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Atomic clusters

Antina Ghosh, Zoe Budrikis, Vijayakumar Chikkadi, Alessandro L Sellerio, Stefano Zapperi, Peter Schall
When strained beyond the linear regime, soft colloidal glasses yield to steady-state plastic flow in a way that is similar to the deformation of conventional amorphous solids. Because of the much larger size of the colloidal particles with respect to the atoms comprising an amorphous solid, colloidal glasses allow us to obtain microscopic insight into the nature of the yielding transition, as we illustrate here combining experiments, atomistic simulations, and mesoscopic modeling. Our results unanimously show growing clusters of nonaffine deformation percolating at yielding...
April 7, 2017: Physical Review Letters
Ji-Kun Li, Jing Dong, Chuan-Ping Wei, Song Yang, Ying-Nan Chi, Yan-Qing Xu, Chang-Wen Hu
Six alkoxohexavanadate-based Cu- or Co-POVs [Cu(dpa)(acac)(H2O)]2[V6O13(OMe)6] (1), [Cu(phen)(acac)(MeOH)]2[V6O13(OMe)6] (2), [Co(dpa)(acac)2]2[V6O13(OMe)6]·2MeOH (3), [Co(phen)(acac)2]2[V6O13(OMe)6] (4), [Cu(dpa)(acac)]2[V(IV)2V(V)4O12(OMe)7] (5), and [Cu(dpa)(acac)(MeOH)]2[V(IV)2V(V)4O11(OMe)8] (6) (POV = polyoxovanadate; dpa = 2,2'-dipyridine amine; phen = 1,10-phenanthroline; acac = acetylacetone anion) have been synthesized by controlling the reaction conditions and characterized by single-crystal X-ray diffraction and powder X-ray diffraction analyses, FT-IR spectroscopy, element analyses, and X-ray photoelectron spectroscopy...
April 21, 2017: Inorganic Chemistry
Richard Wayne Leggett
The transition metal yttrium (Y, atomic number 39) is chemically similar to elements in the lanthanide family (atomic numbers 57-71) and is found with the lanthanides in rare earth ores. Yttrium and the lanthanide holmium are referred to as geochemical twins because they generally show little fractionation from metamorphic or weathering processes, due to their closely similar chemical properties and nearly identical ionic radii. Extensive measurements on rocks, soils, and meteorites indicate that the Y/Ho mass concentration ratio rarely falls far from the so-called chondritic or solar system ratio of ~26...
April 21, 2017: Journal of Radiological Protection: Official Journal of the Society for Radiological Protection
Serhii I Vasylevskyi, Sonja Kracht, Paula Corcosa, Katharina M Fromm, Bernd Giese, Michael Füeg
The reduction of Ag(+) ions to Ag(0) atoms is a highly endergonic reaction step, only the aggregation to Agn clusters leads to an exergonic process. These elementary chemical reactions play a decisive role if Ag nanoparticles (AgNPs) are generated by electron transfer (ET) reactions to Ag(+) ions. We studied the formation of AgNPs in peptides by photoinduced ET, and in c-cytochromes by ET from their Fe(2+) /hemes. Our earlier photoinduced experiments in peptides had demonstrated that histidine prevents AgNP formation...
April 21, 2017: Angewandte Chemie
Martin K Schmitt, Oliver Janka, Rainer Pöttgen, Christopher Benndorf, Marcos de Oliveira, Hellmut Eckert, Florian Pielnhofer, Amadeus-Samuel Tragl, Richard Weihrich, Bastian Joachim, Dirk Johrendt, Hubert Huppertz
We report on the first thoroughly characterized molybdenum borate, which was synthesized in a high-pressure/high-temperature experiment at 12.3 GPa/1300 °C using a Walker-type multianvil apparatus. Mo2 B4 O9 incorporates tetrahedral molybdenum clusters into an anionic borate crystal structure-a structural motif that has never been observed before in the wide field of borate crystal chemistry. The six bonding molecular orbitals of the [Mo4 ] tetrahedron are completely filled with 12 electrons, which are fully delocalized over the four molybdenum atoms...
April 21, 2017: Angewandte Chemie
Nancy Y Acelas, Cacier Hadad, Albeiro Restrepo, César Ibarguen, Elizabeth Flórez
In this work, we used density functional theory calculations to study the resulting complexes of adsorption and of inner- and outer-sphere adsorption-like of bicarbonate and nitrate over Fe-(hydr)oxide surfaces using acidic, neutral, and basic simulated pH conditions. High-spin states that follow the 5N + 1 (N is the number of Fe atoms, each having five unpaired electrons) rule are preferred. Monodentate mononuclear (MM1) surface complexes are shown to lead to the most favorable thermodynamic adsorption for both bicarbonate and nitrate with -63...
April 20, 2017: Inorganic Chemistry
L Li, Q Zheng, Q Zou, S Rajput, A O Ijaduola, Z Wu, X P Wang, H B Cao, S Somnath, S Jesse, M Chi, Z Gai, D Parker, A S Sefat
Quantum materials such as antiferromagnets or superconductors are complex in that chemical, electronic, and spin phenomena at atomic scales can manifest in their collective properties. Although there are some clues for designing such materials, they remain mainly unpredictable. In this work, we find that enhancement of transition temperatures in BaFe2As2-based crystals are caused by removing local-lattice strain and electronic-structure disorder by thermal annealing. While annealing improves Néel-ordering temperature in BaFe2As2 crystal (T N  = 132 K to 136 K) by improving in-plane electronic defects and reducing overall a-lattice parameter, it increases superconducting-ordering temperature in optimally cobalt-doped BaFe2As2 crystal (T c = 23 to 25 K) by precipitating-out the cobalt dopants and giving larger overall a-lattice parameter...
April 19, 2017: Scientific Reports
Jeong Hyun Lee, Raiees Andrabi, Ching-Yao Su, Anila Yasmeen, Jean-Philippe Julien, Leopold Kong, Nicholas C Wu, Ryan McBride, Devin Sok, Matthias Pauthner, Christopher A Cottrell, Travis Nieusma, Claudia Blattner, James C Paulson, Per Johan Klasse, Ian A Wilson, Dennis R Burton, Andrew B Ward
Broadly neutralizing antibodies (bnAbs) to HIV delineate vaccine targets and are prophylactic and therapeutic agents. Some of the most potent bnAbs target a quaternary epitope at the apex of the surface HIV envelope (Env) trimer. Using cryo-electron microscopy, we solved the atomic structure of an apex bnAb, PGT145, in complex with Env. We showed that the long anionic HCDR3 of PGT145 penetrated between glycans at the trimer 3-fold axis, to contact peptide residues from all three Env protomers, and thus explains its highly trimer-specific nature...
April 18, 2017: Immunity
Michael J Servis, David T Wu, Jenifer C Braley
Extraction of polar molecules by amphiphilic species results in a complex variety of clusters whose topologies and energetics control phase behavior and efficiency of liquid-liquid separations. A computational approach including quantum mechanical vibrational frequency calculations and molecular dynamics simulation with intermolecular network theory is used to provide a robust assessment of extractant and polar solute association through hydrogen bonding in the tributyl phosphate (TBP)/HNO3/H2O/dodecane system for the first time...
April 18, 2017: Physical Chemistry Chemical Physics: PCCP
Zainul Aabdin, XiuMei Xu, Soumyo Sen, Utkarsh Anand, Petr Kral, Frank Holsteyns, Utkur Mirsaidov
Wet chemical etching is a key process in fabricating silicon (Si) nanostructures. Currently, wet etching of Si is proposed to occur through the reaction of Si surface atoms with etchant molecules, forming etch intermediates that dissolve directly into the bulk etchant solution. Here, using in situ transmission electron microscopy we follow the nanoscale wet etch dynamics of amorphous Si (a-Si) nanopillars in real-time and show that intermediates generated during alkaline wet etching first aggregate as nanoclusters on the Si surface then detach from the surface before dissolving in the bulk solution...
April 18, 2017: Nano Letters
Chaouki Siouani, Sofiane Mahtout, Sofiane Safer, Franck Rabilloud
We systematically study the equilibrium geometries, electronic and magnetic properties of Gen+1 and VGen (n = 1-19) clusters using the density functional theory approach (DFT) within the generalized gradient approximation (GGA). Endohedral structures in which the vanadium atom is encapsulated inside a Gen cage are predicted to be favored for n ≥ 10. The dopant V atom in the Gen clusters has not an immediate effect on the stability of small germanium clusters (n<6) but it largely contributes to strengthen the stability for n ≥ 7...
April 18, 2017: Journal of Physical Chemistry. A
David J Wales
A general scheme is derived to connect transitions in configuration space with features in the heat capacity. A formulation in terms of occupation probabilities for local minima that define the potential energy landscape provides a quantitative description of how contributions arise from competition between different states. The theory does not rely on a structural interpretation for the local minima, so it is equally applicable to molecular energy landscapes and the landscapes defined by abstract functions...
March 2017: Physical Review. E
Xiang Ma, Shuai Zhang, Fang Jiao, Christina J Newcomb, Yuliang Zhang, Arushi Prakash, Zhihao Liao, Marcel D Baer, Christopher J Mundy, James Pfaendtner, Aleksandr Noy, Chun-Long Chen, James J De Yoreo
Two-step nucleation pathways in which disordered, amorphous, or dense liquid states precede the appearance of crystalline phases have been reported for a wide range of materials, but the dynamics of such pathways are poorly understood. Moreover, whether these pathways are general features of crystallizing systems or a consequence of system-specific structural details that select for direct versus two-step processes is unknown. Using atomic force microscopy to directly observe crystallization of sequence-defined polymers, we show that crystallization pathways are indeed sequence dependent...
April 17, 2017: Nature Materials
Weifeng Tu, Mireille Ghoussoub, Chandra Veer Singh, Ya-Huei Cathy Chin
This study describes a new C-H bond activation pathway during CH4-CO2 reactions on oxophilic Ni-Co and Co clusters, unlike those established previously on Ni clusters. The initial C-H bond activation remains as the sole kinetically relevant step on Ni-Co, Ni, and Co clusters, but their specific reaction path varies. On Ni clusters, C-H bond activation occurs via an oxidative addition step that involves a three center (H3C∙∙∙*∙∙∙H)(‡) transition state, during which a Ni atom inserts into the C-H bond and donates its electron density into the C-H bond anti-bonding orbital...
April 17, 2017: Journal of the American Chemical Society
Hannes Steinkellner, Himanshu Narayan Singh, Martina U Muckenthaler, Hans Goldenberg, Rajeswari R Moganty, Barbara Scheiber-Mojdehkar, Brigitte Sturm
Friedreich's ataxia (FRDA) is a neurodegenerative disease caused by reduced expression of the protein frataxin. Frataxin is thought to play a role in iron-sulfur cluster biogenesis and heme synthesis. In this study, we used erythroid progenitor stem cells obtained from FRDA patients and healthy donors to investigate the putative role, if any, of frataxin deficiency in heme synthesis. We used electrochemiluminescence and qRT-PCR for frataxin protein and mRNA quantification. We used atomic absorption spectrophotometry for iron levels and a photometric assay for hemoglobin levels...
April 12, 2017: Gene
Mario Fernández-Fernández, Pablo Rodríguez-González, David Hevia Sánchez, Pedro González-Menéndez, Rosa M Sainz Menéndez, J Ignacio García Alonso
This work describes a methodology based on multiple linear regression and GC-MS for the determination of molar fractions of isotopically-labeled intracellular metabolites in cell cultures. Novel aspects of this work are: i) the calculation of theoretical isotopic distributions of the different isotopologues from an experimentally measured value of % 13C enrichment of the labeled precursor ii) the calculation of the contribution of lack of mass resolution of the mass spectrometer and different fragmentation mechanism such as the loss or gain of hydrogen atoms in the EI source to measure the purity of the selected cluster for each metabolite and iii) the validation of the methodology not only by the analysis of gravimetrically prepared mixtures of isotopologues but also by the comparison of the obtained molar fractions with experimental values obtained by GC-Combustion-IRMS based on (13)C/(12)C isotope ratio measurements...
May 29, 2017: Analytica Chimica Acta
Luan Feitoza, Marcos A Castro, Salviano A Leão, Tertius L Fonseca
In this work, we report results for the static second hyperpolarizability of magnesium oxide clusters including electronic and vibrational contributions. The comparison between second-order Møller-Plesset (MP2) perturbation theory and coupled cluster results to the electronic contribution points out that MP2 is a suitable method to compute this property. When computed at the MP2 level, the electronic contribution per atom converges to approximately 5000 a.u. Vibrational corrections were computed at the MP2 level through the perturbation theoretical method of Bishop and Kirtman...
April 14, 2017: Journal of Chemical Physics
Aldo Cervantes-Flores, Heriberto Cruz-Martínez, Omar Solorza-Feria, Patrizia Calaminici
A first-principle investigation of structures and properties of Ni n Pd n (n=1-5) clusters is presented. For this study, the linear combination of Gaussian-type orbitals auxiliary density functional theory (LCGTO-ADFT) method has been employed. In order to determine the lowest energy structures, several isomers in different spin multiplicities were studied, for each cluster size. Initial structures, for which successive geometry optimization was computed without any constrain, were taken along Born-Oppenheimer molecular dynamics (BOMD) trajectories...
May 2017: Journal of Molecular Modeling
Dipta B Ghosh, Suraj K Bajgain, Mainak Mookherjee, Bijaya B Karki
Knowledge about the incorporation and role of carbon in silicate magmas is crucial for our understanding of the deep mantle processes. CO2 bearing silicate melting and its relevance in the upper mantle regime have been extensively explored. Here we report first-principles molecular dynamics simulations of MgSiO3 melt containing carbon in three distinct oxidation states - CO2, CO, and C at conditions relevant for the whole mantle. Our results show that at low pressures up to 15 GPa, the carbon dioxide speciation is dominated by molecular form and carbonate ions...
April 12, 2017: Scientific Reports
Chunhui Liu, Hongyan Si, Peilin Han, Mingsheng Tang
The geometries and stabilities of BeBn(+) (up to n = 8) clusters, have been systematically investigated by using the B3LYP and CCSD(T) method. All the possible geometrical structures of BeBn(+) clusters were optimized at B3LYP/6-311 + G(d) level. The single point energies of all the structures were computed at CCSD(T)/aug-cc-pVDZ level. The calculated results showed the most stable structures of the BeBn(+) clusters are planar; the B atoms tend to aggregate to form the boron ring and the Be atoms as coordination atoms are in the periphery of the clusters...
April 12, 2017: Rapid Communications in Mass Spectrometry: RCM
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