New triethoxysilylated 10-vertex closo-decaborate clusters. Synthesis and controlled immobilization into mesoporous silica.

PubMed

Abi-Ghaida, Fatima; Laila, Zahra; Ibrahim, Ghassan; Naoufal, Daoud; Mehdi, Ahmad

2014-09-14

Novel silylated hydroborate clusters comprising the closo-decaborate cage were prepared and characterized by (1)H, (13)C, (11)B, (29)Si NMR and mass spectroscopy ESI. The synthesis of such silylated clusters was achieved using reactive derivatives of [B10H10](2-), [1-B10H9N2](-) and [2-B10H9CO](-). These silylated decaborate clusters constitute a new class of precursors that can be covalently anchored onto various silica supports without any prior surface modification. As a proof of concept, the synthesized precursors were successfully anchored on mesoporous silica, SBA-15 type, in different percentages, where the mesoporous material retained its structure. All materials modified with closo-decaborate were characterized by (11)B and (29)Si solid state NMR, XRD, TEM and nitrogen sorption.

Dispersed metal cluster catalysts by design. Synthesis, characterization, structure, and performance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arslan, Ilke; Dixon, David A.; Gates, Bruce C.

2015-09-30

To understand the class of metal cluster catalysts better and to lay a foundation for the prediction of properties leading to improved catalysts, we have synthesized metal catalysts with well-defined structures and varied the cluster structures and compositions systematically—including the ligands bonded to the metals. These ligands include supports and bulky organics that are being tuned to control both the electron transfer to or from the metal and the accessibility of reactants to influence catalytic properties. We have developed novel syntheses to prepare these well-defined catalysts with atomic-scale control the environment by choice and placement of ligands and applied state-of-themore » art spectroscopic, microscopic, and computational methods to determine their structures, reactivities, and catalytic properties. The ligands range from nearly flat MgO surfaces to enveloping zeolites to bulky calixarenes to provide controlled coverages of the metal clusters, while also enforcing unprecedented degrees of coordinative unsaturation at the metal site—thereby facilitating bonding and catalysis events at exposed metal atoms. With this wide range of ligand properties and our arsenal of characterization tools, we worked to achieve a deep, fundamental understanding of how to synthesize robust supported and ligand-modified metal clusters with controlled catalytic properties, thereby bridging the gap between active site structure and function in unsupported and supported metal catalysts. We used methods of organometallic and inorganic chemistry combined with surface chemistry for the precise synthesis of metal clusters and nanoparticles, characterizing them at various stages of preparation and under various conditions (including catalytic reaction conditions) and determining their structures and reactivities and how their catalytic properties depend on their compositions and structures. Key characterization methods included IR, NMR, and EXAFS spectroscopies to identify ligands on the metals and their reactions; EXAFS spectroscopy and high-resolution STEM to determine cluster framework structures and changes resulting from reactant treatment and locations of metal atoms on support surfaces; X-ray diffraction crystallography to determine full structures of cluster-ligand combinations in the absence of a support, and TEM with tomographic methods to observe individual metal atoms and determine three-dimensional structures of catalysts. Electronic structure calculations were used to verify and interpret spectra and extend the understanding of reactivity beyond what is measurable experimentally.« less

Electrolytic synthesis of aqueous aluminum nanoclusters and in situ characterization by femtosecond Raman spectroscopy and computations

PubMed Central

Wang, Wei; Liu, Weimin; Chang, I-Ya; Wills, Lindsay A.; Zakharov, Lev N.; Boettcher, Shannon W.; Cheong, Paul Ha-Yeon; Fang, Chong; Keszler, Douglas A.

2013-01-01

The selective synthesis and in situ characterization of aqueous Al-containing clusters is a long-standing challenge. We report a newly developed integrated platform that combines (i) a selective, atom-economical, step-economical, scalable synthesis of Al-containing nanoclusters in water via precision electrolysis with strict pH control and (ii) an improved femtosecond stimulated Raman spectroscopic method covering a broad spectral range of ca. 350–1,400 cm−1 with high sensitivity, aided by ab initio computations, to elucidate Al aqueous cluster structures and formation mechanisms in real time. Using this platform, a unique view of flat [Al13(μ3-OH)6(μ2-OH)18(H2O)24](NO3)15 nanocluster formation is observed in water, in which three distinct reaction stages are identified. The initial stage involves the formation of an [Al7(μ3-OH)6(μ2-OH)6(H2O)12]9+ cluster core as an important intermediate toward the flat Al13 aqueous cluster. PMID:24167254

Structure and formation of highly luminescent protein-stabilized gold clusters† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc05086k

PubMed Central

Chevrier, D. M.; Thanthirige, V. D.; Luo, Z.; Driscoll, S.; Cho, P.; MacDonald, M. A.; Yao, Q.; Guda, R.; Xie, J.; Johnson, E. R.; Chatt, A.; Zheng, N.

2018-01-01

Highly luminescent gold clusters simultaneously synthesized and stabilized by protein molecules represent a remarkable category of nanoscale materials with promising applications in bionanotechnology as sensors. Nevertheless, the atomic structure and luminescence mechanism of these gold clusters are still unknown after several years of developments. Herein, we report findings on the structure, luminescence and biomolecular self-assembly of gold clusters stabilized by the large globular protein, bovine serum albumin. We highlight the surprising identification of interlocked gold-thiolate rings as the main gold structural unit. Importantly, such gold clusters are in a rigidified state within the protein scaffold, offering an explanation for their highly luminescent character. Combined free-standing cluster synthesis (without protecting protein scaffold) with rigidifying and un-rigidifying experiments, were designed to further verify the luminescence mechanism and gold atomic structure within the protein. Finally, the biomolecular self-assembly process of the protein-stabilized gold clusters was elucidated by time-dependent X-ray absorption spectroscopy measurements and density functional theory calculations. PMID:29732064

Facile Route to Rare Heterobimetallic Aluminum-Copper and Aluminum-Zinc Selenide Clusters.

PubMed

Li, Bin; Li, Jiancheng; Liu, Rui; Zhu, Hongping; Roesky, Herbert W

2017-03-20

Heterobimetallic aluminum-copper and aluminum-zinc clusters were prepared from the reaction of LAl(SeH) 2 [1; L = HC(CMeNAr) 2 and Ar = 2,6-iPr 2 C 6 H 3 ] with (MesCu) 4 and ZnEt 2 , respectively. The resulting clusters with the core structures of Al 2 Se 4 Cu 4 and Al 2 Se 4 Zn 3 exhibit unique metal-organic frameworks. This is a novel pathway for the synthesis of aluminum-copper and aluminum-zinc selenides. The products have been characterized by spectroscopic methods and single-crystal X-ray structural characterization.

Tuning the Emission and Quantum Yield of Gold and Silver Nanoclusters Through Ligand Design and Doping

NASA Astrophysics Data System (ADS)

Mishra, Dinesh

Nanoparticles have been extensively studied in the past few decades due to the possibilities they offer in applications ranging from medicine to energy generation. A new class of ultra-small noble metal nanoparticles consisting of tens to hundreds of atoms, commonly known as clusters or nanoclusters, have drawn interest of the research community recently due to their unique optical, electronic and structural properties. Over the past few years, advances have been made in the synthesis of atomically precise noble metal clusters (for example, silver and gold) with distinct optical properties. Their ultra-small size distinguishes them from conventional plasmonic nanoparticles and the properties are very sensitive to the slight variation in the compositon of the cluster, i.e. the number of the metal atoms and/or the nature of the ligands. These clusters are interesting because of their potential applications in field such as sensing, imaging, catalysis, clean energy, photonics, etc. as well as they provide fundamental insight into the evolution of the optical and electronic properties of these clusters. In this project, we explored the strategies to synthesize luminescent metallic clusters of gold and silver and to promote their solubility and stability in aqueous and biological medium. We focused particularly on the thiolate protected clusters due to the higher affinity of gold and silver to sulfur. Lipoic acid (Thioctic acid) is a bio-molecule with a cyclic disulfide ring, which also acts as a chelating ligand. Due to the higher binding affinity of the cyclic disulfide ring to nanocrystal surface, lipoic acid and chemically modified lipoic acid molecules have been widely reported for the synthesis and functionalization of inorganic nanocrystals. Here, we describe the use of bidentate lipoic acid ligands in the one phase growth of luminescent gold and silver nanoclusters. In addition, we have synthesized a new set of monothiol ligands containing PEG and zwitterion for the functionalization of fluorescent clusters. Chapter 1 introduces the fundamental properties of metallic clusters and the origin of these properties from electronic and structural point of view. The optical properties of ultra-small nanocrystals (<2 nm) in comparison to the plasmonic particles is described. In addition, the variation of optical and structural properties from one metal to another as well as one ligand to another is also compared. Chapter 2 describes the synthesis of ultra-small size gold clusters with different optical emission (ranging from blue to red) using photo-activated LA-PEG ligands. The influence of various factors on the growth of the clusters is also studied. Optical properties of the clusters were studied by UV-visible absorption, PL emission and excitation and time resolved fluorescence spectroscopy. XPS and DOSY NMR were used to characterize the oxidation states and sizes of these clusters. The photo-chemical transformation of LA-PEG ligands to thiols and the effect of various experimental parameters such as solvent, oxygen, ligand functional group and effect of acid are described in chapter 3. Thiol yield percentage was quantified using ellman assay. Chapter 4 describes the one phase aqueous synthesis of Ag29 clusters capped with bidentate dihydrolipoic acid (DHLA). We also describe the drastic enhancement of the PL intensity upon gold doping of the Ag29 clusters. Optical properties along with the size characterization by electrospray ionization mass spectrometry is also described. We further describe the growth of these clusters using DHLA-PEG molecules. Chapter 5 describes the synthesis of highly fluorescent Au25-xAgx clusters stabilized with two types of ligands (triphenylphosphine and thiols). We designed a set of monothiolate ligands appended with PEG and zwitterionic moieties. This approach allows to prepare water soluble and stable metallic clusters with enhanced photoluminescence and well defined optical properties. Chapter 6 is the overall summary of our findings and prospects and outlook.

A grand unified model for liganded gold clusters

NASA Astrophysics Data System (ADS)

Xu, Wen Wu; Zhu, Beien; Zeng, Xiao Cheng; Gao, Yi

2016-12-01

A grand unified model (GUM) is developed to achieve fundamental understanding of rich structures of all 71 liganded gold clusters reported to date. Inspired by the quark model by which composite particles (for example, protons and neutrons) are formed by combining three quarks (or flavours), here gold atoms are assigned three `flavours' (namely, bottom, middle and top) to represent three possible valence states. The `composite particles' in GUM are categorized into two groups: variants of triangular elementary block Au3(2e) and tetrahedral elementary block Au4(2e), all satisfying the duet rule (2e) of the valence shell, akin to the octet rule in general chemistry. The elementary blocks, when packed together, form the cores of liganded gold clusters. With the GUM, structures of 71 liganded gold clusters and their growth mechanism can be deciphered altogether. Although GUM is a predictive heuristic and may not be necessarily reflective of the actual electronic structure, several highly stable liganded gold clusters are predicted, thereby offering GUM-guided synthesis of liganded gold clusters by design.

Iridium clusters in KLTL zeolite: Synthesis, structural characterization, and catalysis of toluene hydrogenation and n-hexane dehydrocyclization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, A.; Jentoft, R.E.; Gates, B.C.

Iridium clusters incorporating about six atoms each, on average, were prepared in KLTL zeolite by decarbonylation (in H{sub 2} at 400{degrees}C) of iridium carbonyl clusters formed by treatment of adsorbed [Ir(CO){sub 2}(acac)] in CO at 1 atm and 175{degrees}C. The supported species were characterized by infrared and extended X-ray absorption fine structure (EXAFS) spectroscopies. The iridium carbonyls formed from [Ir(CO){sub 2}(acac)] were predominantly [HIr{sub 4}(CO){sub 11}]{sup -} with a small amount of [Ir(CO){sub 4}]{sup -}. The synthesis chemistry of iridium carbonyls in the basic KLTL zeolite parallels that in basic solutions. Shifts of the {nu}{sub CO} bands of the iridiummore » carbonyl clusters relative to those of the same clusters in solution indicate strong interactions between the clusters and zeolite cations. The decarbonylated sample, approximated as Ir{sub 6}/KLTL zeolite, is catalytically active for toluene hydrogenation at 60-100{degrees}C, with the activity being approximately the same as those of Ir{sub 4} and Ir{sub 6} clusters supported on metal oxides, but an order of magnitude less than that of a conventional supported iridium catalyst consisting of aggregates of about 50 atoms each, on average. The catalyst is also active for conversion of n-hexane + H{sub 2} at 340-420{degrees}C, but the selectivity for aromatization is low and that for hydrogenolysis is high, consistent with earlier results for conventionally prepared (salt-derived) iridium clusters of about the same size supported in KLTL zeolite. The zeolite-supported iridium clusters are the first prepared from both salt and organometallic precursors; the results indicate that the organometallic and conventional preparation routes lead to supported iridium clusters having similar structures and catalytic properties. 59 refs., 6 figs., 7 tabs.« less

Synthesis and molecular structure of a spheroidal binary nanoscale copper sulfide cluster.

PubMed

Bestgen, Sebastian; Fuhr, Olaf; Roesky, Peter W; Fenske, Dieter

2016-09-27

The reaction of copper(4-(tert-butyl)phenyl)methanethiolate [CuSCH 2 C 6 H 4 t Bu] with bis(trimethylsilyl)sulfide S(SiMe 3 ) 2 in the presence of triphenylphosphine PPh 3 afforded the binary 52 nuclear copper cluster [Cu 52 S 12 (SCH 2 C 6 H 4 t Bu) 28 (PPh 3 ) 8 ]. The molecular structure of this intensely red coloured nanoscale Cu 2 S mimic was established by single crystal X-ray diffraction.

Molecular Cloning and Functional Analysis of Gene Clusters for the Biosynthesis of Indole-Diterpenes in Penicillium crustosum and P. janthinellum

PubMed Central

Nicholson, Matthew J.; Eaton, Carla J.; Stärkel, Cornelia; Tapper, Brian A.; Cox, Murray P.; Scott, Barry

2015-01-01

The penitremane and janthitremane families of indole-diterpenes are abundant natural products synthesized by Penicillium crustosum and P. janthinellum. Using a combination of PCR, cosmid library screening, and Illumina sequencing we have identified gene clusters encoding enzymes for the synthesis of these compounds. Targeted deletion of penP in P. crustosum abolished the synthesis of penitrems A, B, D, E, and F, and led to accumulation of paspaline, a key intermediate for paxilline biosynthesis in P. paxilli. Similarly, deletion of janP and janD in P. janthinellum abolished the synthesis of prenyl-elaborated indole-diterpenes, and led to accumulation in the latter of 13-desoxypaxilline, a key intermediate for the synthesis of the structurally related aflatremanes synthesized by Aspergillus flavus. This study helps resolve the genetic basis for the complexity of indole-diterpene natural products found within the Penicillium and Aspergillus species. All indole-diterpene gene clusters identified to date have a core set of genes for the synthesis of paspaline and a suite of genes encoding multi-functional cytochrome P450 monooxygenases, FAD dependent monooxygenases, and prenyl transferases that catalyse various regio- and stereo- specific oxidations that give rise to the diversity of indole-diterpene products synthesized by this group of fungi. PMID:26213965

A Polymerase With Potential: The Fe-S Cluster in Human DNA Primase.

PubMed

Holt, Marilyn E; Salay, Lauren E; Chazin, Walter J

2017-01-01

Replication of DNA in eukaryotes is primarily executed by the combined action of processive DNA polymerases δ and ɛ. These enzymes cannot initiate synthesis of new DNA without the presence of a primer on the template ssDNA. The primers on both the leading and lagging strands are generated by DNA polymerase α-primase (pol-prim). DNA primase is a DNA-dependent RNA polymerase that synthesizes the first ~10 nucleotides and then transfers the substrate to polymerase α to complete primer synthesis. The mechanisms governing the coordination and handoff between primase and polymerase α are largely unknown. Isolated DNA primase contains a [4Fe-4S] 2+ cluster that has been shown to serve as a redox switch modulating DNA binding affinity. This discovery suggests a mechanism for modulating the priming activity of primase and handoff to polymerase α. In this chapter, we briefly discuss the current state of knowledge of primase structure and function, including the role of its iron-sulfur cluster. This is followed by providing the methods for expressing, purifying, and biophysically/structurally characterizing primase and its iron-sulfur cluster-containing domain, p58C. © 2017 Elsevier Inc. All rights reserved.

Towards Cluster-Assembled Materials of True Monodispersity in Size and Chemical Environment: Synthesis, Dynamics and Activity

DTIC Science & Technology

2016-10-27

AFRL-AFOSR-UK-TR-2016-0037 Towards cluster-assembled materials of true monodispersity in size and chemical environment: Synthesis, Dynamics and...Towards cluster-assembled materials of true monodispersity in size and chemical environment: synthesis, dynamics and activity 5a.  CONTRACT NUMBER 5b...report Towards cluster-assembled materials of true monodispersity in size and chemical environment: Synthesis, Dynamics and Activity Ulrich Heiz

Gas-phase synthesis of singly and multiply charged polyoxovanadate anions employing electrospray ionization and collision induced dissociation.

PubMed

Al Hasan, Naila M; Johnson, Grant E; Laskin, Julia

2013-09-01

Electrospray ionization mass spectrometry (ESI-MS) combined with in-source fragmentation and tandem mass spectrometry (MS/MS) experiments were used to generate a wide range of singly and multiply charged vanadium oxide cluster anions including VxOy(n-) and VxOyCl(n-) ions (x = 1-14, y = 2-36, n = 1-3), protonated clusters, and ligand-bound polyoxovanadate anions. The cluster anions were produced by electrospraying a solution of tetradecavanadate, V14O36Cl(L)5 (L = Et4N(+), tetraethylammonium), in acetonitrile. Under mild source conditions, ESI-MS generates a distribution of doubly and triply charged VxOyCl(n-) and VxOyCl(L)((n-1)-) clusters predominantly containing 14 vanadium atoms as well as their protonated analogs. Accurate mass measurement using a high-resolution LTQ/Orbitrap mass spectrometer (m/Δm = 60,000 at m/z 410) enabled unambiguous assignment of the elemental composition of the majority of peaks in the ESI-MS spectrum. In addition, high-sensitivity mass spectrometry allowed the charge state of the cluster ions to be assigned based on the separation of the major from the much less abundant minor isotope of vanadium. In-source fragmentation resulted in facile formation of smaller VxOyCl((1-2)-) and VxOy ((1-2)-) anions. Collision-induced dissociation (CID) experiments enabled systematic study of the gas-phase fragmentation pathways of the cluster anions originating from solution and from in-source CID. Surprisingly simple fragmentation patterns were obtained for all singly and doubly charged VxOyCl and VxOy species generated through multiple MS/MS experiments. In contrast, cluster anions originating directly from solution produced comparatively complex CID spectra. These results are consistent with the formation of more stable structures of VxOyCl and VxOy anions through low-energy CID. Furthermore, our results demonstrate that solution-phase synthesis of one precursor cluster anion combined with gas-phase CID is an efficient approach for the top-down synthesis of a wide range of singly and multiply charged gas-phase metal oxide cluster anions for subsequent investigations of structure and reactivity using mass spectrometry and ion spectroscopy techniques.

Gas-Phase Synthesis of Singly and Multiply Charged Polyoxovanadate Anions Employing Electrospray Ionization and Collision Induced Dissociation

NASA Astrophysics Data System (ADS)

Al Hasan, Naila M.; Johnson, Grant E.; Laskin, Julia

2013-09-01

Electrospray ionization mass spectrometry (ESI-MS) combined with in-source fragmentation and tandem mass spectrometry (MS/MS) experiments were used to generate a wide range of singly and multiply charged vanadium oxide cluster anions including VxOy n- and VxOyCln- ions (x = 1-14, y = 2-36, n = 1-3), protonated clusters, and ligand-bound polyoxovanadate anions. The cluster anions were produced by electrospraying a solution of tetradecavanadate, V14O36Cl(L)5 (L = Et4N+, tetraethylammonium), in acetonitrile. Under mild source conditions, ESI-MS generates a distribution of doubly and triply charged VxOyCln- and VxOyCl(L)(n-1)- clusters predominantly containing 14 vanadium atoms as well as their protonated analogs. Accurate mass measurement using a high-resolution LTQ/Orbitrap mass spectrometer (m/Δm = 60,000 at m/z 410) enabled unambiguous assignment of the elemental composition of the majority of peaks in the ESI-MS spectrum. In addition, high-sensitivity mass spectrometry allowed the charge state of the cluster ions to be assigned based on the separation of the major from the much less abundant minor isotope of vanadium. In-source fragmentation resulted in facile formation of smaller VxOyCl(1-2)- and VxOy (1-2)- anions. Collision-induced dissociation (CID) experiments enabled systematic study of the gas-phase fragmentation pathways of the cluster anions originating from solution and from in-source CID. Surprisingly simple fragmentation patterns were obtained for all singly and doubly charged VxOyCl and VxOy species generated through multiple MS/MS experiments. In contrast, cluster anions originating directly from solution produced comparatively complex CID spectra. These results are consistent with the formation of more stable structures of VxOyCl and VxOy anions through low-energy CID. Furthermore, our results demonstrate that solution-phase synthesis of one precursor cluster anion combined with gas-phase CID is an efficient approach for the top-down synthesis of a wide range of singly and multiply charged gas-phase metal oxide cluster anions for subsequent investigations of structure and reactivity using mass spectrometry and ion spectroscopy techniques.

B38: an all-boron fullerene analogue

NASA Astrophysics Data System (ADS)

Lv, Jian; Wang, Yanchao; Zhu, Li; Ma, Yanming

2014-09-01

Fullerene-like structures formed by elements other than carbon have long been sought. Finding all-boron (B) fullerene-like structures is challenging due to the geometrical frustration arising from competitions among various structural motifs. We report here the prediction of a B38 fullerene analogue found through first-principles swarm structure searching calculations. The structure is highly symmetric and consists of 56 triangles and four hexagons, which provide an optimal void in the center of the cage. Energetically, it is more favorable than the planar and tubular structures, and possesses an unusually high chemical stability: a large energy gap (~2.25 eV) and a high double aromaticity, superior to those of most aromatic quasi-planar B12 and double-ring B20 clusters. Our findings represent a key step forward towards to the understanding of structures of medium-sized B clusters and map out the experimental direction of the synthesis of an all-B fullerene analogue.Fullerene-like structures formed by elements other than carbon have long been sought. Finding all-boron (B) fullerene-like structures is challenging due to the geometrical frustration arising from competitions among various structural motifs. We report here the prediction of a B38 fullerene analogue found through first-principles swarm structure searching calculations. The structure is highly symmetric and consists of 56 triangles and four hexagons, which provide an optimal void in the center of the cage. Energetically, it is more favorable than the planar and tubular structures, and possesses an unusually high chemical stability: a large energy gap (~2.25 eV) and a high double aromaticity, superior to those of most aromatic quasi-planar B12 and double-ring B20 clusters. Our findings represent a key step forward towards to the understanding of structures of medium-sized B clusters and map out the experimental direction of the synthesis of an all-B fullerene analogue. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr01846j

Aromaticity and Antiaromaticity in Zintl Clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sun, Zhong -Ming; Liu, Chao; Popov, Ivan Aleksandrovich

Originally, the concepts of aromaticity and antiaromaticity were introduced to explain the stability and reactivity of unsaturated organic compounds. Since then, they have been extended to other species with delocalized electrons including various saturated systems, organometallic compounds, and even inorganic clusters and molecules. In this study, we focus on the most recent progress of using these concepts to guide experimental synthesis and rationalize geometrical and electronic structures of a particular family of polyanions composed of Group 14 and 15 elements, namely Zintl clusters.

Archimedean Synthesis and Magic Numbers: "Sizing" Giant Molybdenum-Oxide-Based Molecular Spheres of the Keplerate Type.

PubMed

Müller; Sarkar; Shah; Bögge; Schmidtmann; Kögerler; Hauptfleisch; Trautwein; Schünemann

1999-11-02

Pythagorean harmony can be found in the spherical polyoxometalate clusters described here (see illustration for an example of a structure), since there are interesting relationships between the so-called magic numbers (12, 32, 42, 72, 132) relevant for spherical viruses and the number of the building blocks in the cluster. The size of these Keplerate clusters can be tailored by varying the type of connections between the pentagons by means of different spacers.

Aromaticity and Antiaromaticity in Zintl Clusters

DOE PAGES

Sun, Zhong -Ming; Liu, Chao; Popov, Ivan Aleksandrovich; ...

2018-05-18

Originally, the concepts of aromaticity and antiaromaticity were introduced to explain the stability and reactivity of unsaturated organic compounds. Since then, they have been extended to other species with delocalized electrons including various saturated systems, organometallic compounds, and even inorganic clusters and molecules. In this study, we focus on the most recent progress of using these concepts to guide experimental synthesis and rationalize geometrical and electronic structures of a particular family of polyanions composed of Group 14 and 15 elements, namely Zintl clusters.

Methanol Synthesis from CO2 Hydrogenation over a Pd4/In2O3 Model Catalyst: A Combined DFT and Kinetic Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ye, Jingyun; Liu, Changjun; Mei, Donghai

2014-08-01

Methanol synthesis from CO2 hydrogenation on Pd4/In2O3 has been investigated using density functional theory (DFT) and microkinetic modeling. In this study, three possible routes in the reaction network of CO2 + H2 → CH3OH + H2O have been examined. Our DFT results show that the HCOO route competes with the RWGS route whereas a high activation barrier kinetically blocks the HCOOH route. DFT results also suggest that H2COO* + H* ↔ H2CO* +OH* and cis-COOH* + H* ↔CO* + H2O* are the rate limiting steps in the HCOO route and the RWGS route, respectively. Microkinetic modeling results demonstrate that themore » HCOO route is the dominant reaction route for methanol synthesis from CO2 hydrogenation. We found that the activation of H adatom on the small Pd cluster and the presence of H2O on the In2O3 substrate play important roles in promoting the methanol synthesis. The hydroxyl adsorbed at the interface of Pd4/In2O3 induces the transformation of the supported Pd4 cluster from a butterfly structure into a tetrahedron structure. This important structure change not only indicates the dynamical nature of the supported nanoparticle catalyst structure during the reaction but also shifts the final hydrogenation step from H2COH to CH3O.« less

Clusters, Assemble: Growth of Intermetallic Compounds from Metal Flux Reactions.

PubMed

Latturner, Susan E

2018-01-16

Metal flux synthesis involves the reaction of metals and metalloids in a large excess of a low-melting metal that acts as a solvent. This technique makes use of an unusual temperature regime (above the temperatures used for solvothermal methods and below the temperatures used in traditional solid state synthesis) and facilitates the growth of products as large crystals. It has proven to be a fruitful method to discover new intermetallic compounds. However, little is known about the chemistry occurring within a molten metal solvent; without an understanding of the nature of precursor formation and assembly, it is difficult to predict product structures and target properties. Organic chemists have a vast toolbox of well-known reagents and reaction mechanisms to use in directing their synthesis toward a desired molecular structure. This is not yet the case for the synthesis of inorganic extended structures. We have carried out extensive explorations of the growth of new magnetic intermetallic compounds from a variety of metal fluxes. This Account presents a review of some of our results and recent reports by other groups; this work indicates that products with common building blocks and homologous series with identical structural motifs are repeatedly seen in metal flux chemistry. For instance, fluorite-type layers comprised of transition metals coordinated by eight main group metal atoms are found in the Th 2 (Au x Si 1-x )[AuAl 2 ] n Si 2 and R[AuAl 2 ] n Al 2 (Au x Si 1-x ) 2 series grown from aluminum flux, the Ce n PdIn 3n+2 series grown from indium flux, and CePdGa 6 and Ce 2 PdGa 10 grown from gallium flux. Similarly, our investigations of reactions of heavy main group metals, M, in rare earth/transition metal eutectic fluxes reveal that the R/T/M/M' products usually feature M-centered rare earth clusters M@R 8-12 , which share faces to form layers and networks that surround transition metal building blocks. These structural trends, temperature dependence of products formed in the flux, and interconversions observed by differential scanning calorimetry support the idea that these clusters likely form in the melt, existing as precursors and assembling into different crystalline products depending on time, temperature, and reaction ratio. Proof of this mechanism will require future investigations using techniques such as pair distribution function analysis of flux melts to observe cluster formation and in situ diffraction during cooling to detect various phases as they crystallize and interconvert. These data will aid in understanding the parameters that control cluster formation and assembly in metal melts, allow for prediction of products of flux reactions, and will potentially enable the tailoring of reaction conditions to promote the formation of structures with desirable properties.

Structural genes for thiamine biosynthetic enzymes (thiCEFGH) in Escherichia coli K-12.

PubMed Central

Vander Horn, P B; Backstrom, A D; Stewart, V; Begley, T P

1993-01-01

Escherichia coli K-12 synthesizes thiamine pyrophosphate (vitamin B1) de novo. Two precursors [4-methyl-5-(beta-hydroxyethyl)thiazole monophosphate and 4-amino-5-hydroxymethyl-2-methylpyrimidine pyrophosphate] are coupled to form thiamine monophosphate, which is then phosphorylated to make thiamine pyrophosphate. Previous studies have identified two classes of thi mutations, clustered at 90 min on the genetic map, which result in requirements for the thiazole or the hydroxymethylpryimidine. We report here our initial molecular genetic analysis of the thi cluster. We cloned the thi cluster genes and examined their organization, structure, and function by a combination of phenotypic testing, complementation analysis, polypeptide expression, and DNA sequencing. We found five tightly linked genes, designated thiCEFGH. The thiC gene product is required for the synthesis of the hydroxymethylpyrimidine. The thiE, thiF, thiG, and thiH gene products are required for synthesis of the thiazole. These mutants did not respond to 1-deoxy-D-threo-2-pentulose, indicating that they are blocked in the conversion of this precursor compound to the thiazole itself. Images PMID:8432721

Water-soluble Au13 clusters protected by binary thiolates: Structural accommodation and the use for chemosensing

NASA Astrophysics Data System (ADS)

Ding, Weihua; Huang, Chuanqi; Guan, Lingmei; Liu, Xianhu; Luo, Zhixun; Li, Weixue

2017-05-01

Here we report a successful synthesis of water-soluble 13-atoms gold clusters under the monolayer protection of binary thiolates, glutathione and penicillamine, under a molecular formula of Au13(SG)5(PA)7. This monolayer-protected cluster (MPC) finds decent stability and is demonstrated to possess an icosahedral geometry pertaining to structural accommodation in contrast to a planar bare Au13 of local minima energy. Natural bond orbital (NBO) analysis depicts the interaction patterns between gold and the ligands, enlightening to understand the origin of enhanced stability of the Au13 MPCs. Further, the water-soluble Au13 MPCs are found to be a decent candidate for chemosensing and bioimaging.

A grand unified model for liganded gold clusters

PubMed Central

Xu, Wen Wu; Zhu, Beien; Zeng, Xiao Cheng; Gao, Yi

2016-01-01

A grand unified model (GUM) is developed to achieve fundamental understanding of rich structures of all 71 liganded gold clusters reported to date. Inspired by the quark model by which composite particles (for example, protons and neutrons) are formed by combining three quarks (or flavours), here gold atoms are assigned three ‘flavours' (namely, bottom, middle and top) to represent three possible valence states. The ‘composite particles' in GUM are categorized into two groups: variants of triangular elementary block Au3(2e) and tetrahedral elementary block Au4(2e), all satisfying the duet rule (2e) of the valence shell, akin to the octet rule in general chemistry. The elementary blocks, when packed together, form the cores of liganded gold clusters. With the GUM, structures of 71 liganded gold clusters and their growth mechanism can be deciphered altogether. Although GUM is a predictive heuristic and may not be necessarily reflective of the actual electronic structure, several highly stable liganded gold clusters are predicted, thereby offering GUM-guided synthesis of liganded gold clusters by design. PMID:27910848

Transfer-free synthesis of graphene-like atomically thin carbon films on SiC by ion beam mixing technique

NASA Astrophysics Data System (ADS)

Zhang, Rui; Chen, Fenghua; Wang, Jinbin; Fu, Dejun

2018-03-01

Here we demonstrate the synthesis of graphene directly on SiC substrates at 900 °C using ion beam mixing technique with energetic carbon cluster ions on Ni/SiC structures. The thickness of 7-8 nm Ni films was evaporated on the SiC substrates, followed by C cluster ion bombarding. Carbon cluster ions C4 were bombarded at 16 keV with the dosage of 4 × 1016 atoms/cm2. After thermal annealing process Ni silicides were formed, whereas C atoms either from the decomposition of the SiC substrates or the implanted contributes to the graphene synthesis by segregating and precipitating process. The limited solubility of carbon atoms in silicides, involving SiC, Ni2Si, Ni5Si2, Ni3Si, resulted in diffusion and precipitation of carbon atoms to form graphene on top of Ni and the interface of Ni/SiC. The ion beam mixing technique provides an attractive production method of a transfer-free graphene growth on SiC and be compatible with current device fabrication.

A discrete Cu cluster and a 3D MnII-CuII framework based on assembly of Mn2Cu4 clusters: synthesis, structure and magnetic properties.

PubMed

Chakraborty, Anindita; Escuer, Albert; Ribas, Joan; Maji, Tapas Kumar

2016-10-04

The synthesis, single-crystal structure characterization and detailed magnetic study of a homometallic hexanuclear Cu II cluster [Cu 6 (μ 3 -OH) 2 (ppk) 6 (H 2 O) 2 (NO 3 ) 4 ] (1) and a three-dimensional (3D) compound [{MnCu 2 (dpkO 2 H) 2 (dpkO 2 )N 3 }·(NO 3 )·H 2 O] n (2) (ppk = phenyl-2-pyridyl ketoxime; dpk = di-2-pyridyl ketone) consisting of heterometallic Mn II -Cu II hexanuclear cores as secondary building units are reported in this paper. In compound 1, two symmetry-related Cu 3 triangles consisting of a hydroxido-bridged trinuclear unit, [Cu 3 (μ 3 -OH)(ppk) 3 (H 2 O)(NO 3 )] + , are assembled through nitrate bridging giving rise to the homometallic Cu 6 cluster. Compound 2 contains heterometallic {MnCu} cores, which are further connected to each other through an azido bridging ligand in all the crystallographic directions, resulting in a 3D metal-organic framework. Construction of such a heterometallic 3D framework from {MnCu} units is until now, unknown. Magnetic studies of both 1 and 2 were performed in detail and both compounds show dominant antiferromagnetic interaction in the respective clusters. Compound 1 reveals significant spin frustration and anti-symmetric exchange interaction in the trinuclear cores, with a significantly high value of J av (-655 cm -1 ). Furthermore, compound 2 exhibits a dominant antiferromagnetic interaction, which is also supported by an extensive magneto-structural correlation which considers the different magnetic pathways.

Cluster synthesis and direct ordering of rare-earth transition-metal nanomagnets.

PubMed

Balasubramanian, Balamurugan; Skomski, Ralph; Li, Xingzhong; Valloppilly, Shah R; Shield, Jeffrey E; Hadjipanayis, George C; Sellmyer, David J

2011-04-13

Rare-earth transition-metal (R-TM) alloys show superior permanent magnetic properties in the bulk, but the synthesis and application of R-TM nanoparticles remains a challenge due to the requirement of high-temperature annealing above about 800 °C for alloy formation and subsequent crystalline ordering. Here we report a single-step method to produce highly ordered R-TM nanoparticles such as YCo(5) and Y(2)Co(17), without high-temperature thermal annealing by employing a cluster-deposition system and investigate their structural and magnetic properties. The direct ordering is highly desirable to create and assemble R-TM nanoparticle building blocks for future permanent-magnet and other significant applications.

Effect of mitochondrial complex I inhibition on Fe-S cluster protein activity.

PubMed

Mena, Natalia P; Bulteau, Anne Laure; Salazar, Julio; Hirsch, Etienne C; Núñez, Marco T

2011-06-03

Iron-sulfur (Fe-S) clusters are small inorganic cofactors formed by tetrahedral coordination of iron atoms with sulfur groups. Present in numerous proteins, these clusters are involved in key biological processes such as electron transfer, metabolic and regulatory processes, DNA synthesis and repair and protein structure stabilization. Fe-S clusters are synthesized mainly in the mitochondrion, where they are directly incorporated into mitochondrial Fe-S cluster-containing proteins or exported for cytoplasmic and nuclear cluster-protein assembly. In this study, we tested the hypothesis that inhibition of mitochondrial complex I by rotenone decreases Fe-S cluster synthesis and cluster content and activity of Fe-S cluster-containing enzymes. Inhibition of complex I resulted in decreased activity of three Fe-S cluster-containing enzymes: mitochondrial and cytosolic aconitases and xanthine oxidase. In addition, the Fe-S cluster content of glutamine phosphoribosyl pyrophosphate amidotransferase and mitochondrial aconitase was dramatically decreased. The reduction in cytosolic aconitase activity was associated with an increase in iron regulatory protein (IRP) mRNA binding activity and with an increase in the cytoplasmic labile iron pool. Since IRP activity post-transcriptionally regulates the expression of iron import proteins, Fe-S cluster inhibition may result in a false iron deficiency signal. Given that inhibition of complex I and iron accumulation are hallmarks of idiopathic Parkinson's disease, the findings reported here may have relevance for understanding the pathophysiology of this disease. Copyright © 2011 Elsevier Inc. All rights reserved.

Linked supramolecular building blocks for enhanced cluster formation

DOE PAGES

McLellan, Ross; Palacios, Maria A.; Beavers, Christine M.; ...

2015-01-09

Methylene-bridged calix[4]arenes have emerged as extremely versatile ligand supports in the formation of new polymetallic clusters possessing fascinating magnetic properties. Metal ion binding rules established for this building block allow one to partially rationalise the complex assembly process. The ability to covalently link calix[4]arenes at the methylene bridge provides significantly improved control over the introduction of different metal centres to resulting cluster motifs. Clusters assembled from bis-calix[4]arenes and transition metal ions or 3d-4f combinations display characteristic features of the analogous calix[4]arene supported clusters, thereby demonstrating an enhanced and rational approach towards the targeted synthesis of complex and challenging structures.

Nanophase materials assembled from clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Siegel, R.W.

1992-02-01

The preparation of metal and ceramic atom clusters by means of the gas-condensation method, followed by their in situ collection and consolidation under high-vacuum conditions, has recently led to the synthesis of a new class of ultrafine-grained materials. These nanophase materials, with typical average grain sizes of 5 to 50 nm and, hence, a large fraction of their atoms in interfaces, exhibit properties that are often considerably improved relative to those of conventional materials. Furthermore, their synthesis and processing characteristics should enable the design of new materials with unique properties. Some examples are ductile ceramics that can be formed andmore » sintered to full density at low temperatures without the need for binding or sintering aids, and metals with dramatically increased strength. The synthesis of these materials is briefly described along with what is presently known of their structure and properties. Their future impact on materials science and technology is also considered.« less

Synthesis and morphology of hydroxyapatite/polyethylene oxide nanocomposites with block copolymer compatibilized interfaces

NASA Astrophysics Data System (ADS)

Lee, Ji Hoon; Shofner, Meisha

2012-02-01

In order to exploit the promise of polymer nanocomposites, special consideration should be given to component interfaces during synthesis and processing. Previous results from this group have shown that nanoparticles clustered into larger structures consistent with their native shape when the polymer matrix crystallinity was high. Therefore in this research, the nanoparticles are disguised from a highly-crystalline polymer matrix by cloaking them with a matrix-compatible block copolymer. Specifically, spherical and needle-shaped hydroxyapatite nanoparticles were synthesized using a block copolymer templating method. The block copolymer used, polyethylene oxide-b-polymethacrylic acid, remained on the nanoparticle surface following synthesis with the polyethylene oxide block exposed. These nanoparticles were subsequently added to a polyethylene oxide matrix using solution processing. Characterization of the nanocomposites indicated that the copolymer coating prevented the nanoparticles from assembling into ordered clusters and that the matrix crystallinity was decreased at a nanoparticle spacing of approximately 100 nm.

Synthesis, characterization and optical properties of an amino-functionalized gold thiolate cluster: Au10(SPh-pNH2)10.

PubMed

Lavenn, Christophe; Albrieux, Florian; Tuel, Alain; Demessence, Aude

2014-03-15

Research interest in ultra small gold thiolate clusters has been rising in recent years for the challenges they offer to bring together properties of nanoscience and well-defined materials from molecular chemistry. Here, a new atomically well-defined Au10 gold nanocluster surrounded by ten 4-aminothiophenolate ligands is reported. Its synthesis followed the similar conditions reported for the elaboration of Au144(SR)60, but because the reactivity of thiophenol ligands is different from alkanethiol derivates, smaller Au10 clusters were formed. Different techniques, such as ESI-MS, elemental analysis, XRD, TGA, XPS and UV-vis-NIR experiments, have been carried out to determine the Au10(SPh-pNH2)10 formula. Photoemission experiment has been done and reveals that the Au10 clusters are weakly luminescent as opposed to the amino-based ultra-small gold clusters. This observation points out that the emission of gold thiolate clusters is highly dependent on both the structure of the gold core and the type of the ligands at the surface. In addition, ultra-small amino-functionalized clusters offer the opportunity for extended work on self-assembling networks or deposition on substrates for nanotechnologies or catalytic applications. Copyright © 2013 Elsevier Inc. All rights reserved.

Synthesis, Characterization and Application of Water-soluble Gold and Silver Nanoclusters

NASA Astrophysics Data System (ADS)

Kumar, Santosh

The term `nanotechnology' has emerged as a buzzword since the last few decades. It has found widespread applications across disciplines, from medicine to energy. The synthesis of gold and silver nanoclusters has found much excitement, due to their novel material properties. Seminal work by various groups, including ours, has shown that the size of these clusters can be controlled with atomic precision. This control gives access to tuning the optical and electronic properties. The majority of nanoclusters reported thus far are not water soluble, which limit their applications in biology that requires water-solubility. Going from organic to aqueous phase is by no means a simple task, as it is associated with many challenges. Their stability in the presence of oxygen, difficulty in characterization, and separation of pure nanoclusters are some of the major bottlenecks associated with the synthesis of water-soluble gold nanoclusters. Water-soluble gold nanoclusters hold great potential in biological labeling, bio-catalysis and nano-bioconjugates. To overcome this problem, a new ligand with structural rigidity is needed. After considering various possibilities, we chose Captopril as a candidate ligand. In my thesis research, the synthesis of Au25 nanocluster capped with captopril has been reported. Captopril-protected Au25 nanocluster showed significantly higher thermal stability and enhanced chiroptical properties than the Glutathione-capped cluster, which confirms our initial rationale, that the ligand is critical in protecting the nanocluster. The optical absorption properties of these Au25 nanoclusters are studied and compared to the plasmonic nanoparticles. The high thermal stability and solubility of Au25 cluster capped with Captopril motivated us to explore this ligand for the synthesis of other gold clusters. Captopril is a chiral molecule with two chiral centers. The chiral ligand can induce chirality to the overall cluster, even if the core is achiral. Therefore, to obtain Au38 clusters as an enantiomer, the ligand employed should be chiral. The enantioselective synthesis of Au 38 capped with different chiral ligands has been reported and their chiroptical properties have been compared. The synthesis of a series of water-soluble Au nanoclusters has motivated us to study the effect of capping ligands and the core-size on their steady-state and time-resolved fluorescence properties, since the photoluminescence properties are particularly important for bioimaging and biomedical applications of nanoclusters. To gain fundamental insights into the origin of luminescence in nanoclusters, the effect of temperature on the fluorescence properties of these clusters has also been studied. The different sized nanoclusters ranging from a few dozen atoms to hundreds of atoms form a bridge between discrete atoms and the plasmonic nanocrystals; the latter involves essentially collective electron excitation-a phenomenon well explained by classical physics as opposed to quantum physics. The central question is: at what size does this transition from quantum behavior to classical behavior occur? To unravel this, we have successfully synthesized a series of silver nanoclusters. The precise formula assignment and their structural determination are still ongoing. We have successfully demonstrated the application of these water-soluble Au nanoclusters in photodynamic therapy for the treatment of cancer. We have successfully demonstrated that Au nanocluster system can produce singlet oxygen without the presence of any organic photosensitizers. In a collaborative project with Dr. Peteanu's group, the quenching efficiency of organic dyes by these water soluble nanoclusters is studied in different systems. Overall, this thesis outlines the successful synthesis of a family of water-soluble nanoclusters, their optical, chiroptical and fluorescence properties, as well as some applications of these nanoclusters.

The first octahedral cluster complexes with terminal formate ligands: synthesis, structure, and properties of K4[Re6S8(HCOO)6] and Cs4[Re6S8(HCOO)6].

PubMed

Brylev, Konstantin A; Mironov, Yuri V; Kozlova, Svetlana G; Fedorov, Vladimir E; Kim, Sung-Jin; Pietzsch, Hans-Jürgen; Stephan, Holger; Ito, Akitaka; Ishizaka, Shoji; Kitamura, Noboru

2009-03-02

The hexarhenium anionic cluster complex with terminal formate ligands [Re6S8(HCOO)6]4- was obtained by the room-temperature reaction between [Re6S8(OH)6]4- and formic acid in an aqueous solution. The cluster was crystallized as a potassium or cesium salt and characterized by X-ray single-crystal diffraction and elemental analyses, IR, 1H NMR, UV/vis, and luminescence spectroscopies. In particular, the emission quantum yield of the potassium salt of the Re6 cluster anion in the solid phase was determined for the first time. The electronic structures of [Re6S8(HCOO)6]4- and [Re6S8(OH)6]4- were also elucidated by DFT calculations.

Titanium oxo-clusters: precursors for a Lego-like construction of nanostructured hybrid materials.

PubMed

Rozes, Laurence; Sanchez, Clément

2011-02-01

Titanium oxo-clusters, well-defined monodispersed nano-objects, are appropriate nano-building blocks for the preparation of organic-inorganic materials by a bottom up approach. This critical review proposes to present the different structures of titanium oxo-clusters referenced in the literature and the different strategies followed to build up hybrid materials with these versatile building units. In particular, this critical review cites and reports on the most important papers in the literature, concentrating on recent developments in the field of synthesis, characterization, and the use of titanium oxo-clusters for the construction of advanced hybrid materials (137 references).

Gas-Phase Synthesis of Singly and Multiply Charged Polyoxovanadate Anions Employing Electrospray Ionization and Collision Induced Dissociation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Al Hasan, Naila M.; Johnson, Grant E.; Laskin, Julia

2013-07-02

Electrospray ionization mass spectrometry (ESI-MS) combined with in-source fragmentation and tandem mass spectrometry (MS/MS) experiments were used to generate a wide range of singly and multiply charged vanadium oxide cluster anions including V xO y n– and V xO yCl n– ions (x = 1–14, y = 2–36, n = 1–3), protonated clusters, and ligand-bound polyoxovanadate anions. The cluster anions were produced by electrospraying a solution of tetradecavanadate, V 14O 36Cl(L) 5 (L = Et 4N +, tetraethylammonium), in acetonitrile. Under mild source conditions, ESI-MS generates a distribution of doubly and triply charged V xO yCl n– and V xOmore » yCl(L) (n–1)– clusters predominantly containing 14 vanadium atoms as well as their protonated analogs. Accurate mass measurement using a high-resolution LTQ/Orbitrap mass spectrometer (m/Δm = 60,000 at m/z 410) enabled unambiguous assignment of the elemental composition of the majority of peaks in the ESI-MS spectrum. In addition, high-sensitivity mass spectrometry allowed the charge state of the cluster ions to be assigned based on the separation of the major from the much less abundant minor isotope of vanadium. In-source fragmentation resulted in facile formation of smaller V xO yCl (1–2)– and V xO y (1–2)– anions. Collision-induced dissociation (CID) experiments enabled systematic study of the gas-phase fragmentation pathways of the cluster anions originating from solution and from in-source CID. Surprisingly simple fragmentation patterns were obtained for all singly and doubly charged V xO yCl and V xO y species generated through multiple MS/MS experiments. In contrast, cluster anions originating directly from solution produced comparatively complex CID spectra. These results are consistent with the formation of more stable structures of V xO yCl and V xO y anions through low-energy CID. Finally and furthermore, our results demonstrate that solution-phase synthesis of one precursor cluster anion combined with gas-phase CID is an efficient approach for the top-down synthesis of a wide range of singly and multiply charged gas-phase metal oxide cluster anions for subsequent investigations of structure and reactivity using mass spectrometry and ion spectroscopy techniques.« less

A new (4, 6)-connected Cu(I) coordination polymer based on rare tetranuclear [Cu4I2] clusters: Synthesis, crystal structure, luminescent and photocatalytic properties

NASA Astrophysics Data System (ADS)

Cui, Li-Jing; Liu, Chun-Yan; Bian, Ming; Yu, Li-Jun

2018-03-01

A new Cu(I) coordination polymer, namely [Cu5I3(L)2]n (1 HL = 3-(4-pyridyl)-5-(3-pyridyl)-1,2,4-triazolyl), was solvothermally synthesized using CuI, HL and NaI as the starting materials. Single crystal X-ray structural analysis shows that compound 1 features a (4, 6)-connected 3D framework employing rare tetranuclear [Cu4I2] clusters as building subunits. It exhibits intense metal-to-ligand luminescence and excellent photocatalytic activity on degradation of methylene blue (MB).

From hormones to secondary metabolism: the emergence of metabolic gene clusters in plants.

PubMed

Chu, Hoi Yee; Wegel, Eva; Osbourn, Anne

2011-04-01

Gene clusters for the synthesis of secondary metabolites are a common feature of microbial genomes. Well-known examples include clusters for the synthesis of antibiotics in actinomycetes, and also for the synthesis of antibiotics and toxins in filamentous fungi. Until recently it was thought that genes for plant metabolic pathways were not clustered, and this is certainly true in many cases; however, five plant secondary metabolic gene clusters have now been discovered, all of them implicated in synthesis of defence compounds. An obvious assumption might be that these eukaryotic gene clusters have arisen by horizontal gene transfer from microbes, but there is compelling evidence to indicate that this is not the case. This raises intriguing questions about how widespread such clusters are, what the significance of clustering is, why genes for some metabolic pathways are clustered and those for others are not, and how these clusters form. In answering these questions we may hope to learn more about mechanisms of genome plasticity and adaptive evolution in plants. It is noteworthy that for the five plant secondary metabolic gene clusters reported so far, the enzymes for the first committed steps all appear to have been recruited directly or indirectly from primary metabolic pathways involved in hormone synthesis. This may or may not turn out to be a common feature of plant secondary metabolic gene clusters as new clusters emerge. © 2011 The Authors. The Plant Journal © 2011 Blackwell Publishing Ltd.

Stabilization of Si_60 Cage Structure: The Agony and the Ecstasy

NASA Astrophysics Data System (ADS)

Kawazoe, Y.; Sun, Q.; Wang, Q.; Rao, B. K.; Jena, P.

2003-03-01

The unique role of silicon in the micro-electronics industry has motivated many researchers to find ways to stabilize Si_60 with fullerene structure. In spite of numerous experimental attempts, synthesis of a theoretically predicted C_60-supported Si_60 cluster (C_60@Si_60) has not been possible. Using a state-of-the-art theoretical method, we provide the first answer for this long-standing contradiction between the experimental observation and the theoretical prediction. The flaws in earlier theoretical works are pointed out, and Si_60 is shown to be unstable in the fullerene structure either on its own or when supported on a C_60 fullerene (C_60@Si_60). On the other hand, we show that Si_60 cage can be stabilized by using magic clusters such as Al_12X (X = Si, Ge, Sn, Pb) as endohedral units, which have been identified in recent experiment as stable clusters and as suitable building blocks for cluster-assembled materials.

Computational Design of Clusters for Catalysis

NASA Astrophysics Data System (ADS)

Jimenez-Izal, Elisa; Alexandrova, Anastassia N.

2018-04-01

When small clusters are studied in chemical physics or physical chemistry, one perhaps thinks of the fundamental aspects of cluster electronic structure, or precision spectroscopy in ultracold molecular beams. However, small clusters are also of interest in catalysis, where the cold ground state or an isolated cluster may not even be the right starting point. Instead, the big question is: What happens to cluster-based catalysts under real conditions of catalysis, such as high temperature and coverage with reagents? Myriads of metastable cluster states become accessible, the entire system is dynamic, and catalysis may be driven by rare sites present only under those conditions. Activity, selectivity, and stability are highly dependent on size, composition, shape, support, and environment. To probe and master cluster catalysis, sophisticated tools are being developed for precision synthesis, operando measurements, and multiscale modeling. This review intends to tell the messy story of clusters in catalysis.

Synthesis, structures, and solution dynamics of tetrasubstituted nine-atom germanium deltahedral clusters.

PubMed

Li, Feng; Sevov, Slavi C

2014-08-27

Reported are the rational synthesis, structures, and solution dynamics of three tetrasubstituted and neutral Ge9-based deltahedral clusters [Ge9R3R'](0), where R = Si(SiMe3)3 and R' = Et (1), Sn(n)Bu3 (2), or Tl (3). The first step of the synthesis is a reaction of an acetonitrile suspension of the intermetallic precursor compound K4Ge9 with {Si(SiMe3)3}Cl which produces the trisubstituted monoanions [Ge9{Si(SiMe3)3}](-). A benzene suspension of the latter is then reacted with Sn(n)Bu3Cl or TlCp to produce 2 and 3, respectively, while the same acetonitrile solution is reacted with EtBr in order to produce 1. All three structures can be viewed as tricapped trigonal prisms of Ge9 with the three "hypersilyl" substituents, Si(SiMe3)3, exo-bonded to the capping atoms. The fourth substituent in 1, the ethyl group, is exo-bonded to one of the six available Ge atoms with the Ge-C bond positioned radially to the Ge9 core. In the case of 2, on the other hand, the tin fragment is found above one of the triangular bases of the prism interacting with one or more Ge atoms in three crystallographically different molecules in the structure. Lastly, the Tl atom in the structure of 3 is found capping a pseudosquare face between two hypersilyl substituents. NMR spectroscopy indicates that all three compounds are dynamic at room temperature. Variable-temperature studies suggest that the process in 1 and 2 is intramolecular while the process in 3 involves dissociation of the Tl(+) ion from the molecule followed by association at the same or another equivalent pseudosquare face of the molecule. Thus, the latter compound may be considered to a large extent to be ionic as it is made of a thallium cation and a trisubstituted cluster anion.

Cluster-to-cluster transformation among Au6, Au8 and Au11 nanoclusters.

PubMed

Ren, Xiuqing; Fu, Junhong; Lin, Xinzhang; Fu, Xuemei; Yan, Jinghui; Wu, Ren'an; Liu, Chao; Huang, Jiahui

2018-05-22

We present the cluster-to-cluster transformations among three gold nanoclusters, [Au6(dppp)4]2+ (Au6), [Au8(dppp)4Cl2]2+ (Au8) and [Au11(dppp)5]3+ (Au11). The conversion process follows a rule that states that the transformation of a small cluster to a large cluster is achieved through an oxidation process with an oxidizing agent (H2O2) or with heating, while the conversion of a large cluster to a small one occurs through a reduction process with a reducing agent (NaBH4). All the reactions were monitored using UV-Vis spectroscopy and ESI-MS. This work may provide an alternative approach to the synthesis of novel gold nanoclusters and a further understanding of the structural transformation relationship of gold nanoclusters.

Endohedral clusterfullerenes--playing with cluster and cage sizes.

PubMed

Dunsch, Lothar; Yang, Shangfeng

2007-06-28

The family of endohedral fullerenes was significantly enlarged within the past six years by the clusterfullerenes containing structures like the M(2)C(2) carbides and the M(3)N nitrides. While the carbide clusters are generated under the standard arc burning conditions according to the stabilisation energy the nitride clusterfullerene type is formed by varying the composition of the cooling gas atmosphere in the arc burning process. The special situation in nitride clusterfullerene synthesis is described in detail and the optimum conditions for the production of nitride clusterfullerenes as the main product in fullerene synthesis are discussed. A review of new nitride clusterfullerenes reported recently is given summarizing the structures, properties and the stability of metal nitride clusterfullerenes. It is shown that all cages with even carbon atoms of C(68) and beyond are available as endohedral nitride clusterstructures. Furthermore the nitride clusterfullerenes are that class of endohedral fullerenes forming the largest number of non-IPR structures. Finally the prospects of this evolving field are briefly discussed taking the superior stability of these endohedral clusterfullerenes into account.

Synthesis of MFe3S4 clusters containing a planar M(II) site (M = Ni, Pd, Pt), a structural element in the C-cluster of carbon monoxide dehydrogenase.

PubMed

Panda, Rashmishree; Berlinguette, Curtis P; Zhang, Yugen; Holm, Richard H

2005-08-10

Synthesis of an analogue of the C-cluster of C. hydrogenoformans carbon monoxide dehydrogenase requires formation of a planar Ni(II) site and attachment of an exo iron atom in the core unit NiFe(4)S(5). The first objective has been achieved by two reactions: (i) displacement of Ph(3)P or Bu(t)()NC at tetrahedral Ni(II) sites of cubane-type [NiFe(3)S(4)](+) clusters with chelating diphosphines, and (ii) metal atom incorporation into a cuboidal [Fe(3)S(4)](0) cluster with a M(0) reactant in the presence of bis(1,2-dimethylphosphino)ethane (dmpe). The isolated product clusters [(dmpe)MFe(3)S(4)(LS(3))](2-) (M = Ni(II) (9), Pd(II) (12), Pt(II) (13); LS(3) = 1,3,5-tris((4,6-dimethyl-3-mercaptophenyl)thio)-2,4,6-tris(p-tolylthio)benzene(3-)) contain the cores [MFe(3)(mu(2)-S)(mu(3)-S)(3)](+) having planar M(II)P(2)S(2) sites and variable nonbonding M...S distances of 2.6-3.4 A. Reaction (i) involves a tetrahedral --> planar Ni(II) structural change between isomeric cubane and cubanoid [NiFe(3)S(4)](+) cores. Based on the magnetic properties of 12 and earlier considerations, the S = (5)/(2) ground state of the cubanoid cluster arises from the [Fe(3)S(4)](-) fragment, whereas the S = (3)/(2) ground state of the cubane cluster is a consequence of antiferromagnetic coupling between the spins of Ni(2+) (S = 1) and [Fe(3)S(4)](-). Other substitution reactions of [NiFe(3)S(4)](+) clusters and 1:3 site-differentiated [Fe(4)S(4)](2+) clusters are described, as are the structures of 12, 13, [(Me(3)P)NiFe(3)S(4)(LS(3))](2-), and [Fe(4)S(4)(LS(3))L'](2-) (L' = Me(2)NC(2)H(4)S(-), Ph(2)P(O)C(2)H(4)S(-)). This work significantly expands our initial report of cluster 9 (Panda et al. J. Am. Chem. Soc. 2004, 126, 6448-6459) and further demonstrates that a planar M(II) site can be stabilized within a cubanoid [NiFe(3)S(4)](+) core.

Two Ti13-oxo-clusters showing non-compact structures, film electrode preparation and photocurrent properties.

PubMed

Hou, Jin-Le; Luo, Wen; Wu, Yin-Yin; Su, Hu-Chao; Zhang, Guang-Lin; Zhu, Qin-Yu; Dai, Jie

2015-12-14

Two benzene dicarboxylate (BDC) and salicylate (SAL) substituted titanium-oxo-clusters, Ti13O10(o-BDC)4(SAL)4(O(i)Pr)16 (1) and Ti13O10(o-BDC)4(SAL-Cl)4(O(i)Pr)16 (2), are prepared by one step in situ solvothermal synthesis. Single crystal analysis shows that the two Ti13 clusters take a paddle arrangement with an S4 symmetry. The non-compact (non-sphere) structure is stabilized by the coordination of BDC and SAL. Film photoelectrodes are prepared by the wet coating process using the solution of the clusters and the photocurrent response properties of the electrodes are studied. It is found that the photocurrent density and photoresponsiveness of the electrodes are related to the number of coating layers and the annealing temperature. Using ligand coordinated titanium-oxo-clusters as the molecular precursors of TiO2 anatase films is found to be effective due to their high solubility, appropriate stability in solution and hence the easy controllability.

Synthesis of multifunctional clustered nano-Fe3O4 chitosan nanocomposite for biomedical applications

NASA Astrophysics Data System (ADS)

Villamin, Maria Emma; Kitamoto, Yoshitaka

2018-01-01

Clustered iron oxide nanoparticles covered with chitosan hydrogel (FeOx/Ch NC) have multiple potential functionalities in biomedical applications such as pH-controlled drug release, magnetic hyperthermia, and magnetic non-contact pH sensing. In the present study, the synthesis and characterization of FeOx/Ch NC are demonstrated. Moreover, the heating capability of the nanocomposites is also explored for the potential magnetic hyperthermia application by measuring the temperature curves under different AC frequencies (900 kHz to 2500 kHz). Monodispersed FeOx NPs are first synthesized via thermal decomposition. Then, dried FeOx NPs are combined with chitosan using a homogenizer to form the clustered composites. Synthesized composites are then characterized using XRD, TEM, and FTIR. Temperature curves are measured via a custom-built hyperthermia setup. Results show successful synthesis of clustered Fe3O4-chitosan nanocomposite with XRD peaks corresponding to magnetite (Fe3O4) structure. FTIR results show the presence of functional groups of chitosan (N-H, C-O) and FeOx NPs (Fe-O). These confirms the successful fabrication of FeOx/Ch NC. The temperature curves show maximum temperature changes of about 2°C to 22°C depending on the AC frequency. The heating rate is found to increase with the frequency, which suggests that the resonance frequency is higher than 2500 kHz.

His86 from the N-terminus of frataxin coordinates iron and is required for Fe-S cluster synthesis.

PubMed

Gentry, Leslie E; Thacker, Matthew A; Doughty, Reece; Timkovich, Russell; Busenlehner, Laura S

2013-09-03

Human frataxin has a vital role in the biosynthesis of iron-sulfur (Fe-S) clusters in mitochondria, and its deficiency causes the neurodegenerative disease Friedreich's ataxia. Proposed functions for frataxin in the Fe-S pathway include iron donation to the Fe-S cluster machinery and regulation of cysteine desulfurase activity to control the rate of Fe-S production, although further molecular detail is required to distinguish these two possibilities. It is well established that frataxin can coordinate iron using glutamate and aspartate side chains on the protein surface; however, in this work we identify a new iron coordinating residue in the N-terminus of human frataxin using complementary spectroscopic and structural approaches. Further, we demonstrate that His86 in this N-terminal region is required for high affinity iron coordination and iron assembly of Fe-S clusters by ISCU as part of the Fe-S cluster biosynthetic complex. If a binding site that includes His86 is important for Fe-S cluster synthesis as part of its chaperone function, this raises the possibility that either iron binding at the acidic surface of frataxin may be spurious or that it is required for protein-protein interactions with the Fe-S biosynthetic quaternary complex. Our data suggest that iron coordination to frataxin may be significant to the Fe-S cluster biosynthesis pathway in mitochondria.

Cluster-assembled metallic glasses

PubMed Central

2013-01-01

A bottom-up approach to nanofabricate metallic glasses from metal clusters as building blocks is presented. Considering metallic glasses as a subclass of cluster-assembled materials, the relation between the two lively fields of metal clusters and metallic glasses is pointed out. Deposition of selected clusters or collections of them, generated by state-of-the-art cluster beam sources, could lead to the production of a well-defined amorphous material. In contrast to rapidly quenched glasses where only the composition of the glass can be controlled, in cluster-assembled glasses, one can precisely control the structural building blocks. Comparing properties of glasses with similar compositions but differing in building blocks and therefore different in structure will facilitate the study of structure–property correlation in metallic glasses. This bottom-up method provides a novel alternative path to the synthesis of glassy alloys and will contribute to improving fundamental understanding in the field of metallic glasses. It may even permit the production of glassy materials for alloys that cannot be quenched rapidly enough to circumvent crystallization. Additionally, gaining deeper insight into the parameters governing the structure–property relation in metallic glasses can have a great impact on understanding and design of other cluster-assembled materials. PMID:23899019

Au13(8e): A secondary block for describing a special group of liganded gold clusters containing icosahedral Au13 motifs

NASA Astrophysics Data System (ADS)

Xu, Wen Wu; Zeng, Xiao Cheng; Gao, Yi

2017-05-01

A grand unified model (GUM) has been proposed recently to understand structure anatomy and evolution of liganded gold clusters. In this work, besides the two types of elementary blocks (triangular Au3(2e) and tetrahedral Au4(2e)), we introduce a secondary block, namely, the icosahedral Au13 with 8e valence electrons, noted as Au13(8e). Using this secondary block, structural anatomy and evolution of a special group of liganded gold nanoclusters containing icosahedral Au13 motifs can be conveniently analyzed. In addition, a new ligand-protected cluster Au49(PR3)10(SR)15Cl2 is predicted to exhibit high chemical and thermal stability, suggesting likelihood of its synthesis in the laboratory.

Route to the Smallest Doped Semiconductor: Mn(2+)-Doped (CdSe)13 Clusters.

PubMed

Yang, Jiwoong; Fainblat, Rachel; Kwon, Soon Gu; Muckel, Franziska; Yu, Jung Ho; Terlinden, Hendrik; Kim, Byung Hyo; Iavarone, Dino; Choi, Moon Kee; Kim, In Young; Park, Inchul; Hong, Hyo-Ki; Lee, Jihwa; Son, Jae Sung; Lee, Zonghoon; Kang, Kisuk; Hwang, Seong-Ju; Bacher, Gerd; Hyeon, Taeghwan

2015-10-14

Doping semiconductor nanocrystals with magnetic transition-metal ions has attracted fundamental interest to obtain a nanoscale dilute magnetic semiconductor, which has unique spin exchange interaction between magnetic spin and exciton. So far, the study on the doped semiconductor NCs has usually been conducted with NCs with larger than 2 nm because of synthetic challenges. Herein, we report the synthesis and characterization of Mn(2+)-doped (CdSe)13 clusters, the smallest doped semiconductors. In this study, single-sized doped clusters are produced in large scale. Despite their small size, these clusters have semiconductor band structure instead of that of molecules. Surprisingly, the clusters show multiple excitonic transitions with different magneto-optical activities, which can be attributed to the fine structure splitting. Magneto-optically active states exhibit giant Zeeman splittings up to elevated temperatures (128 K) with large g-factors of 81(±8) at 4 K. Our results present a new synthetic method for doped clusters and facilitate the understanding of doped semiconductor at the boundary of molecules and quantum nanostructure.

Synthesis and characterization of Mn quantum dots by bioreduction with water hyacinth.

PubMed

Rosano-Ortega, G; Schabes-Retchkiman, P; Zorrilla, C; Liu, H B; Canizal, G; Avila-Pérez, P; Ascencio, J A

2006-01-01

The bio-reduction method is reported as a part of a complimentary self-sustained technology, where bioremediation and metal particle production are related. The use of the characterization methods in this self sustainable technique open the expectative to be used for several other elements and with other plants, which will be discussed. However, the particular case of Mn nanoparticles involves an important option to generate nanoparticles in the range of 1-4 nanometers with a well controlled size and with a structure based on an fcc-like geometry for the smallest clusters and with more complex arrays for cluster greater than four shells, which involves magnetic moments significantly related to their atomistic configuration. At the same time, the use of the characterization methods establishes the dependence of the nanoparticle's size on the pH conditions used during the synthesis; small clusters in the range of 1-2 nm were generated using pH=5, and it was shown that for the smallest aggregates, simple polyhedron shapes are stable.

Unprecedented reduction of the uranyl ion [UO2]2+ into a polyoxo uranium(IV) cluster: synthesis and crystal structure of the first f-element oxide with a M6(micro3-O)8 core.

PubMed

Berthet, Jean-Claude; Thuéry, Pierre; Ephritikhine, Michel

2005-07-21

The smooth comproportionation reaction of the U(VI) and U(III) complexes UO2(OTf)2 and U(OTf)3, afforded the hexanuclear U(IV) oxide cluster [U6(micro3-O)8(micro2-OTf)8(py)8], a rare example of a metal oxide with a M6(micro3-O)8 core.

B38: an all-boron fullerene analogue.

PubMed

Lv, Jian; Wang, Yanchao; Zhu, Li; Ma, Yanming

2014-10-21

Fullerene-like structures formed by elements other than carbon have long been sought. Finding all-boron (B) fullerene-like structures is challenging due to the geometrical frustration arising from competitions among various structural motifs. We report here the prediction of a B38 fullerene analogue found through first-principles swarm structure searching calculations. The structure is highly symmetric and consists of 56 triangles and four hexagons, which provide an optimal void in the center of the cage. Energetically, it is more favorable than the planar and tubular structures, and possesses an unusually high chemical stability: a large energy gap (∼2.25 eV) and a high double aromaticity, superior to those of most aromatic quasi-planar B12 and double-ring B20 clusters. Our findings represent a key step forward towards to the understanding of structures of medium-sized B clusters and map out the experimental direction of the synthesis of an all-B fullerene analogue.

Heteronuclear Metal Cluster Compounds Synthesis and Reactivity

DTIC Science & Technology

1990-08-10

important role in the formation of complexes with heteronuclear metal - metal bonds. Since this is our Final Report recent results are reported and...DTe FL’ Copy AFOSR-86-0125 Lfl X’ HETERONUCLEAR METAL CLUSTER COMPOUNDS00 SYNTHESIS AND REACTIVITY F. Gordon A. Stone, IDepartment of Inorganic...Security Classification) HETERONUCLEAR METAL CLUSTER COMPOUNDS: SYNTHESIS AND REACTIVITY 12. PERSONAL AUTHOR(S) F. GORDON A. STONE 13a. TYPE OF REPORT

Molecular details of the yeast frataxin-Isu1 interaction during mitochondrial Fe-S cluster assembly

PubMed Central

Cook, Jeremy D.; Kondapalli, Kalyan C.; Rawat, Swati; Childs, William C.; Murugesan, Yogapriya; Dancis, Andrew; Stemmler, Timothy L.

2010-01-01

Frataxin, a conserved nuclear encoded mitochondrial protein, plays a direct role in iron-sulfur cluster biosynthesis within the ISC assembly pathway. Humans with frataxin deficiency have Friedreich’s ataxia, a neurodegenerative disorder characterized by mitochondrial iron overload and disruption in Fe-S cluster synthesis. Biochemical and genetic studies have shown frataxin interacts with the iron-sulfur cluster assembly scaffold protein (in yeast, there are two: Isu1 and Isu2), indicating frataxin plays a direct role in cluster assembly, possibly by serving as an iron chaperone n the assembly pathway. Here we provide molecular details of how yeast frataxin (Yfh1) interacts with Isu1 as a structural module to better understand the multiprotein complex assembly that completes Fe-S cluster assembly; this complex also includes the cysteine desulfurase (Nfs1 in yeast) and the accessory protein (Isd11), together in the mitochondria. Thermodynamic binding parameters for protein partner and iron binding were measured for the yeast orthologs using isothermal titration calorimetry (ITC). Nuclear magnetic resonance spectroscopy was used to provide the molecular details to understand how Yfh1 interacts with Isu1. X-ray absorption studies were used to electronically and structurally characterize how iron is transferred to Isu1 and then incorporated into a Fe-S cluster. These results were combined with previously published data to generate a structural model for how the Fe-S cluster protein assembly complex can come together to accomplish Fe-S cluster assembly. PMID:20815377

Molecular Details of the Yeast Frataxin-Isu1 Interaction during Mitochondrial Fe-S Cluster Assembly

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cook, J.; Kondapalli, K; Rawat, S

2010-01-01

Frataxin, a conserved nuclear-encoded mitochondrial protein, plays a direct role in iron-sulfur cluster biosynthesis within the ISC assembly pathway. Humans with frataxin deficiency have Friedreich's ataxia, a neurodegenerative disorder characterized by mitochondrial iron overload and disruption in Fe-S cluster synthesis. Biochemical and genetic studies have shown frataxin interacts with the iron-sulfur cluster assembly scaffold protein (in yeast, there are two, Isu1 and Isu2), indicating frataxin plays a direct role in cluster assembly, possibly by serving as an iron chaperone in the assembly pathway. Here we provide molecular details of how yeast frataxin (Yfh1) interacts with Isu1 as a structural modulemore » to improve our understanding of the multiprotein complex assembly that completes Fe-S cluster assembly; this complex also includes the cysteine desulfurase (Nfs1 in yeast) and the accessory protein (Isd11), together in the mitochondria. Thermodynamic binding parameters for protein partner and iron binding were measured for the yeast orthologs using isothermal titration calorimetry. Nuclear magnetic resonance spectroscopy was used to provide the molecular details to understand how Yfh1 interacts with Isu1. X-ray absorption studies were used to electronically and structurally characterize how iron is transferred to Isu1 and then incorporated into an Fe-S cluster. These results were combined with previously published data to generate a structural model for how the Fe-S cluster protein assembly complex can come together to accomplish Fe-S cluster assembly.« less

Molecular details of the yeast frataxin-Isu1 interaction during mitochondrial Fe-S cluster assembly.

PubMed

Cook, Jeremy D; Kondapalli, Kalyan C; Rawat, Swati; Childs, William C; Murugesan, Yogapriya; Dancis, Andrew; Stemmler, Timothy L

2010-10-12

Frataxin, a conserved nuclear-encoded mitochondrial protein, plays a direct role in iron-sulfur cluster biosynthesis within the ISC assembly pathway. Humans with frataxin deficiency have Friedreich's ataxia, a neurodegenerative disorder characterized by mitochondrial iron overload and disruption in Fe-S cluster synthesis. Biochemical and genetic studies have shown frataxin interacts with the iron-sulfur cluster assembly scaffold protein (in yeast, there are two, Isu1 and Isu2), indicating frataxin plays a direct role in cluster assembly, possibly by serving as an iron chaperone in the assembly pathway. Here we provide molecular details of how yeast frataxin (Yfh1) interacts with Isu1 as a structural module to improve our understanding of the multiprotein complex assembly that completes Fe-S cluster assembly; this complex also includes the cysteine desulfurase (Nfs1 in yeast) and the accessory protein (Isd11), together in the mitochondria. Thermodynamic binding parameters for protein partner and iron binding were measured for the yeast orthologs using isothermal titration calorimetry. Nuclear magnetic resonance spectroscopy was used to provide the molecular details to understand how Yfh1 interacts with Isu1. X-ray absorption studies were used to electronically and structurally characterize how iron is transferred to Isu1 and then incorporated into an Fe-S cluster. These results were combined with previously published data to generate a structural model for how the Fe-S cluster protein assembly complex can come together to accomplish Fe-S cluster assembly.

STRUCTURAL PARAMETERS FOR 10 HALO GLOBULAR CLUSTERS IN M33

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ma, Jun, E-mail: majun@nao.cas.cn

2015-05-15

In this paper, we present the properties of 10 halo globular clusters (GCs) with luminosities L ≃ 5–7 × 10{sup 5} L{sub ⊙} in the Local Group galaxy M33 using images from the Hubble Space Telescope WFPC2 in the F555W and F814W bands. We obtained the ellipticities, position angles, and surface brightness profiles for each GC. In general, the ellipticities of the M33 sample clusters are similar to those of the M31 clusters. The structural and dynamical parameters are derived by fitting the profiles to three different models combined with mass-to-light ratios (M/L values) from population-synthesis models. The structural parametersmore » include core radii, concentration, half-light radii, and central surface brightness. The dynamical parameters include the integrated cluster mass, integrated binding energy, central surface mass density, and predicted line of sight velocity dispersion at the cluster center. The velocity dispersions of the four clusters predicted here agree well with the observed dispersions by Larsen et al. The results here showed that the majority of the sample halo GCs are better fitted by both the King model and the Wilson model than the Sérsic model. In general, the properties of the clusters in M33, M31, and the Milky Way fall in the same regions of parameter spaces. The tight correlations of cluster properties indicate a “fundamental plane” for clusters, which reflects some universal physical conditions and processes operating at the epoch of cluster formation.« less

Synthesis of borophenes: Anisotropic, two-dimensional boron polymorphs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mannix, A. J.; Zhou, X. -F.; Kiraly, B.

At the atomic-cluster scale, pure boron is markedly similar to carbon, forming simple planar molecules and cage-like fullerenes. Theoretical studies predict that two-dimensional (2D) boron sheets will adopt an atomic configuration similar to that of boron atomic clusters. We synthesized atomically thin, crystalline 2D boron sheets (i.e., borophene) on silver surfaces under ultrahigh-vacuum conditions. Atomic-scale characterization, supported by theoretical calculations, revealed structures reminiscent of fused boron clusters with multiple scales of anisotropic, out-of-plane buckling. Unlike bulk boron allotropes, borophene shows metallic characteristics that are consistent with predictions of a highly anisotropic, 2D metal.

Structural and Genetic Analyses of O Polysaccharide from Actinobacillus actinomycetemcomitans Serotype f

PubMed Central

Kaplan, Jeffrey B.; Perry, Malcolm B.; MacLean, Leann L.; Furgang, David; Wilson, Mark E.; Fine, Daniel H.

2001-01-01

The oral bacterium Actinobacillus actinomycetemcomitans is implicated as a causative agent of localized juvenile periodontitis (LJP). A. actinomycetemcomitans is classified into five serotypes (a to e) corresponding to five structurally and antigenically distinct O polysaccharide (O-PS) components of their respective lipopolysaccharide molecules. Serotype b has been reported to be the dominant serotype isolated from LJP patients. We determined the lipopolysaccharide O-PS structure from A. actinomycetemcomitans CU1000, a strain isolated from a 13-year-old African-American female with LJP which had previously been classified as serotype b. The O-PS of strain CU1000 consisted of a trisaccharide repeating unit composed of l-rhamnose and 2-acetamido-2-deoxy-d-galactose (molar ratio, 2:1) with the structure →2)-α-l-Rhap-(1–3)-2-O-(β-d-GalpNAc)-α-l-Rhap-(1→. O-PS from strain CU1000 was structurally and antigenically distinct from the O-PS molecules of the five known A. actinomycetemcomitans serotypes. Strain CU1000 was mutagenized with transposon IS903φkan, and three mutants that were deficient in O-PS synthesis were isolated. All three transposon insertions mapped to a single 1-kb region on the chromosome. The DNA sequence of a 13.1-kb region surrounding these transposon insertions contained a cluster of 14 open reading frames that was homologous to gene clusters responsible for the synthesis of A. actinomycetemcomitans serotype b, c, and e O-PS antigens. The CU1000 gene cluster contained two genes that were not present in serotype-specific O-PS antigen clusters of the other five known A. actinomycetemcomitans serotypes. These data indicate that strain CU1000 should be assigned to a new A. actinomycetemcomitans serotype, designated serotype f. A PCR assay using serotype-specific PCR primers showed that 3 out of 20 LJP patients surveyed (15%) harbored A. actinomycetemcomitans strains carrying the serotype f gene cluster. The finding of an A. actinomycetemcomitans serotype showing serological cross-reactivity with anti-serotype b-specific antiserum suggests that a reevaluation of strains previously classified as serotype b may be warranted. PMID:11500407

Structural evolution and properties of small-size thiol-protected gold nanoclusters

NASA Astrophysics Data System (ADS)

Ma, Miaomiao; Liu, Liren; Zhu, Hengjiang; Lu, Junzhe; Tan, Guiping

2018-07-01

Ligand-protected gold clusters are widely used in biosensors and catalysis. Understanding the structural evolution of these kinds of nanoclusters is important for experimental synthesis. Herein, based on the particle swarm optimisation algorithm and density functional theory method, we use [Au1(SH)2]n, [Au2(SH)3]n, [Au3(SH)4]n (n = 1-3) as basic units to research the structural evolution relationships from building blocks to the final whole structures. Results show that there is a 'line-ring-core' structural evolution pattern in the growth process of the nanoclusters. The core structures of the ligand-protected gold clusters consist of Au3, Au4, Au6 and Au7 atoms. The electronics and optics analysis reflects that stability and optical properties gradually enhance with increase in size. These results can be used to understand the initial growth stage and design new ligand-protected nanoclusters.

The preparation and characterization of novel Pt/C electrocatalysts with controlled porosity and cluster size

DOE PAGES

Coker, Eric N.; Steen, William A.; Miller, Jeffrey T.; ...

2007-05-23

Small platinum clusters have been prepared in zeolite hosts through ion exchange and controlled calcination/reduction processes. In order to enable electrochemical application, the pores of the Pt-zeolite were filled with electrically conductive carbon via infiltration with carbon precursors, polymerization, and pyrolysis. The zeolite host was then removed by acid washing, to leave a Pt/C electrocatalyst possessing quasi-zeolitic porosity and Pt clusters of well-controlled size. The electrocatalysts were characterized by TEM, XRD, EXAFS, nitrogen adsorption and electrochemical techniques. Depending on the synthesis conditions, average Pt cluster sizes in the Pt/C catalysts ranged from 1.3 to 2.0 nm. The presence of orderedmore » porosity/structure in the catalysts was evident in TEM images as lattice fringes, and in XRD as a low-angle diffraction peak with d-spacing similar to the parent zeolite. The catalysts possess micro- and meso-porosity, with pore size distributions that depend upon synthesis variables. Finally, electroactive surface areas as high as 112 m 2 g Pt -1 have been achieved in Pt/C electrocatalysts which show oxygen reduction performance comparable to standard industrial catalysts.« less

Fluid synthesis and structure of a new polymorphic modification of boron nitride

NASA Astrophysics Data System (ADS)

Pokropivny, V. V.; Smolyar, A. S.; Ovsiannikova, L. I.; Pokropivny, A. V.; Kuts, V. A.; Lyashenko, V. I.; Nesterenko, Yu. V.

2013-04-01

A new previously unknown phase of boron nitride with a hardness of 0.41-0.63 GPa has been pre-pared by the supercritical fluid synthesis. The presence of a new phase is confirmed by the X-ray spectra and IR absorption spectra, where new reflections and bands are distinguished. The fundamental reflection of the X-ray diffraction pattern is d = 0.286-0.291 nm, and the characteristic band in the infrared absorption spectrum is observed at 704 cm-1. The X-ray diffraction pattern and the experimental and theoretical infrared absorption spectra show that a new synthesized boron nitride phase can be a cluster crystal (space group 211) with a simple cubic lattice. Cage clusters of a fullerene-like morphology B24N24 with point symmetry O are arranged in lattice sites.

Synthesis and Ligand-Exchange Reactions of a Tri-Tungsten Cluster with Applications in Biomedical Imaging

ERIC Educational Resources Information Center

Noey, Elizabeth; Curtis, Jeff C.; Tam, Sylvia; Pham, David M.; Jones, Ella F.

2011-01-01

In this experiment students are exposed to concepts in inorganic synthesis and various spectroscopies as applied to a tri-tungsten cluster with applications in biomedical imaging. The tungsten-acetate cluster, Na[W[superscript 3](mu-O)[subscript 2](CH[superscript 3]COO)[superscript 9

Biomimetic Chemistry of Iron, Nickel, Molybdenum, and Tungsten in Sulfur-Ligated Protein Sites†

PubMed Central

Groysman, Stanislav; Holm, R. H.

2009-01-01

Biomimetic inorganic chemistry has as its primary goal the synthesis of molecules that approach or achieve the structures, oxidation states, and electronic and reactivity features of native metal-containing sites of variant nuclearity. Comparison of properties of accurate analogues and these sites ideally provides insight into the influence of protein structure and environment on intrinsic properties as represented by the analogue. For polynuclear sites in particular, the goal provides a formidable challenge for, with the exception of iron-sulfur clusters, all such site structures have never been achieved and few even closely approximated by chemical synthesis. This account describes the current status of the synthetic analogue approach as applied to the mononuclear sites in certain molybdoenzymes and the polynuclear sites in hydrogenases, nitrogenase, and carbon monoxide dehydrogenases. PMID:19206188

Effect of mitochondrial complex I inhibition on Fe-S cluster protein activity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mena, Natalia P.; Millennium Institute of Cell Dynamics and Biotechnology, Santiago; Bulteau, Anne Laure

2011-06-03

Highlights: {yields} Mitochondrial complex I inhibition resulted in decreased activity of Fe-S containing enzymes mitochondrial aconitase and cytoplasmic aconitase and xanthine oxidase. {yields} Complex I inhibition resulted in the loss of Fe-S clusters in cytoplasmic aconitase and of glutamine phosphoribosyl pyrophosphate amidotransferase. {yields} Consistent with loss of cytoplasmic aconitase activity, an increase in iron regulatory protein 1 activity was found. {yields} Complex I inhibition resulted in an increase in the labile cytoplasmic iron pool. -- Abstract: Iron-sulfur (Fe-S) clusters are small inorganic cofactors formed by tetrahedral coordination of iron atoms with sulfur groups. Present in numerous proteins, these clusters aremore » involved in key biological processes such as electron transfer, metabolic and regulatory processes, DNA synthesis and repair and protein structure stabilization. Fe-S clusters are synthesized mainly in the mitochondrion, where they are directly incorporated into mitochondrial Fe-S cluster-containing proteins or exported for cytoplasmic and nuclear cluster-protein assembly. In this study, we tested the hypothesis that inhibition of mitochondrial complex I by rotenone decreases Fe-S cluster synthesis and cluster content and activity of Fe-S cluster-containing enzymes. Inhibition of complex I resulted in decreased activity of three Fe-S cluster-containing enzymes: mitochondrial and cytosolic aconitases and xanthine oxidase. In addition, the Fe-S cluster content of glutamine phosphoribosyl pyrophosphate amidotransferase and mitochondrial aconitase was dramatically decreased. The reduction in cytosolic aconitase activity was associated with an increase in iron regulatory protein (IRP) mRNA binding activity and with an increase in the cytoplasmic labile iron pool. Since IRP activity post-transcriptionally regulates the expression of iron import proteins, Fe-S cluster inhibition may result in a false iron deficiency signal. Given that inhibition of complex I and iron accumulation are hallmarks of idiopathic Parkinson's disease, the findings reported here may have relevance for understanding the pathophysiology of this disease.« less

Comparison of nano-sized Mn oxides with the Mn cluster of photosystem II as catalysts for water oxidation.

PubMed

Najafpour, Mohammad Mahdi; Ghobadi, Mohadeseh Zarei; Haghighi, Behzad; Tomo, Tatsuya; Shen, Jian-Ren; Allakhverdiev, Suleyman I

2015-02-01

"Back to Nature" is a promising way to solve the problems that we face today, such as air pollution and shortage of energy supply based on conventional fossil fuels. A Mn cluster inside photosystem II catalyzes light-induced water-splitting leading to the generation of protons, electrons and oxygen in photosynthetic organisms, and has been considered as a good model for the synthesis of new artificial water-oxidizing catalysts. Herein, we surveyed the structural and functional details of this cluster and its surrounding environment. Then, we review the mechanistic findings concerning the cluster and compare this biological catalyst with nano-sized Mn oxides, which are among the best artificial Mn-based water-oxidizing catalysts. Copyright © 2014 Elsevier B.V. All rights reserved.

Early stage structural development of prototypical zeolitic imidazolate framework (ZIF) in solution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Terban, Maxwell W.; Banerjee, Debasis; Ghose, Sanjit

Given the wide-ranging potential applications of metal organic frameworks (MOFs), an emerging imperative is to understand their formation with atomic scale precision. This will aid in designing syntheses for next-generation MOFs with enhanced properties and functionalities. Major challenges are to characterize the early-stage seeds, and the pathways to framework growth, which require synthesis coupled with in situ structural characterization sensitive to nanoscale structures in solution. Here we report measurements of an in situ synthesis of a prototypical MOF, ZIF-8, utilizing synchrotron X-ray atomic pair distribution function (PDF) analysis optimized for sensitivity to dilute species, complemented by mass spectrometry, electron microscopy,more » and density functional theory calculations. We observe that despite rapid formation of the crystalline product, a high concentration of Zn(2-MeIm) 4(2-MeIm=2-methylimidazolate) initially forms and persists as stable clusters over long times. A secondary, amorphous phase also pervades during the synthesis, which has a structural similarity to the final ZIF-8 and may act as an intermediate to the final product.« less

Early stage structural development of prototypical zeolitic imidazolate framework (ZIF) in solution

DOE PAGES

Terban, Maxwell W.; Banerjee, Debasis; Ghose, Sanjit; ...

2018-02-05

Given the wide-ranging potential applications of metal organic frameworks (MOFs), an emerging imperative is to understand their formation with atomic scale precision. This will aid in designing syntheses for next-generation MOFs with enhanced properties and functionalities. Major challenges are to characterize the early-stage seeds, and the pathways to framework growth, which require synthesis coupled with in situ structural characterization sensitive to nanoscale structures in solution. Here we report measurements of an in situ synthesis of a prototypical MOF, ZIF-8, utilizing synchrotron X-ray atomic pair distribution function (PDF) analysis optimized for sensitivity to dilute species, complemented by mass spectrometry, electron microscopy,more » and density functional theory calculations. We observe that despite rapid formation of the crystalline product, a high concentration of Zn(2-MeIm) 4(2-MeIm=2-methylimidazolate) initially forms and persists as stable clusters over long times. A secondary, amorphous phase also pervades during the synthesis, which has a structural similarity to the final ZIF-8 and may act as an intermediate to the final product.« less

Synthesis of borophenes: Anisotropic, two-dimensional boron polymorphs.

PubMed

Mannix, Andrew J; Zhou, Xiang-Feng; Kiraly, Brian; Wood, Joshua D; Alducin, Diego; Myers, Benjamin D; Liu, Xiaolong; Fisher, Brandon L; Santiago, Ulises; Guest, Jeffrey R; Yacaman, Miguel Jose; Ponce, Arturo; Oganov, Artem R; Hersam, Mark C; Guisinger, Nathan P

2015-12-18

At the atomic-cluster scale, pure boron is markedly similar to carbon, forming simple planar molecules and cage-like fullerenes. Theoretical studies predict that two-dimensional (2D) boron sheets will adopt an atomic configuration similar to that of boron atomic clusters. We synthesized atomically thin, crystalline 2D boron sheets (i.e., borophene) on silver surfaces under ultrahigh-vacuum conditions. Atomic-scale characterization, supported by theoretical calculations, revealed structures reminiscent of fused boron clusters with multiple scales of anisotropic, out-of-plane buckling. Unlike bulk boron allotropes, borophene shows metallic characteristics that are consistent with predictions of a highly anisotropic, 2D metal. Copyright © 2015, American Association for the Advancement of Science.

Roles of Fe-S proteins: from cofactor synthesis to iron homeostasis to protein synthesis.

PubMed

Pain, Debkumar; Dancis, Andrew

2016-06-01

Fe-S cluster assembly is an essential process for all cells. Impairment of Fe-S cluster assembly creates diseases in diverse and surprising ways. In one scenario, the loss of function of lipoic acid synthase, an enzyme with Fe-S cluster cofactor in mitochondria, impairs activity of various lipoamide-dependent enzymes with drastic consequences for metabolism. In a second scenario, the heme biosynthetic pathway in red cell precursors is specifically targeted, and iron homeostasis is perturbed, but lipoic acid synthesis is unaffected. In a third scenario, tRNA modifications arising from action of the cysteine desulfurase and/or Fe-S cluster proteins are lost, which may lead to impaired protein synthesis. These defects can then result in cancer, neurologic dysfunction or type 2 diabetes. Copyright © 2016 Elsevier Ltd. All rights reserved.

Scanning the potential energy surface for synthesis of dendrimer-wrapped gold clusters: design rules for true single-molecule nanostructures.

PubMed

Thompson, Damien; Hermes, Jens P; Quinn, Aidan J; Mayor, Marcel

2012-04-24

The formation of true single-molecule complexes between organic ligands and nanoparticles is challenging and requires careful design of molecules with size, shape, and chemical properties tailored for the specific nanoparticle. Here we use computer simulations to describe the atomic-scale structure, dynamics, and energetics of ligand-mediated synthesis and interlinking of 1 nm gold clusters. The models help explain recent experimental results and provide insight into how multidentate thioether dendrimers can be employed for synthesis of true single-ligand-nanoparticle complexes and also nanoparticle-molecule-nanoparticle "dumbbell" nanostructures. Electronic structure calculations reveal the individually weak thioether-gold bonds (325 ± 36 meV), which act collectively through the multivalent (multisite) anchoring to stabilize the ligand-nanoparticle complex (∼7 eV total binding energy) and offset the conformational and solvation penalties involved in this "wrapping" process. Molecular dynamics simulations show that the dendrimer is sufficiently flexible to tolerate the strained conformations and desolvation penalties involved in fully wrapping the particle, quantifying the subtle balance between covalent anchoring and noncovalent wrapping in the assembly of ligand-nanoparticle complexes. The computed preference for binding of a single dendrimer to the cluster reveals the prohibitively high dendrimer desolvation barrier (1.5 ± 0.5 eV) to form the alternative double-dendrimer structure. Finally, the models show formation of an additional electron transfer channel between nitrogen and gold for ligands with a central pyridine unit, which gives a stiff binding orientation and explains the recently measured larger interparticle distances for particles synthesized and interlinked using linear ligands with a central pyridine rather than a benzene moiety. The findings stress the importance of organic-inorganic interactions, the control of which is central to the rational engineering and eventual large-scale production of functional building blocks for nano(bio)electronics.

Synthesis and energetics of gold nanoclusters tailored by interfacial bonding structure

NASA Astrophysics Data System (ADS)

Tang, Zhenghua

In addition to the well known quantum confinement effects resulted from size and shape, interfacial bond structure is another factor, affecting the properties of the nanomaterial that is rarely studied. Inspired by the "Au-S-Au" staple motif discovered from the crystal structure of monothiol protected Au102 nanocluster (Science, 2007, 318, 430), dithiol molecules (e.g. 1, 2-dithiol, 1, 4-dithiol, etc.) with molecular structural constraint have been employed to create dithiolate protected clusters or mixed monothiolate and dithiolate protected clusters. The structure and properties of the Au clusters are expected to change due to two effects: The entropy gain of dithiol over monothiol protection and the constraint to the formation of the thiol bridging motif. DMPS (1, 2-dithiol molecule) stabilized clusters with characteristic absorption bands have been obtained, and characterized by multiple techniques. Monolayer reaction on gold core surface between the monothiol tiopronin and dithiol DMPS has been performed, and the mechanism has been probed. Mixed phenylethanethiolate and durene-dithiolate (1, 4-dithiol molecule) protected Au130 clusters with rich electrochemical features have been created, and the optical and electrochemical energetics have been successfully correlated based on core and core-ligand energy states. Furthermore, the impact of 1, 4-dithiolate-Au bonding on the near infrared luminescence has been studied. INDEX WORDS: Au MPCs, Staple motif, DMPS, Au DTCs, Au4, Tiopronin, Monolayer reaction, Durene-DT, Au MTCs, Au130, Optical energetic, Electrochemistry, Near infrared luminescence, 1, 4-Dithiolate-Au bonding.

Influence of silver and copper doping on luminescent properties of zinc-phosphate glasses after x-ray irradiation

NASA Astrophysics Data System (ADS)

Murashov, Alexander A.; Sidorov, Alexander I.; Shakhverdov, Teimur A.; Stolyarchuk, Maxim V.

2017-11-01

It is shown, experimentally, that in silver- and copper-containing zinc-phosphate glasses, metal molecular clusters are formed during the glass synthesis. X-ray irradiation of these glasses led to the considerable increase of its luminescence in visible spectral range. This effect is caused by the transformation of the charged metal molecular clusters into the neutral state. Luminescence and excitation spectra of the glass, doped with silver and copper simultaneously, change significantly in comparison with the spectra of glasses doped with one metal. The reason for this can be the formation of hybrid AgnCum molecular clusters. The computer simulation of the structure and optical properties of such clusters by the time-dependent density functional theory method is presented. It is shown that the optimal luminescent material for photonics application, in comparison with other studied materials, is glass, containing hybrid molecular clusters.

FWP executive summaries, Basic Energy Sciences Materials Sciences Programs (SNL/NM)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Samara, G.A.

1997-05-01

The BES Materials Sciences Program has the central theme of Scientifically Tailored Materials. The major objective of this program is to combine Sandia`s expertise and capabilities in the areas of solid state sciences, advanced atomic-level diagnostics and materials synthesis and processing science to produce new classes of tailored materials as well as to enhance the properties of existing materials for US energy applications and for critical defense needs. Current core research in this program includes the physics and chemistry of ceramics synthesis and processing, the use of energetic particles for the synthesis and study of materials, tailored surfaces and interfacesmore » for materials applications, chemical vapor deposition sciences, artificially-structured semiconductor materials science, advanced growth techniques for improved semiconductor structures, transport in unconventional solids, atomic-level science of interfacial adhesion, high-temperature superconductors, and the synthesis and processing of nano-size clusters for energy applications. In addition, the program includes the following three smaller efforts initiated in the past two years: (1) Wetting and Flow of Liquid Metals and Amorphous Ceramics at Solid Interfaces, (2) Field-Structured Anisotropic Composites, and (3) Composition-Modulated Semiconductor Structures for Photovoltaic and Optical Technologies. The latter is a joint effort with the National Renewable Energy Laboratory. Separate summaries are given of individual research areas.« less

Cluster-assembled materials based on M12N12 (M = Al, Ga) fullerene-like clusters.

PubMed

Yong, Yongliang; Song, Bin; He, Pimo

2011-09-28

We report the results of density functional theory calculations on cluster-assembled materials based on M(12)N(12) (M = Al, Ga) fullerene-like clusters. Our results show that the M(12)N(12) fullerene-like structure with six isolated four-membered rings (4NRs) and eight six-membered rings (6NRs) has a T(h) symmetry and a large HOMO-LUMO gap, indicating that the M(12)N(12) cluster would be ideal building blocks for the synthesis of cluster-assembled materials. Via the coalescence of M(12)N(12) building blocks, we find that the M(12)N(12) clusters can bind into stable assemblies by either 6NR or 4NR face coalescence, which enables the construction of rhombohedral or cubic nanoporous framework of varying porosity. The rhombohedral-MN phase is energetically more favorable than the cubic-MN phase. The M(12)N(12) fullerene-like structures in both phases are maintained and the M-N bond lengths between M(12)N(12) monomers are slightly larger than that in isolated M(12)N(12) clusters and the bulk wurtzite phases. The band analysis of both phases reveals that they are all wide-gap semiconductors. Because of the nanoporous character of these phases, they could be used for gas storage, heterogeneous catalysis, filtration and so on.

A Novel Coordination Polymer Based on Trinuclear Cobalt Building Blocks Cluster: Synthesis, Crystal Structure, and Properties

NASA Astrophysics Data System (ADS)

Lu, J. F.; Tang, Z. H.; Shi, J.; Ge, H. G.; Jiang, M.; Song, J.; Jin, L. X.

2017-12-01

The title compound {[Co3(μ3-OH)(μ2-H2O)2(H2O)5(BTC)2] · 6H2O} n (H3BTC is a 1,3,5-benzenetricarboxylic acid) was prepared and characterized by single crystal and powder X-ray diffraction, Fourier transform infrared spectroscopy, thermogravimetric and elemental analyses. The single crystal X-ray diffraction reveals that the title compound consists of 1D infinite zigzag chains which were constructed by trinuclear cobalt cluster and BTC3- ligand. Neighbouring above-mentioned 1D infinite zigzag chains are further linked by intermolecular hydrogen bonding to form a 3D supermolecular structure. In addition, the luminescent properties of the title compound were investigated.

More than anticipated - production of antibiotics and other secondary metabolites by Bacillus amyloliquefaciens FZB42.

PubMed

Chen, Xiao-Hua; Koumoutsi, Alexandra; Scholz, Romy; Borriss, Rainer

2009-01-01

The genome of environmental Bacillus amyloliquefaciens FZB42 harbors numerous gene clusters involved in synthesis of antifungal and antibacterial acting secondary metabolites. Five gene clusters, srf, bmy, fen, nrs, dhb, covering altogether 137 kb, direct non-ribosomal synthesis of the cyclic lipopeptides surfactin, bacillomycin, fengycin, an unknown peptide, and the iron siderophore bacillibactin. Bacillomycin and fengycin were shown to act against phytopathogenic fungi in a synergistic manner. Three gene clusters, mln, bae, and dif, with a total length of 199 kb were shown to direct synthesis of the antibacterial acting polyketides macrolactin, bacillaene, and difficidin. Both, non-ribosomal synthesis of cyclic lipopeptides and synthesis of polyketides are dependent on the presence of a functional sfp gene product, 4'-phosphopantetheinyl transferase, as evidenced by knockout mutation of the sfp gene resulting in complete absence of all those eight compounds. In addition, here we present evidence that a gene cluster encoding enzymes involved in synthesis and export of the antibacterial acting dipeptide bacilysin is also functional in FZB42. In summary, environmental FZB42 devoted about 340 kb, corresponding to 8.5% of its total genetic capacity, to synthesis of secondary metabolites useful to cope with other competing microorganisms present in the plant rhizosphere. Copyright (c) 2008 S. Karger AG, Basel.

Diamond family of colloidal supercrystals as phononic metamaterials

NASA Astrophysics Data System (ADS)

Aryana, Kiumars; Zanjani, Mehdi B.

2018-05-01

Colloidal crystals provide a versatile platform for designing phononic metamaterials with exciting applications for sound and heat management. New advances in the synthesis and self-assembly of anisotropic building blocks such as colloidal clusters have expanded the library of available micro- and nano-scale ordered multicomponent structures. Diamond-like supercrystals formed by such clusters and spherical particles are notable examples that include a rich family of crystal symmetries such as diamond, double diamond, zinc-blende, and MgCu2. This work investigates the design of phononic supercrystals by predicting and analyzing phonon transport properties. In addition to size variation and structural diversity, these supercrystals encapsulate different sub-lattice types within one structure. Computational models are used to calculate the effect of various parameters on the phononic spectrum of diamond-like supercrystals. The results show that structures with relatively small or large filling factors (f > 0.65 or f < 0.45) include smaller bandgaps compared to those with medium filling factors (0.65 > f > 0.45). The double diamond and zinc-blende structures render the largest bandgap size compared to the other supercrystals studied in this paper. Additionally, this article discusses the effect of incorporating various configurations of sub-lattices by selecting different material compositions for the building blocks. The results suggest that, for the same structure, there exist multiple phononic variants with drastically different band structures. This study provides a valuable insight for evaluating novel colloidal supercrystals for phononic applications and guides the future experimental work for the synthesis of colloidal structures with desired phononic behavior.

The cluster compound In{sub 4}Ti{sub 1.5}Mo{sub 0.5}Mo{sub 14}O{sub 26} containing Mo{sub 14} clusters and the new mono- and bi-capped trioctahedral Mo{sub 15} and Mo{sub 16} clusters: Synthesis, crystal structure, and electrical and magnetic properties

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gall, Philippe; Guizouarn, Thierry; Gougeon, Patrick, E-mail: Patrick.Gougeon@univ-rennes1.fr

2015-07-15

Single crystals of the new quaternary compound In{sub 4}Ti{sub 1.5}Mo{sub 0.5}Mo{sub 14}O{sub 26} were obtained by solid state reaction. The crystal structure was determined by single-crystal X-ray diffraction. In{sub 4}Ti{sub 1.5}Mo{sub 0.5}Mo{sub 14}O{sub 26} crystallizes in the orthorhombic space group Pbca with unit-cell parameters a=9.4432(14) Å, b=11.4828(12) Å, c=20.299(4) Å and Z=4. Full-matrix least-squares refinement on F{sup 2} using 3807 independent reflections for 219 refinable parameters resulted in R{sub 1}=0.0259 and wR{sub 2}=0.0591. The crystal structure contains in addition to Mo{sub 14} clusters the first examples of mono- and bi-capped trioctahedral Mo{sub 14} i.e. Mo{sub 15} and Mo{sub 16} clusters.more » The oxygen framework derives from a stacking along the a direction of close-packed layers with sequence (…ABAC…). The Mo–Mo distances range between 2.6938(5) and 2.8420(6) Å and the Mo–O distances between 1.879(5) and 2.250(3) Å, as usually observed in molybdenum oxide clusters. The indium atoms form In{sub 4}{sup 6+} bent chains with In–In distances of 2.6682(5) and 2.6622(8) Å and the Ti atoms are in highly distorted octahedral sites of oxygen atoms with Ti–O distances ranging between 1.865(4) and 2.161(4) Å. Magnetic susceptibility measurements confirm the presence of Ti{sup 4+} cations and the absence of localized moments on the Mo network. Electrical resistivity measurements on a single crystal of In{sub 4}Ti{sub 1.5}Mo{sub 0.5}Mo{sub 14}O{sub 26} show a semimetallic behavior. - Graphical abstract: We present here the synthesis, the crystal structure, and the electrical and magnetic properties of the new compound In{sub 4}Ti{sub 1.5}Mo{sub 0.5}Mo{sub 14}O{sub 26} in which Mo{sub 14} clusters coexist statistically with mono- and bi-capped trioctahedral Mo{sub 14} that is Mo{sub 15} and Mo{sub 16} clusters. - Highlights: • Single crystals of In{sub 4}Ti{sub 1.5}Mo{sub 0.5}Mo{sub 14}O{sub 26} were obtained by solid state reaction. • The crystal structure contains Mo{sub 14}, Mo{sub 15} and Mo{sub 16} clusters. • The indium atoms form In{sub 4}{sup 6+} bent chains. • Poorly metallic behavior. • Absence of localized moments on the Mo network as well as on the Ti atoms.« less

Theoretical Analysis of Photoelectron Spectra of Pure and Mixed Metal Clusters: Disentangling Size, Structure, and Composition Effects

DOE PAGES

Acioli, Paulo H.; Jellinek, Julius

2017-07-14

A theoretical/computational description and analysis of the spectra of electron binding energies of Al 12 -, Al 13 - and Al 12Ni- clusters, which differ in size and/or composition by a single atom yet possess strikingly different measured photoelectron spectra, is presented. It is shown that the measured spectra can not only be reproduced computationally with quantitative fidelity – this is achieved through a combination of state-of-the-art density functional theory with a highly accurate scheme for conversion of the Kohn-Sham eigenenergies into electron binding energies – but also explained in terms of the effects of size, structure/symmetry and composition. Furthermore,more » a new methodology is developed and applied that provides for disentanglement and differential assignment of the separate roles played by size, structure/symmetry and composition in defining the observed differences in the measured spectra. The methodology is general and applicable to any finite system, homogeneous or heterogeneous. Finally, we project that in combination with advances in synthesis techniques this methodology will become an indispensable computation-based aid in the design of controlled synthesis protocols for manufacture of nanosystems and nanodevices with precisely desired electronic and other characteristics.« less

Theoretical Analysis of Photoelectron Spectra of Pure and Mixed Metal Clusters: Disentangling Size, Structure, and Composition Effects

DOE Office of Scientific and Technical Information (OSTI.GOV)

Acioli, Paulo H.; Jellinek, Julius

A theoretical/computational description and analysis of the spectra of electron binding energies of Al 12 -, Al 13 - and Al 12Ni- clusters, which differ in size and/or composition by a single atom yet possess strikingly different measured photoelectron spectra, is presented. It is shown that the measured spectra can not only be reproduced computationally with quantitative fidelity – this is achieved through a combination of state-of-the-art density functional theory with a highly accurate scheme for conversion of the Kohn-Sham eigenenergies into electron binding energies – but also explained in terms of the effects of size, structure/symmetry and composition. Furthermore,more » a new methodology is developed and applied that provides for disentanglement and differential assignment of the separate roles played by size, structure/symmetry and composition in defining the observed differences in the measured spectra. The methodology is general and applicable to any finite system, homogeneous or heterogeneous. Finally, we project that in combination with advances in synthesis techniques this methodology will become an indispensable computation-based aid in the design of controlled synthesis protocols for manufacture of nanosystems and nanodevices with precisely desired electronic and other characteristics.« less

Stable platinum nanoclusters on genomic DNA–graphene oxide with a high oxygen reduction reaction activity

PubMed Central

Tiwari, Jitendra N.; Nath, Krishna; Kumar, Susheel; Tiwari, Rajanish N.; Kemp, K. Christian; Le, Nhien H.; Youn, Duck Hyun; Lee, Jae Sung; Kim, Kwang S.

2013-01-01

Nanosize platinum clusters with small diameters of 2–4 nm are known to be excellent catalysts for the oxygen reduction reaction. The inherent catalytic activity of smaller platinum clusters has not yet been reported due to a lack of preparation methods to control their size (<2 nm). Here we report the synthesis of platinum clusters (diameter ≤1.4 nm) deposited on genomic double-stranded DNA–graphene oxide composites, and their high-performance electrocatalysis of the oxygen reduction reaction. The electrochemical behaviour, characterized by oxygen reduction reaction onset potential, half-wave potential, specific activity, mass activity, accelerated durability test (10,000 cycles) and cyclic voltammetry stability (10,000 cycles) is attributed to the strong interaction between the nanosize platinum clusters and the DNA–graphene oxide composite, which induces modulation in the electronic structure of the platinum clusters. Furthermore, we show that the platinum cluster/DNA–graphene oxide composite possesses notable environmental durability and stability, vital for high-performance fuel cells and batteries. PMID:23900456

Tetravalent Ce in the Nitrate-Decorated Hexanuclear Cluster [Ce 6 (μ 3 -O) 4 (μ 3 -OH) 4 ] 12+ : A Structural End Point for Ceria Nanoparticles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Estes, Shanna L.; Antonio, Mark R.; Soderholm, L.

2016-03-17

We describe the synthesis and characterization of three glycine-stabilized hexanuclear Cely cluster compounds, each containing the [Ce-6(mu(3)-O)(4)(mu(3)-OH)(4)](12+) core structure. Crystallized from aqueous nitrate solutions with pH < 0, the core cluster structures exhibit variable decoration by nitrate, glycine, and water ligands depending on solution conditions, where increased nitrate and glycine decoration of the cluster core was observed for crystals synthesized at high Ce and nitrate concentrations. No other crystalline products were observed using this synthetic route. In addition to confirming the tetravalent oxidation state of cerium in one of the reported clusters, cyclic voltammetry also indicates that Ce-IV is reducedmore » at similar to+0.60 V vs Ag/AgCl (3 M NaCl), which is significantly less than the standard electrode potential. This large decrease in the Ce-IV/Ce-III reduction potential suggests that Ce-IV is significantly stabilized relative to Ce-III within the examined cluster. These compounds are discussed in terms of their importance as small, end member, ceric oxide nanoparticles. Single-crystal structural solutions, together with voltammetry and electrolysis data, permit the decoupling of Ce-III defects and substoichiometry. In addition, Ce-Ce distances can be used to determine an "effective" CeO2-x lattice constant, providing a simple method for comparing literature descriptions. The results are discussed in terms of their potential implications for the mechanisms by which nanoparticle ceria serve as catalysts and oxygen-storage materials.« less

Platinum clusters with precise numbers of atoms for preparative-scale catalysis.

PubMed

Imaoka, Takane; Akanuma, Yuki; Haruta, Naoki; Tsuchiya, Shogo; Ishihara, Kentaro; Okayasu, Takeshi; Chun, Wang-Jae; Takahashi, Masaki; Yamamoto, Kimihisa

2017-09-25

Subnanometer noble metal clusters have enormous potential, mainly for catalytic applications. Because a difference of only one atom may cause significant changes in their reactivity, a preparation method with atomic-level precision is essential. Although such a precision with enough scalability has been achieved by gas-phase synthesis, large-scale preparation is still at the frontier, hampering practical applications. We now show the atom-precise and fully scalable synthesis of platinum clusters on a milligram scale from tiara-like platinum complexes with various ring numbers (n = 5-13). Low-temperature calcination of the complexes on a carbon support under hydrogen stream affords monodispersed platinum clusters, whose atomicity is equivalent to that of the precursor complex. One of the clusters (Pt 10 ) exhibits high catalytic activity in the hydrogenation of styrene compared to that of the other clusters. This method opens an avenue for the application of these clusters to preparative-scale catalysis.The catalytic activity of a noble metal nanocluster is tied to its atomicity. Here, the authors report an atom-precise, fully scalable synthesis of platinum clusters from molecular ring precursors, and show that a variation of only one atom can dramatically change a cluster's reactivity.

Synthesis and Structure of an Extended Cluster Lead(II) Carboxylate, [Pb{(CO)(9)Co(3)(&mgr;(3)-CCO(2))}(2)](n)(). Role of Core Metals in Cluster-Derived Hydrogenation Catalysts.

PubMed

Lei, Xinjian; Shang, Maoyu; Patil, Atul; Wolf, Eduardo E.; Fehlner, Thomas P.

1996-05-22

The reaction of lead acetate with (CO)(9)Co(3)(&mgr;(3)-CCOOH) leads to the formation of [Pb{(CO)(9)Co(3)(&mgr;(3)-CCO(2))}(2)](n)(), I, in high yield. The structure of I exhibits unusual six-coordinate Pb(II) centers with two asymmetrical chelating cluster carboxylates (C(22)Co(6)PbO(22); triclinic P&onemacr;; a = 8.119(1), b = 14.346(2), c = 14.660(2) Å; alpha = 102.18(1), beta = 99.01(1), gamma = 97.30(1) degrees; Z = 2). One oxygen of each cluster carboxylate ligand bridges between adjacent lead atoms such that a chainlike extended structure is found in the solid state without the presence of solvent or water. I is converted stepwise on pyrolysis into two metastable forms of solid materials (designated LT and HT), each of which has been characterized spectroscopically. The hydrogenation of 2-butenal as a test reaction shows that the LT catalyst exhibits selectivities similar to previous LT materials derived from other cobalt cluster metal carboxylates and that the HT material is totally inactive. The observed release of the lead core metal under HT activation conditions totally inactivates the catalyst and demonstrates exposure of the core metal in the HT form of these novel catalysts.

The role of FeS clusters for molybdenum cofactor biosynthesis and molybdoenzymes in bacteria

PubMed Central

Yokoyama, Kenichi; Leimkühler, Silke

2016-01-01

Molybdenum is the only second row transition metal essential for biological systems, which is biologically available as molybdate ion. In eukarya, bacteria and archaea, molybdenum is bound to either to a tricyclic pyranopterin, thereby forming the molybdenum cofactor (Moco), or in some bacteria to the FeS cluster based iron-molybdenum cofactor (FeMoco), which forms the active site of nitrogenase. To date more than 50 Moco-containing enzymes have been purified and biochemically or structurally characterized. The physiological role of molybdenum in these enzymes is fundamental to organisms, since the reactions include the catalysis of key steps in carbon, nitrogen and sulfur metabolism. The catalyzed reactions are in most cases oxo-transfer reactions or the hydroxylation of carbon centers. The biosynthesis of Moco has been intensively studied, in addition to its insertion into molybdoenzymes. In particular, a link between the biosynthesis and maturation of molybdoenzymes and the biosynthesis and distribution of FeS clusters has been identified in the last years: 1) The synthesis of the first intermediate in Moco biosynthesis requires an FeS-cluster containing protein, 2) The sulfurtransferase for the dithiolene group in Moco is common also for the synthesis of FeS clusters, thiamin and thiolated tRNAs, 3) the modification of the active site with a sulfur atom additionally involves a sulfurtransferase, 4) most molybdoenzymes in bacteria require FeS clusters as additional redox active cofactors. In this review we will focus on the biosynthesis of the molybdenum cofactor in bacteria, its modification and insertion into molybdoenzymes, with an emphasis to its link to FeS cluster biosynthesis and sulfur transfer. PMID:25268953

Identification of a Nfs1p-bound persulfide intermediate in Fe-S cluster synthesis by intact mitochondria.

PubMed

Pandey, Alok; Yoon, Heeyong; Lyver, Elise R; Dancis, Andrew; Pain, Debkumar

2012-09-01

Cysteine desulfurases generate a covalent persulfide intermediate from cysteine, and this activated form of sulfur is essential for the synthesis of iron-sulfur (Fe-S) clusters. In yeast mitochondria, there is a complete machinery for Fe-S cluster synthesis, including a cysteine desulfurase, Nfs1p. Here we show that following supplementation of isolated mitochondria with [(35)S]cysteine, a radiolabeled persulfide could be detected on Nfs1p. The persulfide persisted under conditions that did not permit Fe-S cluster formation, such as nucleotide and/or iron depletion of mitochondria. By contrast, under permissive conditions, the radiolabeled Nfs1p persulfide was greatly reduced and radiolabeled aconitase was formed, indicating transfer of persulfide to downstream Fe-S cluster recipients. Nfs1p in mitochondria was found to be relatively more resistant to inactivation by N-ethylmaleimide (NEM) as compared with a prokaryotic cysteine desulfurase. Mitochondria treated with NEM (1 mM) formed the persulfide on Nfs1p but failed to generate Fe-S clusters on aconitase, likely due to inactivation of downstream recipient(s) of the Nfs1p persulfide. Thus the Nfs1p-bound persulfide as described here represents a precursor en route to Fe-S cluster synthesis in mitochondria. Copyright © 2012 Elsevier B.V. and Mitochondria Research Society. All rights reserved.

Role of Anions Associated with the Formation and Properties of Silver Clusters.

PubMed

Wang, Quan-Ming; Lin, Yu-Mei; Liu, Kuan-Guan

2015-06-16

Metal clusters have been very attractive due to their aesthetic structures and fascinating properties. Different from nanoparticles, each cluster of a macroscopic sample has a well-defined structure with identical composition, size, and shape. As the disadvantages of polydispersity are ruled out, informative structure-property relationships of metal clusters can be established. The formation of a high-nuclearity metal cluster involves the organization of metal ions into a complex entity in an ordered way. To achieve controllable preparation of metal clusters, it is helpful to introduce a directing agent in the formation process of a cluster. To this end, anion templates have been used to direct the formation of high nuclearity clusters. In this Account, the role of anions played in the formation of a variety of silver clusters has been reviewed. Silver ions are positively charged, so anionic species could be utilized to control the formation of silver clusters on the basis of electrostatic interactions, and the size and shape of the resulted clusters can be dictated by the templating anions. In addition, since the anion is an integral component in the silver clusters described, the physical properties of the clusters can be modulated by functional anions. The templating effects of simple inorganic anions and polyoxometales are shown in silver alkynyl clusters and silver thiolate clusters. Intercluster compounds are also described regarding the importance of anions in determining the packing of the ion pairs and making contribution to electron communications between the positive and negative counterparts. The role of the anions is threefold: (a) an anion is advantageous in stabilizing a cluster via balancing local positive charges of the metal cations; (b) an anion template could help control the size and shape of a cluster product; (c) an anion can be a key factor in influencing the function of a cluster through bringing in its intrinsic properties. Properties including electron communication, luminescent thermochromism, single-molecule magnet, and intercluster charge transfer associated with anion-directed silver clusters have been discussed. We intend to attract chemists' attention to the role that anions could play in determining the structures and properties of metal complexes, especially clusters. We hope that this Account will stimulate more efforts in exploiting new role of anions in various metal cluster systems. Anions can do much more than counterions for charge balance, and they should be considered in the design and synthesis of cluster-based functional materials.

Stepwise assembly of a semiconducting coordination polymer [Cd8S(SPh)14(DMF)(bpy)]n and its photodegradation of organic dyes.

PubMed

Xu, Chao; Hedin, Niklas; Shi, Hua-Tian; Xin, ZhiFeng; Zhang, Qian-Feng

2015-04-14

Chalcogenolate clusters can be interlinked with organic linkers into semiconducting coordination polymers with photocatalytic properties. Here, discrete clusters of Cd8S(SPh)14(DMF)3 were interlinked with 4,4'-bipyridine into a one dimensional coordination polymer of [Cd8S(SPh)14(DMF)(bpy)]n with helical chains. A stepwise mechanism for the assembly of the coordination polymer in DMF was revealed by an ex situ dynamic light scattering study. The cluster was electrostatically neutral and showed a penta-supertetrahedral structure. During the assembly each cluster was interlinked with two 4,4'-bipyridine molecules, which replaced the two terminal DMF molecules of the clusters. In their solid-state forms, the cluster and the coordination polymer were semiconductors with wide band gaps of 3.08 and 2.80 ev. They photocatalytically degraded rhodamine B and methylene blue in aqueous solutions. The moderate conditions used for the synthesis could allow for further in situ studies of the reaction-assembly of related clusters and coordination polymers.

Site-Directed Synthesis of Cobalt Oxide Clusters in a Metal–Organic Framework

DOE PAGES

Peters, Aaron W.; Otake, Kenichi; Platero-Prats, Ana E.; ...

2018-04-19

Here, direct control over structure and location of catalytic species deposited on amorphous supports represents a formidable challenge in heterogeneous catalysis. In contrast, a structurally well-defined, crystalline metal–organic framework (MOF) can be rationally designed using post-synthetic techniques to allow for desired structural or locational changes of deposited metal ions. Herein, naphthalene dicarboxylate linkers are incorporated in the MOF, NU-1000, to block the small cavities where few-atom clusters of cobalt oxide preferentially grow, inducing catalyst deposition towards hither-to ill-favored grafting sites orientated toward NU-1000’s mesoporous channels. Despite the different cobalt oxide location, the resulting material is still an active propane oxidativemore » dehydrogenation catalyst at low temperature, reaching a turnover frequency of 0.68 ± 0.05 h –1 at 230 °C and confirming the utility of MOFs as crystalline supports to guide rational design of catalysts.« less

Paenilamicin: structure and biosynthesis of a hybrid nonribosomal peptide/polyketide antibiotic from the bee pathogen Paenibacillus larvae.

PubMed

Müller, Sebastian; Garcia-Gonzalez, Eva; Mainz, Andi; Hertlein, Gillian; Heid, Nina C; Mösker, Eva; van den Elst, Hans; Overkleeft, Herman S; Genersch, Elke; Süssmuth, Roderich D

2014-09-26

The spore-forming bacterium Paenibacillus larvae is the causative agent of American Foulbrood (AFB), a fatal disease of honey bees that occurs worldwide. Previously, we identified a complex hybrid nonribosomal peptide/polyketide synthesis (NRPS/PKS) gene cluster in the genome of P. larvae. Herein, we present the isolation and structure elucidation of the antibacterial and antifungal products of this gene cluster, termed paenilamicins. The unique structures of the paenilamicins give deep insight into the underlying complex hybrid NRPS/PKS biosynthetic machinery. Bee larval co-infection assays reveal that the paenilamicins are employed by P. larvae in fighting ecological niche competitors and are not directly involved in killing the bee larvae. Their antibacterial and antifungal activities qualify the paenilamicins as attractive candidates for drug development. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Site-Directed Synthesis of Cobalt Oxide Clusters in a Metal–Organic Framework

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peters, Aaron W.; Otake, Kenichi; Platero-Prats, Ana E.

Here, direct control over structure and location of catalytic species deposited on amorphous supports represents a formidable challenge in heterogeneous catalysis. In contrast, a structurally well-defined, crystalline metal–organic framework (MOF) can be rationally designed using post-synthetic techniques to allow for desired structural or locational changes of deposited metal ions. Herein, naphthalene dicarboxylate linkers are incorporated in the MOF, NU-1000, to block the small cavities where few-atom clusters of cobalt oxide preferentially grow, inducing catalyst deposition towards hither-to ill-favored grafting sites orientated toward NU-1000’s mesoporous channels. Despite the different cobalt oxide location, the resulting material is still an active propane oxidativemore » dehydrogenation catalyst at low temperature, reaching a turnover frequency of 0.68 ± 0.05 h –1 at 230 °C and confirming the utility of MOFs as crystalline supports to guide rational design of catalysts.« less

Investigating the synthesis of ligated metal clusters in solution using a flow reactor and electrospray ionization mass spectrometry.

PubMed

Olivares, Astrid; Laskin, Julia; Johnson, Grant E

2014-09-18

The scalable synthesis of ligated subnanometer metal clusters containing an exact number of atoms is of interest due to the highly size-dependent catalytic, electronic, and optical properties of these species. While significant research has been conducted on the batch preparation of clusters through reduction synthesis in solution, the processes of metal complex reduction as well as cluster nucleation, growth, and postreduction etching are still not well understood. Herein, we demonstrate a prototype temperature-controlled flow reactor for qualitatively studying cluster formation in solution at steady-state conditions. Employing this technique, methanol solutions of a chloro(triphenylphosphine)gold precursor, 1,4-bis(diphenylphosphino)butane capping ligand, and borane-tert-butylamine reducing agent were combined in a mixing tee and introduced into a heated capillary with a known length. In this manner, the temperature dependence of the relative abundance of different ionic reactants, intermediates, and products synthesized in real time was characterized qualitatively using online mass spectrometry. A wide distribution of doubly and triply charged cationic gold clusters was observed as well as smaller singly charged organometallic complexes. The results demonstrate that temperature plays a crucial role in determining the relative population of cationic gold clusters and, in general, that higher temperature promotes the formation of doubly charged clusters and singly charged organometallic complexes while reducing the abundance of triply charged species. Moreover, the distribution of clusters observed at elevated temperatures is found to be consistent with that obtained at longer reaction times at room temperature, thereby demonstrating that heating may be used to access cluster distributions characteristic of different stages of batch reduction synthesis in solution.

Petit-High Pressure Carbon Dioxide stress increases synthesis of S-Adenosylmethionine and phosphatidylcholine in yeast Saccharomyces cerevisiae.

PubMed

Niu, Liyuan; Nomura, Kazuki; Iwahashi, Hitoshi; Matsuoka, Hiroyuki; Kawachi, Satoshi; Suzuki, Yoshihisa; Tamura, Katsuhiro

2017-12-01

Petit-High Pressure Carbon Dioxide (p-HPCD) is a promising nonthermal technology for foods pasteurization. Cluster analysis of gene expression profiles of Saccharomyces cerevisiae exposed to various stresses exhibited that gene expression profile for p-HPCD stress (0.5MPa, 25°C) was grouped into a cluster including profiles for Sodium Dodecyl Sulfate and Roundup herbicide. Both are detergents that can disorder membrane structurally and functionally, which suggests that cell membrane may be a target of p-HPCD stress to cause cell growth inhibition. Through metabolomic analysis, amount of S-Adenosylmethionine (AdoMet) that is used as methyl donor to participate in phosphatidylcholine synthesis via phosphatidylethanolamine (PE) methylation pathway, was increased after p-HPCD treatment for 2h. The key gene OPI3 encoding phospholipid methyltransferase that catalyzes the last two steps in PE methylation pathway was confirmed significantly induced by RT-PCR. Transcriptional expression of genes (MET13, MET16, MET10, MET17, MET6 and SAM2) related to AdoMet biosynthesis was also significantly induced. Choline as the PC precursor and ethanolamine as PE precursor in Kennedy pathway were also found increased under p-HPCD condition. We also found that amounts of most of amino acids involving protein synthesis were found decreased after p-HPCD treatment for 2h. Moreover, morphological changes on cell surface were observed by scanning electron microscope. In conclusion, the effects of p-HPCD stress on cell membrane appear to be a very likely cause of yeast growth inhibition and the enhancement of PC synthesis could contribute to maintain optimum structure and functions of cell membrane and improve cell resistance to inactivation. Copyright © 2017 Elsevier B.V. All rights reserved.

Integrated self-organization of transitional ER and early Golgi compartments.

PubMed

Glick, Benjamin S

2014-02-01

COPII coated vesicles bud from an ER domain termed the transitional ER (tER), but the mechanism that clusters COPII vesicles at tER sites is unknown. tER sites are closely associated with early Golgi or pre-Golgi structures, suggesting that the clustering of nascent COPII vesicles could be achieved by tethering to adjacent membranes. This model challenges the prevailing view that COPII vesicles are clustered by a scaffolding protein at the ER surface. Although Sec16 was proposed to serve as such a scaffolding protein, recent data suggest that rather than organizing COPII into higher-order structures, Sec16 acts at the level of individual COPII vesicles to regulate COPII turnover. A plausible synthesis is that tER sites are created by tethering to Golgi membranes and are regulated by Sec16. Meanwhile, the COPII vesicles that bud from tER sites are thought to nucleate new Golgi cisternae. Thus, an integrated self-organization process may generate tER-Golgi units. © 2014 WILEY Periodicals, Inc.

Cluster-mediated assembly enables step-growth copolymerization from binary nanoparticle mixtures with rationally designed architectures† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c8sc00220g

PubMed Central

Zhang, Xianfeng; Lv, Longfei; Wu, Guanhong; Yang, Dong

2018-01-01

Directed co-assembly of binary nanoparticles (NPs) into one-dimensional copolymer-like chains is fascinating but challenging in the realm of material science. While many strategies have been developed to induce the polymerization of NPs, it remains a grand challenge to produce colloidal copolymers with widely tailored compositions and precisely controlled architectures. Herein we report a robust colloidal polymerization strategy, which enables the growth of sophisticated NP chains with elaborately designed structures. By quantifying NP assembly statistics and kinetics, we establish that the linear assembly of colloidal NPs, with the assistance of PbSO4 clusters, follows a step-growth polymerization mechanism, and on the basis of this, we design and fabricate NP chains structurally analogous to random, block, and alternating copolymers, respectively. Our studies offer mechanistic insights into cluster-mediated colloidal polymerization, paving the way toward the rational synthesis of colloidal copolymers with quantitatively predicted architectures and functionalities. PMID:29862003

Extrachromosomal Nucleolus-Like Compartmentalization by a Plasmid-Borne Ribosomal RNA Operon and Its Role in Nucleoid Compaction.

PubMed

Mata Martin, Carmen; Sun, Zhe; Zhou, Yan Ning; Jin, Ding Jun

2018-01-01

In the fast-growing Escherichia coli cells, RNA polymerase (RNAP) molecules are concentrated and form foci at clusters of ribosomal RNA (rRNA) operons resembling eukaryotic nucleolus. The bacterial nucleolus-like organization, spatially compartmentalized at the surface of the compact bacterial chromosome (nucleoid), serves as transcription factories for rRNA synthesis and ribosome biogenesis, which influences the organization of the nucleoid. Unlike wild type that has seven rRNA operons in the genome in a mutant that has six (Δ6 rrn ) rRNA operons deleted in the genome, there are no apparent transcription foci and the nucleoid becomes uncompacted, indicating that formation of RNAP foci requires multiple copies of rRNA operons clustered in space and is critical for nucleoid compaction. It has not been determined, however, whether a multicopy plasmid-borne rRNA operon (p rrnB ) could substitute the multiple chromosomal rRNA operons for the organization of the bacterial nucleolus-like structure in the mutants of Δ6 rrn and Δ7 rrn that has all seven rRNA operons deleted in the genome. We hypothesized that extrachromosomal nucleolus-like structures are similarly organized and functional in trans from p rrnB in these mutants. In this report, using multicolor images of three-dimensional superresolution Structured Illumination Microscopy (3D-SIM), we determined the distributions of both RNAP and NusB that are a transcription factor involved in rRNA synthesis and ribosome biogenesis, p rrnB clustering, and nucleoid structure in these two mutants in response to environmental cues. Our results found that the extrachromosomal nucleolus-like organization tends to be spatially located at the poles of the mutant cells. In addition, formation of RNAP foci at the extrachromosomal nucleolus-like structure condenses the nucleoid, supporting the idea that active transcription at the nucleolus-like organization is a driving force in nucleoid compaction.

Structure and gene cluster of the O-antigen of Escherichia coli O54.

PubMed

Naumenko, Olesya I; Guo, Xi; Senchenkova, Sof'ya N; Geng, Peng; Perepelov, Andrei V; Shashkov, Alexander S; Liu, Bin; Knirel, Yuriy A

2018-06-15

Mild acid hydrolysis of the lipopolysaccharide of Escherichia coli O54 afforded an O-polysaccharide, which was studied by sugar analysis, solvolysis with anhydrous trifluoroacetic acid, and 1 H and 13 C NMR spectroscopy. Solvolysis cleaved predominantly the linkage of β-d-Ribf and, to a lesser extent, that of β-d-GlcpNAc, whereas the other linkages, including the linkage of α-l-Rhap, were stable under selected conditions (40 °C, 5 h). The following structure of the O-polysaccharide was established: →4)-α-d-GalpA-(1 → 2)-α-l-Rhap-(1 → 2)-β-d-Ribf-(1 → 4)-β-d-Galp-(1 → 3)-β-d-GlcpNAc-(1→ The O-antigen gene cluster of E. coli O54 was analyzed and found to be consistent in general with the O-polysaccharide structure established but there were two exceptions: i) in the cluster, there were genes for phosphoserine phosphatase and serine transferase, which have no apparent role in the O-polysaccharide synthesis, and ii) no ribofuranosyltransferase gene was present in the cluster. Both uncommon features are shared by some other enteric bacteria. Copyright © 2018 Elsevier Ltd. All rights reserved.

Reaction dynamics analysis of a reconstituted Escherichia coli protein translation system by computational modeling

PubMed Central

Matsuura, Tomoaki; Tanimura, Naoki; Hosoda, Kazufumi; Yomo, Tetsuya; Shimizu, Yoshihiro

2017-01-01

To elucidate the dynamic features of a biologically relevant large-scale reaction network, we constructed a computational model of minimal protein synthesis consisting of 241 components and 968 reactions that synthesize the Met-Gly-Gly (MGG) peptide based on an Escherichia coli-based reconstituted in vitro protein synthesis system. We performed a simulation using parameters collected primarily from the literature and found that the rate of MGG peptide synthesis becomes nearly constant in minutes, thus achieving a steady state similar to experimental observations. In addition, concentration changes to 70% of the components, including intermediates, reached a plateau in a few minutes. However, the concentration change of each component exhibits several temporal plateaus, or a quasi-stationary state (QSS), before reaching the final plateau. To understand these complex dynamics, we focused on whether the components reached a QSS, mapped the arrangement of components in a QSS in the entire reaction network structure, and investigated time-dependent changes. We found that components in a QSS form clusters that grow over time but not in a linear fashion, and that this process involves the collapse and regrowth of clusters before the formation of a final large single cluster. These observations might commonly occur in other large-scale biological reaction networks. This developed analysis might be useful for understanding large-scale biological reactions by visualizing complex dynamics, thereby extracting the characteristics of the reaction network, including phase transitions. PMID:28167777

Selenium as a Structural Surrogate of Sulfur: Template-Assisted Assembly of Five Types of Tungsten-Iron-Sulfur/Selenium Clusters and the Structural Fate of Chalcogenide Reactants

PubMed Central

Zheng, Bo; Chen, Xu-Dong; Zheng, Shao-Liang; Holm, R. H.

2012-01-01

Syntheses of five types of tungsten-iron-sulfur/selenium clusters–incomplete cubanes, single cubanes, edge-bridged double cubanes (EBDCs), PN-type clusters, and double-cuboidal clusters–have been devised based on the concept of template-assisted assembly. The template reactant is six-coordinate [(Tp*)WVIS3]1−, which in the assembly systems organizes FeII,III and sulfide/selenide into cuboidal [(Tp*)WFe2S3] or cubane [(Tp*)WFe3S3Q] units. With appropriate terminal iron ligation, these units are capable of independent existence or may be transformed into higher nuclearity species. Selenide is used as a surrogate for sulfide in cluster assembly in order to determine by X-ray structures the position occupied by an external chalcogenide nucleophile or an internal chalcogenide atom in product clusters. Specific incorporation of selenide is demonstrated by formation of [WFe3S3Se]2+,3+ cubane cores. Reductive dimerization of the cubane leads to the EBDC core [W2Fe6S6Se2]2+ containing μ4-Se sites. Reaction of these species with HSe− affords the PN-type cores [W2Fe6S6Se3]1+ in which selenide occupies μ6-Se and μ2-Se sites. Reaction of [(Tp*)WS3]1−, FeCl2, and Na2Se results in the double cuboidal [W2Fe4S6Se3]2+,0 core with μ2-Se and μ4-Se bridges. It is highly probable that in analogous sulfide-only assembly systems, external and internal sulfide reactants occupy corresponding positions in cluster products. The results further demonstrate the viability of template-assisted cluster synthesis inasmuch as the reduced (Tp*)WS3 unit is present in all clusters. Structures, zero-field Mössbauer data, and redox potentials are presented for all cluster types. (Tp* = tris(pyrazolyl)hydroborate(1−)) PMID:22424175

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liebhaber, S.A.; Weiss, I.; Cash, F.E.

Synthesis of normal human hemoglobin A, {alpha}{sub 2}{beta}{sub 2}, is based upon balanced expression of genes in the {alpha}-globin gene cluster on chromosome 15 and the {beta}-globin gene cluster on chromosome 11. Full levels of erythroid-specific activation of the {beta}-globin cluster depend on sequences located at a considerable distance 5{prime} to the {beta}-globin gene, referred to as the locus-activating or dominant control region. The existence of an analogous element(s) upstream of the {alpha}-globin cluster has been suggested from observations on naturally occurring deletions and experimental studies. The authors have identified an individual with {alpha}-thalassemia in whom structurally normal {alpha}-globin genesmore » have been inactivated in cis by a discrete de novo 35-kilobase deletion located {approximately}30 kilobases 5{prime} from the {alpha}-globin gene cluster. They conclude that this deletion inactivates expression of the {alpha}-globin genes by removing one or more of the previously identified upstream regulatory sequences that are critical to expression of the {alpha}-globin genes.« less

Nanomanufacturing of titania interfaces with controlled structural and functional properties by supersonic cluster beam deposition

NASA Astrophysics Data System (ADS)

Podestà, Alessandro; Borghi, Francesca; Indrieri, Marco; Bovio, Simone; Piazzoni, Claudio; Milani, Paolo

2015-12-01

Great emphasis is placed on the development of integrated approaches for the synthesis and the characterization of ad hoc nanostructured platforms, to be used as templates with controlled morphology and chemical properties for the investigation of specific phenomena of great relevance in interdisciplinary fields such as biotechnology, medicine, and advanced materials. Here, we discuss the crucial role and the advantages of thin film deposition strategies based on cluster-assembling from supersonic cluster beams. We select cluster-assembled nanostructured titania (ns-TiO2) as a case study to demonstrate that accurate control over morphological parameters can be routinely achieved, and consequently, over several relevant interfacial properties and phenomena, like surface charging in a liquid electrolyte, and proteins and nanoparticles adsorption. In particular, we show that the very good control of nanoscale morphology is obtained by taking advantage of simple scaling laws governing the ballistic deposition regime of low-energy, mass-dispersed clusters with reduced surface mobility.

Nanomanufacturing of titania interfaces with controlled structural and functional properties by supersonic cluster beam deposition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Podestà, Alessandro, E-mail: alessandro.podesta@mi.infn.it, E-mail: pmilani@mi.infn.it; Borghi, Francesca; Indrieri, Marco

Great emphasis is placed on the development of integrated approaches for the synthesis and the characterization of ad hoc nanostructured platforms, to be used as templates with controlled morphology and chemical properties for the investigation of specific phenomena of great relevance in interdisciplinary fields such as biotechnology, medicine, and advanced materials. Here, we discuss the crucial role and the advantages of thin film deposition strategies based on cluster-assembling from supersonic cluster beams. We select cluster-assembled nanostructured titania (ns-TiO{sub 2}) as a case study to demonstrate that accurate control over morphological parameters can be routinely achieved, and consequently, over several relevantmore » interfacial properties and phenomena, like surface charging in a liquid electrolyte, and proteins and nanoparticles adsorption. In particular, we show that the very good control of nanoscale morphology is obtained by taking advantage of simple scaling laws governing the ballistic deposition regime of low-energy, mass-dispersed clusters with reduced surface mobility.« less

Keeping the ball rolling: fullerene-like molecular clusters.

PubMed

Kong, Xiang-Jian; Long, La-Sheng; Zheng, Zhiping; Huang, Rong-Bin; Zheng, Lan-Sun

2010-02-16

The discovery of fullerenes in 1985 opened a new chapter in the chemistry of highly symmetric molecules. Fullerene-like metal clusters, characterized by (multi)shell-like structures, are one rapidly developing class of molecules that share this shape. In addition to creating aesthetically pleasing molecular structures, the ordered arrangement of metal atoms within such frameworks provides the opportunity to develop materials with properties not readily achieved in corresponding mononuclear or lower-nuclearity complexes. In this Account, we survey the great variety of fullerene-like metal-containing clusters with an emphasis on their synthetic and structural chemistry, a first step in the discussion of this fascinating field of cluster chemistry. We group the compounds of interest into three categories based on the atomic composition of the cluster core: those with formal metal-metal bonding, those characterized by ligand participation, and those supported by polyoxometalate building blocks. The number of clusters in the first group, containing metal-metal bonds, is relatively small. However, because of the unique and complex bonding scenarios observed for some of these species, these metalloid clusters present a number of research questions with significant ramifications. Because these cores contain molecular clusters of precious metals at the nanoscale, they offer an opportunity to study chemical properties at size ranges from the molecular to nanoscale and to gain insights into the electronic structures and properties of nanomaterials of similar chemical compositions. Clusters of the second type, whose core structures are facilitated by ligand participation, could aid in the development of functional materials. Of particular interest are the magnetic clusters containing both transition and lanthanide elements. A series of such heterometallic clusters that we prepared demonstrates diverse magnetic properties including antiferromagnetism, ferrimagnetism, and ferromagnetism. Considering the diversity of their composition, their distinct electronic structures, and the disparate coordination behaviors of the different metal elements, these materials suggest abundant opportunities for designing multifunctional materials with varied structures. The third type of clusters that we discuss are based on polyoxometalates, in particular those containing pentagonal units. However, unlike in fullerene chemistry, which does not allow the use of discrete pentagonal building blocks, the metal oxide-based pentagonal units can be used as fundamental building blocks for constructing various Keplerate structures. These structures also have a variety of functions, including intriguing magnetic properties in some cases. Coupled with different linking groups, such pentagonal units can be used for the assembly of a large number of spherical molecules whose properties can be tuned and optimized. Although this Account focuses on the topological aspects of fullerene-like metal clusters, we hope that this topical review will stimulate more efforts in the exploratory synthesis of new fullerene-like clusters. More importantly, we hope that further study of the bonding interactions and properties of these molecules will lead to the development of new functional materials.

Repair of Clustered Damage and DNA Polymerase Iota.

PubMed

Belousova, E A; Lavrik, O I

2015-08-01

Multiple DNA lesions occurring within one or two turns of the DNA helix known as clustered damage are a source of double-stranded DNA breaks, which represent a serious threat to the cells. Repair of clustered lesions is accomplished in several steps. If a clustered lesion contains oxidized bases, an individual DNA lesion is repaired by the base excision repair (BER) mechanism involving a specialized DNA polymerase after excising DNA damage. Here, we investigated DNA synthesis catalyzed by DNA polymerase iota using damaged DNA templates. Two types of DNA substrates were used as model DNAs: partial DNA duplexes containing breaks of different length, and DNA duplexes containing 5-formyluracil (5-foU) and uracil as a precursor of apurinic/apyrimidinic sites (AP) in opposite DNA strands. For the first time, we showed that DNA polymerase iota is able to catalyze DNA synthesis using partial DNA duplexes having breaks of different length as substrates. In addition, we found that DNA polymerase iota could catalyze DNA synthesis during repair of clustered damage via the BER system by using both undamaged and 5-foU-containing templates. We found that hPCNA (human proliferating cell nuclear antigen) increased efficacy of DNA synthesis catalyzed by DNA polymerase iota.

Synthesis and structures of new niobium cluster compounds with pyridinium cations: (PyrH){sub 2}[Nb{sub 6}Cl{sub 18}].EtOH (Pyr: pyridine, Et: ethyl) and the cubic modification of (PyrH){sub 2}[Nb{sub 6}Cl{sub 18}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Flemming, Anke; Hoppe, Alessandra; Koeckerling, Martin

2008-10-15

Slow crystallization of (PyrH){sub 2}[Nb{sub 6}Cl{sub 18}] from hot ethanol solution affords triclinic (PyrH){sub 2}[Nb{sub 6}Cl{sub 18}].EtOH. Treatment of [Nb{sub 6}Cl{sub 14}(H{sub 2}O){sub 4}].4H{sub 2}O with pyridine in a methanol solution gives the second title compound, the cubic modification of (PyrH){sub 2}[Nb{sub 6}Cl{sub 18}]. Both structures were determined by single crystal X-ray diffraction, (PyrH){sub 2}[Nb{sub 6}Cl{sub 18}].EtOH: P1-bar , a=9.3475(3), b=9.3957(3), c=10.8600(3) A, {alpha}=82.582(1){sup o}, {beta}=78.608(1){sup o}, and {gamma}=78.085(1){sup o}, Z=1, R{sub 1}(F)/wR{sub 2}(F{sup 2})=0.0254/0.0573, cub.-(PyrH){sub 2}[Nb{sub 6}Cl{sub 18}]: Fd3-bar m, a=19.935(2) A, Z=8, R{sub 1}(F)/wR{sub 2}(F{sup 2})=0.0557/0.1796. The cluster compounds contain isolated, molecular [Nb{sub 6}Cl{sup i}{sub 12}Cl{sup a}{sub 6}]{supmore » 2-} cluster anions with an octahedron of metal atoms edge bridged by chlorido ligands with additional ones on all the six exo positions. These cluster anions are separated by the pyridinium cations and ethanol solvent molecules, respectively. For the cubic modification of (PyrH){sub 2}[Nb{sub 6}Cl{sub 18}], a structural comparison is given to the known rhombohedral modification using the group-subgroup relations as expressed by a Baernighausen tree. - Graphical abstract: The synthesis and structure of a second cubic modification of (PyrH){sub 2}[Nb{sub 6}Cl{sub 18}] and of the new (PyrH){sub 2}[Nb{sub 6}Cl{sub 18}].EtOH are reported, both of which contain isolated niobium halide cluster anions with an octahedral core of metal atoms.« less

Trimetallic nitride template endohedral metallofullerenes: discovery, structural characterization, reactivity, and applications.

PubMed

Zhang, Jianyuan; Stevenson, Steven; Dorn, Harry C

2013-07-16

Shortly after the discovery of the carbon fullerene allotrope, C₆₀, researchers recognized that the hollow spheroidal shape could accommodate metal atoms, or clusters, which quickly led to the discovery of endohedral metallofullerenes (EMFs). In the past 2 decades, the unique features of EMFs have attracted broad interest in many fields, including inorganic chemistry, organic chemistry, materials chemistry, and biomedical chemistry. Some EMFs produce new metallic clusters that do not exist outside of a fullerene cage, and some other EMFs can boost the efficiency of magnetic resonance (MR) imaging 10-50-fold, in comparison with commercial contrast agents. In 1999, the Dorn laboratory discovered the trimetallic nitride template (TNT) EMFs, which consist of a trimetallic nitride cluster and a host fullerene cage. The TNT-EMFs (A₃N@C2n, n = 34-55, A = Sc, Y, or lanthanides) are typically formed in relatively high yields (sometimes only exceeded by empty-cage C₆₀ and C₇₀, but yields may decrease with increasing TNT cluster size), and exhibit high chemical and thermal stability. In this Account, we give an overview of TNT-EMF research, starting with the discovery of these structures and then describing their synthesis and applications. First, we describe our serendipitous discovery of the first member of this class, Sc₃N@Ih-C₈₀. Second, we discuss the methodology for the synthesis of several TNT-EMFs. These results emphasize the importance of chemically adjusting plasma temperature, energy, and reactivity (CAPTEAR) to optimize the type and yield of TNT-EMFs produced. Third, we review the approaches that are used to separate and purify pristine TNT-EMF molecules from their corresponding product mixtures. Although we used high-performance liquid chromatography (HPLC) to separate TNT-EMFs in early studies, we have more recently achieved facile separation based on the reduced chemical reactivity of the TNT-EMFs. These improved production yields and separation protocols have allowed industrial researchers to scale up the production of TNT-EMFs for commercial use. Fourth, we summarize the structural features of individual members of the TNT-EMF class, including cage structures, cluster arrangement, and dynamics. Fifth, we illustrate typical functionalization reactions of the TNT-EMFs, particularly cycloadditions and radical reactions, and describe the characterization of their derivatives. Finally, we illustrate the unique magnetic and electronic properties of specific TNT-EMFs for biomedicine and molecular device applications.

Theoretical studies on Grignard reagent formation: radical mechanism versus non-radical mechanism.

PubMed

Chen, Zhe-Ning; Fu, Gang; Xu, Xin

2012-12-21

Here we present a systematic theoretical investigation on the mechanisms of Grignard reagent formation (GRF) for CH(3)Cl reacting with Mg atom, Mg(2) and a series of Mg clusters (Mg(4)-Mg(20)). Our calculations reveal that the ground state Mg atom is inactive under matrix condition, whereas it is active under metal vapor synthesis (MVS) conditions. On the other hand, the excited state Mg ((3)P) atom, as produced by laser-ablation, can react with CH(3)Cl barrierlessly, and hence is active under matrix condition. We predict that the bimagnesium Grignard reagent, though often proposed, can barely be observed experimentally, due to its high reactivity towards additional CH(3)Cl to produce more stable Grignard reagent dimer, and that the cluster Grignard reagent RMg(4)X possesses a flat Mg(4) unit rather than a tetrahedral geometry. Our calculations further reveal that the radical pathway (T4) is prevalent on Mg, Mg(2) and Mg(n) clusters of small size, while the no-radical pathway (T2), which starts at Mg(4), becomes competitive with T4 as the cluster size increases. A structure-reactivity relationship between barrier heights and ionization potentials of Mg(n) is established. These findings not only resolve controversy in experiment and theory, but also provide insights which can be used in the design of effective synthesis approaches for the preparation of chiral Grignard reagents.

The Hoyle state in 12C

NASA Astrophysics Data System (ADS)

Freer, M.; Fynbo, H. O. U.

2014-09-01

The 7.65 MeV, Jπ =0+, second excited state in 12C is known as the Hoyle-state after Fred Hoyle. In the 1950s Hoyle proposed the existence of the state in order to account for the stellar abundance of carbon. Aside from its key role in the synthesis of the elements it is believed to possess a rather unusual structure, where the dominant degrees of freedom are those of α-particle clusters rather than nucleons. An understanding of the properties of the Hoyle state, for example its radius and excitations, has been the focus of a major experimental activity. Similarly, unravelling precisely why a cluster state should arise at precisely the right energy to promote synthesis of carbon has been a central theoretical challenge. To a significant extent, the Hoyle-state has become a cornerstone for state-of-the-art nuclear theory. This review examines the present status of both theory and experiment and indicates directions for future developments to resolve some of the remaining open questions.

Design and synthesis of polyoxometalate-framework materials from cluster precursors

NASA Astrophysics Data System (ADS)

Vilà-Nadal, Laia; Cronin, Leroy

2017-10-01

Inorganic oxide materials are used in semiconductor electronics, ion exchange, catalysis, coatings, gas sensors and as separation materials. Although their synthesis is well understood, the scope for new materials is reduced because of the stability limits imposed by high-temperature processing and top-down synthetic approaches. In this Review, we describe the derivatization of polyoxometalate (POM) clusters, which enables their assembly into a range of frameworks by use of organic or inorganic linkers. Additionally, bottom-up synthetic approaches can be used to make metal oxide framework materials, and the features of the molecular POM precursors are retained in these structures. Highly robust all-inorganic frameworks can be made using metal-ion linkers, which combine molecular synthetic control without the need for organic components. The resulting frameworks have high stability, and high catalytic, photochemical and electrochemical activity. Conceptually, these inorganic oxide materials bridge the gap between zeolites and metal-organic frameworks (MOFs) and establish a new class of all-inorganic POM frameworks that can be designed using topological and reactivity principles similar to MOFs.

Dark Matter and Extragalactic Gas Clouds in the NGC 4532/DDO 137 System

NASA Technical Reports Server (NTRS)

Hoffman, G. L.; Lu, N. Y.; Salpeter, E. E.; Connell, B. M.

1998-01-01

H I synthesis mapping of NGC 4532 and DDO 137, a pair of Sm galaxies on the edge of the Virgo cluster, is used to determine rotation curves for each of the galaxies and to resolve the structure and kinematics of three extragalactic H I clouds embedded in an extended envelope of diffuse HI discovered in earlier Arecibo studies of the system.

Synthesis and Catalytic Properties of Au Pd Nanoflowers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Jianguang; Wilson, Adria; Howe, Jane Y

2011-01-01

Reduction of Pd ions by hydroquinone in the presence of gold nanoparticles and polyvinylpyrrolidone resulted in the formation of nanoflowers with a Au core and Pd petals. Addition of HCl to the synthesis halted the reduction by hydroquinone and enabled the acquisition of snapshots of the nanoflowers at different stages of growth. TEM images of the reaction after 10 s show that the nanoflower morphology resulted from the homogeneous nucleation of Pd clusters in solution and their subsequent attachment to gold seeds coated with a thin (0.8 0.1 nm) shell of Pd. UV visible spectra also indicate Pd clusters formedmore » in the early stages of the reaction and disappeared as the nanoflowers grew. The speed at which this reaction can be halted is useful not only for producing a variety of bimetallic nanostructures with precisely controlled dimensions and morphologies but also for understanding the growth mechanism of these structures. The ability of the AuPd core shell structure to catalyze the Suzuki coupling reaction of iodobenzene to phenylboronic acid was probed and compared against the activity of Pd nanocubes and thin-shelled AuPd core shell nanoparticles. The results of this study suggest that Suzuki coupling was not affected by the surface structure or subsurface composition of the nanoparticles, but instead was primarily catalyzed by molecular Pd species that leached from the nanostructures.« less

Synthesis of Au-Pd Nanoflowers Through Nanocluster Assembly

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Jianguang; Howe, Jane Y; Chi, Miaofang

2011-01-01

Reduction of Pd ions by hydroquinone in the presence of gold nanoparticles and polyvinylpyrrolidone resulted in the formation of nanoflowers with a Au core and Pd petals. Addition of HCl to the synthesis halted the reduction by hydroquinone and enabled the acquisition of snapshots of the nanoflowers at different stages of growth. TEM images of the reaction after 10 s show that the nanoflower morphology resulted from the homogeneous nucleation of Pd clusters in solution and their subsequent attachment to gold seeds coated with a thin (0.8 {+-} 0.1 nm) shell of Pd. UV-visible spectra also indicate Pd clusters formedmore » in the early stages of the reaction and disappeared as the nanoflowers grew. The speed at which this reaction can be halted is useful not only for producing a variety of bimetallic nanostructures with precisely controlled dimensions and morphologies but also for understanding the growth mechanism of these structures. The ability of the AuPd core-shell structure to catalyze the Suzuki coupling reaction of iodobenzene to phenylboronic acid was probed and compared against the activity of Pd nanocubes and thin-shelled AuPd core-shell nanoparticles. The results of this study suggest that Suzuki coupling was not affected by the surface structure or subsurface composition of the nanoparticles, but instead was primarily catalyzed by molecular Pd species that leached from the nanostructures.« less

Synthesis of Densely Packaged, Ultrasmall Pt02 Clusters within a Thioether-Functionalized MOF: Catalytic Activity in Industrial Reactions at Low Temperature.

PubMed

Mon, Marta; Rivero-Crespo, Miguel A; Ferrando-Soria, Jesús; Vidal-Moya, Alejandro; Boronat, Mercedes; Leyva-Pérez, Antonio; Corma, Avelino; Hernández-Garrido, Juan C; López-Haro, Miguel; Calvino, José J; Ragazzon, Giulio; Credi, Alberto; Armentano, Donatella; Pardo, Emilio

2018-05-22

The gram-scale synthesis, stabilization, and characterization of well-defined ultrasmall subnanometric catalytic clusters on solids is a challenge. The chemical synthesis and X-ray snapshots of Pt 0 2 clusters, homogenously distributed and densely packaged within the channels of a metal-organic framework, is presented. This hybrid material catalyzes efficiently, and even more importantly from an economic and environmental viewpoint, at low temperature (25 to 140 °C), energetically costly industrial reactions in the gas phase such as HCN production, CO 2 methanation, and alkene hydrogenations. These results open the way for the design of precisely defined catalytically active ultrasmall metal clusters in solids for technically easier, cheaper, and dramatically less-dangerous industrial reactions. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

[Ag115S34(SCH2C6H4 t Bu)47(dpph)6]: synthesis, crystal structure and NMR investigations of a soluble silver chalcogenide nanocluster.

PubMed

Bestgen, Sebastian; Fuhr, Olaf; Breitung, Ben; Kiran Chakravadhanula, Venkata Sei; Guthausen, Gisela; Hennrich, Frank; Yu, Wen; Kappes, Manfred M; Roesky, Peter W; Fenske, Dieter

2017-03-01

With the aim to synthesize soluble cluster molecules, the silver salt of (4-( tert -butyl)phenyl)methanethiol [AgSCH 2 C 6 H 4 t Bu] was applied as a suitable precursor for the formation of a nanoscale silver sulfide cluster. In the presence of 1,6-(diphenylphosphino)hexane (dpph), the 115 nuclear silver cluster [Ag 115 S 34 (SCH 2 C 6 H 4 t Bu) 47 (dpph) 6 ] was obtained. The molecular structure of this compound was elucidated by single crystal X-ray analysis and fully characterized by spectroscopic techniques. In contrast to most of the previously published cluster compounds with more than a hundred heavy atoms, this nanoscale inorganic molecule is soluble in organic solvents, which allowed a comprehensive investigation in solution by UV-Vis spectroscopy and one- and two-dimensional NMR spectroscopy including 31 P/ 109 Ag-HSQC and DOSY experiments. These are the first heteronuclear NMR investigations on coinage metal chalcogenides. They give some first insight into the behavior of nanoscale silver sulfide clusters in solution. Additionally, molecular weight determinations were performed by 2D analytical ultracentrifugation and HR-TEM investigations confirm the presence of size-homogeneous nanoparticles present in solution.

Sinter-Resistant Platinum Catalyst Supported by Metal-Organic Framework.

PubMed

Kim, In Soo; Li, Zhanyong; Zheng, Jian; Platero-Prats, Ana E; Mavrandonakis, Andreas; Pellizzeri, Steven; Ferrandon, Magali; Vjunov, Aleksei; Gallington, Leighanne C; Webber, Thomas E; Vermeulen, Nicolaas A; Penn, R Lee; Getman, Rachel B; Cramer, Christopher J; Chapman, Karena W; Camaioni, Donald M; Fulton, John L; Lercher, Johannes A; Farha, Omar K; Hupp, Joseph T; Martinson, Alex B F

2018-01-22

Single atoms and few-atom clusters of platinum are uniformly installed on the zirconia nodes of a metal-organic framework (MOF) NU-1000 via targeted vapor-phase synthesis. The catalytic Pt clusters, site-isolated by organic linkers, are shown to exhibit high catalytic activity for ethylene hydrogenation while exhibiting resistance to sintering up to 200 °C. In situ IR spectroscopy reveals the presence of both single atoms and few-atom clusters that depend upon synthesis conditions. Operando X-ray absorption spectroscopy and X-ray pair distribution analyses reveal unique changes in chemical bonding environment and cluster size stability while on stream. Density functional theory calculations elucidate a favorable reaction pathway for ethylene hydrogenation with the novel catalyst. These results provide evidence that atomic layer deposition (ALD) in MOFs is a versatile approach to the rational synthesis of size-selected clusters, including noble metals, on a high surface area support. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

X-ray and Neutron Scattering Study of the Formation of Core–Shell-Type Polyoxometalates

DOE PAGES

Yin, Panchao; Wu, Bin; Mamontov, Eugene; ...

2016-02-05

A typical type of core-shell polyoxometalates can be obtained through the Keggin-type polyoxometalate-templated growth of a layer of spherical shell structure of {Mo 72Fe 30}. Small angle X-ray scattering is used to study the structural features and stability of the core-shell structures in aqueous solutions. Time-resolved small angle X-ray scattering is applied to monitor the synthetic reactions and a three-stage formation mechanism is proposed to describe the synthesis of the core-shell polyoxometalates based on the monitoring results. Quasi-elastic and inelastic neutron scattering are used to probe the dynamics of water molecules in the core-shell structures and two different types ofmore » water molecules, the confined and structured water, are observed. These water molecules play an important role in bridging core and shell structures and stabilizing the cluster structures. A typical type of core shell polyoxometalates can be obtained through the Keggin-type polyoxometalate-templated growth of a layer of spherical shell structure of {Mo 72Fe 30}. Small-angle X-ray scattering is used to study the structural features and stability of the core shell structures in aqueous solutions. Time-resolved small-angle X-ray scattering is applied to monitor the synthetic reactions, and a three-stage formation mechanism is proposed to describe the synthesis of the core shell polyoxometalates based on the monitoring results. New protocols have been developed by fitting the X-ray data with custom physical models, which provide more convincing, objective, and completed data interpretation. Quasi-elastic and inelastic neutron scattering are used to probe the dynamics of water molecules in the core shell structures, and two different types of water molecules, the confined and structured water, are observed. These water molecules play an important role in bridging core and shell structures and stabilizing the cluster structures.« less

Zintl Clusters as Wet-Chemical Precursors for Germanium Nanomorphologies with Tunable Composition.

PubMed

Bentlohner, Manuel M; Waibel, Markus; Zeller, Patrick; Sarkar, Kuhu; Müller-Buschbaum, Peter; Fattakhova-Rohlfing, Dina; Fässler, Thomas F

2016-02-12

[Ge9](4-) Zintl clusters are used as soluble germanium source for a bottom-up fabrication of Ge nanomorphologies such as inverse opal structures with tunable composition. The method is based on the assembly and oxidation of [Ge9 ](4-) clusters in a template mold using SiCl4 , GeCl4 , and PCl3 leading to Si and P-containing Ge phases as shown by X-ray diffraction, Raman spectroscopy, and energy-dispersive X-ray analysis. [Ge9](4-) clusters are retained using ethylenediamine (en) as a transfer medium to a mold after removal of the solvent if water is thoroughly excluded, but are oxidized to amorphous Ge in presence of water traces. (1)H NMR spectroscopy reveals the oxidative deprotonation of en by [Ge9](4-). Subsequent annealing leads to crystalline Ge. As an example for wet-chemical synthesis of complex Ge nanomorphologies, we describe the fabrication of undoped and P-doped inverse opal-structured Ge films with a rather low oxygen contents. The morphology of the films with regular volume porosity is characterized by SEM, TEM, and grazing incidence small-angle X-ray scattering. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Ligand-free gold atom clusters adsorbed on graphene nano sheets generated by oxidative laser fragmentation in water

NASA Astrophysics Data System (ADS)

Lau, Marcus; Haxhiaj, Ina; Wagener, Philipp; Intartaglia, Romuald; Brandi, Fernando; Nakamura, Junji; Barcikowski, Stephan

2014-08-01

Over three decades after the first synthesis of stabilized Au55-clusters many scientific questions about gold cluster properties are still unsolved and ligand-free colloidal clusters are difficult to fabricate. Here we present a novel route to produce ultra-small gold particles by using a green technique, the laser ablation and fragmentation in water, without using reductive or stabilizing agents at any step of the synthesis. For fabrication only a pulsed laser, a gold-target, pure water, sodium hydroxide and hydrogen peroxide are deployed. The particles are exemplarily hybridized to graphene supports showing that these carbon-free colloidal clusters might serve as versatile building blocks.

Synthesis, structure and magnetic study of a novel mixed-valent Co(II)10Co(III)4 shield constructed by mixed pyridine-alcoholate ligands.

PubMed

Peng, Yan; Tian, Chong-Bin; Zhang, Hua-Bin; Li, Zhi-Hua; Lin, Ping; Du, Shao-Wu

2012-04-28

A novel tetradecanuclear mixed-valent cobalt cluster, formulated as [Co(II)(10)Co(III)(4)(OH)(2)O(6)(hmp)(10)(pdm)(4)(CH(3)OH)(2)]·5H(2)O (1), was obtained using mixed ligands of 2-(hydroxymethyl)pyridine (hmpH) and 2,6-pyridinedimethanol (pdmH(2)). The cobalt ions in 1 are connected by ten chelating hmp(-) ligands, four tris-chelating pdm(2-) ligands and six μ(3)-oxide/hydroxide anions, forming a unique shield-like planar structure that is rarely observed for Co-based clusters. Compound 1 displays slight frequency dependence at static zero field below 4.5 K, suggesting that it might be a single molecule magnet (SMM). This journal is © The Royal Society of Chemistry 2012

Sinter-Resistant Platinum Catalyst Supported by Metal-Organic Framework

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, In Soo; Li, Zhanyong; Zheng, Jian

Installed on the zirconia nodes of a metal-organic framework (MOF) NU-1000 via targeted vapor-phase synthesis. The catalytic Pt clusters, site-isolated by organic linkers, are shown to exhibit high catalytic activity for ethylene hydrogenation while exhibiting resistance to sintering up to 200 degrees C. In situ IR spectroscopy reveals the presence of both single atoms and few-atom clusters that depend upon synthesis conditions. Operando X-ray absorption spectroscopy and Xray pair distribution analyses reveal unique changes in chemical bonding environment and cluster size stability while on stream. Density functional theory calculations elucidate a favorable reaction pathway for ethylene hydrogenation with the novelmore » catalyst. These results provide evidence that atomic layer deposition (ALD) in MOFs is a versatile approach to the rational synthesis of size-selected clusters, including noble metals, on a high surface area support.« less

Synthesis, crystal structure and magnetic properties of a novel tetranuclear oxo-bridged iron(III) butterfly

NASA Astrophysics Data System (ADS)

Arizaga, Livia; Gancheff, Jorge S.; Faccio, Ricardo; Cañón-Mancisidor, Walter; González, Ricardo; Kremer, Carlos; Chiozzone, Raúl

2014-01-01

A novel carboxylate/picolinate oxo-bridged iron(III) cluster, namely [Na2(H2O)8][Fe4(μ-O)2(O2CPh)7(pic)2]2·2H2O (1) where pic = picolinate, has been obtained by reacting "basic iron benzoate" [Fe3O(O2CPh)6(H2O)3](O2CPh) with sodium picolinate in acetonitrile. The compound has been characterized by elemental analysis and IR spectroscopy and its crystal structure has been determined by single-crystal X-ray diffraction.

NifX and NifEN exchange NifB cofactor and the VK-cluster, a newly isolated intermediate of the iron-molybdenum cofactor biosynthetic pathway.

PubMed

Hernandez, Jose A; Igarashi, Robert Y; Soboh, Basem; Curatti, Leonardo; Dean, Dennis R; Ludden, Paul W; Rubio, Luis M

2007-01-01

The iron-molybdenum cofactor of nitrogenase (FeMo-co) is synthesized in a multistep process catalysed by several Nif proteins and is finally inserted into a pre-synthesized apo-dinitrogenase to generate mature dinitrogenase protein. The NifEN complex serves as scaffold for some steps of this synthesis, while NifX belongs to a family of small proteins that bind either FeMo-co precursors or FeMo-co during cofactor synthesis. In this work, the binding of FeMo-co precursors and their transfer between purified Azotobacter vinelandii NifX and NifEN proteins was studied to shed light on the role of NifX on FeMo-co synthesis. Purified NifX binds NifB cofactor (NifB-co), a precursor to FeMo-co, with high affinity and is able to transfer it to the NifEN complex. In addition, NifEN and NifX exchange another [Fe-S] cluster that serves as a FeMo-co precursor, and we have designated it as the VK-cluster. In contrast to NifB-co, the VK-cluster is electronic paramagnetic resonance (EPR)-active in the reduced and the oxidized states. The NifX/VK-cluster complex is unable to support in vitro FeMo-co synthesis in the absence of NifEN because further processing of the VK-cluster into FeMo-co requires the simultaneous activities of NifEN and NifH. Our in vitro studies suggest that the role of NifX in vivo is to serve as transient reservoir of FeMo-co precursors and thus help control their flux during FeMo-co synthesis.

The Suf Iron-Sulfur Cluster Biosynthetic System Is Essential in Staphylococcus aureus, and Decreased Suf Function Results in Global Metabolic Defects and Reduced Survival in Human Neutrophils.

PubMed

Roberts, Christina A; Al-Tameemi, Hassan M; Mashruwala, Ameya A; Rosario-Cruz, Zuelay; Chauhan, Unnati; Sause, William E; Torres, Victor J; Belden, William J; Boyd, Jeffrey M

2017-06-01

Staphylococcus aureus remains a causative agent for morbidity and mortality worldwide. This is in part a result of antimicrobial resistance, highlighting the need to uncover novel antibiotic targets and to discover new therapeutic agents. In the present study, we explored the possibility that iron-sulfur (Fe-S) cluster synthesis is a viable antimicrobial target. RNA interference studies established that Suf ( su l f ur mobilization)-dependent Fe-S cluster synthesis is essential in S. aureus We found that sufCDSUB were cotranscribed and that suf transcription was positively influenced by sigma factor B. We characterized an S. aureus strain that contained a transposon inserted in the intergenic space between sufC and sufD ( sufD *), resulting in decreased transcription of sufSUB Consistent with the transcriptional data, the sufD * strain had multiple phenotypes associated with impaired Fe-S protein maturation. They included decreased activities of Fe-S cluster-dependent enzymes, decreased growth in media lacking metabolites that require Fe-S proteins for synthesis, and decreased flux through the tricarboxylic acid (TCA) cycle. Decreased Fe-S cluster synthesis resulted in sensitivity to reactive oxygen and reactive nitrogen species, as well as increased DNA damage and impaired DNA repair. The sufD * strain also exhibited perturbed intracellular nonchelated Fe pools. Importantly, the sufD* strain did not exhibit altered exoprotein production or altered biofilm formation, but it was attenuated for survival upon challenge by human polymorphonuclear leukocytes. The results presented are consistent with the hypothesis that Fe-S cluster synthesis is a viable target for antimicrobial development. Copyright © 2017 American Society for Microbiology.

The Suf Iron-Sulfur Cluster Biosynthetic System Is Essential in Staphylococcus aureus, and Decreased Suf Function Results in Global Metabolic Defects and Reduced Survival in Human Neutrophils

PubMed Central

Roberts, Christina A.; Al-Tameemi, Hassan M.; Mashruwala, Ameya A.; Rosario-Cruz, Zuelay; Chauhan, Unnati; Sause, William E.; Torres, Victor J.; Belden, William J.

2017-01-01

ABSTRACT Staphylococcus aureus remains a causative agent for morbidity and mortality worldwide. This is in part a result of antimicrobial resistance, highlighting the need to uncover novel antibiotic targets and to discover new therapeutic agents. In the present study, we explored the possibility that iron-sulfur (Fe-S) cluster synthesis is a viable antimicrobial target. RNA interference studies established that Suf (sulfur mobilization)-dependent Fe-S cluster synthesis is essential in S. aureus. We found that sufCDSUB were cotranscribed and that suf transcription was positively influenced by sigma factor B. We characterized an S. aureus strain that contained a transposon inserted in the intergenic space between sufC and sufD (sufD*), resulting in decreased transcription of sufSUB. Consistent with the transcriptional data, the sufD* strain had multiple phenotypes associated with impaired Fe-S protein maturation. They included decreased activities of Fe-S cluster-dependent enzymes, decreased growth in media lacking metabolites that require Fe-S proteins for synthesis, and decreased flux through the tricarboxylic acid (TCA) cycle. Decreased Fe-S cluster synthesis resulted in sensitivity to reactive oxygen and reactive nitrogen species, as well as increased DNA damage and impaired DNA repair. The sufD* strain also exhibited perturbed intracellular nonchelated Fe pools. Importantly, the sufD* strain did not exhibit altered exoprotein production or altered biofilm formation, but it was attenuated for survival upon challenge by human polymorphonuclear leukocytes. The results presented are consistent with the hypothesis that Fe-S cluster synthesis is a viable target for antimicrobial development. PMID:28320837

Rational synthesis of high nuclearity Mo/Fe/S clusters: the reductive coupling approach in the convenient synthesis of (Cl(4)-cat)(2)Mo(2)Fe(6)S(8)(PR(3))(6) [R = Et, (n)Pr, (n)Bu] and the new [(Cl(4)-cat)(2)Mo(2)Fe(2)S(3)O(PEt(3))(3)Cl]-1/2(Fe(PEt(3))(2)(MeCN)(4)) and (Cl(4)-cat)(2)Mo(2)Fe(3)S(5)(PEt(3))(5) clusters.

PubMed

Han, J; Koutmos, M; Ahmad, S A; Coucouvanis, D

2001-11-05

A general method for the synthesis of high nuclearity Mo/Fe/S clusters is presented and involves the reductive coupling of the (Et(4)N)(2)[(Cl(4)-cat)MoOFeS(2)Cl(2)] (I) and (Et(4)N)(2)[Fe(2)S(2)Cl(4)] (II) clusters. The reaction of I and II with Fe(PR(3))(2)Cl(2) or sodium salts of noncoordinating anions such as NaPF(6) or NaBPh(4) in the presence of PR(3) (R = Et, (n)Pr, or (n)Bu) affords (Cl(4)-cat)(2)Mo(2)Fe(6)S(8)(PR(3))(6) [R = Et (IIIa), (n)Pr (IIIb), (n)Bu (IIIc)], Fe(6)S(6)(PEt(3))(4)Cl(2) (IV) and (PF(6))[Fe(6)S(8)(P(n)Pr(3))(6)] (V) as byproducts. The isolation of (Et(4)N)[Fe(PEt(3))Cl(3)] (VI), NaCl, and SPEt(3) supports a reductive coupling mechanism. Cluster IV and V also have been synthesized by the reductive self-coupling of compound II. The reductive coupling reaction between I and II by PEt(3) and NaPF(6) in a 1:1 ratio produces the (Et(4)N)(2)[(Cl(4)-cat)Mo(L)Fe(3)S(4)Cl(3)] clusters [L = MeCN (VIIa), THF (VIIb)]. The hitherto unknown [(Cl(4)-cat)(2)Mo(2)Fe(2)S(3)O(PEt(3))(3)Cl](+) cluster (VIII) has been isolated as the 2:1 salt of the (Fe(PEt(3))(2)(MeCN)(4))(2+) cation after the reductive self-coupling reaction of I in the presence of Fe(PEt(3))(2)Cl(2). Cluster VIII crystallizes in the monoclinic space group P2(1)/c with a = 11.098(3) A, b = 22.827(6) A, c = 25.855(6) A, beta = 91.680(4) degrees, and Z = 4. The formal oxidation states of metal atoms in VIII have been assigned as Mo(III), Mo(IV), Fe(II), and Fe(III) on the basis of zero-field Mössbauer spectra. The Fe(PEt(3))(2)(MeCN)(4) cation of VIII is also synthesized independently, isolated as the BPh(4)(-) salt (IX), and has been structurally characterized. The reductive coupling of compound I also affords in low yield the new (Cl(4)-cat)(2)Mo(2)Fe(3)S(5)(PEt(3))(5) cluster (X) as a byproduct. Cluster X crystallizes in the monoclinic space group P2(1)/n with a = 14.811(3) A, b = 22.188(4) A, c = 21.864(4) A, beta = 100.124(3) degrees, and Z = 4 and the structure shows very short Mo-Fe, Fe-Fe, Mo-S, Fe-S bonds. The oxidation states of the metal atoms in this neutral cluster (X) have been assigned as Mo(IV)Mo(III)Fe(II)Fe(II)Fe(III) based on zero-field Mössbauer and magnetic measurement. All Fe atoms are high spin and two of the three Fe-Fe distances are found at 2.4683(9) A and 2.4721(9) A.

On the size-dependent magnetism and all-optical magnetization switching of transition-metal silicide nanostructures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Glushkov, G. I.; Tuchin, A. V.; Popov, S. V.

Theoretical investigations of the electronic structure, synthesis, and all-optical magnetization switching of transition-metal silicide nanostructures are reported. The magnetic moment of the nanostructures is studied as a function of the silicide cluster size and configuration. The experimentally demonstrated magnetization switching of nanostructured nickel silicide by circularly polarized light makes it possible to create high-speed storage devices with high density data recording.

Synthesis, Characterization, and Reactivity of Functionalized Trinuclear Iron–Sulfur Clusters – A New Class of Bioinspired Hydrogenase Models

PubMed Central

Kaiser, Manuel; Knör, Günther

2015-01-01

The air- and moisture-stable iron–sulfur carbonyl clusters Fe3S2(CO)7(dppm) (1) and Fe3S2(CO)7(dppf) (2) carrying the bisphosphine ligands bis(diphenylphosphanyl)methane (dppm) and 1,1′-bis(diphenylphosphanyl)ferrocene (dppf) were prepared and fully characterized. Two alternative synthetic routes based on different thionation reactions of triiron dodecacarbonyl were tested. The molecular structures of the methylene-bridged compound 1 and the ferrocene-functionalized derivative 2 were determined by single-crystal X-ray diffraction. The catalytic reactivity of the trinuclear iron–sulfur cluster core for proton reduction in solution at low overpotential was demonstrated. These deeply colored bisphosphine-bridged sulfur-capped iron carbonyl systems are discussed as promising candidates for the development of new bioinspired model compounds of iron-based hydrogenases. PMID:26512211

UV-light-driven prebiotic synthesis of iron-sulfur clusters

NASA Astrophysics Data System (ADS)

Bonfio, Claudia; Valer, Luca; Scintilla, Simone; Shah, Sachin; Evans, David J.; Jin, Lin; Szostak, Jack W.; Sasselov, Dimitar D.; Sutherland, John D.; Mansy, Sheref S.

2017-12-01

Iron-sulfur clusters are ancient cofactors that play a fundamental role in metabolism and may have impacted the prebiotic chemistry that led to life. However, it is unclear whether iron-sulfur clusters could have been synthesized on prebiotic Earth. Dissolved iron on early Earth was predominantly in the reduced ferrous state, but ferrous ions alone cannot form polynuclear iron-sulfur clusters. Similarly, free sulfide may not have been readily available. Here we show that UV light drives the synthesis of [2Fe-2S] and [4Fe-4S] clusters through the photooxidation of ferrous ions and the photolysis of organic thiols. Iron-sulfur clusters coordinate to and are stabilized by a wide range of cysteine-containing peptides and the assembly of iron-sulfur cluster-peptide complexes can take place within model protocells in a process that parallels extant pathways. Our experiments suggest that iron-sulfur clusters may have formed easily on early Earth, facilitating the emergence of an iron-sulfur-cluster-dependent metabolism.

Understanding ligand effects in gold clusters using mass spectrometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnson, Grant E.; Laskin, Julia

This review summarizes recent research on the influence of phosphine ligands on the size, stability, and reactivity of gold clusters synthesized in solution. Sub-nanometer clusters exhibit size- and composition-dependent properties that are unique from those of larger nanoparticles. The highly tunable properties of clusters and their high surface-to-volume ratio make them promising candidates for a variety of technological applications. However, because “each-atom-counts” toward defining cluster properties it is critically important to develop robust synthesis methods to efficiently prepare clusters of predetermined size. For decades phosphines have been known to direct the size-selected synthesis of gold clusters. Despite the preparation ofmore » numerous species it is still not understood how different functional groups at phosphine centers affect the size and properties of gold clusters. Using electrospray ionization mass spectrometry (ESI-MS) it is possible to characterize the effect of ligand substitution on the distribution of clusters formed in solution at defined reaction conditions. In addition, ligand exchange reactions on preformed clusters may be monitored using ESI-MS. Collision induced dissociation (CID) may also be employed to obtain qualitative insight into the fragmentation of mixed ligand clusters and the relative binding energies of differently substituted phosphines. Quantitative ligand binding energies and cluster stability may be determined employing surface induced dissociation (SID) in a custom-built Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR-MS). Rice-Ramsperger-Kassel-Marcus (RRKM) based modeling of the SID data allows dissociation energies and entropy values to be extracted that may be compared with the results of high-level theoretical calculations. The charge reduction and reactivity of atomically precise gold clusters, including partially ligated species generated in the gas-phase by in source CID, on well-defined surfaces may be explored using ion soft landing (SL) in a custom-built instrument combined with in situ time of flight secondary ion mass spectrometry (TOF-SIMS). Jointly, this multipronged experimental approach allows characterization of the full spectrum of relevant phenomena including cluster synthesis, ligand exchange, thermochemistry, surface immobilization, and reactivity. The fundamental insights obtained from this work will facilitate the directed synthesis of gold clusters with predetermined size and properties for specific applications.« less

Fluorescent DNA-templated silver nanoclusters

NASA Astrophysics Data System (ADS)

Lin, Ruoqian

Because of the ultra-small size and biocompatibility of silver nanoclusters, they have attracted much research interest for their applications in biolabeling. Among the many ways of synthesizing silver nanoclusters, DNA templated method is particularly attractive---the high tunability of DNA sequences provides another degree of freedom for controlling the chemical and photophysical properties. However, systematic studies about how DNA sequences and concentrations are controlling the photophysical properties are still lacking. The aim of this thesis is to investigate the binding mechanisms of silver clusters binding and single stranded DNAs. Here in this thesis, we report synthesis and characterization of DNA-templated silver nanoclusters and provide a systematic interrogation of the effects of DNA concentrations and sequences, including lengths and secondary structures. We performed a series of syntheses utilizing five different sequences to explore the optimal synthesis condition. By characterizing samples with UV-vis and fluorescence spectroscopy, we achieved the most proper reactants ratio and synthesis conditions. Two of them were chosen for further concentration dependence studies and sequence dependence studies. We found that cytosine-rich sequences are more likely to produce silver nanoclusters with stronger fluorescence signals; however, sequences with hairpin secondary structures are more capable in stabilizing silver nanoclusters. In addition, the fluorescence peak emission intensities and wavelengths of the DNA templated silver clusters have sequence dependent fingerprints. This potentially can be applied to sequence sensing in the future. However all the current conclusions are not warranted; there is still difficulty in formulating general rules in DNA strand design and silver nanocluster production. Further investigation of more sequences could solve these questions in the future.

Monodisperse Iron Oxide Nanoparticles by Thermal Decomposition: Elucidating Particle Formation by Second-Resolved in Situ Small-Angle X-ray Scattering

PubMed Central

2017-01-01

The synthesis of iron oxide nanoparticles (NPs) by thermal decomposition of iron precursors using oleic acid as surfactant has evolved to a state-of-the-art method to produce monodisperse, spherical NPs. The principles behind such monodisperse syntheses are well-known: the key is a separation between burst nucleation and growth phase, whereas the size of the population is set by the precursor-to-surfactant ratio. Here we follow the thermal decomposition of iron pentacarbonyl in the presence of oleic acid via in situ X-ray scattering. This method allows reaction kinetics and precursor states to be followed with high time resolution and statistical significance. Our investigation demonstrates that the final particle size is directly related to a phase of inorganic cluster formation that takes place between precursor decomposition and particle nucleation. The size and concentration of clusters were shown to be dependent on precursor-to-surfactant ratio and heating rate, which in turn led to differences in the onset of nucleation and concentration of nuclei after the burst nucleation phase. This first direct observation of prenucleation formation of inorganic and micellar structures in iron oxide nanoparticle synthesis by thermal decomposition likely has implications for synthesis of other NPs by similar routes. PMID:28572705

A Role for Iron-Sulfur Clusters in the Regulation of Transcription Factor Yap5-dependent High Iron Transcriptional Responses in Yeast*

PubMed Central

Li, Liangtao; Miao, Ren; Bertram, Sophie; Jia, Xuan; Ward, Diane M.; Kaplan, Jerry

2012-01-01

Yeast respond to increased cytosolic iron by activating the transcription factor Yap5 increasing transcription of CCC1, which encodes a vacuolar iron importer. Using a genetic screen to identify genes involved in Yap5 iron sensing, we discovered that a mutation in SSQ1, which encodes a mitochondrial chaperone involved in iron-sulfur cluster synthesis, prevented expression of Yap5 target genes. We demonstrated that mutation or reduced expression of other genes involved in mitochondrial iron-sulfur cluster synthesis (YFH1, ISU1) prevented induction of the Yap5 response. We took advantage of the iron-dependent catalytic activity of Pseudaminobacter salicylatoxidans gentisate 1,2-dioxygenase expressed in yeast to measure changes in cytosolic iron. We determined that reductions in iron-sulfur cluster synthesis did not affect the activity of cytosolic gentisate 1,2-dioxygenase. We show that loss of activity of the cytosolic iron-sulfur cluster assembly complex proteins or deletion of cytosolic glutaredoxins did not reduce expression of Yap5 target genes. These results suggest that the high iron transcriptional response, as well as the low iron transcriptional response, senses iron-sulfur clusters. PMID:22915593

Complete genome sequence of Nitrosospira multiformis, an ammonia-oxidizing bacterium from the soil environment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Norton, Jeanette M.; Klotz, Martin G; Stein, Lisa Y

2008-01-01

The complete genome of the ammonia-oxidizing bacterium, Nitrosospira multiformis (ATCC 25196T), consists of a circular chromosome and three small plasmids totaling 3,234,309 bp and encoding 2827 putative proteins. Of these, 2026 proteins have predicted functions and 801 are without conserved functional domains, yet 747 of these have similarity to other predicted proteins in databases. Gene homologs from Nitrosomonas europaea and N. eutropha were the best match for 42% of the predicted genes in N. multiformis. The genome contains three nearly identical copies of amo and hao gene clusters as large repeats. Distinguishing features compared to N. europaea include: the presencemore » of gene clusters encoding urease and hydrogenase, a RuBisCO-encoding operon of distinctive structure and phylogeny, and a relatively small complement of genes related to Fe acquisition. Systems for synthesis of a pyoverdine-like siderophore and for acyl-homoserine lactone were unique to N. multiformis among the sequenced AOB genomes. Gene clusters encoding proteins associated with outer membrane and cell envelope functions including transporters, porins, exopolysaccharide synthesis, capsule formation and protein sorting/export were abundant. Numerous sensory transduction and response regulator gene systems directed towards sensing of the extracellular environment are described. Gene clusters for glycogen, polyphosphate and cyanophycin storage and utilization were identified providing mechanisms for meeting energy requirements under substrate-limited conditions. The genome of N. multiformis encodes the core pathways for chemolithoautotrophy along with adaptations for surface growth and survival in soil environments.« less

Synthesis and characterization of mangan oxide coated sand from Capkala kaolin

NASA Astrophysics Data System (ADS)

Destiarti, Lia; Wahyuni, Nelly; Prawatya, Yopa Eka; Sasri, Risya

2017-03-01

Synthesis and characterization of mangan oxide coated sand from quartz sand fraction of Capkala kaolin has been conducted. There were two methods on synthesis of Mangan Oxide Coated Sand (MOCS) from Capkala Kaolin compared in this research. Characterization of MOCS was done by using Scanning Electron Microscope/Energy Dispersive X-Ray Spectrometer (SEM/EDX) and X-Ray Diffraction (XRD). The MOCS was tested to reduce phosphate in laundry waste. The result showed that the natural sand had bigger agregates and a relatively uniform structural orientation while both MOCS had heterogen structural orientation and manganese oxide formed in cluster. Manganese in first and second methods were 1,93% and 2,63%, respectively. The XRD spectrum showed clear reflections at 22,80°, 36,04°, 37,60° and a broad band at 26,62° (SiO2). Based on XRD spectrum, it can be concluded that mineral constituents of MOCS was verified corresponding to pyrolusite (MnO2). The former MOCS could reduce almost 60% while the later could reduce 70% phosphate in laundry waste.

Synthesis of Nine-atom Deltahedral Zintl Ions of Germanium and their Functionalization with Organic Groups

PubMed Central

Gillett-Kunnath, Miriam M.; Sevov, Slavi C.

2012-01-01

Although the first studies of Zintl ions date between the late 1890's and early 1930's they were not structurally characterized until many years later.1,2 Their redox chemistry is even younger, just about ten years old, but despite this short history these deltahedral clusters ions E9n- (E = Si, Ge, Sn, Pb; n = 2, 3, 4) have already shown interesting and diverse reactivity and have been at the forefront of rapidly developing and exciting new chemistry.3-6 Notable milestones are the oxidative coupling of Ge94- clusters to oligomers and infinite chains,7-19 their metallation,14-16,20-25 capping by transition-metal organometallic fragments,26-34 insertion of a transition-metal atom at the center of the cluster which is sometimes combined with capping and oligomerization,35-47 addition of main-group organometallic fragments as exo-bonded substituents,48-50 and functionalization with various organic residues by reactions with organic halides and alkynes.51-58 This latter development of attaching organic fragments directly to the clusters has opened up a new field, namely organo-Zintl chemistry, that is potentially fertile for further synthetic explorations, and it is the step-by-step procedure for the synthesis of germanium-divinyl clusters described herein. The initial steps outline the synthesis of an intermetallic precursor of K4Ge9 from which the Ge94- clusters are extracted later in solution. This involves fused-silica glass blowing, arc-welding of niobium containers, and handling of highly air-sensitive materials in a glove box. The air-sensitive K4Ge9 is then dissolved in ethylenediamine in the box and then alkenylated by a reaction with Me3SiC≡CSiMe3. The reaction is followed by electrospray mass spectrometry while the resulting solution is used for obtaining single crystals containing the functionalized clusters [H2C=CH-Ge9-CH=CH2]2-. For this purpose the solution is centrifuged, filtered, and carefully layered with a toluene solution of 18-crown-6. Left undisturbed for a few days, the so-layered solutions produced orange crystalline blocks of [K(18-crown-6)]2[Ge9(HCCH2)2]•en which were characterized by single-crystal X-ray diffraction. The process highlights standard reaction techniques, work-up, and analysis towards functionalized deltahedral Zintl clusters. It is hoped that it will help towards further development and understanding of these compounds in the community at large. PMID:22349121

Elimination-Fusion Self-Assembly of a Nanometer-Scale 72-Nucleus Silver Cluster Caging a Pair of [EuW10 O36 ]9- Polyoxometalates.

PubMed

Zhang, Shan-Shan; Su, Hai-Feng; Wang, Zhi; Wang, Xing-Po; Chen, Wen-Xian; Zhao, Quan-Qin; Tung, Chen-Ho; Sun, Di; Zheng, Lan-Sun

2018-02-06

The largest known polyoxometalate (POM)-templated silver-alkynyl cluster, [(EuW 10 O 36 ) 2 @Ag 72 (tBuC≡C) 48 Cl 2 ⋅4 BF 4 ] (SD/Ag20), was isolated under solvothermal conditions and structurally characterized. It was confirmed by single-crystal X-ray diffraction (SCXRD) as a {EuW 10 } 2 -in-{Ag 72 } clusters-in-cluster rod-like compound. The high-resolution electrospray ionization mass spectrometry (HR-ESI-MS) shows that such a double anion-templated cluster is assembled from a crucial single anion-templated Ag 42 intermediate in the solution. The crystallization of Ag 42 species (SD/Ag21), followed by SCXRD, gave an important clue about the assembly route of SD/Ag20 in solution: the Ag 42 cluster eliminates six silver atoms laterally, then fuses together at the vacant face to form the final Ag 72 cluster (elimination-fusion mechanism). The characteristic emission of [EuW 10 O 36 ] 9- is well maintained in SD/Ag20. This work not only provides a new method for the synthesis of larger silver clusters as well as the functional integration of the silver cluster and POMs, but also gives deep insights about the high-nuclear silver cluster assembly mechanism. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Synthesis, Structure and Electrochemistry of Tetranuclear Oxygen-Centered Copper(II) Clusters with Acetylacetone and Benz-pyrazole Hydrolyzed Derivatives as Ligand.

PubMed

Vafazadeh, Rasoul; Willis, Anthony C

2016-01-01

Two copper(II) clusters Cu(4)OCl(6)(pyrazole)4, 1, and Cu(4)OBr(6)(Br-pyrazole)4, 2, have been synthesized by reacting acetylacetone and benzohydrazide (1:1 ratio) with CuX(2) (X = Cl for 1 and X= Br for 2) in methanol solutions. The structures of both clusters have been established by X-ray crystallography. The clusters contain four Cu, one O, six μ(2)-X atoms, and four pyrazole ligands. The pyrazoles was prepared in situ by the reaction of acetylacetone with benzohydrazide in methanol under reflux. In 2, the methine hydrogens of the pyrazole ligands have been replaced by bromine atoms. The four copper atoms encapsulate the central O atom in a tetrahedral arrangement. All copper atoms are five-coordinate and have similar coordination environments with slightly distorted trigonal bipyramidal geometry. The cyclic voltammogram of the clusters 1 and 2 show a one-electron quasi-reversible reduction wave in the region 0.485 to 0.731 V, and a one-electron quasi-reversible oxidation wave in the region 0.767 to 0.898 V. In 1, one irreversible oxidative response is observed on the positive of side of the voltammogram at 1.512 V and this can be assigned to Cu(II) to Cu(III) oxidation.

Conductivity and properties of polysiloxane-polyether cluster-LiTFSI networks as hybrid polymer electrolytes

NASA Astrophysics Data System (ADS)

Boaretto, Nicola; Joost, Christine; Seyfried, Mona; Vezzù, Keti; Di Noto, Vito

2016-09-01

This report describes the synthesis and the properties of a series of polymer electrolytes, composed of a hybrid inorganic-organic matrix doped with LiTFSI. The matrix is based on ring-like oligo-siloxane clusters, bearing pendant, partially cross-linked, polyether chains. The dependency of the thermo-mechanic and of the transport properties on several structural parameters, such as polyether chains' length, cross-linkers' concentration, and salt concentration is studied. Altogether, the materials show good thermo-mechanical and electrochemical stabilities, with conductivities reaching, at best, 8·10-5 S cm-1 at 30 °C. In conclusion, the cell performances of one representative sample are shown. The scope of this report is to analyze the correlations between structure and properties in networked and hybrid polymer electrolytes. This could help the design of optimized polymer electrolytes for application in lithium metal batteries.

Structure of mono- and bimetallic heterogeneous catalysts based on noble metals obtained by means of fluid technology and metal-vapor synthesis

NASA Astrophysics Data System (ADS)

Said-Galiev, E. E.; Vasil'kov, A. Yu.; Nikolaev, A. Yu.; Lisitsyn, A. I.; Naumkin, A. V.; Volkov, I. O.; Abramchuk, S. S.; Lependina, O. L.; Khokhlov, A. R.; Shtykova, E. V.; Dembo, K. A.; Erkey, C.

2012-10-01

Monometallic nanocomposites are obtained with the use of supercritical carbon dioxide (fluid technique) and metal-vapor synthesis (MVS), while bimetallic nanocomposites of Pt and Au noble metals and γ-Al2O3 oxide matrix are synthesized by a combination of these two methods. The structures, concentrations, and chemical states of metal atoms in composites are studied by means of small-angle X-ray scattering (SAXS), transparent electron microscopy (TEM), X-ray fluorescent analysis (XFA), and X-ray photoelectron spectroscopy (XPS). The neutral state of metal atoms in clusters is shown by XPS and their size distribution is found according to SAXS; as is shown, it is determined by the pore sizes of the oxide matrices and lies in the range of 1 to 50 nm. The obtained composites manifest themselves as effective catalysts in the oxidation of CO to CO2.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuzmin, Stanislav L.; Wesolowski, Michal J.; Duley, Walter W.

A new type of metal-organic composition consisting of clusters of nanoparticles has been synthesised by laser irradiation of metallocene/benzene solutions. The metallocene molecules in this reaction become the source of the metal. Exposure to high-energy femtosecond laser pulses dehydrogenate benzene molecules and initiate the high-temperature high-pressure conditions that results in the synthesis of new materials. Irradiation experiments have been carried out on ferrocene/benzene and on other solutions. With ferrocene the synthesis of a new compound has been confirmed by X-ray powder diffraction as the peaks detected do not correspond to any known substance in the Crystallography Open Database. Theoretical simulationmore » of the periodic structure of this new carbide predicts that it has hexagonal symmetry and a unit cell with a = 3.2A and c =2.8A. The exact structure is still uncertain but may be determined from scanning tunneling microscope (STM) studies.« less

Genome sequencing and secondary metabolism of the postharvest pathogen Penicillium griseofulvum.

PubMed

Banani, Houda; Marcet-Houben, Marina; Ballester, Ana-Rosa; Abbruscato, Pamela; González-Candelas, Luis; Gabaldón, Toni; Spadaro, Davide

2016-01-05

Penicillium griseofulvum is associated in stored apples with blue mould, the most important postharvest disease of pome fruit. This pathogen can simultaneously produce both detrimental and beneficial secondary metabolites (SM). In order to gain insight into SM synthesis in P. griseofulvum in vitro and during disease development on apple, we sequenced the genome of P. griseofulvum strain PG3 and analysed important SM clusters. PG3 genome sequence (29.3 Mb) shows that P. griseofulvum branched off after the divergence of P. oxalicum but before the divergence of P. chrysogenum. Genome-wide analysis of P. griseofulvum revealed putative gene clusters for patulin, griseofulvin and roquefortine C biosynthesis. Furthermore, we quantified the SM production in vitro and on apples during the course of infection. The expression kinetics of key genes of SM produced in infected apple were examined. We found additional SM clusters, including those potentially responsible for the synthesis of penicillin, yanuthone D, cyclopiazonic acid and we predicted a cluster putatively responsible for the synthesis of chanoclavine I. These findings provide relevant information to understand the molecular basis of SM biosynthesis in P. griseofulvum, to allow further research directed to the overexpression or blocking the synthesis of specific SM.

Synthesis and structure of an extended cluster lead(II) carboxylate, [Pb((CO){sub 9}Co{sub 3}({mu}{sub 3}-CCO{sub 2})){sub 2}]{sub n}. Role of core metals in cluster-derived hydrogenation catalysts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xinjian Lei; Maoyu Shang; Fehlner, T.P.

The reaction of lead acetate with (CO){sub 9}Co{sub 3}({mu}{sub 3}-CCOOH) leads to the formation of [Pb((CO){sub 9}Co{sub 3}({mu}{sub 3}-CCO{sub 2})){sub 2}]{sub n}, I, in high yield. The structure of I exhibits unusual six-coordinate Pb(II) centers with two asymmetrical chelating cluster carboxylates (C{sub 22}Co{sub 6}PbO{sub 22}; triclinic P1; a = 8.119(1), b = 14.346(2), c = 14.660(2) {Angstrom}; {alpha} = 102.18(1), {beta} = 99.01(1), {gamma} = 97.30(1){degrees}; Z = 2). One oxygen of each cluster carboxylate ligand bridges between adjacent lead atoms such that a chainlike extended structure is found in the solid state without the presence of solvent or water.more » I is converted stepwide on pyrolysis into two metastable forms of solid materials (designated LT and HT), each of which has been characterized spectroscopically. The hydrogenation of 2-butenal as a test reaction shows that the LT catalyst exhibits selectivities similar to previous LT materials derived from other cobalt cluster metal carboxylates and that the HT material is totally inactive. The observed release of the lead core metal under HT activation conditions totally inactivates the catalyst and demonstrates exposure of the core metal in the HT form of these novel catalysts.« less

Dppm-Assisted synthesis and reactivity of bimetallic M-Mo, M-W, M-Co, and M-Mn (M = Pt, Pd) complexes. Crystal structure of [([eta][sup 2]-dppm)[ovr Pt([mu]-dppm)W](CO)[sub 2]Cp][PF[sub 6

DOE Office of Scientific and Technical Information (OSTI.GOV)

Braunstein, P.; de Meric de Bellefon, C.; Oswald, B.

1993-04-28

Heterometallic carbonyl complexes and clusters were prepared by reaction of dppm (dppm = Ph[sub 2]PCH[sub 2]PPh[sub 2]) with linear trinuclear chain complexes trans-[Pt(or Pd)[l brace]m(CO)[r brace][sub 2](NCPh)[sub 2

Genetic and Biochemical Map for the Biosynthesis of Occidiofungin, an Antifungal Produced by Burkholderia contaminans Strain MS14 ▿†

PubMed Central

Gu, Ganyu; Smith, Leif; Liu, Aixin; Lu, Shi-En

2011-01-01

A striking feature of Burkholderia contaminans strain MS14 is the production of a glycolipopeptide named occidiofungin. Occidiofungin has a broad range of antifungal activities against plant and animal pathogens. In this study, a complete covalent structure characterization and identification of the whole genomic DNA region for the occidiofungin gene (ocf) cluster are described. Discovery of the presence of 2,4-diaminobutyric acid and 3-chloro-β-hydroxytyrosine and elucidation of the structure of a novel C18 fatty amino acid residue have been achieved. In addition, seven additional putative open reading frames (the genes from ocfI to ocfN [ocfI-N] and ORF16) were identified. Transcription of all the putative genes ocfI-N identified in the region except ORF16 was regulated by both ambR1 and ambR2. Elucidation of the structure and the ocf gene cluster provides insight into the biosynthesis of occidiofungin and promotes future aims at understanding the biosynthetic machinery. This work provides new avenues for optimizing the production and synthesis of structural analogs of occidiofungin. PMID:21742901

Structural direction of hybrid organic-inorganic materials: Synthesis of vanadium oxyfluoride, copper vanadate, and copper molybdate solid state materials through solvuthermal and solution methods

NASA Astrophysics Data System (ADS)

Deburgomaster, Paul

The vast structural complexity of inorganic oxides with structure directing organocations, nitrogen containing ligands and organophosphonate ligands was explored. The hydrothermal reaction conditions utilized herein include the variables of temperature, pH, fill volume and stoichiometry. The systems studied included: (1) the complex materials rendered from reactions of organoamine cations on the structure of vanadium oxides, oxyfluorides and fluorides. As with other systems, the influence of the mineralizer HF was not limited to pH as fluorine incorporation was not uncommon. In specific cases this coincided with reduction of vanadium sites. (2) The copper-organonitrogen ligand/vanadium oxide/aromatic phosphonate system has been studied. The rigid aromatic di- and tri-phosphonate tethers have provided a series of materials which are structurally distinct from the previously investigated aliphatic series. The inclusion of copper-coordinated nitrogen bi- and tri-dentate ligands also provided structural diversity. Product composition was highly influenced by the HF/V ratio. A similar study was conducted with the ligand 1,4-carboxy-phenylphosphonic acid. (3) The preparation of a series of bimetallic organic-inorganic hybrid materials of the M(II)/VxOy/organonitrogen ligand class was further evidence of the utility of thermodynamically driven hydrothermal synthesis. (4) While decomposition of the spherical Keplerate molybdenum clusters is encountered under hydrothermal conditions, this highly soluble form of molybdate was investigated for the development of hybrid organic-inorganic room temperature solution synthesis.

Giant Virus Megavirus chilensis Encodes the Biosynthetic Pathway for Uncommon Acetamido Sugars*

PubMed Central

Piacente, Francesco; De Castro, Cristina; Jeudy, Sandra; Molinaro, Antonio; Salis, Annalisa; Damonte, Gianluca; Bernardi, Cinzia; Abergel, Chantal; Tonetti, Michela G.

2014-01-01

Giant viruses mimicking microbes, by the sizes of their particles and the heavily glycosylated fibrils surrounding their capsids, infect Acanthamoeba sp., which are ubiquitous unicellular eukaryotes. The glycans on fibrils are produced by virally encoded enzymes, organized in gene clusters. Like Mimivirus, Megavirus glycans are mainly composed of virally synthesized N-acetylglucosamine (GlcNAc). They also contain N-acetylrhamnosamine (RhaNAc), a rare sugar; the enzymes involved in its synthesis are encoded by a gene cluster specific to Megavirus close relatives. We combined activity assays on two enzymes of the pathway with mass spectrometry and NMR studies to characterize their specificities. Mg534 is a 4,6-dehydratase 5-epimerase; its three-dimensional structure suggests that it belongs to a third subfamily of inverting dehydratases. Mg535, next in the pathway, is a bifunctional 3-epimerase 4-reductase. The sequential activity of the two enzymes leads to the formation of UDP-l-RhaNAc. This study is another example of giant viruses performing their glycan synthesis using enzymes different from their cellular counterparts, raising again the question of the origin of these pathways. PMID:25035429

Discovery of a widely distributed toxin biosynthetic gene cluster

PubMed Central

Lee, Shaun W.; Mitchell, Douglas A.; Markley, Andrew L.; Hensler, Mary E.; Gonzalez, David; Wohlrab, Aaron; Dorrestein, Pieter C.; Nizet, Victor; Dixon, Jack E.

2008-01-01

Bacteriocins represent a large family of ribosomally produced peptide antibiotics. Here we describe the discovery of a widely conserved biosynthetic gene cluster for the synthesis of thiazole and oxazole heterocycles on ribosomally produced peptides. These clusters encode a toxin precursor and all necessary proteins for toxin maturation and export. Using the toxin precursor peptide and heterocycle-forming synthetase proteins from the human pathogen Streptococcus pyogenes, we demonstrate the in vitro reconstitution of streptolysin S activity. We provide evidence that the synthetase enzymes, as predicted from our bioinformatics analysis, introduce heterocycles onto precursor peptides, thereby providing molecular insight into the chemical structure of streptolysin S. Furthermore, our studies reveal that the synthetase exhibits relaxed substrate specificity and modifies toxin precursors from both related and distant species. Given our findings, it is likely that the discovery of similar peptidic toxins will rapidly expand to existing and emerging genomes. PMID:18375757

Analysis of the project synthesis goal cluster orientation and inquiry emphasis of elementary science textbooks

NASA Astrophysics Data System (ADS)

Staver, John R.; Bay, Mary

The purpose of this descriptive study was to examine selected units of commonly used elementary science texts, using the Project Synthesis goal clusters as a framework for part of the examination. An inquiry classification scheme was used for the remaining segment. Four questions were answered: (1) To what extent do elementary science textbooks focus on each Project Synthesis goal cluster? (2) In which part of the text is such information found? (3) To what extent are the activities and experiments merely verifications of information already introduced in the text? (4) If inquiry is present in an activity, then what is the level of such inquiry?Eleven science textbook series, which comprise approximately 90 percent of the national market, were selected for analysis. Two units, one primary (K-3) and one intermediate (4-6), were selected for analysis by first identifying units common to most series, then randomly selecting one primary and one intermediate unit for analysis.Each randomly selected unit was carefully read, using the sentence as the unit of analysis. Each declarative and interrogative sentence in the body of the text was classified as: (1) academic; (2) personal; (3) career; or (4) societal in its focus. Each illustration, except those used in evaluation items, was similarly classified. Each activity/experiment and each miscellaneous sentence in end-of-chapter segments labelled review, summary, evaluation, etc., were similarly classified. Finally, each activity/experiment, as a whole, was categorized according to a four-category inquiry scheme (confirmation, structured inquiry, guided inquiry, open inquiry).In general, results of the analysis are: (1) most text prose focuses on academic science; (2) most remaining text prose focuses on the personal goal cluster; (3) the career and societal goal clusters receive only minor attention; (4) text illustrations exhibit a pattern similar to text prose; (5) text activities/experiments are academic in orientation, almost to the exclusion of other goal clusters; (6) end-of-chapter sentences are largely academic; (7) inquiry is absent or present only in limited forms in text activities/experiments; and (8) texts allocate only a minor portion of space to activities/experiments. Detailed findings are given as numeral, percentage, and decimal values. Discussion focuses on the implications of the results and a comparison of NSTA recommendations with the results of this analysis.

Silver Clusters in Zeolites: From Self-Assembly to Ground-Breaking Luminescent Properties.

PubMed

Coutiño-Gonzalez, Eduardo; Baekelant, Wouter; Steele, Julian A; Kim, Cheol Woong; Roeffaers, Maarten B J; Hofkens, Johan

2017-09-19

Interest for functional silver clusters (Ag-CLs) has rapidly grown over years due to large advances in the field of nanoscale fabrication and materials science. The continuous development of strategies to fabricate small-scale silver clusters, together with their interesting physicochemical properties (molecule-like discrete energy levels, for example), make them very attractive for a wide variety of applied research fields, from biotechnology and the environmental sciences to fundamental chemistry and physics. Apart from useful catalytic properties, silver clusters (Ag n , n < 10) were recently shown to also exhibit exceptional optical properties. The optical properties and performance of Ag-CLs offer strong potential for their integration into appealing micro(nano)-optoelectronic devices. To date, however, the rational design and directed synthesis of Ag-CLs with specific functionalities has remained elusive. The inability for rational design stems mainly from a lack of understanding of their novel atomic-scale phenomena. This is because accurately studying silver cluster systems at such a scale is hindered by the perturbations introduced during exposure to various experimental probes. For instance, silver possesses a strong tendency to cluster and form ever-larger Ag aggregates while probed with high-energy electron beams and X-ray irradiation. As well, there exists a need to provide a stabilizing environment for which Ag n δ+ clusters can persist, setting up a complex interacting guest-host system, as isolated silver clusters are confined within a suitable hosting medium. Fundamental research into Ag n δ+ formation mechanisms and their important optical properties is paramount to establishing truly informed synthesis protocols. Over recent years, we have developed several protocols for the ship-in-a-bottle synthesis of highly luminescent Ag-CLs within the microporous interiors of zeolite frameworks. This approach has yielded materials displaying a wide variety of optical properties, offering a spectrum of possible applications, from nano(micro)photonic devices to smart luminescent labels and sensors. The versatility of the Ag-zeolite multicomponent system is directly related to the intrinsic and complex tunability of the system as a whole. There are several key zeolite parameters that confer properties to the clusters, namely, the framework Si/Al ratio, choice of counterbalancing ions, silver loading, and zeolite topology, and cannot be overlooked. This Account is intended to shed light on the current state-of-the-art of luminescent Ag-CLs confined in zeolitic matrices, emphasizing the use of combinatorial approaches to overcome problems associated with the correct characterization and correlation of their structural, electronic, and photoluminescence properties, all to establish the important design principles for developing functional silver-zeolite-based materials. Additionally, examples of emerging applications and future perspectives for functional luminescent Ag-zeolite materials are addressed in this Account.

The properties and applications of nanodiamonds.

PubMed

Mochalin, Vadym N; Shenderova, Olga; Ho, Dean; Gogotsi, Yury

2011-12-18

Nanodiamonds have excellent mechanical and optical properties, high surface areas and tunable surface structures. They are also non-toxic, which makes them well suited to biomedical applications. Here we review the synthesis, structure, properties, surface chemistry and phase transformations of individual nanodiamonds and clusters of nanodiamonds. In particular we discuss the rational control of the mechanical, chemical, electronic and optical properties of nanodiamonds through surface doping, interior doping and the introduction of functional groups. These little gems have a wide range of potential applications in tribology, drug delivery, bioimaging and tissue engineering, and also as protein mimics and a filler material for nanocomposites.

Chemical evolution of Mg isotopes versus the time variation of the fine structure constant.

PubMed

Ashenfelter, T; Mathews, Grant J; Olive, Keith A

2004-01-30

We show that the synthesis of (25,26)Mg at the base of the convective envelope in low-metallicity asymptotic giant branch stars can produce the isotopic ratios needed to explain the low-z subset (with z<1.8) of the many-multiplet data from quasar absorption systems without invoking a time variation of the fine structure constant. This is supported by observations of high abundances of the neutron-rich Mg isotopes in metal-poor globular-cluster stars. We conclude that the quasar absorption spectra may be providing interesting information on the nucleosynthetic history of such systems.

Stabilization of flat aromatic Si6 rings analogous to benzene: ab initio theoretical prediction.

PubMed

Zdetsis, Aristides D

2007-12-07

It is shown by ab initio calculations, based on density functional (DFT/B3LYP), and high level coupled-cluster [CCSD(T)] and quadratic CI [QCISD(T)] methods, that flat aromatic silicon structures analogous to benzene (C6H6) can be stabilized in the presence of lithium. The resulting planar Si6Li6 structure is both stable and aromatic, sharing many key characteristics with benzene. To facilitate possible synthesis and characterization of these species, routes of formation with high exothermicity are suggested and several spectral properties (including optical absorption, infrared, and Raman) are calculated.

Hyperfine Structure and Abundances of Heavy Elements in 68 Tauri (HD 27962)

NASA Astrophysics Data System (ADS)

Martinet, S.; Monier, R.

2017-12-01

HD 27962, also known as 68 Tauri, is a Chemically Peculiar Am star member of the Hyades Open Cluster in the local arm of the Galaxy. We have modeled the high resolution SOPHIE (R=75000) spectrum of 68 Tauri using updated model atmosphere and spectrum synthesis to derive chemical abundances in its atmosphere. In particular, we have studied the effect of the inclusion of Hyperfine Structure of various Baryum isotopes on the determination of the Baryum abundance in 68 Tauri. We have also derived new abundances using updated accurate atomic parameters retrieved from the NIST database.

Developmental Physiology of Cluster-Root Carboxylate Synthesis and Exudation in Harsh Hakea. Expression of Phosphoenolpyruvate Carboxylase and the Alternative Oxidase1

PubMed Central

Shane, Michael W.; Cramer, Michael D.; Funayama-Noguchi, Sachiko; Cawthray, Gregory R.; Millar, A. Harvey; Day, David A.; Lambers, Hans

2004-01-01

Harsh hakea (Hakea prostrata R.Br.) is a member of the Proteaceae family, which is highly represented on the extremely nutrient-impoverished soils in southwest Australia. When phosphorus is limiting, harsh hakea develops proteoid or cluster roots that release carboxylates that mobilize sparingly soluble phosphate in the rhizosphere. To investigate the physiology underlying the synthesis and exudation of carboxylates from cluster roots in Proteaceae, we measured O2 consumption, CO2 release, internal carboxylate concentrations and carboxylate exudation, and the abundance of the enzymes phosphoenolpyruvate carboxylase and alternative oxidase (AOX) over a 3-week time course of cluster-root development. Peak rates of citrate and malate exudation were observed from 12- to 13-d-old cluster roots, preceded by a reduction in cluster-root total protein levels and a reduced rate of O2 consumption. In harsh hakea, phosphoenolpyruvate carboxylase expression was relatively constant in cluster roots, regardless of developmental stage. During cluster-root maturation, however, the expression of AOX protein increased prior to the time when citrate and malate exudation peaked. This increase in AOX protein levels is presumably needed to allow a greater flow of electrons through the mitochondrial electron transport chain in the absence of rapid ATP turnover. Citrate and isocitrate synthesis and accumulation contributed in a major way to the subsequent burst of citrate and malate exudation. Phosphorus accumulated by harsh hakea cluster roots was remobilized during senescence as part of their efficient P cycling strategy for growth on nutrient impoverished soils. PMID:15122030

Super Star Clusters and H II Regions in Nuclear Rings

NASA Astrophysics Data System (ADS)

Filippenko, Alex

1996-07-01

We propose to obtain WFPC2 optical broad-band {F547M and F814W} and narrow-band Halpha+ionN2 {F658N} images of nuclear starburst rings in four nearby galaxies for which we already have ultraviolet {F220W} FOC data. Nuclear rings {or ``hot- spot'' regions} in barred spirals are some of the nearest and least obscured starburst regions, and HST images of nuclear rings in several galaxies show that the rings contain large populations of super star clusters similar to those recently discovered in other types of starburst systems. These compact clusters, many having luminosities exceeding that of the R136 cluster in 30 Doradus, represent a violent mode of star formation distinct from that seen in ordinary disk ionH2 regions, and the nuclear rings present us with an opportunity to study large numbers of these extreme clusters in relatively unobscured starburst environments. It has been suggested that super star clusters are present-day versions of young globular clusters. To evaluate this hypothesis, it is important to understand the physical properties and stellar contents of the clusters, but previous HST studies of nuclear ring galaxies have only used single-filter observations. Together with our UV data, new WFPC2 images will enable us to determine the H II region and cluster luminosity functions within nuclear rings, measure cluster radii, derive age and mass estimates for the clusters by comparison with evolutionary synthesis models, and study the structure and evolution of nuclear rings.

Frataxin Accelerates [2Fe-2S] Cluster Formation on the Human Fe–S Assembly Complex

PubMed Central

Fox, Nicholas G.; Das, Deepika; Chakrabarti, Mrinmoy; Lindahl, Paul A.; Barondeau, David P.

2015-01-01

Iron–sulfur (Fe–S) clusters function as protein cofactors for a wide variety of critical cellular reactions. In human mitochondria, a core Fe–S assembly complex [called SDUF and composed of NFS1, ISD11, ISCU2, and frataxin (FXN) proteins] synthesizes Fe–S clusters from iron, cysteine sulfur, and reducing equivalents and then transfers these intact clusters to target proteins. In vitro assays have relied on reducing the complexity of this complicated Fe–S assembly process by using surrogate electron donor molecules and monitoring simplified reactions. Recent studies have concluded that FXN promotes the synthesis of [4Fe-4S] clusters on the mammalian Fe–S assembly complex. Here the kinetics of Fe–S synthesis reactions were determined using different electron donation systems and by monitoring the products with circular dichroism and absorbance spectroscopies. We discovered that common surrogate electron donor molecules intercepted Fe–S cluster intermediates and formed high-molecular weight species (HMWS). The HMWS are associated with iron, sulfide, and thiol-containing proteins and have properties of a heterogeneous solubilized mineral with spectroscopic properties remarkably reminiscent of those of [4Fe-4S] clusters. In contrast, reactions using physiological reagents revealed that FXN accelerates the formation of [2Fe-2S] clusters rather than [4Fe-4S] clusters as previously reported. In the preceding paper [Fox, N. G., et al. (2015) Biochemistry 54, DOI: 10.1021/bi5014485], [2Fe-2S] intermediates on the SDUF complex were shown to readily transfer to uncomplexed ISCU2 or apo acceptor proteins, depending on the reaction conditions. Our results indicate that FXN accelerates a rate-limiting sulfur transfer step in the synthesis of [2Fe-2S] clusters on the human Fe–S assembly complex. PMID:26016518

Frataxin Accelerates [2Fe-2S] Cluster Formation on the Human Fe-S Assembly Complex.

PubMed

Fox, Nicholas G; Das, Deepika; Chakrabarti, Mrinmoy; Lindahl, Paul A; Barondeau, David P

2015-06-30

Iron-sulfur (Fe-S) clusters function as protein cofactors for a wide variety of critical cellular reactions. In human mitochondria, a core Fe-S assembly complex [called SDUF and composed of NFS1, ISD11, ISCU2, and frataxin (FXN) proteins] synthesizes Fe-S clusters from iron, cysteine sulfur, and reducing equivalents and then transfers these intact clusters to target proteins. In vitro assays have relied on reducing the complexity of this complicated Fe-S assembly process by using surrogate electron donor molecules and monitoring simplified reactions. Recent studies have concluded that FXN promotes the synthesis of [4Fe-4S] clusters on the mammalian Fe-S assembly complex. Here the kinetics of Fe-S synthesis reactions were determined using different electron donation systems and by monitoring the products with circular dichroism and absorbance spectroscopies. We discovered that common surrogate electron donor molecules intercepted Fe-S cluster intermediates and formed high-molecular weight species (HMWS). The HMWS are associated with iron, sulfide, and thiol-containing proteins and have properties of a heterogeneous solubilized mineral with spectroscopic properties remarkably reminiscent of those of [4Fe-4S] clusters. In contrast, reactions using physiological reagents revealed that FXN accelerates the formation of [2Fe-2S] clusters rather than [4Fe-4S] clusters as previously reported. In the preceding paper [Fox, N. G., et al. (2015) Biochemistry 54, DOI: 10.1021/bi5014485], [2Fe-2S] intermediates on the SDUF complex were shown to readily transfer to uncomplexed ISCU2 or apo acceptor proteins, depending on the reaction conditions. Our results indicate that FXN accelerates a rate-limiting sulfur transfer step in the synthesis of [2Fe-2S] clusters on the human Fe-S assembly complex.

Synthesis and characterization of sulfur-voided cubanes. Structural analogues for the MoFe(3)S(3) subunit in the nitrogenase cofactor.

PubMed

Coucouvanis, Dimitri; Han, Jaehong; Moon, Namdoo

2002-01-16

A new class of Mo/Fe/S clusters with the MoFe(3)S(3) core has been synthesized in attempts to model the FeMo-cofactor in nitrogenase. These clusters are obtained in reactions of the (Cl(4)-cat)(2)Mo(2)Fe(6)S(8)(PR(3))(6) [R = Et (I), (n)Pr (II)] clusters with CO. The new clusters include those preliminarily reported: (Cl(4)-cat)MoFe(3)S(3)(PEt(3))(2)(CO)(6) (III), (Cl(4)-cat)(O)MoFe(3)S(3)(PEt(3))(3)(CO)(5) (IV), (Cl(4)-cat)(Pyr)MoFe(3)S(3)(PEt(3))(2)(CO)(6) (VI), and (Cl(4)-cat)(Pyr)MoFe(3)S(3)(P(n)Pr(3))(3)(CO)(4) (VIII). In addition the new (Cl(4)-cat)(O)MoFe(3)S(3)(P(n)Pr(3))(3)(CO)(5) cluster (IVa), the (Cl(4)-cat)(O)MoFe(3)S(3)(PEt(3))(2)(CO)(6)cluster (V), the (Cl(4)-cat)(O)MoFe(3)S(3)(P(n)Pr(3))(2)(CO)(6) cluster (Va), the (Cl(4)-cat)(Pyr)MoFe(3)S(3)(P(n)Pr(3))(2)(CO)(6) cluster (VIa), and the (Cl(4)-cat)(P(n)Pr(3))MoFe(3)S(3)(P(n)Pr(3))(2)(CO)(6) cluster (VII) also are reported. Clusters III-VIII have been structurally and spectroscopically characterized. EPR, zero-field (57)Fe-Mössbauer spectroscopic characterizations, and magnetic susceptibility measurements have been used for a tentative assignment of the electronic and oxidation states of the MoFe(3)S(3) sulfur-voided cuboidal clusters. A structural comparison of the clusters with the MoFe(3)S(3) subunit of the FeMo-cofactor has led to the suggestion that the storage of reducing equivalents into M-M bonds, and their use in the reduction of substrates, may occur with the FeMo-cofactor, which also appears to have M-M bonding. On the basis of this argument, a possible N(2)-binding and reduction mechanism on the FeMoco-cofactor is proposed.

Hydrothermal Synthesis and Characterization of Ni-Al Montmorillonite-Like Phyllosilicates

PubMed Central

Reinholdt, Marc X.; Brendlé, Jocelyne; Tuilier, Marie-Hélène; Kaliaguine, Serge; Ambroise, Emmanuelle

2013-01-01

This work describes the first hydrothermal synthesis in fluoride medium of Ni-Al montmorillonite-like phyllosilicates, in which the only metallic elements in the octahedral sheet are Ni and Al. X-ray diffraction , chemical analysis, thermogravimetric and differential thermal analysis, scanning electron microscopy and transmission electron microscopy confirm that the synthesized samples are montmorillonite-like phyllosilicates having the expected chemical composition. The specific surface areas of the samples are relatively large (>100 m2 g−1) compared to naturally occurring montmorillonites. 29Si and 27Al nuclear magnetic resonance (NMR) indicate substitutions of Al for Si in the tetrahedral sheet. 19F NMR and Ni K-edge extended X-ray absorption fine structure (EXAFS) local probes highlight a clustering of the metal elements and of the vacancies in the octahedral sheet of the samples. These Ni-Al phyllosilicates exhibit a higher local order than in previously synthesized Zn-Al phyllosilicates. Unlike natural montmorillonites, where the distribution of transition metal cations ensures a charge equilibrium allowing a stability of the framework, synthetic montmorillonites entail clustering and instability of the lattice when the content of divalent element in the octahedral sheet exceeds ca. 20%. Synthesis of Ni-Al montmorillonite-like phyllosilicates, was successfully achieved for the first time. These new synthetic materials may find potential applications as catalysts or as materials with magnetic, optical or staining properties. PMID:28348321

Optical signatures of high-redshift galaxy clusters

NASA Technical Reports Server (NTRS)

Evrard, August E.; Charlot, Stephane

1994-01-01

We combine an N-body and gasdynamic simulation of structure formation with an updated population synthesis code to explore the expected optical characteristics of a high-redshift cluster of galaxies. We examine a poor (2 keV) cluster formed in a biased, cold dark matter cosmology and employ simple, but plausible, threshold criteria to convert gas into stars. At z = 2, the forming cluster appears as a linear chain of very blue (g-r approximately equals 0) galaxies, with 15 objects brighter than r = 25 within a 1 square arcmin field of view. After 2 Gyr of evolution, the cluster viewed at z = 1 displays both freshly infalling blue galaxies and red galaxies robbed of recent accretion by interaction with the hot intracluster medium. The range in G-R colors is approximately 3 mag at z = 1, with the reddest objects lying at sites of highest galaxy density. We suggest that red, high-redshift galaxies lie in the cores of forming clusters and that their existence indicates the presence of a hot intracluster medium at redshifts z approximately equals 2. The simulated cluster viewed at z = 2 has several characteristics similar to the collection of faint, blue objects identified by Dressler et al. in a deep Hubble Space Telescope observation. The similarities provide some support for the interpretation of this collection as a high-redshift cluster of galaxies.

Type III Pilus of Corynebacteria: Pilus Length Is Determined by the Level of Its Major Pilin Subunit

PubMed Central

Swierczynski, Arlene; Ton-That, Hung

2006-01-01

Multiple pilus gene clusters have been identified in several gram-positive bacterial genomes sequenced to date, including the Actinomycetales, clostridia, streptococci, and corynebacteria. The genome of Corynebacterium diphtheriae contains three pilus gene clusters, two of which have been previously characterized. Here, we report the characterization of the third pilus encoded by the spaHIG cluster. By using electron microscopy and biochemical analysis, we demonstrate that SpaH forms the pilus shaft, while SpaI decorates the structure and SpaG is largely located at the pilus tip. The assembly of the SpaHIG pilus requires a specific sortase located within the spaHIG pilus gene cluster. Deletion of genes specific for the synthesis and polymerization of the other two pilus types does not affect the SpaHIG pilus. Moreover, SpaH but not SpaI or SpaG is essential for the formation of the filament. When expressed under the control of an inducible promoter, the amount of the SpaH pilin regulates pilus length; no pili are assembled from an SpaH precursor that has an alanine in place of the conserved lysine of the SpaH pilin motif. Thus, the spaHIG pilus gene cluster encodes a pilus structure that is independently assembled and antigenically distinct from other pili of C. diphtheriae. We incorporate these findings in a model of sortase-mediated pilus assembly that may be applicable to many gram-positive pathogens. PMID:16923899

Type III pilus of corynebacteria: Pilus length is determined by the level of its major pilin subunit.

PubMed

Swierczynski, Arlene; Ton-That, Hung

2006-09-01

Multiple pilus gene clusters have been identified in several gram-positive bacterial genomes sequenced to date, including the Actinomycetales, clostridia, streptococci, and corynebacteria. The genome of Corynebacterium diphtheriae contains three pilus gene clusters, two of which have been previously characterized. Here, we report the characterization of the third pilus encoded by the spaHIG cluster. By using electron microscopy and biochemical analysis, we demonstrate that SpaH forms the pilus shaft, while SpaI decorates the structure and SpaG is largely located at the pilus tip. The assembly of the SpaHIG pilus requires a specific sortase located within the spaHIG pilus gene cluster. Deletion of genes specific for the synthesis and polymerization of the other two pilus types does not affect the SpaHIG pilus. Moreover, SpaH but not SpaI or SpaG is essential for the formation of the filament. When expressed under the control of an inducible promoter, the amount of the SpaH pilin regulates pilus length; no pili are assembled from an SpaH precursor that has an alanine in place of the conserved lysine of the SpaH pilin motif. Thus, the spaHIG pilus gene cluster encodes a pilus structure that is independently assembled and antigenically distinct from other pili of C. diphtheriae. We incorporate these findings in a model of sortase-mediated pilus assembly that may be applicable to many gram-positive pathogens.

Azole Functionalized Polyoxo-Titanium Clusters with Sunlight-Driven Dye Degradation Applications: Synthesis, Structure, and Photocatalytic Studies.

PubMed

Narayanam, Nagaraju; Chintakrinda, Kalpana; Fang, Wei-Hui; Kang, Yao; Zhang, Lei; Zhang, Jian

2016-10-06

Six polyoxo-titanium clusters (PTCs) with varying nuclearities containing Ti-N bonds and heteronuclearity, namely, [Ti 6 (μ 3 -O) 2 (μ 2 -O) 2 (O 3 P-Phen) 2 (OiPr) 10 (1-hbta) 2 ] (PTC-37), Ti 8 (μ 3 -O) 2 (μ 2 -O) 2 (O 3 P-Phen) 2 (OiPr) 16 (adn) 2 (NO 3 ) 2 ] (PTC-38), [Ti 4 (μ 3 -O)(μ 2 -O)(μ 2 -OiPr) 2 (OiPr) 4 (O 3 P-Phen) 3 (1,10-phn)](HOiPr) (PTC-39), [Ti 4 (μ 3 -O)(μ 2 -OiPr) 3 (OiPr) 5 (O 3 P-Phen) 3 (Im)] (PTC-40), [Ti 4 (μ 3 -O)(μ 2 -OiPr) 3 (OiPr) 5 (O 3 P-Phen) 3 (Im)][Ti 3 M(μ 3 -O)(μ 2 -OiPr) 3 (OiPr) 3 (O 3 P-Phen) 3 (Im)] (M = Co for PTC-41 and M = Zn for PTC-42; O 3 P-Phen = phenyl phosphonate, 1-hbta = 1-hydroxy benzotriazolate, adn = adenine, 1,10-phn = 1,10-phenanthroline, Im = imidazolate, and OiPr = isopropoxide) were prepared as crystalline samples and structurally characterized. Simultaneous doping of nitrogen and transition metal heteroatoms into the Ti-O clusters created complex chemical environments in the resulting hybrid materials. Thus, photocatalytic methylene blue degradation studies were performed to understand structure-property relationships in these Ti cluster-based materials. The complex chemical environment created in these novel molecular clusters had proved to exhibit ligand-dependent photocatalytic activities under normal sunlight. Adenine-functionalized PTC-38 presented moderate activities, while other PTCs all show rapid dye degradation.

Zinc and the iron donor frataxin regulate oligomerization of the scaffold protein to form new Fe-S cluster assembly centers.

PubMed

Galeano, B K; Ranatunga, W; Gakh, O; Smith, D Y; Thompson, J R; Isaya, G

2017-06-21

Early studies of the bacterial Fe-S cluster assembly system provided structural details for how the scaffold protein and the cysteine desulfurase interact. This work and additional work on the yeast and human systems elucidated a conserved mechanism for sulfur donation but did not provide any conclusive insights into the mechanism for iron delivery from the iron donor, frataxin, to the scaffold. We previously showed that oligomerization is a mechanism by which yeast frataxin (Yfh1) can promote assembly of the core machinery for Fe-S cluster synthesis both in vitro and in cells, in such a manner that the scaffold protein, Isu1, can bind to Yfh1 independent of the presence of the cysteine desulfurase, Nfs1. Here, in the absence of Yfh1, Isu1 was found to exist in two forms, one mostly monomeric with limited tendency to dimerize, and one with a strong propensity to oligomerize. Whereas the monomeric form is stabilized by zinc, the loss of zinc promotes formation of dimer and higher order oligomers. However, upon binding to oligomeric Yfh1, both forms take on a similar symmetrical trimeric configuration that places the Fe-S cluster coordinating residues of Isu1 in close proximity of iron-binding residues of Yfh1. This configuration is suitable for docking of Nfs1 in a manner that provides a structural context for coordinate iron and sulfur donation to the scaffold. Moreover, distinct structural features suggest that in physiological conditions the zinc-regulated abundance of monomeric vs. oligomeric Isu1 yields [Yfh1]·[Isu1] complexes with different Isu1 configurations that afford unique functional properties for Fe-S cluster assembly and delivery.

Reduction-Triggered Self-Assembly of Nanoscale Molybdenum Oxide Molecular Clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yin, Panchao; Wu, Bin; Li, Tao

A 2.9 nm molybdenum oxide cluster {Mo 132} (Formula: [Mo VI 72Mo V 60O 372(CH 3COO) 30(H 2O) 72] 42-) can be obtained by reducing ammonium molybdate with hydrazine sulfate in weakly acidic CH 3COOH/CH 3COO- buffers. This reaction has been monitored by time-resolved UV-Vis, 1H-NMR, small angle X-ray/neutron scattering, and X-ray absorption near edge structure spectroscopy. The growth of {Mo 132} cluster shows a typical sigmoid curve, suggesting a multi-step assembly mechanism for this reaction. The reaction starts with a lag phase period when partial MoVI centers of molybdate precursors are reduced to form {MoV2(acetate)} structures under the coordinationmore » effect of the acetate groups. Once the concentration of {Mo V 2(acetate)} reaches a critical value, it triggers the assembly of Mo V and Mo VI species into {Mo 132} clusters. Parameters such as the type and amount of reducing agent, the pH, the type of cation, and the type of organic ligand in the reaction buffer, have been studied for the roles they play in the formation of the target clusters.Understanding the formation mechanism of giant molecular clusters is essential for rational design and synthesis of cluster-based nanomaterials with required morphologies and functionalities. Here, typical synthetic reactions of a 2.9 nm spherical molybdenum oxide cluster, {Mo 132} (formula: [Mo VI 72Mo V 60O 372(CH 3COO) 30(H 2O) 72] 42), with systematically varied reaction parameters have been fully explored to determine the morphologies and concentration of products, reduction of metal centers, and chemical environments of the organic ligands. The growth of these clusters shows a typical sigmoid curve, suggesting a general multistep self-assembly mechanism for the formation of giant molecular clusters. The reaction starts with a lag phase period when partial MoVI centers of molybdate precursors are reduced to form {Mo V 2(acetate)} structures under the coordination effect of the acetate groups. Once the concentration of {MoV2(acetate)} reaches a critical value, it triggers the co-assembly of Mo V and Mo VI species into the giant clusters.« less

Reduction-Triggered Self-Assembly of Nanoscale Molybdenum Oxide Molecular Clusters

DOE PAGES

Yin, Panchao; Wu, Bin; Li, Tao; ...

2016-07-26

A 2.9 nm molybdenum oxide cluster {Mo 132} (Formula: [Mo VI 72Mo V 60O 372(CH 3COO) 30(H 2O) 72] 42-) can be obtained by reducing ammonium molybdate with hydrazine sulfate in weakly acidic CH 3COOH/CH 3COO- buffers. This reaction has been monitored by time-resolved UV-Vis, 1H-NMR, small angle X-ray/neutron scattering, and X-ray absorption near edge structure spectroscopy. The growth of {Mo 132} cluster shows a typical sigmoid curve, suggesting a multi-step assembly mechanism for this reaction. The reaction starts with a lag phase period when partial MoVI centers of molybdate precursors are reduced to form {MoV2(acetate)} structures under the coordinationmore » effect of the acetate groups. Once the concentration of {Mo V 2(acetate)} reaches a critical value, it triggers the assembly of Mo V and Mo VI species into {Mo 132} clusters. Parameters such as the type and amount of reducing agent, the pH, the type of cation, and the type of organic ligand in the reaction buffer, have been studied for the roles they play in the formation of the target clusters.Understanding the formation mechanism of giant molecular clusters is essential for rational design and synthesis of cluster-based nanomaterials with required morphologies and functionalities. Here, typical synthetic reactions of a 2.9 nm spherical molybdenum oxide cluster, {Mo 132} (formula: [Mo VI 72Mo V 60O 372(CH 3COO) 30(H 2O) 72] 42), with systematically varied reaction parameters have been fully explored to determine the morphologies and concentration of products, reduction of metal centers, and chemical environments of the organic ligands. The growth of these clusters shows a typical sigmoid curve, suggesting a general multistep self-assembly mechanism for the formation of giant molecular clusters. The reaction starts with a lag phase period when partial MoVI centers of molybdate precursors are reduced to form {Mo V 2(acetate)} structures under the coordination effect of the acetate groups. Once the concentration of {MoV2(acetate)} reaches a critical value, it triggers the co-assembly of Mo V and Mo VI species into the giant clusters.« less

Different water clusters dependent on long-chain dicarboxylates in two Ag(I) coordination polymers: Synthesis, structure and thermal stability

NASA Astrophysics Data System (ADS)

Sun, Di; Liu, Fu-Jing; Hao, Hong-Jun; Huang, Rong-Bin; Zheng, Lan-Sun

2011-10-01

Two mixed-ligand Ag(I) coordination polymers (CPs), [Ag 2(bipy) 2(sub)·5H 2O] n ( 1), [Ag 2(bipy) 2(aze)·3H 2O] n ( 2), (bipy = 4,4'-bipyridine, H 2sub = suberic acid, H 2aze = azelaic acid) have been synthesized and structurally characterized by elemental analysis, infrared (IR) spectroscopy, powder X-ray diffraction (PXRD), thermogravimetric (TG) analysis, and single crystal X-ray diffraction. Both 1 and 2 are two-dimensional (2D) sheets based on infinite [Ag(bipy)] n double chain incorporating Ag⋯Ag interactions. Interestingly, two different water clusters are encapsulated in the voids between the sheets of 1 and 2. For 1, one water decamer (H 2O) 10 based on a cyclic water tetramer was hydrogen-bonded with the host 2D sheet. While, one water hexamer (H 2O) 6 also based on a cyclic water tetramer was observed in 2. Comparing the experimental results, it is comprehensible that the dicarboxylates play a crucial role in the formation of the different water clusters. Moreover, the thermal stabilities of them were also discussed.

Hexanuclear gold(I) phosphide complexes as platforms for multiple redox-active ferrocenyl units.

PubMed

Lee, Terence Kwok-Ming; Cheng, Eddie Chung-Chin; Zhu, Nianyong; Yam, Vivian Wing-Wah

2014-01-03

The synthesis, X-ray crystal structures, electrochemical, and spectroscopic studies of a series of hexanuclear gold(I) μ(3)-ferrocenylmethylphosphido complexes stabilized by bridging phosphine ligands, [Au(6)(P-P)(n)(Fc-CH(2)-P)(2)][PF(6)](2) (n=3, P-P=dppm (bis(diphenylphosphino)methane) (1), dppe (1,2-bis(diphenylphosphino)ethane) (2), dppp (1,3-bis(diphenylphosphino)propane) (3), Ph(2)PN(C(3)H(7))-PPh(2) (4), Ph(2)PN(Ph-CH(3)-p)PPh(2) (5), dppf (1,1′-bis(diphenylphosphino)ferrocene) (6); n=2, P-P=dpepp (bis(2-diphenylphosphinoethyl)phenylphosphine) (7)), as platforms for multiple redox-active ferrocenyl units, are reported. The investigation of the structural changes of the clusters has been probed by introducing different bridging phosphine ligands. This class of gold(I) μ(3)-ferrocenylmethylphosphido complexes has been found to exhibit one reversible oxidation couple, suggestive of the absence of electronic communication between the ferrocene units through the Au(6)P(2) cluster core, providing an understanding of the electronic properties of the hexanuclear Au(I) cluster linkage. The present complexes also serve as an ideal system for the design of multi-electron reservoir and molecular battery systems.

Synthesis of Two-Electron Bimetallic Cu-Ag and Cu-Au Clusters by using [Cu13 (S2 CNn Bu2 )6 (C≡CPh)4 ]+ as a Template.

PubMed

Silalahi, Rhone P Brocha; Chakrahari, Kiran Kumarvarma; Liao, Jian-Hong; Kahlal, Samia; Liu, Yu-Chiao; Chiang, Ming-Hsi; Saillard, Jean-Yves; Liu, C W

2018-03-02

Atomically precise Cu-rich bimetallic superatom clusters have been synthesized by adopting a galvanic exchange strategy. [Cu@Cu 12 (S 2 CN n Bu 2 ) 6 (C≡CPh) 4 ][CuCl 2 ] (1) was used as a template to generate compositionally uniform clusters [M@Cu 12 (S 2 CN n Bu 2 ) 6 (C≡CPh) 4 ][CuCl 2 ], where M=Ag (2), Au (3). Structures of 1, 2 and 3 were determined by single crystal X-ray diffraction and the results were supported by ESI-MS. The anatomies of clusters 1-3 are very similar, with a centred cuboctahedral cationic core that is surrounded by six di-butyldithiocarbamate (dtc) and four phenylacetylide ligands. The doped Ag and Au atoms were found to preferentially occupy the centre of the 13-atom cuboctahedral core. Experimental and theoretical analyses of the synthesized clusters revealed that both Ag and Au doping result in significant changes in cluster stability, optical characteristics and enhancement in luminescence properties. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Laser ablation synthesis of new gold phosphides using red phosphorus and nanogold as precursors. Laser desorption ionisation time-of-flight mass spectrometry.

PubMed

Panyala, Nagender Reddy; Peña-Méndez, Eladia María; Havel, Josef

2012-05-15

Gold phosphides show unique optical or semiconductor properties and there are extensive high technology applications, e.g. in laser diodes, etc. In spite of the various AuP structures known, the search for new materials is wide. Laser ablation synthesis is a promising screening and synthetic method. Generation of gold phosphides via laser ablation of red phosphorus and nanogold mixtures was studied using laser desorption ionisation time-of-flight mass spectrometry (LDI TOFMS). Gold clusters Au(m)(+) (m = 1 to ~35) were observed with a difference of one gold atom and their intensities were in decreasing order with respect to m. For P(n)(+) (n = 2 to ~111) clusters, the intensities of odd-numbered phosphorus clusters are much higher than those for even-numbered phosphorus clusters. During ablation of P-nanogold mixtures, clusters Au(m)(+) (m = 1-12), P(n)(+) (n = 2-7, 9, 11, 13-33, 35-95 (odd numbers)), AuP(n)(+) (n = 1, 2-88 (even numbers)), Au(2)P(n)(+) (n = 1-7, 14-16, 21-51 (odd numbers)), Au(3)P(n)(+) (n = 1-6, 8, 9, 14), Au(4)P(n)(+) (n = 1-9, 14-16), Au(5)P(n)(+) (n = 1-6, 14, 16), Au(6)P(n)(+) (n = 1-6), Au(7)P(n)(+) (n = 1-7), Au(8)P(n)(+) (n = 1-6, 8), Au(9)P(n)(+) (n = 1-10), Au(10)P(n)(+) (n = 1-8, 15), Au(11)P(n)(+) (n = 1-6), and Au(12)P(n)(+) (n = 1, 2, 4) were detected in positive ion mode. In negative ion mode, Au(m)(-) (m = 1-5), P(n)(-) (n = 2, 3, 5-11, 13-19, 21-35, 39, 41, 47, 49, 55 (odd numbers)), AuP(n)(-) (n = 4-6, 8-26, 30-36 (even numbers), 48), Au(2)P(n)(-) (n = 2-5, 8, 11, 13, 15, 17), A(3) P(n)(-) (n = 6-11, 32), Au(4)P(n)(-) (n = 1, 2, 4, 6, 10), Au(6)P(5)(-), and Au(7)P(8)(-) clusters were observed. In both modes, phosphorus-rich Au(m)P(n) clusters prevailed. The first experimental evidence for formation of AuP(60) and gold-covered phosphorus Au(12)P(n) (n = 1, 2, 4) clusters is given. The new gold phosphides generated might inspire synthesis of new Au-P materials with specific properties. Copyright © 2012 John Wiley & Sons, Ltd.

Peptide protected gold clusters: chemical synthesis and biomedical applications

NASA Astrophysics Data System (ADS)

Yuan, Qing; Wang, Yaling; Zhao, Lina; Liu, Ru; Gao, Fuping; Gao, Liang; Gao, Xueyun

2016-06-01

Bridging the gap between atoms and nanoparticles, noble metal clusters with atomic precision continue to attract considerable attention due to their important applications in catalysis, energy transformation, biosensing and biomedicine. Greatly different to common chemical synthesis, a one-step biomimetic synthesis of peptide-conjugated metal clusters has been developed to meet the demand of emerging bioapplications. Under mild conditions, multifunctional peptides containing metal capturing, reactive and targeting groups are rationally designed and elaborately synthesized to fabricate atomically precise peptide protected metal clusters. Among them, peptide-protected Au Cs (peptide-Au Cs) possess a great deal of exceptional advantages such as nanometer dimensions, high photostability, good biocompatibility, accurate chemical formula and specific protein targeting capacity. In this review article, we focus on the recent advances in potential theranostic fields by introducing the rising progress of peptide-Au Cs for biological imaging, biological analysis and therapeutic applications. The interactions between Au Cs and biological systems as well as potential mechanisms are also our concerned theme. We expect that the rapidly growing interest in Au Cs-based theranostic applications will attract broader concerns across various disciplines.

Exploring the Molecular Growth of Two Gigantic Half‐Closed Polyoxometalate Clusters {Mo180} and {Mo130Ce6}

PubMed Central

Xuan, Weimin; Pow, Robert; Long, De‐Liang

2017-01-01

Abstract Understanding the process of the self‐assembly of gigantic polyoxometalates and their subsequent molecular growth, by the addition of capping moieties onto the oxo‐frameworks, is critical for the development of the designed assembly of complex high‐nuclearity cluster species, yet such processes remain far from being understood. Herein we describe the molecular growth from {Mo150} and {Mo120Ce6} to afford two half‐closed gigantic molybdenum blue clusters {Mo180} (1) and {Mo130Ce6} (2), respectively. Compound 1 features a hat‐shaped structure with the parent wheel‐shaped {Mo150} being capped by a {Mo30} unit on one side. Similarly, 2 exhibits an elliptical lanthanide‐doped wheel {Mo120Ce6} that is sealed by a {Mo10} unit on one side. Moreover, the observation of the parent uncapped {Mo150} and {Mo120Ce6} clusters as minor products during the synthesis of 1 and 2 strongly suggests that the molecular growth process can be initialized from {Mo150} and {Mo120Ce6} in solution, respectively. PMID:28508585

Modularity of Plant Metabolic Gene Clusters: A Trio of Linked Genes That Are Collectively Required for Acylation of Triterpenes in Oat[W][OA

PubMed Central

Mugford, Sam T.; Louveau, Thomas; Melton, Rachel; Qi, Xiaoquan; Bakht, Saleha; Hill, Lionel; Tsurushima, Tetsu; Honkanen, Suvi; Rosser, Susan J.; Lomonossoff, George P.; Osbourn, Anne

2013-01-01

Operon-like gene clusters are an emerging phenomenon in the field of plant natural products. The genes encoding some of the best-characterized plant secondary metabolite biosynthetic pathways are scattered across plant genomes. However, an increasing number of gene clusters encoding the synthesis of diverse natural products have recently been reported in plant genomes. These clusters have arisen through the neo-functionalization and relocation of existing genes within the genome, and not by horizontal gene transfer from microbes. The reasons for clustering are not yet clear, although this form of gene organization is likely to facilitate co-inheritance and co-regulation. Oats (Avena spp) synthesize antimicrobial triterpenoids (avenacins) that provide protection against disease. The synthesis of these compounds is encoded by a gene cluster. Here we show that a module of three adjacent genes within the wider biosynthetic gene cluster is required for avenacin acylation. Through the characterization of these genes and their encoded proteins we present a model of the subcellular organization of triterpenoid biosynthesis. PMID:23532069

A novel asymmetric chair-like hydroxyl-bridged tetra-copper compound: Synthesis, supramolecular structure and magnetic property

NASA Astrophysics Data System (ADS)

Wang, Xiao-Feng; Du, Ke-Jie; Wang, Hong-Qing; Zhang, Xue-Li; Nie, Chang-Ming

2017-06-01

A new polynuclear Cu(II) compound, [Cu4(bpy)4(OH)4(H2O)(BTC)]NO3·8H2O (1), was prepared by self-assembly from the solution of copper(II) nitrate and two kinds of ligands, 2,2‧-bipyridine (bpy) and benzene-tricarboxylic acid (H3BTC). Single crystal structure analysis reveals that 1 features a rare asymmetric chair-like hydroxyl-bridged tetra-copper cluster: [Cu4(OH)4] core along with one H2O and one BTC3- occupied each terminal coordinated site. In addition, the magnetic property has been investigated.

The Properties and Applications of Nanodiamonds.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mochalin, Vadym N.; Shenderova, Olga; Ho, Dean

Nanodiamonds have excellent mechanical and optical properties, high surface areas and tunable surface structures. They are also non-toxic, which makes them well suited to biomedical applications. Here we review the synthesis, structure, properties, surface chemistry and phase transformations of individual nanodiamonds and clusters of nanodiamonds. In particular we discuss the rational control of the mechanical, chemical, electronic and optical properties of nanodiamonds through surface doping, interior doping and the introduction of functional groups. These little gems have a wide range of potential applications in tribology, drug delivery, bioimaging and tissue engineering, and also as protein mimics and a filler materialmore » for nanocomposites.« less

The properties and applications of nanodiamonds.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mochalin, Vadym; Shenderova, Olga; Ho, Dean

Nanodiamonds have excellent mechanical and optical properties, high surface areas and tunable surface structures. They are also non-toxic, which makes them well suited to biomedical applications. Here we review the synthesis, structure, properties, surface chemistry and phase transformations of individual nanodiamonds and clusters of nanodiamonds. In particular we discuss the rational control of the mechanical, chemical, electronic and optical properties of nanodiamonds through surface doping, interior doping and the introduction of functional groups. These little gems have a wide range of potential applications in tribology, drug delivery, bioimaging and tissue engineering, and also as protein mimics and a filler materialmore » for nanocomposites.« less

Towards a methodology for cluster searching to provide conceptual and contextual "richness" for systematic reviews of complex interventions: case study (CLUSTER).

PubMed

Booth, Andrew; Harris, Janet; Croot, Elizabeth; Springett, Jane; Campbell, Fiona; Wilkins, Emma

2013-09-28

Systematic review methodologies can be harnessed to help researchers to understand and explain how complex interventions may work. Typically, when reviewing complex interventions, a review team will seek to understand the theories that underpin an intervention and the specific context for that intervention. A single published report from a research project does not typically contain this required level of detail. A review team may find it more useful to examine a "study cluster"; a group of related papers that explore and explain various features of a single project and thus supply necessary detail relating to theory and/or context.We sought to conduct a preliminary investigation, from a single case study review, of techniques required to identify a cluster of related research reports, to document the yield from such methods, and to outline a systematic methodology for cluster searching. In a systematic review of community engagement we identified a relevant project - the Gay Men's Task Force. From a single "key pearl citation" we conducted a series of related searches to find contextually or theoretically proximate documents. We followed up Citations, traced Lead authors, identified Unpublished materials, searched Google Scholar, tracked Theories, undertook ancestry searching for Early examples and followed up Related projects (embodied in the CLUSTER mnemonic). Our structured, formalised procedure for cluster searching identified useful reports that are not typically identified from topic-based searches on bibliographic databases. Items previously rejected by an initial sift were subsequently found to inform our understanding of underpinning theory (for example Diffusion of Innovations Theory), context or both. Relevant material included book chapters, a Web-based process evaluation, and peer reviewed reports of projects sharing a common ancestry. We used these reports to understand the context for the intervention and to explore explanations for its relative lack of success. Additional data helped us to challenge simplistic assumptions on the homogeneity of the target population. A single case study suggests the potential utility of cluster searching, particularly for reviews that depend on an understanding of context, e.g. realist synthesis. The methodology is transparent, explicit and reproducible. There is no reason to believe that cluster searching is not generalizable to other review topics. Further research should examine the contribution of the methodology beyond improved yield, to the final synthesis and interpretation, possibly by utilizing qualitative sensitivity analysis.

Alpha chymotrypsin coated clusters of Fe3O4 nanoparticles for biocatalysis in low water media.

PubMed

Mukherjee, Joyeeta; Gupta, Munishwar N

2012-11-08

Enzymes in low water containing non aqueous media are useful for organic synthesis. For example, hydrolases in such media can be used for synthetic purposes. Initial work in this area was carried out with lyophilized powders of enzymes. These were found to have poor activity. Drying (removing bulk water) by precipitation turned out to be a better approach. As enzymes in such media are heterogeneous catalysts, spreading these precipitates over a large surface gave even better results. In this context, nanoparticles with their better surface to volume ratio provide obvious advantage. Magnetic nanoparticles have an added advantage of easy separation after the reaction. Keeping this in view, alpha chymotrypsin solution in water was precipitated over a stirred population of Fe3O4 nanoparticles in n-propanol. This led to alpha chymotrypsin activity coated over clusters of Fe3O4 nanoparticles. These preparations were found to have quite high transesterification activity in low water containing n-octane. Precipitation of alpha chymotrypsin over a stirred suspension of Fe3O4 nanoparticles (3.6 nm diameter) led to the formation of enzyme coated clusters of nanoparticles (ECCNs). These clusters were also magnetic and their hydrodynamic diameter ranged from 1.2- 2.6 microns (as measured by dynamic light scattering). Transmission electron microscopy (TEM), showed that these clusters had highly irregular shapes. Transesterification assay of various clusters in anhydrous n-octane led to optimization of concentration of nanoparticles in suspension during precipitation. Optimized design of enzyme coated magnetic clusters of nanoparticles (ECCN 3) showed the highest initial rate of 465 nmol min-1 mg-1protein which was about 9 times higher as compared to the simple precipitates with an initial rate of 52 nmol min-1 mg-1 protein.Circular Dichroism (CD)(with a spinning cell accessory) showed that secondary structure content of the alpha Chymotrypsin in ECCN 3 [15% α-helix, 37% β-sheet and 48% random coil] was identical to the simple precipitates of alpha chymotrypsin. A strategy for obtaining a high activity preparation of alpha chymotrypsin for application in low water media is described. Such high activity biocatalysts are useful in organic synthesis.

Heptacopper(II) and dicopper(II)-adenine complexes: synthesis, structural characterization, and magnetic properties

DOE PAGES

Leite Ferreira, B. J. M.; Brandão, Paula; Dos Santos, A. M.; ...

2015-07-13

The syntheses, crystal structures, and magnetic properties of two new copper(II) complexes with molecular formulas [Cu 7(μ 2-OH 2) 6(μ 3-O) 6(adenine) 6(NO 3) 26H 2O (1) and [Cu 2(μ 2-H 2O) 2(adenine) 2(H 2O) 4](NO 3) 42H 2O (2) are reported. We composed the heptanuclear compound of a central octahedral CuO 6 core sharing edges with six adjacent copper octahedra. In 2, the copper octahedra shares one equatorial edge. In both compounds, these basic copper cluster units are further linked by water bridges and bridging adenine ligands through N3 and N9 donors. All copper(II) centers exhibit Jahn-Teller distorted octahedralmore » coordination characteristic of a d 9 center. Our study of the magnetic properties of the heptacopper complex revealed a dominant ferromagnetic intra-cluster interaction, while the dicopper complex exhibits antiferromagnetic intra-dimer interactions with weakly ferromagnetic inter-dimer interaction.« less

Giant virus Megavirus chilensis encodes the biosynthetic pathway for uncommon acetamido sugars.

PubMed

Piacente, Francesco; De Castro, Cristina; Jeudy, Sandra; Molinaro, Antonio; Salis, Annalisa; Damonte, Gianluca; Bernardi, Cinzia; Abergel, Chantal; Tonetti, Michela G

2014-08-29

Giant viruses mimicking microbes, by the sizes of their particles and the heavily glycosylated fibrils surrounding their capsids, infect Acanthamoeba sp., which are ubiquitous unicellular eukaryotes. The glycans on fibrils are produced by virally encoded enzymes, organized in gene clusters. Like Mimivirus, Megavirus glycans are mainly composed of virally synthesized N-acetylglucosamine (GlcNAc). They also contain N-acetylrhamnosamine (RhaNAc), a rare sugar; the enzymes involved in its synthesis are encoded by a gene cluster specific to Megavirus close relatives. We combined activity assays on two enzymes of the pathway with mass spectrometry and NMR studies to characterize their specificities. Mg534 is a 4,6-dehydratase 5-epimerase; its three-dimensional structure suggests that it belongs to a third subfamily of inverting dehydratases. Mg535, next in the pathway, is a bifunctional 3-epimerase 4-reductase. The sequential activity of the two enzymes leads to the formation of UDP-l-RhaNAc. This study is another example of giant viruses performing their glycan synthesis using enzymes different from their cellular counterparts, raising again the question of the origin of these pathways. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Controlled synthesis of the DSF cell–cell signal is required for biofilm formation and virulence in Xanthomonas campestris

PubMed Central

Torres, Pablo S; Malamud, Florencia; Rigano, Luciano A; Russo, Daniela M; Marano, María Rosa; Castagnaro, Atilio P; Zorreguieta, Angeles; Bouarab, Kamal; Dow, John Maxwell; Vojnov, Adrián A

2007-01-01

Virulence of the black rot pathogen Xanthomonas campestris pv. campestris (Xcc) is regulated by cell–cell signalling involving the diffusible signal factor DSF. Synthesis and perception of DSF require products of genes within the rpf cluster (for regulation of pathogenicity factors). RpfF directs DSF synthesis whereas RpfC and RpfG are involved in DSF perception. Here we have examined the role of the rpf/DSF system in biofilm formation in minimal medium using confocal laser-scanning microscopy of GFP-labelled bacteria. Wild-type Xcc formed microcolonies that developed into a structured biofilm. In contrast, an rpfF mutant (DSF-minus) and an rpfC mutant (DSF overproducer) formed only unstructured arrangements of bacteria. A gumB mutant, defective in xanthan biosynthesis, was also unable to develop the typical wild-type biofilm. Mixed cultures of gumB and rpfF mutants formed a typical biofilm in vitro. In contrast, in mixed cultures the rpfC mutant prevented the formation of the structured biofilm by the wild-type and did not restore wild-type biofilm phenotypes to gumB or rpfF mutants. These effects on structured biofilm formation were correlated with growth and disease development by Xcc strains in Nicotiana benthamiana leaves. These findings suggest that DSF signalling is finely balanced during both biofilm formation and virulence. PMID:17635553

Comparative analyses of Xanthomonas and Xylella complete genomes.

PubMed

Moreira, Leandro M; De Souza, Robson F; Digiampietri, Luciano A; Da Silva, Ana C R; Setubal, João C

2005-01-01

Computational analyses of four bacterial genomes of the Xanthomonadaceae family reveal new unique genes that may be involved in adaptation, pathogenicity, and host specificity. The Xanthomonas genus presents 3636 unique genes distributed in 1470 families, while Xylella genus presents 1026 unique genes distributed in 375 families. Among Xanthomonas-specific genes, we highlight a large number of cell wall degrading enzymes, proteases, and iron receptors, a set of energy metabolism genes, second copy of the type II secretion system, type III secretion system, flagella and chemotactic machinery, and the xanthomonadin synthesis gene cluster. Important genes unique to the Xylella genus are an additional copy of a type IV pili gene cluster and the complete machinery of colicin V synthesis and secretion. Intersections of gene sets from both genera reveal a cluster of genes homologous to Salmonella's SPI-7 island in Xanthomonas axonopodis pv citri and Xylella fastidiosa 9a5c, which might be involved in host specificity. Each genome also presents important unique genes, such as an HMS cluster, the kdgT gene, and O-antigen in Xanthomonas axonopodis pv citri; a number of avrBS genes and a distinct O-antigen in Xanthomonas campestris pv campestris, a type I restriction-modification system and a nickase gene in Xylella fastidiosa 9a5c, and a type II restriction-modification system and two genes related to peptidoglycan biosynthesis in Xylella fastidiosa temecula 1. All these differences imply a considerable number of gene gains and losses during the divergence of the four lineages, and are associated with structural genome modifications that may have a direct relation with the mode of transmission, adaptation to specific environments and pathogenicity of each organism.

Biomimetic Synthesis of Gelatin Polypeptide-Assisted Noble-Metal Nanoparticles and Their Interaction Study

NASA Astrophysics Data System (ADS)

Liu, Ying; Liu, Xiaoheng; Wang, Xin

2011-12-01

Herein, the generation of gold, silver, and silver-gold (Ag-Au) bimetallic nanoparticles was carried out in collagen (gelatin) solution. It first showed that the major ingredient in gelatin polypeptide, glutamic acid, acted as reducing agent to biomimetically synthesize noble metal nanoparticles at 80°C. The size of nanoparticles can be controlled not only by the mass ratio of gelatin to gold ion but also by pH of gelatin solution. Interaction between noble-metal nanoparticles and polypeptide has been investigated by TEM, UV-visible, fluorescence spectroscopy, and HNMR. This study testified that the degradation of gelatin protein could not alter the morphology of nanoparticles, but it made nanoparticles aggregated clusters array (opposing three-dimensional α-helix folding structure) into isolated nanoparticles stabilized by gelatin residues. This is a promising merit of gelatin to apply in the synthesis of nanoparticles. Therefore, gelatin protein is an excellent template for biomimetic synthesis of noble metal/bimetallic nanoparticle growth to form nanometer-sized device.

All-gas-phase synthesis of UiO-66 through modulated atomic layer deposition

NASA Astrophysics Data System (ADS)

Lausund, Kristian Blindheim; Nilsen, Ola

2016-11-01

Thin films of stable metal-organic frameworks (MOFs) such as UiO-66 have enormous application potential, for instance in microelectronics. However, all-gas-phase deposition techniques are currently not available for such MOFs. We here report on thin-film deposition of the thermally and chemically stable UiO-66 in an all-gas-phase process by the aid of atomic layer deposition (ALD). Sequential reactions of ZrCl4 and 1,4-benzenedicarboxylic acid produce amorphous organic-inorganic hybrid films that are subsequently crystallized to the UiO-66 structure by treatment in acetic acid vapour. We also introduce a new approach to control the stoichiometry between metal clusters and organic linkers by modulation of the ALD growth with additional acetic acid pulses. An all-gas-phase synthesis technique for UiO-66 could enable implementations in microelectronics that are not compatible with solvothermal synthesis. Since this technique is ALD-based, it could also give enhanced thickness control and the possibility to coat irregular substrates with high aspect ratios.

Biomimetic Synthesis of Gelatin Polypeptide-Assisted Noble-Metal Nanoparticles and Their Interaction Study

PubMed Central

2011-01-01

Herein, the generation of gold, silver, and silver–gold (Ag–Au) bimetallic nanoparticles was carried out in collagen (gelatin) solution. It first showed that the major ingredient in gelatin polypeptide, glutamic acid, acted as reducing agent to biomimetically synthesize noble metal nanoparticles at 80°C. The size of nanoparticles can be controlled not only by the mass ratio of gelatin to gold ion but also by pH of gelatin solution. Interaction between noble-metal nanoparticles and polypeptide has been investigated by TEM, UV–visible, fluorescence spectroscopy, and HNMR. This study testified that the degradation of gelatin protein could not alter the morphology of nanoparticles, but it made nanoparticles aggregated clusters array (opposing three-dimensional α-helix folding structure) into isolated nanoparticles stabilized by gelatin residues. This is a promising merit of gelatin to apply in the synthesis of nanoparticles. Therefore, gelatin protein is an excellent template for biomimetic synthesis of noble metal/bimetallic nanoparticle growth to form nanometer-sized device. PMID:27502645

Redundant synthesis of a conidial polyketide by two distinct secondary metabolite clusters in Aspergillus fumigatus

PubMed Central

Throckmorton, Kurt; Lim, Fang Yun; Kontoyiannis, Dimitrios P.; Zheng, Weifa; Keller, Nancy P.

2016-01-01

Summary Filamentous fungi are renowned for the production of bioactive secondary metabolites. Typically, one distinct metabolite is generated from a specific secondary metabolite cluster. Here, we characterize the newly described trypacidin (tpc) cluster in the opportunistic human pathogen Aspergillus fumigatus. We find that this cluster as well as the previously characterized endocrocin (enc) cluster both contribute to the production of the spore metabolite endocrocin. Whereas trypacidin is eliminated when only tpc cluster genes are deleted, endocrocin production is only eliminated when both the tpc and enc non-reducing polyketide synthase-encoding genes, tpcC and encA, respectively, are deleted. EncC, an anthrone oxidase, converts the product released from EncA to endocrocin as a final product. In contrast, endocrocin synthesis by the tpc cluster likely results from incomplete catalysis by TpcK (a putative decarboxylase), as its deletion results in a nearly 10-fold increase in endocrocin production. We suggest endocrocin is likely a shunt product in all related non-reducing polyketide synthase clusters containing homologues of TpcK and TpcL (a putative anthrone oxidase), e.g. geodin and monodictyphenone. This finding represents an unusual example of two physically discrete secondary metabolite clusters generating the same natural product in one fungal species by distinct routes. PMID:26242966

Facile Syntheses of Monodisperse Ultra-Small Au Clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bertino, Massimo F.; Sun, Zhong-Ming; Zhang, Rui

2006-11-02

During our effort to synthesize the tetrahedral Au20 cluster, we found a facile synthetic route to prepare monodisperse suspensions of ultra-small Au clusters AuN (N<12) using diphosphine ligands. In our monophasic and single-pot synthesis, a Au precursor ClAu(I)PPh3 and a bidentate phosphine ligand P(Ph)2(CH2)MP(Ph)2 (Ph = phenyl) are dissolved in an organic solvent. Au(I) is reduced slowly by a borane-tert-butylamine complex to form Au clusters coordinated by the diphosphine ligand. The Au clusters are characterized by both high resolution mass spectrometry and UV-Vis absorption spectroscopy. We found that the mean cluster size obtained depends on the chain length M ofmore » the ligand. In particular, a single monodispersed Au11 cluster is obtained with the P(Ph)2(CH2)3P(Ph)2 ligand, whereas P(Ph)2(CH2)MP(Ph)2 ligands with M = 5 and 6 yield Au10 and Au8 clusters. The simplicity of our synthetic method makes it suitable for large-scale production of nearly monodisperse ultrasmall Au clusters. It is suggested that diphosphines provide a set of flexible ligands to allow size-controlled synthesis of Au nanoparticles.« less

Synthesis, Delivery and Regulation of Eukaryotic Heme and Fe-S Cluster Cofactors

PubMed Central

Barupala, Dulmini P.; Dzul, Stephen P.; Riggs-Gelasco, Pamela Jo; Stemmler, Timothy L.

2016-01-01

In humans, the bulk of iron in the body (over 75%) is directed towards heme- or Fe-S cluster cofactor synthesis, and the complex, highly regulated pathways in place to accomplish biosynthesis have evolved to safely assemble and load these cofactors into apoprotein partners. In eukaryotes, heme biosynthesis is both initiated and finalized within the mitochondria, while cellular Fe-S cluster assembly is controlled by correlated pathways both within the mitochondria and within the cytosol. Iron plays a vital role in a wide array of metabolic processes and defects in iron cofactor assembly leads to human diseases. This review describes progress towards our molecular-level understanding of cellular heme and Fe-S cluster biosynthesis, focusing on the regulation and mechanistic details that are essential for understanding human disorders related to the breakdown in these essential pathways. PMID:26785297

Investigating the internal structure of galaxies and clusters through strong gravitational lensing

NASA Astrophysics Data System (ADS)

Jigish Gandhi, Pratik; Grillo, Claudio; Bonamigo, Mario

2018-01-01

Gravitational lensing studies have radically improved our understanding of the internal structure of galaxies and cluster-scale systems. In particular, the combination of strong lensing and stellar dynamics or stellar population synthesis models have made it possible to characterize numerous fundamental properties of the galaxies as well as dark matter halos and subhalos with unprecedented robustness and accuracy. Here we demonstrate the usefulness and accuracy of strong lensing as a probe for characterising the properties of cluster members as well as dark matter halos, to show that such characterisation carried out via lensing analyses alone is as viable as those carried out through a combination of spectroscopy and lensing analyses.Our study uses focuses on the early-type galaxy cluster MACS J1149.5+2223 at redshift 0.54 in the Hubble Frontier Fields (HFF) program, where the first magnified and spatially resolved multiple images of supernova (SN) “Refsdal” and its late-type host galaxy at redshift 1.489 were detected. The Refsdal system is unique in being the first ever multiply-imaged supernova, with it’s first four images appearing in an Einstein Cross configuration around one of the cluster members in 2015. In our lensing analyses we use HST data of the multiply-imaged SN Refsdal to constrain the dynamical masses, velocity dispersions, and virial radii of individual galaxies and dark matter halos in the MACS J1149.5+2223 cluster. For our lensing models we select a sample of 300 cluster members within approximately 500 kpc from the BCG, and a set of reliable multiple images associated with 18 distinct knots in the SN host spiral galaxy, as well as multiple images of the supernova itself. Our results provide accurate measurements of the masses, velocity dispersions, and radii of the cluster’s dark matter halo as well as three chosen members galaxies, in strong agreement with those obtained by Grillo et al 2015, demonstrating the usefulness of strong lensing in characterising the properties of cluster-scale systems.

Mammographic texture synthesis using genetic programming and clustered lumpy background

NASA Astrophysics Data System (ADS)

Castella, Cyril; Kinkel, Karen; Descombes, François; Eckstein, Miguel P.; Sottas, Pierre-Edouard; Verdun, Francis R.; Bochud, François O.

2006-03-01

In this work we investigated the digital synthesis of images which mimic real textures observed in mammograms. Such images could be produced in an unlimited number with tunable statistical properties in order to study human performance and model observer performance in perception experiments. We used the previously developed clustered lumpy background (CLB) technique and optimized its parameters with a genetic algorithm (GA). In order to maximize the realism of the textures, we combined the GA objective approach with psychophysical experiments involving the judgments of radiologists. Thirty-six statistical features were computed and averaged, over 1000 real mammograms regions of interest. The same features were measured for the synthetic textures, and the Mahalanobis distance was used to quantify the similarity of the features between the real and synthetic textures. The similarity, as measured by the Mahalanobis distance, was used as GA fitness function for evolving the free CLB parameters. In the psychophysical approach, experienced radiologists were asked to qualify the realism of synthetic images by considering typical structures that are expected to be found on real mammograms: glandular and fatty areas, and fiber crossings. Results show that CLB images found via optimization with GA are significantly closer to real mammograms than previously published images. Moreover, the psychophysical experiments confirm that all the above mentioned structures are reproduced well on the generated images. This means that we can generate an arbitrary large database of textures mimicking mammograms with traceable statistical properties.

Synthesis, characterization and magnetic behavior of Co/MCM-41 nano-composites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cuello, N.; Elías, V.; CONICET

2013-09-15

Synthesis, structure and magnetic properties of Co/MCM-41 as magnetic nano-composites have been investigated. Mesoporous materials with different degrees of metal loading were prepared by wet impregnation and characterized by ICP, XRD, N{sub 2} adsorption, UV–vis DRS, TPR and EPMA-EDS. Cobalt oxide clusters and Co{sub 3}O{sub 4} nano-particles could be confined inside the mesopores of MCM-41, being this fact favored by the Co loading increasing. In addition, larger crystals of Co{sub 3}O{sub 4} detectable by XRD also grow on the surface when the Co loading is enhanced. The magnetic characterization was performed in a SQUID magnetometer using a maximum magnetic appliedmore » field µ{sub 0}Ha=1 T. While the samples with the higher Co loadings showed a behavior typically paramagnetic, a superparamagnetic contribution is more notorious for lower loadings, suggesting high Co species dispersion. - Graphical abstract: Room temperature hysteresis loops as a function of the Co content. Display Omitted - Highlights: • Co species as isolated Co{sup 2+}, oxide clusters and Co{sub 3}O{sub 4} nano-particles were detected. • For higher Co loads were detected, by XRD, Co{sub 3}O{sub 4} particles on the external surface. • The confining of Co species inside the mesopores was achieved by increasing Co load. • Paramagnetism from oxide clusters/nano-particles becomes dominant for higher Co loads. • Superparamagnetism can be assigned to Co species of small size and finely dispersed.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rana, Abhinandan; Jana, Swapan Kumar; Datta, Sayanti

The synthesis of two new lead(II) coordination polymers, [Pb{sub 2}(mpic){sub 4}(H{sub 2}O)]·0.5H{sub 2}O (1) and [Pb{sub 2}(phen){sub 2}(cit)(mes)]·2H{sub 2}O (2) has been reported, where mpic=3-methyl picolinate, phen=o-phenanthroline, H{sub 2}cit=citraconic acid, H{sub 2}mes mesaconic acid. X-ray single crystal diffraction analyses showed that the complexes comprise topologically different 1D polymeric chains stabilized by weak interactions and both containing tetranuclear Pb{sub 4} units connected by carboxylate groups. In compound 1 3-methylpicolinic acid is formed in situ from 3-methyl piconitrile, and mesaconate and citraconate anions were surprisingly formed from itaconic acid during the synthesis of 2. The photoluminescence and thermal properties of the complexesmore » have been studied. - Graphical abstract: Two new topologically different 1D coordination polymers formed by Pb{sub 4} clusters have been synthesized and characterized by X-ray analysis. The luminescence and thermal properties have been studied. Display Omitted - Highlights: • Both the complexes, made up of different ligands, forms topologycally different 1D polymeric chains containing Pb{sub 4} clusters. • The final structures are stabilized by weak interactions (H-bond, π∙∙∙π stacking). • In complex 1, the 3-methylpicolinic acid is generated in situ from 3-methyl piconitrile. • Mesaconate and citraconate anions are surprisingly formed in situ from itaconic acid during the synthesis of complex 2, indicating an exceptional transformation.« less

Chirality specific and spatially uniform synthesis of single-walled carbon nanotubes from a sputtered Co-W bimetallic catalyst

NASA Astrophysics Data System (ADS)

An, Hua; Kumamoto, Akihito; Takezaki, Hiroki; Ohyama, Shinnosuke; Qian, Yang; Inoue, Taiki; Ikuhara, Yuichi; Chiashi, Shohei; Xiang, Rong; Maruyama, Shigeo

2016-07-01

Synthesis of single-walled carbon nanotubes (SWNTs) with well-defined atomic arrangements has been widely recognized in the past few decades as the biggest challenge in the SWNT community, and has become a bottleneck for the application of SWNTs in nano-electronics. Here, we report a selective synthesis of (12, 6) SWNTs with an enrichment of 50%-70% by chemical vapor deposition (CVD) using sputtered Co-W as a catalyst. This is achieved under much milder reduction and growth conditions than those in the previous report using transition-metal molecule clusters as catalyst precursors (Nature, 2014, 510, 522). Meanwhile, in-plane transmission electron microscopy unambiguously identified an intermediate structure of Co6W6C, which is strongly associated with selective growth. However, most of the W atoms disappear after a 5 min CVD growth, which implies that anchoring W may be important in this puzzling Co-W system.Synthesis of single-walled carbon nanotubes (SWNTs) with well-defined atomic arrangements has been widely recognized in the past few decades as the biggest challenge in the SWNT community, and has become a bottleneck for the application of SWNTs in nano-electronics. Here, we report a selective synthesis of (12, 6) SWNTs with an enrichment of 50%-70% by chemical vapor deposition (CVD) using sputtered Co-W as a catalyst. This is achieved under much milder reduction and growth conditions than those in the previous report using transition-metal molecule clusters as catalyst precursors (Nature, 2014, 510, 522). Meanwhile, in-plane transmission electron microscopy unambiguously identified an intermediate structure of Co6W6C, which is strongly associated with selective growth. However, most of the W atoms disappear after a 5 min CVD growth, which implies that anchoring W may be important in this puzzling Co-W system. Electronic supplementary information (ESI) available: Raman spectroscopy (G-band) of SWNTs grown from Co and Co-W catalyst; Kataura plot for chirality assignment; Raman spectra (RBM region) of SWNTs grown from low temperature reduced monometallic Co; relative intensities of the 197 cm-1 peak with respect to the total sum intensity; TEM image of Co-W catalyst reduced at six different temperatures (600, 650, 700, 750, 800, and 850 °C) TEM images of SWNTs grown from Co monometallic catalyst. See DOI: 10.1039/c6nr02749k

Structural variation from heterometallic cluster-based 1D chain to heterometallic tetranuclear cluster: Syntheses, structures and magnetic properties

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Shu-Hua, E-mail: zsh720108@163.com; Zhao, Ru-Xia; Li, He-Ping

Using the solvothermal method, we present the comparative preparation of ([Co{sub 3}Na(dmaep){sub 3}(ehbd)(N{sub 3}){sub 3}]·DMF){sub n} (1) and [Co{sub 2}Na{sub 2}(hmbd){sub 4}(N{sub 3}){sub 2}(DMF){sub 2}] (2), where Hehbd is 3-ethoxy-2-hydroxy-benzaldehyde, Hhmbd is 3-methoxy-2-hydroxy-benzaldehyde, and Hdmaep is 2-dimethylaminomethyl-6-ethoxy-phenol, which was synthesized by an in-situ reaction. Complexes 1 and 2 were characterized by elemental analysis, IR spectroscopy, and X-ray single-crystal diffraction. Complex 1 is a novel heterometallic cluster-based 1-D chain and 2 is a heterometallic tetranuclear cluster. The (Co{sub 3}{sup II}Na) and (Co{sub 2}{sup II}Na{sub 2}) cores display dominant ferromagnetic interaction from the nature of the binding modes through μ{sub 1,1,1}-N{sub 3}{supmore » –} (end-on, EO). - Graphical abstract: Two novel cobalt complexes have been prepared. Compound 1 consists of tetranuclear (Co{sub 3}{sup II}Na) units, which further formed a 1-D chain. Compound 2 is heterometallic tetranuclear cluster. Two complexes display dominant ferromagnetic interaction. - Highlights: • Two new heterometallic complexes have been synthesized by solvothermal method. • The stereospecific blockade of the ligands in the synthesis system seems to be the most important synthetic parameter. • The magnetism studies show that 1 and 2 exhibit ferromagnetic interactions. • Complex 1 shows slowing down of magnetization and not blocking of magnetization.« less

Organization of the capsule biosynthesis gene locus of the oral streptococcus Streptococcus anginosus.

PubMed

Tsunashima, Hiroyuki; Miyake, Katsuhide; Motono, Makoto; Iijima, Shinji

2012-03-01

The capsular polysaccharide (CPS) of the important oral streptococcus Streptococcus anginosus, which causes endocarditis, and the genes for its synthesis have not been clarified. In this study, we investigated the gene locus required for CPS synthesis in S. anginosus. Southern hybridization using the cpsE gene of the well-characterized bacterium S. agalactiae revealed that there is a similar gene in the genome of S. anginosus. By using the colony hybridization technique and inverse PCR, we isolated the CPS synthesis (cps) genes of S. anginosus. This gene cluster consisted of genes containing typical regulatory genes, cpsA-D, and glycosyltransferase genes coding for glucose, rhamnose, N-acetylgalactosamine, and galactofuranose transferases. Furthermore, we confirmed that the cps locus is required for CPS synthesis using a mutant strain with a defective cpsE gene. The cps cluster was found to be located downstream the nrdG gene, which encodes ribonucleoside triphosphate reductase activator, as is the case in other oral streptococci such as S. gordonii and S. sanguinis. However, the location of the gene cluster was different from those of S. pneumonia and S. agalactiae. Copyright © 2011 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Synthesis efficiency of heavy carbon clusters from ETFE ablated by different numbers of laser pulse in vacuum

NASA Astrophysics Data System (ADS)

Shibagaki, K.; Takada, N.; Sasaki, K.; Kadota, K.

2002-09-01

We have carried out mass spectral analysis of positive ions produced by laser ablation of a copolymer of ethylene and tetrafluoroethylene (ETFE: [CH 2CH 2CF 2CF 2] n) in vacuum using time-of-flight mass spectrometry (TOF-MS). The surfaces of the ETFE targets irradiated by different numbers of laser pulse were analyzed by X-ray photoelectron spectroscopy (XPS) and scanning electron microscopy (SEM). Heavy carbon cluster ions C n+ with n≥30 were observed in the mass spectra. The fractional abundance of heavy clusters in the mass spectrum decreased with the number of laser pulse. On the other hand, carbon became rich in the atomic composition of the laser-irradiated surface, and the eroded area on the surface increased with the number of laser pulse. From these results, it is suggested that the carbon-rich material surface results in the less efficient production of heavy carbon clusters. In addition, it is also suggested that clustering reactions in eroded craters do not contribute to the synthesis of heavy clusters.

Bacillus amyloliquefaciens GA1 as a source of potent antibiotics and other secondary metabolites for biocontrol of plant pathogens

PubMed Central

2009-01-01

Background Phytopathogenic fungi affecting crop and post-harvested vegetables are a major threat to food production and food storage. To face these drawbacks, producers have become increasingly dependent on agrochemicals. However, intensive use of these compounds has led to the emergence of pathogen resistance and severe negative environmental impacts. There are also a number of plant diseases for which chemical solutions are ineffective or non-existent as well as an increasing demand by consumers for pesticide-free food. Thus, biological control through the use of natural antagonistic microorganisms has emerged as a promising alternative to chemical pesticides for more rational and safe crop management. Results The genome of the plant-associated B. amyloliquefaciens GA1 was sample sequenced. Several gene clusters involved in the synthesis of biocontrol agents were detected. Four gene clusters were shown to direct the synthesis of the cyclic lipopeptides surfactin, iturin A and fengycin as well as the iron-siderophore bacillibactin. Beside these non-ribosomaly synthetised peptides, three additional gene clusters directing the synthesis of the antibacterial polyketides macrolactin, bacillaene and difficidin were identified. Mass spectrometry analysis of culture supernatants led to the identification of these secondary metabolites, hence demonstrating that the corresponding biosynthetic gene clusters are functional in strain GA1. In addition, genes encoding enzymes involved in synthesis and export of the dipeptide antibiotic bacilysin were highlighted. However, only its chlorinated derivative, chlorotetaine, could be detected in culture supernatants. On the contrary, genes involved in ribosome-dependent synthesis of bacteriocin and other antibiotic peptides were not detected as compared to the reference strain B. amyloliquefaciens FZB42. Conclusion The production of all of these antibiotic compounds highlights B. amyloliquefaciens GA1 as a good candidate for the development of biocontrol agents. PMID:19941639

Bacillus amyloliquefaciens GA1 as a source of potent antibiotics and other secondary metabolites for biocontrol of plant pathogens.

PubMed

Arguelles-Arias, Anthony; Ongena, Marc; Halimi, Badre; Lara, Yannick; Brans, Alain; Joris, Bernard; Fickers, Patrick

2009-11-26

Phytopathogenic fungi affecting crop and post-harvested vegetables are a major threat to food production and food storage. To face these drawbacks, producers have become increasingly dependent on agrochemicals. However, intensive use of these compounds has led to the emergence of pathogen resistance and severe negative environmental impacts. There are also a number of plant diseases for which chemical solutions are ineffective or non-existent as well as an increasing demand by consumers for pesticide-free food. Thus, biological control through the use of natural antagonistic microorganisms has emerged as a promising alternative to chemical pesticides for more rational and safe crop management. The genome of the plant-associated B. amyloliquefaciens GA1 was sample sequenced. Several gene clusters involved in the synthesis of biocontrol agents were detected. Four gene clusters were shown to direct the synthesis of the cyclic lipopeptides surfactin, iturin A and fengycin as well as the iron-siderophore bacillibactin. Beside these non-ribosomaly synthetised peptides, three additional gene clusters directing the synthesis of the antibacterial polyketides macrolactin, bacillaene and difficidin were identified. Mass spectrometry analysis of culture supernatants led to the identification of these secondary metabolites, hence demonstrating that the corresponding biosynthetic gene clusters are functional in strain GA1. In addition, genes encoding enzymes involved in synthesis and export of the dipeptide antibiotic bacilysin were highlighted. However, only its chlorinated derivative, chlorotetaine, could be detected in culture supernatants. On the contrary, genes involved in ribosome-dependent synthesis of bacteriocin and other antibiotic peptides were not detected as compared to the reference strain B. amyloliquefaciens FZB42. The production of all of these antibiotic compounds highlights B. amyloliquefaciens GA1 as a good candidate for the development of biocontrol agents.

A cryptic pigment biosynthetic pathway uncovered by heterologous expression is essential for conidial development in Pestalotiopsis fici.

PubMed

Zhang, Peng; Wang, Xiuna; Fan, Aili; Zheng, Yanjing; Liu, Xingzhong; Wang, Shihua; Zou, Huixi; Oakley, Berl R; Keller, Nancy P; Yin, Wen-Bing

2017-08-01

Spore pigmentation is very common in the fungal kingdom. The best studied pigment in fungi is melanin which coats the surface of single cell spores. What and how pigments function in a fungal species with multiple cell conidia is poorly understood. Here, we identified and deleted a polyketide synthase (PKS) gene PfmaE and showed that it is essential for multicellular conidial pigmentation and development in a plant endophytic fungus, Pestalotiopsis fici. To further characterize the melanin pathway, we utilized an advanced Aspergillus nidulans heterologous system for the expression of the PKS PfmaE and the Pfma gene cluster. By structural elucidation of the pathway metabolite scytalone in A. nidulans, we provided chemical evidence that the Pfma cluster synthesizes DHN melanin. Combining genetic deletion and combinatorial gene expression of Pfma cluster genes, we determined that the putative reductase PfmaG and the PKS are sufficient for the synthesis of scytalone. Feeding scytalone back to the P. fici ΔPfmaE mutant restored pigmentation and multicellular adherence of the conidia. These results cement a growing understanding that pigments are essential not simply for protection of spores from biotic and abiotic stresses but also for spore structural development. © 2017 John Wiley & Sons Ltd.

Synthesis, delivery and regulation of eukaryotic heme and Fe-S cluster cofactors.

PubMed

Barupala, Dulmini P; Dzul, Stephen P; Riggs-Gelasco, Pamela Jo; Stemmler, Timothy L

2016-02-15

In humans, the bulk of iron in the body (over 75%) is directed towards heme- or Fe-S cluster cofactor synthesis, and the complex, highly regulated pathways in place to accomplish biosynthesis have evolved to safely assemble and load these cofactors into apoprotein partners. In eukaryotes, heme biosynthesis is both initiated and finalized within the mitochondria, while cellular Fe-S cluster assembly is controlled by correlated pathways both within the mitochondria and within the cytosol. Iron plays a vital role in a wide array of metabolic processes and defects in iron cofactor assembly leads to human diseases. This review describes progress towards our molecular-level understanding of cellular heme and Fe-S cluster biosynthesis, focusing on the regulation and mechanistic details that are essential for understanding human disorders related to the breakdown in these essential pathways. Copyright © 2016 Elsevier Inc. All rights reserved.

Origin and chemical composition of the amorphous material from the intergrain pores of self-assembled cubic ZnS:Mn nanocrystals

NASA Astrophysics Data System (ADS)

Stefan, Mariana; Vlaicu, Ioana Dorina; Nistor, Leona Cristina; Ghica, Daniela; Nistor, Sergiu Vasile

2017-12-01

We have shown in previous investigations that the low temperature collective magnetism observed in mesoporous cubic ZnS:Mn nanocrystalline powders prepared by colloidal synthesis, with nominal doping concentrations above 0.2 at.%, is due to the formation of Mn2+ clusters with distributed antiferromagnetic coupling localized in an amorphous phase found between the cubic ZnS:Mn nanocrystals. Here we investigate the composition, origin and thermal annealing behavior of this amorphous phase in such a mesoporous ZnS:Mn sample doped with 5 at.% Mn nominal concentration. Correlated analytical transmission electron microscopy, multifrequency electron paramagnetic resonance and Fourier transform infrared spectroscopy data show that the amorphous nanomaterial consists of unreacted precursor hydrated zinc and manganese acetates trapped inside the pores and on the surface of the cubic ZnS nanocrystals. The decomposition of the acetates under isochronal annealing up to 270 °C, where the mesoporous structure is still preserved, lead to changes in the nature and strength of the magnetic interactions between the aggregated Mn2+ ions. These results strongly suggest the possibility to modulate the magnetic properties of such transition metal ions doped II-VI mesoporous structures by varying the synthesis conditions and/or by post-synthesis thermochemical treatments.

Transcriptome Analysis of Aspergillus flavus Reveals veA-Dependent Regulation of Secondary Metabolite Gene Clusters, Including the Novel Aflavarin Cluster

PubMed Central

Cary, J. W.; Han, Z.; Yin, Y.; Lohmar, J. M.; Shantappa, S.; Harris-Coward, P. Y.; Mack, B.; Ehrlich, K. C.; Wei, Q.; Arroyo-Manzanares, N.; Uka, V.; Vanhaecke, L.; Bhatnagar, D.; Yu, J.; Nierman, W. C.; Johns, M. A.; Sorensen, D.; Shen, H.; De Saeger, S.; Diana Di Mavungu, J.

2015-01-01

The global regulatory veA gene governs development and secondary metabolism in numerous fungal species, including Aspergillus flavus. This is especially relevant since A. flavus infects crops of agricultural importance worldwide, contaminating them with potent mycotoxins. The most well-known are aflatoxins, which are cytotoxic and carcinogenic polyketide compounds. The production of aflatoxins and the expression of genes implicated in the production of these mycotoxins are veA dependent. The genes responsible for the synthesis of aflatoxins are clustered, a signature common for genes involved in fungal secondary metabolism. Studies of the A. flavus genome revealed many gene clusters possibly connected to the synthesis of secondary metabolites. Many of these metabolites are still unknown, or the association between a known metabolite and a particular gene cluster has not yet been established. In the present transcriptome study, we show that veA is necessary for the expression of a large number of genes. Twenty-eight out of the predicted 56 secondary metabolite gene clusters include at least one gene that is differentially expressed depending on presence or absence of veA. One of the clusters under the influence of veA is cluster 39. The absence of veA results in a downregulation of the five genes found within this cluster. Interestingly, our results indicate that the cluster is expressed mainly in sclerotia. Chemical analysis of sclerotial extracts revealed that cluster 39 is responsible for the production of aflavarin. PMID:26209694

[Topography structure and flocculation mechanism of polymeric phosphate ferric sulfate (PPFS)].

PubMed

Zheng, Huai-li; Zhang, Hui-qin; Jiang, Shao-jie; Li, Fang; Jiao, Shi-jun; Fang, Hui-li

2011-05-01

Characteristics of polymeric phosphate ferric sulfate (PPFS) were investigated using FTIR (Fourier transform infrared spectrometer), XRD (X-ray diffraction) and SEM (scanning electron microscope) in the present study. The formed PPFS structure and morphology were stereo meshwork, which was clustered and close to coral reef, synthesis of high charge density, bioactive polyhydroxy and mixed polynuclear complex PPFS. The results showed that charge neutralization of PPFS had not played a decisive role in the coagulation beaker test and the zeta potential proved that PPFS was largely affected by bridging and netting sweep. Therefore, the coagulation mechanisms of PPFS were mainly composed of charge neutralization, adsorption bridging and netting sweep mechanisms.

Hydrothermal Synthesis of Nanostructured Vanadium Oxides

PubMed Central

Livage, Jacques

2010-01-01

A wide range of vanadium oxides have been obtained via the hydrothermal treatment of aqueous V(V) solutions. They exhibit a large variety of nanostructures ranging from molecular clusters to 1D and 2D layered compounds. Nanotubes are obtained via a self-rolling process while amazing morphologies such as nano-spheres, nano-flowers and even nano-urchins are formed via the self-assembling of nano-particles. This paper provides some correlation between the molecular structure of precursors in the solution and the nanostructure of the solid phases obtained by hydrothermal treatment. PMID:28883325

Green Synthesis of Silver Nanoparticles Decorated by Fe₃O₄/GO with Enhanced Catalytic Activity.

PubMed

Guo, Jian; Wang, Yu; Liu, Dan-Dan; Wan, Rong; Han, Guo-Zhi

2018-05-01

We report a simple and green approach to synthesize stable water-dispersible silver nanoparticles decorated by magnetic Fe3O4 and graphene oxide (GO). These results of UV-Vis spectra, along with TEM and SEM indicated that the water-dispersible silver nanoparticles had cluster flat structure and retained the optical properties of the original silver particle. Combining the advantages of Fe3O4 and GO, the composite nanoparticles showed enhanced catalytic activity with good recycling utilization rate by magnetic separation.

Au38Cu1(2-PET)24 nanocluster: synthesis, enantioseparation and luminescence.

PubMed

Kazan, Rania; Zhang, Bei; Bürgi, Thomas

2017-06-20

A CuAu 38 bimetallic nanocluster was synthesized by adding a single copper atom to the Au 38 (2-PET) 24 nanocluster. The absence of Cu x Au 38-x (2-PET) 24 doped species was demonstrated by MALDI-TOF mass spectrometry. A separation of bimetallic clusters was attained for the first time where isomers of the E2 enantiomer of the Au 38 Cu 1 (2-PET) 24 adduct were successfully isolated from their parent cluster using chiral HPLC. The CD of the isolated isomers revealed a change in their electronic structure upon copper addition. The luminescence of the Au 38 Cu 1 adduct is significantly enhanced in comparison with the parent Au 38 nanocluster. The stability of the newly formed adduct is strongly dependent on the coexistence of the Au 38 nanoclusters.

Process for producing dimethyl ether from synthesis gas

DOEpatents

Pierantozzi, R.

1985-06-04

This invention pertains to a Fischer Tropsch process for converting synthesis gas to an oxygenated hydrocarbon with particular emphasis on dimethyl ether. Synthesis gas comprising carbon monoxide and hydrogen are converted to dimethyl ether by carrying out the reaction in the presence of an alkali metal-manganese-iron carbonyl cluster incorporated onto a zirconia-alumina support.

Process for producing dimethyl ether form synthesis gas

DOEpatents

Pierantozzi, Ronald

1985-01-01

This invention pertains to a Fischer Tropsch process for converting synthesis gas to an oxygenated hydrocarbon with particular emphasis on dimethyl ether. Synthesis gas comprising carbon monoxide and hydrogen are converted to dimethyl ether by carrying out the reaction in the presence of an alkali metal-manganese-iron carbonyl cluster incorporated onto a zirconia-alumina support.

Synthesis, crystal structure and third-order non-linear optical property of heterobimetallic cluster compound [MoOICu 3S 3(2,2'-bipy) 2

NASA Astrophysics Data System (ADS)

Li, Yong; Lu, Jing; Xu, Jiqing; Cui, Xiaobing; Sun, Yinghua; Yang, Qingxin; Pan, Lingyun

2004-03-01

Nest-shaped cluster [MoOICu 3S 3(2,2'-bipy) 2] ( 1) was synthesized by the treatment of (NH 4) 2MoS 4, CuI, ( n-Bu) 4NI, and 2,2'-bipyridine (2,2'-bipy) through a solid-state reaction. It crystallizes in monoclinic space group P2 1/ n, a=9.591(2) Å, b=14.820(3) Å, c=17.951(4) Å, β=91.98(2)°, V=2549.9(10) Å3, and Z=4. The nest-shaped cluster was obtained for the first time with a neutral skeleton containing 2,2'-bipy ligand. The non-linear optical (NLO) property of [MoOICu 3S 3(2,2'-bipy) 2] in DMF solution was measured by using a Z-scan technique with 15 ns and 532 nm laser pulses. The cluster has large third-order NLO absorption and the third-order NLO refraction, its α2 and n2 values were calculated as 6.2×10 -10 and -3.8×10 -17 m 2 W -1 in a 3.7×10 -4 M DMF solution.

Synthesis, structure and research on quasi-aromaticity of a new organically templated aluminoborate: [NH0.5C4H4NH0.5][AlB12O14(OH)12

NASA Astrophysics Data System (ADS)

Hu, HengBin; Chen, XiangYi; Deng, Song; Cai, Feng; Sun, YanQiong; Chen, YiPing

2012-02-01

By employing hydrothermal method, we identify a new organically templated aluminoborate [NH0.5C4H4NH0.5][AlB12O14(OH)12] which is structurally determined by single crystal X-ray diffraction and characterized by simulated and experimental IR, 2D IR COS (two-dimensional infrared correlation spectroscopy), NICS (nucleus-independent chemical shifts) and Mulliken charges calculations. Although the cluster anions [AlB12O14(OH)12]- is identical to the counterpart of compound reported by Lin et al. at 2008, we firstly bring up its quasi-aromaticity, discuss and confirm it by NICS, Mulliken charges calculations and magnetic-induced 2D IR COS, and conclude that three isolated and non-coplanar four-center six-electron π bonds of cluster could cooperate and interact with each other to form a closed conjugated large π orbital system, endowing the cluster anions with quasi-aromaticity. Thus, a one-dimensional chain is constructed by π-π stacked interaction between quasi-aromatic clusters and aromatic pyrazine along [1 0¯ 1] direction. The title compound crystallizes in monoclinic space group C2/c with a = 18.397(4), b = 12.0670(16), c = 11.075(2) Å, α = 90.00, β = 116.483(11), γ = 90.00°, Z = 4, V = 2200.6(7) Å, R = 0.0442 and wR = 0.1128 for 2689 observed reflections.

Undecametallic and hexadecametallic ferric oxo–hydroxo/ethoxo pivalate clusters

DOE PAGES

Baca, Svetlana G.; Speldrich, Manfred; van Leusen, Jan; ...

2015-03-27

The synthesis strategies for highly condensed {Fe 11} and {Fe 16} pivalate clusters have been developed based on archetypal geometrically frustrated triangular {Fe 3(μ 3-O)} motifs that are interlinked via oxo, hydroxo, ethoxo, and carboxylate groups.

Atomically Precise Metal Nanoclusters for Catalytic Application

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jin, Rongchao

2016-11-18

The central goal of this project is to explore the catalytic application of atomically precise gold nanoclusters. By solving the total structures of ligand-protected nanoclusters, we aim to correlate the catalytic properties of metal nanoclusters with their atomic/electronic structures. Such correlation unravel some fundamental aspects of nanocatalysis, such as the nature of particle size effect, origin of catalytic selectivity, particle-support interactions, the identification of catalytically active centers, etc. The well-defined nanocluster catalysts mediate the knowledge gap between single crystal model catalysts and real-world conventional nanocatalysts. These nanoclusters also hold great promise in catalyzing certain types of reactions with extraordinarily highmore » selectivity. These aims are in line with the overall goals of the catalytic science and technology of DOE and advance the BES mission “to support fundamental research to understand, predict, and ultimately control matter and energy at the level of electrons, atoms, and molecules”. Our group has successfully prepared different sized, robust gold nanoclusters protected by thiolates, such as Au 25(SR) 18, Au 28(SR) 20, Au 38(SR) 24, Au 99(SR) 42, Au 144(SR) 60, etc. Some of these nanoclusters have been crystallographically characterized through X-ray crystallography. These ultrasmall nanoclusters (< 2 nm diameter) exhibit discrete electronic structures due to quantum size effect, as opposed to quasicontinuous band structure of conventional metal nanoparticles or bulk metals. The available atomic structures (metal core plus surface ligands) of nanoclusters serve as the basis for structure-property correlations. We have investigated the unique catalytic properties of nanoclusters (i.e. not observed in conventional nanogold catalysts) and revealed the structure-selectivity relationships. Highlights of our works include: i) Effects of ligand, cluster charge state, and size on the catalytic reactivity in CO oxidation, semihydrogenation of alkynes; ii) Size-controlled synthesis of Au-n clusters and structural elucidation; iii) Catalytic mechanisms and correlation with structures of cluster catalyst; iv) Catalytic properties of Au nanorods in chemoselective hydrogenation of nitrobenzaldehyde and visible light driven photocatalytic reactions.« less

Au10(SG)10: A Chiral Gold Catenane Nanocluster with Zero Confined Electrons. Optical Properties and First-Principles Theoretical Analysis.

PubMed

Bertorelle, Franck; Russier-Antoine, Isabelle; Calin, Nathalie; Comby-Zerbino, Clothilde; Bensalah-Ledoux, Amina; Guy, Stephan; Dugourd, Philippe; Brevet, Pierre-François; Sanader, Željka; Krstić, Marjan; Bonačić-Koutecký, Vlasta; Antoine, Rodolphe

2017-05-04

We report facile synthesis of the Au 10 (SG) 10 nanoclusters, where SG stands for glutathione, found to be promising as a new class of radiosensitizers for cancer radiotherapy. The homoleptic catenane structure with two Au 5 SG 5 interconnected rings, among different isomer structures, gives the best agreement between theoretical and experimental optical spectra and XRD patterns. This catenane structure exhibits a centrosymmetry-broken structure, resulting in enhanced second harmonic response and new characteristic circular dichroism signals in the spectral region of 250-400 nm. This is the first determination of the nonlinear optical properties of a ligated cluster with an equal Au-to-ligand ratio, thus without a metallic core and therefore zero confined electrons. Insight into the nonlinear and chiroptical efficiencies arising from interplay between structural and electronic properties is provided by the TD-DFT approach.

Coalescence and Collisions of Gold Nanoparticles

PubMed Central

Antúnez-García, Joel; Mejía-Rosales, Sergio; Pérez-Tijerina, Eduardo; Montejano-Carrizales, Juan Martín; José-Yacamán, Miguel

2011-01-01

We study the assembling of small gold clusters subject to collisions and close contact coalescence by using molecular dynamics simulations to simulate events that occur typically in the sputtering process of synthesis. Our results support the notion that the kinetics of coalescence processes strongly determine the geometry and structure of the final particle. While impact velocities, relative orientations, and the initial shape of the interacting particles are unlikely to strictly determine the structural details of the newly formed particle, we found that high initial temperatures and/or impact velocities increase the probability of appearance of icosahedral-like structures, Wulff polyhedra are likely to be formed as a product of the interactions between nanospheres, while the appearance of fcc particles of approximately cuboctahedral shape is mainly due to the interaction between icosahedra. PMID:28879995

Coalescence and Collisions of Gold Nanoparticles.

PubMed

Antúnez-García, Joel; Mejía-Rosales, Sergio; Pérez-Tijerina, Eduardo; Montejano-Carrizales, Juan Martín; José-Yacamán, Miguel

2011-01-28

We study the assembling of small gold clusters subject to collisions and close contact coalescence by using molecular dynamics simulations to simulate events that occur typically in the sputtering process of synthesis. Our results support the notion that the kinetics of coalescence processes strongly determine the geometry and structure of the final particle. While impact velocities, relative orientations, and the initial shape of the interacting particles are unlikely to strictly determine the structural details of the newly formed particle, we found that high initial temperatures and/or impact velocities increase the probability of appearance of icosahedral-like structures, Wulff polyhedra are likely to be formed as a product of the interactions between nanospheres, while the appearance of fcc particles of approximately cuboctahedral shape is mainly due to the interaction between icosahedra.

Knowledge based identification of MAO-B selective inhibitors using pharmacophore and structure based virtual screening models.

PubMed

Boppana, Kiran; Dubey, P K; Jagarlapudi, Sarma A R P; Vadivelan, S; Rambabu, G

2009-09-01

Monoamine Oxidase B interaction with known ligands was investigated using combined pharmacophore and structure based modeling approach. The docking results suggested that the pharmacophore and docking models are in good agreement and are used to identify the selective MAO-B inhibitors. The best model, Hypo2 consists of three pharmacophore features, i.e., one hydrogen bond acceptor, one hydrogen bond donor and one ring aromatic. The Hypo2 model was used to screen an in-house database of 80,000 molecules and have resulted in 5500 compounds. Docking studies were performed, subsequently, on the cluster representatives of 530 hits from 5500 compounds. Based on the structural novelty and selectivity index, we have suggested 15 selective MAO-B inhibitors for further synthesis and pharmacological screening.

New double molybdate Na9Fe(MoO4)6: Synthesis, structure, properties

NASA Astrophysics Data System (ADS)

Savina, Aleksandra A.; Solodovnikov, Sergey F.; Basovich, Olga M.; Solodovnikova, Zoya A.; Belov, Dmitry A.; Pokholok, Konstantin V.; Gudkova, Irina A.; Stefanovich, Sergey Yu.; Lazoryak, Bogdan I.; Khaikina, Elena G.

2013-09-01

A new double molybdate Na9Fe(MoO4)6 was synthesized using solid state reactions and studied with X-ray powder diffraction, second harmonic generation (SHG) technique, differential scanning calorimetry, X-ray fluorescence analysis, Mössbauer and dielectric impedance spectroscopy. Single crystals of Na9Fe(MoO4)6 were obtained and its structure was solved (the space group R3¯, a=14.8264(2), c=19.2402(3) Å, V=3662.79(9) Å3, Z=6, R=0.0132). The structure is related to that of sodium ion conductor II-Na3Fe2(AsO4)3. The basic structure units are polyhedral clusters composed of central FeО6 octahedron sharing edges with three Na(1)О6 octahedra. The clusters share common vertices with bridging МоО4 tetrahedra to form an open 3D framework where the cavities are occupied by Na(2) and Na(3) atoms. The compound melts incongruently at 904.7±0.2 K. Arrhenius type temperature dependence of electric conductivity σ has been registered in solid state (σ=6.8×10-2 S сm-1 at 800 K), thus allowing considering Na9Fe(MoO4)6 as a new sodium ion conductor.

Tetrahydrolipstatin Inhibition, Functional Analyses, and Three-dimensional Structure of a Lipase Essential for Mycobacterial Viability

DOE Office of Scientific and Technical Information (OSTI.GOV)

Crellin, Paul K.; Vivian, Julian P.; Scoble, Judith

2010-09-17

The highly complex and unique mycobacterial cell wall is critical to the survival of Mycobacteria in host cells. However, the biosynthetic pathways responsible for its synthesis are, in general, incompletely characterized. Rv3802c from Mycobacterium tuberculosis is a partially characterized phospholipase/thioesterase encoded within a genetic cluster dedicated to the synthesis of core structures of the mycobacterial cell wall, including mycolic acids and arabinogalactan. Enzymatic assays performed with purified recombinant proteins Rv3802c and its close homologs from Mycobacterium smegmatis (MSMEG{_}6394) and Corynebacterium glutamicum (NCgl2775) show that they all have significant lipase activities that are inhibited by tetrahydrolipstatin, an anti-obesity drug that coincidentlymore » inhibits mycobacterial cell wall biosynthesis. The crystal structure of MSMEG{_}6394, solved to 2.9 {angstrom} resolution, revealed an {alpha}/{beta} hydrolase fold and a catalytic triad typically present in esterases and lipases. Furthermore, we demonstrate direct evidence of gene essentiality in M. smegmatis and show the structural consequences of loss of MSMEG{_}6394 function on the cellular integrity of the organism. These findings, combined with the predicted essentiality of Rv3802c in M. tuberculosis, indicate that the Rv3802c family performs a fundamental and indispensable lipase-associated function in mycobacteria.« less

Tetrahydrolipstatin inhibition, functional analyses, and three-dimensional structure of a lipase essential for mycobacterial viability.

PubMed

Crellin, Paul K; Vivian, Julian P; Scoble, Judith; Chow, Frances M; West, Nicholas P; Brammananth, Rajini; Proellocks, Nicholas I; Shahine, Adam; Le Nours, Jerome; Wilce, Matthew C J; Britton, Warwick J; Coppel, Ross L; Rossjohn, Jamie; Beddoe, Travis

2010-09-24

The highly complex and unique mycobacterial cell wall is critical to the survival of Mycobacteria in host cells. However, the biosynthetic pathways responsible for its synthesis are, in general, incompletely characterized. Rv3802c from Mycobacterium tuberculosis is a partially characterized phospholipase/thioesterase encoded within a genetic cluster dedicated to the synthesis of core structures of the mycobacterial cell wall, including mycolic acids and arabinogalactan. Enzymatic assays performed with purified recombinant proteins Rv3802c and its close homologs from Mycobacterium smegmatis (MSMEG_6394) and Corynebacterium glutamicum (NCgl2775) show that they all have significant lipase activities that are inhibited by tetrahydrolipstatin, an anti-obesity drug that coincidently inhibits mycobacterial cell wall biosynthesis. The crystal structure of MSMEG_6394, solved to 2.9 Å resolution, revealed an α/β hydrolase fold and a catalytic triad typically present in esterases and lipases. Furthermore, we demonstrate direct evidence of gene essentiality in M. smegmatis and show the structural consequences of loss of MSMEG_6394 function on the cellular integrity of the organism. These findings, combined with the predicted essentiality of Rv3802c in M. tuberculosis, indicate that the Rv3802c family performs a fundamental and indispensable lipase-associated function in mycobacteria.

A starburst region at the tip of the Galactic bar around l=347-350

NASA Astrophysics Data System (ADS)

Marco, Amparo; Negueruela, Ignacio; González-Fernández, Carlos; Maíz-Apellániz, Jesús; Dorda, Ricardo; Clark, J. Simon

2015-08-01

In the past few years, several clusters of red supergiants have been discovered in a small region of the Milky Way, close to the base of the Scutum-Crux Arm and the tip of the Long Bar, between l=24º and l=29º. According to the number of observed red supergiants and using population synthesis models, they must contain very large stellar populations to harbour so many RSGs, some of them being candidates to the most massive young clusters in the Galaxy. These massive open clusters are part of a huge structure most likely containing hundreds of red supergiants. These results suggest that the Scutum complex represents a giant star formation region triggered by dynamical excitation by the Galactic bar, whose tip is believed to intersect the Scutum-Crux Arm close to this region. If this scenario is correct, a similar structure would be expected close to the opposite end of the Galactic long bar. We must find in an area between l=347º-350º (these sight lines include the expected location of the far tip of the Galactic bar in the model of González-Fernández et al. (2012)) likely candidates to very massive open clusters.We are carrying out a comprehensive optical and infrared photometric and spectroscopic study of this region containing the open clusters VdBH 222, Teutsch 85 and their surroundings. We have analyzed the population of VdBH 222 and we have found a large population of luminous supergiants and OB stars. The cluster lies behind ~7.5 mag of extinction and has a probable distance of ~ 10 kpc and an age of ~12 Ma. VdBH 222 is a young massive cluster with a likely mass > 20000 Msolar. Now, we are analyzing the population of the open cluster Teutsch 85 and surroundings, finding a numerous population of supergiants.In this work, we will discuss the possible role of the Galactic bar in triggering the formation of starburst clusters.

Solid state, thermal synthesis of site-specific protein-boron cluster conjugates and their physicochemical and biochemical properties.

PubMed

Goszczyński, Tomasz M; Kowalski, Konrad; Leśnikowski, Zbigniew J; Boratyński, Janusz

2015-02-01

Boron clusters represent a vast family of boron-rich compounds with extraordinary properties that provide the opportunity of exploitation in different areas of chemistry and biology. In addition, boron clusters are clinically used in boron neutron capture therapy (BNCT) of tumors. In this paper, a novel, in solid state (solvent free), thermal method for protein modification with boron clusters has been proposed. The method is based on a cyclic ether ring opening in oxonium adduct of cyclic ether and a boron cluster with nucleophilic centers of the protein. Lysozyme was used as the model protein, and the physicochemical and biological properties of the obtained conjugates were characterized. The main residues of modification were identified as arginine-128 and threonine-51. No significant changes in the secondary or tertiary structures of the protein after tethering of the boron cluster were found using mass spectrometry and circular dichroism measurements. However, some changes in the intermolecular interactions and hydrodynamic and catalytic properties were observed. To the best of our knowledge, we have described the first example of an application of cyclic ether ring opening in the oxonium adducts of a boron cluster for protein modification. In addition, a distinctive feature of the proposed approach is performing the reaction in solid state and at elevated temperature. The proposed methodology provides a new route to protein modification with boron clusters and extends the range of innovative molecules available for biological and medical testing. Copyright © 2014 Elsevier B.V. All rights reserved.

Musical sound analysis/synthesis using vector-quantized time-varying spectra

NASA Astrophysics Data System (ADS)

Ehmann, Andreas F.; Beauchamp, James W.

2002-11-01

A fundamental goal of computer music sound synthesis is accurate, yet efficient resynthesis of musical sounds, with the possibility of extending the synthesis into new territories using control of perceptually intuitive parameters. A data clustering technique known as vector quantization (VQ) is used to extract a globally optimum set of representative spectra from phase vocoder analyses of instrument tones. This set of spectra, called a Codebook, is used for sinusoidal additive synthesis or, more efficiently, for wavetable synthesis. Instantaneous spectra are synthesized by first determining the Codebook indices corresponding to the best least-squares matches to the original time-varying spectrum. Spectral index versus time functions are then smoothed, and interpolation is employed to provide smooth transitions between Codebook spectra. Furthermore, spectral frames are pre-flattened and their slope, or tilt, extracted before clustering is applied. This allows spectral tilt, closely related to the perceptual parameter ''brightness,'' to be independently controlled during synthesis. The result is a highly compressed format consisting of the Codebook spectra and time-varying tilt, amplitude, and Codebook index parameters. This technique has been applied to a variety of harmonic musical instrument sounds with the resulting resynthesized tones providing good matches to the originals.

Human mitochondrial MIA40 (CHCHD4) is a component of the Fe-S cluster export machinery.

PubMed

Murari, Anjaneyulu; Thiriveedi, Venkata Ramana; Mohammad, Fareed; Vengaldas, Viswamithra; Gorla, Madhavi; Tammineni, Prasad; Krishnamoorthy, Thanuja; Sepuri, Naresh Babu V

2015-10-15

Mitochondria play an essential role in synthesis and export of iron-sulfur (Fe-S) clusters to other sections of a cell. Although the mechanism of Fe-S cluster synthesis is well elucidated, information on the identity of the proteins involved in the export pathway is limited. The present study identifies hMIA40 (human mitochondrial intermembrane space import and assembly protein 40), also known as CHCHD4 (coiled-coil-helix-coiled-coil-helix domain-containing 4), as a component of the mitochondrial Fe-S cluster export machinery. hMIA40 is an iron-binding protein with the ability to bind iron in vivo and in vitro. hMIA40 harbours CPC (Cys-Pro-Cys) motif-dependent Fe-S clusters that are sensitive to oxidation. Depletion of hMIA40 results in accumulation of iron in mitochondria concomitant with decreases in the activity and stability of Fe-S-containing cytosolic enzymes. Intriguingly, overexpression of either the mitochondrial export component or cytosolic the Fe-S cluster assembly component does not have any effect on the phenotype of hMIA40-depleted cells. Taken together, our results demonstrate an indispensable role for hMIA40 for the export of Fe-S clusters from mitochondria. © 2015 Authors; published by Portland Press Limited.

Nontoxic strains of cyanobacteria are the result of major gene deletion events induced by a transposable element.

PubMed

Christiansen, Guntram; Molitor, Carole; Philmus, Benjamin; Kurmayer, Rainer

2008-08-01

Blooms that are formed by cyanobacteria consist of toxic and nontoxic strains. The mechanisms that result in the occurrence of nontoxic strains are enigmatic. All the nontoxic strains of the filamentous cyanobacterium Planktothrix that were isolated from 9 European countries were found to have lost 90% of a large microcystin synthetase (mcy) gene cluster that encoded the synthesis of the toxic peptide microcystin (MC). Those strains still contain the flanking regions of the mcy gene cluster along with remnants of the transposable elements that are found in between. The majority of the strains still contain a gene coding for a distinct thioesterase type II (mcyT), which is putatively involved in MC synthesis. The insertional inactivation of mcyT in an MC-producing strain resulted in the reduction of MC synthesis by 94 +/- 2% (1 standard deviation). Nontoxic strains that occur in shallow lakes throughout Europe form a monophyletic lineage. A second lineage consists of strains that contain the mcy gene cluster but differ in their photosynthetic pigment composition, which is due to the occurrence of strains that contain phycocyanin or large amounts of phycoerythrin in addition to phycocyanin. Strains containing phycoerythrin typically occur in deep-stratified lakes. The rare occurrence of gene cluster deletion, paired with the evolutionary diversification of the lineages of strains that lost or still contain the mcy gene cluster, needs to be invoked in order to explain the absence or dominance of toxic cyanobacteria in various habitats.

Cobalt coordination and clustering in alpha-Co(OH)(2) revealed by synchrotron X-ray total scattering.

PubMed

Neilson, James R; Kurzman, Joshua A; Seshadri, Ram; Morse, Daniel E

2010-09-03

Structures of layered metal hydroxides are not well described by traditional crystallography. Total scattering from a synthesis-controlled subset of these materials, as described here, reveals that different cobalt coordination polyhedra cluster within each layer on short length scales, offering new insights and approaches for understanding the properties of these and related layered materials. Structures related to that of brucite [Mg(OH)(2)] are ubiquitous in the mineral world and offer a variety of useful functions ranging from catalysis and ion-exchange to sequestration and energy transduction, including applications in batteries. However, it has been difficult to resolve the atomic structure of these layered compounds because interlayer disorder disrupts the long-range periodicity necessary for diffraction-based structure determination. For this reason, traditional unit-cell-based descriptions have remained inaccurate. Here we apply, for the first time to such layered hydroxides, synchrotron X-ray total scattering methods-analyzing both the Bragg and diffuse components-to resolve the intralayer structure of three different alpha-cobalt hydroxides, revealing the nature and distribution of metal site coordination. The different compounds with incorporated chloride ions have been prepared with kinetic control of hydrolysis to yield different ratios of octahedrally and tetrahedrally coordinated cobalt ions within the layers, as confirmed by total scattering. Real-space analyses indicate local clustering of polyhedra within the layers, manifested in the weighted average of different ordered phases with fixed fractions of tetrahedrally coordinated cobalt sites. These results, hidden from an averaged unit-cell description, reveal new structural characteristics that are essential to understanding the origin of fundamental material properties such as color, anion exchange capacity, and magnetic behavior. Our results also provide further insights into the detailed mechanisms of aqueous hydrolysis chemistry of hydrated metal salts. We emphasize the power of the methods used here for establishing structure-property correlations in functional materials with related layered structures.

Alpha chymotrypsin coated clusters of Fe3O4 nanoparticles for biocatalysis in low water media

PubMed Central

2012-01-01

Background Enzymes in low water containing non aqueous media are useful for organic synthesis. For example, hydrolases in such media can be used for synthetic purposes. Initial work in this area was carried out with lyophilized powders of enzymes. These were found to have poor activity. Drying (removing bulk water) by precipitation turned out to be a better approach. As enzymes in such media are heterogeneous catalysts, spreading these precipitates over a large surface gave even better results. In this context, nanoparticles with their better surface to volume ratio provide obvious advantage. Magnetic nanoparticles have an added advantage of easy separation after the reaction. Keeping this in view, alpha chymotrypsin solution in water was precipitated over a stirred population of Fe3O4 nanoparticles in n-propanol. This led to alpha chymotrypsin activity coated over clusters of Fe3O4 nanoparticles. These preparations were found to have quite high transesterification activity in low water containing n-octane. Results Precipitation of alpha chymotrypsin over a stirred suspension of Fe3O4 nanoparticles (3.6 nm diameter) led to the formation of enzyme coated clusters of nanoparticles (ECCNs). These clusters were also magnetic and their hydrodynamic diameter ranged from 1.2- 2.6 microns (as measured by dynamic light scattering). Transmission electron microscopy (TEM), showed that these clusters had highly irregular shapes. Transesterification assay of various clusters in anhydrous n-octane led to optimization of concentration of nanoparticles in suspension during precipitation. Optimized design of enzyme coated magnetic clusters of nanoparticles (ECCN 3) showed the highest initial rate of 465 nmol min-1 mg-1protein which was about 9 times higher as compared to the simple precipitates with an initial rate of 52 nmol min-1 mg-1 protein. Circular Dichroism (CD)(with a spinning cell accessory) showed that secondary structure content of the alpha Chymotrypsin in ECCN 3 [15% α-helix, 37% β-sheet and 48% random coil] was identical to the simple precipitates of alpha chymotrypsin. Conclusion A strategy for obtaining a high activity preparation of alpha chymotrypsin for application in low water media is described. Such high activity biocatalysts are useful in organic synthesis. PMID:23137100

[Ag115S34(SCH2C6H4 tBu)47(dpph)6]: synthesis, crystal structure and NMR investigations of a soluble silver chalcogenide nanocluster† †Dedicated to Evamarie Hey-Hawkins on the occasion of her 60th birthday. ‡ ‡Electronic supplementary information (ESI) available: CCDC 1507868. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c6sc04578b Click here for additional data file. Click here for additional data file.

PubMed Central

Fuhr, Olaf; Breitung, Ben; Kiran Chakravadhanula, Venkata Sei; Guthausen, Gisela; Hennrich, Frank; Yu, Wen; Kappes, Manfred M.; Roesky, Peter W.

2017-01-01

With the aim to synthesize soluble cluster molecules, the silver salt of (4-(tert-butyl)phenyl)methanethiol [AgSCH2C6H4 tBu] was applied as a suitable precursor for the formation of a nanoscale silver sulfide cluster. In the presence of 1,6-(diphenylphosphino)hexane (dpph), the 115 nuclear silver cluster [Ag115S34(SCH2C6H4 tBu)47(dpph)6] was obtained. The molecular structure of this compound was elucidated by single crystal X-ray analysis and fully characterized by spectroscopic techniques. In contrast to most of the previously published cluster compounds with more than a hundred heavy atoms, this nanoscale inorganic molecule is soluble in organic solvents, which allowed a comprehensive investigation in solution by UV-Vis spectroscopy and one- and two-dimensional NMR spectroscopy including 31P/109Ag-HSQC and DOSY experiments. These are the first heteronuclear NMR investigations on coinage metal chalcogenides. They give some first insight into the behavior of nanoscale silver sulfide clusters in solution. Additionally, molecular weight determinations were performed by 2D analytical ultracentrifugation and HR-TEM investigations confirm the presence of size-homogeneous nanoparticles present in solution. PMID:28507679

Synthesis of colloidal silver nanoparticle clusters and their application in ascorbic acid detection by SERS.

PubMed

Cholula-Díaz, Jorge L; Lomelí-Marroquín, Diana; Pramanick, Bidhan; Nieto-Argüello, Alfonso; Cantú-Castillo, Luis A; Hwang, Hyundoo

2018-03-01

Ascorbic acid (vitamin C) has an essential role in the human body mainly due to its antioxidant function. In this work, metallic silver nanoparticle (AgNP) colloids were used in SERS experiments to detect ascorbic acid in aqueous solution. The AgNPs were synthesized by a green method using potato starch as reducing and stabilizing agent, and water as the solvent. The optical properties of the yellowish as-synthesized silver colloids were characterized by UV-vis spectroscopy, in which besides a typical band at 410 nm related to the localized surface plasmon resonance of the silver nanoparticles, a shoulder band around 500 nm, due to silver nanoparticle cluster formation, is presented when relatively higher concentrations of starch are used in the synthesis. These starch-capped silver nanoparticles show an intrinsic Raman peak at 1386 cm -1 assigned to deformation modes of the starch structure. The increase of the intensity of the SERS peak at 1386 cm -1 with an increase in the concentration of the ascorbic acid is related to a decrease of the gap between dimers and trimers of the silver nanoparticle clusters produced by the presence of ascorbic acid in the colloid. The limit of detection of this technique for ascorbic acid is 0.02 mM with a measurement concentration range of 0.02-10 mM, which is relevant for the application of this method for detecting ascorbic acid in biological specimen. Copyright © 2017 Elsevier B.V. All rights reserved.

Copper cluster size effect in methanol synthesis from CO 2

DOE PAGES

Yang, Bing; Liu, Cong; Halder, Avik; ...

2017-05-08

Here, size-selected Cu n catalysts ( n = 3, 4, 20) were synthesized on Al 2O 3 thin films using mass-selected cluster deposition. A systematic study of size and support effects was carried out for CO 2 hydrogenation at atmospheric pressure using a combination of in situ grazing incidence X-ray absorption spectroscopy, catalytic activity measurement, and first-principles calculations. The catalytic activity for methanol synthesis is found to strongly vary as a function of the cluster size; the Cu 4/Al 2O 3 catalyst shows the highest turnover rate for CH 3OH production. With only one atom less than Cu 4, Cumore » 3 showed less than 50% activity. Density functional theory calculations predict that the activities of the gas-phase Cu clusters increase as the cluster size decreases; however, the stronger charge transfer interaction with Al 2O 3 support for Cu 3 than for Cu 4 leads to remarkably reduced binding strength between the adsorbed intermediates and supported Cu 3, which subsequently results in a less favorable energetic pathway to transform carbon dioxide to methanol.« less

Iron-based magnetic superhalogens with pseudohalogens as ligands: An unbiased structure search

PubMed Central

Ping Ding, Li; Shao, Peng; Lu, Cheng; Hui Zhang, Fang; Wang, Li Ya

2017-01-01

We have performed an unbiased structure search for a series of neutral and anionic FeL4 (L = BO2, CN, NO2, NO3, OH, CH3, NH2, BH4 and Li2H3) clusters using the CALYPSO (Crystal structure Analysis by Particle Swarm Optimization) structure search method. To probe the superhalogen properties of neutral and anionic FeL4 clusters, we used density-functional theory with the B3LYP functional to examine three factors, including distribution of extra electron, pattern of bonding and the nature of the ligands. Theoretical results show that Fe(BO2)4, Fe(NO3)4 and Fe(NO2)4 can be classified as magnetic superhalogen due to that their electron affinities even exceed those of the constituent ligands. The magnetic moment of Fe atom is almost entirly maintained when it is decorated with various ligands except for neutral and anionic (Li2H3)4. Moreover, the current work is also extended to the salt moieties formed by hyperhalogen/superhalogen anion and Na+ ion. It is found that these salts against dissociation into Na + FeL4 are thermodynamic stable except for Na[Fe(OH)4]. These results provides a wealth of electronic structure information about FeL4 magnetic superhalogens and offer insights into the synthesis mechanisms. PMID:28327547

Hypo-electronic triple-decker sandwich complexes: synthesis and structural characterization of [(Cp*Mo)2{μ-η(6):η(6)-B4H4E-Ru(CO)3}] (E = S, Se, Te or Ru(CO)3 and Cp* = η(5)-C5Me5).

PubMed

Mondal, Bijan; Bhattacharyya, Moulika; Varghese, Babu; Ghosh, Sundargopal

2016-07-05

The syntheses and structural characterization of hypo-electronic di-molybdenum triple-decker sandwich clusters are reported. Thermolysis of [Ru3(CO)12] with an in situ generated intermediate obtained from the reaction of [Cp*MoCl4] with [LiBH4·THF] yielded an electron deficient triple-decker sandwich complex, [(Cp*Mo)2{μ-η(6):η(6)-B4H4Ru2(CO)6}], . In an effort to generate analogous triple-deckers containing group-16 elements, we isolated [(Cp*Mo)2{μ-η(6):η(6)-B4H4ERu(CO)3}] (: E = Te; : E = S; : E = Se). These clusters show a high metal coordination number and cross cluster Mo-Mo bond. The formal cluster electron count of these compounds is four or three skeletal electron pairs less than required for a canonical closo-structure of the same nuclearity. Therefore, these compounds represent a novel class of triple-decker sandwich complex with 22 or 24 valence-electrons (VE), wherein the "chair" like hexagonal middle ring is composed of B, Ru and chalcogen. One of the key differences among the synthesized triple-decker molecules is the puckering nature of the middle ring [B4RuE], which increases in the order S < Se < Ru(CO)3 < Te. In addition, Fenske-Hall and quantum-chemical calculations with DFT methods at the BP86 level of theory have been used to analyze the bonding of these novel complexes. The studies not only explain the electron unsaturation of the molecules, but also reveal the reason for the significant puckering of the middle deck. All the compounds have been characterized by IR, (1)H, (11)B, and (13)C NMR spectroscopy in solution and the solid state structures were established by crystallographic analysis.

Synthesis of Cluster-Derived PtFe/SiO(2) Catalysts for the Oxidation of CO

DOE Office of Scientific and Technical Information (OSTI.GOV)

Siani, A.; Alexeev, O.S.; Captain, B.

2009-05-27

Infrared (FTIR) and extended X-ray absorption fine structure (EXAFS) spectroscopy measurements were used to characterize the species formed after impregnation of Pt{sub 5}Fe{sub 2}(COD){sub 2}(CO){sub 12} onto silica, before and after removal of the organic ligands. The results indicate that the Pt{sub 5}Fe{sub 2}(COD){sub 2}(CO){sub 12} cluster adsorbs weakly on the SiO{sub 2} surface. Nevertheless, partial disintegration of the cluster was observed during aging even under He and at room temperature, related to the loss of CO ligands due to their interactions with silanol groups of the support. The organic ligands can be removed from a freshly impregnated cluster bymore » thermal treatment in either He or H{sub 2}, but the surface species formed in each case have different structures. Treatment in He at 350 {sup o}C leads to a complete disintegration of the Pt-Fe bimetallic core and results in the formation of highly dispersed Pt clusters with a nuclearity of six, along with surface Fe oxide-like species. In contrast, bimetallic PtFe nanoparticles with an average size of approximately 1 nm were formed when a similar H{sub 2} treatment was used. In this case, a greater degree of metal dispersion and a larger fraction of Pt-Fe interactions were observed compared to the PtFe/SiO{sub 2} samples prepared by co-impregnation of monometallic salt precursors. Electronic interactions between Pt and Fe atoms in such cluster-derived samples led to an increased electron density on platinum, as indicated by a red shift of the frequencies of FTIR bands for adsorbed NO and CO. These electronic interactions affect the strength of the CO adsorption on platinum. All bimetallic samples were found to be more active than Pt/SiO{sub 2} for the oxidation of CO in air; however, the activity depends strongly on the structure of the surface species, the fraction of Pt-Fe bimetallic contributions, the degree of electronic interactions between Pt and Fe, and the strength of the CO adsorption on platinum.« less

Yeast Mitoribosome Large Subunit Assembly Proceeds by Hierarchical Incorporation of Protein Clusters and Modules on the Inner Membrane.

PubMed

Zeng, Rui; Smith, Erin; Barrientos, Antoni

2018-03-06

Mitoribosomes are specialized for the synthesis of hydrophobic membrane proteins encoded by mtDNA, all essential for oxidative phosphorylation. Despite their linkage to human mitochondrial diseases and the recent cryoelectron microscopy reconstruction of yeast and mammalian mitoribosomes, how they are assembled remains obscure. Here, we dissected the yeast mitoribosome large subunit (mtLSU) assembly process by systematic genomic deletion of 44 mtLSU proteins (MRPs). Analysis of the strain collection unveiled 37 proteins essential for functional mtLSU assembly, three of which are critical for mtLSU 21S rRNA stability. Hierarchical cluster analysis of mtLSU subassemblies accumulated in mutant strains revealed co-operative assembly of protein sets forming structural clusters and preassembled modules. It also indicated crucial roles for mitochondrion-specific membrane-binding MRPs in anchoring newly transcribed 21S rRNA to the inner membrane, where assembly proceeds. Our results define the yeast mtLSU assembly landscape in vivo and provide a foundation for studies of mitoribosome assembly across evolution. Copyright © 2018 Elsevier Inc. All rights reserved.

Size-Induced Segregation in the Stepwise Microhydration of Hydantoin and Its Role in Proton-Induced Charge Transfer

NASA Astrophysics Data System (ADS)

Calvo, Florent; Bacchus-Montabonel, Marie-Christine

2018-01-01

Recent photochemistry experiments provided evidence for the formation of hydantoin by irradiation of interstellar ice analogues. The significance of these results and the importance of hydantoin in prebiotic chemistry and polypeptide synthesis motivate the present theoretical investigation, in which we analyzed the effects of stepwise hydration on the electronic and thermodynamical properties of the structure of microhydrated hydantoin using a variety of computational approaches. We generally find microhydration to proceed around the hydantoin heterocycle until 5 water molecules are reached, at which stage hydration becomes segregated with a water cluster forming aside the heterocycle. The reactivity of microhydrated hydantoin caused by an impinging proton was evaluated through charge transfer collision cross sections for microhydrated compounds but also for hydantoin on icy grains modeled using a cluster approach mimicking the true hexagonal ice surface. The effects of hydration on charge transfer efficiency are mostly significant when few water molecules are present, and they progressively weaken and stabilize in larger clusters. On the ice substrate, charge transfer essentially contributes to a global increase in the cross sections.

Discovery and introduction of a (3,18)-connected net as an ideal blueprint for the design of metal-organic frameworks.

PubMed

Guillerm, Vincent; Weseliński, Łukasz J; Belmabkhout, Youssef; Cairns, Amy J; D'Elia, Valerio; Wojtas, Łukasz; Adil, Karim; Eddaoudi, Mohamed

2014-08-01

Metal-organic frameworks (MOFs) are a promising class of porous materials because it is possible to mutually control their porous structure, composition and functionality. However, it is still a challenge to predict the network topology of such framework materials prior to their synthesis. Here we use a new rare earth (RE) nonanuclear carboxylate-based cluster as an 18-connected molecular building block to form a gea-MOF (gea-MOF-1) based on a (3,18)-connected net. We then utilized this gea net as a blueprint to design and assemble another MOF (gea-MOF-2). In gea-MOF-2, the 18-connected RE clusters are replaced by metal-organic polyhedra, peripherally functionalized so as to have the same connectivity as the RE clusters. These metal-organic polyhedra act as supermolecular building blocks when they form gea-MOF-2. The discovery of a (3,18)-connected MOF followed by deliberate transposition of its topology to a predesigned second MOF with a different chemical system validates the prospective rational design of MOFs.

Spheroidal Populated Star Systems

NASA Astrophysics Data System (ADS)

Angeletti, Lucio; Giannone, Pietro

2008-10-01

Globular clusters and low-ellipticity early-type galaxies can be treated as systems populated by a large number of stars and whose structures can be schematized as spherically symmetric. Their studies profit from the synthesis of stellar populations. The computation of synthetic models makes use of various contributions from star evolution and stellar dynamics. In the first sections of the paper we present a short review of our results on the occurrence of galactic winds in star systems ranging from globular clusters to elliptical galaxies, and the dynamical evolution of a typical massive globular cluster. In the subsequent sections we describe our approach to the problem of the stellar populations in elliptical galaxies. The projected radial behaviours of spectro-photometric indices for a sample of eleven galaxies are compared with preliminary model results. The best agreement between observation and theory shows that our galaxies share a certain degree of heterogeneity. The gas energy dissipation varies from moderate to large, the metal yield ranges from solar to significantly oversolar, the dispersion of velocities is isotropic in most of the cases and anisotropic in the remaining instances.

All-gas-phase synthesis of UiO-66 through modulated atomic layer deposition

PubMed Central

Lausund, Kristian Blindheim; Nilsen, Ola

2016-01-01

Thin films of stable metal-organic frameworks (MOFs) such as UiO-66 have enormous application potential, for instance in microelectronics. However, all-gas-phase deposition techniques are currently not available for such MOFs. We here report on thin-film deposition of the thermally and chemically stable UiO-66 in an all-gas-phase process by the aid of atomic layer deposition (ALD). Sequential reactions of ZrCl4 and 1,4-benzenedicarboxylic acid produce amorphous organic–inorganic hybrid films that are subsequently crystallized to the UiO-66 structure by treatment in acetic acid vapour. We also introduce a new approach to control the stoichiometry between metal clusters and organic linkers by modulation of the ALD growth with additional acetic acid pulses. An all-gas-phase synthesis technique for UiO-66 could enable implementations in microelectronics that are not compatible with solvothermal synthesis. Since this technique is ALD-based, it could also give enhanced thickness control and the possibility to coat irregular substrates with high aspect ratios. PMID:27876797

A comprehensive comparative test of seven widely used spectral synthesis models against multi-band photometry of young massive-star clusters

NASA Astrophysics Data System (ADS)

Wofford, A.; Charlot, S.; Bruzual, G.; Eldridge, J. J.; Calzetti, D.; Adamo, A.; Cignoni, M.; de Mink, S. E.; Gouliermis, D. A.; Grasha, K.; Grebel, E. K.; Lee, J. C.; Östlin, G.; Smith, L. J.; Ubeda, L.; Zackrisson, E.

2016-04-01

We test the predictions of spectral synthesis models based on seven different massive-star prescriptions against Legacy ExtraGalactic UV Survey (LEGUS) observations of eight young massive clusters in two local galaxies, NGC 1566 and NGC 5253, chosen because predictions of all seven models are available at the published galactic metallicities. The high angular resolution, extensive cluster inventory, and full near-ultraviolet to near-infrared photometric coverage make the LEGUS data set excellent for this study. We account for both stellar and nebular emission in the models and try two different prescriptions for attenuation by dust. From Bayesian fits of model libraries to the observations, we find remarkably low dispersion in the median E(B - V) (˜0.03 mag), stellar masses (˜104 M⊙), and ages (˜1 Myr) derived for individual clusters using different models, although maximum discrepancies in these quantities can reach 0.09 mag and factors of 2.8 and 2.5, respectively. This is for ranges in median properties of 0.05-0.54 mag, 1.8-10 × 104 M⊙, and 1.6-40 Myr spanned by the clusters in our sample. In terms of best fit, the observations are slightly better reproduced by models with interacting binaries and least well reproduced by models with single rotating stars. Our study provides a first quantitative estimate of the accuracies and uncertainties of the most recent spectral synthesis models of young stellar populations, demonstrates the good progress of models in fitting high-quality observations, and highlights the needs for a larger cluster sample and more extensive tests of the model parameter space.

Rotational spectra of tetracyclic quinolizidine alkaloids: does a water molecule flip sparteine?

PubMed

Lesarri, Alberto; Pinacho, Ruth; Enríquez, Lourdes; Rubio, José E; Jaraíz, Martín; Abad, José L; Gigosos, Marco A

2017-07-21

Sparteine is a quinolizidine alkaloid used as a chiral auxiliary in asymmetric synthesis. We examine whether hydration by a single molecule can flip sparteine from the most stable trans conformation to the bidentate cis arrangement observed in catalytic complexation to a metal center. Sparteine and the sparteine-water dimer were generated in a supersonic jet expansion with H 2 16 O and H 2 18 O, and characterized by broadband chirped-pulse microwave spectroscopy. Even though the bidentate water dimer was predicted with larger binding energy, a single isomer was observed for the monohydrated cluster, with sparteine retaining the trans conformation observed for the free molecule. The absence of the bidentate dimer is attributed to the kinetic control of cluster formation, favoring the pre-expansion most abundant monomer. The structural properties of the O-HN hydrogen bond in the dimer are compared with those of complexes of other secondary and tertiary amines.

Evolution of an adenine-copper cluster to a highly porous cuboidal framework: solution-phase ripening and gas-adsorption properties.

PubMed

Venkatesh, V; Pachfule, Pradip; Banerjee, Rahul; Verma, Sandeep

2014-09-15

The synthesis and directed evolution of a tetranuclear copper cluster, supported by 8-mercapto-N9-propyladenine ligand, to a highly porous three-dimensional cubic framework in the solid state is reported. The structure of this porous framework was unambiguously characterized by X-ray crystallography. The framework contains about 62 % solvent-accessible void; the presence of a free exocyclic amino group in the porous framework facilitates reversible adsorption of gas and solvent molecules. Oriented growth of framework in solution was also tracked by force and scanning electron microscopy studies, leading to identification of an intriguing ripening process, over a period of 30 days, which also revealed formation of cuboidal aggregates in solution. The elemental composition of these cuboidal aggregates was ascertained by EDAX analysis. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Identification of the Main Regulator Responsible for Synthesis of the Typical Yellow Pigment Produced by Trichoderma reesei

PubMed Central

Derntl, Christian; Rassinger, Alice; Srebotnik, Ewald; Mach, Robert L.

2016-01-01

ABSTRACT The industrially used ascomycete Trichoderma reesei secretes a typical yellow pigment during cultivation, while other Trichoderma species do not. A comparative genomic analysis suggested that a putative secondary metabolism cluster, containing two polyketide-synthase encoding genes, is responsible for the yellow pigment synthesis. This cluster is conserved in a set of rather distantly related fungi, including Acremonium chrysogenum and Penicillium chrysogenum. In an attempt to silence the cluster in T. reesei, two genes of the cluster encoding transcription factors were individually deleted. For a complete genetic proof-of-function, the genes were reinserted into the genomes of the respective deletion strains. The deletion of the first transcription factor (termed yellow pigment regulator 1 [Ypr1]) resulted in the full abolishment of the yellow pigment formation and the expression of most genes of this cluster. A comparative high-pressure liquid chromatography (HPLC) analysis of supernatants of the ypr1 deletion and its parent strain suggested the presence of several yellow compounds in T. reesei that are all derived from the same cluster. A subsequent gas chromatography/mass spectrometry analysis strongly indicated the presence of sorbicillin in the major HPLC peak. The presence of the second transcription factor, termed yellow pigment regulator 2 (Ypr2), reduces the yellow pigment formation and the expression of most cluster genes, including the gene encoding the activator Ypr1. IMPORTANCE Trichoderma reesei is used for industry-scale production of carbohydrate-active enzymes. During growth, it secretes a typical yellow pigment. This is not favorable for industrial enzyme production because it makes the downstream process more complicated and thus increases operating costs. In this study, we demonstrate which regulators influence the synthesis of the yellow pigment. Based on these data, we also provide indication as to which genes are under the control of these regulators and are finally responsible for the biosynthesis of the yellow pigment. These genes are organized in a cluster that is also found in other industrially relevant fungi, such as the two antibiotic producers Penicillium chrysogenum and Acremonium chrysogenum. The targeted manipulation of a secondary metabolism cluster is an important option for any biotechnologically applied microorganism. PMID:27520818

Electronic conductivity studies on oxyhalide glasses containing TMO

NASA Astrophysics Data System (ADS)

Vijayatha, D.; Viswanatha, R.; Sujatha, B.; Narayana Reddy, C.

2016-05-01

Microwave-assisted synthesis is cleaner, more economical and much faster than conventional methods. The development of new routes for the synthesis of solid materials is an integral part of material science and technology. The electronic conductivity studies on xPbCl2 - 60 PbO - (40-x) V2O5 (1 ≥ x ≤ 10) glass system has been carried out over a wide range of composition and temperature (300 K to 423 K). X-ray diffraction study confirms the amorphous nature of the samples. The Scanning electron microscopic studies reveal the formation of cluster like morphology in PbCl2 containing glasses. The d.c conductivity exhibits Arrhenius behaviour and increases with V2O5 concentration. Analysis of the results is interpreted in view Austin-Mott's small polaron model of electron transport. Activation energies calculated using regression analysis exhibit composition dependent trend and the variation is explained in view of the structure of lead-vanadate glass.

Efficient Synthesis of Ir-Polyoxometalate Cluster Using a Continuous Flow Apparatus and STM Investigation of Its Coassembly Behavior on HOPG Surface.

PubMed

Zhang, Junyong; Chang, Shaoqing; Suryanto, Bryan H R; Gong, Chunhua; Zeng, Xianghua; Zhao, Chuan; Zeng, Qingdao; Xie, Jingli

2016-06-06

Taking advantage of a continuous-flow apparatus, the iridium(III)-containing polytungstate cluster K12Na2H2[Ir2Cl8P2W20O72]·37H2O (1) was obtained in a reasonable yield (13% based on IrCl3·H2O). Compound 1 was characterized by Fourier transform IR, UV-visible, (31)P NMR, electrospray ionization mass spectrometry (ESI-MS), and thermogravimetric analysis measurements. (31)P NMR, ESI-MS, and elemental analysis all indicated 1 was a new polytungstate cluster compared with the reported K14[(IrCl4)KP2W20O72] compound. Intriguingly, the successful isolation of 1 relied on the custom-built flow apparatus, demonstrating the uniqueness of continuous-flow chemistry to achieve crystalline materials. The catalytic properties of 1 were assessed by investigating the activity on catalyzing the electro-oxidation of ruthenium tris-2,2'-bipyridine [Ru(bpy)3](2+/3+). The voltammetric behavior suggested a coupled catalytic behavior between [Ru(bpy)3](3+/2+) and 1. Furthermore, on the highly oriented pyrolytic graphite surface, 1,3,5-tris(10-carboxydecyloxy) benzene (TCDB) was used as the two-dimensional host network to coassemble cluster 1; the surface morphology was observed by scanning tunneling microscope technique. "S"-shape of 1 was observed, indicating that the cluster could be accommodated in the cavity formed by two TCDB host molecules, leading to a TCDB/cluster binary structure.

The Dickeya dadantii biofilm matrix consists of cellulose nanofibres, and is an emergent property dependent upon the type III secretion system and the cellulose synthesis operon.

PubMed

Jahn, Courtney E; Selimi, Dija A; Barak, Jeri D; Charkowski, Amy O

2011-10-01

Dickeya dadantii is a plant-pathogenic bacterium that produces cellulose-containing biofilms, called pellicles, at the air-liquid interface of liquid cultures. D. dadantii pellicle formation appears to be an emergent property dependent upon at least three gene clusters, including cellulose synthesis, type III secretion system (T3SS) and flagellar genes. The D. dadantii cellulose synthesis operon is homologous to that of Gluconacetobacter xylinus, which is used for industrial cellulose production, and the cellulose nanofibres produced by D. dadantii were similar in diameter and branching pattern to those produced by G. xylinus. Salmonella enterica, an enterobacterium closely related to D. dadantii, encodes a second type of cellulose synthesis operon, and it produced biofilm strands that differed in width and branching pattern from those of D. dadantii and G. xylinus. Unlike any previously described cellulose fibre, the D. dadantii cellulose nanofibres were decorated with bead-like structures. Mutation of the cellulose synthesis operon genes resulted in loss of cellulose synthesis and production of a cellulase-resistant biofilm. Mutation of other genes required for pellicle formation, including those encoding FliA (a sigma factor that regulates flagella production), HrpL (a sigma factor that regulates the T3SS), and AdrA, a GGDEF protein, affected both biofilm and cell morphology. Mutation of the cellulose synthase bcsA or of bcsC resulted in decreased accumulation of the T3SS-secreted protein HrpN.

Binaphthyl-containing Schiff base complexes with carboxyl groups for dye sensitized solar cell: An experimental and theoretical study

NASA Astrophysics Data System (ADS)

Tsaturyan, Arshak; Machida, Yosuke; Akitsu, Takashiro; Gozhikova, Inna; Shcherbakov, Igor

2018-06-01

We report on synthesis and characterization of binaphthyl containing Schiff base Ni(II), Cu(II), and Zn(II) complexes as promising photosensitizers for dye-sensitized solar cells (DSSC). Based on theoretical and experimental data, the possibility of their application in DSSC was confirmed. To our knowledge, we find dye performance of complex is steric and rigid structure widely spread to efficiency. The spatial and electronic structures of the complexes were studied by means of the quantum chemical modeling using DFT and TD-DFT approaches. The adsorption energies of the complexes on TiO2 cluster were calculated and appeared to be very close in value. The Zn(II) complex has the biggest value of molar extinction.

Amyotrophic lateral sclerosis, gene deregulation in the anterior horn of the spinal cord and frontal cortex area 8: implications in frontotemporal lobar degeneration

PubMed Central

Andrés-Benito, Pol; Moreno, Jesús; Aso, Ester; Povedano, Mónica; Ferrer, Isidro

2017-01-01

Transcriptome arrays identifies 747 genes differentially expressed in the anterior horn of the spinal cord and 2,300 genes differentially expressed in frontal cortex area 8 in a single group of typical sALS cases without frontotemporal dementia compared with age-matched controls. Main up-regulated clusters in the anterior horn are related to inflammation and apoptosis; down-regulated clusters are linked to axoneme structures and protein synthesis. In contrast, up-regulated gene clusters in frontal cortex area 8 involve neurotransmission, synaptic proteins and vesicle trafficking, whereas main down-regulated genes cluster into oligodendrocyte function and myelin-related proteins. RT-qPCR validates the expression of 58 of 66 assessed genes from different clusters. The present results: a. reveal regional differences in de-regulated gene expression between the anterior horn of the spinal cord and frontal cortex area 8 in the same individuals suffering from sALS; b. validate and extend our knowledge about the complexity of the inflammatory response in the anterior horn of the spinal cord; and c. identify for the first time extensive gene up-regulation of neurotransmission and synaptic-related genes, together with significant down-regulation of oligodendrocyte- and myelin-related genes, as important contributors to the pathogenesis of frontal cortex alterations in the sALS/frontotemporal lobar degeneration spectrum complex at stages with no apparent cognitive impairment. PMID:28283675

Synthesis and Molecular Structure of a Novel Compound Containing a Carbonate-Bridged Hexacalcium Cluster Cation Assembled on a Trimeric Trititanium(IV)-Substituted Wells-Dawson Polyoxometalate.

PubMed

Hoshino, Takahiro; Isobe, Rina; Kaneko, Takuya; Matsuki, Yusuke; Nomiya, Kenji

2017-08-21

A novel compound containing a hexacalcium cluster cation, one carbonate anion, and one calcium cation assembled on a trimeric trititanium(IV)-substituted Wells-Dawson polyoxometalate (POM), [{Ca 6 (CO 3 )(μ 3 -OH)(OH 2 ) 18 }(P 2 W 15 Ti 3 O 61 ) 3 Ca(OH 2 ) 3 ] 19- (Ca 7 Ti 9 Trimer), was obtained as the Na 7 Ca 6 salt (NaCa-Ca 7 Ti 9 Trimer) by the reaction of calcium chloride with the monomeric trititanium(IV)-substituted Wells-Dawson POM species "[P 2 W 15 Ti 3 O 59 (OH) 3 ] 9- " (Ti 3 Monomer). Ti 3 Monomer was generated in situ under basic conditions from the separately prepared tetrameric species with bridging Ti(OH 2 ) 3 groups and an encapsulated Cl - ion, [{P 2 W 15 Ti 3 O 59 (OH) 3 } 4 {μ 3 -Ti(H 2 O) 3 } 4 Cl] 21- (Ti 16 Tetramer). The Na 7 Ca 6 salt of Ca 7 Ti 9 Trimer was characterized by complete elemental analysis, thermogravimetric (TG) and differential thermal analyses (DTA), FTIR, single-crystal X-ray structure analysis, and solution 183 W and 31 P NMR spectroscopy. X-ray crystallography revealed that the [Ca 6 (CO 3 )(μ 3 -OH)(OH 2 ) 18 ] 9+ cluster cation was composed of six calcium cations linked by one μ 6 -carbonato anion and one μ 3 -OH - anion. The cluster cation was assembled, together with one calcium ion, on a trimeric species composed of three tri-Ti(IV)-substituted Wells-Dawson subunits linked by Ti-O-Ti bonds. Ca 7 Ti 9 Trimer is an unprecedented POM species containing an alkaline-earth-metal cluster cation and is the first example of alkaline-earth-metal ions clustered around a titanium(IV)-substituted POM.

Polymerization in the gas phase, in clusters, and on nanoparticle surfaces.

PubMed

El-Shall, M Samy

2008-07-01

Gas phase and cluster experiments provide unique opportunities to quantitatively study the effects of initiators, solvents, chain transfer agents, and inhibitors on the mechanisms of polymerization. Furthermore, a number of important phenomena, unique structures, and novel properties may exist during gas-phase and cluster polymerization. In this regime, the structure of the growing polymer may change dramatically and the rate coefficient may vary significantly upon the addition of a single molecule of the monomer. These changes would be reflected in the properties of the oligomers deposited from the gas phase. At low pressures, cationic and radical cationic polymerizations may proceed in the gas phase through elimination reactions. In the same systems at high pressure, however, the ionic intermediates may be stabilized, and addition without elimination may occur. In isolated van der Waals clusters of monomer molecules, sequential polymerization with several condensation steps can occur on a time scale of a few microseconds following the ionization of the gas-phase cluster. The cluster reactions, which bridge gas-phase and condensed-phase chemistry, allow examination of the effects of controlled states of aggregation. This Account describes several examples of gas-phase and cluster polymerization studies where the most significant results can be summarized as follows: (1) The carbocation polymerization of isobutene shows slower rates with increasing polymerization steps resulting from entropy barriers, which could explain the need for low temperatures for the efficient propagation of high molecular weight polymers. (2) Radical cation polymerization of propene can be initiated by partial charge transfer from an ionized aromatic molecule such as benzene coupled with covalent condensation of the associated propene molecules. This novel mechanism leads exclusively to the formation of propene oligomer ions and avoids other competitive products. (3) Structural information on the oligomers formed by gas-phase polymerization can be obtained using the mass-selected ion mobility technique where the measured collision cross-sections of the selected oligomer ions and collision-induced dissociation can provide fairly accurate structural identifications. The identification of the structures of the dimers and trimers formed in the gas-phase thermal polymerization of styrene confirms that the polymerization proceeds according to the Mayo mechanism. Similarly, the ion mobility technique has been utilized to confirm the formation of benzene cations by intracluster polymerization following the ionization of acetylene clusters. Finally, it has been shown that polymerization of styrene vapor on the surface of activated nanoparticles can lead to the incorporation of a variety of metal and metal oxide nanoparticles within polystyrene films. The ability to probe the reactivity and structure of the small growing oligomers in the gas phase can provide fundamental insight into mechanisms of polymerization that are difficult to obtain from condensed-phase studies. These experiments are also important for understanding the growth mechanisms of complex organics in flames, combustion processes, interstellar clouds, and solar nebula where gas-phase reactions, cluster polymerization, and surface catalysis on dust nanoparticles represent the major synthetic pathways. This research can lead to the discovery of novel initiation mechanisms and reaction pathways with applications in the synthesis of oligomers and nanocomposites with unique and improved properties.

Engineering of EPA/DHA omega-3 fatty acid production by Lactococcus lactis subsp. cremoris MG1363.

PubMed

Amiri-Jami, Mitra; Lapointe, Gisele; Griffiths, Mansel W

2014-04-01

Eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) have been shown to be of major importance in human health. Therefore, these essential polyunsaturated fatty acids have received considerable attention in both human and farm animal nutrition. Currently, fish and fish oils are the main dietary sources of EPA/DHA. To generate sustainable novel sources for EPA and DHA, the 35-kb EPA/DHA synthesis gene cluster was isolated from a marine bacterium, Shewanella baltica MAC1. To streamline the introduction of the genes into food-grade microorganisms such as lactic acid bacteria, unnecessary genes located upstream and downstream of the EPA/DHA gene cluster were deleted. Recombinant Escherichia coli harboring the 20-kb gene cluster produced 3.5- to 6.1-fold more EPA than those carrying the 35-kb DNA fragment coding for EPA/DHA synthesis. The 20-kb EPA/DHA gene cluster was cloned into a modified broad-host-range low copy number vector, pIL252m (4.7 kb, Ery) and expressed in Lactococcus lactis subsp. cremoris MG1363. Recombinant L. lactis produced DHA (1.35 ± 0.5 mg g(-1) cell dry weight) and EPA (0.12 ± 0.04 mg g(-1) cell dry weight). This is believed to be the first successful cloning and expression of EPA/DHA synthesis gene cluster in lactic acid bacteria. Our findings advance the future use of EPA/DHA-producing lactic acid bacteria in such applications as dairy starters, silage adjuncts, and animal feed supplements.

Spectroscopic Assessment of the Reliability of Metal/Metal Oxide Interfaces

DTIC Science & Technology

1994-10-01

vapor deposition(LCVD)1, 2 of thin films, clusters and ultrafine particles offers many unique opportunities in materials synthesis. As precursors for LCVD...films, the chemistry is directly applicable to other oxidizable metals. Puretsky and Demyanenko9 reported that gas phase clusters and ultrafine ... particles can be synthesized using excimer laser dissociation of all group six metal hexacarbonyls. Our earlier work on platinum clusters and our current

Synthesis, characterization, and reactivity of pentamethylcyclopentadienyl complexes of divalent cobalt and nickel

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, Michael Edward

1993-10-01

The thesis is divided into the following 4 chapters: synthesis, characterization, and reactivity of trinuclear pentamethylcyclopentadienyl cobalt and nickel clusters with triply-bridging methylidyne groups; chemical and physical properties of pentamethylcyclopentadienyl acetylacetonate complexes of Co(II) and Ni(II); synthesis, characterization, and reactivity of pentamethylcyclopentadienyl halide complexes of Co and Ni; and crystallographic studies of distortions in metallocenes with C 5-symmetrical cyclopentadienyl rings.

Characterization of the Saccharomyces Golgi complex through the cell cycle by immunoelectron microscopy.

PubMed Central

Preuss, D; Mulholland, J; Franzusoff, A; Segev, N; Botstein, D

1992-01-01

The membrane compartments responsible for Golgi functions in wild-type Saccharomyces cerevisiae were identified and characterized by immunoelectron microscopy. Using improved fixation methods, Golgi compartments were identified by labeling with antibodies specific for alpha 1-6 mannose linkages, the Sec7 protein, or the Ypt1 protein. The compartments labeled by each of these antibodies appear as disk-like structures that are apparently surrounded by small vesicles. Yeast Golgi typically are seen as single, isolated cisternae, generally not arranged into parallel stacks. The location of the Golgi structures was monitored by immunoelectron microscopy through the yeast cell cycle. Several Golgi compartments, apparently randomly distributed, were always observed in mother cells. During the initiation of new daughter cells, additional Golgi structures cluster just below the site of bud emergence. These Golgi enter daughter cells at an early stage, raising the possibility that much of the bud's growth might be due to secretory vesicles formed as well as consumed entirely within the daughter. During cytokinesis, the Golgi compartments are concentrated near the site of cell wall synthesis. Clustering of Golgi both at the site of bud formation and at the cell septum suggests that these organelles might be directed toward sites of rapid cell surface growth. Images PMID:1381247

Synthesis, Magnetism, and X-ray Molecular Structure of the Mixed-Valence Vanadium(IV/V)-Oxygen Cluster [VO(4) subset(V(18)O(45))](9-).

PubMed

Suber, Lorenza; Bonamico, Mario; Fares, Vincenzo

1997-05-07

Within the transition metal oxide systems, vanadium presents a unique chemistry due to its capacity to form a great number of mixed-valence oxo clusters which often have the peculiarity to incorporate species that function, for size, shape, and charge, as templates. Prismatic, lustrous dark brown crystals of [(n-C(4)H(9))NH(3)](9)[V(19)O(49)].7H(2)O are obtained by reacting (n-C(4)H(9)NH(3))VO(3), VOSO(4), and (n-C(4)H(9))NH(2) in H(2)O. The X-ray crystal structure shows an ellipsoidal metal-oxo cluster formed by 15 VO(5) and 3 VO(4) polyhedra surrounding an almost regular VO(4) tetrahedron located on the 3-fold axis of a trigonal cell of dimensions a = 19.113(5) Å and c = 13.743(5) Å with space group P&thremacr; and Z = 2. Exponentially weighted bond valence sum calculations, manganometric titration of the V(IV) centers, and magnetic measurements are consistent with the presence of three localized and three delocalized electrons. Variable-temperature solid-state susceptibility studies indicate antiferromagnetic coupling between V(IV) centers. Cyclic voltammetry in acetonitrile shows a irreversible reduction at -1.24 V and a reversible oxidation at +0.17 V (vs Ag/AgCl). The title compound converts quantitatively to the metal oxide K(2)V(3)O(8) with an extended layered structure as soon as a potassium salt is added to a neutral aqueous solution of the polyoxoanion.

Comparative genomic analysis in the fungus Fusarium for production of toxins of concern to food safety

USDA-ARS?s Scientific Manuscript database

SUMMARY Comparative analysis of 207 genomes representing 159 species of the fungus Fusarium detected 9403 known and putative secondary metabolite (SM) biosynthetic gene clusters. The clusters included those responsible for synthesis of mycotoxins, plant hormones and pigments, and varied in distribut...

Preparation and Luminescence Thermochromism of Tetranuclear Copper(I)-Pyridine-Iodide Clusters

ERIC Educational Resources Information Center

Parmeggiani, Fabio; Sacchetti, Alessandro

2012-01-01

A simple and straightforward synthesis of a tetranuclear copper(I)-pyridine-iodide cluster is described as a laboratory experiment for advanced inorganic chemistry undergraduate students. The product is used to demonstrate the fascinating and visually impressive phenomenon of luminescence thermochromism: exposed to long-wave UV light, the…

Bis(dicyclohexylselenophosphinyl)selenide, [Cy2P(Se)]2Se: Synthesis, molecular structure and application for self-assembly of a tetrahedral Cu(I) cluster

NASA Astrophysics Data System (ADS)

Artem'ev, Alexander V.; Doronina, Evgeniya P.; Bagryanskaya, Irina Yu; Klyba, Lyudmila V.

2018-05-01

The molecular structure of the selenides of [R2P(Se)]2Se type has been systematically studied on example of bis(dicyclohexylselenophosphinyl)selenide, [Cy2P(Se)]2Se. This selenide has been synthesized in 65% yield by oxidation of Cy2PH with elemental selenium in 1:2 M ratio. Its structure has been investigated by X-ray diffractometry (XRD), NMR, FT-IR and MALDI-TOF/MS techniques. In the solid, the Se1sbnd Psbnd Se2sbnd Psbnd Se3 chain of (Cy2P = Se)2Se molecule adopts a syn-anti conformation with the Se1sbnd Psbnd Se2sbnd P and Psbnd Se2sbnd Psbnd Se3 torsion angles of -179.64 (3)° and 4.69 (4)°. The vibrational band assignments, performing at B3LYP/6-311++G (d,p) theory level, are in a good agreement with the experimental FT-IR frequencies. The synthetic utility of the prepared selenide has been exemplified by its reaction with CuCl2 resulted in the formation of [Cu4(Se2PCy2)4] cluster in 53% yield. The structure of latter is formed by a Cu4 tetrahedron, wherein each triangular face is bridged by a [Se2PCy2] ligand in a trimetallic triconnective (μ2, μ1) pattern.

Evolution of atomic structure during nanoparticle formation

DOE PAGES

Tyrsted, Christoffer; Lock, Nina; Jensen, Kirsten M. Ø.; ...

2014-04-14

Understanding the mechanism of nanoparticle formation during synthesis is a key prerequisite for the rational design and engineering of desirable materials properties, yet remains elusive due to the difficulty of studying structures at the nanoscale under real conditions. Here, the first comprehensive structural description of the formation of a nanoparticle, yttria-stabilized zirconia (YSZ), all the way from its ionic constituents in solution to the final crystal, is presented. The transformation is a complicated multi-step sequence of atomic reorganizations as the material follows the reaction pathway towards the equilibrium product. Prior to nanoparticle nucleation, reagents reorganize into polymeric species whose structuremore » is incompatible with the final product. Instead of direct nucleation of clusters into the final product lattice, a highly disordered intermediate precipitate forms with a local bonding environment similar to the product yet lacking the correct topology. During maturation, bond reforming occurs by nucleation and growth of distinct domains within the amorphous intermediary. The present study moves beyond kinetic modeling by providing detailed real-time structural insight, and it is demonstrated that YSZ nanoparticle formation and growth is a more complex chemical process than accounted for in conventional models. This level of mechanistic understanding of the nanoparticle formation is the first step towards more rational control over nanoparticle synthesis through control of both solution precursors and reaction intermediaries.« less

Vibrational properties of gold nanoparticles obtained by green synthesis

NASA Astrophysics Data System (ADS)

Alvarez, Ramón A. B.; Cortez-Valadez, M.; Bueno, L. Oscar Neira; Britto Hurtado, R.; Rocha-Rocha, O.; Delgado-Beleño, Y.; Martinez-Nuñez, C. E.; Serrano-Corrales, Luis Ivan; Arizpe-Chávez, H.; Flores-Acosta, M.

2016-10-01

This study reports the synthesis and characterization of gold nanoparticles through an ecological method to obtain nanostructures from the extract of the plant Opuntia ficus-indica. Colloidal nanoparticles show sizes that vary between 10-20 nm, and present various geometric morphologies. The samples were characterized through optical absorption, Raman Spectroscopy and Transmission Electron Microscopy (TEM). Additionally, low energy metallic clusters of Aun (n=2-20 atoms) were modeled by computational quantum chemistry. The theoretical results were obtained with Density Functional Theory (DFT). The predicted results of Au clusters show a tendency and are correlated with the experimental results concerning the optical absorption bands and Raman spectroscopy in gold nanoparticles.

Photoassisted Synthesis of Mixed-Metal Clusters;(PPN)(CoOs3(CO)13), H2RuOs3(CO13, and H2FeOs3(CO)13.

DTIC Science & Technology

1980-05-30

8 -1 Photoassisted Synthesis of Mixed-Metal Clusters: Interim echnicalfe 0M [PPN][ Cofs (CO) H OP]CC andF F ’ " 13 2 136. PERFORMING ORG. REPORT NUMBER...the reaction conditions.2 A low yield of the unstable protonated derivative HCoOs3 (CO)13 was obtained in a single experiment in which K[Co(CO)4] was...data.1 Apparently [V(CO)6]" is a sufficiently strong reducing agent to reduce both of these trimers to their respective anions, although the 6 proton

Synthesis and first use of pyridine-2,6-diylbis(pyrazine-2-ylmethanone) in metal cluster chemistry: a {Mn(III)3Na2} complex with an ideal trigonal bipyramidal geometry.

PubMed

Giannopoulos, Dimosthenis P; Wilson-Konderka, Cody; Gagnon, Kevin J; Teat, Simon J; Escuer, Albert; Metallinos, Costa; Stamatatos, Theocharis C

2015-03-07

The successful organic synthesis of a new dipyrazole/pyridine-dicarbonyl organic molecule, namely pyridine-2,6-diylbis(pyrazine-2-ylmethanone) [(pz)CO(py)CO(pz)], followed by its employment in Mn coordination chemistry has yielded the neutral cluster compound [Mn3Na2O(N3)3(L)3] (1), where L(2-) is the (pz)C(CH2COCH3)(O(-))(py)C(CH2COCH3)(O(-))(pz) dianion. The latter group was formed in situ, presumably by the nucleophilic attack of the carbanion (-)CH2COCH3 to the carbonyl carbon atoms of (pz)CO(py)CO(pz), in the presence of Mn(n+) ions under basic conditions and in solvent Me2CO. Complex 1 possesses an almost ideal trigonal bipyramidal topology, with the two Na(I) ions occupying the apical positions and the three Mn(III) ions residing in the equatorial trigonal plane. The bridging ligation about the metal ions is provided by a μ3-O(2-) ion and six μ-OR(-) groups from the L(2-) ligand, while peripheral ligation is completed by three terminal azido groups and the pyridine N and carbonyl O atoms of L(2-). Magnetic susceptibility studies revealed the presence of predominant antiferromagnetic exchange interactions between the paramagnetic Mn(III) centres; the use of an anisotropic, equilateral Mn(III)3 triangle model allowed us to fit the magnetic data and obtain the best-fit parameters: J = -10.8 cm(-1), D = -5.3 cm(-1), and g = 1.99. The combined results demonstrate the rich chemical reactivity of carbonyl groups and the ability of poly-ketone ligands to stabilize cluster compounds with unprecedented structural motifs and interesting architectures.

Spider-web amphiphiles as artificial lipid clusters: design, synthesis, and accommodation of lipid components at the air-water interface.

PubMed

Ariga, Katsuhiko; Urakawa, Toshihiro; Michiue, Atsuo; Kikuchi, Jun-ichi

2004-08-03

As a novel category of two-dimensional lipid clusters, dendrimers having an amphiphilic structure in every unit were synthesized and labeled "spider-web amphiphiles". Amphiphilic units based on a Lys-Lys-Glu tripeptide with hydrophobic tails at the C-terminal and a polar head at the N-terminal are dendrically connected through stepwise peptide coupling. This structural design allowed us to separately introduce the polar head and hydrophobic tails. Accordingly, we demonstrated the synthesis of the spider-web amphiphile series in three combinations: acetyl head/C16 chain, acetyl head/C18 chain, and ammonium head/C16 chain. All the spider-web amphiphiles were synthesized in satisfactory yields, and characterized by 1H NMR, MALDI-TOFMS, GPC, and elemental analyses. Surface pressure (pi)-molecular area (A) isotherms showed the formation of expanded monolayers except for the C18-chain amphiphile at 10 degrees C, for which the molecular area in the condensed phase is consistent with the cross-sectional area assigned for all the alkyl chains. In all the spider-web amphiphiles, the molecular areas at a given pressure in the expanded phase increased in proportion to the number of units, indicating that alkyl chains freely fill the inner space of the dendritic core. The mixing of octadecanoic acid with the spider-web amphiphiles at the air-water interface induced condensation of the molecular area. From the molecular area analysis, the inclusion of the octadecanoic acid bears a stoichiometric characteristic; i.e., the number of captured octadecanoic acids in the spider-web amphiphile roughly agrees with the number of branching points in the spider-web amphiphile.

1,2,3-triazolate-bridged tetradecametallic transition metal clusters [M14(L)6O6(OMe)18X6] (M=FeIII, CrIII and VIII/IV) and related compounds: ground-state spins ranging from S=0 to S=25 and spin-enhanced magnetocaloric effect.

PubMed

Shaw, Rachel; Laye, Rebecca H; Jones, Leigh F; Low, David M; Talbot-Eeckelaers, Caytie; Wei, Qiang; Milios, Constantinos J; Teat, Simon; Helliwell, Madeleine; Raftery, James; Evangelisti, Marco; Affronte, Marco; Collison, David; Brechin, Euan K; McInnes, Eric J L

2007-06-11

We report the synthesis, by solvothermal methods, of the tetradecametallic cluster complexes [M14(L)6O6(OMe)18Cl6] (M=FeIII, CrIII) and [V14(L)6O6(OMe)18Cl6-xOx] (L=anion of 1,2,3-triazole or derivative). Crystal structure data are reported for the {M14} complexes [Fe14(C2H2N3)6O6(OMe)18Cl6], [Cr14(bta)6O6(OMe)18Cl6] (btaH=benzotriazole), [V14O6(Me2bta)6(OMe)18Cl6-xOx] [Me2btaH=5,6-Me2-benzotriazole; eight metal sites are VIII, the remainder are disordered between {VIII-Cl}2+ and {VIV=O}2+] and for the distorted [FeIII14O9(OH)(OMe)8(bta)7(MeOH)5(H2O)Cl8] structure that results from non-solvothermal synthetic methods, highlighting the importance of temperature regime in cluster synthesis. Magnetic studies reveal the {Fe14} complexes to have ground state electronic spins of S

Size-Selected Ag Nanoparticles with Five-Fold Symmetry

PubMed Central

2009-01-01

Silver nanoparticles were synthesized using the inert gas aggregation technique. We found the optimal experimental conditions to synthesize nanoparticles at different sizes: 1.3 ± 0.2, 1.7 ± 0.3, 2.5 ± 0.4, 3.7 ± 0.4, 4.5 ± 0.9, and 5.5 ± 0.3 nm. We were able to investigate the dependence of the size of the nanoparticles on the synthesis parameters. Our data suggest that the aggregation of clusters (dimers, trimer, etc.) into the active zone of the nanocluster source is the predominant physical mechanism for the formation of the nanoparticles. Our experiments were carried out in conditions that kept the density of nanoparticles low, and the formation of larges nanoparticles by coalescence processes was avoided. In order to preserve the structural and morphological properties, the impact energy of the clusters landing into the substrate was controlled, such that the acceleration energy of the nanoparticles was around 0.1 eV/atom, assuring a soft landing deposition. High-resolution transmission electron microscopy images showed that the nanoparticles were icosahedral in shape, preferentially oriented with a five-fold axis perpendicular to the substrate surface. Our results show that the synthesis by inert gas aggregation technique is a very promising alternative to produce metal nanoparticles when the control of both size and shape are critical for the development of practical applications. PMID:20596397

Size-selected ag nanoparticles with five-fold symmetry.

PubMed

Gracia-Pinilla, Miguelángel; Ferrer, Domingo; Mejía-Rosales, Sergio; Pérez-Tijerina, Eduardo

2009-05-15

Silver nanoparticles were synthesized using the inert gas aggregation technique. We found the optimal experimental conditions to synthesize nanoparticles at different sizes: 1.3 ± 0.2, 1.7 ± 0.3, 2.5 ± 0.4, 3.7 ± 0.4, 4.5 ± 0.9, and 5.5 ± 0.3 nm. We were able to investigate the dependence of the size of the nanoparticles on the synthesis parameters. Our data suggest that the aggregation of clusters (dimers, trimer, etc.) into the active zone of the nanocluster source is the predominant physical mechanism for the formation of the nanoparticles. Our experiments were carried out in conditions that kept the density of nanoparticles low, and the formation of larges nanoparticles by coalescence processes was avoided. In order to preserve the structural and morphological properties, the impact energy of the clusters landing into the substrate was controlled, such that the acceleration energy of the nanoparticles was around 0.1 eV/atom, assuring a soft landing deposition. High-resolution transmission electron microscopy images showed that the nanoparticles were icosahedral in shape, preferentially oriented with a five-fold axis perpendicular to the substrate surface. Our results show that the synthesis by inert gas aggregation technique is a very promising alternative to produce metal nanoparticles when the control of both size and shape are critical for the development of practical applications.

Fischer–Tropsch Synthesis at a Low Pressure on Subnanometer Cobalt Oxide Clusters: The Effect of Cluster Size and Support on Activity and Selectivity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Sungsik; Lee, Byeongdu; Seifert, Sönke

2015-05-21

In this study, the catalytic activity and changes in the oxidation state during the Fischer Tropsch (FT) reaction was investigated on subnanometer size-selected cobalt clusters deposited on oxide (Al2O3, MgO) and carbon-based (ultrananocrystalline diamond UNCD) supports by temperature programmed reaction (TPRx) combined with in-situ grazing-incidence X-ray absorption characterization (GIXAS). The activity and selectivity of ultrasmall cobalt clusters exhibits a very strong dependence on cluster size and support. The evolution of the oxidation state of metal cluster during the reaction reveals that metal-support interaction plays a key role in the reaction.

Testing Feedback Models with Nearby Star Forming Regions

NASA Astrophysics Data System (ADS)

Doran, E.; Crowther, P.

2012-12-01

The feedback from massive stars plays a crucial role in the evolution of galaxies. Accurate modelling of this feedback is essential in understanding distant star forming regions. Young nearby, high mass (> 104 M⊙) clusters such as R136 (in the 30 Doradus region) are ideal test beds for population synthesis since they host large numbers of spatially resolved massive stars at a pre-supernovae stage. We present a quantitative comparison of empirical calibrations of radiative and mechanical feedback from individual stars in R136, with instantaneous burst predictions from the popular Starburst99 evolution synthesis code. We find that empirical results exceed predictions by factors of ˜3-9, as a result of limiting simulations to an upper limit of 100 M⊙. 100-300 M⊙ stars should to be incorporated in population synthesis models for high mass clusters to bring predictions into close agreement with empirical results.

Green Synthesis of Ag-Cu Nanoalloys Using Opuntia ficus- indica

NASA Astrophysics Data System (ADS)

Rocha-Rocha, O.; Cortez-Valadez, M.; Hernández-Martínez, A. R.; Gámez-Corrales, R.; Alvarez, Ramón A. B.; Britto-Hurtado, R.; Delgado-Beleño, Y.; Martinez-Nuñez, C. E.; Pérez-Rodríguez, A.; Arizpe-Chávez, H.; Flores-Acosta, M.

2017-02-01

Bimetallic Ag/Cu nanoparticles have been obtained by green synthesis using Opuntia ficus- indica plant extract. Two synthesis methods were applied to obtain nanoparticles with core-shell and Janus morphologies by reversing the order of precursors. Transmission electronic microscopy revealed size of 10 nm and 20 nm for the core-shell and Janus nanoparticles, respectively. Other small particles with size of up to 2 nm were also observed. Absorption bands attributed to surface plasmon resonance were detected at 440 nm and 500 nm for the core-shell and Janus nanoparticles, respectively. Density functional theory predicted a breathing mode type (BMT) located at low wavenumber due to small, low-energy clusters of (AgCu) n with n = 2 to 9, showing a certain correlation with the experimental one (at 220 cm-1). The dependence of the BMT on the number of atoms constituting the cluster is also studied.

Studies on the magnetic ground state of a spin Mobius strip

DOE PAGES

Newton, Graham N.; Hoshino, Norihisa; Matsumoto, Takuto; ...

2016-08-22

In this paper, we report the synthesis, structure and detailed characterisation of three n-membered oxovanadium rings, Na n[(V=O) nNa n(H 2O) n(α, β, or γ-CD) 2]•m H 2O (n=6, 7, or 8), prepared by the reactions of (V=O)SO 4•x H 2O with α, β, or γ-cyclodextrins (CDs) and NaOH in water. Their alternating heterometallic vanadium/sodium cyclic core structures were sandwiched between two CD moieties such that O-Na-O groups separated the neighbouring vanadyl ions. Antiferromagnetic interactions between the S=1/2 vanadyl ions led to S=0 ground states for the even-membered rings, but to two quasi-degenerate S=1/2 states for the spin-frustrated heptanuclear cluster.

The O-antigen structure of bacterium Comamonas aquatica CJG.

PubMed

Wang, Xiqian; Kondakova, Anna N; Zhu, Yutong; Knirel, Yuriy A; Han, Aidong

2017-11-01

Genus Comamonas is a group of bacteria that are able to degrade a variety of environmental waste. Comamonas aquatica CJG (C. aquatica) in this genus is able to absorb low-density lipoprotein but not high-density lipoprotein of human serum. Using 1 H and 13 C NMR spectroscopy, we found that the O-polysaccharide (O-antigen) of this bacterium is comprised of a disaccharide repeat (O-unit) of d-glucose and 2-O-acetyl-l-rhamnose, which is shared by Serratia marcescens O6. The O-antigen gene cluster of C. aquatica, which is located between coaX and tnp4 genes, contains rhamnose synthesis genes, glycosyl and acetyl transferase genes, and ATP-binding cassette transporter genes, and therefore is consistent with the O-antigen structure determined here.

Morphology-controlled synthesis of self-assembled LiFePO4/C/RGO for high-performance Li-ion batteries.

PubMed

Lin, Mei; Chen, Yuming; Chen, Bolei; Wu, Xiao; Kam, Kifung; Lu, Wei; Chan, Helen Lai Wa; Yuan, Jikang

2014-10-22

Novel architectured LiFePO4 (LFP) that consisted of ordered LFP nanocubes was prepared through a facile hydrothermal method using polyethylene glycol (PEG) as a surfactant. The micro/nanostructured LFP with various morphologies ranging from cube cluster to rugby-like structure was synthesized via controlling the pH values of the precursor. A reasonable assembly process elucidating the formation of the hierarchical structure is also provided based on the experimental results. After a combination of carbon (C) coating and reduced graphene oxide (RGO) wrapping, the obtained LFP/C/RGO composites exhibit enhanced electrochemical performance compared to that of blank LFP synthesized under the same condition. Among as-synthesized cube-cluster-like, dumbbell-like, rod-like, and rugby-like composites, the rugby-like LFP/C/RGO reveal the best electrochemical properties with the discharge specific capacity of ∼150 mA h g(-1) after 100 cycles and a high reversible specific capacity of 152 mA h g(-1) at 0.1 C. The prepared LFP/C/RGO composite can be a promising cathode material for high energy, low cost, and environmentally friendly lithium-ion batteries.

Structure of the ribosome post-recycling complex probed by chemical cross-linking and mass spectrometry

PubMed Central

Kiosze-Becker, Kristin; Ori, Alessandro; Gerovac, Milan; Heuer, André; Nürenberg-Goloub, Elina; Rashid, Umar Jan; Becker, Thomas; Beckmann, Roland; Beck, Martin; Tampé, Robert

2016-01-01

Ribosome recycling orchestrated by the ATP binding cassette (ABC) protein ABCE1 can be considered as the final—or the first—step within the cyclic process of protein synthesis, connecting translation termination and mRNA surveillance with re-initiation. An ATP-dependent tweezer-like motion of the nucleotide-binding domains in ABCE1 transfers mechanical energy to the ribosome and tears the ribosome subunits apart. The post-recycling complex (PRC) then re-initiates mRNA translation. Here, we probed the so far unknown architecture of the 1-MDa PRC (40S/30S·ABCE1) by chemical cross-linking and mass spectrometry (XL-MS). Our study reveals ABCE1 bound to the translational factor-binding (GTPase) site with multiple cross-link contacts of the helix–loop–helix motif to the S24e ribosomal protein. Cross-linking of the FeS cluster domain to the ribosomal protein S12 substantiates an extreme lever-arm movement of the FeS cluster domain during ribosome recycling. We were thus able to reconstitute and structurally analyse a key complex in the translational cycle, resembling the link between translation initiation and ribosome recycling. PMID:27824037

Nano-sized manganese oxides as biomimetic catalysts for water oxidation in artificial photosynthesis: a review

PubMed Central

Najafpour, Mohammad Mahdi; Rahimi, Fahimeh; Aro, Eva-Mari; Lee, Choon-Hwan; Allakhverdiev, Suleyman I.

2012-01-01

There has been a tremendous surge in research on the synthesis of various metal compounds aimed at simulating the water-oxidizing complex (WOC) of photosystem II (PSII). This is crucial because the water oxidation half reaction is overwhelmingly rate-limiting and needs high over-voltage (approx. 1 V), which results in low conversion efficiencies when working at current densities required for hydrogen production via water splitting. Particular attention has been given to the manganese compounds not only because manganese has been used by nature to oxidize water but also because manganese is cheap and environmentally friendly. The manganese–calcium cluster in PSII has a dimension of about approximately 0.5 nm. Thus, nano-sized manganese compounds might be good structural and functional models for the cluster. As in the nanometre-size of the synthetic models, most of the active sites are at the surface, these compounds could be more efficient catalysts than micrometre (or bigger) particles. In this paper, we focus on nano-sized manganese oxides as functional and structural models of the WOC of PSII for hydrogen production via water splitting and review nano-sized manganese oxides used in water oxidation by some research groups. PMID:22809849

Low pressure bottom-up synthesis of metal@oxide and oxide nanoparticles: control of structure and functional properties

NASA Astrophysics Data System (ADS)

D'Addato, Sergio; Chiara Spadaro, Maria

2018-03-01

Experimental activity on core@shell, metal@oxide, and oxide nanoparticles (NPs) grown with physical synthesis, and more specifically by low pressure gas aggregation sources (LPGAS) is reviewed, through a selection of examples encompassing some potential applications in nanotechnology. After an introduction to the applications of NPs, a brief description of the main characteristics of the growth process of clusters and NPs in LPGAS is given. Thereafter, some relevant case studies are reported: • Formation of native oxide shells around the metal cores in core@shell NPs. • Experimental efforts to obtain magnetic stabilization in magnetic core@shell NPs by controlling their structure and morphology. • Recent advancements in NP source design and new techniques of co-deposition, with relevant results in the realization of NPs with a greater variety of functionalities. • Recent results on reducible oxide NPs, with potentialities in nanocatalysis, energy storage, and other applications. Although this list is far from being exhaustive, the aim of the authors is to provide the reader a descriptive glimpse into the physics behind the growth and studies of low pressure gas-phase synthesized NPs, with their ever-growing potentialities for the rational design of new functional materials.

The synthesis and electronic structure of a novel [NiS4Fe2(CO)6] radical cluster: implications for the active site of the [NiFe] hydrogenases.

PubMed

Wang, Qiang; Barclay, J Elaine; Blake, Alexander J; Davies, E Stephen; Evans, David J; Marr, Andrew C; McInnes, Eric J L; McMaster, Jonathan; Wilson, Claire; Schröder, Martin

2004-07-19

A novel [NiS4Fe2(CO)6]cluster (1: 'S(4)'=(CH(3)C(6)H(3)S(2))(2)(CH(2))(3)) has been synthesised, structurally characterised and has been shown to undergo a chemically reversible reduction process at -1.31 V versus Fc(+)/Fc to generate the EPR-active monoanion 1(-). Multifrequency Q-, X- and S-band EPR spectra of (61)Ni-enriched 1(-) show a well-resolved quartet hyperfine splitting in the low-field region due to the interaction with a single (61)Ni (I=3/2) nucleus. Simulations of the EPR spectra require the introduction of a single angle of non-coincidence between g(1) and A(1), and g(3) and A(3) to reproduce all of the features in the S- and X-band spectra. This behaviour provides a rare example of the detection and measurement of non-coincidence effects from frozen-solution EPR spectra without the need for single-crystal measurements, and in which the S-band experiment is sensitive to the non-coincidence. An analysis of the EPR spectra of 1(-) reveals a 24 % Ni contribution to the SOMO in 1(-), supporting a delocalisation of the spin-density across the NiFe(2) cluster. This observation is supported by IR spectroscopic results which show that the CO stretching frequencies, nu(CO), shift to lower frequency by about 70 cm(-1) when 1 is reduced to 1(-). Density functional calculations provide a framework for the interpretation of the spectroscopic properties of 1(-) and suggest that the SOMO is delocalised over the whole cluster, but with little S-centre participation. This electronic structure contrasts with that of the Ni-A, -B, -C and -L forms of [NiFe] hydrogenase in which there is considerable S participation in the SOMO.

A powerful double radio relic system discovered in PSZ1 G108.18-11.53: evidence for a shock with non-uniform Mach number?

DOE PAGES

de Gasperin, F.; Intema, H. T.; van Weeren, R. J.; ...

2015-09-09

Diffuse radio emission in the form of radio haloes and relics has been found in a number of merging galaxy clusters. These structures indicate that shock and turbulence associated with the merger accelerate electrons to relativistic energies. We report the discovery of a radio relic + radio halo system in PSZ1 G108.18-11.53 (z = 0.335). This cluster hosts the second most powerful double radio relic system ever discovered. We observed PSZ1 G108.18-11.53 with the Giant Meterwave Radio Telescope and the Westerbork Synthesis Radio Telescope. We obtained radio maps at 147, 323, 607 and 1380 MHz. We also observed the cluster with the Keck telescope, obtaining the spectroscopic redshift for 42 cluster members. From the injection index, we obtained the Mach number of the shocks generating the two radio relics. For the southern shock, we foundmore » $M$ = 2.33 $$+0.19\\atop{-0.26}$$ while the northern shock Mach number goes from $M$2.20 $$+0.07\\atop{-0.14}$$ in the north part down to $M$ = 200 $$+0.03\\atop{-0.08}$$ in the southern region. Finally, if the relation between the injection index and the Mach number predicted by diffusive shock acceleration theory holds, this is the first observational evidence for a gradient in the Mach number along a galaxy cluster merger shock.« less

COMPARING MID-INFRARED GLOBULAR CLUSTER COLORS WITH POPULATION SYNTHESIS MODELS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barmby, P.; Jalilian, F. F.

2012-04-15

Several population synthesis models now predict integrated colors of simple stellar populations in the mid-infrared bands. To date, the models have not been extensively tested in this wavelength range. In a comparison of the predictions of several recent population synthesis models, the integrated colors are found to cover approximately the same range but to disagree in detail, for example, on the effects of metallicity. To test against observational data, globular clusters (GCs) are used as the closest objects to idealized groups of stars with a single age and single metallicity. Using recent mass estimates, we have compiled a sample ofmore » massive, old GCs in M31 which contain enough stars to guard against the stochastic effects of small-number statistics, and measured their integrated colors in the Spitzer/IRAC bands. Comparison of the cluster photometry in the IRAC bands with the model predictions shows that the models reproduce the cluster colors reasonably well, except for a small (not statistically significant) offset in [4.5] - [5.8]. In this color, models without circumstellar dust emission predict bluer values than are observed. Model predictions of colors formed from the V band and the IRAC 3.6 and 4.5 {mu}m bands are redder than the observed data at high metallicities and we discuss several possible explanations. In agreement with model predictions, V - [3.6] and V - [4.5] colors are found to have metallicity sensitivity similar to or slightly better than V - K{sub s}.« less

Pseudomonas syringae Phytotoxins: Mode of Action, Regulation, and Biosynthesis by Peptide and Polyketide Synthetases

PubMed Central

Bender, Carol L.; Alarcón-Chaidez, Francisco; Gross, Dennis C.

1999-01-01

Coronatine, syringomycin, syringopeptin, tabtoxin, and phaseolotoxin are the most intensively studied phytotoxins of Pseudomonas syringae, and each contributes significantly to bacterial virulence in plants. Coronatine functions partly as a mimic of methyl jasmonate, a hormone synthesized by plants undergoing biological stress. Syringomycin and syringopeptin form pores in plasma membranes, a process that leads to electrolyte leakage. Tabtoxin and phaseolotoxin are strongly antimicrobial and function by inhibiting glutamine synthetase and ornithine carbamoyltransferase, respectively. Genetic analysis has revealed the mechanisms responsible for toxin biosynthesis. Coronatine biosynthesis requires the cooperation of polyketide and peptide synthetases for the assembly of the coronafacic and coronamic acid moieties, respectively. Tabtoxin is derived from the lysine biosynthetic pathway, whereas syringomycin, syringopeptin, and phaseolotoxin biosynthesis requires peptide synthetases. Activation of phytotoxin synthesis is controlled by diverse environmental factors including plant signal molecules and temperature. Genes involved in the regulation of phytotoxin synthesis have been located within the coronatine and syringomycin gene clusters; however, additional regulatory genes are required for the synthesis of these and other phytotoxins. Global regulatory genes such as gacS modulate phytotoxin production in certain pathovars, indicating the complexity of the regulatory circuits controlling phytotoxin synthesis. The coronatine and syringomycin gene clusters have been intensively characterized and show potential for constructing modified polyketides and peptides. Genetic reprogramming of peptide and polyketide synthetases has been successful, and portions of the coronatine and syringomycin gene clusters could be valuable resources in developing new antimicrobial agents. PMID:10357851

Fe-S Cluster Biogenesis in Isolated Mammalian Mitochondria

PubMed Central

Pandey, Alok; Pain, Jayashree; Ghosh, Arnab K.; Dancis, Andrew; Pain, Debkumar

2015-01-01

Iron-sulfur (Fe-S) clusters are essential cofactors, and mitochondria contain several Fe-S proteins, including the [4Fe-4S] protein aconitase and the [2Fe-2S] protein ferredoxin. Fe-S cluster assembly of these proteins occurs within mitochondria. Although considerable data exist for yeast mitochondria, this biosynthetic process has never been directly demonstrated in mammalian mitochondria. Using [35S]cysteine as the source of sulfur, here we show that mitochondria isolated from Cath.A-derived cells, a murine neuronal cell line, can synthesize and insert new Fe-35S clusters into aconitase and ferredoxins. The process requires GTP, NADH, ATP, and iron, and hydrolysis of both GTP and ATP is necessary. Importantly, we have identified the 35S-labeled persulfide on the NFS1 cysteine desulfurase as a genuine intermediate en route to Fe-S cluster synthesis. In physiological settings, the persulfide sulfur is released from NFS1 and transferred to a scaffold protein, where it combines with iron to form an Fe-S cluster intermediate. We found that the release of persulfide sulfur from NFS1 requires iron, showing that the use of iron and sulfur for the synthesis of Fe-S cluster intermediates is a highly coordinated process. The release of persulfide sulfur also requires GTP and NADH, probably mediated by a GTPase and a reductase, respectively. ATP, a cofactor for a multifunctional Hsp70 chaperone, is not required at this step. The experimental system described here may help to define the biochemical basis of diseases that are associated with impaired Fe-S cluster biogenesis in mitochondria, such as Friedreich ataxia. PMID:25398879

Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase from Shewanella oneidensis at 1.6 angstrom: Identification of Farnesyl pyrophosphate Trapped in a Hydrophobic Cavity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ni, Shuisong; Robinson, Howard; Marsing, Gregory C.

2004-11-01

1. Introduction Enzymes in the non-mevalonate pathway for isoprenoid synthesis have gained recent attention because of their potential value as targets for antibiotic drug development. 2C-methyl-D-erythritol-2,4 cyclophosphate (MECDP) synthase is the fifth enzyme in the seven enzyme non-mevalonate pathway for synthesis of isopentenyl diphosphate. Four groups have published structures of MECDP synthase at resolutions varying from 1.6Å to 2.8Å, either in the presence or absence of substrate from Escherichia coli (Richard et al., 2002; Kemp et al., 2002; Steinbacher et al., 2002) or from Thermus thermophilus (Kishida et al., 2003). Among these structures, the protein always exists as a homotrimermore » either with a crystallographic or a non-crystallographic three-fold symmetry axis and an active site formed in a cleft between adjacent monomers. While the overall shape of the proteins is highly similar among these structures, each of the four reported structures contain different combinations of metal ions in the active site including a Zn2+ ion only (Steinbacher et al., 2002), a Mn2+ ion only (Richard et al., 2002), Zn2+ and Mn2+ ions (Kemp et al., 2002) or two Mg2+ ions (Kishida et al., 2003). Furthermore, two of the structures are reported to contain a hydrophobic channel along the three-fold symmetry axis that is capped by a cluster of three arginine side chains (one from each monomer) at one end of the cavity and a cluster of three glutamic acid side chains (one from each monomer) at the other side of the cavity. In a 1.8Å resolution structure, Kemp et al. (2002) reported a sulfate ion coordinated to the arginine cap and solvent trapped in a hydrophobic cavity. In a lower 2.8Å resolution structure, Richard et al. (2002) concluded that geranyl diphosphate, GPP, was most likely trapped by the arginine cap and hydrophobic cavity (Richard et al., 2002), however, the low resolution of the data together with the presence of the crystallographic symmetry axis prohibited a definitive analysis of the identity and mode of binding of the bound molecule. Kishida et al. (2003) reported that no cavity existed in a 1.6Å structure of the SO3437 homolog from Thermus thermophilus, presumably due to tighter packing of the protein from the thermophilic organism. Steinbacher et al. (2002) make no description of a hydrophobic cavity in a lower resolution (2.5-3.2Å) of the Escherichia coli protein. Here, we report a high-resolution (1.6Å) structure of MECDP synthase from Shewanella oneidensis in the absence of substrate in the active site. We provide unambiguous data that confirms the presence of Zn2+ in one of the metal binding sites and observe what appears to be farnesyl diphosphate (FPP) bound in the hydrophobic cavity along the non-crystallographic three-fold symmetry axis of the homotrimer. The high-resolution structure clarifies the mode of binding of the pyrophosphate of FPP in the arginine cluster that caps the hydrophobic cavity.« less

Bacilysin from Bacillus amyloliquefaciens FZB42 Has Specific Bactericidal Activity against Harmful Algal Bloom Species

PubMed Central

Wu, Liming; Wu, Huijun; Chen, Lina; Xie, Shanshan; Zang, Haoyu; Borriss, Rainer

2014-01-01

Harmful algal blooms, caused by massive and exceptional overgrowth of microalgae and cyanobacteria, are a serious environmental problem worldwide. In the present study, we looked for Bacillus strains with sufficiently strong anticyanobacterial activity to be used as biocontrol agents. Among 24 strains, Bacillus amyloliquefaciens FZB42 showed the strongest bactericidal activity against Microcystis aeruginosa, with a kill rate of 98.78%. The synthesis of the anticyanobacterial substance did not depend on Sfp, an enzyme that catalyzes a necessary processing step in the nonribosomal synthesis of lipopeptides and polyketides, but was associated with the aro gene cluster that is involved in the synthesis of the sfp-independent antibiotic bacilysin. Disruption of bacB, the gene in the cluster responsible for synthesizing bacilysin, or supplementation with the antagonist N-acetylglucosamine abolished the inhibitory effect, but this was restored when bacilysin synthesis was complemented. Bacilysin caused apparent changes in the algal cell wall and cell organelle membranes, and this resulted in cell lysis. Meanwhile, there was downregulated expression of glmS, psbA1, mcyB, and ftsZ—genes involved in peptidoglycan synthesis, photosynthesis, microcystin synthesis, and cell division, respectively. In addition, bacilysin suppressed the growth of other harmful algal species. In summary, bacilysin produced by B. amyloliquefaciens FZB42 has anticyanobacterial activity and thus could be developed as a biocontrol agent to mitigate the effects of harmful algal blooms. PMID:25261512

Colossal permittivity behavior and its origin in rutile (Mg1/3Ta2/3)xTi1-xO2.

PubMed

Dong, Wen; Chen, Dehong; Hu, Wanbiao; Frankcombe, Terry J; Chen, Hua; Zhou, Chao; Fu, Zhenxiao; Wei, Xiaoyong; Xu, Zhuo; Liu, Zhifu; Li, Yongxiang; Liu, Yun

2017-08-30

This work investigates the synthesis, chemical composition, defect structures and associated dielectric properties of (Mg 2+ , Ta 5+ ) co-doped rutile TiO 2 polycrystalline ceramics with nominal compositions of (Mg 2+ 1/3 Ta 5+ 2/3 ) x Ti 1-x O 2 . Colossal permittivity (>7000) with a low dielectric loss (e.g. 0.002 at 1 kHz) across a broad frequency/temperature range can be achieved at x = 0.5% after careful optimization of process conditions. Both experimental and theoretical evidence indicates such a colossal permittivity and low dielectric loss intrinsically originate from the intragrain polarization that links to the electron-pinned [Formula: see text] defect clusters with a specific configuration, different from the defect cluster form previously reported in tri-/pent-valent ion co-doped rutile TiO 2 . This work extends the research on colossal permittivity and defect formation to bi-/penta-valent ion co-doped rutile TiO 2 and elucidates a likely defect cluster model for this system. We therefore believe these results will benefit further development of colossal permittivity materials and advance the understanding of defect chemistry in solids.

Cleavage of Sn-C and S-C(alkyl) bonds on an organotin scaffold: synthesis and characterization of a novel organotin-sulfite cluster bearing methyltin- and dimethyltin fragments.

PubMed

Shankar, Ravi; Jain, Archana; Kociok-Köhn, Gabriele; Mahon, Mary F; Molloy, Kieran C

2010-05-17

Hydrolysis of the mixed-ligand dimethyltin(ethoxy)ethanesulfonate, [Me(2)Sn(OEt)(OSO(2)Et)](n) (1a) in moist hexane proceeds via disproportionation and partial cleavage of Sn-C and S-C bonds to afford a novel oxo-/hydroxo- organotin cluster of the composition [(Me(2)Sn)(MeSn)(4)(OSO(2)Et)(2)(OH)(4)(O)(2)(SO(3))(2)] (1) bearing both mono- and dimethyltin fragments and in situ generated sulfite (SO(3)(2-)) anion in the structural framework. On the other hand, similar reactions with analogous mixed ligand diorganotin precursors, [R(2)Sn(OR(1))(OSO(2)R(1))](n) (R = n-Bu, R(1) = Et (2a); R = Et, R(1) = Me (3a)), result in the formation of tetranuclear diorganotin clusters, [{(n-Bu(2)Sn)(2)(OH)(OSO(2)Et)}O](2) (2) and [(Et(2)Sn)(4)(OH)(O)(2)(OSO(2)Me)(3)] (3), respectively. The activation of the Sn-C or S-C bond is not observed in these cases. These findings provide a preliminary insight into the unusual reactivity of 1a under hydrolytic conditions.

Synthesis, characterization and optical non-linearity of two heterobimetallic copper clusters containing tetraselenometalates

NASA Astrophysics Data System (ADS)

Zhang, Qian-Feng; Zhang, Chi; Song, Ying-Lin; Xin, Xin-Quan

2000-07-01

Cluster [{MoCu 3Se 3Br}(PPh 3) 3Se]·3THF·H 2O ( 1·3THF·H 2O) was prepared from reaction of [Et 4N] 2[MoSe] 4, Cu(PPh 3) 2NO 3 and Et 4N·Br in CH 2Cl 2 solution; also, 1 can be also obtained from the reaction of [MoSe 4Cu 4Py 6Br 2] and excess PPh 3 in a DMF-CH 2Cl 2 mixture solvent. The 95Mo NMR technique was used to monitor the above two reaction processes. X-ray crystallographic structure determination shows that it contains a strongly distorted cubane-like {MoCu 3Se 3Br} core. The coordination of the central Mo atom and each Cu atom are distorted from tetrahedral. Cluster [{WCu 3Se 3Cl}(PPh 3) 3Se] ( 2) was synthesized by the reaction of [Et 4N] 2[WSe] 4 and Cu(PPh 3) 2Cl in the solid state for nonlinear optical (NLO) studies. Its structure was reported by Ibers (Inorg. Chem. 31 (1992) 4365). The NLO properties of clusters 1 and 2 were studied. Both NLO absorption and refraction were obtained, and their effective third-order non-linearities were detected with α2=3.4×10 -10 and 5.9×10 -10 m/W and n2=-1.5×10 -17 and -1.3×10 -17 m 2/W , respectively, for the same concentration CH 2Cl 2 solution of 1 and 2. Influence of skeletal atoms to nonlinear absorption is also discussed in the paper.

Valence and charge-transfer optical properties for some SinCm (m, n ≤ 12) clusters: Comparing TD-DFT, complete-basis-limit EOMCC, and benchmarks from spectroscopy

NASA Astrophysics Data System (ADS)

Lutz, Jesse J.; Duan, Xiaofeng F.; Ranasinghe, Duminda S.; Jin, Yifan; Margraf, Johannes T.; Perera, Ajith; Burggraf, Larry W.; Bartlett, Rodney J.

2018-05-01

Accurate optical characterization of the closo-Si12C12 molecule is important to guide experimental efforts toward the synthesis of nano-wires, cyclic nano-arrays, and related array structures, which are anticipated to be robust and efficient exciton materials for opto-electronic devices. Working toward calibrated methods for the description of closo-Si12C12 oligomers, various electronic structure approaches are evaluated for their ability to reproduce measured optical transitions of the SiC2, Si2Cn (n = 1-3), and Si3Cn (n = 1, 2) clusters reported earlier by Steglich and Maier [Astrophys. J. 801, 119 (2015)]. Complete-basis-limit equation-of-motion coupled-cluster (EOMCC) results are presented and a comparison is made between perturbative and renormalized non-iterative triples corrections. The effect of adding a renormalized correction for quadruples is also tested. Benchmark test sets derived from both measurement and high-level EOMCC calculations are then used to evaluate the performance of a variety of density functionals within the time-dependent density functional theory (TD-DFT) framework. The best-performing functionals are subsequently applied to predict valence TD-DFT excitation energies for the lowest-energy isomers of SinC and Sin-1C7-n (n = 4-6). TD-DFT approaches are then applied to the SinCn (n = 4-12) clusters and unique spectroscopic signatures of closo-Si12C12 are discussed. Finally, various long-range corrected density functionals, including those from the CAM-QTP family, are applied to a charge-transfer excitation in a cyclic (Si4C4)4 oligomer. Approaches for gauging the extent of charge-transfer character are also tested and EOMCC results are used to benchmark functionals and make recommendations.

Biosynthetic pathway for γ-cyclic sarcinaxanthin in Micrococcus luteus: heterologous expression and evidence for diverse and multiple catalytic functions of C(50) carotenoid cyclases.

PubMed

Netzer, Roman; Stafsnes, Marit H; Andreassen, Trygve; Goksøyr, Audun; Bruheim, Per; Brautaset, Trygve

2010-11-01

We report the cloning and characterization of the biosynthetic gene cluster (crtE, crtB, crtI, crtE2, crtYg, crtYh, and crtX) of the γ-cyclic C(50) carotenoid sarcinaxanthin in Micrococcus luteus NCTC2665. Expression of the complete and partial gene cluster in Escherichia coli hosts revealed that sarcinaxanthin biosynthesis from the precursor molecule farnesyl pyrophosphate (FPP) proceeds via C(40) lycopene, C(45) nonaflavuxanthin, C(50) flavuxanthin, and C(50) sarcinaxanthin. Glucosylation of sarcinaxanthin was accomplished by the crtX gene product. This is the first report describing the biosynthetic pathway of a γ-cyclic C(50) carotenoid. Expression of the corresponding genes from the marine M. luteus isolate Otnes7 in a lycopene-producing E. coli host resulted in the production of up to 2.5 mg/g cell dry weight sarcinaxanthin in shake flasks. In an attempt to experimentally understand the specific difference between the biosynthetic pathways of sarcinaxanthin and the structurally related ε-cyclic decaprenoxanthin, we constructed a hybrid gene cluster with the γ-cyclic C(50) carotenoid cyclase genes crtYg and crtYh from M. luteus replaced with the analogous ε-cyclic C(50) carotenoid cyclase genes crtYe and crtYf from the natural decaprenoxanthin producer Corynebacterium glutamicum. Surprisingly, expression of this hybrid gene cluster in an E. coli host resulted in accumulation of not only decaprenoxanthin, but also sarcinaxanthin and the asymmetric ε- and γ-cyclic C(50) carotenoid sarprenoxanthin, described for the first time in this work. Together, these data contributed to new insight into the diverse and multiple functions of bacterial C(50) carotenoid cyclases as key catalysts for the synthesis of structurally different carotenoids.

Electrochemical oxygen reduction behavior of selectively deposited platinum atoms on gold nanoparticles.

PubMed

Sarkar, A; Kerr, J B; Cairns, E J

2013-07-22

Carbon-supported Pt@Au "core-shell" nanoparticles with varying surface concentration of platinum atoms have been synthesized using a novel redox-mediated synthesis approach. The synthesis technique allows for a selective deposition of platinum atoms on the surface of prefabricated gold nanoparticles. Energy dispersive spectroscopic analyses in a scanning electron microscope reveal that the platinum to gold atomic ratios are close to the nominal values, validating the synthesis scheme. X-ray diffraction data indicate an un-alloyed structure. The platinum to gold surface atomic ratio determined from cyclic voltammetry and copper under-potential deposition experiments reveal good agreement with the calculated values at low platinum concentration. However, there is an increase in non-uniformity in the deposition process upon increasing the platinum concentration. Koutecky-Levich analysis of the samples indicates a transition of the total number of electrons transferred (n) in the electrochemical oxygen reduction reaction from two to four electrons upon increasing the surface concentration of platinum atoms. Furthermore, the data indicate that isolated platinum atoms can reduce molecular oxygen but via a two-electron route. Moreover, successful four-electron reduction of molecular oxygen requires clusters of platinum atoms. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular Clusters: Nanoscale Building Blocks for Solid-State Materials.

PubMed

Pinkard, Andrew; Champsaur, Anouck M; Roy, Xavier

2018-04-17

The programmed assembly of nanoscale building blocks into multicomponent hierarchical structures is a powerful strategy for the bottom-up construction of functional materials. To develop this concept, our team has explored the use of molecular clusters as superatomic building blocks to fabricate new classes of materials. The library of molecular clusters is rich with exciting properties, including diverse functionalization, redox activity, and magnetic ordering, so the resulting cluster-assembled solids, which we term superatomic crystals (SACs), hold the promise of high tunability, atomic precision, and robust architectures among a diverse range of other material properties. Molecular clusters have only seldom been used as precursors for functional materials. Our team has been at the forefront of new developments in this exciting research area, and this Account focuses on our progress toward designing materials from cluster-based precursors. In particular, this Account discusses (1) the design and synthesis of molecular cluster superatomic building blocks, (2) their self-assembly into SACs, and (3) their resulting collective properties. The set of molecular clusters discussed herein is diverse, with different cluster cores and ligand arrangements to create an impressive array of solids. The cluster cores include octahedral M 6 E 8 and cubane M 4 E 4 (M = metal; E = chalcogen), which are typically passivated by a shell of supporting ligands, a feature upon which we have expanded upon by designing and synthesizing more exotic ligands that can be used to direct solid-state assembly. Building from this library, we have designed whole families of binary SACs where the building blocks are held together through electrostatic, covalent, or van der Waals interactions. Using single-crystal X-ray diffraction (SCXRD) to determine the atomic structure, a remarkable range of compositional variability is accessible. We can also use this technique, in tandem with vibrational spectroscopy, to ascertain features about the constituent superatomic building blocks, such as the charge of the cluster cores, by analysis of bond distances from the SCXRD data. The combination of atomic precision and intercluster interactions in these SACs produces novel collective properties, including tunable electrical transport, crystalline thermal conductivity, and ferromagnetism. In addition, we have developed a synthetic strategy to insert redox-active guests into the superstructure of SACs via single-crystal-to-single-crystal intercalation. This intercalation process allows us to tune the optical and electrical transport properties of the superatomic crystal host. These properties are explored using a host of techniques, including Raman spectroscopy, SQUID magnetometry, electrical transport measurements, electronic absorption spectroscopy, differential scanning calorimetry, and frequency-domain thermoreflectance. Superatomic crystals have proven to be both robust and tunable, representing a new method of materials design and architecture. This Account demonstrates how precisely controlling the structure and properties of nanoscale building blocks is key in developing the next generation of functional materials; several examples are discussed and detailed herein.

Microwave plasma chemical synthesis of nanocrystalline carbon film structures and study their properties

NASA Astrophysics Data System (ADS)

Bushuev, N.; Yafarov, R.; Timoshenkov, V.; Orlov, S.; Starykh, D.

2015-08-01

The self-organization effect of diamond nanocrystals in polymer-graphite and carbon films is detected. The carbon materials deposition was carried from ethanol vapors out at low pressure using a highly non-equilibrium microwave plasma. Deposition processes of carbon film structures (diamond, graphite, graphene) is defined. Deposition processes of nanocrystalline structures containing diamond and graphite phases in different volume ratios is identified. The solid film was obtained under different conditions of microwave plasma chemical synthesis. We investigated the electrical properties of the nanocrystalline carbon films and identified it's from various factors. Influence of diamond-graphite film deposition mode in non-equilibrium microwave plasma at low pressure on emission characteristics was established. This effect is justified using the cluster model of the structure of amorphous carbon. It was shown that the reduction of bound hydrogen in carbon structures leads to a decrease in the threshold electric field of emission from 20-30 V/m to 5 V/m. Reducing the operating voltage field emission can improve mechanical stability of the synthesized film diamond-graphite emitters. Current density emission at least 20 A/cm2 was obtained. Nanocrystalline carbon film materials can be used to create a variety of functional elements in micro- and nanoelectronics and photonics such as cold electron source for emission in vacuum devices, photonic devices, cathodoluminescent flat display, highly efficient white light sources. The obtained graphene carbon net structure (with a net size about 6 μm) may be used for the manufacture of large-area transparent electrode for solar cells and cathodoluminescent light sources

A generalized analysis of hydrophobic and loop clusters within globular protein sequences

PubMed Central

Eudes, Richard; Le Tuan, Khanh; Delettré, Jean; Mornon, Jean-Paul; Callebaut, Isabelle

2007-01-01

Background Hydrophobic Cluster Analysis (HCA) is an efficient way to compare highly divergent sequences through the implicit secondary structure information directly derived from hydrophobic clusters. However, its efficiency and application are currently limited by the need of user expertise. In order to help the analysis of HCA plots, we report here the structural preferences of hydrophobic cluster species, which are frequently encountered in globular domains of proteins. These species are characterized only by their hydrophobic/non-hydrophobic dichotomy. This analysis has been extended to loop-forming clusters, using an appropriate loop alphabet. Results The structural behavior of hydrophobic cluster species, which are typical of protein globular domains, was investigated within banks of experimental structures, considered at different levels of sequence redundancy. The 294 more frequent hydrophobic cluster species were analyzed with regard to their association with the different secondary structures (frequencies of association with secondary structures and secondary structure propensities). Hydrophobic cluster species are predominantly associated with regular secondary structures, and a large part (60 %) reveals preferences for α-helices or β-strands. Moreover, the analysis of the hydrophobic cluster amino acid composition generally allows for finer prediction of the regular secondary structure associated with the considered cluster within a cluster species. We also investigated the behavior of loop forming clusters, using a "PGDNS" alphabet. These loop clusters do not overlap with hydrophobic clusters and are highly associated with coils. Finally, the structural information contained in the hydrophobic structural words, as deduced from experimental structures, was compared to the PSI-PRED predictions, revealing that β-strands and especially α-helices are generally over-predicted within the limits of typical β and α hydrophobic clusters. Conclusion The dictionary of hydrophobic clusters described here can help the HCA user to interpret and compare the HCA plots of globular protein sequences, as well as provides an original fundamental insight into the structural bricks of protein folds. Moreover, the novel loop cluster analysis brings additional information for secondary structure prediction on the whole sequence through a generalized cluster analysis (GCA), and not only on regular secondary structures. Such information lays the foundations for developing a new and original tool for secondary structure prediction. PMID:17210072

Studies on tridecaptin B(1), a lipopeptide with activity against multidrug resistant Gram-negative bacteria.

PubMed

Cochrane, Stephen A; Lohans, Christopher T; van Belkum, Marco J; Bels, Manon A; Vederas, John C

2015-06-07

Previously other groups had reported that Paenibacillus polymyxa NRRL B-30507 produces SRCAM 37, a type IIA bacteriocin with antimicrobial activity against Campylobacter jejuni. Genome sequencing and isolation of antimicrobial compounds from this P. polymyxa strain show that the antimicrobial activity is due to polymyxins and tridecaptin B1. The complete structural assignment, synthesis, and antimicrobial profile of tridecaptin B1 is reported, as well as the putative gene cluster responsible for its biosynthesis. This peptide displays strong activity against multidrug resistant Gram-negative bacteria, a finding that is timely to the current problem of antibiotic resistance.

Microwave-assisted synthesis of water-soluble, fluorescent gold nanoclusters capped with small organic molecules and a revealing fluorescence and X-ray absorption study

NASA Astrophysics Data System (ADS)

Helmbrecht, C.; Lützenkirchen-Hecht, D.; Frank, W.

2015-03-01

Colourless solutions of blue light-emitting, water-soluble gold nanoclusters (AuNC) were synthesized from gold colloids under microwave irradiation using small organic molecules as ligands. Stabilized by 1,3,5-triaza-7-phosphaadamantane (TPA) or l-glutamine (GLU), fluorescence quantum yields up to 5% were obtained. AuNC are considered to be very promising for biological labelling, optoelectronic devices and light-emitting materials but the structure-property relationships have still not been fully clarified. To expand the knowledge about the AuNC apart from their fluorescent properties they were studied by X-ray absorption spectroscopy elucidating the oxidation state of the nanoclusters' gold atoms. Based on curve fitting of the XANES spectra in comparison to several gold references, optically transparent fluorescent AuNC are predicted to be ligand-stabilized Au5+ species. Additionally, their near edge structure compared with analogous results of polynuclear clusters known from the literature discloses an increasing intensity of the feature close to the absorption edge with decreasing cluster size. As a result, a linear relationship between the cluster size and the X-ray absorption coefficient can be established for the first time.Colourless solutions of blue light-emitting, water-soluble gold nanoclusters (AuNC) were synthesized from gold colloids under microwave irradiation using small organic molecules as ligands. Stabilized by 1,3,5-triaza-7-phosphaadamantane (TPA) or l-glutamine (GLU), fluorescence quantum yields up to 5% were obtained. AuNC are considered to be very promising for biological labelling, optoelectronic devices and light-emitting materials but the structure-property relationships have still not been fully clarified. To expand the knowledge about the AuNC apart from their fluorescent properties they were studied by X-ray absorption spectroscopy elucidating the oxidation state of the nanoclusters' gold atoms. Based on curve fitting of the XANES spectra in comparison to several gold references, optically transparent fluorescent AuNC are predicted to be ligand-stabilized Au5+ species. Additionally, their near edge structure compared with analogous results of polynuclear clusters known from the literature discloses an increasing intensity of the feature close to the absorption edge with decreasing cluster size. As a result, a linear relationship between the cluster size and the X-ray absorption coefficient can be established for the first time. Electronic supplementary information (ESI) available: The deconvoluted reference spectra are given in ESI Fig. 1-9. See DOI: 10.1039/c4nr07051h

Fast large-scale clustering of protein structures using Gauss integrals.

PubMed

Harder, Tim; Borg, Mikael; Boomsma, Wouter; Røgen, Peter; Hamelryck, Thomas

2012-02-15

Clustering protein structures is an important task in structural bioinformatics. De novo structure prediction, for example, often involves a clustering step for finding the best prediction. Other applications include assigning proteins to fold families and analyzing molecular dynamics trajectories. We present Pleiades, a novel approach to clustering protein structures with a rigorous mathematical underpinning. The method approximates clustering based on the root mean square deviation by first mapping structures to Gauss integral vectors--which were introduced by Røgen and co-workers--and subsequently performing K-means clustering. Compared to current methods, Pleiades dramatically improves on the time needed to perform clustering, and can cluster a significantly larger number of structures, while providing state-of-the-art results. The number of low energy structures generated in a typical folding study, which is in the order of 50,000 structures, can be clustered within seconds to minutes.

Integrating K-means Clustering with Kernel Density Estimation for the Development of a Conditional Weather Generation Downscaling Model

NASA Astrophysics Data System (ADS)

Chen, Y.; Ho, C.; Chang, L.

2011-12-01

In previous decades, the climate change caused by global warming increases the occurrence frequency of extreme hydrological events. Water supply shortages caused by extreme events create great challenges for water resource management. To evaluate future climate variations, general circulation models (GCMs) are the most wildly known tools which shows possible weather conditions under pre-defined CO2 emission scenarios announced by IPCC. Because the study area of GCMs is the entire earth, the grid sizes of GCMs are much larger than the basin scale. To overcome the gap, a statistic downscaling technique can transform the regional scale weather factors into basin scale precipitations. The statistic downscaling technique can be divided into three categories include transfer function, weather generator and weather type. The first two categories describe the relationships between the weather factors and precipitations respectively based on deterministic algorithms, such as linear or nonlinear regression and ANN, and stochastic approaches, such as Markov chain theory and statistical distributions. In the weather type, the method has ability to cluster weather factors, which are high dimensional and continuous variables, into weather types, which are limited number of discrete states. In this study, the proposed downscaling model integrates the weather type, using the K-means clustering algorithm, and the weather generator, using the kernel density estimation. The study area is Shihmen basin in northern of Taiwan. In this study, the research process contains two steps, a calibration step and a synthesis step. Three sub-steps were used in the calibration step. First, weather factors, such as pressures, humidities and wind speeds, obtained from NCEP and the precipitations observed from rainfall stations were collected for downscaling. Second, the K-means clustering grouped the weather factors into four weather types. Third, the Markov chain transition matrixes and the conditional probability density function (PDF) of precipitations approximated by the kernel density estimation are calculated respectively for each weather types. In the synthesis step, 100 patterns of synthesis data are generated. First, the weather type of the n-th day are determined by the results of K-means clustering. The associated transition matrix and PDF of the weather type were also determined for the usage of the next sub-step in the synthesis process. Second, the precipitation condition, dry or wet, can be synthesized basing on the transition matrix. If the synthesized condition is dry, the quantity of precipitation is zero; otherwise, the quantity should be further determined in the third sub-step. Third, the quantity of the synthesized precipitation is assigned as the random variable of the PDF defined above. The synthesis efficiency compares the gap of the monthly mean curves and monthly standard deviation curves between the historical precipitation data and the 100 patterns of synthesis data.

Architecture of the Human Mitochondrial Iron-Sulfur Cluster Assembly Machinery.

PubMed

Gakh, Oleksandr; Ranatunga, Wasantha; Smith, Douglas Y; Ahlgren, Eva-Christina; Al-Karadaghi, Salam; Thompson, James R; Isaya, Grazia

2016-09-30

Fe-S clusters, essential cofactors needed for the activity of many different enzymes, are assembled by conserved protein machineries inside bacteria and mitochondria. As the architecture of the human machinery remains undefined, we co-expressed in Escherichia coli the following four proteins involved in the initial step of Fe-S cluster synthesis: FXN 42-210 (iron donor); [NFS1]·[ISD11] (sulfur donor); and ISCU (scaffold upon which new clusters are assembled). We purified a stable, active complex consisting of all four proteins with 1:1:1:1 stoichiometry. Using negative staining transmission EM and single particle analysis, we obtained a three-dimensional model of the complex with ∼14 Å resolution. Molecular dynamics flexible fitting of protein structures docked into the EM map of the model revealed a [FXN 42-210 ] 24 ·[NFS1] 24 ·[ISD11] 24 ·[ISCU] 24 complex, consistent with the measured 1:1:1:1 stoichiometry of its four components. The complex structure fulfills distance constraints obtained from chemical cross-linking of the complex at multiple recurring interfaces, involving hydrogen bonds, salt bridges, or hydrophobic interactions between conserved residues. The complex consists of a central roughly cubic [FXN 42-210 ] 24 ·[ISCU] 24 sub-complex with one symmetric ISCU trimer bound on top of one symmetric FXN 42-210 trimer at each of its eight vertices. Binding of 12 [NFS1] 2 ·[ISD11] 2 sub-complexes to the surface results in a globular macromolecule with a diameter of ∼15 nm and creates 24 Fe-S cluster assembly centers. The organization of each center recapitulates a previously proposed conserved mechanism for sulfur donation from NFS1 to ISCU and reveals, for the first time, a path for iron donation from FXN 42-210 to ISCU. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Architecture of the Human Mitochondrial Iron-Sulfur Cluster Assembly Machinery*

PubMed Central

Gakh, Oleksandr; Ranatunga, Wasantha; Smith, Douglas Y.; Ahlgren, Eva-Christina; Al-Karadaghi, Salam; Thompson, James R.; Isaya, Grazia

2016-01-01

Fe-S clusters, essential cofactors needed for the activity of many different enzymes, are assembled by conserved protein machineries inside bacteria and mitochondria. As the architecture of the human machinery remains undefined, we co-expressed in Escherichia coli the following four proteins involved in the initial step of Fe-S cluster synthesis: FXN42–210 (iron donor); [NFS1]·[ISD11] (sulfur donor); and ISCU (scaffold upon which new clusters are assembled). We purified a stable, active complex consisting of all four proteins with 1:1:1:1 stoichiometry. Using negative staining transmission EM and single particle analysis, we obtained a three-dimensional model of the complex with ∼14 Å resolution. Molecular dynamics flexible fitting of protein structures docked into the EM map of the model revealed a [FXN42–210]24·[NFS1]24·[ISD11]24·[ISCU]24 complex, consistent with the measured 1:1:1:1 stoichiometry of its four components. The complex structure fulfills distance constraints obtained from chemical cross-linking of the complex at multiple recurring interfaces, involving hydrogen bonds, salt bridges, or hydrophobic interactions between conserved residues. The complex consists of a central roughly cubic [FXN42–210]24·[ISCU]24 sub-complex with one symmetric ISCU trimer bound on top of one symmetric FXN42–210 trimer at each of its eight vertices. Binding of 12 [NFS1]2·[ISD11]2 sub-complexes to the surface results in a globular macromolecule with a diameter of ∼15 nm and creates 24 Fe-S cluster assembly centers. The organization of each center recapitulates a previously proposed conserved mechanism for sulfur donation from NFS1 to ISCU and reveals, for the first time, a path for iron donation from FXN42–210 to ISCU. PMID:27519411

Planet population synthesis driven by pebble accretion in cluster environments

NASA Astrophysics Data System (ADS)

Ndugu, N.; Bitsch, B.; Jurua, E.

2018-02-01

The evolution of protoplanetary discs embedded in stellar clusters depends on the age and the stellar density in which they are embedded. Stellar clusters of young age and high stellar surface density destroy protoplanetary discs by external photoevaporation and stellar encounters. Here, we consider the effect of background heating from newly formed stellar clusters on the structure of protoplanetary discs and how it affects the formation of planets in these discs. Our planet formation model is built on the core accretion scenario, where we take the reduction of the core growth time-scale due to pebble accretion into account. We synthesize planet populations that we compare to observations obtained by radial velocity measurements. The giant planets in our simulations migrate over large distances due to the fast type-II migration regime induced by a high disc viscosity (α = 5.4 × 10-3). Cold Jupiters (rp > 1 au) originate preferably from the outer disc, due to the large-scale planetary migration, while hot Jupiters (rp < 0.1 au) preferably form in the inner disc. We find that the formation of gas giants via pebble accretion is in agreement with the metallicity correlation, meaning that more gas giants are formed at larger metallicity. However, our synthetic population of isolated stars host a significant amount of giant planets even at low metallicity, in contradiction to observations where giant planets are preferably found around high metallicity stars, indicating that pebble accretion is very efficient in the standard pebble accretion framework. On the other hand, discs around stars embedded in cluster environments hardly form any giant planets at low metallicity in agreement with observations, where these changes originate from the increased temperature in the outer parts of the disc, which prolongs the core accretion time-scale of the planet. We therefore conclude that the outer disc structure and the planet's formation location determines the giant planet occurrence rate and the formation efficiency of cold and hot Jupiters.

An Aspergillus flavus secondary metabolic gene cluster containing a hybrid PKS-NRPS is necessary for synthesis of the 2-pyridones, leporins

USDA-ARS?s Scientific Manuscript database

The genome of the filamentous fungus, Aspergillus flavus, has been shown to harbor as many as 55 putative secondary metabolic gene clusters including the one responsible for production of the toxic and carcinogenic, polyketide synthase (PKS)-derived family of secondary metabolites termed aflatoxins....

Binary Populations and Stellar Dynamics in Young Clusters

NASA Astrophysics Data System (ADS)

Vanbeveren, D.; Belkus, H.; Van Bever, J.; Mennekens, N.

2008-06-01

We first summarize work that has been done on the effects of binaries on theoretical population synthesis of stars and stellar phenomena. Next, we highlight the influence of stellar dynamics in young clusters by discussing a few candidate UFOs (unconventionally formed objects) like intermediate mass black holes, η Car, ζ Pup, γ2 Velorum and WR 140.

Surfactant-assisted synthesis of mono-dispersed cubic BaTiO{sub 3} nanoparticles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hai, Chunxi; Inukai, Koji; Takahashi, Yosuke

2014-09-15

Mono-dispersed BaTiO{sub 3} nanoparticles have been prepared via the assistance of capping agent poly(vinylpyrrolidone) (PVP). - Highlights: • BaTiO{sub 3} nanoparticles with single cubic crystal structure. • Poor dispersibility of nanoparticles has been overcome by in situ modification way. • Growth competition between BaTiO3 core and polymer shell. - Abstract: In this study, poly(vinylpyrrolidone)-assisted synthesis of mono-dispersed BaTiO{sub 3} nanoparticles have been reported. The various processing parameters, namely, refluxing temperature, KOH concentration, and poly(vinylpyrrolidone) concentration, have been varied, and the effects on the growth of BaTiO{sub 3} particles have been analyzed systematically. X-ray diffraction studies indicated that poly(vinylpyrrolidone) did notmore » affect the crystal structure, but rather influenced the crystal lattice structure. In addition, the use of surfactant poly(vinylpyrrolidone) hindered the agglomeration of the nanoparticles, and facilitated the formation of mono-dispersed core–shell organic/inorganic hybrid nanocomposite. Furthermore, the mineralizer KOH promoted the dissolution of reactants and promoted the crystallization of BaTiO{sub 3} particles. Accordingly, the dissolution-precipitation scheme was believed to be the mechanism underlying the formation of BaTiO{sub 3} particles. This was further substantiated by the experimental observations, which indicated that the nucleation and crystallization of the particles was affected by the KOH concentration in the reaction system. Finally, the formation of mono-dispersed core–shell nanocomposites proceeded via reaction limited cluster aggregation. We believe that the method proposed in this study could be extended for the synthesis of mono-dispersed nanoparticles for industrial applications.« less

Simulations of the synthesis of boron-nitride nanostructures in a hot, high pressure gas volume† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c8sc00667a

PubMed Central

Han, Longtao; Irle, Stephan; Nakai, Hiromi

2018-01-01

We performed nanosecond timescale computer simulations of clusterization and agglomeration processes of boron nitride (BN) nanostructures in hot, high pressure gas, starting from eleven different atomic and molecular precursor systems containing boron, nitrogen and hydrogen at various temperatures from 1500 to 6000 K. The synthesized BN nanostructures self-assemble in the form of cages, flakes, and tubes as well as amorphous structures. The simulations facilitate the analysis of chemical dynamics and we are able to predict the optimal conditions concerning temperature and chemical precursor composition for controlling the synthesis process in a high temperature gas volume, at high pressure. We identify the optimal precursor/temperature choices that lead to the nanostructures of highest quality with the highest rate of synthesis, using a novel parameter of the quality of the synthesis (PQS). Two distinct mechanisms of BN nanotube growth were found, neither of them based on the root-growth process. The simulations were performed using quantum-classical molecular dynamics (QCMD) based on the density-functional tight-binding (DFTB) quantum mechanics in conjunction with a divide-and-conquer (DC) linear scaling algorithm, as implemented in the DC-DFTB-K code, enabling the study of systems as large as 1300 atoms in canonical NVT ensembles for 1 ns time. PMID:29780513

Three-chain B{sub 6n+14} cages as possible precursors for the syntheses of boron fullerenes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lu, Haigang, E-mail: luhg@sxu.edu.cn; Li, Si-Dian

Using the first principle methods, we proposed a series of three-chain boron cages B{sub 6n+14} (n = 1–12) which are mainly built by fusing three boron semi-double-rings. Their simple geometric structures (approximate D{sub 3} or C{sub 3} symmetry) facilitate their bottom-up syntheses from the hexagonal B{sub 7} and the double-chain boron clusters, such as B{sub 2}, B{sub 4}, B{sub 6}, B{sub 8}H{sub 2}, B{sub 10}H{sub 2}, B{sub 12}H{sub 2}, and the double ring B{sub 20}. The spherical shapes of these three-chain boron cages show that they could be taken as the possible precursors to further synthesize the boron fullerenes, suchmore » as B{sub 80}. Therefore, these three-chain boron cages provide a possible synthesis pathway of the boron fullerenes from the experimentally synthesized small planar boron clusters.« less

Platinum single-atom and cluster catalysis of the hydrogen evolution reaction

NASA Astrophysics Data System (ADS)

Cheng, Niancai; Stambula, Samantha; Wang, Da; Banis, Mohammad Norouzi; Liu, Jian; Riese, Adam; Xiao, Biwei; Li, Ruying; Sham, Tsun-Kong; Liu, Li-Min; Botton, Gianluigi A.; Sun, Xueliang

2016-11-01

Platinum-based catalysts have been considered the most effective electrocatalysts for the hydrogen evolution reaction in water splitting. However, platinum utilization in these electrocatalysts is extremely low, as the active sites are only located on the surface of the catalyst particles. Downsizing catalyst nanoparticles to single atoms is highly desirable to maximize their efficiency by utilizing nearly all platinum atoms. Here we report on a practical synthesis method to produce isolated single platinum atoms and clusters using the atomic layer deposition technique. The single platinum atom catalysts are investigated for the hydrogen evolution reaction, where they exhibit significantly enhanced catalytic activity (up to 37 times) and high stability in comparison with the state-of-the-art commercial platinum/carbon catalysts. The X-ray absorption fine structure and density functional theory analyses indicate that the partially unoccupied density of states of the platinum atoms' 5d orbitals on the nitrogen-doped graphene are responsible for the excellent performance.

Formation of a sodium bicarbonate cluster in the structure of sodium-substituted hydroxyapatite

NASA Astrophysics Data System (ADS)

Tkachenko, M. V.; Kamzin, A. S.

2015-02-01

Ceramic sodium-substituted carbonated hydroxyapatite has been synthesized using the method of the solid-phase reaction in the temperature range of 640-820°C in water vapor. It has been established that substitutions of Ca2+ ions in the cation and anion subsystems with Na+ ions and the PO{4/3-} and OH- groups with CO{3/2-} ions lead to a considerable acceleration of the shrinkage and synthesis of dense ceramics at substantially lower temperatures than in the case of unsubstituted hydroxyapatite. Sintering in water vapor leads to densification of carbonate groups in channel positions, which induces the appearance of orderings of A2 and B2 types (bands with wave numbers 867 and 865 cm-1 in IR spectra, respectively) as well as the protonation of carbonate groups both in A and B sites and the formation of sodium bicarbonate clusters (856 and 859 cm-1) in addition to carbonate ordering of A1 and B1 types (879 and 872 cm-1).

Platinum single-atom and cluster catalysis of the hydrogen evolution reaction

PubMed Central

Cheng, Niancai; Stambula, Samantha; Wang, Da; Banis, Mohammad Norouzi; Liu, Jian; Riese, Adam; Xiao, Biwei; Li, Ruying; Sham, Tsun-Kong; Liu, Li-Min; Botton, Gianluigi A.; Sun, Xueliang

2016-01-01

Platinum-based catalysts have been considered the most effective electrocatalysts for the hydrogen evolution reaction in water splitting. However, platinum utilization in these electrocatalysts is extremely low, as the active sites are only located on the surface of the catalyst particles. Downsizing catalyst nanoparticles to single atoms is highly desirable to maximize their efficiency by utilizing nearly all platinum atoms. Here we report on a practical synthesis method to produce isolated single platinum atoms and clusters using the atomic layer deposition technique. The single platinum atom catalysts are investigated for the hydrogen evolution reaction, where they exhibit significantly enhanced catalytic activity (up to 37 times) and high stability in comparison with the state-of-the-art commercial platinum/carbon catalysts. The X-ray absorption fine structure and density functional theory analyses indicate that the partially unoccupied density of states of the platinum atoms' 5d orbitals on the nitrogen-doped graphene are responsible for the excellent performance. PMID:27901129

CFA-1: the first chiral metal-organic framework containing Kuratowski-type secondary building units.

PubMed

Schmieder, Phillip; Denysenko, Dmytro; Grzywa, Maciej; Baumgärtner, Benjamin; Senkovska, Irena; Kaskel, Stefan; Sastre, German; van Wüllen, Leo; Volkmer, Dirk

2013-08-14

The novel homochiral metal-organic framework CFA-1 (Coordination Framework Augsburg-1), [Zn5(OAc)4(bibta)3], containing the achiral linker {H2-bibta = 1H,1'H-5,5'-bibenzo[d][1,2,3]triazole}, has been synthesised. The reaction of H2-bibta and Zn(OAc)2·2H2O in N-methylformamide (NMF) (90 °C, 3 d) yields CFA-1 as trigonal prismatic single crystals. CFA-1 serves as a convenient precursor for the synthesis of isostructural frameworks with redox-active metal centres, which is demonstrated by the postsynthetic exchange of Zn(2+) by Co(2+) ions. The framework is robust to solvent removal and has been structurally characterized by synchrotron single-crystal X-ray diffraction and solid state NMR measurements ((13)C MAS- and (1)H MAS-NMR at 10 kHz). Results from MAS-NMR and IR spectroscopy studies are corroborated by cluster and periodic DFT calculations performed on CFA-1 cluster fragments.

Robust Control Design for Systems With Probabilistic Uncertainty

NASA Technical Reports Server (NTRS)

Crespo, Luis G.; Kenny, Sean P.

2005-01-01

This paper presents a reliability- and robustness-based formulation for robust control synthesis for systems with probabilistic uncertainty. In a reliability-based formulation, the probability of violating design requirements prescribed by inequality constraints is minimized. In a robustness-based formulation, a metric which measures the tendency of a random variable/process to cluster close to a target scalar/function is minimized. A multi-objective optimization procedure, which combines stability and performance requirements in time and frequency domains, is used to search for robustly optimal compensators. Some of the fundamental differences between the proposed strategy and conventional robust control methods are: (i) unnecessary conservatism is eliminated since there is not need for convex supports, (ii) the most likely plants are favored during synthesis allowing for probabilistic robust optimality, (iii) the tradeoff between robust stability and robust performance can be explored numerically, (iv) the uncertainty set is closely related to parameters with clear physical meaning, and (v) compensators with improved robust characteristics for a given control structure can be synthesized.

Electronic conductivity studies on oxyhalide glasses containing TMO

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vijayatha, D.; Department of Physics, Gurunanak Institute of Technology, Hyderabad -040; Viswanatha, R.

2016-05-06

Microwave-assisted synthesis is cleaner, more economical and much faster than conventional methods. The development of new routes for the synthesis of solid materials is an integral part of material science and technology. The electronic conductivity studies on xPbCl{sub 2} – 60 PbO – (40-x) V{sub 2}O{sub 5} (1 ≥ x ≤ 10) glass system has been carried out over a wide range of composition and temperature (300 K to 423 K). X-ray diffraction study confirms the amorphous nature of the samples. The Scanning electron microscopic studies reveal the formation of cluster like morphology in PbCl{sub 2} containing glasses. The d.c conductivity exhibitsmore » Arrhenius behaviour and increases with V{sub 2}O{sub 5} concentration. Analysis of the results is interpreted in view Austin-Mott’s small polaron model of electron transport. Activation energies calculated using regression analysis exhibit composition dependent trend and the variation is explained in view of the structure of lead-vanadate glass.« less

A systematic literature review of the effectiveness of occupational health and safety regulatory enforcement.

PubMed

Tompa, Emile; Kalcevich, Christina; Foley, Michael; McLeod, Chris; Hogg-Johnson, Sheilah; Cullen, Kim; MacEachen, Ellen; Mahood, Quenby; Irvin, Emma

2016-11-01

We aimed to determine the strength of evidence on the effectiveness of legislative and regulatory policy levers in creating incentives for organizations to improve occupational health and safety processes and outcomes. A systematic review was undertaken to assess the strength of evidence on the effectiveness of specific policy levers using a "best-evidence" synthesis approach. A structured literature search identified 11,947 citations from 13 peer-reviewed literature databases. Forty-three studies were retained for synthesis. Strong evidence was identified for three out of nine clusters. There is strong evidence that several OHS policy levers are effective in terms of reducing injuries and/or increasing compliance with legislation. This study adds to the evidence on OHS regulatory effectiveness from an earlier review. In addition to new evidence supporting previous study findings, it included new categories of evidence-compliance as an outcome, nature of enforcement, awareness campaigns, and smoke-free workplace legislation. Am. J. Ind. Med. 59:919-933, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Particle dynamics during nanoparticle synthesis by laser ablation in a background gas

NASA Astrophysics Data System (ADS)

Nakata, Yoshiki; Muramoto, Junichi; Okada, Tatsuo; Maeda, Mitsuo

2002-02-01

Particle dynamics during Si nanoparticle synthesis in a laser-ablation plume in different background gases were investigated by laser-spectroscopic imaging techniques. Two-dimensional laser induced fluorescence and ultraviolet Rayleigh scattering techniques were used to visualize the spatial distribution of the Si atoms and nanoparticles grown, respectively. We have developed a visualization technique called re-decomposition laser-induced fluorescence to observe small nanoparticles (hereafter called clusters) which are difficult to observe by the conventional imaging techniques. In this article, the whole process of nanoparticle synthesis in different background gases of He, Ne, Ar, N2 and O2 was investigated by these techniques. In He, Ne, Ar and N2 background gases at 10 Torr, the clustering of the Si atoms started 200, 250, 300 and 800 μs after ablation, respectively. The growth rate of the clusters in He background gas was much larger than that in the other gases. The spatial distributions of the Si nanoparticles were mushroom like in He, N2 and O2, and column like in Ne and Ar. It is thought that the difference in distribution was caused by differences in the flow characteristics of the background gases, which would imply that the viscosity of the background gas is one of the main governing parameters.

Cluster structures influenced by interaction with a surface.

PubMed

Witt, Christopher; Dieterich, Johannes M; Hartke, Bernd

2018-05-30

Clusters on surfaces are vitally important for nanotechnological applications. Clearly, cluster-surface interactions heavily influence the preferred cluster structures, compared to clusters in vacuum. Nevertheless, systematic explorations and an in-depth understanding of these interactions and how they determine the cluster structures are still lacking. Here we present an extension of our well-established non-deterministic global optimization package OGOLEM from isolated clusters to clusters on surfaces. Applying this approach to intentionally simple Lennard-Jones test systems, we produce a first systematic exploration that relates changes in cluster-surface interactions to resulting changes in adsorbed cluster structures.

Soft context clustering for F0 modeling in HMM-based speech synthesis

NASA Astrophysics Data System (ADS)

Khorram, Soheil; Sameti, Hossein; King, Simon

2015-12-01

This paper proposes the use of a new binary decision tree, which we call a soft decision tree, to improve generalization performance compared to the conventional `hard' decision tree method that is used to cluster context-dependent model parameters in statistical parametric speech synthesis. We apply the method to improve the modeling of fundamental frequency, which is an important factor in synthesizing natural-sounding high-quality speech. Conventionally, hard decision tree-clustered hidden Markov models (HMMs) are used, in which each model parameter is assigned to a single leaf node. However, this `divide-and-conquer' approach leads to data sparsity, with the consequence that it suffers from poor generalization, meaning that it is unable to accurately predict parameters for models of unseen contexts: the hard decision tree is a weak function approximator. To alleviate this, we propose the soft decision tree, which is a binary decision tree with soft decisions at the internal nodes. In this soft clustering method, internal nodes select both their children with certain membership degrees; therefore, each node can be viewed as a fuzzy set with a context-dependent membership function. The soft decision tree improves model generalization and provides a superior function approximator because it is able to assign each context to several overlapped leaves. In order to use such a soft decision tree to predict the parameters of the HMM output probability distribution, we derive the smoothest (maximum entropy) distribution which captures all partial first-order moments and a global second-order moment of the training samples. Employing such a soft decision tree architecture with maximum entropy distributions, a novel speech synthesis system is trained using maximum likelihood (ML) parameter re-estimation and synthesis is achieved via maximum output probability parameter generation. In addition, a soft decision tree construction algorithm optimizing a log-likelihood measure is developed. Both subjective and objective evaluations were conducted and indicate a considerable improvement over the conventional method.

Design, Synthesis, and Mechanistic Evaluation of Iron-Based Catalysis for Synthesis Gas Conversion to Fuels and Chemicals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Enrique Iglesia; Akio Ishikawa; Manual Ojeda

2007-09-30

A detailed study of the catalyst composition, preparation and activation protocol of Fe-based catalysts for the Fischer-Tropsch Synthesis (FTS) have been carried out in this project. We have studied the effects of different promoters on the catalytic performance of Fe-based catalysts. Specifically, we have focused on how their sequence of addition dramatically influences the performance of these materials in the Fischer-Tropsch synthesis. The resulting procedures have been optimized to improve further upon the already unprecedented rates and C{sub 5+} selectivities of the Fe-based catalysts that we have developed as part of this project. Selectivity to C{sub 5+} hydrocarbon was closemore » to 90 % (CO{sub 2}-free basis) and CO conversion rate was about 6.7 mol h{sup -1} g-at Fe{sup -1} at 2.14 MPa, 508 K and with substoichiometric synthesis gas; these rates were larger than any reported previously for Fe-based FTS catalysts at these conditions. We also tested the stability of Fe-based catalysts during FTS reaction (10 days); as a result, the high hydrocarbon formation rates were maintained during 10 days, though the gradual deactivation was observed. Our investigation has also focused on the evaluation of Fe-based catalysts with hydrogen-poor synthesis gas streams (H{sub 2}/CO=1). We have observed that the Fe-based catalysts prepared in this project display also a high hydrocarbon synthesis rate with substoichiometric synthesis gas (H{sub 2}/CO=1) stream, which is a less desirable reactant mixture than stoichiometric synthesis gas (H{sub 2}/CO=2). We have improved the catalyst preparation protocols and achieved the highest FTS reaction rates and selectivities so far reported at the low temperatures required for selectivity and stability. Also, we have characterized the catalyst structural change and active phases formed, and their catalytic behavior during the activation process to evaluate their influences on FTS reaction. The efforts of this project led to (i) structural evolution of Fe-Zn oxide promoted with K and Cu, and (ii) evaluation of hydrocarbon and CH{sub 4} formation rates during activation procedures at various temperature and H{sub 2}/CO ratios. On the basis of the obtained results, we suggest that lower reactor temperature can be sufficient to activate catalysts and lead to the high FTS performance. In this project, we have also carried out a detailed kinetic and mechanistic study of the Fischer-Tropsch Synthesis with Fe-based catalysts. We have proposed a reaction mechanism with two CO activation pathways: unassisted and H-assisted. Both routes lead to the formation of the same surface monomers (CH{sub 2}). However, the oxygen removal mechanism is different. In the H-assisted route, oxygen is removed exclusively as water, while oxygen is rejected as carbon dioxide in the unassisted CO dissociation. The validity of the mechanism here proposed has been found to be in agreement with the experimental observation and with theoretical calculations over a Fe(110) surface. Also, we have studied the validity of the mechanism that we propose by analyzing the H{sub 2}/D{sub 2} kinetic isotope effect (r{sub H}/r{sub D}) over a conventional iron-based Fischer-Tropsch catalyst Fe-Zn-K-Cu. We have observed experimentally that the use of D{sub 2} instead of H{sub 2} leads to higher hydrocarbons formation rates (inverse kinetic isotopic effect). On the contrary, primary carbon dioxide formation is not influenced. These experimental observations can be explained by two CO activation pathways. We have also explored the catalytic performance of Co-based catalysts prepared by using inverse micelles techniques. We have studied several methods in order to terminate the silanol groups on SiO{sub 2} support including impregnation, urea homogeneous deposition-precipitation, or zirconium (IV) ethoxide titration. Although hydroxyl groups on the SiO{sub 2} surface are difficult to be stoichiometrically titrated by ZrO{sub 2}, a requirement to prevent the formation of strongly-interacting Co oxide species on SiO{sub 2}, modification of ZrO{sub 2} on SiO{sub 2} surface can improve the Co clusters dispersion leading to a marked increase in the number of accessible Co sites. Inverse micelle method allowed the synthesis of small Co clusters on SiO{sub 2}, but the required surfactant removal steps led to the re-oxidation of Co metal clusters and to the formation of difficult to reduce CoO{sub x} species.« less

Two molecular wheels 12-MC-6 complexes: Synthesis, structure and magnetic property of [Co(μ{sub 2}-SEt){sub 2}]{sub 6} and [Fe(μ{sub 2}-SEt){sub 2}]{sub 6}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Jing; Jian, Fangfang, E-mail: ffj2003@163169.net; Huang, Baoxin

2013-08-15

The syntheses and structures of two ethyl mercaptan molecular wheels complexes, [M(μ{sub 2}-SCH{sub 2}CH{sub 3}){sub 2}]{sub 6} (M=Fe, Co), have been reported. Each metal atom is surrounded by four S atoms of the μ{sub 2}-SCH{sub 2}CH{sub 3} ligands in a distorted square plane fashion. The edge-sharing S{sub 4} square planes connect with each other to form a ring. Six metal atoms are located at the vertices of an almost hexagon, with M···M separations in the range of 2.903(1)∼2.936(2) Å for Fe and 2.889(2)∼2.962(2) Å for Co. The diameter of the ring, defined as the average distance between two opposing metalmore » atoms, is 5.850(1) Å for Fe and 5.780(1) Å for Co, respectively. The magnetic property behaves of cobalt(II) cluster complex is studied. Highlights: • Two new ethyl mercaptan cyclic hexanuclear complexes were reported. • The crystal structures shown center formation of M{sub 6}S{sub 12} molecular wheels. • The Co{sub 6} ring cluster complex represents as weak ferromagnet.« less

Synthesis and structure of cesium complexes of nitrilotris(methylenephosphonic) acid [Cs-μ6-NH(CH2PO3)3H4] and [Cs2-μ10-NH(CH2PO3H)3] · H2O

NASA Astrophysics Data System (ADS)

Somov, N. V.; Chausov, F. F.; Zakirov, R. M.

2017-07-01

3D coordination polymers cesium nitrilotris(methylenephosphonate) and dicesium nitrilotris( methylenephosphonate) are synthesized and their crystal structure is determined. In the crystal of [Cs-μ6-NH(CH2PO3)3H4] (space group P, Z = 2), cesium atoms occupy two crystallographically inequivalent positions with c.n. = 10 and c.n. = 14. The phosphonate ligand plays the bridging function; its denticity is nine. The crystal packing consists of alternating layers of Cs atoms in different environments with layers of ligand molecules between them. A ligand is bound to three Cs atoms of one layer and three Cs atoms of another layer. In the crystal of [Cs2-μ10-NH(CH2PO3H)3] · H2O (space group P, Z = 2), the complex has a dimeric structure: the bridging phosphonate ligand coordinates Cs to form a three-dimensional Cs4O6 cluster. The denticity of the ligand is equal to nine; the coordination numbers of cesium atoms are seven and nine. Two-dimensional corrugated layers of Cs4O6 clusters lie in the (002) plane, and layers of ligand molecules are located between them. Each ligand molecule coordinates eight Cs atoms of one layer and two Cs atoms of the neighboring layer.

Synthesis of Fucosylated Chondroitin Sulfate Glycoclusters: A Robust Route to New Anticoagulant Agents.

PubMed

Zhang, Xiao; Yao, Wang; Xu, Xiaojiang; Sun, Huifang; Zhao, Jinhua; Meng, Xiangbao; Wu, Mingyi; Li, Zhongjun

2018-02-01

Fucosylated chondroitin sulfate (FuCS) is a structurally distinct glycosaminoglycan with excellent anticoagulant activity. Studies show that FuCS and its depolymerized fragments exhibit a different anticoagulant mechanism from that of heparin derivatives, with decreased risks of adverse effects and bleeding. However, further exploitation has been hindered by the scarcity of structurally defined oligosaccharides. Herein, facile method is reported for the synthesis of the repeating trisaccharide unit of FuCS based on the degradation of chondroitin sulfate polymers. A series of simplified FuCS glycomimetics that have highly tunable structures, controllable branches, and defined sulfation motifs were generated by copper-catalyzed alkyne-azide cycloaddition. Remarkable improvement in activated partial thromboplastin time (APTT) assay activities was observed as the branches increased, but no significant influences were observed for prothrombin time (PT) and thrombin time (TT) assay activities. Further FXase inhibition tests suggested that glycoclusters 33 b-40 b selectively inhibited intrinsic anticoagulant activities, but had little effect on the extrinsic and common coagulation pathways. Notably, glycoclusters with the 2,4-di-O-sulfated fucosyl residue displayed the most potency, which was in consistent with that of natural polysaccharides. These FuCS clusters demonstrated potency to mimic linear glycosaminoglycans and offer a new framework for the development of novel anticoagulant agents. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Novel genomic island modifies DNA with 7-deazaguanine derivatives

PubMed Central

Thiaville, Jennifer J.; Kellner, Stefanie M.; Yuan, Yifeng; Hutinet, Geoffrey; Thiaville, Patrick C.; Jumpathong, Watthanachai; Mohapatra, Susovan; Brochier-Armanet, Celine; Letarov, Andrey V.; Hillebrand, Roman; Malik, Chanchal K.; Rizzo, Carmelo J.; Dedon, Peter C.; de Crécy-Lagard, Valérie

2016-01-01

The discovery of ∼20-kb gene clusters containing a family of paralogs of tRNA guanosine transglycosylase genes, called tgtA5, alongside 7-cyano-7-deazaguanine (preQ0) synthesis and DNA metabolism genes, led to the hypothesis that 7-deazaguanine derivatives are inserted in DNA. This was established by detecting 2’-deoxy-preQ0 and 2’-deoxy-7-amido-7-deazaguanosine in enzymatic hydrolysates of DNA extracted from the pathogenic, Gram-negative bacteria Salmonella enterica serovar Montevideo. These modifications were absent in the closely related S. enterica serovar Typhimurium LT2 and from a mutant of S. Montevideo, each lacking the gene cluster. This led us to rename the genes of the S. Montevideo cluster as dpdA-K for 7-deazapurine in DNA. Similar gene clusters were analyzed in ∼150 phylogenetically diverse bacteria, and the modifications were detected in DNA from other organisms containing these clusters, including Kineococcus radiotolerans, Comamonas testosteroni, and Sphingopyxis alaskensis. Comparative genomic analysis shows that, in Enterobacteriaceae, the cluster is a genomic island integrated at the leuX locus, and the phylogenetic analysis of the TgtA5 family is consistent with widespread horizontal gene transfer. Comparison of transformation efficiencies of modified or unmodified plasmids into isogenic S. Montevideo strains containing or lacking the cluster strongly suggests a restriction–modification role for the cluster in Enterobacteriaceae. Another preQ0 derivative, 2’-deoxy-7-formamidino-7-deazaguanosine, was found in the Escherichia coli bacteriophage 9g, as predicted from the presence of homologs of genes involved in the synthesis of the archaeosine tRNA modification. These results illustrate a deep and unexpected evolutionary connection between DNA and tRNA metabolism. PMID:26929322

Ionothermal synthesis of discrete supertetrahedral Tn (n = 4, 5) clusters with tunable components, band gaps, and fluorescence properties.

PubMed

Yang, Dan-Dan; Li, Wei; Xiong, Wei-Wei; Li, Jian-Rong; Huang, Xiao-Ying

2018-05-01

The preparation of crystalline molecularly supertetrahedral Tn clusters with variable sizes and components is of vital importance for the fundamental study of their physicochemical properties. However, setting up an efficient method to stabilize large discrete Tn clusters is a challenge due to their high negative charges and polymerization nature. In this work, we report on the ionothermal synthesis of three discrete T4 cluster compounds, namely [Bmmim]5[(CH3)2NH2]4[NH4][M4In16S31(SH)4]·6H2O (M = Mn (1), Zn (2), Cd (3), Bmmim = 1-buty-2,3-dimethyl-imidazolium), and four discrete T5 cluster compounds, namely [Bmmim]10[NH4]3[Cu5Ga30-xInxS52(SH)4] (x = 6.6 (5), 14.5 (6), 23.8 (7), and 30 (8)). The compound [Bmmim]10[NH4]3[Cu5Ga30S52(SH)4] (4) previously reported by us features a discrete T5 cluster. The steep UV-Vis absorption edges indicate band gaps of 2.20 eV for 1, 2.64 eV for 2, 2.69 eV for 3, 3.04 eV for 4, 2.65 eV for 5, 2.48 eV for 6, 2.32 eV for 7, and 2.30 eV for 8. The compositions of T5 clusters could be varied with the ratios of Ga : In in the starting reagents, providing an opportunity to systematically control the band gaps and fluorescence performances of T5 cluster-based compounds. This research might advance the understanding of the ionothermal preparation and functionality tuning of crystalline chalcogenides.

Fe-S cluster biogenesis in isolated mammalian mitochondria: coordinated use of persulfide sulfur and iron and requirements for GTP, NADH, and ATP.

PubMed

Pandey, Alok; Pain, Jayashree; Ghosh, Arnab K; Dancis, Andrew; Pain, Debkumar

2015-01-02

Iron-sulfur (Fe-S) clusters are essential cofactors, and mitochondria contain several Fe-S proteins, including the [4Fe-4S] protein aconitase and the [2Fe-2S] protein ferredoxin. Fe-S cluster assembly of these proteins occurs within mitochondria. Although considerable data exist for yeast mitochondria, this biosynthetic process has never been directly demonstrated in mammalian mitochondria. Using [(35)S]cysteine as the source of sulfur, here we show that mitochondria isolated from Cath.A-derived cells, a murine neuronal cell line, can synthesize and insert new Fe-(35)S clusters into aconitase and ferredoxins. The process requires GTP, NADH, ATP, and iron, and hydrolysis of both GTP and ATP is necessary. Importantly, we have identified the (35)S-labeled persulfide on the NFS1 cysteine desulfurase as a genuine intermediate en route to Fe-S cluster synthesis. In physiological settings, the persulfide sulfur is released from NFS1 and transferred to a scaffold protein, where it combines with iron to form an Fe-S cluster intermediate. We found that the release of persulfide sulfur from NFS1 requires iron, showing that the use of iron and sulfur for the synthesis of Fe-S cluster intermediates is a highly coordinated process. The release of persulfide sulfur also requires GTP and NADH, probably mediated by a GTPase and a reductase, respectively. ATP, a cofactor for a multifunctional Hsp70 chaperone, is not required at this step. The experimental system described here may help to define the biochemical basis of diseases that are associated with impaired Fe-S cluster biogenesis in mitochondria, such as Friedreich ataxia. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

TESTING STELLAR POPULATION SYNTHESIS MODELS WITH SLOAN DIGITAL SKY SURVEY COLORS OF M31's GLOBULAR CLUSTERS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peacock, Mark B.; Zepf, Stephen E.; Maccarone, Thomas J.

2011-08-10

Accurate stellar population synthesis models are vital in understanding the properties and formation histories of galaxies. In order to calibrate and test the reliability of these models, they are often compared with observations of star clusters. However, relatively little work has compared these models in the ugriz filters, despite the recent widespread use of this filter set. In this paper, we compare the integrated colors of globular clusters in the Sloan Digital Sky Survey (SDSS) with those predicted from commonly used simple stellar population (SSP) models. The colors are based on SDSS observations of M31's clusters and provide the largestmore » population of star clusters with accurate photometry available from the survey. As such, it is a unique sample with which to compare SSP models with SDSS observations. From this work, we identify a significant offset between the SSP models and the clusters' g - r colors, with the models predicting colors which are too red by g - r {approx} 0.1. This finding is consistent with previous observations of luminous red galaxies in the SDSS, which show a similar discrepancy. The identification of this offset in globular clusters suggests that it is very unlikely to be due to a minority population of young stars. The recently updated SSP model of Maraston and Stroembaeck better represents the observed g - r colors. This model is based on the empirical MILES stellar library, rather than theoretical libraries, suggesting an explanation for the g - r discrepancy.« less

Structure based alignment and clustering of proteins (STRALCP)

DOEpatents

Zemla, Adam T.; Zhou, Carol E.; Smith, Jason R.; Lam, Marisa W.

2013-06-18

Disclosed are computational methods of clustering a set of protein structures based on local and pair-wise global similarity values. Pair-wise local and global similarity values are generated based on pair-wise structural alignments for each protein in the set of protein structures. Initially, the protein structures are clustered based on pair-wise local similarity values. The protein structures are then clustered based on pair-wise global similarity values. For each given cluster both a representative structure and spans of conserved residues are identified. The representative protein structure is used to assign newly-solved protein structures to a group. The spans are used to characterize conservation and assign a "structural footprint" to the cluster.

Self-assembly of a tetrahedral 58-nuclear barium vanadium oxide cluster.

PubMed

Kastner, Katharina; Puscher, Bianka; Streb, Carsten

2013-01-07

We report the synthesis and characterization of a molecular barium vanadium oxide cluster featuring high nuclearity and high symmetry. The tetrameric, 2.3 nm cluster H(5)[Ba(10)(NMP)(14)(H(2)O)(8)[V(12)O(33)](4)Br] is based on a bromide-centred, octahedral barium scaffold which is capped by four previously unknown [V(12)O(33)](6-) clusters in a tetrahedral fashion. The compound represents the largest polyoxovanadate-based heterometallic cluster known to date. The cluster is formed in organic solution and it is suggested that the bulky N-methyl-2-pyrrolidone (NMP) solvent ligands allow the isolation of this giant molecule and prevent further condensation to a solid-state metal oxide. The cluster is fully characterized using single-crystal XRD, elemental analysis, ESI mass spectrometry and other spectroscopic techniques.

Lysozyme encapsulated gold nanoclusters: effects of cluster synthesis on natural protein characteristics.

PubMed

Russell, B A; Jachimska, B; Komorek, P; Mulheran, P A; Chen, Y

2017-03-08

The study of gold nanoclusters (AuNCs) has seen much interest in recent history due to their unique fluorescence properties and environmentally friendly synthesis method using proteins as a growth scaffold. The differences in the physicochemical properties of lysozyme encapsulated AuNCs in comparison to natural lysozyme are characterised in order to determine the effects AuNCs have on natural protein behaviour. The hydrodynamic radius (dynamic light scattering), light absorbance (UV-Vis), electrophoretic mobility, relative density, dynamic viscosity, adsorption (quartz crystal microbalance) and circular dichroism (CD) characteristics of the molecules were studied. It was found that lysozyme forms small dimer/trimer aggregates upon the synthesis of AuNCs within the protein. The diameter of Ly-AuNCs was found to be 8.0 nm across a pH range of 2-11 indicating dimer formation, but larger aggregates with diameters >20 nm were formed between pH 3 and 6. The formation of larger aggregates limits the use of Ly-AuNCs as a fluorescent probe in this pH range. A large shift in the protein's isoelectric point was also observed, shifting from 11.0 to 4.0 upon AuNC synthesis. This resulted in major changes to the adsorption characteristics of lysozyme, observed using a QCM. A monolayer of 8 nm was seen for Ly-AuNCs at pH 4, offering further evidence that the proteins form small aggregates, unlike the natural monomer form of lysozyme. The adsorption of Ly-AuNCs was seen to decrease as pH was increased; this is in major contrast to the lysozyme adsorption behaviour. A decrease in the α-helix content was observed from 25% in natural lysozyme to 1% in Ly-AuNCs. This coincided with an increase in the β-sheet content after AuNC synthesis indicating that the natural structure of lysozyme was lost. The formation of protein dimers, the change in the protein surface charge from positive to negative, and secondary structure alteration caused by the AuNC synthesis must be considered before attempting to utilise Ly-AuNCs as in vivo probes.

Using Massive Star Clusters in Merger Remnants To Provide Reference Colors of Intermediate-Age Stellar Populations

NASA Astrophysics Data System (ADS)

Goudfrooij, Paul

2009-07-01

Much current research in cosmology and galaxy formation relies on an accurate interpretation of colors of galaxies in terms of their evolutionary state, i.e., in terms of ages and metallicities. One particularly important topic is the ability to identify early-type galaxies at "intermediate" ages { 500 Myr - 5 Gyr}, i.e., the period between the end of star formation and half the age of the universe. Currently, integrated-light studies must rely on population synthesis models which rest upon spectral libraries of stars in the solar neighborhood. These models have a difficult time correctly incorporating short-lived evolutionary phases such as thermally pulsing AGB stars, which produce up to 80% of the flux in the near-IR in this age range. Furthermore, intermediate-age star clusters in the Local Group do not represent proper templates against which to calibrate population synthesis models in this age range, because their masses are too low to render the effect of stochastic fluctuations due to the number of bright RGB and AGB stars negligible. As a consequence, current population synthesis models have trouble reconciling the evolutionary state of high-redshift galaxies from optical versus near-IR colors. We propose a simple and effective solution to this issue, namely obtaining high-quality EMPIRICAL colors of massive globular clusters in galaxy merger remnants which span this important age range. These colors should serve as relevant references, both to identify intermediate-age objects in the local and distant universe and as calibrators for population synthesis modellers.

Thermodynamics of the Coma Cluster Outskirts

NASA Astrophysics Data System (ADS)

Simionescu, A.; Werner, N.; Urban, O.; Allen, S. W.; Fabian, A. C.; Mantz, A.; Matsushita, K.; Nulsen, P. E. J.; Sanders, J. S.; Sasaki, T.; Sato, T.; Takei, Y.; Walker, S. A.

2013-09-01

We present results from a large mosaic of Suzaku observations of the Coma Cluster, the nearest and X-ray brightest hot (~8 keV), dynamically active, non-cool core system, focusing on the thermodynamic properties of the intracluster medium on large scales. For azimuths not aligned with an infalling subcluster toward the southwest, our measured temperature and X-ray brightness profiles exhibit broadly consistent radial trends, with the temperature decreasing from about 8.5 keV at the cluster center to about 2 keV at a radius of 2 Mpc, which is the edge of our detection limit. The southwest merger significantly boosts the surface brightness, allowing us to detect X-ray emission out to ~2.2 Mpc along this direction. Apart from the southwestern infalling subcluster, the surface brightness profiles show multiple edges around radii of 30-40 arcmin. The azimuthally averaged temperature profile, as well as the deprojected density and pressure profiles, all show a sharp drop consistent with an outwardly-propagating shock front located at 40 arcmin, corresponding to the outermost edge of the giant radio halo observed at 352 MHz with the Westerbork Synthesis Radio Telescope. The shock front may be powering this radio emission. A clear entropy excess inside of r 500 reflects the violent merging events linked with these morphological features. Beyond r 500, the entropy profiles of the Coma Cluster along the relatively relaxed directions are consistent with the power-law behavior expected from simple models of gravitational large-scale structure formation. The pressure is also in agreement at these radii with the expected values measured from Sunyaev-Zel'dovich data from the Planck satellite. However, due to the large uncertainties associated with the Coma Cluster measurements, we cannot yet exclude an entropy flattening in this system consistent with that seen in more relaxed cool core clusters.

Machine-learned cluster identification in high-dimensional data.

PubMed

Ultsch, Alfred; Lötsch, Jörn

2017-02-01

High-dimensional biomedical data are frequently clustered to identify subgroup structures pointing at distinct disease subtypes. It is crucial that the used cluster algorithm works correctly. However, by imposing a predefined shape on the clusters, classical algorithms occasionally suggest a cluster structure in homogenously distributed data or assign data points to incorrect clusters. We analyzed whether this can be avoided by using emergent self-organizing feature maps (ESOM). Data sets with different degrees of complexity were submitted to ESOM analysis with large numbers of neurons, using an interactive R-based bioinformatics tool. On top of the trained ESOM the distance structure in the high dimensional feature space was visualized in the form of a so-called U-matrix. Clustering results were compared with those provided by classical common cluster algorithms including single linkage, Ward and k-means. Ward clustering imposed cluster structures on cluster-less "golf ball", "cuboid" and "S-shaped" data sets that contained no structure at all (random data). Ward clustering also imposed structures on permuted real world data sets. By contrast, the ESOM/U-matrix approach correctly found that these data contain no cluster structure. However, ESOM/U-matrix was correct in identifying clusters in biomedical data truly containing subgroups. It was always correct in cluster structure identification in further canonical artificial data. Using intentionally simple data sets, it is shown that popular clustering algorithms typically used for biomedical data sets may fail to cluster data correctly, suggesting that they are also likely to perform erroneously on high dimensional biomedical data. The present analyses emphasized that generally established classical hierarchical clustering algorithms carry a considerable tendency to produce erroneous results. By contrast, unsupervised machine-learned analysis of cluster structures, applied using the ESOM/U-matrix method, is a viable, unbiased method to identify true clusters in the high-dimensional space of complex data. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Clustering of low-valence particles: structure and kinetics.

PubMed

Markova, Olga; Alberts, Jonathan; Munro, Edwin; Lenne, Pierre-François

2014-08-01

We compute the structure and kinetics of two systems of low-valence particles with three or six freely oriented bonds in two dimensions. The structure of clusters formed by trivalent particles is complex with loops and holes, while hexavalent particles self-organize into regular and compact structures. We identify the elementary structures which compose the clusters of trivalent particles. At initial stages of clustering, the clusters of trivalent particles grow with a power-law time dependence. Yet at longer times fusion and fission of clusters equilibrates and clusters form a heterogeneous phase with polydispersed sizes. These results emphasize the role of valence in the kinetics and stability of finite-size clusters.

Chemical and structural evolution in the Th-SeO3(2-)/SeO4(2-) system: from simple selenites to cluster-based selenate compounds.

PubMed

Xiao, Bin; Langer, Eike; Dellen, Jakob; Schlenz, Hartmut; Bosbach, Dirk; Suleimanov, Evgeny V; Alekseev, Evgeny V

2015-03-16

While extensive success has been gained in the structural chemistry of the U-Se system, the synthesis and characterization of Th-based Se structures are widely unexplored. Here, four new Th-Se compounds, α-Th(SeO3)2, β-Th(SeO3)2, Th(Se2O5)2, and Th3O2(OH)2(SeO4)3, have been obtained from mild hydrothermal or low-temperature (180-220 °C) flux conditions and were subsequently structurally and spectroscopically characterized. The crystal structures of α-Th(SeO3)2 and β-Th(SeO3)2 are based on ThO8 and SeO3 polyhedra, respectively, featuring a three-dimensional (3D) network with selenite anions filling in the Th channels along the a axis. Th(Se2O5)2 is a 3D framework composed of isolated ThO8 polyhedra interconnected by [Se2O5](2-) dimers. Th3O2(OH)2(SeO4)3 is also a 3D framework constructed by octahedral hexathorium clusters [Th6(μ3-O)4(μ3-OH)4](12+), which are interlinked by selenate groups SeO4(2-). The positions of the vibrational modes associated with both Se(IV)O3(2-) and Se(VI)O4(2-) units, respectively, were determined for four compounds, and the Raman spectra of α- and β-Th(SeO3)2 are compared and discussed in detail.

Mitochondria and Iron: Current Questions

PubMed Central

Paul, Bibbin T.; Manz, David H.; Torti, Frank M.; Torti, Suzy V.

2017-01-01

Introduction Mitochondria are cellular organelles that perform numerous bioenergetic, biosynthetic, and regulatory functions and play a central role in iron metabolism. Extracellular iron is taken up by cells and transported to the mitochondria, where it is utilized for synthesis of cofactors essential to the function of enzymes involved in oxidation-reduction reactions, DNA synthesis and repair, and a variety of other cellular processes. Areas Covered This article reviews the trafficking of iron to the mitochondria and normal mitochondrial iron metabolism, including heme synthesis and iron-sulfur cluster biogenesis. Much of our understanding of mitochondrial iron metabolism has been revealed by pathologies that disrupt normal iron metabolism. These conditions affect not only iron metabolism but mitochondrial function and systemic health. Therefore, this article also discusses these pathologies, including conditions of systemic and mitochondrial iron dysregulation as well as cancer. Literature covering these areas was identified via PubMed searches using keywords: Iron, mitochondria, Heme Synthesis, Iron-sulfur Cluster, and Cancer. References cited by publications retrieved using this search strategy were also consulted. Expert Commentary While much has been learned about mitochondrial iron, key questions remain. Developing a better understanding of mitochondrial iron regulation will be paramount in developing therapies for syndromes that affect mitochondrial iron. PMID:27911100

Alternative Lengthening of Telomeres Mediated by Mitotic DNA Synthesis Engages Break-Induced Replication Processes

PubMed Central

Min, Jaewon; Wright, Woodring E.

2017-01-01

ABSTRACT Alternative lengthening of telomeres (ALT) is a telomerase-independent telomere maintenance mechanism that occurs in a subset of cancers. By analyzing telomerase-positive cells and their human TERC knockout-derived ALT human cell lines, we show that ALT cells harbor more fragile telomeres representing telomere replication problems. ALT-associated replication defects trigger mitotic DNA synthesis (MiDAS) at telomeres in a RAD52-dependent, but RAD51-independent, manner. Telomeric MiDAS is a conservative DNA synthesis process, potentially mediated by break-induced replication, similar to type II ALT survivors in Saccharomyces cerevisiae. Replication stresses induced by ectopic oncogenic expression of cyclin E, G-quadruplexes, or R-loop formation facilitate the ALT pathway and lead to telomere clustering, a hallmark of ALT cancers. The TIMELESS/TIPIN complex suppresses telomere clustering and telomeric MiDAS, whereas the SMC5/6 complex promotes them. In summary, ALT cells exhibit more telomere replication defects that result in persistent DNA damage responses at telomeres, leading to the engagement of telomeric MiDAS (spontaneous mitotic telomere synthesis) that is triggered by DNA replication stress, a potential driver of genomic duplications in cancer. PMID:28760773

How Is Fe-S Cluster Formation Regulated?

PubMed

Mettert, Erin L; Kiley, Patricia J

2015-01-01

Iron-sulfur (Fe-S) clusters are fundamental to numerous biological processes in most organisms, but these protein cofactors can be prone to damage by various oxidants (e.g., O2, reactive oxygen species, and reactive nitrogen species) and toxic levels of certain metals (e.g., cobalt and copper). Furthermore, their synthesis can also be directly influenced by the level of available iron in the environment. Consequently, the cellular need for Fe-S cluster biogenesis varies with fluctuating growth conditions. To accommodate changes in Fe-S demand, microorganisms employ diverse regulatory strategies to tailor Fe-S cluster biogenesis according to their surroundings. Here, we review the mechanisms that regulate Fe-S cluster formation in bacteria, primarily focusing on control of the Isc and Suf Fe-S cluster biogenesis systems in the model bacterium Escherichia coli.

Porphyrin network materials: Chemical exploration in the supramolecular solid-state

NASA Astrophysics Data System (ADS)

Kosal, Margaret Elizabeth

Rational design of solid-state materials from molecular building blocks possessing desired physical and chemical characteristics remains among the most challenging tasks for the synthetic chemist. Using p-carboxylic acid tetraphenyl porphyrin molecules, H2T(p-CO 2H)PP, as the organic building block, the synthesis of novel microporous coordination framework materials has been pursued for this work. The self-assembly of the anionic carboxylate with divalent alkaline earth or transition metal cations yielded clathrate, lamellar and three-dimensional network materials. The solvothermal synthesis, characterization, and selective sorption properties of a 3-dimensional metalloporphyrin network solid, [CoT( p-CO2)PPCo1.5], named PIZA-1 for Porphyrinic Illinois Zeolite Analogue 1, have been investigated. The extended structure reveals a single, independent, neutral network with large, bi-directional oval-shaped channels (9 x 7 A) along the crystallographic b - and c-axes and another set of channels (14 x 7 A) along the a-axis. At the intersection of channels, an internal chamber (31 x 31 x 10 A) is realized. Channel-shape is attributable to ruffling of the metalloporphyrin macrocycles when coordinated to the bridging trinuclear Co(II)-carboxylate clusters. The void volume of the stable, thermally robust, solvate-free material is calculated to be 74% of the total unit cell volume. Size-, shape- and functional-group-selective sorption indicates a preference for water and amines. This organic zeolite analogue also demonstrates remarkable ability as a molecular sieve for removal of water from common organic solvents. By powder X-ray diffraction, BET gas adsorption studies and FTIR, this material has been shown to maintain its porous structure as a guest-free solid when heated under vacuum to 250°C. PIZA-1 demonstrates extremely high capacity for repeated selective sorption of water. In comparison to 4A molecular sieves, PIZA-1 exhibits higher capacity and faster response for the selective adsorption of water from common organic solvents. Molecular modeling of corroborates experimental results. The large internal cavities of PIZA-1 are a consequence of the trinuclear Co(II)carboxylate cluster forcing the ruffling of the porphyrin building blocks. The linear trinuclear metal-carboxylate cluster of PIZA-1 is contrasted with the bent trinuclear M(II) carboxylate clusters (M = Co, Mn) of isostructural 3-dimensional frameworks: PIZA-2 and PIZA-3. Containing near-planar metalloporphyrin macrocycles, PIZA-2 and PIZA-3 manifest lower void volumes (56%).

Analysis of local bond-orientational order for liquid gallium at ambient pressure: Two types of cluster structures.

PubMed

Chen, Lin-Yuan; Tang, Ping-Han; Wu, Ten-Ming

2016-07-14

In terms of the local bond-orientational order (LBOO) parameters, a cluster approach to analyze local structures of simple liquids was developed. In this approach, a cluster is defined as a combination of neighboring seeds having at least nb local-orientational bonds and their nearest neighbors, and a cluster ensemble is a collection of clusters with a specified nb and number of seeds ns. This cluster analysis was applied to investigate the microscopic structures of liquid Ga at ambient pressure (AP). The liquid structures studied were generated through ab initio molecular dynamics simulations. By scrutinizing the static structure factors (SSFs) of cluster ensembles with different combinations of nb and ns, we found that liquid Ga at AP contained two types of cluster structures, one characterized by sixfold orientational symmetry and the other showing fourfold orientational symmetry. The SSFs of cluster structures with sixfold orientational symmetry were akin to the SSF of a hard-sphere fluid. On the contrary, the SSFs of cluster structures showing fourfold orientational symmetry behaved similarly as the anomalous SSF of liquid Ga at AP, which is well known for exhibiting a high-q shoulder. The local structures of a highly LBOO cluster whose SSF displayed a high-q shoulder were found to be more similar to the structure of β-Ga than those of other solid phases of Ga. More generally, the cluster structures showing fourfold orientational symmetry have an inclination to resemble more to β-Ga.

Large Hexadecametallic {Mn(III) -Ln(III) } Wheels: Synthesis, Structural, Magnetic, and Theoretical Characterization.

PubMed

Vignesh, Kuduva R; Langley, Stuart K; Moubaraki, Boujemaa; Murray, Keith S; Rajaraman, Gopalan

2015-11-09

The synthesis, gas sorption studies, magnetic properties, and theoretical studies of new molecular wheels of core type {Mn(III) 8 Ln(III) 8 } (Ln=Dy, Ho, Er, Y and Yb), using the ligand mdeaH2 , in the presence of ortho-toluic or benzoic acid are reported. From the seven wheels studied the {Mn8 Dy8 } and {Mn8 Y8 } analogues exhibit SMM behavior as determined from ac susceptibility experiments in a zero static magnetic field. From DFT calculations a S=16 ground state was determined for the {Mn8 Y8 } complex due to weak ferromagnetic Mn(III) -Mn(III) interactions. Ab initio CASSCF+RASSI-SO calculations on the {Mn8 Dy8 } wheel estimated the Mn(III) -Dy(III) exchange interaction as -0.1 cm(-1) . This weak exchange along with unfavorable single-ion anisotropy of Dy(III) /Mn(III) ions, however, led to the observation of SMM behavior with fast magnetic relaxation. The orientation of the g-anisotropy of the Dy(III) ions is found to be perpendicular to the plane of the wheel and this suggests the possibility of toroidal magnetic moments in the cluster. The {Mn8 Ln8 } clusters reported here are the largest heterometallic Mn(III) Ln(III) wheels and the largest {3d-4f} wheels to exhibit SMM behavior reported to date. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Complete Genomic Structure of the Bloom-forming Toxic Cyanobacterium Microcystis aeruginosa NIES-843

PubMed Central

Kaneko, Takakazu; Nakajima, Nobuyoshi; Okamoto, Shinobu; Suzuki, Iwane; Tanabe, Yuuhiko; Tamaoki, Masanori; Nakamura, Yasukazu; Kasai, Fumie; Watanabe, Akiko; Kawashima, Kumiko; Kishida, Yoshie; Ono, Akiko; Shimizu, Yoshimi; Takahashi, Chika; Minami, Chiharu; Fujishiro, Tsunakazu; Kohara, Mitsuyo; Katoh, Midori; Nakazaki, Naomi; Nakayama, Shinobu; Yamada, Manabu; Tabata, Satoshi; Watanabe, Makoto M.

2007-01-01

Abstract The nucleotide sequence of the complete genome of a cyanobacterium, Microcystis aeruginosa NIES-843, was determined. The genome of M. aeruginosa is a single, circular chromosome of 5 842 795 base pairs (bp) in length, with an average GC content of 42.3%. The chromosome comprises 6312 putative protein-encoding genes, two sets of rRNA genes, 42 tRNA genes representing 41 tRNA species, and genes for tmRNA, the B subunit of RNase P, SRP RNA, and 6Sa RNA. Forty-five percent of the putative protein-encoding sequences showed sequence similarity to genes of known function, 32% were similar to hypothetical genes, and the remaining 23% had no apparent similarity to reported genes. A total of 688 kb of the genome, equivalent to 11.8% of the entire genome, were composed of both insertion sequences and miniature inverted-repeat transposable elements. This is indicative of a plasticity of the M. aeruginosa genome, through a mechanism that involves homologous recombination mediated by repetitive DNA elements. In addition to known gene clusters related to the synthesis of microcystin and cyanopeptolin, novel gene clusters that may be involved in the synthesis and modification of toxic small polypeptides were identified. Compared with other cyanobacteria, a relatively small number of genes for two component systems and a large number of genes for restriction-modification systems were notable characteristics of the M. aeruginosa genome. PMID:18192279

Radical S-Adenosyl-l-methionine Chemistry in the Synthesis of Hydrogenase and Nitrogenase Metal Cofactors*

PubMed Central

Byer, Amanda S.; Shepard, Eric M.; Peters, John W.; Broderick, Joan B.

2015-01-01

Nitrogenase, [FeFe]-hydrogenase, and [Fe]-hydrogenase enzymes perform catalysis at metal cofactors with biologically unusual non-protein ligands. The FeMo cofactor of nitrogenase has a MoFe7S9 cluster with a central carbon, whereas the H-cluster of [FeFe]-hydrogenase contains a 2Fe subcluster coordinated by cyanide and CO ligands as well as dithiomethylamine; the [Fe]-hydrogenase cofactor has CO and guanylylpyridinol ligands at a mononuclear iron site. Intriguingly, radical S-adenosyl-l-methionine enzymes are vital for the assembly of all three of these diverse cofactors. This minireview presents and discusses the current state of knowledge of the radical S-adenosylmethionine enzymes required for synthesis of these remarkable metal cofactors. PMID:25477518

Horizontal acquisition of toxic alkaloid synthesis in a clade of plant associated fungi.

PubMed

Marcet-Houben, Marina; Gabaldón, Toni

2016-01-01

Clavicipitaceae is a fungal group that comprises species that closely interact with plants as pathogens, parasites or symbionts. A key factor in these interactions is the ability of these fungi to synthesize toxic alkaloid compounds that contribute to the protection of the plant host against herbivores. Some of these compounds such as ergot alkaloids are toxic to humans and have caused important epidemics throughout history. The gene clusters encoding the proteins responsible for the synthesis of ergot alkaloids and lolines in Clavicipitaceae have been elucidated. Notably, homologs to these gene clusters can be found in distantly related species such as Aspergillus fumigatus and Penicillium expansum, which diverged from Clavicipitaceae more than 400 million years ago. We here use a phylogenetic approach to analyze the evolution of these gene clusters. We found that the gene clusters conferring the ability to synthesize ergot alkaloids and loline emerged first in Eurotiomycetes and were then likely transferred horizontally to Clavicipitaceae. Horizontal gene transfer is known to play a role in shaping the distribution of secondary metabolism clusters across distantly related fungal species. We propose that HGT events have played an important role in the capability of Clavicipitaceae to produce two key secondary metabolites that have enhanced the ability of these species to protect their plant hosts, therefore favoring their interactions. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Design and synthesis of tetranuclear cluster monophosphine-cyclopalladated ferrocenylpyrimidinone complexes from the palladium-catalyzed hydroxylation of chloropyrimidine.

PubMed

Xu, Chen; Zhang, Ya-Peng; Wang, Zhi-Qiang; Fu, Wei-Jun; Hao, Xin-Qi; Xu, Yan; Ji, Bao-Ming

2010-09-28

Hydroxylation of a monomeric triphenylphosphine-cyclopalladated ferrocenylchloropyrimidine [PdCl{[(eta(5)-C(5)H(5))]Fe[(eta(5)-C(5)H(3))-N(2)C(4)H(2)-Cl]}(PPh(3))] with KOH gave the first example of a tetranuclear cluster monophosphine-palladacycle [Pd{[(eta(5)-C(5)H(5))]Fe[(eta(5)-C(5)H(3))-N(2)C(4)H(2)O]}(PPh(3))](4). Additionally, the analogous tricyclohexylphosphine tetranuclear cluster palladacycle has also been successfully synthesized by the same method.

RNA Polymerase II cluster dynamics predict mRNA output in living cells

PubMed Central

Cho, Won-Ki; Jayanth, Namrata; English, Brian P; Inoue, Takuma; Andrews, J Owen; Conway, William; Grimm, Jonathan B; Spille, Jan-Hendrik; Lavis, Luke D; Lionnet, Timothée; Cisse, Ibrahim I

2016-01-01

Protein clustering is a hallmark of genome regulation in mammalian cells. However, the dynamic molecular processes involved make it difficult to correlate clustering with functional consequences in vivo. We developed a live-cell super-resolution approach to uncover the correlation between mRNA synthesis and the dynamics of RNA Polymerase II (Pol II) clusters at a gene locus. For endogenous β-actin genes in mouse embryonic fibroblasts, we observe that short-lived (~8 s) Pol II clusters correlate with basal mRNA output. During serum stimulation, a stereotyped increase in Pol II cluster lifetime correlates with a proportionate increase in the number of mRNAs synthesized. Our findings suggest that transient clustering of Pol II may constitute a pre-transcriptional regulatory event that predictably modulates nascent mRNA output. DOI: http://dx.doi.org/10.7554/eLife.13617.001 PMID:27138339

Biosynthesis and Heterologous Production of Epothilones

NASA Astrophysics Data System (ADS)

Müller, Rolf

Although a variety of chemical syntheses for the epothilones and various derivatives have been described, modifying the backbone of those natural products remains a major challenge. One alternative to chemical alteration is the elucidation and subsequent manipulation of the biosynthetic pathway via genetic engineering in the producing organism. This type of approach is known as “combinatorial biosynthesis” and holds great promise, especially in conjunction with semi-synthesis methods to alter the structure of the natural product. In parallel, production can be optimized in the natural producer if the regulatory mechanisms governing the biosynthesis are understood. Alternatively, the entire gene cluster can be transferred into a heterologous host, more amenable both to genetic alteration and overexpression.

Heterobimetallic Catalysis: Platinum-Gold-Catalyzed Tandem Cyclization/C-X Coupling Reaction of (Hetero)Arylallenes with Nucleophiles.

PubMed

Alonso, José Miguel; Muñoz, María Paz

2018-04-16

Heterobimetallic catalysis offers new opportunities for reactivity and selectivity but still presents challenges, and only a few metal combinations have been explored so far. Reported here is a Pt-Au heterobimetallic catalyst system for the synthesis of a family of multi-heteroaromatic structures through tandem cyclization/C-X coupling reaction. Au-catalyzed 6-endo-cyclization takes place as the first fast step. Pt-Au clusters are proposed to be responsible for the increased reactivity in the second step, that is, the intermolecular nucleophilic addition which occurs through an outer-sphere mechanism by hybrid homogeneous-heterogeneous catalysis. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Cellulose Nanofibrils and Mechanism of their Mineralization in Biomimetic Synthesis of Hydroxyapatite/Native Bacterial Cellulose Nanocomposites: Molecular Dynamics Simulations.

PubMed

Lukasheva, N V; Tolmachev, D A

2016-01-12

Molecular dynamics (MD) simulation of a nanofibril of native bacterial cellulose (BC) in solutions of mineral ions is presented. The supersaturated calcium-phosphate (CP) solution with the ionic composition of hydroxyapatite and CaCl2 solutions with the concentrations below, equal to, and above the solubility limits are simulated. The influence of solvation models (TIP3P and TIP4P-ew water models) on structural characteristics of the simulated nanofibril and on the crystal nucleation process is assessed. The structural characteristics of cellulose nanofibrils (in particular, of the surface layer) are found to be nearly independent of the solvation models used in the simulation and on the presence of ions in the solutions. It is shown that ionic clusters are formed in the solution rather than on the fibril surface. The cluster sizes are slightly different for the two water models. The effect of the ion-ion interaction parameters on the results is discussed. The main conclusion is that the activity of hydroxyl groups on the BC fibril surface is not high enough to cause adsorption of Ca(2+) ions from the solution. Therefore, the nucleation of CP crystals takes place initially in solution, and then the crystallites formed can be adsorbed on BC nanofibril surfaces.

Chemistry of group 9 dimetallaborane analogues of octaborane(12).

PubMed

Barik, Subrat Kumar; Roy, Dipak Kumar; Ghosh, Sundargopal

2015-01-14

We report the synthesis, isolation and structural characterization of several moderately air stable nido-metallaboranes that represent boron rich open cage systems. The reaction of [Cp*CoCl]2, (Cp* = η(5)-C5Me5), with [BH3·thf] in toluene at ice cold temperature, followed by thermolysis in boiling toluene produced [(Cp*Co)B9H13], 1 [(Cp*Co)2B8H12], 2 and [(Cp*Co)2B6H10] 3. Building upon our earlier reactivity studies on rhodaboranes, we continue to explore the reactivity of dicobalt analogues of octaborane(12) cluster 3 with [Fe2(CO)9] and [Ru3(CO)12] at ambient conditions that yielded novel fused clusters [Fe2(CO)6(Cp*Co)2B6H10], 4 and [Ru4(CO)11(Cp*Co)2B3H3], 5 respectively. In an attempt to synthesize a heterometallic metallaborane compound we performed the reaction of [(Cp*Rh)2B6H10], 6 with [Cp*IrH4] that yielded a Ir-Ir double bonded compound [(Cp*Ir)2H3][B(OH)4], 7. All the new compounds have been characterized by IR, (1)H, (11)B, (13)C NMR spectroscopy, and the molecular structures were unambiguously established by X-ray diffraction analysis.

Three 3D metal coordination polymers based on triazol-functionalized rigid ligand: Synthesis, topological structure and properties

NASA Astrophysics Data System (ADS)

Meng, Lingkun; Liu, Kang; Liang, Chen; Guo, Xiaolei; Han, Xu; Ren, Siyuan; Ma, Dingxuan; Li, Guanghua; Shi, Zhan; Feng, Shouhua

2018-02-01

By using a triazol-functionalized tricarboxylate, three novel metal coordination polymers, namely, [Zn2L(OH)]·0.5H2O (1), [Co2L(OH)(H2O)]·5.5H2O (2), [Cu2(HL)] (3) L = ［5-(3-(4-carboxyphenyl)-5-methyl-4H-1,2,4-triazol-4-yl)isophthalate］ were synthesized under hydrothermal reactions. All the compounds were characterized by element analysis, IR spectroscopy, thermogravimetric analysis, power X-ray diffrcation and single-crystal X-ray diffrcation. Structural analysis reveals that compounds 1 and 2 have 3D networks with flu topologies where rigid trizaol-functionalized ligands as 4-connected nodes and Zn4(COO)6 or Co4(COO)6 clusters serves as 8-connected secondary building units. Compound 3 has 3D network with pcu topology where Cu4(COO)4 clusters serve as 6-connected secondary building units. Gas adsorption studies reveal that desolvated compoud 1 exhibits high H2 absorption capacity at 77 K and highly selective separation abilities of CO2 and C3H8 over CH4 at room temperature. The results suggest that 1 has potential application in gas storage and separation. In addition, the magnetic properties of compound 2 were also investigated.

Synthesis of SiV-diamond particulates via the microwave plasma chemical deposition of ultrananocrystalline diamond on soda-lime glass fibers

NASA Astrophysics Data System (ADS)

Kunuku, Srinivasu; Chen, Yen-Chun; Yeh, Chien-Jui; Chang, Wen-Hao; Manoharan, Divinah; Leou, Keh-Chyang; Lin, I.-Nan

2016-10-01

We report the synthesis of silicon-vacancy (SiV) incorporated spherical shaped ultrananocrystalline diamond (SiV-UNCD) particulates (size ∼1 μm) with bright luminescence at 738 nm. For this purpose, different granular structured polycrystalline diamond films and particulates were synthesized by using three different kinds of growth plasma conditions on the three types of substrate materials in the microwave plasma enhanced CVD process. The grain size dependent photoluminescence properties of nitrogen vacancy (NV) and SiV color centers have been investigated for different granular structured diamond samples. The luminescence of NV center and the associated phonon sidebands, which are usually observed in microcrystalline diamond and nanocrystalline diamond films, were effectively suppressed in UNCD films and UNCD particulates. Micron sized SiV-UNCD particulates with bright SiV emission has been attained by transfer of SiV-UNCD clusters on soda-lime glass fibers to inverted pyramidal cavities fabricated on Si substrates by the simple crushing of UNCD/soda-lime glass fibers in deionized water and ultrasonication. Such a plasma enhanced CVD process for synthesizing SiV-UNCD particulates with suppressed NV emission is simple and robust to attain the bright SiV-UNCD particulates to employ in practical applications.

Vibration Sensor Data Denoising Using a Time-Frequency Manifold for Machinery Fault Diagnosis

PubMed Central

He, Qingbo; Wang, Xiangxiang; Zhou, Qiang

2014-01-01

Vibration sensor data from a mechanical system are often associated with important measurement information useful for machinery fault diagnosis. However, in practice the existence of background noise makes it difficult to identify the fault signature from the sensing data. This paper introduces the time-frequency manifold (TFM) concept into sensor data denoising and proposes a novel denoising method for reliable machinery fault diagnosis. The TFM signature reflects the intrinsic time-frequency structure of a non-stationary signal. The proposed method intends to realize data denoising by synthesizing the TFM using time-frequency synthesis and phase space reconstruction (PSR) synthesis. Due to the merits of the TFM in noise suppression and resolution enhancement, the denoised signal would have satisfactory denoising effects, as well as inherent time-frequency structure keeping. Moreover, this paper presents a clustering-based statistical parameter to evaluate the proposed method, and also presents a new diagnostic approach, called frequency probability time series (FPTS) spectral analysis, to show its effectiveness in fault diagnosis. The proposed TFM-based data denoising method has been employed to deal with a set of vibration sensor data from defective bearings, and the results verify that for machinery fault diagnosis the method is superior to two traditional denoising methods. PMID:24379045

SPATIALLY RESOLVED SPECTROSCOPY AND CHEMICAL HISTORY OF STAR-FORMING GALAXIES IN THE HERCULES CLUSTER: THE EFFECTS OF THE ENVIRONMENT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Petropoulou, V.; Vilchez, J.; Iglesias-Paramo, J.

2011-06-10

Spatially resolved spectroscopy has been obtained for a sample of 27 star-forming (SF) galaxies selected from our deep H{alpha} survey of the Hercules cluster. We have applied spectral synthesis models to all emission-line spectra of this sample using the population synthesis code STARLIGHT and have obtained fundamental parameters of stellar components such as mean metallicity and age. The emission-line spectra were corrected for underlying stellar absorption using these spectral synthesis models. Line fluxes were measured and O/H and N/O gas chemical abundances were obtained using the latest empirical calibrations. We have derived the masses and total luminosities of the galaxiesmore » using available Sloan Digital Sky Survey broadband photometry. The effects of cluster environment on the chemical evolution of galaxies and on their mass-metallicity (MZ) and luminosity-metallicity (LZ) relations were studied by combining the derived gas metallicities, the mean stellar metallicities and ages, the masses and luminosities of the galaxies, and their existing H I data. Our Hercules SF galaxies are divided into three main subgroups: (1) chemically evolved spirals with truncated ionized-gas disks and nearly flat oxygen gradients, demonstrating the effect of ram-pressure stripping; (2) chemically evolved dwarfs/irregulars populating the highest local densities, possible products of tidal interactions in preprocessing events; and (3) less metallic dwarf galaxies that appear to be 'newcomers' to the cluster and are experiencing pressure-triggered star formation. Most Hercules SF galaxies follow well-defined MZ and LZ sequences (for both O/H and N/O), though the dwarf/irregular galaxies located at the densest regions appear to be outliers to these global relations, suggesting a physical reason for the dispersion in these fundamental relations. The Hercules cluster appears to be currently assembling via the merger of smaller substructures, providing an ideal laboratory where the local environment has been found to be a key parameter in understanding the chemical history of galaxies.« less

Synthesis and Characterization of Novel Compound Clusters

DTIC Science & Technology

1997-08-26

also be intrinsically stable, they cannot be formed by this plasma chemistry presumably because the metals are less reactive. Plasma chemistry reactions...samples without the presence of hydrogen. Vaporization of these composite samples produces the metal carbide clusters in many cases where plasma chemistry does...antimony or bismuth cannot be produced by the hydrocarbon plasma chemistry method, but they are produced readily from composite sample (metal film on

A novel complex networks clustering algorithm based on the core influence of nodes.

PubMed

Tong, Chao; Niu, Jianwei; Dai, Bin; Xie, Zhongyu

2014-01-01

In complex networks, cluster structure, identified by the heterogeneity of nodes, has become a common and important topological property. Network clustering methods are thus significant for the study of complex networks. Currently, many typical clustering algorithms have some weakness like inaccuracy and slow convergence. In this paper, we propose a clustering algorithm by calculating the core influence of nodes. The clustering process is a simulation of the process of cluster formation in sociology. The algorithm detects the nodes with core influence through their betweenness centrality, and builds the cluster's core structure by discriminant functions. Next, the algorithm gets the final cluster structure after clustering the rest of the nodes in the network by optimizing method. Experiments on different datasets show that the clustering accuracy of this algorithm is superior to the classical clustering algorithm (Fast-Newman algorithm). It clusters faster and plays a positive role in revealing the real cluster structure of complex networks precisely.

Polymorphism in alkali metal uranyl nitrates: Synthesis and crystal structure of gamma-K(UO2)(NO3)3

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jouffret, Laurent J.; Krivovichev, Sergey V.; Burns, Peter C.

2011-07-20

Single crystals of γ-K(UO₂)(NO₃)₃ were prepared from aqueous solutions by evaporation. The crystal structure [orthorhombic, Pbca (61), a = 9.2559(3) Å, b = 12.1753(3) Å, c = 15.8076(5) Å, V = 1781.41(9) ų, Z = 8] was determined by direct methods and refined to R₁ = 0.0267 on the basis of 3657 unique observed reflections. The structure is composed of isolated anionic uranyl trinitrate units, [(UO₂)(NO₃)₃] –, that are linked through eleven-coordinated K + cations. Both known polymorphs of K(UO₂)(NO₃)₃ (α- and γ-phases) can be considered as based upon sheets of isolated complex [(UO₂)(NO₃)₃] – ions separated by K +more » cations. The existence of polymorphism in the two K[UO₂(NO₃)₃] polymorphs is due to the different packing modes of uranyl trinitrate clusters that adopt the same two-dimensional but different three-dimensional arrangements.« less

Hydrothermal synthesis and photoluminescent properties of hierarchical GdPO4·H2O:Ln3+ (Ln3+ = Eu3+, Ce3+, Tb3+) flower-like clusters

NASA Astrophysics Data System (ADS)

Amurisana, Bao.; Zhiqiang, Song.; Haschaolu, O.; Yi, Chen; Tegus, O.

2018-02-01

3D hierarchical GdPO4·H2O:Ln3+ (Ln3+ = Eu3+, Ce3+, Tb3+) flower clusters were successfully prepared on glass slide substrate by a simple, economical hydrothermal process with the assistance of disodium ethylenediaminetetraacetic acid (Na2H2L, where L4- = (CH2COO)2N(CH2)2N(CH2COO)24-). In this process, Na2H2L was used as both a chelating agent and a structure-director. The hierarchical flower clusters have an average diameter of 7-12 μm and are composed of well-aligned microrods. The influence of the molar ratio of Na2H2L/Gd3+ and reaction time on the morphology was systematically studied. A possible crystal growth and formation mechanism of hierarchical flower clusters is proposed based on the evolution of morphology as a function of reaction time. The self-assembled GdPO4·H2O:Ln3+ superstructures exhibit strong orange-red (Eu3+, 5D0 → 7F1), green (Tb3+, 5D4 → 7F5) and near ultraviolet emissions (Ce3+, 5d → 7F5/2) under ultraviolet excitation, respectively. This study may provide a new channel for building hierarchically superstructued oxide micro/nanomaterials with optical and new properties.

A framework for graph-based synthesis, analysis, and visualization of HPC cluster job data.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mayo, Jackson R.; Kegelmeyer, W. Philip, Jr.; Wong, Matthew H.

The monitoring and system analysis of high performance computing (HPC) clusters is of increasing importance to the HPC community. Analysis of HPC job data can be used to characterize system usage and diagnose and examine failure modes and their effects. This analysis is not straightforward, however, due to the complex relationships that exist between jobs. These relationships are based on a number of factors, including shared compute nodes between jobs, proximity of jobs in time, etc. Graph-based techniques represent an approach that is particularly well suited to this problem, and provide an effective technique for discovering important relationships in jobmore » queuing and execution data. The efficacy of these techniques is rooted in the use of a semantic graph as a knowledge representation tool. In a semantic graph job data, represented in a combination of numerical and textual forms, can be flexibly processed into edges, with corresponding weights, expressing relationships between jobs, nodes, users, and other relevant entities. This graph-based representation permits formal manipulation by a number of analysis algorithms. This report presents a methodology and software implementation that leverages semantic graph-based techniques for the system-level monitoring and analysis of HPC clusters based on job queuing and execution data. Ontology development and graph synthesis is discussed with respect to the domain of HPC job data. The framework developed automates the synthesis of graphs from a database of job information. It also provides a front end, enabling visualization of the synthesized graphs. Additionally, an analysis engine is incorporated that provides performance analysis, graph-based clustering, and failure prediction capabilities for HPC systems.« less

Specialized Computer Systems for Environment Visualization

NASA Astrophysics Data System (ADS)

Al-Oraiqat, Anas M.; Bashkov, Evgeniy A.; Zori, Sergii A.

2018-06-01

The need for real time image generation of landscapes arises in various fields as part of tasks solved by virtual and augmented reality systems, as well as geographic information systems. Such systems provide opportunities for collecting, storing, analyzing and graphically visualizing geographic data. Algorithmic and hardware software tools for increasing the realism and efficiency of the environment visualization in 3D visualization systems are proposed. This paper discusses a modified path tracing algorithm with a two-level hierarchy of bounding volumes and finding intersections with Axis-Aligned Bounding Box. The proposed algorithm eliminates the branching and hence makes the algorithm more suitable to be implemented on the multi-threaded CPU and GPU. A modified ROAM algorithm is used to solve the qualitative visualization of reliefs' problems and landscapes. The algorithm is implemented on parallel systems—cluster and Compute Unified Device Architecture-networks. Results show that the implementation on MPI clusters is more efficient than Graphics Processing Unit/Graphics Processing Clusters and allows real-time synthesis. The organization and algorithms of the parallel GPU system for the 3D pseudo stereo image/video synthesis are proposed. With realizing possibility analysis on a parallel GPU-architecture of each stage, 3D pseudo stereo synthesis is performed. An experimental prototype of a specialized hardware-software system 3D pseudo stereo imaging and video was developed on the CPU/GPU. The experimental results show that the proposed adaptation of 3D pseudo stereo imaging to the architecture of GPU-systems is efficient. Also it accelerates the computational procedures of 3D pseudo-stereo synthesis for the anaglyph and anamorphic formats of the 3D stereo frame without performing optimization procedures. The acceleration is on average 11 and 54 times for test GPUs.

Heterometal cubane-type MFe(3)S(4) clusters (M = Mo, V) trigonally symmetrized with hydrotris(pyrazolyl)borate(1-) and tris(pyrazolyl)methanesulfonate(1-) capping ligands.

PubMed

Fomitchev, Dmitry V; McLauchlan, Craig C; Holm, R H

2002-02-25

A series of heterometal cubane-type clusters containing [VFe(3)S(4)](2+) and [MoFe(3)S(4)](3+,2+) cores has been prepared. Ligand substitution of [(DMF)(3)VFe(3)S(4)Cl(3)](-) affords [(Tpms)VFe(3)S(4)L(3)](2)(-) (L = Cl(-) (8), EtS(-) (9), p-MeC(6)H(4)S(-), p-MeC(6)H(4)O(-)). A new procedure for the preparation of molybdenum single cubanes is introduced by the reaction of recently reported [(Tp)MoS(S(4))](-) with FeCl(2)/NaSEt to afford [(Tp)MoFe(3)S(4)Cl(3)](-) (1, 75% yield). This procedure is more efficient that the existing multistep synthesis of single cubanes, which generally affords clusters of mirror symmetry. Also prepared were [(Tp)MoFe(3)S(4)L(3)](-) (L = EtS(-) (2), p-MeC(6)H(4)S(-)). Reduction of 1 with borohydride gives [(Tp)MoFe(3)S(4)Cl(3)](2-) (5, 67%). Owing to the nature of the heterometal ligand, all clusters have idealized trigonal symmetry, reflected in their (1)H NMR spectra. Trigonal structures are demonstrated by crystallography of (Bu(4)N)[1,2], (Bu(4)N)(2)[5] x MeCN, and (Me(4)N)(2)[8,9]. The availability of 1 and 5 allows the first comparison of structures and (57)Fe isomer shifts of [MoFe(3)S(4)](3+,2+) in a constant ligand environment. Small increases in most bond distances indicate that an antibonding electron is added in the reduction of 1. Collective synthetic and electrochemical results from this and other studies demonstrate the existence of the series of oxidation states [VFe(3)S(4)](3+,2+,1+) and [MoFe(3)S(4)](4+,3+,2+) whose relative stabilities within a given series are strongly ligand dependent. Isomer shifts indicate that the reduction of 1 largely affects the Fe(3) subcluster and are consistent with the formal descriptions [MoFe(3+)(2)Fe(2+)S(4)](3+) (1) and [MoFe(3+)Fe(2+)(2)S(4)](2+) (5). Reaction of 1 with excess Li(2)S in acetonitrile affords the double cubane [[(Tp)MoFe(3)S(4)Cl(2)](2)(mu(2)(-)S)](2)(-), whose sulfide-bridged structure is supported by two sequential reductions separated by 290 mV, in analogy with previously reported double cubanes of higher charge. Trigonally symmetric single cubanes eliminate isomers in the formation of double cubanes and other cluster structures, and may be of considerable value in the preparation of new types of M-Fe-S clusters. (Tpms = tris(pyrazolyl)methanesulfonate(1-); Tp = hydrotris(pyrazolyl)borate(1-).)

Atomic scale simulations of vapor cooled carbon clusters

NASA Astrophysics Data System (ADS)

Bogana, M. P.; Colombo, L.

2007-03-01

By means of atomistic simulations we observed the formation of many topologically non-equivalent carbon clusters formed by the condensation of liquid droplets, including: (i) standard fullerenes and onion-like structures, (ii) clusters showing extremely complex surfaces with both positive and negative curvatures and (iii) complex endohedral structures. In this work we offer a thorough structural characterization of the above systems, as well as an attempt to correlate the resulting structure to the actual protocol of growth. The IR and Raman responses of some exotic linear carbon structures have been further investigated, finding good agreement with experimental evidence of carbinoid structures in cluster-assembled films. Towards the aim of fully understanding the process of cluster-to-cluster coalescence dynamics, we further simulated an aerosol of amorphous carbon clusters at controlled temperatures. Various annealing temperatures and times have been observed, identifying different pathways for cluster ripening, ranging from simple coalescence to extensive reconstruction.

Cytoskeletal perturbation induced by herbicides, 2,4-dichlorophenoxyacetic acid (2,4-D) and 2,4,5-trichlorophenoxyacetic acid (2,4,5-T).

PubMed

Zhao, Y; Li, W; Chou, I N

1987-01-01

To understand the mechanisms of toxicity of 2,4-dichlorophenoxyacetic acid (2,4-D) and 2,4,5-trichlorophenoxyacetic acid (2,4,5-T), we have studied their effects on the cytoskeletal organization, particularly microtubules (MT) and microfilaments (MF), DNA synthesis, and the synthesis and composition of cytoskeletal proteins in mouse 3T3 cells. Exposure of cells to 2,4-D or 2,4,5-T resulted in a dose-dependent inhibition of DNA synthesis; 50% inhibition occurred at 2.21 mM and 0.90 mM for 2,4-D and 2,4,5-T, respectively. Furthermore, a strong synergistic inhibition of DNA synthesis was produced by mixtures (each having a total concentration of 1.25 mM) of 2,4-D with 2,4,5-T. Similarly, 2,4,5-T is more potent than 2,4-D in causing cytoskeletal perturbation as revealed by fluorescence microscopy. Treatment of cells with 2,4-D (2.5 mM) or 2,4,5-T (1.25 mM) for 20 h resulted in severe MT aggregation and the appearance of large bundles, which were organized in a rope-like structure in the former and a dramatic octopus-like pattern in the latter. Further, MT bundling is particularly severe in the cell center. Under these conditions, marked changes in MF organization also occurred as evidenced by clustering and crisscrossing of MF in the perinuclear region. A 1:1 mixture (final = 1.25 mM) of 2,4-D and 2,4,5-T, a formulation equivalent to Agent Orange composition, also induced a dramatic perturbation to the organization of MT and MF, resulting in the formation of ring-like structures. MT bundling is still apparent, especially around the outer edge of the "rings." MF are localized predominantly along the cell periphery, where they appear to be aggregated tightly forming patches. Surprisingly, the synthesis and composition of cytoskeletal proteins, which are resistant to detergent extraction but released by CaCl2, are essentially unaffected by 2,4-D or 2,4,5-T. These results suggest that the dramatic perturbation of the cytoskeletal morphology caused by these herbicides probably only results from a structural reorganization and redistribution of MT and MF.

Synthesis and Characterization of Platinum-Ruthenium-Tin Catalysts

NASA Astrophysics Data System (ADS)

Uffalussy, Karen

Magnesia-supported trimetallic Pt-Ru-Sn catalysts prepared through a cluster and a conventional synthetic route have been investigated in terms of their structural properties and their catalytic activity for the hydrogenation of citral and crotonaldehyde. FTIR results indicate that the majority of the stabilizing ligands remain attached to the PtRu5(μ-SnPh 2)(C)(CO)15 cluster used following impregnation onto the MgO support. Under H2 reduction conditions, partial and full ligand removal are both observed at 473 and 573 K, respectively. HRSTEM analysis shows that cluster-derived samples exhibit significantly smaller average metal particle sizes, as well as narrower particle size distributions than the corresponding conventionally prepared ones. EDX measurements show that in the cluster-derived catalysts, the majority of the metal particles present are trimetallic in nature, with metal compositions similar to those of the original cluster. In contrast, the conventionally prepared materials contain mostly bimetallic and monometallic particles with variable compositions. XPS was used to determine how the variation in method of Sn addition to bimetallic Pt-Ru affects the electronic state for the trimetallic Pt-Ru-Sn/MgO system prepared by impregnation using multimetallic clusters, metal-salts, and the combination of both precursor types. Results show that the PtRu5Sn/MgO material has a significantly higher percentage of Sn0 in comparison to Pt-Ru-Sn/MgO and PtRu5-Sn/MgO, and a corresponding shift in both Pt and Ru peaks can be correlated to this relative change in Sn oxidation state. The formation of smaller metal particles and electronic modification of Pt and Ru by Sn in the cluster-derived catalysts and the presence of the three metals in these particles in close proximity result in higher activity and selectivity to the unsaturated alcohols for the hydrogenation of both citral and crotonaldehyde.

O2 reduction to H2O by the multicopper oxidases.

PubMed

Solomon, Edward I; Augustine, Anthony J; Yoon, Jungjoo

2008-08-14

In nature the four electron reduction of O2 to H2O is carried out by Cytochrome c oxidase (CcO) and the multicopper oxidases (MCOs). In the former, Cytochrome c provides electrons for pumping protons to produce a gradient for ATP synthesis, while in the MCOs the function is the oxidation of substrates, either organic or metal ions. In the MCOs the reduction of O2 is carried out at a trinuclear Cu cluster (TNC). Oxygen intermediates have been trapped which exhibit unique spectroscopic features that reflect novel geometric and electronic structures. These intermediates have both intact and cleaved O-O bonds, allowing the reductive cleavage of the O-O bond to be studied in detail both experimentally and computationally. These studies show that the topology of the TNC provides a unique geometric and electronic structure particularly suited to carry out this key reaction in nature.

O2 Reduction to H2O by the Multicopper Oxidases

PubMed Central

Solomon, Edward I.; Augustine, Anthony J.; Yoon, Jungjoo

2010-01-01

In nature the four electron reduction of O2 to H2O is carried out by Cytochrome c Oxidase (CcO) and the multicopper oxidases (MCOs). In the former, Cytochrome c provides electrons for pumping protons to produce a gradient for ATP synthesis, while in the MCOs the function is the oxidation of substrates, either organic or metal ions. In the MCOs the reduction of O2 is carried out at a trinuclear Cu cluster (TNC). Oxygen intermediates have been trapped which exhibit unique spectroscopic features that reflect novel geometric and electronic structures. These intermediates have both intact and cleaved O-O bonds, allowing the reductive cleavage of the O-O bond to be studied in detail both experimentally and computationally. These studies show that the topology of the TNC provides a unique geometric and electronic structure particularly suited to carry out this key reaction in Nature. PMID:18648693

L-Tryptophan on Cu(111): engineering a molecular labyrinth driven by indole groups

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yitamben, E. N.; Clayborne, A.; Darling, Seth B.

2015-05-21

The present article investigates the adsorption and molecular orientation of L-Tryptophan, which is both an essential amino acid important for protein synthesis and of particular interest for the development of chiral molecular electronics and biocompatible processes and devices, on Cu(111) using scanning tunneling microscopy and spectroscopy at 55 K and at room temperature. The arrangement of chemisorbed L-Tryptophan on the copper surface varies with both temperature and surface coverage. At low coverage, small clusters form on the surface irrespective of temperature, while at high coverage an ordered chain structure emerges at room temperature, and a tightly packed structure forms amore » molecular labyrinth at low temperature. The dominating superstructure of the adsorbates arises from intermolecular hydrogen bonding, and pi-bonding interactions between the indole groups of neighboring molecules and the Cu surface.« less

Spatial structure and electronic spectrum of TiSi{/n -} clusters ( n = 6-18)

NASA Astrophysics Data System (ADS)

Borshch, N. A.; Pereslavtseva, N. S.; Kurganskii, S. I.

2014-10-01

Results from optimizing the spatial structure and calculated electronic spectra of anion clusters TiSi{/n -} ( n = 6-18) are presented. Calculations are performed within the density functional theory. Spatial structures of clusters detected experimentally are established by comparing the calculated and experimental data. It is shown that prismatic and fullerene-like structures are the ones most energetically favorable for clusters TiSi{/n -}. It is concluded that these structures are basic when building clusters with close numbers of silicon atoms.

Aureolib — A Proteome Signature Library: Towards an Understanding of Staphylococcus aureus Pathophysiology

PubMed Central

Pané-Farré, Jan; Kusch, Harald; Wolf, Carmen; Reiß, Swantje; Binh, Le Thi Nguyen; Albrecht, Dirk; Riedel, Katharina; Hecker, Michael; Engelmann, Susanne

2013-01-01

Gel-based proteomics is a powerful approach to study the physiology of Staphylococcus aureus under various growth restricting conditions. We analyzed 679 protein spots from a reference 2-dimensional gel of cytosolic proteins of S. aureus COL by mass spectrometry resulting in 521 different proteins. 4,692 time dependent protein synthesis profiles were generated by exposing S. aureus to nine infection-related stress and starvation stimuli (H2O2, diamide, paraquat, NO, fermentation, nitrate respiration, heat shock, puromycin, mupirocin). These expression profiles are stored in an online resource called Aureolib (http://www.aureolib.de). Moreover, information on target genes of 75 regulators and regulatory elements were included in the database. Cross-comparisons of this extensive data collection of protein synthesis profiles using the tools implemented in Aureolib lead to the identification of stress and starvation specific marker proteins. Altogether, 226 protein synthesis profiles showed induction ratios of 2.5-fold or higher under at least one of the tested conditions with 157 protein synthesis profiles specifically induced in response to a single stimulus. The respective proteins might serve as marker proteins for the corresponding stimulus. By contrast, proteins whose synthesis was increased or repressed in response to more than four stimuli are rather exceptional. The only protein that was induced by six stimuli is the universal stress protein SACOL1759. Most strikingly, cluster analyses of synthesis profiles of proteins differentially synthesized under at least one condition revealed only in rare cases a grouping that correlated with known regulon structures. The most prominent examples are the GapR, Rex, and CtsR regulon. In contrast, protein synthesis profiles of proteins belonging to the CodY and σB regulon are widely distributed. In summary, Aureolib is by far the most comprehensive protein expression database for S. aureus and provides an essential tool to decipher more complex adaptation processes in S. aureus during host pathogen interaction. PMID:23967085

Sulfur in Cometary Dust

NASA Technical Reports Server (NTRS)

Fomenkova, M. N.

1997-01-01

The computer-intensive project consisted of the analysis and synthesis of existing data on composition of comet Halley dust particles. The main objective was to obtain a complete inventory of sulfur containing compounds in the comet Halley dust by building upon the existing classification of organic and inorganic compounds and applying a variety of statistical techniques for cluster and cross-correlational analyses. A student hired for this project wrote and tested the software to perform cluster analysis. The following tasks were carried out: (1) selecting the data from existing database for the proposed project; (2) finding access to a standard library of statistical routines for cluster analysis; (3) reformatting the data as necessary for input into the library routines; (4) performing cluster analysis and constructing hierarchical cluster trees using three methods to define the proximity of clusters; (5) presenting the output results in different formats to facilitate the interpretation of the obtained cluster trees; (6) selecting groups of data points common for all three trees as stable clusters. We have also considered the chemistry of sulfur in inorganic compounds.

Large stability and high catalytic activities of sub-nm metal (0) clusters: implications into the nucleation and growth theory.

PubMed

Piñeiro, Yolanda; Buceta, David; Calvo, Javier; Huseyinova, Shahana; Cuerva, Miguel; Pérez, Ángel; Domínguez, Blanca; López-Quintela, M Arturo

2015-07-01

Clusters are stable catalytic species, which are produced during the synthesis of nanoparticles (NPs). Their existence contradicts the thermodynamic principles used to explain the formation of NPs by the classical nucleation and growth theories (NGTs). Using chemical and electrochemical methods we will show that depending on the experimental conditions one can produce either Ag clusters or Ag NPs. Moreover, using already prepared Ag clusters one can observe the disappearance of the usual induction period observed for the kinetics of NP formation, indicating that clusters catalyze the formation of NPs. Taking these data together with some previous examples of cluster-catalyzed anisotropic growth, we derived a qualitative approach to include the catalytic activities of clusters into the formation of NPs, which is incorporated into the NGT. Some qualitative conclusions about the main experimental parameters, which affect the formation of clusters versus NPs, as well as the catalytic mechanism versus the non-catalytic one, are also described. Copyright © 2015 Elsevier Inc. All rights reserved.

Dopamine synapse is a neuroligin-2–mediated contact between dopaminergic presynaptic and GABAergic postsynaptic structures

PubMed Central

Uchigashima, Motokazu; Ohtsuka, Toshihisa; Kobayashi, Kazuto; Watanabe, Masahiko

2016-01-01

Midbrain dopamine neurons project densely to the striatum and form so-called dopamine synapses on medium spiny neurons (MSNs), principal neurons in the striatum. Because dopamine receptors are widely expressed away from dopamine synapses, it remains unclear how dopamine synapses are involved in dopaminergic transmission. Here we demonstrate that dopamine synapses are contacts formed between dopaminergic presynaptic and GABAergic postsynaptic structures. The presynaptic structure expressed tyrosine hydroxylase, vesicular monoamine transporter-2, and plasmalemmal dopamine transporter, which are essential for dopamine synthesis, vesicular filling, and recycling, but was below the detection threshold for molecules involving GABA synthesis and vesicular filling or for GABA itself. In contrast, the postsynaptic structure of dopamine synapses expressed GABAergic molecules, including postsynaptic adhesion molecule neuroligin-2, postsynaptic scaffolding molecule gephyrin, and GABAA receptor α1, without any specific clustering of dopamine receptors. Of these, neuroligin-2 promoted presynaptic differentiation in axons of midbrain dopamine neurons and striatal GABAergic neurons in culture. After neuroligin-2 knockdown in the striatum, a significant decrease of dopamine synapses coupled with a reciprocal increase of GABAergic synapses was observed on MSN dendrites. This finding suggests that neuroligin-2 controls striatal synapse formation by giving competitive advantage to heterologous dopamine synapses over conventional GABAergic synapses. Considering that MSN dendrites are preferential targets of dopamine synapses and express high levels of dopamine receptors, dopamine synapse formation may serve to increase the specificity and potency of dopaminergic modulation of striatal outputs by anchoring dopamine release sites to dopamine-sensing targets. PMID:27035941

The WAGGS project - I. The WiFeS Atlas of Galactic Globular cluster Spectra

NASA Astrophysics Data System (ADS)

Usher, Christopher; Pastorello, Nicola; Bellstedt, Sabine; Alabi, Adebusola; Cerulo, Pierluigi; Chevalier, Leonie; Fraser-McKelvie, Amelia; Penny, Samantha; Foster, Caroline; McDermid, Richard M.; Schiavon, Ricardo P.; Villaume, Alexa

2017-07-01

We present the WiFeS Atlas of Galactic Globular cluster Spectra, a library of integrated spectra of Milky Way and Local Group globular clusters. We used the WiFeS integral field spectrograph on the Australian National University 2.3 m telescope to observe the central regions of 64 Milky Way globular clusters and 22 globular clusters hosted by the Milky Way's low-mass satellite galaxies. The spectra have wider wavelength coverage (3300-9050 Å) and higher spectral resolution (R = 6800) than existing spectral libraries of Milky Way globular clusters. By including Large and Small Magellanic Cloud star clusters, we extend the coverage of parameter space of existing libraries towards young and intermediate ages. While testing stellar population synthesis models and analysis techniques is the main aim of this library, the observations may also further our understanding of the stellar populations of Local Group globular clusters and make possible the direct comparison of extragalactic globular cluster integrated light observations with well-understood globular clusters in the Milky Way. The integrated spectra are publicly available via the project website.

Clusters of Galaxies and the Cosmic Web with Square Kilometre Array

NASA Astrophysics Data System (ADS)

Kale, Ruta; Dwarakanath, K. S.; Vir Lal, Dharam; Bagchi, Joydeep; Paul, Surajit; Malu, Siddharth; Datta, Abhirup; Parekh, Viral; Sharma, Prateek; Pandey-Pommier, Mamta

2016-12-01

The intra-cluster and inter-galactic media that pervade the large scale structure of the Universe are known to be magnetized at sub-micro Gauss to micro Gauss levels and to contain cosmic rays. The acceleration of cosmic rays and their evolution along with that of magnetic fields in these media is still not well understood. Diffuse radio sources of synchrotron origin associated with the Intra-Cluster Medium (ICM) such as radio halos, relics and mini-halos are direct probes of the underlying mechanisms of cosmic ray acceleration. Observations with radio telescopes such as the Giant Metrewave Radio Telescope, the Very Large Array and the Westerbork Synthesis Radio Telescope have led to the discoveries of about 80 such sources and allowed detailed studies in the frequency range 0.15-1.4 GHz of a few. These studies have revealed scaling relations between the thermal and non-thermal properties of clusters and favour the role of shocks in the formation of radio relics and of turbulent re-acceleration in the formation of radio halos and mini-halos. The radio halos are known to occur in merging clusters and mini-halos are detected in about half of the cool-core clusters. Due to the limitations of current radio telescopes, low mass galaxy clusters and galaxy groups remain unexplored as they are expected to contain much weaker radio sources. Distinguishing between the primary and the secondary models of cosmic ray acceleration mechanisms requires spectral measurements over a wide range of radio frequencies and with high sensitivity. Simulations have also predicted weak diffuse radio sources associated with filaments connecting galaxy clusters. The Square Kilometre Array (SKA) is a next generation radio telescope that will operate in the frequency range of 0.05-20 GHz with unprecedented sensitivities and resolutions. The expected detection limits of SKA will reveal a few hundred to thousand new radio halos, relics and mini-halos providing the first large and comprehensive samples for their study. The wide frequency coverage along with sensitivity to extended structures will be able to constrain the cosmic ray acceleration mechanisms. The higher frequency (>5 GHz) observations will be able to use the Sunyaev-Zel'dovich effect to probe the ICM pressure in addition to tracers such as lobes of head-tail radio sources. The SKA also opens prospects to detect the `off-state' or the lowest level of radio emission from the ICM predicted by the hadronic models and the turbulent re-acceleration models.

Cyclic tetraureas with variable flexibility--synthesis, crystal structures and properties.

PubMed

Meshcheryakov, Denys; Arnaud-Neu, Françoise; Böhmer, Volker; Bolte, Michael; Cavaleri, Julien; Hubscher-Bruder, Véronique; Thondorf, Iris; Werner, Sabine

2008-09-21

Macrocyclic molecules containing several amide or urea functions may serve as anion receptors. We describe the synthesis of 32-membered macrocycles, in which four rigid xanthene units (X) and/or diphenyl ether units (D) as flexible analogues are linked via urea groups. All six possible combinations of these units (XXXX, XXXD, XXDD, XDXD, XDDD and DDDD) were synthesized and two examples were characterised by single-crystal X-ray analyses (DDDD and two structures for XXXD). Both macrocycles showed distinct differences in their overall conformation and consequently in their hydrogen-bonding pattern. Hydrogen-bonded solvent molecules are found for both compounds and intramolecular hydrogen bonds for the two structures of XXXD, but surprisingly no direct intermolecular hydrogen bonds between the macrocyclic tetraurea molecules. The interaction with various anions was studied by (1)H NMR spectroscopy. Stability constants for all tetramers were determined by UV spectroscopy for complexes with chloride, bromide, acetate and dihydrogenphosphate in acetonitrile-THF (3:1). The strongest binding was found for XXXD and acetate (log beta = 7.4 +/- 0.2), the weakest for XXXX and acetate (log beta = 5.1 +/- 0.5). MD simulations in chloroform and acetonitrile boxes show that all molecules except DDDD adopt very similar conformations characterized by an up-down-up-down arrangement of the spacer groups. Clustered solvation shells of acetonitrile molecules around XXXX and DDDD suggest their preorganization for spherical/planar and tetrahedral/bidentate anions, respectively, which in turn was corroborated by simulation of the corresponding complexes with chloride and dihydrogenphosphate.

Synthesis and characterization of Fe-Ti-Sb intermetallic compounds: Discovery of a new Slater-Pauling phase

NASA Astrophysics Data System (ADS)

Naghibolashrafi, N.; Keshavarz, S.; Hegde, Vinay I.; Gupta, A.; Butler, W. H.; Romero, J.; Munira, K.; LeClair, P.; Mazumdar, D.; Ma, J.; Ghosh, A. W.; Wolverton, C.

2016-03-01

Compounds of Fe, Ti, and Sb were prepared using arc melting and vacuum annealing. Fe2TiSb , expected to be a full Heusler compound crystallizing in the L 21 structure, was shown by XRD and SEM analyses to be composed of weakly magnetic grains of nominal composition Fe1.5TiSb with iron-rich precipitates in the grain boundaries. FeTiSb, a composition consistent with the formation of a half-Heusler compound, also decomposed into Fe1.5TiSb grains with Ti-Sb rich precipitates and was weakly magnetic. The dominant Fe1.5TiSb phase appears to crystallize in a defective L 21 -like structure with iron vacancies. Based on this finding, a first-principles DFT-based binary cluster expansion of Fe and vacancies on the Fe sublattice of the L 21 structure was performed. Using the cluster expansion, we computationally scanned >103 configurations and predict a novel, stable, nonmagnetic semiconductor phase to be the zero-temperature ground state. This new structure is an ordered arrangement of Fe and vacancies, belonging to the space group R 3 m , with composition Fe1.5TiSb , i.e., between the full- and half-Heusler compositions. This phase can be visualized as alternate layers of L 21 phase Fe2TiSb and C 1b phase FeTiSb, with layering along the [111] direction of the original cubic phases. Our experimental results on annealed samples support this predicted ground-state composition, but further work is required to confirm that the R 3 m structure is the ground state.

Zr 2Ir 6B with an eightfold superstructure of the cubic perovskite-like boride ZrIr 3B 0.5: Synthesis, crystal structure and bonding analysis

NASA Astrophysics Data System (ADS)

Hermus, Martin; Fokwa, Boniface P. T.

2010-04-01

Single phase powder samples and single crystals of Zr 2Ir 6B were successfully synthesized by arc-melting the elements in a water-cooled copper crucible under an argon atmosphere. Superstructure reflections were observed both on powder and on single crystal diffraction data, leading to an eightfold superstructure of ZrIr 3B x phase. The new phase, which has a metallic luster, crystallizes in space group Fm3¯m (no. 225) with the lattice parameters a=7.9903(4) Å, V=510.14(4) Å 3. Its crystal structure was refined on the basis of powder as well as single crystal data. The single crystal refinement converged to R1=0.0239 and w R2=0.0624 for all 88 unique reflections and 6 parameters. Zr 2Ir 6B is isotypic to Ti 2Rh 6B and its structure can be described as a defect double perovskite, A2BB' O6, where the A site is occupied by zirconium, the B site by boron, the O site by iridium but the B' site is vacant, leading to the formation of empty and boron-filled octahedral Ir 6 clusters. According to the result of tight-binding electronic structure calculations, Ir-B and Ir-Zr interactions are mainly responsible for the structural stability of the phase. According to COHP bonding analysis, the strongest bonding occurs for the Ir-B contacts, and the Ir-Ir bonding within the empty clusters is two times stronger than that in the BIr 6 octahedra.

Substrate morphology induced self-organization into carbon nanotube arrays, ropes, and agglomerates.

PubMed

Huang, Jia-Qi; Zhang, Qiang; Xu, Guang-Hui; Qian, Wei-Zhong; Wei, Fei

2008-10-29

In this paper, hydrophobic carbon nanotube (CNT) arrays, ropes, and agglomerates were synthesized through self-organization on quartz substrates with different micro-structures under the same growth condition. On a flat substrate, a uniform woven structure was formed which resulted in a synchronous growth into an array. When the substrate with 10 µm round concaves distributed on the surface was adopted, the woven structure was sporadic and a CNT cluster was grown in the concave. With further growth, CNT ropes were self-organized. Subsequently, when the substrate consisting of irregular ∼100 nm gaps was used, the initial woven structure was high density, thus resulting in the formation of CNT agglomerates. Study results showed that CNT arrays grown on the flat substrate were of the highest purity and had a contact angle of 153.8 ± 0.9°. Thus, the self-organization behavior among CNTs was in situ modulated by different substrate morphology without further treatments. This provides us with an additional understanding of the self-organization of CNTs during growth, as well as strategies for the controllable synthesis of CNTs with fixed properties.

Synthesis and Electrochemistry of Cyclopentadienylcarbonyliron Tetramer: An Advanced Experiment.

ERIC Educational Resources Information Center

White, A. J.; Cunningham, Alice J.

1980-01-01

Describes an advanced level experiment in which a transition metal cluster compound, cyclopentadienylcarbonyliron tetramer, is synthesized and characterized spectroscopically. Its redox properties are then explored through cyclic voltammetry. (CS)

Catalysis by clusters with precise numbers of atoms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tyo, Eric C.; Vajda, Stefan

2015-07-03

Clusters that contain only a small number of atoms can exhibit unique and often unexpected properties. The clusters are of particular interest in catalysis because they can act as individual active sites, and minor changes in size and composition – such as the addition or removal of a single atom – can have a substantial influence on the activity and selectivity of a reaction. Here we review recent progress in the synthesis, characterization and catalysis of well-defined sub-nanometre clusters. We examine work on size-selected supported clusters in ultra-high vacuum environments and under realistic reaction conditions, and explore the use ofmore » computational methods to provide a mechanistic understanding of their catalytic properties. We also highlight the potential of size-selected clusters to provide insights into important catalytic processes and their use in the development of novel catalytic systems.« less

Composition formulas of binary eutectics

PubMed Central

Ma, Y. P.; Dong, D. D.; Dong, C.; Luo, L. J.; Wang, Q.; Qiang, J. B.; Wang, Y. M.

2015-01-01

The present paper addresses the long-standing composition puzzle of eutectic points by introducing a new structural tool for the description of short-range-order structural unit, the cluster-plus-glue-atom model. In this model, any structure is dissociated into a 1st-neighbor cluster and a few glue atoms between the clusters, expressed by a cluster formula [cluster]gluex. This model is applied here to establish the structural model for eutectic liquids, assuming that a eutectic liquid consist of two subunits issued from the relevant eutectic phases, each being expressed by the cluster formula for ideal metallic glasses, i.e., [cluster](glue atom)1 or 3. A structural unit is then composed of two clusters from the relevant eutectic phases plus 2, 4, or 6 glue atoms. Such a dual cluster formulism is well validated in all boron-containing (except those located by the extreme phase diagram ends) and in some commonly-encountered binary eutectics, within accuracies below 1 at.%. The dual cluster formulas vary extensively and are rarely identical even for eutectics of close compositions. They are generally formed with two distinctly different cluster types, with special cluster matching rules such as cuboctahedron plus capped trigonal prism and rhombidodecahedron plus octahedral antiprism. PMID:26658618

Seipin is involved in the regulation of phosphatidic acid metabolism at a subdomain of the nuclear envelope in yeast.

PubMed

Wolinski, Heimo; Hofbauer, Harald F; Hellauer, Klara; Cristobal-Sarramian, Alvaro; Kolb, Dagmar; Radulovic, Maja; Knittelfelder, Oskar L; Rechberger, Gerald N; Kohlwein, Sepp D

2015-11-01

Yeast Fld1 and Ldb16 resemble mammalian seipin, implicated in neutral lipid storage. Both proteins form a complex at the endoplasmic reticulum-lipid droplet (LD) interface. Malfunction of this complex either leads to LD clustering or to the generation of supersized LD (SLD) in close vicinity to the nuclear envelope, in response to altered phospholipid (PL) composition. We show that similar to mutants lacking Fld1, deletion of LDB16 leads to abnormal proliferation of a subdomain of the nuclear envelope, which is tightly associated with clustered LD. The human lipin-1 ortholog, the PAH1 encoded phosphatidic acid (PA) phosphatase, and its activator Nem1 are highly enriched at this site. The specific accumulation of PA-binding marker proteins indicates a local enrichment of PA in the fld1 and ldb16 mutants. Furthermore, we demonstrate that clustered LD in fld1 or ldb16 mutants are transformed to SLD if phosphatidylcholine synthesis is compromised by additional deletion of the phosphatidylethanolamine methyltransferase, Cho2. Notably, treatment of wild-type cells with oleate induced a similar LD clustering and nuclear membrane proliferation phenotype as observed in fld1 and ldb16 mutants. These data suggest that the Fld1-Ldb16 complex affects PA homeostasis at an LD-forming subdomain of the nuclear envelope. Lack of Fld1-Ldb16 leads to locally elevated PA levels that induce an abnormal proliferation of nER membrane structures and the clustering of associated LD. We suggest that the formation of SLD is a consequence of locally altered PL metabolism at this site. Copyright © 2015. Published by Elsevier B.V.

Synthesis and characterization of new fluorescent styrene-containing carborane derivatives: the singular quenching role of a phenyl substituent.

PubMed

Ferrer-Ugalde, Albert; Juárez-Pérez, Emilio José; Teixidor, Francesc; Viñas, Clara; Sillanpää, Reijo; Pérez-Inestrosa, Ezequiel; Núñez, Rosario

2012-01-09

A set of neutral and anionic carborane derivatives in which the styrenyl fragment is introduced as a fluorophore group has been successfully synthesized and characterized. The reaction of the monolithium salts of 1-Ph-1,2-C(2)B(10)H(11), 1-Me-1,2-C(2)B(10)H(11) and 1,2-C(2)B(10)H(12) with one equivalent of 4-vinylbenzyl chloride leads to the formation of compounds 1-3, whereas the reaction of the dilithium salt of 1,2-C(2)B(10)H(12) with two equivalents of 4-vinylbenzyl chloride gives disubstituted compound 4. The closo clusters were degraded using the classical method, KOH in EtOH, to afford the corresponding nido species, which were isolated as tetramethylammonium salts. The crystal structure of the four closo compounds 1-4 were analyzed by X-ray diffraction. All compounds, except 1, display emission properties, with quantum yields dependent on the nature of the cluster (closo or nido) and the substituent on the second C(cluster) atom. In general, closo compounds 2-4 exhibit high fluorescence emission, whereas the presence of a nido cluster produces a decrease of the emission intensity. The presence of a phenyl group bonded to the C(cluster) results in an excellent electron-acceptor unit that produces a quenching of the fluorescence. DFT calculations have confirmed the charge-separation state in 1 to explain the quenching of the fluorescence and the key role of the carboranyl fragment in this luminescent process. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Designed topology and site-selective metal composition in tetranuclear [MM'...M'M] linear complexes.

PubMed

Barrios, Leoní A; Aguilà, David; Roubeau, Olivier; Gamez, Patrick; Ribas-Ariño, Jordi; Teat, Simon J; Aromí, Guillem

2009-10-26

The ligand 1,3-bis[3-oxo-3-(2-hydroxyphenyl)propionyl]benzene (H(4)L), designed to align transition metals into tetranuclear linear molecules, reacts with M(II) salts (M=Ni, Co, Cu) to yield complexes with the expected [MMMM] topology. The novel complexes [Co(4)L(2)(py)(6)] (2; py=pyridine) and [Na(py)(2)][Cu(4)L(2)(py)(4)](ClO(4)) (3) have been crystallographically characterised. The metal sites in complexes 2 and 3, together with previously characterised [Ni(4)L(2)(py)(6)] (1), favour different coordination geometries. These have been exploited for the deliberate synthesis of the heterometallic complex [Cu(2)Ni(2)L(2)(py)(6)] (4). Complexes 1, 2, 3 and 4 exhibit antiferromagnetic interactions between pairs of metals within each cluster, leading to S=0 spin ground states, except for the latter cluster, which features two quasi-independent S=1/2 moieties within the molecule. Complex 4 gathers the structural and physical conditions, thus allowing it to be considered as prototype of a two-qbit quantum gate.

Protactinium and the intersection of actinide and transition metal chemistry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wilson, Richard E.; De Sio, Stephanie; Vallet, Valérie

The role of the 5f and 6d orbitals in the chemistry of the actinide elements has been of considerable interest since their discovery and synthesis. Relativistic effects cause the energetics of the 5f and 6d orbitals to change as the actinide series is traversed left to right imparting a rich and complex chemistry. The 5f and 6d atomic states cross in energy at protactinium (Pa), making it a potential intersection between transition metal and actinide chemistries. Herein, we report the synthesis of a Pa-peroxo cluster, A(6)(Pa4O(O-2)(6)F-12) [A = Rb, Cs, (CH3)(4)N], formed in pursuit of an actinide polyoxometalate. Quantum chemicalmore » calculations at the density functional theory level demonstrate equal 5f and 6d orbital participation in the chemistry of Pa and increasing 5f orbital participation for the heavier actinides. Periodic changes in orbital character to the bonding in the early actinides highlights the influence of the 5f orbitals in their reactivity and chemical structure.« less

Surface Structure Characterization of Aspergillus fumigatus Conidia Mutated in the Melanin Synthesis Pathway and Their Human Cellular Immune Response

PubMed Central

Bayry, Jagadeesh; Beaussart, Audrey; Dufrêne, Yves F.; Sharma, Meenu; Bansal, Kushagra; Kniemeyer, Olaf; Aimanianda, Vishukumar; Brakhage, Axel A.; Kaveri, Srini V.; Kwon-Chung, Kyung J.

2014-01-01

In Aspergillus fumigatus, the conidial surface contains dihydroxynaphthalene (DHN)-melanin. Six-clustered gene products have been identified that mediate sequential catalysis of DHN-melanin biosynthesis. Melanin thus produced is known to be a virulence factor, protecting the fungus from the host defense mechanisms. In the present study, individual deletion of the genes involved in the initial three steps of melanin biosynthesis resulted in an altered conidial surface with masked surface rodlet layer, leaky cell wall allowing the deposition of proteins on the cell surface and exposing the otherwise-masked cell wall polysaccharides at the surface. Melanin as such was immunologically inert; however, deletion mutant conidia with modified surfaces could activate human dendritic cells and the subsequent cytokine production in contrast to the wild-type conidia. Cell surface defects were rectified in the conidia mutated in downstream melanin biosynthetic pathway, and maximum immune inertness was observed upon synthesis of vermelone onward. These observations suggest that although melanin as such is an immunologically inert material, it confers virulence by facilitating proper formation of the A. fumigatus conidial surface. PMID:24818666

Ab initio investigation on hydrogen adsorption capability in Zn and Cu-based metal organic frameworks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tanuwijaya, V. V., E-mail: viny.veronika@gmail.com; Hidayat, N. N., E-mail: avantgarde.vee@gmail.com; Agusta, M. K., E-mail: kemal@fti.itb.ac.id

2015-09-30

One of the biggest challenge in material technology for hydrogen storage application is to increase hydrogen uptake in room temperature and pressure. As a class of highly porous material, Metal-Organic Frameworks (MOF) holds great potential with its tunable structure. However, little is known about the effect of metal cluster to its hydrogen storage capability. Investigation on this matter has been carried out carefully on small cluster of Zn and Cu-based MOF using first principles method. The calculation of two distinct building units of MOFs, namely octahedral and paddle-wheel models, have been done with B3LYP density functional method using 6-31G(d,p) andmore » LANL2DZ basis sets. From geometry optimization of Zn-based MOF linked by benzene-dicarboxylate (MOF-5), it is found that hydrogen tends to keep distance from metal cluster group and stays above benzene ring. In the other hand, hydrogen molecule prefers to stay atop of the exposed Cu atom in Cu-based MOF system linked by the same linker group (Cu-bdc). Calculated hydrogen binding enthalpies for Zn and Cu octahedral cages at ZnO{sub 3} sites are 1.64kJ/mol and 2.73kJ/mol respectively, while hydrogen binding enthalpies for Zn and Cu paddle-wheel cages calculated on top of metal atoms are found to be at 6.05kJ/mol and 6.10kJ/mol respectively. Major difference between Zn-MOF-5 and Cu-bdc hydrogen uptake performance might be caused by unsaturated metal sites present in Cu-bdc system and the influence of their geometric structures, although a small difference on binding energy in the type of transition metal used is also observed. The comparison between Zn and Cu-based MOF may contribute to a comprehensive understanding of metal clusters and the importance of selecting best transition metal for design and synthesis of metal-organic frameworks.« less

Valence and charge-transfer optical properties for some SinCm (m, n ≤ 12) clusters: Comparing TD-DFT, complete-basis-limit EOMCC, and benchmarks from spectroscopy.

PubMed

Lutz, Jesse J; Duan, Xiaofeng F; Ranasinghe, Duminda S; Jin, Yifan; Margraf, Johannes T; Perera, Ajith; Burggraf, Larry W; Bartlett, Rodney J

2018-05-07

Accurate optical characterization of the closo-Si 12 C 12 molecule is important to guide experimental efforts toward the synthesis of nano-wires, cyclic nano-arrays, and related array structures, which are anticipated to be robust and efficient exciton materials for opto-electronic devices. Working toward calibrated methods for the description of closo-Si 12 C 12 oligomers, various electronic structure approaches are evaluated for their ability to reproduce measured optical transitions of the SiC 2 , Si 2 C n (n = 1-3), and Si 3 C n (n = 1, 2) clusters reported earlier by Steglich and Maier [Astrophys. J. 801, 119 (2015)]. Complete-basis-limit equation-of-motion coupled-cluster (EOMCC) results are presented and a comparison is made between perturbative and renormalized non-iterative triples corrections. The effect of adding a renormalized correction for quadruples is also tested. Benchmark test sets derived from both measurement and high-level EOMCC calculations are then used to evaluate the performance of a variety of density functionals within the time-dependent density functional theory (TD-DFT) framework. The best-performing functionals are subsequently applied to predict valence TD-DFT excitation energies for the lowest-energy isomers of Si n C and Si n-1 C 7-n (n = 4-6). TD-DFT approaches are then applied to the Si n C n (n = 4-12) clusters and unique spectroscopic signatures of closo-Si 12 C 12 are discussed. Finally, various long-range corrected density functionals, including those from the CAM-QTP family, are applied to a charge-transfer excitation in a cyclic (Si 4 C 4 ) 4 oligomer. Approaches for gauging the extent of charge-transfer character are also tested and EOMCC results are used to benchmark functionals and make recommendations.

Effects of manganese doping on the structure evolution of small-sized boron clusters

NASA Astrophysics Data System (ADS)

Zhao, Lingquan; Qu, Xin; Wang, Yanchao; Lv, Jian; Zhang, Lijun; Hu, Ziyu; Gu, Guangrui; Ma, Yanming

2017-07-01

Atomic doping of clusters is known as an effective approach to stabilize or modify the structures and properties of resulting doped clusters. We herein report the effect of manganese (Mn) doping on the structure evolution of small-sized boron (B) clusters. The global minimum structures of both neutral and charged Mn doped B cluster \\text{MnB}nQ (n  =  10-20 and Q  =  0, ±1) have been proposed through extensive first-principles swarm-intelligence based structure searches. It is found that Mn doping has significantly modified the grow behaviors of B clusters, leading to two novel structural transitions from planar to tubular and then to cage-like B structures in both neutral and charged species. Half-sandwich-type structures are most favorable for small \\text{MnB}n-/0/+ (n  ⩽  13) clusters and gradually transform to Mn-centered double-ring tubular structures at \\text{MnB}16-/0/+ clusters with superior thermodynamic stabilities compared with their neighbors. Most strikingly, endohedral cages become the ground-state structures for larger \\text{MnB}n-/0/+ (n  ⩾  19) clusters, among which \\text{MnB}20+ adopts a highly symmetric structure with superior thermodynamic stability and a large HOMO-LUMO gap of 4.53 eV. The unique stability of the endohedral \\text{MnB}\\text{20}+ cage is attributed to the geometric fit and formation of 18-electron closed-shell configuration. The results significantly advance our understanding about the structure and bonding of B-based clusters and strongly suggest transition-metal doping as a viable route to synthesize intriguing B-based nanomaterials.

Clustering and visualizing similarity networks of membrane proteins.

PubMed

Hu, Geng-Ming; Mai, Te-Lun; Chen, Chi-Ming

2015-08-01

We proposed a fast and unsupervised clustering method, minimum span clustering (MSC), for analyzing the sequence-structure-function relationship of biological networks, and demonstrated its validity in clustering the sequence/structure similarity networks (SSN) of 682 membrane protein (MP) chains. The MSC clustering of MPs based on their sequence information was found to be consistent with their tertiary structures and functions. For the largest seven clusters predicted by MSC, the consistency in chain function within the same cluster is found to be 100%. From analyzing the edge distribution of SSN for MPs, we found a characteristic threshold distance for the boundary between clusters, over which SSN of MPs could be properly clustered by an unsupervised sparsification of the network distance matrix. The clustering results of MPs from both MSC and the unsupervised sparsification methods are consistent with each other, and have high intracluster similarity and low intercluster similarity in sequence, structure, and function. Our study showed a strong sequence-structure-function relationship of MPs. We discussed evidence of convergent evolution of MPs and suggested applications in finding structural similarities and predicting biological functions of MP chains based on their sequence information. © 2015 Wiley Periodicals, Inc.

α clustering with a hollow structure: Geometrical structure of α clusters from platonic solids to fullerene shape

NASA Astrophysics Data System (ADS)

Tohsaki, Akihiro; Itagaki, Naoyuki

2018-01-01

We study α -cluster structure based on the geometric configurations with a microscopic framework, which takes full account of the Pauli principle, and which also employs an effective internucleon force including finite-range three-body terms suitable for microscopic α -cluster models. Here, special attention is focused upon the α clustering with a hollow structure; all the α clusters are put on the surface of a sphere. All the platonic solids (five regular polyhedra) and the fullerene-shaped polyhedron coming from icosahedral structure are considered. Furthermore, two configurations with dual polyhedra, hexahedron-octahedron and dodecahedron-icosahedron, are also scrutinized. When approaching each other from large distances with these symmetries, α clusters create certain local energy pockets. As a consequence, we insist on the possible existence of α clustering with a geometric shape and hollow structure, which is favored from Coulomb energy point of view. Especially, two configurations, that is, dual polyhedra of dodecahedron-icosahedron and fullerene, have a prominent hollow structure compared with the other six configurations.

Decay analysis of compound nuclei formed in reactions with exotic neutron-rich 9Li projectile and the synthesis of 217At* within the dynamical cluster-decay model

NASA Astrophysics Data System (ADS)

Kaur, Arshdeep; Kaushal, Pooja; Hemdeep; Gupta, Raj K.

2018-01-01

The decay of various compound nuclei formed via exotic neutron-rich 9Li projectile is studied within the dynamical cluster-decay model (DCM). Following the earlier work of one of us (RKG) and collaborators (M. Kaur et al. (2015) [1]), for an empirically fixed neck-length parameter ΔRemp, the only parameter in the DCM, at a given incident laboratory energy ELab, we are able to fit almost exactly the (total) fusion cross section σfus =∑x=16σxn for 9Li projectile on 208Pb and other targets, with σfus depending strongly on the target mass of the most abundant isotope and its (magic) shell structure. This result shows the predictable nature of the DCM. The neck-length parameter ΔRemp is fixed empirically for the decay of 217At* formed in 9Li + 208Pb reaction at a fixed laboratory energy ELab, and then the total fusion cross section σfus calculated for all other reactions using 9Li as a projectile on different targets. Apparently, this procedure could be used to predict σfus for 9Li-induced reactions where experimental data are not available. Furthermore, optimum choice of "cold" target-projectile combinations, forming "hot" compact configurations, are predicted for the synthesis of compound nucleus 217At* with 8Li + 209Pb as one of the target-projectile combination, or another (t , p) combination 48Ca + 169Tb, with a doubly magic 48Ca, as the best possibility.

New Convex and Spherical Structures of Bare Boron Clusters

NASA Astrophysics Data System (ADS)

Boustani, Ihsan

1997-10-01

New stable structures of bare boron clusters can easily be obtained and constructed with the help of an "Aufbau Principle" suggested by a systematicab initioHF-SCF and direct CI study. It is concluded that boron cluster formation can be established by elemental units of pentagonal and hexagonal pyramids. New convex and small spherical clusters different from the classical known forms of boron crystal structures are obtained by a combination of both basic units. Convex structures simulate boron surfaces which can be considered as segments of open or closed spheres. Both convex clusters B16and B46have energies close to those of their conjugate quasi-planar clusters, which are relatively stable and can be considered to act as a calibration mark. The closed spherical clusters B12, B22, B32, and B42are less stable than the corresponding conjugated quasi-planar structures. As a consequence, highly stable spherical boron clusters can systematically be predicted when their conjugate quasi-planar clusters are determined and energies are compared.

Structural transition of (InSb)n clusters at n = 6-10

NASA Astrophysics Data System (ADS)

Lu, Qi Liang; Luo, Qi Quan; Huang, Shou Guo; Li, Yi De

2016-10-01

An optimization strategy combining global semi-empirical quantum mechanical search with all-electron density functional theory was adopted to determine the lowest energy structure of (InSb)n clusters with n = 6-10. A new structural growth pattern of the clusters was observed. The lowest energy structures of (InSb)6 and (InSb)8 were different from that of previously reported results. Competition existed between core-shell and cage-like structures of (InSb)8. The structural transition of (InSb)n clusters occurred at size n = 8-9. For (InSb)9 and (InSb)10 clusters, core-shell structure were more energetically favorable than the cage. The corresponding electronic properties were investigated.

Ligand induced structural isomerism in phosphine coordinated gold clusters revealed by ion mobility mass spectrometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ligare, Marshall R.; Baker, Erin S.; Laskin, Julia

Structural isomerism in ligated gold clusters is revealed using electrospray ionization ion mobility spectrometry mass spectrometry. Phosphine ligated Au8 clusters are shown to adopt more “extended” type structures with increasing exchange of methyldiphenylphosphine (MePPh2) for triphenylphosphine (PPh3). These ligand-dependant structure-property relationships are critical to applications of clusters in catalysis.

bcl::Cluster : A method for clustering biological molecules coupled with visualization in the Pymol Molecular Graphics System.

PubMed

Alexander, Nathan; Woetzel, Nils; Meiler, Jens

2011-02-01

Clustering algorithms are used as data analysis tools in a wide variety of applications in Biology. Clustering has become especially important in protein structure prediction and virtual high throughput screening methods. In protein structure prediction, clustering is used to structure the conformational space of thousands of protein models. In virtual high throughput screening, databases with millions of drug-like molecules are organized by structural similarity, e.g. common scaffolds. The tree-like dendrogram structure obtained from hierarchical clustering can provide a qualitative overview of the results, which is important for focusing detailed analysis. However, in practice it is difficult to relate specific components of the dendrogram directly back to the objects of which it is comprised and to display all desired information within the two dimensions of the dendrogram. The current work presents a hierarchical agglomerative clustering method termed bcl::Cluster. bcl::Cluster utilizes the Pymol Molecular Graphics System to graphically depict dendrograms in three dimensions. This allows simultaneous display of relevant biological molecules as well as additional information about the clusters and the members comprising them.

Association between seed dormancy and pericarp color is controlled by a pleiotropic gene that regulates ABA and flavonoid synthesis in weedy red rice

USDA-ARS?s Scientific Manuscript database

Seed dormancy has been associated with red grain color in cereal crops. The association was linked to the cluster of quantitative trait loci qSD7-1/qPC7 in weedy red rice. This research delimited the cluster to Os07g11020 or Rc encoding a predicted bHLH family transcription factor by intragenic reco...

Supported cluster catalysts synthesized to be small, simple, selective, and stable

DOE PAGES

Guan, Erjia; Fang, Chia-Yu; Yang, Dong; ...

2018-01-01

Molecular metal complexes on supports have drawn wide attention as catalysts offering new properties and opportunities for precise synthesis to make uniform catalytic species that can be understood in depth.

Theoretical prediction of a new stable structure of Au28(SR)20 cluster

NASA Astrophysics Data System (ADS)

Sun, Xiangxiang; Wang, Pu; Xiong, Lin; Pei, Yong

2018-07-01

A new stable structure of Au28(SR)20 cluster is predicted, which has the same gold core as two known structures but different Au-S framework. The new Au28(SR)20 cluster is proposed to be a key link in the evolution of Au22(SR)18, Au34(SR)22 and Au40(SR)24 clusters. The four clusters belong to a homogenous Au16+6N(SR)16+2N series (N = 1-4). The relative stabilities of the new Au28 isomer structure were confirmed by density functional theory calculations including dispersion corrections (DFT-D). It is found that upon protection of certain SR ligands, the new isomer structure has lower or comparable energies to two known cluster structures.

Visualizing and Clustering Protein Similarity Networks: Sequences, Structures, and Functions.

PubMed

Mai, Te-Lun; Hu, Geng-Ming; Chen, Chi-Ming

2016-07-01

Research in the recent decade has demonstrated the usefulness of protein network knowledge in furthering the study of molecular evolution of proteins, understanding the robustness of cells to perturbation, and annotating new protein functions. In this study, we aimed to provide a general clustering approach to visualize the sequence-structure-function relationship of protein networks, and investigate possible causes for inconsistency in the protein classifications based on sequences, structures, and functions. Such visualization of protein networks could facilitate our understanding of the overall relationship among proteins and help researchers comprehend various protein databases. As a demonstration, we clustered 1437 enzymes by their sequences and structures using the minimum span clustering (MSC) method. The general structure of this protein network was delineated at two clustering resolutions, and the second level MSC clustering was found to be highly similar to existing enzyme classifications. The clustering of these enzymes based on sequence, structure, and function information is consistent with each other. For proteases, the Jaccard's similarity coefficient is 0.86 between sequence and function classifications, 0.82 between sequence and structure classifications, and 0.78 between structure and function classifications. From our clustering results, we discussed possible examples of divergent evolution and convergent evolution of enzymes. Our clustering approach provides a panoramic view of the sequence-structure-function network of proteins, helps visualize the relation between related proteins intuitively, and is useful in predicting the structure and function of newly determined protein sequences.

The Mass Function of Young Star Clusters in the "Antennae" Galaxies.

PubMed

Zhang; Fall

1999-12-20

We determine the mass function of young star clusters in the merging galaxies known as the "Antennae" (NGC 4038/9) from deep images taken with the Wide Field Planetary Camera 2 on the refurbished Hubble Space Telescope. This is accomplished by means of reddening-free parameters and a comparison with stellar population synthesis tracks to estimate the intrinsic luminosity and age, and hence the mass, of each cluster. We find that the mass function of the young star clusters (with ages less, similar160 Myr) is well represented by a power law of the form psi&parl0;M&parr0;~M-2 over the range 104 less, similarM less, similar106 M middle dot in circle. This result may have important implications for our understanding of the origin of globular clusters during the early phases of galactic evolution.

CHIMERA: Top-down model for hierarchical, overlapping and directed cluster structures in directed and weighted complex networks

NASA Astrophysics Data System (ADS)

Franke, R.

2016-11-01

In many networks discovered in biology, medicine, neuroscience and other disciplines special properties like a certain degree distribution and hierarchical cluster structure (also called communities) can be observed as general organizing principles. Detecting the cluster structure of an unknown network promises to identify functional subdivisions, hierarchy and interactions on a mesoscale. It is not trivial choosing an appropriate detection algorithm because there are multiple network, cluster and algorithmic properties to be considered. Edges can be weighted and/or directed, clusters overlap or build a hierarchy in several ways. Algorithms differ not only in runtime, memory requirements but also in allowed network and cluster properties. They are based on a specific definition of what a cluster is, too. On the one hand, a comprehensive network creation model is needed to build a large variety of benchmark networks with different reasonable structures to compare algorithms. On the other hand, if a cluster structure is already known, it is desirable to separate effects of this structure from other network properties. This can be done with null model networks that mimic an observed cluster structure to improve statistics on other network features. A third important application is the general study of properties in networks with different cluster structures, possibly evolving over time. Currently there are good benchmark and creation models available. But what is left is a precise sandbox model to build hierarchical, overlapping and directed clusters for undirected or directed, binary or weighted complex random networks on basis of a sophisticated blueprint. This gap shall be closed by the model CHIMERA (Cluster Hierarchy Interconnection Model for Evaluation, Research and Analysis) which will be introduced and described here for the first time.

Comparison of Ergot Alkaloid Biosynthesis Gene Clusters in Claviceps Species Indicates Loss of Late Pathway Steps in Evolution of C. fusiformis▿

PubMed Central

Lorenz, Nicole; Wilson, Ella V.; Machado, Caroline; Schardl, Christopher L.; Tudzynski, Paul

2007-01-01

The grass parasites Claviceps purpurea and Claviceps fusiformis produce ergot alkaloids (EA) in planta and in submerged culture. Whereas EA synthesis (EAS) in C. purpurea proceeds via clavine intermediates to lysergic acid and the complex ergopeptines, C. fusiformis produces only agroclavine and elymoclavine. In C. purpurea the EAS gene (EAS) cluster includes dmaW (encoding the first pathway step), cloA (elymoclavine oxidation to lysergic acid), and the lpsA/lpsB genes (ergopeptine formation). We analyzed the corresponding C. fusiformis EAS cluster to investigate the evolutionary basis for chemotypic differences between the Claviceps species. Other than three peptide synthetase genes (lpsC and the tandem paralogues lpsA1 and lpsA2), homologues of all C. purpurea EAS genes were identified in C. fusiformis, including homologues of lpsB and cloA, which in C. purpurea encode enzymes for steps after clavine synthesis. Rearrangement of the cluster was evident around lpsB, which is truncated in C. fusiformis. This and several frameshift mutations render CflpsB a pseudogene (CflpsBΨ). No obvious inactivating mutation was identified in CfcloA. All C. fusiformis EAS genes, including CflpsBΨ and CfcloA, were expressed in culture. Cross-complementation analyses demonstrated that CfcloA and CflpsBΨ were expressed in C. purpurea but did not encode functional enzymes. In contrast, CpcloA catalyzed lysergic acid biosynthesis in C. fusiformis, indicating that C. fusiformis terminates its EAS pathway at elymoclavine because the cloA gene product is inactive. We propose that the C. fusiformis EAS cluster evolved from a more complete cluster by loss of some lps genes and by rearrangements and mutations inactivating lpsB and cloA. PMID:17720822

Comparison of ergot alkaloid biosynthesis gene clusters in Claviceps species indicates loss of late pathway steps in evolution of C. fusiformis.

PubMed

Lorenz, Nicole; Wilson, Ella V; Machado, Caroline; Schardl, Christopher L; Tudzynski, Paul

2007-11-01

The grass parasites Claviceps purpurea and Claviceps fusiformis produce ergot alkaloids (EA) in planta and in submerged culture. Whereas EA synthesis (EAS) in C. purpurea proceeds via clavine intermediates to lysergic acid and the complex ergopeptines, C. fusiformis produces only agroclavine and elymoclavine. In C. purpurea the EAS gene (EAS) cluster includes dmaW (encoding the first pathway step), cloA (elymoclavine oxidation to lysergic acid), and the lpsA/lpsB genes (ergopeptine formation). We analyzed the corresponding C. fusiformis EAS cluster to investigate the evolutionary basis for chemotypic differences between the Claviceps species. Other than three peptide synthetase genes (lpsC and the tandem paralogues lpsA1 and lpsA2), homologues of all C. purpurea EAS genes were identified in C. fusiformis, including homologues of lpsB and cloA, which in C. purpurea encode enzymes for steps after clavine synthesis. Rearrangement of the cluster was evident around lpsB, which is truncated in C. fusiformis. This and several frameshift mutations render CflpsB a pseudogene (CflpsB(Psi)). No obvious inactivating mutation was identified in CfcloA. All C. fusiformis EAS genes, including CflpsB(Psi) and CfcloA, were expressed in culture. Cross-complementation analyses demonstrated that CfcloA and CflpsB(Psi) were expressed in C. purpurea but did not encode functional enzymes. In contrast, CpcloA catalyzed lysergic acid biosynthesis in C. fusiformis, indicating that C. fusiformis terminates its EAS pathway at elymoclavine because the cloA gene product is inactive. We propose that the C. fusiformis EAS cluster evolved from a more complete cluster by loss of some lps genes and by rearrangements and mutations inactivating lpsB and cloA.

Chirally directed formation of nanometer-scale proline clusters.

PubMed

Myung, Sunnie; Fioroni, Marco; Julian, Ryan R; Koeniger, Stormy L; Baik, Mu-Hyun; Clemmer, David E

2006-08-23

Ion mobility measurements, combined with molecular mechanics simulations, are used to study enantiopure and racemic proline clusters formed by electrospray ionization. Broad distributions of cluster sizes and charge states are observed, ranging from clusters containing only a few proline units to clusters that contain more than 100 proline units (i.e., protonated clusters of the form [xPro + nH](n+) with x = 1 to >100 and n = 1-7). As the sizes of clusters increase, there is direct evidence for nanometer scale, chirally induced organization into specific structures. For n = 4 and 5, enantiopure clusters of approximately 50 to 100 prolines assemble into structures that are more elongated than the most compact structure that is observed from the racemic proline clusters. A molecular analogue, cis-4-hydroxy-proline, displays significantly different behavior, indicating that in addition to the rigidity of the side chain ring, intermolecular interactions are important in the formation of chirally directed clusters. This is the first case in which assemblies of chirally selective elongated structures are observed in this size range of amino acid clusters. Relationships between enantiopurity, cluster shape, and overall energetics are discussed.

Beyond Low-Rank Representations: Orthogonal clustering basis reconstruction with optimized graph structure for multi-view spectral clustering.

PubMed

Wang, Yang; Wu, Lin

2018-07-01

Low-Rank Representation (LRR) is arguably one of the most powerful paradigms for Multi-view spectral clustering, which elegantly encodes the multi-view local graph/manifold structures into an intrinsic low-rank self-expressive data similarity embedded in high-dimensional space, to yield a better graph partition than their single-view counterparts. In this paper we revisit it with a fundamentally different perspective by discovering LRR as essentially a latent clustered orthogonal projection based representation winged with an optimized local graph structure for spectral clustering; each column of the representation is fundamentally a cluster basis orthogonal to others to indicate its members, which intuitively projects the view-specific feature representation to be the one spanned by all orthogonal basis to characterize the cluster structures. Upon this finding, we propose our technique with the following: (1) We decompose LRR into latent clustered orthogonal representation via low-rank matrix factorization, to encode the more flexible cluster structures than LRR over primal data objects; (2) We convert the problem of LRR into that of simultaneously learning orthogonal clustered representation and optimized local graph structure for each view; (3) The learned orthogonal clustered representations and local graph structures enjoy the same magnitude for multi-view, so that the ideal multi-view consensus can be readily achieved. The experiments over multi-view datasets validate its superiority, especially over recent state-of-the-art LRR models. Copyright © 2018 Elsevier Ltd. All rights reserved.

Substructural controller synthesis

NASA Technical Reports Server (NTRS)

Su, Tzu-Jeng; Craig, Roy R., Jr.

1989-01-01

A decentralized design procedure which combines substructural synthesis, model reduction, decentralized controller design, subcontroller synthesis, and controller reduction is proposed for the control design of flexible structures. The structure to be controlled is decomposed into several substructures, which are modeled by component mode synthesis methods. For each substructure, a subcontroller is designed by using the linear quadratic optimal control theory. Then, a controller synthesis scheme called Substructural Controller Synthesis (SCS) is used to assemble the subcontrollers into a system controller, which is to be used to control the whole structure.

Deep multi-frequency rotation measure tomography of the galaxy cluster A2255

NASA Astrophysics Data System (ADS)

Pizzo, R. F.; de Bruyn, A. G.; Bernardi, G.; Brentjens, M. A.

2011-01-01

Aims: By studying the polarimetric properties of the radio galaxies and the radio filaments belonging to the galaxy cluster Abell 2255, we aim to unveil their 3-dimensional location within the cluster. Methods: We performed WSRT observations of A2255 at 18, 21, 25, 85, and 200 cm. The polarization images of the cluster were processed through rotation measure (RM) synthesis, producing three final RM cubes. Results: The radio galaxies and the filaments at the edges of the halo are detected in the high-frequency RM cube, obtained by combining the data at 18, 21, and 25 cm. Their Faraday spectra show different levels of complexity. The radio galaxies lying near by the cluster center have Faraday spectra with multiple peaks, while those at large distances show only one peak, as do the filaments. Similar RM distributions are observed for the external radio galaxies and for the filaments, with much lower average RM values and RM variance than those found in previous works for the central radio galaxies. The 85 cm RM cube is dominated by the Galactic foreground emission, but it also shows features associated with the cluster. At 2 m, no polarized emission from A2255 nor our Galaxy is detected. Conclusions: The radial trend observed in the RM distributions of the radio galaxies and in the complexity of their Faraday spectra favors the interpretation that the external Faraday screen for all the sources in A2255 is the ICM. Its differential contribution depends on the amount of medium that the radio signal crosses along the line of sight. The filaments should therefore be located at the periphery of the cluster, and their apparent central location comes from projection effects. Their high fractional polarization and morphology suggest that they are relics rather than part of a genuine radio halo. Their inferred large distance from the cluster center and their geometry could argue for an association with large-scale structure (LSS) shocks. The RM cubes in gif format are only available in electronic form at http://www.aanda.org. To request the RM cubes in FITS format, please contact R. F. Pizzo at: pizzo@astron.nl

Probing the Structures and Electronic Properties of Dual-Phosphorus-Doped Gold Cluster Anions (AunP-2, n = 1–8): A Density functional Theory Investigation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Kang-Ming; Huang, Teng; Liu, Yi-Rong

2015-07-29

The geometries of gold clusters doped with two phosphorus atoms, (AunP-2, n = 1–8) were investigated using density functional theory (DFT) methods. Various two-dimensional (2D) and three-dimensional (3D) structures of the doped clusters were studied. The results indicate that the structures of dual-phosphorus-doped gold clusters exhibit large differences from those of pure gold clusters with small cluster sizes. In our study, as for Au6P-2, two cis–trans isomers were found. The global minimum of Au8P-2 presents a similar configuration to that of Au-20, a pyramid-shaped unit, and the potential novel optical and catalytic properties of this structure warrant further attention. Themore » higher stability of AunP-2 clusters relative to Au-n+2 (n = 1–8) clusters was verified based on various energy parameters, and the results indicate that the phosphorus atom can improve the stabilities of the gold clusters. We then explored the evolutionary path of (n = 1–8) clusters. We found that AunP-2 clusters exhibit the 2D–3D structural transition at n = 6, which is much clearer and faster than that of pure gold clusters and single-phosphorus-doped clusters. The electronic properties of AunP-2 (n = 1–8) were then investigated. The photoelectron spectra provide additional fundamental information on the structures and molecular orbitals shed light on the evolution of AunP-2 (n = 1–8). Natural bond orbital (NBO) described the charge distribution in stabilizing structures and revealed the strong relativistic effects of the gold atoms.« less

Two worlds collide: Image analysis methods for quantifying structural variation in cluster molecular dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Steenbergen, K. G., E-mail: kgsteen@gmail.com; Gaston, N.

2014-02-14

Inspired by methods of remote sensing image analysis, we analyze structural variation in cluster molecular dynamics (MD) simulations through a unique application of the principal component analysis (PCA) and Pearson Correlation Coefficient (PCC). The PCA analysis characterizes the geometric shape of the cluster structure at each time step, yielding a detailed and quantitative measure of structural stability and variation at finite temperature. Our PCC analysis captures bond structure variation in MD, which can be used to both supplement the PCA analysis as well as compare bond patterns between different cluster sizes. Relying only on atomic position data, without requirement formore » a priori structural input, PCA and PCC can be used to analyze both classical and ab initio MD simulations for any cluster composition or electronic configuration. Taken together, these statistical tools represent powerful new techniques for quantitative structural characterization and isomer identification in cluster MD.« less

Two worlds collide: image analysis methods for quantifying structural variation in cluster molecular dynamics.

PubMed

Steenbergen, K G; Gaston, N

2014-02-14

Inspired by methods of remote sensing image analysis, we analyze structural variation in cluster molecular dynamics (MD) simulations through a unique application of the principal component analysis (PCA) and Pearson Correlation Coefficient (PCC). The PCA analysis characterizes the geometric shape of the cluster structure at each time step, yielding a detailed and quantitative measure of structural stability and variation at finite temperature. Our PCC analysis captures bond structure variation in MD, which can be used to both supplement the PCA analysis as well as compare bond patterns between different cluster sizes. Relying only on atomic position data, without requirement for a priori structural input, PCA and PCC can be used to analyze both classical and ab initio MD simulations for any cluster composition or electronic configuration. Taken together, these statistical tools represent powerful new techniques for quantitative structural characterization and isomer identification in cluster MD.

Ages and structural and dynamical parameters of two globular clusters in the M81 group

NASA Astrophysics Data System (ADS)

Ma, Jun; Wang, Song; Wu, Zhenyu; Zhang, TianMeng; Zou, Hu; Zhou, Zhimin; Nie, Jundan; Zhou, Xu; Peng, Xiyang; Wang, Jiali; Wu, Jianghua; Du, Cuihua; Yuan, Qirong

2017-07-01

GC-1 and GC-2 are two globular clusters (GCs) in the remote halo of M81 and M82 in the M81 group discovered by Jang et al. using the Hubble Space Telescope (HST) images. These two GCs were observed as part of the Beijing-Arizona-Taiwan-Connecticut (BATC) Multicolor Sky Survey using 14 intermediate-band filters covering a wavelength range of 4000-10 000 Å. We accurately determine these two clusters' ages and masses by comparing their spectral energy distributions (from 2267 to 20 000 Å, comprising photometric data in the near-ultraviolet of the Galaxy Evolution Explorer, 14 BATC intermediate-band and Two Micron All Sky Survey near-infrared JHKs filters) with theoretical stellar population-synthesis models, resulting in ages of 15.50 ± 3.20 for GC-1 and 15.10 ± 2.70 Gyr for GC-2. The masses of GC-1 and GC-2 obtained here are 1.77-2.04 × 106 and 5.20-7.11 × 106 M⊙, respectively. In addition, the deep observations with the Advanced Camera for Surveys and Wide Field Camera 3 on the HST are used to provide the surface brightness profiles of GC-1 and GC-2. The structural and dynamical parameters are derived from fitting the profiles to three different models; in particular, the internal velocity dispersions of GC-1 and GC-2 are derived, which can be compared with ones obtained based on spectral observations in the future. For the first time, in this paper, the rh versus MV diagram shows that GC-2 is an ultra-compact dwarf in the M81 group.

Synthesis, structural characterization and conversion of dinuclear iron-sulfur clusters containing the disulfide ligand: [Cp*Fe(μ-η2:η2-bdt)(cis-μ-η1:η1-S2)FeCp*], [Cp*Fe(μ-S(C6H4S2))(cis-μ-η1:η1-S2)FeCp*], and [{Cp*Fe(bdt)}2(trans-μ-η1:η1-S2)].

PubMed

Ji, Xiaoxiao; Tong, Peng; Yang, Dawei; Wang, Baomin; Zhao, Jinfeng; Li, Yang; Qu, Jingping

2017-03-21

The treatment of [Cp*Fe(μ-η 2 :η 4 -bdt)FeCp*] (1, Cp* = η 5 -C 5 Me 5 , bdt = benzene-1,2-dithiolate) with 1/4 equiv. of elemental sulfur (S 8 ) gave a dinuclear iron-sulfur cluster [Cp*Fe(μ-η 2 :η 2 -bdt)(cis-μ-η 1 :η 1 -S 2 )FeCp*] (2), which contains a cis-1,2-disulfide ligand. When complex 2 further interacted with 1/8 equiv. of S 8 , another sulfur atom inserted into an Fe-S bond to give a rare product [Cp*Fe(μ-S(C 6 H 4 S 2 ))(cis-μ-η 1 :η 1 -S 2 )FeCp*] (3). Unexpectedly, a trans-1,2 disulfide-bridged diiron complex [{Cp*Fe(bdt)} 2 (trans-μ-η 1 :η 1 -S 2 )] (4) was isolated from the reaction of complex 1 with 1/2 equiv. of S 8 , which represents a structural isomer of [2Fe-2S] ferredoxin-type clusters. In addition, cis-1,2-disulfide-bridged complex 3 can slowly convert into trans-1,2-disulfide-bridged complex 4 and the complex [Cp*Fe(μ-η 2 :η 2 -S 2 )(cis-μ-η 1 :η 1 -S 2 )FeCp*] (5) by self-assembly reaction at ambient temperature, which is evidenced by time-dependent 1 H NMR spectroscopy.

Structures of undecagold clusters: Ligand effect

NASA Astrophysics Data System (ADS)

Spivey, Kasi; Williams, Joseph I.; Wang, Lichang

2006-12-01

The most stable structure of undecagold, or Au 11, clusters was predicted from our DFT calculations to be planar [L. Xiao, L. Wang, Chem. Phys. Lett. 392 (2004) 452; L. Xiao, B. Tollberg, X. Hu, L. Wang, J. Chem. Phys. 124 (2005) 114309.]. The structures of ligand protected undecagold clusters were shown to be three-dimensional experimentally. In this work, we used DFT calculations to study the ligand effect on the structures of Au 11 clusters. Our results show that the most stable structure of Au 11 is in fact three-dimensional when SCH 3 ligands are attached. This indicates that the structures of small gold clusters are altered substantially in the presence of ligands.

Ensemble clustering in visual working memory biases location memories and reduces the Weber noise of relative positions.

PubMed

Lew, Timothy F; Vul, Edward

2015-01-01

People seem to compute the ensemble statistics of objects and use this information to support the recall of individual objects in visual working memory. However, there are many different ways that hierarchical structure might be encoded. We examined the format of structured memories by asking subjects to recall the locations of objects arranged in different spatial clustering structures. Consistent with previous investigations of structured visual memory, subjects recalled objects biased toward the center of their clusters. Subjects also recalled locations more accurately when they were arranged in fewer clusters containing more objects, suggesting that subjects used the clustering structure of objects to aid recall. Furthermore, subjects had more difficulty recalling larger relative distances, consistent with subjects encoding the positions of objects relative to clusters and recalling them with magnitude-proportional (Weber) noise. Our results suggest that clustering improved the fidelity of recall by biasing the recall of locations toward cluster centers to compensate for uncertainty and by reducing the magnitude of encoded relative distances.

Facile synthesis of CsPbBr3/PbSe composite clusters

PubMed Central

Nguyen, Thang Phan; Ozturk, Abdullah; Park, Jongee; Sohn, Woonbae; Lee, Tae Hyung; Jang, Ho Won; Kim, Soo Young

2018-01-01

Abstract In this work, CsPbBr3 and PbSe nanocomposites were synthesized to protect perovskite material from self-enlargement during reaction. UV absorption and photoluminescence (PL) spectra indicate that the addition of Se into CsPbBr3 quantum dots modified the electronic structure of CsPbBr3, increasing the band gap from 2.38 to 2.48 eV as the Cs:Se ratio increased to 1:3. Thus, the emission color of CsPbBr3 perovskite quantum dots was modified from green to blue by increasing the Se ratio in composites. According to X-ray diffraction patterns, the structure of CsPbBr3 quantum dots changed from cubic to orthorhombic due to the introduction of PbSe at the surface. Transmission electron microscopy and X-ray photoemission spectroscopy confirmed that the atomic distribution in CsPbBr3/PbSe composite clusters is uniform and the composite materials were well formed. The PL intensity of a CsPbBr3/PbSe sample with a 1:1 Cs:Se ratio maintained 50% of its initial intensity after keeping the sample for 81 h in air, while the PL intensity of CsPbBr3 reduced to 20% of its initial intensity. Therefore, it is considered that low amounts of Se could improve the stability of CsPbBr3 quantum dots. PMID:29296127

Synthesis of Novel Aza-aromatic Curcuminoids with Improved Biological Activities towards Various Cancer Cell Lines.

PubMed

Theppawong, Atiruj; Van de Walle, Tim; Grootaert, Charlotte; Bultinck, Margot; Desmet, Tom; Van Camp, John; D'hooghe, Matthias

2018-05-01

Curcumin, a natural compound extracted from the rhizomes of Curcuma longa , displays pronounced anticancer properties but lacks good bioavailability and stability. In a previous study, we initiated structure modification of the curcumin scaffold by imination of the labile β-diketone moiety to produce novel β-enaminone derivatives. These compounds showed promising properties for elaborate follow-up studies. In this work, we focused on another class of nitrogen-containing curcuminoids with a similar objective: to address the bioavailability and stability issues and to improve the biological activity of curcumin. This paper thus reports on the synthesis of new pyridine-, indole-, and pyrrole-based curcumin analogues (aza-aromatic curcuminoids) and discusses their water solubility, antioxidant activity, and antiproliferative properties. In addition, multivariate statistics, including hierarchical clustering analysis and principal component analysis, were performed on a broad set of nitrogen-containing curcuminoids. Compared to their respective mother structures, that is, curcumin and bisdemethoxycurcumin, all compounds, and especially the pyridin-3-yl β-enaminone analogues, showed better water solubility profiles. Interestingly, the pyridine-, indole-, and pyrrole-based curcumin derivatives demonstrated improved biological effects in terms of mitochondrial activity impairment and protein content, in addition to comparable or decreased antioxidant properties. Overall, the biologically active N -alkyl β-enaminone aza-aromatic curcuminoids were shown to offer a desirable balance between good solubility and significant bioactivity.

THERMODYNAMICS OF THE COMA CLUSTER OUTSKIRTS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Simionescu, A.; Werner, N.; Urban, O.

2013-09-20

We present results from a large mosaic of Suzaku observations of the Coma Cluster, the nearest and X-ray brightest hot ({approx}8 keV), dynamically active, non-cool core system, focusing on the thermodynamic properties of the intracluster medium on large scales. For azimuths not aligned with an infalling subcluster toward the southwest, our measured temperature and X-ray brightness profiles exhibit broadly consistent radial trends, with the temperature decreasing from about 8.5 keV at the cluster center to about 2 keV at a radius of 2 Mpc, which is the edge of our detection limit. The southwest merger significantly boosts the surface brightness,more » allowing us to detect X-ray emission out to {approx}2.2 Mpc along this direction. Apart from the southwestern infalling subcluster, the surface brightness profiles show multiple edges around radii of 30-40 arcmin. The azimuthally averaged temperature profile, as well as the deprojected density and pressure profiles, all show a sharp drop consistent with an outwardly-propagating shock front located at 40 arcmin, corresponding to the outermost edge of the giant radio halo observed at 352 MHz with the Westerbork Synthesis Radio Telescope. The shock front may be powering this radio emission. A clear entropy excess inside of r{sub 500} reflects the violent merging events linked with these morphological features. Beyond r{sub 500}, the entropy profiles of the Coma Cluster along the relatively relaxed directions are consistent with the power-law behavior expected from simple models of gravitational large-scale structure formation. The pressure is also in agreement at these radii with the expected values measured from Sunyaev-Zel'dovich data from the Planck satellite. However, due to the large uncertainties associated with the Coma Cluster measurements, we cannot yet exclude an entropy flattening in this system consistent with that seen in more relaxed cool core clusters.« less

Analysis of the Structures and Properties of (GaSb)n (n = 4-9) Clusters through Density Functional Theory.

PubMed

Lu, Qi Liang; Luo, Qi Quan; Huang, Shou Guo; Li, Yi De; Wan, Jian Guo

2016-07-07

An optimization strategy combining global semiempirical quantum mechanical search with all-electron density functional theory was adopted to determine the lowest energy structure of (GaSb)n clusters up to n = 9. The growth pattern of the clusters differed from those of previously reported group III-V binary clusters. A cagelike configuration was found for cluster sizes n ≤ 7. The structure of (GaSb)6 deviated from that of other III-V clusters. Competition existed between core-shell and hollow cage structures of (GaSb)7. Novel noncagelike structures were energetically preferred over the cages for the (GaSb)8 and (GaSb)9 clusters. Electronic properties, such as vertical ionization potential, adiabatic electron affinities, HOMO-LUMO gaps, and average on-site charges on Ga or Sb atoms, as well as binding energies, were computed.

Vapor-phase photo-oxidation of methanol over nanosize titanium dioxide clusters dispersed in MCM-41 host material part 1: synthesis and characterization.

PubMed

Bhattacharya, K; Tripathi, A K; Dey, G K; Gupta, N M

2005-05-01

Nanosize clusters of titania were dispersed in mesoporous MCM-41 silica matrix with the help of the incipient wet-impregnation route, using an isopropanol solution of titanium isopropoxide as precursor. The clusters thus formed were of pure anatase phase and their size depended upon the titania loading. In the case of low (< 15 wt %) loadings, the TiO2 particles were X-ray and laser-Raman amorphous, confirming very high dispersion. These particles were mostly of < or = 2 nm size. On the other hand, larger size clusters (2-15 nm) were present in a sample with a higher loading of approximately 21 wt %. These particles of titania, irrespective of their size, exhibited an absorbance behavior similar to that of bulk TiO2. Powder X-ray diffraction, N2-adsorption and transmission electron microscopy results showed that while smaller size particles were confined mostly inside the pore system, the larger size particles occupied the external surface of the host matrix. At the same time, the structural integrity of the host was maintained even though some deformation in the pore system was noticed in the case of the sample having highest loading. The core level X-ray photoelectron spectroscopy results revealed a + 4 valence state of Ti in all the samples. A positive binding energy shift and the increase of the width of Ti 2p peaks were observed, however, with the decrease in the particle size of supported titania crystallites, indicative of a microenvironment for surface sites that is different from that of the bulk.

Extended utility of molten-salt chemistry: unprecedented synthesis of a water-soluble salt-inclusion solid comprised of high-nuclearity vanadium oxide clusters.

PubMed

Queen, Wendy L; West, J Palmer; Hudson, Joan; Hwu, Shiou-Jyh

2011-11-07

Polyoxometallates (POMs) are desirable in materials applications ranging from uses as catalysts in selective oxidation reactions to molecular-like building blocks for the preparation of new extended solids. With the use of an unprecedented approach involving high temperature, molten salt methods, a fascinating series of salt-inclusion solids (SISs) that contain high nuclearity POMs has been isolated for the first time. Cs(11)Na(3)(V(15)O(36))Cl(6) (1) was synthesized using the eutectic NaCl/CsCl flux (mp 493 °C) which serves as a reactive solvent in crystal growth and allows for the SIS formation. Its framework can be viewed as an "ionic" lattice composed of alternately packed counterions of Cl-centered [V(15)O(36)Cl](9-) clusters (V15; S = 11/2) and multinuclear [Cs(9)Na(3)Cl(5)](7+) cations. In light of the structural analysis, 1 was proven to be soluble in water giving rise to a dark green solution that is similar in color to single crystals of the title compound. Infrared spectroscopy of the solid formed from fast evaporation of the solution supports the presence of dissolved V15 clusters. Also noteworthy is the magnetization of 1 at 2 K, which reveals an s-shaped plot resembling that of superparamagnetic materials. © 2011 American Chemical Society

Synthesis and chemistry of the open-cage cobaltaheteroborane cluster [{(η(5)-C5Me5)Co}2B2H2Se2]: a combined experimental and theoretical study.

PubMed

Barik, Subrat Kumar; Dorcet, Vincent; Roisnel, Thierry; Halet, Jean-François; Ghosh, Sundargopal

2015-08-28

Reaction of [(η(5)-C5Me5)CoCl]2 with a two-fold excess of [LiBH4·thf] followed by heating with an excess of Se powder produces the dicobaltaselenaborane species [{(η(5)-C5Me5)Co}2B2H2Se2], , in good yield. The geometry of resembles a nido pentagonal [Co2B2Se2] bipyramid with a missing equatorial vertex. It can alternatively be seen as an open cage triple-decker cluster. Isolation of permits its reaction with [Fe2(CO)9] to give heterometallic diselenametallaborane [{(η(5)-C5Me5)Co}Fe(CO)3B2H2Se2], . The geometry of is similar to that of with one of the [(η(5)-C5Me5)Co] groups replaced by the isolobal, two-electron fragment [Fe(CO)3]. Both new compounds have been characterized by mass spectrometry, and by (1)H, (11)B and (13)C NMR spectroscopy. The structural architectures have been unequivocally established by crystallographic analysis. In addition, density functional theory calculations were performed to investigate the bonding and electronic properties. The large HOMO-LUMO gaps computed for both clusters are consistent with their thermodynamic stability. Natural bond order calculations predict the absence of metal-metal bonding interaction.

Synthesis and characterization of Fe colloid catalysts in inverse micelle solutions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Martino, A.; Stoker, M.; Hicks, M.

1995-12-31

Surfactant molecules, possessing a hydrophilic head group and a hydrophobic tail group, aggregate in various solvents to form structured solutions. In two component mixtures of surfactant and organic solvents (e.g., toluene and alkanes), surfactants aggregate to form inverse micelles. Here, the hydrophilic head groups shield themselves by forming a polar core, and the hydrophobic tails groups are free to move about in the surrounding oleic phase. The formation of Fe clusters in inverse miscelles was studied.Iron salts are solubilized within the polar interior of inverse micelles, and the addition of the reducing agent LiBH{sub 4} initiates a chemical reduction tomore » produce monodisperse, nanometer sized Fe based particles. The reaction sequence is sustained by material exchange between inverse micelles. The surfactant interface provides a spatial constraint on the reaction volume, and reactions carried out in these micro-heterogeneous solutions produce colloidal sized particles (10-100{Angstrom}) stabilized in solution against flocculation of surfactant. The clusters were stabilized with respect to size with transmission electron microscopy (TEM) and with respect to chemical composition with Mossbauer spectroscopy, electron diffraction, and x-ray photoelectron spectroscopy (XPS). In addition, these iron based clusters were tested for catalytic activity in a model hydrogenolysis reaction. The hydrogenolysis of naphthyl bibenzyl methane was used as a model for coal pyrolysis.« less

A platonic solid templating Archimedean solid: an unprecedented nanometre-sized Ag37 cluster

NASA Astrophysics Data System (ADS)

Li, Xiao-Yu; Su, Hai-Feng; Yu, Kai; Tan, Yuan-Zhi; Wang, Xing-Po; Zhao, Ya-Qin; Sun, Di; Zheng, Lan-Sun

2015-04-01

The spontaneous formation of discrete spherical nanosized molecules is prevalent in nature, but the authentic structural mimicry of such highly symmetric polyhedra from edge sharing of regular polygons has remained elusive. Here we present a novel ball-shaped {(HNEt3)[Ag37S4(SC6H4tBu)24(CF3COO)6(H2O)12]} cluster (1) that is assembled via a one-pot process from polymeric {(HNEt3)2[Ag10(SC6H4tBu)12]}n and CF3COOAg. Single crystal X-ray analysis confirmed that 1 is a Td symmetric spherical molecule with a [Ag36(SC6H4tBu)24] anion shell enwrapping a AgS4 tetrahedron. The shell topology of 1 belongs to one of 13 Archimedean solids, a truncated tetrahedron with four edge-shared hexagons and trigons, which are supported by a AgS4 Platonic solid in the core. Interestingly, the cluster emits green luminescence centered at 515 nm at room temperature. Our investigations have provided a promising synthetic protocol for a high-nuclearity silver cluster based on underlying geometrical principles.The spontaneous formation of discrete spherical nanosized molecules is prevalent in nature, but the authentic structural mimicry of such highly symmetric polyhedra from edge sharing of regular polygons has remained elusive. Here we present a novel ball-shaped {(HNEt3)[Ag37S4(SC6H4tBu)24(CF3COO)6(H2O)12]} cluster (1) that is assembled via a one-pot process from polymeric {(HNEt3)2[Ag10(SC6H4tBu)12]}n and CF3COOAg. Single crystal X-ray analysis confirmed that 1 is a Td symmetric spherical molecule with a [Ag36(SC6H4tBu)24] anion shell enwrapping a AgS4 tetrahedron. The shell topology of 1 belongs to one of 13 Archimedean solids, a truncated tetrahedron with four edge-shared hexagons and trigons, which are supported by a AgS4 Platonic solid in the core. Interestingly, the cluster emits green luminescence centered at 515 nm at room temperature. Our investigations have provided a promising synthetic protocol for a high-nuclearity silver cluster based on underlying geometrical principles. Electronic supplementary information (ESI) available: detailed synthesis procedure, tables, crystal data in CIF files, IR data, TGA results and powder X-ray diffractogram for 1. CCDC 1042228. See DOI: 10.1039/c5nr01222h

The [(AI 2O 3) 2] - Anion Cluster: Electron Localization-Delocalization Isomerism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sierka, Marek; Dobler, Jens; Sauer, Joachim

2009-10-05

Three-dimensional bulk alumina and its two-dimensional thin films show great structural diversity, posing considerable challenges to their experimental structural characterization and computational modeling. Recently, structural diversity has also been demonstrated for zerodimensional gas phase aluminum oxide clusters. Mass-selected clusters not only make systematic studies of the structural and electronic properties as a function of size possible, but lately have also emerged as powerful molecular models of complex surfaces and solid catalysts. In particular, the [(Al 2O 3) 3-5] + clusters were the first example of polynuclear maingroup metal oxide cluster that are able to thermally activate CH 4. Over themore » past decades gas phase aluminum oxide clusters have been extensively studied both experimentally and computationally, but definitive structural assignments were made for only a handful of them: the planar [Al 3O 3] - and [Al 5O 4] - cluster anions, and the [(Al 2O 3) 1-4(AlO)] + cluster cations. For stoichiometric clusters only the atomic structures of [(Al 2O 3) 4] +/0 have been nambiguously resolved. Here we report on the structures of the [(Al 2O 3) 2] -/0 clusters combining photoelectron spectroscopy (PES) and quantum chemical calculations employing a genetic algorithm as a global optimization technique. The [(Al 2O 3) 2] - cluster anion show energetically close lying but structurally distinct cage and sheet-like isomers which differ by delocalization/localization of the extra electron. The experimental results are crucial for benchmarking the different computational methods applied with respect to a proper description of electron localization and the relative energies for the isomers which will be of considerable value for future computational studies of aluminum oxide and related systems.« less

Cell-targeted platinum nanoparticles and nanoparticle clusters.

PubMed

Papst, Stefanie; Brimble, Margaret A; Evans, Clive W; Verdon, Daniel J; Feisst, Vaughan; Dunbar, P Rod; Tilley, Richard D; Williams, David E

2015-06-21

Herein, we report the facile preparation of cell-targeted platinum nanoparticles (PtNPs), through the design of peptides that, as a single molecule added in small concentration during the synthesis, control the size of PtNP clusters during their growth, stabilise the PtNPs in aqueous suspension and enable the functionalisation of the PtNPs with a versatile range of cell-targeting ligands. Water-soluble PtNPs targeted respectively at blood group antigens and at integrin receptors are demonstrated.

Multielectron donors based on TTF-phosphine and ferrocene-phosphine hybrid complexes of a hexarhenium(III) octahedral cluster core.

PubMed

Perruchas, Sandrine; Avarvari, Narcis; Rondeau, David; Levillain, Eric; Batail, Patrick

2005-05-16

Electroactive molecular materials precursors are obtained through coordination chemistry of the hexarhenium cluster core [Re(6)Se(8)](2+) on the six available apical positions with redox-active phosphines bearing tetrathiafulvalene- or ferrocene-based moieties. Single-crystal X-ray diffraction study and electrospray mass spectrometry ascertain the synthesis of these hexasubstituted electroactive clusters, containing up to 12 redox active sites. Cyclic voltammetry experiments demonstrate that these compounds can be reversibly oxidized at rather low potentials, thus allowing an easy access to the corresponding radical species which should provide new conducting and/or magnetic molecular materials.

Structural and electronic properties of Aun-xPtx (n = 2-14; x ⩽ n) clusters: The density functional theory investigation

NASA Astrophysics Data System (ADS)

Yuan, H. K.; Kuang, A. L.; Tian, C. L.; Chen, H.

2014-03-01

The structural evolutions and electronic properties of bimetallic Aun-xPtx (n = 2-14; x ⩽ n) clusters are investigated by using the density functional theory (DFT) with the generalized gradient approximation (GGA). The monatomic doping Aun-1Pt clusters are emphasized and compared with the corresponding pristine Aun clusters. The results reveal that the planar configurations are favored for both Aun-1Pt and Aun clusters with size up to n = 13, and the former often employ the substitution patterns based on the structures of the latter. The most stable clusters are Au6 and Au6Pt, which adopt regular planar triangle (D3h) and hexagon-ring (D6h) structures and can be regarded as the preferential building units in designing large clusters. For Pt-rich bimetallic clusters, their structures can be obtained from the substitution of Pt atoms by Au atoms from the Ptn structures, where Pt atoms assemble together and occupy the center yet Au atoms prefer the apex positions showing a segregation effect. With respect to pristine Au clusters, AunPt clusters exhibit somewhat weaker and less pronounced odd-even oscillations in the highest occupied and lowest unoccupied molecular-orbital gaps (HOMO-LUMO gap), electron affinity (EA), and ionization potential (IP) due to the partially released electron pairing effect. The analyses of electronic structure indicate that Pt atoms in AuPt clusters would delocalize their one 6s and one 5d electrons to contribute the electronic shell closure. The sp-d hybridizations as well as the d-d interactions between the host Au and dopant Pt atoms result in the enhanced stabilities of AuPt clusters.

Line-of-sight structure toward strong lensing galaxy clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bayliss, Matthew B.; Johnson, Traci; Sharon, Keren

2014-03-01

We present an analysis of the line-of-sight structure toward a sample of 10 strong lensing cluster cores. Structure is traced by groups that are identified spectroscopically in the redshift range, 0.1 ≤ z ≤ 0.9, and we measure the projected angular and comoving separations between each group and the primary strong lensing clusters in each corresponding line of sight. From these data we measure the distribution of projected angular separations between the primary strong lensing clusters and uncorrelated large-scale structure as traced by groups. We then compare the observed distribution of angular separations for our strong lensing selected lines ofmore » sight against the distribution of groups that is predicted for clusters lying along random lines of sight. There is clear evidence for an excess of structure along the line of sight at small angular separations (θ ≤ 6') along the strong lensing selected lines of sight, indicating that uncorrelated structure is a significant systematic that contributes to producing galaxy clusters with large cross sections for strong lensing. The prevalence of line-of-sight structure is one of several biases in strong lensing clusters that can potentially be folded into cosmological measurements using galaxy cluster samples. These results also have implications for current and future studies—such as the Hubble Space Telescope Frontier Fields—that make use of massive galaxy cluster lenses as precision cosmological telescopes; it is essential that the contribution of line-of-sight structure be carefully accounted for in the strong lens modeling of the cluster lenses.« less

Structural, stability, and vibrational properties of BinPm clusters

NASA Astrophysics Data System (ADS)

Shen, Wanting; Han, Lihong; Liang, Dan; Zhang, Chunfang; Ruge, Quhe; Wang, Shumin; Lu, Pengfei

2018-04-01

An in-depth investigation is performed on stability mechanisms, electronic and optical properties of III-V semiconductor vapor phases clusters. First principles electronic structure calculations of CAM-B3LYP are performed on neutral BinPm (n + m ≤ 14) clusters. The geometrical evolution of all stable structures remains amorphous as the clusters size increases. Binding energies (BEs), energy gains and highest occupied molecular orbital and lowest unoccupied molecular orbital (HOMO-LUMO) gaps confirm that all four-atom structures of BinPm clusters have more stable optical properties. Orbitals composition and vibrational spectra of stable clusters are analyzed. Our calculations will contribute to the study of diluted bismuth alloys and compounds.

Hidden electronic rule in the “cluster-plus-glue-atom” model

PubMed Central

Du, Jinglian; Dong, Chuang; Melnik, Roderick; Kawazoe, Yoshiyuki; Wen, Bin

2016-01-01

Electrons and their interactions are intrinsic factors to affect the structure and properties of materials. Based on the “cluster-cluster-plus-glue-atom” model, an electron counting rule for complex metallic alloys (CMAs) has been revealed in this work (i. e. the CPGAMEC rule). Our results on the cluster structure and electron concentration of CMAs with apparent cluster features, indicate that the valence electrons’ number per unit cluster formula for these CMAs are specific constants of eight-multiples and twelve-multiples. It is thus termed as specific electrons cluster formula. This CPGAMEC rule has been demonstrated as a useful guidance to direct the design of CMAs with desired properties, while its practical applications and underlying mechanism have been illustrated on the basis of CMAs’ cluster structural features. Our investigation provides an aggregate picture with intriguing electronic rule and atomic structural features of CMAs. PMID:27642002

Principal Cluster Axes: A Projection Pursuit Index for the Preservation of Cluster Structures in the Presence of Data Reduction

ERIC Educational Resources Information Center

Steinley, Douglas; Brusco, Michael J.; Henson, Robert

2012-01-01

A measure of "clusterability" serves as the basis of a new methodology designed to preserve cluster structure in a reduced dimensional space. Similar to principal component analysis, which finds the direction of maximal variance in multivariate space, principal cluster axes find the direction of maximum clusterability in multivariate space.…

Equilibrium geometries, electronic and magnetic properties of small AunNi- (n = 1-9) clusters

NASA Astrophysics Data System (ADS)

Tang, Cui-Ming; Chen, Xiao-Xu; Yang, Xiang-Dong

2014-05-01

Geometrical, electronic and magnetic properties of small AunNi- (n = 1-9) clusters have been investigated based on density functional theory (DFT) at PW91P86 level. An extensive structural search shows that the relative stable structures of AunNi- (n = 1-9) clusters adopt 2D structure for n = 1-5, 7 and 3D structure for n = 6, 8-9. And the substitution of a Ni atom for an Au atom in the Au-n+1 cluster obviously changes the structure of the host cluster. Moreover, an odd-even alternation phenomenon has been found for HOMO-LUMO energy gaps, indicating that the relative stable structures of the AunNi- clusters with odd-numbered gold atoms have a higher relative stability. Finally, the natural population analysis (NPA) and the vertical detachment energies (VDE) are studied, respectively. The theoretical values of VDE are reported for the first time to our best knowledge.

Lipoic acid biosynthesis defects.

PubMed

Mayr, Johannes A; Feichtinger, René G; Tort, Frederic; Ribes, Antonia; Sperl, Wolfgang

2014-07-01

Lipoate is a covalently bound cofactor essential for five redox reactions in humans: in four 2-oxoacid dehydrogenases and the glycine cleavage system (GCS). Two enzymes are from the energy metabolism, α-ketoglutarate dehydrogenase and pyruvate dehydrogenase; and three are from the amino acid metabolism, branched-chain ketoacid dehydrogenase, 2-oxoadipate dehydrogenase, and the GCS. All these enzymes consist of multiple subunits and share a similar architecture. Lipoate synthesis in mitochondria involves mitochondrial fatty acid synthesis up to octanoyl-acyl-carrier protein; and three lipoate-specific steps, including octanoic acid transfer to glycine cleavage H protein by lipoyl(octanoyl) transferase 2 (putative) (LIPT2), lipoate synthesis by lipoic acid synthetase (LIAS), and lipoate transfer by lipoyltransferase 1 (LIPT1), which is necessary to lipoylate the E2 subunits of the 2-oxoacid dehydrogenases. The reduced form dihydrolipoate is reactivated by dihydrolipoyl dehydrogenase (DLD). Mutations in LIAS have been identified that result in a variant form of nonketotic hyperglycinemia with early-onset convulsions combined with a defect in mitochondrial energy metabolism with encephalopathy and cardiomyopathy. LIPT1 deficiency spares the GCS, and resulted in a combined 2-oxoacid dehydrogenase deficiency and early death in one patient and in a less severely affected individual with a Leigh-like phenotype. As LIAS is an iron-sulphur-cluster-dependent enzyme, a number of recently identified defects in mitochondrial iron-sulphur cluster synthesis, including NFU1, BOLA3, IBA57, GLRX5 presented with deficiency of LIAS and a LIAS-like phenotype. As in DLD deficiency, a broader clinical spectrum can be anticipated for lipoate synthesis defects depending on which of the affected enzymes is most rate limiting.

Atomically precise cluster catalysis towards quantum controlled catalysts

PubMed Central

Watanabe, Yoshihide

2014-01-01

Catalysis of atomically precise clusters supported on a substrate is reviewed in relation to the type of reactions. The catalytic activity of supported clusters has generally been discussed in terms of electronic structure. Several lines of evidence have indicated that the electronic structure of clusters and the geometry of clusters on a support, including the accompanying cluster-support interaction, are strongly correlated with catalytic activity. The electronic states of small clusters would be easily affected by cluster–support interactions. Several studies have suggested that it is possible to tune the electronic structure through atomic control of the cluster size. It is promising to tune not only the number of cluster atoms, but also the hybridization between the electronic states of the adsorbed reactant molecules and clusters in order to realize a quantum-controlled catalyst. PMID:27877723

Where Water Is Oxidized to Dioxygen: Structure of the Photosynthetic Mn4Ca Cluster

PubMed Central

Yano, Junko; Kern, Jan; Sauer, Kenneth; Latimer, Matthew J.; Pushkar, Yulia; Biesiadka, Jacek; Loll, Bernhard; Saenger, Wolfram; Messinger, Johannes; Zouni, Athina; Yachandra, Vittal K.

2014-01-01

The oxidation of water to dioxygen is catalyzed within photosystem II (PSII) by a Mn4Ca cluster, the structure of which remains elusive. Polarized extended x-ray absorption fine structure (EXAFS) measurements on PSII single crystals constrain the Mn4Ca cluster geometry to a set of three similar high-resolution structures. Combining polarized EXAFS and x-ray diffraction data, the cluster was placed within PSII, taking into account the overall trend of the electron density of the metal site and the putative ligands. The structure of the cluster from the present study is unlike either the 3.0 or 3.5 angstrom–resolution x-ray structures or other previously proposed models. PMID:17082458

Versatile Method for the Site-Specific Modification of DNA with Boron Clusters: Anti-Epidermal Growth Factor Receptor (EGFR) Antisense Oligonucleotide Case.

PubMed

Ebenryter-Olbińska, Katarzyna; Kaniowski, Damian; Sobczak, Milena; Wojtczak, Błażej A; Janczak, Sławomir; Wielgus, Ewelina; Nawrot, Barbara; Leśnikowski, Zbigniew J

2017-11-21

A general and convenient approach for the incorporation of different types of boron clusters into specific locations of the DNA-oligonucleotide chain based on the automated phosphoramidite method of oligonucleotide synthesis and post-synthetic "click chemistry" modification has been developed. Pronounced effects of boron-cluster modification on the physico- and biochemical properties of the antisense oligonucleotides were observed. The silencing activity of antisense oligonucleotides bearing a single boron cluster modification in the middle of the oligonucleotide chain was substantially higher than that of unmodified oligonucleotides. This finding may be of importance for the design of therapeutic nucleic acids with improved properties. The proposed synthetic methodology broadens the availability of nucleic acid-boron cluster conjugates and opens up new avenues for their potential practical use. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Open Cluster Chemical Abundances and Mapping (OCCAM) Survey: Current Status

NASA Astrophysics Data System (ADS)

Frinchaboy, Peter; O'Connell, Julia; Donor, John; Cunha, Katia; Thompson, Benjamin; Melendez, Matthew; Shetrone, Matthew; Zasowski, Gail; Majewski, Steven R.; APOGEE TEAM

2018-01-01

The Open Cluster Chemical Analysis and Mapping (OCCAM) survey aims to produce a comprehensive, uniform, infrared-based data set forhundreds of open clusters, and constrain key Galactic dynamical and chemical parameters using the SDSS/APOGEE survey and follow-up from the McDonald Observatory Otto Struve 2.1-m telescope and Sandiford Cass Echelle Spectrograph (R ~ 60,000). We report on multi-element radial abundance gradients obtained from a sample of over 30 disk open clusters. The APOGEE chemical abundances were derived automatically by the ASPCAP pipeline and these are part of the SDSS IV Data Release 14, optical follow-up were analyzed using equivalent width analysis and spectral synthesis. We present the current open cluster sample that spans a significant range in age allowing exploration of the evolution of the Galactic abundance gradients. This work is supported by an NSF AAG grants AST-1311835 & AST-1715662.

α decay and cluster radioactivity of nuclei of interest to the synthesis of Z =119 , 120 isotopes

NASA Astrophysics Data System (ADS)

Poenaru, D. N.; Gherghescu, R. A.

2018-04-01

Super-heavy nuclei of interest for the forthcoming synthesis of the isotopes with Z =119 , 120 are investigated. One of the very interesting latest experiments was performed at the velocity filter SHIP (GSI Darmstadt) trying to produce 299120 in a fusion reaction 248Cm(54Cr,3 n )299120 . We report calculations of α -decay half-lives using four models: AKRA (Akrawy), ASAF (analytical superasymmetric fission), UNIV (universal formula), and semFIS (semi-empirical formula based on fission theory). The released energy, Q , is calculated using the theoretical model of atomic masses, WS4. For Sr,9492 cluster radioactivity of 120,302300 we predict a branching ratio relative to α decay of -0.10 and 0.49, respectively, meaning that it is worth trying to detect such kinds of decay modes in competition with α decay.

A Hierarchical Clustering Methodology for the Estimation of Toxicity

EPA Science Inventory

A Quantitative Structure Activity Relationship (QSAR) methodology based on hierarchical clustering was developed to predict toxicological endpoints. This methodology utilizes Ward's method to divide a training set into a series of structurally similar clusters. The structural sim...

Diffuse radio emission in the complex merging galaxy cluster Abell2069

NASA Astrophysics Data System (ADS)

Drabent, A.; Hoeft, M.; Pizzo, R. F.; Bonafede, A.; van Weeren, R. J.; Klein, U.

2015-03-01

Context. Galaxy clusters with signs of a recent merger in many cases show extended diffuse radio features. This emission originates from relativistic electrons that suffer synchrotron losses due to the intracluster magnetic field. The mechanisms of particle acceleration and the properties of the magnetic field are still poorly understood. Aims: We search for diffuse radio emission in galaxy clusters. Here, we study the complex galaxy cluster Abell 2069, for which X-ray observations indicate a recent merger. Methods: We investigate the cluster's radio continuum emission by deep Westerbork Synthesis Radio Telescope (WSRT) observations at 346 MHz and Giant Metrewave Radio Telescope (GMRT) observations at 322 MHz. Results: We find an extended diffuse radio feature roughly coinciding with the main component of the cluster. We classify this emission as a radio halo and estimate its lower limit flux density at 25 ± 9 mJy. Moreover, we find a second extended diffuse source located at the cluster's companion and estimate its flux density at 15 ± 2 mJy. We speculate that this is a small halo or a mini-halo. If true, this cluster is the first example of a double-halo in a single galaxy cluster.

Exploring the atomic structure of 1.8nm monolayer-protected gold clusters with aberration-corrected STEM.

PubMed

Liu, Jian; Jian, Nan; Ornelas, Isabel; Pattison, Alexander J; Lahtinen, Tanja; Salorinne, Kirsi; Häkkinen, Hannu; Palmer, Richard E

2017-05-01

Monolayer-protected (MP) Au clusters present attractive quantum systems with a range of potential applications e.g. in catalysis. Knowledge of the atomic structure is needed to obtain a full understanding of their intriguing physical and chemical properties. Here we employed aberration-corrected scanning transmission electron microscopy (ac-STEM), combined with multislice simulations, to make a round-robin investigation of the atomic structure of chemically synthesised clusters with nominal composition Au 144 (SCH 2 CH 2 Ph) 60 provided by two different research groups. The MP Au clusters were "weighed" by the atom counting method, based on their integrated intensities in the high angle annular dark field (HAADF) regime and calibrated exponent of the Z dependence. For atomic structure analysis, we compared experimental images of hundreds of clusters, with atomic resolution, against a variety of structural models. Across the size range 123-151 atoms, only 3% of clusters matched the theoretically predicted Au 144 (SR) 60 structure, while a large proportion of the clusters were amorphous (i.e. did not match any model structure). However, a distinct ring-dot feature, characteristic of local icosahedral symmetry, was observed in about 20% of the clusters. Copyright © 2017. Published by Elsevier B.V.

Carbon nitride supported Fe2 cluster catalysts with superior performance for alkene epoxidation.

PubMed

Tian, Shubo; Fu, Qiang; Chen, Wenxing; Feng, Quanchen; Chen, Zheng; Zhang, Jian; Cheong, Weng-Chon; Yu, Rong; Gu, Lin; Dong, Juncai; Luo, Jun; Chen, Chen; Peng, Qing; Draxl, Claudia; Wang, Dingsheng; Li, Yadong

2018-06-15

Sub-nano metal clusters often exhibit unique and unexpected properties, which make them particularly attractive as catalysts. Herein, we report a "precursor-preselected" wet-chemistry strategy to synthesize highly dispersed Fe 2 clusters that are supported on mesoporous carbon nitride (mpg-C 3 N 4 ). The obtained Fe 2 /mpg-C 3 N 4 sample exhibits superior catalytic performance for the epoxidation of trans-stilbene to trans-stilbene oxide, showing outstanding selectivity of 93% at high conversion of 91%. Molecular oxygen is the only oxidant and no aldehyde is used as co-reagent. Under the same condition, by contrast, iron porphyrin, single-atom Fe, and small Fe nanoparticles (ca. 3 nm) are nearly reactively inert. First-principles calculations reveal that the unique reactivity of the Fe 2 clusters originates from the formation of active oxygen species. The general applicability of the synthesis approach is further demonstrated by producing other diatomic clusters like Pd 2 and Ir 2 , which lays the foundation for discovering diatomic cluster catalysts.

Calculation of the structure of carbon clusters based on fullerene-like C24 and C48 molecules

NASA Astrophysics Data System (ADS)

Krylova, K. A.; Baimova, Yu. A.; Dmitriev, S. V.; Mulyukov, R. R.

2016-02-01

Equilibrium structures obtained by linking with valence bonds the carbon carcasses of two fullerene-like molecules have been studied by molecular dynamics simulation. In free fullerene, carbon atoms form sp 2 hybridized bonds, but at places of links between fullerenes, sp 3 hybridized bonds are formed, which determines the changes in the properties of such structures. In the literature, the topology of diamond-like phases is described, but equilibrium clusters based on fullerene-like molecules are underexplored. The right angles between the C-C bonds are energetically unfavorable, and the reduction in the energy of clusters in the process of relaxation is connected with the optimization of valence angles, which leads to a reduction in the symmetry of clusters and, in a number of cases, even to disruption of some valence bonds. It is shown that different fashions of linking two fullerenes result in the formation of clusters with different structures and energies. Different initial conditions can lead to different configurations of clusters with the same topology. Among the analyzed clusters, a structure with the minimum potential energy per atom was found. The results of this work contribute to the study of the real structure of carbon clusters.

Structural features of small benzene clusters (C6H6)n (n ≤ 30) as investigated with the all-atom OPLS potential.

PubMed

Takeuchi, Hiroshi

2012-10-18

The structures of the simplest aromatic clusters, benzene clusters (C(6)H(6))(n), are not well elucidated. In the present study, benzene clusters (C(6)H(6))(n) (n ≤ 30) were investigated with the all-atom optimized parameters for liquid simulation (OPLS) potential. The global minima and low-lying minima of the benzene clusters were searched with the heuristic method combined with geometrical perturbations. The structural features and growth sequence of the clusters were examined by carrying out local structure analyses and structural similarity evaluation with rotational constants. Because of the anisotropic interaction between the benzene molecules, the local structures consisting of 13 molecules are considerably deviated from regular icosahedron, and the geometries of some of the clusters are inconsistent with the shapes constructed by the interior molecules. The distribution of the angle between the lines normal to two neighboring benzene rings is anisotropic in the clusters, whereas that in the liquid benzene is nearly isotropic. The geometries and energies of the low-lying configurations and the saddle points between them suggest that most of the configurations previously detected in supersonic expansions take different orientations for one to four neighboring molecules.

The Effects of Environmental Characteristics on the Structure of Hospital Clusters.

ERIC Educational Resources Information Center

Fennell, Mary L.

1980-01-01

The population ecology view that variation in sets or clusters of organizations should be isomorphic with variation in cluster environment was used to explain structural variation among hospital clusters. Cluster differentiation seems to be casually affected by range of services, average hospital size, and the periodic closing of hospitals.…

Multiple co-clustering based on nonparametric mixture models with heterogeneous marginal distributions

PubMed Central

Yoshimoto, Junichiro; Shimizu, Yu; Okada, Go; Takamura, Masahiro; Okamoto, Yasumasa; Yamawaki, Shigeto; Doya, Kenji

2017-01-01

We propose a novel method for multiple clustering, which is useful for analysis of high-dimensional data containing heterogeneous types of features. Our method is based on nonparametric Bayesian mixture models in which features are automatically partitioned (into views) for each clustering solution. This feature partition works as feature selection for a particular clustering solution, which screens out irrelevant features. To make our method applicable to high-dimensional data, a co-clustering structure is newly introduced for each view. Further, the outstanding novelty of our method is that we simultaneously model different distribution families, such as Gaussian, Poisson, and multinomial distributions in each cluster block, which widens areas of application to real data. We apply the proposed method to synthetic and real data, and show that our method outperforms other multiple clustering methods both in recovering true cluster structures and in computation time. Finally, we apply our method to a depression dataset with no true cluster structure available, from which useful inferences are drawn about possible clustering structures of the data. PMID:29049392

Statistical Significance for Hierarchical Clustering

PubMed Central

Kimes, Patrick K.; Liu, Yufeng; Hayes, D. Neil; Marron, J. S.

2017-01-01

Summary Cluster analysis has proved to be an invaluable tool for the exploratory and unsupervised analysis of high dimensional datasets. Among methods for clustering, hierarchical approaches have enjoyed substantial popularity in genomics and other fields for their ability to simultaneously uncover multiple layers of clustering structure. A critical and challenging question in cluster analysis is whether the identified clusters represent important underlying structure or are artifacts of natural sampling variation. Few approaches have been proposed for addressing this problem in the context of hierarchical clustering, for which the problem is further complicated by the natural tree structure of the partition, and the multiplicity of tests required to parse the layers of nested clusters. In this paper, we propose a Monte Carlo based approach for testing statistical significance in hierarchical clustering which addresses these issues. The approach is implemented as a sequential testing procedure guaranteeing control of the family-wise error rate. Theoretical justification is provided for our approach, and its power to detect true clustering structure is illustrated through several simulation studies and applications to two cancer gene expression datasets. PMID:28099990

Fe2+ chelator proferrorosamine A: a gene cluster of Erwinia rhapontici P45 involved in its synthesis and its impact on growth of Erwinia amylovora CFBP1430.

PubMed

Born, Yannick; Remus-Emsermann, Mitja N P; Bieri, Marco; Kamber, Tim; Piel, Jörn; Pelludat, Cosima

2016-02-01

Proferrorosamine A (proFRA) is an iron (Fe2+) chelator produced by the opportunistic plant pathogen Erwinia rhapontici P45. To identify genes involved in proFRA synthesis, transposon mutagenesis was performed. The identified 9.3 kb gene cluster, comprising seven genes, designated rosA-rosG, encodes proteins that are involved in proFRA synthesis. Based on gene homologies, a biosynthetic pathway model for proFRA is proposed. To obtain a better understanding of the effect of proFRA on non-proFRA producing bacteria, E. rhapontici P45 was co-cultured with Erwinia amylovora CFBP1430, a fire-blight-causing plant pathogen. E. rhapontici P45, but not corresponding proFRA-negative mutants, led to a pink coloration of E. amylovora CFBP1430 colonies on King's B agar, indicating accumulation of the proFRA-iron complex ferrorosamine, and growth inhibition in vitro. By saturating proFRA-containing extracts with Fe2+, the inhibitory effect was neutralized, suggesting that the iron-chelating capability of proFRA is responsible for the growth inhibition of E. amylovora CFBP1430.

Genetics and evolution of Yersinia pseudotuberculosis O-specific polysaccharides: a novel pattern of O-antigen diversity

PubMed Central

Kenyon, Johanna J.; Cunneen, Monica M.

2017-01-01

Abstract O-antigen polysaccharide is a major immunogenic feature of the lipopolysaccharide of Gram-negative bacteria, and most species produce a large variety of forms that differ substantially from one another. There are 18 known O-antigen forms in the Yersinia pseudotuberculosis complex, which are typical in being composed of multiple copies of a short oligosaccharide called an O unit. The O-antigen gene clusters are located between the hemH and gsk genes, and are atypical as 15 of them are closely related, each having one of five downstream gene modules for alternative main-chain synthesis, and one of seven upstream modules for alternative side-branch sugar synthesis. As a result, many of the genes are in more than one gene cluster. The gene order in each module is such that, in general, the earlier a gene product functions in O-unit synthesis, the closer the gene is to the 5΄ end for side-branch modules or the 3΄ end for main-chain modules. We propose a model whereby natural selection could generate the observed pattern in gene order, a pattern that has also been observed in other species. PMID:28364730

Chaperone-Usher Pili Loci of Colonization Factor-Negative Human Enterotoxigenic Escherichia coli

PubMed Central

Del Canto, Felipe; O'Ryan, Miguel; Pardo, Mirka; Torres, Alexia; Gutiérrez, Daniela; Cádiz, Leandro; Valdés, Raul; Mansilla, Aquiles; Martínez, Rodrigo; Hernández, Daniela; Caro, Benjamin; Levine, Myron M.; Rasko, David A.; Hill, Christopher M.; Pop, Mihai; Stine, O. Colin; Vidal, Roberto

2017-01-01

Enterotoxigenic Escherichia coli (ETEC) is one of the most common causes of diarrhea worldwide. Among the 25 different ETEC adhesins, 22 are known as “colonization factors” (CFs), of which 17 are assembled by the chaperone-usher (CU) mechanism. Currently, there is no preventive therapy against ETEC, and CFs have been proposed as components for vaccine development. However, studies of diarrhea-causing ETEC strains worldwide indicate that between 15 and 50% of these are negative for known CFs, hindering the selection of the most widespread structures and suggesting that unknown adhesins remain to be identified. Here, we report the result of a comprehensive analysis of 35 draft genomes of ETEC strains which do not carry known adhesin genes; our goal was to find new CU pili loci. The phylogenetic profiles and serogroups of these strains were highly diverse, a majority of which produced only the heat-labile toxin. We identified 10 pili loci belonging to CU families β (1 locus), γ2 (7 loci), κ (1 locus), and π (1 locus), all of which contained the required number of open reading frames (ORFs) to encode functional structures. Three loci were variants of previously-known clusters, three had been only-partially described, and four are novel loci. Intra-loci genetic variability identified would allow the synthesis of up to 14 different structures. Clusters of putative γ2-CU pili were most common (23 strains), followed by putative β-CU pili (12 strains), which have not yet been fully characterized. Overall, our findings significantly increase the number of ETEC adhesion genes associated with human infections. PMID:28111618

Polymorphism in Alkali Metal Uranyl Nitrates: Synthesis and Crystal Structure of γ-K(UO2)(NO3)3

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jouffret, Laurent J.; Krivovichev, Sergey V.; Burns, Peter C.

2011-07-20

Single crystals of γ-K(UO2)(NO3)3 were prepared from aqueous solutions by evaporation. The crystal structure [orthorhombic, Pbca (61), a = 9.2559(3) Å, b = 12.1753(3) Å, c = 15.8076(5) Å, V = 1781.41(9) Å3, Z = 8] was determined by direct methods and refined to R1 = 0.0267 on the basis of 3657 unique observed reflections. The structure is composed of isolated anionic uranyl trinitrate units, [(UO2)(NO3)3]–, that are linked through eleven-coordinated K+ cations. Both known polymorphs of K(UO2)(NO3)3 (α- and γ-phases) can be considered as based upon sheets of isolated complex [(UO2)(NO3)3]– ions separated by K+ cations. The existence ofmore » polymorphism in the two K[UO2(NO3)3] polymorphs is due to the different packing modes of uranyl trinitrate clusters that adopt the same two-dimensional but different three-dimensional arrangements.« less

Triosmium Clusters on a Support: Determination of Structure by X-Ray Absorption Spectroscopy and High-Resolution Microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shareghe, Mehraeen; Chi, Miaofang; Browning, Nigel D.

2011-01-01

The structures of small, robust metal clusters on a solid support were determined by a combination of spectroscopic and microscopic methods: extended X-ray absorption fine structure (EXAFS) spectroscopy, scanning transmission electron microscopy (STEM), and aberration-corrected STEM. The samples were synthesized from [Os{sub 3}(CO){sub 12}] on MgO powder to provide supported clusters intended to be triosmium. The results demonstrate that the supported clusters are robust in the absence of oxidants. Conventional high-angle annular dark-field (HAADF) STEM images demonstrate a high degree of uniformity of the clusters, with root-mean-square (rms) radii of 2.03 {+-} 0.06 {angstrom}. The EXAFS OsOs coordination number ofmore » 2.1 {+-} 0.4 confirms the presence of triosmium clusters on average and correspondingly determines an average rms cluster radius of 2.02 {+-} 0.04 {angstrom}. The high-resolution STEM images show the individual Os atoms in the clusters, confirming the triangular structures of their frames and determining OsOs distances of 2.80 {+-} 0.14 {angstrom}, matching the EXAFS value of 2.89 {+-} 0.06 {angstrom}. IR and EXAFS spectra demonstrate the presence of CO ligands on the clusters. This set of techniques is recommended as optimal for detailed and reliable structural characterization of supported clusters.« less

Supported Dendrimer-Encapsulated Metal Clusters: Toward Heterogenizing Homogeneous Catalysts

DOE PAGES

Ye, Rong; Zhukhovitskiy, Aleksandr V.; Deraedt, Christophe V.; ...

2017-07-13

Recyclable catalysts, especially those that display selective reactivity, are vital for the development of sustainable chemical processes. Among available catalyst platforms, heterogeneous catalysts are particularly well-disposed toward separation from the reaction mixture via filtration methods, which renders them readily recyclable. Furthermore, heterogeneous catalysts offer numerous handles—some without homogeneous analogues—for performance and selectivity optimization. These handles include nanoparticle size, pore profile of porous supports, surface ligands and interface with oxide supports, and flow rate through a solid catalyst bed. Despite these available handles, however, conventional heterogeneous catalysts are themselves often structurally heterogeneous compared to homogeneous catalysts, which complicates efforts to optimizemore » and expand the scope of their reactivity and selectivity. Ongoing efforts in our laboratories are aimed to address the above challenge by heterogenizing homogeneous catalysts, which can be defined as the modification of homogeneous catalysts to render them in a separable (solid) phase from the starting materials and products. Specifically, we grow the small nanoclusters in dendrimers, a class of uniform polymers with the connectivity of fractal trees and generally radial symmetry. Thanks to their dense multivalency, shape persistence, and structural uniformity, dendrimers have proven to be versatile scaffolds for the synthesis and stabilization of small nanoclusters. Then these dendrimer-encapsulated metal clusters (DEMCs) are adsorbed onto mesoporous silica. Through this method, we have achieved selective transformations that had been challenging to accomplish in a heterogeneous setting, e.g., π-bond activation and aldol reactions. Extensive investigation into the catalytic systems under reaction conditions allowed us to correlate the structural features (e.g., oxidation states) of the catalysts and their activity. Moreover, we have demonstrated that supported DEMCs are also excellent catalysts for typical heterogeneous reactions, including hydrogenation and alkane isomerization. Critically, these investigations also confirmed that the supported DEMCs are heterogeneous and stable against leaching. Catalysts optimization is achieved through the modulation of various parameters. The clusters are oxidized (e.g., with PhICl 2) or reduced (e.g., with H 2) in situ. Changing the dendrimer properties (e.g., generation, terminal functional groups) is analogous to ligand modification in homogeneous catalysts, which affect both catalytic activity and selectivity. Similarly, pore size of the support is another factor in determining product distribution. In a flow reactor, the flow rate is adjusted to control the residence time of the starting material and intermediates, and thus the final product selectivity. Our approach to heterogeneous catalysis affords various advantages: (1) the catalyst system can tap into the reactivity typical to homogeneous catalysts, which conventional heterogeneous catalysts could not achieve; (2) unlike most homogeneous catalysts with comparable performance, the heterogenized homogeneous catalysts can be recycled; (3) improved activity or selectivity compared to conventional homogeneous catalysts is possible because of uniquely heterogeneous parameters for optimization. Here in this Account, we will briefly introduce metal clusters and describe the synthesis and characterizations of supported DEMCs. We will present the catalysis studies of supported DEMCs in both the batch and flow modes. Lastly, we will summarize the current state of heterogenizing homogeneous catalysis and provide future directions for this area of research.« less

Fluorescence detection of a protein-bound 2Fe2S cluster.

PubMed

Hoff, Kevin G; Goodlitt, Rochelle; Li, Rui; Smolke, Christina D; Silberg, Jonathan J

2009-03-02

A fluorescent biosensor is described for 2Fe2S clusters that is composed of green fluorescent protein (GFP) fused to glutaredoxin 2 (Grx2), as illustrated here. 2Fe2S detection is based on the reduction of GFP fluorescence upon the 2Fe2S-induced dimerization of GFP-Grx2. This assay is sufficiently sensitive to detect submicromolar changes in 2Fe2S levels, thus making it suitable for high-throughput measurements of metallocluster degradation and synthesis reactions.

Biosynthesis and Total Synthesis of Pyrronazol B: a Secondary Metabolite from Nannocystis pusilla.

PubMed

Witte, Swjatoslaw N R; Hug, Joachim J; Géraldy, Magalie N E; Müller, Rolf; Kalesse, Markus

2017-11-13

The first stereoselective total synthesis of the natural product pyrronazol B, which contains a chlorinated pyrrole-oxazole-pyrone framework, has been achieved. Genome sequencing of the myxobacterial producer strain Nannocystis pusilla Ari7 led to the identification of the putative biosynthetic gene cluster. The proposed biosynthetic pathway was supported by feeding experiments with stable isotopes of three biosynthetic building blocks, namely l-proline, l-serine, and l-methionine. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structural properties and glass transition in Aln clusters

NASA Astrophysics Data System (ADS)

Sun, D. Y.; Gong, X. G.

1998-02-01

We have studied the structural and dynamical properties of several Aln clusters by the molecular-dynamics method combined with simulated annealing. The well-fitted glue potential is used to describe the interatomic interaction. The obtained atomic structures for n=13, 55, and 147 are in agreement with results from ab initio calculations. Our results have demonstrated that the disordered cluster Al43 can be considered as a glass cluster. The obtained thermal properties of glass cluster Al43 are clearly different from the results for high-symmetry clusters, its melting behavior has properties similar to those of a glass solid. The present studies also show that the surface melting behavior does not exist in the studied Aln clusters.

Structural and electronic properties Te62+ and Te82+: A DFT study

NASA Astrophysics Data System (ADS)

Sharma, Tamanna; Tamboli, Rohit; Kanhere, D. G.; Sharma, Raman

2018-05-01

Structural and electronic properties of Tellurium cluster (Ten) and their cations (Ten2+) (n = 6, 8) have been studied theoretically using VASP within generalized gradient approximation. Ground state geometries and higher energy isomers of these clusters have been examined on the basis of total free energy calculations. Lowest energy isomers of neutral clusters are ring like structures whereas the lowest energy isomers of cations are polyhedral cages. HOMO-LUMO gap in cationic clusters is small compared to its neutral clusters. Removal of two electrons from the neutral cluster raises the free energy. Analysis of free energy, HOMO-LUMO gap and density of states (DOS) show that neutral cluster are more stable than their cations.

Clustering Aspects in Nuclear Structure and Collisions

NASA Astrophysics Data System (ADS)

Horiuchi, H.

Four topics on nuclear clustering are discussed. The first subject is about the cluster formation in dilute matter which we think is now observed in heavy ion collisions at hundreds MeV/nucleon. The second subject is about our new proposal of the existense of alpha condensed states in light nuclei. Two other subjects are both about the clustering in neutron-rich nuclei. One is the cluster structures in neutron-rich Be and B isotopes. In these isotopes, the clustering prevails as fundamental characters of nuclear structure. The other is the report of our recent study about the possible relation of the clustering with the breaking of the neutron magic number N=20 in 32Mg and 30Ne.

Structures of small Pd Pt bimetallic clusters by Monte Carlo simulation

NASA Astrophysics Data System (ADS)

Cheng, Daojian; Huang, Shiping; Wang, Wenchuan

2006-11-01

Segregation phenomena of Pd-Pt bimetallic clusters with icosahedral and decahedral structures are investigated by using Monte Carlo method based on the second-moment approximation of the tight-binding (TB-SMA) potentials. The simulation results indicate that the Pd atoms generally lie on the surface of the smaller clusters. The three-shell onion-like structures are observed in 55-atom Pd-Pt bimetallic clusters, in which a single Pd atom is located in the center, and the Pt atoms are in the middle shell, while the Pd atoms are enriched on the surface. With the increase of Pd mole fraction in 55-atom Pd-Pt bimetallic clusters, the Pd atoms occupy the vertices of clusters first, then edge and center sites, and finally the interior shell. It is noticed that some decahedral structures can be transformed into the icosahedron-like structure at 300 and 500 K. Comparisons are made with previous experiments and theoretical studies of Pd-Pt bimetallic clusters.

Medium resolution spectroscopy and chemical composition of Galactic globular clusters

NASA Astrophysics Data System (ADS)

Khamidullina, D. A.; Sharina, M. E.; Shimansky, V. V.; Davoust, E.

We used integrated-light medium-resolution spectra of six Galactic globular clusters and model stellar atmospheres to carry out population synthesis and to derive chemical composition and age of the clusters. We used medium-resolution spectra of globular clusters published by Schiavon et al. (2005), as well as our long-slit observations with the 1.93 m telescope of the Haute Provence Observatory. The observed spectra were fitted to the theoretical ones interactively. As an initial approach, we used masses, radii and log g of stars in the clusters corresponding to the best fitting isochrones in the observed color-magnitude diagrams. The computed synthetic blanketed spectra of stars were summed according to the Chabrier mass function. To improve the determination of age and helium content, the shape and depth of the Balmer absorption lines was analysed. The abundances of Mg, Ca, C and several other elements were derived. A reasonable agreement with the literature data both in chemical composition and in age of the clusters is found. Our method might be useful for the development of stellar population models and for a better understanding of extragalactic star clusters.

Neutral and charged gallium clusters: structures, physical properties and implications for the melting features

NASA Astrophysics Data System (ADS)

Núñez, Sara; López, José M.; Aguado, Andrés

2012-09-01

We report the putative Global Minimum (GM) structures and electronic properties of GaN+, GaN and GaN- clusters with N = 13-37 atoms, obtained from first-principles density functional theory structural optimizations. The calculations include spin polarization and employ an exchange-correlation functional which accounts for van der Waals dispersion interactions (vdW-DFT). We find a wide diversity of structural motifs within the located GM, including decahedral, polyicosahedral, polytetrahedral and layered structures. The GM structures are also extremely sensitive to the number of electrons in the cluster, so that the structures of neutral and charged clusters differ for most sizes. The main magic numbers (clusters with an enhanced stability) are identified and interpreted in terms of electronic and geometric shell closings. The theoretical results are consistent with experimental abundance mass spectra of GaN+ and with photoelectron spectra of GaN-. The size dependence of the latent heats of melting, the shape of the heat capacity peaks, and the temperature dependence of the collision cross-sections, all measured for GaN+ clusters, are properly interpreted in terms of the calculated cohesive energies, spectra of configurational excitations, and cluster shapes, respectively. The transition from ``non-melter'' to ``magic-melter'' behaviour, experimentally observed between Ga30+ and Ga31+, is traced back to a strong geometry change. Finally, the higher-than-bulk melting temperatures of gallium clusters are correlated with a more typically metallic behaviour of the clusters as compared to the bulk, contrary to previous theoretical claims.We report the putative Global Minimum (GM) structures and electronic properties of GaN+, GaN and GaN- clusters with N = 13-37 atoms, obtained from first-principles density functional theory structural optimizations. The calculations include spin polarization and employ an exchange-correlation functional which accounts for van der Waals dispersion interactions (vdW-DFT). We find a wide diversity of structural motifs within the located GM, including decahedral, polyicosahedral, polytetrahedral and layered structures. The GM structures are also extremely sensitive to the number of electrons in the cluster, so that the structures of neutral and charged clusters differ for most sizes. The main magic numbers (clusters with an enhanced stability) are identified and interpreted in terms of electronic and geometric shell closings. The theoretical results are consistent with experimental abundance mass spectra of GaN+ and with photoelectron spectra of GaN-. The size dependence of the latent heats of melting, the shape of the heat capacity peaks, and the temperature dependence of the collision cross-sections, all measured for GaN+ clusters, are properly interpreted in terms of the calculated cohesive energies, spectra of configurational excitations, and cluster shapes, respectively. The transition from ``non-melter'' to ``magic-melter'' behaviour, experimentally observed between Ga30+ and Ga31+, is traced back to a strong geometry change. Finally, the higher-than-bulk melting temperatures of gallium clusters are correlated with a more typically metallic behaviour of the clusters as compared to the bulk, contrary to previous theoretical claims. Electronic supplementary information (ESI) available: Atomic coordinates (in xyz format and Å units) and point group symmetries for the global minimum structures reported in this paper. See DOI: 10.1039/c2nr31222k

Regulation of the Synthesis of the Angucyclinone Antibiotic Alpomycin in Streptomyces ambofaciens by the Autoregulator Receptor AlpZ and Its Specific Ligand▿

PubMed Central

Bunet, Robert; Mendes, Marta V.; Rouhier, Nicolas; Pang, Xiuhua; Hotel, Laurence; Leblond, Pierre; Aigle, Bertrand

2008-01-01

Streptomyces ambofaciens produces an orange pigment and the antibiotic alpomycin, both of which are products of a type II polyketide synthase gene cluster identified in each of the terminal inverted repeats of the linear chromosome. Five regulatory genes encoding Streptomyces antibiotic regulatory proteins (alpV, previously shown to be an essential activator gene; alpT; and alpU) and TetR family receptors (alpZ and alpW) were detected in this cluster. Here, we demonstrate that AlpZ, which shows high similarity to γ-butyrolactone receptors, is at the top of a pathway-specific regulatory hierarchy that prevents synthesis of the alp polyketide products. Deletion of the two copies of alpZ resulted in the precocious production of both alpomycin and the orange pigment, suggesting a repressor role for AlpZ. Consistent with this, expression of the five alp-located regulatory genes and of two representative biosynthetic structural genes (alpA and alpR) was induced earlier in the alpZ deletion strain. Furthermore, recombinant AlpZ was shown to bind to specific DNA sequences within the promoter regions of alpZ, alpV, and alpXW, suggesting direct transcriptional control of these genes by AlpZ. Analysis of solvent extracts of S. ambofaciens cultures identified the existence of a factor which induces precocious production of alpomycin and pigment in the wild-type strain and which can disrupt the binding of AlpZ to its DNA targets. This activity is reminiscent of γ-butyrolactone-type molecules. However, the AlpZ-interacting molecule(s) was shown to be resistant to an alkali treatment capable of inactivating γ-butyrolactones, suggesting that the AlpZ ligand(s) does not possess a lactone functional group. PMID:18296523

Local ordering and magnetism in Ga{sub 0.9}Fe{sub 3.1}N

DOE Office of Scientific and Technical Information (OSTI.GOV)

Burghaus, Jens; Sougrati, Moulay T., E-mail: moulay-tahar.sougrati@univ-montp2.fr; Moechel, Anne

Prior investigations of the ternary nitride series Ga{sub 1-x}Fe{sub 3+x}N (0{<=}x{<=}1) have indicated a transition from ferromagnetic {gamma}'-Fe{sub 4}N to antiferromagnetic 'GaFe{sub 3}N'. The ternary nitride 'GaFe{sub 3}N' has been magnetically and spectroscopically reinvestigated in order to explore the weakening of the ferromagnetic interactions through the gradual incorporation of gallium into {gamma}'-Fe{sub 4}N. A hysteretic loop at RT reveals the presence of a minority phase of only 0.1-0.2 at%, in accord with the sound two-step synthesis. The composition of the gallium-richest phase 'GaFe{sub 3}N' was clarified by Prompt Gamma-ray Activation Analysis and leads to the berthollide formula Ga{sub 0.91(1)}Fe{sub 3.09(10)}N{submore » 1.05(7)}. Magnetic measurements indicate a transition around 8 K, further supported by Moessbauer spectral data. The weakening of the ferromagnetic coupling through an increasing gallium concentration is explained by a simple Stoner argument. In Ga{sub 0.9}Fe{sub 3.1}N, the presence of iron on the gallium site affects the magnetism by the formation of 13-atom iron clusters. - Graphical Abstract: The crystal structure of GaFe{sub 3}N with green nitrogen atoms in the very center, red iron atoms at the face centers, and gray gallium atoms at the corner positions. Highlights: > Almost phase-pure synthesis of Ga{sub 0.9}Fe{sub 3.1}N. > Prompt gamma-ray activation analysis yields precise composition. > Magnetic ordering of the facial Fe atoms at the lowest temperatures. > Moessbauer spectroscopy suggests percolation or RKKY-type interaction. > Fe{sub 13} clusters due to berthollide character.« less

Two-Step Nucleation and Growth of InP Quantum Dots via Magic-Sized Cluster Intermediates

DOE PAGES

Gary, Dylan C.; Terban, Maxwell W.; Billinge, Simon J. L.; ...

2015-01-30

We report on the role of magic-sized clusters (MSCs) as key intermediates in the synthesis of indium phosphide quantum dots (InP QDs) from molecular precursors. These observations suggest that previous efforts to control nucleation and growth by tuning precursor reactivity have been undermined by formation of these kinetically persistent MSCs prior to QD formation. The thermal stability of InP MSCs is influenced by the presence of exogenous bases as well as choice of the anionic ligand set. Addition of a primary amine, a common additive in previous InP QD syntheses, to carboxylate terminated MSCs was found to bypass the formationmore » of MSCs, allowing for homogeneous growth of InP QDs through a continuum of isolable sizes. Substitution of the carboxylate ligand set for a phosphonate ligand set increased the thermal stability of one particular InP MSC to 400°C. The structure and optical properties of the MSCs with both carboxylate and phosphonate ligand sets were studied by UV-Vis absorption spectroscopy, powder XRD analysis, and solution ³¹P{¹H} and ¹H NMR spectroscopy. Finally, the carboxylate terminated MSCs were identified as effective single source precursors (SSPs) for the synthesis of high quality InP QDs. Employing InP MSCs as SSPs for QDs effectively decouples the formation of MSCs from the subsequent second nucleation event and growth of InP QDs. The concentration dependence of this SSP reaction, as well as the shape uniformity of particles observed by TEM suggests that the stepwise growth from MSCs directly to QDs proceeds via a second nucleation event rather than an aggregative growth mechanism.« less

Regulation of the synthesis of the angucyclinone antibiotic alpomycin in Streptomyces ambofaciens by the autoregulator receptor AlpZ and its specific ligand.

PubMed

Bunet, Robert; Mendes, Marta V; Rouhier, Nicolas; Pang, Xiuhua; Hotel, Laurence; Leblond, Pierre; Aigle, Bertrand

2008-05-01

Streptomyces ambofaciens produces an orange pigment and the antibiotic alpomycin, both of which are products of a type II polyketide synthase gene cluster identified in each of the terminal inverted repeats of the linear chromosome. Five regulatory genes encoding Streptomyces antibiotic regulatory proteins (alpV, previously shown to be an essential activator gene; alpT; and alpU) and TetR family receptors (alpZ and alpW) were detected in this cluster. Here, we demonstrate that AlpZ, which shows high similarity to gamma-butyrolactone receptors, is at the top of a pathway-specific regulatory hierarchy that prevents synthesis of the alp polyketide products. Deletion of the two copies of alpZ resulted in the precocious production of both alpomycin and the orange pigment, suggesting a repressor role for AlpZ. Consistent with this, expression of the five alp-located regulatory genes and of two representative biosynthetic structural genes (alpA and alpR) was induced earlier in the alpZ deletion strain. Furthermore, recombinant AlpZ was shown to bind to specific DNA sequences within the promoter regions of alpZ, alpV, and alpXW, suggesting direct transcriptional control of these genes by AlpZ. Analysis of solvent extracts of S. ambofaciens cultures identified the existence of a factor which induces precocious production of alpomycin and pigment in the wild-type strain and which can disrupt the binding of AlpZ to its DNA targets. This activity is reminiscent of gamma-butyrolactone-type molecules. However, the AlpZ-interacting molecule(s) was shown to be resistant to an alkali treatment capable of inactivating gamma-butyrolactones, suggesting that the AlpZ ligand(s) does not possess a lactone functional group.

The Cer-cqu gene cluster determines three key players in a β-diketone synthase polyketide pathway synthesizing aliphatics in epicuticular waxes.

PubMed

Schneider, Lizette M; Adamski, Nikolai M; Christensen, Caspar Elo; Stuart, David B; Vautrin, Sonia; Hansson, Mats; Uauy, Cristobal; von Wettstein-Knowles, Penny

2016-03-09

Aliphatic compounds on plant surfaces, called epicuticular waxes, are the first line of defense against pathogens and pests, contribute to reducing water loss and determine other important phenotypes. Aliphatics can form crystals affecting light refraction, resulting in a color change and allowing identification of mutants in their synthesis or transport. The present study discloses three such Eceriferum (cer) genes in barley - Cer-c, Cer-q and Cer-u - known to be tightly linked and functioning in a biochemical pathway forming dominating amounts of β-diketone and hydroxy-β-diketones plus some esterified alkan-2-ols. These aliphatics are present in many Triticeae as well as dicotyledons such as Eucalyptus and Dianthus. Recently developed genomic resources and mapping populations in barley defined these genes to a small region on chromosome arm 2HS. Exploiting Cer-c and -u potential functions pinpointed five candidates, of which three were missing in apparent cer-cqu triple mutants. Sequencing more than 50 independent mutants for each gene confirmed their identification. Cer-c is a chalcone synthase-like polyketide synthase, designated diketone synthase (DKS), Cer-q is a lipase/carboxyl transferase and Cer-u is a P450 enzyme. All were highly expressed in pertinent leaf sheath tissue of wild type. A physical map revealed the order Cer-c, Cer-u, Cer-q with the flanking genes 101kb apart, confirming they are a gene cluster, Cer-cqu. Homology-based modeling suggests that many of the mutant alleles affect overall protein structure or specific active site residues. The rich diversity of identified mutations will facilitate future studies of three key enzymes involved in synthesis of plant apoplast waxes. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.

The Cer-cqu gene cluster determines three key players in a β-diketone synthase polyketide pathway synthesizing aliphatics in epicuticular waxes

PubMed Central

Schneider, Lizette M; Adamski, Nikolai M; Christensen, Caspar Elo; Stuart, David B; Vautrin, Sonia; Hansson, Mats; Uauy, Cristobal; von Wettstein-Knowles, Penny

2016-01-01

Aliphatic compounds on plant surfaces, called epicuticular waxes, are the first line of defense against pathogens and pests, contribute to reducing water loss and determine other important phenotypes. Aliphatics can form crystals affecting light refraction, resulting in a color change and allowing identification of mutants in their synthesis or transport. The present study discloses three such Eceriferum (cer) genes in barley – Cer-c, Cer-q and Cer-u – known to be tightly linked and functioning in a biochemical pathway forming dominating amounts of β-diketone and hydroxy-β-diketones plus some esterified alkan-2-ols. These aliphatics are present in many Triticeae as well as dicotyledons such as Eucalyptus and Dianthus. Recently developed genomic resources and mapping populations in barley defined these genes to a small region on chromosome arm 2HS. Exploiting Cer-c and -u potential functions pinpointed five candidates, of which three were missing in apparent cer-cqu triple mutants. Sequencing more than 50 independent mutants for each gene confirmed their identification. Cer-c is a chalcone synthase-like polyketide synthase, designated diketone synthase (DKS), Cer-q is a lipase/carboxyl transferase and Cer-u is a P450 enzyme. All were highly expressed in pertinent leaf sheath tissue of wild type. A physical map revealed the order Cer-c, Cer-u, Cer-q with the flanking genes 101kb apart, confirming they are a gene cluster, Cer-cqu. Homology-based modeling suggests that many of the mutant alleles affect overall protein structure or specific active site residues. The rich diversity of identified mutations will facilitate future studies of three key enzymes involved in synthesis of plant apoplast waxes. PMID:26962211

A Geometric and Electrostatic Study of the [4Fe-4S] Cluster of Adenosine-5´-Phosphosulfate Reductase from Broken Symmetry Density Functional Calculations and Extended X-ray Absorption Fine Structure Spectroscopy

PubMed Central

Bhave, Devayani P.; Han, Wen-Ge; Pazicni, Samuel; Penner-Hahn, James E.; Carroll, Kate S.; Noodleman, Louis

2011-01-01

Adenosine-5’-phosphosulfate reductase (APSR) is an iron-sulfur protein that catalyses the reduction of adenosine-5’-phosphosulfate (APS) to sulfite. APSR coordinates to a [4Fe-4S] cluster via a conserved CC-X~80-CXXC motif and the cluster is essential for catalysis. Despite extensive functional, structural and spectroscopic studies, the exact role of the iron-sulfur cluster in APS reduction remains unknown. To gain an understanding into the role of the cluster, density functional theory (DFT) analysis and extended X-ray fine structure spectroscopy (EXAFS) have been performed to reveal insights into the coordination, geometry and electrostatics of the [4Fe-4S] cluster. XANES data confirms that the cluster is in the [4Fe-4S]2+ state in both native and substrate-bound APSR while EXAFS data recorded at ~0.1 Å resolution indicates that there is no significant change in the structure of the [4Fe-4S] cluster between the native and substrate-bound forms of the protein. On the other hand, DFT calculations provide an insight into the subtle differences between the geometry of the cluster in the native and APS-bound forms of APSR. A comparison between models with and without the tandem cysteine pair coordination of the cluster suggests a role for the unique coordination in facilitating a compact geometric structure and ‘fine-tuning’ the electronic structure to prevent reduction of the cluster. Further, calculations using models in which residue Lys144 is mutated to Ala confirm the finding that Lys144 serves as a crucial link in the interactions involving the [4Fe-4S] cluster and APS. PMID:21678934

Clusternomics: Integrative context-dependent clustering for heterogeneous datasets

PubMed Central

Wernisch, Lorenz

2017-01-01

Integrative clustering is used to identify groups of samples by jointly analysing multiple datasets describing the same set of biological samples, such as gene expression, copy number, methylation etc. Most existing algorithms for integrative clustering assume that there is a shared consistent set of clusters across all datasets, and most of the data samples follow this structure. However in practice, the structure across heterogeneous datasets can be more varied, with clusters being joined in some datasets and separated in others. In this paper, we present a probabilistic clustering method to identify groups across datasets that do not share the same cluster structure. The proposed algorithm, Clusternomics, identifies groups of samples that share their global behaviour across heterogeneous datasets. The algorithm models clusters on the level of individual datasets, while also extracting global structure that arises from the local cluster assignments. Clusters on both the local and the global level are modelled using a hierarchical Dirichlet mixture model to identify structure on both levels. We evaluated the model both on simulated and on real-world datasets. The simulated data exemplifies datasets with varying degrees of common structure. In such a setting Clusternomics outperforms existing algorithms for integrative and consensus clustering. In a real-world application, we used the algorithm for cancer subtyping, identifying subtypes of cancer from heterogeneous datasets. We applied the algorithm to TCGA breast cancer dataset, integrating gene expression, miRNA expression, DNA methylation and proteomics. The algorithm extracted clinically meaningful clusters with significantly different survival probabilities. We also evaluated the algorithm on lung and kidney cancer TCGA datasets with high dimensionality, again showing clinically significant results and scalability of the algorithm. PMID:29036190

Clusternomics: Integrative context-dependent clustering for heterogeneous datasets.

PubMed

Gabasova, Evelina; Reid, John; Wernisch, Lorenz

2017-10-01

Integrative clustering is used to identify groups of samples by jointly analysing multiple datasets describing the same set of biological samples, such as gene expression, copy number, methylation etc. Most existing algorithms for integrative clustering assume that there is a shared consistent set of clusters across all datasets, and most of the data samples follow this structure. However in practice, the structure across heterogeneous datasets can be more varied, with clusters being joined in some datasets and separated in others. In this paper, we present a probabilistic clustering method to identify groups across datasets that do not share the same cluster structure. The proposed algorithm, Clusternomics, identifies groups of samples that share their global behaviour across heterogeneous datasets. The algorithm models clusters on the level of individual datasets, while also extracting global structure that arises from the local cluster assignments. Clusters on both the local and the global level are modelled using a hierarchical Dirichlet mixture model to identify structure on both levels. We evaluated the model both on simulated and on real-world datasets. The simulated data exemplifies datasets with varying degrees of common structure. In such a setting Clusternomics outperforms existing algorithms for integrative and consensus clustering. In a real-world application, we used the algorithm for cancer subtyping, identifying subtypes of cancer from heterogeneous datasets. We applied the algorithm to TCGA breast cancer dataset, integrating gene expression, miRNA expression, DNA methylation and proteomics. The algorithm extracted clinically meaningful clusters with significantly different survival probabilities. We also evaluated the algorithm on lung and kidney cancer TCGA datasets with high dimensionality, again showing clinically significant results and scalability of the algorithm.

Cationic Gold Clusters Ligated with Differently Substituted Phosphines: Effect of Substitution on Ligand Reactivity and Binding

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnson, Grant E.; Olivares, Astrid M.; Hill, David E.

2015-01-01

We present a systematic study of the effect of the number of methyl (Me) and cyclohexyl (Cy) functional groups in monodentate phosphine ligands on the solution-phase synthesis of ligated sub-nanometer gold clusters and their gas-phase fragmentation pathways. Small mixed ligand cationic gold clusters were synthesized using ligand exchange reactions between pre-formed triphenylphosphine ligated (PPh3) gold clusters and monodentate Me- and Cy-substituted ligands in solution and characterized using electrospray ionization mass spectrometry (ESI-MS) and collision-induced dissociation (CID) experiments. Under the same experimental conditions, larger gold-PPh3 clusters undergo efficient exchange of unsubstituted PPh3 ligands for singly Me- and Cy-substituted PPh2Me and PPh2Cymore » ligands. The efficiency of ligand exchange decreases with an increasing number of Me or Cy groups in the substituted phosphine ligands. CID experiments performed for a series of ligand-exchanged gold clusters indicate that loss of a neutral Me-substituted ligand is preferred over loss of a neutral PPh¬3 ligand while the opposite trend is observed for Cy-substituted ligands. The branching ratio of the competing ligand loss channels is strongly correlated with the electron donating ability of the phosphorous lone pair as determined by the relative proton affinity of the ligand. The results indicate that the relative ligand binding energies increase in the order PMe3 < PPhMe2 < PPh2Me < PPh3< PPh2Cy < PPhCy2< PCy3. Furthermore, the difference in relative ligand binding energies increases with the number of substituted PPh3-mMem or PPh3-mCym ligands (L) exchanged onto each cluster. This study provides the first experimental determination of the relative binding energies of ligated gold clusters containing differently substituted monophosphine ligands, which are important to controlling their synthesis and reactivity in solution. The results also indicate that ligand substitution is an important parameter that must be considered in theoretical modeling of these complex systems« less

Essential multimeric enzymes in kinetoplastid parasites: A host of potentially druggable protein-protein interactions.

PubMed

Wachsmuth, Leah M; Johnson, Meredith G; Gavenonis, Jason

2017-06-01

Parasitic diseases caused by kinetoplastid parasites of the genera Trypanosoma and Leishmania are an urgent public health crisis in the developing world. These closely related species possess a number of multimeric enzymes in highly conserved pathways involved in vital functions, such as redox homeostasis and nucleotide synthesis. Computational alanine scanning of these protein-protein interfaces has revealed a host of potentially ligandable sites on several established and emerging anti-parasitic drug targets. Analysis of interfaces with multiple clustered hotspots has suggested several potentially inhibitable protein-protein interactions that may have been overlooked by previous large-scale analyses focusing solely on secondary structure. These protein-protein interactions provide a promising lead for the development of new peptide and macrocycle inhibitors of these enzymes.

Synthesis, structure and sensing behavior of a Cd-coordination polymer based on 1,10-phenanthroline and 2-aminoterephthalic acid

NASA Astrophysics Data System (ADS)

Meng, Xing; Wang, Hai-Feng; Chen, He; Zhou, Zi-Yan; Wang, Hai-Ning

The reaction of 2-aminoterephthalic acid and 1,10-phenanthroline with Cd(NO3)2ṡ4H2O under solvothermal conditions leads to the formation of [Cd(2-aip)(phen)]ṡ0.5C2H5OH ( 1). In the compound, dimetallic cluster [Cd2(COO)4] exists and is linked by 2-aip ligands to stretch into a 2D flat layer. These layers are lined parallel to each other via N-HṡṡṡOCO hydrogen bond interactions, generating a 3D supramolecular architecture. The sensing property has been investigated. The experimental results show that the compound can be used as a luminescent probe to detect Co2+ and organic small molecules acetone.

Rhenium ion beam for implantation into semiconductors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kulevoy, T. V.; Seleznev, D. N.; Alyoshin, M. E.

2012-02-15

At the ion source test bench in Institute for Theoretical and Experimental Physics the program of ion source development for semiconductor industry is in progress. In framework of the program the Metal Vapor Vacuum Arc ion source for germanium and rhenium ion beam generation was developed and investigated. It was shown that at special conditions of ion beam implantation it is possible to fabricate not only homogenous layers of rhenium silicides solid solutions but also clusters of this compound with properties of quantum dots. At the present moment the compound is very interesting for semiconductor industry, especially for nanoelectronics andmore » nanophotonics, but there is no very developed technology for production of nanostructures (for example quantum sized structures) with required parameters. The results of materials synthesis and exploration are presented.« less

Optically enhanced SnO{sub 2}/CdSe core/shell nanostructures grown by sol-gel spin coating method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kumar, Vijay, E-mail: vijaynadda83@gmail.com; Goswami, Y. C.; Rajaram, P.

2015-08-28

Synthesis of SnO{sub 2}/CdSe metal oxide/ chalcogenide nanostructures on glass micro slides using ultrasonic sol-gel process followed by spin coating has been reported. Stannous chloride, cadmium chloride and selenium dioxide compounds were used for Sn, Cd and Se precursors respectively. Ethylene glycol was used as complexing agent. The samples were characterized by XRD, SEM, AFM and UV-spectrophotometer. All the peaks shown in diffractograms are identified for SnO{sub 2}. Peak broadening observed in core shell due to stress behavior of CdSe lattice. Scanning electron microscope and AFM exhibits the conversion of cluster in to nanorods structures forms. Atomic force microscope showsmore » the structures in nanorods form and a roughness reduced 1.5194 nm by the deposition of CdSe. Uv Visible spectra shows a new absorption edge in the visible region make them useful for optoelectronic applications.« less

Physics in ordered and disordered colloidal matter composed of poly(N-isopropylacrylamide) microgel particles.

PubMed

Yunker, Peter J; Chen, Ke; Gratale, Matthew D; Lohr, Matthew A; Still, Tim; Yodh, A G

2014-05-01

This review collects and describes experiments that employ colloidal suspensions to probe physics in ordered and disordered solids and related complex fluids. The unifying feature of this body of work is its clever usage of poly(N-isopropylacrylamide) (PNIPAM) microgel particles. These temperature-sensitive colloidal particles provide experimenters with a 'knob' for in situ control of particle size, particle interaction and particle packing fraction that, in turn, influence the structural and dynamical behavior of the complex fluids and solids. A brief summary of PNIPAM particle synthesis and properties is given, followed by a synopsis of current activity in the field. The latter discussion describes a variety of soft matter investigations including those that explore formation and melting of crystals and clusters, and those that probe structure, rearrangement and rheology of disordered (jammed/glassy) and partially ordered matter. The review, therefore, provides a snapshot of a broad range of physics phenomenology which benefits from the unique properties of responsive microgel particles.

Atomic Layer Deposition of Pd Nanoparticles on TiO₂ Nanotubes for Ethanol Electrooxidation: Synthesis and Electrochemical Properties.

PubMed

Assaud, Loïc; Brazeau, Nicolas; Barr, Maïssa K S; Hanbücken, Margrit; Ntais, Spyridon; Baranova, Elena A; Santinacci, Lionel

2015-11-11

Palladium nanoparticles are grown on TiO2 nanotubes by atomic layer deposition (ALD), and the resulting three-dimensional nanostructured catalysts are studied for ethanol electrooxidation in alkaline media. The morphology, the crystal structure, and the chemical composition of the Pd particles are fully characterized using scanning and transmission electron microscopies, X-ray diffraction, and X-ray photoelectron spectroscopy. The characterization revealed that the deposition proceeds onto the entire surface of the TiO2 nanotubes leading to the formation of well-defined and highly dispersed Pd nanoparticles. The electrooxidation of ethanol on Pd clusters deposited on TiO2 nanotubes shows not only a direct correlation between the catalytic activity and the particle size but also a steep increase of the response due to the enhancement of the metal-support interaction when the crystal structure of the TiO2 nanotubes is modified by annealing at 450 °C in air.

Atomic layer deposition in a metal–organic framework: Synthesis, characterization, and performance of a solid acid

DOE PAGES

Rimoldi, Martino; Bernales, Varinia; Borycz, Joshua; ...

2017-01-05

NU-1000, a zirconium-based metal-organic framework featuring mesoporous channels, has been post-synthetically metalated via atomic layer deposition in MOF (AIM) employing dimethylaluminum iso-propoxide ([AlMe 2 iOPr] 2 – DMAI), a milder precursor than widely used trimethylaluminum (AlMe 3 - TMA). The aluminum-modified NU-1000 (Al-NU-1000) has been characterized with a comprehensive suite of techniques that points to the formation of aluminum oxide clusters well dispersed through the framework and stabilized by confinement within small pores intrinsic to the NU-1000 structure. Experimental evidence allows for identification of spectroscopic similarities between Al-NU-1000 and γ-Al 2O 3. Density functional theory modeling provides structures and simulatedmore » spectra the relevance of which can be assessed via comparison to experimental IR and EXAFS data. As a result, the catalytic performance of Al-NU-1000 has been benchmarked against γ-Al 2O 3, with promising results in terms of selectivity.« less

Design and synthesis of tetraol derivatives of 1,12-dicarba-closo-dodecaborane as non-secosteroidal vitamin D analogs.

PubMed

Fujii, Shinya; Kano, Atsushi; Masuno, Hiroyuki; Songkram, Chalermkiat; Kawachi, Emiko; Hirano, Tomoya; Tanatani, Aya; Kagechika, Hiroyuki

2014-09-15

Vitamin D receptor (VDR), a nuclear receptor for 1α,25-dihydroxyvitamin D3 (1α,25(OH)2D3, 1), is a promising target for multiple clinical applications. We recently developed non-secosteroidal VDR ligands based on a carbon-containing boron cluster, 1,12-dicarba-closo-dodecaborane (p-carborane), and examined the binding of one of them to VDR by means of crystallographic analysis. Here, we utilized that X-ray structure to design novel p-carborane-based tetraol-type vitamin D analogs, and we examined the biological activities of the synthesized compounds. Structure-activity relationship study revealed that introduction of an ω-hydroxyalkoxy functionality enhanced the biological activity, and the configuration of the substituent significantly influenced the potency. Among the synthesized compounds, 4-hydroxybutoxy derivative 9a exhibited the most potent activity, which was equal to that of the secosteroidal vitamin D analog, 19-nor-1α,25-dihydroxyvitamin D3 (2). Copyright © 2014 Elsevier Ltd. All rights reserved.

X-ray Absorption Spectroscopy Reveals an Organometallic Ni–C Bond in the CO-Treated Form of Acetyl-CoA Synthase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Can, Mehmet; Giles, Logan J.; Ragsdale, Stephen W.

Acetyl-CoA synthase (ACS) is a key enzyme in the Wood–Ljungdahl pathway of anaerobic CO 2 fixation, which has long been proposed to operate by a novel mechanism involving a series of protein-bound organometallic (Ni–CO, methyl–Ni, and acetyl–Ni) intermediates. Here we report the first direct structural evidence of the proposed metal–carbon bond. We describe the preparation of the highly active metal-replete enzyme and near-quantitative generation of the kinetically competent carbonylated intermediate. This advance has allowed a combination of Ni and Fe K-edge X-ray absorption spectroscopy and extended X-ray absorption fine structure experiments along with density functional theory calculations. The data revealmore » that CO binds to the proximal Ni of the six-metal metallocenter at the active site and undergoes dramatic structural and electronic perturbation in forming this organometallic Ni–CO intermediate. This direct identification of a Ni–carbon bond in the catalytically competent CO-bound form of the In conclusion, a cluster of ACS provides definitive experimental structural evidence supporting the proposed organometallic mechanism of anaerobic acetyl-CoA synthesis.« less

X-ray Absorption Spectroscopy Reveals an Organometallic Ni–C Bond in the CO-Treated Form of Acetyl-CoA Synthase

DOE PAGES

Can, Mehmet; Giles, Logan J.; Ragsdale, Stephen W.; ...

2017-02-10

Acetyl-CoA synthase (ACS) is a key enzyme in the Wood–Ljungdahl pathway of anaerobic CO 2 fixation, which has long been proposed to operate by a novel mechanism involving a series of protein-bound organometallic (Ni–CO, methyl–Ni, and acetyl–Ni) intermediates. Here we report the first direct structural evidence of the proposed metal–carbon bond. We describe the preparation of the highly active metal-replete enzyme and near-quantitative generation of the kinetically competent carbonylated intermediate. This advance has allowed a combination of Ni and Fe K-edge X-ray absorption spectroscopy and extended X-ray absorption fine structure experiments along with density functional theory calculations. The data revealmore » that CO binds to the proximal Ni of the six-metal metallocenter at the active site and undergoes dramatic structural and electronic perturbation in forming this organometallic Ni–CO intermediate. This direct identification of a Ni–carbon bond in the catalytically competent CO-bound form of the In conclusion, a cluster of ACS provides definitive experimental structural evidence supporting the proposed organometallic mechanism of anaerobic acetyl-CoA synthesis.« less

Unexpected self-sorting self-assembly formation of a [4:4] sulfate:ligand cage from a preorganized tripodal urea ligand.

PubMed

Pandurangan, Komala; Kitchen, Jonathan A; Blasco, Salvador; Boyle, Elaine M; Fitzpatrick, Bella; Feeney, Martin; Kruger, Paul E; Gunnlaugsson, Thorfinnur

2015-04-07

The design and synthesis of tripodal ligands 1-3 based upon the N-methyl-1,3,5-benzenetricarboxamide platform appended with three aryl urea arms is reported. This ligand platform gives rise to highly preorganized structures and is ideally suited for binding SO4 (2-) and H2 PO4 (-) ions through multiple hydrogen-bonding interactions. The solid-state crystal structures of 1-3 with SO4 (2-) show the encapsulation of a single anion within a cage structure, whereas the crystal structure of 1 with H2 PO4 (-) showed that two anions are encapsulated. We further demonstrate that ligand 4, based on the same platform but consisting of two bis-urea moieties and a single ammonium moiety, also recognizes SO4 (2-) to form a self-assembled capsule with [4:4] SO4 (2-) :4 stoichiometry in which the anions are clustered within a cavity formed by the four ligands. This is the first example of a self-sorting self-assembled capsule where four tetrahedrally arranged SO4 (2-) ions are embedded within a hydrophobic cavity. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Crossover from disordered to core-shell structures of nano-oxide Y{sub 2}O{sub 3} dispersed particles in Fe

DOE Office of Scientific and Technical Information (OSTI.GOV)

Higgins, M. P.; Wang, L. M.; Gao, F., E-mail: gaofeium@umich.edu

Molecular dynamic simulations of Y{sub 2}O{sub 3} in bcc Fe and transmission electron microscopy (TEM) observations were used to understand the structure of Y{sub 2}O{sub 3} nano-clusters in an oxide dispersion strengthened steel matrix. The study showed that Y{sub 2}O{sub 3} nano-clusters below 2 nm were completely disordered. Y{sub 2}O{sub 3} nano-clusters above 2 nm, however, form a core-shell structure, with a shell thickness of 0.5–0.7 nm that is independent of nano-cluster size. Y{sub 2}O{sub 3} nano-clusters were surrounded by off-lattice Fe atoms, further increasing the stability of these nano-clusters. TEM was used to corroborate our simulation results and showed a crossover frommore » a disordered nano-cluster to a core-shell structure.« less

Spanish Dyslexic Spelling Abilities: The Case of Consonant Clusters

ERIC Educational Resources Information Center

Serrano, Francisca; Defior, Sylvia

2012-01-01

This paper investigates Spanish dyslexic spelling abilities: specifically, the influence of syllabic linguistic structure (simple vs consonant cluster) on children's spelling performance. Consonant clusters are phonologically complex structures, so it was anticipated that there would be lower spelling performance for these syllabic structures than…

Interactions of small platinum clusters with the TiC(001) surface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mao, Jianjun; Li, Shasha; Chu, Xingli

2015-11-14

Density functional theory calculations are used to elucidate the interactions of small platinum clusters (Pt{sub n}, n = 1–5) with the TiC(001) surface. The results are analyzed in terms of geometric, energetic, and electronic properties. It is found that a single Pt atom prefers to be adsorbed at the C-top site, while a Pt{sub 2} cluster prefers dimerization and a Pt{sub 3} cluster forms a linear structure on the TiC(001). As for the Pt{sub 4} cluster, the three-dimensional distorted tetrahedral structure and the two-dimensional square structure almost have equal stability. In contrast with the two-dimensional isolated Pt{sub 5} cluster, the adsorbed Pt{submore » 5} cluster prefers a three-dimensional structure on TiC(001). Substantial charge transfer takes place from TiC(001) surface to the adsorbed Pt{sub n} clusters, resulting in the negatively charged Pt{sub n} clusters. At last, the d-band centers of the absorbed Pt atoms and their implications in the catalytic activity are discussed.« less

Optimizing weak lensing mass estimates for cluster profile uncertainty

DOE PAGES

Gruen, D.; Bernstein, G. M.; Lam, T. Y.; ...

2011-09-11

Weak lensing measurements of cluster masses are necessary for calibrating mass-observable relations (MORs) to investigate the growth of structure and the properties of dark energy. However, the measured cluster shear signal varies at fixed mass M 200m due to inherent ellipticity of background galaxies, intervening structures along the line of sight, and variations in the cluster structure due to scatter in concentrations, asphericity and substructure. We use N-body simulated halos to derive and evaluate a weak lensing circular aperture mass measurement M ap that minimizes the mass estimate variance <(M ap - M 200m) 2> in the presence of allmore » these forms of variability. Depending on halo mass and observational conditions, the resulting mass estimator improves on M ap filters optimized for circular NFW-profile clusters in the presence of uncorrelated large scale structure (LSS) about as much as the latter improve on an estimator that only minimizes the influence of shape noise. Optimizing for uncorrelated LSS while ignoring the variation of internal cluster structure puts too much weight on the profile near the cores of halos, and under some circumstances can even be worse than not accounting for LSS at all. As a result, we discuss the impact of variability in cluster structure and correlated structures on the design and performance of weak lensing surveys intended to calibrate cluster MORs.« less