Ab initio Molecular Dynamics

Water oxidation or oxygen evolution reaction (OER) in electrochemical cells is considered to be a major bottleneck in the way of hydrogen production by electro-synthesis, mainly due to a sluggish kinetics that characterizes the OER steps. Layered transition metal dichalcogenides, such as WSe2 , are emerging as promising non-precious electrocatalysts for water splitting due to their excellent activity and stability. This paper aims to shed light on the (100) WSe 2-aqueous interface in catalyzing the slow kinetics of the OER in the context of water splitting electro-catalysis. We employ state-of-the-art DFT-metadynamics to explore reaction mechanisms, activation free energies, and catalytic sites. This study reveals an energetically preferred water-assisted OER mechanism, where proton transfer is facilitated by the surrounding aqueous environment. Our findings not only provide insights into the OER process but also offer a design strategy for optimizing WSe2-based catalysts and a modeling protocol for future DFT-based OER investigations.

Experimental evidence exists for the enhancement of the hydrogen storage capacity of porous carbons when these materials are doped with metal nanoparticles. One of the most studied dopants is palladium. Dissociation of the hydrogen molecules and spillover of the H atoms towards the carbon substrate has been advocated as the reason for the enhancement of the storage capacity. We have investigated this mechanism by performing ab initio density functional molecular dynamics (AIMD) simulations of the deposition of molecular hydrogen on Pd 6 clusters anchored on graphene vacancies. The clusters are initially near-saturated with atomic and molecular hydrogen. This condition would facilitate the occurrence of spillover, since our energy calculations based on density functional theory indicate that migration of preadsorbed H atoms towards the graphene substrate becomes exothermic on Pd clusters with high hydrogen coverages. However, AIMD simulations show that the H atoms prefer to intercalate and absorb within the Pd cluster rather than migrate to the carbon substrate. These results reveal that high activation barriers exist preventing the spillover of hydrogen from the anchored Pd clusters to the carbon substrate.

Shock compression of silicon (Si) under extremely high pressures (>100 Mbar) was investigated by using two first-principles methods of orbital-free molecular dynamics (OFMD) and path integral Monte Carlo (PIMC). While pressures from the two methods agree very well, PIMC predicts a second compression maximum because of 1s electron ionization that is absent in OFMD calculations since Thomas-Fermi-based theories lack shell structure. The Kohn-Sham density functional theory is used to calculate the equation of state (EOS) of warm dense silicon for low-pressure loadings (P < 100 Mbar). Combining these first-principles EOS results, the principal shock Hugoniot curve of silicon for pressures varying from ~1 Mbar to above ~10 Gbar was derived. We find that silicon is ~20% or more softer than what was predicted by widely-used EOS models. Existing high-pressure experimental data (P ≈ 1 -2 Mbar) seem to indicate this softening behavior of Si, which calls for future strong-shock experiments (P > 10 Mbar) to benchmark our results.

A detailed chemical kinetic mechanism has been developed to describe the pyrolysis and oxidation of the hydrogen/NOx and syngas/NOx systems. The thermodynamic data of nitrogenous compounds have been updated based on the study of Bugler et al. [

Photoelectron (PES) spectra from aluminum cluster anions, Al - n (12 ≤ n ≤ 15), at various temperature regimes, were studied using ab-initio molecular dynamics simulations and experimentally. The calculated PES spectra, obtained via shifting of the simulated electronic densities of states by the self-consistently determined values of the asymptotic exchange-correlation potential, agree well with the measured ones, allowing reliable structural assignments and theoretical estimation of the clusters' temperatures.

The amorphous structure of four Ca 60 Mg X Zn 40-X (X=10, 15, 20, and 25 at. %) ternary metallic glasses (MGs) has been investigated by neutron and x-ray diffraction, using Reverse Monte Carlo modeling to simulate the results. A critical analysis of the resultant models, corroborated by ab initio molecular-dynamics simulations, indicate that the glass structure for this system can be described as a mixture of Mg-and Zn-centered clusters, with Ca dominating in the first coordination shell of these clusters. A coordination number (CN) of 10 [with about 7 Ca and 3(Mg+Zn) atoms] is most common for the Zn-centered clusters. CN=11 and 12 [with about 7-8 Ca and 4 (Mg+Zn) atoms] are most common for Mg-centered clusters. Fivefold bond configurations (pentagonal pyramids) dominate (~60%) in the first coordination shell of the clusters, suggesting dense atomic packing. Bond-angle distributions suggest near-equilateral triangles and pentagonal bipyramids to be the most common nearest atom configurations. This is the systematic characterization of the structure of Ca-Mg-Zn MGs, a category of bulk MGs with interesting properties and intriguing applications. It is also the experimental verification of the principle of efficient packing of solute-centered clusters in ternary MGs. 15. SUBJECT TERMS bulk metallic glasses (BMGs), molecular-dynamics simulations, phase diagrams 16. SECURITY CLASSIFICATION OF: 17. LIMITATION

In this work, we study vacancy energetics in the equiatomic Nb-Mo-Ta-W alloy, especially vacancy formation and migration energies, using molecular statics calculations based on a spectral neighbor analysis potential specifically developed for Nb-Mo-Ta-W. We consider vacancy properties in bulk environments as well as near edge dislocation cores, including the effect of short-range order (SRO) by preparing supercells through Metropolis Monte-Carlo relaxations and temperature on the calculation. The nudged elastic band (NEB) method is applied to study vacancy migration energies. Our results show that both vacancy formation energies and vacancy migration energies are statistically distributed with a wide spread, on the order of 1.0 eV in some cases, and display a noticeable dependence on SRO. We find that, in some cases, vacancies can form with very low energies at edge dislocation cores, from which we hypothesize the formation of stable ‘superjogs’ on edge dislocation lines. Moreover, ...

Gas-phase H9O4(+) has been considered an archetypal Eigen cation, H3O(+)(H2O)3. Yet ab initio molecular dynamics (AIMD) suggested that its infrared spectrum is explained by a linear-chain Zundel isomer, alone or in a mixture with the Eigen cation. Recently, hole-burning experiments suggested a single isomer, with a second-order vibrational perturbation theory (VPT2) spectrum agreeing with the Eigen cation. To resolve this discrepancy, we have extended both calculations to more advanced DFT functionals, better basis sets, and dispersion correction. For Zundel-isomers, we find VPT2 anharmonic frequencies for four low-frequency modes involving the excess proton unreliable, including the 1750 cm(-1) band that is pivotal for differentiating between Zundel and Eigen isomers. Because the analogous bands of the H5O2(+) cation show little effect of anharmonicity, we utilize the harmonic frequencies for these modes. With this caveat, both AIMD and VPT2 agree on the spectrum as originating fro...

We introduce a machine-learning interatomic potential for tungsten using the Gaussian Approximation Potential framework. We specifically focus on properties relevant for simulations of radiationinduced collision cascades and the damage they produce, including a realistic repulsive potential for the short-range many-body cascade dynamics and a good description of the liquid phase. Furthermore, the potential accurately reproduces surface properties and the energetics of vacancy and self-interstitial clusters, which have been long-standing deficiencies of existing potentials. The potential enables molecular dynamics simulations of radiation damage in tungsten with unprecedented accuracy.

Water is the best general solvent due to its molecular structure and distribution of electric charge Solute-solute and solute-solvent reactions lead to: complexation, binding, local ordering; clustering Features probed by scattering: interatomic distances; coordination numbers; extent of local ordering around a particular atom; orientation (tilt angle) Local structure divided into several parts: contact distance, nearest neighbor distance; end of short range order

En este trabajo, presentamos el estudio de las propiedades estructurales y electrónicas del compuesto YIn 3 N 4 en las fases NaCl (B1) y wurtzita para una presión anterior al cambio de fase de wurtzita hacia NaCl y para una posterior. Los cálculos se han realizado en el marco de la teoría de la densidad funcional, usado el método FP-LAPW. Los efectos de intercambio y correlación son tratados usando la aproximación del Gradiente Generalizado (GGA) implementado en Perdew-Burke-Ernzerhof.

Recibido para revisar D-M-A, aceptado D-M-A, versión final D-M-A. RESUMEN: Estudiamos las propiedades estructurales y electrónicas del carburo del ytrio (YC) en el volumen. El estudio se realiza a partir de primeros principios utilizando la teoría del funcional densidad con la aproximación de gradiente generalizado (GGA), esta última con el potencial Wu-Cohen en 2006 Tran et al. 2007 (WC). Los cálculos se realizaron en las fases Arseniuro de Niquel (NiAs), Cloruro de Sodio (NaCl), Cloruro de Cesio (CsCl) y zinc blenda (ZB) (incluyendo spin). Calculamos la densidad de estados y su estructura de bandas en la fase más estable del compuesto con los potenciales señalados.

A new class of sodium-water clusters with a low lying ionization potential (IP) is characterized by their photoionization spectra in molecular beam experiments. This implies that Na(H2O)n clusters coexist for n≥15 in two forms of significant abundances being distinguished by their IPs of ∼2.8 and ∼3.2 eV. A tentative quantum chemical characterization was achieved by simulating ionization spectra for selected cluster sizes using an ab initio molecular dynamics approach. Experiment and theory suggest that the Na+-e− distance is significantly larger in the clusters with the lower IP. This indicates that the solvated electron in Na(H2O)n clusters very probably forms with the Na+ counterion both a solvent separated and a contact ion pair.

Ab initio molecular dynamics simulations modeling low-energy collisions of a sodium atom with a cluster with more than 30 water molecules are presented. We follow the dynamics of the atom-cluster interaction and the delocalization of the valence electron of sodium together with the changes in the electron binding energy. This electron tends to be shared by the nascent sodium cation and the water cluster. IR spectra of the sodium-water cluster are both computationally and experimentally obtained, with a good agreement between the two approaches.

Olivia F. Dippo, Materials Science and Engineering Program, University of California San Diego [email protected] Tyler J. Harrington, Materials Science and Engineering Program, University of California San Diego Pranab Sarker, Mechanical Engineering and Materials Science, Duke University Cormac Toher, Department of Mechanical Engineering and Materials Science, Duke University Eduardo Marin, Dept. of NanoEngineering, University of California San Diego William M. Mellor, Dept. of NanoEngineering, University of California San Diego Matthew C. Quinn, Dept. of NanoEngineering, University of California San Diego Stefano Curtarolo, Materials Science, Electrical Engineering, Physics and Chemistry, Duke University Kenneth S. Vecchio, Dept. of NanoEngineering, University of California San Diego

The geometric and electronic structure of the Pb n clusters ͑n =2-15͒ has been calculated to elucidate its structural evolution and compared with other group-IV elemental clusters. The search for several low-lying isomers was carried out using the ab initio molecular dynamics simulations under the framework of the density functional theory formalism. The results suggest that unlike Si, Ge, and Sn clusters, which favor less compact prolate shape in the small size range, Pb clusters favor compact spherical structures consisting of fivefold or sixfold symmetries. The difference in the growth motif can be attributed to their bulk crystal structure, which is diamond-like for Si, Ge, and Sn but fcc for Pb. The relative stability of Pb n clusters is analyzed based on the calculated binding energies and second difference in energy. The results suggest that n = 4, 7, 10, and 13 clusters are more stable than their respective neighbors, reflecting good agreement with experimental observation. Based on the fragmentation pattern it is seen that small clusters up to n = 12 favor monomer evaporation, larger ones fragment into two stable daughter products. The experimental observation of large abundance for n = 7 and lowest abundance of n = 14 have been demonstrated from their fragmentation pattern. Finally a good agreement of our theoretical results with that of the experimental findings reported earlier implies accurate predictions of the ground state geometries of these clusters.

High-energy x-ray diffraction and ab initio molecular-dynamics simulations demonstrate that the short-range order in the deeply undercooled Zr 2 Ni liquid is quite nuanced. The second diffuse scattering peak in the total structure factory sharpens with supercooling, revealing a shoulder on the high-Q side that is often taken to be a hallmark of increasing icosahedral order. However, a Voronoi tessellation indicates that only approximately 3.5% of all the atoms are in an icosahedral or icosahedral-like environment. In contrast, a Honeycutt-Andersen analysis indicates that a much higher fraction of the atoms is in icosahedral ͑15%-18%͒ or distorted icosahedral ͑25%-28%͒ bond-pair environments. These results indicate that the liquid contains a large population of fragmented clusters with pentagonal and distorted pentagonal faces, but the fully developed icosahedral fragments are rare. Interestingly, in both cases, the ordering changes little over the 500 K of cooling. All metrics show that the nearest-neighbor atomic configurations of the most deeply supercooled simulated liquid ͑1173 K͒ differ topologically and chemically from those in the stable C16 compound, even though the partial pair distributions are similar. The most significant structural change upon decreasing the temperature from 1673 to 1173 K is an increase in the population of Zr in Ni-centered clusters. The structural differences between the liquid and the C16 increase the nucleation barrier, explaining glass formation in the rapidly quenched alloys.

The atomic structures in equilibrium and supercooled liquids of Zr 80 Pt 20 were determined as a function of temperature by in-situ high-energy synchrotron diffraction studies of the levitated liquids (containerless processing) using the beamline electrostatic levitation (BESL) technique. The presence of a pronounced pre-peak at q ~ 1.7 Å-1 in the static structure factor indicates medium range order (MRO) in the liquid. The position and intensity of the pre-peak remain constant with cooling, indicating that the MRO is already present in the liquid above its melting temperature. An analysis of the liquid atomic structures obtained using the Reverse Monte Carlo (RMC) method utilizing both the structure factor, S(q), from x-ray diffraction experiments and the partial pair-correlation functions from ab initio molecular dynamics (MD) simulations show that the pre-peak arises from a Pt-Pt correlation that can be indentified with icosahedral short-range order around the Pt atoms. The local atomic ordering is dominated by icosahedral-like structures, raising the nucleation barrier between the liquid and these phases, thus assisting glass formation.

Double-walled carbon and boron nitride hetero-nanotube Boron nitride doping Ab initio molecular dynamics method Electronic band structures a b s t r a c t The effect of boron nitride (BN) doping on electronic properties of armchair double-walled carbon and hetero-nanotubes is studied using ab initio molecular dynamics method. The armchair double-walled hetero-nanotubes are predicted to be semiconductor and their electronic structures depend strongly on the electronic properties of the single-walled carbon nanotube. It is found that electronic structures of BN-doped double-walled hetero-nanotubes are intermediate between those of double-walled boron nitride nanotubes and double-walled carbon and boron nitride hetero-nanotubes. Increasing the amount of doping leads to a stronger intertube interaction and also increases the energy gap.

The response to compression of the synthetic zeolite Li-ABW (LiAlSiO 4 Á H 2 O, Z = 4, s.g. Pna2 1 ) was explored by synchrotron X-ray powder diffraction experiments, using silicone oil as non-penetrating pressure transmitting medium, and Car Parrinello Molecular Dynamics simulations. In the range P amb -8.9 GPa, a nearly isotropic compression for the axial parameters and a cell volume decrease of approximately 12% are observed. A discontinuity in the cell parameters vs P behaviour can be detected between 5 and 6 GPa. As a consequence, the bulk modulus was calculated separately in the P amb -4.9 GPa and 5.6-8.9 GPa pressure ranges. The corresponding values (72(2) GPa and 80(2) GPa, respectively) are among the highest found up to now for zeolites studied with non-penetrating P-transmitting media. Molecular Dynamics simulations were performed at volumes corresponding to P amb , 1.5, 5.6, and 7.6 GPa, respectively. At 1.5 GPa the channel system is already elliptically deformed, and the zig-zag trend of the 4-ring tetrahedral chains is enhanced. Moreover, the water molecule chain running along the channel becomes interrupted and the water molecules are more strongly connected to the framework oxygen atoms. The four-fold coordination of Li cation is maintained up to the highest pressure and only a slight bond distance decrease is observed above 1.5 GPa. In the P amb -5.6 GPa range, all T-O-T angles decrease with pressure, and hence the Li-ABW structure can be defined as collapsible. Otherwise, at higher compression, average T-O-T angles increase slightly. Overall, the deformation of the Li-ABW upon compression resembles that achieved by anhydrous Li-ABW in the high temperature regimes.

The process of intermolecular electronic excitation transfer (EET) in a monodimensional supramolecular arrangement of molecules in confined space has been modelled and investigated by means of first‐principles molecular dynamics simulations. The chosen model system consists of a wire of chlorine molecules hosted in the noncrossing channels of the zeolite bikitaite. The time evolution of the system in its first excited singlet state has been described by the restricted open shell Kohn–Sham formalism. Simulation results have highlighted that excitation, initially localized on a guest molecule, is transferred to an adjacent moiety in the molecular wire on the picosecond scale via a collision‐induced Dexter‐type short range EET. Analysis of the modifications of the electronic structure of the system brought about by EET has given insight into the microscopic details of the process.

We show that new aspects of the physics of microclusters can be investigated accurately with ab initio molecular dynamics. We present results on a number of properties of Sin aggregates (N up to 10) at both zero and finite temperatures. The results of dynamical simulated annealing for the ground state point to a complex growth sequence. Simulations at finite temperatures show the existence of two regimes, solidlike and liquidlike, with substantially dift'erent electronic and structural properties.

We studied water on the rutile (110) surface using ab-initio molecular dynamics simulations in NVT ensemble at 280K, 300K, and 320K. Water adsorbs on the 5-fold coordinated titanium atoms or dissociates transferring a proton to a bridging-oxygen atom. The equilibrium between ...

Graphene (Gr) is known to be an excellent barrier preventing atoms and molecules to diffuse through it. This is due to the carbon atom arrangement in a two-dimensional (2D) honeycomb structure with a very small lattice parameter thus forming an electron cloud that prevents atoms and molecules crossing. Nonetheless at high annealing temperatures, intercalation of atoms through graphene occurs, opening the path for formation of vertical heterojunctions constituted of two-dimensional layers. In this paper, we report on the ability of silicon atoms to penetrate the graphene network, fully epitaxially grown on a Ni(111) surface, even at room temperature. Our scanning tunneling microscopy (STM) experiments show that the presence of defects like vacancies and dislocations in the graphene lattice favor the Si atoms intercalation, thus forming two-dimensional, flat and disordered islands below the Gr layer. Ab-initio molecular dynamics calculations confirm that Gr defects are necessary for Si intercalation at room temperature and show that: i) a hypothetical intercalated silicene layer cannot be stable for more than 8 ps and ii) the corresponding Si atoms completely lose their in-plane order resulting in a random planar distribution and form strong covalent bonds with Ni atoms.

Ab initio molecular dynamics (CPMD) coupled with metadynamics (MTD) simulations were used to investigate the free-energy surfaces of acid-catalyzed hydrolysis reactions of xylobiose disaccharide in the gas phase and in aqueous solution. Water and water structures were found to play a critical role in the hydrolysis reaction barrier. Proton partial desolvation associated with its migration to the ether linkage site, the protonation of the ether bond, and the subsequent breaking of the C-O bond were found to be the rate-limiting steps. The significant contribution to the reaction barrier caused by partial proton desolvation and migration could partially explain the biphasic phenomenon in xylan hydrolysis and highlight the importance of mass transport during biomass pretreatment.

Bimetallic catalysts are extensively sought as alternatives to the use of platinum in lowtemperature fuel cell electrodes, particularly for the cathode, where the kinetically-slow oxygen electroreduction takes place. One of the first questions that arise in trying to search for alternative catalysts relates to the understanding of the mechanism of the oxygen four-electron reduction on Pt, the best catalyst currently known, and how the mechanism would be altered (if at all) by the presence of other catalyst active sites. We discuss the nature of O 2 adsorption, and of the various intermediates, such as OOH, OH, O, H 2 O 2 , and H 2 O in the presence of hydrated protons (acid medium) on Pt and Pt-alloy catalysts, on the basis of density functional theory on small clusters and extended surfaces, and Car-Parrinello molecular dynamics simulations. We conclude with an overview of the current status and future perspectives for the design of new efficient and less expensive fuel cell catalysts.

We have employed ab initio molecular dynamics simulations in an attempt to study a temperature-induced order-disorder structural phase transformation that occurs in Li 2 NH at about 385 K. A structural phase transition was observed by us in the temperature range 300-400 K, in good agreement with experiment. This transition is associated with a melting of the cation sublattice ͑Li + ͒, giving rise to a superionic phase, which in turn is accompanied by an order-disorder transition of the N-H bond orientation. The results obtained here can contribute to a better understanding of the hydrogen storage reactions involving Li 2 NH and furthermore broaden its possible technological applications toward batteries and fuel cells.

High-energy x-ray diffraction and ab initio molecular-dynamics simulations demonstrate that the short-range order in the deeply undercooled Zr 2 Ni liquid is quite nuanced. The second diffuse scattering peak in the total structure factory sharpens with supercooling, revealing a shoulder on the high-Q side that is often taken to be a hallmark of increasing icosahedral order. However, a Voronoi tessellation indicates that only approximately 3.5% of all the atoms are in an icosahedral or icosahedral-like environment. In contrast, a Honeycutt-Andersen analysis indicates that a much higher fraction of the atoms is in icosahedral ͑15%-18%͒ or distorted icosahedral ͑25%-28%͒ bond-pair environments. These results indicate that the liquid contains a large population of fragmented clusters with pentagonal and distorted pentagonal faces, but the fully developed icosahedral fragments are rare. Interestingly, in both cases, the ordering changes little over the 500 K of cooling. All metrics show that the nearest-neighbor atomic configurations of the most deeply supercooled simulated liquid ͑1173 K͒ differ topologically and chemically from those in the stable C16 compound, even though the partial pair distributions are similar. The most significant structural change upon decreasing the temperature from 1673 to 1173 K is an increase in the population of Zr in Ni-centered clusters. The structural differences between the liquid and the C16 increase the nucleation barrier, explaining glass formation in the rapidly quenched alloys.

A planar honeycomb monolayer of siligraphene (SiC 7) could be a prospective medium for clean energy storage due to its light weight, and its remarkable mechanical and unique electronic properties. By employing van der Waalsinduced first principles calculations based on density functional theory (DFT), we have explored the structural, electronic, and hydrogen (H 2) storage characteristics of SiC 7 sheets decorated with various light metals. The binding energies of lithium (Li), sodium (Na), potassium (K), magnesium (Mg), calcium (Ca), scandium (Sc), and titanium (Ti) dopants on a SiC 7 monolayer were studied at various doping concentrations, and found to be strong enough to counteract the metal clustering effect. We further verified the stabilities of the metallized SiC 7 sheets at room temperature using ab initio molecular dynamics (MD) simulations. Bader charge analysis revealed that upon adsorption, due to the difference in electronegativity, all the metal adatoms donated a fraction of their electronic charges to the SiC 7 sheet. Each partially charged metal center on the SiC 7 sheets could bind a maximum of 4 to 5 H 2 molecules. A high H 2 gravimetric density was achieved for several dopants at a doping concentration of 12.50%. The H 2 binding energies were found to fall within the ideal range of 0.2-0.6 eV. Based on these findings, we propose that metal-doped SiC 7 sheets can operate as efficient H 2 storage media under ambient conditions.

In the present work, the liquid‐solid interaction of liquid N‐heteroaromatic compounds, commonly present in the petroleum feedstocks of the refineries, with Y zeolites used as hydrocracking catalysts was followed using IR‐ATR spectroscopy. The inhibition of the zeolitic acid sites by strongly basic pyridine and weakly basic indole was highlighted using a continuous flow IR‐ATR cell. Results were assessed by Density Functional Theory calculations to compute the vibrational frequencies of pyridine and indole according to the nature of the interaction sites: silanol groups or acidic OH groups. The study points out that IR‐ATR spectroscopy opens the way for investigating the interaction modes of low vapor pressure molecules (e. g. indole) that present an inherent difficulty to be operated in the gas phase. Moreover, the IR‐ATR makes possible the analysis of the little‐explored low wavenumber zone (&lt;800 cm−1), that presents informative vibrational modes on the adsorption mode of N‐mol...

Computing the k dominant eigenvalues and eigenvectors of massive graphs is a key operation in numerous machine learning applications; however, popular solvers suffer from slow convergence, especially when k is reasonably large. In this paper, we propose and analyze a novel multi-scale spectral decomposition method (MSEIGS), which first clusters the graph into smaller clusters whose spectral decomposition can be computed efficiently and independently. We show theoretically as well as empirically that the union of all cluster's subspaces has significant overlap with the dominant subspace of the original graph, provided that the graph is clustered appropriately. Thus, eigenvectors of the clusters serve as good initializations to a block Lanczos algorithm that is used to compute spectral decomposition of the original graph. We further use hierarchical clustering to speed up the computation and adopt a fast early termination strategy to compute quality approximations. Our method outperforms widely used solvers in terms of convergence speed and approximation quality. Furthermore, our method is naturally parallelizable and exhibits significant speedups in shared-memory parallel settings. For example, on a graph with more than 82 million nodes and 3.6 billion edges, MSEIGS takes less than 3 hours on a single-core machine while Randomized SVD takes more than 6 hours, to obtain a similar approximation of the top-50 eigenvectors. Using 16 cores, we can reduce this time to less than 40 minutes.

We highlight that machine-learning interatomic potentials trained over short AIMD trajectories enable first-principles multiscale modeling, bridging DFT level accuracy to the continuum level and empowering the study of complex/novel nanostructures.

The combination of experimental and simulation techniques becomes essential for refining structural models that are consistent with all the available experimental data. In this work we investigated the structure of liquid CaAl 2 O 4 above its melting point by ab initio molecular dynamics (AIMD), carried out using the VASP code where the interatomic forces are obtained from density functional theory. Neutron diffraction and simulation results are compared. By using the AIMD model we determined structural parameters such as coordination numbers, interatomic distances and bond angle distributions.

We use the aerodynamic levitation technique combined with CO 2 laser heating to study the structure of liquid calcium aluminates using neutron diffraction. We determine the structure factors and corresponding pair correlation functions describing the short-range order in the liquids above the melting points. The combination of the experiments with ab initio molecular dynamics simulations makes possible to get a detailed description of the liquid structure. We find that ordered tetrahedral sites around the Al atoms become more prevalent with increasing CaO concentration, while the Ca atoms present highly distorted environments at all compositions studied.

Ionic liquids (ILs) are promising materials for application in a new generation of Li-batteries. They can be used as electrolyte, interlayer, or incorporated into other materials. ILs have ability to form a stable Solid Electrochemical Interface (SEI) which plays an important role, preventing Li-based electrode from oxidation and electrolyte from extensive decomposition. Experimentally, it is hardly possible to elicit fine details of the SEI structure. To remedy this situation, we have performed a comprehensive computational study (DFT-MD) to determine the composition and structure of the SEI compact layer formed between Li anode and [Pyr14][TFSI] IL. We found that the [TFSI] anions quickly reacted with Li and decomposed, unlike the [Pyr14] cations which remained stable. The obtained SEI compact layer structure is non-homogeneous and consists of the atomized S, N, O, F, and C anions oxidized by Li atoms.

We present evidence of homogenization of atomic diffusion properties caused by C and N interstitials in an equiatomic single-phase high entropy alloy (FeMnNiCoCr). This phenomenon is manifested by an unexpected interstitial-induced reduction and narrowing of the directly experimentally determined migration barrier distribution of mono-vacancy defects introduced by particle irradiation. Our observation by positron annihilation spectroscopy is explained by state-of-the-art theoretical calculations that predict preferential localization of C/N interstitials in regions rich in Mn and Cr, leading to a narrowing and reduction of the mono-vacancy size distribution in the random alloy. This phenomenon is likely to have a significant impact on the mechanical behavior under irradiation, as the local variations in elemental motion have a profound effect on the solute strengthening in high entropy alloys.

We present the results of ab-initio study on the structural, elastic, thermodynamics, and electronic properties of the nonmagnetic Lanthanum nitride (LaN) using the plane-wave pseudopotential approach to the density-functional theory within the generalized-gradient approximation implemented in VASP (Viena Ab-initio Simulation Package). The calculated structural parameters (the lattice constant, bulk modulus, cohesive energy), the phase transition pressure from NaCl (B1) to CsCl (B2) phase, elastic constants, Zener anisotropy factor (A), Poisson ratio (ν), Young's modulus (Y), Shear modulus (C), Debye temperature, and band structures are presented. The obtained results are compared with the available experimental and the other theoretical results.

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We describe the intermediate of the reaction between a ruthenium complex and the 1-propen-3-ol in water by an atomistic approach for gaining information about the conformation and dynamics of complex molecules in aqueous solution, which combines DFT based ab initio molecular dynamics (AIMD) and neutron scattering data based on Empirical Potential Structure Refinement (EPSR) simulations. We apply our method to the study of the water soluble h 2-allylic complex [RuCp(exo-h 2-CH2=CH-CH2-OH)(PTA)2] + (2) (PTA = 1,3,5-triaza-7-phosphaadamantane), a significant intermediate in the isomerisation of 1-propen-3-ol into propanal catalysed by {RuCp(H2O-κO)(PTA)2} +. We identify the factors responsible for the stabilisation of a specific conformer of 2 in water solution and, for the first time, we demonstrate the direct involvement of water molecules in the formation of this species. In particular, we show that long-lived (ca. 10 ps) bonded chains of water molecules play a crucial role in influencing the conformation and, potentially, the chemical reactivity of 2.

The density anomaly of liquid Ge 0:15 Te 0:85 measured between 633 and 733 K is investigated with ab initio molecular dynamics calculations at four temperatures and at the corresponding experimental densities. For box sizes ranging from 56 to 112 atoms, an 8 k-points sampling of the Brillouin zone is necessary to obtain reliable results. Contrary to other Ge chalcogenides, no sp 3 hybridization of the Ge bonding is observed. As a consequence, the negative thermal expansion of the liquid is not related to a tetrahedral bonding as in the case of water or silica. We show that it results from the symmetry recovery of the local environment of Ge atoms that is distorted at low temperature by a Peierls-like mechanism acting in the liquid state in the same way as in the parent solid phases.

The reaction mechanism of the human P450 CYP1A2 enzyme plays a fundamental role in understanding the effects of environmental carcinogens and mutagens on humans. Despite extensive experimental research on this enzyme system, key questions regarding its catalytic cycle and oxygen activation mechanism remain unanswered. In order to elucidate the reaction mechanism in human P450, new computational methods are needed to accurately represent this system. To enable us to perform computational simulations of unprecedented accuracy on these systems, we developed a dynamic quantum-classical (QM/MM) hybrid method, in which ab initio molecular dynamics are coupled with classical molecular mechanics. This will provide the accuracy needed to address such a complex, large biological system in a fully dynamic environment. We also present detailed calculations of the P450 active site, including the relative charge transfer between iron porphine and tetraphenyl porphyrin.

We study the relation between the hydrogen bonding and the vibrational frequency spectra of water on the (110) surface of rutile (R-TiO 2) with three structural layers of adsorbed water. Using ab initio molecular dynamics simulations at 280, 300, and 320 K, we find strong, crystallographically controlled adsorption sites, in general agreement with synchrotron X-ray and classical molecular dynamics simulations. We demonstrate that these sites are produced by strong hydrogen bonds formed between the surface oxygen atoms and the sorbed water molecules. The strength of these bonds is manifested by substantial broadening of the stretching mode vibrational band. The overall vibrational spectrum obtained from our simulations is in good agreement with inelastic neutron scattering experiments. We correlate the vibrational spectrum with different bonds at the surface to transform these vibrational measurements into a spectroscopy of surface interactions.

We studied water on the rutile (110) surface using ab-initio molecular dynamics simulations in NVT ensemble at 280K, 300K, and 320K. Water adsorbs on the 5-fold coordinated titanium atoms or dissociates transferring a proton to a bridging-oxygen atom. The equilibrium between ...

We have calculated the frequencies of the normal vibrations of the complementary nucleic acid base pairs adenine-thymine, guanine-cytosine, adenine-uracil, corresponding to the Watson-Crick structure, and the adenine-uracil pair, corresponding to the Hoogsteen structure, in condensed states and we interpret the spectra. We determine the contributions of hydrogen bonds to the vibrational modes of the complementary pairs. We have analyzed the nature of the relative displacements of the nucleic acid bases as integral molecular units along the hydrogen bonds. We show the role of hydrogen bonds in tautomeric interconversions of complementary nucleic acid base pairs.

Chemical vapor deposition growth of amorphous ruthenium-phosphorus films on SiO 2 containing ∼ 15% phosphorus is reported. cis-Ruthenium(II)dihydridotetrakis-(trimethylphosphine), cis-RuH 2 (PMe 3) 4 (Me = CH 3) was used at growth temperatures ranging from 525 to 575 K. Both Ru and P are zero-valent. The films are metastable, becoming increasingly more polycrystalline upon annealing to 775 and 975 K. Surface studies illustrate that demethylation is quite efficient near 560 K. Precursor adsorption at 135 K or 210 K and heating reveal the precursor undergoes a complex decomposition process in which the hydride and trimethylphosphine ligands are lost at temperatures as low at 280 K. Phosphorus and its manner of incorporation appear responsible for the amorphous-like character. Molecular dynamics simulations are presented to suggest the local structure in the films and the causes for phosphorus stabilizing the amorphous phase.