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Atomic clusters

Wojciech Pulawski, Michal Jamroz, Michal Kolinski, Andrzej Kolinski, Sebastian Kmiecik
The CABS coarse-grained model is a well-established tool for modeling globular proteins (predicting their structure, dynamics and interactions). Here we introduce an extension of CABS representation and force field (CABS-membrane) to the modeling of the effect of biological membrane environment on the structure of membrane proteins. We validate the CABS-membrane model in folding simulations of 10 short helical membrane proteins not using any knowledge about their structure. The simulations start from random protein conformations placed outside the membrane environment and allow for full flexibility of the modeled proteins during their spontaneous insertion into the membrane...
October 24, 2016: Journal of Chemical Information and Modeling
Hong-Xu Na, Pei-Yu Yang, Zheng Yin, Yun-Hong Wang, Li-Xian Chang, Rui Si, Mohamedally Kurmoo, Ming-Hua Zeng
The square-planar monomer NiL2 (Ni1 ), L=2-ethoxy-6-(N-methyl-iminomethyl)phenolate, reacts with M(H2 O)6 (ClO4 )2 , M=Ni or Co, to form heptanuclear disks [Cox Ni7-x (OH)6 (L)6 ](ClO4 )2 ⋅2 CH3 CN (Cox Ni7-x , x=0-7) and the co-crystal [Cox Ni7-x (OH)6 L6 ][NiL2 ](ClO4 )2 ⋅2 CH3 CN (Cox Ni7-x -Ni1 ) under ambient conditions. It has proved possible to explore the bottom-up assembly process of Cox Ni7-x and Cox Ni7-x -Ni1 in real time. The final products have been characterized by thermogravimetric analysis, IR, elemental analysis, ICP-MS, and single-crystal X-ray diffraction...
October 24, 2016: Chemistry: a European Journal
B E Husic, D Schebarchov, D J Wales
We use the harmonic superposition approach to examine how a single atom substitution affects low-temperature anomalies in the vibrational heat capacity (CV) of model nanoclusters. Each anomaly is linked to competing solidlike "phases", where crossover of the corresponding free energies defines a solid-solid transition temperature (Ts). For selected Lennard-Jones clusters we show that Ts and the corresponding CV peak can be tuned over a wide range by varying the relative atomic size and binding strength of the impurity, but excessive atom-size mismatch can destroy a transition and may produce another...
October 24, 2016: Nanoscale
Daniela Rupp, Leonie Flückiger, Marcus Adolph, Tais Gorkhover, Maria Krikunova, Jan Philippe Müller, Maria Müller, Tim Oelze, Yevheniy Ovcharenko, Benjamin Röben, Mario Sauppe, Sebastian Schorb, David Wolter, Rolf Mitzner, Michael Wöstmann, Sebastian Roling, Marion Harmand, Rolf Treusch, Mathias Arbeiter, Thomas Fennel, Christoph Bostedt, Thomas Möller
We studied the nanoplasma formation and explosion dynamics of single large xenon clusters in ultrashort, intense x-ray free-electron laser pulses via ion spectroscopy. The simultaneous measurement of single-shot diffraction images enabled a single-cluster analysis that is free from any averaging over the cluster size and laser intensity distributions. The measured charge state-resolved ion energy spectra show narrow distributions with peak positions that scale linearly with final ion charge state. These two distinct signatures are attributed to highly efficient recombination that eventually leads to the dominant formation of neutral atoms in the cluster...
October 7, 2016: Physical Review Letters
Mangesh I Chaudhari, Jijeesh R Nair, Lawrence R Pratt, Fernando A Soto, Perla B Balbuena, Susan Rempe
Lithium ion solvation and diffusion properties in ethylene carbonate (EC) and propylene carbonate (PC) are studied by molecular simulation, experiments, and electronic structure calculations. Studies carried out in water provide a reference for interpretation. Classical molecular dynamics simulation results are compared to ab initio molecular dynamics to as- sess non-polarizable force field parameters for solvation structure of the carbonate solvents. Quasi-chemical theory (QCT) is adapted to take advantage of four-fold occupancy of the near-neighbor solvation structure observed in simulations, and used to calculate solvation free energies...
October 21, 2016: Journal of Chemical Theory and Computation
Taizo Mori, Torsten Hegmann
ABSTRACT: Size, shape, overall composition, and surface functionality largely determine the properties and applications of metal nanoparticles. Aside from well-defined metal clusters, their composition is often estimated assuming a quasi-spherical shape of the nanoparticle core. With decreasing diameter of the assumed circumscribed sphere, particularly in the range of only a few nanometers, the estimated nanoparticle composition increasingly deviates from the real composition, leading to significant discrepancies between anticipated and experimentally observed composition, properties, and characteristics...
2016: Journal of Nanoparticle Research: An Interdisciplinary Forum for Nanoscale Science and Technology
Zhizhao Che, Panagiotis E Theodorakis
Surface nanobubbles are stable gaseous phases in liquids that form on solid substrates. While their existence has been confirmed, there are many open questions related to their formation and dissolution processes along with their structures and properties, which are difficult to investigate experimentally. To address these issues, we carried out molecular dynamics simulations based on atomistic force fields for systems comprised of water, air (N2 and O2), and a Highly Oriented Pyrolytic Graphite (HOPG) substrate...
October 14, 2016: Journal of Colloid and Interface Science
Antonella Caivano, Francesco La Rocca, Vittorio Simeon, Marco Girasole, Simone Dinarelli, Ilaria Laurenzana, Angelo De Stradis, Luciana De Luca, Stefania Trino, Antonio Traficante, Giovanni D'Arena, Giovanna Mansueto, Oreste Villani, Giuseppe Pietrantuono, Luca Laurenti, Luigi Del Vecchio, Pellegrino Musto
PURPOSE: The use of extracellular vesicles (EVs) from body fluids as "liquid biopsies" is emerging as a promising approach for the diagnosis, prognosis and therapeutic monitoring of cancer patients. MicroRNA-155 (miR155), a non-coding transcript of the B-cell integration cluster (BIC) gene, has been reported to play a critical role in the pathogenesis of several types of hematologic malignancies (HMs) in which high miR155 levels have been found. At yet, however, the EV miR155 level and its putative clinical relevance in sera of HM patients have not been reported...
October 19, 2016: Cellular Oncology (Dordrecht)
Liyuan Chai, Huan Li, Zhihui Yang, Xiaobo Min, Qi Liao, Yi Liu, Shuhui Men, Yanan Yan, Jixin Xu
Here, we aim to determine the distribution, ecological risk and sources of heavy metals and metalloids in the surface sediments of the Xiangjiang River, Hunan Province, China. Sixty-four surface sediment samples were collected in 16 sites of the Xiangjiang River, and the concentrations of ten heavy metals and metalloids (Mn, Zn, Cr, V, Pb, Cu, As, Ni, Co, and Cd) in the sediment samples were investigated using an inductively coupled plasma mass spectrometer (ICP-MS) and an atomic fluorescence spectrophotometer (AFS), respectively...
October 19, 2016: Environmental Science and Pollution Research International
Vahid Sokhanvaran, Saeid Yeganegi
The quantum mechanics (QM) method and Grand Canonical Monte Carlo (GCMC) simulations were performed to study the effect of lithium cation doping on the adsorption and separation of CO2, CH4 and H2 on 2-fold interwoven metal-organic framework (MOF) Zn2(NDC)2(diPyNI). The second order Moller-Plesset (MP2) calculations on the (Li+-diPyNI) cluster model showed that the energetically most favorable lithium binding site is above the pyridine ring side and at a distance of 1.817 Å from the oxygen atom. The results revealed that the adsorption capacity of Zn2(NDC)2(diPyNI) for carbon dioxide is higher than that of hydrogen and methane at room temperature...
October 19, 2016: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
Donato Belmonte, Carlo Gatti, Giulio Armando Ottonello, Pascal Richet, Marino Vetuschi Zuccolini
Thermodynamic and thermophysical properties of Na2SiO3 in the Cmc21 structural state are computed ab-initio using the hybrid B3LYP density functional method. The static properties at the athermal limit are first evaluated through a symmetry-preserving relaxation procedure. The thermodynamic properties that depend on vibrational frequencies viz, heat capacities, thermal expansion, thermal derivative of the bulk modulus, thermal correction to internal energy, enthalpy, Gibbs free energy, are then computed in the framework of quasi-harmonic approximation...
October 19, 2016: Journal of Physical Chemistry. A
Chris Jeynes, Julien L Colaux
The analysis of thin films is of central importance for functional materials, including the very large and active field of nanomaterials. Quantitative elemental depth profiling is basic to analysis, and many techniques exist, but all have limitations and quantitation is always an issue. We here review recent significant advances in ion beam analysis (IBA) which now merit it a standard place in the analyst's toolbox. Rutherford backscattering spectrometry (RBS) has been in use for half a century to obtain elemental depth profiles non-destructively from the first fraction of a micron from the surface of materials: more generally, "IBA" refers to the cluster of methods including elastic scattering (RBS; elastic recoil detection, ERD; and non-Rutherford elastic backscattering, EBS), nuclear reaction analysis (NRA: including particle-induced gamma-ray emission, PIGE), and also particle-induced X-ray emission (PIXE)...
October 17, 2016: Analyst
Parnia Abyar Ghamsari, Milad Nouraliei, Sara Soleimani Gorgani
Adsorption of hydrogen (H2) and nitrogen (N2) molecules was analyzed on a new fullerene-like C16Mg8O8 nano-cage, composed of magnesium, oxygen, and carbon, using density functional theory. A detailed analysis of the energy, geometry, and electronic structure of various H2 and N2 adsorptions on the cluster surface was performed. The adsorption energies of H2 and N2 were estimated to ranging from -0.16 to -0.52eV, respectively. The most stable adsorption configurations were those in which the H or N atoms of the adsorbates were located near the Mg atom of the cluster surface at different sides...
August 13, 2016: Journal of Molecular Graphics & Modelling
Katsuyuki Nobusada
A simple and efficient method to inhibit aggregation of Pt clusters supported on metal-oxide is presented and assessed. This method preserves the accessible clusters surface where catalytic active sites are located and is effective even at relatively high temperatures up to 700K. The key idea is the inclusion of transition metal atoms, such as Ni, into the Pt clusters realizing the anchoring via the formation of strong chemical bonds with oxygen atoms of the metal-oxide support. To elucidate the efficiency of the method, we use first-principles molecular dynamics enhanced with free-energy sampling methods...
October 15, 2016: Chemistry: a European Journal
Laurent Piccolo, Z Y Li, Ilker Demiroglu, Florian Moyon, Zere Konuspayeva, Gilles Berhault, Pavel Afanasiev, Williams Lefebvre, Jun Yuan, Roy L Johnston
Heterogeneous catalysis, which is widely used in the chemical industry, makes a great use of supported late-transition-metal nanoparticles, and bimetallic catalysts often show superior catalytic performances as compared to their single metal counterparts. In order to optimize catalyst efficiency and discover new active combinations, an atomic-level understanding and control of the catalyst structure is desirable. In this work, the structure of catalytically active AuRh bimetallic nanoparticles prepared by colloidal methods and immobilized on rutile titania nanorods was investigated using aberration-corrected scanning transmission electron microscopy...
October 14, 2016: Scientific Reports
Eduardo Ortega, Arturo Ponce, Ulises Santiago, Diego Alducin, Alfredo Benitez-Lara, Germán Plascencia-Villa, Miguel José-Yacamán
The present work explores electron diffraction methods for studying the structure of metallic clusters stabilized with thiol groups, which are susceptible to structural damage caused by electron beam irradiation. There is a compromise between the electron dose used and the size of the clusters since they have small interaction volume with electrons and as a consequence weak reflections in the diffraction patterns. The common approach of recording individual clusters using nanobeam diffraction has the problem of an increased current density...
2017: Adv Struct Chem Imaging
Kohei Koyama, Toshiaki Nagata, Satoshi Kudoh, Ken Miyajima, Douwe M M Huitema, Valeriy Chernyy, Joost M Bakker, Fumitaka Mafune
Infrared multiple photon dissociation (IR-MPD) spectra of Rh6Om+ (m = 4-10) are obtained in the 300-1000 cm-1 spectral range using the free electron laser for infrared experiments (FELIX) via dissociation of Rh6Om+ or Rh6Om+-Ar complexes. The spectra are compared with the calculated spectra of several stable geometries obtained by density functional theory (DFT) structural optimization. The spectrum for Rh6O4+ shows prominent bands at 620 and 690 cm-1, and is assigned to a capped-square pyramidal Rh atom geometry with three bridging O atoms and one O atom in a hollow site...
October 13, 2016: Journal of Physical Chemistry. A
Katsuaki Konishi, Mitsuhiro Iwasaki, Mizuho Sugiuchi, Yukatsu Shichibu
Recent advances in the crystal structure determination of ligand-protected metal clusters have revealed that their electronic structures and optical features are essentially governed by the nuclearity and geometries of the inorganic frameworks. In this perspective, we point out the definite effects of the exterior ligand moieties on the properties of small gold clusters. Based on the systematic experimental studies on the optical properties of Au8 and Au13 clusters with various anionic ligands, it was shown that not only the "through-bond" electronic effects of coordinating atoms but also the non-bonding interaction with neighboring heteroatoms and the electronic coupling with π-systems cause substantial perturbations...
October 13, 2016: Journal of Physical Chemistry Letters
Marta Cavo, Marco Fato, Leonardo Peñuela, Francesco Beltrame, Roberto Raiteri, Silvia Scaglione
Three-dimensional (3D) cell cultures represent fundamental tools for the comprehension of cellular phenomena both in normal and in pathological conditions. In particular, mechanical and chemical stimuli play a relevant role on cell fate, cancer onset and malignant evolution. Here, we use mechanically-tuned alginate hydrogels to study the role of substrate elasticity on breast adenocarcinoma cell activity. The hydrogel elastic modulus (E) was measured via atomic force microscopy (AFM) and a remarkable range (150-4000 kPa) was obtained...
October 13, 2016: Scientific Reports
Sebastian D Pike, Edward R White, Milo S P Shaffer, Charlotte K Williams
The bottom-up synthesis of ligand-stabilized functional nanoparticles from molecular precursors is widely applied but is difficult to study mechanistically. Here we use (31)P NMR spectroscopy to follow the trajectory of phosphinate ligands during the synthesis of a range of ligated zinc oxo clusters, containing 4, 6 and 11 zinc atoms. Using an organometallic route, the clusters interconvert rapidly and self-assemble in solution based on thermodynamic equilibria rather than nucleation kinetics. These clusters are also identified in situ during the synthesis of phosphinate-capped zinc oxide nanoparticles...
October 13, 2016: Nature Communications
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