Phonocatalysis. An ab initio simulation experiment
NASA Astrophysics Data System (ADS)
Kim, Kwangnam; Kaviany, Massoud
2016-06-01
Using simulations, we postulate and show that heterocatalysis on large-bandgap semiconductors can be controlled by substrate phonons, i.e., phonocatalysis. With ab initio calculations, including molecular dynamic simulations, the chemisorbed dissociation of XeF6 on h-BN surface leads to formation of XeF4 and two surface F/h-BN bonds. The reaction pathway and energies are evaluated, and the sorption and reaction emitted/absorbed phonons are identified through spectral analysis of the surface atomic motion. Due to large bandgap, the atomic vibration (phonon) energy transfer channels dominate and among them is the match between the F/h-BN covalent bond stretching and the optical phonons. We show that the chemisorbed dissociation (the pathway activation ascent) requires absorption of large-energy optical phonons. Then using progressively heavier isotopes of B and N atoms, we show that limiting these high-energy optical phonons inhibits the chemisorbed dissociation, i.e., controllable phonocatalysis.
Ab initio simulation of transport phenomena in rarefied gases.
Sharipov, Felix; Strapasson, José L
2012-09-01
Ab initio potentials are implemented into the direct simulation Monte Carlo (DSMC) method. Such an implementation allows us to model transport phenomena in rarefied gases without any fitting parameter of intermolecular collisions usually extracted from experimental data. Applying the method proposed by Sharipov and Strapasson [Phys. Fluids 24, 011703 (2012)], the use of ab initio potentials in the DSMC requires the same computational efforts as the widely used potentials such as hard spheres, variable hard sphere, variable soft spheres, etc. At the same time, the ab initio potentials provide more reliable results than any other one. As an example, the transport coefficients of a binary mixture He-Ar, viz., viscosity, thermal conductivity, and thermal diffusion factor, have been calculated for several values of the mole fraction. PMID:23030889
AB INITIO SIMULATIONS FOR MATERIAL PROPERTIES ALONG THE JUPITER ADIABAT
French, Martin; Becker, Andreas; Lorenzen, Winfried; Nettelmann, Nadine; Bethkenhagen, Mandy; Redmer, Ronald; Wicht, Johannes
2012-09-15
We determine basic thermodynamic and transport properties of hydrogen-helium-water mixtures for the extreme conditions along Jupiter's adiabat via ab initio simulations, which are compiled in an accurate and consistent data set. In particular, we calculate the electrical and thermal conductivity, the shear and longitudinal viscosity, and diffusion coefficients of the nuclei. We present results for associated quantities like the magnetic and thermal diffusivity and the kinematic shear viscosity along an adiabat that is taken from a state-of-the-art interior structure model. Furthermore, the heat capacities, the thermal expansion coefficient, the isothermal compressibility, the Grueneisen parameter, and the speed of sound are calculated. We find that the onset of dissociation and ionization of hydrogen at about 0.9 Jupiter radii marks a region where the material properties change drastically. In the deep interior, where the electrons are degenerate, many of the material properties remain relatively constant. Our ab initio data will serve as a robust foundation for applications that require accurate knowledge of the material properties in Jupiter's interior, e.g., models for the dynamo generation.
Ab initio simulations of peptide-mineral interactions
NASA Astrophysics Data System (ADS)
Hug, Susanna; Hunter, Graeme K.; Goldberg, Harvey; Karttunen, Mikko
We performed Car-Parrinello Molecular Dynamics (CPMD) simulations of two amino acids, aspartic acid (Asp) and phophoserine (pSer), on a calcium oxalate monohydrate (COM) surface as a model of the interactions of phosphoproteins with biominerals. In our earlier work using in vitro experiments and classical Molecular Dynamics (MD) simulations we have demonstrated the importance of phosphorylation of serine on the interactions of osteopontin (OPN) with COM. We used configurations from our previous classical MD simulations as a starting point for the ab initio simulations. In the case of Asp we found that the α-carboxyl and amine groups form temporary close contacts with the surface. For the dipeptide Asp-pSer the carboxyl groups form permanent close contacts with the surface and the distances of its other functional groups do not vary much. We show how the interaction of carboxyl groups with COM crystal is established and confirm the importance of phosphorylation in mediating the interactions between COM surfaces and OPN.
Ab Initio Simulation of the Photoelectron Spectrum for Methoxy Radical
NASA Astrophysics Data System (ADS)
Cheng, Lan; Weichman, Marissa L.; Kim, Jongjin B.; Ichino, Takatoshi; Neumark, Daniel; Stanton, John F.
2015-06-01
A theoretical simulation of the photoelectron spectrum for the ground state of methoxy radical is reported based on the quasidiabatic model Hamiltonian originally proposed by Köppel, Domcke, and Cederbaum. The parameters in the model Hamiltonian have been obtained from ab initio coupled-cluster calculations. The linear and quadratic force constants have been calculated using equation-of-motion coupled-cluster ionization potential method with the singles, doubles, and triples (EOMIP-CCSDT) truncation scheme together with atomic natural orbital basis sets of triple-zeta quality (ANO1). The cubic and quartic force constants have been obtained from EOMIP-CCSD calculations with ANO basis sets of double-zeta quality (ANO0), and the spin-orbit coupling constant has been computed at the EOMIP-CCSD/pCVTZ level. The nuclear Schroedinger equation has been solved using the Lanzcos algorithm to obtain vibronic energy levels as well as the corresponding intensities. The simulated spectrum compares favorably with the recent high-resolution slow electron velocity-map imaging experiment for vibronic levels up to 2000 cm-1.
Ab initio simulations on rutile-based titania nanowires
NASA Astrophysics Data System (ADS)
Zhukovskii, Yu F.; Evarestov, R. A.
2012-08-01
The rod symmetry groups for monoperiodic (1D) nanostructures have been applied for construction of models for bulk-like TiO2 nanowires (NWs) cut from a rutile-based 3D crystal along the chosen [001] and [110] directions of crystallographic axes. In this study, we have considered nanowires described by both the Ti-atom centered rotation axes as well as the hollow site centered axes passing through the interstitial positions between the Ti and O atoms closest to the axes. The most stable [001]-oriented TiO2 NWs with rhombic cross sections are found to display the energetically preferable {110} facets only while the nanowires with quasi-square sections across the [110] axis are formed by the alternating { 1bar 10 } and {001} facets. For simulations on rutile-based nanowires possessing different diameters for each NW type, we have performed large-scale ab initio Density Functional Theory (DFT) and hybrid DFT-Hartree Fock (DFT-HF) calculations with total geometry optimization within the Generalized Gradient Approximation (GGA) in the form of the Perdew-Becke-Ernzenhof (PBE) exchange-correlation functionals (PBE and PBE0, respectively), using the formalism of linear combination of localized atomic functions (LCAO). We have simulated both structural and electronic properties of TiO2 NWs depending both on orientation and position of symmetry axes as well as on diameter and morphology of nanowires.
Ab initio simulation of gap discrete breathers in strained graphene
NASA Astrophysics Data System (ADS)
Lobzenko, I. P.; Chechin, G. M.; Bezuglova, G. S.; Baimova, Yu. A.; Korznikova, E. A.; Dmitriev, S. V.
2016-03-01
The methods of the density functional theory were used for the first time for the simulation of discrete breathers in graphene. It is demonstrated that breathers can exist with frequencies lying in the gap of the phonon spectrum, induced by uniaxial tension of a monolayer graphene sheet in the "zigzag" direction (axis X), polarized in the "armchair" direction (axis Y). The found gap breathers are highly localized dynamic objects, the core of which is formed by two adjacent carbon atoms located on the Y axis. The atoms surrounding the core vibrate at much lower amplitudes along both the axes ( X and Y). The dependence of the frequency of these breathers on amplitude is found, which shows a soft type of nonlinearity. No breathers of this type were detected in the gap induced by stretching along the Y axis. It is shown that the breather vibrations may be approximated by the Morse oscillators, the parameters of which are determined from ab initio calculations. The results are of fundamental importance, as molecular dynamics calculations based on empirical potentials cannot serve as a reliable proof of the existence of breathers in crystals.
Ab initio simulations of pseudomorphic silicene and germanene bidimensional heterostructures
NASA Astrophysics Data System (ADS)
Debernardi, Alberto; Marchetti, Luigi
2016-06-01
Among the novel two-dimensional (2D) materials, silicene and germanene, which are two honeycomb crystal structures composed of a monolayer of Si and Ge, respectively, have attracted the attention of material scientists because they combine the advantages of the new 2D ultimate-scaled electronics with their compatibility with industrial processes presently based on Si and Ge. We envisage pseudomorphic lateral heterostructures based on ribbons of silicene and germanene, which are the 2D analogs of conventional 3D Si/Ge superlattices and quantum wells. In spite of the considerable lattice mismatch (˜4 % ) between free-standing silicene and germanene, our ab initio simulations predict that, considering striped 2D lateral heterostructures made by alternating silicene and germanene ribbons of constant width, the silicene/germanene junction remains pseudomorphic—i.e., it maintains lattice-matched edges—up to critical ribbon widths that can reach some tens of nanometers. Such critical widths are one order of magnitude larger than the critical thickness measured in 3D pseudomorphic Si/Ge heterostructures and the resolution of state-of-the-art lithography, thus enabling the possibility of lithography patterned silicene/germanene junctions. We computed how the strain produced by the pseudomorphic growth modifies the crystal structure and electronic bands of the ribbons, providing a mechanism for band-structure engineering. Our results pave the way for lithography patterned lateral heterostructures that can serve as the building blocks of novel 2D electronics.
Efficient conformational space exploration in ab initio protein folding simulation.
Ullah, Ahammed; Ahmed, Nasif; Pappu, Subrata Dey; Shatabda, Swakkhar; Ullah, A Z M Dayem; Rahman, M Sohel
2015-08-01
Ab initio protein folding simulation largely depends on knowledge-based energy functions that are derived from known protein structures using statistical methods. These knowledge-based energy functions provide us with a good approximation of real protein energetics. However, these energy functions are not very informative for search algorithms and fail to distinguish the types of amino acid interactions that contribute largely to the energy function from those that do not. As a result, search algorithms frequently get trapped into the local minima. On the other hand, the hydrophobic-polar (HP) model considers hydrophobic interactions only. The simplified nature of HP energy function makes it limited only to a low-resolution model. In this paper, we present a strategy to derive a non-uniform scaled version of the real 20×20 pairwise energy function. The non-uniform scaling helps tackle the difficulty faced by a real energy function, whereas the integration of 20×20 pairwise information overcomes the limitations faced by the HP energy function. Here, we have applied a derived energy function with a genetic algorithm on discrete lattices. On a standard set of benchmark protein sequences, our approach significantly outperforms the state-of-the-art methods for similar models. Our approach has been able to explore regions of the conformational space which all the previous methods have failed to explore. Effectiveness of the derived energy function is presented by showing qualitative differences and similarities of the sampled structures to the native structures. Number of objective function evaluation in a single run of the algorithm is used as a comparison metric to demonstrate efficiency. PMID:26361554
Efficient conformational space exploration in ab initio protein folding simulation
Ullah, Ahammed; Ahmed, Nasif; Pappu, Subrata Dey; Shatabda, Swakkhar; Ullah, A. Z. M. Dayem; Rahman, M. Sohel
2015-01-01
Ab initio protein folding simulation largely depends on knowledge-based energy functions that are derived from known protein structures using statistical methods. These knowledge-based energy functions provide us with a good approximation of real protein energetics. However, these energy functions are not very informative for search algorithms and fail to distinguish the types of amino acid interactions that contribute largely to the energy function from those that do not. As a result, search algorithms frequently get trapped into the local minima. On the other hand, the hydrophobic–polar (HP) model considers hydrophobic interactions only. The simplified nature of HP energy function makes it limited only to a low-resolution model. In this paper, we present a strategy to derive a non-uniform scaled version of the real 20×20 pairwise energy function. The non-uniform scaling helps tackle the difficulty faced by a real energy function, whereas the integration of 20×20 pairwise information overcomes the limitations faced by the HP energy function. Here, we have applied a derived energy function with a genetic algorithm on discrete lattices. On a standard set of benchmark protein sequences, our approach significantly outperforms the state-of-the-art methods for similar models. Our approach has been able to explore regions of the conformational space which all the previous methods have failed to explore. Effectiveness of the derived energy function is presented by showing qualitative differences and similarities of the sampled structures to the native structures. Number of objective function evaluation in a single run of the algorithm is used as a comparison metric to demonstrate efficiency. PMID:26361554
Exploring complex chemical reactions by ab-initio simulation
NASA Astrophysics Data System (ADS)
Parrinello, Michele
1998-03-01
Recent progress in the ab-initio molecular dynamics method and the power of parallel computing, allow the detailed study of complex chemical reaction of great industrial relevance. We illustrate this unprecedented capability by investigating the second generation Ziegler-Natta catalytic process. In this inhomogeneous catalyst, a polymerization reaction is induced by TiCl4 molecules deposited on an MgCl2 solid support. A density functional based ab-initio molecular dynamics calculation conducted with a minimum of initial assumption allows to understand the nature of the catalytic center and to determine the reaction path with the associated free energy barrier. Furthermore our calculation can explain in a nontrivial way the stereo-selectivity of the process.
Ab Initio Simulations of Hydrogen in Crystalline and Amorphous Metal Membranes
NASA Astrophysics Data System (ADS)
Huhn, William; Widom, Mike
2011-03-01
Solid metallic membranes are used to separate hydrogen from other gases for clean energy applications. In order to create cheaper, more effective membranes for hydrogen separation, it is desirable to model hydrogen transport through the membrane. Amorphous metal membranes in particular have potential for this type of application due to low expense and high theoretical hydrogen capacity. We computationally model hydrogen absorption and transport through materials in order to find materials that can be used to construct effective membranes for hydrogen capture. In this talk, we will obtain hydrogen binding sites and diffusion barriers in order to model the hydrogen diffusion through various nickel-based amorphous alloys and compare them to associated crystalline structures as well as elemental palladium, which is favored for this application despite its high expense. Ab initio methods (specifically the Vienna Ab Initio Simulation Package, VASP) are used to develop the hydrogen binding energy spectrum, from which thermodynamic models can be constructed. Kinetic Monte Carlo methods are used to model the hydrogen transport through the bulk, from which we can obtain the permeability.
i-PI: A Python interface for ab initio path integral molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Ceriotti, Michele; More, Joshua; Manolopoulos, David E.
2014-03-01
Recent developments in path integral methodology have significantly reduced the computational expense of including quantum mechanical effects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of these developments requires a considerable programming effort, which has hindered their adoption. Here we describe i-PI, an interface written in Python that has been designed to minimise the effort required to bring state-of-the-art path integral techniques to an electronic structure program. While it is best suited to first principles calculations and path integral molecular dynamics, i-PI can also be used to perform classical molecular dynamics simulations, and can just as easily be interfaced with an empirical forcefield code. To give just one example of the many potential applications of the interface, we use it in conjunction with the CP2K electronic structure package to showcase the importance of nuclear quantum effects in high-pressure water. Catalogue identifier: AERN_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AERN_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 138626 No. of bytes in distributed program, including test data, etc.: 3128618 Distribution format: tar.gz Programming language: Python. Computer: Multiple architectures. Operating system: Linux, Mac OSX, Windows. RAM: Less than 256 Mb Classification: 7.7. External routines: NumPy Nature of problem: Bringing the latest developments in the modelling of nuclear quantum effects with path integral molecular dynamics to ab initio electronic structure programs with minimal implementational effort. Solution method: State-of-the-art path integral molecular dynamics techniques are implemented in a Python interface. Any electronic structure code can be patched to receive the atomic
An Efficient Time-Stepping Scheme for Ab Initio Molecular Dynamics Simulations
NASA Astrophysics Data System (ADS)
Tsuchida, Eiji
2016-08-01
In ab initio molecular dynamics simulations of real-world problems, the simple Verlet method is still widely used for integrating the equations of motion, while more efficient algorithms are routinely used in classical molecular dynamics. We show that if the Verlet method is used in conjunction with pre- and postprocessing, the accuracy of the time integration is significantly improved with only a small computational overhead. We also propose several extensions of the algorithm required for use in ab initio molecular dynamics. The validity of the processed Verlet method is demonstrated in several examples including ab initio molecular dynamics simulations of liquid water. The structural properties obtained from the processed Verlet method are found to be sufficiently accurate even for large time steps close to the stability limit. This approach results in a 2× performance gain over the standard Verlet method for a given accuracy. We also show how to generate a canonical ensemble within this approach.
An efficient approach to ab initio Monte Carlo simulation
Leiding, Jeff; Coe, Joshua D.
2014-01-21
We present a Nested Markov chain Monte Carlo (NMC) scheme for building equilibrium averages based on accurate potentials such as density functional theory. Metropolis sampling of a reference system, defined by an inexpensive but approximate potential, was used to substantially decorrelate configurations at which the potential of interest was evaluated, thereby dramatically reducing the number needed to build ensemble averages at a given level of precision. The efficiency of this procedure was maximized on-the-fly through variation of the reference system thermodynamic state (characterized here by its inverse temperature β{sup 0}), which was otherwise unconstrained. Local density approximation results are presented for shocked states of argon at pressures from 4 to 60 GPa, where—depending on the quality of the reference system potential—acceptance probabilities were enhanced by factors of 1.2–28 relative to unoptimized NMC. The optimization procedure compensated strongly for reference potential shortcomings, as evidenced by significantly higher speedups when using a reference potential of lower quality. The efficiency of optimized NMC is shown to be competitive with that of standard ab initio molecular dynamics in the canonical ensemble.
NASA Astrophysics Data System (ADS)
Timko, Jeff; Kuyucak, Serdar
2012-11-01
Polarization is an important component of molecular interactions and is expected to play a particularly significant role in inhomogeneous environments such as pores and interfaces. Here we investigate the effects of polarization in the gramicidin A ion channel by performing quantum mechanics/molecular mechanics molecular dynamics (MD) simulations and comparing the results with those obtained from classical MD simulations with non-polarizable force fields. We consider the dipole moments of backbone carbonyl groups and channel water molecules as well as a number of structural quantities of interest. The ab initio results show that the dipole moments of the carbonyl groups and water molecules are highly sensitive to the hydrogen bonds (H-bonds) they participate in. In the absence of a K+ ion, water molecules in the channel are quite mobile, making the H-bond network highly dynamic. A central K+ ion acts as an anchor for the channel waters, stabilizing the H-bond network and thereby increasing their average dipole moments. In contrast, the K+ ion has little effect on the dipole moments of the neighboring carbonyl groups. The weakness of the ion-peptide interactions helps to explain the near diffusion-rate conductance of K+ ions through the channel. We also address the sampling issue in relatively short ab initio MD simulations. Results obtained from a continuous 20 ps ab initio MD simulation are compared with those generated by sampling ten windows from a much longer classical MD simulation and running each window for 2 ps with ab initio MD. Both methods yield similar results for a number of quantities of interest, indicating that fluctuations are fast enough to justify the short ab initio MD simulations.
Hu, Hao; Yang, Weitao
2013-01-01
Determining the free energies and mechanisms of chemical reactions in solution and enzymes is a major challenge. For such complex reaction processes, combined quantum mechanics/molecular mechanics (QM/MM) method is the most effective simulation method to provide an accurate and efficient theoretical description of the molecular system. The computational costs of ab initio QM methods, however, have limited the application of ab initio QM/MM methods. Recent advances in ab initio QM/MM methods allowed the accurate simulation of the free energies for reactions in solution and in enzymes and thus paved the way for broader application of the ab initio QM/MM methods. We review here the theoretical developments and applications of the ab initio QM/MM methods, focusing on the determination of reaction path and the free energies of the reaction processes in solution and enzymes. PMID:24146439
Ab initio calculations on twisted graphene/hBN: Electronic structure and STM image simulation
NASA Astrophysics Data System (ADS)
Correa, J. D.; Cisternas, E.
2016-09-01
By performing ab initio calculations we obtained theoretical scanning tunneling microscopy (STM) images and studied the electronic properties of graphene on a hexagonal boron-nitrite (hBN) layer. Three different stack configurations and four twisted angles were considered. All calculations were performed using density functional theory, including van der Waals interactions as implemented in the SIESTA ab initio package. Our results show that the electronic structure of graphene is preserved, although some small changes are induced by the interaction with the hBN layer, particularly in the total density of states at 1.5 eV under the Fermi level. When layers present a twisted angle, the density of states shows several van Hove singularities under the Fermi level, which are associated to moiré patterns observed in theoretical STM images.
Ab initio molecular dynamics simulation of liquid water by quantum Monte Carlo
Zen, Andrea; Luo, Ye Mazzola, Guglielmo Sorella, Sandro; Guidoni, Leonardo
2015-04-14
Although liquid water is ubiquitous in chemical reactions at roots of life and climate on the earth, the prediction of its properties by high-level ab initio molecular dynamics simulations still represents a formidable task for quantum chemistry. In this article, we present a room temperature simulation of liquid water based on the potential energy surface obtained by a many-body wave function through quantum Monte Carlo (QMC) methods. The simulated properties are in good agreement with recent neutron scattering and X-ray experiments, particularly concerning the position of the oxygen-oxygen peak in the radial distribution function, at variance of previous density functional theory attempts. Given the excellent performances of QMC on large scale supercomputers, this work opens new perspectives for predictive and reliable ab initio simulations of complex chemical systems.
Matsushita, Y. Murakawa, T. Shimamura, K. Oishi, M. Ohyama, T. Kurita, N.
2015-02-27
The catabolite activator protein (CAP) is one of the regulatory proteins controlling the transcription mechanism of gene. Biochemical experiments elucidated that the complex of CAP with cyclic AMP (cAMP) is indispensable for controlling the mechanism, while previous molecular simulations for the monomer of CAP+cAMP complex revealed the specific interactions between CAP and cAMP. However, the effect of cAMP-binding to CAP on the specific interactions between CAP and DNA is not elucidated at atomic and electronic levels. We here considered the ternary complex of CAP, cAMP and DNA in solvating water molecules and investigated the specific interactions between them at atomic and electronic levels using ab initio molecular simulations based on classical molecular dynamics and ab initio fragment molecular orbital methods. The results highlight the important amino acid residues of CAP for the interactions between CAP and cAMP and between CAP and DNA.
Properties of metals during the heating by intense laser irradiation using ab initio simulations
NASA Astrophysics Data System (ADS)
Holst, Bastian; Recoules, Vanina; Torrent, Marc; Mazevet, Stephane
2011-10-01
Ultrashort laser pulses irradiating a target heat the electrons to very high temperatures. In contrast, the ionic lattice is unaffected on the time scale of the laser pulse since the heat capacity of electrons is much smaller than that of the lattice. This non-equilibrium system can be described as a composition of two subsystems: one consisting of hot electrons and the other of an ionic lattice at low temperature. We studied the effect of this intense electronic excitations on the optical properties of gold using ab initio simulations. We additionally use ab initio linear response to compute the phonon spectrum and the electron-phonon coupling constant within Density Functional Theory for several electronic temperatures of few eV. LULI, Ecole Polytechnique, CNRS, CEA, UPMC, 91128 Palaiseau, France.
PSI3: an open-source Ab Initio electronic structure package.
Crawford, T Daniel; Sherrill, C David; Valeev, Edward F; Fermann, Justin T; King, Rollin A; Leininger, Matthew L; Brown, Shawn T; Janssen, Curtis L; Seidl, Edward T; Kenny, Joseph P; Allen, Wesley D
2007-07-15
PSI3 is a program system and development platform for ab initio molecular electronic structure computations. The package includes mature programming interfaces for parsing user input, accessing commonly used data such as basis-set information or molecular orbital coefficients, and retrieving and storing binary data (with no software limitations on file sizes or file-system-sizes), especially multi-index quantities such as electron repulsion integrals. This platform is useful for the rapid implementation of both standard quantum chemical methods, as well as the development of new models. Features that have already been implemented include Hartree-Fock, multiconfigurational self-consistent-field, second-order Møller-Plesset perturbation theory, coupled cluster, and configuration interaction wave functions. Distinctive capabilities include the ability to employ Gaussian basis functions with arbitrary angular momentum levels; linear R12 second-order perturbation theory; coupled cluster frequency-dependent response properties, including dipole polarizabilities and optical rotation; and diagonal Born-Oppenheimer corrections with correlated wave functions. This article describes the programming infrastructure and main features of the package. PSI3 is available free of charge through the open-source, GNU General Public License. PMID:17420978
Ab Initio Simulation Beryllium in Solid Molecular Hydrogen: Elastic Constant
NASA Astrophysics Data System (ADS)
Guerrero, Carlo L.; Perlado, Jose M.
2016-03-01
In systems of inertial confinement fusion targets Deuterium-Tritium are manufactured with a solid layer, it must have specific properties to increase the efficiency of ignition. Currently there have been some proposals to model the phases of hydrogen isotopes and hence their high pressure, but these works do not allow explaining some of the structures present at the solid phase change effect of increased pressure. By means of simulation with first principles methods and Quantum Molecular Dynamics, we compare the structural difference of solid molecular hydrogen pure and solid molecular hydrogen with beryllium, watching beryllium inclusion in solid hydrogen matrix, we obtain several differences in mechanical properties, in particular elastic constants. For C11 the difference between hydrogen and hydrogen with beryllium is 37.56%. This may produce a non-uniform initial compression and decreased efficiency of ignition.
The ab initio simulation of the Earth's core.
Alfè, D; Gillan, M J; Vocadlo, L; Brodholt, J; Price, G D
2002-06-15
The Earth has a liquid outer and solid inner core. It is predominantly composed of Fe, alloyed with small amounts of light elements, such as S, O and Si. The detailed chemical and thermal structure of the core is poorly constrained, and it is difficult to perform experiments to establish the properties of core-forming phases at the pressures (ca. 300 GPa) and temperatures (ca. 5000-6000 K) to be found in the core. Here we present some major advances that have been made in using quantum mechanical methods to simulate the high-P/T properties of Fe alloys, which have been made possible by recent developments in high-performance computing. Specifically, we outline how we have calculated the Gibbs free energies of the crystalline and liquid forms of Fe alloys, and so conclude that the inner core of the Earth is composed of hexagonal close packed Fe containing ca. 8.5% S (or Si) and 0.2% O in equilibrium at 5600 K at the boundary between the inner and outer cores with a liquid Fe containing ca. 10% S (or Si) and 8% O. PMID:12804276
Ab initio based force field and molecular dynamics simulations of crystalline TATB.
Gee, Richard H; Roszak, Szczepan; Balasubramanian, Krishnan; Fried, Laurence E
2004-04-15
An all-atom force field for 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) is presented. The classical intermolecular interaction potential for TATB is based on single-point energies determined from high-level ab initio calculations of TATB dimers. The newly developed potential function is used to examine bulk crystalline TATB via molecular dynamics simulations. The isobaric thermal expansion and isothermal compression under hydrostatic pressures obtained from the molecular dynamics simulations are in good agreement with experiment. The calculated volume-temperature expansion is almost one dimensional along the c crystallographic axis, whereas under compression, all three unit cell axes participate, albeit unequally. PMID:15267608
Debela, T. T.; Wang, X. D.; Cao, Q. P.; Zhang, D. X.; Wang, S. Y.; Wang, Cai-Zhuang; Jiang, J. Z.
2013-12-12
Atomic structure transitions of liquid niobium during solidification, at different temperatures from 3200 to 1500 K, were studied by using ab initio molecular dynamics simulations. The local atomic structure variations with temperature are investigated by using the pair-correlation function, the structure factor, the bond-angle distribution function, the Honeycutt–Anderson index, Voronoi tessellation and the cluster alignment methods. Our results clearly show that, upon quenching, the icosahedral short-range order dominates in the stable liquid and supercooled liquid states before the system transforms to crystalline body-center cubic phase at a temperature of about 1830 K.
The role of Metals in Amyloid Aggregation: A Test Case for ab initio Simulations
Minicozzi, V.; Rossi, G. C.; Stellato, F.; Morante, S.
2007-12-26
First principle ab initio molecular dynamics simulations of the Car-Parrinello type have proved to be of invaluable help in understanding the microscopic mechanisms of chemical bonding both in solid state physics and in structural biophysics. In this work we present as test cases the study of the Cu coordination mode in two especially important examples: Prion protein and {beta}-amyloids. Using medium size PC-clusters as well as larger parallel platforms, we are able to deal with systems comprising 300 to 500 atoms and 1000 to 1500 electrons for as long as 2-3 ps. We present structural results which confirm indications coming from NMR and XAS data.
NASA Astrophysics Data System (ADS)
Ishimura, Hiromi; Kadoya, Ryushi; Suzuki, Tomoya; Murakawa, Takeru; Shulga, Sergiy; Kurita, Noriyuki
2015-07-01
Alzheimer's disease is caused by accumulation of amyloid-β (Aβ) peptides in a brain. To suppress the production of Aβ peptides, it is effective to inhibit the cleavage of amyloid precursor protein (APP) by secretases. However, because the secretases also play important roles to produce vital proteins for human body, inhibitors for the secretases may have side effects. To propose new agents for protecting the cleavage site of APP from the attacking of the γ-secretase, we have investigated here the specific interactions between a short APP peptide and curcumin derivatives, using protein-ligand docking as well as ab initio molecular simulations.
NASA Astrophysics Data System (ADS)
Pham, Thi Nu; Ono, Shota; Ohno, Kaoru
2016-04-01
Doing ab initio molecular dynamics simulations, we demonstrate a possibility of hydrogenation of carbon monoxide producing methanol step by step. At first, the hydrogen atom reacts with the carbon monoxide molecule at the excited state forming the formyl radical. Formaldehyde was formed after adding one more hydrogen atom to the system. Finally, absorption of two hydrogen atoms to formaldehyde produces methanol molecule. This study is performed by using the all-electron mixed basis approach based on the time dependent density functional theory within the adiabatic local density approximation for an electronic ground-state configuration and the one-shot GW approximation for an electronic excited state configuration.
Holst, Bastian; French, Martin; Redmer, Ronald
2011-06-15
Using Kubo's linear response theory, we derive expressions for the frequency-dependent electrical conductivity (Kubo-Greenwood formula), thermopower, and thermal conductivity in a strongly correlated electron system. These are evaluated within ab initio molecular dynamics simulations in order to study the thermoelectric transport coefficients in dense liquid hydrogen, especially near the nonmetal-to-metal transition region. We also observe significant deviations from the widely used Wiedemann-Franz law, which is strictly valid only for degenerate systems, and give an estimate for its valid scope of application toward lower densities.
Ab initio molecular simulations on specific interactions between amyloid beta and monosaccharides
NASA Astrophysics Data System (ADS)
Nomura, Kazuya; Okamoto, Akisumi; Yano, Atsushi; Higai, Shin'ichi; Kondo, Takashi; Kamba, Seiji; Kurita, Noriyuki
2012-09-01
Aggregation of amyloid β (Aβ) peptides, which is a key pathogenetic event in Alzheimer's disease, can be caused by cell-surface saccharides. We here investigated stable structures of the solvated complexes of Aβ with some types of monosaccharides using molecular simulations based on protein-ligand docking and classical molecular mechanics methods. Moreover, the specific interactions between Aβ and the monosaccharides were elucidated at an electronic level by ab initio fragment molecular orbital calculations. Based on the results, we proposed which type of monosaccharide prefers to have large binding affinity to Aβ and inhibit the Aβ aggregation.
NASA Astrophysics Data System (ADS)
Venâncio, Mateus F.; Rocha, Willian R.
2015-10-01
Ab initio molecular dynamics simulations were used to investigate the early chemical events involved in the dynamics of nitric oxide (NOrad), nitrosonium cation (NO+) and nitroxide anion (NO-) in aqueous solution. The NO+ ion is very reactive in aqueous solution having a lifetime of ∼4 × 10-13 s, which is shorter than the value of 3 × 10-10 s predicted experimentally. The NO+ reacts generating the nitrous acid as an intermediate and the NO2- ion as the final product. The dynamics of NOrad revealed the reversibly formation of a transient anion radical species HONOrad -.
Structure and Raman spectra in cryolitic melts: simulations with an ab initio interaction potential.
Cikit, Serpil; Akdeniz, Zehra; Madden, Paul A
2014-01-30
The Raman spectra of cryolitic melts have been calculated from molecular dynamics computer simulations using a polarizable ionic potential obtained by force-fitting to ab initio electronic structure calculations. Simulations which made use of this ab initio derived polarizable interaction potential reproduced the structure and dynamical properties of crystalline cryolite, Na3AlF6, rather well. The transferability of the potential model from solid state to the molten state is tested by comparing results for the Raman spectra of melts of various compositions with those previously obtained with empirically developed potentials and with experimental data. The shapes of the spectra and their evolution with composition in the mixtures conform quite well to those seen experimentally, and we discuss the relationship between the bands seen in the spectra and the vibrational modes of the AlFn((3–n)) coordination complexes which are found in the NaF/AlF3 mixtures. The simulations thus enable a link between the structure of the melt as derived through Raman spectroscopy and through diffraction experiments. We report results for quantities which relate to the degree of cross-linking between these coordination complexes and the diffusive properties of ions. PMID:24432905
Ab Initio simulations of nonstoichiometric CdxTe1-x liquids
NASA Astrophysics Data System (ADS)
Ko, Eunjung; Alemany, M. M. G.; Derby, Jeffrey J.; Chelikowsky, James R.
2005-08-01
We present ab initio molecular-dynamics simulations for CdxTe1-x liquids where the composition is nonstoichiometric. The simulations are performed following Born-Oppenheimer molecular dynamics. The required forces are obtained from a solution of the Kohn-Sham equation using ab initio pseudopotentials. We consider stoichiometries of the form: CdxTe1-x, where x =0.2, 0.4, 0.6, and 0.8. For each composition of the melt, we consider a range of temperatures near the experimentally determined liquid temperatures. We examine the microstructural properties of the melt, the viscosity, and self-diffusion properties of the liquid as a function of the stoichiometry and temperature. We also perform an analysis of the distribution of the electronic density of states in these liquids. We find that structural changes in the local order, experimentally predicted to occur when the concentration of Cd is increased, are closely related to changes in the electronic properties of the melt.
Accelerating Ab Initio Path Integral Simulations via Imaginary Multiple-Timestepping.
Cheng, Xiaolu; Herr, Jonathan D; Steele, Ryan P
2016-04-12
This work investigates the use of multiple-timestep schemes in imaginary time for computationally efficient ab initio equilibrium path integral simulations of quantum molecular motion. In the simplest formulation, only every n(th) path integral replica is computed at the target level of electronic structure theory, whereas the remaining low-level replicas still account for nuclear motion quantum effects with a more computationally economical theory. Motivated by recent developments for multiple-timestep techniques in real-time classical molecular dynamics, both 1-electron (atomic-orbital basis set) and 2-electron (electron correlation) truncations are shown to be effective. Structural distributions and thermodynamic averages are tested for representative analytic potentials and ab initio molecular examples. Target quantum chemistry methods include density functional theory and second-order Møller-Plesset perturbation theory, although any level of theory is formally amenable to this framework. For a standard two-level splitting, computational speedups of 1.6-4.0x are observed when using a 4-fold reduction in time slices; an 8-fold reduction is feasible in some cases. Multitiered options further reduce computational requirements and suggest that quantum mechanical motion could potentially be obtained at a cost not significantly different from the cost of classical simulations. PMID:26966920
Xiong, L H; Yoo, H; Lou, H B; Wang, X D; Cao, Q P; Zhang, D X; Jiang, J Z; Xie, H L; Xiao, T Q; Jeon, S; Lee, G W
2015-01-28
X-ray diffraction and electrostatic levitation measurements, together with the ab initio molecular dynamics simulation of liquid Al(75)Cu(25) alloy have been performed from 800 to 1600 K. Experimental and ab initio molecular dynamics simulation results match well with each other. No abnormal changes were experimentally detected in the specific heat capacity over total hemispheric emissivity and density curves in the studied temperature range for a bulk liquid Al(75)Cu(25) alloy measured by the electrostatic levitation technique. The structure factors gained by the ab initio molecular dynamics simulation precisely coincide with the experimental data. The atomic structure analyzed by the Honeycutt-Andersen index and Voronoi tessellation methods shows that icosahedral-like atomic clusters prevail in the liquid Al(75)Cu(25) alloy and the atomic clusters evolve continuously. All results obtained here suggest that no liquid-liquid transition appears in the bulk liquid Al(75)Cu(25) alloy in the studied temperature range. PMID:25524926
Ab Initio Classical Dynamics Simulations of CO_2 Line-Mixing Effects in Infrared Bands
NASA Astrophysics Data System (ADS)
Lamouroux, Julien; Hartmann, Jean-Michel; Tran, Ha; Snels, Marcel; Stefani, Stefania; Piccioni, Giuseppe
2013-06-01
Ab initio calculations of line-mixing effects in CO_2 infrared bands are presented and compared with experiments. The predictions were carried using requantized Classical Dynamics Molecular Simulations (rCDMS) based on an approach previously developed and successfully tested for CO_2 isolated line shapes. Using classical dynamics equations, the force and torque applied to each molecule by the surrounding molecules (described by an ab initio intermolecular potential) are computed at each time step. This enables, using a requantization procedure, to predict dipole and isotropic polarizability auto-correlation functions whose Fourier-Laplace transforms yield the spectra. The quality of the rCDMS calculations is demonstrated by comparisons with measured spectra in the spectral regions of the 3ν_3 and 2ν_1+2ν_2+ν_3 Infrared bands. J.-M. Hartmann, H. Tran, N. H. Ngo, et al., Phys. Rev. Lett. A {87} (2013), 013403. H. Tran, C. Boulet, M. Snels, S. Stefani, J. Quant. Spectrosc. Radiat. Transfer {112} (2011), 925-936.
Ab initio molecular dynamics simulations of ion-solid interactions in zirconate pyrochlores
Xiao, Haiyan Y.; Weber, William J.; Zhang, Yanwen; Zu, X. T.
2015-01-31
In this paper, an ab initio molecular dynamics method is employed to study low energy recoil events in zirconate pyrochlores (A2Zr2O7, A = La, Nd and Sm). It shows that both cations and anions in Nd2Zr2O7 and Sm2Zr2O7 are generally more likely to be displaced than those in La2Zr2O7. The damage end states mainly consist of Frenkel pair defects, and the Frenkel pair formation energies in Nd2Zr2O7 and Sm2Zr2O7 are lower than those in La2Zr2O7. These results suggest that the order–disorder structural transition more easily occurs in Nd2Zr2O7 and Sm2Zr2O7 resulting in a defect-fluorite structure, which agrees well with experimentalmore » observations. Our calculations indicate that oxygen migration from 48f and 8b to 8a sites is dominant under low energy irradiation. A number of new defects, including four types of cation Frenkel pairs and six types of anion Frenkel pairs, are revealed by ab initio molecular dynamics simulations. The present findings may help to advance the fundamental understanding of the irradiation response behavior of zirconate pyrochlores.« less
Xiao, Haiyan J.; Gao, Fei; Zu, Xiaotao T.; Weber, William J.
2009-06-17
The high-pressure induced phase transformation from the zinc blende to rocksalt structure in SiC has been studied by ab initio molecular dynamics. The simulations show that SiC passes through tetragonal and then monoclinic intermediate states before finally forming the rock salt structure at 160 GPa. The mechanism for this phase transformation agrees well with recent ab initio MD simulations, in which the applied pressure was as high as ~600 GPa, but in the present study the transformation occurs at much lower pressure. It is found that the phase transition has to overcome an energy barrier of 0.44 eV/pair.
Shimamura, K; Shibuta, Y; Ohmura, S; Arifin, R; Shimojo, F
2016-04-13
The atomistic mechanism of dissociative adsorption of ethylene molecules on a Ni cluster is investigated by ab initio molecular-dynamics simulations. The activation free energy to dehydrogenate an ethylene molecule on the Ni cluster and the corresponding reaction rate is estimated. A remarkable finding is that the adsorption energy of ethylene molecules on the Ni cluster is considerably larger than the activation free energy, which explains why the actual reaction rate is faster than the value estimated based on only the activation free energy. It is also found from the dynamic simulations that hydrogen molecules and an ethane molecule are formed from the dissociated hydrogen atoms, whereas some exist as single atoms on the surface or in the interior of the Ni cluster. On the other hand, the dissociation of the C-C bonds of ethylene molecules is not observed. On the basis of these simulation results, the nature of the initial stage of carbon nanotube growth is discussed. PMID:26953616
NASA Astrophysics Data System (ADS)
Shimamura, K.; Shibuta, Y.; Ohmura, S.; Arifin, R.; Shimojo, F.
2016-04-01
The atomistic mechanism of dissociative adsorption of ethylene molecules on a Ni cluster is investigated by ab initio molecular-dynamics simulations. The activation free energy to dehydrogenate an ethylene molecule on the Ni cluster and the corresponding reaction rate is estimated. A remarkable finding is that the adsorption energy of ethylene molecules on the Ni cluster is considerably larger than the activation free energy, which explains why the actual reaction rate is faster than the value estimated based on only the activation free energy. It is also found from the dynamic simulations that hydrogen molecules and an ethane molecule are formed from the dissociated hydrogen atoms, whereas some exist as single atoms on the surface or in the interior of the Ni cluster. On the other hand, the dissociation of the C-C bonds of ethylene molecules is not observed. On the basis of these simulation results, the nature of the initial stage of carbon nanotube growth is discussed.
Makhov, Dmitry V.; Saita, Kenichiro; Martinez, Todd J.; Shalashilin, Dmitrii V.
2014-12-11
In this study, we report a detailed computational simulation of the photodissociation of pyrrole using the ab initio Multiple Cloning (AIMC) method implemented within MOLPRO. The efficiency of the AIMC implementation, employing train basis sets, linear approximation for matrix elements, and Ehrenfest configuration cloning, allows us to accumulate significant statistics. We calculate and analyze the total kinetic energy release (TKER) spectrum and Velocity Map Imaging (VMI) of pyrrole and compare the results directly with experimental measurements. Both the TKER spectrum and the structure of the velocity map image (VMI) are well reproduced. Previously, it has been assumed that the isotropicmore » component of the VMI arises from long time statistical dissociation. Instead, our simulations suggest that ultrafast dynamics contributes significantly to both low and high energy portions of the TKER spectrum.« less
Thomas, Martin; Kirchner, Barbara
2016-02-01
We present a new approach for calculating vibrational circular dichroism spectra by ab initio molecular dynamics. In the context of molecular dynamics, these spectra are given by the Fourier transform of the cross-correlation function of magnetic dipole moment and electric dipole moment. We obtain the magnetic dipole moment from the electric current density according to the classical definition. The electric current density is computed by solving a partial differential equation derived from the continuity equation and the condition that eddy currents should be absent. In combination with a radical Voronoi tessellation, this yields an individual magnetic dipole moment for each molecule in a bulk phase simulation. Using the chiral alcohol 2-butanol as an example, we show that experimental spectra are reproduced very well. Our approach requires knowing only the electron density in each simulation step, and it is not restricted to any particular electronic structure method. PMID:26771403
Decarboxylation of furfural on Pd(111): Ab initio molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Xue, Wenhua; Dang, Hongli; Shields, Darwin; Liu, Yingdi; Jentoft, Friederike; Resasco, Daniel; Wang, Sanwu
2013-03-01
Furfural conversion over metal catalysts plays an important role in the studies of biomass-derived feedstocks. We report ab initio molecular dynamics simulations for the decarboxylation process of furfural on the palladium surface at finite temperatures. We observed and analyzed the atomic-scale dynamics of furfural on the Pd(111) surface and the fluctuations of the bondlengths between the atoms in furfural. We found that the dominant bonding structure is the parallel structure in which the furfural plane, while slightly distorted, is parallel to the Pd surface. Analysis of the bondlength fluctuations indicates that the C-H bond is the aldehyde group of a furfural molecule is likely to be broken first, while the C =O bond has a tendency to be isolated as CO. Our results show that the reaction of decarbonylation dominates, consistent with the experimental measurements. Supported by DOE (DE-SC0004600). Simulations and calculations were performed on XSEDE's and NERSC's supercomputers.
Hydrogen-water mixtures in giant planet interiors studied with ab initio simulations
NASA Astrophysics Data System (ADS)
Soubiran, F.; Militzer, B.
2015-12-01
We study water-hydrogen mixtures under planetary interior conditions using ab initio molecular dynamics simulations. We determine the thermodynamic properties of various water-hydrogen mixing ratios at temperatures of 2000 and 6000 K for pressures of a few tens of GPa. These conditions are relevant for ice giant planets and for the outer envelope of the gas giants. We find that at 2000 K the mixture is in a molecular regime, while at 6000 K the dissociation of hydrogen and water is important and affects the thermodynamic properties. We study the structure of the liquid and analyze the radial distribution function. We provide estimates for the transport properties, diffusion and viscosity, based on autocorrelation functions. We obtained viscosity estimates of the order of a few tenths of mPa s for the conditions under consideration. These results are relevant for dynamo simulations of ice giant planets.
Ab initio simulation of photoinduced transformation of small rings in amorphous silica
NASA Astrophysics Data System (ADS)
Donadio, Davide; Bernasconi, Marco
2005-02-01
We have studied the photoinduced transformation of small rings (three membered) in amorphous silica by Car-Parrinello simulations. The process of ring opening leading to the formation of a couple of paramagnetic centers, namely an E' and a nonbridging-oxygen hole center (NBOHC), has been proposed experimentally to occur in silica exposed to F2 laser irradiation (at 7.9eV ). By using a scheme for the simulation of rare events in ab initio molecular dynamics [M. Iannuzzi, A. Laio, and M. Parrinello, Phys. Rev. Lett. 90, 238303 (2003)], we have identified a transformation path for the opening of a three-membered ring induced by a self-trapped triplet exciton, the migration of NBOHC and formation of a couple of stable E' and NBOHC paramagnetic defects.
Brandt, Erik G; Agosta, Lorenzo; Lyubartsev, Alexander P
2016-07-21
Small-sized wet TiO2 nanoparticles have been investigated by ab initio molecular dynamics simulations. Chemical and physical adsorption of water on the TiO2-water interface was studied as a function of water content, ranging from dry nanoparticles to wet nanoparticles with monolayer coverage of water. The surface reactivity was shown to be a concave function of water content and driven by surface defects. The local coordination number at the defect was identified as the key factor to decide whether water adsorption proceeds through dissociation or physisorption on the surface. A consistent picture of TiO2 nanoparticle wetting at the microscopic level emerges, which corroborates existing experimental data and gives further insight into the molecular mechanisms behind nanoparticle wetting. These calculations will facilitate the engineering of metal oxide nanoparticles with a controlled catalytic water activity. PMID:27341183
Ab Initio Molecular-Dynamics Simulation of Neuromorphic Computing in Phase-Change Memory Materials.
Skelton, Jonathan M; Loke, Desmond; Lee, Taehoon; Elliott, Stephen R
2015-07-01
We present an in silico study of the neuromorphic-computing behavior of the prototypical phase-change material, Ge2Sb2Te5, using ab initio molecular-dynamics simulations. Stepwise changes in structural order in response to temperature pulses of varying length and duration are observed, and a good reproduction of the spike-timing-dependent plasticity observed in nanoelectronic synapses is demonstrated. Short above-melting pulses lead to instantaneous loss of structural and chemical order, followed by delayed partial recovery upon structural relaxation. We also investigate the link between structural order and electrical and optical properties. These results pave the way toward a first-principles understanding of phase-change physics beyond binary switching. PMID:26040531
Mahmoud, A; Erba, A; Doll, K; Dovesi, R
2014-06-21
A general methodology has been devised and implemented into the solid-state ab initio quantum-mechanical Crystal program for studying the evolution under geophysical pressure of the elastic anisotropy of crystalline materials. This scheme, which fully exploits both translational and point symmetry of the crystal, is developed within the formal frame of one-electron Hamiltonians and atom-centered basis functions. Six silicate garnet end-members, among the most important rock-forming minerals of the Earth's mantle, are considered, whose elastic anisotropy is fully characterized under high hydrostatic compressions, up to 60 GPa. The pressure dependence of azimuthal anisotropy and shear-wave birefringence of seismic wave velocities for these minerals are accurately simulated and compared with available single-crystal measurements. PMID:24952556
Mahmoud, A.; Erba, A. Dovesi, R.; Doll, K.
2014-06-21
A general methodology has been devised and implemented into the solid-state ab initio quantum-mechanical CRYSTAL program for studying the evolution under geophysical pressure of the elastic anisotropy of crystalline materials. This scheme, which fully exploits both translational and point symmetry of the crystal, is developed within the formal frame of one-electron Hamiltonians and atom-centered basis functions. Six silicate garnet end-members, among the most important rock-forming minerals of the Earth's mantle, are considered, whose elastic anisotropy is fully characterized under high hydrostatic compressions, up to 60 GPa. The pressure dependence of azimuthal anisotropy and shear-wave birefringence of seismic wave velocities for these minerals are accurately simulated and compared with available single-crystal measurements.
Equation of state and phase diagram of ammonia at high pressures from ab initio simulations.
Bethkenhagen, Mandy; French, Martin; Redmer, Ronald
2013-06-21
We present an equation of state as well as a phase diagram of ammonia at high pressures and high temperatures derived from ab initio molecular dynamics simulations. The predicted phases of ammonia are characterized by analyzing diffusion coefficients and structural properties. Both the phase diagram and the subsequently computed Hugoniot curves are compared to experimental results. Furthermore, we discuss two methods that allow us to take into account nuclear quantum effects, which are of considerable importance in molecular fluids. Our data cover pressures up to 330 GPa and a temperature range from 500 K to 10,000 K. This regime is of great interest for interior models of the giant planets Uranus and Neptune, which contain, besides water and methane, significant amounts of ammonia. PMID:23802968
NASA Astrophysics Data System (ADS)
Brandt, Erik G.; Agosta, Lorenzo; Lyubartsev, Alexander P.
2016-07-01
Small-sized wet TiO2 nanoparticles have been investigated by ab initio molecular dynamics simulations. Chemical and physical adsorption of water on the TiO2-water interface was studied as a function of water content, ranging from dry nanoparticles to wet nanoparticles with monolayer coverage of water. The surface reactivity was shown to be a concave function of water content and driven by surface defects. The local coordination number at the defect was identified as the key factor to decide whether water adsorption proceeds through dissociation or physisorption on the surface. A consistent picture of TiO2 nanoparticle wetting at the microscopic level emerges, which corroborates existing experimental data and gives further insight into the molecular mechanisms behind nanoparticle wetting. These calculations will facilitate the engineering of metal oxide nanoparticles with a controlled catalytic water activity.Small-sized wet TiO2 nanoparticles have been investigated by ab initio molecular dynamics simulations. Chemical and physical adsorption of water on the TiO2-water interface was studied as a function of water content, ranging from dry nanoparticles to wet nanoparticles with monolayer coverage of water. The surface reactivity was shown to be a concave function of water content and driven by surface defects. The local coordination number at the defect was identified as the key factor to decide whether water adsorption proceeds through dissociation or physisorption on the surface. A consistent picture of TiO2 nanoparticle wetting at the microscopic level emerges, which corroborates existing experimental data and gives further insight into the molecular mechanisms behind nanoparticle wetting. These calculations will facilitate the engineering of metal oxide nanoparticles with a controlled catalytic water activity. Electronic supplementary information (ESI) available: Simulation data on equilibration of energies and structures (root-mean-square-deviations and
Born-Oppenheimer Ab Initio QM/MM Molecular Dynamics Simulations of Enzyme Reactions.
Zhou, Y; Wang, S; Li, Y; Zhang, Y
2016-01-01
There are two key requirements for reliably simulating enzyme reactions: one is a reasonably accurate potential energy surface to describe the bond-forming/breaking process as well as to adequately model the heterogeneous enzyme environment; the other is to perform extensive sampling since an enzyme system consists of at least thousands of atoms and its energy landscape is very complex. One attractive approach to meet both daunting tasks is Born-Oppenheimer ab initio QM/MM molecular dynamics (aiQM/MM-MD) simulation with umbrella sampling. In this chapter, we describe our recently developed pseudobond Q-Chem-Amber interface, which employs a combined electrostatic-mechanical embedding scheme with periodic boundary condition and the particle mesh Ewald method for long-range electrostatics interactions. In our implementation, Q-Chem and the sander module of Amber are combined at the source code level without using system calls, and all necessary data communications between QM and MM calculations are achieved via computer memory. We demonstrate the applicability of this pseudobond Q-Chem-Amber interface by presenting two examples, one reaction in aqueous solution and one enzyme reaction. Finally, we describe our established aiQM/MM-MD enzyme simulation protocol, which has been successfully applied to study more than a dozen enzymes. PMID:27498636
Ab initio molecular dynamics simulation of proton hopping in a model polymer membrane.
Devanathan, Ram; Idupulapati, Nagesh; Baer, Marcel D; Mundy, Christopher J; Dupuis, Michel
2013-12-27
We report the results of ab initio molecular dynamics simulations of a model Nafion polymer membrane initially equilibrated using classical molecular dynamics simulations. We studied three hydration levels (λ) of 3, 9, and 15 H2O/SO3(-) corresponding to dry, hydrated, and saturated fuel cell membrane, respectively. The barrier for proton transfer from the SO3(-)-H3O(+) contact ion pair to a solvent-separated ion pair decreased from 2.3 kcal/mol for λ = 3 to 0.8 kcal/mol for λ = 15. The barrier for proton transfer between two water molecules was in the range from 0.7 to 0.8 kcal/mol for the λ values studied. The number of proton shuttling events between a pair of water molecules is an order of magnitude more than the number of proton hops across three distinct water molecules. The proton diffusion coefficient at λ = 15 is about 0.9 × 10(-5) cm(2)/s, which is in good agreement with experiment and our previous quantum hopping molecular dynamics simulations. PMID:24320080
How fragility makes phase-change data storage robust: insights from ab initio simulations
Zhang, Wei; Ronneberger, Ider; Zalden, Peter; Xu, Ming; Salinga, Martin; Wuttig, Matthias; Mazzarello, Riccardo
2014-01-01
Phase-change materials are technologically important due to their manifold applications in data storage. Here we report on ab initio molecular dynamics simulations of crystallization of the phase change material Ag4In3Sb67Te26 (AIST). We show that, at high temperature, the observed crystal growth mechanisms and crystallization speed are in good agreement with experimental data. We provide an in-depth understanding of the crystallization mechanisms at the atomic level. At temperatures below 550 K, the computed growth velocities are much higher than those obtained from time-resolved reflectivity measurements, due to large deviations in the diffusion coefficients. As a consequence of the high fragility of AIST, experimental diffusivities display a dramatic increase in activation energies and prefactors at temperatures below 550 K. This property is essential to ensure fast crystallization at high temperature and a stable amorphous state at low temperature. On the other hand, no such change in the temperature dependence of the diffusivity is observed in our simulations, down to 450 K. We also attribute this different behavior to the fragility of the system, in combination with the very fast quenching times employed in the simulations. PMID:25284316
Feng, Wen-Ling; Tian, Shan Xi
2015-03-12
Dissociative electron attachment (DEA) processes of six low-lying conformers (1-6) of dialanine in the gas phase are investigated by using ab initio molecular dynamics simulations. The incoming electron is captured and primarily occupies the virtual molecular orbital π*, which is followed by the different dissociation processes. The electron attachments to conformers 1 and 2 having the stronger N-H···N and O-H···O intramolecular hydrogen bonds do not lead to fragmentations, but two different backbone bonds are broken in the DEAs to conformers 3 (or 4) and 6, respectively. It is interesting that the hydrogen abstraction of -NH from the terminal methyl group -CH3 is found in the roaming dissociation of the temporary anion of conformer 3. The present simulations enable us to have more insights into the peptide backbone bond breaks in the DEA process and demonstrate a promising way toward understanding of the radiation damages of complicated biological system. PMID:25679256
NASA Astrophysics Data System (ADS)
Erba, A.; Ferrabone, M.; Baima, J.; Orlando, R.; Rérat, M.; Dovesi, R.
2013-02-01
The vibration spectrum of single-walled zigzag boron nitride (BN) nanotubes is simulated with an ab initio periodic quantum chemical method. The trend towards the hexagonal monolayer (h-BN) in the limit of large tube radius R is explored for a variety of properties related to the vibrational spectrum: vibration frequencies, infrared intensities, oscillator strengths, and vibration contributions to the polarizability tensor. The (n,0) family is investigated in the range from n = 6 (24 atoms in the unit cell and tube radius R = 2.5 Å) to n = 60 (240 atoms in the cell and R = 24.0 Å). Simulations are performed using the CRYSTAL program which fully exploits the rich symmetry of this class of one-dimensional periodic systems: 4n symmetry operators for the general (n,0) tube. Three sets of infrared active phonon bands are found in the spectrum. The first one lies in the 0-600 cm-1 range and goes regularly to zero when R increases; the connection between these normal modes and the elastic and piezoelectric constants of h-BN is discussed. The second (600-800 cm-1) and third (1300-1600 cm-1) sets tend regularly, but with quite different speed, to the optical modes of the h-BN layer. The vibrational contribution of these modes to the two components (parallel and perpendicular) of the polarizability tensor is also discussed.
Direct molecular simulation of nitrogen dissociation based on an ab initio potential energy surface
Valentini, Paolo Schwartzentruber, Thomas E. Bender, Jason D. Nompelis, Ioannis Candler, Graham V.
2015-08-15
The direct molecular simulation (DMS) approach is used to predict the internal energy relaxation and dissociation dynamics of high-temperature nitrogen. An ab initio potential energy surface (PES) is used to calculate the dynamics of two interacting nitrogen molecules by providing forces between the four atoms. In the near-equilibrium limit, it is shown that DMS reproduces the results obtained from well-established quasiclassical trajectory (QCT) analysis, verifying the validity of the approach. DMS is used to predict the vibrational relaxation time constant for N{sub 2}–N{sub 2} collisions and its temperature dependence, which are in close agreement with existing experiments and theory. Using both QCT and DMS with the same PES, we find that dissociation significantly depletes the upper vibrational energy levels. As a result, across a wide temperature range, the dissociation rate is found to be approximately 4–5 times lower compared to the rates computed using QCT with Boltzmann energy distributions. DMS calculations predict a quasi-steady-state distribution of rotational and vibrational energies in which the rate of depletion of high-energy states due to dissociation is balanced by their rate of repopulation due to collisional processes. The DMS approach simulates the evolution of internal energy distributions and their coupling to dissociation without the need to precompute rates or cross sections for all possible energy transitions. These benchmark results could be used to develop new computational fluid dynamics models for high-enthalpy flow applications.
Köster, Andreas; Spura, Thomas; Rutkai, Gábor; Kessler, Jan; Wiebeler, Hendrik; Vrabec, Jadran; Kühne, Thomas D
2016-07-15
The accuracy of water models derived from ab initio molecular dynamics simulations by means on an improved force-matching scheme is assessed for various thermodynamic, transport, and structural properties. It is found that although the resulting force-matched water models are typically less accurate than fully empirical force fields in predicting thermodynamic properties, they are nevertheless much more accurate than generally appreciated in reproducing the structure of liquid water and in fact superseding most of the commonly used empirical water models. This development demonstrates the feasibility to routinely parametrize computationally efficient yet predictive potential energy functions based on accurate ab initio molecular dynamics simulations for a large variety of different systems. © 2016 Wiley Periodicals, Inc. PMID:27232117
He, Rongxing; Li, Lei; Zhong, Jie; Zhu, Chongqin; Francisco, Joseph S; Zeng, Xiao Cheng
2016-04-26
Solar emission produces copious nitrosonium ions (NO(+)) in the D layer of the ionosphere, 60 to 90 km above the Earth's surface. NO(+) is believed to transfer its charge to water clusters in that region, leading to the formation of gaseous nitrous acid (HONO) and protonated water cluster. The dynamics of this reaction at the ionospheric temperature (200-220 K) and the associated mechanistic details are largely unknown. Using ab initio molecular dynamics (AIMD) simulations and transition-state search, key structures of the water hydrates-tetrahydrate NO(+)(H2O)4 and pentahydrate NO(+)(H2O)5-are identified and shown to be responsible for HONO formation in the ionosphere. The critical tetrahydrate NO(+)(H2O)4 exhibits a chain-like structure through which all of the lowest-energy isomers must go. However, most lowest-energy isomers of pentahydrate NO(+)(H2O)5 can be converted to the HONO-containing product, encountering very low barriers, via a chain-like or a three-armed, star-like structure. Although these structures are not the global minima, at 220 K, most lowest-energy NO(+)(H2O)4 and NO(+)(H2O)5 isomers tend to channel through these highly populated isomers toward HONO formation. PMID:27071120
Carbon and proton Overhauser DNP from MD simulations and ab initio calculations: TEMPOL in acetone.
Küçük, Sami Emre; Biktagirov, Timur; Sezer, Deniz
2015-10-14
A computational analysis of the Overhauser effect is reported for the proton, methyl carbon, and carbonyl carbon nuclei of liquid acetone doped with the nitroxide radical TEMPOL. A practical methodology for calculating the dynamic nuclear polarization (DNP) coupling factors by accounting for both dipole-dipole and Fermi-contact interactions is presented. The contribution to the dipolar spectral density function of nuclear spins that are not too far from TEMPOL is computed through classical molecular dynamics (MD) simulations, whereas the contribution of distant spins is included analytically. Fermi contacts are obtained by subjecting a few molecules from every MD snapshot to ab initio quantum mechanical calculations. Scalar interaction is found to be an essential part of the (13)C Overhauser DNP. While mostly detrimental to the carbonyl carbon of acetone it is predicted to result in large enhancements of the methyl carbon signal at magnetic fields of 9 T and beyond. In contrast, scalar coupling is shown to be negligible for the protons of acetone. The additional influence of proton polarization on the carbon DNP (three-spin effect) is also analyzed computationally. Its effect, however, is concluded to be practically insignificant for liquid acetone. PMID:26343351
NASA Astrophysics Data System (ADS)
Zeng, Xiancheng; Hu, Hao; Hu, Xiangqian; Cohen, Aron J.; Yang, Weitao
2008-03-01
Electron transfer (ET) reactions are one of the most important processes in chemistry and biology. Because of the quantum nature of the processes and the complicated roles of the solvent, theoretical study of ET processes is challenging. To simulate ET processes at the electronic level, we have developed an efficient density functional theory (DFT) quantum mechanical (QM)/molecular mechanical (MM) approach that uses the fractional number of electrons as the order parameter to calculate the redox free energy of ET reactions in solution. We applied this method to study the ET reactions of the aqueous metal complexes Fe(H2O)62+/3+ and Ru(H2O)62+/3+. The calculated oxidation potentials, 5.82 eV for Fe(II/III) and 5.14 eV for Ru(II/III), agree well with the experimental data, 5.50 and 4.96 eV, for iron and ruthenium, respectively. Furthermore, we have constructed the diabatic free energy surfaces from histogram analysis based on the molecular dynamics trajectories. The resulting reorganization energy and the diabatic activation energy also show good agreement with experimental data. Our calculations show that using the fractional number of electrons (FNE) as the order parameter in the thermodynamic integration process leads to efficient sampling and validate the ab initio QM/MM approach in the calculation of redox free energies.
Ab Initio Molecular Dynamics Simulations and GIPAW NMR Calculations of a Lithium Borate Glass Melt.
Ohkubo, Takahiro; Tsuchida, Eiji; Takahashi, Takafumi; Iwadate, Yasuhiko
2016-04-14
The atomic structure of a molten 0.3Li2O-0.7B2O3 glass at 1250 K was investigated using ab initio molecular dynamics (AIMD) simulations. The gauge including projector augmented wave (GIPAW) method was then employed for computing the chemical shift and quadrupolar coupling constant of (11)B, (17)O, and (7)Li from 764 AIMD derived structures. The chemical shift and quadrupolar coupling constant distributions were directly estimated from the dynamical structure of the molten glass. (11)B NMR parameters of well-known structural units such as the three-coordinated ring, nonring, and four-coordinated tetrahedron were found to be in good agreement with the experimental results. In this study, more detailed classification of B units was presented based on the number of O species bonded to the B atoms. This highlights the limitations of (11)B NMR sensitivity for resolving (11)B local environment using the experimentally obtained spectra only. The (17)O NMR parameter distributions can theoretically resolve the bridging and nonbridging O atoms with different structural units such as nonring, single boroxol ring, and double boroxol ring. Slight but clear differences in the number of bridging O atoms surrounding Li that have not been reported experimentally were observed in the theoretically obtained (7)Li NMR parameters. PMID:27010637
Ab initio molecular dynamics simulations of threshold displacement energies in SrTiO3
Liu, Bin; Xiao, Haiyan; Zhang, Yanwen; Aidhy, Dilpuneet S; Weber, William J
2013-01-01
Ab initio molecular dynamics simulations have been carried out to study low-energy recoil events in SrTiO3. The threshold displacement energies are shown to be strongly dependent on both the orientation and the corresponding atomic arrangement. The minimum threshold displacement energies are 13 eV for an O recoil along the <100> O-O chain, 25 eV for a Sr recoil along the <100> Sr-Sr chain and 38 eV for a Ti recoil along the <110> Ti-Ti chain. The weighted average threshold displacement energies along the primary crystallographic directions are 35.7, 53.5 and > 64.9 eV for O, Sr and Ti, respectively. The interstitial configurations produced by the recoil events are <100> and <111> split-interstitials for O and Sr, respectively, together with a Ti interstitial occupying a distorted bridge position between two Sr sites. It is found that the recoil events in SrTiO3 are partial- charge transfer assisted processes, and the partial- charge transfer plays an important role in these recoil events.
Xie, Binbin; Liu, Lihong; Cui, Ganglong; Fang, Wei-Hai; Cao, Jun; Feng, Wei; Li, Xin-qi
2015-11-21
In this work, the recently introduced quantum trajectory mean-field (QTMF) approach is implemented and employed to explore photodissociation dynamics of diazirinone (N2CO), which are based on the high-level ab initio calculation. For comparison, the photodissociation process has been simulated as well with the fewest-switches surface hopping (FSSH) and the ab initio multiple spawning (AIMS) methods. Overall, the dynamical behavior predicted by the three methods is consistent. The N2CO photodissociation at λ > 335 nm is an ultrafast process and the two C-N bonds are broken in a stepwise way, giving birth to CO and N2 as the final products in the ground state. Meanwhile, some noticeable differences were found in the QTMF, FSSH, and AIMS simulated time constants for fission of the C-N bonds, excited-state lifetime, and nonadiabatic transition ratios in different intersection regions. These have been discussed in detail. The present study provides a clear evidence that direct ab initio QTMF approach is one of the reliable tools for simulating nonadiabatic dynamics processes. PMID:26590527
The role of metals in amyloid aggregation - Experiments and ab initio simulations
NASA Astrophysics Data System (ADS)
Minicozzi, V.; Morante, S.; Rossi, G. C.; Stellato, F.; Christian, N.; Jansen, K.
With a combination of modern spectroscopic techniques and numerical first principle simulations it is possible to investigate the physico-chemical basis of the beta-amyloid aggregation phenomenon, which is suspected to be at the basis of the development of the Alzheimer disease. On the experimental side, in fact, X-ray absorption spectroscopy can be successfully used to determine the atomic structure around the metal binding site in samples where beta-amyloid peptides are complexed with either Cu2+ or Zn2+ ions. Exploiting spectroscopic information obtained on a selected set of fragments of the natural Abeta-peptide, the residues that along the sequence are coordinated to the metal are identified. Although copper data can be consistently interpreted assuming that oligopeptides encompassing the minimal 1-16 amino acidic sequence display a metal coordination mode which involves three Histidines (His6, His13, and His14), in complexes with zinc a four Histidines coordination mode is seen to be preferred. Lacking a fourth Histidine in the Abeta1-16 fragment, this geometrical arrangement hints to a Zn2+ promoted inter-peptide aggregation mode. On the theoretical side, first principle ab initio molecular dynamics simulations of the Car-Parrinello type, which have proved to be of invaluable help in understanding the microscopic mechanisms of chemical bonding both in solid-state physics and structural biophysics, have been employed in an effort to give a microscopic basis and find a phenomenological interpretation of the body of available experimental data on Abeta-peptides-metal complexes. Using medium size PC-clusters as well as larger parallel platforms, it is possible to deal with systems comprising 300-500 atoms and 1,000-2,000 electrons for simulation times as long as 2-3 ps. We present structural results that nicely compare with NMR and XAS data.
Diffusion within α-CuI studied using ab initio molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Mohn, Chris E.; Stølen, Svein; Hull, Stephen
2009-08-01
The structure and dynamics of superionic α-CuI are studied in detail by means of ab initio Born-Oppenheimer molecular dynamics simulations. The extreme cation disorder and a soft immobile face centred cubic sublattice are evident from the highly diffuse atomic density profiles. The Cu-Cu pair distribution function and distribution of Cu-I-Cu bond angles possess distinct peaks at 2.6 Å and 60° respectively, which are markedly lower than the values expected from the average cationic density, pointing to the presence of pronounced short-range copper-copper correlations. Comparison with lattice static calculations shows that these correlations and the marked shift in the cationic density profile in the lang111rang directions are associated with a locally distorted cation sublattice, and that the movements within the tetrahedral cavities involve rapid jumps into and out of shallow basins on the system potential energy surface. On average, the iodines are surrounded by three coppers within their first coordination shell, with the fourth copper being located in a transition zone between two neighbouring iodine cavities. However, time-resolved analysis reveals that the local structure actually involves a mixture of threefold-, fourfold- and fivefold-coordinated iodines. Examination of the ionic trajectories shows that the copper ions jump rapidly to nearest neighbouring tetrahedral cavities (aligned in the lang100rang directions) following a markedly curved trajectory and often involving short-lived (~1 ps) interstitial positions. The nature of the correlated diffusion underlying the unusually high fraction of coppers with short residence time can be attributed to the presence of a large number of 'unsuccessful' jumps and the likelihood of cooperative motion of pairs of coppers. The calculated diffusion coefficient at 750 K, DCu = 2.8 × 10-5 cm2 s-1, is in excellent agreement with that found experimentally.
Axisymmetric Ab Initio Core-Collapse Supernova Simulations of 12--25 Solar Mass Stars
Bruenn, S. W.; Mezzacappa, Anthony; Hix, William Raphael; Lentz, E. J.; Messer, Bronson; Lingerfelt, Eric J; Blondin, J. M.; Endeve, Eirik; Marronetti, Pedro; Yakunin, Konstantin
2013-01-01
We present an overview of four ab initio axisymmetric core-collapse supernova simulations employing detailed spectral neutrino transport computed with our CHIMERA code and initiated from Woosley & Heger (2007) progenitors of mass 12, 15, 20, and 25 M_sun. All four models exhibit shock revival over ~ 200 ms (leading to the possibility of explosion), driven by neutrino energy deposition. Hydrodynamic instabilities that impart substantial asymmetries to the shock aid these revivals, with convection appearing first in the 12 solar mass model and the standing accretion shock instability (SASI) appearing first in the 25 solar mass model. Three of the models have developed pronounced prolate morphologies (the 20 solar mass model has remained approximately spherical). By 500 ms after bounce the mean shock radii in all four models exceed 3,000 km and the diagnostic explosion energies are 0.33, 0.66, 0.65, and 0.70 Bethe (B=10^{51} ergs) for the 12, 15, 20, and 25 solar mass models, respectively, and are increasing. The three least massive of our models are already sufficiently energetic to completely unbind the envelopes of their progenitors (i.e., to explode), as evidenced by our best estimate of their explosion energies, which first become positive at 320, 380, and 440 ms after bounce. By 850 ms the 12 solar mass diagnostic explosion energy has saturated at 0.38 B, and our estimate for the final kinetic energy of the ejecta is ~ 0.3 B, which is comparable to observations for lower-mass progenitors.
Ab initio quantum Monte Carlo simulations of the uniform electron gas without fixed nodes
NASA Astrophysics Data System (ADS)
Groth, S.; Schoof, T.; Dornheim, T.; Bonitz, M.
2016-02-01
The uniform electron gas (UEG) at finite temperature is of key relevance for many applications in the warm dense matter regime, e.g., dense plasmas and laser excited solids. Also, the quality of density functional theory calculations crucially relies on the availability of accurate data for the exchange-correlation energy. Recently, results for N =33 spin-polarized electrons at high density, rs=r ¯/aB≲4 , and low temperature have been obtained with the configuration path integral Monte Carlo (CPIMC) method [T. Schoof et al., Phys. Rev. Lett. 115, 130402 (2015), 10.1103/PhysRevLett.115.130402]. To achieve these results, the original CPIMC algorithm [T. Schoof et al., Contrib. Plasma Phys. 51, 687 (2011), 10.1002/ctpp.201100012] had to be further optimized to cope with the fermion sign problem (FSP). It is the purpose of this paper to give detailed information on the manifestation of the FSP in CPIMC simulations of the UEG and to demonstrate how it can be turned into a controllable convergence problem. In addition, we present new thermodynamic results for higher temperatures. Finally, to overcome the limitations of CPIMC towards strong coupling, we invoke an independent method—the recently developed permutation blocking path integral Monte Carlo approach [T. Dornheim et al., J. Chem. Phys. 143, 204101 (2015), 10.1063/1.4936145]. The combination of both approaches is able to yield ab initio data for the UEG over the entire density range, above a temperature of about one half of the Fermi temperature. Comparison with restricted path integral Monte Carlo data [E. W. Brown et al., Phys. Rev. Lett. 110, 146405 (2013), 10.1103/PhysRevLett.110.146405] allows us to quantify the systematic error arising from the free particle nodes.
Icosahedral short-range order in amorphous Cu80Si20 by ab initio molecular dynamics simulation study
Wu, S.; Kramer, Matthew J.; Fang, Xiaowei; Wang, Shy-Guey; Wang, Cai-Zhuang; Ho, Kai-Ming; Ding, Z.J.; Chen, L.Y.
2012-04-26
Short-range order in liquid and amorphous structures of Cu80Si20 is studied by ab initio molecular dynamics simulations. We performed the simulations at 1140 and 300 K respectively to investigate the local structure change from liquid to amorphous. The result of structure factor in comparison with experimental data indicates that our simulation of amorphous Cu80Si20 is reliable. By using the bond-angle distribution function, Honeycutt–Andersen index, Voronoi tessellation method, and the atomistic cluster alignment method, the icosahedral short-range order in the system is revealed. Strong Cu–Si interaction was also observed.
NASA Astrophysics Data System (ADS)
Shibuta, Yasushi; Shimamura, Kohei; Arifin, Rizal; Shimojo, Fuyuki
2015-09-01
Ethanol decomposition on a platinum cluster is investigated by ab initio MD simulation. As the dehydrogenation proceeds, the Mulliken charge of the methylene carbon becomes a positive value, whereas that of the methyl carbon keeps a negative value. Especially, the Mulliken charge of the methylene carbon in CHxCO (x = 0, 1, 2 and 3) fragment molecules takes a large positive value. These fragment molecules correspond to those with Csbnd C bond that dissociated in the MD simulation. It suggests the large deviation in the Mulliken charge between methylene and methyl carbons is the key factor inducing the Csbnd C bond dissociation.
Structure and mechanical properties of cement and intermetallic compounds via ab-initio simulations
NASA Astrophysics Data System (ADS)
Dharmawardhana, Chamila Chathuranga
Calcium silicate hydrates comprise a class of minerals formed synthetically during Portland cement hydration or naturally through various geological processes. The importance of these minerals is immense since they are the primary binding phases for Portland cement derived construction materials. Efforts spanning centuries have been devoted to understand the structural aspects of cohesion in these minerals. In recent years, the focus has progressively turned to atomic level comprehension. Structurally these minerals can range from crystalline to highly disordered amorphous phases. This thesis focuses upon unraveling the nature of chemical bonding in a large subset of calcium silicate hydrate (CSH) crystals. Thus their electronic structure was calculated and bonding mechanisms were investigated quantitatively. Results highlight a wide range of contributions from each type of bonding (Si-O, Ca-O, O-H and hydrogen bond) with respect to silicate polymerization, crystal symmetry, water and OH content. Consequently, total bond order density (TBOD) was designated as the overall single criterion for characterizing crystal cohesion. The TBOD categorization indicates that a rarely known orthorhombic phase Suolunite is closest to the ideal composition and structure of cement. Present work finds the relationship of partial bond order density (PBOD) of each bond species, especially HBs to the mechanical properties of CSH crystals. This can be used as a basis to validate existing C-S-H models and to build improved ones. This work goes further and validates the recently proposed models (2014) for C-S-H (I) phase on the same basis of proposed electronic structure parameters. Then the respective Calcium aluminosilicate hydrates C-A-S-H (I) phase models are proposed. Finally, these results lead to improved interpretations and construction of realistic atomistic models of cement hydrates. Ab initio molecular dynamics (AIMD) could be vital to solve critical problems in complex
NASA Astrophysics Data System (ADS)
Siraleartmukul, Krisana; Siriwong, Khatcharin; Remsungnen, Tawun; Muangsin, Nongnuj; Udomkichdecha, Werasak; Hannongbua, Supot
2004-09-01
The solvation structure of glucosamine in aqueous solution was investigated using Monte Carlo simulation at 298 K. The MCY rigid water model and ab initio glucosamine-water fitted potential were applied. The first hydration shell appears at 4.6 Å from the center of glucosamine with a coordination number of seven water molecules where one water lies in the ligand's plane while two and four of them are about 2-4 Å above and below the plane, respectively. Furthermore, the mobility distribution and orientation of the water molecules around the ligand have been intensively investigated and reported.
NASA Astrophysics Data System (ADS)
Koizumi, Kenichi; Nobusada, Katsuyuki; Boero, Mauro
2015-12-01
Ab initio molecular dynamics simulations have been used to inspect the adsorption of O2 to a small gold-copper alloy cluster supported on graphene. The exposed Cu atom in this cluster acts as a crucial attractive site for the approaching of O2 and consequently widens the reaction channel for the adsorption process. Conversely, a pure Au cluster on the same graphene support is inactive for the O2 adsorption because the corresponding reaction channel for the adsorption is very narrow. These results clearly indicate that doping a different metal to the Au cluster is a way to enhance the oxygen adsorption and to promote catalytic reactions.
NASA Astrophysics Data System (ADS)
Kritayakornupong, Chinapong; Hannongbua, Supot
2007-01-01
The structural and dynamical properties of high-spin Ru 2+ in aqueous solution have been theoretically studied using molecular dynamics (MD) simulations. The conventional MD simulation based on pair potentials gives the overestimated average first shell coordination number of 9, whereas the value of 5.9 was observed when the three-body corrected function was included. A combined ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulation has been performed to take into account the many-body effects on the hydration shell structure of Ru 2+. The most important region, the first hydration shell, was treated by ab initio quantum mechanics at UHF level using the SBKJC VDZ ECP basis set for Ru 2+ and the 6-31G ∗ basis sets for water. An exact coordination number of 6 for the first hydration shell was obtained from the QM/MM simulation. The QM/MM simulation predicts the average Ru 2+-O distance of 2.42 Å for the first hydration shell, whereas the values of 2.34 and 2.46 Å are resulted from the pair potentials without and with the three-body corrected simulations, respectively. Several other structural properties representing position and orientation of the solvate molecules were evaluated for describing the hydration shell structure of the Ru 2+ ion in dilute aqueous solution. A mean residence time of 7.1 ps was obtained for water ligands residing in the second hydration shell.
The many-body Wigner Monte Carlo method for time-dependent ab-initio quantum simulations
Sellier, J.M. Dimov, I.
2014-09-15
The aim of ab-initio approaches is the simulation of many-body quantum systems from the first principles of quantum mechanics. These methods are traditionally based on the many-body Schrödinger equation which represents an incredible mathematical challenge. In this paper, we introduce the many-body Wigner Monte Carlo method in the context of distinguishable particles and in the absence of spin-dependent effects. Despite these restrictions, the method has several advantages. First of all, the Wigner formalism is intuitive, as it is based on the concept of a quasi-distribution function. Secondly, the Monte Carlo numerical approach allows scalability on parallel machines that is practically unachievable by means of other techniques based on finite difference or finite element methods. Finally, this method allows time-dependent ab-initio simulations of strongly correlated quantum systems. In order to validate our many-body Wigner Monte Carlo method, as a case study we simulate a relatively simple system consisting of two particles in several different situations. We first start from two non-interacting free Gaussian wave packets. We, then, proceed with the inclusion of an external potential barrier, and we conclude by simulating two entangled (i.e. correlated) particles. The results show how, in the case of negligible spin-dependent effects, the many-body Wigner Monte Carlo method provides an efficient and reliable tool to study the time-dependent evolution of quantum systems composed of distinguishable particles.
Giese, Timothy J; York, Darrin M
2016-06-14
A new approach for performing Particle Mesh Ewald in ab initio quantum mechanical/molecular mechanical (QM/MM) simulations with extended atomic orbital basis sets is presented. The new approach, the Ambient-Potential Composite Ewald (CEw) method, does not perform the QM/MM interaction with Mulliken charges nor electrostatically fit charges. Instead the nuclei and electron density interact directly with the MM environment, but in a manner that avoids the use of dense Fourier transform grids. By performing the electrostatics with the underlying QM density, the CEw method avoids self-consistent field instabilities that have been encountered with simple charge mapping procedures. Potential of mean force (PMF) profiles of the p-nitrophenyl phosphate dissociation reaction in explicit solvent are computed from PBE0/6-31G* QM/MM molecular dynamics simulations with various electrostatic protocols. The CEw profiles are shown to be stable with respect to real-space Ewald cutoff, whereas the PMFs computed from truncated and switched electrostatics produce artifacts. PBE0/6-311G**, AM1/d-PhoT, and DFTB2 QM/MM simulations are performed to generate two-dimensional PMF profiles of the phosphoryl transesterification reactions with ethoxide and phenoxide leaving groups. The semiempirical models incorrectly produce a concerted ethoxide mechanism, whereas PBE0 correctly produces a stepwise mechanism. The ab initio reaction barriers agree more closely to experiment than the semiempirical models. The failure of Mulliken-charge QM/MM-Ewald is analyzed. PMID:27171914
NASA Technical Reports Server (NTRS)
Smith, Grant D.; Jaffe, R. L.; Yoon, D. Y.; Arnold, James O. (Technical Monitor)
1994-01-01
Molecular dynamics simulations of POE melts have been performed utilizing a potential force field parameterized to reproduce conformer energies and rotational energy barriers in dimethoxyethane as determined from ab initio electronic structure calculations. Chain conformations and dimensions of POE from the simulations were found to be in good agreement with predictions of a rotational isomeric state (RIS) model based upon the ab initio conformational. energies. The melt chains were found to be somewhat extended relative to chains at theta conditions. This effect will be discussed in light of neutron scattering experiments which indicate that POE chains are extended in the melt relative to theta solutions. The conformational characteristics of POE chains will also be compared with those of other poly (alkylethers), namely poly(oxymethylene), poly(oxytrimethylene) and poly(oxytetramethylene). Local conformational dynamics were found to be more rapid than in polymethylene. Calculated C-H vector correlation times were found to be in reasonable agreement with experimental values from C-13 NMR spin-lattice relaxation times. The influence of ionic salts on local conformations and dynamics will also be discussed.
Rio, Beatriz G del; González, Luis E
2014-11-19
We have performed a comprehensive study of the properties of liquid Be, Ca and Ba, through the use of orbital free ab initio simulations. To this end we have developed a force-matching method to construct the necessary local pseudopotentials from standard ab initio calculations. The structural magnitudes are analyzed, including the average and local structures and the dynamic properties are studied. We find several common features, like an asymmetric second peak in the structure factor, a large amount of local structures with five-fold symmetry, a quasi-universal behaviour of the single-particle dynamic properties and a large degree of positive dispersion in the propagation of collective density fluctuations, whose damping is dictated by slow thermal relaxations and fast viscoelastic ones. Some peculiarities in the dynamic properties are however observed, like a very high sound velocity and a large violation of the Stokes-Einstein relation for Be, or an extremely high positive dispersion and a large slope in the dispersion relation of shear waves at the onset of the wavevector region where they are supported for Ba. PMID:25347355
NASA Astrophysics Data System (ADS)
Kumar, Anupriya; Kołaski, Maciej; Kim, Kwang S.
2008-01-01
Structures of the ground state pyrrole-(H2O)n clusters are investigated using ab initio calculations. The charge-transfer driven femtosecond scale dynamics are studied with excited state ab initio molecular dynamics simulations employing the complete-active-space self-consistent-field method for pyrrole-(H2O)n clusters. Upon the excitation of these clusters, the charge density is located over the farthest water molecule which is repelled by the depleted π-electron cloud of pyrrole ring, resulting in a highly polarized complex. For pyrrole-(H2O), the charge transfer is maximized (up to 0.34a.u.) around ˜100fs and then oscillates. For pyrrole-(H2O)2, the initial charge transfer occurs through the space between the pyrrole and the π H-bonded water molecule and then the charge transfer takes place from this water molecule to the σ H-bonded water molecule. The total charge transfer from the pyrrole to the water molecules is maximized (up to 0.53a.u.) around ˜100fs.
Ab Initio Atomic Simulations of Antisite Pair Recovery in Cubic Silicon Carbide
Gao, Fei; Du, Jincheng; Bylaska, Eric J.; Posselt, Matthias; Weber, William J.
2007-05-28
The thermal stability of an antisite pair in 3C-SiC is studied using ab initio molecular dynamics within the framework of density functional theory. The lifetime of the antisite pair configuration is calculated for temperatures between 1800 and 2250 K, and the effective activation energy for antisite pair recombination is determined to be 2.52 eV. The recombination energy path and static energy barrier are also calculated using the nudged elastic band method, along with the dimer method to accurately locate the transition states. The consistency of the results suggests that the antisite pair cannot be correlated with the DI photoluminescence center, as proposed by previously theoretical interpretations. An extended exchange mechanism is found for the antisite pair recombination, and this may be a dominant mechanism for antisite pair recombination and diffusion of impurities in compound semiconductors.
Casolo, S; Tantardini, G F; Martinazzo, R
2016-07-14
We studied Eley-Rideal molecular hydrogen formation on graphite using ab initio molecular dynamics, in the energy range relevant for the chemistry of the interstellar medium and for terrestrial experiments employing cold plasma (0.02-1 eV). We found substantial projectile steering effects that prevent dimer formation at low energies, thereby ruling out any catalytic synthetic pathways that form hydrogen molecules. Ortho and para dimers do form efficiently thanks to preferential sticking, but only at energies that are too high to be relevant for the chemistry of the interstellar medium. Computed reaction cross sections and ro-vibrational product populations are in good agreement with available experimental data and capable of generating adsorbate configurations similar to those observed with scanning tunneling microscopy techniques. PMID:26905385
Impact of oxygen on the 300-K isotherm of Laser Megajoule ablator using ab initio simulation
NASA Astrophysics Data System (ADS)
Colin-Lalu, P.; Recoules, V.; Salin, G.; Huser, G.
2015-11-01
The ablator material for inertial confinement fusion (ICF) capsules on the Laser Mégajoule is a glow-discharge polymer (GDP) plastic. Its equation of state (EOS) is of primary importance for the design of such capsules, since it has direct consequences on shock timing and is essential to mitigate hydrodynamic instabilities. Using ab initio molecular dynamics (AIMD), we have investigated the 300-K isotherm of amorphous CH1.37O0.08 plastic, whose structure is close to GDP plastic. The 300-K isotherm, which is often used as a cold curve within tabular EOS, is an important contribution of the EOS in the multimegabar pressure range. AIMD results are compared to analytic models within tabular EOS, pointing out large discrepancies. In addition, we show that the effect of oxygen decreases 300-K isotherm pressure by 10%-15%. The implication of these observations is the ability to improve ICF target performance, which is essential to achieve fusion ignition.
High-pressure crystalline polyethylene studied by x-ray diffraction and ab initio simulations
Fontana, L.; Vinh, Diep Q.; Santoro, M.; Gorelli, F. A.; Hanfland, M.
2007-05-01
Crystalline polyethylene was investigated under pressure between 0 and 40 GPa, up to 280 deg. C, by means of synchrotron x-ray powder diffraction and ab initio calculations. A rich polymorphism was unveiled, consisting of two new high-pressure monoclinic phases, in addition to the well-known orthorhombic one, which appear reversibly, although with strong hysteresis, upon increasing pressure above 6 GPa (P2{sub 1}/m, Z{sub chain}=1) and 14-16 GPa (A2/m, Z{sub chain}=2), respectively. The equation of state was determined for the three solid phases. We find that polyethylene is characterized by a sharp separation between strong covalent intrachain and weaker interchain interactions up to the maximum investigated pressure, which, in turn, places the ultimate chemical stability limit of polyethylene far beyond these thermodynamic conditions.
NASA Astrophysics Data System (ADS)
Xue, Wenhua; Dang, Hongli; Liu, Yingdi; Jentoft, Friederike; Resasco, Daniel; Wang, Sanwu
2014-03-01
In the study of catalytic reactions of biomass, furfural conversion over metal catalysts with the presence of hydrogen has attracted wide attention. We report ab initio molecular dynamics simulations for furfural and hydrogen on the Pd(111) surface at finite temperatures. The simulations demonstrate that the presence of hydrogen is important in promoting furfural conversion. In particular, hydrogen molecules dissociate rapidly on the Pd(111) surface. As a result of such dissociation, atomic hydrogen participates in the reactions with furfural. The simulations also provide detailed information about the possible reactions of hydrogen with furfural. Supported by DOE (DE-SC0004600). This research used the supercomputer resources of the XSEDE, the NERSC Center, and the Tandy Supercomputing Center.
NASA Astrophysics Data System (ADS)
Cerdeira, M. A.; Palacios, S. L.; González, C.; Fernández-Pello, D.; Iglesias, R.
2016-09-01
The formation, binding and migration energetics of helium clusters inside a niobium crystal have been analysed via ab initio simulations. The effect of placing several He atoms within an n-vacancy previously formed or as interstitials inside the initial perfect bulk matrix has been studied. DFT-based results show that He atoms prefer to aggregate forming small clusters at n-vacancy sites rather than at interstitial positions in the perfect crystal. The minimum formation energy is found when NHe is equal to the number of vacancies, n. It follows that vacancies act as almost perfect traps for He atoms, as is well known for other metals. The migration barriers of He atoms inside vacancies increase considerably when compared to what happens for vacancies alone. A secondary consequence is that the full set of energies obtained will be highly relevant as an input for new approaches to KMC simulations of defects in Nb.
Wang, S.Y.; Kramer, M.J.; Xu, M.; Wu, S.; Hao, S.G.; Sordelet, D.J.; Ho, K.M.; Wang, C.Z.
2009-06-12
X-ray diffraction and ab initio molecular dynamics simulation studies of molten Al{sub 60}Cu{sub 40} have been carried out between 973 and 1323 K. The structures obtained from our simulated atomic models are fully consistent with the experimental results. The local structures of the models analyzed using Honeycutt-Andersen and Voronoi tessellation methods clearly demonstrate that as the temperatures of the liquid is lowered it becomes more ordered. While no one cluster-type dominates the local structure of this liquid, the most prevalent polyhedra in the liquid structure can be described as distorted icosahedra. No obvious correlations between the clusters observed in the liquid and known stable crystalline phases in this system were observed.
Wikfeldt, K. T.; Michaelides, A.
2014-01-28
Ab initio simulations that account for nuclear quantum effects have been used to examine the order-disorder transition in squaric acid, a prototypical H-bonded antiferroelectric crystal. Our simulations reproduce the >100 K difference in transition temperature observed upon deuteration as well as the strong geometrical isotope effect observed on intermolecular separations within the crystal. We find that collective transfer of protons along the H-bonding chains – facilitated by quantum mechanical tunneling – is critical to the order-disorder transition and the geometrical isotope effect. This sheds light on the origin of isotope effects and the importance of tunneling in squaric acid which likely extends to other H-bonded ferroelectrics.
Makhov, Dmitry V.; Saita, Kenichiro; Martinez, Todd J.; Shalashilin, Dmitrii V.
2014-12-11
In this study, we report a detailed computational simulation of the photodissociation of pyrrole using the ab initio Multiple Cloning (AIMC) method implemented within MOLPRO. The efficiency of the AIMC implementation, employing train basis sets, linear approximation for matrix elements, and Ehrenfest configuration cloning, allows us to accumulate significant statistics. We calculate and analyze the total kinetic energy release (TKER) spectrum and Velocity Map Imaging (VMI) of pyrrole and compare the results directly with experimental measurements. Both the TKER spectrum and the structure of the velocity map image (VMI) are well reproduced. Previously, it has been assumed that the isotropic component of the VMI arises from long time statistical dissociation. Instead, our simulations suggest that ultrafast dynamics contributes significantly to both low and high energy portions of the TKER spectrum.
Koizumi, Kenichi; Nobusada, Katsuyuki; Boero, Mauro
2015-12-31
Ab initio molecular dynamics simulations have been used to inspect the adsorption of O{sub 2} to a small gold-copper alloy cluster supported on graphene. The exposed Cu atom in this cluster acts as a crucial attractive site for the approaching of O{sub 2} and consequently widens the reaction channel for the adsorption process. Conversely, a pure Au cluster on the same graphene support is inactive for the O{sub 2} adsorption because the corresponding reaction channel for the adsorption is very narrow. These results clearly indicate that doping a different metal to the Au cluster is a way to enhance the oxygen adsorption and to promote catalytic reactions.
Guo, Xun; Zhang, Xitong; Zhao, Shijun; Huang, Qing; Xue, Jianming
2016-01-01
Density functional theory (DFT) calculation is employed to study the adsorption properties of Pb and Cu on recently synthesized two-dimensional materials MXenes, including Ti3C2, V2C1 and Ti2C1. The influence of surface decoration with functional groups such as H, OH and F have also been investigated. Most of these studied MXenes exhibit excellent capability to adsorb Pb and Cu, especially the adsorption capacity of Pb on Ti2C1 is as high as 2560 mg g(-1). Both the binding energies and the adsorption capacities are sensitive to the functional groups attached to the MXenes' surface. Ab initio molecular dynamics (ab-init MD) simulation confirms that Ti2C1 remains stable at room temperature after adsorbing Pb atoms. Our calculations imply that these newly emerging two-dimensional MXenes are promising candidates for wastewater treatment and ion separation. PMID:26602974
Erba, A; Mahmoud, A; Belmonte, D; Dovesi, R
2014-03-28
A computational strategy is devised for the accurate ab initio simulation of elastic properties of crystalline materials under pressure. The proposed scheme, based on the evaluation of the analytical stress tensor and on the automated computation of pressure-dependent elastic stiffness constants, is implemented in the CRYSTAL solid state quantum-chemical program. Elastic constants and related properties (bulk, shear and Young moduli, directional seismic wave velocities, elastic anisotropy index, Poisson's ratio, etc.) can be computed for crystals of any space group of symmetry. We apply such a technique to the study of high-pressure elastic properties of three silicate garnet end-members (namely, pyrope, grossular, and andradite) which are of great geophysical interest, being among the most important rock-forming minerals. The reliability of this theoretical approach is proved by comparing with available experimental measurements. The description of high-pressure properties provided by several equations of state is also critically discussed. PMID:24697466
Jakse, N.; Pasturel, A.
2014-12-21
In the present work, the structural and dynamic properties of liquid and undercooled boron are investigated by means of ab initio molecular dynamics simulation. Our results show that both liquid and undercooled states present a well pronounced short-range order (SRO) mainly due to the formation of inverted umbrella structural units. Moreover, we observe the development of a medium-range order (MRO) in the undercooling regime related to the increase of inverted umbrella structural units and of their interconnection as the temperature decreases. We also evidence that this MRO leads to a partial crystallization in the β-rhombohedral crystal below T = 1900 K. Finally, we discuss the role played by the SRO and MRO in the nearly Arrhenius evolution of the diffusion and the non-Arrhenius temperature dependence of the shear viscosity, in agreement with the experiment.
Alemany, Manuel M. G.; Longo, Roberto; Gallego, Luis; Gonzales, D. J.; Gonzales, L. E.; Tiago, Murilo L; Chelikowsky, James
2007-01-01
We performed a comprehensive study of the static, dynamic and electronic properties of liquid Pb at T = 650 kelvins, density 0.0309 angstroms^{-3} by means of 216-particle ab initio molecular dynamics simulations based on a real-space implementation of pseudopotentials constructed within density-functional theory. The predicted results and available experimental data are very in good agreement, which confirms the adequacy of this technique to achieve a reliable description of the behavior of liquid metals, including their dynamic properties. Although some of the computed properties of liquid Pb are similar to those of simple liquid metals, others differ markedly. Our results show that an appropriate description of liquid Pb requires the inclusion of relativistic effects in the determination of the pseudopotentials of Pb.
Feng, Ya-Juan; Huang, Teng; Wang, Chao; Liu, Yi-Rong; Jiang, Shuai; Miao, Shou-Kui; Chen, Jiao; Huang, Wei
2016-07-14
Molecular level insight into the interaction between volatile organic compounds (VOCs) and aerosols is crucial for improvement of atmospheric chemistry models. In this paper, the interaction between adsorbed toluene, one of the most significant VOCs in the urban atmosphere, and the aqueous surface of aerosols was studied by means of combined molecular dynamics simulations and ab initio quantum chemistry calculations. It is revealed that toluene can be stably adsorbed on the surface of aqueous droplets via hydroxyl-π hydrogen bonding between the H atoms of the water molecules and the C atoms in the aromatic ring. Further, significant modifications on the electrostatic potential map and frontier molecular orbital are induced by the solvation effect of surface water molecules, which would affect the reactivity and pathway of the atmospheric photooxidation of toluene. This study demonstrates that the surface interactions should be taken into consideration in the atmospheric chemical models on oxidation of aromatics. PMID:27280740
Erba, A. Mahmoud, A.; Dovesi, R.; Belmonte, D.
2014-03-28
A computational strategy is devised for the accurate ab initio simulation of elastic properties of crystalline materials under pressure. The proposed scheme, based on the evaluation of the analytical stress tensor and on the automated computation of pressure-dependent elastic stiffness constants, is implemented in the CRYSTAL solid state quantum-chemical program. Elastic constants and related properties (bulk, shear and Young moduli, directional seismic wave velocities, elastic anisotropy index, Poisson's ratio, etc.) can be computed for crystals of any space group of symmetry. We apply such a technique to the study of high-pressure elastic properties of three silicate garnet end-members (namely, pyrope, grossular, and andradite) which are of great geophysical interest, being among the most important rock-forming minerals. The reliability of this theoretical approach is proved by comparing with available experimental measurements. The description of high-pressure properties provided by several equations of state is also critically discussed.
Impact of oxygen on the 300-K isotherm of Laser Megajoule ablator using ab initio simulation.
Colin-Lalu, P; Recoules, V; Salin, G; Huser, G
2015-11-01
The ablator material for inertial confinement fusion (ICF) capsules on the Laser Mégajoule is a glow-discharge polymer (GDP) plastic. Its equation of state (EOS) is of primary importance for the design of such capsules, since it has direct consequences on shock timing and is essential to mitigate hydrodynamic instabilities. Using ab initio molecular dynamics (AIMD), we have investigated the 300-K isotherm of amorphous CH(1.37)O(0.08) plastic, whose structure is close to GDP plastic. The 300-K isotherm, which is often used as a cold curve within tabular EOS, is an important contribution of the EOS in the multimegabar pressure range. AIMD results are compared to analytic models within tabular EOS, pointing out large discrepancies. In addition, we show that the effect of oxygen decreases 300-K isotherm pressure by 10%-15%. The implication of these observations is the ability to improve ICF target performance, which is essential to achieve fusion ignition. PMID:26651799
Chen Shilu; Fang Weihai
2009-08-07
In the present paper we report a theoretical study on mechanistic photodissociation of acetaldehyde (CH{sub 3}CHO). Stationary structures for H{sub 2} and CO eliminations in the ground state (S{sub 0}) have been optimized with density functional theory method, which is followed by the intrinsic reaction coordinate and ab initio molecular dynamics calculations to confirm the elimination mechanism. Equilibrium geometries, transition states, and intersection structures for the C-C and C-H dissociations in excited states were determined by the complete-active-space self-consistent field (CASSCF) method. Based on the CASSCF optimized structures, the potential energy profiles for the dissociations were refined by performing the single-point calculations using the multireference configuration interaction method. Upon the low-energy irradiation of CH{sub 3}CHO (265 nm<{lambda}<318 nm), the T{sub 1} C-C bond fission following intersystem crossing from the S{sub 1} state is the predominant channel and the minor channel, the ground-state elimination to CH{sub 4}+CO after internal conversion (IC) from S{sub 1} to S{sub 0}, could not be excluded. With the photon energy increasing, another pathway of IC, achieved via an S{sub 1}/S{sub 0} intersection point resulting from the S{sub 1} C-C bond fission, becomes accessible and increases the yield of CH{sub 4}+CO.
Simulating ionic thermal trasport by equilibrium ab-initio molecular dynamics
NASA Astrophysics Data System (ADS)
Marcolongo, Aris; Umari, Paolo; Baroni, Stefano
2014-03-01
The Green-Kubo approach to thermal transport is often considered to be incompatible with ab-initio molecular dynamics (AIMD) because a suitable quantum-mechanical definition of the heat current is not readily available, due to the ill-definedness of the microscopic energy density to which it is related by the continuity equation. We argue that a similar difficulty actually exists in classical mechanics as well, and we address the conditions that have to be fulfilled in order for the physically well defined transport coefficients to be independent of the ill defined microscopic energy density from which they derive. We then provide two alternative approaches to calculating thermal conductivites from equilibrium AIMD. The first is based on the Green-Kubo formula, supplemented with an expression for the energy current, which is a generalization of Thouless' expression for the adiabatic charge current. The second approach, which avoids the recourse to an energy current altogether, rests on an efficient and accurate extrapolation to infinite wavelengths of the energy-density time correlation functions. The two methods are compared on a simple classical test bed, and their implementation in AIMD is demonstrated with the calculation of the thermal conductivity of simple fluids.
Ab initio molecular dynamics simulations of ion-solid interactions in zirconate pyrochlores
Xiao, Haiyan Y.; Weber, William J.; Zhang, Yanwen; Zu, X. T.
2015-01-31
In this paper, an ab initio molecular dynamics method is employed to study low energy recoil events in zirconate pyrochlores (A_{2}Zr_{2}O_{7}, A = La, Nd and Sm). It shows that both cations and anions in Nd_{2}Zr_{2}O_{7} and Sm_{2}Zr_{2}O_{7} are generally more likely to be displaced than those in La_{2}Zr_{2}O_{7}. The damage end states mainly consist of Frenkel pair defects, and the Frenkel pair formation energies in Nd_{2}Zr_{2}O_{7} and Sm_{2}Zr_{2}O_{7} are lower than those in La_{2}Zr_{2}O_{7}. These results suggest that the order–disorder structural transition more easily occurs in Nd_{2}Zr_{2}O_{7} and Sm_{2}Zr_{2}O_{7} resulting in a defect-fluorite structure, which agrees well with experimental observations. Our calculations indicate that oxygen migration from 48f and 8b to 8a sites is dominant under low energy irradiation. A number of new defects, including four types of cation Frenkel pairs and six types of anion Frenkel pairs, are revealed by ab initio molecular dynamics simulations. The present findings may help to advance the fundamental understanding of the irradiation response behavior of zirconate pyrochlores.
Grenier, Romain; To, Quy-Dong; de Lara-Castells, María Pilar; Léonard, Céline
2015-07-01
Global potentials for the interaction between the Ar atom and gold surfaces are investigated and Ar-Au pair potentials suitable for molecular dynamics simulations are derived. Using a periodic plane-wave representation of the electronic wave function, the nonlocal van-der-Waals vdW-DF2 and vdW-OptB86 approaches have been proved to describe better the interaction. These global interaction potentials have been decomposed to produce pair potentials. Then, the pair potentials have been compared with those derived by combining the dispersionless density functional dlDF for the repulsive part with an effective pairwise dispersion interaction. These repulsive potentials have been obtained from the decomposition of the repulsive interaction between the Ar atom and the Au2 and Au4 clusters and the dispersion coefficients have been evaluated by means of ab initio calculations on the Ar+Au2 complex using symmetry adapted perturbation theory. The pair potentials agree very well with those evaluated through periodic vdW-DF2 calculations. For benchmarking purposes, CCSD(T) calculations have also been performed for the ArAu and Ar+Au2 systems using large basis sets and extrapolations to the complete basis set limit. This work highlights that ab initio calculations using very small surface clusters can be used either as an independent cross-check to compare the performance of state-of-the-art vdW-corrected periodic DFT approaches or, directly, to calculate the pair potentials necessary in further molecular dynamics calculations. PMID:26046588
Ab initio simulation of radiation damage in nuclear reactor pressure vessel materials
NASA Astrophysics Data System (ADS)
Watts, Daniel; Finkenstadt, Daniel
2012-02-01
Using Kinetic Monte Carlo we developed a code to study point defect hopping in BCC metallic alloys using energetics and attempt frequencies calculated using VASP, an electronic structure software package. Our code provides a way of simulating the effects of neutron radiation on potential reactor materials. Specifically we will compare the Molybdenum-Chromium alloy system to steel alloys for use in nuclear reactor pressure vessels.
Caturla, M. J.; Diaz de la Rubia, T.; Griffin, P. B.; Johnson, M. C.; Theiss, S.; Ural, A.
1998-12-16
We have developed a kinetic Monte Carlo (kMC) simulator that links atomic migration and binding energies determined primarily from first principles calculations to macroscopic phenomena and laboratory time scales. Input for the kMC simulation is obtained from a combination of ab initio planewave pseudopotential calculations, molecular dynamics simulations, and experimental data. The simulator is validated against an extensive series of experimental studies of the diffusion of B spikes in self-implanted Si. The implant energy, dose, and dose rate, as well as the detailed thermal history of the sample, are included. Good agreement is obtained with the experimental data for temperatures between 750 and 950 C and times from 15 to 255 s. At 1050o C we predict too little diffusion after 105 s compared to experiment: apparently, some mechanism which is not adequately represented by our model becomes important at this temperature. Below 1050o C, the kMC simulation produces a complete description over macroscopic time scales of the atomic level diffusion and defect reaction phenomena that operate during the anneals. This simulator provides a practical method for predicting technologically interesting phenomena, such as transient enhanced diffusion of B, over a wide range of conditions, using energetics determined from first-principles approaches.
Ab initio molecular dynamics simulations of low energy recoil events in ceramics
Gao, Fei; Xiao, Haiyan Y.; Weber, William J.
2011-07-15
The recent progress in the use of large-scale ab initio molecular dynamics (AIMD) to investigate low energy recoil events and determine threshold displacement energies, Ed, in ceramics is reviewed. In general, Ed shows a significant dependence on recoil direction and atom. In 3C-SiC, the minimum Ed for both C and Si atoms is found along the <100> direction, with a value of 20 and 49 eV, respectively. The results demonstrate that significant charge transfer occurs during the dynamics process, and defects can enhance charge transfer to surrounding atoms, which provides important insights into the formation of charged defects. It is found that the C vacancy is a positively charged defect, whereas the Si vacancy is in its neutral state. The minimum Ed in GaN is determined to be 17 and 39 eV for N and Ga atoms, respectively, both along the direction. The average Ed for N atoms (32.4 eV) is smaller than that for Ga atoms (73.2 eV). It is of interest to note that the N defects created along different crystallographic directions have a similar configuration (a N-N dumbbell configuration), but various configurations for Ga defects are formed. In Y2Ti2O7 prochlore, the minimum Ed for Y atoms is determined to be 27 eV for a recoil along the <100> direction, 31.5 eV for Ti atoms along the <100> direction, 14.5 eV for O48f atoms along the <110> direction and 13 eV for O8b atoms along the <111> direction. The average Ed values determined are 32.7, 34.2, 14.2 and 16.1 eV for yttrium, titanium, O48f and O8b atoms, respectively. Cation interstitials at vacant 8a sites, which are generally occupied by oxygen anions, and at the bridge sites between two neighboring cations along the <010> direction are observed after low energy recoil events.
Ab initio molecular dynamics simulations of low energy recoil events in ceramics
Gao, Fei; Xiao, Haiyan; Weber, William J
2011-01-01
The recent progress in the use of large-scale ab initio molecular dynamics (AIMD) to investigate low energy recoil events and determine threshold displacement energies, Ed, in ceramics is reviewed. In general, Ed shows a significant dependence on recoil direction and atom. In SiC, the minimum Ed for both C and Si atoms is found along the <100> direction, with a value of 20 and 49 eV, respectively. The results demonstrate that significant charge transfer occurs during the dynamics process, and defects can enhance charge transfer to surrounding atoms, which provides important insights into the formation of charged defects. It is found that the C vacancy is a positively charged defect, whereas the Si vacancy is in its neutral state. The minimum Ed in GaN is determined to be 17 and 39 eV for N and Ga atoms, respectively, both along the direction. The average Ed for N atoms (32.4 eV) is smaller than that for Ga atoms (73.2 eV). It is of interest to note that the N defects created along different crystallographic directions have a similar configuration (a N-N dumbbell configuration), but various configurations for Ga defects are formed. In Y2Ti2O7 prochlore, the minimum Ed for Y atoms is determined to be 27 eV for a recoil along the <100> direction, 31.5 eV for Ti atoms along the <100> direction, 14.5 eV for O48f atoms along the <110> direction and 13 eV for O8b atoms along the <111> direction. The average Ed values determined are 32.7, 34.2, 14.2 and 16.1 eV for yttrium, titanium, O48f and O8b atoms, respectively. Cation interstitials at vacant 8a sites, which are generally occupied by oxygen anions, and at the bridge sites between two neighboring cations along the <010> direction are observed after low energy recoil events.
NASA Astrophysics Data System (ADS)
Nikolopoulos, L. A. A.
2003-02-01
A package is presented for the fully ab-initio calculation of one- and two-photon ionization cross sections for two-electron atomic systems (H -, He, Mg, Ca, …) under strong laser fields, within lowest-order perturbation theory (LOPT) and in the dipole approximation. The atomic structure is obtained through configuration interaction (CI) of antisymmetrized two-electron states expanded in a B-spline finite basis. The formulation of the theory and the relevant codes presented here represent the accumulation of work over the last ten years [1-11,13-15]. Extensions to more than two-photon ionization is straightforward. Calculation is possible for both the length and velocity form of the laser-atom interaction operator. The package is mainly, written in standard FORTRAN language and uses the publicly available libraries SLATEC, LAPACK and BLAS.
NASA Astrophysics Data System (ADS)
Santos, Iván; Aboy, María; López, Pedro; Marqués, Luis A.; Pelaz, Lourdes
2016-02-01
We have used atomistic simulations to identify and characterize interstitial defect cluster configurations candidate for W and X photoluminescence centers in crystalline Si. The configurational landscape of small self-interstitial defect clusters has been explored through nanosecond annealing and implantation recoil simulations using classical molecular dynamics. Among the large collection of defect configurations obtained, we have selected those defects with the trigonal symmetry of the W center, and the tetrahedral and tetragonal symmetry of the X center. These defect configurations have been characterized using ab initio simulations in terms of their donor levels, their local vibrational modes, the defect induced modifications of the electronic band structure, and the transition amplitudes at band edges. We have found that the so-called I 3-V is the most likely candidate for the W PL center. It has a donor level and local vibrational modes in better agreement with experiments, a lower formation energy, and stronger transition amplitudes than the so-called I 3-I, which was previously proposed as the W center. With respect to defect candidates for the X PL center, our calculations have shown that none of the analyzed defect candidates match all of the experimental characteristics of the X center. Although the Arai tetra-interstitial configuration previously proposed as the X center cannot be excluded, the other defect candidates for the X center found, I 3-C and I 3-X, cannot be discarded either.
NASA Astrophysics Data System (ADS)
Marini, Andrea
Density functional theory and many-body perturbation theory methods (such as GW and Bethe-Selpether equation) are standard approaches to the equilibrium ground and excited state properties of condensed matter systems, surfaces, molecules and other several kind of materials. At the same time ultra-fast optical spectroscopy is becoming a widely used and powerful tool for the observation of the out-of-equilibrium dynamical processes. In this case the theoretical tools (such as the Baym-Kadanoff equation) are well known but, only recently, have been merged with the ab-Initio approach. And, for this reason, highly parallel and efficient codes are lacking. Nevertheless, the combination of these two areas of research represents, for the ab-initio community, a challenging prespective as it requires the development of advanced theoretical, methodological and numerical tools. Yambo is a popular community software implementing the above methods using plane-waves and pseudo-potentials. Yambo is available to the community as open-source software, and oriented to high-performance computing. The Yambo project aims at making the simulation of these equilibrium and out-of-equilibrium complex processes available to a wide community of users. Indeed the code is used, in practice, in many countries and well beyond the European borders. Yambo is a member of the suite of codes of the MAX European Center of Excellence (Materials design at the exascale) . It is also used by the user facilities of the European Spectroscopy Facility and of the NFFA European Center (nanoscience foundries & fine analysis). In this talk I will discuss some recent numerical and methodological developments that have been implemented in Yambo towards to exploitation of next generation HPC supercomputers. In particular, I will present the hybrid MPI+OpenMP parallelization and the specific case of the response function calculation. I will also discuss the future plans of the Yambo project and its potential use as
Ma, Xiaoyan; Cai, Kaicong; Wang, Jianping
2011-02-10
Infrared (IR) experiment, ab initio computations, and molecular dynamics (MD) simulations were used to examine the dynamical structures of ethylene glycol (EG) and 1,2-ethanedithiol (EDT) in carbon tetrachloride and deuterated chloroform. Using the O-H and S-H stretching modes as structural probes, EG and EDT were found to exhibit different conformational preferences, even though they share similar molecular formula. Results suggest that the gauche conformation of EG presents and is stabilized by the intramolecular hydrogen bond (IHB), while both the trans and gauche EDT are possible in the two solvents. Exchangeable IHB donor and acceptor pairs were predicted in the case of EG. Anharmonic vibrational frequencies, anharmonicities, and couplings of the O-H and S-H stretching modes were predicted and found to be structurally dependent. Linear IR and two-dimensional IR spectra containing these structural signatures were simulated and discussed. These results demonstrate that a combination of the methods used here is very useful in revealing structural dynamics of small molecules in condensed phases. PMID:21208002
Ab initio simulation of the electronic structure of Ta{sub 2}O{sub 5} crystal modifications
Perevalov, T. V. Shaposhnikov, A. V.
2013-06-15
Ab initio simulation of the electronic structure crystalline {beta} and {delta} phases of tantalum(V) oxide (Ta{sub 2}O{sub 5}), representing a promising dielectric material for microelectronics, has been carried out. Both ideal crystals and those with neutral oxygen vacancies in various coordination positions have been studied. The simulation has been performed using the density functional theory with hybrid functionals involving the Hartree-Fock exchange energy. This approach gives a correct description of the bandgap width: 4.1 eV for {beta}-Ta{sub 2}O{sub 5} and 3.1 eV for {delta}-Ta{sub 2}O{sub 5}. The energy levels related to oxygen vacancies in various positions have been determined for the spectra of electron states in {beta}- and {delta}-Ta{sub 2}O{sub 5} polymorphs. It is established that the presence of oxygen vacancies in Ta{sub 2}O{sub 5} crystal modifications leads to the formation of characteristic absorption peaks in their electron energy loss spectra.
NASA Astrophysics Data System (ADS)
Kent, P. R. C.; Ganesh, P.; Jiang, De-En; Borodin, O.
2012-02-01
Optimizing the choice of electrolyte in lithium ion batteries and an understanding of the solid-electrolyte interphase (SEI) is required to optimize the balance between high-energy storage, high rate capability, and lifetime. We perform accurate ab initio molecular-dynamics simulations of common cyclic carbonates and LiPF6 to build solvation models which explain available Neutron and NMR spectroscopies. Our results corroborate why ethylene carbonate is a preferred choice for battery applications over propylene carbonate and how mixtures with dimethyl carbonate improve Li-ion diffusion. We study the role of functionalization of graphite-anode edges on the reducibility of the electrolyte and the ease of Li-ion intercalation at the initial stages of SEI formation. We find that oxygen terminated edges readily act as strong reductive sites, while hydrogen terminated edges are less reactive and allow faster Li diffusion. Orientational ordering of the solvent molecules precedes reduction at the interphase. Inorganic reductive components are seen to readily migrate to the anode edges, leading to increased surface passivation of the anode. We are currently quantifying Li-intercalation barriers across realistic SEI models, and progress along these lines will be presented.
NASA Astrophysics Data System (ADS)
Burresi, E.; Celino, M.
2012-05-01
A single wurtzite phase of cadmium sulfide cluster is investigated by ab-initio molecular dynamics simulations at different temperatures, ranging from 100 K to 600 K. In this study we propose a possible procedure to characterize the CdS quantum dots system by means of molecular dynamics calculations using a standard Car-Parrinello scheme. In order to ensure the accuracy of the numerical approach, preliminary calculations to test pseudopotentials, cutoff and box size on both single atoms systems and Cd-Cd, S-S, Cd-S dimers have been performed. Calculated binding energies and bond lengths are obtained in good agreement with experimental data. Subsequently, an uncapped CdS cluster with size below 2 nm, 48 atoms of cadmium and 48 atoms of sulfur, in a wurtzite geometry was structurally optimized to minimize internal stresses. The CdS cluster has been carefully characterized structurally at several temperatures up to T = 600 K. At the temperature of 340 K atomic diffusion on the surface allows the onset of a new stable atomic configuration.
NASA Astrophysics Data System (ADS)
Lee, Mal-Soon; Peter McGrail, B.; Rousseau, Roger; Glezakou, Vassiliki-Alexandra
2015-10-01
The boundary layer at solid-liquid interfaces is a unique reaction environment that poses significant scientific challenges to characterize and understand by experimentation alone. Using ab initio molecular dynamics (AIMD) methods, we report on the structure and dynamics of boundary layer formation, cation mobilization and carbonation under geologic carbon sequestration scenarios (T = 323 K and P = 90 bar) on a prototypical anorthite (001) surface. At low coverage, water film formation is enthalpically favored, but entropically hindered. Simulated adsorption isotherms show that a water monolayer will form even at the low water concentrations of water-saturated scCO2. Carbonation reactions readily occur at electron-rich terminal Oxygen sites adjacent to cation vacancies that readily form in the presence of a water monolayer. These results point to a carbonation mechanism that does not require prior carbonic acid formation in the bulk liquid. This work also highlights the modern capabilities of theoretical methods to address structure and reactivity at interfaces of high chemical complexity.
Lee, Mal-Soon; Peter McGrail, B.; Rousseau, Roger; Glezakou, Vassiliki-Alexandra
2015-01-01
The boundary layer at solid-liquid interfaces is a unique reaction environment that poses significant scientific challenges to characterize and understand by experimentation alone. Using ab initio molecular dynamics (AIMD) methods, we report on the structure and dynamics of boundary layer formation, cation mobilization and carbonation under geologic carbon sequestration scenarios (T = 323 K and P = 90 bar) on a prototypical anorthite (001) surface. At low coverage, water film formation is enthalpically favored, but entropically hindered. Simulated adsorption isotherms show that a water monolayer will form even at the low water concentrations of water-saturated scCO2. Carbonation reactions readily occur at electron-rich terminal Oxygen sites adjacent to cation vacancies that readily form in the presence of a water monolayer. These results point to a carbonation mechanism that does not require prior carbonic acid formation in the bulk liquid. This work also highlights the modern capabilities of theoretical methods to address structure and reactivity at interfaces of high chemical complexity. PMID:26456362
NASA Astrophysics Data System (ADS)
Song, Bingyi; Jiang, Wenlong; Yang, Bin; Chen, Xiumin; Xu, Baoqiang; Kong, Lingxin; Liu, Dachun; Dai, Yongnian
2016-07-01
The possibility of the separation of Pb-Sb alloys by vacuum distillation was investigated theoretically. The results show that Pb and Sb can be separated by vacuum distillation. However, the experimental results show that vacuum distillation technique does not provide clear separation. According to the literature, Pb-Sb alloys belong to azeotropic compounds under some certain temperature; the experiment and computer simulation were carried out based on the exceptional condition so as to analyze the reason from the experiment and microstructure of Pb-Sb alloys perspective. The separation of Pb-Sb alloys by vacuum distillation was experimentally carried out to probe the azeotropic point. Also, the functions, such as partial radial distributions functions, the structure factor, mean square displacement, and the density of state, were calculated by ab-initio molecular dynamics for the representation of the structure and properties of Pb-Sb alloys with different composition of Sb. The experimental results indicate that there exists common volatilization for Pb-Sb alloys when Sb content is 16.5 wt pct. On the other hand, the calculation results show that there is an intense interaction between Pb and Sb when Sb content is 22 wt pct, which supports the experimental results although Sb content is slightly deviation.
Hydration structures of U(III) and U(IV) ions from ab initio molecular dynamics simulations
Leung, Kevin; Nenoff, Tina M.
2012-08-21
We apply DFT+U-based ab initio molecular dynamics simulations to study the hydration structures of U(III) and U(IV) ions, pertinent to redox reactions associated with uranium salts in aqueous media. U(III) is predicted to be coordinated to 8 water molecules, while U(IV) has a hydration number between 7 and 8. At least one of the innershell water molecules of the hydrated U(IV) complex becomes spontaneously deprotonated. As a result, the U(IV)-O pair correlation function exhibits a satellite peak at 2.15 A associated with the shorter U(IV)-(OH{sup -}) bond. This feature is not accounted for in analysis of extended x-ray absorption fine structure and x-ray adsorption near edge structure measurements, which yield higher estimates of U(IV) hydration numbers. This suggests that it may be useful to include the effect of possible hydrolysis in future interpretation of experiments, especially when the experimental pH is close to the reported hydrolysis equilibrium constant value.
NASA Astrophysics Data System (ADS)
Izvekov, Sergei; Swanson, Jessica M. J.
2011-05-01
The exchange-correlation (XC) functional and value of the electronic fictitious mass μ can be two major sources of systematic errors in ab initio Car-Parrinello Molecular Dynamics (CPMD) simulations, and have a significant impact on the structural and dynamic properties of condensed-phase systems. In this work, an attempt is made to identify the origin of differences in liquid water properties generated from CPMD simulations run with the BLYP and HCTH/120 XC functionals and two different values of μ (representative of "small" and "large" limits) by analyzing the effective pairwise atom-atom interactions. The force-matching (FM) algorithm is used to map CPMD interactions into non-polarizable, empirical potentials defined by bonded interactions, pairwise short-ranged interactions in numerical form, and Coulombic interactions via atomic partial charges. The effective interaction models are derived for the BLYP XC functional with μ = 340 a.u. and μ = 1100 a.u. (BLYP-340 and BLYP-1100 simulations) and the HCTH/120 XC functional with μ = 340 a.u. (HCTH-340 simulation). The BLYP-340 simulation results in overstructured water with slow dynamics. In contrast, the BLYP-1100 and HCTH-340 simulations both produce radial distribution functions (indicative of structure) that are in reasonably good agreement with experiment. It is shown that the main difference between the BLYP-340 and HCTH-340 effective potentials arises in the short-ranged nonbonded interactions (in hydrogen bonding regions), while the difference between the BLYP-340 and BLYP-1100 interactions is mainly in the long-ranged electrostatic components. Collectively, these results demonstrate how the FM method can be used to further characterize various simulation ensembles (e.g., density-functional theory via CPMD). An analytical representation of each effective interaction water model, which is easy to implement, is presented.
Xie, Binbin; Liu, Lihong; Cui, Ganglong; Fang, Wei-Hai; Cao, Jun; Feng, Wei; Li, Xin-qi
2015-11-21
In this work, the recently introduced quantum trajectory mean-field (QTMF) approach is implemented and employed to explore photodissociation dynamics of diazirinone (N{sub 2}CO), which are based on the high-level ab initio calculation. For comparison, the photodissociation process has been simulated as well with the fewest-switches surface hopping (FSSH) and the ab initio multiple spawning (AIMS) methods. Overall, the dynamical behavior predicted by the three methods is consistent. The N{sub 2}CO photodissociation at λ > 335 nm is an ultrafast process and the two C—N bonds are broken in a stepwise way, giving birth to CO and N{sub 2} as the final products in the ground state. Meanwhile, some noticeable differences were found in the QTMF, FSSH, and AIMS simulated time constants for fission of the C—N bonds, excited-state lifetime, and nonadiabatic transition ratios in different intersection regions. These have been discussed in detail. The present study provides a clear evidence that direct ab initio QTMF approach is one of the reliable tools for simulating nonadiabatic dynamics processes.
NASA Astrophysics Data System (ADS)
Bruenn, Stephen W.; Lentz, Eric J.; Hix, W. Raphael; Mezzacappa, Anthony; Harris, J. Austin; Messer, O. E. Bronson; Endeve, Eirik; Blondin, John M.; Chertkow, Merek Austin; Lingerfelt, Eric J.; Marronetti, Pedro; Yakunin, Konstantin N.
2016-02-01
We present four ab initio axisymmetric core-collapse supernova simulations initiated from 12, 15, 20, and 25 {M}⊙ zero-age main sequence progenitors. All of the simulations yield explosions and have been evolved for at least 1.2 s after core bounce and 1 s after material first becomes unbound. These simulations were computed with our Chimera code employing RbR spectral neutrino transport, special and general relativistic transport effects, and state-of-the-art neutrino interactions. Continuing the evolution beyond 1 s after core bounce allows the explosions to develop more fully and the processes involved in powering the explosions to become more clearly evident. We compute explosion energy estimates, including the negative gravitational binding energy of the stellar envelope outside the expanding shock, of 0.34, 0.88, 0.38, and 0.70 Bethe (B ≡ {10}51 erg) and increasing at 0.03, 0.15, 0.19, and 0.52 {\\text{B s}}-1, respectively, for the 12, 15, 20, and 25 {M}⊙ models at the endpoint of this report. We examine the growth of the explosion energy in our models through detailed analyses of the energy sources and flows. We discuss how the explosion energies may be subject to stochastic variations as exemplfied by the effect of the explosion geometry of the 20 {M}⊙ model in reducing its explosion energy. We compute the proto-neutron star masses and kick velocities. We compare our results for the explosion energies and ejected {}56{Ni} masses against some observational standards despite the large error bars in both models and observations.
Bruenn, Stephen W.; Lentz, Eric J.; Hix, William Raphael; Mezzacappa, Anthony; Harris, James Austin; Messer, O. E. Bronson; Endeve, Eirik; Blondin, John M.; Chertkow, Merek Austin; Lingerfelt, Eric J.; et al
2016-02-16
We present four ab initio axisymmetric core-collapse supernova simulations initiated from 12, 15, 20, and 25 M⊙ zero-age main sequence progenitors. All of the simulations yield explosions and have been evolved for at least 1.2 s after core bounce and 1 s after material first becomes unbound. These simulations were computed with our Chimera code employing RbR spectral neutrino transport, special and general relativistic transport effects, and state-of-the-art neutrino interactions. Continuing the evolution beyond 1 s after core bounce allows the explosions to develop more fully and the processes involved in powering the explosions to become more clearly evident. Wemore » compute explosion energy estimates, including the negative gravitational binding energy of the stellar envelope outside the expanding shock, of 0.34, 0.88, 0.38, and 0.70 Bethe (B ≡ 1051 erg) and increasing at 0.03, 0.15, 0.19, and 0.52 BS–1, respectively, for the 12, 15, 20, and 25 M⊙ models at the endpoint of this report. We examine the growth of the explosion energy in our models through detailed analyses of the energy sources and flows. We discuss how the explosion energies may be subject to stochastic variations as exemplfied by the effect of the explosion geometry of the 20 M⊙ model in reducing its explosion energy. We compute the proto-neutron star masses and kick velocities. In conclusion, we compare our results for the explosion energies and ejected 56Ni masses against some observational standards despite the large error bars in both models and observations.« less
Zhou, Yanzi; Wang, Shenglong; Zhang, Yingkai
2010-01-01
Acetylcholinesterase (AChE) is a remarkably efficient serine hydrolase responsible for the termination of impulse signaling at cholinergic synapses. By employing Born-Oppenheimer molecular dynamics simulations with B3LYP/6-31G(d) QM/MM potential and the umbrella sampling method, we have characterized its complete catalytic reaction mechanism for hydrolyzing neurotransmitter acetylcholine (ACh) and determined its multi-step free energy reaction profiles for the first time. In both acylation and deacylation reaction stages, the first step involves the nucleophilic attack to the carbonyl carbon with the triad His447 serving as the general base, and leads to a tetrahedral covalent intermediate stabilized by the oxyanion hole. From the intermediate to the product, the orientation of His447 ring needs to be adjusted very slightly, and then the proton transfers from His447 to the product and the break of the scissile bond happen spontaneously. For the three-pronged oxyanion hole, it only makes two hydrogen bonds with the carbonyl oxygen at either the initial reactant or the final product state, but the third hydrogen bond is formed and stable at all transition and intermediate states during the catalytic process. At the intermediate state of the acylation reaction, a short and low-barrier hydrogen bond (LBHB) is found to be formed between two catalytic triad residues His447 and Glu334, and the spontaneous proton transfer between two residues has been observed. However, it is only about 1 ~ 2 kcal/mol stronger than the normal hydrogen bond. In comparison with previous theoretical investigations of the AChE catalytic mechanism, our current study clearly demonstrates the power and advantages of employing Born-Oppenheimer ab initio QM/MM MD simulations in characterizing enzyme reaction mechanisms. PMID:20550161
AXISYMMETRIC AB INITIO CORE-COLLAPSE SUPERNOVA SIMULATIONS OF 12-25 M{sub Sun} STARS
Bruenn, Stephen W.; Yakunin, Konstantin N.; Mezzacappa, Anthony; Hix, W. Raphael; Lingerfelt, Eric J.; Lentz, Eric J.; Messer, O. E. Bronson; Blondin, John M.; Endeve, Eirik; Marronetti, Pedro
2013-04-10
We present an overview of four ab initio axisymmetric core-collapse supernova simulations employing detailed spectral neutrino transport computed with our CHIMERA code and initiated from Woosley and Heger progenitors of mass 12, 15, 20, and 25 M{sub Sun }. All four models exhibit shock revival over {approx}200 ms (leading to the possibility of explosion), driven by neutrino energy deposition. Hydrodynamic instabilities that impart substantial asymmetries to the shock aid these revivals, with convection appearing first in the 12 M{sub Sun} model and the standing accretion shock instability appearing first in the 25 M{sub Sun} model. Three of the models have developed pronounced prolate morphologies (the 20 M{sub Sun} model has remained approximately spherical). By 500 ms after bounce the mean shock radii in all four models exceed 3000 km and the diagnostic explosion energies are 0.33, 0.66, 0.65, and 0.70 Bethe (B = 10{sup 51} erg) for the 12, 15, 20, and 25 M{sub Sun} models, respectively, and are increasing. The three least massive of our models are already sufficiently energetic to completely unbind the envelopes of their progenitors (i.e., to explode), as evidenced by our best estimate of their explosion energies, which first become positive at 320, 380, and 440 ms after bounce. By 850 ms the 12 M{sub Sun} diagnostic explosion energy has saturated at 0.38 B, and our estimate for the final kinetic energy of the ejecta is {approx}0.3 B, which is comparable to observations for lower mass progenitors.
NASA Astrophysics Data System (ADS)
Harchaoui, N.; Hellal, S.; Grosdidier, B.; Gasser, J. G.
2008-02-01
The physical properties of disordered matter depend on the 'atomic structure' i.e. the arrangement of the atoms. This arrangement is described by the structure factor S (q) in reciprocal space and by the pair correlation function g(r) in real space. The structure factor is obtained experimentally while the numerical simulation enables us to obtain the pair correlation function. Liquid sodium is one of the elements the most studied and one can wonder about new scientific contribution appropriateness. The majority of theoretical calculations are compared with the experiment of Waseda. However two other posterior measurements have been published and give different results, in particular with regard to the height of the first peak of the structure factor. Three models of pseudopotential are considered to describe the electron-ion interaction. The first is a local pseudopotential with the alternative known as 'individual' of the model suggested by Fiolhais et al. The second model considered is that of Bachelet et al. This one, ab-initio and 'norm conserving', is non local. The last model is that proposed by Shaw known as 'first principles' and 'energy dependent'. Various static dielectric functions characteristic of the effects of exchange and correlation have been used and developed by Hellal et al. We calculated the form factors (pseudopotential in reciprocal space) and deduce the normalized energy-wave-number characteristic FN (q), the interatomic pair potential Veff (r), then the pair correlation function g(r) by molecular dynamics. The structure factor S(q) is obtained by Fourier transform and is compared with the experiment. Our calculations with the Bachelet and Shaw pseudopotentials are close to the last experiments of Greenfield et al. and of Huijben et al. Our results are discussed.
Influence of ab initio chemistry models on simulations of the Ionian atmosphere
NASA Astrophysics Data System (ADS)
Parsons, Neal; Levin, Deborah A.; Walker, Andrew C.; Moore, Chris H.; Goldstein, David B.; Varghese, Philip L.; Trafton, Laurence
2014-09-01
There is significant scientific interest in simulating the unique atmospheric conditions on the Jovian moon Io that range from cold surface temperatures to hyperthermal interactions which possibly supply the Jovian plasma torus. The Direct Simulation Monte Carlo (DSMC) method is well suited to model the rarefied, predominantly SO2, Ionian atmosphere. High speed collisions between SO2 and the hypervelocity O atoms and ions that compose the plasma torus are a significant mechanism in determining the composition of the atmosphere; therefore, high-fidelity modeling of their interactions is crucial to the accuracy of such simulations. Typically, the Total Collision Energy (TCE) model is used to determine molecular dissociation probabilities and the Variable Hard Sphere (VHS) model is used to determine collision cross sections. However, the parameters for each of these baseline models are based on low-temperature experimental data and thus have unknown reliability for the hyperthermal conditions in the Ionian atmosphere. Recently, Molecular Dynamics/Quasi-Classical Trajectory (MD/QCT) studies have been conducted to generate accurate collision and chemistry models for the SO2-O collision pair in order to replace the baseline models. However, the influence of MD/QCT models on Ionian simulations compared to the previously used models is not well understood. In this work, 1D simulations are conducted using both the MD/QCT-based and baseline models in order to determine the effect of MD/QCT models on Ionian simulations. It is found that atmospheric structure predictions are highly sensitive to the chemistry and collision models. Specifically, the MD/QCT model predicts approximately half the SO2 atmospheric dissociation due to O and O+ bombardment compared to TCE models, and also predicts a temperature rise due to plasma heating further from the Ionian surface than the existing baseline methodologies. These findings indicate that the accurate MD/QCT chemistry and collision
Thermal Decomposition of the Solid Phase of Nitromethane: Ab Initio Molecular Dynamics Simulations
NASA Astrophysics Data System (ADS)
Chang, Jing; Lian, Peng; Wei, Dong-Qing; Chen, Xiang-Rong; Zhang, Qing-Ming; Gong, Zi-Zheng
2010-10-01
The Car-Parrinello molecular dynamics simulations were employed to investigate thermal decomposition of the solid nitromethane. It is found that it undergoes chemical decomposition at about 2200 K under ambient pressure. The initiation of reactions involves both proton transfer and commonly known C-N bond cleavage. About 75 species and 100 elementary reactions were observed with the final products being H2O, CO2, N2, and CNCNC. It represents the first complete simulation of solid-phase explosive reactions reported to date, which is of far-reaching implication for design and development of new energetic materials.
Non-equilibrium dynamics in disordered materials: Ab initio molecular dynamics simulations
Ohmura, Satoshi; Nagaya, Kiyonobu; Yao, Makoto; Shimojo, Fuyuki
2015-08-17
The dynamic properties of liquid B{sub 2}O{sub 3} under pressure and highly-charged bromophenol molecule are studied by using molecular dynamics (MD) simulations based on density functional theory (DFT). Diffusion properties of covalent liquids under high pressure are very interesting in the sense that they show unexpected pressure dependence. It is found from our simulation that the magnitude relation of diffusion coefficients for boron and oxygen in liquid B{sub 2}O{sub 3} shows the anomalous pressure dependence. The simulation clarified the microscopic origin of the anomalous diffusion properties. Our simulation also reveals the dissociation mechanism in the coulomb explosion of the highly-charged bromophenol molecule. When the charge state n is 6, hydrogen atom in the hydroxyl group dissociates at times shorter than 20 fs while all hydrogen atoms dissociate when n is 8. After the hydrogen dissociation, the carbon ring breaks at about 100 fs. There is also a difference on the mechanism of the ring breaking depending on charge states, in which the ring breaks with expanding (n = 6) or shrink (n = 8)
Ab initio simulation of diffractometer instrumental function for high-resolution X-ray diffraction1
Mikhalychev, Alexander; Benediktovitch, Andrei; Ulyanenkova, Tatjana; Ulyanenkov, Alex
2015-01-01
Modeling of the X-ray diffractometer instrumental function for a given optics configuration is important both for planning experiments and for the analysis of measured data. A fast and universal method for instrumental function simulation, suitable for fully automated computer realization and describing both coplanar and noncoplanar measurement geometries for any combination of X-ray optical elements, is proposed. The method can be identified as semi-analytical backward ray tracing and is based on the calculation of a detected signal as an integral of X-ray intensities for all the rays reaching the detector. The high speed of calculation is provided by the expressions for analytical integration over the spatial coordinates that describe the detection point. Consideration of the three-dimensional propagation of rays without restriction to the diffraction plane provides the applicability of the method for noncoplanar geometry and the accuracy for characterization of the signal from a two-dimensional detector. The correctness of the simulation algorithm is checked in the following two ways: by verifying the consistency of the calculated data with the patterns expected for certain simple limiting cases and by comparing measured reciprocal-space maps with the corresponding maps simulated by the proposed method for the same diffractometer configurations. Both kinds of tests demonstrate the agreement of the simulated instrumental function shape with the measured data. PMID:26089760
Phenylalanine ab initio models for the simulation of skin natural moisturizing factor
NASA Astrophysics Data System (ADS)
Carvalho, B. G.; Raniero, L. J.; Martin, A. A.; Favero, P. P.
2013-04-01
In this study, we evaluated models that can be used to simulate amino acids in biological environments via density functional theory (DFT). The goal was to obtain realistic representations that combine computational economy and result quality when compared to experimental data. We increased the complexity of the models by using a model of an amino acid in a vacuum, followed by a water-solvated amino acid model. To consider pH variation, we simulated zwitterionic and nonionic amino acid configurations. The amino acid chosen for testing was phenylalanine, an aromatic amino acid present in high concentrations in the natural moisturizing factor of skin that plays a fundamental role in ultraviolet protection and vitiligo disease. To validate the models, vibrational modes and electronic properties were calculated and compared to experimental results.
Miller, J.; Miaskiewicz, K.; Osman, R.
1993-12-01
Studies of ring-saturated pyrimidine base lesions are used to illustrate an integrated modeling approach that combines quantum-chemical calculations with molecular dynamics simulation. Electronic-structure calculations on the lesions in Isolation reveal strong conformational preferences due to interactions between equatorial substituents to the pyrimidine ring. Large distortions of DNA should result when these interactions force the methyl group of thymine to assume an axial orientation, as is the case for thymine glycol but not for dihydrothymine. Molecular dynamics simulations of the dodecamer d(CGCGAATTCGCG){sub 2} with and without a ring-saturated thymine lesion at position T7 support this conclusion. Implications of these studies for recognition of thymine lesions by endonuclease III are also discussed.
Intramolecular hydrogen bonds: ab initio Car Parrinello simulations of arylamide torsions
NASA Astrophysics Data System (ADS)
Doerksen, Robert J.; Chen, Bin; Klein, Michael L.
2003-10-01
Gas-phase, room temperature Car-Parrinello molecular dynamics simulations using the HCTH density functional are reported for the arylamides acetanilide ( 1) and ortho-methylthioacetanilide ( 2). The simulations show that in 1, rotation around the ring-amide bond is relatively unrestricted. By contrast, in 2 the methylthio side chain encourages the amide to be directed with N-H pointing toward S, not to flip by 360°, and furthermore to remain close to coplanar with the benzene ring. Because of an intramolecular N-H⋯S hydrogen bond, the N-H stretch frequency of 2 is red-shifted by ˜78 cm -1 compared to that of 1.
Ab initio simulations for the ion-ion structure factor of warm dense aluminum.
Rüter, Hannes R; Redmer, Ronald
2014-04-11
We perform ab initio simulations based on finite-temperature density functional theory in order to determine the static and dynamic ion-ion structure factor in aluminum. We calculate the dynamic structure factor via the intermediate scattering function and extract the dispersion relation for the collective excitations. The results are compared with available experimental x-ray scattering data. Very good agreement is obtained for the liquid metal domain. In addition we perform simulations for warm dense aluminum in order to obtain the ion dynamics in this strongly correlated quantum regime. We determine the sound velocity for both liquid and warm dense aluminum which can be checked experimentally using narrow-bandwidth free electron laser radiation. PMID:24765982
Study of correlations from Ab-Initio Simulations of Liquid Water
NASA Astrophysics Data System (ADS)
Soto, Adrian; Fernandez-Serra, Marivi; Lu, Deyu; Yoo, Shinjae
An accurate understanding of the dynamics and the structure of H2O molecules in the liquid phase is of extreme importance both from a fundamental and from a practical standpoint. Despite the successes of Molecular Dynamics (MD) with Density Functional Theory (DFT), liquid water remains an extremely difficult material to simulate accurately and efficiently because of fine balance between the covalent O-H bond, the hydrogen bond and the attractive the van der Waals forces. Small errors in those produce dramatic changes in the macroscopic properties of the liquid or in its structural properties. Different density functionals produce answers that differ by as much as 35% in ambient conditions, with none producing quantitative results in agreement with experiment at different mass densities. In order to understand these differences we perform an exhaustive scanning of the geometrical coordinates of MD simulations and study their statistical correlations with the simulation output quantities using advanced correlation analyses and machine learning techniques. This work was partially supported by DOE Award No. DE-FG02-09ER16052, by DOE Early Career Award No. DE-SC0003871, by BNL LDRD 16-039 project and BNL Contract No. DE-SC0012704.
Study of correlations from Ab-Initio Simulations of Liquid Water
NASA Astrophysics Data System (ADS)
Soto, Adrian; Fernandez-Serra, Marivi; Lu, Deyu; Yoo, Shinjae
An accurate understanding of the dynamics and the structure of H2O molecules in the liquid phase is of extreme importance both from a fundamental and from a practical standpoint. Despite the successes of Molecular Dynamics (MD) with Density Functional Theory (DFT), liquid water remains an extremely difficult material to simulate accurately and efficiently because of fine balance between the covalent O-H bond, the hydrogen bond and the attractive the van der Waals forces. Small errors in those produce dramatic changes in the macroscopic properties of the liquid or in its structural properties. Different density functionals produce answers that differ by as much as 35% in ambient conditions, with none producing quantitative results in agreement with experiment at different mass densities [J. Chem Phys. 139, 194502(2013)]. In order to understand these differences we perform an exhaustive scanning of the geometrical coordinates of MD simulations and study their statistical correlations with the simulation output quantities using advanced correlation analyses and machine learning techniques. This work was partially supported by DOE Award No. DE-FG02-09ER16052, by DOE Early Career Award No. DE-SC0003871, by BNL LDRD 16-039 project and BNL Contract No. DE-SC0012704.
Ab initio simulation of the equation of state and kinetics of shocked water
Goldman, Nir; Reed, Evan; Kuo, I-F W.; Fried, Larry; Mundy, Christopher J.; Curioni, Alessandro
2009-03-28
We report herein first principles simulations of water under shock loading of pressures from ca. 9 - 69 GPa. Accurate description of the chemical mechanism for the ionic conductivity at high pressures and temperatures is of particular importance to models of the planetary dynamo mechanism in Neptune and Uranus. Using a novel simulation technique for shock compression, we are able to make excellent comparison to the experimental results for the Hugoniot pressure, temperature and density final states. Our simulations resolve controversy regarding the molecular mechanism for electric conduction at high pressures along the shock Hugoniot. At the approximate intersection of the Hugoniot and Neptune isentrope we observe high concentrations of negatively charges species that contribute electronic states near the band gap. Our results provide a microscopic picture of the chemistry in planetary interiors, which could impact models of Neptune and Uranus. This work was supported by the US Department of Energy's Office of Basic Energy Sciences' Chemical Sciences program. Battelle operates Pacific Northwest National Laboratory for the US Department of Energy.
LETTER TO THE EDITOR: Ab initio simulations of cation ordering in oxides: application to spinel
NASA Astrophysics Data System (ADS)
Warren, Michele C.; Dove, Martin T.; Redfern, Simon A. T.
2000-01-01
At high temperature, MgAl2 O4 spinel is stabilized by disorder of Mg and Al between octahedral and tetrahedral sites. Recent neutron experiments cover only a limited temperature range and are not sufficient to discriminate between analytic models. Electronic structure calculations have been used to parametrize on-site and short-ranged cluster potentials from a small number of disordered configuations. These potentials were then used in Monte Carlo simulations at finite temperatures to predict disordering thermodynamics beyond the range of experimental measurements. Within the temperature range of the experiment, good agreement is obtained for the degree of order.
Diffusion Mechanism of Hydrogen in Amorphous Silicon:
Su, Y.-S.; Pantelides, Sokrates T
2002-01-01
The mechanism of H migration in amorphous Si has remained an unresolved problem. The main issue is the small activation energy (1.5 eV) relative to the known strength of Si-H bonds (2--3.5 eV). We report first-principles finite-temperature simulations which demonstrate vividly that H is not released spontaneously, as proposed by most models, but awaits the arrival of a floating bond (FB). The 'migrating species' is an FB-H complex, with H jumping from Si to Si and the FB literally floating around it. Migration stops when the FB veers away.
Philippov, Alexander A.; Spitkovsky, Anatoly
2014-04-20
We perform ''first-principles'' relativistic particle-in-cell simulations of aligned pulsar magnetosphere. We allow free escape of particles from the surface of a neutron star and continuously populate the magnetosphere with neutral pair plasma to imitate pair production. As pair plasma supply increases, we observe the transition from a charge-separated ''electrosphere'' solution with trapped plasma and no spin-down to a solution close to the ideal force-free magnetosphere with electromagnetically dominated pulsar wind. We calculate the magnetospheric structure, current distribution, and spin-down power of the neutron star. We also discuss particle acceleration in the equatorial current sheet.
Campetella, Marco; Bodo, Enrico; Montagna, Maria; De Santis, Serena; Gontrani, Lorenzo
2016-03-14
We have explored by means of ab initio molecular dynamics the homologue series of 11 different ionic liquids based on the combination of the cholinium cation with deprotonated amino acid anions. We present a structural analysis of the liquid states of these compounds as revealed by accurate ab initio computations of the forces. We highlight the persistent structural motifs that see the ionic couple as the basic building block of the liquid whereby a strong hydrogen bonding network substantially determines the short range structural behavior of the bulk state. Other minor docking features of the interaction network are also discovered and described. Special cases along the series such as Cysteine and Phenylalanine are discussed in the view of their peculiar properties due to zwitterion formation and additional long-range structural organization. PMID:26979694
NASA Astrophysics Data System (ADS)
Campetella, Marco; Bodo, Enrico; Montagna, Maria; De Santis, Serena; Gontrani, Lorenzo
2016-03-01
We have explored by means of ab initio molecular dynamics the homologue series of 11 different ionic liquids based on the combination of the cholinium cation with deprotonated amino acid anions. We present a structural analysis of the liquid states of these compounds as revealed by accurate ab initio computations of the forces. We highlight the persistent structural motifs that see the ionic couple as the basic building block of the liquid whereby a strong hydrogen bonding network substantially determines the short range structural behavior of the bulk state. Other minor docking features of the interaction network are also discovered and described. Special cases along the series such as Cysteine and Phenylalanine are discussed in the view of their peculiar properties due to zwitterion formation and additional long-range structural organization.
Fermi level influence on the adsorption at semiconductor surfaces—ab initio simulations
NASA Astrophysics Data System (ADS)
Krukowski, Stanisław; Kempisty, Paweł; Strąk, Paweł
2013-08-01
Chemical adsorption of the species at semiconductor surfaces is analyzed showing the existence of the two contributions to adsorption energy: bond creation and charge transfer. It is shown that the energy of quantum surface states is affected by the electric field at the surface, nevertheless, the potential contribution of electron and nuclei cancels out. The charge transfer contribution is Fermi level independent for pinned surfaces. Thus for Fermi level pinned at the surface, the adsorption energy is independent on the Fermi energy, i.e., the doping in the bulk. The DFT simulations of adsorption of hydrogen at clean GaN(0001) and silicon at SiC(0001) surfaces confirmed independence of adsorption energy on the doping in the bulk. For the Fermi level nonpinned surfaces, the charge contribution depends on the position of Fermi level in the bulk. Thus adsorption energy is sensitive to change of the Fermi energy in the bulk, i.e., the doping. The DFT simulations of adsorption of atomic hydrogen at 0.75 ML hydrogen covered GaN(0001) surface confirmed that the adsorption energy may be changed by about 2 eV by the doping change from n- to p-type.
NASA Astrophysics Data System (ADS)
Schiffmann, Florian; VandeVondele, Joost
2015-06-01
We present an improved preconditioning scheme for electronic structure calculations based on the orbital transformation method. First, a preconditioner is developed which includes information from the full Kohn-Sham matrix but avoids computationally demanding diagonalisation steps in its construction. This reduces the computational cost of its construction, eliminating a bottleneck in large scale simulations, while maintaining rapid convergence. In addition, a modified form of Hotelling's iterative inversion is introduced to replace the exact inversion of the preconditioner matrix. This method is highly effective during molecular dynamics (MD), as the solution obtained in earlier MD steps is a suitable initial guess. Filtering small elements during sparse matrix multiplication leads to linear scaling inversion, while retaining robustness, already for relatively small systems. For system sizes ranging from a few hundred to a few thousand atoms, which are typical for many practical applications, the improvements to the algorithm lead to a 2-5 fold speedup per MD step.
Ab Initio Simulations of Silica Alpha Quartz Surfaces and their Interaction with Water
NASA Astrophysics Data System (ADS)
Chen, Yun-Wen; Cheng, Hai-Ping
2008-03-01
Two types of dry silica alpha quartz (0001) surfaces have been investigated through density functional calculations. One is the dense surface proposed by Rignanese et al.[1] that has 3-fold flower like six-member rings on the top and the three-member rings underneath. The other one is a newfound surface that has zigzag-shape six-member rings on the top and the three-member rings underneath. It is found that the new one is energetically more stable than the dense surface. The interactions of the surfaces with water molecules have also been concerned. Both of the surfaces have the similar hydrophilic properties. We report our results from MD simulations at a temperature of 300K. [1]. G.-M. Rignanese, Alessandro De Vita, J.-C. Charlier, Roberto Car, Phys. Rev. B 61, 13250 (2000)
Schiffmann, Florian; VandeVondele, Joost
2015-06-28
We present an improved preconditioning scheme for electronic structure calculations based on the orbital transformation method. First, a preconditioner is developed which includes information from the full Kohn-Sham matrix but avoids computationally demanding diagonalisation steps in its construction. This reduces the computational cost of its construction, eliminating a bottleneck in large scale simulations, while maintaining rapid convergence. In addition, a modified form of Hotelling's iterative inversion is introduced to replace the exact inversion of the preconditioner matrix. This method is highly effective during molecular dynamics (MD), as the solution obtained in earlier MD steps is a suitable initial guess. Filtering small elements during sparse matrix multiplication leads to linear scaling inversion, while retaining robustness, already for relatively small systems. For system sizes ranging from a few hundred to a few thousand atoms, which are typical for many practical applications, the improvements to the algorithm lead to a 2-5 fold speedup per MD step. PMID:26133420
Ab initio simulations of subatomic resolution images in noncontact atomic force microscopy
NASA Astrophysics Data System (ADS)
Kim, Minjung; Chelikowsky, James R.
2015-03-01
Direct imaging of polycyclic aromatic molecules with a subatomic resolution has recently been achieved with noncontact atomic force microscopy (nc-AFM). Specifically, nc-AFM employing a CO functionalized tip has provided details of the chemical bond in aromatic molecules, including the discrimination of bond order. However, the underlying physics of such high resolution imaging remains problematic. By employing new, efficient algorithms based on real space pseudopotentials, we calculate the forces between the nc-AFM tip and specimen. We simulate images of planar organic molecules with two different approaches: 1) with a chemically inert tip and 2) with a CO functionalized tip. We find dramatic differences in the resulting images, which are consistent with recent experimental work. Our work is supported by the DOE under DOE/DE-FG02-06ER46286 and by the Welch Foundation under Grant F-1837. Computational resources were provided by NERSC and XSEDE.
Ab initio simulations on migration paths of interstitial oxygen in corundum
NASA Astrophysics Data System (ADS)
Zhukovskii, Yuri F.; Platonenko, Alexander; Piskunov, Sergei; Kotomin, Eugene A.
2016-05-01
Ionizing radiation produces in Al2O3 (corundum) crystals primary Frenkel pairs of complementary defects (in oxygen sublattice these are oxygen vacancies and interstitial oxygen ions, VO - Oi). The interstitial Oi atoms begin to migrate above certain temperature and create the dumbbell pairs with regular oxygen atoms (Oreg - Oi). We have calculated the optimal dumbbell configurations and optimized further migration paths (i.e., Oi interstitial can break the bond with one Oreg atom and moves towards another, one of four next-neighbor Oreg atoms). To simulate all possible Oi migration trajectories, we have performed large-scale hybrid DFT-LCAO PBE0 calculations on 2 × 2 × 1 supercells of defective α-Al2O3 crystals using CRYSTAL14 computer code. The limiting barrier height for oxygen interstitial 3D migration is estimated as 1.3 eV.
Schiffmann, Florian; VandeVondele, Joost
2015-06-28
We present an improved preconditioning scheme for electronic structure calculations based on the orbital transformation method. First, a preconditioner is developed which includes information from the full Kohn-Sham matrix but avoids computationally demanding diagonalisation steps in its construction. This reduces the computational cost of its construction, eliminating a bottleneck in large scale simulations, while maintaining rapid convergence. In addition, a modified form of Hotelling’s iterative inversion is introduced to replace the exact inversion of the preconditioner matrix. This method is highly effective during molecular dynamics (MD), as the solution obtained in earlier MD steps is a suitable initial guess. Filtering small elements during sparse matrix multiplication leads to linear scaling inversion, while retaining robustness, already for relatively small systems. For system sizes ranging from a few hundred to a few thousand atoms, which are typical for many practical applications, the improvements to the algorithm lead to a 2-5 fold speedup per MD step.
Derivatization and diffusive motion of molecular fullerenes: Ab initio and atomistic simulations
NASA Astrophysics Data System (ADS)
Berdiyorov, G.; Harrabi, K.; Mehmood, U.; Peeters, F. M.; Tabet, N.; Zhang, J.; Hussein, I. A.; McLachlan, M. A.
2015-07-01
Using first principles density functional theory in combination with the nonequilibrium Green's function formalism, we study the effect of derivatization on the electronic and transport properties of C60 fullerene. As a typical example, we consider [6,6]-phenyl-C61-butyric acid methyl ester (PCBM), which forms one of the most efficient organic photovoltaic materials in combination with electron donating polymers. Extra peaks are observed in the density of states (DOS) due to the formation of new electronic states localized at/near the attached molecule. Despite such peculiar behavior in the DOS of an isolated molecule, derivatization does not have a pronounced effect on the electronic transport properties of the fullerene molecular junctions. Both C60 and PCBM show the same response to finite voltage biasing with new features in the transmission spectrum due to voltage induced delocalization of some electronic states. We also study the diffusive motion of molecular fullerenes in ethanol solvent and inside poly(3-hexylthiophene) lamella using reactive molecular dynamics simulations. We found that the mobility of the fullerene reduces considerably due to derivatization; the diffusion coefficient of C60 is an order of magnitude larger than the one for PCBM.
The activation of phosphoramide mustard anticancer drugs from ab initio simulations.
NASA Astrophysics Data System (ADS)
Allesch, Markus; Schwegler, Eric; Colvin, Mike; Gygi, Francois; Galli, Giulia
2007-03-01
The nitrogen mustard based DNA alkylating agents were the first nonhormonal drugs to be used effectively in the treatment of cancer and remain one of the most important drugs for the chemotherapeutic management of many common malignancies today. An understanding of the activation of these compounds is, in itself, of scientific interest, but also critical in designing improved analogs of greater selectivity and efficacy. We have investigated the activation pathways of one of the most active metabolites, phosphoramide mustard (PM), and its methylated ester (PMME). In particular, we have examined the activation barrier and reaction free energy for the intramolecular cyclization reaction using first principles molecular dynamics simulations with explicit and continuum solvation models. Structural, dynamical and electronic properties along the reaction path have been computed mainly to address the question why de-esterification is required to activate these drugs. This work was performed under the auspices of the U.S. Dept. of Energy at the University of California/Lawrence Livermore National Laboratory under contract no. W-7405-Eng-48.
Ab initio metadynamics simulations of oxygen/ligand interactions in organoaluminum clusters.
Alnemrat, Sufian; Hooper, Joseph P
2014-10-14
Car-Parrinello molecular dynamics combined with a metadynamics algorithm is used to study the initial interaction of O2 with the low-valence organoaluminum clusters Al4Cp4 (Cp=C5H5) and Al4Cp4* (Cp*=C5[CH3]5). Prior to reaction with the aluminum core, simulations suggest that the oxygen undergoes a hindered crossing of the steric barrier presented by the outer ligand monolayer. A combination of two collective variables based on aluminum/oxygen distance and lateral oxygen displacement was found to produce distinct reactant, product, and transition states for this process. In the methylated cluster with Cp* ligands, a broad transition state of 45 kJ/mol was observed due to direct steric interactions with the ligand groups and considerable oxygen reorientation. In the non-methylated cluster the ligands distort away from the oxidizer, resulting in a barrier of roughly 34 kJ/mol with minimal O2 reorientation. A study of the oxygen/cluster system fixed in a triplet multiplicity suggests that the spin state does not affect the initial steric interaction with the ligands. The metadynamics approach appears to be a promising means of analyzing the initial steps of such oxidation reactions for ligand-protected clusters. PMID:25318719
Wang, Zhiguo; Zhou, Yungang; Bang, Junhyeok; Prange, Micah P.; Zhang, Shengbai; Gao, Fei
2012-08-02
Defects play an important role on the unique properties of the sp2-bonded materials, such as graphene. The creation and evolution of mono-vacancy, di-vacancy, Stone-Wales (SW) and grain boundaries (GBs) under irradiation in graphene are investigated using density functional theory and time-dependent density functional theory molecular dynamics simulations. It is of great interest to note that the patterns of these defects can be controlled through electron irradiation. The SW defects can be created by electron irradiation with energy of above the displacement threshold energy (Td, {approx}19 eV) and can be healed with an energy (14-18 eV) lower than Td. The transformation between four types of divacancies, V2(5-8-5), V2(555-777), V2(5555-6-7777), and V2(55-77) can be realized through bond rotation induced by electron irradiation. The migrations of divancancies, SW defects, and GBs can also be controlled by electron irradiation. Thus, electron irradiation can serve as an important tool to modify morphology in a controllable manner, and to tailor the physical properties of graphene.
Derivatization and diffusive motion of molecular fullerenes: Ab initio and atomistic simulations
Berdiyorov, G. Tabet, N.; Harrabi, K.; Mehmood, U.; Hussein, I. A.; Peeters, F. M.; Zhang, J.; McLachlan, M. A.
2015-07-14
Using first principles density functional theory in combination with the nonequilibrium Green's function formalism, we study the effect of derivatization on the electronic and transport properties of C{sub 60} fullerene. As a typical example, we consider [6,6]-phenyl-C{sub 61}-butyric acid methyl ester (PCBM), which forms one of the most efficient organic photovoltaic materials in combination with electron donating polymers. Extra peaks are observed in the density of states (DOS) due to the formation of new electronic states localized at/near the attached molecule. Despite such peculiar behavior in the DOS of an isolated molecule, derivatization does not have a pronounced effect on the electronic transport properties of the fullerene molecular junctions. Both C{sub 60} and PCBM show the same response to finite voltage biasing with new features in the transmission spectrum due to voltage induced delocalization of some electronic states. We also study the diffusive motion of molecular fullerenes in ethanol solvent and inside poly(3-hexylthiophene) lamella using reactive molecular dynamics simulations. We found that the mobility of the fullerene reduces considerably due to derivatization; the diffusion coefficient of C{sub 60} is an order of magnitude larger than the one for PCBM.
Evidence for plasma phase transition in high pressure hydrogen from ab-initio simulations
Morales, M; Pierleoni, C; Schwegler, E; Ceperley, D
2010-02-08
We have performed a detailed study of molecular dissociation in liquid hydrogen using both Born-Oppenheimer molecular dynamics with Density Functional Theory and Coupled Electron-Ion Monte Carlo simulations. We observe a range of densities where (dP/d{rho}){sub T} = 0 that coincides with sharp discontinuities in the electronic conductivity, which is clear evidence of the plasma phase transition for temperatures 600K {le} T {le} 1500K. Both levels of theory exhibit the transition, although Quantum Monte Carlo predicts higher transition pressures. Based on the temperature dependence of the discontinuity in the electronic conductivity, we estimate the critical point of the transition at temperatures slightly below 2000 K. We examine the influence of proton zero point motion by using Path Integral Molecular Dynamics with Density Functional Theory; the main effect is to shift the transition to lower pressures. Furthermore, we calculate the melting curve of molecular hydrogen up to pressures of 200 GPa, finding a reentrant melting line in good agreement with previous calculations. The melting line crosses the metalization line at 700 K and 220 GPa using density functional energetics and at 550 K and 290 GPa using Quantum Monte Carlo energetics.
Ab initio metadynamics simulations of oxygen/ligand interactions in organoaluminum clusters
Alnemrat, Sufian; Hooper, Joseph P.
2014-10-14
Car-Parrinello molecular dynamics combined with a metadynamics algorithm is used to study the initial interaction of O{sub 2} with the low-valence organoaluminum clusters Al{sub 4}Cp{sub 4} (Cp=C{sub 5}H{sub 5}) and Al{sub 4}Cp{sub 4}{sup *} (Cp{sup *}=C{sub 5}[CH{sub 3}]{sub 5}). Prior to reaction with the aluminum core, simulations suggest that the oxygen undergoes a hindered crossing of the steric barrier presented by the outer ligand monolayer. A combination of two collective variables based on aluminum/oxygen distance and lateral oxygen displacement was found to produce distinct reactant, product, and transition states for this process. In the methylated cluster with Cp{sup *} ligands, a broad transition state of 45 kJ/mol was observed due to direct steric interactions with the ligand groups and considerable oxygen reorientation. In the non-methylated cluster the ligands distort away from the oxidizer, resulting in a barrier of roughly 34 kJ/mol with minimal O{sub 2} reorientation. A study of the oxygen/cluster system fixed in a triplet multiplicity suggests that the spin state does not affect the initial steric interaction with the ligands. The metadynamics approach appears to be a promising means of analyzing the initial steps of such oxidation reactions for ligand-protected clusters.
Infrared Spectroscopy of N-Methylacetamide Revisited by ab Initio Molecular Dynamics Simulations.
Gaigeot, M P; Vuilleumier, R; Sprik, M; Borgis, D
2005-09-01
The density functional theory based molecular dynamics simulation method ("Car-Parrinello") was applied in a numerical study of the electronic properties, hydrogen bonding, and infrared spectroscopy of the trans and cis isomer of N-methylacetamide in aqueous solution. A detailed analysis of the electronic structure of the solvated molecules, in terms of localized Wannier functions and Born atomic charges, is presented. Two schemes for the computation of the solute infrared absorption spectrum are investigated: In the first method the spectrum is determined by Fourier transforming the time correlation function of the solute dipole as determined from the Wannier function analysis. The second method uses instead the molecular current-current correlation function computed from the Born charges and atomic velocities. The resulting spectral properties of trans- and cis-NMA are carefully compared to each other and to experimental results. We find that the two solvated isomers can be clearly distinguished by their infrared spectral profile in the 1000-2000 cm(-)(1) range. PMID:26641894
Ab Initio Pulsar Magnetosphere: Three-dimensional Particle-in-cell Simulations of Oblique Pulsars
NASA Astrophysics Data System (ADS)
Philippov, Alexander A.; Spitkovsky, Anatoly; Cerutti, Benoit
2015-03-01
We present “first-principles” relativistic particle-in-cell simulations of the oblique pulsar magnetosphere with pair formation. The magnetosphere starts to form with particles extracted from the surface of the neutron star. These particles are accelerated by surface electric fields and emit photons capable of producing electron-positron pairs. We inject secondary pairs at the locations of primary energetic particles whose energy exceeds the threshold for pair formation. We find solutions that are close to the ideal force-free magnetosphere with the Y-point and current sheet. Solutions with obliquities ≤40° do not show pair production in the open field line region because the local current density along the magnetic field is below the Goldreich-Julian value. The bulk outflow in these solutions is charge-separated, and pair formation happens in the current sheet and return current layer only. Solutions with higher inclinations show pair production in the open field line region, with high multiplicity of the bulk flow and the size of the pair-producing region increasing with inclination. We observe the spin-down of the star to be comparable to MHD model predictions. The magnetic dissipation in the current sheet ranges between 20% for the aligned rotator and 3% for the orthogonal rotator. Our results suggest that for low obliquity neutron stars with suppressed pair formation at the light cylinder, the presence of phenomena related to pair activity in the bulk of the polar region, e.g., radio emission, may crucially depend on the physics beyond our simplified model, such as the effects of curved spacetime or multipolar surface fields.
NASA Astrophysics Data System (ADS)
Seifitokaldani, Ali
oxidizing potential (more than 2 volts vs. NHE). X-ray Photoelectron Spectroscopy (XPS) showed that the nitrogen amount on the surface of the electro-catalyst decreased from 11 % before the oxidation to 5 % after the oxidation, whereas the catalytic activity for the ORR decreased after the oxidation. Thus, decreasing the titanium nitride's amount in the titanium oxy-nitride surface reduced its catalytic activity. In the second phase of this project, electro-catalytic activity of the titanium nitride for the ORR was investigated via a density functional theory (DFT) computation. To the best of our knowledge, there is no theoretical and computational quantum chemistry study of the transition metal's nitride as the electro-catalyst in PEM fuel cells. ORR was considered to take place in three different sequential steps namely oxygen adsorption, hydroxide production and water desorption. Based on the XRD results, TiN(111) and TiN(200) were considered as the two major facets of the TiN. Simulation was done by the Vienna ab initio Simulation Package (VASP) based on the Plane-Wave basis sets and periodic boundary condition, while the PBE exchangecorrelational functional was used to describe the interactions among electrons. Comparing the adsorption energies proved existence of a strong dissociative adsorption of oxygen on the TiN(111) regardless of the adsorption sites. However, because of a relatively strong OH adsorption, TiN(111) loses the active sites to proceed the ORR, while on the TiN(200) surface, water production and desorption came about easily. Electron density of states (DOS) was obtained to calculate the d-band center and fractional filling in different situations. Considering two possible bridge and top adsorption sites on the TiN(200), these information indicated the hydroxide production and water desorption as the rate determining steps for the ORR in bridge and top sites, respectively. Therefore, it was shown that the TiN, specially TiN(200) had exhibited good
Gao, Fei; Xiao, H. Y.; Zu, Xiaotao T.; Posselt, Matthias; Weber, William J.
2009-07-10
Large-scale ab initio molecular dynamics simulations of ion-solid interactions in SiC reveal that significant charge-transfer occurs between atoms and defects can enhance charge transfer to surrounding atoms. The results demonstrate that charge transfer to and from recoiling atoms can alter the energy barriers and dynamics for stable defect formation. The present simulations illustrate in detail the dynamic processes for charged defect formation. The averaged values of displacement threshold energies along four main crystallographic directions are smaller than those determined by empirical potentials due to charge transfer effects on recoil atoms.
Gao Fei; Weber, William J.; Xiao Haiyan; Zu Xiaotao; Posselt, Matthias
2009-07-10
Large-scale ab initio molecular dynamics simulations of ion-solid interactions in SiC reveal that significant charge transfer occurs between atoms, and defects can enhance charge transfer to surrounding atoms. The results demonstrate that charge transfer to and from recoiling atoms can alter the energy barriers and dynamics for stable defect formation. The present simulations illustrate in detail the dynamic processes for charged defect formation. The averaged values of displacement threshold energies along four main crystallographic directions are smaller than those determined by empirical potentials due to charge-transfer effects on recoil atoms.
Fakhraee, Mostafa; Zandkarimi, Borna; Salari, Hadi; Gholami, Mohammad Reza
2014-12-11
The influences of hydroxyl functional group (-OH) on the thermodynamic and structural properties of ionic liquids (ILs) composed of 1-(2-Hydroxyethyl)-3-methyl imidazolium ([C2OHmim](+)) cation and the six different conventional anions, including [Cl](-), [NO3](-), [BF4](-), [PF6](-), [TfO](-), and [Tf2N](-) have been extensively investigated using classical molecular dynamics (MD) simulations combined with ab initio calculations over a wide range of temperature (298-550 K). The volumetric thermodynamic properties, enthalpy of vaporization, cohesive energy density, Hildebrand solubility parameter, and heat capacity at constant pressure were estimated at desired temperature. The simulated densities were in good agreement with the experimental data with a slight overestimation. The interionic interaction of selected ILs was also computed using both the MD simulations and ab initio calculations. It was found that the highest association of cation and anion is attributed to [C2OHmim][Cl] followed by [C2OHmim][NO3], and [C2OHmim][Tf2N] with the bulkiest anion has the weakest interionic interaction among chosen ILs. The similar trend of interactions energies was nearly observed from cohesive energy density results. Additional structural details were comprehensively yielded by calculating radial distribution functions (RDFs) and spatial distribution function (SDFs) at 358 K. The most stable configurations of isolated and dimer ion pairs of these ILs were in excellent consistency with RDFs and SDFs results. Significant changes in arrangement of anions around the [C2OHmim](+) cation in comparison with conventional imidazolium-based ILs can be inferred from the MD simulations and ab initio results. Also, microscopic structural properties disclosed that the most strong cation-cation interaction is ascribed to the hydroxyl-functionalized ILs composed of bulkier anions, whereas ILs incorporating [Cl](-) and [NO3](-) anions are mainly involved in cation-anion interactions. The
NASA Astrophysics Data System (ADS)
Mei, Yuan; Etschmann, Barbara; Liu, Weihua; Sherman, David M.; Testemale, Denis; Brugger, Joël
2016-04-01
Chlorine and sulfur are the main elements involved in the complexing of metals in ore-forming fluids. The nature and thermodynamic properties of the Zn(II)-Cl complexes have been investigated by previous experimental and theoretical studies and are now well established up to high temperatures (600 °C). In contrast, the role of bisulfide complexes for zinc speciation in sulfur-bearing fluids remains poorly known, and a better understanding of Zn(II)-HS complexation is required for modeling zinc transport in magmatic and metamorphic fluids and for optimizing the hydrometallurgical processing of sulfide ores. We have conducted ab initio molecular dynamics (MD) simulations to calculate the speciation of Zn(II)-HS complexes from ambient to hydrothermal-magmatic conditions (25-600 °C, up to 2000 bar). These theoretical calculations were complemented by X-ray absorption spectroscopy (XAS) measurements of Zn(II) in HS--rich solutions at 200-500 °C and 600-1000 bar. The speciation and geometrical properties predicted by the ab initio MD simulations and the in situ XAS data are in excellent agreement. Upon heating from room temperature to 250 °C, Zn(II) speciation in HS--rich solutions shows a transition from the sixfold octahedral hexaaquo complex [Zn(H2O)6]2+ to fourfold tetrahedral [Zn(HS)n(H2O)4-n]2-n complexes (n = 1-4). Ab initio MD simulations also show that at temperatures > 250 °C, the threefold trigonal-planar [Zn(HS)3]- complex becomes increasingly stable, and predominates in S-rich solutions; in contrast, chloro-complexes display a tetrahedral geometry at 25-500 °C, while trigonal planar ZnCl3- predominates at temperatures > 500 °C. The stability constants of Zn(II)-HS complexes were calculated by thermodynamic integration of constrained ab initio MD simulations at 200, 350 and 600 °C. The stability constants generated from this study predict that zinc can be transported by HS- at high temperature in reduced, neutral to alkaline solutions, while Zn
NASA Astrophysics Data System (ADS)
Suwardi; Pranowo, Harno Dwi; Armunanto, Ria
2015-09-01
The structure and dynamics of Hf4+ ion in liquid ammonia have been investigated by an ab initio quantum mechanics molecular mechanics (QM/MM) molecular dynamics simulation. The structural data was obtained in terms of radial distribution, coordination number and angular distribution, and then the dynamics in mean ligand residence time. The Hf4+ ion is coordinated by five ammonia molecules in the first solvation shell showing a distorted square pyramidal structure with an average Hf4+-N distance of 2.38 Å. No ammonia ligand was observed for exchange processes between the first and second shells.
Kessler, Jan; Elgabarty, Hossam; Spura, Thomas; Karhan, Kristof; Partovi-Azar, Pouya; Hassanali, Ali A; Kühne, Thomas D
2015-08-01
The structure and dynamics of the water/vapor interface is revisited by means of path-integral and second-generation Car-Parrinello ab initio molecular dynamics simulations in conjunction with an instantaneous surface definition [Willard, A. P.; Chandler, D. J. Phys. Chem. B 2010, 114, 1954]. In agreement with previous studies, we find that one of the OH bonds of the water molecules in the topmost layer is pointing out of the water into the vapor phase, while the orientation of the underlying layer is reversed. Therebetween, an additional water layer is detected, where the molecules are aligned parallel to the instantaneous water surface. PMID:26174102
Xiao, Hai Yan; Gao, Fei; Zu, Xiaotao T.; Weber, William J.
2010-02-04
High-pressure induced zinc blende to rocksalt phase transition in GaN has been investigated by ab initio molecular dynamics method to characterize the transformation mechanism at the atomic level. It was shown that at 100 GPa GaN passes through tetragonal and monoclinic states before rocksalt structure is formed. The transformation mechanism is consistent with that for other zinc blende semiconductors obtained from the same method. Detailed structural analysis showed that there is no bond breaking involved in the phase transition.
NASA Astrophysics Data System (ADS)
Fischer, Dominik; Kersch, Alfred
2008-10-01
By means of ab initio simulations we investigate the influence of dopants (Si, C, Ge, Sn, Ti, and Ce) on the transition from the monoclinic to the tetragonal phase in HfO2. In this study we focus first on the internal energy only, an approach common to ab initio simulations. In the second step we go beyond this approach in considering the Helmholtz free energy by additionally taking into account the contribution of the phonon density of states. Finally we discuss the change in transition temperature in the regime of thin films based on an empirical model. We find that both the contributions of the internal energy and phonons can be understood in terms of a model relying on the ionic radius of the dopants. Among the investigated dopants silicon is identified to promote the tetragonal phase most efficiently. The effectiveness of the various dopants is compared on the basis of a qualitative phase diagram for doping concentrations up to ˜12%.
NASA Astrophysics Data System (ADS)
Oguri, Tomoya; Shimamura, Kohei; Shibuta, Yasushi; Shimojo, Fuyuki; Yamaguchi, Shu
2014-03-01
Dissociation of ethanol on a nickel cluster is investigated by ab initio molecular dynamics simulation to reveal the bond dissociation mechanism of carbon source molecules during carbon nanotube synthesis. C-C bonds in only CHxCO fragments are dissociated on the nickel cluster, whereas there is no preferential structure among the fragments for C-O bond dissociation. The dissociation preference is uncorrelated with the bond dissociation energy of corresponding bonds in freestanding molecules but is correlated with the energy difference between fragment molecules before and after dissociation on the nickel surface. Moreover, carbon-chain formation occurs after C-C bond dissociation in a continuous simulation. What determines the chirality of CNTs? What happens at the dissociation stage of carbon source molecules? Regarding the former question, many researchers have pointed out the good epitaxial relationship between a graphite network and a close-packed facet (i.e., fcc(1 1 1) or hcp(0 0 0 1)) of transition metals [17-19]. Therefore, the correlation between the chirality of CNTs and the angle of the step edge on metal (or metal carbide) surfaces has been closely investigated [20-22]. In association with this geometric matching, the epitaxial growth of graphene on Cu(1 1 1) and Ni(1 1 1) surfaces has recently been achieved via CCVD technique [23-25], which is a promising technique for the synthesis of large-area and monolayer graphene.Regarding the latter question, it is empirically known that the yield and quality of CNT products strongly depend on the choice of carbon source molecules and additives. For example, it is well known that the use of ethanol as carbon source molecules yields a large amount of SWNTs without amorphous carbons (called the alcohol CCVD (ACCVD) technique) compared with the CCVD process using hydrocarbons [4]. Moreover, the addition of a small amount of water dramatically enhances the activity and lifetime of the catalytic metal (called the
NASA Astrophysics Data System (ADS)
Wang, Yaocen; Takeuchi, Akira; Makino, Akihiro; Liang, Yunye; Kawazoe, Yoshiyuki
2014-05-01
Iron-based amorphous and nano-crystalline alloys have attracted a growing interest due to their potential in the application of magnetic coil production. However, fundamental understanding of the nano-crystallization mechanisms and magnetic features in the amorphous structure are still lack of knowledge. In the present work, we performed ab initio molecular dynamics simulation to clarify the ionic and electronic structure in atomic scale, and to derive the origin of the good magnetic property of Fe85Si2B8P4Cu1 amorphous alloy. The simulation gave a direct evidence of the Cu-P bonding preference in the amorphous alloy, which may promote nucleation in nano-crystallization process. On the other hand, the electron transfer and the band/orbital features in the amorphous alloy suggests that alloying elements with large electronegativity and the potential to expand Fe disordered matrix are preferred for enhancing the magnetization.
Long, Run; Fang, Weihai; Prezhdo, Oleg V
2016-08-18
Experiments show both positive and negative changes in performance of hybrid organic-inorganic perovskite solar cells upon exposure to moisture. Ab initio nonadiabatic molecular dynamics reveals the influence of humidity on nonradiative electron-hole recombination. In small amounts, water molecules perturb perovskite surface and localize photoexcited electron close to the surface. Importantly, deep electron traps are avoided. The electron-hole overlap decreases, and the excited state lifetime increases. In large amounts, water forms stable hydrogen-bonded networks, has a higher barrier to enter perovskite, and produces little impact on charge localization. At the same time, by contributing high frequency polar vibrations, water molecules increase nonadiabatic coupling and accelerate recombination. In general, short coherence between electron and hole benefits photovoltaic response of the perovskites. The calculated recombination time scales show excellent agreement with experiment. The time-domain atomistic simulations reveal the microscopic effects of humidity on perovskite excited-state lifetimes and rationalize the conflicting experimental observations. PMID:27485025
NASA Technical Reports Server (NTRS)
Bowman, Joel M.; Gazdy, Bela; Bentley, Joseph A.; Lee, Timothy J.; Dateo, Christopher E.
1993-01-01
A potential energy surface for the HCN/HNC system which is a fit to extensive, high-quality ab initio, coupled-cluster calculations is presented. All HCN and HNC states with energies below the energy of the first delocalized state are reported and characterized. Vibrational transition energies are compared with all available experimental data on HCN and HNC, including high CH-overtone states up to 23,063/cm. A simulation of the (A-tilde)-(X-tilde) stimulated emission pumping (SEP) spectrum is also reported, and the results are compared to experiment. Franck-Condon factors are reported for odd bending states of HCN, with one quantum of vibrational angular momentum, in order to compare with the recent assignment by Jonas et al. (1992), on the basis of axis-switching arguments of a number of previously unassigned states in the SEP spectrum.
Fediai, Artem; Ryndyk, Dmitry A; Cuniberti, Gianaurelio
2016-10-01
Up to now, the electrical properties of the contacts between 3D metals and 2D materials have never been computed at a fully ab initio level due to the huge number of atomic orbitals involved in a current path from an electrode to a pristine 2D material. As a result, there are still numerous open questions and controversial theories on the electrical properties of systems with 3D/2D interfaces-for example, the current path and the contact length scalability. Our work provides a first-principles solution to this long-standing problem with the use of the modular approach, a method which rigorously combines a Green function formalism with the density functional theory (DFT) for this particular contact type. The modular approach is a general approach valid for any 3D/2D contact. As an example, we apply it to the most investigated among 3D/2D contacts-metal/graphene contacts-and show its abilities and consistency by comparison with existing experimental data. As it is applicable to any 3D/2D interface, the modular approach allows the engineering of 3D/2D contacts with the pre-defined electrical properties. PMID:27502169
NASA Astrophysics Data System (ADS)
Souto, J.; Alemany, M. M. G.; Gallego, L. J.; Gonzalez, L. E.; Gonzalez, D. J.
2013-03-01
We perform an ab initio molecular dynamics study of the static, dynamic and electronic properties of the liquid Bi-Pb alloy at three concentrations, including the eutectic one. This alloy is of particular technological interest for its possible use as coolant in fast reactors. Our predictions are in good agreement with the available experimental data. In particular, the computed total static structure factors reproduce accurately the neutron diffraction results, and the predicted adiabatic sound velocity and shear viscosity compare well with the experimental values. The partial dynamic structure factors exhibit clear side peaks indicative of propagating density fluctuations, and the longitudinal and transverse dispersion relations show several branches.The electronic density of states show that the liquid Bi-Pb alloy is a good metal, but with strong deviations from the free-electron parabolic curve. Supported by FIS2008-02490/FIS, FIS2008-04894/FIS, VA068A06, GR120, INCITE09E2R206033ES and INCITE08PXIB206107PR
NASA Astrophysics Data System (ADS)
Hüter, Claas; Friák, Martin; Weikamp, Marc; Neugebauer, Jörg; Goldenfeld, Nigel; Svendsen, Bob; Spatschek, Robert
2016-06-01
We investigate nonlinear elastic deformations in the phase field crystal model and derived amplitude equation formulations. Two sources of nonlinearity are found, one of them is based on geometric nonlinearity expressed through a finite strain tensor. This strain tensor is based on the inverse right Cauchy-Green deformation tensor and correctly describes the strain dependence of the stiffness for anisotropic and isotropic behavior. In isotropic one- and two-dimensional situations, the elastic energy can be expressed equivalently through the left deformation tensor. The predicted isotropic low-temperature nonlinear elastic effects are directly related to the Birch-Murnaghan equation of state with bulk modulus derivative K'=4 for bcc. A two-dimensional generalization suggests K2D '=5 . These predictions are in agreement with ab initio results for large strain bulk deformations of various bcc elements and graphene. Physical nonlinearity arises if the strain dependence of the density wave amplitudes is taken into account and leads to elastic weakening. For anisotropic deformation, the magnitudes of the amplitudes depend on their relative orientation to the applied strain.
Ab initio molecular dynamics simulations of ion–solid interactions in Gd2Zr2O7 and Gd2Ti2O7
Wang, X. J.; Xiao, Haiyan Y.; Zu, Xiaotao; Zhang, Yanwen; Weber, William J.
2012-12-21
The development of the ab initio molecular dynamics (AIMD) method has made it a powerful tool in describing ion–solid interactions in materials, with the determination of threshold displacement energies with ab initio accuracy, and prediction of a new mechanism for defect generation and new defective states that are different from classical molecular dynamics (MD) simulations. In the present work, this method is employed to study the low energy recoil events in Gd2Zr2O7 and Gd2Ti2O7. The weighted average threshold displacement energies in Gd2Zr2O7 are determined to be 38.8 eV for Gd, 41.4 eV for Zr, 18.6 eV for O48f, and 15.6 eV for O8b, which are smaller than the respective values of 41.8, >53.8, 22.6 and 16.2 eV in Gd2Ti2O7. It reveals that all the ions in Gd2Zr2O7 are more easily displaced than those in Gd2Ti2O7, and anion order–disorder is more likely to be involved in the displacement events than cation disordering. The average charge transfer from the primary knock-on atom to its neighbors is estimated to be [similar]0.15, [similar]0.11 to 0.27 and [similar]0.1 to 0.13 |e| for Gd, Zr (or Ti), and O, respectively. Neglecting the charge transfer in the interatomic potentials may result in the larger threshold displacement energies in classical MD.
Ab initio molecular dynamics simulations of ion-solid interactions in Gd2Zr2O7 and Gd2Ti2O7
Wang, X J; Xiao, Haiyan; Zu, X T; Zhang, Yanwen; Weber, William J
2013-01-01
The development of ab initio molecular dynamics (AIMD) method has made it a powerful tool in describing ion-solid interactions in materials, with identification determination of threshold displacement energies with ab initio accuracy, and prediction of new mechanism for defect generation and new defective states that are different from classical molecular dynamics (MD) simulations. In the present work, this method is employed to study the low energy recoil events in Gd2Zr2O7 and Gd2Ti2O7. The weighted average threshold displacement energies in Gd2Zr2O7 are determined to be 38.8 eV for Gd, 41.4 eV for Zr, 18.6 eV for O48f, and 15.6 eV for O8b, which are smaller than the respective values of 41.8, >53.8, 22.6 and 16.2 eV in Gd2Ti2O7. It reveals that all the ions in Gd2Zr2O7 are more easily displaced than those in Gd2Ti2O7, and anion order-disorder are more likely to be involved in the displacement events than cation disordering. The average charge transfer from the primary knock-on atom to its neighbors is estimated to be ~0.15, ~0.11-0.27 and ~0.1-0.13 |e| for Gd, Zr (or Ti), and O, respectively. Negligence of the charge transfer in the interatomic potentials may result in the larger threshold displacement energies in classical MD.
Wood, Geoffrey P F; Sreedhara, Alavattam; Moore, Jamie M; Wang, John; Trout, Bernhardt L
2016-05-12
An assessment of the mechanisms of (•)OH and (•)OOH radical-mediated oxidation of tryptophan was performed using density functional theory calculations and ab initio plane-wave Quantum Mechanics/Molecular Mechanics (QM/MM) molecular dynamics simulations. For the (•)OH reactions, addition to the pyrrole ring at position 2 is the most favored site with a barrierless reaction in the gas phase. The subsequent degradation of this adduct through a H atom transfer to water was intermittently observed in aqueous-phase molecular dynamics simulations. For the (•)OOH reactions, addition to the pyrrole ring at position 2 is the most favored pathway, in contrast to the situation in the model system ethylene, where concerted addition to the double bond is preferred. From the (•)OOH position 2 adduct QM/MM simulations show that formation of oxy-3-indolanaline occurs readily in an aqueous environment. The observed transformation starts from an initial rupture of the O-O bond followed by a H atom transfer with the accompanying loss of an (•)OH radical to solution. Finally, classical molecular dynamics simulations were performed to equate observed differential oxidation rates of various tryptophan residues in monoclonal antibody fragments. It was found that simple parameters derived from simulation correlate well with the experimental data. PMID:27082439
Brüssel, Marc; di Dio, Philipp J.; Muñiz, Kilian; Kirchner, Barbara
2011-01-01
We carried out ab initio molecular dynamic simulations in order to determine the free energy surfaces of two selected reactions including solvents, namely a rearrangement of a ruthenium oxoester in water and a carbon dioxide addition to a palladium complex in carbon dioxide. For the latter reaction we also investigated the gas phase reaction in order to take solvent effects into account. We used two techniques to reconstruct the free energy surfaces: thermodynamic integration and metadynamics. Furthermore, we gave a reasonable error estimation of the computed free energy surface. We calculated a reaction barrier of ΔF = 59.5 ± 8.5 kJ mol−1 for the rearrangement of a ruthenium oxoester in water from thermodynamic integration. For the carbon dioxide addition to the palladium complex in carbon dioxide we found a ΔF = 44.9 ± 3.3 kJ mol−1 from metadynamics simulations with one collective variable. The investigation of the same reactions in the gas phase resulted in ΔF = 24.9 ± 6.7 kJ mol−1 from thermodynamic integration, in ΔF = 26.7 ± 2.3 kJ mol−1 from metadynamics simulations with one collective variable, and in ΔF = 27.1 ± 5.9 kJ mol−1 from metadynamics simulations with two collective variables. PMID:21541065
Lee, Hee-Seung; Tuckerman, Mark E
2008-12-14
An efficient computational approach to perform Car-Parrinello ab initio molecular dynamics (CPAIMD) simulations under cluster (free) boundary conditions is presented. The general approach builds upon a recent real-space CPAIMD formalism using discrete variable representation (DVR) basis sets [Y. Liu et al., Phys. Rev. B 12, 125110 (2003); H.-S. Lee and M. E. Tuckerman, J. Phys. Chem. A 110, 5549 (2006)]. In order to satisfy cluster boundary conditions, a DVR based on sinc functions is utilized to expand the Kohn-Sham orbitals and electron density. Poisson's equation is solved in order to calculate the Hartree potential via an integral representation of the 1/r singularity. Excellent convergence properties are achieved with respect to the number of grid points (or DVR functions) and the size of the simulation cell. A straightforward implementation of the present approach leads to near linear scaling [O(N(4/3))] of the computational cost with respect to the system size (N) for the solution of Poisson's equation. The accuracy and stability of CPAIMD simulations based on sinc DVR are tested for a model problem as well as for N(2) and a water dimer. PMID:19071908
Motif based Hessian matrixfor ab initio geometry optimization ofnanostructures
Zhao, Zhengji; Wang, Lin-Wang; Meza, Juan
2006-04-05
A simple method to estimate the atomic degree Hessian matrixof a nanosystem is presented. The estimated Hessian matrix, based on themotif decomposition of the nanosystem, can be used to accelerate abinitio atomic relaxations with speedups of 2 to 4 depending on the sizeof the system. In addition, the programing implementation for using thismethod in a standard ab initio package is trivial.
Wu, Xiuxiu; Gao, Liang; Liu, Jinxiang; Yang, Hongfang; Wang, Shoushan; Bu, Yuxiang
2015-10-28
Studies on the structure, states, and reactivity of excess electrons (EEs) in biological media are of great significance. Although there is information about EE interaction with desolvated biological molecules, solution effects are hardly explored. In this work, we present an ab initio molecular dynamics simulation study on the interaction and reactivity of an EE with glycine in solution. Our simulations reveal two striking results. Firstly, a pre-solvated EE partially localizes on the negatively charged -COO(-) group of the zwitterionic glycine and the remaining part delocalizes over solvent water molecules, forming an anion-centered quasi-localized structure, due to relative alignment of the lowest unoccupied molecular orbital energy levels of potential sites for EE residence in the aqueous solution. Secondly, after a period of anion-centered localization of an EE, the zwitterionic glycine is induced to spontaneously fragment through the cleavage of the N-Cα bond, losing ammonia (deamination), and leaving a ˙CH2-COO(-) anion radical, in good agreement with experimental observations. Introduction of the same groups (-COO(-) or -NH3(+)) in the side chain (taking lysine and aspartic acid as examples) can affect EE localization, with the fragmentation of the backbone part of these amino acids dependent on the properties of the side chain groups. These findings provide insights into EE interaction mechanisms with the backbone parts of amino acids and low energy EE induced fragmentation of amino acids and even peptides and proteins. PMID:26399512
NASA Astrophysics Data System (ADS)
Lee, T. H.; Simdyankin, S. I.; Hegedus, J.; Heo, J.; Elliott, S. R.
2010-03-01
The spatial distribution of Nd3+ ions and GaS4 tetrahedral units in Nd-doped Ge-As-Ga-S glasses has been studied by laser spectroscopy and ab initio molecular dynamics (MD) simulations. A sharp increase in Nd3+ fluorescence intensities and lifetimes was observed with increasing Ga content, and attributed to the formation of tightly bound Nd3+ clusters in Ga-free glasses and the subsequent dissolution of such clusters upon Ga doping. A large modification in Nd3+ sites was also identified from low-temperature site-selective excitation spectra, suggesting preferential spatial correlations between Nd3+ and GaS4 tetrahedra even at low Ga-doping levels. MD simulations of these materials in the liquid state showed a tendency for Ga cluster formation as well as spatial correlations between Nd and Ga atoms consistent with the experimental results. On the basis of this result, a comprehensive structural model for Nd- and Ga-doped sulfide glasses is proposed.
Zhang, Ru; Bu, Yuxiang
2016-07-28
In this work, we conduct ab initio molecular dynamics simulations on the localization dynamics of an excess electron (EE) in acetamide/Ca(2+) aqueous solutions with three different interaction modes of Ca(2+) with acetamide: tight contact, solvent-shared state, and separated interaction. The simulated results reveal that an EE could exhibit two different localization behaviors in these acetamide/Ca(2+) aqueous solutions depending on different amideCa(2+) interactions featuring different contact distances. For the tight contact and solvent-shared state of amideCa(2+) solutions, vertically injected diffuse EEs follow different mechanisms with different dynamics, forming a cavity-shaped hydrated electron or a hydrated amide anion, respectively. Meanwhile, for the separated state, only one localization pattern of a vertically injected diffuse EE towards the formation of hydrated amide anion is observed. The hindrance of hydrated Ca(2+) and the attraction of the hydrated amide group originating from its polarity and low energy π* orbital are the main driving forces. Additionally, different EE localization modes have different effects on the interaction between the amide group and Ca(2+) in turn. This work provides an important basis for further understanding the mechanisms and dynamics of localizations/transfers of radiation-produced EEs and associated EE-induced lesions and damage to biological species in real biological environments or other aqueous solutions. PMID:27351489
Ab initio melting curve of osmium
NASA Astrophysics Data System (ADS)
Burakovsky, L.; Burakovsky, N.; Preston, D. L.
2015-11-01
The melting curve of osmium up to a pressure P of 500 GPa is obtained from an extensive suite of ab initio quantum molecular dynamics (QMD) simulations using the Z method. The ab initio P =0 melting point of Os is 3370 ±75 K; this range encompasses all of the available data in the literature and corroborates the conclusion of J. W. Arblaster [Platinum Metals Rev. 49, 166 (2005)], 10.1595/147106705X70264 that the melting temperature of pure Os is 3400 ±50 K and that the 3300 K typically quoted in the literature is the melting point of impure Os. The T =0 equation of state (EOS) of Os and the P dependence of the optimized c /a ratio for the hexagonal unit cell, both to pressures ˜900 GPa, are obtained in the ab initio approach as validation of its use. Although excellent agreement with the available experimental data (P ≲80 GPa) is found, it is the third-order Birch-Murnaghan EOS with B0'=5 rather than the more widely accepted B0'=4 that describes the QMD data to higher pressures, in agreement with the more recent experimental EOS by Godwal et al. The theoretical melting curve of Os obtained earlier by Joshi et al. is shown to be inconsistent with our QMD results, and the possible reason for this discrepancy is suggested. Regularities in the melting curves of Os and five other third-row transition metals (Ta, W, Re, Pt, Au) could be used to estimate the currently unknown melting curves of Hf and Ir.
Huang, Yuxiang; Huang, Li; Wang, C Z; Kramer, M J; Ho, K M
2016-03-01
Comparative analysis between Zr-rich Zr50Cu45Al5 and Cu-rich Cu50Zr45Al5 metallic glasses (MGs) is extensively performed to locate the key structural motifs accounting for their difference of glass forming ability. Here we adopt ab initio molecular dynamics simulations to investigate the local atomic structures of Zr50Cu45Al5 and Cu50Zr45Al5 MGs. A high content of icosahedral-related (full and distorted) orders was found in both samples, while in the Zr-rich MG full icosahedrons [Formula: see text] is dominant, and in the Cu-rich one the distorted icosahedral orders, especially [Formula: see text] and [Formula: see text], are prominent. And the [Formula: see text] polyhedra in Cu50Zr45Al5 MG mainly originate from Al-centered clusters, while the [Formula: see text] in Zr50Cu45Al5 derives from both Cu-centered clusters and Al-centered clusters. These difference may be ascribed to the atomic size difference and chemical property between Cu and Zr atoms. The relatively large size of Zr and large negative heat of mixing between Zr and Al atoms, enhancing the packing density and stability of metallic glass system, may be responsible for the higher glass forming ability of Zr50Cu45Al5. PMID:26828778
NASA Astrophysics Data System (ADS)
Huang, Yuxiang; Huang, Li; Wang, C. Z.; Kramer, M. J.; Ho, K. M.
2016-03-01
Comparative analysis between Zr-rich Zr50Cu45Al5 and Cu-rich Cu50Zr45Al5 metallic glasses (MGs) is extensively performed to locate the key structural motifs accounting for their difference of glass forming ability. Here we adopt ab initio molecular dynamics simulations to investigate the local atomic structures of Zr50Cu45Al5 and Cu50Zr45Al5 MGs. A high content of icosahedral-related (full and distorted) orders was found in both samples, while in the Zr-rich MG full icosahedrons < 0,0,12,0> is dominant, and in the Cu-rich one the distorted icosahedral orders, especially < 0,2,8,2> and < 0,2,8,1> , are prominent. And the < 0,2,8,2> polyhedra in Cu50Zr45Al5 MG mainly originate from Al-centered clusters, while the < 0,0,12,0> in Zr50Cu45Al5 derives from both Cu-centered clusters and Al-centered clusters. These difference may be ascribed to the atomic size difference and chemical property between Cu and Zr atoms. The relatively large size of Zr and large negative heat of mixing between Zr and Al atoms, enhancing the packing density and stability of metallic glass system, may be responsible for the higher glass forming ability of Zr50Cu45Al5.
Huang, Yuxiang; Huang, Li; Wang, C. Z.; Kramer, M. J.; Ho, K. M.
2016-02-01
Comparative analysis between Zr-rich Zr50Cu45Al5 and Cu-rich Cu50Zr45Al5 metallic glasses (MGs) is extensively performed to locate the key structural motifs accounting for their difference of glass forming ability. Here we adopt ab initio molecular dynamics simulations to investigate the local atomic structures of Zr50Cu45Al5 and Cu50Zr45Al5 MGs. A high content of icosahedral-related (full and distorted) orders was found in both samples, while in the Zr-rich MG full icosahedrons < 0,0,12,0 > is dominant, and in the Cu-rich one the distorted icosahedral orders, especially < 0,2,8,2 > and < 0,2,8,1 >, are prominent. And the < 0,2,8,2 > polyhedra in Cu50Zr45Al5more » MG mainly originate from Al-centered clusters, while the < 0,0,12,0 > in Zr50Cu45Al5 derives from both Cu-centered clusters and Al-centered clusters. These difference may be ascribed to the atomic size difference and chemical property between Cu and Zr atoms. Lastly, the relatively large size of Zr and large negative heat of mixing between Zr and Al atoms, enhancing the packing density and stability of metallic glass system, may be responsible for the higher glass forming ability of Zr50Cu45Al5.« less
Xin, H.; LaRue, J.; Oberg, H.; Beye, M.; Dell'Angela, M.; Turner, J. J.; Gladh, J.; Ng, M. L.; Sellberg, J. A.; Kaya, S.; Mercurio, G.; Hieke, F.; Nordlund, D.; Schlotter, W. F.; Dakovski, G. L.; Minitti, M. P.; Fohlisch, A.; Wolf, M.; Wurth, W.; Ogasawara, H.; Norskov, J. K.; Ostrom, H.; Pettersson, L. G. M.; Nilsson, A.; Ablid-Pedersen, F.
2015-04-16
We show that coadsorbed oxygen atoms have a dramatic influence on the CO desorption dynamics from Ru(0001). In contrast to the precursor-mediated desorption mechanism on Ru(0001), the presence of surface oxygen modifies the electronic structure of Ru atoms such that CO desorption occurs predominantly via the direct pathway. This phenomenon is directly observed in an ultrafast pump-probe experiment using a soft x-ray free-electron laser to monitor the dynamic evolution of the valence electronic structure of the surface species. This is supported with the potential of mean force along the CO desorption path obtained from density-functional theory calculations. Charge density distribution and frozen-orbital analysis suggest that the oxygen-induced reduction of the Pauli repulsion, and consequent increase of the dative interaction between the CO 5σ and the charged Ru atom, is the electronic origin of the distinct desorption dynamics. Ab initio molecular dynamics simulations of CO desorption from Ru(0001) and oxygen-coadsorbed Ru(0001) provide further insights into the surface bond-breaking process.
Huang, Yuxiang; Huang, Li; Wang, C. Z.; Kramer, M. J.; Ho, K. M.
2016-02-01
In this study, comparative analysis between Zr-rich Zr50Cu45Al5 and Cu-rich Cu50Zr45Al5 metallic glasses (MGs) is extensively performed to locate the key structural motifs accounting for their difference of glass forming ability. Here we adopt ab initio molecular dynamics simulations to investigate the local atomic structures of Zr50Cu45Al5 and Cu50Zr45Al5 MGs. A high content of icosahedral-related (full and distorted) orders was found in both samples, while in the Zr-rich MG full icosahedrons <0,0,12,0> is dominant, and in the Cu-rich one the distorted icosahedral orders, especially <0,2,8,2> and <0,2,8,1>, are prominent. And the <0,2,8,2> polyhedra in Cu50Zr45Al5 MG mainly originate from Al-centeredmore » clusters, while the <0,0,12,0> in Zr50Cu45Al5 derives from both Cu-centered clusters and Al-centered clusters. These difference may be ascribed to the atomic size difference and chemical property between Cu and Zr atoms. The relatively large size of Zr and large negative heat of mixing between Zr and Al atoms, enhancing the packing density and stability of metallic glass system, may be responsible for the higher glass forming ability of Zr50Cu45Al5.« less
Wang, Zhiping; Zhang, Liang; Cukier, Robert I; Bu, Yuxiang
2010-02-28
The structural and electronic properties of an excess electron (EE) in the ionic liquid (IL) 1-methylpyridinium chloride were explored using ab initio molecular dynamics simulations and quantum chemical calculations to give an overall understanding of the solvation and transport behavior of an EE in this IL. The results show that the EE resides in cation pi*-type orbitals and that the electronic states can be characterized by the alternating appearance of localized and delocalized states during the time evolution. The characters of the EE electronic states are determined by the number of cations contributing to the LUMO of the IL. In a localized state one or two cations contribute to the LUMO of the bulk ionic liquid, while in the delocalized state the IL LUMO is composed of pi*-type orbitals spanning nearly all the cations in the cell. The arrangement and fluctuation-induced changes of the orbital components in the empty band produce an alternation of different states and leads to the migration of the excess electron. These findings can be attributed to the special features of the electronic structures and geometries of the IL, and they can be used to explain similarities and differences between pyridinium-based and imidazolium-based ILs in mediating electron migration. PMID:20145852
Xin, Xukai; Li, Bo; Jung, Jaehan; Yoon, Young Jun; Biswas, Rana; Lin, Zhiqun
2014-07-24
Quantum dot-sensitized solar cells (QDSSCs) have emerged as a promising solar architecture for next-generation solar cells. The QDSSCs exhibit a remarkably fast electron transfer from the quantum dot (QD) donor to the TiO2 acceptor with size quantization properties of QDs that allows for the modulation of band energies to control photoresponse and photoconversion efficiency of solar cells. In order to understand the mechanisms that underpin this rapid charge transfer, the electronic properties of CdSe and PbSe QDs with different sizes on the TiO2 substrate are simulated using a rigorous ab initio density functional method. Our method capitalizes on localized orbitalmore » basis set, which is computationally less intensive. Quite intriguingly, a remarkable set of electron bridging states between QDs and TiO2 occurring via the strong bonding between the conduction bands of QDs and TiO2 is revealed. Such bridging states account for the fast adiabatic charge transfer from the QD donor to the TiO2 acceptor, and may be a general feature for strongly coupled donor/acceptor systems. All the QDs/TiO2 systems exhibit type II band alignments, with conduction band offsets that increase with the decrease in QD size. This facilitates the charge transfer from QDs donors to TiO2 acceptors and explains the dependence of the increased charge transfer rate with the decreased QD size.« less
Qian, X.; Nimlos, M. R.; Davis, M.; Johnson, D. K.; Himmel, M. E.
2005-01-01
Ab initio molecular dynamics simulations were employed to investigate, with explicit solvent water molecules, {beta}-d-glucose and {beta}-d-xylose degradation mechanisms in acidic media. The rate-limiting step in sugar degradation was found to be protonation of the hydroxyl groups on the sugar ring. We found that the structure of water molecules plays a significant role in the acidic sugar degradation pathways. Firstly, a water molecule competes with the hydroxyl group on the sugar ring for protons. Secondly, water forms hydrogen bonds with the hydroxyl groups on the sugar rings, thus weakening the C-C and C-O bonds (each to a different degree). Note that the reaction pathways could be altered due to the change of relative stability of the C-C and C-O bonds. Thirdly, water molecules that are hydrogen-bonded to sugar hydroxyls could easily extract a proton from the reaction intermediate, terminating the reaction. Indeed, the sugar degradation pathway is complex due to multiple protonation probabilities and the surrounding water structure. Our experimental data support multiple sugar acidic degradation pathways.
AB INITIO AND CALPHAD THERMODYNAMICS OF MATERIALS
Turchi, P A
2004-04-14
Ab initio electronic structure methods can supplement CALPHAD in two major ways for subsequent applications to stability in complex alloys. The first one is rather immediate and concerns the direct input of ab initio energetics in CALPHAD databases. The other way, more involved, is the assessment of ab initio thermodynamics {acute a} la CALPHAD. It will be shown how these results can be used within CALPHAD to predict the equilibrium properties of multi-component alloys.
Ab initio non-relativistic spin dynamics
Ding, Feizhi; Goings, Joshua J.; Li, Xiaosong; Frisch, Michael J.
2014-12-07
Many magnetic materials do not conform to the (anti-)ferromagnetic paradigm where all electronic spins are aligned to a global magnetization axis. Unfortunately, most electronic structure methods cannot describe such materials with noncollinear electron spin on account of formally requiring spin alignment. To overcome this limitation, it is necessary to generalize electronic structure methods and allow each electron spin to rotate freely. Here, we report the development of an ab initio time-dependent non-relativistic two-component spinor (TDN2C), which is a generalization of the time-dependent Hartree-Fock equations. Propagating the TDN2C equations in the time domain allows for the first-principles description of spin dynamics. A numerical tool based on the Hirshfeld partitioning scheme is developed to analyze the time-dependent spin magnetization. In this work, we also introduce the coupling between electron spin and a homogenous magnetic field into the TDN2C framework to simulate the response of the electronic spin degrees of freedom to an external magnetic field. This is illustrated for several model systems, including the spin-frustrated Li{sub 3} molecule. Exact agreement is found between numerical and analytic results for Larmor precession of hydrogen and lithium atoms. The TDN2C method paves the way for the ab initio description of molecular spin transport and spintronics in the time domain.
Ab initio non-relativistic spin dynamics
NASA Astrophysics Data System (ADS)
Ding, Feizhi; Goings, Joshua J.; Frisch, Michael J.; Li, Xiaosong
2014-12-01
Many magnetic materials do not conform to the (anti-)ferromagnetic paradigm where all electronic spins are aligned to a global magnetization axis. Unfortunately, most electronic structure methods cannot describe such materials with noncollinear electron spin on account of formally requiring spin alignment. To overcome this limitation, it is necessary to generalize electronic structure methods and allow each electron spin to rotate freely. Here, we report the development of an ab initio time-dependent non-relativistic two-component spinor (TDN2C), which is a generalization of the time-dependent Hartree-Fock equations. Propagating the TDN2C equations in the time domain allows for the first-principles description of spin dynamics. A numerical tool based on the Hirshfeld partitioning scheme is developed to analyze the time-dependent spin magnetization. In this work, we also introduce the coupling between electron spin and a homogenous magnetic field into the TDN2C framework to simulate the response of the electronic spin degrees of freedom to an external magnetic field. This is illustrated for several model systems, including the spin-frustrated Li3 molecule. Exact agreement is found between numerical and analytic results for Larmor precession of hydrogen and lithium atoms. The TDN2C method paves the way for the ab initio description of molecular spin transport and spintronics in the time domain.
Wang, Shenglong; Hu, Po; Zhang, Yingkai
2008-01-01
In order to elucidate enzyme catalysis through computer simulation, a prerequisite is to reliably compute free energy barriers for both enzyme and solution reactions. By employing on-the-fly Born-Oppenheimer molecular dynamics simulations with the ab initio QM/MM approach and the umbrella sampling method, we have determined free energy profiles for the methyl-transfer reaction catalyzed by the histone lysine methyl- transferase SET7/9 and its corresponding uncatalyzed reaction in aqueous solution, respectively. Our calculated activation free energy barrier for the enzyme catalyzed reaction is 22.5 kcal/mol, which agrees very well with the experimental value of 20.9 kcal/mol. The difference in potential of mean force between a corresponding pre-reaction state and the transition state for the solution reaction is computed to be 30.9 kcal/mol. Thus our simulations indicate that the enzyme SET7/9 plays an essential catalytic role in significantly lowering the barrier for the methyl-transfer reaction step. For the reaction in solution, it is found that the hydrogen bond network near the reac- tion center undergoes a significant change and there is a strong shift in electrostatic field from the pre-reaction state to the transition state. While for the enzyme reaction, such an effect is much smaller and the enzyme SET7/9 is found to provide a pre-organized electrostatic environment to facilitate the methyl-transfer reaction. Meanwhile, we find that the transition state in the enzyme reaction is a little more dissociative than that in solution. PMID:17388541
Atta-Fynn, Raymond; Johnson, Donald F.; Bylaska, Eric J.; Ilton, Eugene S.; Schenter, Gregory K.; De Jong, Wibe A.
2012-03-05
Ab initio molecular dynamics simulations at 300 K based on density functional theory have been used to study the hydration shell geometries, solvent dipole, and first hydrolysis of the Uranium(IV) (U{sup 4+}) and Uranyl(V) (UO{sub 2}{sup +}) ions in aqueous solution. The solvent dipole and first of hydrolysis of aqueous Uranium(VI) (UO{sub 2}{sup 2+}) has also been probed. The first shell of U{sup 4+} is coordinated by 8-9 water ligands with an average U-O distance of 2.42 {angstrom}. The average first shell coordination number and distance are in agreement with experimental estimates of 8-11 and 2.40-2.44 {angstrom} respectively. The simulated EXAFS spectra of U{sup 4+} matched well with recent experimental data. The first shell of UO{sub 2}{sup +} is coordinated by 5 water ligands in the equatorial plane, with the average U=O{sub ax} and U-O distances being 1.85 {angstrom} and 2.54 {angstrom} respectively. Overall, the hydration shell structure of UO{sub 2}{sup +} matches closely with that of UO{sub 2}{sup 2+} except for small expansions in the average U=O{sub ax} and U-O distances. Each ion strongly polarizes their respective first shell water ligands. The computed acidity constant (pK{sub a}) of U{sup 4+} and UO{sub 2}{sup 2+} are 0.93 and 4.95, in good agreement with the experimental values of 0.54 and 5.24 respectively. The predicted pK{sub a} of UO{sub 2}{sup +} is 8.5.
Choudhary, Ashu; Chandra, Amalendu
2016-02-17
The anisotropic structure and dynamics of the hydration shell of a benzene solute in liquid water have been investigated by means of ab initio molecular dynamics simulations using the BLYP (Becke-Lee-Yang-Parr) and dispersion corrected BLYP-D functionals. The main focus has been to look at the influence of π-hydrogen-bonding and hydrophobic interactions on the distance and angle resolved various structural and dynamic properties of solvation shell. The structure of hydration shell water molecules around benzene is found to be highly anisotropic as revealed by the radial distribution functions of different conical regions and joint radial/angular distribution functions. The benzene-water dimer potential energy curves are calculated for a variety of orientations of water along the axial and equatorial directions for both BLYP and BLYP-D functionals. The simulation results of the hydration shell structure of benzene, particularly the axial and equatorial benzene-water RDFs are discussed based on the differences in the benzene-water potential energies for different orientations and functionals. The inter-particle distance/angle correlations show an enhanced water structure in the solvation shell of benzene compared to that between the solvation shell and bulk and also between the bulk molecules. On average, a single πH-bond is found to be formed between water and benzene in the 45° axial conical region of the solvation shell. The πH-bonded water molecules are found to have faster translational dynamics and also found to follow a fast jump mechanism of reorientation to change their hydrogen bonded partners. The presence of π-hydrogen-bonded water makes the overall dynamics of the axial region faster than that of the equatorial region where the water molecules are hydrophobically solvated and hydrogen bonded to other water molecules. PMID:26847163
Xin, Xukai; Li, Bo; Jung, Jaehan; Yoon, Young Jun; Biswas, Rana; Lin, Zhiqun
2014-07-24
Quantum dot-sensitized solar cells (QDSSCs) have emerged as a promising solar architecture for next-generation solar cells. The QDSSCs exhibit a remarkably fast electron transfer from the quantum dot (QD) donor to the TiO_{2} acceptor with size quantization properties of QDs that allows for the modulation of band energies to control photoresponse and photoconversion efficiency of solar cells. In order to understand the mechanisms that underpin this rapid charge transfer, the electronic properties of CdSe and PbSe QDs with different sizes on the TiO_{2} substrate are simulated using a rigorous ab initio density functional method. Our method capitalizes on localized orbital basis set, which is computationally less intensive. Quite intriguingly, a remarkable set of electron bridging states between QDs and TiO_{2} occurring via the strong bonding between the conduction bands of QDs and TiO_{2} is revealed. Such bridging states account for the fast adiabatic charge transfer from the QD donor to the TiO_{2} acceptor, and may be a general feature for strongly coupled donor/acceptor systems. All the QDs/TiO_{2} systems exhibit type II band alignments, with conduction band offsets that increase with the decrease in QD size. This facilitates the charge transfer from QDs donors to TiO_{2} acceptors and explains the dependence of the increased charge transfer rate with the decreased QD size.
Bankura, Arindam; Chandra, Amalendu
2015-01-28
The dynamics of proton transfer (PT) through hydrogen bonds in a two-dimensional water layer confined between two graphene sheets at room temperature are investigated through ab initio and quantum-classical simulations. The excess proton is found to be mostly solvated as an Eigen cation where the hydronium ion donates three hydrogen bonds to the neighboring water molecules. In the solvation shell of the hydronium ion, the three coordinated water molecules with two donor hydrogen bonds are found to be properly presolvated to accept a proton. Although no hydrogen bond needs to be broken for transfer of a proton to such presolvated water molecules from the hydronium ion, the PT rate is still found to be not as fast as it is for one-dimensional chains. Here, the PT is slowed down as the probability of finding a water with two donor hydrogen bonds in the solvation shell of the hydronium ion is found to be only 25%-30%. The hydroxide ion is found to be solvated mainly as a complex anion where it accepts four H-bonds through its oxygen atom and the hydrogen atom of the hydroxide ion remains free all the time. Here, the presolvation of the hydroxide ion to accept a proton requires that one of its hydrogen bonds is broken and the proton comes from a neighboring water molecule with two acceptor and one donor hydrogen bonds. The coordination number reduction by breaking of a hydrogen bond is a slow process, and also the population of water molecules with two acceptor and one donor hydrogen bonds is only 20%-25% of the total number of water molecules. All these factors together tend to slow down the hydroxide ion migration rate in two-dimensional water layers compared to that in three-dimensional bulk water.
Towards SiC Surface Functionalization: An Ab Initio Study
Cicero, G; Catellani, A
2005-01-28
We present a microscopic model of the interaction and adsorption mechanism of simple organic molecules on SiC surfaces as obtained from ab initio molecular dynamics simulations. Our results open the way to functionalization of silicon carbide, a leading candidate material for bio-compatible devices.
NASA Astrophysics Data System (ADS)
Prasetyo, Niko; Armunanto, Ria
2016-05-01
Structures and dynamics of Ag+ in 18.6% aqueous ammonia have been studied using Quantum Mechanical Charge Field Molecular Dynamics (QMCF-MD) simulation at the Hartree-Fock (HF) level theory employing LANL2DZ ECP basis set for Ag+ and Dunning DZP for solvent molecules. Structural properties are in excellent agreement with previous QM/MM and experiments studies. [Ag(NH3)2(H2O)3]+ was found as dominant species during simulation time. For 20 ps of simulation time, a labile first solvation shell was observed with both fast ammonia and water ligands exchanges. QMCF-MD framework describes first solvation shell more labile than conventional QM/MM MD simulation.
Kowalewski, Markus Mukamel, Shaul
2015-07-28
Femtosecond Stimulated Raman Spectroscopy (FSRS) signals that monitor the excited state conical intersections dynamics of acrolein are simulated. An effective time dependent Hamiltonian for two C—H vibrational marker bands is constructed on the fly using a local mode expansion combined with a semi-classical surface hopping simulation protocol. The signals are obtained by a direct forward and backward propagation of the vibrational wave function on a numerical grid. Earlier work is extended to fully incorporate the anharmonicities and intermode couplings.
NASA Astrophysics Data System (ADS)
Kowalewski, Markus; Mukamel, Shaul
2015-07-01
Femtosecond Stimulated Raman Spectroscopy (FSRS) signals that monitor the excited state conical intersections dynamics of acrolein are simulated. An effective time dependent Hamiltonian for two C—H vibrational marker bands is constructed on the fly using a local mode expansion combined with a semi-classical surface hopping simulation protocol. The signals are obtained by a direct forward and backward propagation of the vibrational wave function on a numerical grid. Earlier work is extended to fully incorporate the anharmonicities and intermode couplings.
Demmel, F; Mukhopadhyay, S
2016-01-01
The ionic stochastic motions in the molten alkali halide NaF are investigated by quasielastic neutron scattering and first principles molecular dynamics simulation. Quasielastic neutron scattering was employed to extract the diffusion behavior of the sodium ions in the melt. An extensive first principles based simulation on a box of up to 512 particles has been performed to complement the experimental data. From that large box, a smaller 64-particle box has then been simulated over a runtime of 60 ps. A good agreement between calculated and neutron data on the level of spectral shape has been obtained. The obtained sodium diffusion coefficients agree very well. The simulation predicts a fluorine diffusion coefficient similar to the sodium one. Applying the Nernst-Einstein equation, a remarkable large cross correlation between both ions can be deduced. The velocity cross correlations demonstrate a positive correlation between the ions over a period of 0.1 ps. That strong correlation is evidence that the unlike ions do not move completely statistically independent and have a strong association over a short period of time. PMID:26747811
NASA Astrophysics Data System (ADS)
Demmel, F.; Mukhopadhyay, S.
2016-01-01
The ionic stochastic motions in the molten alkali halide NaF are investigated by quasielastic neutron scattering and first principles molecular dynamics simulation. Quasielastic neutron scattering was employed to extract the diffusion behavior of the sodium ions in the melt. An extensive first principles based simulation on a box of up to 512 particles has been performed to complement the experimental data. From that large box, a smaller 64-particle box has then been simulated over a runtime of 60 ps. A good agreement between calculated and neutron data on the level of spectral shape has been obtained. The obtained sodium diffusion coefficients agree very well. The simulation predicts a fluorine diffusion coefficient similar to the sodium one. Applying the Nernst-Einstein equation, a remarkable large cross correlation between both ions can be deduced. The velocity cross correlations demonstrate a positive correlation between the ions over a period of 0.1 ps. That strong correlation is evidence that the unlike ions do not move completely statistically independent and have a strong association over a short period of time.
Haskins, Justin B; Bauschlicher, Charles W; Lawson, John W
2015-11-19
Density functional theory (DFT), density functional theory molecular dynamics (DFT-MD), and classical molecular dynamics using polarizable force fields (PFF-MD) are employed to evaluate the influence of Li(+) on the structure, transport, and electrochemical stability of three potential ionic liquid electrolytes: N-methyl-N-butylpyrrolidinium bis(trifluoromethanesulfonyl)imide ([pyr14][TFSI]), N-methyl-N-propylpyrrolidinium bis(fluorosulfonyl)imide ([pyr13][FSI]), and 1-ethyl-3-methylimidazolium boron tetrafluoride ([EMIM][BF4]). We characterize the Li(+) solvation shell through DFT computations of [Li(Anion)n]((n-1)-) clusters, DFT-MD simulations of isolated Li(+) in small ionic liquid systems, and PFF-MD simulations with high Li-doping levels in large ionic liquid systems. At low levels of Li-salt doping, highly stable solvation shells having two to three anions are seen in both [pyr14][TFSI] and [pyr13][FSI], whereas solvation shells with four anions dominate in [EMIM][BF4]. At higher levels of doping, we find the formation of complex Li-network structures that increase the frequency of four anion-coordinated solvation shells. A comparison of computational and experimental Raman spectra for a wide range of [Li(Anion)n]((n-1)-) clusters shows that our proposed structures are consistent with experiment. We then compute the ion diffusion coefficients and find measures from small-cell DFT-MD simulations to be the correct order of magnitude, but influenced by small system size and short simulation length. Correcting for these errors with complementary PFF-MD simulations, we find DFT-MD measures to be in close agreement with experiment. Finally, we compute electrochemical windows from DFT computations on isolated ions, interacting cation/anion pairs, and liquid-phase systems with Li-doping. For the molecular-level computations, we generally find the difference between ionization energy and electron affinity from isolated ions and interacting cation/anion pairs to
NASA Astrophysics Data System (ADS)
Gao, L. L.; Wang, F.; Jiang, L.; Qu, L. T.; Lu, Y. F.
2016-01-01
The electric current has been switched in diamond by a dual-laser field with an attosecond pulse train and a femtosecond laser, respectively serving to excite and drive electrons. The optical-induced current is simulated by the developed method based on the time-dependent density functional theory. The electric current is induced within several attoseconds with the diamond’s conductivity increased by 16~23 orders of magnitude. Our work opens the way to extending electronic signal processing from the present gigahertz domain into the exahertz domain.
Koubsky, T.; Kalvoda, L.; Drab, M.
2013-07-01
For hydrometallurgical treatment of the high level liquid waste (HLLW) in the DIAMEX and SANEX processes, organic compounds of the bis-DGA family are used as cation extractants in apolar solvents. For the compound of m-xylylene-bis-diglycolamide high distribution coefficients for Eu and Am were found. Since the environment of the process is highly radioactive and acidic (nitric acid), it is necessary to ensure the stability of the extractants. In order to analyse the process theoretically, the molecule of m-xylylene-bis- diglycolamide and two of its degradation products were simulated by the DFT computational methods (PBE, RPBE, BLYP, B3LYP) available within the simulation environment DMol{sup 3} 6.1 and Gaussian 09 software. The local chemical stability of some locations of the molecule was assessed from the calculated stability indicators (electrostatic potential, Fukui function, HOMO localization). In connection with the chemical treatment, especially the stability against an electrophilic attack was tested. The results of calculated bond orders and spatial distribution of electrostatic potential and HOMO were are successfully correlated with the local and general stability determined by the experiment. These results should be helpful for the further development of the separation process. (authors)
NASA Astrophysics Data System (ADS)
Bensadiq, A.; Zaari, H.; Benyoussef, A.; El Kenz, A.
2016-09-01
Using the density functional theory, the electronic structure; density of states, band structure and exchange couplings of Tb Ni4 Si compound have been investigated. Magnetic and magnetocaloric properties of this material have been studied using Monte Carlo Simulation (MCS) and Mean Field Approximation (MFA) within a three dimensional Ising model. We calculated the isothermal magnetic entropy change, adiabatic temperature change and relative cooling power (RCP) for different external magnetic field and temperature. The highest obtained isothermal magnetic entropy change is of -14.52 J kg-1 K-1 for a magnetic field of H=4 T. The adiabatic temperature reaches a maximum value equal to 3.7 K and the RCP maximum value is found to be 125.12 J kg-1 for a field magnetic of 14 T.
Martins-Costa, Marilia T C; García-Prieto, Francisco F; Ruiz-López, Manuel F
2015-02-14
Understanding the influence of solute-solvent interactions on chemical reactivity has been a subject of intense research in the last few decades. Theoretical studies have focused on bulk solvation phenomena and a variety of models and methods have been developed that are now widely used by both theoreticians and experimentalists. Much less attention has been paid, however, to processes that occur at liquid interfaces despite the important role such interfaces play in chemistry and biology. In this study, we have carried out sequential molecular dynamics simulations and quantum mechanical calculations to analyse the influence of the air-water interface on the reactivity of formaldehyde, acetaldehyde and benzaldehyde, three simple aldehydes of atmospheric interest. The calculated free-energy profiles exhibit a minimum at the interface, where the average reactivity indices may display large solvation effects. The study emphasizes the role of solvation dynamics, which are responsible for large fluctuations of some molecular properties. We also show that the photolysis rate constant of benzaldehyde in the range 290-308 nm increases by one order of magnitude at the surface of a water droplet, from 2.7 × 10(-5) s(-1) in the gas phase to 2.8 × 10(-4) s(-1) at the air-water interface, and we discuss the potential impact of this result on the chemistry of the troposphere. Experimental data in this domain are still scarce and computer simulations like those presented in this work may provide some insights that can be useful to design new experiments. PMID:25451554
Fang, Qiu; Shen, Lin; Fang, Wei-Hai
2013-07-14
Photo-induced multiple body dissociation is of fundamental interest in chemistry and physics. A description of the mechanism associated with n-body (n ≥ 3) photodissociation has proven to be an intriguing and yet challenging issue in the field of chemical dynamics. Oxalyl chloride, (ClCO)2, is the sole molecule reported up to date that can undergo four-body dissociation following absorption of a single UV photon, with a rich history of mechanistic debate. In the present work, the combined electronic structure calculations and dynamics simulations have been performed at the advanced level, which provides convincing evidence for resolving the mechanistic debate. More importantly, synchronous and asynchronous concertedness were explored for the first time for the (ClCO)2 photodissociation, which is based on the simulated time constants for the C-C and C-Cl bond fissions. Upon photoexcitation of (ClCO)2 to the S1 state, the adiabatic C-C or C-Cl fission takes place with little possibility. The four-body dissociation to 2Cl((2)P) and 2CO((1)Σ) was determined to a dominant channel with its branch of ∼0.7, while the three-body dissociation to ClCO((2)A(')) + CO((1)Σ) + Cl((2)P) was predicted to play a minor role in the (ClCO)2 photodissociation at 193 nm. Both the four-body and three-body dissociations are non-adiabatic processes, which proceed in a synchronous concerted way as a result of the S1 → S0 internal conversion. There is a little possibility for two-body dissociation to occur in the S0 and S1 states. PMID:23862946
Discovering chemistry with an ab initio nanoreactor
Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; Liu, Fang; Pande, Vijay S.; Martínez, Todd J.
2014-11-02
Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provides detailed physical insight. While theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor – a highly accelerated, first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor we show new pathways for glycine synthesis frommore » primitive compounds proposed to exist on the early Earth, providing new insight into the classic Urey-Miller experiment. Ultimately, these results highlight the emergence of theoretical and computational chemistry as a tool for discovery in addition to its traditional role of interpreting experimental findings.« less
Discovering chemistry with an ab initio nanoreactor
Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; Liu, Fang; Pande, Vijay S.; Martínez, Todd J.
2014-01-01
Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provides detailed physical insight. While theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor – a highly accelerated, first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, providing new insight into the classic Urey-Miller experiment. These results highlight the emergence of theoretical and computational chemistry as a tool for discovery in addition to its traditional role of interpreting experimental findings. PMID:25411881
Discovering chemistry with an ab initio nanoreactor.
Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; Liu, Fang; Pande, Vijay S; Martínez, Todd J
2014-12-01
Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provide detailed physical insight. Although theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor--a highly accelerated first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor, we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, which provide new insight into the classic Urey-Miller experiment. These results highlight the emergence of theoretical and computational chemistry as a tool for discovery, in addition to its traditional role of interpreting experimental findings. PMID:25411881
Discovering chemistry with an ab initio nanoreactor
NASA Astrophysics Data System (ADS)
Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; Liu, Fang; Pande, Vijay S.; Martínez, Todd J.
2014-12-01
Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provide detailed physical insight. Although theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor—a highly accelerated first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor, we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, which provide new insight into the classic Urey-Miller experiment. These results highlight the emergence of theoretical and computational chemistry as a tool for discovery, in addition to its traditional role of interpreting experimental findings.
Discovering chemistry with an ab initio nanoreactor
Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; Liu, Fang; Pande, Vijay S.; Martínez, Todd J.
2014-11-02
Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provides detailed physical insight. While theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor – a highly accelerated, first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, providing new insight into the classic Urey-Miller experiment. Ultimately, these results highlight the emergence of theoretical and computational chemistry as a tool for discovery in addition to its traditional role of interpreting experimental findings.
Ab Initio Calculation of the Hoyle State
Epelbaum, Evgeny; Krebs, Hermann; Lee, Dean; Meissner, Ulf-G.
2011-05-13
The Hoyle state plays a crucial role in the helium burning of stars heavier than our Sun and in the production of carbon and other elements necessary for life. This excited state of the carbon-12 nucleus was postulated by Hoyle as a necessary ingredient for the fusion of three alpha particles to produce carbon at stellar temperatures. Although the Hoyle state was seen experimentally more than a half century ago nuclear theorists have not yet uncovered the nature of this state from first principles. In this Letter we report the first ab initio calculation of the low-lying states of carbon-12 using supercomputer lattice simulations and a theoretical framework known as effective field theory. In addition to the ground state and excited spin-2 state, we find a resonance at -85(3) MeV with all of the properties of the Hoyle state and in agreement with the experimentally observed energy.
NASA Astrophysics Data System (ADS)
Dornheim, T.; Groth, S.; Schoof, T.; Hann, C.; Bonitz, M.
2016-05-01
In a recent publication [S. Groth et al., Phys. Rev. B 93, 085102 (2016), 10.1103/PhysRevB.93.085102], we have shown that the combination of two complementary quantum Monte Carlo approaches, namely configuration path integral Monte Carlo [T. Schoof et al., Phys. Rev. Lett. 115, 130402 (2015), 10.1103/PhysRevLett.115.130402] and permutation blocking path integral Monte Carlo [T. Dornheim et al., New J. Phys. 17, 073017 (2015), 10.1088/1367-2630/17/7/073017], allows for the accurate computation of thermodynamic properties of the spin-polarized uniform electron gas over a wide range of temperatures and densities without the fixed-node approximation. In the present work, we extend this concept to the unpolarized case, which requires nontrivial enhancements that we describe in detail. We compare our simulation results with recent restricted path integral Monte Carlo data [E. W. Brown et al., Phys. Rev. Lett. 110, 146405 (2013), 10.1103/PhysRevLett.110.146405] for different energy contributions and pair distribution functions and find, for the exchange correlation energy, overall better agreement than for the spin-polarized case, while the separate kinetic and potential contributions substantially deviate.
Ab initio simulation of ammonia monohydrate (NH3ṡH2O) and ammonium hydroxide (NH4OH)
NASA Astrophysics Data System (ADS)
Fortes, A. D.; Brodholt, J. P.; Wood, I. G.; Vočadlo, L.; Jenkins, H. D. B.
2001-10-01
We report the results of the first pseudopotential plane-wave simulations of the static properties of ammonia monohydrate phase I (AMH I) and ammonium hydroxide. Our calculated fourth-order logarithmic equation of state, at zero pressure and temperature, has molar volume, V0=36.38(3) cm3 mol-1, bulk modulus, K0=9.59(9) GPa, and the first derivative of the bulk modulus with respect to pressure, K0'=5.73(21). Both this and the lattice parameters are in very good agreement with experimental values. The monohydrate transforms, via a solid-state proton transfer reaction, to ammonium hydroxide (NH4OH) at 5.0(4) GPa. The equation of state of ammonium hydroxide is, V0=31.82(5) cm3 mol-1, K0=14.78(62) GPa, K0'=2.69(48). We calculate the reaction enthalpy, ΔH(NH4OH,s→NH3ṡH2O,s)=-14.8(5) kJ mol-1 at absolute zero, and thus estimate the enthalpy of formation, ΔfH⊖(NH4OH,s)=-356 kJ mol-1 at 298 K. This result places an upper limit of 84 kJ mol-1 on the barrier to rotation of the ammonium cation, and yields an average hydrogen bond enthalpy of ˜23 kJ mol-1.
Accurate path integral molecular dynamics simulation of ab-initio water at near-zero added cost
NASA Astrophysics Data System (ADS)
Elton, Daniel; Fritz, Michelle; Soler, José; Fernandez-Serra, Marivi
It is now established that nuclear quantum motion plays an important role in determining water's structure and dynamics. These effects are important to consider when evaluating DFT functionals and attempting to develop better ones for water. The standard way of treating nuclear quantum effects, path integral molecular dynamics (PIMD), multiplies the number of energy/force calculations by the number of beads, which is typically 32. Here we introduce a method whereby PIMD can be incorporated into a DFT molecular dynamics simulation at virtually zero cost. The method is based on the cluster (many body) expansion of the energy. We first subtract the DFT monomer energies, using a custom DFT-based monomer potential energy surface. The evolution of the PIMD beads is then performed using only the more-accurate Partridge-Schwenke monomer energy surface. The DFT calculations are done using the centroid positions. Various bead thermostats can be employed to speed up the sampling of the quantum ensemble. The method bears some resemblance to multiple timestep algorithms and other schemes used to speed up PIMD with classical force fields. We show that our method correctly captures some of key effects of nuclear quantum motion on both the structure and dynamics of water. We acknowledge support from DOE Award No. DE-FG02-09ER16052 (D.E.) and DOE Early Career Award No. DE-SC0003871 (M.V.F.S.).
NASA Astrophysics Data System (ADS)
Mok, Daniel K. W.; Chau, Foo-tim; Lee, Edmond P. F.; Dyke, John M.
2006-09-01
Geometry optimization calculations were carried out on the X˜A11 state of SCl2 and the X˜B12, ÃB22, B˜A12, C˜A12, D˜A22, and ẼB22 states of SCl2+ at the restricted-spin coupled-cluster single-double plus perturbative triple excitation [RCCSD(T)] level with basis sets of up to the augmented correlation-consistent polarized quintuple-zeta [aug-cc-pV(5+d )Z] quality. Effects of core electron correlation, basis set extension to the complete basis set limit, and relativistic contributions on computed minimum-energy geometrical parameters and/or relative electronic energies were also investigated. RCCSD(T) potential energy functions (PEFs) were calculated for the X˜A11 state of SCl2 and the low-lying states of SCl2+ listed above employing the aug-cc-pV(5+d )Z basis set. Anharmonic vibrational wave functions of these neutral and cationic states of SCl2, and Franck-Condon (FC) factors of the lowest four one-electron allowed neutral photoionizations were computed employing the RCCSD(T )/aug-cc-pV(5+d)Z PEFs. Calculated FC factors with allowance for the Duschinsky rotation and anharmonicity were used to simulate the first four photoelectron (PE) bands of SCl2. The agreement between simulated and observed He I PE spectra reported by Colton et al. [J. Electron Spectrosc. Relat. Phenom. 3, 345 (1974)] and Solouki et al. [Chem. Phys. Lett. 26, 20 (1974)] is excellent. However, our FC spectral simulations indicate that the first observed vibrational component in the first PE band of SCl2 is a "hot" band arising from the SCl2+X˜B12(0,0,0)←SCl2X˜A11(1,0,0) ionization. Consequently, the experimental adiabatic ionization energy of SCl2 is revised to 9.55±0.01eV, in excellent agreement with results obtained from state-of-the-art ab initio calculations in this work.
Ab initio alpha-alpha scattering
NASA Astrophysics Data System (ADS)
Elhatisari, Serdar; Lee, Dean; Rupak, Gautam; Epelbaum, Evgeny; Krebs, Hermann; Lähde, Timo A.; Luu, Thomas; Meißner, Ulf-G.
2015-12-01
Processes such as the scattering of alpha particles (4He), the triple-alpha reaction, and alpha capture play a major role in stellar nucleosynthesis. In particular, alpha capture on carbon determines the ratio of carbon to oxygen during helium burning, and affects subsequent carbon, neon, oxygen, and silicon burning stages. It also substantially affects models of thermonuclear type Ia supernovae, owing to carbon detonation in accreting carbon-oxygen white-dwarf stars. In these reactions, the accurate calculation of the elastic scattering of alpha particles and alpha-like nuclei—nuclei with even and equal numbers of protons and neutrons—is important for understanding background and resonant scattering contributions. First-principles calculations of processes involving alpha particles and alpha-like nuclei have so far been impractical, owing to the exponential growth of the number of computational operations with the number of particles. Here we describe an ab initio calculation of alpha-alpha scattering that uses lattice Monte Carlo simulations. We use lattice effective field theory to describe the low-energy interactions of protons and neutrons, and apply a technique called the ‘adiabatic projection method’ to reduce the eight-body system to a two-cluster system. We take advantage of the computational efficiency and the more favourable scaling with system size of auxiliary-field Monte Carlo simulations to compute an ab initio effective Hamiltonian for the two clusters. We find promising agreement between lattice results and experimental phase shifts for s-wave and d-wave scattering. The approximately quadratic scaling of computational operations with particle number suggests that it should be possible to compute alpha scattering and capture on carbon and oxygen in the near future. The methods described here can be applied to ultracold atomic few-body systems as well as to hadronic systems using lattice quantum chromodynamics to describe the interactions of
Ab initio alpha-alpha scattering.
Elhatisari, Serdar; Lee, Dean; Rupak, Gautam; Epelbaum, Evgeny; Krebs, Hermann; Lähde, Timo A; Luu, Thomas; Meißner, Ulf-G
2015-12-01
Processes such as the scattering of alpha particles ((4)He), the triple-alpha reaction, and alpha capture play a major role in stellar nucleosynthesis. In particular, alpha capture on carbon determines the ratio of carbon to oxygen during helium burning, and affects subsequent carbon, neon, oxygen, and silicon burning stages. It also substantially affects models of thermonuclear type Ia supernovae, owing to carbon detonation in accreting carbon-oxygen white-dwarf stars. In these reactions, the accurate calculation of the elastic scattering of alpha particles and alpha-like nuclei--nuclei with even and equal numbers of protons and neutrons--is important for understanding background and resonant scattering contributions. First-principles calculations of processes involving alpha particles and alpha-like nuclei have so far been impractical, owing to the exponential growth of the number of computational operations with the number of particles. Here we describe an ab initio calculation of alpha-alpha scattering that uses lattice Monte Carlo simulations. We use lattice effective field theory to describe the low-energy interactions of protons and neutrons, and apply a technique called the 'adiabatic projection method' to reduce the eight-body system to a two-cluster system. We take advantage of the computational efficiency and the more favourable scaling with system size of auxiliary-field Monte Carlo simulations to compute an ab initio effective Hamiltonian for the two clusters. We find promising agreement between lattice results and experimental phase shifts for s-wave and d-wave scattering. The approximately quadratic scaling of computational operations with particle number suggests that it should be possible to compute alpha scattering and capture on carbon and oxygen in the near future. The methods described here can be applied to ultracold atomic few-body systems as well as to hadronic systems using lattice quantum chromodynamics to describe the interactions of
Multiple time step integrators in ab initio molecular dynamics
Luehr, Nathan; Martínez, Todd J.; Markland, Thomas E.
2014-02-28
Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we present two schemes that enable efficient time-scale separation in ab initio calculations: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynamics. This permits computational speedups of up to 4.4x, compared to standard Born-Oppenheimer ab initio molecular dynamics with a 0.5 fs time step, while maintaining the same energy conservation and accuracy.
Collective rotation from ab initio theory
NASA Astrophysics Data System (ADS)
Caprio, M. A.; Maris, P.; Vary, J. P.; Smith, R.
2015-08-01
Through ab initio approaches in nuclear theory, we may now seek to quantitatively understand the wealth of nuclear collective phenomena starting from the underlying internucleon interactions. No-core configuration interaction (NCCI) calculations for p-shell nuclei give rise to rotational bands, as evidenced by rotational patterns for excitation energies, electromagnetic moments and electromagnetic transitions. In this review, NCCI calculations of 7-9Be are used to illustrate and explore ab initio rotational structure, and the resulting predictions for rotational band properties are compared with experiment. We highlight the robustness of ab initio rotational predictions across different choices for the internucleon interaction.
Liu, Ping; Zhao, Jing; Liu, Jinxiang; Zhang, Meng; Bu, Yuxiang
2014-01-28
In view of the important implications of excess electrons (EEs) interacting with CO{sub 2}–H{sub 2}O clusters in many fields, using ab initio molecular dynamics simulation technique, we reveal the structures and dynamics of an EE associated with its localization and subsequent time evolution in heterogeneous CO{sub 2}–H{sub 2}O mixed media. Our results indicate that although hydration can increase the electron-binding ability of a CO{sub 2} molecule, it only plays an assisting role. Instead, it is the bending vibrations that play the major role in localizing the EE. Due to enhanced attraction of CO{sub 2}, an EE can stably reside in the empty, low-lying π{sup *} orbital of a CO{sub 2} molecule via a localization process arising from its initial binding state. The localization is completed within a few tens of femtoseconds. After EE trapping, the ∠OCO angle of the core CO{sub 2}{sup −} oscillates in the range of 127°∼142°, with an oscillation period of about 48 fs. The corresponding vertical detachment energy of the EE is about 4.0 eV, which indicates extreme stability of such a CO{sub 2}-bound solvated EE in [CO{sub 2}(H{sub 2}O){sub n}]{sup −} systems. Interestingly, hydration occurs not only on the O atoms of the core CO{sub 2}{sup −} through formation of O⋯H–O H–bond(s), but also on the C atom, through formation of a C⋯H–O H–bond. In the latter binding mode, the EE cloud exhibits considerable penetration to the solvent water molecules, and its IR characteristic peak is relatively red-shifted compared with the former. Hydration on the C site can increase the EE distribution at the C atom and thus reduce the C⋯H distance in the C⋯H–O H–bonds, and vice versa. The number of water molecules associated with the CO{sub 2}{sup −} anion in the first hydration shell is about 4∼7. No dimer-core (C{sub 2}O{sub 4}{sup −}) and core-switching were observed in the double CO{sub 2} aqueous media. This work provides molecular dynamics
Ab initio nuclear structure theory
NASA Astrophysics Data System (ADS)
Negoita, Gianina Alina
Ab initio no core methods have become major tools for understanding the properties of light nuclei based on realistic nucleon-nucleon (NN) and three-nucleon (NNN) interactions. A brief description is provided for the inter-nucleon interactions that fit two-body scattering and bound state data, as well as NNN interactions. Major new progress, including the goal of applying these interactions to solve for properties of nuclei, is limited by convergence issues. That is, with the goal of obtaining high precision solutions of the nuclear many-body Hamiltonian with no core methods (all nucleons treated on the same footing), one needs to proceed to very large basis spaces to achieve a convergence pattern suitable for extrapolation to the exact result. This thesis investigates (1) the similarity renormalization group (SRG) approach to soften the interaction, while preserving its phase shift properties, and (2) adoption of a realistic basis space using Woods-Saxon (WS) single-particle wavefunctions. Both have their advantages and limitations, discussed here. For (1), SRG was demonstrated by applying it to a realistic NN interaction, JISP16, in a harmonic oscillator (HO) representation. The degree of interaction softening achieved through a regulator parameter is examined. For (2), new results are obtained with the realistic JISP16 NN interaction in ab initio calculations of light nuclei 4He, 6He and 12C, using a WS basis optimized to minimize the ground-state energy within the truncated no core shell model. These are numerically-intensive many-body calculations. Finally, to gain insight into the potential for no core investigations of heavier nuclei, an initial investigation was obtained for the odd mass A = 47 - 49 region nuclei straddling 48Ca. The motivation for selecting these nuclei stems from the aim of preparing for nuclear double beta-decay studies of 48Ca. In these heavier systems, phenomenological additions to the realistic NN interaction determined by previous
Ab initio phonon limited transport
NASA Astrophysics Data System (ADS)
Verstraete, Matthieu
We revisit the thermoelectric (TE) transport properties of two champion materials, PbTe and SnSe, using fully first principles methods. In both cases the performance of the material is due to subtle combinations of structural effects, scattering, and phase space reduction. In PbTe anharmonic effects are completely opposite to the predicted quasiharmonic evolution of phonon frequencies and to frequently (and incorrectly) cited extrapolations of experiments. This stabilizes the material at high T, but also tends to enhance its thermal conductivity, in a non linear manner, above 600 Kelvin. This explains why PbTe is in practice limited to room temperature applications. SnSe has recently been shown to be the most efficient TE material in bulk form. This is mainly due to a strongly enhanced carrier concentration and electrical conductivity, after going through a phase transition from 600 to 800 K. We calculate the transport coefficients as well as the defect concentrations ab initio, showing excellent agreement with experiment, and elucidating the origin of the double phase transition as well as the new charge carriers. AH Romero, EKU Gross, MJ Verstraete, and O Hellman PRB 91, 214310 (2015) O. Hellman, IA Abrikosov, and SI Simak, PRB 84 180301 (2011)
NASA Astrophysics Data System (ADS)
Li, Hongfei; Guo, Yuzheng; Robertson, John; Okuno, Y.
2016-02-01
Models of three representative higher Miller index interfaces, Si(310):SiO2, Si(410):SiO2, and Si(331):SiO2, have been built by an ab-initio molecular dynamics method. We show that each interface can be made as a fully bonded network without any defects and has a reasonable electronic structure for use in fin field effect transistors or gate-all-around nanowire devices. The differences in numbers of oxygen bridges are attributed to the intermediate sub-oxide components and the atomic step structure. The interface bonding schemes to passivate different densities of dangling bonds on different facets are also analyzed.
Hamama, Wafaa S.; Gouda, Moustafa A.; Soliman, Mamdouh S.; Badr, Marwa H.; Zoorob, Hanafi H.
2012-01-01
Michael addition reaction of the 2-amino-1,3,4-thiadiazole to chalcone as biselectrophile afforded 5,7-diphenyl-6-[1,3-diphenylpropan-1-on-3-yl][1,3,4]thiadiazolo[3,2-a]pyrimidine (3) instead of 5,7-diphenyl-5H-[1,3,4]thiadiazolo[3,2-a]pyrimidine (5) via further Michael addition at C5 in pyrimidine moiety. The structure 3 was established through the aspect of ab initio calculations, elemental analysis and spectral data. PMID:25685403
Zabidi, Noriza Ahmad; Kassim, Hasan Abu; Shrivastava, Keshav N.
2008-05-20
Polonium is the only element with a simple cubic (sc) crystal structure. Atoms in solid polonium sit at the corners of a simple cubic unit cell and no where else. Polonium has a valence electron configuration 6s{sup 2}6p{sup 4} (Z = 84). The low temperature {alpha}-phase transforms into the rhombohedral (trigonal) {beta} structure at {approx}348 K. The sc {alpha}-Po unit cell constant is a = 3.345 A. The beta form of polonium ({beta}-Po) has the lattice parameters, a{sub R} = 3.359 A and a rhombohedral angle 98 deg. 13'. We have performed an ab initio electronic structure calculation by using the density functional theory. We have performed the calculation with and without spin-orbit (SO) coupling by using both the LDA and the GGA for the exchange-correlations. The k-points in a simple cubic BZ are determined by R (0.5, 0.5, 0.5), {gamma} (0, 0, 0), X (0.5, 0, 0), M (0.5, 0.5, 0) and {gamma} (0, 0, 0). Other directions of k-points are {gamma} (0, 0, 0), X (0.5, 0, 0), R (0.5, 0.5, 0.5) and {gamma} (0, 0, 0). The SO splittings of p states at the {gamma} point in the GGA+SO scheme for {alpha}-Po are 0.04 eV and 0.02 eV while for the {beta}-Po these are 0.03 eV and 0.97 eV. We have also calculated the vibrational spectra for the unit cells in both the structures. We find that exchanging of a Po atom by Pb atom produces several more bands and destabilizes the {beta} phase.
Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics
Makhov, Dmitry V.; Shalashilin, Dmitrii V.; Glover, William J.; Martinez, Todd J.
2014-08-07
We present a new algorithm for ab initio quantum nonadiabatic molecular dynamics that combines the best features of ab initio Multiple Spawning (AIMS) and Multiconfigurational Ehrenfest (MCE) methods. In this new method, ab initio multiple cloning (AIMC), the individual trajectory basis functions (TBFs) follow Ehrenfest equations of motion (as in MCE). However, the basis set is expanded (as in AIMS) when these TBFs become sufficiently mixed, preventing prolonged evolution on an averaged potential energy surface. We refer to the expansion of the basis set as “cloning,” in analogy to the “spawning” procedure in AIMS. This synthesis of AIMS and MCE allows us to leverage the benefits of mean-field evolution during periods of strong nonadiabatic coupling while simultaneously avoiding mean-field artifacts in Ehrenfest dynamics. We explore the use of time-displaced basis sets, “trains,” as a means of expanding the basis set for little cost. We also introduce a new bra-ket averaged Taylor expansion (BAT) to approximate the necessary potential energy and nonadiabatic coupling matrix elements. The BAT approximation avoids the necessity of computing electronic structure information at intermediate points between TBFs, as is usually done in saddle-point approximations used in AIMS. The efficiency of AIMC is demonstrated on the nonradiative decay of the first excited state of ethylene. The AIMC method has been implemented within the AIMS-MOLPRO package, which was extended to include Ehrenfest basis functions.
Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics
NASA Astrophysics Data System (ADS)
Makhov, Dmitry V.; Glover, William J.; Martinez, Todd J.; Shalashilin, Dmitrii V.
2014-08-01
We present a new algorithm for ab initio quantum nonadiabatic molecular dynamics that combines the best features of ab initio Multiple Spawning (AIMS) and Multiconfigurational Ehrenfest (MCE) methods. In this new method, ab initio multiple cloning (AIMC), the individual trajectory basis functions (TBFs) follow Ehrenfest equations of motion (as in MCE). However, the basis set is expanded (as in AIMS) when these TBFs become sufficiently mixed, preventing prolonged evolution on an averaged potential energy surface. We refer to the expansion of the basis set as "cloning," in analogy to the "spawning" procedure in AIMS. This synthesis of AIMS and MCE allows us to leverage the benefits of mean-field evolution during periods of strong nonadiabatic coupling while simultaneously avoiding mean-field artifacts in Ehrenfest dynamics. We explore the use of time-displaced basis sets, "trains," as a means of expanding the basis set for little cost. We also introduce a new bra-ket averaged Taylor expansion (BAT) to approximate the necessary potential energy and nonadiabatic coupling matrix elements. The BAT approximation avoids the necessity of computing electronic structure information at intermediate points between TBFs, as is usually done in saddle-point approximations used in AIMS. The efficiency of AIMC is demonstrated on the nonradiative decay of the first excited state of ethylene. The AIMC method has been implemented within the AIMS-MOLPRO package, which was extended to include Ehrenfest basis functions.
Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics.
Makhov, Dmitry V; Glover, William J; Martinez, Todd J; Shalashilin, Dmitrii V
2014-08-01
We present a new algorithm for ab initio quantum nonadiabatic molecular dynamics that combines the best features of ab initio Multiple Spawning (AIMS) and Multiconfigurational Ehrenfest (MCE) methods. In this new method, ab initio multiple cloning (AIMC), the individual trajectory basis functions (TBFs) follow Ehrenfest equations of motion (as in MCE). However, the basis set is expanded (as in AIMS) when these TBFs become sufficiently mixed, preventing prolonged evolution on an averaged potential energy surface. We refer to the expansion of the basis set as "cloning," in analogy to the "spawning" procedure in AIMS. This synthesis of AIMS and MCE allows us to leverage the benefits of mean-field evolution during periods of strong nonadiabatic coupling while simultaneously avoiding mean-field artifacts in Ehrenfest dynamics. We explore the use of time-displaced basis sets, "trains," as a means of expanding the basis set for little cost. We also introduce a new bra-ket averaged Taylor expansion (BAT) to approximate the necessary potential energy and nonadiabatic coupling matrix elements. The BAT approximation avoids the necessity of computing electronic structure information at intermediate points between TBFs, as is usually done in saddle-point approximations used in AIMS. The efficiency of AIMC is demonstrated on the nonradiative decay of the first excited state of ethylene. The AIMC method has been implemented within the AIMS-MOLPRO package, which was extended to include Ehrenfest basis functions. PMID:25106573
Ab initio Monte Carlo investigation of small lithium clusters.
Srinivas, S.
1999-06-16
Structural and thermal properties of small lithium clusters are studied using ab initio-based Monte Carlo simulations. The ab initio scheme uses a Hartree-Fock/density functional treatment of the electronic structure combined with a jump-walking Monte Carlo sampling of nuclear configurations. Structural forms of Li{sub 8} and Li{sub 9}{sup +} clusters are obtained and their thermal properties analyzed in terms of probability distributions of the cluster potential energy, average potential energy and configurational heat capacity all considered as a function of the cluster temperature. Details of the gradual evolution with temperature of the structural forms sampled are examined. Temperatures characterizing the onset of structural changes and isomer coexistence are identified for both clusters.
Towards AB Initio Calculation of the Circular Dichroism of Peptides
NASA Astrophysics Data System (ADS)
Molteni, E.; Onida, G.; Tiana, G.
2012-08-01
In this work we plan to use ab initio spectroscopy calculations to compute circular dichroism (CD) spectra of peptides. CD provides information on protein secondary structure content; peptides, instead, remain difficult to address, due to their tendency to adopt multiple conformations in equilibrium. Therefore peptides are an interesting test-case for ab initio calculation of CD spectra. As a first application, we focus on the (83-92) fragment of HIV-1 protease, which is known to be involved in the folding and dimerization of this protein. As a preliminary step, we performed classical molecular dynamics (MD) simulations, in order to obtain a set of representative conformers of the peptide. Then, on some of the obtained conformations, we calculated absorption spectra at the independent particle, RPA and TDLDA levels, showing the presence of charge transfer excitations, and their influence on spectral features.
NASA Astrophysics Data System (ADS)
Vincent, E.; Becquart, C. S.; Domain, C.
2007-02-01
The embrittlement of pressure vessel steels under radiation has been long ago correlated with the presence of Cu solutes. Other solutes such as Ni, Mn and Si are now suspected to contribute also to the embrittlement. The interactions of these solutes with radiation induced point defects thus need to be characterized properly in order to understand the elementary mechanisms behind the formation of the clusters formed upon radiation. Ab initio calculations based on the density functional theory have been performed to determine the interactions of point defects with solute atoms in dilute FeX alloys (X = Cu, Mn, Ni or Si) in order to build a database used to parameterise an atomic kinetic Monte Carlo model. Some results of irradiation damage in dilute Fe-CuNiMnSi alloys obtained with this model are presented.
Li, Zi; Li, Chuanying; Wang, Cong; Zhang, Ping; Kang, Wei
2015-11-15
Ultrafast laser experiments on metals usually induce a high electron temperature and a low ion temperature and, thus, an energy relaxation process. The electron heat capacity and electron-phonon coupling factor are crucial thermal quantities to describe this process. We perform ab initio theoretical studies to determine these thermal quantities and their dependence on density and electron temperature for the metals aluminum and beryllium. The heat capacity shows an approximately linear dependence on the temperature, similar to free electron gas, and the compression only slightly affects the capacity. The electron-phonon coupling factor increases with both temperature and density, and the change observed for beryllium is more obvious than that for aluminum. The connections between thermal quantities and electronic/atomic structures are discussed in detail, and the different behaviors of aluminum and beryllium are well explained.
NASA Astrophysics Data System (ADS)
Li, Zi; Wang, Cong; Kang, Wei; Li, Chuanying; Zhang, Ping
2015-11-01
Ultrafast laser experiments on metals usually induce a high electron temperature and a low ion temperature and, thus, an energy relaxation process. The electron heat capacity and electron-phonon coupling factor are crucial thermal quantities to describe this process. We perform ab initio theoretical studies to determine these thermal quantities and their dependence on density and electron temperature for the metals aluminum and beryllium. The heat capacity shows an approximately linear dependence on the temperature, similar to free electron gas, and the compression only slightly affects the capacity. The electron-phonon coupling factor increases with both temperature and density, and the change observed for beryllium is more obvious than that for aluminum. The connections between thermal quantities and electronic/atomic structures are discussed in detail, and the different behaviors of aluminum and beryllium are well explained.
Ab Initio Studies of Calcium Carbonate Hydration.
Lopez-Berganza, Josue A; Diao, Yijue; Pamidighantam, Sudhakar; Espinosa-Marzal, Rosa M
2015-11-25
Ab initio simulations of large hydrated calcium carbonate clusters are challenging due to the existence of multiple local energy minima. Extensive conformational searches around hydrated calcium carbonate clusters (CaCO3·nH2O for n = 1-18) were performed to find low-energy hydration structures using an efficient combination of Monte Carlo searches, density-functional tight binding (DFTB+) method, and density-functional theory (DFT) at the B3LYP level, or Møller-Plesset perturbation theory at the MP2 level. This multilevel optimization yields several low-energy structures for hydrated calcium carbonate. Structural and energetics analysis of the hydration of these clusters revealed a first hydration shell composed of 12 water molecules. Bond-length and charge densities were also determined for different cluster sizes. The solvation of calcium carbonate in bulk water was investigated by placing the explicitly solvated CaCO3·nH2O clusters in a polarizable continuum model (PCM). The findings of this study provide new insights into the energetics and structure of hydrated calcium carbonate and contribute to the understanding of mechanisms where calcium carbonate formation or dissolution is of relevance. PMID:26505205
Wang, Yaocen; Takeuchi, Akira; Makino, Akihiro; Liang, Yunye; Kawazoe, Yoshiyuki
2015-05-07
In the work reported in this paper, ab initio molecular dynamics simulation was performed on Fe{sub 85}Si{sub 2}B{sub 9}P{sub 4} amorphous alloy. Preferred atomic environment of the elements was analyzed with Voronoi polyhedrons. It showed that B and P atoms prefer less neighbors compared with Fe and Si, making them structurally incompatible with Fe rich structure and repulsive to the formation of α-Fe. However, due to the low bonding energy of B and P caused by low coordination number, the diffusion rates of them were considerably large, resulting in the requirement of fast annealing for achieving optimum nano-crystallization for its soft magnetic property. The simulation work also indicates that diffusion rate in amorphous alloy is largely determined by bonding energy rather than atomic size.
Antol, Ivana; Eckert-Maksić, Mirjana; Barbatti, Mario; Lischka, Hans
2007-12-21
The short-time photodynamics (1 ps) of formamide in its low-lying singlet excited n(O)-pi(*) and pi-pi(*) states have been investigated by the direct trajectory surface-hopping method based on multiconfigurational ab initio calculations. The simulations showed that in both states, the primary deactivation process is C-N bond dissociation. In the ground state, the energy is transferred to (a) translational motion of the HCO and NH(2) fragments, (b) additional C-H dissociation from the vibrationally hot HCO fragment, or (c) formation of NH(3) and CO. In addition to the C-N dissociation pathway, C-O bond fission is found to be an additional primary deactivation path in the pi-pi(*) dynamics. From fractional occupations of trajectories, lifetimes of formamide were estimated: tau(S(1))=441 fs and tau(S(2))=66 fs. PMID:18154378
Bylaska, Eric J.; Glass, Kevin A.; Baxter, Douglas J.; Baden, Scott B.; Weare, John H.
2010-09-16
An overview of the parallel algorithms for ab initio molecular dynamics (AIMD) used in the NWChem program package is presented, including recent developments for computing exact exchange. These algorithms make use of a two-dimensional processor geometry proposed by Gygi et al for use in AIMD algorithms. Using this strategy, a highly scalable algorithm for exact exchange has been developed and incorporated it into AIMD. This new algorithm for exact exchange employs an incomplete butterfly to overcome the bottleneck associated with exact exchange term, and it makes judicious use of data replication. Initial testing has shown that this algorithm can scale to over 20,000 CPUs even for modest size simulation.
Jiang, M.; Peng, S. M.; Zhang, H. B.; Xu, C. H.; Xiao, H. Y.; Zhao, F. A.; Liu, Z. J.; Zu, X. T.
2016-01-01
In this study, an ab initio molecular dynamics method is employed to investigate how the existence of stacking faults (SFs) influences the response of SiC to low energy irradiation. It reveals that the C and Si atoms around the SFs are generally more difficult to be displaced than those in unfaulted SiC, and the corresponding threshold displacement energies for them are generally larger, indicative of enhanced radiation tolerance caused by the introduction of SFs, which agrees well with the recent experiment. As compared with the unfaulted state, more localized point defects are generated in faulted SiC. Also, the efficiency of damage production for Si recoils is generally higher than that of C recoils. The calculated potential energy increases for defect generation in SiC with intrinsic and extrinsic SFs are found to be higher than those in unfaulted SiC, due to the stronger screen-Coulomb interaction between the PKA and its neighbors. The presented results provide a fundamental insight into the underlying mechanism of displacement events in faulted SiC and will help to advance the understanding of the radiation response of SiC with and without SFs. PMID:26880027
Ab initio infrared and Raman spectra
NASA Astrophysics Data System (ADS)
Fredkin, Donald R.; Komornicki, Andrew; White, Steven R.; Wilson, Kent R.
1983-06-01
We discuss several ways in which molecular absorption and scattering spectra can be computed ab initio, from the fundamental constants of nature. These methods can be divided into two general categories. In the first, or sequential, type of approach, one first solves the electronic part of the Schrödinger equation in the Born-Oppenheimer approximation, mapping out the potential energy, dipole moment vector (for infrared absorption) and polarizability tensor (for Raman scattering) as functions of nuclear coordinates. Having completed the electronic part of the calculation, one then solves the nuclear part of the problem either classically or quantum mechanically. As an example of the sequential ab initio approach, the infrared and Raman rotational and vibrational-rotational spectral band contours for the water molecule are computed in the simplest rigid rotor, normal mode approximation. Quantum techniques are used to calculate the necessary potential energy, dipole moment, and polarizability information at the equilibrium geometry. A new quick, accurate, and easy to program classical technique involving no reference to Euler angles or special functions is developed to compute the infrared and Raman band contours for any rigid rotor, including asymmetric tops. A second, or simultaneous, type of ab initio approach is suggested for large systems, particularly those for which normal mode analysis is inappropriate, such as liquids, clusters, or floppy molecules. Then the curse of dimensionality prevents mapping out in advance the complete potential, dipole moment, and polarizability functions over the whole space of nuclear positions of all atoms, and a solution in which the electronic and nuclear parts of the Born-Oppenheimer approximation are simultaneously solved is needed. A quantum force classical trajectory (QFCT) molecular dynamic method, based on linear response theory, is described, in which the forces, dipole moment, and polarizability are computed quantum
Ab initio based investigation of interstitial interactions and Snoek relaxation in Nb-O
NASA Astrophysics Data System (ADS)
Dmitriev, V. V.; Blanter, M. S.; Ruban, A. V.; Johansson, B.
2012-02-01
Chemical and strain-induced effective pair interactions of interstitial oxygen atoms in bcc Nb have been determined in supercell first-principles calculations using Vienna ab initio simulation package (VASP). The strain-induced interactions are in reasonable agreement with those obtained earlier within a phenomenological microscopic Krivoglaz-Kanzaki-Khachaturyan model (KKKM). At the same time, the chemical interactions, which have been considered to be small in earlier theoretical considerations, turned out to be dominating at the first several coordination shells. The obtained interactions have been used in calculations of the concentration- and temperature-dependence of the internal friction Snoek peak. The theoretical results are found to be in good agreement with the existing experimental data.
Collective rotation from ab initio theory
NASA Astrophysics Data System (ADS)
Caprio, Mark A.; Maris, Pieter; Vary, James P.
2015-10-01
The challenge of ab initio nuclear theory is to quantitatively predict the complex and highly-correlated behavior of the nuclear many-body system, starting from the underlying internucleon interactions. We may now seek to understand the wealth of nuclear collective phenomena through ab initio approaches. No-core configuration interaction (NCCI) calculations for p-shell nuclei give rise to rotational bands, as evidenced by rotational patterns for excitation energies, electromagnetic moments, and electromagnetic transitions. In this talk, the intrinsic structure of these bands is discussed, and the predicted rotational bands are compared to experiment. Supported by the US DOE under Award Nos. DE-FG02-95ER-40934, DESC0008485 (SciDAC/NUCLEI), and DE-FG02-87ER40371 and the US NSF under Award No. 0904782. Computational resources provided by NERSC (US DOE Contract No. DE-AC02-05CH11231).
Ab initio infrared and Raman spectra
NASA Technical Reports Server (NTRS)
Fredkin, D. R.; White, S. R.; Wilson, K. R.; Komornicki, A.
1983-01-01
It is pointed out that with increased computer power and improved computational techniques, such as the gradients developed in recent years, it is becoming practical to compute spectra ab initio, from the fundamental constants of nature, for systems of increasing complexity. The present investigation has the objective to explore several possible ab initio approaches to spectra, giving particular attention to infrared and nonresonance Raman. Two approaches are discussed. The sequential approach, in which first the electronic part and then later the nuclear part of the Born-Oppenheimer approximation is solved, is appropriate for small systems. The simultaneous approach, in which the electronic and nuclear parts are solved at the same time, is more appropriate for many-atom systems. A review of the newer quantum gradient techniques is provided, and the infrared and Raman spectral band contours for the water molecule are computed.
NASA Astrophysics Data System (ADS)
Thiessen, P. A.; Treder, H.-J.
Jedes initium wird durch experimenta crucis zum eventus. Jedes theoretisch interpretierbare ex-eventu-Resultat führt auf ein neues Initium. Gerade dies ist die gemeinsame Aussage von Atomistik, Quantenmechanik und Relativitätstheorie.Translated AbstractAb initio vel ex eventu. IIEvery initium becomes an eventus by experimenta crucis. Every theoretically interpretable ex-eventu result leads to a new initium. Right this is the joint assertion of atomism, quantum mechanics, and relativity.
Ab initio Bogoliubov coupled cluster theory
NASA Astrophysics Data System (ADS)
Signoracci, Angelo; Hagen, Gaute; Duguet, Thomas
2014-09-01
Coupled cluster (CC) theory has become a standard method in nuclear theory for realistic ab initio calculations of medium mass nuclei, but remains limited by its requirement of a Slater determinant reference state which reasonably approximates the nuclear system of interest. Extensions of the method, such as equation-of-motion CC, permit the calculation of nuclei with one or two nucleons added or removed from a doubly magic core, yet still only a few dozen nuclei are accessible with modern computational restrictions. In order to extend the applicability of ab initio methods to open-shell systems, the superfluid nature of nuclei must be taken into account. By utilizing Bogoliubov algebra and employing spontaneous symmetry breaking with respect to particle number conservation, superfluid systems can be treated by a single reference state. An ab initio theory to include correlations on top of a Bogoliubov reference state has been developed in the guise of standard CC theory. The formalism and first results of this Bogoliubov coupled cluster theory will be presented to demonstrate the applicability of the method.
Entropy of Liquid Water from Ab Initio Molecular Dynamics
NASA Astrophysics Data System (ADS)
Spanu, Leonardo; Zhang, Cui; Galli, Giulia
2012-02-01
The debate on the structural properties of water has been mostly based on the calculation of pair correlation functions. However, the simulation of thermodynamic and spectroscopic quantities may be of great relevance for the characterization of liquid water properties. We have computed the entropy of liquid water using a two-phase thermodynamic model and trajectories generated by ab initio molecular dynamics simulations [1]. In an attempt to better understand the performance of several density functionals in simulating liquid water, we have performed ab initio molecular dynamics using semilocal, hybrid [2] and van der Waals density functionals [3]. We show that in all cases, at the experimental equilibrium density and at temperatures in the vicinity of 300 K, the computed entropies are underestimated, with respect to experiment, and the liquid exhibits a degree of tetrahedral order higher than in experiments. We also discuss computational strategies to simulate spectroscopic properties of water, including infrared and Raman spectra.[4pt] [1] C.Zhang, L.Spanu and G.Galli, J.Phys.Chem. B 2011 (in press)[0pt] [2] C.Zhang, D.Donadio, F.Gygi and G.Galli, J. Chem. Theory Comput. 7, 1443 (2011)[0pt] [3] C.Zhang, J.Wu, G.Galli and F.Gygi, J. Chem. Theory Comput. 7, 3061 (2011)
Ab initio dynamics of the cytochrome P450 hydroxylation reaction
Elenewski, Justin E.; Hackett, John C
2015-01-01
The iron(IV)-oxo porphyrin π-cation radical known as Compound I is the primary oxidant within the cytochromes P450, allowing these enzymes to affect the substrate hydroxylation. In the course of this reaction, a hydrogen atom is abstracted from the substrate to generate hydroxyiron(IV) porphyrin and a substrate-centered radical. The hydroxy radical then rebounds from the iron to the substrate, yielding the hydroxylated product. While Compound I has succumbed to theoretical and spectroscopic characterization, the associated hydroxyiron species is elusive as a consequence of its very short lifetime, for which there are no quantitative estimates. To ascertain the physical mechanism underlying substrate hydroxylation and probe this timescale, ab initio molecular dynamics simulations and free energy calculations are performed for a model of Compound I catalysis. Semiclassical estimates based on these calculations reveal the hydrogen atom abstraction step to be extremely fast, kinetically comparable to enzymes such as carbonic anhydrase. Using an ensemble of ab initio simulations, the resultant hydroxyiron species is found to have a similarly short lifetime, ranging between 300 fs and 3600 fs, putatively depending on the enzyme active site architecture. The addition of tunneling corrections to these rates suggests a strong contribution from nuclear quantum effects, which should accelerate every step of substrate hydroxylation by an order of magnitude. These observations have strong implications for the detection of individual hydroxylation intermediates during P450 catalysis. PMID:25681906