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Atomic clusters

K Nagaya, D Iablonskyi, N V Golubev, K Matsunami, H Fukuzawa, K Motomura, T Nishiyama, T Sakai, T Tachibana, S Mondal, S Wada, K C Prince, C Callegari, C Miron, N Saito, M Yabashi, Ph V Demekhin, L S Cederbaum, A I Kuleff, M Yao, K Ueda
In high-intensity laser light, matter can be ionized by direct multiphoton absorption even at photon energies below the ionization threshold. However on tuning the laser to the lowest resonant transition, the system becomes multiply excited, and more efficient, indirect ionization pathways become operative. These mechanisms are known as interatomic Coulombic decay (ICD), where one of the species de-excites to its ground state, transferring its energy to ionize another excited species. Here we show that on tuning to a higher resonant transition, a previously unknown type of interatomic Coulombic decay, intra-Rydberg ICD occurs...
December 5, 2016: Nature Communications
Dinh Bao Nguyen, Thanh Danh Nguyen, Sangsoo Kim, Sang-Woo Joo
Spectral differences between cytosine (Cyt) and 5-methylcytosine (5MC) were investigated by means of Raman spectroscopy with a combination of density functional theory (DFT) calculations. Surface-enhanced Raman scattering (SERS) revealed discriminating peaks of 5MC from those of Cyt upon adsorption on gold nanoparticles (AuNPs). Among the notable features, the multiple bands between 850 and 700cm(-1) for the ring-breathing modes of 5MC and Cyt could be correlated well with the simulated spectra based on the DFT calculations of the adsorbates on the gold cluster atoms...
November 9, 2016: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
Wen Wu Xu, Beien Zhu, Xiao Cheng Zeng, Yi Gao
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...
December 2, 2016: Nature Communications
Colin Harthcock, Abdolreza Jahanbekam, Jeremy R Eskelsen, David Y Lee
We describe an example of a piecewise gas chamber that can be customized to incorporate a low flux of gas-phase radicals with an existing surface analysis chamber for in situ and stepwise gas-surface interaction experiments without any constraint in orientation. The piecewise nature of this gas chamber provides complete angular freedom and easy alignment and does not require any modification of the existing surface analysis chamber. In addition, the entire gas-surface system is readily differentially pumped with the surface chamber kept under ultra-high-vacuum during the gas-surface measurements...
November 2016: Review of Scientific Instruments
M J MacDonald, T Gorkhover, B Bachmann, M Bucher, S Carron, R N Coffee, R P Drake, K R Ferguson, L B Fletcher, E J Gamboa, S H Glenzer, S Göde, S P Hau-Riege, D Kraus, J Krzywinski, A L Levitan, K-H Meiwes-Broer, C P O'Grady, T Osipov, T Pardini, C Peltz, S Skruszewicz, M Swiggers, C Bostedt, T Fennel, T Döppner
Atomic clusters can serve as ideal model systems for exploring ultrafast (∼100 fs) laser-driven ionization dynamics of dense matter on the nanometer scale. Resonant absorption of optical laser pulses enables heating to temperatures on the order of 1 keV at near solid density conditions. To date, direct probing of transient states of such nano-plasmas was limited to coherent x-ray imaging. Here we present the first measurement of spectrally resolved incoherent x-ray scattering from clusters, enabling measurements of transient temperature, densities, and ionization...
November 2016: Review of Scientific Instruments
Shaodong Zhou, Jilai Li, Maria Schlangen, Helmut Schwarz
The thermal gas-phase reactions of the closed-shell heteronuclear metal-oxide clusters [AlCeOx ](+) (x=2-4) with methane have been explored by FT-ICR mass spectrometry and high-level quantum-chemical calculation. Whereas [AlCeO2 ](+) and [AlCeO4 ](+) are inert towards methane under ambient conditions, [AlCeO3 ](+) spontaneously abstracts one hydrogen atom from methane. Mechanistic aspects have been addressed to reveal the reasons for the rather distinct reactivities of the [AlCeOx ](+) /CH4 couples, and the electronic origins of the unprecedented single hydrogen-atom abstraction from methane by closed-shell [AlCeO3 ](+) are discussed...
December 2, 2016: Angewandte Chemie
Eszter Makkos, Andrew Kerridge, Jonathan Austin, Nikolas Kaltsoyannis
Density functional theory (DFT) at the generalised gradient approximation level is employed within the periodic electrostatic embedded cluster method (PEECM) to model the brucite (0001) surface. Three representative studies are then used to demonstrate the reliability of the PEECM for the description of the interactions of various ionic species with the layered Mg(OH)2 structure, and its performance is compared with periodic DFT, an approach known to be challenging for the adsorption of charged species. The adsorption energies of a series of s block cations, including Sr(2+) and Cs(+) which are known to coexist with brucite in nuclear waste storage ponds, are well described by the embedded cluster model, provided that basis sets of triple-zeta quality are employed for the adsorbates...
November 28, 2016: Journal of Chemical Physics
Yu Xia, Zhibing Li
To understand laser-assisted field evaporation of semiconductors and insulators at the microscopic level, we study the time evolution of the electronic and atomic structure of a MgO cluster in high electrostatic fields subjected to strong laser pulses. We find that the critical laser intensity for evaporation decreases linearly as the electrostatic field strength increases. The optical absorption enhancement in high electrostatic field is confirmed by the redshift of the optical absorption spectra, the reduction of the energy gap, and the increase of the absorption cross section...
November 28, 2016: Journal of Chemical Physics
Y Zhang, R Ashcraft, M I Mendelev, C Z Wang, K F Kelton
The state-of-the-art experimental and atomistic simulation techniques were utilized to study the structure of the liquid and amorphous Ni62Nb38 alloy. First, the ab initio molecular dynamics (AIMD) simulation was performed at rather high temperature where the time limitations of the AIMD do not prevent to reach the equilibrium liquid structure. A semi-empirical potential of the Finnis-Sinclair (FS) type was developed to almost exactly reproduce the AIMD partial pair correlation functions (PPCFs) in a classical molecular dynamics simulation...
November 28, 2016: Journal of Chemical Physics
Hans-Joachim Werner
The accuracy of multipole approximations for distant pair energies in local second-order Møller-Plesset perturbation theory (LMP2) as introduced by Hetzer et al. [Chem. Phys. Lett. 290, 143 (1998)] is investigated for three chemical reactions involving molecules with up to 92 atoms. Various iterative and non-iterative approaches are compared, using different energy thresholds for distant pair selection. It is demonstrated that the simple non-iterative dipole-dipole approximation, which has been used in several recent pair natural orbitals (PNO)-LMP2 and PNO-LCCSD (local coupled-cluster with singles and doubles) methods, may underestimate the distant pair energies by up to 50% and can lead to significant errors in relative energies, unless very tight thresholds are used...
November 28, 2016: Journal of Chemical Physics
John F Dobson, Andreas Savin, János G Ángyán, Ru-Fen Liu
We consider the zero-temperature van der Waals (vdW) interaction between two molecules, each of which has a zero or near-zero electronic gap between a ground state and the first excited state, using a toy model molecule (equilateral H3) as an example. We show that the van der Waals energy between two ground state molecules falls off as D(-3) instead of the usual D(-6) dependence, when the molecules are separated by distance D. We show that this is caused by a perfect "spooky" correlation between the two fluctuating electric dipoles...
November 28, 2016: Journal of Chemical Physics
Dzmitry S Firaha, Martin Thomas, Oldamur Hollóczki, Martin Korth, Barbara Kirchner
In this study, we aim at understanding the influence of dispersion correction on the ab initio molecular dynamics simulations of ionic liquid (IL) systems. We investigated a large bulk system of the 1-butyl-3-methylimidazolium triflate IL and a small cluster system of ethylamine in ethylammonium nitrate both under periodic boundary conditions. The large system displays several changes upon neglect of dispersion correction, the most striking one is the surprising decrease of the well-known microheterogeneity which is accompanied by an increase of side chain hydrogen atom-anion interplay...
November 28, 2016: Journal of Chemical Physics
Kota Kasahara, Kengo Kinoshita
Ion conduction mechanisms of ion channels are a long-standing conundrum. Although the molecular dynamics (MD) method has been extensively used to simulate ion conduction dynamics at the atomic level, analysis and interpretation of MD results are not straightforward due to complexity of the dynamics. In our previous reports, we proposed an analytical method called ion-binding state analysis to scrutinize and summarize ion conduction mechanisms by taking advantage of a variety of analytical protocols, e.g., the complex network analysis, sequence alignment, and hierarchical clustering...
2016: PloS One
Avelino Corma, Antonio Leyva, Miguel Angel Rivero
The Pt-catalysed hydrosilylation of alkynes is the procedure of choice to obtain vinylsilanes, and this is claimed to be the most relevant application of Pt in organic synthesis. More than half a century after its discovery, only -vinylsilanes (anti-Markovnikov addition) are obtained with simple Pt catalysts, while -vinylsilanes (Markovnikov addition) remain elusive compounds. Here we report that Pt3 clusters, in part-per-million (ppm) amounts, catalyse the Markovnikov hydrosilylation of terminal alkynes to give a wide variety of -vinylsilanes in reasonable isolated yields and with turnover frequencies that can reach up to one million per hour...
December 1, 2016: Chemistry: a European Journal
Amirul Edham Roslee, Saifful Kamaluddin Muzakir, Jamil Ismail, Mashitah M Yusoff, Rajan Jose
This article addresses the heat capacity of quantum dots (QDs) using density functional theory (DFT). By analyzing the evolution of phonon density of states and heat capacity as CdSe clusters grow from a molecular cluster into larger quantum confined solids, we have shown that their heat capacity does not fit very well with the Debye T(3) model. We observed that the number of phonon modes, which is discrete, increases as the particles grow, and the dispersion relation shows a quadratic behavior in contrast to the bulk solids whose dispersion relation is linear and equal to the sound velocity...
December 1, 2016: Physical Chemistry Chemical Physics: PCCP
Dylan C Gary, Alessio Petrone, Xiaosong Li, Brandi M Cossairt
The reaction of primary amines with In37P20(O2CR)51 is found to remove In(O2CR)3 subunits from In37P20(O2CR)51. This loss of Z-type ligands coincides with structural rearrangement to alleviate core strain and passivate phosphorus atoms. This result consolidates conflicting claims that primary amines both promote and retard precursor conversion rates for InP nanocrystals.
December 1, 2016: Chemical Communications: Chem Comm
Xizi Cao, Mengyi Chen, Jun Ma, Baoqi Yin, Xiaopeng Xing
Atomic oxygen on silver is the crucial active species in many catalytic oxidation processes, while it is a big challenge to explore the relationship between its activity and molecular-level structures in condensed phases. We carried out kinetic measurements of the gas phase reactions between AgnO(-) (n = 1-8) and CO, in which the oxygen atoms were predicted to be terminal ones in AgO(-) and Ag2O(-), in quasi-Ag-O-Ag chains for Ag3O(-) and Ag4O(-), and on the two-fold or three-fold bridging positions in AgnO(-) (n = 5-8)...
November 30, 2016: Physical Chemistry Chemical Physics: PCCP
Luca Evangelisti, Lorenzo Spada, Weixing Li, Susana Blanco, Juan Carlos López, Alberto Lesarri, Jens-Uwe Grabow, Walther Caminati
Upon supersonic expansion, formic acid and cyclobutanone (CBU) form a molecular cluster in which the two constituent molecules, linked by OHO and CHO hydrogen bonds, undergo a rapid interconversion between two equivalent forms. The tunneling motion takes place through the rupture and reformation of the C-HO hydrogen bond between the carbonyl oxygen of HCOOH and one of the two hydrogen atoms of the methylenic group adjacent to the cyclobutanone keto group. From the microwave spectra, tunneling energy splittings (ΔE01) have been determined for the parent (1122...
November 30, 2016: Physical Chemistry Chemical Physics: PCCP
Niancai Cheng, Samantha Stambula, Da Wang, Mohammad Norouzi Banis, Jian Liu, Adam Riese, Biwei Xiao, Ruying Li, Tsun-Kong Sham, Li-Min Liu, Gianluigi A Botton, Xueliang Sun
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...
November 30, 2016: Nature Communications
Mona Habibi, Jörg Rottler, Steven S Plotkin
Mechanical unfolding of a single domain of loop-truncated superoxide dismutase protein has been simulated via force spectroscopy techniques with both all-atom (AA) models and several coarse-grained models having different levels of resolution: A Gō model containing all heavy atoms in the protein (HA-Gō), the associative memory, water mediated, structure and energy model (AWSEM) which has 3 interaction sites per amino acid, and a Gō model containing only one interaction site per amino acid at the Cα position (Cα-Gō)...
November 2016: PLoS Computational Biology
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