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Atomic clusters

Brian J Vaccaro, Sonya M Clarkson, James F Holden, Dong-Woo Lee, Chang-Hao Wu, Farris L Poole Ii, Julien J H Cotelesage, Mark J Hackett, Sahel Mohebbi, Jingchuan Sun, Huilin Li, Michael K Johnson, Graham N George, Michael W W Adams
Iron-sulfur clusters are ubiquitous in biology and function in electron transfer and catalysis. They are assembled from iron and cysteine sulfur on protein scaffolds. Iron is typically stored as iron oxyhydroxide, ferrihydrite, encapsulated in 12 nm shells of ferritin, which buffers cellular iron availability. Here we have characterized IssA, a protein that stores iron and sulfur as thioferrate, an inorganic anionic polymer previously unknown in biology. IssA forms nanoparticles reaching 300 nm in diameter and is the largest natural metalloprotein complex known...
July 20, 2017: Nature Communications
K R Krishnadas, Ananya Baksi, Atanu Ghosh, Ganapati Natarajan, Anirban Som, Thalappil Pradeep
Nanoparticles exhibit a rich variety in terms of structure, composition, and properties. However, reactions between them remain largely unexplored. In this Account, we discuss an emerging aspect of nanomaterials chemistry, namely, interparticle reactions in solution phase, similar to reactions between molecules, involving atomically precise noble metal clusters. A brief historical account of the developments, starting from the bare, gas phase clusters, which led to the synthesis of atomically precise monolayer protected clusters in solution, is presented first...
July 20, 2017: Accounts of Chemical Research
Mahdie Mollazade, Thibault Tabarin, Philip R Nicovich, Alexander Soeriyadi, Daniel J Nieves, J Justin Gooding, Katharina Gaus
Cells sense and respond to nanoscale variations in the distribution of ligands to adhesion receptors. This makes single molecule localization microscopy (SMLM) an attractive tool to map the distribution of ligands on nanopatterned surfaces. We explore the use of SMLM spatial cluster analysis to detect nanodomains of the cell adhesion-stimulating tripeptide arginine-glycine-aspartic acid (RGD). These domains were formed by the phase separation of block copolymers with controllable spacing on the scale of tens of nanometers...
2017: PloS One
Evgeny Loginov, Luis F Gomez, Boris G Sartakov, Andrey F Vilesov
Ethane core - silver shell clusters consisting of several thousand particles have been assembled in helium droplets upon capture of first ethane molecules, followed by Ag atoms. The composite clusters were studied via infrared laser spectroscopy in the range of C-H stretching vibrations of ethane molecules. The spectra show the splitting of the vibrational bands, which was assigned to different environment of the molecules, such as in contact or devoid of a contact with Ag atoms. The analysis of the band intensities for different number of trapped ethane molecules and Ag atoms indicates that the composite clusters consist of ethane core covered with small Ag clusters having different degree of submergence on the surface...
July 19, 2017: Journal of Physical Chemistry. A
B Leedahl, D W Boukhvalov, E Z Kurmaev, A Kukharenko, I S Zhidkov, N V Gavrilov, S O Cholakh, P Huu Le, C Wei Luo, A Moewes
Topological insulators have become one of the most prominent research topics in materials science in recent years. Specifically, Bi2Te3 is one of the most promising for technological applications due to its conductive surface states and insulating bulk properties. Herein, we contrast the bulk and surface structural environments of dopant ions Cr, Mn, Fe, Co, Ni, and Cu in Bi2Te3 thin films in order to further elucidate this compound. Our measurements show the preferred oxidation state and surrounding crystal environment of each 3d-metal atomic species, and how they are incorporated into Bi2Te3...
July 18, 2017: Scientific Reports
Fude Sun, Long Chen, Xiufang Ding, Lida Xu, Xirui Zhou, Peng Wei, Jun-Feng Liang, Shi-Zhong Luo
Peptide self-assembly has a profound biological significance since self-assembled bioactive peptides are gifted with improved bioactivity as well as life-span. In this study, peptide self-assembly was investigated using a therapeutic peptide, PTP-7S (EENFLGALFKALSKLL). Combining experiments of atomic force microscopy (AFM), circular dichroism (CD) and 8-anilino-1-naphthalenesulfonic acid (ANS) fluorescence spectra, PTP-7S showing α-helix was found self-assembling into nanofibers in solution. Relying on the coarse-grained (CG) dynamic simulations, the self-assembling of PTP-7S was revealed as a stepwise process that peptide monomers first clustered into peptide-assembling units (PUs) with charged surface, and then the PUs integrated together to construct nano-fibril aggregates...
July 18, 2017: Journal of Physical Chemistry. B
Adam Philips, Alex Marchenko, Lionel Alexandre Truflandier, Jochen Autschbach
Quadrupolar NMR relaxation rates are computed for (17)O, (2)H nuclei of liquid water, and of (23)Na(+) , and (35)Cl(-) in aqueous solution, via Kohn-Sham (KS) density functional theory ab-initio molecular dynamics (aiMD) and subsequent KS electric field gradient (EFG) calculations along the trajectories. The calculated relaxation rates are within about a factor of two of experimental results, and improved over previous aiMD simulations. The relaxation rates are assessed with regard to the lengths of the simulations as well as configurational sampling...
July 18, 2017: Journal of Chemical Theory and Computation
Nan Jian, Karl Bauer, Richard E Palmer
A multilayer deposition method has been developed with the potential to capture and process atomic clusters generated by a high flux cluster beam source. In this deposition mode a series of sandwich structures each consisting of three layers-a carbon support layer, cluster layer and polymer release layer-is sequentially deposited to form a stack of isolated cluster layers, as confirmed by through-focal aberration-corrected HAADF STEM analysis. The stack can then be diced into small pieces by a mechanical saw...
August 11, 2017: Nanotechnology
Syed Taseer Abbas Jaffar, Long-Zhu Chen, Hassan Younas
Urbanization and industrialization increase the concentrations of heavy metals in soils, which affect human health. A total of 127 topsoil samples were collected from the massively urbanized and industrialized district of Shanghai: Baoshan District. The sampling sites were isolated based on the land-use practice: industrial area, roadside area, residential area, and agricultural area. The absolute concentrations of heavy metals (Zn, Cr, Ni, Mn, Cu, Pb, and Cd) were determined using atomic absorption spectrometry and compared with Shanghai and the National soil background values...
July 17, 2017: Archives of Environmental Contamination and Toxicology
Tingting You, Xiufeng Lang, Anping Huang, Penggang Yin
A computational study on aromatic dithiol derivatives (HS-Ar-X-Ar-SH, X=O, S, Se, NH, CH2, NN, CHCH, CC) interacting with gold cluster(s) was presented to investigate the chemical enhancement mechanism related to surface-enhanced Raman spectroscopy (SERS) for molecular junctions. Density functional theory (DFT) were performed on derivatives molecules as well as their single-end-linked (SEL) or double-end-linked (DEL) complexes for geometric, spectra, electronic and excitation properties, leading to discussions on dominant factor during SERS process...
July 12, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
Gaoxiang Liu, Sandra M Ciborowski, Kit Hansell Bowen
Pyridine-ligated gold cluster anions were studied through a combination of negative ion photoelectron spectroscopy and density functional theory calculations. Small gold cluster anions ligated by pyridine, Aun(py) were generated with a ligation cell coupled to a laser vaporization source (LVS). We showed that pyridine is weakly bound (physisorbed) to the Au2(-) moiety of Au2(py)(-) by interactions between its gold atoms and either the hydrogen atoms or the π-ring of pyridine. We also found that pyridine's lone electron pair strongly binds (chemisorbs) to both Au3(py)(-) and Au4(py)(-) through single gold atoms on each of these clusters...
July 17, 2017: Journal of Physical Chemistry. A
Xiaojun Li, Shuna Li, Hongjiang Ren, Juxiang Yang, Yongqiang Tang
A new series of alkali-based complexes, AM@GenAu (AM = Li, Na, and K), have been theoretically designed and investigated by means of the density functional theory calculations. The geometric structures and electronic properties of the species are systematically analyzed. The adsorption of alkali metals maintains the structural framework of the gold-germanium bimetallic clusters, and the alkali metals prefer energetically to be attached on clusters' surfaces or edges. The high chemical stability of Li@Ge12Au is revealed by the spherical aromaticity, the hybridization between the Ge atoms and Au-4d states, and delocalized multi-center bonds, as well as large binding energies...
July 17, 2017: Nanomaterials
Ayako Nakata, Yasunori Futamura, Tetsuya Sakurai, David R Bowler, Tsuyoshi Miyazaki
We propose an efficient way to calculate the electronic structure of large systems by combining a large-scale first-principles density functional theory code, CONQUEST, and an efficient interior eigenproblem solver, the Sakurai-Sugiura method. The electronic Hamiltonian and charge density of large systems are obtained by CONQUEST and the eigenstates of the Hamiltonians are then obtained by the Sakurai-Sugiura method. Applications to a hydrated DNA system, and adsorbed P2 molecules and Ge hut clusters on large Si substrates demonstrate the applicability of this combination on systems with 10,000+ atoms with high accuracy and efficiency...
July 17, 2017: Journal of Chemical Theory and Computation
Furong Wang, Pascal Pernot, Pierre Archirel, Daniel Ortiz, Sophie Le Caer, Mehran Mostafavi
NMR measurements show that diethyl carbonate (DEC, a solvent with a low dielectric constant) solutions of LiClO4 contain (LiClO4)n oligomers. The reduction of these species by solvated electrons and pre-solvated electrons is followed by picosecond pulse radiolysis measurements. The data analysis shows that several anions absorbing in the NIR and visible range are formed after the 7 ps electron pulse. In contrast with THF solutions of LiClO4, the anionic monomer (LiClO4)- is not observed in DEC solutions. This is due to the fact that DEC is a non-polar solvent favoring the clustering of the monomers in the non-irradiated solution as shown by NMR results, and also due to the instability of the anionic monomer...
July 15, 2017: Journal of Physical Chemistry. B
Daniel R Martin, Dmitry V Matyushov
Complex I is a part of the respiration energy chain converting the redox energy into the cross-membrane proton gradient. The electron-transfer chain of iron-sulfur cofactors within the water-soluble peripheral part of the complex is responsible for the delivery of electrons to the proton pumping subunit. The protein is porous to water penetration and the hydration level of the cofactors changes when the electron is transferred along the chain. High reaction barriers and trapping of the electrons at the iron-sulfur cofactors are prevented by the combination of intense electrostatic noise produced by the protein-water interface with the high density of quantum states in the iron-sulfur clusters caused by spin interactions between paramagnetic iron atoms...
July 14, 2017: Scientific Reports
Jose Leonardo Gomez-Ballesteros, Perla B Balbuena
Achieving a better control of the nucleation and growth of single-walled carbon nanotubes requires understanding of the changes in the catalyst structure and the interfacial phenomena occurring at the solid surface and the gaseous phase from the early stages of the synthesis process. Carbon nanotubes produced by chemical vapor deposition typically use carbon-philic metal catalysts such as Fe, Ni and Co, in which both surface C and dissolved C atoms contribute to the nanotube formation. We use density functional theory to investigate the interactions of Rh, a noble metal, with carbon both as individual atoms gradually deposited on the catalyst surface from the precursor gas decomposition and as a nucleating seed adhered to the catalyst...
July 14, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
Masahiro Kako, Shigeru Nagase, Takeshi Akasaka
Exohedral derivatization of endohedral metallofullerenes (EMFs) has been exploited as a useful method for characterizing the structural and chemical properties of EMFs, and for functionalizing them for potential applications. The introduction of heteroatoms, such as electropositive silicon atoms, to fullerene cages is a novel functionalization method that remarkably affects the electronic characteristics of fullerenes. This review comprehensively describes the results of the reactions of monometallofullerene, dimetallofullerene, and trimetallic nitride template EMFs with disilirane, silirane, silylene, and digermirane, which afforded the corresponding silylated and germylated fullerenes...
July 14, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Bastian C Krüger, G Barratt Park, Sven Meyer, Roman J V Wagner, Alec M Wodtke, Tim Schäfer
Nonreactive surface scattering of atoms, molecules and clusters can be almost universally described by two mechanisms: trapping-desorption and direct-scattering. A hard cube model with an attractive square well provides a zeroth order description of the branching ratio between these two mechanisms as a function of the incidence energy. However, the trapping process is likely to be enhanced by excitation of internal degrees of freedom during the collision. In this molecular beam surface scattering study, we characterize formaldehyde/Au(111) scattering using angle resolved time-of-flight techniques...
July 14, 2017: Physical Chemistry Chemical Physics: PCCP
F X Kärtner, F Ahr, A-L Calendron, H Çankaya, S Carbajo, G Chang, G Cirmi, K Dörner, U Dorda, A Fallahi, A Hartin, M Hemmer, R Hobbs, Y Hua, W R Huang, R Letrun, N Matlis, V Mazalova, O D Mücke, E Nanni, W Putnam, K Ravi, F Reichert, I Sarrou, X Wu, A Yahaghi, H Ye, L Zapata, D Zhang, C Zhou, R J D Miller, K K Berggren, H Graafsma, A Meents, R W Assmann, H N Chapman, P Fromme
X-ray crystallography is one of the main methods to determine atomic-resolution 3D images of the whole spectrum of molecules ranging from small inorganic clusters to large protein complexes consisting of hundred-thousands of atoms that constitute the macromolecular machinery of life. Life is not static, and unravelling the structure and dynamics of the most important reactions in chemistry and biology is essential to uncover their mechanism. Many of these reactions, including photosynthesis which drives our biosphere, are light induced and occur on ultrafast timescales...
September 1, 2016: Nuclear Instruments & Methods in Physics Research. Section A, Accelerators, Spectrometers, Detectors and Associated Equipment
X J Liu, I P Hamilton
We present a series of intrinsically chiral gold nanocage structures, Au9n+6, which are stable for n ≥ 2. These structures consist of an Au9n tube which is capped with Au3 units at each end. Removing the Au3 caps, we obtain a series of intrinsically chiral gold nanotube structures, Au9n, which are stable for n ≥ 4. The intrinsic chirality of these structures results from the helicity of the gold strands which form the tube and not because an individual Au atom is a chiral center. The symmetry of these structures is C3 and substructures of gold hexagons with a gold atom in the middle are particularly prominent...
July 12, 2017: Nanoscale
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