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Ab Initio

Andrey A Buglak, Ruslan R Ramazanov, Alexei I Kononov
Binding of silver ion (Ag+ ) and two atomic neutral silver cluster (Ag2 ) with a set of amino acids has been studied using Density Functional Theory (DFT) and ab initio MP2 method. We show that binding energy with Ag2 is higher for deprotonated anionic amino acids. Cysteine, aspartic acid, and tyrosine with deprotonated side chain exhibit the highest binding energy (Gbind ) values among all the amino acids: - 30.1 kcal mol-1 , - 30.7 kcal mol-1 , and - 30.9 kcal mol-1 , respectively. Binding energies of deprotonated cysteine, glutamic acid, tyrosine, and aspartic acid with silver ion Ag+ are reported here for the first time...
March 21, 2019: Amino Acids
N Klemke, N Tancogne-Dejean, G M Rossi, Y Yang, F Scheiba, R E Mainz, G Di Sciacca, A Rubio, F X Kärtner, O D Mücke
Attosecond metrology sensitive to sub-optical-cycle electronic and structural dynamics is opening up new avenues for ultrafast spectroscopy of condensed matter. Using intense lightwaves to precisely control the fast carrier dynamics in crystals holds great promise for next-generation petahertz electronics and devices. The carrier dynamics can produce high-order harmonics of the driving field extending up into the extreme-ultraviolet region. Here, we introduce polarization-state-resolved high-harmonic spectroscopy of solids, which provides deeper insights into both electronic and structural sub-cycle dynamics...
March 21, 2019: Nature Communications
S Ohmura, F Shimojo
The structural properties of liquid sulphur under high pressure up to approximately 500 GPa have been investigated by means of ab initio molecular-dynamics (MD) simulations. The obtained pair distribution functions and spatial distribution of electron density under high pressure indicate the existence of a covalent-like interaction even in the metallic state and the covalent-like interaction gradually decreases with increasing pressure. By analyzing the static structure factor, it is found that the covalent-like interaction still remains at approximately 200 GPa, and liquid sulphur has a simple liquid structure at 320 GPa and higher pressures...
March 21, 2019: Journal of Physics. Condensed Matter: An Institute of Physics Journal
Pierre Winter, Jeremy O Richardson
Ring-polymer instanton theory has been developed to simulate the quantum dynamics of molecular systems at low temperatures. Chemical reaction rates can be obtained by locating the dominant tunneling pathway and analyzing fluctuations around it. In the standard method, calculating the fluctuation terms involves the diagonalization of a large matrix, which can be unfeasible for large systems with a high number of ring- polymer beads. Here we present a method for computing the instanton fluctuations with a large reduction in computational scaling...
March 21, 2019: Journal of Chemical Theory and Computation
Francesca Nunzi, Diego Cesario, Leonardo Belpassi, Francesco Tarantelli, Luiz F Roncaratti, Stefano Falcinelli, David Cappelletti, Fernando Pirani
We have carried out molecular-beam scattering experiments and high-level ab initio investigations on the potential energy surfaces of a series of noble-gas-Cl2 adducts. This effort has permitted the construction of a simple, reliable and easily generalizable analytical model potential formulation, which is based on a few physically meaningful parameters of the interacting partners and transparently shows the origin, strength, and stereospecificity of the various interaction components. The results demonstrate quantitatively beyond doubt that the interaction between a noble-gas (Ng) atom - even He - and Cl2 in a collinear configuration is characterized by weak halogen bond (XB) formation, accompanied by charge transfer (CT) from the Ng to chlorine...
March 21, 2019: Physical Chemistry Chemical Physics: PCCP
Daniel Rabin, David Fuks, Yaniv Gelbstein
Half-Heusler, HH, alloys are widely used n-type materials in thermoelectric applications. Today, there is a shortage in p-type HH based materials, which may have an inherent compatibility with the HH n-type pair. Al is a good candidate as an acceptor doping element for this purpose, and the results on alloying of TiNiSn-based HH with Al are reported in details. Combination of CALPHAD and ab initio DFT calculations with an experimental validation was carried out. It is demonstrated that low level Al doping leads to p-type conductivity of the material...
March 21, 2019: Physical Chemistry Chemical Physics: PCCP
Petr Čermák, Astrid Schneidewind, Benqiong Liu, Michael Marek Koza, Christian Franz, Rudolf Schönmann, Oleg Sobolev, Christian Pfleiderer
Nearly a century of research has established the Born-Oppenheimer approximation as a cornerstone of condensed-matter systems, stating that the motion of the atomic nuclei and electrons may be treated separately. Interactions beyond the Born-Oppenheimer approximation are at the heart of magneto-elastic functionalities and instabilities. We report comprehensive neutron spectroscopy and ab initio phonon calculations of the coupling between phonons, CEF-split localized 4f electron states, and conduction electrons in the paramagnetic regime of [Formula: see text], an archetypal Kondo lattice compound...
March 20, 2019: Proceedings of the National Academy of Sciences of the United States of America
Jhon Zapata-Rivera, Carmen J Calzado
Metal dithiolene complexes-M(dmit)₂-are key building blocks for magnetic, conducting, and optical molecular materials, with singular electronic structures resulting from the mixing of the metal and dmit ligand orbitals. Their use in the design of magnetic and conducting materials is linked to the control of the unpaired electrons and their localized/delocalized nature. It has been recently found that UV⁻Vis light can control the spin distribution of some [Cu(dmit)₂]-2 salts in a direct and reversible way...
March 19, 2019: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Lei Tan, Keith Refson, Martin T Dove
The crystal structure of the low-temperature δ phase of crystalline malononitrile, CH2(CN)2 (stable phase below 260 K), has been determined using Rietveld refinement on neutron powder diffraction data. The δ phase has a slightly lower density than the other three low-pressure phases, and unlike those phases it has a polar structure. The reconstructive transition from the β to δ phase involves a major reconstruction of the structure, including establishing a network of hydrogen bonds. DFT simulations of the structure and phonon dispersion curves of both α and δ phases give free energy curves consistent with the phase transitions...
March 20, 2019: Journal of Physics. Condensed Matter: An Institute of Physics Journal
Yutong Wang, Weihai Fang, Run Long, Oleg V Prezhdo
The influence of grain boundaries (GBs) on charge carrier lifetimes in methylammonium lead triiodide perovskite (MAPbI3) remains unclear. Some experiments suggest that GBs promote rapid nonradiative decay and deteriorate device performance, while other measurements indicate that charge recombination happens primarily in non-GB regions, and that GBs facilitate charge separation and collection. By combining time-domain density functional theory and nonadiabatic (NA) molecular dynamics, we demonstrate that charge separation and localization happening at MAPbI3 GBs due to symmetry breaking suppresses charge recombination...
March 20, 2019: Journal of Physical Chemistry Letters
Thomas Northey, Adam Kirrander
A fragment-based approach for the prediction of elastic x-ray scattering is presented. The total diffraction pattern is assembled from anisotropic form factors calculated for individual molecular fragments, optionally including corrections for pair-wise interactions between fragments. The approach is evaluated against full ab-initio scattering calculations in the peptide diphenylalanine, and the optimal selection of fragments is examined in the ethanol molecule. The approach is found to improve significantly on the independent atom model, while remaining conceptually simple and computationally efficient...
March 20, 2019: Journal of Physical Chemistry. A
Sangeeta Sur, Ernesto Quintas-Sánchez, Steve A Ndengué, Richard Dawes
The cycle of formation and destruction of ozone is an important process in the atmosphere. A key step in the formation process is the stabilization of a metastable ozone molecule, which occurs through energy transfer: usually a highly excited ozone molecule loses the excess energy through inelastic collisions with a third body (M). However, the details of this energy transfer mechanism are still not well known and one of the reasons has been the lack of an accurate potential energy surface (PES). In theoretical studies, Ar is often selected as the third body when considering O3-M dynamics...
March 20, 2019: Physical Chemistry Chemical Physics: PCCP
Silvia Amabilino, Lars Andersen Bratholm, Simon Jonathan Bennie, Alain C Vaucher, Markus Reiher, David R Glowacki
Whilst the primary bottleneck to a number of computational workflows was not so long ago limited by processing power, the rise of machine learning technologies has resulted in an interesting paradigm shift, which places increasing value on issues related to data curation - i.e., data size, quality, bias, format, and coverage. Increasingly, data-related issues are equally as important as the algorithmic methods used to process and learn from the data. Here we introduce an open source GPU-accelerated neural network (NN) framework for learning reactive potential energy surfaces (PESs), and investigate the use of real-time interactive ab initio molecular dynamics in virtual reality (iMD-VR) as a new strategy which enables human users to rapidly sample geometries along reaction pathways which can subsequently be used to train NNs to learn efficient reactive PESs...
March 20, 2019: Journal of Physical Chemistry. A
M Meinero, F Caglieris, I Pallecchi, G Lamura, S Ishida, H Eisaki, A Continenza, M Putti
Anisotropy of transport and magnetic properties of parent compounds of iron based superconductors is a key ingredient of superconductivity. In this work, we investigate in-plane and out-of-plane properties, namely thermal, electric, thermoelectric transport and magnetic susceptibility in a high quality BaFe2 As2 single crystal of the 122 parent compound, using a combined experimental and theoretical approach. Combining the ab initio calculation of the band structure and the measured in-plane and out-of-plane resistivity, we evaluate the scattering rates which turn out to be strongly anisotropic and determined by spin excitations in the antiferromagnetic state...
March 19, 2019: Journal of Physics. Condensed Matter: An Institute of Physics Journal
Prashanth Sandineni, Hooman Yaghoobnejad Asl, Nikolay Gerasimchuk, Kartik Ghosh, Amitava Choudhury
New iron phosphates with related structures have been synthesized using hydrothermal and ion-exchange routes, and their electrochemical properties were investigated. First, NaFe(HPO4 )2 was synthesized employing a hydrothermal route and its structure was determined from single-crystal X-ray diffraction data. Subsequent Na+ and partial proton ion exchange with Li+ ion produced a known phase, Li2 Fe(H0.5 PO4 )2 , and complete deprotonation of Li2 Fe(H0.5 PO4 )2 with Li+ by employing a solid-state ion-exchange route produced the new phase Li3 Fe(PO4 )2 ...
March 19, 2019: Inorganic Chemistry
Barbara Marchetti, Tolga N V Karsili, Michael N R Ashfold
Norrish reactions are important photo-induced reactions in mainstream organic chemistry and are implicated in many industrially and biologically relevant processes and in the processing of carbonyl molecules in the atmosphere. The present study reports multi-reference electronic structure calculations designed to assess details of the potential energy profiles associated with the Norrish type-I and type-II reactions of a prototypical ketone 5-methyl-hexan-2-one. We show that the well-established 'triplet state mediated' reaction pathways following initial population of a singlet excited state can be complemented by (hitherto rarely recognized) 'singlet state only' Norrish type-I and type-II reaction mechanisms that involve no spin-forbidden transitions along the respective reaction paths, and suggest how the efficiencies of such reactions might be affected by strategic substitutions at selected sites within the parent ketone...
March 19, 2019: Physical Chemistry Chemical Physics: PCCP
Xiaohu He, Wenliang Li, Huiyan Meng, Chuanliang Li, Guqing Guo, Xuanbing Qiu, Jilin Wei
Quantum time-dependent wave-packet calculations have been carried out to explore the state-to-state dynamics of the ion-molecule (H-(D-),HD) collisions on two accurate ab initio potential energy surfaces in the collision energy range 0.2-1.2 eV. Total and final state-resolved integral and differential cross sections are elaborated in detail. The differential cross sections vary substantially with the collision energy, turning from predominantly backward-scattering at low collision energies to forward and sideways scattering bias at relatively high collision energies...
March 19, 2019: Physical Chemistry Chemical Physics: PCCP
Patrick D Taylor, Dale A Osborne, Sherif Abdulkader Tawfik, Tetsuya Morishita, Michelle J S Spencer
Silicene, the silicon analog of graphene, is an atomically thin two-dimensional material with promising applications in gas sensing, storage and as components in modern electronic devices. Silicene epitaxially grown on the Ag(111) surface can expand the utility of the silver surface by enabling the tuning of its work function through the functionalisation of silicene. Here we examine the electronic and structural properties and the thermodynamic stability of functionalised silicene/4 × 4 Ag(111) using density functional theory calculations coupled with ab initio molecular dynamics (AIMD) simulations...
March 19, 2019: Physical Chemistry Chemical Physics: PCCP
Junjing Gu, Wei Wu, Thijs Stuyver, David Danovich, Roald Hoffmann, Yuta Tsuji, Sason Shaik
This study examined the nature of the electronic structure of representative cross-conjugated polyenes from a Valence Bond (VB) perspective. Our VBSCF calculations on a prototypical dendralene model reveal a remarkable inhibition of the delocalization compared to linear polyenes. Especially along the C-C backbone, the delocalization is virtually quenched, so that these compounds can essentially be considered as sets of isolated butadiene units. In direct contrast to the dendralene chains, quinodimethane compounds exhibit an enhancement in their delocalization compared to linear polyenes...
March 19, 2019: Journal of the American Chemical Society
Xin Yang, Jun Zou, Yifei Wang, Ying Xue, Sheng-Yong Yang
The asymmetric 1,3-dipolar cycloadditions of azomethine ylides with activated olefins are one of the most important and versatile methods for the synthesis of enantioenriched pyrroline and pyrrolidine derivatives. Despite both theoretical and practical importance, the roles of water molecules in reactivity and endo/exo selectivity remain unclear. To explore how water accelerates the reaction rates and improves the endo/exo selectivity of the cycloadditions of 1,3-dipole phthalazinium-2-dicyanomethanide (1) and two dipolarophiles, an ab initio-quality neural network potential that overcomes the computational bottleneck of explicitly considering water molecules has been used...
March 19, 2019: Chemistry: a European Journal
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