam crosslinked PVC : structure property relationships

    International Nuclear Information System (INIS)

    Gupta, Neeraj K.; Sabharwal, Sunil

    2001-01-01

    PVC is used extensively for its insulating properties for the manufacture of wires and cables and for other applications. Its gradual degradation, oxidation and even dehydro chlorination restricts use for long lasting period in installations such as high temperature zones, underground cables, communication systems, electro-nuclear facilities, etc. The technological properties and performance characteristics of PVC based insulation can be improved via crosslinking by high-energy electrons. PVC is however a polymer, which on irradiation predominantly undergoes degradation. To avoid degradation, it needs to be compounded with sensitizing agents or multifunctional monomers so that crosslinking is the predominant reaction. Radiation cross linkable formulations are complex mixtures of resin and various additives incorporated for achieving desired technological and performance characteristics, ease of processing and improving quality. The proper choice of additives and sensitizing agents enable low dose requirements for efficient crosslinking and improvements in various technological properties. The purposes of this work was to investigate the effect of using a binary sensitizer blend of a trifunctional monomer and a rubber in PVC, and develop suitable electron beam cross linkable formulations for wire insulation. This paper presents some aspects of the investigations and development of insulation demonstrated at industrial scale

  17. Electronic structure and isomer shifts of Sn halides

    International Nuclear Information System (INIS)

    Terra, J.; Guenzburger, D.

    1988-01-01

    The all-electron first-principles Discrete Variational method was employed to study the electronic structure of SnF 4 , SnCl 4 , SnBr 4 and SnI 4 . Values of the electronic density at the Sn nucleus were derived and related to 119 Sn Isomer Shifts to obtain the nuclear constant Δ 2 >. Differences in values of ρ(o) area discussed in terms of the chemical bonding between Sn and halogen atoms. (author) [pt

  18. Electronic structure of graphene beyond the linear dispersion regime

    OpenAIRE

    POWER, STEPHEN; FERREIRA, MAURO

    2011-01-01

    PUBLISHED Among the many interesting features displayed by graphene, one of the most attractive is the simplicity with which its electronic structure can be described. The study of its physical properties is significantly simplified by the linear dispersion relation of electrons in a narrow range around the Fermi level. Unfortunately, the mathematical simplicity of graphene electrons is limited only to this narrow energy region and is not very practical when dealing with problems that invo...

  19. Phase stability and electronic structure of transition-metal aluminides

    International Nuclear Information System (INIS)

    Carlsson, A.E.

    1992-01-01

    This paper will describe the interplay between die electronic structure and structural energetics in simple, complex, and quasicrystalline Al-transition metal (T) intermetallics. The first example is the Ll 2 -DO 22 competition in Al 3 T compounds. Ab-initio electronic total-energy calculations reveal surprisingly large structural-energy differences, and show that the phase stability of both stoichiometric and ternary-substituted compounds correlates closely with a quasigap in the electronic density of states (DOS). Secondly, ab-initio calculations for the structural stability of the icosahedrally based Al 12 W structure reveal similar quasigap effects, and provide a simple physical explanation for the stability of the complex aluminide structures. Finally, parametrized tight-binding model calculations for the Al-Mn quasicrystal reveal a large spread in the local Mn DOS behavior, and support a two-site model for the quasicrystal's magnetic behavior

  20. Hemoglobin structural dynamics as monitored by resonance Raman spectroscopy

    International Nuclear Information System (INIS)

    Spiro, T.G.

    1981-01-01

    Resonance Raman spectra of the heme group are now understood at a level sufficient to provide a useful monitor of several heme structural features. Some porphyrin vibrational frequencies are sensitive to Fe oxidation state, or π-electron distribution, and give insight into the electronic structure of O 2 , CO and NO hemes. Others are sensitive to Fe spin-state, via the associated geometry variation, and provide an accurate index of the porphyrin core size. When examined during the photolysis of CO-hemoglobin via short laser pulses, these frequencies indicate that conversion from low- to h+gh-spin Fe 11 takes place within 30 ps of photolysis, presumably via intersystem-crossing in the excited state, but that the subsequent relaxation of the Fe atom out of the heme plane takes longer than 20 ns, probably because of restraint by the protein. Axial ligand modes have been identified for several heme derivatives. The Fe-imidazole frequency in deoxyhemoglobin is appreciably lowered in the T quaternary structure, as determined in both static and kinetic experiments, suggesting molecular tension or proximal imidazole H-bond weakening in the T state. (author)

  1. Electronic structure of filled tetrahedral semiconductors

    NARCIS (Netherlands)

    Wood, D.M.; Zunger, Alex; Groot, R. de

    1985-01-01

    We discuss the susceptibility of zinc-blende semiconductors to band-structure modification by insertion of small atoms at their tetrahedral interstitial states. GaP is found to become a direct-gap semiconductor with two He atoms present at its interstitial sites; Si does not. Analysis of the factors

  2. Electronic Band Structure of Helical Polyisocyanides.

    Science.gov (United States)

    Champagne, Benoît; Liégeois, Vincent; Fripiat, Joseph G; Harris, Frank E

    2017-10-19

    Restricted Hartree-Fock computations are reported for a methyl isocyanide polymer (repeating unit -C═N-CH 3 ), whose most stable conformation is expected to be a helical chain. The computations used a standard contracted Gaussian orbital set at the computational levels STO-3G, 3-21G, 6-31G, and 6-31G**, and studies were made for two line-group configurations motivated by earlier work and by studies of space-filling molecular models: (1) A structure of line-group symmetry L9 5 , containing a 9-fold screw axis with atoms displaced in the axial direction by 5/9 times the lattice constant, and (2) a structure of symmetry L4 1 that had been proposed, containing a 4-fold screw axis with translation by 1/4 of the lattice constant. Full use of the line-group symmetry was employed to cause most of the computational complexity to depend only on the size of the asymmetric repeating unit. Data reported include computed bond properties, atomic charge distribution, longitudinal polarizability, band structure, and the convoluted density of states. Most features of the description were found to be insensitive to the level of computational approximation. The work also illustrates the importance of exploiting line-group symmetry to extend the range of polymer structural problems that can be treated computationally.

  3. Electronic structure and ionicity of actinide oxides from first principles

    DEFF Research Database (Denmark)

    Petit, Leon; Svane, Axel; Szotek, Z.

    2010-01-01

    The ground-state electronic structures of the actinide oxides AO, A2O3, and AO2 (A=U, Np, Pu, Am, Cm, Bk, and Cf) are determined from first-principles calculations, using the self-interaction corrected local spin-density approximation. Emphasis is put on the degree of f-electron localization, whi...

  4. On the electronic structure of high Tc superconductors

    International Nuclear Information System (INIS)

    Fink, J.; Nuecker, N.; Romberg, H.; Alexander, M.; Knupfer, M.; Mante, J.; Claessen, R.; Buslaps, T.; Harm, S.; Manzke, R.; Skibowski, M.

    1992-01-01

    Studies of the electronic structure of high-T c superconductors and related compounds by high-energy spectroscopies are reviewed. In particular, we report on investigations by electron energy-loss, angle-resolved photoemission, and inverse angle-resolved photoemission spectroscopy. Information on the symmetry and the character of states close to the Fermi level has been obtained. 25 refs., 8 figs

  5. Electronic structure and equilibrium properties of hcp titanium

    Indian Academy of Sciences (India)

    The electronic structures of hexagonal-close-packed divalent titanium (3-d) and zirconium (4-d) transition metals are studied by using a non-local model potential method. From the present calculation of energy bands, Fermi energy, density of states and the electronic heat capacity of these two metals are determined and ...

  6. Weiss oscillations in the electronic structure of modulated graphene

    International Nuclear Information System (INIS)

    Tahir, M; Sabeeh, K; MacKinnon, A

    2007-01-01

    We present a theoretical study of the electronic structure of modulated graphene in the presence of a perpendicular magnetic field. The density of states and the bandwidth for the Dirac electrons in this system are determined. The appearance of unusual Weiss oscillations in the bandwidth and density of states is the main focus of this work

  7. Electronic Structure of Au25 Clusters: Between Discrete and Continuous

    KAUST Repository

    Katsiev, Khabiboulakh

    2016-07-15

    Here, an approach based on synchrotron resonant photoemission is emplyed to explore the transition between quantization and hybridization of the electronic structure in atomically precise ligand-stabilized nanoparticles. While the presence of ligands maintains quantization in Au25 clusters, their removal renders increased hybridization of the electronic states at the vicinity of the Fermi level. These observations are supported by DFT studies.

  8. Electronic Structure of Au25 Clusters: Between Discrete and Continuous

    KAUST Repository

    Katsiev, Khabiboulakh; Lozova, Nataliya; Wang, Lu; Katla, Saikrishna; Li, Ruipeng; Mei, Wai Ning; Skrabalak, Sara; Challa, Challa; Losovyj, Yaroslav

    2016-01-01

    Here, an approach based on synchrotron resonant photoemission is emplyed to explore the transition between quantization and hybridization of the electronic structure in atomically precise ligand-stabilized nanoparticles. While the presence of ligands maintains quantization in Au25 clusters, their removal renders increased hybridization of the electronic states at the vicinity of the Fermi level. These observations are supported by DFT studies.

  9. Electronic Structure of Cdse Nanowires Terminated With Gold ...

    African Journals Online (AJOL)

    Bheema

    Owing to their unusual electronic and structural properties, SC clusters have received considerable attention ... performing molecular dynamics simulations. A similar .... Analysis of the charge density, gap, corresponding to states with energies ...

  10. Structures and electronics of buried and unburied semiconductor interfaces

    International Nuclear Information System (INIS)

    Kamiya, Itaru

    2011-01-01

    The structure of interfaces plays an important role in determining the electronic properties of semiconductor nanostructures. Here, such examples are shown and discussed using semiconductor nanostructures prepared by molecular beam epitaxy and colloidal synthesis.

  11. Manganites in Perovskite Superlattices: Structural and Electronic Properties

    KAUST Repository

    Jiwuer, Jilili

    2016-01-01

    Perovskite manganites are widely investigated compounds due to the discovery of the colossal magnetoresistance effect in 1994. They have a broad range of structural, electronic, magnetic properties and potential device applications in sensors

  12. Structure and electron-ion correlation of liquid germanium

    Energy Technology Data Exchange (ETDEWEB)

    Kawakita, Y. [Faculty of Sciences, Kyushu University, 4-2-1 Ropponmatsu, Fukuoka 810-8560 (Japan)]. E-mail: kawakita@rc.kyushu-u.ac.jp; Fujita, S. [Graduate School of Sciences, Kyushu University, 4-2-1 Ropponmatsu, Fukuoka 810-8560 (Japan); Kohara, S. [Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto Mikazuki-cho, Hyogo 679-5198 (Japan); Ohshima, K. [Graduate School of Sciences, Kyushu University, 4-2-1 Ropponmatsu, Fukuoka 810-8560 (Japan); Fujii, H. [Graduate School of Sciences, Kyushu University, 4-2-1 Ropponmatsu, Fukuoka 810-8560 (Japan); Yokota, Y. [Graduate School of Sciences, Kyushu University, 4-2-1 Ropponmatsu, Fukuoka 810-8560 (Japan); Takeda, S. [Faculty of Sciences, Kyushu University, 4-2-1 Ropponmatsu, Fukuoka 810-8560 (Japan)

    2005-08-15

    Structure factor of liquid germanium (Ge) has a shoulder at {theta} = 3.2 A{sup -1} in the high-momentum-transfer region of the first peak. To investigate the origin of such a non-simplicity in the structure, high energy X-ray diffraction measurements have been performed using 113.26 keV incident X-ray, at BL04B2 beamline of SPring-8. By a combination of the obtained structure factor with the reported neutron diffraction data, charge density function and electron-ion partial structure factor have been deduced. The peak position of the charge distribution is located at about 1 A, rather smaller r value than the half value of nearest neighbor distance ({approx}2.7 A), which suggests that valence electrons of liquid Ge play a role of screening electrons around a metallic ion rather than covalently bonding electrons.

  13. Structure functions in electron-nucleon deep inelastic scattering

    Energy Technology Data Exchange (ETDEWEB)

    Saleem, M.; Fazal-E-Aleem (University of the Punjab, Lahore (Pakistan). Dept. of Physics)

    1982-06-26

    The phenomenological expressions for the structure functions in electron-nucleon deep inelastic scattering are proposed and are shown to satisfy the experimental data as well as a number of sum rules.

  14. First-principle calculations of structural, electronic, optical, elastic ...

    Indian Academy of Sciences (India)

    S CHEDDADI

    2017-11-28

    Nov 28, 2017 ... First-principle calculations on the structural, electronic, optical, elastic and thermal properties of the chalcopyrite ... The Kohn–Sham equations were solved using the ... RMTKmax = 7 was used for all the investigated systems,.

  15. Electronic structure of incident carbon ions on a graphite surface

    International Nuclear Information System (INIS)

    Kiuchi, Masato; Takeuchi, Takae; Yamamoto, Masao.

    1997-01-01

    The electronic structure of an incident carbon ion on a graphite surface is discussed on the basis of ab initio molecular orbital calculations. A carbon cation forms a covalent bond with the graphite, and a carbon nonion is attracted to the graphite surface through van der Waals interaction. A carbon anion has no stable state on a graphite surface. The charge effects of incident ions become clear upon detailed examination of the electronic structure. (author)

  16. Heme synthesis in normal mouse liver and mouse liver tumors

    International Nuclear Information System (INIS)

    Stout, D.L.; Becker, F.F.

    1990-01-01

    Hepatic cancers from mice and rats demonstrate decreased levels of delta-aminolevulinic acid synthase, the rate-limiting enzyme in the heme synthetic pathway, and increased heme oxygenase, the heme-catabolizing enzyme. These findings suggest that diminution of P-450, b5, and catalase in these lesions may result from a heme supply that is limited by decreased heme synthesis and increased heme catabolism. Heme synthesis was measured in mouse liver tumors (MLT) and adjacent tumor-free lobes (BKG) by administering the radiolabeled heme precursors 55 FeCl3 and [2- 14 C]glycine and subsequently extracting the heme for determination of specific activity. Despite reduced delta-aminolevulinic acid synthase activity in MLT, both tissues incorporated [2-14C]glycine into heme at similar rates. At early time points, heme extracted from MLT contained less 55Fe than that from BKG. This was attributed to the findings that MLT took up 55Fe at a slower rate than BKG and had larger iron stores than BKG. The amount of heme per milligram of protein was also similar in both tissues. These findings militate against the hypothesis that diminished hemoprotein levels in MLT result from limited availability of heme. It is probable, therefore, that decreased hemoprotein levels in hepatic tumors are linked to a general program of dedifferentiation associated with the cancer phenotype. Diminution of hemoprotein in MLT may result in a relatively increased intracellular heme pool. delta-Aminolevulinic acid synthase and heme oxygenase are, respectively, negatively and positively regulated by heme. Thus, their alteration in MLT may be due to the regulatory influences of the heme pool

  17. The orbital ground state of the azide-substrate complex of human heme oxygenase is an indicator of distal H-bonding: Implications for the enzyme mechanism‡

    OpenAIRE

    Ogura, Hiroshi; Evans, John P.; Peng, Dungeng; Satterlee, James D.; de Montellano, Paul R. Ortiz; Mar, Gerd N. La

    2009-01-01

    The active site electronic structure of the azide complex of substrate-bound human heme oxygenase-1, (hHO) has been investigated by 1H NMR spectroscopy to shed light on the orbital/spin ground state as an indicator of the unique distal pocket environment of the enzyme. 2D 1H NMR assignments of the substrate and substrate-contact residue signals reveal a pattern of substrate methyl contact shifts, that places the lone iron π-spin in the dxz orbital, rather than the dyz orbital found in the cya...

  18. A peroxidase mimic with atom transfer radical polymerization activity constructed through the grafting of heme onto metal-organic frameworks.

    Science.gov (United States)

    Jiang, Wei; Pan, Yue; Yang, Jiebing; Liu, Yong; Yang, Yan; Tang, Jun; Li, Quanshun

    2018-07-01

    Atom transfer radical polymerization (ATRP) has been considered to be an efficient strategy for constructing functional macromolecules owing to its simple operation and versatile monomers, and thus it is of great significance to develop ideal catalysts with higher activity and perfect reusability. We constructed a peroxidase mimic through the grafting of heme onto metal-organic frameworks UiO-66-NH 2 (ZrMOF), namely Heme-ZrMOF. After the systematic characterization of structure, the composite Heme-ZrMOF was demonstrated to possess high peroxidase activity using 2,2'-azinobis-(3-ethylbenzthiazoline-6-sulphonate) and 3,3',5,5'-tetramethylbenzidine as substrates. The enzyme mimic was then used as catalysts in the ATRP reactions of different monomers, in which favorable monomer conversion (44.6-98.0%) and product molecular weight (8600-25,600 g/mol) could be obtained. Compared to free heme, Heme-ZrMOF could efficiently achieve the easy separation of heme from the catalytic system and facilitate the ATRP reaction in an aqueous environment to avoid the utilization of organic solvents. In conclusion, the enzyme mimic Heme-ZrMOF could be potentially used as an effective catalyst for preparing well-defined polymers with biomedical applications. Copyright © 2018 Elsevier Inc. All rights reserved.

  19. Voltammetry and In Situ Scanning Tunnelling Microscopy of De Novo Designed Heme Protein Monolayers on Au(111)-Electrode Surfaces

    DEFF Research Database (Denmark)

    Albrecht, Tim; Li, Wu; Haehnel, Wolfgang

    2006-01-01

    to the tunnelling current, apparently due to slow electron transfer kinetics. As a consequence, STM images of heme-containing and heme-free MOP-C did not reveal any notable differences in apparent height or physical extension. The apparent height of heme-containing MOP-C did not show any dependence on the substrate...... potential being varied around the redox potential of the protein. The mere presence of an accessible molecular energy level is not sufficient to result in detectable tunnelling current modulation. (c) 2006 Elsevier B.V. All rights reserved.......In the present work, we report the electrochemical characterization and in situ scanning tunnelling microscopy (STM) studies of monolayers of an artificial de novo designed heme protein MOP-C, covalently immobilized on modified Au(111) surfaces. The protein forms closely packed monolayers, which...

  20. Heme and non-heme iron transporters in non-polarized and polarized cells

    Directory of Open Access Journals (Sweden)

    Yasui Yumiko

    2010-06-01

    Full Text Available Abstract Background Heme and non-heme iron from diet, and recycled iron from hemoglobin are important products of the synthesis of iron-containing molecules. In excess, iron is potentially toxic because it can produce reactive oxygen species through the Fenton reaction. Humans can absorb, transport, store, and recycle iron without an excretory system to remove excess iron. Two candidate heme transporters and two iron transporters have been reported thus far. Heme incorporated into cells is degraded by heme oxygenases (HOs, and the iron product is reutilized by the body. To specify the processes of heme uptake and degradation, and the reutilization of iron, we determined the subcellular localizations of these transporters and HOs. Results In this study, we analyzed the subcellular localizations of 2 isoenzymes of HOs, 4 isoforms of divalent metal transporter 1 (DMT1, and 2 candidate heme transporters--heme carrier protein 1 (HCP1 and heme responsive gene-1 (HRG-1--in non-polarized and polarized cells. In non-polarized cells, HCP1, HRG-1, and DMT1A-I are located in the plasma membrane. In polarized cells, they show distinct localizations: HCP1 and DMT1A-I are located in the apical membrane, whereas HRG-1 is located in the basolateral membrane and lysosome. 16Leu at DMT1A-I N-terminal cytosolic domain was found to be crucial for plasma membrane localization. HOs are located in smooth endoplasmic reticulum and colocalize with NADPH-cytochrome P450 reductase. Conclusions HCP1 and DMT1A-I are localized to the apical membrane, and HRG-1 to the basolateral membrane and lysosome. These findings suggest that HCP1 and DMT1A-I have functions in the uptake of dietary heme and non-heme iron. HRG-1 can transport endocytosed heme from the lysosome into the cytosol. These localization studies support a model in which cytosolic heme can be degraded by HOs, and the resulting iron is exported into tissue fluids via the iron transporter ferroportin 1, which is

  1. Chemistry and Molecular Dynamics Simulations of Heme b-HemQ and Coproheme-HemQ.

    Science.gov (United States)

    Hofbauer, Stefan; Dalla Sega, Marco; Scheiblbrandner, Stefan; Jandova, Zuzana; Schaffner, Irene; Mlynek, Georg; Djinović-Carugo, Kristina; Battistuzzi, Gianantonio; Furtmüller, Paul G; Oostenbrink, Chris; Obinger, Christian

    2016-09-27

    Recently, a novel pathway for heme b biosynthesis in Gram-positive bacteria has been proposed. The final poorly understood step is catalyzed by an enzyme called HemQ and includes two decarboxylation reactions leading from coproheme to heme b. Coproheme has been suggested to act as both substrate and redox active cofactor in this reaction. In the study presented here, we focus on HemQs from Listeria monocytogenes (LmHemQ) and Staphylococcus aureus (SaHemQ) recombinantly produced as apoproteins in Escherichia coli. We demonstrate the rapid and two-phase uptake of coproheme by both apo forms and the significant differences in thermal stability of the apo forms, coproheme-HemQ and heme b-HemQ. Reduction of ferric high-spin coproheme-HemQ to the ferrous form is shown to be enthalpically favored but entropically disfavored with standard reduction potentials of -205 ± 3 mV for LmHemQ and -207 ± 3 mV for SaHemQ versus the standard hydrogen electrode at pH 7.0. Redox thermodynamics suggests the presence of a pronounced H-bonding network and restricted solvent mobility in the heme cavity. Binding of cyanide to the sixth coproheme position is monophasic but relatively slow (∼1 × 10(4) M(-1) s(-1)). On the basis of the available structures of apo-HemQ and modeling of both loaded forms, molecular dynamics simulation allowed analysis of the interaction of coproheme and heme b with the protein as well as the role of the flexibility at the proximal heme cavity and the substrate access channel for coproheme binding and heme b release. Obtained data are discussed with respect to the proposed function of HemQ in monoderm bacteria.

  2. A Heme-based Redox Sensor in the Methanogenic Archaeon Methanosarcina acetivorans*

    Science.gov (United States)

    Molitor, Bastian; Stassen, Marc; Modi, Anuja; El-Mashtoly, Samir F.; Laurich, Christoph; Lubitz, Wolfgang; Dawson, John H.; Rother, Michael; Frankenberg-Dinkel, Nicole

    2013-01-01

    Based on a bioinformatics study, the protein MA4561 from the methanogenic archaeon Methanosarcina acetivorans was originally predicted to be a multidomain phytochrome-like photosensory kinase possibly binding open-chain tetrapyrroles. Although we were able to show that recombinantly produced and purified protein does not bind any known phytochrome chromophores, UV-visible spectroscopy revealed the presence of a heme tetrapyrrole cofactor. In contrast to many other known cytoplasmic heme-containing proteins, the heme was covalently attached via one vinyl side chain to cysteine 656 in the second GAF domain. This GAF domain by itself is sufficient for covalent attachment. Resonance Raman and magnetic circular dichroism data support a model of a six-coordinate heme species with additional features of a five-coordination structure. The heme cofactor is redox-active and able to coordinate various ligands like imidazole, dimethyl sulfide, and carbon monoxide depending on the redox state. Interestingly, the redox state of the heme cofactor has a substantial influence on autophosphorylation activity. Although reduced protein does not autophosphorylate, oxidized protein gives a strong autophosphorylation signal independent from bound external ligands. Based on its genomic localization, MA4561 is most likely a sensor kinase of a two-component system effecting regulation of the Mts system, a set of three homologous corrinoid/methyltransferase fusion protein isoforms involved in methyl sulfide metabolism. Consistent with this prediction, an M. acetivorans mutant devoid of MA4561 constitutively synthesized MtsF. On the basis of our results, we postulate a heme-based redox/dimethyl sulfide sensory function of MA4561 and propose to designate it MsmS (methyl sulfide methyltransferase-associated sensor). PMID:23661702

  3. Electronic structure of UCl5: A reexamination

    International Nuclear Information System (INIS)

    Soule, E.; Edelstein, N.

    1980-01-01

    On the basis of the absorption spectrum of UCl 5 recorded at 4.2 K, Leung and Poon attempted a determination of both the spin-orbit coupling constant and the crystal field parameters. Their parameters, however, led to a calculated g-tensor at variance with the position of the electron paramagnetic resonance line observed by Miyake et al. It was therefore attempted to simultaneously interpret both spectra (absorption and EPR), assuming the validity of the Newman superposition model, and taking the point symmetry group on each uranium of the (UCl 5 ) 2 dimer as C 2 sub(v). We obtain one and only one satisfactory solution, namely a set of parameters that reasonably reproduce the observed absorption peaks, and lead to the following principal values of the g-tensor: gx = 0.226 (unobservable); gy = 1.187; gz = 1.186. Therefore the paradox stemming from the apparent isotropy of the EPR signal for a species of low point symmetry is resolved. (orig.)

  4. Electronic structure of metal overlayers on rhodium

    International Nuclear Information System (INIS)

    Feibelman, P.J.; Hamann, D.R.

    1983-01-01

    We have evaluated work functions, surface core-level shifts, and surface band dispersions for clean, Ag-covered, and Pd-covered Rh(100) surfaces, and for clean and Ag-covered Rh(111). The calculations were performed self-consistently, using the surface-linearized augmented-plane-wave method. As expected from the Pauling electronegativities, Ag adsorption lowers the work function from the clean Rh value, by several tenths of an eV, while Pd has an almost negligible effect. The values calculated for the core-level shifts of various films are shown to correspond to expectations based on surface band narrowing and layerwise charge neutrality. Using the core-level shifts, we predict heat-of-adsorption differences (for Ag on Pd vs Ag on Rh, etc.) that are in quite good agreement with the empirical predictions of Miedema and Dorleijn. Finally, the chemical inactivity of the Ag-covered Rh surface is associated with the fact that, for that system, the outer-layer local density of states is essentially that of Ag, with a characteristically low value at the Fermi energy. On the other hand, the Pd-covered Rh surface should behave much like clean Rh with an extra electron per surface atom. The surface band dispersions for the Pd-covered and clean Rh surfaces are closely similar. This result contrasts sharply with the case of Pd-covered Nb, for which, because of the appreciable electronegativity difference, the Pd overlayer is effectively ''noble.''

  5. Electronic structure properties of UO2 as a Mott insulator

    Science.gov (United States)

    Sheykhi, Samira; Payami, Mahmoud

    2018-06-01

    In this work using the density functional theory (DFT), we have studied the structural, electronic and magnetic properties of uranium dioxide with antiferromagnetic 1k-, 2k-, and 3k-order structures. Ordinary approximations in DFT, such as the local density approximation (LDA) or generalized gradient approximation (GGA), usually predict incorrect metallic behaviors for this strongly correlated electron system. Using Hubbard term correction for f-electrons, LDA+U method, as well as using the screened Heyd-Scuseria-Ernzerhof (HSE) hybrid functional for the exchange-correlation (XC), we have obtained the correct ground-state behavior as an insulator, with band gaps in good agreement with experiment.

  6. New Insight into Carbon Nanotube Electronic Structure Selectivity

    Energy Technology Data Exchange (ETDEWEB)

    Sumpter, Bobby G [ORNL; Meunier, Vincent [ORNL; Jiang, Deen [ORNL

    2009-01-01

    The fundamental role of aryl diazonium salts for post synthesis selectivity of carbon nanotubes is investigated using extensive electronic structure calculations. The resulting understanding for diazonium salt based selective separation of conducting and semiconducting carbon nanotubes shows how the primary contributions come from the interplay between the intrinsic electronic structure of the carbon nanotubes and that of the anion of the salt. We demonstrate how the electronic transport properties change upon the formation of charge transfer complexes and upon their conversion into covalently attached functional groups. Our results are found to correlate well with experiments and provide for the first time an atomistic description for diazonium salt based chemical separation of carbon nanotubes

  7. Electronic structure of the copper oxides

    International Nuclear Information System (INIS)

    Pickett, W.E.; Cohen, R.E.; Singh, D.; Krakauer, H.

    1989-01-01

    Since the discovery of the high temperature superconducting copper oxides a great deal has been learned from experiment about their behavior. From the theoretical side, there continues to be developments both within the band picture and from the model Hamiltonian viewpoint emphasizing correlations. In this paper the authors discuss these complementary viewpoints in relation to some of the experimental data. Due to their background in the band structure area, they approach the discussion by evaluating which phenomena can be (or has been) accounted for by the standard band approach, and point out which properties appear to require more intricate treatments of correlation

  8. Electronic and geometric structures of calcium metaborates

    International Nuclear Information System (INIS)

    Baranovskij, V.I.; Lopatin, S.I.; Sizov, V.V.

    2000-01-01

    Calculations of geometric structure, vibration frequencies, ionization potentials and atomization energies of CaBO 2 and CaB 2 O 4 molecules were made. It is shown that linear conformations of the molecules are the most stable ones. In the metaborates studied calcium atom coordination with oxygen is a monodentate one, meanwhile CaB 2 O 4 can be considered as a Ca 2+ compound, whereas CaBO 2 - as a Ca + compound, which explains similarity of the molecule (from the viewpoint of its geometry, spectral and energy characteristics) to alkaline metal metaborates [ru

  9. Equilibrium and nonequilibrium solvation and solute electronic structure

    International Nuclear Information System (INIS)

    Kim, H.J.; Hynes, J.T.

    1990-01-01

    When a molecular solute is immersed in a polar and polarizable solvent, the electronic wave function of the solute system is altered compared to its vacuum value; the solute electronic structure is thus solvent-dependent. Further, the wave function will be altered depending upon whether the polarization of the solvent is or is not in equilibrium with the solute charge distribution. More precisely, while the solvent electronic polarization should be in equilibrium with the solute electronic wave function, the much more sluggish solvent orientational polarization need not be. We call this last situation non-equilibrium solvation. We outline a nonlinear Schroedinger equation approach to these issues

  10. Evidence for dynamic behavior of O2 in oxy-heme model compounds

    International Nuclear Information System (INIS)

    Montiel-Montoya, R.; Bill, E.; Trautwein, A.X.; Winkler, H.

    1986-01-01

    The authors have performed Moessbauer studies on several oxy-heme model compounds, and for two of them they have also derived the three dimensional structure from X-ray studies. The X-ray structure analysis of these model compounds provides the information that O 2 occupies three different sites in one and only two sites in the other. (Auth.)

  11. Structure and electronic properties of azadirachtin.

    Science.gov (United States)

    de Castro, Elton A S; de Oliveira, Daniel A B; Farias, Sergio A S; Gargano, Ricardo; Martins, João B L

    2014-02-01

    We performed a combined DFT and Monte Carlo (13)C NMR chemical-shift study of azadirachtin A, a triterpenoid that acts as a natural insect antifeedant. A conformational search using a Monte Carlo technique based on the RM1 semiempirical method was carried out in order to establish its preferred structure. The B3LYP/6-311++G(d,p), wB97XD/6-311++G(d,p), M06/6-311++G(d,p), M06-2X/6-311++G(d,p), and CAM-B3LYP/6-311++G(d,p) levels of theory were used to predict NMR chemical shifts. A Monte Carlo population-weighted average spectrum was produced based on the predicted Boltzmann contributions. In general, good agreement between experimental and theoretical data was obtained using both methods, and the (13)C NMR chemical shifts were predicted highly accurately. The geometry was optimized at the semiempirical level and used to calculate the NMR chemical shifts at the DFT level, and these shifts showed only minor deviations from those obtained following structural optimization at the DFT level, and incurred a much lower computational cost. The theoretical ultraviolet spectrum showed a maximum absorption peak that was mainly contributed by the tiglate group.

  12. Structural complexities in the active layers of organic electronics.

    Science.gov (United States)

    Lee, Stephanie S; Loo, Yueh-Lin

    2010-01-01

    The field of organic electronics has progressed rapidly in recent years. However, understanding the direct structure-function relationships between the morphology in electrically active layers and the performance of devices composed of these materials has proven difficult. The morphology of active layers in organic electronics is inherently complex, with heterogeneities existing across multiple length scales, from subnanometer to micron and millimeter range. A major challenge still facing the organic electronics community is understanding how the morphology across all of the length scales in active layers collectively determines the device performance of organic electronics. In this review we highlight experiments that have contributed to the elucidation of structure-function relationships in organic electronics and also point to areas in which knowledge of such relationships is still lacking. Such knowledge will lead to the ability to select active materials on the basis of their inherent properties for the fabrication of devices with prespecified characteristics.

  13. Interactions between 4-aminoquinoline and heme: Promising mechanism against Trypanosoma cruzi

    Directory of Open Access Journals (Sweden)

    Guilherme Curty Lechuga

    2016-12-01

    Full Text Available Chagas disease is a neglected tropical disease caused by the flagellated protozoan Trypanosoma cruzi. The current drugs used to treat this disease have limited efficacy and produce severe side effects. Quinolines, nitrogen heterocycle compounds that form complexes with heme, have a broad spectrum of antiprotozoal activity and are a promising class of new compounds for Chagas disease chemotherapy. In this study, we evaluated the activity of a series of 4-arylaminoquinoline-3-carbonitrile derivatives against all forms of Trypanosoma cruzi in vitro. Compound 1g showed promising activity against epimastigote forms when combined with hemin (IC50<1 μM, with better performance than benznidazole, the reference drug. This compound also inhibited the viability of trypomastigotes and intracellular amastigotes. The potency of 1g in combination with heme was enhanced against epimastigotes and trypomastigotes, suggesting a similar mechanism of action that occurs in Plasmodium spp. The addition of hemin to the culture medium increased trypanocidal activity of analog 1g without changing the cytotoxicity of the host cell, reaching an IC50 of 11.7 μM for trypomastigotes. The mechanism of action was demonstrated by the interaction of compound 1g with hemin in solution and prevention of heme peroxidation. Compound 1g and heme treatment induced alterations of the mitochondrion-kinetoplast complex in epimastigotes and trypomastigotes and also, accumulation of electron-dense deposits in amastigotes as visualized by transmission electron microscopy. The trypanocidal activity of 4-aminoquinolines and the elucidation of the mechanism involving interaction with heme is a neglected field of research, given the parasite's lack of heme biosynthetic pathway and the importance of this cofactor for parasite survival and growth. The results of this study can improve and guide rational drug development and combination treatment strategies.

  14. Interactions between 4-aminoquinoline and heme: Promising mechanism against Trypanosoma cruzi.

    Science.gov (United States)

    Lechuga, Guilherme Curty; Borges, Júlio Cesar; Calvet, Claudia Magalhães; de Araújo, Humberto Pinheiro; Zuma, Aline Araujo; do Nascimento, Samara Braga; Motta, Maria Cristina Machado; Bernardino, Alice Maria Rolim; Pereira, Mirian Claudia de Souza; Bourguignon, Saulo Cabral

    2016-12-01

    Chagas disease is a neglected tropical disease caused by the flagellated protozoan Trypanosoma cruzi. The current drugs used to treat this disease have limited efficacy and produce severe side effects. Quinolines, nitrogen heterocycle compounds that form complexes with heme, have a broad spectrum of antiprotozoal activity and are a promising class of new compounds for Chagas disease chemotherapy. In this study, we evaluated the activity of a series of 4-arylaminoquinoline-3-carbonitrile derivatives against all forms of Trypanosoma cruzi in vitro. Compound 1g showed promising activity against epimastigote forms when combined with hemin (IC50<1 μM), with better performance than benznidazole, the reference drug. This compound also inhibited the viability of trypomastigotes and intracellular amastigotes. The potency of 1g in combination with heme was enhanced against epimastigotes and trypomastigotes, suggesting a similar mechanism of action that occurs in Plasmodium spp. The addition of hemin to the culture medium increased trypanocidal activity of analog 1g without changing the cytotoxicity of the host cell, reaching an IC50 of 11.7 μM for trypomastigotes. The mechanism of action was demonstrated by the interaction of compound 1g with hemin in solution and prevention of heme peroxidation. Compound 1g and heme treatment induced alterations of the mitochondrion-kinetoplast complex in epimastigotes and trypomastigotes and also, accumulation of electron-dense deposits in amastigotes as visualized by transmission electron microscopy. The trypanocidal activity of 4-aminoquinolines and the elucidation of the mechanism involving interaction with heme is a neglected field of research, given the parasite's lack of heme biosynthetic pathway and the importance of this cofactor for parasite survival and growth. The results of this study can improve and guide rational drug development and combination treatment strategies. Copyright © 2016 The Authors. Published by Elsevier

  15. Conversion of a heme-based oxygen sensor to a heme oxygenase by hydrogen sulfide: effects of mutations in the heme distal side of a heme-based oxygen sensor phosphodiesterase (Ec DOS)

    Czech Academy of Sciences Publication Activity Database

    Du, Y.; Liu, G.; Yan, Y.; Huang, D.; Luo, W.; Martínková, M.; Man, Petr; Shimizu, T.

    2013-01-01

    Roč. 26, č. 5 (2013), s. 839-852 ISSN 0966-0844 Institutional support: RVO:61388971 Keywords : Heme oxygenase * Heme protein * Hydrogen sulfide Subject RIV: CE - Biochemistry Impact factor: 2.689, year: 2013

  16. Atomic and electronic structures of divacancy in graphene nanoribbons

    Energy Technology Data Exchange (ETDEWEB)

    Zhao Jun [College of Physical Science and Technology, Yangtze University, Jingzhou, Hubei 434023 (China); Zeng Hui, E-mail: zenghui@yangtzeu.edu.cn [College of Physical Science and Technology, Yangtze University, Jingzhou, Hubei 434023 (China); Wei Jianwei [School of Mathematics and Physics, Chongqing University of Technology, Chongqing 400054 (China)

    2012-01-15

    First principles calculations have been performed to investigate the electronic structures and transport properties of defective graphene nanoribbons (GNRs) in the presence of pentagon-octagon-pentagon (5-8-5) defects. Electronic band structure results reveal that 5-8-5 defects in the defective zigzag graphene nanoribbon (ZGNR) is unfavorable for electronic transport. However, such defects in the defective armchair graphene nanoribbon (AGNR) give rise to smaller band gap than that in the pristine AGNR, and eventually results in semiconductor to metal-like transition. The distinct roles of 5-8-5 defects in two kinds of edged-GNR are attributed to the different coupling between {pi}{sup Low-Asterisk} and {pi} subbands influenced by the defects. Our findings indicate the possibility of a new route to improve the electronic transport properties of graphene nanoribbons via tailoring the atomic structures by ion irradiation.

  17. Electronic structure of a graphene superlattice with massive Dirac fermions

    International Nuclear Information System (INIS)

    Lima, Jonas R. F.

    2015-01-01

    We study the electronic and transport properties of a graphene-based superlattice theoretically by using an effective Dirac equation. The superlattice consists of a periodic potential applied on a single-layer graphene deposited on a substrate that opens an energy gap of 2Δ in its electronic structure. We find that extra Dirac points appear in the electronic band structure under certain conditions, so it is possible to close the gap between the conduction and valence minibands. We show that the energy gap E g can be tuned in the range 0 ≤ E g  ≤ 2Δ by changing the periodic potential. We analyze the low energy electronic structure around the contact points and find that the effective Fermi velocity in very anisotropic and depends on the energy gap. We show that the extra Dirac points obtained here behave differently compared to previously studied systems

  18. Molecular hijacking of siroheme for the synthesis of heme and d1 heme.

    Science.gov (United States)

    Bali, Shilpa; Lawrence, Andrew D; Lobo, Susana A; Saraiva, Lígia M; Golding, Bernard T; Palmer, David J; Howard, Mark J; Ferguson, Stuart J; Warren, Martin J

    2011-11-08

    Modified tetrapyrroles such as chlorophyll, heme, siroheme, vitamin B(12), coenzyme F(430), and heme d(1) underpin a wide range of essential biological functions in all domains of life, and it is therefore surprising that the syntheses of many of these life pigments remain poorly understood. It is known that the construction of the central molecular framework of modified tetrapyrroles is mediated via a common, core pathway. Herein a further branch of the modified tetrapyrrole biosynthesis pathway is described in denitrifying and sulfate-reducing bacteria as well as the Archaea. This process entails the hijacking of siroheme, the prosthetic group of sulfite and nitrite reductase, and its processing into heme and d(1) heme. The initial step in these transformations involves the decarboxylation of siroheme to give didecarboxysiroheme. For d(1) heme synthesis this intermediate has to undergo the replacement of two propionate side chains with oxygen functionalities and the introduction of a double bond into a further peripheral side chain. For heme synthesis didecarboxysiroheme is converted into Fe-coproporphyrin by oxidative loss of two acetic acid side chains. Fe-coproporphyrin is then transformed into heme by the oxidative decarboxylation of two propionate side chains. The mechanisms of these reactions are discussed and the evolutionary significance of another role for siroheme is examined.

  19. Effects of Structural Correlations on Electronic Properties

    International Nuclear Information System (INIS)

    Pastawski, H.M.; Weisz, J.F.

    1984-01-01

    A one dimensional alloy model is treated in the nearest neighbour tight binding approximation in which the correlation of the atoms can be adjusted. The correlation can be changed from a situation in which there is a tendency for atoms to alternate to a situation in which the atoms are randomly located, consistent with a fixed concentration c for A c B 1-c . The results show that when there is short range order, at certain energies there is a tendency for localized states and formation of structure induced minimum in the density of states. The results for the ordered case are similar to those of Charge Density Wave (CDW). A smooth transition is carried out between this case and the randomly disordered case which behaves like the Anderson model for uncorrelated disorder. (M.W.O.) [pt

  20. The surface electronic structure of Y(0001)

    International Nuclear Information System (INIS)

    Searle, C.

    1998-12-01

    Yttrium has been grown epitaxially on W(110). The growth was monitored by using photoemission spectroscopy with a synchrotron radiation source. The film thickness has been gauged by the attenuation of the W 4f 7/2 bulk component. The films have been grown reproducibly and show a prominent surface state which is indicative of good order and low contamination. Angle-Resolved Ultra-Violet Photoemission Spectroscopy has been used to examine the valence band of these ultra-thin films. The films show a very different structure to the valence band of a bulk crystal of yttrium. The differences have been investigated by a series of model calculations using the LMASA-46 tight-binding LMTO program. The calculations suggest that the ultra-thin film surface state may be hybridised with a tungsten orbital having (x 2 - y 2 ) character. (author)

  1. Structural stability, electronic structure and mechanical properties of actinide carbides AnC (An = U, Np)

    International Nuclear Information System (INIS)

    Manikandan, M.; Santhosh, M.; Rajeswarapalanichamy, R.

    2016-01-01

    Ab initio calculations are performed to investigate the structural stability, electronic structure and mechanical properties of actinide carbides AnC (An=U, Np) for three different crystal structures, namely NaCl, CsCl and ZnS. Among the considered structures, NaCl structure is found to be the most stable structure for these carbides at normal pressure. A pressure induced structural phase transition from NaCl to ZnS is observed. The electronic structure reveals that these carbides are metals. The calculated elastic constants indicate that these carbides are mechanically stable at normal pressure.

  2. Electronic properties in a quantum well structure of Weyl semimetal

    International Nuclear Information System (INIS)

    You, Wen-Long; Zhou, Jiao-Jiao; Wang, Xue-Feng; Oleś, Andrzej M.

    2016-01-01

    We investigate the confined states and transport of three-dimensional Weyl electrons around a one-dimensional external rectangular electrostatic potential. The confined states with finite transverse wave vector exist at energies higher than the half well depth or lower than the half barrier height. The rectangular potential appears completely transparent to the normal incident electrons but not otherwise. The tunneling transmission coefficient is sensitive to their incident angle and shows resonant peaks when their energy coincides with the confined spectra. In addition, for the electrons in the conduction (valence) band through a potential barrier (well), the transmission spectrum has a gap of width increasing with the incident angle. Interestingly, the electron linear zero-temperature conductance over the potential can approach zero when the Fermi energy is aligned to the top and bottom energies of the potential, when only electron beams normal to the potential interfaces can pass through. The considered structure can be used to collimate the Weyl electron beams.

  3. Effect of electron emission on an ion sheath structure

    International Nuclear Information System (INIS)

    Mishra, M K; Phukan, A; Chakraborty, M

    2014-01-01

    This article reports on the variations of ion sheath structures due to the emission of both hot and cold electrons in the target plasma region of a double plasma device. The ion sheath is produced in front of a negatively biased plate. The plasma is produced by hot filament discharge in the source region, and no discharge is created in the target region of the device. The plate is placed in the target (diffused plasma) region where cold electron emitting filaments are present. These cold electrons are free from maintenance of discharge, which is sustained in the source region. The hot ionizing electrons are present in the source region. Three important parameters are changed by both hot and cold electrons i.e. plasma density, plasma potential and electron temperature. The decrease in plasma potential and the increase in plasma density lead to the contraction of the sheath. (paper)

  4. Kidney injury and heme oxygenase-1

    Directory of Open Access Journals (Sweden)

    Hai-xing MAI

    2012-02-01

    Full Text Available     Heme oxygenase-1 (HO-1 is one of the main pathways to degrade heme in mammals, and the main degradation products are free iron (Fe2+, carbon monoxide (CO, and bilirubin. Heme plays an important role in promoting cell survival, circulation of intracellular substrates, and immune regulation. Previous studies suggest that HO-1 pathway is an important internal factor in determining the susceptibility and severity of acute kidney injury (AKI. The induction of HO-1 expression can attenuate the severity of renal ischemia-reperfusion injury (IRI, and the inhibition of HO-1 expression will aggravate IRI. The present article summarizes the latest advances in research abroad and at home on protective mechanism by which HO-1 prevents AKI to further deepen our understanding of the role of HO-1 in the treatment of AKI.   

  5. Structure Identification in High-Resolution Transmission Electron Microscopic Images

    DEFF Research Database (Denmark)

    Vestergaard, Jacob Schack; Kling, Jens; Dahl, Anders Bjorholm

    2014-01-01

    A connection between microscopic structure and macroscopic properties is expected for almost all material systems. High-resolution transmission electron microscopy is a technique offering insight into the atomic structure, but the analysis of large image series can be time consuming. The present ...

  6. Electronic and chemical properties of graphene-based structures:

    DEFF Research Database (Denmark)

    Vanin, Marco

    In the present thesis several aspects of graphene-based structures have been investigated using density functional theory calculations to solve the electronic structure problem. A review of the implementation of a localized basis-set within the projector augmented wave method - the way of describ...... are attractive candidates although issues regarding the poisoning of the active site remain to be addressed....

  7. Electronic structure of palladium and its relation to uv spectroscopy

    DEFF Research Database (Denmark)

    Christensen, N.E.

    1976-01-01

    The electronic-energy-band structure of palladium has been calculated by means of the relativistic augmented-plane-wave method covering energies up to 30 eV above the Fermi level. The optical interband transitions producing structure in the dielectric function up to photon energies of 25 eV have ...

  8. The electron irradiation effects in different structures of diodes

    International Nuclear Information System (INIS)

    Li Quanfen; Wang Jiaxu

    1993-01-01

    This paper describes the different electron irradiation effects in different structures of diodes and the different results produced by different irradiation ways. From this work, we can know how to choose proper manufacture arts and comprehensive factors according to the structures of diodes and the irradiation conditions

  9. Electron vortex magnetic holes: A nonlinear coherent plasma structure

    Energy Technology Data Exchange (ETDEWEB)

    Haynes, Christopher T., E-mail: c.t.haynes@qmul.ac.uk; Burgess, David; Sundberg, Torbjorn [School of Physics and Astronomy, Queen Mary University of London, Mile End Road, London E1 4NS (United Kingdom); Camporeale, Enrico [Multiscale Dynamics, Centrum Wiskunde and Informatica (CWI), Amsterdam (Netherlands)

    2015-01-15

    We report the properties of a novel type of sub-proton scale magnetic hole found in two dimensional particle-in-cell simulations of decaying turbulence with a guide field. The simulations were performed with a realistic value for ion to electron mass ratio. These structures, electron vortex magnetic holes (EVMHs), have circular cross-section. The magnetic field depression is associated with a diamagnetic azimuthal current provided by a population of trapped electrons in petal-like orbits. The trapped electron population provides a mean azimuthal velocity and since trapping preferentially selects high pitch angles, a perpendicular temperature anisotropy. The structures arise out of initial perturbations in the course of the turbulent evolution of the plasma, and are stable over at least 100 electron gyroperiods. We have verified the model for the EVMH by carrying out test particle and PIC simulations of isolated structures in a uniform plasma. It is found that (quasi-)stable structures can be formed provided that there is some initial perpendicular temperature anisotropy at the structure location. The properties of these structures (scale size, trapped population, etc.) are able to explain the observed properties of magnetic holes in the terrestrial plasma sheet. EVMHs may also contribute to turbulence properties, such as intermittency, at short scale lengths in other astrophysical plasmas.

  10. Chemical modulation of electronic structure at the excited state

    Science.gov (United States)

    Li, F.; Song, C.; Gu, Y. D.; Saleem, M. S.; Pan, F.

    2017-12-01

    Spin-polarized electronic structures are the cornerstone of spintronics, and have thus attracted a significant amount of interest; in particular, researchers are looking into how to modulate the electronic structure to enable multifunctional spintronics applications, especially in half-metallic systems. However, the control of the spin polarization has only been predicted in limited two-dimensional systems with spin-polarized Dirac structures and is difficult to achieve experimentally. Here, we report the modulation of the electronic structure in the light-induced excited state in a typical half-metal, L a1 /2S r1 /2Mn O3 -δ . According to the spin-transport measurements, there appears a light-induced increase in magnetoresistance due to the enhanced spin scattering, which is closely associated with the excited spin polarization. Strikingly, the light-induced variation can be enhanced via alcohol processing and reduced by oxygen annealing. X-ray photoelectron spectroscopy measurements show that in the chemical process, a redox reaction occurs with a change in the valence of Mn. Furthermore, first-principles calculations reveal that the change in the valence of Mn alters the electronic structure and consequently modulates the spin polarization in the excited state. Our findings thus report a chemically tunable electronic structure, demonstrating interesting physics and the potential for multifunctional applications and ultrafast spintronics.

  11. Orbital approach to the electronic structure of solids

    CERN Document Server

    Canadell, Enric; Iung, Christophe

    2012-01-01

    This book provides an intuitive yet sound understanding of how structure and properties of solids may be related. The natural link is provided by the band theory approach to the electronic structure of solids. The chemically insightful concept of orbital interaction and the essential machinery of band theory are used throughout the book to build links between the crystal and electronic structure of periodic systems. In such a way, it is shown how important tools for understandingproperties of solids like the density of states, the Fermi surface etc. can be qualitatively sketched and used to ei

  12. Design Considerations for Optimized Lateral Spring Structures for Wearable Electronics

    KAUST Repository

    Hussain, Aftab M.

    2016-03-07

    The market for wearable electronics has been gaining momentum in the recent years. For completely electronic wearable textiles with integrated sensors, actuators, computing units and communication circuitry, it is important that there is significant stretchability. This stretchability can be obtained by introducing periodic stretchable structures between the electronic circuits. In this work, we derive the equations and constraints governing the stretchability in horseshoe lateral spring structures. We have derived the optimum design and the parameters therein, to help develop the best spring structures for a given stretchability. We have also developed a figure of merit, called area efficiency of stretchability, to compare all twodimensional stretchable systems. Finally, we experimentally verify the validity of our equations by fabricating a metal/polymer bilayer thin film based stretchable horseshoe lateral spring structures. We obtain a stretchability of 1.875 which is comparable to the theoretical maxima of 2.01 for the given parameters.

  13. Design Considerations for Optimized Lateral Spring Structures for Wearable Electronics

    KAUST Repository

    Hussain, Aftab M.; Hussain, Muhammad Mustafa

    2016-01-01

    The market for wearable electronics has been gaining momentum in the recent years. For completely electronic wearable textiles with integrated sensors, actuators, computing units and communication circuitry, it is important that there is significant stretchability. This stretchability can be obtained by introducing periodic stretchable structures between the electronic circuits. In this work, we derive the equations and constraints governing the stretchability in horseshoe lateral spring structures. We have derived the optimum design and the parameters therein, to help develop the best spring structures for a given stretchability. We have also developed a figure of merit, called area efficiency of stretchability, to compare all twodimensional stretchable systems. Finally, we experimentally verify the validity of our equations by fabricating a metal/polymer bilayer thin film based stretchable horseshoe lateral spring structures. We obtain a stretchability of 1.875 which is comparable to the theoretical maxima of 2.01 for the given parameters.

  14. Studies on electronic structure of GaN(0001) surface

    CERN Document Server

    Xie Chang Kun; Xu Fa Qiang; Deng Rui; Liu Feng; Yibulaxin, K

    2002-01-01

    An electronic structure investigation on GaN(0001) is reported. The authors employ a full-potential linearized augmented plane-wave (FPLAPW) approach to calculate the partial density of state, which is in agreement with previous experimental results. The effects of the Ga3d semi-core levels on the electronic structure of GaN are discussed. The valence-electronic structure of the wurtzite GaN(0001) surface is investigated using synchrotron radiation excited angle-resolved photoemission spectroscopy. The bulk bands dispersion along GAMMA A direction in the Brillouin zones is measured using normal-emission spectra by changing photon-energy. The band structure derived from authors' experimental data is compared well with the results of authors' FPLAPW calculation. Furthermore, off-normal emission spectra are also measured along the GAMMA K and GAMMA M directions. Two surface states are identified, and their dispersions are characterized

  15. Red meat and colon cancer : how dietary heme initiates hyperproliferation

    NARCIS (Netherlands)

    IJssennagger, N.

    2012-01-01

    Colorectal cancer is a leading cause of cancer deaths in Western countries. The risk to develop colorectal cancer is associated with the intake of red meat. Red meat contains the porphyrin pigment heme. Heme is an irritant for the colonic wall and it is previously shown that the addition of heme

  16. Heme oxygenase activity increases after exercise in healthy volunteers

    Science.gov (United States)

    AbstractHeme oxygenase (HO) is an essential, rate-limiting protein which participates in the catabolism of heme to iron, carbon monoxide (CO), and biliverdin. The alpha methene bridge carbon of the heme is eliminated as CO which can be measured as blood carboxyhemoglobin (COHb)....

  17. Up-regulation of A1M/α1-microglobulin in skin by heme and reactive oxygen species gives protection from oxidative damage.

    Science.gov (United States)

    Olsson, Magnus G; Allhorn, Maria; Larsson, Jörgen; Cederlund, Martin; Lundqvist, Katarina; Schmidtchen, Artur; Sørensen, Ole E; Mörgelin, Matthias; Akerström, Bo

    2011-01-01

    During bleeding the skin is subjected to oxidative insults from free heme and radicals, generated from extracellular hemoglobin. The lipocalin α(1)-microglobulin (A1M) was recently shown to have reductase properties, reducing heme-proteins and other substrates, and to scavenge heme and radicals. We investigated the expression and localization of A1M in skin and the possible role of A1M in the protection of skin tissue from damage induced by heme and reactive oxygen species. Skin explants, keratinocyte cultures and purified collagen I were exposed to heme, reactive oxygen species, and/or A1M and investigated by biochemical methods and electron microscopy. The results demonstrate that A1M is localized ubiquitously in the dermal and epidermal layers, and that the A1M-gene is expressed in keratinocytes and up-regulated after exposure to heme and reactive oxygen species. A1M inhibited the heme- and reactive oxygen species-induced ultrastructural damage, up-regulation of antioxidation and cell cycle regulatory genes, and protein carbonyl formation in skin and keratinocytes. Finally, A1M bound to purified collagen I (K(d) = 0.96×10(-6) M) and could inhibit and repair the destruction of collagen fibrils by heme and reactive oxygen species. The results suggest that A1M may have a physiological role in protection of skin cells and matrix against oxidative damage following bleeding.

  18. Electronic structure of the high-temperature oxide superconductors

    International Nuclear Information System (INIS)

    Pickett, W.E.

    1989-01-01

    Since the discovery of superconductivity above 30 K by Bednorz and Mueller in the La copper oxide system, the critical temperature has been raised to 90 K in YBa 2 Cu 3 O 7 and to 110 and 125 K in Bi-based and Tl-based copper oxides, respectively. In the two years since this Nobel-prize-winning discovery, a large number of electronic structure calculations have been carried out as a first step in understanding the electronic properties of these materials. In this paper these calculations (mostly of the density-functional type) are gathered and reviewed, and their results are compared with the relevant experimental data. The picture that emerges is one in which the important electronic states are dominated by the copper d and oxygen p orbitals, with strong hybridization between them. Photon, electron, and positron spectroscopies provide important information about the electronic states, and comparison with electronic structure calculations indicates that, while many features can be interpreted in terms of existing calculations, self-energy corrections (''correlations'') are important for a more detailed understanding. The antiferromagnetism that occurs in some regions of the phase diagram poses a particularly challenging problem for any detailed theory. The study of structural stability, lattice dynamics, and electron-phonon coupling in the copper oxides is also discussed. Finally, a brief review is given of the attempts so far to identify interaction constants appropriate for a model Hamiltonian treatment of many-body interactions in these materials

  19. Dibromine radical anion reactions with heme enzymes

    International Nuclear Information System (INIS)

    Gebicka, L.; Gebicki, J.L.

    1996-01-01

    Reactions of Br 2 radical anion with heme enzymes, catalase horseradish peroxidase, have been studied by pulse radiolysis. It has been found that Br 2 - does not react with the heme centre of investigated enzymes. Dibromine radical anion reacts with tryptophan residues of catalase without any influence on the activity of catalase. It is suggested that in pulse radiolysis studies, where horseradish peroxidase is at about tenfold excess toward Br 2 - , the enzyme is modified rather by Br 2 , than by Br 2 - . (author). 26 refs., 3 figs

  20. Standardized structure of electronic records for information exchange

    International Nuclear Information System (INIS)

    Galabova, Sevdalina; Trencheva, Tereza; Trenchev, Ivan

    2009-01-01

    In the paper is presented the structure of the electronic record whose form is standardized in ISO 2709:2008. This International Standard describes a generalized structure, a framework designed specially for communications between data processing systems and not for use as a processing format within systems.Basic terms are defined as follows: character, data field, directory, directory map, field, field separator etc. It’s presented the general structure of a record. The application analysis of this structure shows the effective information exchange in the widest range.The purpose of this research is to find out advantages and structure of the information exchange format standardized in ISO 2709:2008. Key words: Standardized structure, electronic records, exchange formats, data field, directory, directory map, indicators, identifiers

  1. The stabilities and electron structures of Al-Mg clusters with 18 and 20 valence electrons

    Science.gov (United States)

    Yang, Huihui; Chen, Hongshan

    2017-07-01

    The spherical jellium model predicts that metal clusters having 18 and 20 valence electrons correspond to the magic numbers and will show specific stabilities. We explore in detail the geometric structures, stabilities and electronic structures of Al-Mg clusters containing 18 and 20 valence electrons by using genetic algorithm combined with density functional theories. The stabilities of the clusters are governed by the electronic configurations and Mg/Al ratios. The clusters with lower Mg/Al ratios are more stable. The molecular orbitals accord with the shell structures predicted by the jellium model but the 2S level interweaves with the 1D levels and the 2S and 1D orbitals form a subgroup. The clusters having 20 valence electrons form closed 1S21P61D102S2 shells and show enhanced stability. The Al-Mg clusters with a valence electron count of 18 do not form closed shells because one 1D orbital is unoccupied. The ionization potential and electron affinity are closely related to the electronic configurations; their values are determined by the subgroups the HOMO or LUMO belong to. Supplementary material in the form of one pdf file available from the Journal web page at http://https://doi.org/10.1140/epjd/e2017-80042-9

  2. Proton NMR investigation of heme pocket mobility in hemoglobin via hydrogen isotope exchange kinetics

    International Nuclear Information System (INIS)

    Han, K.

    1985-01-01

    Dynamic mobility of heme cavity, the active site of Hb, was investigated by analyzing the hydrogen isotope exchange kinetics of the proximal histidyl ring NH of various kinds of Hbs with the aid of the high field Fourier Transform 1 H NMR spectroscopy. The exchange reaction occurs faster in oxy or R-state Hb than in deoxy or T-state Hb and there exists a good correlation between the oxygen affinity of Hb and the heme pocket mobility reflected in the hydrogen exchange rate. The effect of pH on the exchange is dramatically different for the two subunits of Hb A. Studying the exchange characteristics of mutant Hbs and chemically modified Hbs not only showed the existence of three well-defined localized paths for transmission of conformational changes between different heme pockets through a 1 b 2 subunit interface, but also indicated that the heme pocket mobility is regulated by the quaternary state of Hb as well as by the ligation state of Hb. Finally, the effect of the quaternary state on the heme pocket mobility is separated from that of the ligation by following the exchange reactions in Hbs where only their quaternary structure transition can be achieved without changing their ligation states by adjusting experimental conditions such as adding inositol hexaphosphate

  3. Heme Exporter FLVCR1a Regulates Heme Synthesis and Degradation and Controls Activity of Cytochromes P450

    OpenAIRE

    Vinchi, Francesca; Ingoglia, Giada; Chiabrando, Deborah; Mercurio, Sonia; Turco, Emilia; Silengo, Lorenzo; Altruda, Fiorella; Tolosano, Emanuela

    2014-01-01

    Background & Aims The liver has one of the highest rates of heme synthesis of any organ. More than 50% of the heme synthesized in the liver is used for synthesis of P450 enzymes, which metabolize exogenous and endogenous compounds that include natural products, hormones, drugs, and carcinogens. Feline leukemia virus subgroup C cellular receptor 1a (FLVCR1a) is plasma membrane heme exporter that is ubiquitously expressed and controls intracellular heme content in hematopoietic lineages. We inv...

  4. Modeling of the atomic and electronic structures of interfaces

    International Nuclear Information System (INIS)

    Sutton, A.P.

    1988-01-01

    Recent tight binding and Car-Parrinello simulations of grain boundaries in semiconductors are reviewed. A critique is given of some models of embrittlement that are based on electronic structure considerations. The structural unit model of grain boundary structure is critically assessed using some results for mixed tilt and twist grain boundaries. A new method of characterizing interfacial structure in terms of bond angle distribution functions is described. A new formulation of thermodynamic properties of interfaces is presented which focusses on the local atomic environment. Effective, temperature dependent N-body atomic interactions are derived for studying grain boundary structure at elevated temperature

  5. Extremely large magnetoresistance and electronic structure of TmSb

    Science.gov (United States)

    Wang, Yi-Yan; Zhang, Hongyun; Lu, Xiao-Qin; Sun, Lin-Lin; Xu, Sheng; Lu, Zhong-Yi; Liu, Kai; Zhou, Shuyun; Xia, Tian-Long

    2018-02-01

    We report the magnetotransport properties and the electronic structure of TmSb. TmSb exhibits extremely large transverse magnetoresistance and Shubnikov-de Haas (SdH) oscillation at low temperature and high magnetic field. Interestingly, the split of Fermi surfaces induced by the nonsymmetric spin-orbit interaction has been observed from SdH oscillation. The analysis of the angle-dependent SdH oscillation illustrates the contribution of each Fermi surface to the conductivity. The electronic structure revealed by angle-resolved photoemission spectroscopy (ARPES) and first-principles calculations demonstrates a gap at the X point and the absence of band inversion. Combined with the trivial Berry phase extracted from SdH oscillation and the nearly equal concentrations of electron and hole from Hall measurements, it is suggested that TmSb is a topologically trivial semimetal and the observed XMR originates from the electron-hole compensation and high mobility.

  6. Electronic Structure of Large-Scale Graphene Nanoflakes

    OpenAIRE

    Hu, Wei; Lin, Lin; Yang, Chao; Yang, Jinlong

    2014-01-01

    With the help of the recently developed SIESTA-PEXSI method [J. Phys.: Condens. Matter \\textbf{26}, 305503 (2014)], we perform Kohn-Sham density functional theory (DFT) calculations to study the stability and electronic structure of hexagonal graphene nanoflakes (GNFs) with up to 11,700 atoms. We find the electronic properties of GNFs, including their cohesive energy, HOMO-LUMO energy gap, edge states and aromaticity, depend sensitively on the type of edges (ACGNFs and ZZGNFs), size and the n...

  7. Human enamel structure studied by high resolution electron microscopy

    International Nuclear Information System (INIS)

    Wen, S.L.

    1989-01-01

    Human enamel structural features are characterized by high resolution electron microscopy. The human enamel consists of polycrystals with a structure similar to Ca10(PO4)6(OH)2. This article describes the structural features of human enamel crystal at atomic and nanometer level. Besides the structural description, a great number of high resolution images are included. Research into the carious process in human enamel is very important for human beings. This article firstly describes the initiation of caries in enamel crystal at atomic and unit-cell level and secondly describes the further steps of caries with structural and chemical demineralization. The demineralization in fact, is the origin of caries in human enamel. The remineralization of carious areas in human enamel has drawn more and more attention as its potential application is realized. This process has been revealed by high resolution electron microscopy in detail in this article. On the other hand, the radiation effects on the structure of human enamel are also characterized by high resolution electron microscopy. In order to reveal this phenomenon clearly, a great number of electron micrographs have been shown, and a physical mechanism is proposed. 26 references

  8. Study of electronic and structural properties of CaS

    International Nuclear Information System (INIS)

    Mirfenderski, M.; Akbarzdeh, H.; Mokhtari, A.

    2003-01-01

    The electronic and structural properties of CaS are calculated using full potential linearized augmented plane wave method within the local density approximation and generalized gradient approximation for the exchange -correlation energy. For both structures, NaCl structure (B1) and CsCl structure (B2), the obtained values for lattice parameters, bulk modulus and its pressure derivative and transition pressure are in reasonable agreement with the experimental values. For electronic properties, the obtained value for band gap is smaller than the experimental value as well as other calculated results based on density functional theory. Engel and Vosko calculated an exchange potential for some atoms within the so-called optimize-potential model and then used the virial relation and constructed a new exchange-correlation functional. We used that functional and obtained reasonable results for band gap. Finally we investigated the possibility for a third phase ( Zinc Blend structure) for this crystal

  9. Ceramic materials on perovskite-type structure for electronic applications

    International Nuclear Information System (INIS)

    Surowiak, Z.

    2003-01-01

    Ceramic materials exhibiting the perovskite-type structure constitute among others, resource base for many fields of widely understood electronics (i.e., piezoelectronics, accustoelectronics, optoelectronics, computer science, tele- and radioelectronics etc.). Most often they are used for fabrication of different type sensors (detectors), transducers, ferroelectric memories, limiters of the electronic current intensity, etc., and hence they are numbered among so-called intelligent materials. Prototype structure of this group of materials is the structure of the mineral called perovskite (CaTiO 3 ). By means of right choice of the chemical composition of ABO 3 and deforming the regular perovskite structure (m3m) more than 5000 different chemical compounds and solid solutions exhibiting the perovskite-type structure have been fabricated. The concept of perovskite functional ceramics among often things ferroelectric ceramics, pyroelectric ceramics, piezoelectric ceramics, electrostrictive ceramics, posistor ceramics, superconductive ceramics and ferromagnetic ceramics. New possibilities of application of the perovskite-type ceramics are opened by nanotechnology. (author)

  10. Electron confinement in thin metal films. Structure, morphology and interactions

    Energy Technology Data Exchange (ETDEWEB)

    Dil, J.H.

    2006-05-15

    This thesis investigates the interplay between reduced dimensionality, electronic structure, and interface effects in ultrathin metal layers (Pb, In, Al) on a variety of substrates (Si, Cu, graphite). These layers can be grown with such a perfection that electron confinement in the direction normal to the film leads to the occurrence of quantum well states in their valence bands. These quantum well states are studied in detail, and their behaviour with film thickness, on different substrates, and other parameters of growth are used here to characterise a variety of physical properties of such nanoscale systems. The sections of the thesis deal with a determination of quantum well state energies for a large data set on different systems, the interplay between film morphology and electronic structure, and the influence of substrate electronic structure on their band shape; finally, new ground is broken by demonstrating electron localization and correlation effects, and the possibility to measure the influence of electron-phonon coupling in bulk bands. (orig.)

  11. Atomic and electronic structure of exfoliated black phosphorus

    International Nuclear Information System (INIS)

    Wu, Ryan J.; Topsakal, Mehmet; Jeong, Jong Seok; Wentzcovitch, Renata M.; Mkhoyan, K. Andre; Low, Tony; Robbins, Matthew C.; Haratipour, Nazila; Koester, Steven J.

    2015-01-01

    Black phosphorus, a layered two-dimensional crystal with tunable electronic properties and high hole mobility, is quickly emerging as a promising candidate for future electronic and photonic devices. Although theoretical studies using ab initio calculations have tried to predict its atomic and electronic structure, uncertainty in its fundamental properties due to a lack of clear experimental evidence continues to stymie our full understanding and application of this novel material. In this work, aberration-corrected scanning transmission electron microscopy and ab initio calculations are used to study the crystal structure of few-layer black phosphorus. Directly interpretable annular dark-field images provide a three-dimensional atomic-resolution view of this layered material in which its stacking order and all three lattice parameters can be unambiguously identified. In addition, electron energy-loss spectroscopy (EELS) is used to measure the conduction band density of states of black phosphorus, which agrees well with the results of density functional theory calculations performed for the experimentally determined crystal. Furthermore, experimental EELS measurements of interband transitions and surface plasmon excitations are also consistent with simulated results. Finally, the effects of oxidation on both the atomic and electronic structure of black phosphorus are analyzed to explain observed device degradation. The transformation of black phosphorus into amorphous PO 3 or H 3 PO 3 during oxidation may ultimately be responsible for the degradation of devices exposed to atmosphere over time

  12. Atomic and electronic structure of exfoliated black phosphorus

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Ryan J.; Topsakal, Mehmet; Jeong, Jong Seok; Wentzcovitch, Renata M.; Mkhoyan, K. Andre, E-mail: mkhoyan@umn.edu [Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455 (United States); Low, Tony; Robbins, Matthew C.; Haratipour, Nazila; Koester, Steven J. [Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, Minnesota 55455 (United States)

    2015-11-15

    Black phosphorus, a layered two-dimensional crystal with tunable electronic properties and high hole mobility, is quickly emerging as a promising candidate for future electronic and photonic devices. Although theoretical studies using ab initio calculations have tried to predict its atomic and electronic structure, uncertainty in its fundamental properties due to a lack of clear experimental evidence continues to stymie our full understanding and application of this novel material. In this work, aberration-corrected scanning transmission electron microscopy and ab initio calculations are used to study the crystal structure of few-layer black phosphorus. Directly interpretable annular dark-field images provide a three-dimensional atomic-resolution view of this layered material in which its stacking order and all three lattice parameters can be unambiguously identified. In addition, electron energy-loss spectroscopy (EELS) is used to measure the conduction band density of states of black phosphorus, which agrees well with the results of density functional theory calculations performed for the experimentally determined crystal. Furthermore, experimental EELS measurements of interband transitions and surface plasmon excitations are also consistent with simulated results. Finally, the effects of oxidation on both the atomic and electronic structure of black phosphorus are analyzed to explain observed device degradation. The transformation of black phosphorus into amorphous PO{sub 3} or H{sub 3}PO{sub 3} during oxidation may ultimately be responsible for the degradation of devices exposed to atmosphere over time.

  13. Momentum space analysis of the electronic structure of biphenyl

    International Nuclear Information System (INIS)

    Morini, F; Shojaei, S H Reza; Deleuze, M S

    2014-01-01

    The results of a yet to come experimental study of the electronic structure of biphenyl employing electron momentum spectroscopy (EMS) have been theoretically predicted, taking into account complications such as structural mobility in the electronic ground state, electronic correlation and relaxation, and a dispersion of the inner-valence ionization intensity to electronically excited (shake-up) configurations in the cation. The main purpose of this work is to explore the current limits of EMS in unraveling details of the molecular structure, namely the torsional characteristics of large and floppy aromatic molecules. At the benchmark ADC(3)/cc-pVDZ level of theory, the influence of the twist angle between the two phenyl rings is found to be extremely limited, except for individual orbital momentum profiles corresponding to ionization lines at electron binding energies ranging from 15 to 18 eV. When taking band overlap effects into account, this influence is deceptively far too limited to allow for any experimental determination of the torsional characteristics of biphenyl by means of EMS. (paper)

  14. Quasiparticle GW calculations within the GPAW electronic structure code

    DEFF Research Database (Denmark)

    Hüser, Falco

    The GPAW electronic structure code, developed at the physics department at the Technical University of Denmark, is used today by researchers all over the world to model the structural, electronic, optical and chemical properties of materials. They address fundamental questions in material science...... and use their knowledge to design new materials for a vast range of applications. Todays hottest topics are, amongst many others, better materials for energy conversion (e.g. solar cells), energy storage (batteries) and catalysts for the removal of environmentally dangerous exhausts. The mentioned...... properties are to a large extent governed by the physics on the atomic scale, that means pure quantum mechanics. For many decades, Density Functional Theory has been the computational method of choice, since it provides a fairly easy and yet accurate way of determining electronic structures and related...

  15. A multipole acceptability criterion for electronic structure theory

    International Nuclear Information System (INIS)

    Schwegler, E.; Challacombe, M.; Head-Gordon, M.

    1998-01-01

    Accurate and computationally inexpensive estimates of multipole expansion errors are crucial to the success of several fast electronic structure methods. In this paper, a new nonempirical multipole acceptability criterion is described that is directly applicable to expansions of high order moments. Several model calculations typical of electronic structure theory are presented to demonstrate its performance. For cases involving small translation distances, accuracies are increased by up to five orders of magnitude over an empirical criterion. The new multipole acceptance criterion is on average within an order of magnitude of the exact expansion error. Use of the multipole acceptance criterion in hierarchical multipole based methods as well as in traditional electronic structure methods is discussed. copyright 1998 American Institute of Physics

  16. Structural and electronic properties of L-amino acids

    Science.gov (United States)

    Tulip, P. R.; Clark, S. J.

    2005-05-01

    The structural and electronic properties of four L-amino acids alanine, leucine, isoleucine, and valine have been investigated using density functional theory (DFT) and the generalized gradient approximation. Within the crystals, it is found that the constituent molecules adopt zwitterionic configurations, in agreement with experimental work. Lattice constants are found to be in good agreement with experimentally determined values, although certain discrepancies do exist due to the description of van der Waals interactions. We find that these materials possess wide DFT band gaps in the region of 5 eV, with electrons highly localized to the constituent molecules. It is found that the main mechanisms behind crystal formation are dipolar interactions and hydrogen bonding of a primarily electrostatic character, in agreement with current biochemical understanding of these systems. The electronic structure suggests that the amine and carboxy functional groups are dominant in determining band structure.

  17. Electron transfer reactions in structural units of copper proteins

    International Nuclear Information System (INIS)

    Faraggi, M.

    1975-01-01

    In previous pulse radiolysis studies it was suggested that the reduction of the Cu(II) ions in copper proteins by the hydrated electron is a multi-step electron migration process. The technique has been extended to investigate the reduction of some structural units of these proteins. These studies include: the reaction of the hydrated electron with peptides, the reaction of the disulphide bridge with formate radical ion and radicals produced by the reduction of peptides, and the reaction of Cu(II)-peptide complex with esub(aq)sup(-) and CO 2 - . Using these results the reduction mechanism of copper and other proteins will be discussed. (author)

  18. Electronic structure of deep impurity centers in silicon

    International Nuclear Information System (INIS)

    Oosten, A.B. van.

    1989-01-01

    This thesis reports an experimental study of deep level impurity centers in silicon, with much attention for theoretical interpretation of the data. A detailed picture of the electronic structure of several centers was obtained by magnetic resonance techniques, such as electron paramagnetic resonance (EPR), electron-nuclear double resonance (ENDOR) and field scanned ENDOR (FSE). The thesis consists of two parts. The first part deals with chalcogen (sulfur, selenium and tellurium) related impurities, which are mostly double donors. The second part is about late transition metal (nickel, palladium and platinum) impurities, which are single (Pd,Pt) or double (Ni) acceptor centers. (author). 155 refs.; 51 figs.; 23 tabs

  19. Regiospecificity determinants of human heme oxygenase: differential NADPH- and ascorbate-dependent heme cleavage by the R183E mutant.

    Science.gov (United States)

    Wang, Jinling; Lad, Latesh; Poulos, Thomas L; Ortiz de Montellano, Paul R

    2005-01-28

    The ability of the human heme oxygenase-1 (hHO-1) R183E mutant to oxidize heme in reactions supported by either NADPH-cytochrome P450 reductase or ascorbic acid has been compared. The NADPH-dependent reaction, like that of wild-type hHO-1, yields exclusively biliverdin IXalpha. In contrast, the R183E mutant with ascorbic acid as the reductant produces biliverdin IXalpha (79 +/- 4%), IXdelta (19 +/- 3%), and a trace of IXbeta. In the presence of superoxide dismutase and catalase, the yield of biliverdin IXdelta is decreased to 8 +/- 1% with a corresponding increase in biliverdin IXalpha. Spectroscopic analysis of the NADPH-dependent reaction shows that the R183E ferric biliverdin complex accumulates, because reduction of the iron, which is required for sequential iron and biliverdin release, is impaired. Reversal of the charge at position 183 makes reduction of the iron more difficult. The crystal structure of the R183E mutant, determined in the ferric and ferrous-NO bound forms, shows that the heme primarily adopts the same orientation as in wild-type hHO-1. The structure of the Fe(II).NO complex suggests that an altered active site hydrogen bonding network supports catalysis in the R183E mutant. Furthermore, Arg-183 contributes to the regiospecificity of the wild-type enzyme, but its contribution is not critical. The results indicate that the ascorbate-dependent reaction is subject to a lower degree of regiochemical control than the NADPH-dependent reaction. Ascorbate may be able to reduce the R183E ferric and ferrous dioxygen complexes in active site conformations that cannot be reduced by NADPH-cytochrome P450 reductase.

  20. Photoelectron spectra and electronic structure of some spiroborate complexes

    Energy Technology Data Exchange (ETDEWEB)

    Vovna, V.I.; Tikhonov, S.A.; Lvov, I.B., E-mail: lvov.ib@dvfu.ru; Osmushko, I.S.; Svistunova, I.V.; Shcheka, O.L.

    2014-12-15

    Highlights: • The electronic structure of three spiroborate complexes—boron 1,2-dioxyphenylene β-diketonates has been investigated. • UV and X-ray photoelectron spectra have been interpreted. • DFT calculations have been used for interpretation of spectral bands. • The binding energy of nonequivalent carbon and oxygen atoms were measured. • The structure of X-ray photoelectron spectra of the valence electrons is in good agreement with the energies and composition of Kohn–Sham orbitals. - Abstract: The electronic structure of the valence and core levels of three spiroborate complexes – boron 1,2-dioxyphenylene β-diketonates – has been investigated by methods of UV and X-ray photoelectron spectroscopy and quantum chemical density functional theory. The ionization energy of π- and n-orbitals of the dioxyphenylene fragment and β-diketonate ligand were measured from UV photoelectron spectra. This made it possible to determine the effect of substitution of one or two methyl groups by the phenyl in diketone on the electronic structure of complexes. The binding energy of nonequivalent carbon and oxygen atoms were measured from X-ray photoelectron spectra. The results of calculations of the energy of the valence orbitals of complexes allowed us to refer bands observed in the spectra of the valence electrons to the 2s-type levels of carbon and oxygen.

  1. Mononuclear non-heme iron(III)

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 123; Issue 2. Mononuclear non-heme iron(III) complexes of linear and tripodal tridentate ligands as functional models for catechol dioxygenases: Effect of -alkyl substitution on regioselectivity and reaction rate. Mallayan Palaniandavar Kusalendiran Visvaganesan.

  2. Heme pathway evolution in kinetoplastid protists

    Czech Academy of Sciences Publication Activity Database

    Cenci, U.; Moog, D.; Curtis, B.A.; Tanifuji, G.; Eme, L.; Lukeš, Julius; Archibald, J.M.

    2016-01-01

    Roč. 16, MAY 18 (2016), č. článku 109. ISSN 1471-2148 Institutional support: RVO:60077344 Keywords : heme * kinetoplastea * Paramoeba pemaquidensis * Perkinsela * evolution * endosymbiosis * Prokinetoplastina * lateral gene transfer Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.221, year: 2016

  3. Electronic structure of ordered and disordered Fe sub 3 Pt

    CERN Document Server

    Major, Z; Jarlborg, T; Bruno, E; Ginatempo, B; Staunton, J B; Poulter, J

    2003-01-01

    The electronic structure of invar alloys (i.e. materials in which the near absence of thermal expansion is observed) has been the focus of much study, owing both to the technological applications of these materials and interest in the fundamental mechanism that is responsible for the effect. Here, calculations of the magnetic Compton profiles are presented for ordered and disordered Fe sub 3 Pt alloys. Using linear muffin-tin orbital and KKR methods, the latter incorporating the coherent potential approximation to describe the substitutional disorder, the electronic band structure and measurable quantities such as the Fermi surface topology are presented.

  4. Band structure and unconventional electronic topology of CoSi

    Science.gov (United States)

    Pshenay-Severin, D. A.; Ivanov, Y. V.; Burkov, A. A.; Burkov, A. T.

    2018-04-01

    Semimetals with certain crystal symmetries may possess unusual electronic structure topology, distinct from that of the conventional Weyl and Dirac semimetals. Characteristic property of these materials is the existence of band-touching points with multiple (higher than two-fold) degeneracy and nonzero Chern number. CoSi is a representative of this group of materials exhibiting the so-called ‘new fermions’. We report on an ab initio calculation of the electronic structure of CoSi using density functional methods, taking into account the spin-orbit interactions. The linearized \

  5. Comparison of electronic structure between monolayer silicenes on Ag (111)

    Science.gov (United States)

    Chun-Liang, Lin; Ryuichi, Arafune; Maki, Kawai; Noriaki, Takagi

    2015-08-01

    The electronic structures of monolayer silicenes (4 × 4 and ) grown on Ag (111) surface are studied by scanning tunneling spectroscopy (STS) and density functional theory (DFT) calculations. While both phases have similar electronic structures around the Fermi level, significant differences are observed in the higher energy unoccupied states. The DFT calculations show that the contributions of Si 3pz orbitals to the unoccupied states are different because of their different buckled configurations. Project supported by the Ministry of Education, Culture, Sports, Science and Technology (MEXT) through Grants-in-Aid for Scientific Research (Grant Nos. 24241040 and 25110008) and the World Premier International Research Center Initiative (WPI), MEXT, Japan.

  6. Solving complex and disordered surface structures with electron diffraction

    International Nuclear Information System (INIS)

    Van Hove, M.A.

    1987-10-01

    The past of surface structure determination with low-energy electron diffraction (LEED) will be briefly reviewed, setting the stage for a discussion of recent and future developments. The aim of these developments is to solve complex and disordered surface structures. Some efficient solutions to the theoretical and experimental problems will be presented. Since the theoretical problems dominate, the emphasis will be on theoretical approaches to the calculation of the multiple scattering of electrons through complex and disordered surfaces. 49 refs., 13 figs., 1 tab

  7. Electromagnetic Structure and Electron Acceleration in Shock–Shock Interaction

    Energy Technology Data Exchange (ETDEWEB)

    Nakanotani, Masaru [Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, 6-1 Kasuga-Koen, Kasuga, Fukuoka, 816-8580 (Japan); Matsukiyo, Shuichi; Hada, Tohru [Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-Koen, Kasuga, Fukuoka, 816-8580 (Japan); Mazelle, Christian X., E-mail: nakanot@esst.kyushu-u.ac.jp [IRAP, Université Paul Sabatier Toulouse III-CNRS, F-31028 Toulouse Cedex 4 (France)

    2017-09-10

    A shock–shock interaction is investigated by using a one-dimensional full particle-in-cell simulation. The simulation reproduces the collision of two symmetrical high Mach number quasi-perpendicular shocks. The basic structure of the shocks and ion dynamics is similar to that obtained by previous hybrid simulations. The new aspects obtained here are as follows. Electrons are already strongly accelerated before the two shocks collide through multiple reflection. The reflected electrons self-generate waves upstream between the two shocks before they collide. The waves far upstream are generated through the right-hand resonant instability with the anomalous Doppler effect. The waves generated near the shock are due to firehose instability and have much larger amplitudes than those due to the resonant instability. The high-energy electrons are efficiently scattered by the waves so that some of them gain large pitch angles. Those electrons can be easily reflected at the shock of the other side. The accelerated electrons form a power-law energy spectrum. Due to the accelerated electrons, the pressure of upstream electrons increases with time. This appears to cause the deceleration of the approaching shock speed. The accelerated electrons having sufficiently large Larmor radii are further accelerated through the similar mechanism working for ions when the two shocks are colliding.

  8. Pilot-scale tests of HEME and HEPA dissolution process

    Energy Technology Data Exchange (ETDEWEB)

    Qureshi, Z.H.; Strege, D.K.

    1994-06-01

    A series of pilot-scale demonstration tests for the dissolution of High Efficiency Mist Eliminators (HEME`s) and High Efficiency Particulate Airfilters (HEPA) were performed on a 1/5th linear scale. These fiberglass filters are to be used in the Defense Waste Processing Facility (DWPF) to decontaminate the effluents from the off-gases generated during the feed preparation process and vitrification. When removed, these filters will be dissolved in the Decontamination Waste Treatment Tank (DWTT) using 5 wt% NaOH solution. The contaminated fiberglass is converted to an aqueous stream which will be transferred to the waste tanks. The filter metal structure will be rinsed with process water before its disposal as low-level solid waste. The pilot-scale study reported here successfully demonstrated a simple one step process using 5 wt% NaOH solution. The proposed process requires the installation of a new water spray ring with 30 nozzles. In addition to the reduced waste generated, the total process time is reduced to 48 hours only (66% saving in time). The pilot-scale tests clearly demonstrated that the dissolution process of HEMEs has two stages - chemical digestion of the filter and mechanical erosion of the digested filter. The digestion is achieved by a boiling 5 wt% caustic solutions, whereas the mechanical break down of the digested filter is successfully achieved by spraying process water on the digested filter. An alternate method of breaking down the digested filter by increased air sparging of the solution was found to be marginally successful are best. The pilot-scale tests also demonstrated that the products of dissolution are easily pumpable by a centrifugal pump.

  9. The Chemistry and Biochemistry of Heme c: Functional Bases for Covalent Attachment

    OpenAIRE

    Bowman, Sarah E. J.; Bren, Kara L.

    2008-01-01

    A discussion of the literature concerning the synthesis, function, and activity of heme c-containing proteins is presented. Comparison of the properties of heme c, which is covalently bound to protein, is made to heme b, which is bound noncovalently. A question of interest is why nature uses biochemically expensive heme c in many proteins when its properties are expected to be similar to heme b. Considering the effects of covalent heme attachment on heme conformation and on the proximal histi...

  10. Surface electron structure of short-period semiconductor superlattice

    International Nuclear Information System (INIS)

    Bartos, I.; Czech Academy Science, Prague,; Strasser, T.; Schattke, W.

    2004-01-01

    Full text: Semiconductor superlattices represent man-made crystals with unique physical properties. By means of the directed layer-by-layer molecular epitaxy growth their electric properties can be tailored (band structure engineering). Longer translational periodicity in the growth direction is responsible for opening of new electron energy gaps (minigaps) with surface states and resonances localized at superlattice surfaces. Similarly as for the electron structure of the bulk, a procedure enabling to modify the surface electron structure of superlattices is desirable. Short-period superlattice (GaAs) 2 (AlAs) 2 with unreconstructed (100) surface is investigated in detail. Theoretical description in terms of full eigenfunctions of individual components has to be used. The changes of electron surface state energies governed by the termination of a periodic crystalline potential, predicted on simple models, are confirmed for this system. Large surface state shifts are found in the lowest minigap of the superlattice when this is terminated in four different topmost layer configurations. The changes should be observable in angle resolved photoelectron spectroscopy as demonstrated in calculations based on the one step model of photoemission. Surface state in the center of the two dimensional Brillouin zone moves from the bottom of the minigap (for the superlattice terminated by two bilayers of GaAs) to its top (for the superlattice terminated by two bilayers of AlAs) where it becomes a resonance. No surface state/resonance is found for a termination with one bilayer of AlAs. The surface state bands behave similarly in the corresponding gaps of the k-resolved section of the electron band structure. The molecular beam epitaxy, which enables to terminate the superlattice growth with atomic layer precision, provides a way of tuning the superlattice surface electron structure by purely geometrical means. The work was supported by the Grant Agency of the Academy of Sciences

  11. Electronic structure and optical properties of AIN under high pressure

    International Nuclear Information System (INIS)

    Li Zetao; Dang Suihu; Li Chunxia

    2011-01-01

    We have calculated the electronic structure and optical properties of Wurtzite structure AIN under different high pressure with generalized gradient approximation (GGA) in this paper. The total energy, density of state, energy band structure and optical absorption and reflection properties under high pressure are calculated. By comparing the changes of the energy band structure, we obtained AIN phase transition pressure for 16.7 GPa, which is a direct band structure transforming to an indirect band structure. Meanwhile, according to the density of states distribution and energy band structure, we analyzed the optical properties of AIN under high-pressure, the results showed that the absorption spectra moved from low-energy to high-energy. (authors)

  12. Electronic structure of disordered alloys, surfaces and interfaces

    CERN Document Server

    Turek, Ilja; Kudrnovský, Josef; Šob, Mojmír; Weinberger, Peter

    1997-01-01

    At present, there is an increasing interest in the prediction of properties of classical and new materials such as substitutional alloys, their surfaces, and metallic or semiconductor multilayers. A detailed understanding based on a thus of the utmost importance for fu­ microscopic, parameter-free approach is ture developments in solid state physics and materials science. The interrela­ tion between electronic and structural properties at surfaces plays a key role for a microscopic understanding of phenomena as diverse as catalysis, corrosion, chemisorption and crystal growth. Remarkable progress has been made in the past 10-15 years in the understand­ ing of behavior of ideal crystals and their surfaces by relating their properties to the underlying electronic structure as determined from the first principles. Similar studies of complex systems like imperfect surfaces, interfaces, and mul­ tilayered structures seem to be accessible by now. Conventional band-structure methods, however, are of limited use ...

  13. Electronic structure of nitrides PuN and UN

    Science.gov (United States)

    Lukoyanov, A. V.; Anisimov, V. I.

    2016-11-01

    The electronic structure of uranium and plutonium nitrides in ambient conditions and under pressure is investigated using the LDA + U + SO band method taking into account the spin-orbit coupling and the strong correlations of 5 f electrons of actinoid ions. The parameters of these interactions for the equilibrium cubic structure are calculated additionally. The application of pressure reduces the magnetic moment in PuN due to predominance of the f 6 configuration and the jj-type coupling. An increase in the occupancy of the 5 f state in UN leads to a decrease in the magnetic moment, which is also detected in the trigonal structure of the UN x β phase (La2O3-type structure). The theoretical results are in good agreement with the available experimental data.

  14. Redox active molecules cytochrome c and vitamin C enhance heme-enzyme peroxidations by serving as non-specific agents for redox relay

    International Nuclear Information System (INIS)

    Gade, Sudeep Kumar; Bhattacharya, Subarna; Manoj, Kelath Murali

    2012-01-01

    Highlights: ► At low concentrations, cytochrome c/vitamin C do not catalyze peroxidations. ► But low levels of cytochrome c/vitamin C enhance diverse heme peroxidase activities. ► Enhancement positively correlates to the concentration of peroxide in reaction. ► Reducible additives serve as non-specific agents for redox relay in the system. ► Insight into electron transfer processes in routine and oxidative-stress states. -- Abstract: We report that incorporation of very low concentrations of redox protein cytochrome c and redox active small molecule vitamin C impacted the outcome of one-electron oxidations mediated by structurally distinct plant/fungal heme peroxidases. Evidence suggests that cytochrome c and vitamin C function as a redox relay for diffusible reduced oxygen species in the reaction system, without invoking specific or affinity-based molecular interactions for electron transfers. The findings provide novel perspectives to understanding – (1) the promiscuous role of cytochrome b 5 in the metabolism mediated by liver microsomal xenobiotic metabolizing systems and (2) the roles of antioxidant molecules in affording relief from oxidative stress.

  15. Redox active molecules cytochrome c and vitamin C enhance heme-enzyme peroxidations by serving as non-specific agents for redox relay

    Energy Technology Data Exchange (ETDEWEB)

    Gade, Sudeep Kumar; Bhattacharya, Subarna [Heme and Flavo Proteins Laboratory, 204, Center for Biomedical Research, VIT University, Vellore, Tamil Nadu 632014 (India); Manoj, Kelath Murali, E-mail: satyamjayatu@yahoo.com [Heme and Flavo Proteins Laboratory, 204, Center for Biomedical Research, VIT University, Vellore, Tamil Nadu 632014 (India)

    2012-03-09

    Highlights: Black-Right-Pointing-Pointer At low concentrations, cytochrome c/vitamin C do not catalyze peroxidations. Black-Right-Pointing-Pointer But low levels of cytochrome c/vitamin C enhance diverse heme peroxidase activities. Black-Right-Pointing-Pointer Enhancement positively correlates to the concentration of peroxide in reaction. Black-Right-Pointing-Pointer Reducible additives serve as non-specific agents for redox relay in the system. Black-Right-Pointing-Pointer Insight into electron transfer processes in routine and oxidative-stress states. -- Abstract: We report that incorporation of very low concentrations of redox protein cytochrome c and redox active small molecule vitamin C impacted the outcome of one-electron oxidations mediated by structurally distinct plant/fungal heme peroxidases. Evidence suggests that cytochrome c and vitamin C function as a redox relay for diffusible reduced oxygen species in the reaction system, without invoking specific or affinity-based molecular interactions for electron transfers. The findings provide novel perspectives to understanding - (1) the promiscuous role of cytochrome b{sub 5} in the metabolism mediated by liver microsomal xenobiotic metabolizing systems and (2) the roles of antioxidant molecules in affording relief from oxidative stress.

  16. Quantitative vs. qualitative approaches to the electronic structure of solids

    International Nuclear Information System (INIS)

    Oliva, J.M.; Llunell, Miquel; Alemany, Pere; Canadell, Enric

    2003-01-01

    The usefulness of qualitative and quantitative theoretical approaches in solid state chemistry is discussed by considering three different types of problems: (a) the distribution of boron and carbon atoms in MB 2 C 2 (M=Ca, La, etc.) phases, (b) the band structure and Fermi surface of low-dimensional transition metal oxides and bronzes, and (c) the correlation between the crystal and electronic structure of the ternary nitride Ca 2 AuN

  17. Electronic structure of binuclear acetylacetonates of boron difluoride

    Science.gov (United States)

    Tikhonov, Sergey A.; Svistunova, Irina V.; Samoilov, Ilya S.; Osmushko, Ivan S.; Borisenko, Aleksandr V.; Vovna, Vitaliy I.

    2018-05-01

    The electronic structure of boron difluoride acetylacetonate and its three derivatives was studied using photoelectron and absorption spectroscopy, as well as the density functional theory. In a series of binuclear acetylacetonate complexes containing bridge-moieties of sulfur and selenium atoms, it was found an appreciable mixing of the π3-orbital of the chelate cycle with atomic orbitals S 3p and Se 4p resulting in destabilization of the HOMO levels by 0.4-0.6 eV, in comparison with the monomer. The positively charged fragment C(CH3)-CX-C(CH3) causes the field effect, which leads to stabilization of the LUMO levels by 0.3-0.4 eV and C 1s-levels by 0.5-1.2 eV. An analysis of the research results on the electronic structure made it possible to determine the effect of substituents in the γ position on the absorption spectra, which is mainly determined by the electron density transfer from the chalcogen atoms to the chelate cycles. It is shown that the calculated energy intervals between electron levels correlate well with the structure of the photoelectron spectra of valence and core electrons.

  18. The electronic structure of C60 and its derivatives

    International Nuclear Information System (INIS)

    Lichtenberger, D.L.; Rempe, M.E.; Gruhn, N.E.; Wright, L.L.

    1993-01-01

    Molecular orbital calculations are used to examine the electronic structure of C 60 and its interaction with metals and some other atoms. The bonding capabilities of the η 5 , η 6 , and the two possible η 2 sites of C 60 to metals are probed with Fenske-Hall calculations of a silver cation bound in those positions. These results are compared to the bonding capabilities of cyclopentadiene, benzene and ethylene, respectively. It is found that the silver cation bonding to C 60 is favored at the η 2 that is shared between five-membered rings, but that the silver cation bonds more favorably to ethylene than to the η 2 site of C 60 . The electronic structure of the known platinum compound, C 60 Pt(phosphine) 2 , where the bonding is also to this η 2 site, is investigated and compared to the electronic structure of the corresponding ethylene complex. In this more electron-rich metal case, the bonding of the C 60 and ethylene are very similar. A calculation on C 60 OsO 4 (NH 3 ) 2 , where C 60 is bound to two oxygens, shows that the orbital composition correlates with the observed NMR shifts of the carbon atoms. The calculations are used to clarify the interpretations of experimental data obtained from STM, NMR, PES and reactivity. The latest results of these electronic studies will be presented

  19. Nature-Inspired Structural Materials for Flexible Electronic Devices.

    Science.gov (United States)

    Liu, Yaqing; He, Ke; Chen, Geng; Leow, Wan Ru; Chen, Xiaodong

    2017-10-25

    Exciting advancements have been made in the field of flexible electronic devices in the last two decades and will certainly lead to a revolution in peoples' lives in the future. However, because of the poor sustainability of the active materials in complex stress environments, new requirements have been adopted for the construction of flexible devices. Thus, hierarchical architectures in natural materials, which have developed various environment-adapted structures and materials through natural selection, can serve as guides to solve the limitations of materials and engineering techniques. This review covers the smart designs of structural materials inspired by natural materials and their utility in the construction of flexible devices. First, we summarize structural materials that accommodate mechanical deformations, which is the fundamental requirement for flexible devices to work properly in complex environments. Second, we discuss the functionalities of flexible devices induced by nature-inspired structural materials, including mechanical sensing, energy harvesting, physically interacting, and so on. Finally, we provide a perspective on newly developed structural materials and their potential applications in future flexible devices, as well as frontier strategies for biomimetic functions. These analyses and summaries are valuable for a systematic understanding of structural materials in electronic devices and will serve as inspirations for smart designs in flexible electronics.

  20. Electronic Structure of GdCuGe Intermetallic Compound

    Science.gov (United States)

    Lukoyanov, A. V.; Knyazev, Yu. V.; Kuz'min, Yu. I.

    2018-04-01

    The electronic structure of GdCuGe intermetallic compound has been studied. Spin-polarized energy spectrum calculations have been performed by the band method with allowance for strong electron correlations in the 4 f-shell of gadolinium ions. Antiferromagnetic ordering of GdCuGe at low temperatures has been obtained in a theoretical calculation, with the value of the effective magnetic moment of gadolinium ions reproduced in fair agreement with experimental data. The electronic density of states has been analyzed. An optical conductivity spectrum has been calculated for GdCuGe; it reveals specific features that are analogous to the ones discovered previously in the GdCuSi compound with a similar hexagonal structure.

  1. First principle calculations of alkali hydride electronic structures

    International Nuclear Information System (INIS)

    Novakovic, N; Radisavljevic, I; Colognesi, D; Ostojic, S; Ivanovic, N

    2007-01-01

    Electronic structure, volume optimization, bulk moduli, elastic constants, and frequencies of the transversal optical vibrations in LiH, NaH, KH, RbH, and CsH are calculated using the full potential augmented plane wave method, extended with local orbitals, and the full potential linearized augmented plane wave method. The obtained results show some common features in the electronic structure of these compounds, but also clear differences, which cannot be explained using simple empirical trends. The differences are particularly prominent in the electronic distributions and interactions in various crystallographic planes. In the light of these findings we have elaborated some selected experimental results and discussed several theoretical approaches frequently used for the description of various alkali hydride properties

  2. Strontium titanate thin film deposition - structural and electronical characterization

    Energy Technology Data Exchange (ETDEWEB)

    Hanzig, Florian; Hanzig, Juliane; Stoecker, Hartmut; Mehner, Erik; Abendroth, Barbara; Meyer, Dirk C. [TU Bergakademie Freiberg, Institut fuer Experimentelle Physik (Germany); Franke, Michael [TU Bergakademie Freiberg, Institut fuer Elektronik- und Sensormaterialien (Germany)

    2012-07-01

    Strontium titanate is on the one hand a widely-used model oxide for solids which crystallize in perovskite type of structure. On the other hand, with its large band-gap energy and its mixed ionic and electronic conductivity, SrTiO{sub 3} is a promising isolating material in metal-insulator-metal (MIM) structures for resistive switching memory cells. Here, we used physical vapour deposition methods (e. g. electron-beam and sputtering) to produce strontium titanate layers. Sample thicknesses were probed with X-ray reflectometry (XRR) and spectroscopic ellipsometry (SE). Additionally, layer densities and dielectric functions were quantified with XRR and SE, respectively. Using infrared spectroscopy free electron concentrations were obtained. Phase and element composition analysis was carried out with grazing incidence X-ray diffraction and X-ray photoelectron spectroscopy. Subsequent temperature treatment of samples lead to crystallization of the initially amorphous strontium titanate.

  3. Electron Heat Flux in Pressure Balance Structures at Ulysses

    Science.gov (United States)

    Yamauchi, Yohei; Suess, Steven T.; Sakurai, Takashi; Whitaker, Ann F. (Technical Monitor)

    2001-01-01

    Pressure balance structures (PBSs) are a common feature in the high-latitude solar wind near solar minimum. Rom previous studies, PBSs are believed to be remnants of coronal plumes and be related to network activity such as magnetic reconnection in the photosphere. We investigated the magnetic structures of the PBSs, applying a minimum variance analysis to Ulysses/Magnetometer data. At 2001 AGU Spring meeting, we reported that PBSs have structures like current sheets or plasmoids, and suggested that they are associated with network activity at the base of polar plumes. In this paper, we have analyzed high-energy electron data at Ulysses/SWOOPS to see whether bi-directional electron flow exists and confirm the conclusions more precisely. As a result, although most events show a typical flux directed away from the Sun, we have obtained evidence that some PBSs show bi-directional electron flux and others show an isotropic distribution of electron pitch angles. The evidence shows that plasmoids are flowing away from the Sun, changing their flow direction dynamically in a way not caused by Alfven waves. From this, we have concluded that PBSs are generated due to network activity at the base of polar plumes and their magnetic structures axe current sheets or plasmoids.

  4. The structure of spinach Photosystem I studied by electron microscopy

    NARCIS (Netherlands)

    Boekema, Egbert J.; Wynn, R. Max; Malkin, Richard

    1990-01-01

    The structure of three types of Photosystem I (PS I) complex isolated from spinach chloroplasts was studied by electron microscopy and computer image analysis. Molecular projections (top views and side views) of a native PS I complex (PSI-200), an antenna-depleted PS I complex (PSI-100) and the PS I

  5. Ground-state electronic structure of actinide monocarbides and mononitrides

    DEFF Research Database (Denmark)

    Petit, Leon; Svane, Axel; Szotek, Z.

    2009-01-01

    The self-interaction corrected local spin-density approximation is used to investigate the ground-state valency configuration of the actinide ions in the actinide monocarbides, AC (A=U,Np,Pu,Am,Cm), and the actinide mononitrides, AN. The electronic structure is characterized by a gradually increa...

  6. Effects of thickness on electronic structure of titanium thin films

    Indian Academy of Sciences (India)

    using near-edge X-ray absorption fine structure (NEXAFS) technique at titanium L2,3 edge in total electron yield .... the contribution of titanium L2,3 levels to the absorption co- ... all absorption coefficient of a sample is related to the atomic.

  7. Empirical pseudo-potential studies on electronic structure

    Indian Academy of Sciences (India)

    Theoretical investigations of electronic structure of quantum dots is of current interest in nanophase materials. Empirical theories such as effective mass approximation, tight binding methods and empirical pseudo-potential method are capable of explaining the experimentally observed optical properties. We employ the ...

  8. Electronic structure and superconductivity of MgB 2

    Indian Academy of Sciences (India)

    Results of ab initio electronic structure calculations on the compound, MgB2, using the FPLAPW method employing GGA for the exchange–correlation energy are presented. Total energy minimization enables us to estimate the equilibrium volume, / ratio and the bulk modulus, all of which are in excellent agreement with ...

  9. First principles calculations of structural, electronic and thermal ...

    Indian Academy of Sciences (India)

    Home; Journals; Bulletin of Materials Science; Volume 37; Issue 5. First principles calculations of structural, electronic and thermal properties of lead chalcogenides PbS, PbSe and PbTe compounds. N Boukhris H Meradji S Amara Korba S Drablia S Ghemid F El Haj Hassan. Volume 37 Issue 5 August 2014 pp 1159-1166 ...

  10. Structural, elastic, electronic and optical properties of bi-alkali ...

    Indian Academy of Sciences (India)

    The structural parameters, elastic constants, electronic and optical properties of the bi-alkali ... and efficient method for the calculation of the ground-state ... Figure 2. Optimization curve (E–V) of the bi-alkali antimonides: (a) Na2KSb, (b) Na2RbSb, (c) Na2CsSb, .... ical shape of the charge distributions in the contour plots.

  11. First-principle calculations of the structural, electronic ...

    Indian Academy of Sciences (India)

    First-principle calculations were performed to study the structural, electronic, thermodynamic and thermal properties of ... functional theory (DFT) combined with the quasi-harmonic .... is consistent with Vegard's law which assumes that the lat- tice constant varies .... reflects a charge-transfer effect which is due to the different.

  12. Structural, energetic and electronic properties of intercalated boron ...

    Indian Academy of Sciences (India)

    2National Institute for R&D of Isotopic and Molecular Technologies, Cluj-Napoca 400 293, Romania. MS received 8 November 2010; revised 28 March 2012. Abstract. The effects of chirality and the intercalation of transitional metal atoms inside single walled BN nano- tubes on structural, energetic and electronic properties ...

  13. Removal of Vesicle Structures from Transmission Electron Microscope Images

    DEFF Research Database (Denmark)

    Jensen, Katrine Hommelhoff; Sigworth, Fred; Brandt, Sami Sebastian

    2015-01-01

    In this paper, we address the problem of imaging membrane proteins for single-particle cryo-electron microscopy reconstruction of the isolated protein structure. More precisely, we propose a method for learning and removing the interfering vesicle signals from the micrograph, prior to reconstruct...

  14. Small round structured viruses (SRSVs) and transmission electron ...

    African Journals Online (AJOL)

    Administrator

    immune-electron microscopy (IEM) from patients' feces. They reported this virus particle as the causative agent of winter vomiting outbreaks in Norwalk (Kapikian et al.,. 1972). This is the remarkable landmark study of non- bacterial gastroenteritis viruses, especially for small round structured viruses (SRSVs). After that, many.

  15. Electronic structure and optical properties of thorium monopnictides

    Indian Academy of Sciences (India)

    Unknown

    Indian Academy of Sciences. 165. Electronic structure and optical properties of thorium monopnictides. S KUMAR* and S AULUCK†. Physics Department, Institute of Engineering and Technology, M.J.P. Rohilkhand University, Bareilly 243 006,. India. †Department of Physics, Indian Institute of Technology, Roorkee 247 667, ...

  16. Variational cellular model of the molecular and crystal electronic structure

    International Nuclear Information System (INIS)

    Ferreira, L.G.; Leite, J.R.

    1977-12-01

    A variational version of the cellular method is developed to calculate the electronic structure of molecules and crystals. Due to the simplicity of the secular equation, the method is easy to be implemented. Preliminary calculations on the hydrogen molecular ion suggest that it is also accurate and of fast convergence [pt

  17. CLOPW; a mixed basis set full potential electronic structure method

    NARCIS (Netherlands)

    Bekker, H.G.; Bekker, Hermie Gerhard

    1997-01-01

    This thesis is about the development of the full potental CLOPW package for electronic structure calculations. Chapter 1 provides the necessary background in the theory of solid state physics. It gives a short overview of the effective one particle model as commonly used in solid state physics. It

  18. The effect of oxygen exposure on pentacene electronic structure

    NARCIS (Netherlands)

    Vollmer, A; Jurchescu, OD; Arfaoui, [No Value; Salzmann, [No Value; Palstra, TTM; Rudolf, P; Niemax, J; Pflaum, J; Rabe, JP; Koch, N; Arfaoui, I.; Salzmann, I.

    We use ultraviolet photoelectron spectroscopy to investigate the effect of oxygen and air exposure on the electronic structure of pentacene single crystals and thin films. it is found that O-2 and water do not react noticeably with pentacene, whereas singlet oxygen/ozone readily oxidize the organic

  19. Electronic structures and photophysics of d8-d8 complexes

    Czech Academy of Sciences Publication Activity Database

    Gray, H. B.; Záliš, Stanislav; Vlček, Antonín

    2017-01-01

    Roč. 345, AUG 2017 (2017), s. 297-317 ISSN 0010-8545 R&D Projects: GA MŠk LH13015 Grant - others:COST(XE) CM1405 Institutional support: RVO:61388955 Keywords : excitation * electronic structures * photophysics Subject RIV: CG - Electrochemistry OBOR OECD: Physical chemistry Impact factor: 13.324, year: 2016

  20. The electronic structure of 4d and 5d silicides

    NARCIS (Netherlands)

    Speier, W.; Kumar, L.; Sarma, D.D.; Groot, R.A. de; Fuggle, J.C.

    1989-01-01

    A systematic experimental and theoretical study of the electronic structure of stoichiometric silicides with Nb, Mo, Ta and W is presented. We have employed x-ray photoemission and bremsstrahlung isochromat spectroscopy as experimental techniques and interpreted the measured data by calculation of

  1. Highlighting material structure with transmission electron diffraction correlation coefficient maps.

    Science.gov (United States)

    Kiss, Ákos K; Rauch, Edgar F; Lábár, János L

    2016-04-01

    Correlation coefficient maps are constructed by computing the differences between neighboring diffraction patterns collected in a transmission electron microscope in scanning mode. The maps are shown to highlight material structural features like grain boundaries, second phase particles or dislocations. The inclination of the inner crystal interfaces are directly deduced from the resulting contrast. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. First principles calculations of structural, electronic and thermal ...

    Indian Academy of Sciences (India)

    Administrator

    2013-07-28

    Jul 28, 2013 ... The structural, electronic and thermal properties of lead chalcogenides PbS, PbSe and BeTe using .... results for all the systems are presented in table 1, along ... as interatomic bonding, equations of state and phonon spectra.

  3. Coordination Chemistry of Linear Oligopyrrolic Fragments Inspired by Heme Metabolites

    Science.gov (United States)

    Gautam, Ritika

    Linear oligopyrroles are degradation products of heme, which is converted in the presence of heme oxygenase to bile pigments, such as biliverdin and bilirubin. These tetrapyrrolic oligopyrroles are ubiquitously present in biological systems and find applications in the fields of catalysis and sensing. These linear tetrapyrrolic scaffolds are further degraded into linear tripyrrolic and dipyrrolic fragments. Although these lower oligopyrroles are abundantly present, their coordination chemistry requires further characterization. This dissertation focuses mainly on two classes of bioinspired linear oligopyrroles, propentdyopent and tripyrrindione, and their transition metal complexes, which present a rich ligand-based redox chemistry. Chapter 1 offers an overview of heme degradation to different classes of linear oligopyrroles and properties of their transition metal complexes. Chapter 2 is focused on the tripyrrin-1,14-dione scaffold of the urinary pigment uroerythrin, which coordinates divalent transition metals palladium and copper with square planar geometry. Specifically, the tripyrrin-1, 14-dione ligand binds Cu(II) and Pd(II) as a dianionic organic radical under ambient conditions. The electrochemical study confirms the presence of ligand based redox chemistry, and one electron oxidation or reduction reactions do not alter the planar geometry around the metal center. The X-Ray analysis and the electron paramagnetic resonance (EPR) studies of the complexes in the solid and solution phase reveals intermolecular interactions between the ligand based unpaired electrons and therefore formation of neutral pi-pi dimers. In Chapter 3, the antioxidant activity and the fluorescence sensor properties of the tripyrrin-1,14-dione ligand in the presence of superoxide are described. We found that the tripyrrindione ligand undergoes one-electron reduction in the presence of the superoxide radical anion (O2•- ) to form highly fluorescent H3TD1•- radical anion, which emits

  4. Heme exporter FLVCR1a regulates heme synthesis and degradation and controls activity of cytochromes P450.

    Science.gov (United States)

    Vinchi, Francesca; Ingoglia, Giada; Chiabrando, Deborah; Mercurio, Sonia; Turco, Emilia; Silengo, Lorenzo; Altruda, Fiorella; Tolosano, Emanuela

    2014-05-01

    The liver has one of the highest rates of heme synthesis of any organ. More than 50% of the heme synthesized in the liver is used for synthesis of P450 enzymes, which metabolize exogenous and endogenous compounds that include natural products, hormones, drugs, and carcinogens. Feline leukemia virus subgroup C cellular receptor 1a (FLVCR1a) is plasma membrane heme exporter that is ubiquitously expressed and controls intracellular heme content in hematopoietic lineages. We investigated the role of Flvcr1a in liver function in mice. We created mice with conditional disruption of Mfsd7b, which encodes Flvcr1a, in hepatocytes (Flvcr1a(fl/fl);alb-cre mice). Mice were analyzed under basal conditions, after phenylhydrazine-induced hemolysis, and after induction of cytochromes P450 synthesis. Livers were collected and analyzed by histologic, quantitative real-time polymerase chain reaction, and immunoblot analyses. Hepatic P450 enzymatic activities were measured. Flvcr1a(fl/fl);alb-cre mice accumulated heme and iron in liver despite up-regulation of heme oxygenase 1, ferroportin, and ferritins. Hepatic heme export activity of Flvcr1a was closely associated with heme biosynthesis, which is required to sustain cytochrome induction. Upon cytochromes P450 stimulation, Flvcr1a(fl/fl);alb-cre mice had reduced cytochrome activity, associated with accumulation of heme in hepatocytes. The expansion of the cytosolic heme pool in these mice was likely responsible for the early inhibition of heme synthesis and increased degradation of heme, which reduced expression and activity of cytochromes P450. In livers of mice, Flvcr1a maintains a free heme pool that regulates heme synthesis and degradation as well as cytochromes P450 expression and activity. These findings have important implications for drug metabolism. Copyright © 2014 AGA Institute. Published by Elsevier Inc. All rights reserved.

  5. Heme Exporter FLVCR1a Regulates Heme Synthesis and Degradation and Controls Activity of Cytochromes P450

    Science.gov (United States)

    Vinchi, Francesca; Ingoglia, Giada; Chiabrando, Deborah; Mercurio, Sonia; Turco, Emilia; Silengo, Lorenzo; Altruda, Fiorella; Tolosano, Emanuela

    2014-01-01

    Background & Aims The liver has one of the highest rates of heme synthesis of any organ. More than 50% of the heme synthesized in the liver is used for synthesis of P450 enzymes, which metabolize exogenous and endogenous compounds that include natural products, hormones, drugs, and carcinogens. Feline leukemia virus subgroup C cellular receptor 1a (FLVCR1a) is plasma membrane heme exporter that is ubiquitously expressed and controls intracellular heme content in hematopoietic lineages. We investigated the role of Flvcr1a in liver function in mice. Methods We created mice with conditional disruption of Mfsd7b, which encodes Flvcr1a, in hepatocytes (Flvcr1afl/fl;alb-cre mice). Mice were analyzed under basal conditions, after phenylhydrazine-induced hemolysis, and after induction of cytochromes P450 synthesis. Livers were collected and analyzed by histologic, quantitative real-time polymerase chain reaction, and immunoblot analyses. Hepatic P450 enzymatic activities were measured. Results Flvcr1afl/fl;alb-cre mice accumulated heme and iron in liver despite up-regulation of heme oxygenase 1, ferroportin, and ferritins. Hepatic heme export activity of Flvcr1a was closely associated with heme biosynthesis, which is required to sustain cytochrome induction. Upon cytochromes P450 stimulation, Flvcr1afl/fl;alb-cre mice had reduced cytochrome activity, associated with accumulation of heme in hepatocytes. The expansion of the cytosolic heme pool in these mice was likely responsible for the early inhibition of heme synthesis and increased degradation of heme, which reduced expression and activity of cytochromes P450. Conclusions In livers of mice, Flvcr1a maintains a free heme pool that regulates heme synthesis and degradation as well as cytochromes P450 expression and activity. These findings have important implications for drug metabolism. PMID:24486949

  6. Structural and Electronic Investigations of Complex Intermetallic Compounds

    Energy Technology Data Exchange (ETDEWEB)

    Ko, Hyunjin [Iowa State Univ., Ames, IA (United States)

    2008-01-01

    In solid state chemistry, numerous investigations have been attempted to address the relationships between chemical structure and physical properties. Such questions include: (1) How can we understand the driving forces of the atomic arrangements in complex solids that exhibit interesting chemical and physical properties? (2) How do different elements distribute themselves in a solid-state structure? (3) Can we develop a chemical understanding to predict the effects of valence electron concentration on the structures and magnetic ordering of systems by both experimental and theoretical means? Although these issues are relevant to various compound classes, intermetallic compounds are especially interesting and well suited for a joint experimental and theoretical effort. For intermetallic compounds, the questions listed above are difficult to answer since many of the constituent atoms simply do not crystallize in the same manner as in their separate, elemental structures. Also, theoretical studies suggest that the energy differences between various structural alternatives are small. For example, Al and Ga both belong in the same group on the Periodic Table of Elements and share many similar chemical properties. Al crystallizes in the fcc lattice with 4 atoms per unit cell and Ga crystallizes in an orthorhombic unit cell lattice with 8 atoms per unit cell, which are both fairly simple structures (Figure 1). However, when combined with Mn, which itself has a very complex cubic crystal structure with 58 atoms per unit cell, the resulting intermetallic compounds crystallize in a completely different fashion. At the 1:1 stoichiometry, MnAl forms a very simple tetragonal lattice with two atoms per primitive unit cell, while MnGa crystallizes in a complicated rhombohedral unit cell with 26 atoms within the primitive unit cell. The mechanisms influencing the arrangements of atoms in numerous crystal structures have been studied theoretically by calculating electronic

  7. Electronic structures of azafullerene C48N12

    International Nuclear Information System (INIS)

    Brena, Barbara; Luo Yi

    2003-01-01

    Two recently proposed low-energy azafullerene C 48 N 12 isomers have been theoretically characterized using x-ray spectroscopies. The x-ray photoelectron spectroscopy, the near-edge absorption fine structure, the x-ray emission spectroscopy, and the ultraviolet photoelectron spectroscopy for both isomers have been predicted at the gradient-corrected density functional theory level. These spectroscopies together give a comprehensive insight of the electronic structure on the core, valence, and unoccupied orbitals. They have also provided a convincing way for identifying the isomer structures

  8. Electronic structure of graphene on Ni surfaces with different orientation

    International Nuclear Information System (INIS)

    Pudikov, D.A.; Zhizhin, E.V.; Rybkin, A.G.; Rybkina, A.A.; Zhukov, Y.M.; Vilkov, O. Yu.; Shikin, A.M.

    2016-01-01

    An experimental study of the graphene, synthesized by propylene cracking on Ni surfaces with different orientation: (100) and (111), using angle-resolved photoemission, has been performed. It has been shown that graphene on Ni(111) had a perfect lateral structure due to consistency of their lattices, whereas graphene/Ni(100) consisted of a lot of domains. For both systems electronic structure was quite similar and demonstrated a strong bonding of graphene to the underlying Ni surface. After Au intercalation the electronic structure of graphene in both systems was shifted to the Fermi level and became linear in the vicinity of the K point of the Brillouin zone. - Highlights: • Graphene on Ni(111) is well-ordered, whereas on Ni(100) – multi-domain. • Graphene on Ni(111) and Ni(100) is strongly bonded with substrate. • Intercalation of Au atoms restores the linearity in dispersion and makes graphene quasi-free on both Ni(100) and Ni(111).

  9. Surface morphology and electronic structure of Ni/Ag(100)

    International Nuclear Information System (INIS)

    Hite, D. A.; Kizilkaya, O.; Sprunger, P. T.; Howard, M. M.; Ventrice, C. A. Jr.; Geisler, H.; Zehner, D. M.

    2000-01-01

    The growth morphology and electronic structure of Ni on Ag(100) has been studied with scanning tunneling microscopy (STM) and synchrotron based angle resolved photoemission spectroscopy. At deposition temperatures at or below 300 K, STM reveals Ni cluster growth on the surface along with some subsurface growth. Upon annealing to 420 K, virtually all Ni segregates into the subsurface region forming embedded nanoclusters. The electronic structure of Ni d bands in the unannealed surface shows dispersion only perpendicular to the surface whereas the annealed surface has Ni d bands that exhibit a three-dimensional-like structure. This is a result of the increased Ni d-Ag sp hybridization bonding and increased coordination of the embedded Ni nanoclusters. (c) 2000 American Vacuum Society

  10. Electronic structure and optical properties of metal doped tetraphenylporphyrins

    Science.gov (United States)

    Shah, Esha V.; Roy, Debesh R.

    2018-05-01

    A density functional scrutiny on the structure, electronic and optical properties of metal doped tetraphenylporphyrins MTPP (M=Fe, Co, Ni) is performed. The structural stability of the molecules is evaluated based on the electronic parameters like HOMO-LUMO gap (HLG), chemical hardness (η) and binding energy of the central metal atom to the molecular frame etc. The computed UltraViolet-Visible (UV-Vis) optical absorption spectra for all the compounds are also compared. The molecular structures reported are the lowest energy configurations. The entire calculations are carried out with a widely reliable functional, viz. B3LYP with a popular basis set which includes a scaler relativistic effect, viz. LANL2DZ.

  11. Electronic structure of multi-walled carbon fullerenes

    International Nuclear Information System (INIS)

    Doore, Keith; Cook, Matthew; Clausen, Eric; Lukashev, Pavel V; Kidd, Tim E; Stollenwerk, Andrew J

    2017-01-01

    Despite an enormous amount of research on carbon based nanostructures, relatively little is known about the electronic structure of multi-walled carbon fullerenes, also known as carbon onions. In part, this is due to the very high computational expense involved in estimating electronic structure of large molecules. At the same time, experimentally, the exact crystal structure of the carbon onion is usually unknown, and therefore one relies on qualitative arguments only. In this work we present the results of a computational study on a series of multi-walled fullerenes and compare their electronic structures to experimental data. Experimentally, the carbon onions were fabricated using ultrasonic agitation of isopropanol alcohol and deposited onto the surface of highly ordered pyrolytic graphite using a drop cast method. Scanning tunneling microscopy images indicate that the carbon onions produced using this technique are ellipsoidal with dimensions on the order of 10 nm. The majority of differential tunneling spectra acquired on individual carbon onions are similar to that of graphite with the addition of molecular-like peaks, indicating that these particles span the transition between molecules and bulk crystals. A smaller, yet sizable number exhibited a semiconducting gap between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) levels. These results are compared with the electronic structure of different carbon onion configurations calculated using first-principles. Similar to the experimental results, the majority of these configurations are metallic with a minority behaving as semiconductors. Analysis of the configurations investigated here reveals that each carbon onion exhibiting an energy band gap consisted only of non-metallic fullerene layers, indicating that the interlayer interaction is not significant enough to affect the total density of states in these structures. (paper)

  12. Characterization of strained semiconductor structures using transmission electron microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Oezdoel, Vasfi Burak

    2011-08-15

    Today's state-of-the-art semiconductor electronic devices utilize the charge transport within very small volumes of the active device regions. The structural, chemical and optical material properties in these small dimensions can critically affect the performance of these devices. The present thesis is focused on the nanometer scale characterization of the strain state in semiconductor structures using transmission electron microscopy (TEM). Although high-resolution TEM has shown to provide the required accuracy at the nanometer scale, optimization of imaging conditions is necessary for accurate strain measurements. An alternative HRTEM method based on strain mapping on complex-valued exit face wave functions is developed to reduce the artifacts arising from objective lens aberrations. However, a much larger field of view is crucial for mapping strain in the active regions of complex structures like latest generation metal-oxide-semiconductor field-effect transistors (MOSFETs). To overcome this, a complementary approach based on electron holography is proposed. The technique relies on the reconstruction of the phase shifts in the diffracted electron beams from a focal series of dark-field images using recently developed exit-face wave function reconstruction algorithm. Combining high spatial resolution, better than 1 nm, with a field of view of about 1 {mu}m in each dimension, simultaneous strain measurements on the array of MOSFETs are possible. Owing to the much lower electron doses used in holography experiments when compared to conventional quantitative methods, the proposed approach allows to map compositional distribution in electron beam sensitive materials such as InGaN heterostructures without alteration of the original morphology and chemical composition. Moreover, dark-field holography experiments can be performed on thicker specimens than the ones required for high-resolution TEM, which in turn reduces the thin foil relaxation. (orig.)

  13. Structure determination of modulated structures by powder X-ray diffraction and electron diffraction

    Czech Academy of Sciences Publication Activity Database

    Zhou, Z.Y.; Palatinus, Lukáš; Sun, J.L.

    2016-01-01

    Roč. 3, č. 11 (2016), s. 1351-1362 ISSN 2052-1553 Institutional support: RVO:68378271 Keywords : electron diffraction * incommensurate structure * powder diffraction Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 4.036, year: 2016

  14. Nano-structured thin films : a Lorentz transmission electron microscopy and electron holography study

    NARCIS (Netherlands)

    Hosson, J.Th.M. de; Raedt, H.A. De; Zhong, ZY; Saka, H; Kim, TH; Holm, EA; Han, YF; Xie, XS

    2005-01-01

    This paper aims at applying advanced transmission electron microscopy (TEM) to functional materials, such as ultra-soft magnetic films for high-frequency inductors, to reveal the structure-property relationship. The ultimate goal is to delineate a more quantitative way to obtain information of the

  15. Electronic structure of a striped nickelate studied by the exact exchange for correlated electrons (EECE) approach

    KAUST Repository

    Schwingenschlö gl, Udo; Schuster, Cosima B.; Fré sard, Raymond

    2009-01-01

    Motivated by a RIXS study of Wakimoto, et al.(Phys. Rev. Lett., 102 (2009) 157001) we use density functional theory to analyze the magnetic order in the nickelate La5/3Sr1/3NiO4 and the details of its crystal and electronic structure. We compare

  16. Heme-containing enzymes and inhibitors for tryptophan metabolism.

    Science.gov (United States)

    Yan, Daojing; Lin, Ying-Wu; Tan, Xiangshi

    2017-09-20

    Iron-containing enzymes such as heme enzymes play crucial roles in biological systems. Three distinct heme-containing dioxygenase enzymes, tryptophan 2,3-dioxygenase (TDO), indoleamine 2,3-dioxygenase 1 (IDO1) and indoleamine 2,3-dioxygenase 2 (IDO2) catalyze the initial and rate-limiting step of l-tryptophan catabolism through the kynurenine pathway in mammals. Overexpression of these enzymes causes depletion of tryptophan and the accumulation of metabolic products, which contributes to tumor immune tolerance and immune dysregulation in a variety of disease pathologies. In the past few decades, IDO1 has garnered the most attention as a therapeutic target with great potential in cancer immunotherapy. Many potential inhibitors of IDO1 have been designed, synthesized and evaluated, among which indoximod (d-1-MT), INCB024360, GDC-0919 (formerly NLG-919), and an IDO1 peptide-based vaccine have advanced to the clinical trial stage. However, recently, the roles of TDO and IDO2 have been elucidated in immune suppression. In this review, the current drug discovery landscape for targeting TDO, IDO1 and IDO2 is highlighted, with particular attention to the recent use of drugs in clinical trials. Moreover, the crystal structures of these enzymes, in complex with inhibitors, and the mechanisms of Trp catabolism in the first step, are summarized to provide information for facilitating the discovery of new enzyme inhibitors.

  17. Interaction between Mitochondrial Reactive Oxygen Species, Heme Oxygenase, and Nitric Oxide Synthase Stimulates Phagocytosis in Macrophages

    Directory of Open Access Journals (Sweden)

    Andrea Müllebner

    2018-01-01

    Full Text Available BackgroundMacrophages are cells of the innate immune system that populate every organ. They are required not only for defense against invading pathogens and tissue repair but also for maintenance of tissue homeostasis and iron homeostasis.AimThe aim of this study is to understand whether heme oxygenase (HO and nitric oxide synthase (NOS contribute to the regulation of nicotinamide adenine dinucleotide phosphate oxidase (NOX activity and phagocytosis, two key components of macrophage function.MethodsThis study was carried out using resting J774A.1 macrophages treated with hemin or vehicle. Activity of NOS, HO, or NOX was inhibited using specific inhibitors. Reactive oxygen species (ROS formation was determined by Amplex® red assay, and phagocytosis was measured using fluorescein isothiocyanate-labeled bacteria. In addition, we analyzed the fate of the intracellular heme by using electron spin resonance.ResultsWe show that both enzymes NOS and HO are essential for phagocytic activity of macrophages. NOS does not directly affect phagocytosis, but stimulates NOX activity via nitric oxide-triggered ROS production of mitochondria. Treatment of macrophages with hemin results in intracellular accumulation of ferrous heme and an inhibition of phagocytosis. In contrast to NOS, HO products, including carbon monoxide, neither clearly affect NOX activity nor clearly affect phagocytosis, but phagocytosis is accelerated by HO-mediated degradation of heme.ConclusionBoth enzymes contribute to the bactericidal activity of macrophages independently, by controlling different pathways.

  18. Slow electron acoustic double layer (SEADL) structures in bi-ion plasma with trapped electrons

    Science.gov (United States)

    Shan, Shaukat Ali; Imtiaz, Nadia

    2018-05-01

    The properties of ion acoustic double layer (IADL) structures in bi-ion plasma with electron trapping are investigated by using the quasi-potential analysis. The κ-distributed trapped electrons number density expression is truncated to some finite order of the electrostatic potential. By utilizing the reductive perturbation method, a modified Schamel equation which describes the evolution of the slow electron acoustic double layer (SEADL) with the modified speed due to the presence of bi-ion species is investigated. The Sagdeev-like potential has been derived which accounts for the effect of the electron trapping and superthermality in a bi-ion plasma. It is found that the superthermality index, the trapping efficiency of electrons, and ion to electron temperature ratio are the inhibiting parameters for the amplitude of the slow electron acoustic double layers (SEADLs). However, the enhanced population of the cold ions is found to play a supportive role for the low frequency DLs in bi-ion plasmas. The illustrations have been presented with the help of the bi-ion plasma parameters in the Earth's ionosphere F-region.

  19. Electronic structure of divacancy-hydrogen complexes in silicon

    International Nuclear Information System (INIS)

    Coutinho, J; Torres, V J B; Jones, R; Oeberg, S; Briddon, P R

    2003-01-01

    Divacancy-hydrogen complexes (V 2 H and V 2 H 2 ) in Si are studied by ab initio modelling using large supercells. Here we pay special attention to their electronic structure, showing that these defects produce deep carrier traps. Calculated electrical gap levels indicate that V 2 H 2 is an acceptor, whereas V 2 H is amphoteric, with levels close to those of the well known divacancy. Finally our results are compared with the available data from deep level transient spectroscopy and electron paramagnetic resonance experiments

  20. Structural defects in laser- and electron-beam annealed silicon

    International Nuclear Information System (INIS)

    Narayan, J.

    1979-01-01

    Laser and electron beam pulses provide almost an ideal source of heat by which thin layers of semiconductors can be rapidly melted and solidified with heating and cooling rates exceeding 10 80 C/sec. Microstructural modifications obtained as a function of laser parameters are examined and it is shown that both laser and electron beam pulses can be used to remove displacement damage, dislocations, dislocation loops and precipitates. Annealing of defects underneath the oxide layers in silicon is possible within a narrow energy window. The formation of cellular structure provides a rather clear evidence of melting which leads to segregation and supercooling, and subsequent cell formation

  1. Synthesis, reactivity, and electronic structure of molecular uranium nitrides

    OpenAIRE

    Cleaves, Peter A.

    2016-01-01

    The study of metal-ligand multiple bonding offers insight into the electronic structure and bond of metal systems. Until recently, for uranium, such systems were limited to uranyl, and terminal chalcogenide, imide and carbene complexes. In 2012, this was extended to nitrides with the first preparation of a uranium–nitride (U≡N) species isolable under standard conditions, namely [U(TrenTIPS)(N)][Na(12C4)2] (52), which is prepared by the two-electron reduction of sodium azide with a trivalent u...

  2. Electronic structure of superlattices of graphene and hexagonal boron nitride

    KAUST Repository

    Kaloni, Thaneshwor P.

    2011-11-14

    We study the electronic structure of superlattices consisting of graphene and hexagonal boron nitride slabs, using ab initio density functional theory. We find that the system favors a short C–B bond length at the interface between the two component materials. A sizeable band gap at the Dirac point is opened for superlattices with single graphene layers but not for superlattices with graphene bilayers. The system is promising for applications in electronic devices such as field effect transistors and metal-oxide semiconductors.

  3. Acceptors in cadmium telluride. Identification and electronic structure

    International Nuclear Information System (INIS)

    Molva, E.

    1983-11-01

    It is shown that electronic properties of CdTe are determined by impurities more than by intrinsic defects like vacancies or interstitials in Cd or Te contrary to classical theories. These results are based on annealing, diffusion, implantation and electron irradiation at 4 K. Centers appearing in treated samples are accurately identified by photoluminescence, cathodoluminescence infra-red absorption, electrical measurements and magneto-optic properties. Acceptors identified are Li, Na, Cu, Ag and Au impurities in Cd and N, P and As in Te. Energy levels of all acceptors and fine structure of excitons are determined [fr

  4. Grid-based electronic structure calculations: The tensor decomposition approach

    Energy Technology Data Exchange (ETDEWEB)

    Rakhuba, M.V., E-mail: rakhuba.m@gmail.com [Skolkovo Institute of Science and Technology, Novaya St. 100, 143025 Skolkovo, Moscow Region (Russian Federation); Oseledets, I.V., E-mail: i.oseledets@skoltech.ru [Skolkovo Institute of Science and Technology, Novaya St. 100, 143025 Skolkovo, Moscow Region (Russian Federation); Institute of Numerical Mathematics, Russian Academy of Sciences, Gubkina St. 8, 119333 Moscow (Russian Federation)

    2016-05-01

    We present a fully grid-based approach for solving Hartree–Fock and all-electron Kohn–Sham equations based on low-rank approximation of three-dimensional electron orbitals. Due to the low-rank structure the total complexity of the algorithm depends linearly with respect to the one-dimensional grid size. Linear complexity allows for the usage of fine grids, e.g. 8192{sup 3} and, thus, cheap extrapolation procedure. We test the proposed approach on closed-shell atoms up to the argon, several molecules and clusters of hydrogen atoms. All tests show systematical convergence with the required accuracy.

  5. Electronic structure of superlattices of graphene and hexagonal boron nitride

    KAUST Repository

    Kaloni, Thaneshwor P.; Cheng, Yingchun; Schwingenschlö gl, Udo

    2011-01-01

    We study the electronic structure of superlattices consisting of graphene and hexagonal boron nitride slabs, using ab initio density functional theory. We find that the system favors a short C–B bond length at the interface between the two component materials. A sizeable band gap at the Dirac point is opened for superlattices with single graphene layers but not for superlattices with graphene bilayers. The system is promising for applications in electronic devices such as field effect transistors and metal-oxide semiconductors.

  6. Electron-Poor Polar Intermetallics: Complex Structures, Novel Clusters, and Intriguing Bonding with Pronounced Electron Delocalization.

    Science.gov (United States)

    Lin, Qisheng; Miller, Gordon J

    2018-01-16

    Intermetallic compounds represent an extensive pool of candidates for energy related applications stemming from magnetic, electric, optic, caloric, and catalytic properties. The discovery of novel intermetallic compounds can enhance understanding of the chemical principles that govern structural stability and chemical bonding as well as finding new applications. Valence electron-poor polar intermetallics with valence electron concentrations (VECs) between 2.0 and 3.0 e - /atom show a plethora of unprecedented and fascinating structural motifs and bonding features. Therefore, establishing simple structure-bonding-property relationships is especially challenging for this compound class because commonly accepted valence electron counting rules are inappropriate. During our efforts to find quasicrystals and crystalline approximants by valence electron tuning near 2.0 e - /atom, we observed that compositions close to those of quasicrystals are exceptional sources for unprecedented valence electron-poor polar intermetallics, e.g., Ca 4 Au 10 In 3 containing (Au 10 In 3 ) wavy layers, Li 14.7 Mg 36.8 Cu 21.5 Ga 66 adopting a type IV clathrate framework, and Sc 4 Mg x Cu 15-x Ga 7.5 that is incommensurately modulated. In particular, exploratory syntheses of AAu 3 T (A = Ca, Sr, Ba and T = Ge, Sn) phases led to interesting bonding features for Au, such as columns, layers, and lonsdaleite-type tetrahedral frameworks. Overall, the breadth of Au-rich polar intermetallics originates, in part, from significant relativistics effect on the valence electrons of Au, effects which result in greater 6s/5d orbital mixing, a small effective metallic radius, and an enhanced Mulliken electronegativity, all leading to ultimate enhanced binding with nearly all metals including itself. Two other successful strategies to mine electron-poor polar intermetallics include lithiation and "cation-rich" phases. Along these lines, we have studied lithiated Zn-rich compounds in which structural

  7. Electronic structure and insulating gap in epitaxial VO2 polymorphs

    Directory of Open Access Journals (Sweden)

    Shinbuhm Lee

    2015-12-01

    Full Text Available Determining the origin of the insulating gap in the monoclinic V O2(M1 is a long-standing issue. The difficulty of this study arises from the simultaneous occurrence of structural and electronic transitions upon thermal cycling. Here, we compare the electronic structure of the M1 phase with that of single crystalline insulating V O2(A and V O2(B thin films to better understand the insulating phase of VO2. As these A and B phases do not undergo a structural transition upon thermal cycling, we comparatively study the origin of the gap opening in the insulating VO2 phases. By x-ray absorption and optical spectroscopy, we find that the shift of unoccupied t2g orbitals away from the Fermi level is a common feature, which plays an important role for the insulating behavior in VO2 polymorphs. The distinct splitting of the half-filled t2g orbital is observed only in the M1 phase, widening the bandgap up to ∼0.6 eV. Our approach of comparing all three insulating VO2 phases provides insight into a better understanding of the electronic structure and the origin of the insulating gap in VO2.

  8. Electronic structure of germanium selenide investigated using ultra-violet photo-electron spectroscopy

    Science.gov (United States)

    Mishra, P.; Lohani, H.; Kundu, A. K.; Patel, R.; Solanki, G. K.; Menon, Krishnakumar S. R.; Sekhar, B. R.

    2015-07-01

    The valence band electronic structure of GeSe single crystals has been investigated using angle resolved photoemission spectroscopy (ARPES) and x-ray photoelectron spectroscopy. The experimentally observed bands from ARPES, match qualitatively with our LDA-based band structure calculations along the Γ-Z, Γ-Y and Γ-T symmetry directions. The valence band maximum occurs nearly midway along the Γ-Z direction, at a binding energy of -0.5 eV, substantiating the indirect band gap of GeSe. Non-dispersive features associated with surface states and indirect transitions have been observed. The difference in hybridization of Se and Ge 4p orbitals leads to the variation of dispersion along the three symmetry directions. The predominance of the Se 4pz orbitals, evidenced from theoretical calculations, may be the cause for highly dispersive bands along the Γ-T direction. Detailed electronic structure analysis reveals the significance of the cation-anion 4p orbitals hybridization in the valence band dispersion of IV-VI semiconductors. This is the first comprehensive report of the electronic structure of a GeSe single crystal using ARPES in conjugation with theoretical band structure analysis.

  9. Electronic structure of germanium selenide investigated using ultra-violet photo-electron spectroscopy

    International Nuclear Information System (INIS)

    Mishra, P; Lohani, H; Sekhar, B R; Kundu, A K; Menon, Krishnakumar S R; Patel, R; Solanki, G K

    2015-01-01

    The valence band electronic structure of GeSe single crystals has been investigated using angle resolved photoemission spectroscopy (ARPES) and x-ray photoelectron spectroscopy. The experimentally observed bands from ARPES, match qualitatively with our LDA-based band structure calculations along the Γ–Z, Γ–Y and Γ–T symmetry directions. The valence band maximum occurs nearly midway along the Γ–Z direction, at a binding energy of −0.5 eV, substantiating the indirect band gap of GeSe. Non-dispersive features associated with surface states and indirect transitions have been observed. The difference in hybridization of Se and Ge 4p orbitals leads to the variation of dispersion along the three symmetry directions. The predominance of the Se 4p z orbitals, evidenced from theoretical calculations, may be the cause for highly dispersive bands along the Γ–T direction. Detailed electronic structure analysis reveals the significance of the cation–anion 4p orbitals hybridization in the valence band dispersion of IV–VI semiconductors. This is the first comprehensive report of the electronic structure of a GeSe single crystal using ARPES in conjugation with theoretical band structure analysis. (paper)

  10. Biosynthesis of heme in immature erythroid cells. The regulatory step for heme formation in the human erythron

    International Nuclear Information System (INIS)

    Gardner, L.C.; Cox, T.M.

    1988-01-01

    Heme formation in reticulocytes from rabbits and rodents is subject to end product negative feedback regulation: intracellular free heme has been shown to control acquisition of transferrin iron for heme synthesis. To identify the site of control of heme biosynthesis in the human erythron, immature erythroid cells were obtained from peripheral blood and aspirated bone marrow. After incubation with human 59Fe transferrin, 2-[14C]glycine, or 4-[14C]delta-aminolevulinate, isotopic incorporation into extracted heme was determined. Addition of cycloheximide to increase endogenous free heme, reduced incorporation of labeled glycine and iron but not delta-aminolevulinate into cell heme. Incorporation of glycine and iron was also sensitive to inhibition by exogenous hematin (Ki, 30 and 45 microM, respectively) i.e. at concentrations in the range which affect cell-free protein synthesis in reticulocyte lysates. Hematin treatment rapidly diminished incorporation of intracellular 59Fe into heme by human erythroid cells but assimilation of 4-[14C]delta-aminolevulinate into heme was insensitive to inhibition by hematin (Ki greater than 100 microM). In human reticulocytes (unlike those from rabbits), addition of ferric salicylaldehyde isonicotinoylhydrazone, to increase the pre-heme iron pool independently of the transferrin cycle, failed to promote heme synthesis or modify feedback inhibition induced by hematin. In human erythroid cells (but not rabbit reticulocytes) pre-incubation with unlabeled delta-aminolevulinate or protoporphyrin IX greatly stimulated utilization of cell 59Fe for heme synthesis and also attenuated end product inhibition. In human erythroid cells heme biosynthesis is thus primarily regulated by feedback inhibition at one or more steps which lead to delta-aminolevulinate formation

  11. Effect of lead on heme synthesis

    Energy Technology Data Exchange (ETDEWEB)

    Neuberger, A.

    1975-01-01

    Recently, a fair amount of work has been done on the effect of lead on porphobilinogen dehydratase, which has been used as a sensitive indicator of lead poisoning. How far this is in itself harmful depends on the Michaelis constants of both the aminolaevulinic synthetase and of the dehydratase, and in addition on the relative activities of the two enzymes in a cell and also on the tissue concentration of glycine. Information on some of these points is still fragmentary, and a reliable judgement is at the present not very easy. Another step in the heme synthesis, which is sensitive to low concentrations of lead, is the incorporation of iron into protoporphyrin. Inhibition of this step may be important in accounting to a large extent for the anaemia found in individuals with lead poisoning. Reduction in the tissue concentration of heme or of heme-like compounds may also explain, through the mechanism of de-repression, the excretion of increased amounts of aminolaevulinic acid in the urine observed in cases of lead poisoning. A third step in heme synthesis, which might be sensitive to lead, is the oxidative decarboxylation of coproporphyrin to protoporphyrin, and this may explain why the former derivative is excreted in the urine. Recent work of the Harvard Medical School has indicated that greatly reduced levels of ALA dehydratase may be found in most cases of severe liver damage due to alcoholism. In most of these cases the level of lead in the blood is within normal limits, and there is no history of exposure to toxic amounts of lead. We therefore have to assume that a reduction in the blood level of this enzyme is not necessarily an indication of lead poisoning.

  12. Electronic structure of p type Delta doped systems

    International Nuclear Information System (INIS)

    Gaggero S, L.M.; Perez A, R.

    1998-01-01

    We summarize of the results obtained for the electronic structure of quantum wells that consist in an atomic layer doped with impurities of p type. The calculations are made within the frame worth of the wrapper function approach to independent bands and with potentials of Hartree. We study the cases reported experimentally (Be in GaAs and B in Si). We present the levels of energy, the wave functions and the rate of the electronic population between the different subbands, as well as the dependence of these magnitudes with the density of impurities in the layer. The participation of the bans of heavy holes is analysed, light and split-off band in the total electronic population. The effect of the temperature is discussed and we give a possible qualitative explanation of the experimental optical properties. (Author)

  13. Valence electronic structure of tantalum carbide and nitride

    Institute of Scientific and Technical Information of China (English)

    FAN; ChangZeng

    2007-01-01

    The valence electronic structures of tantalum carbide (TaC) and tantalum nitride (TaN) are studied by using the empirical electronic theory (EET). The results reveal that the bonds of these compounds have covalent, metallic and ionic characters. For a quantitative analysis of the relative strength of these components, their ionicities have been calculated by implanting the results of EET to the PVL model. It has been found that the ionicity of tantalum carbide is smaller than that of tantalum nitride. The EET results also reveal that the covalent electronic number of the strongest bond in the former is larger than that of the latter. All these suggest that the covalent bond of TaC is stronger than that of TaN, which coincides to that deduced from the first-principles method.……

  14. Valence electronic structure of tantalum carbide and nitride

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    @@ The valence electronic structures of tantalum carbide (TaC) and tantalum nitride (TaN) are studied by using the empirical electronic theory (EET). The results reveal that the bonds of these compounds have covalent, metallic and ionic characters. For a quantitative analysis of the relative strength of these components, their ionicities have been calculated by implanting the results of EET to the PVL model. It has been found that the ionicity of tantalum carbide is smaller than that of tantalum nitride. The EET results also reveal that the covalent electronic number of the strongest bond in the former is larger than that of the latter. All these suggest that the covalent bond of TaC is stronger than that of TaN, which coincides to that deduced from the first-principles method.

  15. Study of polysilane mainchain electronic structure by picosecond pulse radiolysis

    International Nuclear Information System (INIS)

    Habara, H.; Saeki, A.; Kunimi, Y.; Seki, S.; Kozawa, T.; Yoshida, Y.; Tagawa, S.

    2000-01-01

    The electronic structure of a charged polysilane molecle is studied. The transient absorption spectroscopy was carried out for charged radicals of poly (methylphenylsilane): PMPS by pico-second and nanosecond pulse radiolysis technique. It was observed that the peak of the transient absorption spectra shifted to longer wavelength region within a few nsec, and an increase was observed in the optical density at 370 nm, which had been already assigned to the radical anions of PMPS. It is ascribed to inter-segment electron transfer (intra-molecular transfer) through polymer chain. The nanosecond pulse radiolysis experiments gave similar kinetic traces in near-UV and IR region. This suggests the presence of an interband level, that is, a polaron level occupied by an excess electron or a hole. (author)

  16. Anomalous electronic structure and magnetoresistance in TaAs2.

    Science.gov (United States)

    Luo, Yongkang; McDonald, R D; Rosa, P F S; Scott, B; Wakeham, N; Ghimire, N J; Bauer, E D; Thompson, J D; Ronning, F

    2016-06-07

    The change in resistance of a material in a magnetic field reflects its electronic state. In metals with weakly- or non-interacting electrons, the resistance typically increases upon the application of a magnetic field. In contrast, negative magnetoresistance may appear under some circumstances, e.g., in metals with anisotropic Fermi surfaces or with spin-disorder scattering and semimetals with Dirac or Weyl electronic structures. Here we show that the non-magnetic semimetal TaAs2 possesses a very large negative magnetoresistance, with an unknown scattering mechanism. Density functional calculations find that TaAs2 is a new topological semimetal [ℤ2 invariant (0;111)] without Dirac dispersion, demonstrating that a negative magnetoresistance in non-magnetic semimetals cannot be attributed uniquely to the Adler-Bell-Jackiw chiral anomaly of bulk Dirac/Weyl fermions.

  17. Two-particle approach to the electronic structure of solids

    International Nuclear Information System (INIS)

    Gonis, A.

    2007-01-01

    Based on an extension of Hubbard's treatment of the electronic structure of correlated electrons in matter we propose a methodology that incorporates the scattering off the Coulomb interaction through the determination of a two-particle propagator. The Green function equations of motion are then used to obtain single-particle Green functions and related properties such as densities of states. The solutions of the equations of motion in two- and single-particle spaces are accomplished through applications of the coherent potential approximation. The formalism is illustrated by means of calculations for a single-band model system representing a linear arrangement of sites with nearest neighbor hopping and an one-site repulsion when two electrons of opposite spin occupy the same site in the lattice in the manner described by the so-called Hubbard Hamiltonian

  18. Carbon nanotube on Si(001): structural and electronic properties

    International Nuclear Information System (INIS)

    Orellana, W.; Fazzio, A.; Miwa, R.W.

    2003-01-01

    Full text: The promising nanoscale technology based on carbon nanotubes has attracted much attention due to the unique electronic, chemical and mechanical properties of the nanotubes. Single-wall carbon nanotubes (SWCNs) provide an ideal atomically uniform one dimensional (1D) conductors, having a strong electronic confinement around its circumference, which can be retained up to room temperature[1]. This interesting property may lead one to consider SWCNs as 1D conductors for the development of nanoscale electronic devices. In this work the structural and electronic properties of the contact between a metallic (6,6) SWCN adsorbed on a silicon (001) surface are studied from first-principles total-energy calculations. We consider two adsorption sites for the tube on the Si(001) surface: on the top of the Si-dimer rows and on the surface 'trench' between two consecutive dimer rows. Our results show a chemical bond between the nanotube and Si(001) when the tube is located along the 'trench', which corresponds to the only bound structure. We find a binding energy per tube length of 0.21 eV/angstrom. We also verified that the binding energy depends on the rotation of the tube. Typically, a rotation of 15 deg can reduce the binding energy up to 0.07 eV/angstrom. Our calculated electronic properties indicate that the most stable structure shows a subband associated to the tube/surface bond that cross the Fermi level. This result indicates an enhanced metallic behavior along the tube/surface contact characterizing a 1D quantum wire. The charge transfer between the Si surface and the tube is also discussed. [1] Z. Yao, C. Dekker, and P. Avouris in Carbon Nanotubes, M. S. Dresselhaus, G. Dresselhaus, and P. Avouris Eds., (Springer, Berlin 2001), p. 147. (author)

  19. Fast electronic structure methods for strongly correlated molecular systems

    International Nuclear Information System (INIS)

    Head-Gordon, Martin; Beran, Gregory J O; Sodt, Alex; Jung, Yousung

    2005-01-01

    A short review is given of newly developed fast electronic structure methods that are designed to treat molecular systems with strong electron correlations, such as diradicaloid molecules, for which standard electronic structure methods such as density functional theory are inadequate. These new local correlation methods are based on coupled cluster theory within a perfect pairing active space, containing either a linear or quadratic number of pair correlation amplitudes, to yield the perfect pairing (PP) and imperfect pairing (IP) models. This reduces the scaling of the coupled cluster iterations to no worse than cubic, relative to the sixth power dependence of the usual (untruncated) coupled cluster doubles model. A second order perturbation correction, PP(2), to treat the neglected (weaker) correlations is formulated for the PP model. To ensure minimal prefactors, in addition to favorable size-scaling, highly efficient implementations of PP, IP and PP(2) have been completed, using auxiliary basis expansions. This yields speedups of almost an order of magnitude over the best alternatives using 4-center 2-electron integrals. A short discussion of the scope of accessible chemical applications is given

  20. Expression and characterization of truncated human heme oxygenase (hHO-1) and a fusion protein of hHO-1 with human cytochrome P450 reductase.

    Science.gov (United States)

    Wilks, A; Black, S M; Miller, W L; Ortiz de Montellano, P R

    1995-04-04

    A human heme oxygenase (hHO-1) gene without the sequence coding for the last 23 amino acids has been expressed in Escherichia coli behind the pho A promoter. The truncated enzyme is obtained in high yields as a soluble, catalytically-active protein, making it available for the first time for detailed mechanistic studies. The purified, truncated hHO-1/heme complex is spectroscopically indistinguishable from that of the rat enzyme and converts heme to biliverdin when reconstituted with rat liver cytochrome P450 reductase. A self-sufficient heme oxygenase system has been obtained by fusing the truncated hHO-1 gene to the gene for human cytochrome P450 reductase without the sequence coding for the 20 amino acid membrane binding domain. Expression of the fusion protein in pCWori+ yields a protein that only requires NADPH for catalytic turnover. The failure of exogenous cytochrome P450 reductase to stimulate turnover and the insensitivity of the catalytic rate toward changes in ionic strength establish that electrons are transferred intramolecularly between the reductase and heme oxygenase domains of the fusion protein. The Vmax for the fusion protein is 2.5 times higher than that for the reconstituted system. Therefore, either the covalent tether does not interfere with normal docking and electron transfer between the flavin and heme domains or alternative but equally efficient electron transfer pathways are available that do not require specific docking.

  1. Strongly correlated electron materials. I. Theory of the quasiparticle structure

    International Nuclear Information System (INIS)

    Lopez-Aguilar, F.; Costa-Quintana, J.; Puig-Puig, L.

    1993-01-01

    In this paper we give a method for analyzing the renormalized electronic structure of the Hubbard systems. The first step is the determination of effective interactions from the random-phase approximation (RPA) and from an extended RPA (ERPA) that introduces vertex effects within the bubble polarization. The second step is the determination of the density of states deduced from the spectral functions. Its analysis leads us to conclude that these systems can exhibit three types of resonances in their electronic structures: the lower-, middle-, and upper-energy resonances. Furthermore, we analyze the conditions for which there is only one type of resonance and the causes that lead to the disappearance of the heavy-fermion state. We finally introduce the RPA and ERPA effective interactions within the strong-coupling theory and we give the conditions for obtaining coupling and superconductivity

  2. Phase Diagram and Electronic Structure of Praseodymium and Plutonium

    Directory of Open Access Journals (Sweden)

    Nicola Lanatà

    2015-01-01

    Full Text Available We develop a new implementation of the Gutzwiller approximation in combination with the local density approximation, which enables us to study complex 4f and 5f systems beyond the reach of previous approaches. We calculate from first principles the zero-temperature phase diagram and electronic structure of Pr and Pu, finding good agreement with the experiments. Our study of Pr indicates that its pressure-induced volume-collapse transition would not occur without change of lattice structure—contrarily to Ce. Our study of Pu shows that the most important effect originating the differentiation between the equilibrium densities of its allotropes is the competition between the Peierls effect and the Madelung interaction and not the dependence of the electron correlations on the lattice structure.

  3. Relationship between electronic structure and radioprotective activity of some indazoles

    International Nuclear Information System (INIS)

    Sokolov, Yu.A.

    2000-01-01

    The quantum-chemical study of electronic structure of 29 indasoles with complete optimization of geometry and search of quantitative link between the established characteristics and radioprotective activity (RPA) was carried out through the MNDO method with application of multiple linear and nonlinear regression analysis and the basic component method. The equations of correlation relationship between the RPA and electronic characteristics are presented. 10 indasole structures, the forecasted RPA values whereof (survival rate, %) equal 50% and above, are selected. The statistic significance of the obtained correlation equations and their regression coefficients make it possible to conclude, that the established relationships are not accidental and are prospective for forecasting RPA of other close compounds of the indasole series [ru

  4. Electronic structure of C and Si fullerenes and fullerides

    International Nuclear Information System (INIS)

    Saito, S.

    1996-01-01

    Fullerenes, i.e., cage-structure clusters are now studied intensively as a building unit for a new class of materials. The electronic structure of C 60 and Si 20 fullerenes and their fullerides obtained in the framework of the density-functional theory is discussed with emphasis on the electronic as well as the geometrical hierarchy in superconducting fullerides. In both C 60 and Si 20 fullerides, the charge transfer from alkali atoms to fullerenes and the hybridization between alkaline-earth states and fullerene states are observed. Also A 3 C 60 and (Ba 3 Si 3 Na rate at Si 20 ) 2 superconductors are found to have high Fermi-level density of states, although the mechanism giving it is different in two materials. Interesting materials to be produced in the future are also discussed. (orig.)

  5. Comparing two iteration algorithms of Broyden electron density mixing through an atomic electronic structure computation

    International Nuclear Information System (INIS)

    Zhang Man-Hong

    2016-01-01

    By performing the electronic structure computation of a Si atom, we compare two iteration algorithms of Broyden electron density mixing in the literature. One was proposed by Johnson and implemented in the well-known VASP code. The other was given by Eyert. We solve the Kohn-Sham equation by using a conventional outward/inward integration of the differential equation and then connect two parts of solutions at the classical turning points, which is different from the method of the matrix eigenvalue solution as used in the VASP code. Compared to Johnson’s algorithm, the one proposed by Eyert needs fewer total iteration numbers. (paper)

  6. Electronic structure of a striped nickelate studied by the exact exchange for correlated electrons (EECE) approach

    KAUST Repository

    Schwingenschlögl, Udo

    2009-12-01

    Motivated by a RIXS study of Wakimoto, et al.(Phys. Rev. Lett., 102 (2009) 157001) we use density functional theory to analyze the magnetic order in the nickelate La5/3Sr1/3NiO4 and the details of its crystal and electronic structure. We compare the generalized gradient approximation to the hybrid functional approach of exact exchange for correlated electrons (EECE). In contrast to the former, the latter reproduces the insulating state of the compound and the midgap states. The EECE approach, in general, appears to be appropriate for describing stripe phases in systems with orbital degrees of freedom. Copyright © EPLA, 2009.

  7. Role of Heme and Heme-Proteins in Trypanosomatid Essential Metabolic Pathways

    Directory of Open Access Journals (Sweden)

    Karina E. J. Tripodi

    2011-01-01

    Full Text Available Around the world, trypanosomatids are known for being etiological agents of several highly disabling and often fatal diseases like Chagas disease (Trypanosoma cruzi, leishmaniasis (Leishmania spp., and African trypanosomiasis (Trypanosoma brucei. Throughout their life cycle, they must cope with diverse environmental conditions, and the mechanisms involved in these processes are crucial for their survival. In this review, we describe the role of heme in several essential metabolic pathways of these protozoans. Notwithstanding trypanosomatids lack of the complete heme biosynthetic pathway, we focus our discussion in the metabolic role played for important heme-proteins, like cytochromes. Although several genes for different types of cytochromes, involved in mitochondrial respiration, polyunsaturated fatty acid metabolism, and sterol biosynthesis, are annotated at the Tritryp Genome Project, the encoded proteins have not yet been deeply studied. We pointed our attention into relevant aspects of these protein functions that are amenable to be considered for rational design of trypanocidal agents.

  8. Electronic structure and superconductivity of FeSe-related superconductors.

    Science.gov (United States)

    Liu, Xu; Zhao, Lin; He, Shaolong; He, Junfeng; Liu, Defa; Mou, Daixiang; Shen, Bing; Hu, Yong; Huang, Jianwei; Zhou, X J

    2015-05-13

    FeSe superconductors and their related systems have attracted much attention in the study of iron-based superconductors owing to their simple crystal structure and peculiar electronic and physical properties. The bulk FeSe superconductor has a superconducting transition temperature (Tc) of ~8 K and it can be dramatically enhanced to 37 K at high pressure. On the other hand, its cousin system, FeTe, possesses a unique antiferromagnetic ground state but is non-superconducting. Substitution of Se with Te in the FeSe superconductor results in an enhancement of Tc up to 14.5 K and superconductivity can persist over a large composition range in the Fe(Se,Te) system. Intercalation of the FeSe superconductor leads to the discovery of the AxFe2-ySe2 (A = K, Cs and Tl) system that exhibits a Tc higher than 30 K and a unique electronic structure of the superconducting phase. A recent report of possible high temperature superconductivity in single-layer FeSe/SrTiO3 films with a Tc above 65 K has generated much excitement in the community. This pioneering work opens a door for interface superconductivity to explore for high Tc superconductors. The distinct electronic structure and superconducting gap, layer-dependent behavior and insulator-superconductor transition of the FeSe/SrTiO3 films provide critical information in understanding the superconductivity mechanism of iron-based superconductors. In this paper, we present a brief review of the investigation of the electronic structure and superconductivity of the FeSe superconductor and related systems, with a particular focus on the FeSe films.

  9. Structural and electronic properties of hydrosilylated silicon surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Baumer, A.

    2005-11-15

    The structural and electronic properties of alkyl-terminated Si surfaces prepared by thermallyinduced hydrosilylation have been studied in detail in the preceding chapters. Various surfaces have been used for the functionalization ranging from crystalline Si over amorphous hydrogenated Si to nanoscaled materials such as Si nanowires and nanoparticles. In each case, the alkyl-terminated surfaces have been compared to the native oxidized and H-terminated surfaces. (orig.)

  10. Thick-Restart Lanczos Method for Electronic Structure Calculations

    International Nuclear Information System (INIS)

    Simon, Horst D.; Wang, L.-W.; Wu, Kesheng

    1999-01-01

    This paper describes two recent innovations related to the classic Lanczos method for eigenvalue problems, namely the thick-restart technique and dynamic restarting schemes. Combining these two new techniques we are able to implement an efficient eigenvalue problem solver. This paper will demonstrate its effectiveness on one particular class of problems for which this method is well suited: linear eigenvalue problems generated from non-self-consistent electronic structure calculations

  11. Electronic structure of ternary hydrides based on light elements

    Energy Technology Data Exchange (ETDEWEB)

    Orgaz, E. [Departamento de Fisica y Quimica Teorica, Facultad de Quimica, Universidad Nacional Autonoma de Mexico, CP 04510 Coyoacan, Mexico, D.F. (Mexico)]. E-mail: orgaz@eros.pquim.unam.mx; Membrillo, A. [Departamento de Fisica y Quimica Teorica, Facultad de Quimica, Universidad Nacional Autonoma de Mexico, CP 04510 Coyoacan, Mexico, D.F. (Mexico); Castaneda, R. [Departamento de Fisica y Quimica Teorica, Facultad de Quimica, Universidad Nacional Autonoma de Mexico, CP 04510 Coyoacan, Mexico, D.F. (Mexico); Aburto, A. [Departamento de Fisica, Facultad de Ciencias, Universidad Nacional Autonoma de Mexico, CP 04510 Coyoacan, Mexico, D.F. (Mexico)

    2005-12-08

    Ternary hydrides based on light elements are interesting owing to the high available energy density. In this work we focused into the electronic structure of a series of known systems having the general formula AMH{sub 4}(A=Li,Na,M=B,Al). We computed the energy bands and the total and partial density of states using the linear-augmented plane waves method. In this report, we discuss the chemical bonding in this series of complex hydrides.

  12. Final Technical Report: Electronic Structure Workshop (ES13)

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Shiwei [College of William and Mary, Williamsburg, VA (United States)

    2015-02-26

    The 25th Annual Workshop on Recent Developments in Electronic Structure Methods (ES2013) was successfully held at the College of William & Mary in Williamsburg VA on June 11-14, 2013. The workshop website is at http://es13.wm.edu/ , which contains updated information on the workshop and a permanent archive of the scientific contents. DOE's continued support has been instrumental to the success of the workshop.

  13. Formalized Medical Guidelines and a Structured Electronic Health Record.

    Czech Academy of Sciences Publication Activity Database

    Peleška, Jan; Anger, Z.; Buchtela, David; Šebesta, K.; Tomečková, Marie; Veselý, Arnošt; Zvára, K.; Zvárová, Jana

    2005-01-01

    Roč. 11, - (2005), s. 4652-4656 ISSN 1727-1983. [EMBEC'05. European Medical and Biomedical Conference /3./. Prague, 20.11.2005-25.11.2005] R&D Projects: GA AV ČR 1ET200300413 Institutional research plan: CEZ:AV0Z10300504 Keywords : formalization of guidelines in cardilogy * GLIF model * structure electronic health record * algorithm in cardiovascular diagnostics and treatment Subject RIV: BD - Theory of Information

  14. Dissociative recombination of interstellar ions: electronic structure calculations for HCO+

    International Nuclear Information System (INIS)

    Kraemer, W.P.; Hazi, A.U.

    1985-01-01

    The present study of the interstellar formyl ion HCO + is the first attempt to investigate dissociative recombination for a triatomic molecular ion using an entirely theoretical approach. We describe a number of fairly extensive electronic structure calculations that were performed to determine the reaction mechanism of the e-HCO + process. Similar calculations for the isoelectronic ions HOC + and HN 2 + are in progress. 60 refs

  15. Strain-induced changes to the electronic structure of germanium

    KAUST Repository

    Tahini, H. A.

    2012-04-17

    Density functional theory calculations (DFT) are used to investigate the strain-induced changes to the electronic structure of biaxially strained (parallel to the (001), (110) and (111) planes) and uniaxially strained (along the [001], [110] and [111] directions) germanium (Ge). It is calculated that a moderate uniaxial strain parallel to the [111] direction can efficiently transform Ge to a direct bandgap material with a bandgap energy useful for technological applications. © 2012 IOP Publishing Ltd.

  16. Structured electron beams from nano-engineered cathodes

    Energy Technology Data Exchange (ETDEWEB)

    Lueangaramwong, A. [NICADD, DeKalb; Mihalcea, D. [NICADD, DeKalb; Andonian, G. [RadiaBeam Tech.; Piot, P. [Fermilab

    2017-03-07

    The ability to engineer cathodes at the nano-scale have open new possibilities such as enhancing quantum eciency via surface-plasmon excitation, forming ultra-low-emittance beams, or producing structured electron beams. In this paper we present numerical investigations of the beam dynamics associated to this class of cathode in the weak- and strong-field regimes.We finally discuss the possible applications of some of the achievable cathode patterns when coupled with other phase space manipulations.

  17. Strain-induced changes to the electronic structure of germanium

    KAUST Repository

    Tahini, H. A.; Chroneos, Alexander I.; Grimes, Robin W.; Schwingenschlö gl, Udo; Dimoulas, Athanasios Dimoulas

    2012-01-01

    Density functional theory calculations (DFT) are used to investigate the strain-induced changes to the electronic structure of biaxially strained (parallel to the (001), (110) and (111) planes) and uniaxially strained (along the [001], [110] and [111] directions) germanium (Ge). It is calculated that a moderate uniaxial strain parallel to the [111] direction can efficiently transform Ge to a direct bandgap material with a bandgap energy useful for technological applications. © 2012 IOP Publishing Ltd.

  18. An automatic chip structure optical inspection system for electronic components

    Science.gov (United States)

    Song, Zhichao; Xue, Bindang; Liang, Jiyuan; Wang, Ke; Chen, Junzhang; Liu, Yunhe

    2018-01-01

    An automatic chip structure inspection system based on machine vision is presented to ensure the reliability of electronic components. It consists of four major modules, including a metallographic microscope, a Gigabit Ethernet high-resolution camera, a control system and a high performance computer. An auto-focusing technique is presented to solve the problem that the chip surface is not on the same focusing surface under the high magnification of the microscope. A panoramic high-resolution image stitching algorithm is adopted to deal with the contradiction between resolution and field of view, caused by different sizes of electronic components. In addition, we establish a database to storage and callback appropriate parameters to ensure the consistency of chip images of electronic components with the same model. We use image change detection technology to realize the detection of chip images of electronic components. The system can achieve high-resolution imaging for chips of electronic components with various sizes, and clearly imaging for the surface of chip with different horizontal and standardized imaging for ones with the same model, and can recognize chip defects.

  19. Atomic structures and electronic properties of phosphorene grain boundaries

    International Nuclear Information System (INIS)

    Guo, Yu; Zhou, Si; Bai, Yizhen; Zhao, Jijun; Zhang, Junfeng

    2016-01-01

    Grain boundary (GB) is one main type of defects in two-dimensional (2D) crystals, and has significant impact on the physical properties of 2D materials. Phosphorene, a recently synthesized 2D semiconductor, possesses a puckered honeycomb lattice and outstanding electronic properties. It is very interesting to know the possible GBs present in this novel material, and how their properties differ from those in the other 2D materials. Based on first-principles calculations, we explore the atomic structure, thermodynamic stability, and electronic properties of phosphorene GBs. A total of 19 GBs are predicted and found to be energetically stable with formation energies much lower than those in graphene. These GBs do not severely affect the electronic properties of phosphorene: the band gap of perfect phosphorene is preserved, and the electron mobilities are only moderately reduced in these defective systems. Our theoretical results provide vital guidance for experimental tailoring the electronic properties of phosphorene as well as the device applications using phosphorene materials. (paper)

  20. Electronic shell structure and chemisorption on gold nanoparticles

    DEFF Research Database (Denmark)

    Larsen, Ask Hjorth; Kleis, Jesper; Thygesen, Kristian Sommer

    2011-01-01

    to distort considerably, creating large band gaps at the Fermi level. For up to 200 atoms we consider structures generated with a simple EMT potential and clusters based on cuboctahedra and icosahedra. All types of cluster geometry exhibit jelliumlike electronic shell structure. We calculate adsorption...... energies of several atoms on the cuboctahedral clusters. Adsorption energies are found to vary abruptly at magic numbers. Using a Newns-Anderson model we find that the effect of magic numbers on adsorption energy can be understood from the location of adsorbate-induced states with respect to the cluster...

  1. DFTB Parameters for the Periodic Table: Part 1, Electronic Structure.

    Science.gov (United States)

    Wahiduzzaman, Mohammad; Oliveira, Augusto F; Philipsen, Pier; Zhechkov, Lyuben; van Lenthe, Erik; Witek, Henryk A; Heine, Thomas

    2013-09-10

    A parametrization scheme for the electronic part of the density-functional based tight-binding (DFTB) method that covers the periodic table is presented. A semiautomatic parametrization scheme has been developed that uses Kohn-Sham energies and band structure curvatures of real and fictitious homoatomic crystal structures as reference data. A confinement potential is used to tighten the Kohn-Sham orbitals, which includes two free parameters that are used to optimize the performance of the method. The method is tested on more than 100 systems and shows excellent overall performance.

  2. Asymptotic convergence for iterative optimization in electronic structure

    International Nuclear Information System (INIS)

    Lippert, Ross A.; Sears, Mark P.

    2000-01-01

    There have recently been a number of proposals for solving large electronic structure problems (local-density approximation, Hartree-Fock, and tight-binding methods) iteratively with a computational effort proportional to the size of the system. The effort needed to perform a single iteration in these schemes is well understood but the convergence rate has been an empirical matter. This paper will show that many of the proposed methods have a single underlying geometrical structure, which has a specific asymptotic convergence behavior, and that behavior can be understood in terms of some simple condition numbers based on the spectrum of the Hamiltonian. (c) 2000 The American Physical Society

  3. Highlighting material structure with transmission electron diffraction correlation coefficient maps

    International Nuclear Information System (INIS)

    Kiss, Ákos K.; Rauch, Edgar F.; Lábár, János L.

    2016-01-01

    Correlation coefficient maps are constructed by computing the differences between neighboring diffraction patterns collected in a transmission electron microscope in scanning mode. The maps are shown to highlight material structural features like grain boundaries, second phase particles or dislocations. The inclination of the inner crystal interfaces are directly deduced from the resulting contrast. - Highlights: • We propose a novel technique to image the structure of polycrystalline TEM-samples. • Correlation coefficients maps highlights the evolution of the diffracting signal. • 3D views of grain boundaries are provided for nano-particles or polycrystals.

  4. Heme metabolism as an integral part of iron homeostasis

    Directory of Open Access Journals (Sweden)

    Paweł Lipiński

    2014-01-01

    Full Text Available Heme, a ferrous iron protoporphyrin IX complex, is employed as a prosthetic group in a number of diverse heme proteins that participate in important cellular and systemic physiological processes. Provision of an adequate amount of iron for heme biosynthesis is one of the elemental hallmarks of intracellular iron homeostasis. In the cell the bioavailability of iron for the two main iron biological pathways – heme synthesis and the biogenesis of iron-sulfur clusters ([Fe-S] – is mainly regulated by the IRP/IRE posttranscriptional system. The biogenesis of [Fe-S] centers is crucial for heme synthesis because these co-factors determine the activity of IRP1 and that of ferrochelatase, an enzyme responsible for the insertion of an iron into protoporphyrin IX to produce heme. On the other hand, delivery of iron for heme and hemoglobin synthesis in erythroblasts, precursors of erythrocytes in bone marrow, is an indispensable element of body iron homeostasis. This process relies on the recovery of iron from senescent red blood cells through the enzymatic degradation of heme molecules and recycling of iron to the circulation. Molecular coordination of these processes involves the activity of heme oxygenase 1, IRP1 and IRP2 as well as the functioning of the hepcidin-ferroportin regulatory axis. Recent studies show in mammals the existence of an expanded system of proteins involved in the transport of intact heme molecules at the cellular and systemic levels. The biological role of this system is of particular importance when the concentration of free heme reaches a toxic level in the body (intravascular hemolysis as well as locally in cells having intensive heme metabolism such as erythroblasts and macrophages.

  5. [Heme metabolism as an integral part of iron homeostasis].

    Science.gov (United States)

    Lipiński, Paweł; Starzyński, Rafał R; Styś, Agnieszka; Gajowiak, Anna; Staroń, Robert

    2014-01-02

    Heme, a ferrous iron protoporphyrin IX complex, is employed as a prosthetic group in a number of diverse heme proteins that participate in important cellular and systemic physiological processes. Provision of an adequate amount of iron for heme biosynthesis is one of the elemental hallmarks of intracellular iron homeostasis. In the cell the bioavailability of iron for the two main iron biological pathways--heme synthesis and the biogenesis of iron-sulfur clusters ([Fe-S])--is mainly regulated by the IRP/IRE posttranscriptional system. The biogenesis of [Fe-S] centers is crucial for heme synthesis because these co-factors determine the activity of IRP1 and that of ferrochelatase, an enzyme responsible for the insertion of an iron into protoporphyrin IX to produce heme. On the other hand, delivery of iron for heme and hemoglobin synthesis in erythroblasts, precursors of erythrocytes in bone marrow, is an indispensable element of body iron homeostasis. This process relies on the recovery of iron from senescent red blood cells through the enzymatic degradation of heme molecules and recycling of iron to the circulation. Molecular coordination of these processes involves the activity of heme oxygenase 1, IRP1 and IRP2 as well as the functioning of the hepcidin-ferroportin regulatory axis. Recent studies show in mammals the existence of an expanded system of proteins involved in the transport of intact heme molecules at the cellular and systemic levels. The biological role of this system is of particular importance when the concentration of free heme reaches a toxic level in the body (intravascular hemolysis) as well as locally in cells having intensive heme metabolism such as erythroblasts and macrophages.

  6. Electronic structures near surfaces of perovskite type oxides

    International Nuclear Information System (INIS)

    Hara, Toru

    2005-01-01

    This work is intended to draw attention to the origin of the electronic structures near surfaces of perovskite type oxides. Deep states were observed by ultraviolet photoelectron spectroscopic measurements. The film thickness dependent electronic structures near surfaces of (Ba 0.5 Sr 0.5 )TiO 3 thin films were observed. As for the 117-308 nm thick (Ba 0.5 Sr 0.5 )TiO 3 films, deep states were lying at 0.20, 0.55, and 0.85 eV below the quasi-fermi level, respectively. However, as for the 40 nm thick (Ba 0.5 Sr 0.5 )TiO 3 film, the states were overlapped. The A-site doping affected electronic structures near surfaces of SrTiO 3 single crystals. No evolution of deep states in non-doped SrTiO 3 single crystal was observed. However, the evolution of deep states in La-doped SrTiO 3 single crystal was observed

  7. Transmission electron microscopy in molecular structural biology: A historical survey.

    Science.gov (United States)

    Harris, J Robin

    2015-09-01

    In this personal, historic account of macromolecular transmission electron microscopy (TEM), published data from the 1940s through to recent times is surveyed, within the context of the remarkable progress that has been achieved during this time period. The evolution of present day molecular structural biology is described in relation to the associated biological disciplines. The contribution of numerous electron microscope pioneers to the development of the subject is discussed. The principal techniques for TEM specimen preparation, thin sectioning, metal shadowing, negative staining and plunge-freezing (vitrification) of thin aqueous samples are described, with a selection of published images to emphasise the virtues of each method. The development of digital image analysis and 3D reconstruction is described in detail as applied to electron crystallography and reconstructions from helical structures, 2D membrane crystals as well as single particle 3D reconstruction of icosahedral viruses and macromolecules. The on-going development of new software, algorithms and approaches is highlighted before specific examples of the historical progress of the structural biology of proteins and viruses are presented. Copyright © 2014 Elsevier Inc. All rights reserved.

  8. Direct electron crystallographic determination of zeolite zonal structures

    International Nuclear Information System (INIS)

    Dorset, Douglas L.; Gilmore, Christopher J.; Jorda, Jose Luis; Nicolopoulos, Stavros

    2007-01-01

    The prospect for improving the success of ab initio zeolite structure investigations with electron diffraction data is evaluated. First of all, the quality of intensities obtained by precession electron diffraction at small hollow cone illumination angles is evaluated for seven representative materials: ITQ-1, ITQ-7, ITQ-29, ZSM-5, ZSM-10, mordenite, and MCM-68. It is clear that, for most examples, an appreciable fraction of a secondary scattering perturbation is removed by precession at small angles. In one case, ZSM-10, it can also be argued that precession diffraction produces a dramatically improved 'kinematical' data set. There seems to no real support for application of a Lorentz correction to these data and there is no reason to expect for any of these samples that a two-beam dynamical scattering relationship between structure factor amplitude and observed intensity should be valid. Removal of secondary scattering by the precession mode appears to facilitate ab initio structure analysis. Most zeolite structures investigated could be solved by maximum entropy and likelihood phasing via error-correcting codes when precession data were used. Examples include the projected structure of mordenite that could not be determined from selected area data alone. One anomaly is the case of ZSM-5, where the best structure determination in projection is made from selected area diffraction data. In a control study, the zonal structure of SSZ-48 could be determined from selected area diffraction data by either maximum entropy and likelihood or traditional direct methods. While the maximum entropy and likelihood approach enjoys some advantages over traditional direct methods (non-dependence on predicted phase invariant sums), some effort must be made to improve the figures of merit used to identify potential structure solutions

  9. Moessbauer spectroscopic evidence on the heme binding to the proximal histidine in unfolded carbonmonoxy myoglobin by guanidine hydrochloride

    Energy Technology Data Exchange (ETDEWEB)

    Harami, Taikan, E-mail: harami.taikan@jaea.go.jp [Japan Atomic Energy Agency (Japan); Kitao, Shinji; Kobayashi, Yasuhiro [Kyoto University, Research Reactor Institute (Japan); Mitsui, Takaya [Japan Atomic Energy Agency (Japan)

    2008-01-15

    The unfolded heme structure in myoglobin is controversial because of no chance of direct X-ray structure analyses. The unfolding of carbonmonoxy myoglobin (MbCO) by guanidine hydrochloride (GdnHCl) was studied by the Moessbauer spectroscopy. The spectra show the presence of a sort of spectrum in the unfolded MbCO, independent on the concentration of GdnHCl from 1 to 6 M and the increase of the fraction of unfolded MbCO, depending on the GdnHCl concentration. The isomer shift of the iron of heme in the unfolded MbCO was identified to be different from that of the native MbCO as the globin structure in Mb collapses under the unfolded conditions. This result and the existing related Moessbauer data proved that the heme in the unfolded MbCO may remain coordinated to the proximal histidine.

  10. Electronic structure of free and doped actinides: N and Z dependences of energy levels and electronic structure parameters

    International Nuclear Information System (INIS)

    Kulagin, N.

    2005-01-01

    Theoretical study of electronic structure of antinide ions and its dependence on N and Z are presented in this paper. The main 5f N and excited 5f N n'l' N' configurations of actinides have been studied using Hartree-Fock-Pauli approximation. Results of calculations of radial integrals and the energy of X-ray lines for all 5f ions with electronic state AC +1 -AC +4 show approximate dependence on N and Z. A square of N and cubic of Z are ewalized for the primary electronic parameters of the actinides. Theoretical values of radial integrals for free actinides and for ions in a cluster AC +n :[L] k are compared, too

  11. Novel Insights in Mammalian Catalase Heme Maturation: Effect of NO and Thioredoxin-1

    Science.gov (United States)

    Chakravarti, Ritu; Gupta, Karishma; Majors, Alana; Ruple, Lisa; Aronica, Mark; Stuehr, Dennis J.

    2016-01-01

    Catalase is a tetrameric heme-containing enzyme with essential antioxidant functions in biology. Multiple factors including nitric oxide (NO) have been shown to attenuate its activity. However, the possible impact of NO in relation to the maturation of active catalase, including its heme acquisition and tetramer formation, has not been investigated. We found that NO attenuates heme insertion into catalase in both short-term and long-term incubations. The NO inhibition in catalase heme incorporation was associated with defective oligomerization of catalase, such that inactive catalase monomers and dimers accumulated in place of the mature tetrameric enzyme. We also found that GAPDH plays a key role in mediating these NO effects on the structure and activity of catalase. Moreover, the NO sensitivity of catalase maturation could be altered up or down by manipulating the cellular expression level or activity of thioredoxin-1, a known protein-SNO denitrosylase enzyme. In a mouse model of allergic inflammatory asthma, we found that lungs from allergen-challenged mice contained a greater percentage of dimeric catalase relative to tetrameric catalase in the unchallenged control, suggesting that the mechanisms described here are in play in the allergic asthma model. Together, our study shows how maturation of active catalase can be influenced by NO, S-nitrosylated GAPDH, and thioredoxin-1, and how maturation may become compromised in inflammatory conditions such as asthma. PMID:25659933

  12. Novel insights in mammalian catalase heme maturation: effect of NO and thioredoxin-1.

    Science.gov (United States)

    Chakravarti, Ritu; Gupta, Karishma; Majors, Alana; Ruple, Lisa; Aronica, Mark; Stuehr, Dennis J

    2015-05-01

    Catalase is a tetrameric heme-containing enzyme with essential antioxidant functions in biology. Multiple factors including nitric oxide (NO) have been shown to attenuate its activity. However, the possible impact of NO in relation to the maturation of active catalase, including its heme acquisition and tetramer formation, has not been investigated. We found that NO attenuates heme insertion into catalase in both short-term and long-term incubations. The NO inhibition in catalase heme incorporation was associated with defective oligomerization of catalase, such that inactive catalase monomers and dimers accumulated in place of the mature tetrameric enzyme. We also found that GAPDH plays a key role in mediating these NO effects on the structure and activity of catalase. Moreover, the NO sensitivity of catalase maturation could be altered up or down by manipulating the cellular expression level or activity of thioredoxin-1, a known protein-SNO denitrosylase enzyme. In a mouse model of allergic inflammatory asthma, we found that lungs from allergen-challenged mice contained a greater percentage of dimeric catalase relative to tetrameric catalase in the unchallenged control, suggesting that the mechanisms described here are in play in the allergic asthma model. Together, our study shows how maturation of active catalase can be influenced by NO, S-nitrosylated GAPDH, and thioredoxin-1, and how maturation may become compromised in inflammatory conditions such as asthma. Copyright © 2015 Elsevier Inc. All rights reserved.

  13. Electronic Structure Approach to Tunable Electronic Properties of Hybrid Organic-Inorganic Perovskites

    Science.gov (United States)

    Liu, Garnett; Huhn, William; Mitzi, David B.; Kanai, Yosuke; Blum, Volker

    We present a study of the electronic structure of layered hybrid organic-inorganic perovskite (HOIP) materials using all-electron density-functional theory. Varying the nature of the organic and inorganic layers should enable systematically fine-tuning the carrier properties of each component. Using the HSE06 hybrid density functional including spin-orbit coupling (SOC), we validate the principle of tuning subsystem-specific parts of the electron band structures and densities of states in CH3NH3PbX3 (X=Cl, Br, I) compared to a modified organic component in layered (C6H5C2H4NH3) 2PbX4 (X=Cl, Br, I) and C20H22S4N2PbX4 (X=Cl, Br, I). We show that tunable shifts of electronic levels indeed arise by varying Cl, Br, I as the inorganic components, and CH3NH3+ , C6H5C2H4NH3+ , C20H22S4N22 + as the organic components. SOC is found to play an important role in splitting the conduction bands of the HOIP compounds investigated here. The frontier orbitals of the halide shift, increasing the gap, when Cl is substituted for Br and I.

  14. The electron-electron instability in a spherical plasma structure with an intermediate double layer

    International Nuclear Information System (INIS)

    Lapuerta, V.; Ahedo, E.

    2003-01-01

    A linear dynamic model of a spherical plasma structure with an intermediate double layer is analyzed in the high-frequency range. The two ion populations tend to stay frozen in their stationary response and this prevents the displacement of the double layer. Different electron modes dominate the plasma dynamics in each quasineutral region. The electrostatic potential and the electron current are the magnitudes most perturbed. The structure develops a reactive electron-electron instability, which is made up of a countable family of eigenmodes. Space-charge effects must be included in the quasineutral regions to determine the eigenmode carrying the maximum growth rate. Except for very small Debye lengths, the fundamental eigenmode governs the instability. The growth rate for the higher harmonics approaches that of an infinite plasma. The instability modes develop mainly on the plasma at the high-potential side of the double layer. The influence of the parameters defining the stationary solution on the instability growth rate is investigated, and the parametric regions of stability are found. The comparison with a couple of experiments on plasma contactors is satisfactory

  15. Electronic structure and electron-phonon coupling in layered copper oxide superconductors

    International Nuclear Information System (INIS)

    Pickett, W.E.; Cohen, R.E.; Krakauer, H.

    1991-01-01

    Experimental data on the layered Cu-O superconductors seem more and more to reflect normal Fermi-liquid behavior and substantial correspondence with band structure predictions. Recent self-consistent, microscopic band theoretic calculations of the electronic structure, lattice instabilities, phonon frequencies, and electron-phonon coupling characteristics and strength for La 2 CuO 4 and YBa 2 Cu 3 O 7 are reviewed. A dominant feature of the coupling is a novel Madelung-like contribution which would be screened out in high density of states superconductors but survives in cuprates because of weak screening. Local density functional theory correctly predicts the instability of (La, Ba) 2 CuO 4 to both the low-temperature orthorhombic phase (below room temperature) and the lower-temperature tetragonal phase (below 50 K). (orig.)

  16. Software abstractions and computational issues in parallel structure adaptive mesh methods for electronic structure calculations

    Energy Technology Data Exchange (ETDEWEB)

    Kohn, S.; Weare, J.; Ong, E.; Baden, S.

    1997-05-01

    We have applied structured adaptive mesh refinement techniques to the solution of the LDA equations for electronic structure calculations. Local spatial refinement concentrates memory resources and numerical effort where it is most needed, near the atomic centers and in regions of rapidly varying charge density. The structured grid representation enables us to employ efficient iterative solver techniques such as conjugate gradient with FAC multigrid preconditioning. We have parallelized our solver using an object- oriented adaptive mesh refinement framework.

  17. Structural and electronic properties of La C[sub 82

    Energy Technology Data Exchange (ETDEWEB)

    Laasonen, K.; Andreoni, W.; Parrinello, M. (Zurich Research Lab., Rueschlikon (Switzerland))

    1992-12-18

    The structural and electronic properties of the La C[sub 82] fullerene have been investigated by means of the Car-Parrinello method, which is based on the local density approximation of the density functional theory. The topological arrangement of the C[sub 82] cage was assumed to be a C[sub 3v] symmetry isomer. Three configurations were considered, one with the lanthanum atom at the center of the cluster, one with it along the threefold axis, and one with it at a low-symmetry, highly coordinated site. The structure was fully relaxed and it was found that the last of these configurations is energetically preferred. In this position, the lanthanum atom is nearly in a La[sup 3+] state and the unpaired electron is somewhat delocalized on the cage, in agreement with available experimental data. This arrangement suggests that the chemical shifts of the 5s and 5p lanthanum states can be used as a structural probe and as a way of further validating this picture. It is argued that this conclusion is not affected by the assumed fullerene structure.

  18. Valence band electronic structure of Pd based ternary chalcogenide superconductors

    Energy Technology Data Exchange (ETDEWEB)

    Lohani, H. [Institute of Physics, Sachivalaya Marg, Bhubaneswar 751005 (India); Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400085 (India); Mishra, P. [Institute of Physics, Sachivalaya Marg, Bhubaneswar 751005 (India); Goyal, R.; Awana, V.P.S. [National Physical Laboratory(CSIR), Dr. K. S. Krishnan Road, New Delhi 110012 (India); Sekhar, B.R., E-mail: sekhar@iopb.res.in [Institute of Physics, Sachivalaya Marg, Bhubaneswar 751005 (India); Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400085 (India)

    2016-12-15

    Highlights: • VB Photoemission study and DFT calculations on Pd based ternary superconductors are presented. • Nb{sub 2}Pd{sub 0.95}S{sub 5} shows a temperature dependent pseudogap. • VB spectral features of ternary superconductors are correlated to their structural geometry. - Abstract: We present a comparative study of the valence band electronic structure of Pd based ternary chalcogenide superconductors Nb{sub 2}Pd{sub 0.95}S{sub 5}, Ta{sub 2}Pd{sub 0.97}S{sub 6} and Ta{sub 2}Pd{sub 0.97}Te{sub 6} using experimental photoemission spectroscopy and density functional based theoretical calculations. We observe a qualitatively similarity between valence band (VB) spectra of Nb{sub 2}Pd{sub 0.95}S{sub 5} and Ta{sub 2}Pd{sub 0.97}S{sub 6}. Further, we find a pseudogap feature in Nb{sub 2}Pd{sub 0.95}S{sub 5} at low temperature, unlike other two compounds. We have correlated the structural geometry with the differences in VB spectra of these compounds. The different atomic packing in these compounds could vary the strength of inter-orbital hybridization among various atoms which leads to difference in their electronic structure as clearly observed in our DOS calculations.

  19. Atomic and electronic structures of an extremely fragile liquid.

    Science.gov (United States)

    Kohara, Shinji; Akola, Jaakko; Patrikeev, Leonid; Ropo, Matti; Ohara, Koji; Itou, Masayoshi; Fujiwara, Akihiko; Yahiro, Jumpei; Okada, Junpei T; Ishikawa, Takehiko; Mizuno, Akitoshi; Masuno, Atsunobu; Watanabe, Yasuhiro; Usuki, Takeshi

    2014-12-18

    The structure of high-temperature liquids is an important topic for understanding the fragility of liquids. Here we report the structure of a high-temperature non-glass-forming oxide liquid, ZrO2, at an atomistic and electronic level. The Bhatia-Thornton number-number structure factor of ZrO2 does not show a first sharp diffraction peak. The atomic structure comprises ZrO5, ZrO6 and ZrO7 polyhedra with a significant contribution of edge sharing of oxygen in addition to corner sharing. The variety of large oxygen coordination and polyhedral connections with short Zr-O bond lifetimes, induced by the relatively large ionic radius of zirconium, disturbs the evolution of intermediate-range ordering, which leads to a reduced electronic band gap and increased delocalization in the ionic Zr-O bonding. The details of the chemical bonding explain the extremely low viscosity of the liquid and the absence of a first sharp diffraction peak, and indicate that liquid ZrO2 is an extremely fragile liquid.

  20. Auger electron spectroscopy analysis of high metal content micro-structures grown by electron beam induced deposition

    International Nuclear Information System (INIS)

    Cicoira, F.; Hoffmann, P.; Olsson, C.O.A.; Xanthopoulos, N.; Mathieu, H.J.; Doppelt, P.

    2005-01-01

    An auger electron spectroscopy study was carried out on Rh-containing micro-structures grown by electron beam induced deposition (EBID) of the iso-structural and iso-electronic precursors [RhCl(PF 3 ) 2 ] 2 and [RhCl(CO) 2 ] 2 . A material containing between 55 and 60 at.% Rh was obtained from both precursors. The chemical composition of structures grown from the two different precursors indicates a similar decomposition mechanism. Deposits grown from [RhCl(PF 3 ) 2 ] 2 showed a chemical composition independent of electron energy and electron dose in the investigated range of conditions

  1. Electronic structure of PPP@ZnO from all-electron quasiarticle calculations

    Science.gov (United States)

    Höffling, Benjamin; Nabok, Dimitri; Draxl, Claudia; Condensed Matter Theory Group, Humboldt University Berlin Team

    We investigate the electronic properties of poly(para-phenylene) (PPP) adsorbed on the non-polar (001) surface of rocksalt (rs) ZnO using all-electron density functional theory (DFT) as well as quasiparticle (QP) calculations within the GW approach. A particular focus is put on the electronic band discontinuities at the interface, where we investigate the impact of quantum confinement, molecular polarization, and charge rearrangement. For our prototypical system, PPP@ZnO, we find a type-I heterostructure. Comparison of the band offsets derived from a QP-treatment of the hybrid system with predictions based on mesoscopic methods, like the Shockley-Anderson model or alignment via the electrostatic potential, reveals the inadequacy of these simple approaches for the prediction of the electronic structure of such inorganic/organic heterosystems. Finally, we explore the optical excitations of the interface compared to the features of the pristine components and discuss the methodological implications for the ab-initio treatment of interface electronics.

  2. Characterization of a gene family encoding SEA (sea-urchin sperm protein, enterokinase and agrin-domain proteins with lectin-like and heme-binding properties from Schistosoma japonicum.

    Directory of Open Access Journals (Sweden)

    Evaristus Chibunna Mbanefo

    Full Text Available BACKGROUND: We previously identified a novel gene family dispersed in the genome of Schistosoma japonicum by retrotransposon-mediated gene duplication mechanism. Although many transcripts were identified, no homolog was readily identifiable from sequence information. METHODOLOGY/PRINCIPAL FINDINGS: Here, we utilized structural homology modeling and biochemical methods to identify remote homologs, and characterized the gene products as SEA (sea-urchin sperm protein, enterokinase and agrin-domain containing proteins. A common extracellular domain in this family was structurally similar to SEA-domain. SEA-domain is primarily a structural domain, known to assist or regulate binding to glycans. Recombinant proteins from three members of this gene family specifically interacted with glycosaminoglycans with high affinity, with potential implication in ligand acquisition and immune evasion. Similar approach was used to identify a heme-binding site on the SEA-domain. The heme-binding mode showed heme molecule inserted into a hydrophobic pocket, with heme iron putatively coordinated to two histidine axial ligands. Heme-binding properties were confirmed using biochemical assays and UV-visible absorption spectroscopy, which showed high affinity heme-binding (K D = 1.605×10(-6 M and cognate spectroscopic attributes of hexa-coordinated heme iron. The native proteins were oligomers, antigenic, and are localized on adult worm teguments and gastrodermis; major host-parasite interfaces and site for heme detoxification and acquisition. CONCLUSIONS: The results suggest potential role, at least in the nucleation step of heme crystallization (hemozoin formation, and as receptors for heme uptake. Survival strategies exploited by parasites, including heme homeostasis mechanism in hemoparasites, are paramount for successful parasitism. Thus, assessing prospects for application in disease intervention is warranted.

  3. Characterization of a Gene Family Encoding SEA (Sea-urchin Sperm Protein, Enterokinase and Agrin)-Domain Proteins with Lectin-Like and Heme-Binding Properties from Schistosoma japonicum

    Science.gov (United States)

    Mbanefo, Evaristus Chibunna; Kikuchi, Mihoko; Huy, Nguyen Tien; Shuaibu, Mohammed Nasir; Cherif, Mahamoud Sama; Yu, Chuanxin; Wakao, Masahiro; Suda, Yasuo; Hirayama, Kenji

    2014-01-01

    Background We previously identified a novel gene family dispersed in the genome of Schistosoma japonicum by retrotransposon-mediated gene duplication mechanism. Although many transcripts were identified, no homolog was readily identifiable from sequence information. Methodology/Principal Findings Here, we utilized structural homology modeling and biochemical methods to identify remote homologs, and characterized the gene products as SEA (sea-urchin sperm protein, enterokinase and agrin)-domain containing proteins. A common extracellular domain in this family was structurally similar to SEA-domain. SEA-domain is primarily a structural domain, known to assist or regulate binding to glycans. Recombinant proteins from three members of this gene family specifically interacted with glycosaminoglycans with high affinity, with potential implication in ligand acquisition and immune evasion. Similar approach was used to identify a heme-binding site on the SEA-domain. The heme-binding mode showed heme molecule inserted into a hydrophobic pocket, with heme iron putatively coordinated to two histidine axial ligands. Heme-binding properties were confirmed using biochemical assays and UV-visible absorption spectroscopy, which showed high affinity heme-binding (K D = 1.605×10−6 M) and cognate spectroscopic attributes of hexa-coordinated heme iron. The native proteins were oligomers, antigenic, and are localized on adult worm teguments and gastrodermis; major host-parasite interfaces and site for heme detoxification and acquisition. Conclusions The results suggest potential role, at least in the nucleation step of heme crystallization (hemozoin formation), and as receptors for heme uptake. Survival strategies exploited by parasites, including heme homeostasis mechanism in hemoparasites, are paramount for successful parasitism. Thus, assessing prospects for application in disease intervention is warranted. PMID:24416467

  4. Structural and electronic properties of carbon nanotubes under hydrostatic pressures

    International Nuclear Information System (INIS)

    Zhang Ying; Cao Juexian; Yang Wei

    2008-01-01

    We studied the structural and electronic properties of carbon nanotubes under hydrostatic pressures based on molecular dynamics simulations and first principles band structure calculations. It is found that carbon nanotubes experience a hard-to-soft transition as external pressure increases. The bulk modulus of soft phase is two orders of magnitude smaller than that of hard phase. The band structure calculations show that band gap of (10, 0) nanotube increases with the increase of pressure at low pressures. Above a critical pressure (5.70GPa), band gap of (10, 0) nanotube drops rapidly and becomes zero at 6.62GPa. Moreover, the calculated charge density shows that a large pressure can induce an sp 2 -to-sp 3 bonding transition, which is confirmed by recent experiments on deformed carbon nanotubes

  5. Geometric and electronic structures of small GaN clusters

    Energy Technology Data Exchange (ETDEWEB)

    Song Bin; Cao Peilin

    2004-08-02

    The geometric and electronic structures of Ga{sub x}N{sub y} (x+y{<=}8) clusters have been calculated using a full-potential linear-muffin-tin-orbital method, combined with molecular dynamics and simulated annealing techniques. It is found that the structures, binding energies and HOMO-LUMO gaps of these clusters strongly depend on their size and composition. The lowest energy structures of these clusters are obtained, and the trends in the geometries are discussed. The binding energy of the cluster increases as the size of cluster increases. N-rich cluster has larger binding energy than Ga-rich ones. The HOMO-LUMO gaps of these clusters are evaluated.

  6. Angle-Resolved Photoemission Spectroscopy on Electronic Structure and Electron-Phonon Coupling in Cuprate Superconductors

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, X.J.

    2010-04-30

    In addition to the record high superconducting transition temperature (T{sub c}), high temperature cuprate superconductors are characterized by their unusual superconducting properties below T{sub c}, and anomalous normal state properties above T{sub c}. In the superconducting state, although it has long been realized that superconductivity still involves Cooper pairs, as in the traditional BCS theory, the experimentally determined d-wave pairing is different from the usual s-wave pairing found in conventional superconductors. The identification of the pairing mechanism in cuprate superconductors remains an outstanding issue. The normal state properties, particularly in the underdoped region, have been found to be at odd with conventional metals which is usually described by Fermi liquid theory; instead, the normal state at optimal doping fits better with the marginal Fermi liquid phenomenology. Most notable is the observation of the pseudogap state in the underdoped region above T{sub c}. As in other strongly correlated electrons systems, these unusual properties stem from the interplay between electronic, magnetic, lattice and orbital degrees of freedom. Understanding the microscopic process involved in these materials and the interaction of electrons with other entities is essential to understand the mechanism of high temperature superconductivity. Since the discovery of high-T{sub c} superconductivity in cuprates, angle-resolved photoemission spectroscopy (ARPES) has provided key experimental insights in revealing the electronic structure of high temperature superconductors. These include, among others, the earliest identification of dispersion and a large Fermi surface, an anisotropic superconducting gap suggestive of a d-wave order parameter, and an observation of the pseudogap in underdoped samples. In the mean time, this technique itself has experienced a dramatic improvement in its energy and momentum resolutions, leading to a series of new discoveries not

  7. Angle-Resolved Photoemission Spectroscopy on Electronic Structure and Electron-Phonon Coupling in Cuprate Superconductors

    International Nuclear Information System (INIS)

    Zhou, X.J.

    2010-01-01

    In addition to the record high superconducting transition temperature (T c ), high temperature cuprate superconductors are characterized by their unusual superconducting properties below T c , and anomalous normal state properties above T c . In the superconducting state, although it has long been realized that superconductivity still involves Cooper pairs, as in the traditional BCS theory, the experimentally determined d-wave pairing is different from the usual s-wave pairing found in conventional superconductors. The identification of the pairing mechanism in cuprate superconductors remains an outstanding issue. The normal state properties, particularly in the underdoped region, have been found to be at odd with conventional metals which is usually described by Fermi liquid theory; instead, the normal state at optimal doping fits better with the marginal Fermi liquid phenomenology. Most notable is the observation of the pseudogap state in the underdoped region above T c . As in other strongly correlated electrons systems, these unusual properties stem from the interplay between electronic, magnetic, lattice and orbital degrees of freedom. Understanding the microscopic process involved in these materials and the interaction of electrons with other entities is essential to understand the mechanism of high temperature superconductivity. Since the discovery of high-T c superconductivity in cuprates, angle-resolved photoemission spectroscopy (ARPES) has provided key experimental insights in revealing the electronic structure of high temperature superconductors. These include, among others, the earliest identification of dispersion and a large Fermi surface, an anisotropic superconducting gap suggestive of a d-wave order parameter, and an observation of the pseudogap in underdoped samples. In the mean time, this technique itself has experienced a dramatic improvement in its energy and momentum resolutions, leading to a series of new discoveries not thought possible

  8. Electronic Structure and Transport in Solids from First Principles

    Science.gov (United States)

    Mustafa, Jamal Ibrahim

    The focus of this dissertation is the determination of the electronic structure and trans- port properties of solids. We first review some of the theory and computational methodology used in the calculation of electronic structure and materials properties. Throughout the dissertation, we make extensive use of state-of-the-art software packages that implement density functional theory, density functional perturbation theory, and the GW approximation, in addition to specialized methods for interpolating matrix elements for extremely accurate results. The first application of the computational framework introduced is the determination of band offsets in semiconductor heterojunctions using a theory of quantum dipoles at the interface. This method is applied to the case of heterojunction formed between a new metastable phase of silicon, with a rhombohedral structure, and cubic silicon. Next, we introduce a novel method for the construction of localized Wannier functions, which we have named the optimized projection functions method (OPFM). We illustrate the method on a variety of systems and find that it can reliably construct localized Wannier functions with minimal user intervention. We further develop the OPFM to investigate a class of materials called topological insulators, which are insulating in the bulk but have conductive surface states. These properties are a result of a nontrivial topology in their band structure, which has interesting effects on the character of the Wannier functions. In the last sections of the main text, the noble metals are studied in great detail, including their electronic properties and carrier dynamics. In particular, we investigate, the Fermi surface properties of the noble metals, specifically electron-phonon scattering lifetimes, and subsequently the transport properties determined by carriers on the Fermi surface. To achieve this, a novel sampling technique is developed, with wide applicability to transport calculations

  9. Electronic structure, bonding and chemisorption in metallic hydrides

    International Nuclear Information System (INIS)

    Ward, J.W.

    1980-01-01

    Problems that can arise during the cycling steps for a hydride storage system usually involve events at surfaces. Chemisorption and reaction processes can be affected by small amounts of contaminants that may act as catalytic poisons. The nature of the poisoning process can vary greatly for the different metals and alloys that form hydrides. A unifying concept is offered, which satisfactorily correlates many of the properties of transition-metal, rare-earth and actinide hydrides. The metallic hydrides can be differentiated on the basis of electronegativity, metallic radius (valence) and electronic structure. For those systems where there are d (transition metals) or f (early actinides) electrons near the Fermi level a broad range of chemical and catalytic behaviors are found, depending on bandwidth and energy. The more electropositive metals (rare-earths, actinides, transition metals with d > 5) dissolve hydrogen and form hydrides by an electronically somewhat different process, and as a class tend to adsorb electrophobic molecules. The net charge-transfer in either situation is subtle; however, the small differences are responsible for many of the observed structural, chemical, and catalytic properties in these hydride systems

  10. Novel electronic structures of superlattice composed of graphene and silicene

    International Nuclear Information System (INIS)

    Yu, S.; Li, X.D.; Wu, S.Q.; Wen, Y.H.; Zhou, S.; Zhu, Z.Z.

    2014-01-01

    Highlights: • Graphene/silicene superlattices exhibit metallic electronic properties. • Dirac point of graphene is folded to the Γ-point in the superlattice system. • Significant changes in the transport properties of the graphene layers are expected. • Small amount of charge transfer from the graphene to the silicene layers is found. - Abstract: Superlattice is a major force in providing man-made materials with unique properties. Here we report a study of the structural and electronic properties of a superlattice made with alternate stacking of graphene and hexagonal silicene. Three possible stacking models, i.e., the top-, bridge- and hollow-stacking, are considered. The top-stacking is found to be the most stable pattern. Although both the free-standing graphene and silicene are semi-metals, our results suggest that the graphene and silicene layers in the superlattice both exhibit metallic electronic properties due to a small amount of charge transfer from the graphene to the silicene layers. More importantly, the Dirac point of graphene is folded to the Γ-point of the superlattice, instead of the K-point in the isolated graphene. Such a change in the Dirac point of graphene could lead to significant change in the transportation property of the graphene layer. Moreover, the band structure and the charge transfer indicate that the interaction between the stacking sheets in the graphene/silicene superlattice is more than just the van der Waals interaction

  11. Structural Fingerprinting of Nanocrystals in the Transmission Electron Microscope

    Science.gov (United States)

    Rouvimov, Sergei; Plachinda, Pavel; Moeck, Peter

    2010-03-01

    Three novel strategies for the structurally identification of nanocrystals in a transmission electron microscope are presented. Either a single high-resolution transmission electron microscopy image [1] or a single precession electron diffractogram (PED) [2] may be employed. PEDs from fine-grained crystal powders may also be utilized. Automation of the former two strategies is in progress and shall lead to statistically significant results on ensembles of nanocrystals. Open-access databases such as the Crystallography Open Database which provides more than 81,500 crystal structure data sets [3] or its mainly inorganic and educational subsets [4] may be utilized. [1] http://www.scientificjournals.org/journals 2007/j/of/dissertation.htm [2] P. Moeck and S. Rouvimov, in: {Drugs and the Pharmaceutical Sciences}, Vol. 191, 2009, 270-313 [3] http://cod.ibt.lt, http://www.crystallography.net, http://cod.ensicaen.fr, http://nanocrystallography.org, http://nanocrystallography.net, http://journals.iucr.org/j/issues/2009/04/00/kk5039/kk5039.pdf [4] http://nanocrystallography.research.pdx.edu/CIF-searchable

  12. HREELS to identify electronic structures of organic thin films.

    Science.gov (United States)

    Oeter, D; Ziegler, C; Göpel, W

    1995-10-01

    The electronic structure of alpha-oligothiophene (alphanT) thin films has been investigated for increasing chain lengths of n= 4-8 thiophene units with high resolution electron energy loss spectroscopy (HREELS) in the specular reflection geometry at a primary energy of 15 eV. The great advantage of this technique in contrast to UV/VIS absorption spectroscopy results from the fact, that the impact scattering mechanism of HREELS makes it possible to also detect optically forbidden electronic transitions. On the other hand, the electrons used as probes in HREELS have a wavelength which is two orders of magnitudes smaller if compared to those of photons used in UV/VIS absorption spectroscopy. Therefore individual molecules are excited by HREELS independent from each other and hence the excitation of collective excitons is not possible. As a result, information about the orientation of the molecules cannot be achieved with HREELS, which, however, is possible in polarization-dependent UV/VIS spectroscopy.

  13. Electronic structure and mechanical properties of plasma nitrided ferrous alloys

    Energy Technology Data Exchange (ETDEWEB)

    Portolan, E. [Centro de Ciencias Exatas e Tecnologia, Universidade de Caxias do Sul, 95070-560 Caxias do Sul-RS (Brazil); Baumvol, I.J.R. [Centro de Ciencias Exatas e Tecnologia, Universidade de Caxias do Sul, 95070-560 Caxias do Sul-RS (Brazil); Instituto de Fisica, Universidade Federal do Rio Grande do Sul, Porto Alegre 91509-970 (Brazil); Figueroa, C.A., E-mail: cafiguer@ucs.br [Centro de Ciencias Exatas e Tecnologia, Universidade de Caxias do Sul, 95070-560 Caxias do Sul-RS (Brazil)

    2009-04-15

    The electronic structures of the near-surface regions of two different nitrided steels (AISI 316 and 4140) were investigated using X-ray photoelectron spectroscopy. Photoelectron groups from all main chemical elements involved were addressed for steel samples with implanted-N concentrations in the range 16-32 at.%. As the implanted-N concentrations were increased, rather contrasting behaviors were observed for the two kinds of steel. The N1s photoelectrons had spectral shifts toward lower (nitrided AISI 316) or higher (nitrided AISI 4140) binding energies, whereas the Fe2p{sub 3/2} photoelectron spectrum remains at a constant binding energy (nitrided AISI 316) or shifts toward higher binding energies (AISI 4140). These trends are discussed in terms of the metallic nitride formation and the overlapping of atomic orbitals. For nitrided AISI 316, a semi-classical approach of charge transfer between Cr and N is used to explain the experimental facts (formation of CrN), while for nitrided AISI 4140 we propose that the interaction between orbitals 4s from Fe and 2p from N promotes electrons to the conduction band increasing the electrical attraction of the N1s and Fe2p electrons in core shells (formation of FeN{sub x}). The increase in hardness of the steel upon N implantation is attributed to the localization of electrons in specific bonds, which diminishes the metallic bond character.

  14. Electronic structure and mechanical properties of plasma nitrided ferrous alloys

    Science.gov (United States)

    Portolan, E.; Baumvol, I. J. R.; Figueroa, C. A.

    2009-04-01

    The electronic structures of the near-surface regions of two different nitrided steels (AISI 316 and 4140) were investigated using X-ray photoelectron spectroscopy. Photoelectron groups from all main chemical elements involved were addressed for steel samples with implanted-N concentrations in the range 16-32 at.%. As the implanted-N concentrations were increased, rather contrasting behaviors were observed for the two kinds of steel. The N1s photoelectrons had spectral shifts toward lower (nitrided AISI 316) or higher (nitrided AISI 4140) binding energies, whereas the Fe2p 3/2 photoelectron spectrum remains at a constant binding energy (nitrided AISI 316) or shifts toward higher binding energies (AISI 4140). These trends are discussed in terms of the metallic nitride formation and the overlapping of atomic orbitals. For nitrided AISI 316, a semi-classical approach of charge transfer between Cr and N is used to explain the experimental facts (formation of CrN), while for nitrided AISI 4140 we propose that the interaction between orbitals 4s from Fe and 2p from N promotes electrons to the conduction band increasing the electrical attraction of the N1s and Fe2p electrons in core shells (formation of FeN x). The increase in hardness of the steel upon N implantation is attributed to the localization of electrons in specific bonds, which diminishes the metallic bond character.

  15. Electronic structure and mechanical properties of plasma nitrided ferrous alloys

    International Nuclear Information System (INIS)

    Portolan, E.; Baumvol, I.J.R.; Figueroa, C.A.

    2009-01-01

    The electronic structures of the near-surface regions of two different nitrided steels (AISI 316 and 4140) were investigated using X-ray photoelectron spectroscopy. Photoelectron groups from all main chemical elements involved were addressed for steel samples with implanted-N concentrations in the range 16-32 at.%. As the implanted-N concentrations were increased, rather contrasting behaviors were observed for the two kinds of steel. The N1s photoelectrons had spectral shifts toward lower (nitrided AISI 316) or higher (nitrided AISI 4140) binding energies, whereas the Fe2p 3/2 photoelectron spectrum remains at a constant binding energy (nitrided AISI 316) or shifts toward higher binding energies (AISI 4140). These trends are discussed in terms of the metallic nitride formation and the overlapping of atomic orbitals. For nitrided AISI 316, a semi-classical approach of charge transfer between Cr and N is used to explain the experimental facts (formation of CrN), while for nitrided AISI 4140 we propose that the interaction between orbitals 4s from Fe and 2p from N promotes electrons to the conduction band increasing the electrical attraction of the N1s and Fe2p electrons in core shells (formation of FeN x ). The increase in hardness of the steel upon N implantation is attributed to the localization of electrons in specific bonds, which diminishes the metallic bond character.

  16. Relationship between natural and heme-mediated antibody polyreactivity

    Energy Technology Data Exchange (ETDEWEB)

    Hadzhieva, Maya; Vassilev, Tchavdar [Stephan Angelov Institute of Microbiology, Bulgarian Academy of Sciences, Sofia 1113 (Bulgaria); Bayry, Jagadeesh; Kaveri, Srinivas; Lacroix-Desmazes, Sébastien [Sorbonne Universités, UPMC Univ Paris 06, UMR-S 1138, Centre de Recherche des Cordeliers, F-75006 Paris (France); INSERM, UMR-S 1138, F-75006 Paris (France); Université Paris Descartes, Sorbonne Paris Cité, UMR-S 1138, F-75006 Paris (France); Dimitrov, Jordan D., E-mail: jordan.dimitrov@crc.jussieu.fr [Sorbonne Universités, UPMC Univ Paris 06, UMR-S 1138, Centre de Recherche des Cordeliers, F-75006 Paris (France); INSERM, UMR-S 1138, F-75006 Paris (France); Université Paris Descartes, Sorbonne Paris Cité, UMR-S 1138, F-75006 Paris (France)

    2016-03-25

    Polyreactive antibodies represent a considerable fraction of the immune repertoires. Some antibodies acquire polyreactivity post-translationally after interaction with various redox-active substances, including heme. Recently we have demonstrated that heme binding to a naturally polyreactive antibody (SPE7) results in a considerable broadening of the repertoire of recognized antigens. A question remains whether the presence of certain level of natural polyreactivity of antibodies is a prerequisite for heme-induced further extension of antigen binding potential. Here we used a second monoclonal antibody (Hg32) with unknown specificity and absence of intrinsic polyreactivity as a model to study the potential of heme to induce polyreactivity of antibodies. We demonstrated that exposure to heme greatly extends the antigen binding potential of Hg32, suggesting that the intrinsic binding promiscuity is not a prerequisite for the induction of polyreactivity by heme. In addition we compared the kinetics and thermodynamics of the interaction of heme-exposed antibodies with a panel of unrelated antigens. These analyses revealed that the two heme-sensitive antibodies adopt different mechanisms of binding to the same set of antigens. This study contributes to understanding the phenomenon of induced antibody polyreactivity. The data may also be of importance for understanding of physiological and pathological roles of polyreactive antibodies. - Highlights: • Exposure of certain monoclonal IgE antibodies to heme results in gain of antigen binding polyreactivity. • Natural polyreactivity of antibodies is dispensable for acquisition of polyreactivity through interaction with heme. • Heme-induced monoclonal IgE antibodies differ in their thermodynamic mechanisms of antigen recognition.

  17. Design and fabrication of a continuous wave electron accelerating structure

    International Nuclear Information System (INIS)

    Takahashi, Jiro

    1997-01-01

    The Physics Institute of Sao Paulo University, SP, Brazil is fabricating a 31 MeV cw racetrack microtron (RTM) designed for nuclear physics research. This is a two-stage microtron that includes a 1.93 MeV injector linac feeding a five-turn microtron booster. After 28 turns, the main microtron delivers a 31 MeV continuous electron beam. The objective of this work is the development and fabrication of an advanced, beta=l, cw accelerating structure for the main microtron. The accelerating structure will be a side-coupled structure (SCS). We have chosen this kind of cavity, because it presents good vacuum properties, allows operation at higher accelerating electric fields and has a shunt impedance better than 81 MQ/m, with a high coupling factor ( 3 - 5%). The engineering design is the Los Alamos one. There will be two tuning plungers placed at both ends of the accelerating structure. They automatically and quickly compensate for the variation in the resonance frequency caused by changes in the structure temperature. Our design represents an advanced accelerating structure with the optimum SCS properties coexisting with the plunger's good tuning properties. (author)

  18. Structural phase transition and electronic properties in samarium chalcogenides

    Energy Technology Data Exchange (ETDEWEB)

    Panwar, Y. S., E-mail: yspanwar2011@gmail.com [Department of Physics, Govt. New Science College Dewas-455001 (India); Aynyas, Mahendra [Department of Physics, C.S.A. Govt. P.G. College, Sehore, 466001 (India); Pataiya, J.; Sanyal, Sankar P. [Department of Physics, Barkatullah University, Bhopal, 462026 (India)

    2016-05-06

    The electronic structure and high pressure properties of samarium monochalcogenides SmS, SmSe and SmTe have been reported by using tight binding linear muffin-tin-orbital (TB-LMTO) method within the local density approximation (LDA). The total energy as a function of volume is evaluated. It is found that these monochalcogenides are stable in NaCl-type structure under ambient pressure. We predict a structural phase transition from NaCl-type (B{sub 1}-phase) structure to CsCl-type (B{sub 2}-type) structure for these compounds. Phase transition pressures were found to be 1.7, 4.4 and 6.6 GPa, for SmS, SmSe and SmTe respectively. Apart from this, the lattice parameter (a{sub 0}), bulk modulus (B{sub 0}), band structure (BS) and density of states (DOS) are calculated. From energy band diagram we observed that these compounds exhibit metallic character. The calculated values of equilibrium lattice parameter and phase transition pressure are in general good agreement with available data.

  19. Electronic structure of benzene adsorbed on Ni and Cu surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Weinelt, M.; Nilsson, A.; Wassdahl, N. [Uppsala Univ. (Sweden)] [and others

    1997-04-01

    Benzene has for a long time served as a prototype adsorption system of large molecules. It adsorbs with the molecular plane parallel to the surface. The bonding of benzene to a transition metal is typically viewed to involve the {pi} system. Benzene adsorbs weakly on Cu and strongly on Ni. It is interesting to study how the adsorption strength is reflected in the electronic structure of the adsorbate-substrate complex. The authors have used X-ray Emission (XE) and X-ray Absorption (XA) spectroscopies to selectively study the electronic states localized on the adsorbed benzene molecule. Using XES the occupied states can be studies and with XAS the unoccupied states. The authors have used beamline 8.0 and the Swedish endstation equipped with a grazing incidence x-ray spectrometer and a partial yield absorption detector. The resolution in the XES and XAS were 0.5 eV and 0.05 eV, respectively.

  20. Electronic structure classifications using scanning tunneling microscopy conductance imaging

    International Nuclear Information System (INIS)

    Horn, K.M.; Swartzentruber, B.S.; Osbourn, G.C.; Bouchard, A.; Bartholomew, J.W.

    1998-01-01

    The electronic structure of atomic surfaces is imaged by applying multivariate image classification techniques to multibias conductance data measured using scanning tunneling microscopy. Image pixels are grouped into classes according to shared conductance characteristics. The image pixels, when color coded by class, produce an image that chemically distinguishes surface electronic features over the entire area of a multibias conductance image. Such open-quotes classedclose quotes images reveal surface features not always evident in a topograph. This article describes the experimental technique used to record multibias conductance images, how image pixels are grouped in a mathematical, classification space, how a computed grouping algorithm can be employed to group pixels with similar conductance characteristics in any number of dimensions, and finally how the quality of the resulting classed images can be evaluated using a computed, combinatorial analysis of the full dimensional space in which the classification is performed. copyright 1998 American Institute of Physics

  1. Microscopical Studies of Structural and Electronic Properties of Semiconductors

    CERN Multimedia

    2002-01-01

    The electronic and structural properties of point defects in semiconductors, e.g. radiation defects, impurities or passivating defects can excellently be studied by the hyperfine technique of Perturbed Angular Correlation (PAC). The serious limitation of this method, the small number of chemically different radioactive PAC probe atoms can be widely overcome by means of ISOLDE. Providing shortliving isotopes, which represent common dopants as well as suitable PAC probe atoms, the ISOLDE facility enables a much broader application of PAC to problems in semiconductor physics.\\\\ Using the probe atom $^{111m}$ Cd , the whole class of III-V compounds becomes accessible for PAC investigations. First successful experiments in GaAs, InP and GaP have been performed, concerning impurity complex formation and plasma induced defects. In Si and Ge, the electronic properties~-~especially their influence on acceptor-donor interaction~-~could be exemplarily st...

  2. Electronic structure of molecules using relativistic effective core potentials

    International Nuclear Information System (INIS)

    Hay, P.J.

    1981-01-01

    Starting with one-component Cowan-Griffin relativistic Hartree-Fock orbitals, which successfully incorporate the mass-velocity and Darwin terms present in more complicated wavefunctions such as Dirac-Hartree-Fock, one can derive relativistic effective core potentials (RECP's) to carry out molecular calculations. These potentials implicitly include the dominant relativistic terms for molecules while allowing one to use the traditional quantum chemical techniques for studying the electronic structure of molecules. The effects of spin-orbit coupling can then be included using orbitals from such calculations using an effective 1-electron, 1-center spin-orbit operator. Applications to molecular systems involving heavy atoms, show good agreement with available spectroscopic data on molecular geometries and excitation energies

  3. Development and application of advanced methods for electronic structure calculations

    DEFF Research Database (Denmark)

    Schmidt, Per Simmendefeldt

    . For this reason, part of this thesis relates to developing and applying a new method for constructing so-called norm-conserving PAW setups, that are applicable to GW calculations by using a genetic algorithm. The effect of applying the new setups significantly affects the absolute band positions, both for bulk......This thesis relates to improvements and applications of beyond-DFT methods for electronic structure calculations that are applied in computational material science. The improvements are of both technical and principal character. The well-known GW approximation is optimized for accurate calculations...... of electronic excitations in two-dimensional materials by exploiting exact limits of the screened Coulomb potential. This approach reduces the computational time by an order of magnitude, enabling large scale applications. The GW method is further improved by including so-called vertex corrections. This turns...

  4. Structural and electronic properties of GaAsBi

    International Nuclear Information System (INIS)

    Achour, H.; Louhibi, S.; Amrani, B.; Tebboune, A.; Sekkal, N.

    2008-05-01

    The structural and electronic properties of the GaAs 1-x Bi x ternary alloy are investigated by means of two first principles and full potential methods, the linear augmented plane waves (FPLAPW) method and a recent version of the full potential linear muffin-tin orbitals method (FPLMTO) which enables an accurate treatment of the interstitial regions. In particular, we have found that the maximal GaBi mole fraction x for which GaBixAs 1-x remains a semiconductor is probably around x = 0.5. The electronic properties of (GaAs) m /(GaBi) n quantum well superlattices (SLs) have also been calculated and it is found that such SLs are semiconductors when m is larger or equal to n. (author)

  5. Protonated serotonin: Geometry, electronic structures and photophysical properties

    Science.gov (United States)

    Omidyan, Reza; Amanollahi, Zohreh; Azimi, Gholamhassan

    2017-07-01

    The geometry and electronic structures of protonated serotonin have been investigated by the aim of MP2 and CC2 methods. The relative stabilities, transition energies and geometry of sixteen different protonated isomers of serotonin have been presented. It has been predicted that protonation does not exhibit essential alteration on the S1 ← S0 electronic transition energy of serotonin. Instead, more complicated photophysical nature in respect to its neutral analogue is suggested for protonated system owing to radiative and non-radiative deactivation pathways. In addition to hydrogen detachment (HD), hydrogen/proton transfer (H/PT) processes from ammonium to indole ring along the NH+⋯ π hydrogen bond have been predicted as the most important photophysical consequences of SERH+ at S1 excited state. The PT processes is suggested to be responsible for fluorescence of SERH+ while the HD driving coordinate is proposed for elucidation of its nonradiative deactivation mechanism.

  6. Electronic structure characterization and bandgap engineering of solar hydrogen materials

    International Nuclear Information System (INIS)

    Guo, Jinghua

    2007-01-01

    Bandgap, band edge positions as well as the overall band structure of semiconductors are of crucial importance in photoelectrochemical and photocatalytic applications. The energy position of the band edge level can be controlled by the electronegativity of the dopants, the pH of the solution (flatband potential variation of 60 mV per pH unit), as well as by quantum confinement effects. Accordingly, band edges and bandgap can be tailored to achieve specific electronic, optical or photocatalytic properties. Synchrotron radiation with photon energy at or below 1 keV is giving new insight into such areas as condensed matter physics and extreme ultraviolet optics technology. In the soft x-ray region, the question tends to be, what are the electrons doing as they migrated between the atoms. In this paper, I will present a number of soft x-ray spectroscopic study of nanostructured 3d metal compounds Fe 2 O 3 and ZnO

  7. Modification of electronic structure, magnetic structure, and topological phase of bismuthene by point defects

    Science.gov (United States)

    Kadioglu, Yelda; Kilic, Sevket Berkay; Demirci, Salih; Aktürk, O. Üzengi; Aktürk, Ethem; Ciraci, Salim

    2017-12-01

    This paper reveals how the electronic structure, magnetic structure, and topological phase of two-dimensional (2D), single-layer structures of bismuth are modified by point defects. We first showed that a free-standing, single-layer, hexagonal structure of bismuth, named h-bismuthene, exhibits nontrivial band topology. We then investigated interactions between single foreign adatoms and bismuthene structures, which comprise stability, bonding, electronic structure, and magnetic structures. Localized states in diverse locations of the band gap and resonant states in band continua of bismuthene are induced upon the adsorption of different adatoms, which modify electronic and magnetic properties. Specific adatoms result in reconstruction around the adsorption site. Single vacancies and divacancies can form readily in bismuthene structures and remain stable at high temperatures. Through rebondings, Stone-Whales-type defects are constructed by divacancies, which transform into a large hole at high temperature. Like adsorbed adatoms, vacancies induce also localized gap states, which can be eliminated through rebondings in divacancies. We also showed that not only the optical and magnetic properties, but also the topological features of pristine h-bismuthene can be modified by point defects. The modification of the topological features depends on the energies of localized states and also on the strength of coupling between point defects.

  8. Quantum Monte Carlo for electronic structure: Recent developments and applications

    International Nuclear Information System (INIS)

    Rodriguez, M.M.S.; Lawrence Berkeley Lab., CA

    1995-04-01

    Quantum Monte Carlo (QMC) methods have been found to give excellent results when applied to chemical systems. The main goal of the present work is to use QMC to perform electronic structure calculations. In QMC, a Monte Carlo simulation is used to solve the Schroedinger equation, taking advantage of its analogy to a classical diffusion process with branching. In the present work the author focuses on how to extend the usefulness of QMC to more meaningful molecular systems. This study is aimed at questions concerning polyatomic and large atomic number systems. The accuracy of the solution obtained is determined by the accuracy of the trial wave function's nodal structure. Efforts in the group have given great emphasis to finding optimized wave functions for the QMC calculations. Little work had been done by systematically looking at a family of systems to see how the best wave functions evolve with system size. In this work the author presents a study of trial wave functions for C, CH, C 2 H and C 2 H 2 . The goal is to study how to build wave functions for larger systems by accumulating knowledge from the wave functions of its fragments as well as gaining some knowledge on the usefulness of multi-reference wave functions. In a MC calculation of a heavy atom, for reasonable time steps most moves for core electrons are rejected. For this reason true equilibration is rarely achieved. A method proposed by Batrouni and Reynolds modifies the way the simulation is performed without altering the final steady-state solution. It introduces an acceleration matrix chosen so that all coordinates (i.e., of core and valence electrons) propagate at comparable speeds. A study of the results obtained using their proposed matrix suggests that it may not be the optimum choice. In this work the author has found that the desired mixing of coordinates between core and valence electrons is not achieved when using this matrix. A bibliography of 175 references is included

  9. Electron microscope investigation into dislocation structure of cast aluminium alloys

    International Nuclear Information System (INIS)

    Zolotorevskij, V.S.; Orelkina, T.A.; Istomin-Kastrovskij, V.V.

    1978-01-01

    By applying the diffraction electron microscopy method, the general specific features of the disclocation structure of cast binary alloys of aluminium with different additions were established. It is shown that in most alloys, when they undergo cooling in the process of crystallization at the rate of about 850 deg/min, the cellular dislocation structure is formed. It is shown that in all the alloys studied, the total density of dislocations of one order is about-10 9 cm -2 , which exceeds by 1 to 2 orders of magnitude the value which follows from the Tiller theory of concentration stresses. It has been experimentally established that the contribution of shrinkage and thermal stresses to the formation of a dislocation structure is rather insignificant; yet the dislocation density values calculated according to the size of dendritic cells and the medium angles of their disorientation are close to those determined by the electron-microscopic method. This is the basis for making a supposition that the greater part of the dislocations in castings are formed as a result of comparing dendritic branches with one another, which are disoriented in respect to each other

  10. Amyloid Structure and Assembly: Insights from Scanning Transmission Electron Microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Goldsbury, C.; Wall, J.; Baxa, U.; Simon, M. N.; Steven, A. C.; Engel, A.; Aebi, U.; Muller, S. A.

    2011-01-01

    Amyloid fibrils are filamentous protein aggregates implicated in several common diseases such as Alzheimer's disease and type II diabetes. Similar structures are also the molecular principle of the infectious spongiform encephalopathies such as Creutzfeldt-Jakob disease in humans, scrapie in sheep, and of the so-called yeast prions, inherited non-chromosomal elements found in yeast and fungi. Scanning transmission electron microscopy (STEM) is often used to delineate the assembly mechanism and structural properties of amyloid aggregates. In this review we consider specifically contributions and limitations of STEM for the investigation of amyloid assembly pathways, fibril polymorphisms and structural models of amyloid fibrils. This type of microscopy provides the only method to directly measure the mass-per-length (MPL) of individual filaments. Made on both in vitro assembled and ex vivo samples, STEM mass measurements have illuminated the hierarchical relationships between amyloid fibrils and revealed that polymorphic fibrils and various globular oligomers can assemble simultaneously from a single polypeptide. The MPLs also impose strong constraints on possible packing schemes, assisting in molecular model building when combined with high-resolution methods like solid-state nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR).

  11. Electronic structure and magnetic properties of zigzag blue phosphorene nanoribbons

    Energy Technology Data Exchange (ETDEWEB)

    Hu, Tao; Hong, Jisang, E-mail: hongj@pknu.ac.kr [Department of Physics, Pukyong National University, Busan 608-737 (Korea, Republic of)

    2015-08-07

    We investigated the electronic structure and magnetism of zigzag blue phosphorene nanoribbons (ZBPNRs) using first principles density functional theory calculations by changing the widths of ZBPNRs from 1.5 to 5 nm. In addition, the effect of H and O passivation was explored as well. The ZBPNRs displayed intra-edge antiferromagnetic ground state with a semiconducting band gap of ∼0.35 eV; and this was insensitive to the edge structure relaxation effect. However, the edge magnetism of ZBPNRs disappeared with H-passivation. Moreover, the band gap of H-passivated ZBPNRs was greatly enhanced because the calculated band gap was ∼1.77 eV, and this was almost the same as that of two-dimensional blue phosphorene layer. For O-passivated ZBPNRs, we also found an intra-edge antiferromagnetic state. Besides, both unpassivated and O-passivated ZBPNRs preserved almost the same band gap. We predict that the electronic band structure and magnetic properties can be controlled by means of passivation. Moreover, the edge magnetism can be also modulated by the strain. Nonetheless, the intrinsic physical properties are size independent. This feature can be an advantage for device applications because it may not be necessary to precisely control the width of the nanoribbon.

  12. X-ray and photoelectron spectroscopy of the structure, reactivity, and electronic structure of semiconductor nanocrystals

    Energy Technology Data Exchange (ETDEWEB)

    Hamad, Kimberly Sue [Univ. of California, Berkeley, CA (United States)

    2000-01-01

    Semiconductor nanocrystals are a system which has been the focus of interest due to their size dependent properties and their possible use in technological applications. Many chemical and physical properties vary systematically with the size of the nanocrystal and thus their study enables the investigation of scaling laws. Due to the increasing surface to volume ratio as size is decreased, the surfaces of nanocrystals are expected to have a large influence on their electronic, thermodynamic, and chemical behavior. In spite of their importance, nanocrystal surfaces are still relatively uncharacterized in terms of their structure, electronic properties, bonding, and reactivity. Investigation of nanocrystal surfaces is currently limited by what techniques to use, and which methods are suitable for nanocrystals is still being determined. This work presents experiments using x-ray and electronic spectroscopies to explore the structure, reactivity, and electronic properties of semiconductor (CdSe, InAs) nanocrystals and how they vary with size. Specifically, x-ray absorption near edge spectroscopy (XANES) in conjunction with multiple scattering simulations affords information about the structural disorder present at the surface of the nanocrystal. X-ray photoelectron spectroscopy (XPS) and ultra-violet photoelectron spectroscopy (UPS) probe the electronic structure in terms of hole screening, and also give information about band lineups when the nanocrystal is placed in electric contact with a substrate. XPS of the core levels of the nanocrystal as a function of photo-oxidation time yields kinetic data on the oxidation reaction occurring at the surface of the nanocrystal.

  13. Structural studies of glasses by transmission electron microscopy and electron diffraction

    International Nuclear Information System (INIS)

    Kashchieva, E.P.

    1997-01-01

    The purpose of this work is to present information about the applications of transmission electron microscopy (TEM) and electron diffraction (ED) for structural investigations of glasses. TEM investigations have been carried out on some binary and on a large number of ternary borate-telluride systems where glass-forming oxides, oxides of transitional elements and modified oxides of elements from I, II and III groups in the periodic table, are used as third component. The large experimental data given by TEM method allows the fine classification of the micro-heterogeneities. A special case of micro-heterogeneous structure with technological origin occurs near the boundary between the 2 immiscible liquids obtained at macro-phase separation. TEM was also used for the direct observation of the glass structure and we have studied the nano-scale structure of borate glasses obtained at slow and fast cooling of the melts. The ED possesses advantages for analysis of amorphous thin films or micro-pastilles and it is a very useful technique for study in materials containing simultaneously light and heavy elements. A comparison between the possibilities of the 3 diffraction techniques (X-ray diffraction, neutron diffraction and ED) is presented

  14. III - V semiconductor structures for biosensor and molecular electronics applications

    Energy Technology Data Exchange (ETDEWEB)

    Luber, S M

    2007-01-15

    The present work reports on the employment of III-V semiconductor structures to biosensor and molecular electronics applications. In the first part a sensor based on a surface-near two dimensional electron gas for a use in biological environment is studied. Such a two dimensional electron gas inherently forms in a molecular beam epitaxy (MBE) grown, doped aluminum gallium arsenide - gallium arsenide (AlGaAs-GaAs) heterostructure. Due to the intrinsic instability of GaAs in aqueous solutions the device is passivated by deposition of a monolayer of 4'-substituted mercaptobiphenyl molecules. The influence of these molecules which bind to the GaAs via a sulfur group is investigated by Kelvin probe measurements in air. They reveal a dependence of GaAs electron affinity on the intrinsic molecular dipole moment of the mercaptobiphenyls. Furthermore, transient surface photovoltage measurements are presented which demonstrate an additional influence of mercaptobiphenyl chemisorption on surface carrier recombination rates. As a next step, the influence of pH-value and salt concentration upon the sensor device is discussed based on the results obtained from sensor conductance measurements in physiological solutions. A dependence of the device surface potential on both parameters due to surface charging is deduced. Model calculations applying Poisson-Boltzmann theory reveal as possible surface charging mechanisms either the adsorption of OH- ions on the surface, or the dissociation of OH groups in surface oxides. A comparison between simulation settings and physical device properties indicate the OH- adsorption as the most probable mechanism. In the second part of the present study the suitability of MBE grown III-V semiconductor structures for molecular electronics applications is examined. In doing so, a method to fabricate nanometer separated, coplanar, metallic electrodes based on the cleavage of a supporting AlGaAs-GaAs heterostructure is presented. This is followed by a

  15. III - V semiconductor structures for biosensor and molecular electronics applications

    Energy Technology Data Exchange (ETDEWEB)

    Luber, S.M.

    2007-01-15

    The present work reports on the employment of III-V semiconductor structures to biosensor and molecular electronics applications. In the first part a sensor based on a surface-near two dimensional electron gas for a use in biological environment is studied. Such a two dimensional electron gas inherently forms in a molecular beam epitaxy (MBE) grown, doped aluminum gallium arsenide - gallium arsenide (AlGaAs-GaAs) heterostructure. Due to the intrinsic instability of GaAs in aqueous solutions the device is passivated by deposition of a monolayer of 4'-substituted mercaptobiphenyl molecules. The influence of these molecules which bind to the GaAs via a sulfur group is investigated by Kelvin probe measurements in air. They reveal a dependence of GaAs electron affinity on the intrinsic molecular dipole moment of the mercaptobiphenyls. Furthermore, transient surface photovoltage measurements are presented which demonstrate an additional influence of mercaptobiphenyl chemisorption on surface carrier recombination rates. As a next step, the influence of pH-value and salt concentration upon the sensor device is discussed based on the results obtained from sensor conductance measurements in physiological solutions. A dependence of the device surface potential on both parameters due to surface charging is deduced. Model calculations applying Poisson-Boltzmann theory reveal as possible surface charging mechanisms either the adsorption of OH- ions on the surface, or the dissociation of OH groups in surface oxides. A comparison between simulation settings and physical device properties indicate the OH- adsorption as the most probable mechanism. In the second part of the present study the suitability of MBE grown III-V semiconductor structures for molecular electronics applications is examined. In doing so, a method to fabricate nanometer separated, coplanar, metallic electrodes based on the cleavage of a supporting AlGaAs-GaAs heterostructure is presented. This is followed

  16. Temperature dependence of the electronic structure of semiconductors and insulators

    Energy Technology Data Exchange (ETDEWEB)

    Poncé, S., E-mail: samuel.pon@gmail.com; Gillet, Y.; Laflamme Janssen, J.; Gonze, X. [European Theoretical Spectroscopy Facility and Institute of Condensed Matter and Nanosciences, Université catholique de Louvain, Chemin des étoiles 8, bte L07.03.01, B-1348 Louvain-la-neuve (Belgium); Marini, A. [Consiglio Nazionale delle Ricerche (CNR), Via Salaria Km 29.3, CP 10, 00016 Monterotondo Stazione (Italy); Verstraete, M. [European Theoretical Spectroscopy Facility and Physique des matériaux et nanostructures, Université de Liège, Allée du 6 Août 17, B-4000 Liège (Belgium)

    2015-09-14

    The renormalization of electronic eigenenergies due to electron-phonon coupling (temperature dependence and zero-point motion effect) is sizable in many materials with light atoms. This effect, often neglected in ab initio calculations, can be computed using the perturbation-based Allen-Heine-Cardona theory in the adiabatic or non-adiabatic harmonic approximation. After a short description of the recent progresses in this field and a brief overview of the theory, we focus on the issue of phonon wavevector sampling convergence, until now poorly understood. Indeed, the renormalization is obtained numerically through a slowly converging q-point integration. For non-zero Born effective charges, we show that a divergence appears in the electron-phonon matrix elements at q → Γ, leading to a divergence of the adiabatic renormalization at band extrema. This problem is exacerbated by the slow convergence of Born effective charges with electronic wavevector sampling, which leaves residual Born effective charges in ab initio calculations on materials that are physically devoid of such charges. Here, we propose a solution that improves this convergence. However, for materials where Born effective charges are physically non-zero, the divergence of the renormalization indicates a breakdown of the adiabatic harmonic approximation, which we assess here by switching to the non-adiabatic harmonic approximation. Also, we study the convergence behavior of the renormalization and develop reliable extrapolation schemes to obtain the converged results. Finally, the adiabatic and non-adiabatic theories, with corrections for the slow Born effective charge convergence problem (and the associated divergence) are applied to the study of five semiconductors and insulators: α-AlN, β-AlN, BN, diamond, and silicon. For these five materials, we present the zero-point renormalization, temperature dependence, phonon-induced lifetime broadening, and the renormalized electronic band structure.

  17. Electronic structure and magnetic properties of Pd sub(3)Fe

    International Nuclear Information System (INIS)

    Kuhnen, C.A.

    1988-01-01

    In this work we study the electronic and magnetic properties of the Pd sub(3)Fe alloy. For the ordered phase of Pd sub(3)Fe we employed the Linear Muffin-Tin Orbitals Method, with the atomic sphere approximation, which is a first principles method and includes spin polarization. The theoretical results for the thermal and magnetic properties show good agreement with experience. Here we explain the formation of the localized magnetic moments from completely itinerant electrons. We investigate the influence of the hydrogen in the physical properties of the compound Pd sub(3)Fe, where we obtain a drastic reduction in the magnetic moments at the Pd and Fe sites. This reduction is confirmed by experience. The self consistent potentials of the Pd sub(3)Fe compound were used for an analysis of the influence of the disorder in the electronic structure of Pd sub(3)Fe alloy. To this end, we employ a spin polarized version of the Green's Function Method with the Coherent Potential Approximation (or KKR-CPA). The results obtained show that in random ferromagnetic alloys different degrees of disorder occurs for the different spin directions. The formation of the magnetic moments in these alloys were explained from the existence of 'virtual crystal' states for spin up electrons and 'split band' states for spin down electrons. Finally we employ the muffin-tin orbitals to calculate the X-ray photoemission spectra of the Pd sub(3)Fe and Pd sub(3)FeH compounds, which allows us a direct comparison between theory and experiment. (author)

  18. Electronic Structure of the Bismuth Family of High Temperature Superconductors

    Energy Technology Data Exchange (ETDEWEB)

    Dunn, Lisa

    2002-03-07

    High temperature superconductivity remains the central intellectual problem in condensed matter physics fifteen years after its discovery. Angle resolved photoemission spectroscopy (ARPES) directly probes the electronic structure, and has played an important role in the field of high temperature superconductors. With the recent advances in sample growth and the photoemission technique, we are able to study the electronic structure in great detail, and address regimes that were previously inaccessible. This thesis work contains systematic photoemission studies of the electronic structure of the Bi-family of high temperature superconductors, which include the single-layer system (Bi2201), the bi-layer system (Bi2212), and the tri-layer system (Bi2223). We show that, unlike conventional BCS superconductors, phase coherence information emerges in the single particle excitation spectrum of high temperature superconductors as the superconducting peak in Bi2212. The universality and various properties of this superconducting peak are studied in various systems. We argue that the origin of the superconducting peak may provide the key to understanding the mechanism of High-Tc superconductors. In addition, we identified a new experimental energy scale in the bilayer material, the anisotropic intra-bilayer coupling energy. For a long time, it was predicted that this energy scale would cause bilayer band splitting. We observe this phenomenon, for the first time, in heavily overdoped Bi2212. This new observation requires the revision of the previous picture of the electronic excitation in the Brillouin zone boundary. As the first ARPES study of a trilayer system, various detailed electronic proper- ties of Bi2223 are examined. We show that, comparing with Bi2212, both superconducting gap and relative superconducting peak intensity become larger in Bi2223, however, the strength of the interlayer coupling within each unit cell is possibly weaker. These results suggest that the

  19. Electronic, structural, and optical properties of crystalline yttria

    International Nuclear Information System (INIS)

    Xu, Y.; Gu, Z.; Ching, W.Y.

    1997-01-01

    The electronic structure of crystalline Y 2 O 3 is investigated by first-principles calculations within the local-density approximation (LDA) of the density-functional theory. Results are presented for the band structure, the total density of states (DOS), the atom- and orbital-resolved partial DOS, effective charges, bond order, and charge-density distributions. Partial covalent character in the Y-O bonding is shown, and the nonequivalency of the two Y sites is demonstrated. The calculated electronic structure is compared with a variety of available experimental data. The total energy of the crystal is calculated as a function of crystal volume. A bulk modulus B of 183 Gpa and a pressure coefficient B ' of 4.01 are obtained, which are in good agreement with compression data. An LDA band gap of 4.54 eV at Γ is obtained which increases with pressure at a rate of dE g /dP=0.012eV/Gpa at the equilibrium volume. Also investigated are the optical properties of Y 2 O 3 up to a photon energy of 20 eV. The calculated complex dielectric function and electron-energy-loss function are in good agreement with experimental data. A static dielectric constant of var-epsilon(0)=3.20 is obtained. It is also found that the bottom of the conduction band consists of a single band, and direct optical transition at Γ between the top of the valence band and the bottom of the conduction band may be symmetry forbidden. copyright 1997 The American Physical Society

  20. Heme oxygenase-1, oxidation, inflammation and atherosclerosis

    Directory of Open Access Journals (Sweden)

    Jesus A Araujo

    2012-07-01

    Full Text Available Atherosclerosis is an inflammatory process of the vascular wall characterized by the infiltration of lipids and inflammatory cells. Oxidative modifications of infiltrating low density lipoproteins and induction of oxidative stress play a major role in lipid retention in the vascular wall, uptake by macrophages and generation of foam cells, a hallmark of this disorder. The vasculature has a plethora of protective resources against oxidation and inflammation, many of them regulated by the Nrf2 transcription factor. Heme oxygenase-1 (HO-1 is a Nrf2-regulated gene that plays a critical role in the prevention of vascular inflammation. It is the inducible isoform of heme oxygenase, responsible for the oxidative cleavage of heme groups leading to the generation of biliverdin, carbon monoxide and release of ferrous iron. HO-1 has important antioxidant, antiinflammatory, antiapoptotic, antiproliferative and immunomodulatory effects in vascular cells, most of which play a significant role in the protection against atherogenesis. HO-1 may also be an important feature in macrophage differentiation and polarization to certain subtypes. The biological effects of HO-1 are largely attributable to its enzymatic activity, which can be conceived as a system with three arms of action, corresponding to its three enzymatic byproducts. HO-1 mediated vascular protection may be due to a combination of systemic and vascular local effects. It is usually expressed at low levels but can be highly upregulated in the presence of several proatherogenic stimuli. The HO-1 system is amenable for use in the development of new therapies, some of them currently under experimental and clinical trials. Interestingly, in contrast to the HO-1 antiatherogenic actions, the expression of its transcriptional regulator Nrf2 leads to proatherogenic effects instead. This article reviews the evidence that supports the antiatherogenic role of HO-1, potential pathways and mechanisms mediating