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Atomic clusters

Jaechang Lim, Sungwoo Kang, Jaewook Kim, Woo Youn Kim, Seol Ryu
Plasmonic nanoparticles in the quantum regime exhibit characteristic optical properties that cannot be described by classical theories. Time-dependent density functional theory (TDDFT) is rising as a versatile tool for study on such systems, but its application has been limited to very small clusters due to rapidly growing computational costs. We propose an atomistic dipole-interaction-model for quantum plasmon simulations as a practical alternative. Namely the atomic dipole approximation represents induced dipoles with atomic polarizabilities obtained from TDDFT without empirical parameters...
November 17, 2017: Scientific Reports
Kazuo Tsutsui, Tomohiro Matsushita, Kotaro Natori, Takayuki Muro, Yoshitada Morikawa, Takuya Hoshii, Kuniyuki Kakushima, Hitoshi Wakabayashi, Kouichi Hayashi, Fumihiko Matsui, Toyohiko Kinoshita
The atomic scale characterization of dopant atoms in semiconductor devices to establish correlations with the electrical activation of these atoms is the essential to the advancement of contemporary semiconductor process technology. Spectro-photoelectron holography combined with first-principles simulations can determine the local three-dimensional atomic structures of dopant elements, which in turn affect their electronic states. In the work reported herein, this technique was used to examine arsenic (As) atoms doped into a silicon (Si) crystal...
November 17, 2017: Nano Letters
Yutaro Kawazu, Hiroshi Hoke, Yasunori Yamada, Tatsuya Umecky, Kazuhiko Ozutsumi, Toshiyuki Takamuku
The thermodynamics of complex formation of Ni(2+) with molecular liquids (ML), dimethyl sulfoxide (DMSO), methanol (MeOH), and acetonitrile (AN) in the ionic liquid (IL) of 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)amide ([C2mim][TFSA]) has been elucidated using ultraviolet (UV)-visible spectroscopy. X-ray structural analyses for single crystals grown from Ni(2+)-[C2mim][TFSA]-DMSO and -AN solutions at high ML contents have shown that six DMSO oxygen or AN nitrogen atoms coordinate with Ni(2+) to form octahedral structures of [Ni(dmso)6](TFSA)2 and [Ni(an)6](TFSA)2, respectively...
November 17, 2017: Physical Chemistry Chemical Physics: PCCP
Bishnu Prasad Mukhopadhyay
Human Ceruloplasmin belongs to the family of multi-copper oxidases and it is involved in different physiological processes, copper ion transport, iron metabolism, iron homeostasis, and biogenic amine metabolism. MD-simulation studies have indicated the higher hydrophilic susceptibility of the trinuclear copper cluster in native CP compared to its oxygen bound form. The copper (T2/T3) atom Cu3047 of the cluster, which is close to T1 copper center Cu3052 (~13 Å) has a higher affinity for water molecules compared to other copper centers...
November 17, 2017: Journal of Biomolecular Structure & Dynamics
Michio Iwaoka, Toshiki Suzuki, Yuya Shoji, Kenichi Dedachi, Taku Shimosato, Toshiya Minezaki, Hironobu Hojo, Hiroyuki Onuki, Hiroshi Hirota
Single amino acid potential (SAAP) would be a prominent factor to determine peptide conformations. To prove this hypothesis, we previously developed SAAP force field for molecular simulation of polypeptides. In this study, the force field was renovated to SAAP3D force field by applying more accurate three-dimensional main-chain parameters, instead of the original two-dimensional ones, for the amino acids having a long side-chain. To demonstrate effectiveness of the SAAP3D force field, replica-exchange Monte Carlo (REMC) simulation was performed for two benchmark short peptides, chignolin (H-GYDPETGTWG-OH) and C-peptide (CHO-AETAAAKFLRAHA-NH2)...
November 17, 2017: Journal of Computer-aided Molecular Design
Michael Rivera Mananghaya, Gil Nonato Santos, Dennis Yu, Catherine Stampfl
The realistic shapes of N doped graphene nanoribbons (GNRs) can be realized by considering nearly zigzag-edged (NZE) imperfections and pyridine defects (3NV). The paper focuses on NZE-GNRs with 3NV that is populated by Scandium abbreviated as Sc/NZE-3NVGNRs. Systematic calculations have clarified roles of the nano-shapes of NZE-3NVGNRs in its formation, energetics, stability and electron states functionalized with Sc using density functional theory (DFT) formalisms. According to DFT calculations, the magnitude of the spin that is attributed to the rise of magnetic order is closely linked to the altered shape of the ribbon edges...
November 16, 2017: Scientific Reports
Yoav Atsmon-Raz, D Peter Tieleman
Peripheral membrane proteins go through various post-translational modifications that covalently bind fatty acid tails to specific amino acids. These post translational modifications significantly alter the lipophilicity of the modified proteins and allow them to anchor to biological membranes. Over 1000 different proteins have been identified to date that require such membrane-protein interactions in order to carry out their biological functions, including members of the Src and Ras superfamilies that play key roles in cell signaling and carcinogenesis...
November 16, 2017: Journal of Physical Chemistry. B
Julian Cruz-Borbolla, Esteban Garcia-Ochoa, Jayanthi Narayanan, Pablo Maldonado-Rivas, Thangarasu Pandiyan, José M Vásquez-Pérez
The capacity of 2,6-bis[((2-pyridylmethyl)oxy)methyl)]pyridine (BPMMP) to inhibit the corrosion of mild carbon steel in HCl was analyzed. In a polarization study, both the cathodic and anodic currents were appreciably decreased in the presence of BPMMP, suggesting that this ligand is effective at inhibiting corrosion at the metal surface. This conclusion is consistent with the results of impedance analysis, where only one time constant corresponding to one depressed capacitive loop was detected, and the diameter of the impedance plot was directly related to the concentration of BPMMP...
November 15, 2017: Journal of Molecular Modeling
Sebastian Dillinger, Jennifer Mohrbach, Gereon Niedner-Schatteburg
We present the cryogenic (26 K) IR spectra of selected [Nin(N2)m](+) (n = 5-20, m = 1 - mmax), which strongly reveal n- and m-dependent features in the N2 stretching region, in conjunction with density functional theory modeling of some of these findings. The observed spectral features allow us to refine the kinetic classification [cf. J. Mohrbach, S. Dillinger, and G. Niedner-Schatteburg, J. Chem. Phys. 147, 184304 (2017)] and to define four classes of structure related surface adsorption behavior: Class (1) of Ni6(+), Ni13(+), and Ni19(+) are highly symmetrical clusters with all smooth surfaces of equally coordinated Ni atoms that entertain stepwise N2 adsorption up to stoichiometric N2:Nisurface saturation...
November 14, 2017: Journal of Chemical Physics
Heejune Park, Giovanni Meloni
The capability of the superalkali Li_3 F_2 to activate dinitrogen (N_2) is presented. The (Li_3 F_2 )_n N_2 clusters (n = 1 - 6) were investigated first at the MP2/6-311+G(3d2f,2df,2p)//B3LYP/6-311G(2d,d,p) level of theory. Clusters up to n = 4 were also optimized through the CBS-QB3 composite model. The complete dissociation of N_2 was confirmed through visualized molecular orbitals and bond order calculation. The N-N bond is weakened by the addition of Li_3 F_2 superalkali units. The enthalpy of atomization (Δ_at H_0^°) and formation (Δ_f H_0^°), charge flows (∆q), binding energies, and the energy gap between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) are calculated to help explaining the N_2 activation...
November 15, 2017: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
Simon Budzak, Giovanni Scalmani, Denis Jacquemin
We present an investigation of the excited-state structural parameters determined for a large set of small compounds with the dual goals of defining reference values for further works and assessing the quality of the geometries obtained with relatively cheap computational approaches. In the first stage, we compare the excited-state geometries obtained with ADC(2), CC2, CCSD, CCSDR(3), CC3 and CASPT2 and large atomic basis sets. It is found that CASPT2 and CC3 results are generally in very good agreement with one another (typical differences of ca...
November 15, 2017: Journal of Chemical Theory and Computation
Manar M Shoshani, Robert Beck, Xiaoping Wang, Matthew J McLaughlin, Samuel A Johnson
Tetranuclear Ni complexes were synthesized with bonding to BH, NR, and O in atypical surface-like geometries. The previously reported electron-deficient cluster [((i)Pr3P)Ni]5H6 (1) reacts with N-methylmorpholine oxide to give [((i)Pr3P)Ni]4H4(μ4-O) (2), which contains O coordinated in the center of a square-plane arrangement of Ni atoms. Reaction of 1 with benzonitrile gave the square-planar tetranuclear Ni cluster [((i)Pr3P)Ni]4H4(μ4-NCH2Ph) (3), which contains an imido donor in a square-based-pyramidal geometry...
November 15, 2017: Inorganic Chemistry
Xin Tang, Kit H Bowen, Florent Calvo
Tungsten oxide cluster anions (WO3)3(-) produced from a magnetron source were soft-landed on highly oriented pyrolytic graphite (HOPG) surfaces at different temperatures, and the structures formed upon deposition were analyzed using ex situ atomic force microscopy. Under liquid nitrogen cooling conditions of 100 K, the clusters form small branched nanostructures extending over a few nanometers with a height not exceeding 1 nm. At 673 K, nanowires approximately 100 nm long and less than 10 nm in diameter are observed...
November 15, 2017: Physical Chemistry Chemical Physics: PCCP
Joshua D Hartman, Ashwin Balaji, Gregory J O Beran
Fragment-based methods predict nuclear magnetic resonance (NMR) chemical shielding tensors in molecular crystals with high accuracy and computational efficiency. Such methods typically employ electrostatic embedding to mimic the crystalline environment, and the quality of the results can be sensitive to the embedding treatment. To improve the quality of this embedding environment for fragment-based molecular crystal property calculations, we borrow ideas from the embedded ion method to incorporate self-consistently polarized Madelung field effects...
November 15, 2017: Journal of Chemical Theory and Computation
Minghao Nie, Yan Wang, Yanhong Lu, Ying Yuan, Yingying Liu, Xiurong Li
High oxygen mechanical ventilation is widely used to treat various lung diseases; however, it may result in hyperoxia, which induces inflammation and lung injury. Fucoidan is an extract of the seaweed Fucus vesiculosus, which has previously been reported to exert effects against diabetic nephropathy. The present study is the first, to the best of our knowledge, to investigate the protective effects of fucoidan against hyperoxic lung injury. Balb/c mice were ventilated with 100% oxygen, with or without the atomization inhalation of fucoidan, for 36 h...
November 10, 2017: Molecular Medicine Reports
Tiia-Riikka Tero, Sami Malola, Benedek Koncz, Emmi Pohjolainen, Saara Lautala, Satu Mustalahti, Perttu Permi, Gerrit Groenhof, Mika Pettersson, Hannu Häkkinen
Ligand-stabilized, atomically precise gold nanoclusters with a metal core of a uniform size of just 1 - 3 nm constitute an interesting class of nanomaterials with versatile possibilities for applications due to their size dependent properties and modifiable ligand layers. The key to extending the usability of the clusters in applications is to understand the chemical bonding in the ligand layer as a function of cluster size and ligand structure. Previously, it has been shown that monodispersed gold nanoclusters, stabilized by meta-mercaptobenzoic acid (m-MBA or 3-MBA) ligands and with sizes of 68 to 144 gold atoms, show ambient stability...
November 14, 2017: ACS Nano
Feridoon Azough, Samuel S Jackson, Dursun Ekren, Robert Freer, Marco Molinari, Stephen R Yeandel, Pooja M Panchmatia, Stephen C Parker, David Hernandez Maldonado, Demie M Kepaptsoglou, Quentin M Ramasse
To help understand the factors controlling the performance of one of the most promising n-type oxide thermoelectrics SrTiO3, we need to explore structural control at the atom level. In Sr1-xLa2x/3TiO3 ceramics (0.0 ≤ x ≤ 0.9), we determined that the thermal conductivity can be reduced and controlled through an interplay of La substitution and A-site vacancies and the formation of a layered structure. The decrease in thermal conductivity with La and A-site vacancy substitution dominates the trend in the overall thermoelectric response...
November 14, 2017: ACS Applied Materials & Interfaces
Shiping Huang
The evolution of the contact area with normal load for rough surfaces has great fundamental and practical importance, ranging from earthquake dynamics to machine wear. This work bridges the gap between the atomic scale and the macroscopic scale for normal contact behavior. The real contact area, which is formed by a large ensemble of discrete contacts (clusters), is proven to be much smaller than the apparent surface area. The distribution of the discrete contact clusters and the interaction between them are key to revealing the mechanism of the contacting solids...
November 13, 2017: Nanoscale Research Letters
(no author information available yet)
The metal abundance of the hot plasma that permeates galaxy clusters represents the accumulation of heavy elements produced by billions of supernovae. Therefore, X-ray spectroscopy of the intracluster medium provides an opportunity to investigate the nature of supernova explosions integrated over cosmic time. In particular, the abundance of the iron-peak elements (chromium, manganese, iron and nickel) is key to understanding how the progenitors of typical type Ia supernovae evolve and explode. Recent X-ray studies of the intracluster medium found that the abundance ratios of these elements differ substantially from those seen in the Sun, suggesting differences between the nature of type Ia supernovae in the clusters and in the Milky Way...
November 13, 2017: Nature
Xin Zhao, Cai-Zhuang Wang, Minsung Kim, Kai-Ming Ho
Fe-cluster-based crystal structures are predicted for chalcogenides Fe3X4 (X = S, Se, Te) using an adaptive genetic algorithm. Topologically different from the well-studied layered structures of iron chalcogenides, the newly predicted structures consist of Fe clusters that are either separated by the chalcogen atoms or connected via sharing of the vertex Fe atoms. Using first-principles calculations, we demonstrate that these structures have competitive or even lower formation energies than the experimentally synthesized Fe3X4 compounds and exhibit interesting magnetic and electronic properties...
November 13, 2017: Inorganic Chemistry
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