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1

SIMPLE: Software for ab initio reconstruction of heterogeneous single-particles.

The open source software suite SIMPLE: Single-particle IMage Processing Linux Engine provides data analysis methods for single-particle cryo-electron microscopy (cryo-EM). SIMPLE addresses the problem of obtaining 3D reconstructions from 2D projections only, without using an input reference volume for approximating orientations. The SIMPLE reconstruction algorithm is tailored to asymmetrical and structurally heterogeneous single-particles. Its basis is global optimization with the use of Fourier common lines. The advance that enables ab initio reconstruction and heterogeneity analysis is the separation of the tasks of in-plane alignment and projection direction determination via bijective orientation search - a new concept in common lines-based strategies. Bijective orientation search divides the configuration space into two groups of paired parameters that are optimized separately. The first group consists of the rotations and shifts in the plane of the projection; the second group consists of the projection directions and state assignments. In SIMPLE, ab initio reconstruction is feasible because the 3D in-plane alignment is approximated using reference-free 2D rotational alignment. The subsequent common lines-based search hence searches projection directions and states only. Thousands of class averages are analyzed simultaneously in a matter of hours. Novice SIMPLE users get a head start via the well documented front-end. The structured, object-oriented back-end invites advanced users to develop new alignment and reconstruction algorithms. An overview of the package is presented together with benchmarks on simulated data. Executable binaries, source code, and documentation are available at http://simple.stanford.edu. PMID:22902564

Elmlund, Dominika; Elmlund, Hans

2012-12-01

2

AUGUSTUS: ab initio prediction of alternative transcripts

AUGUSTUS is a software tool for gene prediction in eukaryotes based on a Generalized Hidden Markov Model, a probabilistic model of a sequence and its gene structure. Like most existing gene finders, the first version of AUGUSTUS returned one transcript per predicted gene and ignored the phenomenon of alternative splicing. Herein, we present a WWW server for an extended version of AUGUSTUS that is able to predict multiple splice variants. To our knowledge, this is the first ab initio gene find...

Stanke, Mario; Keller, Oliver; Gunduz, Irfan; Hayes, Alec; Waack, Stephan; Morgenstern, Burkhard

2006-01-01

3

Energy Technology Data Exchange (ETDEWEB)

This collection of benchmark timings represents a snapshot of the hardware and software capabilities available for ab initio quantum chemical calculations at Pacific Northwest Laboratory`s Molecular Science Research Center in late 1992 and early 1993. The ``snapshot`` nature of these results should not be underestimated, because of the speed with which both hardware and software are changing. Even during the brief period of this study, we were presented with newer, faster versions of several of the codes. However, the deadline for completing this edition of the benchmarks precluded updating all the relevant entries in the tables. As will be discussed below, a similar situation occurred with the hardware. The timing data included in this report are subject to all the normal failures, omissions, and errors that accompany any human activity. In an attempt to mimic the manner in which calculations are typically performed, we have run the calculations with the maximum number of defaults provided by each program and a near minimum amount of memory. This approach may not produce the fastest performance that a particular code can deliver. It is not known to what extent improved timings could be obtained for each code by varying the run parameters. If sufficient interest exists, it might be possible to compile a second list of timing data corresponding to the fastest observed performance from each application, using an unrestricted set of input parameters. Improvements in I/O might have been possible by fine tuning the Unix kernel, but we resisted the temptation to make changes to the operating system. Due to the large number of possible variations in levels of operating system, compilers, speed of disks and memory, versions of applications, etc., readers of this report may not be able to exactly reproduce the times indicated. Copies of the output files from individual runs are available if questions arise about a particular set of timings.

Feller, D.F.

1993-07-01

4

Ab initio generation of thermal neutron scattering cross sections

International Nuclear Information System (INIS)

Quantum mechanical ab initio (i.e., first principle) methods are applied in generating the thermal neutron scattering cross sections of moderators and reflectors that are of interest in nuclear technology. Specifically, this work focuses on graphite and beryllium. In both cases, the ab initio code VASP and the lattice dynamics code PHONON were used to generate the dispersion relations, and the phonon frequency distributions (density of states). This information was then utilized in the LEAPR module of the NJOY code to calculate the thermal neutron scattering cross sections at various temperatures. The use of the ab initio approach represents a major departure from previously applied methods, which depended mainly on fitting simpler dynamical models to experimental data to arrive at the phonon frequency distributions. In this case, much more complicated models of the atomic system of interest can be set up, which allows the establishment of a more complete dynamical matrix. As opposed to the semi-empirical methods used previously, this method represents a fundamental and predictive approach for estimating materials' properties including ones that are of interest in nuclear reactor design. (authors)

5

Ab initio potential for solids

A total-energy theory for a solid is presented. It is based on density-functional theory and consists of a succession of approximations. At the most accurate level, the theory consists of a systematic derivation of an ansatz for the electron density which is best suited for the Harris functional. At the most approximate level, the theory is equivalent to the usual effective-medium theory. At all levels of approximation, every term in the total-energy expression is calculated ab initio, that i...

Chetty, N.; Stokbro, Kurt; Jacobsen, Karsten Wedel; Nørskov, Jens Kehlet

2009-01-01

6

A symmetry-general approach for the least-squares, therefore precise, extraction of elastic coefficients for strained materials is reported. It analyzes stresses calculated ab initio for properly selected strains. The problem, its implementation, and its solution strategy all differ radically from a previous energy-strain approach that we published last year, but the normal equations turn out to be amenable to the same constrainment scheme that makes both approaches symmetry general. The symmetry considerations governing the automated selection of appropriately strained models and their Cartesian systems are detailed. The extension to materials under general stress is discussed and implemented. VASP was used for ab initio calculation of stresses. A comprehensive range of examples includes a triclinic material (kyanite) and simple materials with a range of symmetries at zero pressure, MgO under hydrostatic pressure, Ti4As3 under [001] uniaxial strain, and Si under [001] uniaxial stress. The MgO case agrees with recent experimental work including elastic coefficients as well as their first and second derivatives. The curves of elastic coefficients for Si show a gradual increase in the 33 compliance coefficient, leading to a collapse of the material at -11.7 GPa, compared with -12.0 GPa experimentally. Interpretation of results for Be using two approximations [local density (LDA), generalized gradient (GGA)], two approaches (stress strain and energy strain), two potential types (projector augmented wave and ultrasoft), and two quantum engines (VASP and ORESTES) expose the utmost importance of the cell data used for the elastic calculations and the lesser importance of the other factors. For stiffness at relaxed cell data, differences are shown to originate mostly in the considerable overestimation of the residual compressive stresses at x-ray cell data by LDA, resulting in a smaller relaxed cell, thus larger values for diagonal stiffness coefficients. The symmetry generality of the approach described here enabled the creation of a robust user interface going seamlessly from the database search to the printout of the elastic coefficients. With it, even nonspecialist users can reliably produce technologically relevant results like those discussed here in a simple point-and-click fashion from corresponding entries in the CRYSTMET® and ICSD® structure databases, i.e., for all pure-phase nonorganic materials with known crystal structure. The case of Ti4As3 exposes, on a first cluster of properties, stiffness, compliance, and the isotropic properties that can be derived from them, the current reality of mining crystal structure databases with ab initio software for technological properties that were never measured before. Further developments in that direction are currently underway.

Le Page, Yvon; Saxe, Paul

2002-03-01

7

International Nuclear Information System (INIS)

Formation energies of defects were estimated from an ab initio calculation for uranium dioxide with different valences of the fission products. The VASP (Vienna Ab initio Simulation Package) was used in this study, which is based on a density function theory (DFT) to express the total energy with the density of electrons. One uranium element was replaced with an element of the fission products to calculate the oxygen and uranium defection energy. Additionally, the formation energy of the Schottky defects (two oxygen vacancies and one uranium vacancy) was obtained. This data will be very useful to estimate a diffusion mechanism of fission gases in a nuclear fuel

8

Ab initio potential for solids

DEFF Research Database (Denmark)

A total-energy theory for a solid is presented. It is based on density-functional theory and consists of a succession of approximations. At the most accurate level, the theory consists of a systematic derivation of an ansatz for the electron density which is best suited for the Harris functional. At the most approximate level, the theory is equivalent to the usual effective-medium theory. At all levels of approximation, every term in the total-energy expression is calculated ab initio, that is, without any fitting to experiment or to other calculations. Every step in the approximation procedure can thus be tested independently. The theory is applied to calculations of the surface energies and vacancy formation energy of Al. At the most accurate level, the theory gives results that are in almost complete agreement with self-consistent calculations. At the more approximate, but also computationally much less demanding, level, the theory gives results that are still in excellent agreement with the self-consistent results.

Chetty, N.; Stokbro, Kurt

1992-01-01

9

International Nuclear Information System (INIS)

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 6s26p4 (Z = 84). The low temperature ?-phase transforms into the rhombohedral (trigonal) ? structure at ?348 K. The sc ?-Po unit cell constant is a = 3.345 A. The beta form of polonium (?-Po) has the lattice parameters, aR = 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), ? (0, 0, 0), X (0.5, 0, 0), M (0.5, 0.5, 0) and ? (0, 0, 0). Other directions of k-points are ? (0, 0, 0), X (0.5, 0, 0), R (0.5, 0.5, 0.5) and ? (0, 0, 0). The SO splittings of p states at the ? point in the GGA+SO scheme for ?-Po are 0.04 eV and 0.02 eV while for the ?-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 ? phase

10

Ab initio simulation in extreme conditions

Directory of Open Access Journals (Sweden)

Full Text Available The study of materials properties under extreme conditions has made considerable progress over the past decade as a result of improvements in experimental techniques and advanced modeling methods. The availability of accurate models is crucial for analyzing results obtained in extreme conditions of pressure and temperature, where experimental data can be scarce. Among theoretical models, ab initio simulations are playing an increasingly important role because of their ability to predict materials properties without the need for any experimental input. Ab initio simulations also allow the exploration of materials properties in conditions that are unachievable using controlled experiments – such as, for example, the conditions prevailing in the cores of large planets. In that limit, they constitute the only quantitative model of condensed matter available today. We review the current status of ab initio simulations and discuss examples of recent applications in which numerical simulations have provided an essential complement to experimental data.

François Gygi

2005-11-01

11

Ab initio valence calculations in chemistry

Ab Initio Valence Calculations in Chemistry describes the theory and practice of ab initio valence calculations in chemistry and applies the ideas to a specific example, linear BeH2. Topics covered include the Schrödinger equation and the orbital approximation to atomic orbitals; molecular orbital and valence bond methods; practical molecular wave functions; and molecular integrals. Open shell systems, molecular symmetry, and localized descriptions of electronic structure are also discussed. This book is comprised of 13 chapters and begins by introducing the reader to the use of the Schrödinge

Cook, D B

1974-01-01

12

Accelerating Ab Initio Nuclear Physics Calculations with GPUs

This paper describes some applications of GPU acceleration in ab initio nuclear structure calculations. Specifically, we discuss GPU acceleration of the software package MFDn, a parallel nuclear structure eigensolver. We modify the matrix construction stage to run partly on the GPU. On the Titan supercomputer at the Oak Ridge Leadership Computing Facility, this produces a speedup of approximately 2.2x - 2.7x for the matrix construction stage and 1.2x - 1.4x for the entire run.

Potter, Hugh; Maris, Pieter; Sosonkina, Masha; Vary, James; Binder, Sven; Calci, Angelo; Langhammer, Joachim; Roth, Robert; Çatalyürek, Ümit; Saule, Erik

2014-01-01

13

Ab initio approach of the zircaloy-4 oxidation process

International Nuclear Information System (INIS)

This thesis is linked to the study of fuel cladding corrosion in Pressurized Water Reactors. Despite all the alloys which could be used as fuel cells, we focused on Zircaloy-4 where alloying elements like iron and chromium, insolubles in the zirconium matrice, precipitate in the intermetallic form. The aim of our work is to justified, on a theoretical point of view, the role of iron concentration redistributed in the metal as in the oxide on the oxidation process of the fuel claddings under irradiation. Our approach relies on electronic structure calculations based on the density functional theory and more specifically on the pseudopotentials technique. We use the code VASP (Vienna Ab initio Simulation Package) developed by G. Kresse and J. Hafner at the Institut for Materials Physics of Vienna University. After a quick stage designed to validate our computational approach, we study the early stages of zirconium ? (0001) surface. Performing both static and dynamic calculations, we are able to show that there is one reaction channel which can explained the dissociation of an oxygen molecule on this surface and the incorporation of one of the two oxygen atoms under the metal surface. At least, we used VASP to tackle the technological problem which has motivated this thesis. We first conclude that substoichiometry can explain the stabilisation of the high temperature phases of zirconia (tetragonal and cubic structures), this stabilisation is more evident in the case wheilisation is more evident in the case where oxygen vacancies are doubly charged (this corresponds to extract an O2- ion to the ZrO2 crystal). The second conclusion is that doping zirconia with iron could not lead to the stabilisation of the tetragonal or cubic structures directly. But as iron enhances the formation of oxygen vacancies (which have been shown to have a stabilizing effect) it can indirectly contribute to stabilize these two high temperature polymorphs. (author)

14

Using \\textit{ab initio} calculation, we investigate systematically the structural and electronic properties of Ni$_{2}$Nb$_{1+x}$Sn$_{1-x}$ ($x$ = 0, 0.25, 0.50). Here, projector augmented wave approach (PAW) implemented in the Vienna \\textit{ab initio} simulation package (VASP) within generalized gradient approximation (GGA) for the exchange-correlation functional has been used. In this article, it is reported that though Ni$_{2}$NbSn and Ni$_{2}$Nb$_{1.25}$Sn$_{0.75}$ hav...

Pal, Soumyadipta

2012-01-01

15

Modeling Brown Dwarfs using ab initio equation of state data

We present wide-range equations of state (EOS) for hydrogen and helium including accurate data derived from finite-temperature density functional theory molecular dynamics (FT-DFT-MD) simulations for the warm dense matter regime using the VASP package [1]. This hydrogen/helium Rostock EOS (H/He-REOS) cover a wide range of temperatures and densities with a maximum error of 5%. Based on this ab initio data set we calculate interior models and mass-radius (MR) relations for Giant Planets and particularly for Brown Dwarfs. The latter need EOS data for the 1 bar level (? - 10-5g/cm3, T - 1000 K) as well as for central conditions with - 150 Gbar (? - 250g/cm3, T - 3 MK). We compare our interior models and the MR relations with those based on the Saumon-Chabrier-van Horn (SCvH) EOS [2]. [1] G. Kresse and J. Furthmüller, Phys. Rev. B 54, 11169 (1996) [2] D. Saumon, G. Chabrier, and H. M. van Horn, Astrophys. J. Suppl. Ser. 99, 713 (1995)

Becker, Andreas; Lorenzen, Winfried; Nettelmann, Nadine; Redmer, Ronald

2013-07-01

16

Macromolecular ab initio phasing enforcing secondary and tertiary structure

Directory of Open Access Journals (Sweden)

Full Text Available Ab initio phasing of macromolecular structures, from the native intensities alone with no experimental phase information or previous particular structural knowledge, has been the object of a long quest, limited by two main barriers: structure size and resolution of the data. Current approaches to extend the scope of ab initio phasing include use of the Patterson function, density modification and data extrapolation. The authors' approach relies on the combination of locating model fragments such as polyalanine ?-helices with the program PHASER and density modification with the program SHELXE. Given the difficulties in discriminating correct small substructures, many putative groups of fragments have to be tested in parallel; thus calculations are performed in a grid or supercomputer. The method has been named after the Italian painter Arcimboldo, who used to compose portraits out of fruit and vegetables. With ARCIMBOLDO, most collections of fragments remain a `still-life', but some are correct enough for density modification and main-chain tracing to reveal the protein's true portrait. Beyond ?-helices, other fragments can be exploited in an analogous way: libraries of helices with modelled side chains, ?-strands, predictable fragments such as DNA-binding folds or fragments selected from distant homologues up to libraries of small local folds that are used to enforce nonspecific tertiary structure; thus restoring the ab initio nature of the method. Using these methods, a number of unknown macromolecules with a few thousand atoms and resolutions around 2?Å have been solved. In the 2014 release, use of the program has been simplified. The software mediates the use of massive computing to automate the grid access required in difficult cases but may also run on a single multicore workstation (http://chango.ibmb.csic.es/ARCIMBOLDO_LITE to solve straightforward cases.

Claudia Millán

2015-01-01

17

Macromolecular ab initio phasing enforcing secondary and tertiary structure

Ab initio phasing of macromolecular structures, from the native intensities alone with no experimental phase information or previous particular structural knowledge, has been the object of a long quest, limited by two main barriers: structure size and resolution of the data. Current approaches to extend the scope of ab initio phasing include use of the Patterson function, density modification and data extrapolation. The authors’ approach relies on the combination of locating model fragments such as polyalanine ?-helices with the program PHASER and density modification with the program SHELXE. Given the difficulties in discriminating correct small substructures, many putative groups of fragments have to be tested in parallel; thus calculations are performed in a grid or supercomputer. The method has been named after the Italian painter Arcimboldo, who used to compose portraits out of fruit and vegetables. With ARCIMBOLDO, most collections of fragments remain a ‘still-life’, but some are correct enough for density modification and main-chain tracing to reveal the protein’s true portrait. Beyond ?-helices, other fragments can be exploited in an analogous way: libraries of helices with modelled side chains, ?-strands, predictable fragments such as DNA-binding folds or fragments selected from distant homologues up to libraries of small local folds that are used to enforce nonspecific tertiary structure; thus restoring the ab initio nature of the method. Using these methods, a number of unknown macromolecules with a few thousand atoms and resolutions around 2?Å have been solved. In the 2014 release, use of the program has been simplified. The software mediates the use of massive computing to automate the grid access required in difficult cases but may also run on a single multicore workstation (http://chango.ibmb.csic.es/ARCIMBOLDO_LITE) to solve straightforward cases. PMID:25610631

Millán, Claudia; Sammito, Massimo; Usón, Isabel

2015-01-01

18

Materials Design from ab initio Calculations

This thesis presents a theoretical study of bulk materials using ab initio methods based on the density functional theory (DFT). Crystallographic structural phase transformations and phase stability for 5f-dioxides, ABO3 perovskites, and ABO4 compounds have been extensively studied. Different approaches such as static total energy calculations, elastic stability and dynamical stability (phonon calculations) criteria have been used to determine the phase stability. As a special case, the latti...

Li, Sa

2004-01-01

19

Ab initio conformational study of caffeic acid

A complete conformational analysis of caffeic acid, a phenolic derivative with well known antioxidant properties, was carried out by ab initio calculations, at the density funtional theory (DFT) level. Fourteen different conformers were obtained, the most stable ones being planar, as the conformational preferences of this molecule were found to be mainly determined by the stabilising effect of [pi]-electron delocalisation. Harmonic vibrational frequencies, as well as potential energy profiles...

Vanbesien, E.; Marques, M. P. M.

2003-01-01

20

Operator evolution for ab initio nuclear theory

The past two decades have seen a revolution in ab initio calculations of nuclear properties. One key element has been the development of a rigorous effective interaction theory, applying unitary transformations to soften the nuclear Hamiltonian and hence accelerate the convergence as a function of the model space size. For consistency, however, one ought to apply the same transformation to other operators when calculating transitions and mean values from the eigenstates of t...

Schuster, Micah D.; Quaglioni, Sofia; Johnson, Calvin W.; Jurgenson, Eric D.; Navratil, Petr

2014-01-01

21

Ab initio energetics of nonsubstituted monocyclic pyrones

International Nuclear Information System (INIS)

The monocyclic nonsubstituted pyrones were studied computationally using state-of-the-art ab initio composite computational techniques. Combination of the accurate energies so obtained with conveniently chosen isodesmic or homodesmotic chemical reactions lead to very confident predictions of their corresponding standard enthalpy of formation. The internal consistency of the results obtained from a vast number of independent chemical schemes serves as a further support of the quality of our results, which are thus proposed to establish the energetics of ?-pyrone and ?-pyrone.

22

Ab initio energetics of nonsubstituted monocyclic pyrones

Energy Technology Data Exchange (ETDEWEB)

The monocyclic nonsubstituted pyrones were studied computationally using state-of-the-art ab initio composite computational techniques. Combination of the accurate energies so obtained with conveniently chosen isodesmic or homodesmotic chemical reactions lead to very confident predictions of their corresponding standard enthalpy of formation. The internal consistency of the results obtained from a vast number of independent chemical schemes serves as a further support of the quality of our results, which are thus proposed to establish the energetics of {alpha}-pyrone and {gamma}-pyrone.

Morais, Victor M.F., E-mail: vmmorais@icbas.up.p [Instituto de Ciencias Biomedicas Abel Salazar, ICBAS, Universidade do Porto, P-4099-003 Porto (Portugal); Centro de Investigacao em Quimica, Departamento de Quimica, Faculdade de Ciencias da Universidade do Porto, Rua do Campo Alegre, 687, P-4169-007 Porto (Portugal)

2011-01-15

23

Ab initio structure solution by charge flipping

In this paper we present an extremely simple structure solution method termed charge flipping. It works ab initio on high resolution x-ray diffraction data in the manner of Fourier recycling. The real space modification simply changes the sign of charge density below a threshold, while in reciprocal space the modification is the Fobs map without any weighting. We test the algorithm using synthetic data for a wide range of structures, analyse the solution statistics and check the quality of reconstruction. Finally, we reconsider mathematical aspects of the algorithm in detail, showing that in this chaotic iteration process the solution is a limit cycle and not a fixed point.

Oszlanyi, G; Oszlanyi, Gabor; Suto, Andras

2003-01-01

24

Ab initio non-relativistic spin dynamics

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.

Ding, Feizhi; Goings, Joshua J.; Frisch, Michael J.; Li, Xiaosong

2014-12-01

25

Ab initio non-relativistic spin dynamics.

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. PMID:25481133

Ding, Feizhi; Goings, Joshua J; Frisch, Michael J; Li, Xiaosong

2014-12-01

26

Coupling of DFT- and ab-initio methods

Im Rahmen der Doktorarbeit wurde untersucht, inwieweit die Kopplung von Dichtefunktionalmethoden und ab-initio-Korrelationsmethoden der Quantenchemie eine Verbesserung bezüglich beider Grenzmethoden erbringt. Die Kopplung erfolgt durch eine Aufspaltung des interelektronischen Hamiltonoperators (abstoßende Coulombwechselwirkung). Die kurzreichweitige Wechselwirkung wird mit Dichtefunktionaltheorie behandelt, die langreichweitige mit Hilfe von ab-initio-Methoden. Diese Aufteilung soll dazu di...

Goll, Erich

2008-01-01

27

International Nuclear Information System (INIS)

An optimal integration of modern computational tools and efficient experimentation is presented for the accelerated design of Nb-based superalloys. Integrated within a systems engineering framework, we have used ab initio methods along with alloy theory tools to predict phase stability of solid solutions and intermetallics to accelerate assessment of thermodynamic and kinetic databases enabling comprehensive predictive design of multicomponent multiphase microstructures as dynamic systems. Such an approach is also applicable for the accelerated design and development of other high performance materials. Based on established principles underlying Ni-based superalloys, the central microstructural concept is a precipitation strengthened system in which coherent cubic aluminide phase(s) provide both creep strengthening and a source of Al for Al2O3 passivation enabled by a Nb-based alloy matrix with required ductile-to-brittle transition temperature, atomic transport kinetics and oxygen solubility behaviors. Ultrasoft and PAW pseudopotentials, as implemented in VASP, are used to calculate total energy, density of states and bonding charge densities of aluminides with B2 and L21 structures relevant to this research. Characterization of prototype alloys by transmission and analytical electron microscopy demonstrates the precipitation of B2 or L21 aluminide in a (Nb) matrix. Employing Thermo-Calc and DICTRA software systems, thermod-Calc and DICTRA software systems, thermodynamic and kinetic databases are developed for substitutional alloying elements and interstitial oxygen to enhance the diffusivity ratio of Al to O for promotion of Al2O3 passivation. However, the oxidation study of a Nb-Hf-Al alloy, with enhanced solubility of Al in (Nb) than in binary Nb-Al alloys, at 1300 deg. C shows the presence of a mixed oxide layer of NbAlO4 and HfO2 exhibiting parabolic growth

28

Discovering chemistry with an ab initio nanoreactor

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.

Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; Liu, Fang; Pande, Vijay S.; Martínez, Todd J.

2014-12-01

29

Operator evolution for ab initio nuclear theory

The past two decades have seen a revolution in ab initio calculations of nuclear properties. One key element has been the development of a rigorous effective interaction theory, applying unitary transformations to soften the nuclear Hamiltonian and hence accelerate the convergence as a function of the model space size. For consistency, however, one ought to apply the same transformation to other operators when calculating transitions and mean values from the eigenstates of the renormalized Hamiltonian. Working in a translationally-invariant harmonic oscillator basis for the two- and three-nucleon systems, we evolve the Hamiltonian, square-radius and total dipole strength operators by the similarity renormalization group (SRG). The inclusion of up to three-body matrix elements in the 4He nucleus all but completely restores the invariance of the expectation values under the transformation. We also consider a Gaussian operator with adjustable range and find at short ranges an increased contribution from such ind...

Schuster, Micah D; Johnson, Calvin W; Jurgenson, Eric D; Navratil, Petr

2014-01-01

30

Ab Initio Description of p -Shell Hypernuclei

We present the first ab initio calculations for p -shell single-? hypernuclei. For the solution of the many-baryon problem, we develop two variants of the no-core shell model with explicit ? and ?+,?0,?- hyperons including ? -? conversion, optionally supplemented by a similarity renormalization group transformation to accelerate model-space convergence. In addition to state-of-the-art chiral two- and three-nucleon interactions, we use leading-order chiral hyperon-nucleon interactions and a recent meson-exchange hyperon-nucleon interaction. We validate the approach for s -shell hypernuclei and apply it to p -shell hypernuclei, in particular to Li7? , Be9? , and C13? . We show that the chiral hyperon-nucleon interactions provide ground-state and excitation energies that generally agree with experiment within the cutoff dependence. At the same time we demonstrate that hypernuclear spectroscopy provides tight constraints on the hyperon-nucleon interactions.

Wirth, Roland; Gazda, Daniel; Navrátil, Petr; Calci, Angelo; Langhammer, Joachim; Roth, Robert

2014-11-01

31

Ab-initio nanoplasmonics: atoms matter

We present an ab-initio study of the hybridization of localized surface plasmons in a metal nanoparticle dimer. The atomic structure, which is often neglected in theoretical studies of quantum nanoplasmonics, has a strong impact on the optical absorption properties when sub-nanometric gaps between the nanoparticles are considered. We demonstrate that this influences the hybridization of optical resonances of the dimer, and leads to significantly smaller electric field enhancements as compared to the standard jellium model. In addition we show that the corrugation of the metal surface at a microscopic scale becomes as important as other well-known quantum corrections to the plasmonic response, implying that the atomic structure has to be taken into account to obtain quantitative predictions for realistic nanoplasmonic devices.

Zhang, Pu; Rubio, Angel; Garcia-Gonzalez, Pablo; Garcia-Vidal, F J

2014-01-01

32

Ab initio determination of light hadron masses.

More than 99% of the mass of the visible universe is made up of protons and neutrons. Both particles are much heavier than their quark and gluon constituents, and the Standard Model of particle physics should explain this difference. We present a full ab initio calculation of the masses of protons, neutrons, and other light hadrons, using lattice quantum chromodynamics. Pion masses down to 190 mega-electron volts are used to extrapolate to the physical point, with lattice sizes of approximately four times the inverse pion mass. Three lattice spacings are used for a continuum extrapolation. Our results completely agree with experimental observations and represent a quantitative confirmation of this aspect of the Standard Model with fully controlled uncertainties. PMID:19023076

Dürr, S; Fodor, Z; Frison, J; Hoelbling, C; Hoffmann, R; Katz, S D; Krieg, S; Kurth, T; Lellouch, L; Lippert, T; Szabo, K K; Vulvert, G

2008-11-21

33

Ab Initio Modeling of Molecular Radiation

Radiative emission from excited states of atoms and molecules can comprise a significant fraction of the total heat flux experienced by spacecraft during atmospheric entry at hypersonic speeds. For spacecraft with ablating heat shields, some of this radiative flux can be absorbed by molecular constituents in the boundary layer that are formed by the ablation process. Ab initio quantum mechanical calculations are carried out to predict the strengths of these emission and absorption processes. This talk will describe the methods used in these calculations using, as examples, the 4th positive emission bands of CO and the 1g+ 1u+ absorption in C3. The results of these calculations are being used as input to NASA radiation modeling codes like NeqAir, HARA and HyperRad.

Jaffe, Richard; Schwenke, David

2014-01-01

34

Reconstructions of Ir (110) and (100) an ab initio study

Prediction criteria for surface reconstructions are discussed, with reference to ab initio calculations of the (110)-$1\\times 2$ missing-row and (100)-$5\\times 1$ quasi-hexagonal reconstructions of Ir and Rh.

Filippetti, A; Filippetti, Alessio; Fiorentini, Vincenzo

1996-01-01

35

Reconstructions of Ir (110) and (100): an ab initio study

Prediction criteria for surface reconstructions are discussed, with reference to ab initio calculations of the (110)-$1\\times 2$ missing-row and (100)-$5\\times 1$ quasi-hexagonal reconstructions of Ir and Rh.

Filippetti, Alessio; Fiorentini, Vincenzo

1996-01-01

36

Ab initio Lattice Dynamics : Hydrogen-dense and Other Materials

This thesis presents a theoretical study of materials under high pressure using ab initio lattice dynamics based on density functional theory and density functional perturbation theory using both super-cell and linear response approach. Ab initio lattice dynamics using super-cell approach is applied to compare our theoretical predictions with experimental findings. Phonon dispersion curves of fcc ?-? cerium are calculated and compared with inelastic X-ray scattering data. Pressure dependenc...

Kim, Duck Young

2009-01-01

37

Ab Initio Protein Structure Prediction Using Chunk-TASSER

We have developed an ab initio protein structure prediction method called chunk-TASSER that uses ab initio folded supersecondary structure chunks of a given target as well as threading templates for obtaining contact potentials and distance restraints. The predicted chunks, selected on the basis of a new fragment comparison method, are folded by a fragment insertion method. Full-length models are built and refined by the TASSER methodology, which searches conformational space via parallel hyp...

Zhou, Hongyi; Skolnick, Jeffrey

2007-01-01

38

Ab initio atomistic simulation of metals and multicomponent alloys

Ab initio theory provides a powerful tool to understand and predict the behavior of materials. This thesis contains both of these aspects. First we use ab initio alloy theory to investigate a new kind of complex alloy (high-entropy alloy). Second we introduce a novel potential (interlayer potential), which can be extracted from ab inito total energy calculations using the Chen-Möbius inversion method. High-entropy alloys (HEAs) are composed of four or more metallic elements with nearly equim...

Tian, Fuyang

2013-01-01

39

Ab initio molecular crystal structures, spectra, and phase diagrams.

Conspectus Molecular crystals are chemists' solids in the sense that their structures and properties can be understood in terms of those of the constituent molecules merely perturbed by a crystalline environment. They form a large and important class of solids including ices of atmospheric species, drugs, explosives, and even some organic optoelectronic materials and supramolecular assemblies. Recently, surprisingly simple yet extremely efficient, versatile, easily implemented, and systematically accurate electronic structure methods for molecular crystals have been developed. The methods, collectively referred to as the embedded-fragment scheme, divide a crystal into monomers and overlapping dimers and apply modern molecular electronic structure methods and software to these fragments of the crystal that are embedded in a self-consistently determined crystalline electrostatic field. They enable facile applications of accurate but otherwise prohibitively expensive ab initio molecular orbital theories such as Møller-Plesset perturbation and coupled-cluster theories to a broad range of properties of solids such as internal energies, enthalpies, structures, equation of state, phonon dispersion curves and density of states, infrared and Raman spectra (including band intensities and sometimes anharmonic effects), inelastic neutron scattering spectra, heat capacities, Gibbs energies, and phase diagrams, while accounting for many-body electrostatic (namely, induction or polarization) effects as well as two-body exchange and dispersion interactions from first principles. They can fundamentally alter the role of computing in the studies of molecular crystals in the same way ab initio molecular orbital theories have transformed research practices in gas-phase physical chemistry and synthetic chemistry in the last half century. In this Account, after a brief summary of formalisms and algorithms, we discuss applications of these methods performed in our group as compelling illustrations of their unprecedented power in addressing some of the outstanding problems of solid-state chemistry, high-pressure chemistry, or geochemistry. They are the structure and spectra of ice Ih, in particular, the origin of two peaks in the hydrogen-bond-stretching region of its inelastic neutron scattering spectra, a solid-solid phase transition from CO2-I to elusive, metastable CO2-III, pressure tuning of Fermi resonance in solid CO2, and the structure and spectra of solid formic acid, all at the level of second-order Møller-Plesset perturbation theory or higher. PMID:24754304

Hirata, So; Gilliard, Kandis; He, Xiao; Li, Jinjin; Sode, Olaseni

2014-09-16

40

Why ferroelectricity? synchrotron radiation and ab initio answers

Directory of Open Access Journals (Sweden)

Full Text Available Una pregunta hist´orica de la f´?sica del estado s´olido est´a encontrando respuesta en nuestros tiempos: la explicaci´on a nivel at´omico del origen de la ferroelectricidad. Las ideas tradicionales sobre fen´omenos ferroel´ectricos se relacionan con el ?ablandamiento? de los fonones en el origen de la zona de Brillouin y con funciones en forma de ?W? para la energ´?a libre de Landau. Las contribuciones experimentales (radiaci´on sincrotr´onica, neutrones y te´oricas (Cohen, Resta, Spaldin de la ´ultima d´ecada han esclarecido aspectos del comportamiento at´omico que conducen a la polarizaci´on espont´anea en estructuras perovskitas y asociadas. Se presenta el trabajo desarrollado por nuestro grupo interdisciplinario. Se obtienen fases ferroel´ectricas perovskitas y Aurivillius por diferentes m´etodos. Se investigan detalles finos de las estructuras cristalinas mediante radiaci´on sincrotr´onica en el Laboratorio de Radiaci´on Sincrotr´onica de Stanford. Las estructuras electr´onicas de las fases consideradas se caracterizan por m´etodos ab initio. Los experimentos de difracci´on en alta resoluci´on demuestran ruptura de simetr´?a en un n´umero de sistemas perovskita y Aurivillius. Se discute la relaci ´on estructura-simetr´?a- polarizaci´on. Se presenta una explicaci´on ab initio de la polarizaci´on ferroel´ectrica en perovskitas. La energ´?a del sistema se calcula mediante el c´odigo CASTEP bajo un funcional GGA. La optimizaci´on de la energ´?a conduce a la ruptura de simetr´?a c´ubica, con desplazamiento del cati´on Ti fuera del centro, v´?a una transformaci´on Jahn-Teller de segundo orden. La estructura electr´onica se investiga mediante el software BandLab, bajo un funcional LDA, con el m´etodo LMTO. La causa de la deformaci´on de la perovskita es la degeneraci´on de los orbitales Ti 3d z2 y Ti 3d (x2+y2.

R. Olivera

2007-01-01

41

Skutterudites under pressure: An ab initio study

International Nuclear Information System (INIS)

Ab initio results on the band structure, density of states, and Fermi surface (FS) properties of LaRu4X12 (X?=?P, As, Sb) are presented at ambient pressure as well as under compression. The analysis of density of states reveals the major contribution at the Fermi level to be mainly from the Ru-d and X-p states. We have a complicated Fermi surface with both electron and hole characters for all the three compounds which is derived mainly from the Ru-d and X-p states. There is also a simpler FS with hole character derived from the P-pz orbital for LaRu4P12 and Ru-dz2 orbital in the case of As and Sb containing compounds. More interestingly, Fermi surface nesting feature is observed only in the case of the LaRu4P12. Under compression, we observe the topology of the complicated FS sheet of LaRu4As12 to change around V/V0?=?0.85, leading to a behaviour similar to that of a multiband superconductor, and in addition, we have two more hole pockets centered around ? at V/V0?=?0.8 for the same compound. Apart from this, we find the hole pocket to vanish at V/V0?=?0.8 in the case of LaRu4Sb12 and the opening of the complicated FS sheet gets reduced. The de Haas van Alphen calculation shows the number of extremal orbits in the complicated sheet to change in As and Sb containing compounds under compression, where we also observe the FS topology to change

42

THERMODYNAMICS OF MATERIALS: FROM AB INITIO TO PHENOMENOLOGY

Energy Technology Data Exchange (ETDEWEB)

Quantum mechanical-based (or ab initio) methods are used to predict the stability properties of materials although their application is limited to relatively simple systems in terms of structures and number of alloy components. However thermodynamics of complex multi-component alloys requires a more versatile approach afforded within the CALPHAD formalism. Despite its success, the lack of experimental data very often prevents the design of robust thermodynamic databases. After a brief survey of ab initio methodologies and CALPHAD, it will be shown how ab initio electronic structure methods can supplement in two ways CALPHAD for subsequent applications. 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. Finally, comments will be made on challenges and future prospects.

Turchi, P A

2004-09-24

43

Ab Initio Studies of Stratospheric Ozone Depletion Chemistry

An overview of the current understanding of ozone depletion chemistry, particularly with regards the formation of the so-called Antarctic ozone hole, will be presented together with an outline as to how ab initio quantum chemistry can be used to further our understanding of stratospheric chemistry. The ability of modern state-of-the art ab initio quantum chemical techniques to characterize reliably the gas-phase molecular structure, vibrational spectrum, electronic spectrum, and thermal stability of fluorine, chlorine, bromine and nitrogen oxide species will be demonstrated by presentation of some example studies. The ab initio results will be shown to be in excellent agreement with the available experimental data, and where the experimental data are either not known or are inconclusive, the theoretical results are shown to fill in the gaps and to resolve experimental controversies. In addition, ab initio studies in which the electronic spectra and the characterization of excited electronic states of halogen oxide species will also be presented. Again where available, the ab initio results are compared to experimental observations, and are used to aid in the interpretation of experimental studies.

Lee, Timothy J.; Head-Gordon, Martin; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

44

Energy Technology Data Exchange (ETDEWEB)

A long-standing goal of nuclear theory is to determine the properties of atomic nuclei based on the fundamental interactions among the protons and neutrons (i.e., nucleons). By adopting nucleon-nucleon (NN), three-nucleon (NNN) and higher-nucleon interactions determined from either meson-exchange theory or QCD, with couplings fixed by few-body systems, we preserve the predictive power of nuclear theory. This foundation enables tests of nature's fundamental symmetries and offers new vistas for the full range of complex nuclear phenomena. Basic questions that drive our quest for a microscopic predictive theory of nuclear phenomena include: (1) What controls nuclear saturation; (2) How the nuclear shell model emerges from the underlying theory; (3) What are the properties of nuclei with extreme neutron/proton ratios; (4) Can we predict useful cross sections that cannot be measured; (5) Can nuclei provide precision tests of the fundamental laws of nature; and (6) Under what conditions do we need QCD to describe nuclear structure, among others. Along with other ab initio nuclear theory groups, we have pursued these questions with meson-theoretical NN interactions, such as CD-Bonn and Argonne V18, that were tuned to provide high-quality descriptions of the NN scattering phase shifts and deuteron properties. We then add meson-theoretic NNN interactions such as the Tucson-Melbourne or Urbana IX interactions. More recently, we have adopted realistic NN and NNN interactions with ties to QCD. Chiral perturbation theory within effective field theory ({chi}EFT) provides us with a promising bridge between QCD and hadronic systems. In this approach one works consistently with systems of increasing nucleon number and makes use of the explicit and spontaneous breaking of chiral symmetry to expand the strong interaction in terms of a dimensionless constant, the ratio of a generic small momentum divided by the chiral symmetry breaking scale taken to be about 1 GeV/c. The resulting NN and NNN interactions, characterized by the order of the expansion retained (e.g. 'next-to-next-to leading order' is NNLO), provide a high-quality fit to the NN data and the A = 3 ground-state (g.s.) properties. The derivations of NN, NNN, etc. interactions within meson-exchange and {chi}EFT are well-established but are not subjects of this review. Our focus is solution of the non-relativistic quantum many-body Hamiltonian that includes these interactions using our no core shell model (NCSM) formalism. In the next section we will briefly outline the NCSM formalism and then present applications, results and extensions in later sections.

Barrett, B R; Navratil, P; Vary, J P

2011-04-11

45

Ab initio simulation of transport phenomena in rarefied gases.

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

Sharipov, Felix; Strapasson, José L

2012-09-01

46

Classical and ab initio preparation of organometallic model structures

The detailed investigation of electronic and magnetic properties of organometallic materials with accurate ab initio methods is often computationally extremely demanding because of the large number of atoms in the unit cell. Moreover, usually the available structural data are insufficient or poorly determined specially when the structure contains hydrogen atoms. In order to be able to perform controlled ab initio calculations on reliable structures, we propose a two step approach to prepare systematically model structures for organometallic systems and to relax them to their equilibrium configuration. First, a structure is constructed on the basis of a crystallographic database and optimized by force field methods; in the second step, the structure is relaxed by ab initio quantum mechanical molecular dynamics.

Jeschke, H O; Valenti, R; Buchsbaum, C; Schmidt, M U; Wagner, M; Jeschke, Harald O.; Valenti, Roser; Buchsbaum, Christian; Schmidt, Martin U.; Wagner, Matthias

2006-01-01

47

Energy Technology Data Exchange (ETDEWEB)

We present first-principles VASP calculations of the structural, electronic, vibrational, and optical properties of paraelectric SrTiO{sub 3} and KTaO{sub 3}. The ab initio calculations are performed in the framework of density functional theory with different exchange-correlation potentials. Our calculated lattice parameters, elastic constants, and vibrational frequencies are found to be in good agreement with the available experimental values. Then, the bandstructures are calculated with the GW approximation, and the corresponding band gap is used to obtain the optical properties of SrTiO{sub 3} and KTaO{sub 3}.

Benrekia, A.R., E-mail: benrekia.ahmed@yahoo.com [Faculty of Science and Technology, University of Medea (Algeria); Benkhettou, N. [Laboratoire des Materiaux Magnetiques, Faculte des Sciences, Universite Djillali Liabes de Sidi Bel Abbes (Algeria); Nassour, A. [Laboratoire de Cristallographie, Resonance Magnetique et Modelisations (CRM2, UMR CNRS 7036) Institut Jean Barriol, Nancy Universite BP 239, Boulevard des Aiguillettes, 54506 Vandoeuvre-les-Nancy (France); Driz, M. [Applied Material Laboratory (AML), Electronics Department, University of Sidi bel Abbes (DZ 22000) (Algeria); Sahnoun, M. [Laboratoire de Physique Quantique de la Matiere et Modelisations Mathematique (LPQ3M), Faculty of Science and Technology,University of Mascara (Algeria); Lebegue, S. [Laboratoire de Cristallographie, Resonance Magnetique et Modelisations (CRM2, UMR CNRS 7036) Institut Jean Barriol, Nancy Universite BP 239, Boulevard des Aiguillettes, 54506 Vandoeuvre-les-Nancy (France)

2012-07-01

48

Ab Initio Nuclear Structure Theory: From Few to Many

We summarize recent advances in ab initio nuclear structure theory, aiming to connect few- and many-body systems in a coherent theoretical framework. Starting from chiral effective field theory to construct the nuclear Hamiltonian and the similarity renormalization group to soften it, we address several many-body approaches that have seen major developments over the past few years. We show that the domain of ab initio nuclear structure theory has been pushed well beyond the p-shell and that quantitative predictions connected to QCD via chiral effective field theory are becoming possible all the way from the proton to the neutron drip line up into the medium-mass regime.

Roth, Robert; Calci, Angelo; Langhammer, Joachim; Binder, Sven

2014-08-01

49

Use of ab initio quantum chemical methods in battery technology

Energy Technology Data Exchange (ETDEWEB)

Ab initio quantum chemistry can nowadays predict physical and chemical properties of molecules and solids. An attempt should be made to use this tool more widely for predicting technologically favourable materials. To demonstrate the use of ab initio quantum chemistry in battery technology, the theoretical energy density (energy per volume of active electrode material) and specific energy (energy per mass of active electrode material) of a rechargeable lithium-ion battery consisting of a graphite electrode and a nickel oxide electrode has been calculated with this method. (author) 1 fig., 1 tab., 7 refs.

Deiss, E. [Paul Scherrer Inst. (PSI), Villigen (Switzerland)

1997-06-01

50

P-V Relation for Mercuric Calcogenides: Ab Initio Method

Directory of Open Access Journals (Sweden)

Full Text Available Mercuric Calcogenides found many applications in electronic and optical devices as semiconducting materials. An equation of state provides useful information about the relationship between pressure (P, volume (V and temperature (T that helps to understand the behaviour of materials under the effect of high pressure and high temperature. The present paper sheds light on the electronic structure of Mercuric Calcogenides by simulating its electronic properties through ab initio method. This ab initio method is extended to derive the equation of state for Mercuric Calcogenides. The present equation of state has also been tested for the prediction of End Point. The computed results compare well with Quantum statistical data.

G. Misra

2011-01-01

51

Recent achievements in ab initio modelling of liquid water

The application of newly developed first-principle modeling techniques to liquid water deepens our understanding of the microscopic origins of its unusual macroscopic properties and behaviour. Here, we review two novel ab initio computational methods: second-generation Car-Parrinello molecular dynamics and decomposition analysis based on absolutely localized molecular orbitals. We show that these two methods in combination not only enable ab initio molecular dynamics simulations on previously inaccessible time and length scales, but also provide unprecedented insights into the nature of hydrogen bonding between water molecules. We discuss recent applications of these methods to water clusters and bulk water.

Khaliullin, Rustam Z

2013-01-01

52

Ab Initio Determination of Thermal Conductivity of Dense Hydrogen Plasmas

International Nuclear Information System (INIS)

Ab initio molecular dynamics is used to compute the thermal conductivity of hydrogen at 80 g cm-3 and temperature up to 800 eV. Pressures and ionic structure are compared with orbital-free calculations. Thermal conductivity is evaluated using the Kubo-Greenwood formula and is compared with models currently used in hydrodynamical simulations of inertial confinement fusion

53

Ab initio determination of thermal conductivity of dense hydrogen plasmas.

Ab initio molecular dynamics is used to compute the thermal conductivity of hydrogen at 80 g cm(-3) and temperature up to 800 eV. Pressures and ionic structure are compared with orbital-free calculations. Thermal conductivity is evaluated using the Kubo-Greenwood formula and is compared with models currently used in hydrodynamical simulations of inertial confinement fusion. PMID:19257679

Recoules, Vanina; Lambert, Flavien; Decoster, Alain; Canaud, Benoit; Clérouin, Jean

2009-02-20

54

Experimental, semi-experimental and ab initio equilibrium structures

Abstract The determination of equilibrium structures of molecules by spectroscopic methods or by quantum mechanical calculations is reviewed. The following structures are described in detail: experimental equilibrium structures, empirical structures, semi-experimental structures and ab initio structures. The approximations made by the different methods are discussed and their accuracies are compared.

Demaison, Jean

2007-01-01

55

Multiple time step integrators in ab initio molecular dynamics

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.

Luehr, Nathan; Markland, Thomas E.; Martínez, Todd J.

2014-02-01

56

Multiple time step integrators in ab initio molecular dynamics

International Nuclear Information System (INIS)

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

57

Ab initio simulation of dislocation cores in metals

International Nuclear Information System (INIS)

In the framework of the multi scale simulation of metals and alloys plasticity, the aim of this study is to develop a methodology of ab initio dislocations study and to apply it to the [111] screw dislocation in the bc iron. (A.L.B.)

58

Motif based Hessian matrixfor ab initio geometry optimization ofnanostructures

Energy Technology Data Exchange (ETDEWEB)

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.

Zhao, Zhengji; Wang, Lin-Wang; Meza, Juan

2006-04-05

59

Ab-Initio SCF investigation of glycolic acid

International Nuclear Information System (INIS)

The potential energy surface of glycolic acid was investigated using ab initio 4-31G SCF calculations. Geometries, energies, and wavenumbers for all seven symmetry-unique local minima are reported together with all reaction paths and their energetical barriers

60

Protonated benzene dimer: an experimental and ab initio study.

The excitation spectrum of the protonated benzene dimer has been recorded in the 415-600 nm wavelength range. In contrast to the neutral iso-electronic benzene dimer, its absorption spectrum extends in the visible spectral region. This huge spectral shift has been interpreted with ab initio calculations, which indicate that the first excited states should be charge transfer states. PMID:19621925

Chakraborty, Shamik; Omidyan, Reza; Alata, Ivan; Nielsen, Iben B; Dedonder, Claude; Broquier, Michel; Jouvet, Christophe

2009-08-12

61

Energy Technology Data Exchange (ETDEWEB)

In the framework of the multi scale simulation of metals and alloys plasticity, the aim of this study is to develop a methodology of ab initio dislocations study and to apply it to the [111] screw dislocation in the bc iron. (A.L.B.)

Ventelon, L. [CEA Saclay, Dept. des Materiaux pour le Nucleaire (DEN/DANS/DMN/SRMP), 91 - Gif-sur-Yvette (France)

2008-07-01

62

Spin-orbit decomposition of ab initio wavefunctions

Although the modern shell-model picture of atomic nuclei is built from single-particle orbits with good total angular momentum $j$, leading to $j$-$j$ coupling, phenomenological models suggested decades ago that for $0p$-shell nuclides a simpler picture can be realized via coupling of total spin $S$ and total orbital angular momentum $L$. I revisit this idea with large-basis, no-core shell model (NCSM) calculations using modern \\textit{ab initio} two-body interactions, and dissect the resulting wavefunctions into their component $L$- and $S$-components. Remarkably, there is broad agreement with calculations using the phenomenological Cohen-Kurath forces, despite a gap of nearly fifty years and six orders of magnitude in basis dimensions. I suggest $L$-$S$ may be a useful tool for analyzing \\textit{ab initio} wavefunctions of light nuclei, for example in the case of rotational bands.

Johnson, Calvin W

2014-01-01

63

Ab initio and perturbation treatment studies in different dielectric media

Using ab initio method and perturbation treatment of the Onsager model we have studied the geometrical and spectroscopic changes due to the reaction field in several carbonyl compounds including succinimide, N-chlorophthalimide, and phthalic anhydride. A very good agreement is observed between the results of the ab initio method and those of the perturbation treatment. It is found that the carbonyl bonds in the molecules investigated elongate and red-shifted C dbnd O stretching modes result. Moreover, based on the solvent-induced vibrational Stark effect, the magnitude of the difference dipole moment and the difference polarizability for N-H stretching mode in succinimide are evaluated to be 0.0157 and 0.608 a.u., respectively.

Asghari-Khiavi, M.; Mohammadi, S.; Safinejad, F.

2009-02-01

64

Multiple Time Step Integrators in Ab Initio Molecular Dynamics

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 show that such a timescale separation is possible using two different schemes: 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 dynami...

Luehr, Nathan; Martinez, Todd J

2013-01-01

65

Ab initio anharmonic force field and equilibrium structure of propene

The quadratic, cubic and semi-diagonal quartic force field of propene has been calculated at the MP2 level of theory employing a basis set of triple-? quality. A semi-experimental equilibrium structure has been derived from experimental ground state rotational constants and rovibrational interaction parameters calculated from the ab initio force field. This structure is in excellent agreement with the ab initio structure calculated at the CCSD(T) level of theory using a basis set of quintuple-? quality and a core correlation correction. The experimental mass-dependent rm structures are also determined and their accuracy is discussed. The use of isolated CH stretching frequencies is shown to be a good method to determine CH bond length.

Demaison, J.; Rudolph, H. D.

2008-03-01

66

The density matrix renormalization group for ab initio quantum chemistry

During the past 15 years, the density matrix renormalization group (DMRG) has become increasingly important for ab initio quantum chemistry. Its underlying wavefunction ansatz, the matrix product state (MPS), is a low-rank decomposition of the full configuration interaction tensor. The virtual dimension of the MPS, the rank of the decomposition, controls the size of the corner of the many-body Hilbert space that can be reached with the ansatz. This parameter can be systematically increased until numerical convergence is reached. The MPS ansatz naturally captures exponentially decaying correlation functions. Therefore DMRG works extremely well for noncritical one-dimensional systems. The active orbital spaces in quantum chemistry are however often far from one-dimensional, and relatively large virtual dimensions are required to use DMRG for ab initio quantum chemistry (QC-DMRG). The QC-DMRG algorithm, its computational cost, and its properties are discussed. Two important aspects to reduce the computational co...

Wouters, Sebastian

2014-01-01

67

Ab initio inspection of magnetic and redox hysteresis

Bistable systems are more and more present; part of the reason is to be found in the possible applications in molecular electronics. Some of those systems can exist under two different electronic states under the same conditions. As a consequence its present an hysteresis. Two properties are commonly associated with the hysteresis response, magnetism and redox activity. Even though these phenomena are not new, parts of the mechanisms remains unknown. Thanks to wavefunction-based ab initio cal...

Ke?pe?ne?kian, Mikae?l

2010-01-01

68

Ab initio calculation of tight-binding parameters

Energy Technology Data Exchange (ETDEWEB)

We calculate ab initio values of tight-binding parameters for the f- electron metal Ce and various phases of Si, from local-density functional one-electron Hamiltonian and overlap matrix elements. Our approach allows us to unambiguously test the validity of the common minimal basis and two-center approximations as well as to determine the degree of transferability of both nonorthogonal and orthogonal hopping parameters in the cases considered.

McMahan, A.K.; Klepeis, J.E.

1997-12-01

69

Ab initio modeling of TiO2 nanotubes

TiO2 nanotubes constructed from a lepidocrocite-like TiO2 layer were investigated with ab initio methods employing the periodic CRYSTAL code. The dependence of strain energies, structural and electronic properties on the tube diameter was investigated in the 18–57 A range. Nanotubes constructed by a (0,n) rollup proved to be the most stable at all diameters. All three types of rollup undergo significant reconstruction at diameters <25 A. All investigated structures possess a hig...

Szieberth, Denes; Ferrabone, Matteo; Ferrari, Anna Maria

2010-01-01

70

Ab initio dynamics study of poly-para-phenylene vinylene.

We present an ab initio dynamics investigation within a density-functional perturbation theory framework of the properties of the conjugated polymer poly-para-phenylene vinylene (PPV) in both the isolated chain and crystalline states. The calculated results show that for an isolated chain, most of the vibrational modes correspond to experimentally observed modes in crystalline PPV. However, additional hitherto unidentified modes have been observed in experiment and our calculations on crystal...

Zheng, Guang; Clark, S. J.; Tulip, P. R.; Brand, S.; Abram, R. A.

2005-01-01

71

Ab Initio Description of p-Shell Hypernuclei

We present the first ab initio calculations for p-shell single-Lambda hypernuclei. For the solution of the many-baryon problem, we develop two variants of the no-core shell model with explicit $\\Lambda$ and $\\Sigma^+$, $\\Sigma^0$, $\\Sigma^-$ hyperons including $\\Lambda$-$\\Sigma$ conversion, optionally supplemented by a similarity renormalization group transformation to accelerate model-space convergence. In addition to state-of-the-art chiral two- and three-nucleon interacti...

Wirth, Roland; Gazda, Daniel; Navra?til, Petr; Calci, Angelo; Langhammer, Joachim; Roth, Robert

2014-01-01

72

Reversible relaxation at charged metal surfaces: An ab initio study

Results of an ab initio density functional theory study of atomic and electronic relaxation at electrically charged surfaces of Au suggest that the outward relaxation of the top layer at negative excess charge is driven by electrostatic forces on the surface atoms due to the incomplete screening of the external electric field. The relaxation amplitude agrees well with experiments on Au (111) in electrolyte. Electron redistribution between bonding and antibonding states in the plane containing...

Umeno, Y.; Elsa?sser, C.; Meyer, B.; Gumbsch, P.; Weissmu?ller, J.

2008-01-01

73

Ab initio DFT - the seamless connection between WFT and DFT

Abstract Orbital-dependent exchange-correlation functionals and potentials play an increasingly important role in Density Functional Theory (DFT). Methods which use explicit orbital-dependent functionals can be viewed as a natural extension to the standard Kohn-Sham (KS) procedure in DFT, that traditionally have used functionals with explicit density-dependence but only implicit orbital-dependence. Ab initio DFT, invented at the Quantum Theory Project, is the m...

Grabowski, Ireneusz; Hirata, So; Lotrich, Victor F.

2010-01-01

74

Dissociative recombination of N2+: An ab initio study

Cross sections for the dissociative recombination of N2+ for vi+=0 -3 are computed using multichannel quantum defect theory with molecular data generated using the R -matrix method. The calculation is completely ab initio and includes three electronic cores of the ion. Extensive comparisons are made with previous experimental and theoretical studies. Our cross section is in excellent agreement with experimental results and other theoretical results. Cross sections and isotropic rate coefficients are provided for all computed vibrational levels.

Little, D. A.; Chakrabarti, K.; Mezei, J. Zs.; Schneider, I. F.; Tennyson, J.

2014-11-01

75

Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics

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.

Makhov, Dmitry V.; Glover, William J.; Martinez, Todd J.; Shalashilin, Dmitrii V.

2014-08-01

76

Ab initio simulations for material properties inside Jupiter

The behavior of warm dense matter is of paramount importance for interior and dynamo models for solar and extrasolar giant planets. For instance, nonmetal-to-metal transitions (e.g. metallization in hydrogen), demixing phenomena (in H-He or C-N-O-H mixtures), and new exotic phases (e.g. with proton conduction in water and ammonia) may occur at high pressures and elevated temperatures. These effects have to be taken into account consistently in corresponding planetary models. Therefore, we apply ab initio molecular dynamics simulations based on finite-temperature density functional theory to calculate thermophysical properties of warm dense matter. In particular we determine the equation of state (thermal and caloric), material (sound velocity, specific heat) and transport properties (electrical and thermal conductivity, viscosity, diffusion coefficient) along the adiabat of Jupiter, i.e. from ambient conditions up to the multi-megabar range [1,2]. This ab initio data set can be used as input in future interior (structure) and dynamo models (magnetic fields, flow dynamics) for this planet. Similar data sets can also be compiled for interior conditions of other solar giant planets so that important problems such as the size of planetary cores necessary for the accretion of gaseous (H/He) or icy (C-N-O hydrides) envelopes, the origin, location and stability of layer boundaries, or the source of an excess (e.g. Saturn) or deficit luminosity (e.g. Uranus) can be studied. The increasing sample of extrasolar planets poses new questions that can be addressed based on such ab initio data sets, e.g. to explain the wide range of radii for planets with similar mass. [1] N. Nettelmann, A. Becker, B. Holst, R. Redmer, Astrophys. J. 750, 52 (2012). [2] M. French, A. Becker, W. Lorenzen, N. Nettelmann, M. Bethkenhagen, J. Wicht, R. Redmer, Astrophys. J. Suppl. Ser. 202, 5 (2012).

French, Martin; Becker, Andreas; Lorenzen, Winfried; Nettelmann, Nadine; Bethkenhagen, Mandy; Wicht, Johannes; Redmer, Ronald

2013-07-01

77

Hydrogen bond connectivity in jennite from ab initio simulations

International Nuclear Information System (INIS)

The protonation scheme and the hydrogen bond connectivity in the structure of jennite were investigated by ab initio molecular dynamics simulations. The calculated statistics of hydrogen bonds at ambient conditions is consistent with the protonation scheme proposed by Bonaccorsi et al. (2004) based on the bond valence theory. The protons in the system are associated with the ?2Ca-OH linkage and H2O molecules. The dangling Si-O bond on the bridging tetrahedra is de-protonated. The proton dynamics revealed in the molecular dynamic simulations explains the apparent discrepancies in the NMR and X-ray diffraction studies of jennite

78

Raman intensities in polyphenyls: an ab-initio study

International Nuclear Information System (INIS)

Full text: Among the most prominent features in the normal first order Stokes Raman spectra of poly(para-phenylenes) and its oligomers are the 1220 cm-1 and 1280 cm-1 Ag modes and their intensity ratio. Also the 1600 cm-1 Ag mode, showing a well resolved splitting in the oligomers, has received a lot of attention in terms of electron-phonon coupling in these materials. We discuss these vibrational modes and their Raman intensities in terms of Albrecht' theory and anharmonic coupling effects. By means of quantum chemical ab-initio methods we relate the respective Raman cross sections to the electronic and geometrical structure of the molecules. (author)

79

Ab Initio Studies of Liquid and Amorphous Ge

We review our previous work on the dynamic structure factor S(k,omega) of liquid Ge (l-Ge) at temperature T = 1250 K, and of amorphous Ge (a-Ge) at T = 300 K, using ab initio molecular dynamics [Phys. Rev. B67, 104205 (2003)]. The electronic energy is computed using density-functional theory, primarily in the generalized gradient approximation, together with a plane wave representation of the wave functions and ultra-soft pseudopotentials. We use a 64-atom cell with periodic...

Chai, Jeng-da; Stroud, D.

2004-01-01

80

Symmetry-Adapted Ab Initio Open Core Shell Model Theory

International Nuclear Information System (INIS)

By using only a fraction of the model space, we gain further insight – within a symmetry-guided no-core shell model framework – into the many-body nuclear dynamics that gives rise to important single-particle configurations together with correlated highly-deformed and alpha-cluster structures. We show results of the novel ab initio symmetry-adapted no-core shell model for large-scale nuclear structure computations. In addition, we use the symmetry patterns unveiled in these results to explore ultra-large model spaces.

81

Ab initio and molecular orbital studies of the diuranium molecule

International Nuclear Information System (INIS)

The existence and nature of actinide multiple bonds have been investigated by ab initio relativistic-core-potential SCF, MCSCF, and SRCI calculations on the diuranium molecule. These calculations indicate a double-minimum potential energy surface for diuranium, similar to that reported (and debated) for dichromium. At short bond lengths (2.2 angstrom), the lowest-energy state lies approximately 80 kcal/mol above the separated atoms. At longer bond distances, the 5f orbitals retain their atomic character, and six valence electrons occupy 6d and 7s MOs

82

Ab initio studies of transition-metal dihydrogen chemistry

International Nuclear Information System (INIS)

Examples of transition metal complexes containing dihydrogen ligands are investigated using ab initio electronic structure calculations employing effective core potentials. Calculated geometrical structures and relative energies of various forms of WL5(H2) complexes (L = CO, PR3) are reported, and the influence of the ligand on the relative stabilities of the dihydrogen and dihydride forms is studied. The possible intramolecular mechanisms for H/D scrambling are investigated in another d6 complex, Cr(CO)4(H2)2, where various polyhydride intermediates are possible. 8 refs., 6 figs., 1 tab

83

Ab initio calculations of inelastic losses and optical constants

Ab initio approaches are introduced for calculations of inelastic losses and vibrational damping in core level x-ray and electron spectroscopies. From the dielectric response function we obtain system-dependent self-energies, inelastic mean free paths, and losses due to multiple-electron excitations, while from the dynamical matrix we obtain phonon spectra and Debye-Waller factors. These developments yield various spectra and optical constants from the UV to x-ray energies in aperiodic materials, and significantly improve both the near edge and extended fine structure.

Rehr, J J; Prange, M P; Vila, F D; Ankudinov, A L; Campbell, L W; Sorini, A P

2006-01-01

84

Stretching siloxanes: An ab initio molecular dynamics study

We present an ab initio molecular dynamics study of siloxane elastomers placed under tensile stress for comparison with single molecule AFM experiments. Of particular interest is stress-induced chemical bond breaking in the high force regime, where a description of the molecular electronic structure is essential to determine the rupture mechanism. We predict an ionic mechanism for the bond breaking process with a rupture force of 4.4 nN for an isolated siloxane decamer pulled at a rate of 27.3 m/s and indicate lower values at experimental polymer lengths and pulling rates.

Lupton, E. M.; Nonnenberg, C.; Frank, I.; Achenbach, F.; Weis, J.; Bräuchle, C.

2005-10-01

85

Ab Initio Study of Phase Equilibria in TiCx

The phase diagram for the vacancy-ordered structures in the substoichiometric TiCx ( x = 0.5-1.0) has been established from Monte Carlo simulations with the long-range pair and multisite effective interactions obtained from ab initio calculations. Three ordered superstructures of vacancies ( Ti2C, Ti3C2, and Ti6C5) are found to be ground state configurations. Their stability has been verified by full-potential total energy calculations of the fully relaxed structures.

Korzhavyi, P. A.; Pourovskii, L. V.; Hugosson, H. W.; Ruban, A. V.; Johansson, B.

2002-01-01

86

Ab initio molecular dynamics simulations of Aluminum solvation

The solvation of Al and its hydrolyzed species in water clusters has been studied by means of ab initio molecular dynamics simulations. The hexa-hydrate aluminum ion formed a stable complex in the finite temperature cluster simulation of one aluminum ion and 16 waters. The average dipole moment of strongly polarized hydrated water molecules in the first solvation shell of the hexa-hydrate aluminum ion was found to be 5.02 Debye. The deprotonated hexa-hydrate complex evolves into a tetra-coordinated aluminate ion with two water molecules in the second solvation shell forming hydrogen bonds to the hydroxyl groups in agreement with the observed coordination.

Lubin, M I; Weare, J H

1999-01-01

87

Ab initio studies of electromechanical effects in carbon nanotubes

Scientific Electronic Library Online (English)

Full Text Available SciELO Brazil | Language: English Abstract in english Carbon nanotubes have recently attracted interest for their possible applications as nanoactuators and nanoswitches, as well as possible building blocks for nanoelectronics. We present ab initio calculations for uniformly charged graphene and (11,0),(9,0) and (5,5) carbon nanotubes. We also consider [...] the effects of polaron formation in these systems. The strain-charge coeÆcient is calculated and compared for both graphene and the nanotubes under study.

M. Verissimo, Alves; R.B., Capaz; Belita, Koiller; Emilio, Artacho; H., Chacham.

2002-06-01

88

Ab-initio study of transition metal hydrides

Energy Technology Data Exchange (ETDEWEB)

We have performed ab initio self consistent calculations based on Full potential linearized augmented plane wave (FP-LAPW) method to investigate the optical and thermal properties of yttrium hydrides. From the band structure and density of states, the optical absorption spectra and specific heats have been calculated. The band structure of Yttrium metal changes dramatically due to hybridization of Y sp orbitals with H s orbitals and there is a net charge transfer from metal to hydrogen site. The electrical resistivity and specific heats of yttrium hydrides are lowered but the thermal conductivity is slightly enhanced due to increase in scattering from hydrogen sites.

Sharma, Ramesh [Dept. of Physics, Feroze Gandhi Insititute of Engineering and Technology, Raebareli-229001 (India); Shukla, Seema, E-mail: sharma.yamini62@gmail.com; Dwivedi, Shalini, E-mail: sharma.yamini62@gmail.com; Sharma, Yamini, E-mail: sharma.yamini62@gmail.com [Theoretical Condensed Matter Physics Laboratory, Dept. of Physics Feroze Gandhi College, Raebareli-229001 (India)

2014-04-24

89

The implementation of ab initio quantum chemistry calculations on transporters.

The RHF and geometry optimization sections of the ab initio quantum chemistry code, GAMESS, have been optimized for a network of parallel microprocessors, Inmos T800-20 transputers, using both indirect and direct SCF techniques. The results indicate great scope for implementation of such codes on small parallel computer systems, very high efficiencies having been achieved, particularly in the cases of direct SCF and geometry optimization with large basis sets. The work, although performed upon one particular parallel system, the Meiko Computing Surface, is applicable to a wide range of parallel systems with both shared and distributed memory. PMID:1919615

Cooper, M D; Hillier, I H

1991-06-01

90

Ab initio calculation of the static structural properties of Be

International Nuclear Information System (INIS)

An ab initio calculation of the static structural properties of Be is presented. The total structural energy is calculated using pseudopotentials and the local density-functional formalism with the atomic number as the only input. The lattice constant, Poisson's ratio, and the bulk modulus are predicted by calculating the total energy of the system. The deviations of the calculated results for lattice constants c, a and c/a are approximately 1% when compared with experimental results. Poisson's ratio and the bulk modulus are also in reasonably good agreement with the measured values. (author)

91

Ab-initio study of napthelene based conducting polymer

Energy Technology Data Exchange (ETDEWEB)

In this paper, we have identified structural and electronic properties of conducting polymers by using DFT based ATK-VNL ab-initio tool. Naphthalene derivative structures were stabilized by varying the bond length between two atoms of the molecule C-N and C-C. We have also studied the molecular energy spectrum of naphthalene derivatives and found the HOMOLUMO for the same. A comparison of structural and electronic properties of naphthalene derivatives by attaching the functional group of amine, have been performed and found that they show good semi conducting properties.

Ruhela, Ankur [Advanced Materials Research Group, Computational Nanoscience and Technology Lab (CNTL), ABV-Indian Institute of Information Technology and Management, Gwalior -474010, India and Amity Institute of Nanotechnology, Amity University, Noida-201303 (India); Kanchan, Reena, E-mail: reena.kanchan1977@gmail.com [Department of Chemistry, Jiwaji University, Gwalior-474001 (India); Srivastava, Anurag [Advanced Materials Research Group, Computational Nanoscience and Technology Lab (CNTL), ABV-Indian Institute of Information Technology and Management, Gwalior -474010 (India); Sinha, O. P. [Amity Institute of Nanotechnology, Amity University, Noida-201303 (India)

2014-04-24

92

Ab initio study of phase equilibria in TiCx

DEFF Research Database (Denmark)

The phase diagram for the vacancy-ordered structures in the substoichiometric TiCx (x = 0.5-1.0) has been established from Monte Carlo simulations with the long-range pair and multisite effective interactions obtained from ab initio calculations. Three ordered superstructures of vacancies (Ti2C, Ti3C2, and Ti6C5) are found to be ground state configurations. Their stability has been verified by full-potential total energy calculations of the fully relaxed structures.

Korzhavyi, P.A.; Pourovskii, L.V.

2002-01-01

93

Ab initio Study of He Stability in hcp-Ti

Energy Technology Data Exchange (ETDEWEB)

The stability of He in hcp-Ti was studied using ab initio method based on density functional theory. The results indicate that a single He atom prefers to occupy the tetrahedral site rather than the octahedral site. The interaction of He defects with Ti atoms has been used to explain the relative stabilities of He point defects in hcp-Ti. The relative stability of He defects in hcp-Ti is useful for He clustering and bubble nucleation in metal tritides, which provides the basis for development of improved atomistic models.

Dai, Yunya; Yang, Li; Peng, SM; Long, XG; Gao, Fei; Zu, Xiaotao T.

2010-12-20

94

Ab initio characterization of linear C3Si isomers

Aims. This paper presents an ab initio characterization of linear isomers of C3Si, which are suitable species for astrophysical detection in carbon-rich sources. Methods. By the help of multiconfigurational calculations, two linear minima are characterized, namely l-SiCCC and l-CSiCC, whose relative energy is 3.3 eV, and their electronic ground states have X3? - symmetry, and their electronic spectra present a high density of electronic states at low energy. Anharmonic spectroscopic paramete...

Inostroza, N.; Hochlaf, M.; Senent Di?ez, Mari?a Luisa; Letelier, J. R.

2008-01-01

95

Ab-initio study of napthelene based conducting polymer

International Nuclear Information System (INIS)

In this paper, we have identified structural and electronic properties of conducting polymers by using DFT based ATK-VNL ab-initio tool. Naphthalene derivative structures were stabilized by varying the bond length between two atoms of the molecule C-N and C-C. We have also studied the molecular energy spectrum of naphthalene derivatives and found the HOMOLUMO for the same. A comparison of structural and electronic properties of naphthalene derivatives by attaching the functional group of amine, have been performed and found that they show good semi conducting properties

96

Ab Initio study of neutron drops with chiral Hamiltonians

We report ab initio calculations for neutron drops in a 10 MeV external harmonic-oscillator trap using chiral nucleon-nucleon plus three-nucleon interactions. We present total binding energies, internal energies, radii and odd-even energy differences for neutron numbers N = 2 - 18 using the no-core shell model with and without importance truncation. Furthermore, we present total binding energies for N = 8, 16, 20, 28, 40, 50 obtained in a coupled-cluster approach. Comparisons with Green's Function Monte Carlo results, where available, using Argonne v8' with three-nucleon interactions reveal important dependences on the chosen Hamiltonian.

Potter, H D; Maris, P; Vary, J P; Binder, S; Calci, A; Langhammer, J; Roth, R

2014-01-01

97

The structural, elastic, thermodynamic, electronic and vibrational properties of CsCl-type TbMg have been studied by performing ab initio calculations based on density functional theory using the Vienna Ab initio Simulation Package (VASP). The exchange correlation potential within the generalized-gradient approximation (GGA) of projector augmented wave (PAW) method is used. The calculated structural parameters, such as the lattice constant, bulk modulus, its pressure derivative, formation energy and second-order elastic constants are presented in this paper. The obtained results are compared with related experimental and theoretical studies. The electronic band calculations, total density of states (DOS), partial DOS and charge density are also presented. Formation enthalpy and Cauchy pressure are determined. In order to obtain more information the elastic properties such as Zener anisotropy factor, Poisson’s ratio, Young modulus, isotropic shear modulus, Debye temperature and melting point have been carried out. The elastic constants are calculated in zero and different pressure ranges (0-50 GPa) with bulk modulus. We have performed the thermodynamic properties of TbMg by using quasi-harmonic Debye model. The temperature and pressure variation of the volume, bulk modulus, and thermal expansion coefficient have been predicted over a pressure range of 0-25 GPa for of TbMg. Pressure dependence of the anisotropy factors, Young’s modulus, Poisson’s ratios, bulk modulus and axis compressibility of TbMg are presented along different directions and planes. Finally, the phonon dispersion curves are presented for TbMg.

Mogulkoc, Y.; Ciftci, Y. O.; Kabak, M.; Colakoglu, K.

2014-07-01

98

Ab initio neutron crystallography by the charge flipping method.

In this paper, the charge flipping method is proposed for ab initio structure determination using neutron diffraction data alone. For this purpose, a new variant of the dual-space iterative algorithm is introduced, which is called band flipping. Unlike the basic algorithm, it reverses the sign of scattering density only within a zero-centred band, develops large plateaus without forcing positivity, and often leads to Babinet solutions. Its phasing power was tested on two organic structures. These behave similarly when using X-ray diffraction data and the basic algorithm but, with neutron data and band flipping, their solution becomes orders-of-magnitude more difficult and strongly dependent on the hydrogen content. Surprisingly, when the constraint of positivity is added, convergence speeds up to the point where structure determination using neutron diffraction data is not more difficult than the X-ray case. However, by following the evolution of the R factor, such a solution can be easily missed, and band flipping must be used both as a probe of convergence and as a tool for developing negative densities. Apart from demonstrating the feasibility of charge flipping for ab initio neutron crystallography, the present study also leads to an important byproduct: the type of traps that occasionally block the iterative process are identified and a mathematical analysis of their origin is given. PMID:17301476

Oszlányi, Gábor; Süto, András

2007-03-01

99

Infrared emission spectroscopy and ab initio calculations on VCl

The emission spectrum of VCl has been investigated at high resolution in the 3000-19 400 cm -1 region using a Fourier transform spectrometer. The bands were excited in a high temperature carbon tube furnace by the reaction of vanadium metal vapor and a trace of BCl 3 as well as in a microwave discharge lamp by the reaction of VOCl 3 vapor with active nitrogen. The spectra were recorded using the Fourier transform spectrometer associated with the McMath-Pierce telescope of the National Solar Observatory at Kitt Peak. The analysis of the E 5?-X 5? system of VCl (previously labeled as [7.0] 5?-X 5?) has been extended by analyzing the rotational structure of some additional bands. A rotational analysis of the 5?1- 5?1, 5?3- 5?3, and 5?4- 5?4 subbands of the 0-2, 0-1, 0-0, and 1-0 bands, and the 5?2- 5?2 subband of the 0-1 and 0-0 bands has been obtained and molecular constants have been extracted. The 5?0±- 5?0± subband was not identified in any of the assigned bands. The spectroscopic properties of the low-lying electronic states of VCl have been predicted by CASSCF/CMRCI ab initio calculations and the experimental assignments are supported by the ab initio results.

Ram, R. S.; Liévin, J.; Bernath, P. F.; Davis, S. P.

2003-02-01

100

Why ferro electricity? synchrotron radiation and ab initio answers

International Nuclear Information System (INIS)

An old question of solid state physics is being answered nowadays: the atomic-level understanding of ferro electricity. Traditional ideas about ferroelectric phenomena relate with softening of optical phonons at the Brillouin zone origin and with 'W-shaped' Landau free energy functions. Last decade experimental (synchrotron radiation, neutrons) and quantum-theoretical (Cohen, Resta, Spaldin) contributions have clarified detailed descriptions and explanations for atomic behavior leading to spontaneous polarization in perovskite and perovskite-related crystal structures. Work being performed by our interdisciplinary group on ferro electricity is presented. Perovskite and Aurivillius ferroelectric phases are obtained by different methods. Fine details on crystal structures are investigated by means of synchrotron radiation at Stanford Synchrotron Radiation Laboratory. Electronic structures of considered phases are theoretically characterized by ab initio methods. High-resolution diffraction experiments demonstrate several symmetry break-downs in perovskite and Aurivillius phases. The structure- symmetry-polarization relationship is discussed for a number of representative cases. Ab initio explanation of ferroelectric polarization in perovskite structures is given. Energy calculation is performed by means of CASTEP code under GGA functional. Energy optimization leads to cubic-tetragonal symmetry break-down with off-centering cation displacements via second-order Jahn-Telln displacements via second-order Jahn-Teller effect. Electronic structure is investigated with Band Lab code, under LDA functional with LMTO method. Degeneracy of Ti 3d z2 and Ti 3d (x2 + y2) orbitals is the cause of cubic-perovskite deformation. (Author)

101

New Horizons in Ab Initio Nuclear Structure Theory

International Nuclear Information System (INIS)

Nuclear interactions derived within chiral effective field theory enable nuclear structure and reaction calculations solidly rooted in QCD. Using chiral two- and three-body interactions in ab initio studies of a variety of nuclear observables is, both, promising and challenging. Particularly the inclusion of chiral 3N interactions into exact and approximate many-body calculations is demanding and computationally expensive. We present recent key developments that facilitate ab initio calculations of ground and low-lying excited states of p- and sd-shell nuclei with full 3N interactions in the Importance-Truncated No-Core Shell Model using consistent Similarity Renormalization Group transformations of the NN+3N Hamiltonian. The treatment of 3N interactions without approximations allows for first studies of the dependence of nuclear-structure observables on the details of chiral interactions. Moreover, we present results for heavy nuclei obtained in Coupled Cluster calculations using a normal-ordered two-body approximation of the 3N interaction.

102

Why ferro electricity? synchrotron radiation and ab initio answers

Energy Technology Data Exchange (ETDEWEB)

An old question of solid state physics is being answered nowadays: the atomic-level understanding of ferro electricity. Traditional ideas about ferroelectric phenomena relate with softening of optical phonons at the Brillouin zone origin and with 'W-shaped' Landau free energy functions. Last decade experimental (synchrotron radiation, neutrons) and quantum-theoretical (Cohen, Resta, Spaldin) contributions have clarified detailed descriptions and explanations for atomic behavior leading to spontaneous polarization in perovskite and perovskite-related crystal structures. Work being performed by our interdisciplinary group on ferro electricity is presented. Perovskite and Aurivillius ferroelectric phases are obtained by different methods. Fine details on crystal structures are investigated by means of synchrotron radiation at Stanford Synchrotron Radiation Laboratory. Electronic structures of considered phases are theoretically characterized by ab initio methods. High-resolution diffraction experiments demonstrate several symmetry break-downs in perovskite and Aurivillius phases. The structure- symmetry-polarization relationship is discussed for a number of representative cases. Ab initio explanation of ferroelectric polarization in perovskite structures is given. Energy calculation is performed by means of CASTEP code under GGA functional. Energy optimization leads to cubic-tetragonal symmetry break-down with off-centering cation displacements via second-order Jahn-Teller effect. Electronic structure is investigated with Band Lab code, under LDA functional with LMTO method. Degeneracy of Ti 3d z{sup 2} and Ti 3d (x{sup 2} + y{sup 2}) orbitals is the cause of cubic-perovskite deformation. (Author)

Olivera, R.; Espinosa, F.; Garcia, M.; Macias, E. [Centro de Investigacion en Materiales Avanzados (CIMAV), Chihuahua (Mexico); Fuentes, M.E. [Universidad Autonoma de Chihuahua (UACh), Chihuahua (Mexico); Duran, A.; Siqueiros, J. [Centro de Ciencias de la Materia Condensada (CCMC), Ensenada (Mexico)]. e-mail: luis.fuentes@cimav.edu.mx

2007-07-01

103

Accounting for dynamical effects in ab initio NMR calculations

The ab initio calculation of chemical shifts using density functional theory (DFT) is now routine. For many rigid crystals and molecules isotropic chemical shifts have been computed agreeing with experiment to better than 1ppm. However systems that exhibit greater dynamical motion, such as in biological systems, the computed shifts are found to be in error. We study an example of one such system, an L-Alanine molecular crystal, using the NMR-CASTEP code. A straightforward calculation results in a discrepancy between computed and experimental chemical shifts of nearly 4ppm. Previous work by Dumez and Pickard has shown that dynamics are a contributing factor to this error [1]. To incorporate dynamics into the calculation of the chemical shifts we average over an ensemble of configurations representational of the motion of the system. These configurations are generated using molecular dynamics (MD). This can pose a problem for ab initio MD since the time scale of such dynamics can be of the order of a picosecond. We overcome this by fitting a force field to DFT forces for the system under study. Classical MD is then used to generate uncorrelated configurations from which the chemical shifts are averaged. Using this procedure we are able to improve the computed chemical shifts for L-Alanine significantly. [1] J-N. Dumez and C.J. Pickard, J. Chem. Phys., 130 (2009) 104701.

Robinson, Mark; Haynes, Peter

2010-03-01

104

Accessing the limits of ab initio docking methods

Ab initio protein docking is the prediction of the three dimensional structure of a protein-protein complex from the structures of two interacting proteins, receptor and ligand. Here we report our instigation of the performance of several popular ab initio docking algorithms (ZDOCK, GRAMM and 3D-Garden) in a bound test (lock-and-key) on very large set of 2903 cases taken from ProCom database. The bound test was preferred over the unbound because of two reasons (1) to test the performance of docking algorithms without obscuring the results with the effects originating from possible conformational changes and (2) to expand the benchmarking set since we do not need the 3D structures of isolated monomers. The assessment of the predictions was made by computing the ligand RMSD (L/RMSD). The first ten ranked predictions were taken. It was found that, on average, only 28% of the predictions resulted in L/RMSD < 10 A, which is the standard criterion of acceptable models in CAPRI. The performance of the methods was investigated with respect to physical characteristics of the receptor and ligand as well.

Shyam, Radhey; Alexov, Emil

2009-11-01

105

Ab Initio Simulations for Material Properties along the Jupiter Adiabat

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 Grüneisen 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.

French, Martin; Becker, Andreas; Lorenzen, Winfried; Nettelmann, Nadine; Bethkenhagen, Mandy; Wicht, Johannes; Redmer, Ronald

2012-09-01

106

The density matrix renormalization group for ab initio quantum chemistry

During the past 15 years, the density matrix renormalization group (DMRG) has become increasingly important for ab initio quantum chemistry. Its underlying wavefunction ansatz, the matrix product state (MPS), is a low-rank decomposition of the full configuration interaction tensor. The virtual dimension of the MPS, the rank of the decomposition, controls the size of the corner of the many-body Hilbert space that can be reached with the ansatz. This parameter can be systematically increased until numerical convergence is reached. The MPS ansatz naturally captures exponentially decaying correlation functions. Therefore DMRG works extremely well for noncritical one-dimensional systems. The active orbital spaces in quantum chemistry are however often far from one-dimensional, and relatively large virtual dimensions are required to use DMRG for ab initio quantum chemistry (QC-DMRG). The QC-DMRG algorithm, its computational cost, and its properties are discussed. Two important aspects to reduce the computational cost are given special attention: the orbital choice and ordering, and the exploitation of the symmetry group of the Hamiltonian. With these considerations, the QC-DMRG algorithm allows to find numerically exact solutions in active spaces of up to 40 electrons in 40 orbitals.

Wouters, Sebastian; Van Neck, Dimitri

2014-09-01

107

Surface Segregation Energies of BCC Binaries from Ab Initio and Quantum Approximate Calculations

We compare dilute-limit segregation energies for selected BCC transition metal binaries computed using ab initio and quantum approximate energy method. Ab initio calculations are carried out using the CASTEP plane-wave pseudopotential computer code, while quantum approximate results are computed using the Bozzolo-Ferrante-Smith (BFS) method with the most recent parameterization. Quantum approximate segregation energies are computed with and without atomistic relaxation. The ab initio calculations are performed without relaxation for the most part, but predicted relaxations from quantum approximate calculations are used in selected cases to compute approximate relaxed ab initio segregation energies. Results are discussed within the context of segregation models driven by strain and bond-breaking effects. We compare our results with other quantum approximate and ab initio theoretical work, and available experimental results.

Good, Brian S.

2003-01-01

108

NestedMICA as an ab initio protein motif discovery tool

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Discovering overrepresented patterns in amino acid sequences is an important step in protein functional element identification. We adapted and extended NestedMICA, an ab initio motif finder originally developed for finding transcription binding site motifs, to find short protein signals, and compared its performance with another popular protein motif finder, MEME. NestedMICA, an open source protein motif discovery tool written in Java, is driven by a Monte Carlo technique called Nested Sampling. It uses multi-class sequence background models to represent different "uninteresting" parts of sequences that do not contain motifs of interest. In order to assess NestedMICA as a protein motif finder, we have tested it on synthetic datasets produced by spiking instances of known motifs into a randomly selected set of protein sequences. NestedMICA was also tested using a biologically-authentic test set, where we evaluated its performance with respect to varying sequence length. Results Generally NestedMICA recovered most of the short (3–9 amino acid long test protein motifs spiked into a test set of sequences at different frequencies. We showed that it can be used to find multiple motifs at the same time, too. In all the assessment experiments we carried out, its overall motif discovery performance was better than that of MEME. Conclusion NestedMICA proved itself to be a robust and sensitive ab initio protein motif finder, even for relatively short motifs that exist in only a small fraction of sequences. Availability NestedMICA is available under the Lesser GPL open-source license from: http://www.sanger.ac.uk/Software/analysis/nmica/

Down Thomas A

2008-01-01

109

Ab initio constrained crystal-chemical Rietveld refinement of Ca10(VxP1-xO4)6F2 apatites

International Nuclear Information System (INIS)

Extraction of reliable bond distances and angles for Ca10(VxP1-xO4)6F2 apatites using standard Rietveld refinement with Cu K? X-ray powder data was significantly impaired by large imprecision for the O-atom coordinates. An initial attempt to apply crystal-chemical Rietveld refinements to the same compounds was partly successful, and exposed the problematic determination of two oxygen-metal- oxygen angles. Ab initio modeling with VASP in space groups P63/m, P21/m and Pm showed that both these angular parameters exhibited a linear dependence with the vanadium content. Stable crystal-chemical Rietveld refinements in agreement with quantum results were obtained by fixing these angles at the values from ab initio simulations. Residuals were comparable with the less precise standard refinements. The larger vanadium ion is accommodated primarily by uniform expansion and rotation of BO4 tetrahedra combined with a rotation of the Ca-Ca-Ca triangular units. It is proposed that the reduction of symmetry for the vanadium end-member is necessary to avoid considerable departures from formal valences at the AII and B sites in P63/m. The complementarity of quantum methods and structural analysis by powder diffraction in cases with problematic least-squares extraction of the crystal chemistry is discussed. (orig.)

110

Ab initio calculation of thermodynamic functions for crystals

International Nuclear Information System (INIS)

The knowledge of thermodynamic functions is essential to investigate crystal stability and chemical reactivity. These functions are not always experimentally known, as for some crystalline host phases for radioactive waste. Fortunately, it is possible to calculate them. Although possible, the full ab initio calculation is not realistic because the calculation time rapidly becomes too long. These functions are obtained using an analytical model containing physical quantities determined by ab initio calculations. This enabled us to estimate the main thermodynamic functions of zircon ZrSiO4, fluor-apatite Ca10(PO4)6F2 and stoichiometric iodo-apatite Pb10(VO4)6I2 from the variation of cohesive energy with volume and the harmonic vibration frequencies at the center of the first Brillouin zone for the unit cell corresponding to maximum cohesive energy. These ab initio quantities are calculated with the DMOL3 code that solves the electronic Schroedinger equation using the electronic density functional theory (DFT) in local density approximation, corrected (NLDA) or not (LDA) with its gradient. To limit calculation time, we made additional approximations: - acoustic and optical vibrations beyond the first Brillouin zone center are described by the Debye and Einstein models respectively; - to allow thermal expansion of the crystal we used the quasi-harmonic approximation which assumes that frequency variations are proportional to volume variations. The proportionality coefficients known as Gruneisen coefficients are derived in this study, with specific approximations; - we used the spherical cellular approximation and considered the crystal as isotropic. The thermodynamic functions calculated with this model are the following measurable quantities : enthalpy and free enthalpy, heat capacity at constant pressure, bulk modulus and thermal expansion coefficient. For zircon and fluor-apatite, for which the main thermodynamic functions are experimentally known, the enthalpy of formation are determined with less than 2% uncertainty, and heat capacities at constant pressure are well reproduced: For iodo-apatite, there are as yet no published experimental data to compare with the present theoretical results. This model can be applied to a wide range of crystals. (author)

111

Recent advancements in computational methods for protein-structure prediction have made it possible to generate the high-quality de novo models required for ab initio phasing of crystallographic diffraction data using molecular replacement. Despite those encouraging achievements in ab initio phasing using de novo models, its success is limited only to those targets for which high-quality de novo models can be generated. In order to increase the scope of targets to which ab initio phasing with de novo models can be successfully applied, it is necessary to reduce the errors in the de novo models that are used as templates for molecular replacement. Here, an approach is introduced that can identify and rebuild the residues with larger errors, which subsequently reduces the overall C(?) root-mean-square deviation (CA-RMSD) from the native protein structure. The error in a predicted model is estimated from the average pairwise geometric distance per residue computed among selected lowest energy coarse-grained models. This score is subsequently employed to guide a rebuilding process that focuses on more error-prone residues in the coarse-grained models. This rebuilding methodology has been tested on ten protein targets that were unsuccessful using previous methods. The average CA-RMSD of the coarse-grained models was improved from 4.93 to 4.06 Å. For those models with CA-RMSD less than 3.0 Å, the average CA-RMSD was improved from 3.38 to 2.60 Å. These rebuilt coarse-grained models were then converted into all-atom models and refined to produce improved de novo models for molecular replacement. Seven diffraction data sets were successfully phased using rebuilt de novo models, indicating the improved quality of these rebuilt de novo models and the effectiveness of the rebuilding process. Software implementing this method, called MORPHEUS, can be downloaded from http://www.riken.jp/zhangiru/software.html. PMID:23090401

Shrestha, Rojan; Simoncini, David; Zhang, Kam Y J

2012-11-01

112

The ab-initio density matrix renormalization group in practice

The ab-initio density matrix renormalization group (DMRG) is a tool that can be applied to a wide variety of interesting problems in quantum chemistry. Here, we examine the density matrix renormalization group from the vantage point of the quantum chemistry user. What kinds of problems is the DMRG well-suited to? What are the largest systems that can be treated at practical cost? What sort of accuracies can be obtained, and how do we reason about the computational difficulty in different molecules? By examining a diverse benchmark set of molecules: ?-electron systems, benchmark main-group and transition metal dimers, and the Mn-oxo-salen and Fe-porphine organometallic compounds, we provide some answers to these questions, and show how the density matrix renormalization group is used in practice.

Olivares-Amaya, Roberto; Hu, Weifeng; Nakatani, Naoki; Sharma, Sandeep; Yang, Jun; Chan, Garnet Kin-Lic

2015-01-01

113

Ab initio studies on polymers. V. All-trans-polyethylene

The ab initio crystal orbital method has been applied to study the electronic ground state of an infinite polyethylene chain in the all-trans conformation within the framework of the Hartree-Fock approximation. Gaussian basis sets of minimal and double zeta quality have been used to evaluate equilibrium geometry and longitudinal elastic modulus of this model system. A structure with rCC = 2.952 bohr, rCH = 2.082 bohr, ?CCC = 112.2°, and ?HCH = 107.4° has been found to be most stable and a longitudinal elastic modulus of 345 GPa is predicted. Basis set dependence and the influence of lattice sum truncations on the electronic band structure are thoroughly discussed. Calculations including polarization functions have subsequently been performed in order to obtain electronic band structure and density of states at a near Hartree-Fock limit quality.

Karpfen, Alfred

1981-07-01

114

Ab initio structural, elastic, and vibrational properties of carbon nanotubes

A study based on ab initio calculations is presented on the estructural, elastic, and vibrational properties of single-wall carbon nanotubes with different radii and chiralities. We use SIESTA, an implementation of pseudopotential-density-functional theory which allows calculations on systems with a large number of atoms per cell. Different quantities like bond distances, Young moduli, Poisson ratio and the frequencies of different phonon branches are monitored versus tube radius. The validity of expectations based on graphite is explored down to small radii, where some deviations appear related to the curvature effects. For the phonon spectra, the results are compared with the predictions of the simple zone-folding approximation. Except for the known defficiencies of this approximation in the low-frequency vibrational regions, it offers quite accurate results, even for relatively small radii.

Sánchez-Portál, D; Soler, J M; Rubio, A; Ordejón, P

1999-01-01

115

Ab-initio Determination of Light Hadron Masses

More than 99% of the mass of the visible universe is made up of protons and neutrons. Both particles are much heavier than their quark and gluon constituents, and the Standard Model of particle physics should explain this difference. We present a full ab-initio calculation of the masses of protons, neutrons and other light hadrons, using lattice quantum chromodynamics. Pion masses down to 190 mega electronvolts are used to extrapolate to the physical point with lattice sizes of approximately four times the inverse pion mass. Three lattice spacings are used for a continuum extrapolation. Our results completely agree with experimental observations and represent a quantitative confirmation of this aspect of the Standard Model with fully controlled uncertainties.

Dürr, S; Frison, J; Hölbling, C; Hoffmann, R; Katz, S D; Krieg, S; Kurth, T; Lellouch, L; Lippert, T; Szabó, K K; Vulvert, G

2009-01-01

116

Ab initio and RRKM calculations of o-benzyne pyrolysis

Recently, a new mechanism has been provided in the phenyl pyrolysis, that is, the phenyl dissociation favours the benzyne channel by losing an H atom [H. Wang, M. Frenklach, J. Phys. Chem., 98 (1994) 11465]. In this Letter, the dissociation of o-benzyne has been investigated by means of ab initio theory. The geometries and structures of o-benzyne with its pyrolysis products C 4H 2, C 2H 2 and also the transition state were optimized at the UHF/6-31G* level. The single point energies were refined by B3LYP/6-31G* calculations. The unimolecular rate constants for o-benzyne pyrolysis in different pressures were calculated by the Rice-Ramsperger-Kassel-Marcus (RRKM) method.

Deng, Wei-Qiao; Han, Ke-Li; Zhan, Ji-Ping; He, Guo-Zhong

1998-05-01

117

An Efficient Approach to Ab Initio Monte Carlo Simulation

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, is used to substantially decorrelate configurations at which the potential of interest is evaluated, thereby dramatically reducing the number needed to build ensemble averages at a given level of precision. The efficiency of this procedure is maximized on-the-fly through variation of the reference system thermodynamic state (characterized here by its inverse temperature \\beta^0), which is otherwise unconstrained. Local density approximation (LDA) results are presented for shocked states in argon at pressures from 4 to 60 GPa. Depending on the quality of the reference potential, the acceptance probability is enhanced by factors of 1.2-28 relative to unoptimized NMC sampling, and the procedure's efficiency is found to be competitive with that of standard ab initio...

Leiding, Jeff

2013-01-01

118

Ab initio theoretical optical rotations of small molecules

Optical rotations of small chiral molecules have been calculated ab initio to evaluate the role of substituents and of conformations. The optical rotations of oxaziridines provide a nice correlation between the sign of optical rotation and absolute configuration. Such correlation is not obvious in the case of diaziridines and tetrahydrofurans. The optical rotations obtained for different conformers of 3-butyn-2-ol suggested a possible predominant conformation in liquid solutions. The prediction of optical rotations, as a function of dihedral angle, for H 2O 2 and H 2S 2 reveal that the sign of optical rotation is negative for counter-clockwise dihedral angles (M-helicity) and the magnitude is maximum at a dihedral angle of 90° (in H 2O 2) or 110° (in H 2S 2).

Polavarapu, Prasad L.; Chakraborty, Dilip K.

1999-01-01

119

Ab Initio Large-Basis No-Core Shell Model

Energy Technology Data Exchange (ETDEWEB)

We discuss the motivation, theory, and formulation of the ab initio No-Core Shell Model (NCSM). In this method the effective Hamiltonians are derived microscopically from realistic nucleon-nucleon (NN) and theoretical three-nucleon (NNN) potentials, as a function of the finite harmonic-oscillator (HO) basis space. We present converged results for the A = 3 and 4 nucleon systems, which are in agreement with results obtained by other exact methods, followed by results for p-shell nuclei. Binding energies, rms radii, excitation spectra, and electromagnetic properties are discussed.The favorable comparison with available data is a consequence of the underlying NN and NNN interactions rather than a phenomenological fit.

Barrett, B R; Navratil, P; Nogga, A; Ormand, W E; Stetcu, I; Vary, J P; Zhan, H

2005-02-11

120

Ab initio Potential Energy Surface for H-H2

Ab initio calculations employing large basis sets are performed to determine an accurate potential energy surface for H-H2 interactions for a broad range of separation distances. At large distances, the spherically averaged potential determined from the calculated energies agrees well with the corresponding results determined from dispersion coefficients; the van der Waals well depth is predicted to be 75 +/- (mu)E(sub h). Large basis sets have also been applied to reexamine the accuracy of theoretical repulsive potential energy surfaces. Multipolar expansions of the computed H-H2 potential energy surface are reported for four internuclear separation distances (1.2, 1.401, 1.449, and 1.7a(sub 0) of the hydrogen molecule. The differential elastic scattering cross section calculated from the present results is compared with the measurements from a crossed beam experiment.

Partridge, Harry; Bauschlicher, Charles W., Jr.; Stallcop, James R.; Levin, Eugene

1993-01-01

121

Ab initio electronic and lattice dynamical properties of cerium dihydride

The rare-earth metal hydrides are interesting systems because of the dramatic structural and electronic changes due to the hydrogen absorption and desorption. Among them, cerium dihydride (CeH2) is one of the less studied rare-earth metal-hydride. To have a better understanding, we have performed an ab initio study of electronic and lattice dynamical properties of CeH2 by using pseudopotential density functional theory within local density approximation (LDA) and a plane-wave basis. Electronic band structure of CeH2 have been obtained within LDA and as well as GW approximation. Lattice dynamical properties are calculated using density functional perturbation theory. The phonon spectrum is found to contain a set of high-frequency (˜ 850-1000 cm-1) optical bands, mostly hydrogen related, and low frequency cerium related acoustic modes climbing to 160 cm^ -1 at the zone boundary.

Gurel, Tanju; Eryigit, Resul

2007-03-01

122

Ab initio description of p-shell hypernuclei.

We present the first ab initio calculations for p-shell single-? hypernuclei. For the solution of the many-baryon problem, we develop two variants of the no-core shell model with explicit ? and ?(+),?(0),?(-) hyperons including ?-? conversion, optionally supplemented by a similarity renormalization group transformation to accelerate model-space convergence. In addition to state-of-the-art chiral two- and three-nucleon interactions, we use leading-order chiral hyperon-nucleon interactions and a recent meson-exchange hyperon-nucleon interaction. We validate the approach for s-shell hypernuclei and apply it to p-shell hypernuclei, in particular to (?)(7)Li, (?)(9)Be, and (?)(13)C. We show that the chiral hyperon-nucleon interactions provide ground-state and excitation energies that generally agree with experiment within the cutoff dependence. At the same time we demonstrate that hypernuclear spectroscopy provides tight constraints on the hyperon-nucleon interactions. PMID:25415901

Wirth, Roland; Gazda, Daniel; Navrátil, Petr; Calci, Angelo; Langhammer, Joachim; Roth, Robert

2014-11-01

123

Ab initio study of II-(VI)2 dichalcogenides.

The structural stabilities of the (Zn,Cd)(S,Se,Te)(2) dichalcogenides have been determined ab initio. These compounds are shown to be stable in the pyrite phase, in agreement with available experiments. Structural parameters for the ZnTe(2) pyrite semiconductor compound proposed here are presented. The opto-electronic properties of these dichalcogenide compounds have been calculated using quasiparticle GW theory. Bandgaps, band structures and effective masses are proposed as well as absorption coefficients and refraction indices. The compounds are all indirect semiconductors with very flat conduction band dispersion and high absorption coefficients. The work functions and surface properties are predicted. The Te and Se based compounds could be of interest as absorber materials in photovoltaic applications. PMID:21937783

Olsson, P; Vidal, J; Lincot, D

2011-10-12

124

Ab initio study of helium behavior in titanium tritides

Energy Technology Data Exchange (ETDEWEB)

Ab initio calculations based on density functional theory have been performed to investigate the relative stability of titanium tritides and the helium behavior in stable titanium tritides. The results show that the ?-phase TiT1.5 without two tritium along the [100] direction (TiT1.5[100]) is more stable than other possible structures. The stability of titanium tritides decrease with the increased generation of helium in TiT1.5[100]. In addition, helium generated by tritium decay prefers locating at a tetrahedral site, and favorably migrates between two neighbor vacant tetrahedral sites through an intermediate octahedral site in titanium tritides, with a migration energy of 0.23 eV. Furthermore, helium is easily accumulated on a (100) plane in ?-phase TiT1.5[100].

Liang, J. H.; Dai, Yunya; Yang, Li; Peng, SM; Fan, K. M.; Long, XG; Zhou, X. S.; Zu, Xiaotao; Gao, Fei

2013-03-01

125

Ab initio oscillator strengths and radiative lifetimes for Ca IX

International Nuclear Information System (INIS)

The configuration interaction method realized in the basis of Hartree-Fock functions and transformed radial orbitals with variable parameters is applied to the ab initio calculation of electric dipole transition probabilities from the levels of configurations 3s3p, 3p2, 3s3d, 3p3d, 3d2, 3s4l (l ? 3) and 3p4l (l ? 1) of the Ca IX ion. Relativistic corrections are accounted for within the Breit-Pauli approximation. Using the transition probabilities obtained, the radiative lifetimes of levels of the configurations indicated are determined. The calculated results are compared with the recent experimental data and theoretical results of other authors

126

Ab initio studies on complexes formed by melamine and cyclotrione

Directory of Open Access Journals (Sweden)

Full Text Available Ab initio methods were used to study the binding energies of non-bonded complexes formed by melamine and cyclotrione, with the STO-3G, 3-21G and 6-31G (d basis sets. The electronic spectra were computed using the INDO/CIS method, and the IR spectra, Raman and NMR spectra with the RHF/6-31G (dmethod. It was demonstrated that the complexes could be formed because of the negative binding energies, which were changed with the change in the electronic properties of the monomers. A red-shift of the first absorptions in the electronic spectra and the vibrational frequencies of the N–H bonds in the IR and Raman spectra of the complexes, compared with those of the monomers, occurred; simultaneously, the 1Hand 13C chemical shifts were altered, due to the non-bonded interaction.

LIANGIANG ZHU

2007-04-01

127

Self-vacancies in Gallium Arsenide: an ab initio calculation

We report here a reexamination of the static properties of vacancies in GaAs by means of first-principles density-functional calculations using localized basis sets. Our calculated formation energies yields results that are in good agreement with recent experimental and {\\it ab-initio} calculation and provide a complete description of the relaxation geometry and energetic for various charge state of vacancies from both sublattices. Gallium vacancies are stable in the 0, -, -2, -3 charge state, but V_Ga^-3 remains the dominant charge state for intrinsic and n-type GaAs, confirming results from positron annihilation. Interestingly, Arsenic vacancies show two successive negative-U transitions making only +1, -1 and -3 charge states stable, while the intermediate defects are metastable. The second transition (-/-3) brings a resonant bond relaxation for V_As^-3 similar to the one identified for silicon and GaAs divacancies.

El-Mellouhi, F; El-Mellouhi, Fedwa; Mousseau, Normand

2004-01-01

128

Ab-initio study of fluorine-doped tin dioxide: A prospective catalyst support for water electrolysis

International Nuclear Information System (INIS)

In an attempt to identify new electrochemically stable catalyst supports for electrolysis of water, the electronic structure of SnO2 doped with different fluorine concentrations has been calculated using the Vienna ab-initio simulation package (VASP) in the projector-augmented wave (PAW) method with the general gradient approximation (GGA) for conducting the exchange-correlation corrections. The role of fluorine in improving the electronic conductivity is discussed. An increase in the density of electronic states at the Fermi level with increase in the concentration of fluorine incorporated into the main SnO2 matrix agrees well with published experimental observations. Despite a gradual decrease in the cohesive energies for the fluorine-doped tin oxide with increase in fluorine concentration, the doped material still remains an appropriate candidate for use as catalyst supports in water electrolysis warranting further experimental validation. -- Research Highlights: ? Fluorine-doped tin oxide is a potentially stable catalyst support for water electrolysis. ? Electronic conductivity dependence on fluorine concentration is determined by the electronic structure. ? Chemical and structural stability-marginal decrease compared to undoped oxide. ? Catalyst support-fluorine-doped tin oxide is a promising catalyst support for water electrolysis.

129

Emergence of rotational bands in ab initio no-core configuration interaction calculations

Rotational bands have been observed to emerge in ab initio no-core configuration interaction (NCCI) calculations for p-shell nuclei, as evidenced by rotational patterns for excitation energies, electromagnetic moments, and electromagnetic transitions. We investigate the ab initio emergence of nuclear rotation in the Be isotopes, focusing on 9Be for illustration, and make use of basis extrapolation methods to obtain ab initio predictions of rotational band parameters for comparison with experiment. We find robust signatures for rotational motion, which reproduce both qualitative and quantitative features of the experimentally observed bands.

Caprio, M A; Vary, J P; Smith, R

2015-01-01

130

Heats of Segregation of BCC Binaries from ab Initio and Quantum Approximate Calculations

We compare dilute-limit heats of segregation for selected BCC transition metal binaries computed using ab initio and quantum approximate energy methods. Ab initio calculations are carried out using the CASTEP plane-wave pseudopotential computer code, while quantum approximate results are computed using the Bozzolo-Ferrante-Smith (BFS) method with the most recent LMTO-based parameters. Quantum approximate segregation energies are computed with and without atomistic relaxation, while the ab initio calculations are performed without relaxation. Results are discussed within the context of a segregation model driven by strain and bond-breaking effects. We compare our results with full-potential quantum calculations and with available experimental results.

Good, Brian S.

2004-01-01

131

Hydrogen adsorption on boron doped graphene: an {\\it ab initio} study

The electronic and structural properties of (i) boron doped graphene sheets, and (ii) the chemisorption processes of hydrogen adatoms on the boron doped graphene sheets have been examined by {\\it ab initio} total energy calculations.

Miwa, R. H.; Martins, T. B.; Fazzio, A.

2007-01-01

132

DEFF Research Database (Denmark)

Time-resolved photoelectron spectroscopy and ab initio multiple spawning were applied to the ultrafast non-adiabatic dynamics of hexamethylcyclopentadiene. The high level of agreement between experiment and theory associates wavepacket motion with a distinct degree of freedom.

Wolf, T. J. A.; Kuhlman, Thomas Scheby

133

Ab initio methods to oxides, and atomic orbitals in te PAW framework

International Nuclear Information System (INIS)

The accuracy of ab initio density functional theory calculations depends crucially on the applied exchange-correlation functional. In recent years, a true zoo of functionals has emerged in particular in the quantum chemistry community. All these developments were aimed on an improved description of different properties of molecules, solids and surfaces. In the first part of this thesis we apply four different exchange-correlation functionals (LDA, PBE, PBEsol and HSE03) to two model perovskites, namely SrTiO3 and BaTiO3. We evaluate structural, electronic and phonon properties in the high temperature cubic as well as the tetragonal distorted phase with special attention on the zone-centred phonon mode. Our results show that the ferroelectric instability strongly depends on the volume and to a lesser extent on the applied functional. The second part of the thesis concentrates on the description of the polar oxygen terminated surface of ZnO. In the simple ionic picture the surface is electrostatically unstable due to a diverging electrostatic energy and has to adopt a modified surface structure to compensate for the polarity. In a close collaboration with experiment, a novel reconstruction is suggested. The remarkable observation is that the previously investigated oxygen terminated surface behaves very different than the zinc terminated surface. The difference is explained by the different bond preferences of Zn and O atoms: as a d-element Zn atom of Zn and O atoms: as a d-element Zn atoms are more flexible than O atoms. The final part of the thesis concentrates on the implementation of a local basis set code in VASP. We derive all required formulas for an atomic orbital basis set expanded in spherical Bessel functions within the projector augmented wave framework. Particular emphasis was placed on an implementation that maintains to a very high accuracy the translational invariance of the Hamiltonian. The basis set was optimized to achieve this aim. This is demonstrated for few simple test cases. (author)

134

Ab initio and finite-temperature molecular dynamics studies of lattice resistance in tantalum

This manuscript explores the apparent discrepancy between experimental data and theoretical calculations of the lattice resistance of bcc tantalum. We present the first results for the temperature dependence of the Peierls stress in this system and the first ab initio calculation of the zero-temperature Peierls stress to employ periodic boundary conditions, which are those best suited to the study of metallic systems at the electron-structure level. Our ab initio value for t...

Segall, D. E.; Strachan, Alejandro; Ismail-beigi, Sohrab; Goddard Iii, William A.; Arias, T. A.

2002-01-01

135

Ab initio Defect Energetics in LaBO3 Perovskite Solid Oxide Fuel Cell Materials

Perovskite materials of the form ABO3 are a promising family of compounds for use in solid oxide fuel cell (SOFC) cathodes. Study of the physics of these compounds under SOFC conditions with ab initio methods is particularly challenging due to high temperatures, exchange of oxygen with O2 gas, and correlated electron effects. This paper discusses an approach to performing ab initio studies on these materials for SOFC applications and applies the approach to calculate vacancy formation energi...

Lee, Yueh-lin; Morgan, Dane; Kleis, Jesper; Rossmeisl, Jan

2010-01-01

136

Ab initio simulations of iron-nickel alloys at Earth's core conditions

We report ab initio density functional theory calculations on iron–nickel (Fe?Ni) alloys at conditions representative of the Earth's inner core. We test different concentrations of Ni, up to ?39 wt% using ab initio lattice dynamics, and investigate the thermodynamic and vibrational stability of the three candidate crystal structures (bcc, hcp and fcc). First of all, at inner core pressures, we find that pure Fe transforms from the hcp to the fcc phase at around 6000 K. Secondly, in agre...

Cote, A. S.; Vocadlo, L.; Brodholt, J. P.

2012-01-01

137

Ab-Initio Molecular Dynamics Acceleration Scheme with an Adaptive Machine Learning Framework

Quantum mechanics based ab-initio molecular dynamics (MD) simulation schemes offer an accurate and direct means to monitor the time-evolution of materials. Nevertheless, the expensive and repetitive energy and force computations required in such simulations lead to significant bottlenecks. Here, we lay the foundations for such an accelerated ab-initio MD approach integrated with a machine learning framework. The proposed algorithm learns from previously visited configuration...

Botu, Venkatesh; Ramprasad, Rampi

2014-01-01

138

A biased potential molecular dynamics simulation approach, accelerated molecular dynamics (AMD), has been implemented in the framework of ab initio molecular dynamics for the study of chemical reactions. Using two examples, the double proton transfer reaction in formic acid dimer and the hypothetical adiabatic ring opening and subsequent rearrangement reactions in methylenecyclopropane, it is demonstrated that ab initio AMD can be readily employed to efficiently explore the reactive potential...

Pierce, Levi C. T.; Markwick, Phineus R. L.; Mccammon, J. Andrew; Doltsinis, Nikos L.

2011-01-01

139

Ab initio study of edge sites reactivity on pyrophyllite

Energy Technology Data Exchange (ETDEWEB)

The crystal chemistry and surface site reactivity of the phyllosilicate minerals is a key issue for modelling the ion mobility and retardation in clay sediments. Various cation substitutions in the TOT layer of the 2:1 phyllosilicates result in a permanent structural charge near basal plane which is responsible for swelling and the sorption of ions by a cation exchange mechanism. In contrast, the pH-dependent uptake of cations is controlled by protonation/de-protonation reactions on the edge sites of the TOT layer. Various models have been proposed to explain the reactivity of the edge sites based on macroscopic experiments. A detailed understanding of this process on an atomistic level is still missing. We are using electronic structure calculations and ab initio MD simulations in order to understand the mechanism of pH dependent sorption of cations on edge sites of pyrophyllite and the transport properties of aqueous solutions in compacted pyrophyllite. The calculations provide important constrains for the macroscopic surface complexation models of clay minerals. (authors)

Churakov, S.V. [Paul Scherrer Institute, Nuclear Energy and Safety Department, Lab. for Waste Management, Villigen PSI (Switzerland)

2005-07-01

140

Ab initio calculations of the absorption spectrum of chalcone

The excitation energies and excited states of trans-chalcone ( trans-( s-cis)-1,3-diphenylpropenone), and several related molecules ( trans-( s-cis)-3-phenylpropenal, s-cis-1-phenylpropenone, propenal, trans-( s-cis)-1-(4-hydroxyphenyl)-3-phenylpropenone, trans-( s-cis)3-(4-hydroxyphenyl)-1-phenylpropenone) have been calculated using single reference ab initio molecular orbital methods, and characterized by attachment-detachment density analysis. The results suggest assignments for the lowest three electronic transitions observed experimentally for trans-( s-cis)-chalcone in solution. The extent of localization of the electronic transitions is established by calculations on the excited states of trans-( s-cis)-3-phenylpropenal, s-cis-1-phenylpropenone and propenal, as well as analysis of the chalcone calculations. Contrary to some previous work, none of these excitations are strongly delocalized over the entire molecule. Calculated substituent shifts for the hydroxy chalcones are in qualitative agreement with experimental data, and support the localized interpretation of the main ?? ?* transition.

Oumi, Manabu; Maurice, David; Head-Gordon, Martin

1999-03-01

141

Ab initio simulations of MgO under extreme conditions

We determined the phase diagram of magnesium oxide with finite-temperature density functional theory molecular dynamics simulations up to temperatures and pressures as relevant for the deep interior of super-Earths and in rocky cores of giant planets such as Jupiter. The equation of state data, the Hugoniot, and a ramp compression curve are computed and compared to earlier results from diamond anvil cell and (decaying) shock wave experiments. In addition, the dynamical electrical conductivity and the reflectivity along the experimental Hugoniot curve are calculated in order to characterize electronic structure changes under compression. The structural properties of MgO are identified using pair correlation functions and self-diffusion coefficients. The solid-solid coexistence line is calculated by comparing the free enthalpies of the B1 and the B2 phase. The free energy of the solid phases is determined via thermodynamic relations using the ab initio simulation results and phonon calculations in the harmonic approximation. Our results indicate that the solid B2 phase of MgO does not occur in the interior of the Earth but may play an important role in super-Earths and in rocky planetary cores.

Cebulla, Daniel; Redmer, Ronald

2014-04-01

142

Ab initio calculations on electronic states of Be13

International Nuclear Information System (INIS)

A cluster of 13 beryllium atoms has been studied in ab initio Hartree--Fock calculations. The chosen geometric configuration has D/sub 3h/ symmetry and corresponds to a central Be with 12 atoms situated at the hexagonal close-packed, nearest-neighbor positions. The lowest energy electronic state among those investigated is 5A/sup double-prime/1 and the first excited state is 5E'' lying at 1.12 eV. A total of 14 states were identified below 2.0 eV. The 5A/sup primeprime/1 Hartree--Fock ground state has a binding energy of 12.0 kcal/mol relative to the separated atoms and an ionization potential of 0.54 eV. Total valence energies, orbital energies, binding energies, electric field gradients, diamagnetic shielding constants, nuclear--electron potentials, second moments, and Mulliken populations are reported. In addition, the cluster calculations give a reasonable estimate for the Sternheimer correction to the electric field gradient of the bulk metal

143

Nature of magnetism in iron pnictides: an ab initio study

Energy Technology Data Exchange (ETDEWEB)

While it is commonly believed that magnetic-mediate pairing is the source of superconductivity in the iron-based superconductors, the nature of magnetism is still under debate. We apply ab initio molecular dynamics to investigate physical properties of LaOFePn, BaFe{sub 2}Pn{sub 2} and LiFePn (Pn=As,Sb), so-called 1111, 122 and 111 compounds, respectively. We find that, with substitution of As by Sb, the stripe-type antiferromagnetic orderings are always enhanced. By calculating Pauli susceptibility, we attribute the enhancement of magnetization to the increase of instability at ({pi},{pi}) when As is substituted by Sb. Furthermore, we study the magnetic and lattice properties of LaOFePn (Pn=P,As,Sb,Bi) as well as ScOFeP, ScOFeAs and YOFeP and argue that LaOFeSb would be a candidate for a superconductor with highest transition temperature among the investigated compounds. We further suggest that the absence of antiferromagnetic phase in LaOFeP and the presence in LaOFeAs are due to the competition of instability in Pauli susceptibility between ({pi},{pi}) and (0,0) and therefore argue that superconductivity can only occur through doping in LaOFeSb.

Zhang, Yu-Zhong; Opahle, Ingo; Jeschke, Harald; Valenti, Roser [Goethe-Universitaet Frankfurt, Max-von-Laue-Strasse 1, 60438 Frankfurt am Main (Germany)

2010-07-01

144

Ab initio and kinetic modeling studies of formic acid oxidation

DEFF Research Database (Denmark)

A detailed chemical kinetic model for oxidation of formic acid (HOCHO) in flames has been developed, based on theoretical work and data from literature. Ab initio calculations were used to obtain rate coefficients for reactions of HOCHO with H, O, and HO2. Modeling predictions with the mechanism have been compared to the experimental results of de Wilde and van Tiggelen (1968) who measured the laminar burning velocities for HOCHO flames over a range of stoichiometries and dilution ratios. The modeling predictions are generally satisfactory. The governing reaction mechanisms are outlined based on calculations with the kinetic model. Formic acid is consumed mainly by reaction with OH, yielding OCHO, which dissociates rapidly to CO2 + H, and HOCO, which may dissociate to CO + OH or CO2 + H, or react with H, OH, or O2 to form more stable products. The branching fraction of the HOCHO + OH reaction, as well as the fate of HOCO, determines the oxidation rate of formic acid. At lower temperatures HO2, formed from HOCO + O2, is an important chain carrier and modeling predictions become sensitive to the HOCHO + HO2 reaction. © 2014 The Combustion Institute.

Marshall, Paul; Glarborg, Peter

2015-01-01

145

Magnetic response of carbon nanotubes from ab initio calculations

We present {\\it ab initio} calculations of the magnetic susceptibility and of the $^{13}$C chemical shift for carbon nanotubes, both isolated and in bundles. These calculations are performed using the recently proposed gauge-including projector augmented-wave approach for the calculation of magnetic response in periodic insulating systems. We have focused on the semiconducting zigzag nanotubes with diameters ranging from 0.6 to 1.6 nm. Both the susceptibility and the isotropic shift exhibit a dependence with the diameter (D) and the chirality of the tube (although this dependence is stronger for the susceptibility). The isotropic shift behaves asymptotically as $\\alpha/D + 116.0$, where $\\alpha$ is a different constant for each family of nanotubes. For a tube diameter of around 1.2 nm, a value normally found in experimental samples, our results are in excellent agreement with experiments. Moreover, we calculated the chemical shift of a double-wall tube. We found a diamagnetic shift of the isotropic lines corr...

Marques, M A L; Mauri, F; Marques, Miguel A.L.; Avezac, Mayeul d'; Mauri, Francesco

2005-01-01

146

Ab initio calculation of infrared intensities for hydrogen peroxide

Results of an ab initio SCF quantum mechanical study are used to derive estimates for the infrared intensities of the fundamental vibrations of hydrogen peroxide. Atomic polar tensors (APTs) were calculated on the basis of a 4-31G basis set, and used to derive absolute intensities for the vibrational transitions. Comparison of the APTs calculated for H2O2 with those previously obtained for H2O and CH3OH, and of the absolute intensities derived from the H2O2 APTs with those derived from APTs transferred from H2O and CH3OH, reveals the sets of values to differ by no more than a factor of two, supporting the validity of the theoretical calculation. Values of the infrared intensities obtained correspond to A1 = 14.5 km/mol, A2 = 0.91 km/mol, A3 = 0.058 km/mol, A4 = 123 km/mol, A5 = 46.2 km/mol, and A6 = 101 km/mol. Charge, charge flux and overlap contributions to the dipole moment derivatives are also computed.

Rogers, J. D.; Hillman, J. J.

1982-01-01

147

Operator evolution for ab initio theory of light nuclei

The past two decades have seen a revolution in ab initio calculations of nuclear properties. One key element has been the development of a rigorous effective interaction theory, applying unitary transformations to soften the nuclear Hamiltonian and hence accelerate the convergence as a function of the model space size. For consistency, however, one ought to apply the same transformation to other operators when calculating transitions and mean values from the eigenstates of the renormalized Hamiltonian. Working in a translationally invariant harmonic oscillator basis for the two- and three-nucleon systems, we evolve the Hamiltonian, square radius, and total dipole strength operators by the similarity renormalization group (SRG). The inclusion of up to three-body matrix elements in the 4He nucleus all but completely restores the invariance of the expectation values under the transformation. We also consider a Gaussian operator with adjustable range; short ranges have the largest absolute renormalization when including two- and three-body induced terms, while at long ranges the induced three-body contribution takes on increased relative importance.

Schuster, Micah D.; Quaglioni, Sofia; Johnson, Calvin W.; Jurgenson, Eric D.; Navrátil, Petr

2014-07-01

148

Hydrogen adsorption on the ?-graphyne using ab initio calculations

In this study, we use the Siesta ab initio code based on Density Functional Theory (DFT) to determine the feasibility of hydrogen storage on the ?-graphyne. We examined the effect of hydrogen adsorption on the structural properties, the density of states of this nano structure. Calculations were performed in the GGA and LDA approximations. We find that in the case of chemical adsorption of hydrogen, functional exchange-correlation PBE (GGA) in explaining chemical bonds have more accuracy and leads to more stable structures. Adsorption is chemical and the binding energy of single and double hydrogen adsorption is -2.28 eV and -3.48 eV, respectively. Our calculations show that the adsorption of one hydrogen atom induces a magnetic moment as 1 ?B, because of breaking of ?-bonds and generate unpaired electron and system find ferromagnetic configuration. Further analysis indicates that adsorption of second hydrogen eliminates magnetization and the semi metalic ?-graphyne structure attains a band gap of 2 eV upon hydrogenation.

Drogar, J.; Roknabadi, M. R.; Behdani, M.; Modarresi, M.; Kari, A.

2014-11-01

149

Ab-initio description of p-shell hypernuclei

International Nuclear Information System (INIS)

Tremendous progress is being made on the experimental study of hypernuclei, especially on the spectroscopy of p-shell hypernuclei. Their theoretical description, however, is limited to phenomenological models or very light (i.e. s-shell) systems. We present the first ab-initio calculations of p-shell hypernuclei using chiral Hamiltonians including hyperon-nucleon and two- plus three-nucleon interactions, which to date constitute the most consistent starting-point to solving the hypernuclear many-body problem. The many-body calculations are performed in the framework of the importance-truncated no-core shell model using leading-order (LO) chiral hyperon-nucleon and chiral two- plus three-body nucleon-nucleon interactions at N3LO and N2LO, respectively. To improve convergence with respect to model space size, the interactions are evolved consistently using a similarity renormalization group transformation. We show absolute energies and spectra for selected single-lambda-hypernuclei up to the ?Li isotope chain.

150

Ab-initio description of p-shell hypernuclei

Energy Technology Data Exchange (ETDEWEB)

Tremendous progress is being made on the experimental study of hypernuclei, especially on the spectroscopy of p-shell hypernuclei. Their theoretical description, however, is limited to phenomenological models or very light (i.e. s-shell) systems. We present the first ab-initio calculations of p-shell hypernuclei using chiral Hamiltonians including hyperon-nucleon and two- plus three-nucleon interactions, which to date constitute the most consistent starting-point to solving the hypernuclear many-body problem. The many-body calculations are performed in the framework of the importance-truncated no-core shell model using leading-order (LO) chiral hyperon-nucleon and chiral two- plus three-body nucleon-nucleon interactions at N{sup 3}LO and N{sup 2}LO, respectively. To improve convergence with respect to model space size, the interactions are evolved consistently using a similarity renormalization group transformation. We show absolute energies and spectra for selected single-lambda-hypernuclei up to the {sub ?}Li isotope chain.

Wirth, Roland; Calci, Angelo; Langhammer, Joachim; Roth, Robert [Technische Univ. Darmstadt (Germany). Inst. fuer Kernphysik

2013-07-01

151

Ab Initio Description of p-Shell Hypernuclei

We present the first ab initio calculations for p-shell single-Lambda hypernuclei. For the solution of the many-baryon problem, we develop two variants of the no-core shell model with explicit Lambda and Sigma+, Sigma0, Sigma- hyperons including Lambda-Sigma conversion, optionally supplemented by a similarity renormalization group transformation to accelerate model-space convergence. In addition to state-of-the-art chiral two- and three-nucleon interactions, we use leading-order chiral hyperon-nucleon interactions and a recent meson-exchange hyperon-nucleon interaction. We validate the approach for s-shell hypernuclei and apply it to p-shell hypernuclei, in particular to Lambda-Li-7, Lambda-Be-9 and Lambda-C-13. We show that the chiral hyperon-nucleon interactions provide ground-state and excitation energies that agree with experiment within the cutoff dependence. At the same time we demonstrate that hypernuclear spectroscopy provides tight constraints on the hyperon-nucleon interactions and we discuss the im...

Wirth, Roland; Navratil, Petr; Calci, Angelo; Langhammer, Joachim; Roth, Robert

2014-01-01

152

An Ab Initio Based Potential Energy Surface for Water

We report a new determination of the water potential energy surface. A high quality ab initio potential energy surface (PES) and dipole moment function of water have been computed. This PES is empirically adjusted to improve the agreement between the computed line positions and those from the HITRAN 92 data base. The adjustment is small, nonetheless including an estimate of core (oxygen 1s) electron correlation greatly improves the agreement with experiment. Of the 27,245 assigned transitions in the HITRAN 92 data base for H2(O-16), the overall root mean square (rms) deviation between the computed and observed line positions is 0.125/cm. However the deviations do not correspond to a normal distribution: 69% of the lines have errors less than 0.05/cm. Overall, the agreement between the line intensities computed in the present work and those contained in the data base is quite good, however there are a significant number of line strengths which differ greatly.

Partridge, Harry; Schwenke, David W.; Langhoff, Stephen R. (Technical Monitor)

1996-01-01

153

Ab initio modeling of the motional Stark effect on MASTa)

A multichord motional Stark effect (MSE) system has recently been built on the MAST tokamak. In MAST the ? and ? lines of the MSE spectrum overlap due to the low magnetic field typical for present day spherical tokamaks. Also, the field curvature results in a large change in the pitch angle over the observation volume. The measured polarization angle does not relate to one local pitch angle but to an integration over all pitch angles in the observation volume. The velocity distribution of the neutral beam further complicates the measurement. To take into account volume effects and velocity distribution, an ab initio code was written that simulates the MSE spectrum on MAST. The code is modular and can easily be adjusted for other tokamaks. The code returns the intensity, polarized fraction, and polarization angle as a function of wavelength. Results of the code are presented, showing the effect on depolarization and wavelength dependence of the polarization angle. The code is used to optimize the design and calibration of the MSE diagnostic.

De Bock, M. F. M.; Conway, N. J.; Walsh, M. J.; Carolan, P. G.; Hawkes, N. C.

2008-10-01

154

Ab initio modeling of the motional Stark effect on MAST

International Nuclear Information System (INIS)

A multichord motional Stark effect (MSE) system has recently been built on the MAST tokamak. In MAST the ? and ? lines of the MSE spectrum overlap due to the low magnetic field typical for present day spherical tokamaks. Also, the field curvature results in a large change in the pitch angle over the observation volume. The measured polarization angle does not relate to one local pitch angle but to an integration over all pitch angles in the observation volume. The velocity distribution of the neutral beam further complicates the measurement. To take into account volume effects and velocity distribution, an ab initio code was written that simulates the MSE spectrum on MAST. The code is modular and can easily be adjusted for other tokamaks. The code returns the intensity, polarized fraction, and polarization angle as a function of wavelength. Results of the code are presented, showing the effect on depolarization and wavelength dependence of the polarization angle. The code is used to optimize the design and calibration of the MSE diagnostic.

155

Ab initio simulations of peptide-mineral interactions

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 ?-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.

Hug, Susanna; Hunter, Graeme K.; Goldberg, Harvey; Karttunen, Mikko

156

Ab initio simulations on rutile-based titania nanowires

International Nuclear Information System (INIS)

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 { 11-bar 0 } 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.

157

Ab initio molecular dynamics simulation of ionic liquids

Ab initio Car-Parinnello molecular dynamics is used to simulate the structure and the dynamics of 1-butyl-3-methylimidazolium iodide ([bmim]I) ionic liquid at 300K. Site-site pair correlation functions reveal that the anion has a strong interaction with any three C-H's of the imidazolium ring. The ring bends over and wraps around the anion such that the two nitrogen atoms take a distance to the anion. Electron donating butyl group contributes the electronic polarization in addition to geometrical (out-of-plane) polarization of the ring due to the liquid environment. This facilitates bending of the ring along the axis passing through nitrogen atoms. The average bending angle depends largely on the alkyl chain length and slightly on the anion type. Redistribution of electron density over the ring caused by the electron donating alkyl group provides additional independent evidence to the instability of lattice structure, hence the low melting point of the ionic liquid. Simulated viscosity and diffusion coefficients of [bmim]I are in quite agreement with the experiments.

Ghatee, Mohammad Hadi; Ansari, Younes

2007-04-01

158

Ab initio calculation of double ionization of atoms

The Solov'ev-Vinitsky method was used to perform an ab initio calculation of the triple-differential cross section for the double single-photon photoionization of helium for the case of equal emitted-electron energies. A Gaussian width ? describing angular electron-electron correlations at the total electron energy E taking values in range between 0.1 and 100 eV was obtained for this cross section. The results agree with available experimental data, but they raise a doubt as to whether the well-known Wannier law ? ? E 1/4 is applicable at experimentally accessible energies. The Gaussian width ? was investigated as a function of the total emitted-electron energy for targets that have a strongly asymmetric configuration of the initial state—specifically, a negative atomic-hydrogen ion H- and heliumin the 1 s2 s 1 S and 1 s3 s 1 S excited states. It was found that this function, ?( E), had a maximum at low energies. It was also shown that, at low energies, the dependence of the double-differential cross section on the angle between the emitted-electron momenta for the targets indicated above differed substantially from the Gaussian dependence, featuring maxima whose number was equal to the number of radial nodes in the initial state. This opens new possibilities for a qualitative analysis of the electron structure of targets.

Serov, V. V.

2013-02-01

159

Ab initio calculation of double ionization of atoms

Energy Technology Data Exchange (ETDEWEB)

The Solov'ev-Vinitsky method was used to perform an ab initio calculation of the triple-differential cross section for the double single-photon photoionization of helium for the case of equal emitted-electron energies. A Gaussian width {gamma} describing angular electron-electron correlations at the total electron energy E taking values in range between 0.1 and 100 eV was obtained for this cross section. The results agree with available experimental data, but they raise a doubt as to whether the well-known Wannier law {gamma} {proportional_to} E{sup 1/4} is applicable at experimentally accessible energies. The Gaussian width {gamma} was investigated as a function of the total emitted-electron energy for targets that have a strongly asymmetric configuration of the initial state-specifically, a negative atomic-hydrogen ion H{sup -} and heliumin the 1s2s{sup 1}S and 1s3s{sup 1}S excited states. It was found that this function, {gamma}(E), had a maximum at low energies. It was also shown that, at low energies, the dependence of the double-differential cross section on the angle between the emitted-electron momenta for the targets indicated above differed substantially from the Gaussian dependence, featuring maxima whose number was equal to the number of radial nodes in the initial state. This opens new possibilities for a qualitative analysis of the electron structure of targets.

Serov, V. V., E-mail: vladislav.serov@mail.ru [Saratov State University, Department of Theoretical Physics (Russian Federation)

2013-02-15

160

Ab initio effective interactions for sd-shell valence nucleons

We perform \\textit{ab initio} no core shell model calculations for $A=18$ and $19$ nuclei in a $4\\hbar\\Omega$, or $N_{\\rm max}=4$, model space using the effective JISP16 and chiral N3LO nucleon-nucleon potentials and transform the many-body effective Hamiltonians into the $0\\hbar\\Omega$ model space to construct the $A$-body effective Hamiltonians in the $sd$-shell. We separate the $A$-body effective Hamiltonians with $A=18$ and $A=19$ into inert core, one- and two-body components. Then, we use these core, one- and two-body components to perform standard shell model calculations for the $A=18$ and $A=19$ systems with valence nucleons restricted to the $sd$-shell. Finally, we compare the standard shell model results in the $0\\hbar\\Omega$ model space with the exact no core shell model results in the $4\\hbar\\Omega$ model space for the $A=18$ and $A=19$ systems and find good agreement.

Dikmen, E; Barrett, B R; Maris, P; Shirokov, A M; Vary, J P

2015-01-01

161

Ab-initio calculations of the Optical band-gap of TiO2 thin films

Titanium dioxide has been extensively studied in recent decades for its important photocatalytic application in environmental purification. The search for a method to narrow the optical band-gap of TiO2 plays a key role for enhancing its photocatalytic application. The optical band gap of epitaxial rutile and anatase TiO2 thin films deposited by helicon magnetron sputtering on sapphire and on SrTiO3 substrates was correlated to the lattice constants estimated from HRTEM images and SAED. The optical band-gap of 3.03 eV for bulk-rutile increased for the thin films to 3.37 on sapphire. The band gap of 3.20 eV for bulk-anatase increases to 3.51 on SrTiO3. In order to interpret the optical band gap expansion for both phases, ab-initio calculations were performed using the Vienna ab-initio software. The calculations for rutile as well anatase show an almost linear increase of the band gap width with decreasing volume or increasing lattice constant a. The calculated band gap fits well with the experimental values. T...

Wunderlich, W; Tanemura, M; Tanemura, S; Jin, P; Kaneko, K; Terai, A; Nabatova-Gabin, N; Belkada, R; Wunderlich, Wilfried; Miao, Lei; Tanemura, Masaki; Tanemura, Sakae; Jin, Ping; Kaneko, Kenji; Terai, Asuka; Nabatova-Gabin, Nataliya; Belkada, Rachid

2004-01-01

162

Ab initio quantum chemical design of supermolecule logical devices

The geometrical structure of both the ground and excited state of the azo-dyes: Disperse Orange 3 (DO3) and Ch2- C4H4-N=N-C44/H(subscript 4-CH2 molecules have been investigated applying the Hartree Fock (HF), density functional theory (DFT) methods with the Berny geometry optimization and Ames Laboratory determinant (ALDET)single- double-triple-quadra configuration interaction (SDTQ-CI) method. The investigations proved that the above-mentioned molecules can not rotate around the -N=N- bond. Thus, the alternative mechanism of the isomerization of the DO3 molecule per linear transition state has been suggested and investigated. The obtained one- and many- electron energy diagrams have been drawn. According to these diagrams the above mentioned isomerization way is possible. The mechanism of the isomerization of the azo-dyes molecule per linear transition state is suggested and investigated. The results of light induced internal molecular motions in azo-dyes molecules have been used for the design of light driven logically controlled molecular machines composed form photoactive organic molecules such as carbazole, 1,4- phenylenediamine (PhDA) and 4,5-dinitro- 9(dicyanomethylidene)-fluorene (DN9(CN)2F), Dithieno[3,2-b:2',3'-d]thiphene and Ferocene (C10H10Fe) molecules joined with -CH=CH- or -N=N- bridges. Ab initio DFT B3PW91 model using 6-311G** and Watanabe (WBTS) basis sets calculations show the stability of Sc3N and ErSc2 molecules which exist inside endohedral fullerene C80 derivatives: Sc3NC80. Analysis of electronic structure of inside clusters allowed proposing that these endohedral fullerenes might be used for electro- optical and magneto-optical switches and for information storage. We performed design of molecular logical devices based on organic electron donor and electron acceptor molecules, fullerene C60 substituted derivative CH2C60, electron donor-bridge-electron acceptor dyads and triads. Design of new series molecular implementations (MI) of two variable logic functions: AND (NAND), OR (NOR) is based on geometry optimization procedure. Molecular triggers and molecular dynamic memory were designed based on investigations of photo-excitation movements and charge transfer of aza-fullerene supermolecule (NH2)CH-NC59-NC59-CH(NO2). Our ab initio DFT B3PW91/LanL3DZ calculation of HOMO-LUMO gap in CdS nanocluster without four phenyle fragments gives value equal to 3.85 eV and the same method calculation of CdS nanocluster with four phenyle fragments gives HOMO-LUMO gap value equal to 3.66 eV. 121

Tamulis, Arvydas; Rinkevicius, Zilvinas; Tamuliene, Jelena; Tamulis, Vykintas; Balevicius, Mindaugas L.; Graja, Andrzej

2001-05-01

163

Ab initio study of the thermodynamic properties and the phonon calculations of Zircon and Reidite

Zircon and Reidite are the polymorphs of Zirconium Silicate which find its importance geologically, because of its natural hosting to various radioactive elements in the crust of the earth. High permittivity also makes it a promising material for the gate dielectric material in metal-oxide semiconductors. Knowledge of the thermodynamic properties and the phonon based calculations is very critical to understand the high temperature and high pressure properties in order to consider its application as an effective natural storage for the radioactive wastes. These properties are thoroughly studied both computationally and experimentally for zircon, while significantly less attention was paid to reidite in the literature. The thermodynamic properties and phonon calculations of Zircon and Reidite were studied using ab initio based periodic density-functional theory (DFT) based calculations using the generalized gradient approximation (GGA). Various properties such as free energy, internal energy, entropy, heat capacity and thermal displacement as a function of temperature is calculated using the PHONON software. Various phonon based density of states and dispersion curves are calculated and compared with the experimental data. No first principles based computational results were reported up to now. Calculated bulk properties agree very well with the experimental data in the literature.

Chaudhari, Mrunalkumar; Du, Jincheng

2011-03-01

164

Symplectic ab initio no-core shell model

Scientific Electronic Library Online (English)

Full Text Available SciELO Mexico | Language: English Abstract in spanish En el presente trabajo se confirma la importancia de la simetría simpléctica Sp(3,R) en la dinámica nuclear a través de estudios de interacciones nucleón-nucleón realistas así como de eigenestados calculados en el marco del modelo de capas sin carozo (NCSM, por sus siglas en inglés). Los resultados [...] demuestran para núcleos ligeros un gran traslapo entre la funciones de onda NCSM usando nada más los estados base con simetría Sp(3,R) con mayor deformación, lo cual abre la posibilidad para obtener convergencia de modos colectivos con energías altas y poder describir nucleos más pesados con una extensión del espacio de los estados base NCSM usando estados con simetría Sp(3,R). Además, las interacciones nucleón-nucleón realistas JISP16 y CD-Bonn favorecen la simetría simpléctica lo cual apunta a una explicación a nivel mas fundamental de la simetría simpléctica. Abstract in english The present study confirm the significanc of the symplectic Sp(3,R) symmetry in nuclear dynamics as unveiled, for the firs time, by examinations of realistic nucleon-nucleon (N N) interactions as well as of eigenstates calculated in the framework of the ab initio No-Core Shell Model (NCSM). The resu [...] lts reveal that the NCSM wave functions for light nuclei highly overlap (at the 90% level) with only a few of the most deformed Sp(3,R)-symmetric basis states. This points to the possibility of achieving convergence of higher-lying collective modes and reaching heavier nuclei by expanding the NCSM basis space beyond its current limits through Sp(3,R) basis states. Furthermore, the symplectic symmetry is found to be favored by the JISP16 and CD-Bonn realistic nucleon-nucleon interactions, which points to a more fundamental origin of the symplectic symmetry.

J.P., Draayer; T., Dytrych; K.D., Sviratcheva; C, Bahri; J.P., Vary.

2008-12-01

165

Ab initio molecular dynamics study of ferroelectric phase transitions

We have undertaken the first ever fully first-principles simulations of ferroelectric crystals at finite temperature with an aim to understand the nature of their phase transitions. In particular, we have studied the different aspects of phase transitions in two protypical ferroelectrics - PbTiO3 and KH2PO4. In PbTiO3, we have successfully reproduced the temperature-driven transition from a tetragonal to a cubic phase by using constant-pressure Car-Parrinello molecular dynamics. By defining suitable order parameters in terms of atomic displacements, we are able to monitor the approach of the cubic phase. Using a quasi-harmonic analysis, with the inclusion of a temperature dependent volume and the average thermal atomic displacements as the most basic effects of anharmonicity, we are also able to recover the softening of ferroelectric modes as well as other features seen in experiments. These observations confirm the predominantly displacive nature of the transition, while our simulations also indicate a possible build-up of disorder near the transition temperature. We have also studied the isotope effects in the ferroelectric transition in KH2PO4 by quantifying the temperature and mass dependence of the extent of delocalization of the hydrogens. Using a recently developed ab initio Open Path-integral Molecular Dynamics scheme we have calculated both the real and momentum-space distribution of the hydrogens in both protonated and deuterated KDP above and below their respective transition temperatures. We find that the two crystals not only involve different transition mechanisms but also the fluctuations above the transition temperature are of a qualitatively different nature.

Srinivasan, Varadharajan

166

AN AB INITIO MODEL FOR COSMIC-RAY MODULATION

Energy Technology Data Exchange (ETDEWEB)

A proper understanding of the effects of turbulence on the diffusion and drift of cosmic rays (CRs) is of vital importance for a better understanding of CR modulation in the heliosphere. This study presents an ab initio model for CR modulation, incorporating for the first time the results yielded by a two-component turbulence transport model. This model is solved for solar minimum heliospheric conditions, utilizing boundary values chosen so that model results are in reasonable agreement with spacecraft observations of turbulence quantities in the solar ecliptic plane and along the out-of-ecliptic trajectory of the Ulysses spacecraft. These results are employed as inputs for modeled slab and two-dimensional (2D) turbulence energy spectra. The modeled 2D spectrum is chosen based on physical considerations, with a drop-off at the very lowest wavenumbers. There currently exist no models or observations for the wavenumber where this drop-off occurs, and it is considered to be the only free parameter in this study. The modeled spectra are used as inputs for parallel mean free path expressions based on those derived from quasi-linear theory and perpendicular mean free paths from extended nonlinear guiding center theory. Furthermore, the effects of turbulence on CR drifts are modeled in a self-consistent way, also employing a recently developed model for wavy current sheet drift. The resulting diffusion and drift coefficients are applied to the study of galactic CR protons and antiprotons using a 3D, steady-state CR modulation code, and sample solutions in fair to good agreement with multiple spacecraft observations are presented.

Engelbrecht, N. E.; Burger, R. A. [Center for Space Research, North-West University, Potchefstroom 2520 (South Africa)

2013-07-20

167

An ab initio study of plutonium oxides surfaces

International Nuclear Information System (INIS)

By means of first-principles calculations, we have studied the atomic structure as well as the thermodynamic stability of various plutonium dioxide surfaces in function of their environment (in terms of oxygen partial pressure and temperature). All these simulations have been performed with the ABINIT code. It is well known that DFT fails to describe correctly plutonium-based materials since 5f electrons in such systems are strongly correlated. In order to go beyond DFT, we have treated PuO2 and ?-Pu2O3 in a DFT+U framework. We show that the couple of parameters (U,J) that works well for pure Pu is also well designed for describing ground state (GS) properties of these two oxides. The major improvement with respect with DFT is that we are able to predict an insulating GS in agreement with experiments. The presence of a gap in the DOS (Density of States) of plutonium oxides should play a significant role in the predicted surface reactivity. However, performing DFT+U calculations on surfaces of plutonium oxide from scratch was too ambitious. That is why we decided, as a first step, to study the stability of the (100), (110) and (111) surfaces of PuO2 in a DFT-GGA framework. For each of these orientations, we considered various terminations. These ab initio results have been introduced in a thermodynamic model which allows us to predict the relative stability of the different terminations as a function of temperature and oxygen partial pressure (pO2). We conclude that at room temperature and for pO2?10 atm., the polar O2-(100) termination is favoured. The stabilization of such a polar stoichiometric surface is surprising and should be confirmed by DFT+U calculations before any final conclusion. (authors)

168

Nonlinear elasticity in III-N compounds: Ab initio calculations

We have studied the nonlinear elasticity effects in zinc-blende and wurtzite crystallographic phases of III-N compounds. Particularly, we have determined the pressure dependences of elastic constants in InN, GaN, and AlN by performing ab initio calculations in the framework of plane-wave pseudopotential implementation of the density-functional theory. The calculations have been performed employing two exchange-correlation functionals, one within the local density approximation and the other within the generalized gradient approximation. We have found that C11 , C12 in zinc-blende nitrides and C11 , C12 , C13 , C33 in wurtzite nitrides depend significantly on hydrostatic pressure. Much weaker dependence on pressure has been observed for C44 elastic constant in both zinc-blende and wurtzite phases. Further, we have examined the influence of pressure dependence of elastic constants on the pressure coefficient of light emission, dEE/dP , in wurtzite InGaN/GaN and GaN/AlGaN quantum wells. We have shown that the pressure dependence of elastic constants leads to a significant reduction of dEE/dP in nitride quantum wells. Finally, we have considered the influence of nonlinear elasticity of III-N compounds on the properties of hexagonal nitride quantum dots (QDs). For typical wurtzite GaN/AlN QDs, we have shown that taking into account pressure dependence of elastic constants results in the decrease of volumetric strain in the QD region by about 7%. Simultaneously, the average z component of the piezoelectric polarization in the QDs increases by 0.1MV/cm compared to the case when linear elastic theory is used. Both effects, i.e., decrease of volumetric strain as well as increase of piezoelectric field, decrease the band-to-band transition energies in the QDs.

?epkowski, S. P.; Majewski, J. A.; Jurczak, G.

2005-12-01

169

Our aim is to address the question: how to generate line lists for molecular spectra containing line positions determined within experimental accuracy and predicted ab initio intensities in a consistent way for atmospheric, planetological and astrophysical applications? In this work we have developed a new combined spectroscopic model1 for methane vibrational polyads which involves all resonance terms very accurately derived from the molecular potential energy surface2 via high-order contact transformation (CT) method1. A subsequent "fine tuning" of the diagonal parameters allows achieving experimental accuracy for about 6000 Dyad and Pentad line positions whereas all resonance coupling parameters were held fixed to ab initio values. For determination of dipole transition moment parameters, we have applied two complementary methods. Initial values for the effective dipole moment were first computed from ab initio dipole moment surface (DMS)2, then the final parameters were fitted to selected ab initio line strengths previously computed3 from the same DMS by variational method. The new polyad model allows generating a spectral line list for the Dyad and Pentad bands with the accuracy ˜10-3 cm-1 for line positions combined with ab initio predictions for line intensities. Future prospectives for an application of this approach to other molecules will be discussed.

Tyuterev, V.; Rey, M.; Delahaye, T.; Tashkun, S.; Nikitin, A. V.; Kochanov, R.

2014-06-01

170

An ab initio study of plutonium oxides surfaces; Etude ab initio des surfaces d'oxydes de Pu

Energy Technology Data Exchange (ETDEWEB)

By means of first-principles calculations, we have studied the atomic structure as well as the thermodynamic stability of various plutonium dioxide surfaces in function of their environment (in terms of oxygen partial pressure and temperature). All these simulations have been performed with the ABINIT code. It is well known that DFT fails to describe correctly plutonium-based materials since 5f electrons in such systems are strongly correlated. In order to go beyond DFT, we have treated PuO{sub 2} and {beta}-Pu{sub 2}O{sub 3} in a DFT+U framework. We show that the couple of parameters (U,J) that works well for pure Pu is also well designed for describing ground state (GS) properties of these two oxides. The major improvement with respect with DFT is that we are able to predict an insulating GS in agreement with experiments. The presence of a gap in the DOS (Density of States) of plutonium oxides should play a significant role in the predicted surface reactivity. However, performing DFT+U calculations on surfaces of plutonium oxide from scratch was too ambitious. That is why we decided, as a first step, to study the stability of the (100), (110) and (111) surfaces of PuO{sub 2} in a DFT-GGA framework. For each of these orientations, we considered various terminations. These ab initio results have been introduced in a thermodynamic model which allows us to predict the relative stability of the different terminations as a function of temperature and oxygen partial pressure (p{sub O{sub 2}}). We conclude that at room temperature and for p{sub O{sub 2}}{approx}10 atm., the polar O{sub 2}-(100) termination is favoured. The stabilization of such a polar stoichiometric surface is surprising and should be confirmed by DFT+U calculations before any final conclusion. (authors)

Jomard, G.; Bottin, F.; Amadon, B

2007-07-01

171

Hydrogen adsorption on boron doped graphene: an ab initio study

International Nuclear Information System (INIS)

(i) The electronic and structural properties of boron doped graphene sheets, and (ii) the chemisorption processes of hydrogen adatoms on the boron doped graphene sheets have been examined by ab initio total energy calculations. In (i) we find that the structural deformations are very localized around the boron substitutional sites, and in accordance with previous studies (Endo et al 2001 J. Appl. Phys. 90 5670) there is an increase of the electronic density of states near the Fermi level. Our simulated scanning tunneling microscope (STM) images, for occupied states, indicate the formation of bright (triangular) spots lying on the substitutional boron (center) and nearest-neighbor carbon (edge) sites. Those STM images are attributed to the increase of the density of states within an energy interval of 0.5 eV below the Fermi level. For a boron concentration of ?2.4%, we find that two boron atoms lying on the opposite sites of the same hexagonal ring (B1-B2 configuration) represents the energetically most stable configuration, which is in contrast with previous theoretical findings. Having determined the energetically most stable configuration for substitutional boron atoms on graphene sheets, we next considered the hydrogen adsorption process as a function of the boron concentration, (ii). Our calculated binding energies indicate that the C-H bonds are strengthened near boron substitutional sites. Indeed, the binding energy of hydrogen adatoms forming a dimer-like strydrogen adatoms forming a dimer-like structure on the boron doped B1-B2 graphene sheet is higher than the binding energy of an isolated H2 molecule. Since the formation of the H dimer-like structure may represent the initial stage of the hydrogen clustering process on graphene sheets, we can infer that the formation of H clusters is quite likely not only on clean graphene sheets, which is in consonance with previous studies (Hornekaer et al 2006 Phys. Rev. Lett. 97 186102), but also on B1-B2 boron doped graphene sheets. However, for a low concentration of boron atoms, the formation of H dimer structures is not expected to occur near a single substitutional boron site. That is, the formation (or not) of H clusters on graphene sheets can be tuned by the concentration of substitutional boron atoms

172

Ab initio computational applications to complex biomolecular systems

A series of biomaterial related systems---including water and DNA molecules---have been studied using ab initio (first-principles) methods. By investigating the properties of water as the preliminary step, the hydrogen bond (HB) interactions, which play important roles in biomolecules, were better understood from the quantum mechanical viewpoint. The calculated K-edge x-ray absorption near edge structure (XANES) spectra of all 340 oxygen atoms in the model have been accumulated to reproduce the experimental one. The spectra were shown to be very sensitive to the HB configurations of O atoms, which could be used to elucidate the subtle structural variations in complex biomolecules. The simulation of single-molecule DNA overstretching experiments under torsionally constrained condition has been carried out afterwards. The initial DNA models were stretched stepwisely and eventually gained an extension of 1.5-fold (150% x the original length). The variation of total energy, atomic configuration, and the electronic structure during this process were analyzed in details. At the extension of ˜1.3-fold, the ring opening reactions occurred in the backbones. The backbone nicks appeared at elongations of ˜1.40-fold. The whole process was accompanied by HB breaking and charge transfers. We have proposed an overstretched structure named O-DNA (Opened-DNA) to clarify the confusion in understanding the behavior of DNA under high force load. With more experiences gained, a comprehensive methodology revealing the underlying principles of bioprocesses from the quantum mechanical viewpoint eventually come up. For the purpose of better computational accuracy, the scheme of implementing the generalized gradient approximation (GGA) exchange-correlation functionals into the Orthogonalized Linear Combination of Atomic Orbitals (OLCAO) program suite has been discussed, and the computational efficiency has been analyzed correspondingly. Moreover, the parallel strategy for performing evaluation on a regular mesh and relevant updates to the file system were also presented. All the fundamental works above paved the way for more sophisticated study on wet DNA model and interfaces between biomolecules and bioceramic materials in the future.

Liang, Lei

173

Ab Initio Computation of Dynamical Properties: Pressure Broadening

Rotational spectroscopy of polar molecules is the main observational tool in many areas of astrophysics, for gases of low densities (n ˜ 102 - 108 cm-3). Spectral line shapes in astrophysical media are largely dominated by turbulence-induced Doppler effects and natural line broadening are negligible. However line broadening remains an important tool for denser gases, like planetary high atmospheres. Understanding the excitation schemes of polar molecules requires the knowledge of excitation transfer rate due to collisional excitation, between the polar molecule and the ambient gas, usually H2. Transport properties in ionized media also require a precise knowledge of momentum transfer rates by elastic collisions. In order to assess the theoretically computed cross section and energy/momentum transfer rates, direct absolute experiments are scarce. The best way is to measure not individual scattering events but rather the global effect of the buffer gas, thanks to the pressure broadening cross sections, whose magnitude can be measured without any scaling parameters. At low temperatures, both elastic and inelastic scattering amplitudes are tested. At higher temperature, depending on the interaction strength, only inelastic scattering cross section are shown to play a significant role 1 ,2. Thanks to the advances of computer capabilities, it has become practical to compute spectral line parameters fromab initio quantum chemistry. In particular, the theory of rotational line broadening is readily incorporated into scattering quantum dynamical theory, like close-coupling schemes. The only approximations used in the computation are the isolated collision/isolated line approximations. We compute the non-binding interaction potential with high precision quantum chemistry and fit the resulting ab initio points onto a suitable functional. We have recently computed several such systems, for molecules in H2 buffer gas: H2O,3 H2CO,4 HCO+ .5 Detailed computations taking into account the ortho or para state of H2 were performed, at temperatures ranging from 10 K to 100K, typically. Reliable results are found, that compare favorably to experiments. In particular, the water-molecular hydrogen system has been thoroughly computed and successfully experimentally tested 6. New projects consider other simple molecules as well as heavier systems, relevant for cometary comae and planetary high atmospheres. as part of the GNU EPrints system , and is freely redistributable under the GPL .

Wiesenfeld, Laurent; Drouin, Brian

2014-06-01

174

An ab initio-based Er-He interatomic potential in hcp Er

We have developed an empirical erbium-helium (Er-He) potential by fitting to the results calculated from the ab initio method. Based on the electronic hybridization between Er and He atoms, an s-band model, along with a repulsive pair potential, has been derived to describe the Er-He interaction. The atomic configurations and the formation energies of single He defects, small He interstitial clusters (Hen) and He-vacancy (HenV) clusters obtained by ab initio calculations are used as the fitting database. The binding energies and relative stabilities of the HnVm clusters are studied by the present potential and compared with the ab initio calculations. The Er-He potential is also applied to study the migration of He in hcp Er at different temperatures, and He clustering is found to occur at 600 K in hcp Er crystal, which may be due to the anisotropic migration behavior of He interstitials.

Yang, L.; Ye, Y. T.; Fan, K. M.; Shen, H. H.; Peng, S. M.; Long, X. G.; Zhou, X. S.; Zu, X. T.; Gao, F.

2014-09-01

175

Shear stiffness in nanolaminar Ti3SiC2 challenges ab initio calculations.

Nanolaminates such as the M(n + 1)AX(n) (MAX) phases are a material class with ab initio derived elasticity tensors published for over 250 compounds. We have for the first time experimentally determined the full elasticity tensor of the archetype MAX phase, Ti(3)SiC(2), using polycrystalline samples and in situ neutron diffraction. The experimental elastic constants show extreme shear stiffness, with c(44) more than five times greater than expected for an isotropic material. Such shear stiffness is quite rare in hexagonal materials and strongly contradicts the predictions of all published MAX phase elastic constants derived from ab initio calculations. It is concluded that second order properties such as elastic moduli derived from ab initio calculations require careful experimental verification. The diffraction technique used currently provides the only method of verification for the elasticity tensor for the majority of new materials where single crystals are not available. PMID:21386405

Kisi, E H; Zhang, J F; Kirstein, O; Riley, D P; Styles, M J; Paradowska, A M

2010-04-28

176

Ab initio simulation of paramagnetic NMR spectra: the 31P NMR in oxovanadium phosphates.

A theoretical analysis of the temperature-dependent (31)P NMR signals for the ambient pressure vanadyl pyrophosphate AP-(VO)(2)P(2)O(7) and the oxovanadium hemihydrate hydrogenophosphate VO(HPO(4)).0.5H(2)O phases is reported. The ab initio calculation of the magnetic exchange parameters and the hyperfine constants gives access to an original ab initio simulation of NMR spectra. Such a strategy allows one to clarify the crystallographic nature of the different experimentally studied phases. For the vanadyl pyrophosphate ambient pressure structure, our simulations strongly support the presence of a monoclinic phase. Based on this assumption, hyperfine constants are extracted from the fit of the experimental data. These values are directly compared to the ab initio ones. PMID:12656632

Petit, Sébastien; Borshch, Serguei A; Robert, Vincent

2003-04-01

177

This article focuses on the development of an approach for ab initio protein structure prediction (PSP) without using any earlier knowledge from similar protein structures, as fragment-based statistics or inference of secondary structures. Such an approach is called purely ab initio prediction. The article shows that well-designed multiobjective evolutionary algorithms can predict relevant protein structures in a purely ab initio way. One challenge for purely ab initio PSP is the prediction of structures with ?-sheets. To work with such proteins, this research has also developed procedures to efficiently estimate hydrogen bond and solvation contribution energies. Considering van der Waals, electrostatic, hydrogen bond, and solvation contribution energies, the PSP is a problem with four energetic terms to be minimized. Each interaction energy term can be considered an objective of an optimization method. Combinatorial problems with four objectives have been considered too complex for the available multiobjective optimization (MOO) methods. The proposed approach, called "Multiobjective evolutionary algorithms with many tables" (MEAMT), can efficiently deal with four objectives through the combination thereof, performing a more adequate sampling of the objective space. Therefore, this method can better map the promising regions in this space, predicting structures in a purely ab initio way. In other words, MEAMT is an efficient optimization method for MOO, which explores simultaneously the search space as well as the objective space. MEAMT can predict structures with one or two domains with RMSDs comparable to values obtained by recently developed ab initio methods (GAPFCG , I-PAES, and Quark) that use different levels of earlier knowledge. PMID:23666867

Brasil, Christiane Regina Soares; Delbem, Alexandre Claudio Botazzo; da Silva, Fernando Luís Barroso

2013-07-30

178

We calculate the photoemission spectra of suspended and epitaxial doped graphene using an ab initio cumulant expansion of the Green's function based on the GW self-energy. Our results are compared to experiment and to standard GW calculations. For doped graphene on a silicon carbide substrate, we find, in contrast to earlier calculations, that the spectral function from GW only does not reproduce experimental satellite properties. However, ab initio GW plus cumulant theory combined with an accurate description of the substrate screening results in good agreement with experiment, but gives no plasmaron (i.e., no extra well-defined excitation satisfying Dyson's equation). PMID:25167020

Lischner, Johannes; Vigil-Fowler, Derek; Louie, Steven G

2013-04-01

179

International Nuclear Information System (INIS)

The ab initio/classical free energy perturbation (ABC-FEP) method proposed previously by Wood et al. [J. Chem. Phys. 110, 1329 (1999)] uses classical simulations to calculate solvation free energies within an empirical potential model, then applies free energy perturbation theory to determine the effect of changing the empirical solute-solvent interactions to corresponding interactions calculated from ab initio methods. This approach allows accurate calculation of solvation free energies using an atomistic description of the solvent and solute, with interactions calculated from first principles. Results can be obtained at a feasible computational cost without making use of approximations such as a continuum solvent or an empirical cavity formation energy. As such, the method can be used far from ambient conditions, where the empirical parameters needed for approximate theories of solvation may not be available. The sources of error in the ABC-FEP method are the approximations in the ab initio method, the finite sample of configurations, and the classical solvent model. This article explores the accuracy of various approximations used in the ABC-FEP method by comparing to the experimentally well-known free energy of hydration of water at two state points (ambient conditions, and 973.15 K and 600 kg/m3). The TIP4P-FQ model [J. Chem. Phys. 101, 6141 (1994)] is found to be a reliable solvent model for use with this method, even at supercritical conditions. Results depend supercritical conditions. Results depend strongly on the ab initio method used: a gradient-corrected density functional theory is not adequate, but a localized MP2 method yields excellent agreement with experiment. Computational costs are reduced by using a cluster approximation, in which ab initio pair interaction energies are calculated between the solute and up to 60 solvent molecules, while multi-body interactions are calculated with only a small cluster (5 to 12 solvent molecules). Sampling errors for the ab initio contribution to solvation free energies are ±2 kJ/mol or less when 50-200 configurations are used. Using the largest clusters and most accurate ab initio methods, ABC-FEP predicts hydration free energies of water at both state points that agree with equations of state, within the sampling error. These results are the first calculation of a free energy of solvation at extreme conditions from a fully atomistic model with ab initio methods. (c) 2000 American Institute of Physics

180

X-ray absorption Debye-Waller factors from ab initio molecular dynamics

An ab initio equation of motion method is introduced to calculate the temperature-dependent mean-square vibrational amplitudes ?2 which appear in the Debye-Waller factors in x-ray absorption, x-ray scattering, and related spectra. The approach avoids explicit calculations of phonon modes, and is based instead on calculations of the displacement-displacement time correlation function from ab initio density functional theory molecular dynamics simulations. The method also yields the vibrational density of states and thermal quantities such as the lattice free energy. Illustrations of the method are presented for a number of systems and compared with other methods and experiment.

Vila, F. D.; Lindahl, V. E.; Rehr, J. J.

2012-01-01

181

Estudo da geometria da uréia por métodos ab initio e simulação computacional de líquidos

Directory of Open Access Journals (Sweden)

Full Text Available A study was carried out on the urea geometries using ab initio calculation and Monte Carlo computational simulation of liquids. The ab initio calculated results showed that urea has a non-planar conformation in the gas phase in which the hydrogen atoms are out of the plane formed by the heavy atoms. Free energies associated to the rotation of the amino groups of urea in water were obtained using the Monte Carlo method in which the thermodynamic perturbation theory is implemented. The magnitude of the free energy obtained from this simulation did not permit us to conclude that urea is non-planar in water.

Cirino José Jair Vianna

2002-01-01

182

Ab initio calculations versus polarized neutron diffraction for the spin density of free radicals

International Nuclear Information System (INIS)

The determination of the magnetization distribution using polarized neutron diffraction has played a key role during the last twenty years in the field of molecular magnetism. This distribution can also be obtained by first principle ab initio calculations. Such calculations always rely on approximations and the question that arises is to know whether the obtained results are reliable enough to represent accurately the properties of these molecules. The comparison between polarized neutron experimental results and ab initio calculations has turned to provide stringent tests for these methods. In the resent article a comparison between experimental and theoretical results is made and is illustrated by examples based on magnetic free radicals. (author)

183

Ab initio calculations versus polarized neutron diffraction for the spin density of free radicals

The determination of the magnetization distribution using polarized neutron diffraction has played a key role during the last twenty years in the field of molecular magnetism. This distribution can also be obtained by first principle ab initio calculations. Such calculations always rely on approximations and the question that arises is to know whether the obtained results are reliable enough to represent accurately the properties of these molecules. The comparison between polarized neutron experimental results and ab initio calculations has turned to provide stringent tests for these methods. In the resent article a comparison between experimental and theoretical results is made and is illustrated by examples based on magnetic free radicals. (author)

Ressouche, E

2003-01-01

184

Ab initio Defect Energetics in LaBO3 Perovskite Solid Oxide Fuel Cell Materials

DEFF Research Database (Denmark)

Perovskite materials of the form ABO3 are a promising family of compounds for use in solid oxide fuel cell (SOFC) cathodes. Study of the physics of these compounds under SOFC conditions with ab initio methods is particularly challenging due to high temperatures, exchange of oxygen with O2 gas, and correlated electron effects. This paper discusses an approach to performing ab initio studies on these materials for SOFC applications and applies the approach to calculate vacancy formation energies in LaBO3 (B = Mn, Fe, Co, Ni) compounds.

Lee, Yueh-Lin; Morgan, Dane

2009-01-01

185

Energy Technology Data Exchange (ETDEWEB)

A calcium aluminosilicate glass of molar composition 67 % SiO{sub 2} - 12 % Al{sub 2}O{sub 3} - 21 % CaO was modelled by classical and ab initio molecular dynamics. The size effect study in classical MD shows that the systems of 100 atoms are more ordered than the larger ones. These effects are mainly due to the 3-body terms in the empirical potentials. Nevertheless, these effects are small and the structures generated are in agreement with experimental data. In such kind of glass, we denote an aluminium avoidance and an excess of non bridging oxygens which can be compensated by tri coordinated oxygens. When the dynamics of systems of 100 and 200 atoms is followed by ab initio MD, some local arrangements occurs (bond length, angular distributions). Thus, more realistic vibrational properties are obtained in ab initio MD. The modelling of thin films shows that aluminium atoms extend to the most external part of the surface and they are all tri-coordinated. Calcium atoms are set in the sub layer part of the surface and they produce a depolymerization of the network. In classical MD, tri-coordinated aluminium atoms produce an important electric field above the surface. With non bridging oxygens, they constitute attractive sites for single water molecules. (author)

Ganster, P

2004-10-15

186

Ab initio modelling of UN grain boundary interfaces

International Nuclear Information System (INIS)

The uranium mononitride (UN) is a material considered as a promising candidate for Generation-IV nuclear reactor fuels. Unfortunately, oxygen in air affects UN fuel performance and stability. Therefore, it is necessary to understand the mechanism of oxygen adsorption and further UN oxidation in the bulk and at surface. Recently, we performed a detailed study on oxygen interaction with UN surface using density functional theory (DFT) calculations. We were able to identify an atomistic mechanism of UN surface oxidation consisting of several important steps, starting with the oxygen molecule dissociation and finishing with oxygen atom incorporation into vacancies on the surface. However, in reality most of processes occur at the interfaces and on UN grain boundaries. In this study, we present the results of first DFT calculations on O behaviour inside UN grain boundaries performed using GGA exchange-correlation functional PW91 as implemented into the VASP computer code. We consider a simple interface (310)[001](36.8°) tilt grain boundary. The N vacancy formation energies and energies of O incorporation into pre-existing vacancies in the grain boundaries as well as O solution energies were compared with those obtained for the UN (001) and (110) surfaces

187

Ab initio modelling of UN grain boundary interfaces

The uranium mononitride (UN) is a material considered as a promising candidate for Generation-IV nuclear reactor fuels. Unfortunately, oxygen in air affects UN fuel performance and stability. Therefore, it is necessary to understand the mechanism of oxygen adsorption and further UN oxidation in the bulk and at surface. Recently, we performed a detailed study on oxygen interaction with UN surface using density functional theory (DFT) calculations. We were able to identify an atomistic mechanism of UN surface oxidation consisting of several important steps, starting with the oxygen molecule dissociation and finishing with oxygen atom incorporation into vacancies on the surface. However, in reality most of processes occur at the interfaces and on UN grain boundaries. In this study, we present the results of first DFT calculations on O behaviour inside UN grain boundaries performed using GGA exchange-correlation functional PW91 as implemented into the VASP computer code. We consider a simple interface (310)[001](36.8°) tilt grain boundary. The N vacancy formation energies and energies of O incorporation into pre-existing vacancies in the grain boundaries as well as O solution energies were compared with those obtained for the UN (001) and (110) surfaces

Kotomin, E. A.; Zhukovkii, Yu F.; Bocharov, D.; Gryaznov, D.

2012-08-01

188

Dispersion Interactions between Rare Gas Atoms: Testing the London Equation Using ab Initio Methods

A computational chemistry experiment is described in which students can use advanced ab initio quantum mechanical methods to test the ability of the London equation to account quantitatively for the attractive (dispersion) interactions between rare gas atoms. Using readily available electronic structure applications, students can calculate the…

Halpern, Arthur M.

2011-01-01

189

How does glycine adsorb at hydroxyapatite surfaces? Ab initio simulations based on periodic B3LYP GTO calculations reveal the detailed mechanism of binding to the (001) and (010) surfaces by shedding light on how acid and basic amino acid residues of proteins interact with hydroxyapatite based biomaterials.

Ugliengo, Piero; Corno, Marta

2008-01-01

190

Study on the surface hydroxyl group on solid breeding materials by ab-initio calculations

Energy Technology Data Exchange (ETDEWEB)

The nature of -OH on the surface of Li{sub 2}O was analyzed with the ab-initio quantum chemical calculation technique. Calculation results showed that the stretching vibration of O-H is affected by the chemical species around the -OH. (author)

Tanaka, Satoru; Taniguchi, Masaki [Tokyo Univ. (Japan). Faculty of Engineering

1996-10-01

191

Stabilization of Ab Initio Molecular Dynamics Simulations at Large Time Steps

The Verlet method is still widely used to integrate the equations of motion in ab initio molecular dynamics simulations. We show that the stability limit of the Verlet method may be significantly increased by setting an upper limit on the kinetic energy of each atom with only a small loss in accuracy. The validity of this approach is demonstrated for molten lithium fluoride.

Tsuchida, Eiji

2014-01-01

192

The phonon dispersion relations of bulk hexagonal boron nitride have been determined from inelastic x-ray scattering measurements and analyzed by ab initio calculations. Experimental data and calculations show an outstanding agreement and reconcile the controversies raised by recent experimental data obtained by electron-energy loss spectroscopy and second-order Raman scattering.

Serrano, J.; Bosak, A.; Arenal, R.; Krisch, M.; Watanabe, K.; Taniguchi, M.; Kanda, H.; Rubio Secades, A?ngel; Wirtz, Ludger

2007-01-01

193

Mechanical properties of carbynes investigated by ab initio total-energy calculations

DEFF Research Database (Denmark)

As sp carbon chains (carbynes) are relatively rigid molecular objects, can we exploit them as construction elements in nanomechanics? To answer this question, we investigate their remarkable mechanical properties by ab initio total-energy simulations. In particular, we evaluate their linear response to small longitudinal and bending deformations and their failure limits for longitudinal compression and elongation.

Castelli, Ivano E.; Salvestrini, Paolo

2012-01-01

194

The Use of Ab Initio Wavefunctions in Line-Shape Calculations for Water Vapor

In semi-classical line-shape calculations, the internal motions of the colliding pair are treated via quantum mechanics and the collision trajectory is determined by classical dynamics. The quantum mechanical component, i.e. the determination of reduced matrix elements (RME) for the colliding pair, requires the wavefunctions of the radiating and the perturbing molecules be known. Here the reduced matrix elements for collisions in the ground vibrational state of water vapor are calculated by two methods and compared. First, wavefunctions determined by diagonalizing an effective (Watson) Hamiltonian are used to calculate the RMEs and, second, the ab initio wavefunctions of Partridge and Schwenke are used. While the ground vibrational state will yield the best approximation of the wavefunctions from the effective Hamiltonian approach, this study clearly identifies problems for states not included in the fit of the Hamiltonian and for extrapolated states. RMEs determined using ab initio wavefunctions use ˜100000 times more computational time; however, all ro-vibrational interactions are included. Hence, the ab initio approach will yield better RMEs as the number of vibrational quanta exchanged in the optical transition increases, resulting in improvements in calculated half-widths and line shifts. It is important to note that even for pure rotational transitions the use of ab initio wavefunctions will yield improved results.

Gamache, Robert R.; Lamouroux, Julien; Schwenke, David W.

2014-06-01

195

Dynamical dimer method for the determination of transition states with ab initio molecular dynamics

A dynamical formulation of the dimer method for the determination of transition states is presented. The method is suited for ab-initio molecular dynamics using the fictitious Lagrangian formulation. The method has been applied to the con-rotatory ring opening of chloro-cyclo-butadiene, an example, where the application of the drag method is problematic.

Poddey, Alexander

2007-01-01

196

The Raman spectrum of triclinic low-albite is presented, where all 39 Ag modes are identified. A good agreement is found with ab initio calculations using the CRYSTAL14 program at the hybrid HF/DFT level, using WC1LYP Hamiltonian.

Aliatis, I.; Lambruschi, E.; Mantovani, L.; Bersani, D.; Ando, S.; Gatta, G. D.; Gentile, P.; Salvioli-Mariani, E.; Prencipe, M.; Tribaudino, M.; Lottici, P. P.

2014-06-01

197

Ab initio treatment of ion-water molecule collisions with a three-center pseudo potential

International Nuclear Information System (INIS)

We calculate electron capture cross sections in collisions of protons with water molecules, using two simple ab initio approaches. The formalism involves the calculation of one-electron scattering wave functions and the use of three-center pseudo potential to represent the electron H2O+ interaction. Several methods to obtain many-electron cross sections are considered.

198

Ab Initio Studies of Hydrogen-Bonded Complexes between Uracil and HCl

Ab initio SCF calculations were performed to investigate the hydrogen-bonding characteristics of the two carbonyl groups of the uracil molecule. The calculated interaction energy of the uracil-HCl complexes shows a strong basis-set dependence and provides no evidence for a significant difference between the two carbonyl groups in terms of intrinsic properties.

Latajka, Zdzis?aw; Ratajczak, H.; Zeegers-huyskens, Th; Scheiner, Steve

1991-01-01

199

Combining instanton theory and ab initio data to model tunneling dynamics

International Nuclear Information System (INIS)

To describe tunneling dynamics in polyatomic systems the Instanton formalism is combined with the complete potential-energy surface generated from ab-initio calculations. The applications range from the rate constant of molecular inversion in aziridine molecule, oxyranyl and dioxolanyl radical, to tunneling splittings in malonaldehyde and hydrogenoxalate anion, indoline, and tropolone, including mode-specific effects

200

The electronic structure and bonding of a realistic model of an intergranular glassy film (IGF) was studied with multiple computational methods. The model has a Si-O-N glassy region sandwiched between crystalline basal planes of ?-Si3N4 and contains a total of 798 atoms. It was constructed with periodic boundary conditions via classical molecular dynamics (MD) techniques using an accurate multibody atomic potential. The model was then further relaxed by the VASP (Vienna ab initio simulation package) program. It is shown that the VASP-relaxed structure reduces the total energy from the MD-relaxed structure by only 47.38eV , validating the accuracy of the multiatom potential used. The calculated electronic structure shows the IGF model to be an insulator with a sizable gap of almost 3eV . Quasidefectlike states can be identified near the band edges arising from the more strained Si-N and Si-O bonds at the interface. Calculation of the Mulliken effective charge and bond order values indicates that the bonds in the glassy region and at the interface can be enhanced and weakened by distortions in the bond length and bond angle. The states at the top of the valence band are derived mostly from the crystalline part of the Si-N bonding while the states at the bottom of the conduction band are dominated by the Si-O bonding in the glassy region. Calculation of the electrostatic potential across the interface shows an average band offset of about 1.5eV between the crystalline ?-Si3N4 and the glassy Si-O-N region which could be related to the space charge model for IGF.

Rulis, P.; Chen, J.; Ouyang, L.; Ching, W.-Y.; Su, X.; Garofalini, S. H.

2005-06-01

201

Scientific Electronic Library Online (English)

Full Text Available SciELO Brazil | Language: Portuguese Abstract in portuguese [...] Abstract in english In this paper a methodology for the computation of Raman scattering cross-sections and depolarization ratios within the Placzek Polarizability Theory is described. The polarizability gradients are derived from the values of the dynamic polarizabilities computed at the excitation frequencies using ab [...] initio Linear Response Theory. A sample application of the computational program, at the HF, MP2 and CCSD levels of theory, is presented for H2O and NH3. The results show that high correlated levels of theory are needed to achieve good agreement with experimental data.

Luciano N., Vidal; Pedro A. M., Vazquez.

2003-08-01

202

Energy Technology Data Exchange (ETDEWEB)

As a first step, we calculated ab initio the solubility and mixing energies of iron and chromium that confirm previous calculations. The same methodology is used to calculate free surface energies of iron and chromium (100), (110), (111) and (211). Refuting extrapolations from high temperatures measurements, ab initio calculations show that chromium surface energies are always higher that iron ones. We also calculated the segregation energy of a chromium impurity in iron (100) which is endothermic. Finally, we propose an interaction model parameterized on the ab initio calculations that we use to calculate segregation isotherms. We show that the large difference in surface energies between chromium and iron we highlighted from ab initio calculations causes the surfaces to be always depleted in chromium. (authors)

Levesque, M.; Soisson, F.; Fu, C.C.; Nastar, M. [CEA, DEN, DMN, Service de Recherches de Metallurgie Physique, 91191 Gif-sur-Yvette, (France); Martinez, E. [Los Alamos National Laboratory, 87545 Los Alamos, New Mexico, (United States)

2011-07-01

203

Nuclear quantum effects in liquid water from an ab initio force matching approach

We have applied path integral simulations, in combination with new ab initio based water potentials, to investigate nuclear quantum effects in liquid water. Because direct ab initio path integral simulations are computationally expensive, a flexible water model is parameterized by force-matching to density functional theory-based molecular dynamics simulations. The resulting effective potentials provide an inexpensive replacement for direct \\textit{ab inito} molecular dynamics simulations and furthermore allow an efficient simulation of nuclear quantum effects. Static and dynamic properties of liquid water at ambient conditions are presented and the role of nuclear quantum effects, exchange-correlation functionals and dispersion corrections are discussed in regards to reproducing the experimental properties of liquid water.

Spura, Thomas; Habershon, Scott; Kühne, Thomas D

2014-01-01

204

Ab initio investigations of structure and stability of the LiBeF3 molecule

International Nuclear Information System (INIS)

Ab initio calculations of the potential energy surface of LiBeF3 have been performed using the basis set of Roos and Siegbahn. The extremum and saddle points were made more precise with Huzinaga-Dunning basis sets in double- and triple-zeta contractions. The 'bidentate' structure (symmetry group Csub(2v)) is found to have the lowest energy and is much more advantageous than the others, and the LiBeF3 molecule turns out to be rigid with respect to migration of the cation around the anion. The calculated internuclear distances and the energy of complex formation are in agreement with experimental values within 0.03 Angstroem and 2 kcal/mole. The results are compared with similar ab initio data for LiBeH3 and LiNO3. (orig.)

205

Experimental studies and ab initio calculations on characteristics of the C state of SF2 radical

International Nuclear Information System (INIS)

SF2 radicals were generated by a pulsed dc discharge in the mixture gas beam of SF2 and Ar. The (2+1) resonance-enhanced multiphoton ionization (REMPI) excitation spectroscopy of SF2 radical was obtained between 325 and 365 nm. The SF+ ion signals were also observed in the same wavelength range. The analysis shows that the spectrum can be assigned as the two-photon resonant excitation of SF2 radical (B-tilde1 B1 and (C-tilde1 A1 states). And also, ab initio calculations suggest that the C-tilde state is a bonding state with Rydberg characteristic. The potential energy surfaces (PESs) of SF2 and SF2+ by ab initio calculations suggest that SF+ ions originate from dissociation processes of excited SF2+ ions. (author)

206

Ab Initio No-Core Shell Model Calculations Using Realistic Two- and Three-Body Interactions

Energy Technology Data Exchange (ETDEWEB)

There has been significant progress in the ab initio approaches to the structure of light nuclei. One such method is the ab initio no-core shell model (NCSM). Starting from realistic two- and three-nucleon interactions this method can predict low-lying levels in p-shell nuclei. In this contribution, we present a brief overview of the NCSM with examples of recent applications. We highlight our study of the parity inversion in {sup 11}Be, for which calculations were performed in basis spaces up to 9{Dirac_h}{Omega} (dimensions reaching 7 x 10{sup 8}). We also present our latest results for the p-shell nuclei using the Tucson-Melbourne TM three-nucleon interaction with several proposed parameter sets.

Navratil, P; Ormand, W E; Forssen, C; Caurier, E

2004-11-30

207

Li ion diffusion mechanisms in LiFePO4: an ab initio molecular dynamics study.

The mechanisms for thermal (self) diffusion of Li ions in fully lithiated LiFePO(4) have been investigated with spin polarized ab initio molecular dynamics calculations. The effect of electron correlation is taken into account with the GGA+U formalism. It was found that Li ion diffusion is not a continuous process but through a series of jumps from one site to another. A dominant process is the hopping between neighboring Li sites around the PO(4) groups, which results in a zigzag pathway along the crystallographic b-axis. This observation is in agreement with a recent neutron diffraction experiment. A second process involves the collaborative movements of the Fe ions leading to the formation of antisite defects and promotes Li diffusion across the Li ion channels. The finding of the second mechanism demonstrates the benefit of ab initio molecular dynamics simulation in sampling diffusion pathways that may not be anticipated. PMID:21932862

Yang, Jianjun; Tse, John S

2011-11-17

208

Ab Initio calculations of even oxygen isotopes with chiral two-plus-three-nucleon interactions.

We formulate the in-medium similarity renormalization group (IM-SRG) for open-shell nuclei using a multireference formalism based on a generalized Wick theorem introduced in quantum chemistry. The resulting multireference IM-SRG (MR-IM-SRG) is used to perform the first ab initio study of all even oxygen isotopes with chiral nucleon-nucleon and three-nucleon interactions, from the proton to the neutron drip lines. We obtain an excellent reproduction of experimental ground-state energies with quantified uncertainties, which is validated by results from the importance-truncated no-core shell model and the coupled cluster method. The agreement between conceptually different many-body approaches and experiment highlights the predictive power of current chiral two- and three-nucleon interactions, and establishes the MR-IM-SRG as a promising new tool for ab initio calculations of medium-mass nuclei far from shell closures. PMID:25165916

Hergert, H; Binder, S; Calci, A; Langhammer, J; Roth, R

2013-06-14

209

Ab Initio Calculations of Even Oxygen Isotopes with Chiral Two- Plus Three-Nucleon Interactions

We formulate the In-Medium Similarity Renormalization Group (IM-SRG) for open-shell nuclei using a multi-reference formalism based on a generalized Wick theorem introduced in quantum chemistry. The resulting multi-reference IM-SRG (MR-IM-SRG) is used to perform the first ab initio study of even oxygen isotopes with chiral NN and 3N Hamiltonians, from the proton to the neutron drip lines. We obtain an excellent reproduction of experimental ground-state energies with quantified uncertainties, which is validated by results from the Importance-Truncated No-Core Shell Model and the Coupled Cluster method. The agreement between conceptually different many-body approaches and experiment highlights the predictive power of current chiral two- and three-nucleon interactions, and establishes the MR-IM-SRG as a promising new tool for ab initio calculations of medium-mass nuclei far from shell closures.

Hergert, H; Calci, A; Langhammer, J; Roth, R

2013-01-01

210

An ab initio dynamics study of the CH{sub 3}Cl + OH reaction

Energy Technology Data Exchange (ETDEWEB)

Ab initio calculations have been performed for both H-atom and Cl-atom abstraction reactions by the hydroxyl radical. Geometry optimization and vibrational frequencies analysis were performed for reactants, transition state and products at the MP2(full)/cc-pVTZ level of theory. On the basis of the ab initio data, the rate constants have been deduced over a wide temperature range, 200-2000 K, using conventional transition state theory, including Wigner tunneling correction and the hindered rotor approximation. Calculated transition state rate constants with Wigner tunneling correction are in good agreement with experimental results. The tunneling contribution becomes important at ambient temperatures, resulting in the exhibited non-Arrhenius behavior of the rate constant.

Tzima, Theodora D. [Department of Chemistry, University of Ioannina, GR-451 10, Ioannina (Greece); Papayannis, Demetrios K. [Department of Materials Science and Engineering, University of Ioannina, GR-451 10, Ioannina (Greece); Melissas, Vasilios S. [Department of Chemistry, University of Ioannina, GR-451 10, Ioannina (Greece)]. E-mail: melissas@chem.auth.gr

2005-06-06

211

An ab initio dynamics study of the CH3Cl + OH reaction

International Nuclear Information System (INIS)

Ab initio calculations have been performed for both H-atom and Cl-atom abstraction reactions by the hydroxyl radical. Geometry optimization and vibrational frequencies analysis were performed for reactants, transition state and products at the MP2(full)/cc-pVTZ level of theory. On the basis of the ab initio data, the rate constants have been deduced over a wide temperature range, 200-2000 K, using conventional transition state theory, including Wigner tunneling correction and the hindered rotor approximation. Calculated transition state rate constants with Wigner tunneling correction are in good agreement with experimental results. The tunneling contribution becomes important at ambient temperatures, resulting in the exhibited non-Arrhenius behavior of the rate constant

212

Implementation of ab initio multiple spawning in the MOLPRO quantum chemistry package

International Nuclear Information System (INIS)

The ab initio multiple spawning (AIMS) method has been developed to solve the electronic and nuclear Schrodinger equations simultaneously for application to photochemical reaction dynamics. We discuss some details of the implementation of AIMS in the MOLPRO program package. A few aspects of the implementation are highlighted, including a new multiple timescale integrator and a scheme for solving the coupled-perturbed multiconfiguration self-consistent field (CP-MCSCF) equations in the context of ab initio molecular dynamics. The implementation is very efficient and we demonstrate calculations on the photoisomerization of ethylene using more than 5000 trajectory basis functions. We have included the capability for hybrid quantum mechanics/molecular mechanics (QM/MM) simulations within AIMS, and we investigate the role of an argon solvent in the photoisomerization of ethylene. Somewhat surprisingly, the surrounding argon has little effect on the timescale of non-adiabatic quenching in ethylene

213

Bridging a gap between continuum-QCD and ab initio predictions of hadron observables

Within contemporary hadron physics there are two common methods for determining the momentum-dependence of the interaction between quarks: the top-down approach, which works toward an ab initio computation of the interaction via direct analysis of the gauge-sector gap equations; and the bottom-up scheme, which aims to infer the interaction by fitting data within a well-defined truncation of those equations in the matter sector that are relevant to bound-state properties. We unite these two approaches by demonstrating that the renormalisation-group-invariant running-interaction predicted by contemporary analyses of QCD's gauge sector coincides with that required in order to describe ground-state hadron observables using a nonperturbative truncation of QCD's Dyson-Schwinger equations in the matter sector. This bridges a gap that had lain between nonperturbative continuum-QCD and the ab initio prediction of bound-state properties.

Binosi, Daniele; Papavassiliou, Joannis; Roberts, Craig D

2014-01-01

214

Ab Initio Many-Body Calculations Of Nucleon-Nucleus Scattering

Energy Technology Data Exchange (ETDEWEB)

We develop a new ab initio many-body approach capable of describing simultaneously both bound and scattering states in light nuclei, by combining the resonating-group method with the use of realistic interactions, and a microscopic and consistent description of the nucleon clusters. This approach preserves translational symmetry and Pauli principle. We outline technical details and present phase shift results for neutron scattering on {sup 3}H, {sup 4}He and {sup 10}Be and proton scattering on {sup 3,4}He, using realistic nucleon-nucleon (NN) potentials. Our A = 4 scattering results are compared to earlier ab initio calculations. We find that the CD-Bonn NN potential in particular provides an excellent description of nucleon-{sup 4}He S-wave phase shifts. We demonstrate that a proper treatment of the coupling to the n-{sup 10}Be continuum is successful in explaining the parity-inverted ground state in {sup 11}Be.

Quaglioni, S; Navratil, P

2008-12-17

215

A fully ab initio technique is discussed for the determination of dynamical X-ray structure factors (XSFs) of crystalline materials, which is based on a standard Debye-Waller (DW) harmonic lattice dynamical approach with all-electron atom-centered basis sets, periodic boundary conditions, and one-electron Hamiltonians. This technique requires an accurate description of the lattice dynamics and the electron charge distribution of the system. The main theoretical parameters involved and final accuracy of the technique are discussed with respect to the experimental determinations of the XSFs at 298 K of crystalline silicon. An overall agreement factor of 0.47% between the ab initio predicted values and the experimental determinations is found. The best theoretical determination of the anisotropic displacement parameter, of silicon is here 60.55 × 10(-4) Å(2), corresponding to a DW factor B = 0.4781 Å(2). PMID:23081746

Erba, Alessandro; Ferrabone, Matteo; Orlando, Roberto; Dovesi, Roberto

2013-02-15

216

Ab initio calculation of valley splitting in monolayer \\delta-doped phosphorus in silicon

The differences in energy between electronic bands due to valley splitting are of paramount importance in interpreting transport spectroscopy experiments on state-of-the-art quantum devices defined by scanning tunneling microscope lithography. We develop a plane-wave density functional theory description of these systems which is size-limited due to computational tractability. We then develop a less resource-intensive alternative via localized basis functions, retaining the physics of the plane-wave description, and extend this model beyond the capability of plane-wave methods to determine the ab initio valley splitting of well-isolated \\delta-layers. In obtaining agreement between plane-wave and delocalized methods, we show that the valley splitting has been overestimated in previous ab initio calculations by more than 50%.

Drumm, Daniel W; Per, Manolo C; Russo, Salvy P; Hollenberg, Lloyd C L

2012-01-01

217

Ab-initio molecular dynamics simulation of liquid water by Quantum Monte Carlo

Despite liquid water is ubiquitous in chemical reactions at roots of life and climate on 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 excellent 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.

Zen, Andrea; Mazzola, Guglielmo; Guidoni, Leonardo; Sorella, Sandro

2014-01-01

218

Ab Initio MCSM Calculation for Reduced Matrix Elements of E2 Operator for A = 10 Nuclei

The reduced matrix elements of Ê2 operator for 10Be low-lying states are evaluated with the no-core Monte Carlo shell model, which has been used to investigate the structure of light nuclei in an ab initio sense recently. The MCSM calculation converges within 20 MCSM dimensions. These MCSM results show good agreement with new experimental data and other ab initio calculations. The reduced matrix elements are investigated in terms of single-particle orbits contribution. It is found that the transition among p-shell orbits is dominant. The triaxial deformation of 10Be, as well as its mirror nucleus 10C, is also discussed. Meanwhile, the importance of p-shell orbits to the triaxiality is addressed.

Liu, Lang

2014-08-01

219

Ab initio study of AlxMoNbTiV high-entropy alloys.

The AlxMoNbTiV (x = 0-1.5) high-entropy alloys (HEAs) adopt a single solid-solution phase, having the body centered cubic (bcc) crystal structure. Here we employ the ab initio exact muffin-tin orbitals method in combination with the coherent potential approximation to investigate the equilibrium volume, elastic constants, and polycrystalline elastic moduli of AlxMoNbTiV HEAs. A comparison between the ab initio and experimental equilibrium volumes demonstrates the validity and accuracy of the present approach. Our results indicate that Al addition decreases the thermodynamic stability of the bcc structure with respect to face-centered cubic and hexagonal close packed lattices. For the elastically isotropic Al0.4MoNbTiV HEAs, the valence electron concentration (VEC) is about 4.82, which is slightly different from VEC ? 4.72 obtained for the isotropic Gum metals and refractory-HEAs. PMID:25640032

Cao, Peiyu; Ni, Xiaodong; Tian, Fuyang; Varga, Lajos K; Vitos, Levente

2015-02-25

220

Ab initio model of optical properties of two-temperature warm dense matter

We present a model to describe thermophysical and optical properties of two-temperature systems consisted of heated electrons and cold ions in a solid lattice that occur during ultrafast heating experiments. Our model is based on ab initio simulations within the framework of density functional theory. The optical properties are obtained by evaluating the Kubo-Greenwood formula. By applying the material parameters of our ab initio model to a two-temperature model we are able to describe the temperature relaxation process of femtosecond-laser-heated gold and its optical properties within the same theoretical framework. Recent time-resolved measurements of optical properties of ultrafast heated gold revealed the dynamics of the interaction between femtosecond laser pulses and solid state matter. Different scenarios obtained from simulations of our study are compared with experimental data [Chen, Holst, Kirkwood, Sametoglu, Reid, Tsui, Recoules, and Ng, Phys. Rev. Lett. 110, 135001 (2013), 10.1103/PhysRevLett.110.135001].

Holst, B.; Recoules, V.; Mazevet, S.; Torrent, M.; Ng, A.; Chen, Z.; Kirkwood, S. E.; Sametoglu, V.; Reid, M.; Tsui, Y. Y.

2014-07-01

221

Ab initio Nonequilibrium Molecular Dynamics in the Solid Superionic Conductor LiBH4

The color-diffusion algorithm is applied to ab initio molecular dynamics simulation of hexagonal LiBH4 to determine the lithium diffusion coefficient and diffusion mechanisms. Even in the best solid lithium ion conductors, the time scale of ion diffusion is too long to be readily accessible by ab initio molecular dynamics at a reasonable computational cost. In our nonequilibrium method, rare events are accelerated by the application of an artificial external field acting on the mobile species; the system response to this perturbation is accurately described in the framework of linear response theory and is directly related to the diffusion coefficient, thus resulting in a controllable approximation. The calculated lithium ionic conductivity of LiBH4 closely matches published measurements, and the diffusion mechanism can be elucidated directly from the generated trajectory.

Aeberhard, Philippe C.; Williams, Stephen R.; Evans, Denis J.; Refson, Keith; David, William I. F.

2012-03-01

222

Interface structure of graphene on SiC: an ab initio and STM approach

International Nuclear Information System (INIS)

High temperature treatment of SiC surfaces is a well-established technique for producing graphene directly on top of an insulating substrate. In this domain an important question is the influence of the substrate on the atomic and electronic structure of the graphene layers. This requires a detailed investigation of the interactions at the graphene-SiC interface. Surface science techniques and ab initio calculations are well suited for that purpose. In this paper, we present a brief review of the recent investigations performed in this domain by scanning tunnelling microscopy (STM) and ab initio simulations. It is largely based on the work performed in our group, but it also provides a survey of the literature in these fields. Both the so-called Si and C face of the hexagonal 6H(4H)SiC{0 0 0 1} substrates will be considered, as they show markedly different types of behaviour.

223

Interface structure of graphene on SiC: an ab initio and STM approach

Energy Technology Data Exchange (ETDEWEB)

High temperature treatment of SiC surfaces is a well-established technique for producing graphene directly on top of an insulating substrate. In this domain an important question is the influence of the substrate on the atomic and electronic structure of the graphene layers. This requires a detailed investigation of the interactions at the graphene-SiC interface. Surface science techniques and ab initio calculations are well suited for that purpose. In this paper, we present a brief review of the recent investigations performed in this domain by scanning tunnelling microscopy (STM) and ab initio simulations. It is largely based on the work performed in our group, but it also provides a survey of the literature in these fields. Both the so-called Si and C face of the hexagonal 6H(4H)SiC{l_brace}0 0 0 1{r_brace} substrates will be considered, as they show markedly different types of behaviour.

Veuillen, J-Y; Hiebel, F; Magaud, L; Mallet, P; Varchon, F, E-mail: jean-yves.veuillen@grenoble.cnrs.f, E-mail: fanny.hiebel@grenoble.cnrs.f, E-mail: laurence.magaud@grenoble.cnrs.f, E-mail: pierre.mallet@grenoble.cnrs.f, E-mail: francois.varchon@uclouvain.b [Institut Neel, CNRS-UJF, BoIte Postale 166, 38042 Grenoble (France)

2010-09-22

224

International Nuclear Information System (INIS)

The ab initio Hartree--Fock calculation of the elastic electron scattering cross section of sulphur hexafluoride is reported. The integrals for the Born scattering amplitudes have been evaluated by a new simple technique, based on Gaussian quadrature. Spherical averaging was performed numerically; different techniques for spherical averaging are discussed. An estimated r/sub e/ structure was used and vibrational effects have been neglected. In order to assess the effect of the basis set on the intensities, calculations have been performed for the nitrogen molecule with six different basis sets. Using these results as a guide, a triple-zeta basis set, augmented with polarization functions and diffuse functions, was selected for SF6. The results confirm Bartell's hypothesis that the observed residuals from the independent atom model intensities are due to electronic bonding effects. It is suggested that, for very accurate electron diffraction work, the effect of electron redistribution has to be taken into account by ab initio calculations

225

A Hartree-Fock ab initio band-structure calculation employing Wannier-type orbitals

An ab initio Wannier-function-based approach to electronic ground-state calculations for crystalline solids is outlined. In the framework of the linear combination of atomic orbitals method the infinite character of the solid is rigorously taken into account. The Hartree-Fock ground-state energy, cohesive energy, lattice constant and bulk modulus are calculated in a fully ab initio manner as it is demonstrated for sodium chloride, NaCl, using basis sets close to the Hartree-Fock limit. It is demonstrated that the Hartree-Fock band-structure can easily be recovered with the current approach and agrees with the one obtained from a more conventional Bloch-orbital-based calculation. It is argued that the advantage of the present approach lies in its capability to include electron correlation effects for crystalline insulators by means of well-established quantum chemical procedures.

Albrecht, M; Dolg, M; Fulde, P; Stoll, H; Albrecht, Martin; Shukla, Alok; Dolg, Michael; Fulde, Peter; Stoll, Hermann

1998-01-01

226

{\\it Ab initio} nuclear structure - the large sparse matrix eigenvalue problem

The structure and reactions of light nuclei represent fundamental and formidable challenges for microscopic theory based on realistic strong interaction potentials. Several {\\it ab initio} methods have now emerged that provide nearly exact solutions for some nuclear properties. The {\\it ab initio} no core shell model (NCSM) and the no core full configuration (NCFC) method, frame this quantum many-particle problem as a large sparse matrix eigenvalue problem where one evaluates the Hamiltonian matrix in a basis space consisting of many-fermion Slater determinants and then solves for a set of the lowest eigenvalues and their associated eigenvectors. The resulting eigenvectors are employed to evaluate a set of experimental quantities to test the underlying potential. For fundamental problems of interest, the matrix dimension often exceeds $10^{10}$ and the number of nonzero matrix elements may saturate available storage on present-day leadership class facilities. We survey recent results and advances in solving t...

Vary, James P; Ng, Esmond; Yang, Chao; Sosonkina, Masha

2009-01-01

227

Ab initio modelling of vacancy–solute dragging in dilute irradiated iron-based alloys

International Nuclear Information System (INIS)

The formation of solute–defect nanoclusters in RPV steels is the main cause of radiation induced embrittlement. Solute atoms may diffuse in the alloy by a vacancy drag mechanism, depending on the strength of interaction with point defects. A multifrequency model based on ab initio computed migration barriers was applied in order to investigate the possibility of solute drag in iron-based bcc binary alloys containing Ni, Cr, Cu or Mn, and the obtained solute diffusion coefficients were compared with previous experiments. The results show that Ni is expected to be dragged at temperatures below approximately 900 K, while Cr and Mn are not involved in the dragging mechanism. As for Cu, the results are controversial because the computed migration barriers are strongly affected by the particular choice of the ab initio method

228

A periodic ab initio study of the structure and relative stability of silica polymorphs

The equilibrium geometry and total energy of four all-silica zeolite frameworks, sodalite, chabazite, faujasite and edingtonite, have been obtained at a periodic ab initio all-electron level (CRYSTAL code) and compared with the corresponding quantities for ?- and ?-quartz. The dependence of the results on the adopted basis set and hamiltonian (Hartree-Fock, or with an a posteriori correlation correction; various local and gradient-corrected density functional methods and Becke's hybrid scheme) is discussed. The various methods provide a similar order in the relative stabilities; large quantitative differences are however observed, Hartree-Fock and LDA results being at the extremes. The combined use of force-field and ab initio schemes in the geometry optimization is discussed.

Civalleri, B.; Zicovich-Wilson, C. M.; Ugliengo, P.; Saunders, V. R.; Dovesi, R.

1998-08-01

229

Ab-initio approach to study hydrogen diffusion in 9Cr steels

Energy Technology Data Exchange (ETDEWEB)

We calculate the equilibrium energies and migration barriers of Fe, Cr and H interstitial defects in {alpha}-FeX(X=Cr). We use the ab-initio electronic structure code, SIESTA, coupled to the monomer method to find activated states (or migration barriers), in order to study atomic defects diffusion. Ab-initio calculations reveal that in the presence of Cr the H migration barriers are higher than in pure {alpha}-Fe. On the other hand, our permeation tests on 9%Cr-91%Fe alloys reveal a permeation coefficient 10 times lower and a diffusion coefficient 200 times lower than in pure, annealed iron. Focusing on our experimental results, we explore very simple model of new H trapping sites and possible migration paths that can explain the experimental observations.

Ramunni, Viviana P., E-mail: vpram@cnea.gov.ar [Cons. Nac. de Inv. Cientificas y Tecnologicas (CONICET), Av. Rivadavia 1917 - C1033AAJ, Buenos Aires (Argentina); Departamento de Materiales, CAC-CNEA, Avda. General Paz 1499, 1650 San Martin (Argentina); Hurtado-Norena, Carolina [Cons. Nac. de Inv. Cientificas y Tecnologicas (CONICET), Av. Rivadavia 1917 - C1033AAJ, Buenos Aires (Argentina); Departamento de Materiales, CAC-CNEA, Avda. General Paz 1499, 1650 San Martin (Argentina); Bruzzoni, Pablo [Departamento de Materiales, CAC-CNEA, Avda. General Paz 1499, 1650 San Martin (Argentina)

2012-08-15

230

Ab-initio approach to study hydrogen diffusion in 9Cr steels

International Nuclear Information System (INIS)

We calculate the equilibrium energies and migration barriers of Fe, Cr and H interstitial defects in ?-FeX(X=Cr). We use the ab-initio electronic structure code, SIESTA, coupled to the monomer method to find activated states (or migration barriers), in order to study atomic defects diffusion. Ab-initio calculations reveal that in the presence of Cr the H migration barriers are higher than in pure ?-Fe. On the other hand, our permeation tests on 9%Cr-91%Fe alloys reveal a permeation coefficient 10 times lower and a diffusion coefficient 200 times lower than in pure, annealed iron. Focusing on our experimental results, we explore very simple model of new H trapping sites and possible migration paths that can explain the experimental observations.

231

Automated generation of radical species in crystalline carbohydrate using ab initio MD simulations.

As the chemical structures of radiation damaged molecules may differ greatly from their undamaged counterparts, investigation and description of radiation damaged structures is commonly biased by the researcher. Radical formation from ionizing radiation in crystalline ?-l-rhamnose monohydrate has been investigated using a new method where the selection of radical structures is unbiased by the researcher. The method is based on using ab initio molecular dynamics (MD) studies to investigate how ionization damage can form, change and move. Diversity in the radical production is gained by using different points on the potential energy surface of the intact crystal as starting points for the ionizations and letting the initial velocities of the nuclei after ionization be generated randomly. 160 ab initio MD runs produced 12 unique radical structures for investigation. Out of these, 7 of the potential products have never previously been discussed, and 3 products are found to match with radicals previously observed by electron magnetic resonance experiments. PMID:25012493

Aalbergsjø, Siv G; Pauwels, Ewald; Van Yperen-De Deyne, Andy; Van Speybroeck, Veronique; Sagstuen, Einar

2014-08-28

232

Toward the first ab initio description of the deuterium-tritium fusion

We are building a new capability to describe light-ion fusion reactions from first principles, known as ab initio NCSM/RGM approach [1,2]. Using a recently developed formalism based on nucleon-nucleus basis states, we have completed a promising preliminary study of nucleon-nucleus scattering, particularly n-^4He scattering below the d+^3H threshold [1,2]. Now we are developing the deuterium-nucleus formalism that coupled with the nucleon-nucleus basis will allow us the first ab initio calculation of the ^3H(d,n)^4He fusion. We present recent results and work in progress. [4pt] [1] S. Quaglioni and P. Navratil, Phys. Rev. Lett. 101, 092501 (2008). [0pt] [2] S. Quaglioni and P. Navratil, Phys. Rev. C 79, 044606 (2009).

Quaglioni, Sofia; Navratil, Petr

2009-10-01

233

Topological phases in triangular lattices of Ru adsorbed on graphene: Ab initio calculations

We have performed an ab initio investigation of the electronic properties of the graphene sheet adsorbed by Ru adatoms (Ru/graphene). For a particular set of triangular arrays of Ru adatoms, we find the formation of four (spin-polarized) Dirac cones attributed to a suitable overlap between two hexagonal lattices: one composed by the C sites of the graphene sheet, and the other formed by the surface potential induced by the Ru adatoms. Upon the presence of spin-orbit coupling (SOC) nontrivial band gaps take place at the Dirac cones promoting several topological phases. Depending on the Ru concentration, the system can be topologically characterized among the phases (i) quantum spin Hall (QSH), (ii) quantum anomalous Hall (QAH), (iii) metal, (iv) or trivial insulator. For each concentration, the topological phase is characterized by the ab initio calculation of the Chern number.

Acosta, C. Mera; Lima, Matheus P.; Miwa, R. H.; da Silva, Antônio J. R.; Fazzio, A.

2014-04-01

234

Ab initio modelling of the behaviour of point defects and fission products in nuclear fuel

International Nuclear Information System (INIS)

The aim of this work is to determine precisely the mechanisms of formation and migration of defects and fission products as well as the associated energies. Examples on uranium dioxide UO2 (standard nuclear fuel) and on uranium carbide UC (potential fuel for new generation reactors) are given. The obtained results are discussed and compared with the experimental results carried out. The ab initio method used is the Projector Augmented-Wave (PAW) method based on the density functional theory. The particular electronic properties of actinides are especially studied because, on account of their 5f orbitals more or less localized around the nucleus, it is difficult to model the actinide compounds by the DFT method. In particular, the modelling of the exchange-correlation interaction of the 5f electrons of UO2 requires approximations (as GGA+U) beyond those more currently used in ab initio calculations (LDA or GGA). (O.M.)

235

We present theoretical studies for the third-order elastic constants $C_{ijk}$ in zinc-blende nitrides AlN, GaN, and InN. Our predictions for these compounds are based on detailed ab initio calculations of strain-energy and strain-stress relations in the framework of the density functional theory. To judge the computational accuracy, we compare the ab initio calculated results for $C_{ijk}$ with experimental data available for Si and GaAs. We also underline the relation of the third-order elastic constants to other quantities characterizing anharmonic behaviour of materials, such as pressure derivatives of the second-order elastic constants and the mode Gr\\"uneisen constants for long-wavelength acoustic modes.

Lopuszynski, M; Lopuszynski, Michal; Majewski, Jacek A.

2007-01-01

236

We present theoretical studies for the third-order elastic constants Cijk in zinc-blende nitrides AlN, GaN, and InN. Our predictions for these compounds are based on detailed ab initio calculations of strain-energy and strain-stress relations in the framework of the density functional theory. To judge the computational accuracy, we compare the ab initio calculated results for Cijk with experimental data available for Si and GaAs. We also underline the relation of the third-order elastic constants to other quantities characterizing anharmonic behavior of materials, such as pressure derivatives of the second-order elastic constants cij' and the mode Grüneisen constants for long-wavelength acoustic modes ?(q,j) .

?opuszy?ski, Micha?; Majewski, Jacek A.

2007-07-01

237

Ab initio studies of equations of state and chemical reactions of reactive structural materials

The motivations for the research issues addressed in this thesis are based on the needs of the aerospace structural analysis and the design community. The specific focus is related to the characterization and shock induced chemical reactions of multi-functional structural-energetic materials that are also known as the reactive structural materials and their reaction capabilities. Usually motivation for selection of aerospace structural materials is to realize required strength characteristics and favorable strength to weight ratios. The term strength implies resistance to loads experienced during the service life of the structure, including resistance to fatigue loads, corrosion and other extreme conditions. Thus, basically the structural materials are single function materials that resist loads experienced during the service life of the structure. However, it is desirable to select materials that are capable of offering more than one basic function of strength. Very often, the second function is the capability to provide functions of sensing and actuation. In this thesis, the second function is different. The second function is the energetic characteristics. Thus, the choice of dual functions of the material are the structural characteristics and energetic characteristics. These materials are also known by other names such as the reactive material structures or dual functional structural energetic materials. Specifically the selected reactive materials include mixtures of selected metals and metal oxides that are also known as thermite mixtures, reacting intermetallic combinations and oxidizing materials. There are several techniques that are available to synthesize these structural energetic materials or reactive material structures and new synthesis techniques constitute an open research area. The focus of this thesis, however, is the characterization of chemical reactions of reactive material structures that involve two or more solids (or condensed matter). The subject of studies of the shock or thermally induced chemical reactions of the two solids comprising these reactive materials, from first principles, is a relatively new field of study. The published literature on ab initio techniques or quantum mechanics based approaches consists of the ab initio or ab initio-molecular dynamics studies in related fields that contain a solid and a gas. One such study in the literature involves a gas and a solid. This is an investigation of the adsorption of gasses such as carbon monoxide (CO) on Tungsten. The motivation for these studies is to synthesize alternate or synthetic fuel technology by Fischer-Tropsch process. In this thesis these studies are first to establish the procedure for solid-solid reaction and then to extend that to consider the effects of mechanical strain and temperature on the binding energy and chemisorptions of CO on tungsten. Then in this thesis, similar studies are also conducted on the effect of mechanical strain and temperature on the binding energies of Titanium and hydrogen. The motivations are again to understand the method and extend the method to such solid-solid reactions. A second motivation is to seek strained conditions that favor hydrogen storage and strain conditions that release hydrogen easily when needed. Following the establishment of ab initio and ab initio studies of chemical reactions between a solid and a gas, the next step of research is to study thermally induced chemical reaction between two solids (Ni+Al). Thus, specific new studies of the thesis are as follows: (1) Ab initio Studies of Binding energies associated with chemisorption of (a) CO on W surfaces (111, and 100) at elevated temperatures and strains and (b) adsorption of hydrogen in titanium base. (2) Equations of state of mixtures of reactive material structures from ab initio methods. (3) Ab initio studies of the reaction initiation, transition states and reaction products of intermetallic mixtures of (Ni+Al) at elevated temperatures and strains. (4) Press-cure synthesis of Nano-nickel and nano-aluminum based reacti

Zaharieva, Roussislava

238

Optimized Unrestricted Kohn-Sham Potentials from Ab Initio Spin Densities

The reconstruction of the exchange-correlation potential from accurate ab initio electron densities can provide insights into the limitations of the currently available approximate functionals and provide guidance for devising improved approximations for density-functional theory (DFT). For open-shell systems, the spin density is introduced as an additional fundamental variable in Spin-DFT. Here, we consider the reconstruction of the corresponding unrestricted Kohn-Sham potentials from accurate ab initio spin densities. In particular, we investigate whether it is possible to reconstruct the spin exchange-correlation potential, which determines the spin density in spin-unrestricted Kohn-Sham-DFT, despite the numerical difficulties inherent to the optimization of potentials with finite orbital basis sets. We find that the recently developed scheme for unambiguously singling out an optimal optimized potential [J. Chem. Phys. 135, 244102 (2011)] can provide such spin potentials accurately. This is demonstrated fo...

Boguslawski, Katharina; Reiher, Markus

2012-01-01

239

Next generation sequencing technology is advancing genome sequencing at an unprecedented level. By unravelling the code within a pathogen’s genome, every possible protein (prior to post-translational modifications) can theoretically be discovered, irrespective of life cycle stages and environmental stimuli. Now more than ever there is a great need for high-throughput ab initio gene finding. Ab initio gene finders use statistical models to predict genes and their exon-intron structures from ...

Goodswen, Stephen J.; Kennedy, Paul J.; Ellis, John T.

2012-01-01

240

Ab-initio chemical potentials of solid and liquid solutions and the chemistry of the Earth's core

A general set of methods is presented for calculating chemical potentials in solid and liquid mixtures using {\\em ab initio} techniques based on density functional theory (DFT). The methods are designed to give an {\\em ab initio} approach to treating chemical equilibrium between coexisting solid and liquid solutions, and particularly the partitioning ratio of solutes between such solutions. For the liquid phase, the methods are based on the general technique of thermodynamic...

Alfe, D.; Gillan, M. J.; Price, G. D.

2001-01-01

241

Ab initio calculation of the anomalous Hall conductivity by Wannier interpolation

The intrinsic anomalous Hall conductivity in ferromagnets depends on subtle spin-orbit-induced effects in the electronic structure, and recent ab initio studies found that it was necessary to sample the Brillouin zone at millions of k -points to converge the calculation. We present an efficient first-principles approach for computing this quantity. We start out by performing a conventional electronic-structure calculation including spin-orbit coupling on a uniform and relatively coarse k -poi...

Wang, X.; Yates, Jr; Souza, I.; Vanderbilt, D.

2006-01-01

242

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 wid...

Holst, Bastian; French, Martin; Redmer, Ronald

2012-01-01

243

Forced coalescence phasing: a method for ab initio determination of crystallographic phases.

A method has been developed for ab initio determination of crystallographic phases. This technique, called forced coalescence phasing (FCP), is implemented on a computer and uses an automated iterative procedure that combines real space filtering with numerically seeded Fourier transforms to solve the crystallographic phase problem. This approach is fundamentally different from that of traditional direct methods of phasing, which rely on structure invariant probabilistic phase relationships. ...

Drendel, W. B.; Dave?, R. D.; Jain, S.

1995-01-01

244

Influence of the ab-initio nd cross sections in the critical heavy-water benchmarks

The n-d elastic and breakup cross sections are computed by solving the three-body Faddeev equations for realistic and semi-realistic Nucleon-Nucleon potentials. These cross sections are inserted in the Monte Carlo simulation of the nuclear processes considered in the International Handbook of Evaluated Criticality Safety Benchmark Experiments (ICSBEP). The results obtained using thes ab initio n-d cross sections are compared with those provided by the most renown international libraries.

Morillon, B; Carbonell, J

2013-01-01

245

Influence of the ab-initio nd cross sections in the critical heavy-water benchmarks

The n-d elastic and breakup cross sections are computed by solving the three-body Faddeev equations for realistic and semi-realistic Nucleon-Nucleon potentials. These cross sections are inserted in the Monte Carlo simulation of the nuclear processes considered in the International Handbook of Evaluated Criticality Safety Benchmark Experiments (ICSBEP). The results obtained using thes ab initio n-d cross sections are compared with those provided by the most renown internation...

Morillon, B.; Lazauskas, R.; Carbonell, J.

2013-01-01

246

In this thesis, density functional theory (DFT) calculations and DFT based ab initio molecular dynamics simulations have been employed in order to gain insights into materials properties like diffusion, adsorption, catalysis, and structure. In transition metals, absorbed hydrogen atoms self-trap due to localization of metal d-electrons. The self-trapping state is shown to highly influence hydrogen diffusion in the classical over-barrier jump temperature region. Li diffusion in Li-N-H systems ...

Blomqvist, Andreas

2010-01-01

247

Dynamic Structure Factor of Liquid and Amorphous Ge From Ab Initio Simulations

We calculate the dynamic structure factor S(k,omega) of liquid Ge (l-Ge) at temperature T = 1250 K, and of amorphous Ge (a-Ge) at T = 300 K, using ab initio molecular dynamics. The electronic energy is computed using density-functional theory, primarily in the generalized gradient approximation, together with a plane wave representation of the wave functions and ultra-soft pseudopotentials. We use a 64-atom cell with periodic boundary conditions, and calculate averages over ...

Chai, Jeng-da; Stroud, D.; Hafner, J.; Kresse, G.

2002-01-01

248

The molecular structure and spectra of cubane. An ab initio investigation

The equilibrium geometry and vibrational frequencies of cubane have been studied with accurate ab initio SCF calculations. The calculations confirm the cubic symmetry of the molecule, and the computed bond distances RCC = 1.570 Å, RCH = 1.081 Å compare well with experiment. Intensities and depolarization ratios have also been calculated for the Raman-active fundamentals. The orbital energies are discussed in relation to the photoelectron spectrum.

Almlöf, Jan; Jonvik, Torgeir

1982-10-01

249

Parabolic laws of the surrounded-atom model from ab initio calculations on clusters

The « surrounded-atom » model formulates empirical hypotheses on energies, associated to elementary configurational supports of binary alloys, via parabolic laws which are functions of the local concentration. In this paper, using ab initio MO-CI calculations on clusters, we have shown that these parabolic laws have a microscopic electronic basis. Two binary alloys, [Li, Na] and [Al, Li], were studied and we qualitatively found a correct order for the dissymetry of their enthalpy of mixing ...

Pellegatti, A.; Marinelli, F.; Mathieu, J. -c

1990-01-01

250

Incorporating

Abstract Background Native structures of proteins are formed essentially due to the combining effects of local and distant (in the sense of sequence) interactions among residues. These interaction information are, explicitly or implicitly, encoded into the scoring function in protein structure prediction approaches—threading approaches usually measure an alignment in the sense that how well a sequence adopts an existing structure; while the energy functions in Ab Initio...

Li Shuai; Yuan Xiongying; Wang Chao; Wang Sheng; Shao Mingfu; Zheng Weimou; Bu Dongbo

2011-01-01

251

Embedded-cluster ab-initio study of the neutral oxygen vacancy in quartz and cristobalite.

The oxygen vacancy in silica is characterized theoretically using an ab initio unrestricted Hartree-Fock, embedded-cluster approach. Two models are adopted for the host crystal, ?-quartz and ?-cristobalite. The defect formation energy, the transition energies from the ground to the first excited singlet and triplet states and the corresponding luminescence are considered. The electronic structure of the defect in the different states is analysed, and it is shown that the excitation correspo...

Pisani, Cesare; Casassa, Silvia Maria

2000-01-01

252

Ab-initio study of oxygen vacancies in alpha-quartz

Extrinsic levels, formation energies, and relaxation geometries are calculated ab initio for oxygen vacancies in alpha-quartz SiO2. The vacancy is found to be thermodynamically stable in the charge states Q=+3, Q=0, Q=--2, and Q=-3. The charged states are stabilized by large and asymmetric distortions near the vacancy site. Concurrently, Franck-Condon shifts for absorption and recombination related to these states are found to be strongly asymmetric. In undoped quartz, the g...

Carbonaro, C. M.; Fiorentini, V.; Massidda, S.

1996-01-01

253

Reaction pathways for the decomposition of fluoroformic and chloroformic acids, FC(O)OH and CIC(O)OH, have been studied using ab initio methods. Equilibrium geometries and transition state structures have been fully optimized at the Hartree-Fockand second-order Møller-Plesset levels of theory. The most favorable reaction pathway is molecular dissociation into CO 2 and hydrogen halide (HF or HCl). Dissociation into radical fragments are energetically non-favorable processes.

Francisco, J. S.; Ghoul, W. A.

1991-11-01

254

GlimmerM, Exonomy and Unveil: three ab initio eukaryotic genefinders

We present three programs for ab initio gene prediction in eukaryotes: Exonomy, Unveil and GlimmerM. Exonomy is a 23-state Generalized Hidden Markov Model (GHMM), Unveil is a 283-state standard Hidden Markov Model (HMM) and GlimmerM is a previously-described genefinder which utilizes decision trees and Interpolated Markov Models (IMMs). All three are readily re-trainable for new organisms and have been found to perform well compared to other genefinders. Results are presented for Arabidopsis ...

Majoros, William H.; Pertea, Mihaela; Antonescu, Corina; Salzberg, Steven L.

2003-01-01

255

Ab initio modeling of quantum transport properties of molecular electronic devices

We report on a self-consistent ab initio technique for modeling quantum transport properties of atomic and molecular scale nanoelectronic devices under external bias potentials. The technique is based on density functional theory using norm conserving nonlocal pseudopotentials to define the atomic core and nonequilibrium Green’s functions (NEGF’s) to calculate the charge distribution. The modeling of an open device system is reduced to a calculation defined on a finite region of space usi...

Taylor, J.; Guo, H.; Wang, J.

2001-01-01

256

Ab initio molecular dynamics study of manganese porphine hydration and interaction with nitric oxide

The authors use ab initio molecular dynamics and the density functional theory+U (DFT+U) method to compute the hydration environment of the manganese ion in manganese (II) and manganese (III) porphines (MnP) dispersed in liquid water. These are intended as simple models for more complex water soluble porphyrins, which have important physiological and electrochemical applications. The manganese ion in Mn(II)P exhibits significant out-of-porphine plane displacement and binds s...

Leung, Kevin; Medforth, Craig J.

2007-01-01

257

Direct ab initio MD simulation of silver ion diffusion in chalcogenide glasses

In this paper, we present new models of germanium selenide chalcogenide glasses heavily doped with silver. The models were readily obtained with ab initio molecular dynamics and their structure agrees closely with diffraction measurements. Thermal molecular dynamics simulation reveals the dynamics of Ag+ ions and the existence of trapping centers as conjectured in other theory work. We show that first principles simulation is a powerful tool to reveal the motion of ions in glass.

Tafen, D N; Mitkova, M; Tafen, De Nyago

2005-01-01

258

Direct ab initio MD simulation of silver ion diffusion in chalcogenide glasses

In this paper, we present new models of germanium selenide chalcogenide glasses heavily doped with silver. The models were readily obtained with ab initio molecular dynamics and their structure agrees closely with diffraction measurements. Thermal molecular dynamics simulation reveals the dynamics of Ag+ ions and the existence of trapping centers as conjectured in other theory work. We show that first principles simulation is a powerful tool to reveal the motion of ions in g...

Tafen, Nyago; Drabold, D. A.; Mitkova, M.

2005-01-01

259

Contact dependence of carrier injection in carbon nanotubes: An ab initio study

We combine ab initio density functional theory with transport calculations to provide a microscopic basis for distinguishing between `good' and `poor' metal contacts to nanotubes. Comparing Ti and Pd as examples of different contact metals, we trace back the observed superiority of Pd to the nature of the metal-nanotube hybridization. Based on large scale Landauer transport calculations, we suggest that the `optimum' metal-nanotube contact combines a weak hybridization with a large contact length between the metal and the nanotube.

Nemec, N; Cuniberti, G

2006-01-01

260

Based on a numerical ab initio study, we discuss a structure model for a broad boron sheet, which is the analog of a single graphite sheet, and the precursor of boron nanotubes. The sheet has linear chains of sp hybridized sigma bonds lying only along its armchair direction, a high stiffness, and anisotropic bonds properties. The puckering of the sheet is explained as a mechanism to stabilize the sp sigma bonds. The anisotropic bond properties of the boron sheet lead to a tw...

Kunstmann, Jens; Quandt, Alexander

2005-01-01

261

Strain energy calculations of hexagonal boron nanotubes: An ab-initio approach

An ab initio calculations have been carried out for examining the curvature effect of small diameter hexagonal boron nanotubes. The considered conformations of boron nanotubes are namely armchair (3,3), zigzag (5,0) and chiral (4,2), and consist of 12, 20, and 56 atoms, respectively. The strain energy is evaluated in order to examine the curvature effect. It is found that the strain energy of hexagonal BNT strongly depends upon the radius, whereas the strain energy of triang...

Jain, S. K.; Srivastava, P.

2013-01-01

262

EVAL15: a diffraction data integration method based on ab initio predicted profiles

A novel diffraction data integration method is presented, EVAL15, based upon ab initio calculation of three-dimensional (x, y, ) reflection profiles from a few physical crystal and instrument parameters. Net intensities are obtained by least-squares fitting the observed profile with the calculated standard using singular value decomposition. This paper shows that profiles can be predicted satisfactorily and that accurate intensities are obtained. The detailed profile analysis has the addition...

Schreurs, A. M. M.; Xian, X.; Kroon-batenburg, L. M. J.

2010-01-01

263

Electron transport through Al–ZnO–Al: an ab initio calculation

The electron transport properties of ZnO nanowires coupled by two aluminum electrodes were studied by ab initio method based on nonequilibrium Green’s function approach and density functional theory. A clearly rectifying current-voltage characteristics was observed. It was found that the contact interfaces between Al–O and Al–Zn play important roles in the charge transport at low bias voltage and give very asymmetric I-V characteristics. When the bias voltage increases, the negative dif...

Yang, Zj; Wan, Lh; Wei, Y.; Yu, Y.; Wang, J.

2010-01-01

264

The thermal and lattice dynamical properties of seven silicon clathrate framework structures are investigated with ab initio density functional methods (frameworks I, II, IV, V, VII, VIII, and H). The negative thermal expansion (NTE) phenomenon is investigated by means of quasiharmonic approximation and applying it to equal time displacement correlation functions. The thermal properties of the studied clathrate frameworks, excluding the VII framework, resemble those of the c...

Ha?rko?nen, Ville J.; Karttunen, Antti J.

2014-01-01

265

Ab initio Hartree-Fock study of tetragonal and cubic phases of zirconium dioxide

The structural and electronic properties of cubic and tetragonal zirconia (ZrO2) are studied using a periodic ab initio Hartree-Fock method. Only valence electrons are treated explicitly, while effective core potentials are used for describing core electrons. The equilibrium geometries and elastic properties of the two phases are studied, and the mechanism of phase transition is discussed, with possible effects of applied pressure being taken into consideration. The analysis of the electronic...

Orlando, Roberto

1992-01-01

266

Temperature dependence of TiN elastic constants from ab initio molecular dynamics simulations

Elastic properties of cubic TiN are studied theoretically in a wide temperature interval. First-principles simulations are based on ab initio molecular dynamics (AIMD). Computational efficiency of the method is greatly enhanced by a careful preparation of the initial state of the simulation cell that minimizes or completely removes a need for equilibration and therefore allows for parallel AIMD calculations. Elastic constants C11, C12, and C44 are calculated. A strong dependence on the temper...

Steneteg, Peter; Hellman, Olle; Vekilova, Olga; Shulumba, Nina; Tasna?di, Ferenc; Abrikosov, Igor

2013-01-01

267

Ab initio study of the optical absorption and wave-vector-dependent dielectric response of graphite

We performed ab initio calculations of the optical absorption spectrum and the wave-vector-dependent dielectric and energy-loss functions of graphite in the framework of the random-phase approximation. In the absorption spectrum, the most prominent peaks were analyzed in terms of interband transitions from specific regions of the Brillouin zone. The inclusion of the crystal local-field effects (LFE) in the response had an important influence on the absorption spectrum for light polarization p...

Marinopoulos, A. G.; Reining, Lucia; Rubio Secades, A?ngel; Olevano, Valerio

2004-01-01

268

Ab initio study of ladder-type polymers polythiophene and polypyrrole

This article presents an \\textit{ab initio} study of four polymers, polythiophene, polypyrrole, ladder-type polythiophene, and ladder-type polypyrrole. Upon an analysis of the variation of the band gap when comparing the unconstrained and the ladder-type polymers, a discrepancy was found between the thiophene and the pyrrole polymer families. For polythiophene, the ladder-type polymer has a larger gap than the unconstrained polymer whereas the opposite is found for the pyrro...

Pesant, Simon; Boulanger, Paul; Co?te?, Michel; Ernzerhof, Matthias

2006-01-01

269

Ab initio investigation of the melting line of nitrogen at high pressure

Understanding the behavior of molecular systems under pressure is a fundamental problem in condensed matter physics. In the case of nitrogen, the determination of the phase diagram and in particular of the melting line, are largely open problems. Two independent experiments have reported the presence of a maximum in the nitrogen melting curve, below 90 GPa, however the position and the interpretation of the origin of such maximum differ. By means of ab initio molecular dynam...

Donadio, Davide; Spanu, Leonardo; Duchemin, Ivan; Gygi, Francois; Galli, Giulia

2010-01-01

270

International Nuclear Information System (INIS)

We have devised a technique for spectral imaging using accurate ab initio electron energy loss near edge structure (ELNES) data and function field visualization. The technique is initially applied to a planar defect model in Si with different ring structures and no broken bonds where experimental probes are severely limited. The same model with B doping is also considered. It is shown that specific deviations in different energy ranges of the ELNES spectra are correlated with different structural components of the models.

271

Ab initio calculations of the electronic structure and doubling parameters of BS

International Nuclear Information System (INIS)

Ab initio calculations have been performed to understand the influence of spin-orbit interaction upon the fine structure of the observed valence doublet states of the BS molecule: spin-orbit splittings, ?-type and ?-type doublings. Configuration interaction is shown to be an essential feature in order to account for the observed data. Other properties of the electronic states (transition energies) have also been calculated. (orig.)

272

Energy Technology Data Exchange (ETDEWEB)

The melting and lattice dynamics of sodium are studied by quantum molecular dynamics simulation, i.e., with allowance for anharmonicity, at pressures up to 1 Mbar and temperatures up to 1000 K. The simulation results agree well with the experimental data and our earlier calculation performed ab initio in the quasi-harmonic approximation. The simulation results demonstrate that anharmonic interactions weakly affect the melting curve and the phonon frequencies of Na up to near-melting temperatures.

Lepeshkin, S. V., E-mail: lepeshkin@lpi.ru [Russian Academy of Sciences, Lebedev Physical Institute (Russian Federation); Magnitskaya, M. V. [Vereshchagin Institute for High Pressure Physics (Russian Federation); Matsko, N. L.; Maksimov, E. G. [Russian Academy of Sciences, Lebedev Physical Institute (Russian Federation)

2012-07-15

273

Ab initio large-basis no-core shell model and its applications to light nuclei

International Nuclear Information System (INIS)

We describe the ab initio No-Core Shell Model, in which the effective Hamiltonians are derived microscopically from realistic nucleon-nucleon potentials, as a function of the finite harmonic-oscillator basis space. We give results for the A = 3 nucleon system to demonstrate the viability of the technique. Extending our approach to p-shell nuclei, we present some of our latest results

274

Vibrational properties of ultralong Rydberg Cs$_2$ molecules are investigated on corresponding potential curves obtained by perturbation theory. The Rydberg Cs$_2$ molecules are associated by a Rydberg Cs($nS/nP$) atom $(n=30-70)$ and a ground state Cs($6s$) atom. The starting point for the perturbation treatment of corresponding Rydberg molecular potential curves is to generate accurate atomic Rydberg states from realistic {\\it ab initio} effective core potential. The calcu...

Liu, Xiaomeng; Yang, Yonggang; Zhao, Jianming; Xiao, Liantuan; Jia, Suotang

2012-01-01

275

Ab initio calculations of the parameters of magnetic and electrical hyperfine interactions at the nuclei of magnetic ions 47,49Ti and nonmagnetic ions 139La and 89Y have been performed in the model of a periodic crystal and in the cluster model for lanthanum and yttrium titanates. A comparison has been performed with experimental data and with the results of calculations in the model of crystalline field and with data from calculations in the LDA and LDA + U approximations.

Agzamova, P. A.; Leskova, Yu. V.; Petrov, V. P.; Chernyshev, V. A.; Zakir'yanov, D. O.; Nikiforov, A. E.

2014-12-01

276

Ab initio calculation of Quasi-equilibrium microcracks in cubic boron nitride

International Nuclear Information System (INIS)

A crack in cubic boron nitride crystal was simulated within ab initio density-functional theory. The lattice constant, critical stress intensity factor Kc, which describes crack creation stress, and fracture surface energy ? were calculated from the elongated 2 x 6 x 1 supercell and these quantities agree quite well with the experimental data. We conclude that density-functional theory can be used to estimate crack's material constants. (author)

277

Ab initio derivation of Hubbard models for cold atoms in optical lattices

We derive ab initio local Hubbard models for several optical lattice potentials of current interest, including the honeycomb and Kagom\\'{e} lattices, verifying their accuracy on each occasion by comparing the interpolated band structures against the originals. To achieve this, we calculate the maximally-localized generalized Wannier basis by implementing the steepest-descent algorithm of Marzari and Vanderbilt [N. Marzari and D. Vanderbilt, Phys. Rev. B 56, 12847 (1997)] dir...

Walters, R.; Cotugno, G.; Johnson, Th; Clark, Sr; Jaksch, D.

2013-01-01

278

Experimental and ab initio infrared study of ?-, ? - and ?-aluminas formed from gibbsite

?-, ?- and ?-alumina phases formed by dehydration of micro-grained gibbsite between 773 and 1573 K are studied using infrared spectroscopy (IR). The structural transitions evidenced by X-ray diffraction (XRD) were interpreted by comparing IR measurements with ab initio simulations (except for the ? form whose complexity does not allow a reliable simulation). For each phase, IR spectrum presents specific bands corresponding to transverse optical (TO) modes of Al-O stretching and bending under 900 cm -1. The very complex ? phase, obtained at 773 K, provides a distinctive XRD pattern in contrast with the IR absorbance appearing as a broad structure extending between 200 and 900 cm -1 resembling the equivalent spectra for ?-alumina phase. ?-alumina is forming at 1173 K and its rich IR spectrum is in good qualitative agreement with ab initio simulations. This complexity reflects the large number of atoms in the ?-alumina unit cell and the wide range of internuclear distances as well as the various coordinances of both Al and O atoms. Ab initio simulations suggest that this form of transition alumina demonstrates a strong departure from the simple pattern observed for other transition alumina. At 1573 K, the stable ?-?l 2? 3 develops. Its IR spectra extends in a narrower energy range as compared to transition alumina and presents characteristics features similar to model ?-?l 2? 3? Ab initio calculations show again a very good general agreement with the observed IR spectra for this phase. In addition, for both ?- and ?-?l 2? 3, extra modes, measured at high energy (above 790 cm -1 for ? and above 650 cm -1 for ?), can originate from either remnant ?-alumina or from surface modes.

Favaro, L.; Boumaza, A.; Roy, P.; Lédion, J.; Sattonnay, G.; Brubach, J. B.; Huntz, A. M.; Tétot, R.

2010-04-01

279

Calculation of ab initio of the potential curves between atoms (Li-Li, F-F)

International Nuclear Information System (INIS)

Using ab initio program MONSTERGAUSS and various basis sets, we calculated the potential curves between Li-Li and F-F atoms at wider nuclear distances. We also calculated the equilibrium nuclear distances of ground state molecules Li2(1?g+) and F2(1?g+) and election correlation energy with configuration interaction method (CI). The calculated results were discussed and compared with other's calculated and experimental results

280

We present an efficient and accurate computational approach to study phase-coherent quantum transport in molecular and nanoscale electronics. We formulate a Green’s-function method in the recently developed ab initio nonorthogonal quasiatomic orbital basis set within the Landauer-Büttiker formalism. These quasiatomic orbitals are efficiently and robustly transformed from Kohn-Sham eigenwave functions subject to the maximal atomic-orbital similarity measure. With this minimal ba...

Qian, Xiaofeng; Li, Ju; Yip, Sidney

2010-01-01

281

Structural, electronic, and optical properties of ZrO2 from ab initio calculations

Structural, electronic, and optical properties for the cubic, tetragonal, and monoclinic crystalline phases of ZrO2, as derived from it ab initio full-relativistic calculations, are presented. The electronic structure calculations were carried out by means of the all-electron full potential linear augmented plane wave method, within the framework of the density functional theory and the local density approximation. The calculated carrier effective masses are shown to be high...

Garcia, Joelson Cott; Scolfaro, L. M. R.; Lino, A. T.; Freire, V. N.; Farias, G. A.; Silva, C. C.; Alves, H. W. Leite; Rodrigues, S. C. P.; Silva Jr, E. F. Da

2012-01-01

282

Mechanics properties of Mono-layer Hexagonal Boron Nitride: Ab initio study

We introduced a method to obtain the continuum description of the elastic properties of mono- layer h-BN through ab initio density functional theory. This thermodynamically rigorous contin- uum description of the elastic response is formulated by expanding the elastic strain energy density in a Taylor series in strain truncated after the fifth-order term. we obtained a total of fourteen nonzero independent elastic constants for the up to tenth-order tensor. We predicted the ...

Peng, Qing; Zamiri, Amir R.; De, Suvranu

2011-01-01

283

Ab initio potential energy surface for the highly nonlinear dynamics of the KCN molecule

Energy Technology Data Exchange (ETDEWEB)

An accurate ab initio quantum chemistry study at level of quadratic configuration interaction method of the electronic ground state of the KCN molecule is presented. A fitting of the results to an analytical series expansion was performed to obtain a global potential energy surface suitable for the study of the associated vibrational dynamics. Additionally, classical Poincaré surfaces of section for different energies and quantum eigenstates were calculated, showing the highly nonlinear behavior of this system.

Párraga, H.; Arranz, F. J., E-mail: fj.arranz@upm.es; Benito, R. M., E-mail: rosamaria.benito@upm.es [Grupo de Sistemas Complejos, ETSI Agrónomos, Universidad Politécnica de Madrid, 28040 Madrid (Spain); Borondo, F., E-mail: f.borondo@uam.es [Departamento de Química and Instituto de Ciencias Matemáticas (ICMAT), Universidad Autónoma de Madrid, Cantoblanco, 28049-Madrid (Spain)

2013-11-21

284

Ab initio potential energy surface for the highly nonlinear dynamics of the KCN molecule

International Nuclear Information System (INIS)

An accurate ab initio quantum chemistry study at level of quadratic configuration interaction method of the electronic ground state of the KCN molecule is presented. A fitting of the results to an analytical series expansion was performed to obtain a global potential energy surface suitable for the study of the associated vibrational dynamics. Additionally, classical Poincaré surfaces of section for different energies and quantum eigenstates were calculated, showing the highly nonlinear behavior of this system

285

Ab initio potential energy surface for the highly nonlinear dynamics of the KCN molecule

An accurate ab initio quantum chemistry study at level of quadratic configuration interaction method of the electronic ground state of the KCN molecule is presented. A fitting of the results to an analytical series expansion was performed to obtain a global potential energy surface suitable for the study of the associated vibrational dynamics. Additionally, classical Poincaré surfaces of section for different energies and quantum eigenstates were calculated, showing the highly nonlinear behavior of this system.

Párraga, H.; Arranz, F. J.; Benito, R. M.; Borondo, F.

2013-11-01

286

Spectroscopic and ab initio study of an intramolecular charge transfer (ICT) rhodanine derivative

The steady state absorption and emission studies of the rhodanine derivative 5-( p-dimethylaminobenzylidene) rhodanine (PDR) have been investigated. A dual fluorescence associated with an intramolecular charge transfer (ICT) phenomenon is reported. The characteristic emission band at low temperature (77 K) has also been reported. In support of the experimental results ab initio SCF and DFT calculations have been performed. The theoretical calculations also indicate that the chosen compound has significant non-linear optical (NLO) properties.

Ray, Jayanta; Panja, Nabamita; Nandi, Prasanta K.; Martin, Justin J.; Jones, Wayne E., Jr.

2008-02-01

287

Ab initio calculation of the anomalous Hall conductivity by Wannier interpolation

The intrinsic anomalous Hall effect in ferromagnets depends on subtle spin-orbit-induced effects in the electronic structure, and recent ab-initio studies found that it was necessary to sample the Brillouin zone at millions of k-points to converge the calculation. We present an efficient first-principles approach for computing the anomalous Hall conductivity. We start out by performing a conventional electronic-structure calculation including spin-orbit coupling on a uniform and relatively coarse k-point mesh. From the resulting Bloch states, maximally-localized Wannier functions are constructed which reproduce the ab-initio states up to the Fermi level. The Hamiltonian and position-operator matrix elements, needed to represent the energy bands and Berry curvatures, are then set up between the Wannier orbitals. This completes the first stage of the calculation, whereby the low-energy ab-initio problem is transformed into an effective tight-binding form. The second stage only involves Fourier transforms and un...

Wang, X; Souza, I; Vanderbilt, D; Wang, Xinjie; Yates, Jonathan R.; Souza, Ivo; Vanderbilt, David

2006-01-01

288

International Nuclear Information System (INIS)

The behaviour of silicon carbide under irradiation has been studied using classical and ab initio simulations, focusing on the nano scale elementary processes. First, we have been interested in the calculation of threshold displacement energies, which are difficult to determine both experimentally and theoretically, and also the associated Frenkel pairs. In the framework of this thesis, we have carried out simulations in classical and ab initio molecular dynamics. For the classical approach, two types of potentials have been used: the Tersoff potential, which led to non satisfactory results, and a new one which has been developed during this thesis. This potential allows a better modelling of SiC under irradiation than most of the empirical potentials available for SiC. It is based on the EDIP potential, initially developed to describe defects in silicon, that we have generalized to SiC. For the ab initio approach, the feasibility of the calculations has been validated and average energies of 19 eV for the C and 38 eV for the Si sublattices have been determined, close to the values empirically used in the fusion community. The results obtained with the new potential EDIP are globally in agreement with those values. Finally, the elementary processes involved in the crystal recovery have been studied by calculating the stability of the created Frenkel pairs and determining possible recombination mechanisms with the nudged elastic band method. (author)

289

This study elucidated the in vitro physicomechanical transitions of a crosslinked polylactic-co-glycolic acid (PLGA) scaffold, utilizing quantum mechanics to compute the ab initio energy requirements of a salted-out and subsequently crosslinked PLGA scaffold interacting with simulated physiological fluid, phosphate buffered saline (PBS) (pH 7.4, 37 degrees C) at a molecular level. Twenty-six salted-out PLGA scaffolds were formulated using a four factor, two centerpoint quadratic Face-Centered Central Composite Design (FCCD). PLGA molecular mass, PLGA concentration, water volume and salting-out reaction time were the dependant formulation variables. Subsequent to PLGA solubilization in dimethyl formamide (DMF), protonated water was added to induce salting-out of PLGA into a scaffolds that were immersed in PBS, oscillated at 100 rpm, and analyzed at pre-determined time intervals for their physicomechanical and ab initio quantum energy transitions. Results indicated that the matrix resilience (MR) decreased with longer incubation periods (MR=35-45%) at day 30. Scaffolds salted-out using higher PLGA concentrations exhibited minimal changes in MR and the matrix ability to absorb energy was found to closely correlate with the scaffold residence time in PBS. Spartan-based ab initio quantum energy predictions elucidated the potential scaffold stability from a molecular viewpoint and its suitability for use in rate-modulated drug delivery. PMID:17524474

Sibambo, Sibongile R; Pillay, Viness; Choonara, Yahya E; Khan, Riaz A; Sweet, Joe L

2007-09-01

290

A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics (AI-PIMD) simulation, without compromising the overall accuracy. To validate the method, the internal energy and free energy of an Einstein crystal are calculated and compared with the analytical solutions. As a preliminary application, we assess the performance of the method in a realistic model, the FCC phase of dense atomic hydrogen, in which the calculated result shows that the acceleration rate is about 3 to 4 fold for a two-level implementation, and can be increased to 10 times if extrapolation is used. With only 16 beads used for the ab initio potential sampling, this method gives a well converged internal energy. The residual error in pressure is just about 3 GPa, whereas it is about 20 GPa for a plain AI-PIMD calculation with the same number of beads. The vibration...

Geng, Hua Y

2014-01-01

291

Modeling of nuclear glasses by classical and ab initio molecular dynamics

International Nuclear Information System (INIS)

A calcium aluminosilicate glass of molar composition 67 % SiO2 - 12 % Al2O3 - 21 % CaO was modelled by classical and ab initio molecular dynamics. The size effect study in classical MD shows that the systems of 100 atoms are more ordered than the larger ones. These effects are mainly due to the 3-body terms in the empirical potentials. Nevertheless, these effects are small and the structures generated are in agreement with experimental data. In such kind of glass, we denote an aluminium avoidance and an excess of non bridging oxygens which can be compensated by tri-coordinated oxygens. When the dynamics of systems of 100 and 200 atoms is followed by ab initio MD, some local arrangements occurs (bond length, angular distributions). Thus, more realistic vibrational properties are obtained in ab initio MD. The modelling of thin films shows that aluminum atoms extend to the most external part of the surface and they are all tri-coordinated. Calcium atoms are set in the sub layer part of the surface and they produce a depolymerization of the network. In classical MD, tri-coordinated aluminium atoms produce an important electric field above the surface. With non bridging oxygens, they constitute attractive sites for single water molecules. (author)

292

Dominant Modes in Light Nuclei - Ab Initio View of Emergent Symmetries

An innovative symmetry-guided concept is discussed with a focus on emergent symmetry patterns in complex nuclei. In particular, the ab initio symmetry-adapted no-core shell model (SA-NCSM), which capitalizes on exact as well as partial symmetries that underpin the structure of nuclei, provides remarkable insight into how simple symmetry patterns emerge in the many-body nuclear dynamics from first principles. This ab initio view is complemented by a fully microscopic no-core symplectic shell-model framework (NCSpM), which, in turn, informs key features of the primary physics responsible for the emergent phenomena of large deformation and alpha-cluster substructures in studies of the challenging Hoyle state in Carbon-12 and enhanced collectivity in intermediate-mass nuclei. Furthermore, by recognizing that deformed configurations often dominate the low-energy regime, the SA-NCSM provides a strategy for determining the nature of bound states of nuclei in terms of a relatively small subspace of the symmetry-reorganized complete model space, which opens new domains of nuclei for ab initio investigations, namely, the intermediate-mass region, including isotopes of Ne, Mg, and Si.

Draayer, J. P.; Dytrych, T.; Launey, K. D.; Dreyfuss, A. C.; Langr, D.

2015-01-01

293

Modelling of nuclear glasses by classical and ab initio molecular dynamics

International Nuclear Information System (INIS)

A calcium aluminosilicate glass of molar composition 67 % SiO2 - 12 % Al2O3 - 21 % CaO was modelled by classical and ab initio molecular dynamics. The size effect study in classical MD shows that the systems of 100 atoms are more ordered than the larger ones. These effects are mainly due to the 3-body terms in the empirical potentials. Nevertheless, these effects are small and the structures generated are in agreement with experimental data. In such kind of glass, we denote an aluminium avoidance and an excess of non bridging oxygens which can be compensated by tri coordinated oxygens. When the dynamics of systems of 100 and 200 atoms is followed by ab initio MD, some local arrangements occurs (bond length, angular distributions). Thus, more realistic vibrational properties are obtained in ab initio MD. The modelling of thin films shows that aluminium atoms extend to the most external part of the surface and they are all tri-coordinated. Calcium atoms are set in the sub layer part of the surface and they produce a depolymerization of the network. In classical MD, tri-coordinated aluminium atoms produce an important electric field above the surface. With non bridging oxygens, they constitute attractive sites for single water molecules. (author)

294

Ab initio based thermal property predictions at a low cost: An error analysis

Ab initio calculations often do not straightforwardly yield the thermal properties of a material yet. It requires considerable computational efforts, for example, to predict the volumetric thermal expansion coefficient ?V or the melting temperature Tm from first principles. An alternative is to use semiempirical approaches. They relate the experimental values to first-principles predictors via fits or approximative models. Before applying such methods, however, it is of paramount importance to be aware of the expected errors. We therefore quantify these errors at the density-functional theory level using the Perdew-Burke-Ernzerhof functional for several semiempirical approximations of ?V and Tm, and compare them to the errors from fully ab initio methods, which are computationally more intensive. We base our conclusions on a benchmark set of 71 ground-state elemental crystals. For the thermal expansion coefficient, it appears that simple quasiharmonic theory, in combination with different approximations to the Grüneisen parameter, provides a similar overall accuracy as exhaustive first-principles phonon calculations. For the melting temperature, expensive ab initio molecular-dynamics simulations still outperform semiempirical methods.

Lejaeghere, Kurt; Jaeken, Jan; Van Speybroeck, Veronique; Cottenier, Stefaan

2014-01-01

295

A benchmark ab initio and density functional (DFT) study has been carried out on the electron affinities of the first- and second-row atoms. The ab initio study involves basis sets of $spdfgh$ and $spdfghi$ quality, extrapolations to the 1-particle basis set limit, and a combination of the CCSD(T), CCSDT, and full CI electron correlation methods. Scalar relativistic and spin-orbit coupling effects were taken into account. On average, the best ab initio results agree to better than 0.001 eV with the most recent experimental results. Correcting for imperfections in the CCSD(T) method improves the mean absolute error by an order of magnitude, while for accurate results on the second-row atoms inclusion of relativistic corrections is essential. The latter are significantly overestimated at the SCF level; for accurate spin-orbit splitting constants of second-row atoms inclusion of (2s,2p) correlation is essential. In the DFT calculations it is found that results for the 1st-row atoms are very sensitive to the exch...

De Oliveira, G; De Proft, F; Geerlings, P; Oliveira, Glenisson de; Martin, Jan M.L.; Proft, Frank de; Geerlings, Paul

1999-01-01

296

Iron -chromium alloys and free surfaces: from ab initio calculations to thermodynamic modeling

International Nuclear Information System (INIS)

Ferritic steels possibly strengthened by oxide dispersion are candidates as structural materials for generation IV and fusion nuclear reactors. Their use is limited by incomplete knowledge of the iron-chromium phase diagram at low temperatures and of the phenomena inducing preferential segregation of one element at grain boundaries or at surfaces. In this context, this work contributes to the multi-scale study of the model iron-chromium alloy and their free surfaces by numerical simulations. This study begins with ab initio calculations of properties related to the mixture of atoms of iron and chromium. We highlight complex dependency of the magnetic moments of the chromium atoms on their local chemical environment. Surface properties are also proving sensitive to magnetism. This is the case of impurity segregation of chromium in iron and of their interactions near the surface. In a second step, we construct a simple energy model for high numerical efficiency. It is based on pair interactions on a rigid lattice to which are given local chemical environment and temperature dependencies. With this model, we reproduce the ab initio results at zero temperature and experimental results at high temperature. We also deduce the solubility limits at all intermediate temperatures with mean field approximations that we compare to Monte Carlo simulations. The last step of our work is to introduce free surfaces in our model. We then study the effect of ab initio calculated bulk and surface properties on surface segregation.Finally, we calculate segregation isotherms. We therefore propose an evolution model of surface composition of iron-chromium alloys as a function of bulk composition. which are given local chemical environment and temperature dependencies. With this model, we reproduce the ab initio results at zero temperature and experimental results at high temperature. We also deduce the solubility limits at all intermediate temperatures with mean field approximations that we compare to Monte Carlo simulations. The last step of our work is to introduce free surfaces in our model. We then study the effect of ab initio calculated bulk and surface properties on surface segregation. Finally, we calculate segregation isotherms. We therefore propose an evolution model of surface composition of iron-chromium alloys as a function of bulk composition. (author)

297

FIREBALL is an ab initio technique for fast local orbital simulations of nanotechnological, solid state, and biological systems. We have implemented a convenient interface for new users and software architects in the platform-independent Java language to access FIREBALL's unique and powerful capabilities. The graphical user interface can be run directly from a web server or from within a larger framework such as the Computational Science and Engineering Online (CSE-Online) environment or the Distributed Analysis of Neutron Scattering Experiments (DANSE) framework. We demonstrate its use for high-throughput electronic structure calculations and a multi-100 atom quantum molecular dynamics (MD) simulation. Program summaryProgram title: FireballUI Catalogue identifier: AECF_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AECF_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 279 784 No. of bytes in distributed program, including test data, etc.: 12 836 145 Distribution format: tar.gz Programming language: Java Computer: PC and workstation Operating system: The GUI will run under Windows, Mac and Linux. Executables for Mac and Linux are included in the package. RAM: 512 MB Word size: 32 or 64 bits Classification: 4.14 Nature of problem: The set up and running of many simulations (all of the same type), from the command line, is a slow process. But most research quality codes, including the ab initio tight-binding code FIREBALL, are designed to run from the command line. The desire is to have a method for quickly and efficiently setting up and running a host of simulations. Solution method: We have created a graphical user interface for use with the FIREBALL code. Once the user has created the files containing the atomic coordinates for each system that they are going to run a simulation on, the user can set up and start the computations of up to hundreds of simulations. Running time: 3 to 5 minutes on a 2 GHz Pentium IV processor.

Keith, J. Brandon; Fennick, Jacob R.; Junkermeier, Chad E.; Nelson, Daniel R.; Lewis, James P.

2009-03-01

298

Next generation sequencing technology is advancing genome sequencing at an unprecedented level. By unravelling the code within a pathogen's genome, every possible protein (prior to post-translational modifications) can theoretically be discovered, irrespective of life cycle stages and environmental stimuli. Now more than ever there is a great need for high-throughput ab initio gene finding. Ab initio gene finders use statistical models to predict genes and their exon-intron structures from the genome sequence alone. This paper evaluates whether existing ab initio gene finders can effectively predict genes to deduce proteins that have presently missed capture by laboratory techniques. An aim here is to identify possible patterns of prediction inaccuracies for gene finders as a whole irrespective of the target pathogen. All currently available ab initio gene finders are considered in the evaluation but only four fulfil high-throughput capability: AUGUSTUS, GeneMark_hmm, GlimmerHMM, and SNAP. These gene finders require training data specific to a target pathogen and consequently the evaluation results are inextricably linked to the availability and quality of the data. The pathogen, Toxoplasma gondii, is used to illustrate the evaluation methods. The results support current opinion that predicted exons by ab initio gene finders are inaccurate in the absence of experimental evidence. However, the results reveal some patterns of inaccuracy that are common to all gene finders and these inaccuracies may provide a focus area for future gene finder developers. PMID:23226328

Goodswen, Stephen J; Kennedy, Paul J; Ellis, John T

2012-01-01

299

Conventional density functional theory (DFT) fails for strongly correlated electron systems due to large intra-atomic self-interaction errors. The DFT+U method provides a means of overcoming these errors through the use of a parametrized potential that employs an exact treatment of quantum mechanical exchange interactions. The parameters that enter into this potential correspond to the spherically averaged intra-atomic Coulomb (U) and exchange (J) interactions. Recently, we developed an ab initio approach for evaluating these parameters on the basis of unrestricted Hartree-Fock (UHF) theory, which has the advantage of being free of self-interaction errors and does not require experimental input [Mosey and Carter, Phys. Rev. B 76, 155123 (2007)]. In this work, we build on that method to develop a more robust and convenient ab initio approach for evaluating U and J. The new technique employs a relationship between U and J and the Coulomb and exchange integrals evaluated using the entire set of UHF molecular orbitals (MOs) for the system. Employing the entire set of UHF MOs renders the method rotationally invariant and eliminates the difficulty in selecting unambiguously the MOs that correspond to localized states. These aspects overcome two significant deficiencies of our earlier method. The new technique is used to evaluate U and J for Cr(2)O(3), FeO, and Fe(2)O(3). The resulting values of U-J are close to empirical estimates of this quantity for each of these materials and are also similar to results of constrained DFT calculations. DFT+U calculations using the ab initio parameters yield results that are in good agreement with experiment. As such, this method offers a means of performing accurate and fully predictive DFT+U calculations of strongly correlated electron materials. PMID:18624466

Mosey, Nicholas J; Liao, Peilin; Carter, Emily A

2008-07-01

300

Ab initio calculations of the interaction between CO2 and the acetate ion

Energy Technology Data Exchange (ETDEWEB)

A series of ab initio calculations designed to investigate the interaction of CO{sub 2} with acetate are presented. The lowest energy structure, AC–CO{sub 2}-?{sup 2}, is predicted by CCSD(T)/aVTZ to be bound by ?10.6 kcal/mol. Six of the bound complexes have binding energies on the order of ?8 kcal/mol, but analysis shows that the ?{sup 1}-CT complex is fundamentally different from the others. The ?{sup 1}-CT complex is characterized by geometric distortion, large polarization and induction effects and charge transfer whereas the other five complexes have little geometric distortion and negligible charge transfer. The amount of charge that is transferred from the anion to the CO{sub 2} in the ?{sup 1}-CT complex is estimated to be about half an electron by NPA, DMA, CHELPG, and Mulliken analyses, whereas the EDA-ALMO-CTA (B3LYP) approach predicts a charge transfer of 75 me{sup –}. However, the transfer of this small amount of charge leads to an energy lowering of ?56 kcal/mol, without which the complex would not be bound. The RI-MP2 geometries closely approximate those resulting from the CCSD optimizations, and the optimized second-order opposite spin (O2) method performs well for all the complexes except for the ?{sup 1}-CT complex. DFT methods do not reproduce all the ab initio geometries, binding energies and/or energy ordering of these complexes although the range-separated hybrid meta-GGA (M11) and nonlocal (VV10 and vdwDF10) functionals are shown to yield results significantly better than other functionals considered for this system. The fact that there is such variation among DFT methods has implications for DFT-based ab initio molecular dynamics simulations and for the parametrization of classical force fields based on DFT calculations.

Steckel, Janice A. [U.S. DOE

2012-11-29

301

Gas hydrate deposits are receiving increased attention as potential locations for CO2 sequestration, with CO2 replacing the methane that is recovered as an energy source. In this scenario, it is very important to correctly characterize the cage occupancies of CO2 to correctly assess the sequestration potential as well as the methane recoverability. In order to predict accurate cage occupancies, the guest–host interaction potential must be represented properly. Earlier, these potential parameters were obtained by fitting to experimental equilibrium data and these fitted parameters do not match with those obtained by second virial coefficient or gas viscosity data. Ab initio quantum mechanical calculations provide an independent means to directly obtain accurate intermolecular potentials. A potential energy surface (PES) between H2O and CO2 was computed at the MP2/aug-cc-pVTZ level and corrected for basis set superposition error (BSSE), an error caused due to the lower basis set, by using the half counterpoise method. Intermolecular potentials were obtained by fitting Exponential-6 and Lennard-Jones 6-12 models to the ab initio PES, correcting for many-body interactions. We denoted this model as the “VAS” model. Reference parameters for structure I carbon dioxide hydrate were calculated using the VAS model (site–site ab initio intermolecular potentials) as ??(w)(0) = 1206 ± 2 J/mol and ?H(w)(0) = 1260 ± 12 J/mol. With these reference parameters and the VAS model, pure CO2 hydrate equilibrium pressure was predicted with an average absolute deviation of less than 3.2% from the experimental data. Predictions of the small cage occupancy ranged from 32 to 51%, and the large cage is more than 98% occupied. The intermolecular potentials were also tested by calculating the pure CO2 density and diffusion of CO2 in water using molecular dynamics simulations. PMID:24328234

Velaga, Srinath C; Anderson, Brian J

2014-01-16

302

Intermolecular interaction energy data for the methane dimer have been calculated at a spectroscopic accuracy and employed to construct an ab initio potential energy surface (PES) for molecular dynamics (MD) simulations of fluid methane properties. The full potential curves of the methane dimer at 12 symmetric conformations were calculated by the supermolecule counterpoise-corrected second-order Møller-Plesset (MP2) perturbation theory. Single-point coupled cluster with single and double and perturbative triple excitations [CCSD(T)] calculations were also carried out to calibrate the MP2 potentials. We employed Pople's medium size basis sets [up to 6-311++G(3df, 3pd)] and Dunning's correlation consistent basis sets (cc-pVXZ and aug-cc-pVXZ, X = D, T, Q). For each conformer, the intermolecular carbon-carbon separation was sampled in a step 0.1 A for a range of 3-9 A, resulting in a total of 732 configuration points calculated. The MP2 binding curves display significant anisotropy with respect to the relative orientations of the dimer. The potential curves at the complete basis set (CBS) limit were estimated using well-established analytical extrapolation schemes. A 4-site potential model with sites located at the hydrogen atoms was used to fit the ab initio potential data. This model stems from a hydrogen-hydrogen repulsion mechanism to explain the stability of the dimer structure. MD simulations using the ab initio PES show quantitative agreements on both the atom-wise radial distribution functions and the self-diffusion coefficients over a wide range of experimental conditions. PMID:19090563

Chao, Shih-Wei; Li, Arvin Huang-Te; Chao, Sheng D

2009-09-01

303

Using ab initio 'data' to accurately determine the fourth density virial coefficient of helium

International Nuclear Information System (INIS)

We combine accurate ab initio calculations of the second and third density virial coefficients, B(T) and C(T), of 4He with measurements of its (p-?-T) behavior to determine the fourth density virial coefficient D(T). The measurements were made with a two-sinker, magnetic-suspension densimeter at pressures up to 38 MPa. The measurements on isotherms from T = 223 K to T = 323 K were previously published; new measurements from T = 323 K to T = 500 K are presented here. On each isotherm, a regression of the virial expansion was constrained to the ab initio values of B(T) and C(T); the regression determined D(T) as well as two apparatus-dependent parameters that compensated for systematic errors in the measurements. The percentage uncertainties of D(T) ranged from 2.6% at T = 223 K to 9.5% at T = 400 K to 24.7% at T = 500 K, where these uncertainties are expanded uncertainties with coverage factor of k = 2 corresponding to a 95% confidence interval. These uncertainties are 1/6th of the uncertainty obtained without the ab initio values of B(T) and C(T). The apparatus-dependent parameters can be used to calibrate the densimeter, and this will reduce the uncertainty of other measurements made with this two-sinker densimeter. The new values of D(T) will find applications in accurate gas metrology, such as a primary pressure standard based on the refractive index of helium.

304

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 towards lower densities.

Holst, Bastian; Redmer, Ronald; 10.1103/PhysRevB.83.235120

2012-01-01

305

Ab initio simulation of the solid state for /sup 14/N NQR assignments

International Nuclear Information System (INIS)

Detailed analysis of the microwave spectra (MW) of gases can yield the complete /sup 14/N quadrupole coupling tensor, with signs, magnitudes and directions; and only inertial axis (IA) data is obtained. In contrast /sup 14/N nuclear quadrupole resonance (NQR) leads to the diagonalised tensor, but only with relative signs and no directions. Ab initio SCF calculations with a double zeta or better basis yield good values when compared with MW data for single molecules. In order to assign /sup 14/N NQR data the crystal structure must be known. The application to various H-bonded systems with heterocyclic rings is described

306

Thorium in tungsten: construction of interatomic EAM potentials from ab initio data

The interatomic interaction potential of tungsten and thorium crystals and those of hypothetical tungsten and thorium alloys within the embedded atom approach are considered. The corresponding Ansatz functions are fitted against full potential linear augmented plane wave data of real tungsten- and thorium- and hypothetical tungsten-thorium-crystals. The result is interatomic potentials, ready for use within classical molecular dynamics schemes. A cross check of the resulting force scheme derived by comparison of ab initio and classical molecular dynamics data is provided. Furthermore, we used the potentials to calculate the phonon dispersion relations, which then serve as an additional check.

Eberhard, Bernd; Haider, Ferdinand

2013-07-01

307

Testing the density matrix expansion against ab initio calculations of trapped neutron drops

Microscopic input to a universal nuclear energy density functional can be provided through the density matrix expansion (DME), which has recently been revived and improved. Several DME implementation strategies are tested for neutron drop systems in harmonic traps by comparing to Hartree-Fock (HF) and ab initio no-core full configuration (NCFC) calculations with a model interaction (Minnesota potential). The new DME with exact treatment of Hartree contributions is found to best reproduce HF results and supplementing the functional with fit Skyrme-like contact terms shows systematic improvement toward the full NCFC results.

Bogner, S K; Hergert, H; Kortelainen, M; Maris, P; Stoitsov, M; Vary, J P

2011-01-01

308

A multi-scale model of domain wall velocities based on ab initio parameters

Abstract A new approach is presented to evaluate the velocity of field-driven domain walls by means of ab-initio parameters. This approach makes intensive use of multi-scaling by means of (a) mapping of domain wall formation energies obtained in terms of a fully relativistic method onto a Landau-Ginzburg-type expression, and (b) applying the Landau-Lifshitz-Gilbert equation to evaluate the time needed to move domain walls. In comparison with the "classical" expression for the domai...

Weinberger, Peter; Vedmedenko, Elena; Wieser, Robert; Wiesendanger, Roland

2011-01-01

309

Overlap model and ab initio cluster calculations of polarisabilities of ions in solids

A recently developed overlap model for exchange-induction is used to simulate in-crystal anion polarisabilities for alkali halides and chalcogenides (LiF, NaF, KF, LiCl, NaCl, KCl, LiBr, NaBr, KBr, MgO, CaO, SrO, MgS, CaS and SrS) in overall qualitative agreement with results of ab initio cluster calculations and experiment. Extension to AgF supports the proposal that crystal-field splitting causes significant enhancement of cation polarisability for d10 systems, in contrast to the demonstrat...

Domene, C.; Fowler, Pw; Madden, Pa; Wilson, M.; Wheatley, Rj

1999-01-01

310

Ab initio molecular orbital calculations on ion pair-water complexes of metal halides and oxides

Ab initio MO calculations are performed on a series of ion-molecular and ion pair-molecular complexes of H2O + MX (MX = LiF, LiCl, NaCl, BeO and MgO) systems. BSSE-corrected stabilization energies, optimized geometrical parameters, internal force constants and harmonic vibrational frequencies have been evaluated for all the structures of interest. The trends observed in the geometrical parameters and other properties calculated for the mono-hydrated contact ion pair complexes parallel those c...

Mohandas, P.; Singh, S.; Chandrasekhar, J.

1994-01-01

311

Cálculo Ab-Initio De Parámetros Atómicos En Argón Neutro, Ar I

En este trabajo presentamos resultados parciales tipo ab-initio de parámetros de energía atómicos para ciertas configuraciones de argón neutro, Ar I, utilizando el programa de cálculos de R. D. Cowan bajo la aproximación de campo auto-consistente (SCF) vía método Hartree-Fock no-relativista (HF). Las configuraciones de paridad par introducidas en el cálculo fueron 3p6 + 3p5 [4p+5p+6p+7p] mientras que las configuraciones de paridad opuesta (impar) incluidas en el cálculo fueron 3p5[3...

Bandera, N.; I. Guzm\\u00E1n; Sarmiento, R.

2009-01-01

312

The hydrogen diffusion in liquid aluminum alloys from ab initio molecular dynamics.

We study the hydrogen diffusion in liquid aluminum alloys through extensive ab initio molecular dynamics simulations. At the microscopic scale, we show that the hydrogen motion is characterized by a broad distribution of spatial jumps that does not correspond to a Brownian motion. To determine the self-diffusion coefficient of hydrogen in liquid aluminum alloys, we use a generalized continuous time random walk model recently developed to describe the hydrogen diffusion in pure aluminum. In particular, we show that the model successfully accounts the effects of alloying elements on the hydrogen diffusion in agreement with experimental features. PMID:25194378

Jakse, N; Pasturel, A

2014-09-01

313

Ab-initio density functional theory study of a WO3 NH3-sensing mechanism

International Nuclear Information System (INIS)

WO3 bulk and various surfaces are studied by an ab-initio density functional theory technique. The band structures and electronic density states of WO3 bulk are investigated. The surface energies of different WO3 surfaces are compared and then the (002) surface with minimum energy is computed for its NH3 sensing mechanism which explains the results in the experiments. Three adsorption sites are considered. According to the comparisons of the energy and the charge change between before and after adsorption in the optimal adsorption site O1c, the NH3 sensing mechanism is obtained. (nuclear physics)

314

Effective core potential ab initio calculations on main group heptoxides and large silicate systems

The ab initio molecular structures for several main group heptoxides (X2O7n-, n=0,2,4) are calculated using effective core potentials at the HF and DFT (B3LYP) levels. Particular attention is given to the X-O-X bond angle, as this structural parameter is a key feature for the study of both heptoxides and larger derivatives, such as polysilicate systems. The extent of the p-d interactions, which was found to be the main factor governing the magnitude of the X-O-X angle in transition metal hept...

Ribeiro-claro, P. J. A.; Amado, A. M.

2000-01-01

315

Time-dependent Born charges of lithium borate melts by ab initio molecular dynamics

We present time-dependent Born effective charges of B and O in lithium borate melts determined by ab initio molecular dynamics (AIMD) simulations. The Born charge, based on polarization theory, is calculated from all atoms at each time step of the AIMD run. The time-averaged charge distributions are obtained for specific chemical species such as three-coordinated B, four-coordinated B, bridging O (Ob) and, non-bridging O (Onb). Ob and Onb have similar time-averaged charge distributions, indicating that positively charged Li+ is compensated not only by Onb but also by the glass network of the melt as a whole.

Ohkubo, Takahiro; Tsuchida, Eiji; Iwadate, Yasuhiko

2014-09-01

316

Charge carrier motion in disordered conjugated polymers: a multiscale ab-initio study

Energy Technology Data Exchange (ETDEWEB)

We developed an ab-initio multiscale method for simulation of carrier transport in large disordered systems, based on direct calculation of electronic states and electron-phonon coupling constants. It enabled us to obtain the never seen before rich microscopic details of carrier motion in conjugated polymers, which led us to question several assumptions of phenomenological models, widely used in such systems. The macroscopic mobility of disordered poly(3- hexylthiophene) (P3HT) polymer, extracted from our simulation, is in agreement with experimental results from the literature.

Vukmirovic, Nenad; Wang, Lin-Wang

2009-11-10

317

A quantum chemical ab initio study of the polymerization to polyhydridophosphazenes

International Nuclear Information System (INIS)

Quantum chemical ab initio calculations on the polymerization to polyhydridophosphazenes were carried out using mainly Moller-Plesset perturbation theory. Considering finite clusters of increasing size modeling the infinite system suggests that the isolated polyhydridophosphazenes prefer helical structures. A small bond alternation of 0.02 A was found, whereas amino substituted hydridophosphazenes show a little larger bond alternation of 0.04 A. Our study suggests that a substituent on the phosphorus atom with an electronegativity of about 3, e.g. amino substituents, makes the polymerization energetically favorable. This agrees excellently with the experiments on the polymerization of trisaminophosphines to polyhydridophosphazenes. The theoretical investigations also support a recently proposed polymerization mechanism

318

International Nuclear Information System (INIS)

A general method for the energy-adjustment of accurate relativistic ab initio pseudopotentials to be used in one-, two- or four-component quantum chemical valence-only calculations of the electronic structure and spectra of heavy-element compounds is discussed. The described pseudopotential scheme is completely based on quantum chemical observables, i.e., all parameters are determined by a least-squares adjustment to total valence energies of a multitude of many-electron states from corresponding atomic all-electron calculations. The presentation will include several examples of theoretical investigations of heavy-element compounds, many of them containing lanthanide or actinide atoms

319

The mechanism of the chemical reaction of H2O with three stabilized Criegee intermediates (stabCI-OO, stabCI-CH3-OO and stabCIx-OO) produced via the limonene ozonolysis reaction has been investigated using ab initio and DFT (Density Functional Theory) methods. It has been shown that the formation of the hydrogen-bonded complexes is followed by two different reaction pathways, leading to the formation of either OH radicals via water-catalyzed H migration or of ?-hydroxy hydroperoxide. Both pa...

Wen-Jie Zhang; Wen Yang; Yi-Sheng Xu; Ru Lan; Lei Jiang

2013-01-01

320

Ab initio study of the low-lying electronic states of the CaO molecule

International Nuclear Information System (INIS)

Graphical abstract: Highly correlated ab initio calculations have been performed for an accurate determination of the electronic structure of the low-lying electronic states of the CaO molecule. The computations are done using the aug-cc-pV5Z basis set for O and the cc-pCV5Z for Ca. The potential energy curves for the molecular states correlating to the lowest three asymptotes are calculated at the CASSCF level. The potential curves of the lowest five molecular states, X1?+, a3?, A'1?, b3?+ and A1?+, and the corresponding dipole moment functions have been determined using internally contracted multi-reference configuration interaction approaches. The spectroscopic constants associated with these electronic states are compared to experimental values. The corresponding electronic wavefunctions have also been analyzed using the dipole moment functions. Display Omitted Highlights: ? The five lowest electronic states of Cao have been determined ab initio at a high level of accuracy. ? Large active space, core-valence correlation and configuration interaction are required. ? The multi-configurational nature of the electronic ground state is confirmed as well as its monovalent and divalent ionic nature using dipole moment analysis. ? These interacting potentials will serve for future obtention of spin-rovibronic levels. - Abstract: Highly correlated ab initio calculations haved ab initio calculations have been performed for an accurate determination of the electronic structure of the low-lying electronic states of the CaO molecule. The computations are done using the aug-cc-pV5Z basis set for O and the cc-pCV5Z for Ca. The potential energy curves for the molecular states correlating to the lowest three asymptotes are calculated at the CASSCF level. The potential curves of the lowest five molecular states, X1?+, a3?, A'1?, b3?+ and A1?+, and the corresponding dipole moment functions have been determined using internally contracted multi-reference configuration interaction approaches. The spectroscopic constants associated with these electronic states are compared to experimental values. The corresponding electronic wavefunctions have also been analyzed using the dipole moment functions.

321

Oxygen vacancy formation energies in Sr-doped complex perovskites: ab initio thermodynamic study

La1-xSrxCo0.25Fe0.75O3-delta is known as one of the best cathode materials for permeation membranes and solid oxide fuel cells. Optimization of its chemical composition is a challenging problem. One of the key properties is concentration of oxygen vacancies, controlled by their formation energies. Ab initio calculations were employed in order to study the formation of oxygen vacancies in La1-xSrxCo0.25Fe0.75O3-delta perovskites by varying the Sr content from x = 12.5% to 50%...

Gryaznov, Denis; Finnis, Mike W.; Evarestov, Robert; Maier, Joachim

2012-01-01

322

Electronic and transport properties edge functionalized graphene nanoribbons-An ab initio approach

Energy Technology Data Exchange (ETDEWEB)

With the help of ab initio approach we have investigated the electronic and transport properties of edge functionalized zigzag graphene nanoribbons using density functional theory. We have studied the energetic stability and Fermi energy of ZGNRs. We have reported that the edge functionalization of zigzag graphene nanoribbons can break the degeneracy that can be used to promote the onset of a semiconducting to metal transition or a half metal to semiconducting state. The edge functionalization also promotes a metal-semimetal transition. It has also been observed that the transmission spectrum of the edge functionalized ZGNRs are different from those of pristine.

Chauhan, Satyendra Singh, E-mail: sschauhan-71@rediffmail.com [Institute of Information Technology and Management, ITM University, Gwalior - 474001 (India); Srivastava, Pankaj [ABV Indian Institute of Information Technology and Management, Gwalior - 474010 (India); Shrivastva, A. K. [School of Studies in Physics, Jiwaji University, Gwalior- 474011 (India)

2014-04-24

323

[Ab initio calculations of vibrational frequencies and structures of ion pairs of perchlorate].

Ion association of solutions of lithium perchlorate in N,N-dimethylformamide, acetonitrile, tetrahydrofuran, acetone, methyl acetate and other organic solvents have been investigated by infrared and Raman spectroscopy, respectively. The spectroscopically free ion, contact ion pair and dimer are fingerprint by the curve fitting of upsilon1 band of. The most stable geometries of contact ion pairs and dimmer, and the vibrational frequencies were optimized and calculated using the ab initio methods. The comparison between calculated and experimental data of band position was made. Effect of solvation mode and solvent molecule on the vibrational frequencies of ion pairs was also indicated. PMID:21105435

Xuan, Xiao-peng; Xie, You-hai; Zhao, Yang

2010-09-01

324

Monte Carlo methods in AB initio quantum chemistry quantum Monte Carlo for molecules

This book presents the basic theory and application of the Monte Carlo method to the electronic structure of atoms and molecules. It assumes no previous knowledge of the subject, only a knowledge of molecular quantum mechanics at the first-year graduate level. A working knowledge of traditional ab initio quantum chemistry is helpful, but not essential.Some distinguishing features of this book are: Clear exposition of the basic theory at a level to facilitate independent study. Discussion of the various versions of the theory: diffusion Monte Carlo, Green's function Monte Carlo, and release n

Lester, William A; Reynolds, PJ

1994-01-01

325

Ab initio calculation of BaF2 cross-luminescence spectrum

International Nuclear Information System (INIS)

We present the theoretical calculations of the core hole electronic and spatial structure and cross-luminescence spectrum in [Ba13F32]-6 cluster. The ab initio Hartree-Fock calculation of cross-luminescence has been performed in embedded-cluster approach. The theoretical spectrum reproduces well the characteristics of the experimental one. The valence states corresponding to the 5.6, 6.3 and 7.1 eV emissions is found to be localized. The low-energy tail is shown to be due to transitions between 5p core states of Ba2+ ion and 2p valence states of next-nearest F- ions.

326

Ab initio study of energy-level alignments in polymer-dye blends

Polymers with a small amount of dye blended in offer an attractive possibility to change the color of the emitted light by changing the dye. We present ab initio calculations within density-functional theory of the HOMO/LUMO energies for dipyrrolomethane dyes, polyphenylenevinylene and polyfluorene. Special attention is paid to the trends in these energies with variation of the sidegroups of the dyes as observed in cyclic-voltammetry measurements. From the energy-level alignments between dye and polymer we can understand and predict electron and hole trapping, crucial processes for the functioning of light-emitting devices based on these blends.

Pasveer, W. F.; Bobbert, P. A.; Michels, M. A. J.; Langeveld-Voss, B. M. W.; Schoo, H. F. M.; Bastiaansen, J. J. A. M.

2003-11-01

327

Pride, Prejudice, and Penury of {\\it ab initio} transport calculations for single molecules

Recent progress in measuring the transport properties of individual molecules has triggered a substantial demand for {\\it ab initio} transport calculations. Even though program packages are commercially available and placed on custom tailored to address this task, reliable information often is difficult and very time consuming to attain in the vast majority of cases, namely when the molecular conductance is much smaller than $e^2/h$. The article recapitulates procedures for molecular transport calculations from the point of view of time-dependent density functional theory. Emphasis is describing the foundations of the ``standard method''. Pitfalls will be uncovered and the domain of applicability discussed.

Evers, F

2006-01-01

328

Charge redistribution at Pd surfaces: ab initio grounds for tight-binding interatomic potentials

A simplified tight-binding description of the electronic structure is often necessary for complex studies of surfaces of transition metal compounds. This requires a self-consistent parametrization of the charge redistribution, which is not obvious for late transition series elements (such as Pd, Cu, Au), for which not only d but also s-p electrons have to be taken into account. We show here, with the help of an ab initio FP-LMTO approach, that for these elements the electron...

Sawaya, S.; Goniakowski, J.; Mottet, C.; Saul, A.; Treglia, G.

1997-01-01

329

International Nuclear Information System (INIS)

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.

330

A scalable numerical approach for the Steady-State Ab-Initio Laser Theory

We present an efficient and flexible method for solving the non-linear lasing equations of the steady-state ab-initio laser theory. Unlike previous techniques, we solve the underlying system of partial differential equations directly, without the need of setting up a parametrized basis of constant flux states. We validate our approach in one-dimensional as well as in cylindrical systems, and demonstrate its scalability to full-vector three-dimensional calculations in photonic-crystal slabs. Our approach paves the way for efficient and accurate simulations of lasing structures which were previously inaccessible.

Esterhazy, S; Liertzer, M; Cerjan, A; Ge, L; Makris, K G; Stone, A D; Melenk, J M; Johnson, S G; Rotter, S

2013-01-01

331

A periodic ab initio extended basis set study of ?-Al2O3

Corundum, or ?-Al2O3, is investigated at the ab initio periodic Hartree-Fock LCAO level using the program CRYSTAL. A split valence 6–21G basis set is adopted, and the influence of d polarization functions is explored. The four geometrical parameters of the unit cell are optimized, the difference with respect to the experimental data always being less than 1%. The electric field gradient tensor at both nuclei (Al and O) is calculated; agreement with the experimental data is quite satisfacto...

Dovesi, Roberto; Orlando, Roberto

1991-01-01

332

Ab initio calculations of the optical properties of ions in glass

International Nuclear Information System (INIS)

There is interest in the optical properties of ions in insulating glasses for various applications. This paper addresses the task of predicting optical properties of ions in glass from first principles given only the physics of the constituent atoms. The prospects for developing such ab initio-computation procedures are gleaned from examining the progress made in understanding the properties of dopant ions in crystals. It is probable that in 20 years, there will be reliable procedures for predicting optical properties of ions in crystals, but the development of corresponding procedures for complex glasses is a herculean task. The use of computer simulations is addressed

333

Ab Initio Calculations of Even Oxygen Isotopes with Chiral Two- Plus Three-Nucleon Interactions

We formulate the In-Medium Similarity Renormalization Group (IM-SRG) for open-shell nuclei using a multi-reference formalism based on a generalized Wick theorem introduced in quantum chemistry. The resulting multi-reference IM-SRG (MR-IM-SRG) is used to perform the first ab initio study of even oxygen isotopes with chiral NN and 3N Hamiltonians, from the proton to the neutron drip lines. We obtain an excellent reproduction of experimental ground-state energies with quantifie...

Hergert, H.; Binder, S.; Calci, A.; Langhammer, J.; Roth, R.

2013-01-01

334

The equilibrium structure and spectroscopic constants of HCP - an ab initio study

The molecular parameters of phosphaethyne, HCP, have been determinned in large-scale ab initio calculations using the coupled cluster method, CCSD(T), and basis sets of double- to quintuple-zeta quality. The effect of core correlation on the structural parameters was investigated. The equilibrium structure of the molecule was found to be linear, with the bond lengths r( HC) = 1.0706 Åand r( CP) = 1.5399 Å. The full anharmonic quartic force field was determined. The spectroscopic constants of HCP were calculated using perturbation theory and accounting for the effects of a Fermi resonance. The calculated molecular constants were found to be in excellent agreement with experimental data.

Koput, Jacek

1996-12-01

335

Ab initio calculation of the C1s photoelectron spectrum of C2H2

International Nuclear Information System (INIS)

The C1s photoelectron spectrum of C2H2, measured by Kempgens et al. [Phys. Rev. Lett. 79 (1997) 3617] and characterized by the presence of a core-level splitting, has been calculated and interpreted using an ab initio quantum-mechanical method that allows detailed analysis of photoionization processes and accurate reproduction of spectral profiles. The anisotropy of the electron emission, measured in a hypothetical experiment in which the orientation of the molecules can be established, has been also predicted and analyzed

336

Strain energy calculations of hexagonal boron nanotubes: An ab-initio approach

Directory of Open Access Journals (Sweden)

Full Text Available An ab initio calculations have been carried out for examining the curvature effect of small diameter hexagonal boron nanotubes. The considered conformations of boron nanotubes are namely armchair (3,3, zigzag (5,0 and chiral (4,2, and consist of 12, 20, and 56 atoms, respectively. The strain energy is evaluated in order to examine the curvature effect. It is found that the strain energy of hexagonal BNT strongly depends upon the radius, whereas the strain energy of triangular BNTs depends on both radius and chirality.

S.K. Jain

2013-01-01

337

We predict that iron-based superconductors discovered near d(6) configuration (5 Fe 3d orbitals filled by 6 electrons) is located on the foot of an unexpectedly large dome of correlated electron matter centered at the Mott insulator at d(5) (namely, half filling). This is based on the many-variable variational Monte Carlo results for ab initio low-energy models derived by the downfolding. The d(5) Mott proximity extends to subsequent emergence of incoherent metals, orbital differentiations due to the Mott physics, and Hund's rule coupling, followed by antiferromagnetic quantum criticality, in quantitative accordance with available experiments. PMID:22680899

Misawa, Takahiro; Nakamura, Kazuma; Imada, Masatoshi

2012-04-27

338

Structural Features of Boron-Doped Si(113) Surfaces Simulated by ab initio Calculations

International Nuclear Information System (INIS)

Based on ab initio calculations, boron-doped Si(113) surfaces have been simulated and atomic structures of the surfaces have been proposed. It has been determined that surface features of empty and filled states that are separately localized at pentamers and adatoms indicates a low surface density of B atoms, while it is attributed to heavy doping of B atoms at the second layer that pentamers and adatoms are both present in an image of scanning tunnelling microscopy. B doping at the second layer should be balanced by adsorbed B or Si atoms beside the adatoms and inserted B interstitials below the adatoms. (condensed matter: structure, mechanical and thermal properties)

339

International Nuclear Information System (INIS)

The results of ab initio calculations of the electronic structure of Si nanocrystals doped with shallow donors (Li, P) are reported. It is shown that phosphorus introduces much more significant distortions into the electronic structure of the nanocrystal than lithium, which is due to the stronger central cell potential of the phosphorus ion. It is found that the Li-induced splitting of the ground state in the conduction band of the nanocrystal into the singlet, doublet, and triplet retains its inverse structure typical for bulk silicon

340

Ab initio calculations of Curie temperatures in GdX compounds

International Nuclear Information System (INIS)

We present calculations of Curie temperatures of selected GdX (X = Zn, Rh, Mg, Cd) compounds with a cubic CsCl structure. Exchange interactions are obtained from ab initio electronic structure calculations in the framework of density functional theory. Critical temperatures are evaluated using two approaches, namely the mean-field approximation (MFA) and a more involved, random phase approximation (RPA). Calculated critical temperatures serve as theoretical upper estimate (MFA) and lower estimate (RPA) of an exact critical temperature given by the Heisenberg model. Obtained results are in fair agreement with experimental values

341

Ab initio calculations of Curie temperatures in GdX compounds

Energy Technology Data Exchange (ETDEWEB)

We present calculations of Curie temperatures of selected GdX (X = Zn, Rh, Mg, Cd) compounds with a cubic CsCl structure. Exchange interactions are obtained from ab initio electronic structure calculations in the framework of density functional theory. Critical temperatures are evaluated using two approaches, namely the mean-field approximation (MFA) and a more involved, random phase approximation (RPA). Calculated critical temperatures serve as theoretical upper estimate (MFA) and lower estimate (RPA) of an exact critical temperature given by the Heisenberg model. Obtained results are in fair agreement with experimental values.

Rusz, Jan [Department of Electronic Structures, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, CZ-121 16 Prague 2 (Czech Republic)]. E-mail: rusz@mag.mff.cuni.cz; Turek, Ilja [Department of Electronic Structures, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, CZ-121 16 Prague 2 (Czech Republic); Divis, Martin [Department of Electronic Structures, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, CZ-121 16 Prague 2 (Czech Republic)

2006-02-09

342

HIGH-PRESSURE BEHAVIOUR OF YUGAWARALITE AT DIFFERENT WATER CONTENT: AN AB INITIO STUDY.

The influence of the water content in a partially occupied water site in yugawaralite on the pressure-induced structural modifications of this zeolite has been studied by means of ab initio molecular dynamics simulations. The effect of the water site occupancy has been singled out by comparing results from simulations, performed with the cell parameters determined via XRPD at rP and 8.8 GPa, on two model systems whose cell stoichiometry differs only by the presence of a water molecule in such...

Arletti, Rossella

2004-01-01

343

Ab initio potential-energy surface for the reaction Ca+HCl --> CaCl+H

The potential-energy surface of the ground electronic state of CaHCl has been obtained from 6400 ab initio points calculated at the multireference configuration-interaction level and represented by a global analytical fit. The Ca+HCl --> CaCl+H reaction is endothermic by 5100 cm–1 with a barrier of 4470 cm–1 at bent geometry, taking the zero energy in the Ca+HCl asymptote. On both sides of this barrier are potential wells at linear geometries, a shallow one due to van der Waals interactio...

Verbockhaven, Gilles; Sanz, Cristina; Groenenboom, Gerrit C.; Roncero, Octavio; Avoird, Ad

2005-01-01

344

Ab-initio theory of metal-insulator interfaces in a finite electric field

We present a novel technique for calculating the properties of an electric field applied to a periodic heterostructure with alternating metallic and insulating layers. This scheme allows us to investigate fully from first-principles the microscopic properties of a thin-film capacitor at finite bias potential. We demonstrate how the capacitance and local permittivity profiles can be readily obtained by performing a series of calculations for the Ag(100)/MgO(100) system. Applications range from the emerging field of electronic devices based on ferroelectric materials, to the ab-initio simulation of electrochemical cells.

Stengel, M

2005-01-01

345

Social permutation invariant coordinates are introduced describing the bond network around a given atom. They originate from the largest eigenvalue and the corresponding eigenvector of the contact matrix, are invariant under permutation of identical atoms, and bear a clear signature of an order-disorder transition. Once combined with ab initio metadynamics, these coordinates are shown to be a powerful tool for the discovery of low-energy isomers of molecules and nanoclusters as well as for a blind exploration of isomerization, association, and dissociation reactions.

Pietrucci, Fabio; Andreoni, Wanda

2011-08-01

346

"Ab initio" studies of hydrogen-enhanced oxygen diffusion in silicon

Scientific Electronic Library Online (English)

Full Text Available SciELO Brazil | Language: English Abstract in english A novel microscopic mechanism for hydrogen-enhanced oxygen diffusion in p-doped silicon is proposed. A path for joint diffusion of O and H is obtained from an ab-initio molecular dynamics "kick" simulation. The migration pathway consists of a two-step mechanism, with a maximum energy of 1.46 eV. Thi [...] s path represents a 0.54 eV reduction in the static barrier when compared with the diffusion of isolated O in Si, in excellent agreement with experiments.

R. B., Capaz; L. V. C., Assali; L. C., Kimerling; K., Cho; J. D., Joannopoulos.

1999-12-01

347

Atomic structure of PdNiP bulk metallic glass from ab initio simulations

The atomic structure of Pd40Ni40P20 bulk metallic glass (BMG) has been simulated using ab initio molecular dynamics plane wave method and PAW pseudopotentials. We use generalized gradient approximation to calculate the exchange-correlation energy and a cubic simulation box whose size and shape have been optimized after the BMG has been formed in simulations. The resulting radial distribution function and density agree remarkably well with the experimental data. The structure is analysed in terms of local clusters centered around Pd, Ni and P atoms and their electronic structures have been used to understand the bonding, stability, and the formation of the PdNiP BMG.

Kumar, Vijay; Fujita, T.; Chen, M. W.; Inoue, A.; Kawazoe, Y.

2009-03-01

348

Ab Initio Investigations of the C2F4S Isomers and of Their Interconversions

DEFF Research Database (Denmark)

The transition states and the activation energies for the unobserved isomerization reactions between the three possible C2F4S isomers with divalent sulfur, trifluorothioacetyl fluoride 1, tetrafluorothiirane 2, and trifluoroethenesulfenyl fluoride 3, have been determined by ab initio Hartree-Fock, Møller-Plesset second order perturbation calculations and by Gaussian-3 theory. The results show that the unobserved isomerization reactions are feasible. Furthermore, all three isomers should exist as stable species, but the unknown isomer, 3, is considerably less stable than the known isomers, 1 and 2.

Shim, Irene; Vallano-Lorenzo, Sandra

2003-01-01

349

Ab Initio Theory of NMR Chemical Shifts in Solids and Liquids

International Nuclear Information System (INIS)

We present a theory for the ab initio computation of NMR chemical shifts (?) in condensed matter systems, using periodic boundary conditions. Our approach can be applied to periodic systems such as crystals, surfaces, or polymers and, with a supercell technique, to nonperiodic systems such as amorphous materials, liquids, or solids with defects. We have computed the hydrogen ? for a set of free molecules, for an ionic crystal LiH, and for a H-bonded crystal HF, using density functional theory in the local density approximation. The results are in excellent agreement with experimental data. copyright 1996 The American Physical Society

350

Ab initio study of charge transport of hydrogen functionalized palladium wires.

We present ab initio calculations of transport properties of palladium wires in the presence of hydrogen. Detailed investigations have been conducted with a pure palladium wire and with opening a gap inside the wire in which the transition between point contact regime and tunneling regime occurs. The effect of the presence of hydrogen in the gap is studied for different ranges of the gap size. The hydrogen mediated transport in the contact and tunneling regimes of the gap are analyzed and compared. It is predicted that only in large enough distances the hydrogen presence increases the conductance. The effect of additional hydrogen molecules on the gap is also studied. PMID:18624547

Zhao, Zhen; Dunietz, Barry D

2008-07-14

351

The mechanism of carbonyl reduction by LiBH 4: an AB initio investigation

The minimum energy path and the geometry of the transition state for the first stage of the reduction by LiBH 4 of R 2CO (R?H, CH 3) to alcohol have been determined by ab initio SCF calculations using a small basis set and subsequently confirmed by further calculations using a larger basis set and CI methods. Attention has been focused on the changes of electron distribution during the reaction, the nature of the bonding, and the effect of chemical substituents. The results lend support to one of the proposed reaction mechanisms. Some supplementary data concerning the role of the solvent are also discussed.

Bonaccorsi, R.; Palla, P.; Tomasi, J.

352

Ab initio study of the EFG at the N sites in imidazole

International Nuclear Information System (INIS)

We study the nuclear quadrupole interaction at the nitrogen sites in the molecular and crystalline phases of the imidazole compound. We use PAW which is a state-of-the-art method to calculate the electronic structure and electric field gradient at the nucleus in the framework of the density functional theory. The quadrupole frequencies at both imino and amino N sites are in excellent agreement with measurements. This is the first time that the electric field gradient at crystalline imidazole is correctly treated by an ab initio theoretical approach.

353

Ab initio study of magnesium alanate, Mg(AlH4)2

Magnesium alanate Mg(AlH4)2 has recently raised interest as a potential material for hydrogen storage. We apply ab initio calculations to characterize structural, electronic and energetic properties of Mg(AlH4)2. Density functional theory calculations within the generalized gradient approximation (GGA) are used to optimize the geometry and obtain the electronic structure. The latter is also studied by quasi-particle calculations at the GW level. Mg(AlH4)2 is a large band gap...

Setten, M. J.; Wijs, G. A.; Popa, V. A.; Brocks, G.

2005-01-01

354

Ab initio correlation approach to a ferric wheel-like molecular cluster

We present an ab initio study of electronic correlation effects in a molecular cluster derived from the hexanuclear ferric wheel [LiFe6(OCH3)12-(dbm)6]PF6. The electronic and magnetic properties of this cluster have been studied with all-electron Hartree-Fock, full-potential density functional calculations and multi-reference second-order perturbation theory. For different levels of correlation, a detailed study of the impact of the electronic correlation on the exchange par...

Nieber, H.; Doll, K.; Zwicknagl, G.

2006-01-01

355

Vibrational energy levels for CH4 from an ab initio potential

Many areas of astronomy and astrophysics require an accurate high temperature spectrum of methane (CH4). The goal of the present research is to determine an accurate ab initio potential energy surface (PES) for CH4. As a first step towards this goal, we have determined a PES including up to octic terms. We compare our results with experiment and to a PES based on a quartic expansion. Our octic PES gives good agreement with experiment for all levels, while the quartic PES only for the lower levels.

Schwenke, D. W.; Partridge, H.

2001-01-01

356

Ab initio simulation of particle momentum distributions in high-pressure water

Applying pressure to water reduces the average oxygen-oxygen distance, and facilitates the delocalisation of protons along the hydrogen bond. This pressure-induced delocalisation is further enhanced by the quantum nature of hydrogen nuclei, which is very significant even well above room temperature. Here we will evaluate the quantum kinetic energy and the particle momentum distribution of hydrogen and oxygen nuclei in water at extreme pressure, using ab initio path integral molecular dynamics. We will show that (transient) dissociation of water molecules induce measurable changes in the kinetic energy hydrogen atoms, although current deep inelastic scattering experiments are probably unable to capture the heterogeneity of the sample.

Ceriotti, M.

2014-12-01

357

Ab-initio study of high temperature lattice dynamics of BCC zirconium (?-Zr) and uranium (?-U)

Energy Technology Data Exchange (ETDEWEB)

Using self consistent ab-initio lattice dynamics calculations, we show that bcc structures of Zr and U phases become stable at high temperature by phonon-phonon interactions. The calculated temperature dependent phonon dispersion curve (PDC) of ?-Zr match excellently with experimental PDC. But the calculated PDC for ?-U shows negative phonon frequencies even at solid to liquid transition temperature. We show that this discrepancy is due to an overestimation of instability depth of bcc U phase which is removed by incorporation of spin-orbit coupling in the electronic structure calculations.

Ghosh, Partha S., E-mail: parthasarathi13@gmail.com; Arya, A., E-mail: parthasarathi13@gmail.com; Dey, G. K., E-mail: parthasarathi13@gmail.com [Materials Science Division, Bhabha Atomic Research Centre, Mumbai-400085 (India)

2014-04-24

358

International Nuclear Information System (INIS)

We present exemplary results of extensive studies of mechanical, electronic and transport properties of covalent functionalization of graphene monolayers (GML). We report new results of ab initio studies for covalent functionalization of GML with ?NH2 groups up to 12.5 % concentration. Our studies are performed in the framework of the density functional theory (DFT) and non-equilibrium Green’s function (NEGF). We discuss the stability (adsorption energy), elastic moduli, electronic structure, band gaps, and effective electron masses as a function of the density of the adsorbed molecules. We also show the conductance and current – voltage I(V) characteristics for these systems

359

Electronic and transport properties edge functionalized graphene nanoribbons-An ab initio approach

International Nuclear Information System (INIS)

With the help of ab initio approach we have investigated the electronic and transport properties of edge functionalized zigzag graphene nanoribbons using density functional theory. We have studied the energetic stability and Fermi energy of ZGNRs. We have reported that the edge functionalization of zigzag graphene nanoribbons can break the degeneracy that can be used to promote the onset of a semiconducting to metal transition or a half metal to semiconducting state. The edge functionalization also promotes a metal-semimetal transition. It has also been observed that the transmission spectrum of the edge functionalized ZGNRs are different from those of pristine

360

An acceleration mechanism of silane plasma chemical vapor deposition by diborane is proposed on the basis of an ab initio molecular orbital calculation. Hydrogen abstraction from the growing surface by BH2 is calculated to be much more favorable than that by SiH3 from both the kinetic and thermodynamic viewpoint. Thus, the abstraction by BH2 is predicted to occur frequently, although the concentration of BH2 is considerably lower than that of SiH3. This process creates a dangling bond on the growing surface and then the deposition rate is increased.

Sato, Kota; Kubota, Yasuyo

2011-05-01

361

A study on defect energy in UO2 lattice using ab initio DFT

International Nuclear Information System (INIS)

The behavior of fission gases is an important limiting factor for the nuclear fuel performance, as fission gas release affects the pressure and temperature of the fuel rod. The point defects are a major diffusion channel for fission gases. The defect energies and mobility energies are needed to know the fission gas mobility in point defect. In this study, we performed ab initio total energy calculations to investigate the defect energies and employed a large super cell containing 96 atoms to decrease defect-defect interaction. The formation energy of intrinsic defects indicates that the accuracy of the present modeling is significantly improved, compared with previous studies

362

Estudo ab-initio da a-alanina em meio aquoso

Ab initio Hartree-Fock (HF), Density Functional (B3LYP) and electron correlation (MP2) methods have been used to caracterize the aqueous medium intramolecular hydrogen bond in a-alanine. The 6-31G* and 6-31++G** were taken from Gaussian94 library. We were concerned on the structure of three conformers of a-alanine, in their neutral form plus on the structure of the zwitterionic form (Z). The Z structure is a stationary point at the HF/6-31...

Sambrano Júlio Ricardo; Souza Aguinaldo Robinson de; Queralt Joaquim Josep; Andrés Juan; Longo Elson

1999-01-01

363

Ab initio Hartree-Fock calculations of periodic compounds: application to semiconductors

The ab initio Hartree-Fock crystalline orbital program CRYSTAL is applied to diamond, silicon, BN, BP, SiC and AlP. The effects of the computational parameters controlling the accuracy of the infinite Coulomb and exchange series are analysed; the performances of five standard (but re-optimised in the valence part) molecular basis sets (STO-3G; 3-21G; 3-21G*; 6-21G; 6-21G*) are documented with reference to equilibrium binding energy, lattice parameter and bulk modulus. The analysis is then ext...

Dovesi, Roberto; Orlando, Roberto

1990-01-01

364

This study presents ab initio calculations on six sialic acid derivatives (N-acetylneuraminic acid, 2-deoxy-2,3-didehydro-Nacetylneuraminic acid, N-acetyl-4-O-acetylneuraminic acid, N-glycolylneuraminic acid, N-glycolyl-4-O-acetylneuraminic acid and N-acetyl-9-O-acetylneuraminic acid). The calculations were carried out using the GAMESS-UK-Program. Since the charge distribution of a ligand has an essential impact on the specific interaction with an enzyme or a receptor, the precise re...

Lenthe, J. H.; Boer, D. H. W. Den; Havenith, R. W. A.; Schauer, R.; Siebert, H. -c

2004-01-01

365

A study on defect energy in UO{sub 2} lattice using ab initio DFT

Energy Technology Data Exchange (ETDEWEB)

The behavior of fission gases is an important limiting factor for the nuclear fuel performance, as fission gas release affects the pressure and temperature of the fuel rod. The point defects are a major diffusion channel for fission gases. The defect energies and mobility energies are needed to know the fission gas mobility in point defect. In this study, we performed ab initio total energy calculations to investigate the defect energies and employed a large super cell containing 96 atoms to decrease defect-defect interaction. The formation energy of intrinsic defects indicates that the accuracy of the present modeling is significantly improved, compared with previous studies

Kim, Sung Ryul; Kim, Yong Uhn [Chungbuk National University, Cheongju (Korea, Republic of); Kim, Hee Moon; Park, Chang Je; Jin, Young Gwan; Ahn, Sang Bok [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of); Yun, Youn Suk [Paul Scherrer Institute, Villigen (Switzerland); Park, Kwang Heon [Kyunghee University, Yongin (Korea, Republic of)

2012-05-15

366

Adiabiatic ab initio potential curves for the B' 1?+/subu/ state of H2

International Nuclear Information System (INIS)

There is reported here an accurate ab initio calculation of the fixed nuclei potential curve for the B' 1?+/subu/ state of H2 together with approximate values of the adiabatic corrections to the potential curve for this state. The state is observed to have two minima in its potential with the very small maxima occurring at approximately, R=5.5a0. Dipole transition moments and oscillator strengths for X 1?+/subg/ bold-arrow-left-right B 1?+/subu/ transitions are given for a wide range of internuclear separations

367

An ab initio study of the electronic structure of boron arsenide, BAs

The completely unexplored BAs diatomic has been thoroughly studied by high level multireference variational ab initio methods. Potential energy curves for 42 molecular states dissociating to the first four asymptotic channels and covering an energy range of 5.8 eV have been constructed revealing an interesting morphology and a rich spectroscopy. The ground state is of 3? symmetry while its first excited 1?+ state lies ˜8 kcal/mol higher. A general feature of the potential curves is the presence of avoided crossings that challenge the validity of the Born Oppenheimer approximation.

Magoulas, Ilias; Kalemos, Apostolos

2013-10-01

368

Ab initio theory of NMR chemical shifts in solids and liquids

We present a theory for the ab-initio computation of NMR chemical shifts (sigma) in condensed matter systems, using periodic boundary conditions. Our approach can be applied to periodic systems such as crystals, surfaces, or polymers and, with a super-cell technique, to non-periodic systems such as amorphous materials, liquids, or solids with defects. We have computed the hydrogen sigma for a set of free molecules, for an ionic crystal, LiH, and for a H-bonded crystal, HF, using density functional theory in the local density approximation. The results are in excellent agreement with experimental data.

Mauri, F; Louie, S G; Mauri, Francesco; Pfrommer, Bernd G.; Louie, Steven G.

1996-01-01

369

Ab-initio simulation for the Growth Mechanism of CNx Nanobells

Nitrogen atoms play an important role in the synthesis of carbon nanobells. Without nitrogen atoms in the growth gas mixture, long and pure carbon nanotubes are produced. With nitrogen atoms in otherwise the same growth condition, CNx nanobells are formed. We performed ab-initio total energy calculations to simulation the growth process of short CNx nanobells. We studied the structural stability of short CNx nanobells and identified the related possible growth mechanism. Work funded in part by US NASA (Award No. NCC2-1344), and by NASA/USAR-NACME.

Zhao, G. L.; Bagayoko, D.; Pullen, A.; Wang, E. G.

2003-03-01

370

Ab initio MO studies on the hydration of trivalent curium ion

International Nuclear Information System (INIS)

We have performed a series of ab initio relativistic molecular-orbital calculations to model the hydration of trivalent curium ion. Up to the hexa-hydrate model, Dirac-Hartree-Fock calculations as a four-component recipe were used to investigate the interaction between the ion and water molecules. The fluorescence transition energy was estimated by complete open-shell configuration interaction calculation. Hydrates having more than six water molecules were treated using the B3LYP hybrid density-functional theory with effective-core potential. (author)

371

High-resolution microwave spectroscopic and ab initio studies of propanoic acid and its hydrates.

High-resolution microwave spectra of the propanoic acid monomer (PPA) and two of its hydrates, the PPA-(H2O) and the PPA-(H2O)2, were recorded using a pulsed nozzle Fourier transform microwave spectrometer. The rotational and centrifugal distortion constants of these species were determined. Agreements between the experimental and ab initio results of these constants, and of the planar moment of inertia, the dipole moments, and the orientation of the PPA relative to the H2O confirm the geomet...

Ouyang, B.; Howard, Bj

2008-01-01

372

Ab initio molecular dynamics of Al irradiation-induced processes during Al(2)O(3) growth

Al bombardment induced structural changes in alpha-Al(2)O(3) (R-3c) and gamma-Al(2)O(3) (Fd-3m) were studied using ab initio molecular dynamics. Diffusion and irradiation damage occur for both polymorphs in the kinetic energy range from 3.5 to 40 eV. However, for gamma-Al(2)O(3)(001) subplantation of impinging Al causes significantly larger irradiation damage and hence larger mobility as compared to alpha-Al(2)O(3). Consequently, fast diffusion along gamma-Al(2)O(3)(001) gives rise to prefere...

Music, Denis; Nahif, Farwah; Sarakinos, Kostas; Friederichsen, Niklas; M Schneider, Jochen

2011-01-01

373

Ab initio potential energy surface and vibration-rotation energy levels of lithium monohydroxide

The accurate ground-state potential energy surface of lithium monohydroxide (LiOH) has been determined from ab initio calculations using the coupled-cluster approach in conjunction with the correlation-consistent core-valence basis sets up to septuple-zeta quality. Results obtained with the conventional and explicitly correlated coupled-cluster methods were compared. The higher-order electron correlation, scalar relativistic, and adiabatic effects were taken into account. The vibration-rotation energy levels of the LiOH, LiOD, Li18OH, and 6LiOH isotopologues were predicted to near "spectroscopic" accuracy.

Koput, Jacek

2013-06-01

374

Ab initio calculation of electronic and optical properties of metallic tin

International Nuclear Information System (INIS)

The electronic and optical properties of the metallic bcc and ?-Sn phases of tin are studied using density functional theory. The effects of spin-orbit coupling are examined and significant splittings are found in the band structures for both phases. Based on ab initio band structures we calculate the anisotropic optical response of ?-Sn. Both intra- and interband contributions are included and the plasma frequencies for both the ordinary and extraordinary optical axis are calculated. The theoretical results are found to be in excellent agreement with experimental spectra for the anisotropic optical response. We identify the electronic transitions responsible for the dominant interband resonances in the near-infrared response.

375

Ab initio study of the alkaline hydrolysis of a thio-?-lactam structure

The alkaline hydrolysis of a thio-?-lactam in the gas phase was examined in the light of RHF and DFT ab initio calculations. The solvent effect was considered via IPCM computations. The tetrahedral intermediate for the thio-?-lactam studied is unstable, so the compound evolves directly to the corresponding thio-azethidin-2-one open ring with cleavage of the C-S bond. The end-products obtained bear a carbamate group, which suggests that the thio-?-lactam might be an effective inhibitor for ?-lactamases.

Coll, Miguel; Frau, Juan; Vilanova, Bartolomé; Donoso, Josefa; Muñoz, Francisco

2000-08-01

376

Quantum chemistry the development of ab initio methods in molecular electronic structure theory

This guide is guaranteed to prove of keen interest to the broad spectrum of experimental chemists who use electronic structure theory to assist in the interpretation of their laboratory findings. A list of 150 landmark papers in ab initio molecular electronic structure methods, it features the first page of each paper (which usually encompasses the abstract and introduction). Its primary focus is methodology, rather than the examination of particular chemical problems, and the selected papers either present new and important methods or illustrate the effectiveness of existing methods in predi

Schaefer III, Henry F

2012-01-01

377

The role of Metals in Amyloid Aggregation: A Test Case for ab initio Simulations

International Nuclear Information System (INIS)

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 ?-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

378

VASP-4096: a very high performance programmable device for digital media processing applications

Over the past few years, technology drivers for microprocessors have changed significantly. Media data delivery and processing--such as telecommunications, networking, video processing, speech recognition and 3D graphics--is increasing in importance and will soon dominate the processing cycles consumed in computer-based systems. This paper presents the architecture of the VASP-4096 processor. VASP-4096 provides high media performance with low energy consumption by integrating associative SIMD parallel processing with embedded microprocessor technology. The major innovations in the VASP-4096 is the integration of thousands of processing units in a single chip that are capable of support software programmable high-performance mathematical functions as well as abstract data processing. In addition to 4096 processing units, VASP-4096 integrates on a single chip a RISC controller that is an implementation of the SPARC architecture, 128 Kbytes of Data Memory, and I/O interfaces. The SIMD processing in VASP-4096 implements the ASProCore architecture, which is a proprietary implementation of SIMD processing, operates at 266 MHz with program instructions issued by the RISC controller. The device also integrates a 64-bit synchronous main memory interface operating at 133 MHz (double-data rate), and a 64- bit 66 MHz PCI interface. VASP-4096, compared with other processors architectures that support media processing, offers true performance scalability, support for deterministic and non-deterministic data processing on a single device, and software programmability that can be re- used in future chip generations.

Krikelis, Argy

2001-03-01

379

VASP-E: specificity annotation with a volumetric analysis of electrostatic isopotentials.

Algorithms for comparing protein structure are frequently used for function annotation. By searching for subtle similarities among very different proteins, these algorithms can identify remote homologs with similar biological functions. In contrast, few comparison algorithms focus on specificity annotation, where the identification of subtle differences among very similar proteins can assist in finding small structural variations that create differences in binding specificity. Few specificity annotation methods consider electrostatic fields, which play a critical role in molecular recognition. To fill this gap, this paper describes VASP-E (Volumetric Analysis of Surface Properties with Electrostatics), a novel volumetric comparison tool based on the electrostatic comparison of protein-ligand and protein-protein binding sites. VASP-E exploits the central observation that three dimensional solids can be used to fully represent and compare both electrostatic isopotentials and molecular surfaces. With this integrated representation, VASP-E is able to dissect the electrostatic environments of protein-ligand and protein-protein binding interfaces, identifying individual amino acids that have an electrostatic influence on binding specificity. VASP-E was used to examine a nonredundant subset of the serine and cysteine proteases as well as the barnase-barstar and Rap1a-raf complexes. Based on amino acids established by various experimental studies to have an electrostatic influence on binding specificity, VASP-E identified electrostatically influential amino acids with 100% precision and 83.3% recall. We also show that VASP-E can accurately classify closely related ligand binding cavities into groups with different binding preferences. These results suggest that VASP-E should prove a useful tool for the characterization of specific binding and the engineering of binding preferences in proteins. PMID:25166865

Chen, Brian Y

2014-08-01

380

FAST TRACK COMMUNICATION: Shear stiffness in nanolaminar Ti3SiC2 challenges ab initio calculations

Nanolaminates such as the Mn + 1AXn (MAX) phases are a material class with ab initio derived elasticity tensors published for over 250 compounds. We have for the first time experimentally determined the full elasticity tensor of the archetype MAX phase, Ti3SiC2, using polycrystalline samples and in situ neutron diffraction. The experimental elastic constants show extreme shear stiffness, with c44 more than five times greater than expected for an isotropic material. Such shear stiffness is quite rare in hexagonal materials and strongly contradicts the predictions of all published MAX phase elastic constants derived from ab initio calculations. It is concluded that second order properties such as elastic moduli derived from ab initio calculations require careful experimental verification. The diffraction technique used currently provides the only method of verification for the elasticity tensor for the majority of new materials where single crystals are not available.

Kisi, E. H.; Zhang, J. F.; Kirstein, O.; Riley, D. P.; Styles, M. J.; Paradowska, A. M.

2010-04-01

381

Inelastic neutron scattering an ab-initio calculation of negative thermal expansion in Ag{sub 2}O

Energy Technology Data Exchange (ETDEWEB)

The compound Ag{sub 2}O undergoes large and isotropic negative thermal expansion over 0-500 K. We report temperature dependent inelastic neutron scattering measurements and ab-initio calculations of the phonon spectrum. The temperature dependence of the experimental phonon spectrum shows strong anharmonic nature of phonon modes of energy around 2.4 meV. The ab-initio calculations reveal that the maximum negative Grueneisen parameter, which is a measure of the relevant anharmonicity, occurs for the transverse phonon modes that involve bending motions of the Ag{sub 4}O tetrahedra. The thermal expansion is evaluated from the ab-initio calculation of the pressure dependence of the phonon modes, and found in good agreement with available experimental data.

Gupta, M.K. [Solid State Physics Division, Bhabha Atomic Research Center, Mumbai 400 085 (India); Mittal, R., E-mail: rmittal@barc.gov.in [Solid State Physics Division, Bhabha Atomic Research Center, Mumbai 400 085 (India); Rols, S. [Institut Laue-Langevin, BP 156, 38042 Grenoble Cedex 9 (France); Chaplot, S.L. [Solid State Physics Division, Bhabha Atomic Research Center, Mumbai 400 085 (India)

2012-06-15

382

X-ray diffraction and electrostatic levitation measurements, together with the ab initio molecular dynamics simulation of liquid Al75Cu25 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 Al75Cu25 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 Al75Cu25 alloy and the atomic clusters evolve continuously. All results obtained here suggest that no liquid-liquid transition appears in the bulk liquid Al75Cu25 alloy in the studied temperature range. PMID:25524926

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

383

X-ray diffraction and electrostatic levitation measurements, together with the ab initio molecular dynamics simulation of liquid Al75Cu25 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 Al75Cu25 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 Al75Cu25 alloy and the atomic clusters evolve continuously. All results obtained here suggest that no liquid–liquid transition appears in the bulk liquid Al75Cu25 alloy in the studied temperature range.

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.

2015-01-01

384

Energy Technology Data Exchange (ETDEWEB)

We present a coherent ab initio, i.e. parameter free, description of the anomalous Hall effect (AHE) that is applicable to pure as well as disordered alloy systems by treating all sources of the AHE on equal footing. We employ an implementation of the Kubo-Streda equation using the fully relativistic Korringa-Kohn-Rostoker (KKR) Green's function method in conjunction with the Coherent Potential Approximation (CPA) alloy theory. Applications to the pure elemental ferromagnets bcc-Fe, hcp-Co and fcc-Ni lead to results in full accordance to previous ab initio studies determining the intrinsic contribution only. However, the power of the approach presented is the ability to explicitly treat also extrinsic contributions to the AHE which is demonstrated by an application to the fcc alloy systems Fe{sub x}Pd{sub 1-x}, Co{sub x}Pd{sub 1-x} and Ni{sub x}Pd{sub 1-x}. We obtain a very satisfying qualitative agreement with experiment over the whole concentration range including the sign reversal of the AH-conductivity. A detailed discussion of skew and side-jump scattering processes exemplifies the capability of the proposed method.

Koedderitzsch, Diemo; Chadova, Kristina; Lowitzer, Stephan; Ebert, Hubert [Ludwig-Maximilians-Universitaet Muenchen, Department Chemie und Biochemie, Physikalische Chemie, Butenandtstrasse 11, D-81377 Muenchen (Germany)

2011-07-01

385

Ab initio investigation of the spin Hall effect for non-magnetic alloys

Energy Technology Data Exchange (ETDEWEB)

Spin-orbit coupling is responsible for several interesting phenomena like e.g. the anomalous Hall effect (AHE) in magnetic materials. The AHE results from the interaction between spin-orbit coupling and the spin polarization. In comparison to the AHE the spin Hall effect (SHE) needs no spin polarization and is therefore even present in non-magnetic systems. This was shown by several experimental works e.g. During the last years several publications have appeared which studied the spin Hall effect for pure systems via ab initio e.g. or model calculations. However, up to now no publication is available in which the SHE is calculated for alloy systems on an ab initio level. To calculate the SHE we have implemented the Kubo-Streda equation in our fully relativistic SPR-KKR package. The Kubo-Streda equation gives access to the full anti-symmetric conductivity tensor what is necessary for the calculation of the SHE. The disorder is treated via the coherent potential approximation (CPA). We show first results for several non-magnetic 3d and 4d transition metal alloys.

Lowitzer, Stephan; Koedderitzsch, Diemo; Ebert, Hubert [Department Chemie, Physikalische Chemie, Universitaet Muenchen, Butenandstr. 5-13, 81377 Muenchen (Germany)

2010-07-01

386

Ab initio investigation on a promising transparent conductive oxide, Nb:SnO2

International Nuclear Information System (INIS)

The effects of Nb dopant on the lattice structure, thermal, electronic, and optical properties of rutile-phased SnO2 were investigated via ab initio calculations. The corresponding effects of Sb and Ta dopants were also studied for comparison. Results indicated that after SnO2 was doped with Nb, the differences in ionic radii, electron configurations, and electronegativities between the native element and the heterogeneous dopant led to the variations in lattice structure, thermal stability, and electron distribution, while the tetragonal symmetry of the rutile phase is conserved. The partially filled bands around Ef originated from Nb dopant led to the severe enhancement of conductivity, electron excitation in infrared region, and the consequent optical properties except for the band gaps and the selection rule restricting the electron excitation in the visible light region. Therefore, the visible transparency of Nb:SnO2 is expected to be comparable with or even better than Ta:SnO2. - Highlights: ? In this study we model rutile-phased Nb:SnO2 with ab initio methods. ? Nb dopants cause the variations in lattice structure and thermal stability. ? Bands around Ef enhance the conductivity and infrared electron excitation. ? Band gaps and selection rule restrict the electron excitation in visible region.

387

Magnetism of small Co clusters as a probe of ab initio theory

We report ab initio calculations of the electronic and magnetic properties of small Co clusters. We performed pseudopotential-based and all-electron calculations. In view of the ``unwritten theorem'' that electron localization enhances the electronic correlations, we have also considered the LDA+U functional, which is tailored for the strong-correlation problem associated with, e.g., partially-filled d shells. As a result of the weak dependence of the total energy on the calculated magnetic moment, the latter is very sensitive to the method employed. Thus, the magnetic moments obtained in the all-electron and pseudopotential calculations are quite different. Furthermore, the on-site Hubbard U enhances the magnetic moment significantly. The available experimental data for the magnetic moment of small clusters [Billas et al., Science 265, 1682 (1994)] are consistent with this enhancement. Additional Stern-Gerlach measurements for smaller clusters would, in combination with our ab initio results, constitute a direct determination of the U for these prototypes of correlated-electron behavior. (*) Supported by NSF Grant ITR DMR-0219332 (+) Managed by UT-Battelle for the U.S. DOE under contract DE- AC05-00OR22725

Troparevsky, Claudia

2007-03-01

388

Ab initio and DFT studies of the molecular structures and vibrational spectra of succinonitrile

The Molecular structure, conformational stability and vibrational frequencies of succinonitrile NCCH 2CH 2CN have been investigated with ab initio and density functional theory (DFT) methods implementing the standard 6-311++G * basis set. The potential energy surfaces (PES) have been explored at DFT-B3LYP, HF and MP2 levels of theory. In agreements with previous experimental results, the molecule was predicted to exist in equilibrium mixture of trans and gauche conforms with the trans form being slightly lower in energy. The vibrational frequencies and the corresponding vibrational assignments of succinonitrile in both C 2h and C 2 symmetry were examined theoretically and the calculated Infrared and Raman spectra of the molecule were plotted. Observed frequencies for normal modes were compared with those calculated from normal mode coordinate analysis carried out on the basis of ab initio and DFT force fields using the standard 6-311++G * basis set of the theoretical optimized geometry. Theoretical IR intensities and Raman activities are reported.

Umar, Yunusa; Morsy, M. A.

2007-04-01

389

Ab initio Reconstructions of the Shape of Cellobiose Dehydrogenase and its Domains in Solution

Three-dimensional low-resolution models of the biochemically and biotechno- logically significant enzyme cellobiose dehydrogenase (CDH) were predicted by advanced modeling approaches based on experimental one-dimensional low-resolution small-angle x-ray scattering (SAXS) data. In particular, the ab initio modeling program DAMMIN by Svergun was used to predict the shape of both the whole protein and the two major constituent units (heme and FAD domains). The validity of the approach applied was tested in a systematic way by a critical assessment of scattering profiles (scattering intensities, pair-distance distribution functions) and structural and hydrodynamic parameters (hydrated particle volume, radius of gyration, maximum particle diameter, sedimentation and diffusion coefficients) and a comparison to available experimental data. Obviously, the applied approach enables the prediction of the solution structure of both CDH and its domains with a high degree of probability, though the problem of shape uniqueness remains crucial, similar to the use of other solution methods. The obtained results demonstrate the possibility to unravel particle shapes by ab initio calculations, without knowledge of high-resolution data, and confirm earlier trial-and-error models.

Zipper, P.; Durchschlag, H.

2005-01-01

390

A methodology, Quantum Wavepacket Ab Initio Molecular Dynamics (QWAIMD), for the efficient, simultaneous dynamics of electrons and nuclei is presented. This approach allows for the quantum-dynamical treatment of a subset of nuclei in complex, molecular systems while treating the remaining nuclei and electrons within in the ab initio molecular dynamics (AIMD) paradigm. Developments of QWAIMD discussed within include: (a) a novel sampling algorithm dubbed Time-Dependent Deterministic Sampling (TDDS), which increases the computational efficiency by several orders of magnitude; (b) generalizations to hybrid QM/QM and QM/MM electronic structure methods via a combination of the ONIOM and empirical valence bond approaches, which may allow for the accurate simulation of large molecules; and (c) a novel velocity-flux autocorrelation function to calculate the vibrational density-of-states of quantum-classical systems. These techniques are benchmarked on calculations of small, hydrogen-bound clusters. Furthermore, since many chemical processes occur over time-scales inaccessible to computation, a scheme is discussed and benchmarked here which can bias both QWAIMD and classical-AIMD dynamics to sample these long time-scale events, like proton transfer in enzyme catalysis. Finally, hydrogen tunneling in an enzyme, soybean lipoxygenase-1 (SLO-1) is examined by calculating the orbitals (eigenstates) of the transferring proton along the reaction coordinate. This orbital analysis is then supplemented by using quantum measurement theory to reexamine the transfer.

Sumner, Isaiah

391

Vibrational predissociation dynamics of the aniline-neon Van der Waals complex: an ab initio study

International Nuclear Information System (INIS)

The aniline-neon van der Waals complex has been investigated from a theoretical point of view. The intermolecular distance, structure and rotational constants in the ground electronic state have been obtained by ab initio calculations using second-order Moeller-Plesset (MP2) theory. The potential energy surface has also been determined. It has been found that two conformers exist: the anti, where the neon atom and the NH bonds are located on opposite sides of the ring, is slightly more stable than the syn conformer. All the ab initio results agree with those obtained by the analysis of the rotational and laser induced fluorescence spectra of this complex. We have also modeled the interaction of the van der Waals bending mode with others internal motions of the aniline molecule such as the inversion mode of the amino group and the breathing mode of the ring. The theoretical results predict that there is a significant coupling between the van der Waals bending and the inversion mode in agreement with the experimental behavior found in both the ground and the first excited electronic states of this complex

392

A means to take advantage of molecular similarity to lower the computational cost of electronic structure theory is proposed, in which parameters are embedded into a low-cost, low-level (LL) ab initio theory and adjusted to obtain agreement with a higher level (HL) ab initio theory. This approach is explored by training such a model on data for ethane and testing the resulting model on methane, propane and butane. The electronic distribution of the molecules is varied by placing them in strong electrostatic environments consisting of random charges placed on the corners of a cube. The results find that parameters embedded in HF/STO-3G theory can be adjusted to obtain agreement, to within about 2 kcal/mol, with results of HF/6-31G theory. Obtaining this level of agreement requires the use of parameters that are functions of the bond lengths, atomic charges, and bond orders within the molecules. The argument is made that this approach provides a well-controlled means to take advantage of molecular similarity in...

Tanha, Matteus; Cappiello, Alex; Gordon, Geoffrey J; Yaron, David J

2013-01-01

393

Ab initio study of hydrogen adsorption on benzenoid linkers in metal-organic framework materials

Energy Technology Data Exchange (ETDEWEB)

We have computed the energies of adsorption of molecular hydrogen on a number of molecular linkers in metal-organic framework solid materials using density functional theory (DFT) and ab initio molecular orbital methods. We find that the hybrid B3LYP (Becke three-parameter Lee-Yang-Parr) DFT method gives a qualitatively incorrect prediction of the hydrogen binding with benzenoid molecular linkers. Both local-density approximation (LDA) and generalized gradient approximation (GGA) DFT methods are inaccurate in predicting the values of hydrogen binding energies, but can give a qualitatively correct prediction of the hydrogen binding. When compared to the more accurate binding-energy results based on the ab initio Moeller-Plesset second-order perturbation (MP2) method, the LDA results may be viewed as an upper limit while the GGA results may be viewed as a lower limit. Since the MP2 calculation is impractical for realistic metal-organic framework systems, the combined LDA and GGA calculations provide a cost-effective way to assess the hydrogen binding capability of these systems.

Gao Yi; Zeng, X C [Department of Chemistry and Nebraska Center for Materials and Nanoscience, University of Lincoln-Nebraska, Lincoln, NE 68588 (United States)

2007-09-26

394

Comment on 'Shear stiffness in nanolaminar Ti3SiC2 challenges ab initio calculations'

In a recent publication by Kisi et al (2010 J. Phys.: Condens. Matter 22 162202) the authors present experimentally measured elastic constants for the Mn + 1AXn (MAX) phase, Ti3SiC2, that differ from density functional theory calculations. They then conclude that 'prediction [by ab initio calculation] of the full elasticity tensor for Ti3SiC2 has not been successful'. However the authors do not compare with previous experimental work in which Finkel et al measure the elastic moduli (Finkel et al 2000 J. Appl. Phys. 87 1701). The predictions of ab initio calculations (Yu et al 2005 J. Mater. Res. 20 1180) agree with the measurements of Finkel et al as well as with most other experimentally measured elastic moduli for MAX phases (Cover et al 2008 10 935; Cover et al 2009 J. Phys.: Condens. Matter 21 305403). The unrealistically high value of the C44 constant obtained by Kisi et al, which would mean that Ti3SiC2 is almost as resistant to shear as diamond, undermines confidence in their results.

Cover, M. F.; Bilek, M. M. M.; McKenzie, D. R.

2011-07-01

395

International Nuclear Information System (INIS)

The applicability of ab initio multireference wavefunction-based methods to the study of magnetic complexes has been restricted by the quickly rising active-space requirements of oligonuclear systems and dinuclear complexes with S > 1 spin centers. Ab initio density matrix renormalization group (DMRG) methods built upon an efficient parameterization of the correlation network enable the use of much larger active spaces, and therefore may offer a way forward. Here, we apply DMRG-CASSCF to the dinuclear complexes [Fe2OCl6]2? and [Cr2O(NH3)10]4+. After developing the methodology through systematic basis set and DMRG M testing, we explore the effects of extended active spaces that are beyond the limit of conventional methods. We find that DMRG-CASSCF with active spaces including the metal d orbitals, occupied bridging-ligand orbitals, and their virtual double shells already capture a major portion of the dynamic correlation effects, accurately reproducing the experimental magnetic coupling constant (J) of [Fe2OCl6]2? with (16e,26o), and considerably improving the smaller active space results for [Cr2O(NH3)10]4+ with (12e,32o). For comparison, we perform conventional MRCI+Q calculations and find the J values to be consistent with those from DMRG-CASSCF. In contrast to previous studies, the higher spin states of the two systems show similar deviations from the Heisenberg spectrum, regardless of the computational method

396

Ab initio molecular dynamics study of dissociation of water under an electric field

The behavior of liquid water under an electric field is a crucial phenomenon in science and engineering. However, its detailed description at a microscopic level is difficult to achieve experimentally. Here we report on the first ab initio molecular-dynamics study on water under an electric field. We observe that the hydrogen-bond length and the molecular orientation are significantly modified at low-to-moderate field intensities. Fields beyond a threshold of about 0.35 V/\\AA are able to dissociate molecules and sustain an ionic current via a series of correlated proton jumps. Upon applying even more intense fields (1.0 V/\\AA), a 15-20% fraction of molecules are instantaneously dissociated and the resulting ionic flow yields a conductance of about 7.8 $\\Omega^{-1}cm^{-1}$, in good agreement with experimental values. This result paves the way to quantum-accurate microscopic studies of the effect of electric fields on aqueous solutions and, thus, to massive applications of ab initio molecular dynamics in neurob...

Saitta, A Marco; Giaquinta, Paolo V

2012-01-01

397

Deviational simulation of phonon transport in graphene ribbons with ab initio scattering

International Nuclear Information System (INIS)

We present a deviational Monte Carlo method for solving the Boltzmann-Peierls equation with ab initio 3-phonon scattering, for temporally and spatially dependent thermal transport problems in arbitrary geometries. Phonon dispersion relations and transition rates for graphene are obtained from density functional theory calculations. The ab initio scattering operator is simulated by an energy-conserving stochastic algorithm embedded within a deviational, low-variance Monte Carlo formulation. The deviational formulation ensures that simulations are computationally feasible for arbitrarily small temperature differences, while the stochastic treatment of the scattering operator is both efficient and exhibits no timestep error. The proposed method, in which geometry and phonon-boundary scattering are explicitly treated, is extensively validated by comparison to analytical results, previous numerical solutions and experiments. It is subsequently used to generate solutions for heat transport in graphene ribbons of various geometries and evaluate the validity of some common approximations found in the literature. Our results show that modeling transport in long ribbons of finite width using the homogeneous Boltzmann equation and approximating phonon-boundary scattering using an additional homogeneous scattering rate introduces an error on the order of 10% at room temperature, with the maximum deviation reaching 30% in the middle of the transition regime.

398

Energy Technology Data Exchange (ETDEWEB)

The objective of the FP6 Perfect Project was to develop a first example of integrated multiscale computational models, capable of describing the effects of irradiation in nuclear reactor components, namely vessel and internals. The use of ab initio techniques to study, in the most reliable way currently possible, atomic-level interactions between species and defects, and the transfer of this knowledge to interatomic potentials, of use for large scale dynamic simulations, lie at the core of this effort. The target materials of the Project were bainitic steels (vessel) and austenitic steels (internals), i.e. iron alloys. In this article, the advances made within the Project in the understanding of defect properties in Fe alloys, by means of ab initio calculations, and in the development of interatomic potentials for Fe and Fe alloys are overviewed, thereby providing a reference basis for further progress in the field. Emphasis is put in showing how the produced data have enhanced our level of understanding of microstructural processes occurring under irradiation in model alloys and steels used in existing nuclear power plants.

Malerba, L., E-mail: lmalerba@sckcen.b [Structural Materials Group, Institute of Nuclear Materials Science, SCK-CEN, Boeretang 200, B-2400 Mol (Belgium); Ackland, G.J. [School of Physics, CSEC and SUPA, Univ. of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ (United Kingdom); Becquart, C.S. [Unite de Materiaux et Techniques, UMR 8207, Universite Lille-1, F-59655 Villeneuve d' Ascq Cedex (France); Bonny, G. [Structural Materials Group, Institute of Nuclear Materials Science, SCK-CEN, Boeretang 200, B-2400 Mol (Belgium); Domain, C. [Dept. MMC, EDF-R and D, Site des Renardieres, F-77218 Moret-sur-Loing (France); Dudarev, S.L. [EURATOM/UKAEA Fusion Association, Culham Science Centre, Oxfordshire OX14 3DB (United Kingdom); Fu, C.-C. [CEA, DEN, Service de Recherches de Metallurgie Physique, F- 91191 Gif-sur-Yvette (France); Hepburn, D. [School of Physics, CSEC and SUPA, Univ. of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ (United Kingdom); Marinica, M.C. [CEA, DEN, Service de Recherches de Metallurgie Physique, F- 91191 Gif-sur-Yvette (France); Olsson, P. [Dept. MMC, EDF-R and D, Site des Renardieres, F-77218 Moret-sur-Loing (France); Pasianot, R.C. [CAC-CNEA, Depto. de Materiales, Avda. Gral. Paz 1499, 1650 San Martin, Pcia. Buenos Aires (Argentina); CONICET, Avda. Rivadavia 1917, 1033 Buenos Aires (Argentina); Raulot, J.M. [Institut Superieur de Genie Mecanique et Productique, UMR CNRS 7078, Bat. B, Ile du Saulcy, F57045 Metz, Cedex 1 (France); Terentyev, D. [Structural Materials Group, Institute of Nuclear Materials Science, SCK-CEN, Boeretang 200, B-2400 Mol (Belgium); Vincent, E. [Unite de Materiaux et Techniques, UMR 8207, Universite Lille-1, F-59655 Villeneuve d' Ascq Cedex (France); Dept. MMC, EDF-R and D, Site des Renardieres, F-77218 Moret-sur-Loing (France); Soisson, F.; Willaime, F. [CEA, DEN, Service de Recherches de Metallurgie Physique, F- 91191 Gif-sur-Yvette (France)

2010-11-01

399

Ionization dynamics of the water trimer: A direct ab initio MD study

International Nuclear Information System (INIS)

Highlights: ? We calculated ionization dynamics of water trimer. ? Direct ab initio molecular dynamics (MD) method is applied. ? Proton transfer dynamics were discussed. ? The proton transfer process calculated are well reproduced in recent experiments. - Abstract: Ionization dynamics of the cyclic water trimer (H2O)3 have been investigated by means of direct ab initio molecular dynamics (AIMD) method. Two reaction channels, complex formation and OH dissociation, were found following the ionization of (H2O)3. In both channels, first, a proton was rapidly transferred from H2O+ to H2O (time scale is ?15 fs after the ionization). In complex channel, an ion–radical contact pair (H3O+–OH) solvated by the third water molecule was formed as a long-lived H3O+(OH)H2O complex. In OH dissociation channel, the second proton transfer further takes place from H3O+(OH) to H2O (time scale is 50–100 fs) and the OH radical is separated from the H3O+. At the same time, the OH dissociation takes place when the excess energy is efficiently transferred into the kinetic energy of OH radical. The OH dissociation channel is significantly minor, and almost all product channels were the complex formation. The reaction mechanism was discussed on the basis of theoretical results

400

Ab initio study of Pd carbonyls and CO/Pd(110)

Energy Technology Data Exchange (ETDEWEB)

Carbon monoxide chemisorption on transition metal surfaces has been one of the most extensively studied in surface science in past years due to its importance in a variety of catalytic processes, especially, automotive catalytic converters using Pt or Pd. The authors have performed ab initio studies to understand the electronic and geometric aspects of the Pd-CO bond in small carbonyl clusters and the CO covered (2 x 1)p2mg superstructure of the Pd(110) surface. They have used the standard quantum chemistry package Gaussian to study the former system and a LDA (local density approximation) formalism using ab initio pseudopotentials and a plane wave basis to study the latter. The latter results are preliminary; the authors intended to study thicker slabs in the future. The organization of the paper is as follows. The authors describe the methods used in their calculation in Sec. 2. In Sec. 3, they present results and discussion; here, they first look at the smallest possible clusters, viz, Pd{sub 2} and PdCO, take a brief look at the orbital chemistry involved and then move on to the study of the CO covered Pd(110) surface and examine the geometry of the near equilibrium structure.

Ramprasad, R.; Glassford, K.M.; Adams, J.B. [Univ. of Illinois, Urbana, IL (United States). Dept. of Materials Science and Engineering

1994-12-31

401

Variable temperature (-60 to -100°C) studies of ethyldichlorophosphine, CH3CH2PCl2, of the infrared spectra (4000-400cm(-1)) dissolved in liquid xenon have been carried out. From these data, the two conformers have been identified and the enthalpy difference has been determined between the more stable trans conformer and the less stable gauche form to be 88±9cm(-1) (1.04±0.11kJ/mol). The percentage of abundance of the gauche conformer is estimated to be 57% at ambient temperature. The conformational stabilities have been predicted from ab initio calculations by utilizing many different basis sets up to aug-cc-pVTZ for both MP2(full) and density functional theory calculations by the B3LYP method. Vibrational assignments have been provided for both conformers which have been predicted by MP2(full)/6-31G(d) ab initio calculations to predict harmonic force fields, wavenumbers of the fundamentals, infrared intensities, Raman activities and depolarization ratios for both conformers. Estimated r0 structural parameters have been obtained from adjusted MP2(full)/6-311+G(d,p) calculations. The results are discussed and compared to the corresponding properties of some related molecules. PMID:24618201

Darkhalil, Ikhlas D; Paquet, Charles; Waqas, Mohammad; Gounev, Todor K; Durig, James R

2015-02-01

402

Ab Initio Potential Energy Surfaces and the Calculation of Accurate Vibrational Frequencies

Due to advances in quantum mechanical methods over the last few years, it is now possible to determine ab initio potential energy surfaces in which fundamental vibrational frequencies are accurate to within plus or minus 8 cm(exp -1) on average, and molecular bond distances are accurate to within plus or minus 0.001-0.003 Angstroms, depending on the nature of the bond. That is, the potential energy surfaces have not been scaled or empirically adjusted in any way, showing that theoretical methods have progressed to the point of being useful in analyzing spectra that are not from a tightly controlled laboratory environment, such as vibrational spectra from the interstellar medium. Some recent examples demonstrating this accuracy will be presented and discussed. These include the HNO, CH4, C2H4, and ClCN molecules. The HNO molecule is interesting due to the very large H-N anharmonicity, while ClCN has a very large Fermi resonance. The ab initio studies for the CH4 and C2H4 molecules present the first accurate full quartic force fields of any kind (i.e., whether theoretical or empirical) for a five-atom and six-atom system, respectively.

Lee, Timothy J.; Dateo, Christopher E.; Martin, Jan M. L.; Taylor, Peter R.; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

403

Ab Initio Based Understanding of the Segregation and Diffusion Mechanisms of Hydrogen in Steels

A microscopic understanding of the processes that lead to hydrogen embrittlement is of critical importance for developing new generations of high-strength steels. With this article, we provide an overview of insights that can be gained from ab initio based methods when investigating the segregation and diffusion mechanisms of hydrogen in steels. We first discuss the solubility and diffusion behavior of hydrogen in the ferrite, austenite, and martensite phases. We consider not only defect-free bulk phases but also the influence of alloying elements and geometric defects such as vacancies and grain boundaries. In the second part, the behavior of hydrogen in the presence of precipitates, the solubility, the surface absorption, and the influence of hydrogen on the interface cohesion are studied. Finally, we provide simulation results for the interaction of hydrogen with dislocations. For all these applications, we will comment on advantages and shortcomings of ab initio methods and will demonstrate how the obtained data and insights can complement experimental approaches to extract general trends and to identify causes of hydrogen embrittlement.

Hickel, T.; Nazarov, R.; McEniry, E. J.; Leyson, G.; Grabowski, B.; Neugebauer, J.

2014-08-01

404

Ab initio prediction of the critical thickness of a precipitate.

Segregation and precipitation of second phases in metals and metallic alloys is an important phenomenon that has a strong influence on the mechanical properties of the material. Models exist that describe the growth of coherent, semi-coherent and incoherent precipitates. One important parameter of these models is the energy of the interface between matrix and precipitate. In this work we apply ab initio density functional theory calculations to obtain this parameter and to understand how it depends on chemical composition and mechanical strain at the interface.Our example is a metastable Mo-C phase, the body-centred tetragonal structure, which exists as a semi-coherent precipitate in body-centred cubic molybdenum. The interface of this precipitate is supposed to change from coherent to semi-coherent during the growth of the precipitate. We predict the critical thickness of the precipitate by calculating the different contributions to a semi-coherent interface energy by means of ab initio density functional theory calculations. The parameters in our model include the elastic strain energy stored in the precipitate, as well as a misfit dislocation energy that depends on the dislocation core width and the dislocation spacing. Our predicted critical thickness agrees well with experimental observations. PMID:23896820

Sampath, S; Janisch, R

2013-09-01

405

International Nuclear Information System (INIS)

The objective of the FP6 Perfect Project was to develop a first example of integrated multiscale computational models, capable of describing the effects of irradiation in nuclear reactor components, namely vessel and internals. The use of ab initio techniques to study, in the most reliable way currently possible, atomic-level interactions between species and defects, and the transfer of this knowledge to interatomic potentials, of use for large scale dynamic simulations, lie at the core of this effort. The target materials of the Project were bainitic steels (vessel) and austenitic steels (internals), i.e. iron alloys. In this article, the advances made within the Project in the understanding of defect properties in Fe alloys, by means of ab initio calculations, and in the development of interatomic potentials for Fe and Fe alloys are overviewed, thereby providing a reference basis for further progress in the field. Emphasis is put in showing how the produced data have enhanced our level of understanding of microstructural processes occurring under irradiation in model alloys and steels used in existing nuclear power plants.

406

Ab Initio Calculations and Raman and SERS Spectral Analyses of Amphetamine Species

DEFF Research Database (Denmark)

For the first time, the differences between the spectra of amphetamine and amphetamine-H+ and between different conformers are thoroughly studied by ab initio model calculations, and Raman and surface-enhanced Raman spectroscopy (SERS) spectra are measured for different species of amphetamine. The spectra of amphetamine and amphetamine-H+ sampleswere obtained and assigned according to a comparison of the experimental spectra and the ab initio MO calculations, performed using the Gaussian 03W program (Gaussian, Inc., Pittsburgh, PA). The analyses were based on complete geometry minimization of the conformational energy of the S-plus-amphetamine molecule and the S-plus-amphetamine-H+ ion. The harmonic frequency calculations provide information about the characteristic features of the Raman spectra and the nature of the bonding in the molecule. It is concluded that vibrational bands from salt anions with internal bonds (sulfates, hydrogen phosphates, etc.) need to be taken into account when employing these spectra for identification purposes. These results also show how Raman spectroscopy can assist the forensic community in drug profiling studies. Furthermore, because their spectra are different, discrimination between the free and protonated forms of amphetamine salts can be observed. Here, we provide evidence for this difference and show experimentally how it has been overseen.

Berg, Rolf W.; NØrbygaard, Thomas

2011-01-01

407

Nonadiabatic ab initio molecular dynamics including spin-orbit coupling and laser fields.

Nonadiabatic ab initio molecular dynamics (MD) including spin-orbit coupling (SOC) and laser fields is investigated as a general tool for studies of excited-state processes. Up to now, SOCs are not included in standard ab initio MD packages. Therefore, transitions to triplet states cannot be treated in a straightforward way. Nevertheless, triplet states play an important role in a large variety of systems and can now be treated within the given framework. The laser interaction is treated on a non-perturbative level that allows nonlinear effects like strong Stark shifts to be considered. As MD allows for the handling of many atoms, the interplay between triplet and singlet states of large molecular systems will be accessible. In order to test the method, IBr is taken as a model system, where SOC plays a crucial role for the shape of the potential curves and thus the dynamics. Moreover, the influence of the nonresonant dynamic Stark effect is considered. The latter is capable of controlling reaction barriers by electric fields in time-reversible conditions, and thus a control laser using this effect acts like a photonic catalyst. In the IBr molecule, the branching ratio at an avoided crossing, which arises from SOC, can be influenced. PMID:22452086

Marquetand, Philipp; Richter, Martin; González-Vázquez, Jesús; Sola, Ignacio; González, Leticia

2011-01-01

408

Towards the first ab initio description of the deuterium-tritium fusion

The deuterium-tritium reaction is important for the future fusion energy generation. It is used in laser-induced fusion at NIF and magnetic-confinement fusion at ITER. Even though it has been well studied experimentally, its first principles theoretical understanding is important. We are building a new capability to describe light-ion fusion reactions from first principles, known as ab initio NCSM/RGM approach [1,2]. We have completed a promising preliminary study of nucleon-nucleus scattering, particularly n-^4He scattering below the d+^3H threshold [1,2]. Now we are developing the deuterium-nucleus formalism that coupled with the nucleon-nucleus basis will allow us the first ab initio calculation of the ^3H(d,n)^4He fusion. We will present recent results and work in progress. [4pt] [1] S. Quaglioni and P. Navratil, Phys. Rev. Lett. 101, 092501 (2008). [0pt] [2] S. Quaglioni and P. Navratil, Phys. Rev. C 79, 044606 (2009).

Navratil, Petr; Quaglioni, Sofia

2009-11-01

409

A new full-dimensional global potential energy surface (PES) for the acetylene-vinylidene isomerization on the ground (S0) electronic state has been constructed by fitting ?37 000 high-level ab initio points using the permutation invariant polynomial-neural network method with a root mean square error of 9.54 cm(-1). The geometries and harmonic vibrational frequencies of acetylene, vinylidene, and all other stationary points (two distinct transition states and one secondary minimum in between) have been determined on this PES. Furthermore, acetylene vibrational energy levels have been calculated using the Lanczos algorithm with an exact (J = 0) Hamiltonian. The vibrational energies up to 12 700 cm(-1) above the zero-point energy are in excellent agreement with the experimentally derived effective Hamiltonians, suggesting that the PES is approaching spectroscopic accuracy. In addition, analyses of the wavefunctions confirm the experimentally observed emergence of the local bending and counter-rotational modes in the highly excited bending vibrational states. The reproduction of the experimentally derived effective Hamiltonians for highly excited bending states signals the coming of age for the ab initio based PES, which can now be trusted for studying the isomerization reaction. PMID:25554156

Han, Huixian; Li, Anyang; Guo, Hua

2014-12-28

410

Estudio ab initio del mecanismo de la reacción HSO + O3

La reacción entre el radical HSO y el ozono ha sido ampliamente estudiada desde el punto de vista experimental debido a la importancia que tiene el radical HSO en la oxidación de los compuestos de azufre reductores y a que puede contribuir a la producción de H2SO4 [1-4]. Se realizaron diversos estudios teóricos sobre la cinética de la reacción entre el radical HSO y el ozono. La reacción del HSO con el ozono presenta tres canales diferentes : HSO + O3 &rightarrow &HSO2 + O2 &rightarrow &HS + 2 O2 &rightarrow &SO + OH + O2 La controversia existente entre los grupos experimentales sobre cuál de las tres vías es la predominante, se ha resuelto mediante un estudio teórico de todas ellas utilizando métodos ab initio. La estructura de todos los reactivos, productos, intermedios y estados de transición ha sido optimizada a nivel ab initio utilizando los métodos UMP2 /6-31G** y QCISD/6-31G**.

Nebot Gil, I.

411

We present the first systematic {\\em ab initio} study of anti-ferrodistortive (AFD) order in Ruddlesden-Popper (RP) phases of strontium titanate, Sr$_{1+n}$Ti$_n$O$_{3n+1}$, as a function of both compressive epitaxial strain and phase number $n$. We find all RP phases to exhibit AFD order under a significant range of strains, recovering the bulk AFD order as $\\sim 1/n^2$. A Ginzburg-Landau Hamiltonian generalized to include inter-octahedral interactions reproduces our {\\em ab initio} results well, opening a pathway to understanding other nanostructured perovskite systems.

Lee, Jeehye

2010-01-01

412

International Nuclear Information System (INIS)

Ab initio molecular orbital calculations on the structure and stability of the nitrate and sulfate complexes of uranyl (UO22+) and plutonyl (PuO22+) using effective core potentials are reported. It is found that the binding energy of sulfate is greater than that of nitrate to both uranyl and plutonyl, with a slight preference for plutonyl. A method of decomposing the binding energy into electrostatic, Pauli repulsion, polarization, and charge-transfer components is described which predicts that electrostatic forces are dominant. A simple molecular mechanics potential is developed by using this finding, which is successful in reproducing the ab initio results. 38 refs., 2 figs., 6 tabs

413

We have performed ab-initio tensile tests of bulk Al along different tensile axes, as well as perpendicular to different grain boundaries to determine mechanical properties such as interface energy, work of separation and theoretical strength. We show that all the different investigated geometries exhibit energy-displacement curves that can be brought into coincindence in the spirit of the well known UBER curve. This simplyfies significantly the calculation of ab-initio tensile strengths for the whole parameter space of grain boundaries.

Janisch, Rebecca; Hartmaier, Alexander

2010-01-01

414

We have obtained accurate ab initio quartet potentials for the diatomic metastable triplet helium + alkali-metal (Li, Na, K, Rb) systems, using all-electron restricted open-shell coupled cluster singles and doubles with noniterative triples corrections [CCSD(T)] calculations and accurate calculations of the long-range $C_6$ coefficients. These potentials provide accurate ab initio quartet scattering lengths, which for these many-electron systems is possible, because of the small reduced masses and shallow potentials that results in a small amount of bound states. Our results are relevant for ultracold metastable triplet helium + alkali-metal mixture experiments.

K?dziera, Dariusz; ?uchowski, Piotr S; Knoop, Steven

2015-01-01

415

AB initio calculations of the structure and stability of the non-rigid LiBF 4 molecule

Ab initio calculations of the potential energy surface, equilibrium geometry and energetic stability of the non-rigid LiBF4 molecule have been performed using the basis sets of Roos and Siegbahn, and Huzinaga and Dunning in a doublezeta contraction. The results are compared with similar ab initio data for LiBH 4, LiAlH 4, LiBeH -4, LiCH +4, Li 2 F 2, and LiBeF 3 ‡The geometry of the most disadvantageous configuration (m) was not optimized completely

Zakzhevzskii, V. G.; Boldyrev, A. I.; Charkin, O. P.

1980-07-01

416

Ab initio path integral molecular dynamics simulation was performed to understand the nuclear quantum effect on the hydrogen bond of hydrogen malonate anion. Static calculation predicted the proton transfer barrier as 0.12 kcal/mol. Conventional ab initio molecular dynamics simulation at 300 K found proton distribution with a double peak on the proton transfer coordinate. Inclusion of thermal effect alone elongates the hydrogen bond length, which increases the barrier height. Inclusion of nuclear quantum effect washes out this barrier, and distributes a single broad peak in the center. H/D isotope effect on the proton transfer is also discussed.

Kawashima, Yukio; Tachikawa, Masanori

2013-05-01

417

Hydroxyapatite [HA, Ca10(PO4)6(OH)2] is the main constituent of the mineral phase in mammalian bones and teeth enamel. In the present work, in order to study the interfacial reactions between HA and bioglasses (Hench’s mechanism), ab-initio electronic structure methods have been applied to describe hydroxyapatite (001) and (100) surfaces, with the periodic ab-initio CRYSTAL code (Gaussian basis set and B3LYP functional). Actually, HA growth is elongated in the [0001] direction in bone...

Corno, Marta; Ugliengo, Piero; Busco, Claudia

2005-01-01

418

Electron-ion structure factors, calculated in ab initio molecular dynamics simulations, are reported for several binary liquids with different kinds of chemical bonding: metallic liquid alloy Bi-Pb, molten salt RbF, and liquid water. We derive analytical expressions for the long-wavelength asymptotes of the partial electron-ion structure factors of binary systems and show that the analytical results are in good agreement with the ab initio simulation data. The long-wavelength behaviour of the total charge structure factors for the three binary liquids is discussed.

Klevets, Ivan; Bryk, Taras

2014-12-01

419

i-PI: A Python interface for ab initio path integral molecular dynamics simulations

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 coordinates from the Python interface, and to return the forces and energy that are used to integrate the equations of motion. Restrictions: This code only deals with distinguishable particles. It does not include fermonic or bosonic exchanges between equivalent nuclei, which can become important at very low temperatures. Running time: Depends dramatically on the nature of the simulation being performed. A few minutes for short tests with empirical force fields, up to several weeks for production calculations with ab initio forces. The examples provided with the code run in less than an hour.

Ceriotti, Michele; More, Joshua; Manolopoulos, David E.

2014-03-01

420

Comparative studies of the spectroscopy of CuCl2: DFT versus standard ab initio approaches.

The X2Pi g-2Sigma g+, X2Pi g-2Delta g, X2Pi g-2Sigma u+, X2Pi g-2Pi u transitions on CuCl2 have been studied using several exchange-correlation functionals from the various types of density functional theory (DFT) approaches like local density approximation (LDA), generalized gradient approximation (GGA), hybrid and meta-GGA. The results are compared with the experience and with those coming from the most sophisticated nondynamic and dynamic electronic correlation treatments using the same relativistic effective core potentials and especially developed basis sets to study the electronic structure of the five lowest states and the corresponding vertical and adiabatic transition energies. The calculated transition energies for three of the hybrid functionals (B3LYP, B97-2, and PBE0) are in very good agreement with the benchmark ab initio results and experimental figures. All of the other functionals largely overestimate the X2Pi g-2Sigma g+ and X2Pi g-2Delta g transition energies, many of them even placing the 2Delta g ligand field state above the charge transfer 2Pi u and 2Sigma u+ states. The relative weight of the Hartree-Fock exchange in the definition of the functional used appears to play a key role in the accurate description of the LambdaSSigma density defined by the orientation of the 3d hole (sigma, pi, or delta) on Cu in the field of both chlorine atoms, but no simple connection of this weight with the quality of the spectra has been found. Mulliken charges and spin densities are carefully analyzed; a possible link between the extent of spin density on the metal for the X2Pi g state and the performance of the various functionals was observed, suggesting that those that lead to the largest values (close to 0.65) are the ones that best reproduce these four transitions. Most functionals lead to a remarkably low ionicity for the three ligand field states even for the best performing functionals, compared to the complete active space (SCF) (21, 14) ab initio values. These findings show that not only large variational ab initio calculations can produce reliable spectroscopic results for extremely complex systems where delicate electronic correlation effects have to be carefully dealt with. However, those functionals that were recently shown to perform best for a series of molecular properties [J. Chem. Phys. 121 3405 (2004)] are not the ones that produce the best transition energies for this complex case. PMID:15945683

Ramírez-Solís, A; Poteau, R; Vela, A; Daudey, J P

2005-04-22

421

Ab initio study of the low-lying electronic states of the CaO molecule

Energy Technology Data Exchange (ETDEWEB)

Graphical abstract: Highly correlated ab initio calculations have been performed for an accurate determination of the electronic structure of the low-lying electronic states of the CaO molecule. The computations are done using the aug-cc-pV5Z basis set for O and the cc-pCV5Z for Ca. The potential energy curves for the molecular states correlating to the lowest three asymptotes are calculated at the CASSCF level. The potential curves of the lowest five molecular states, X{sup 1}{Sigma}{sup +}, a{sup 3}{Pi}, A'{sup 1{Pi}}, b{sup 3}{Sigma}{sup +} and A{sup 1}{Sigma}{sup +}, and the corresponding dipole moment functions have been determined using internally contracted multi-reference configuration interaction approaches. The spectroscopic constants associated with these electronic states are compared to experimental values. The corresponding electronic wavefunctions have also been analyzed using the dipole moment functions. Display Omitted Highlights: {yields} The five lowest electronic states of Cao have been determined ab initio at a high level of accuracy. {yields} Large active space, core-valence correlation and configuration interaction are required. {yields} The multi-configurational nature of the electronic ground state is confirmed as well as its monovalent and divalent ionic nature using dipole moment analysis. {yields} These interacting potentials will serve for future obtention of spin-rovibronic levels. - Abstract: Highly correlated ab initio calculations have been performed for an accurate determination of the electronic structure of the low-lying electronic states of the CaO molecule. The computations are done using the aug-cc-pV5Z basis set for O and the cc-pCV5Z for Ca. The potential energy curves for the molecular states correlating to the lowest three asymptotes are calculated at the CASSCF level. The potential curves of the lowest five molecular states, X{sup 1}{Sigma}{sup +}, a{sup 3}{Pi}, A'{sup 1}{Pi}, b{sup 3}{Sigma}{sup +} and A{sup 1}{Sigma}{sup +}, and the corresponding dipole moment functions have been determined using internally contracted multi-reference configuration interaction approaches. The spectroscopic constants associated with these electronic states are compared to experimental values. The corresponding electronic wavefunctions have also been analyzed using the dipole moment functions.

Khalil, Hossain; Brites, Vincent; Quere, Frederic Le [Universite Paris-Est, Laboratoire de Modelisation et Simulation Multi Echelle, UMR 8208 CNRS, Batiment Lavoisier, 5 boulevard Descartes, Champs sur Marne, 77454 Marne-la-Vallee, Cedex 2 (France); Leonard, Celine, E-mail: celine.leonard@univ-paris-est.fr [Universite Paris-Est, Laboratoire de Modelisation et Simulation Multi Echelle, UMR 8208 CNRS, Batiment Lavoisier, 5 boulevard Descartes, Champs sur Marne, 77454 Marne-la-Vallee, Cedex 2 (France)

2011-07-28

422

International Nuclear Information System (INIS)

Principal values of magnetic shielding tensors of acetylenic carbon nuclei for butadiynyltrimethylsilane and its reorientation rate in solution have been obtained from the interpretation of the 13C longitudinal relaxation data. The ab initio GIAO-CHF calculations of shielding parameters have been performed and the experimental and theoretical results have been compared. (author)

423

Energy Technology Data Exchange (ETDEWEB)

Iterative ab initio structure solution algorithms were tested on their performance power in phasing diffraction data. Statistical investigations on the reproducibility of the recovered phases allow an estimate about the reliability of the results. The working principle is demonstrated on synthetic structures and on experimental diffraction data of decagonal AlCuCo, AlFeNi and AlCoNi quasicrystals.

Fleischer, F; Weber, T; Steurer, W, E-mail: frank.fleischer@mat.ethz.c [Laboratory of Crystallography, Department of Materials, ETH Zurich, 8093 Zurich (Switzerland)

2010-04-01

424

Ab initio approach is used to describe the time evolution of the amplitudes of whispering gallery modes in a system of coupled microdisk resonators with Kerr nonlinearity. It is shown that this system demonstrates a transition between Josephson-like nonlinear oscillations and self-trapping behavior. Manifestation of this transition in the dynamics of radiative losses is studied.

Ramezani, Hamidreza; Shuvayev, Vladimir; Deych, Lev

2011-01-01

425

International Nuclear Information System (INIS)

An ab initio approach is used to describe the time evolution of the amplitudes of whispering gallery modes in a system of coupled microdisk resonators with Kerr nonlinearity. It is shown that this system demonstrates a transition between Josephson-like nonlinear oscillations and self-trapping behavior. Manifestation of this transition in the dynamics of radiative losses is studied.

426

Ab initio nuclear shielding parameters and spin-rotation coupling constants of FBO, ClBO and FBS

Ab initio nuclear shielding parameters and nuclear spin-rotation coupling constants of FBO, ClBO and FBS have been calculated using the multi-configuration self consistent field (MCSCF) method. The dependence of these parameters upon the basis set and active space employed in the calculation was investigated. The results are compared with the experimental values obtained from microwave spectra.

Gatehouse, Bethany

1998-05-01

427

Dynamical screening and ionic conductivity in water from ab initio simulations.

We present a method to calculate ionic conductivities of complex fluids from ab initio simulations. This is achieved by combining density functional theory molecular dynamics simulations with polarization theory. Conductivities are then obtained via a Green-Kubo formula using time-dependent effective charges of electronically screened ions. The method is applied to two different phases of warm dense water. We observe large fluctuations in the effective charges; protons can transport effective charges greater than +e for ultrashort time scales. Furthermore, we compare our results with a simpler model of ionic conductivity in water that is based on diffusion coefficients. Our approach can be directly applied to study ionic conductivities of electronically insulating materials of arbitrary composition, e.g., complex molecular mixtures under such extreme conditions that occur deep inside giant planets. PMID:22107646

French, Martin; Hamel, Sebastien; Redmer, Ronald

2011-10-28

428

This work is devoted to the \\textit{ab initio} calculation of transport and optical properties of aluminum. The calculation is based on the quantum molecular dynamics simulation, density functional theory and the Kubo-Greenwood formula. Mainly the calculations are performed for liquid aluminum at near-normal densities for the temperatures from melting up to 20000 K. The results on dynamic electrical conductivity, static electrical conductivity and thermal conductivity are obtained and compared with available reference and experimental data and the calculations of other authors. The influence of the technical parameters on the results is investigated in detail. The error of static electrical conductivity calculation is estimated to be about 20%; more accurate results require bigger number of atoms.

Knyazev, D V

2013-01-01

429

Ab initio theory of galvanomagnetic phenomena in ferromagnetic metals and disordered alloys

We present an ab initio theory of transport quantities of metallic ferromagnets developed in the framework of the fully relativistic tight-binding linear muffin-tin orbital method. The approach is based on the Kubo-St?eda formula for the conductivity tensor, on the coherent potential approximation for random alloys, and on the concept of interatomic electron transport. The developed formalism is applied to pure 3d transition metals (Fe, Co, Ni) and to random Ni-based ferromagnetic alloys (Ni-Fe, Ni-Co, Ni-Mn). High values of the anisotropic magnetoresistance (AMR), found for Ni-rich alloys, are explained by a negligible disorder in the majority spin channel, while a change of the sign of the anomalous Hall effect (AHE) on alloying is interpreted as a band-filling effect without a direct relation to the high AMR. The influence of disorder on the AHE in concentrated alloys is investigated as well.

Turek, I.; Kudrnovský, J.; Drchal, V.

2012-07-01

430

International Nuclear Information System (INIS)

Experimental measurements and theoretical calculations of the electrical conductivity of aluminum are presented in the strongly coupled partially degenerate regime (?=0.3 g/cm3, 5000< T<15 000 K). The experiments were performed in an isochoric plasma closed vessel designed to confine electrical plasma discharges up to 1.5 GPa. Aluminum properties were determined theoretically by ab initio molecular dynamics simulations in the local density approximation, from which the conductivity was computed using the Kubo-Greenwood formula. The theoretical results were validated in the dense coupled regime against previously published experimental results and then applied to our experimental low density regime, showing that the theoretical results overestimate the experimental conductivities

431

Lattice thermal conductivity of UO2 using ab-initio and classical molecular dynamics

International Nuclear Information System (INIS)

We applied the non-equilibrium ab-initio molecular dynamics and predict the lattice thermal conductivity of the pristine uranium dioxide for up to 2000?K. We also use the equilibrium classical molecular dynamics and heat-current autocorrelation decay theory to decompose the lattice thermal conductivity into acoustic and optical components. The predicted optical phonon transport is temperature independent and small, while the acoustic component follows the Slack relation and is in good agreement with the limited single-crystal experimental results. Considering the phonon grain-boundary and pore scatterings, the effective lattice thermal conductivity is reduced, and we show it is in general agreement with the sintered-powder experimental results. The charge and photon thermal conductivities are also addressed, and we find small roles for electron, surface polaron, and photon in the defect-free structures and for temperatures below 1500?K

432

Ab initio studies on the mechanic and magnetic properties of PdHx

International Nuclear Information System (INIS)

Based on ab initio total energy calculations, the structural, electronic, mechanic, and magnetic properties of PdHx are investigated. It is found that bulk modulus of PdHx is larger than the metal Pd with the hydrogen storage except Pd4H2. The calculated results for the magnetic moments show that the hydrogen addition weakens the magnetic properties of the PdHx systems. A strong magneto-volume effect is found in PdHx structures as well as Pd. The transition from paramagnetism to ferromagnetism is discussed. The corresponding densities of states for both structures are also shown to understand the magnetic behaviour. (condensed matter: structure, thermal and mechanical properties)

433

The density functional theory (DFT)+U method is an efficient and effective way to calculate the ground-state properties of strongly correlated transition metal compounds, with the effective U parameters typically determined empirically. Two ab initio methods have been developed to compute the U parameter based on either constrained DFT (CDFT) or unrestricted Hartree-Fock (UHF) theory. Previous studies have demonstrated the success of both methods in typical open-shell materials such as FeO and NiO. In this Communication we report numerical instability issues that arise for the CDFT method when applied to closed-shell transition metals, by using ZnO and Cu2O as examples. By contrast, the UHF method behaves much more robustly for both closed- and open-shell materials, making it more suitable for treating closed-shell transition metals, as well as main group elements.

Yu, Kuang; Carter, Emily A.

2014-03-01

434

Ab initio lattice dynamics of zinc-blende GaxIn1-xN alloys

International Nuclear Information System (INIS)

Using ab initio calculations in the framework of plane-wave pseudopotential implementation of the density-functional theory within the local density approximation under the virtual crystal approximation, we present a theoretical study of the elastic and dielectric properties and zone-center optical phonons in zinc-blende GaxIn1-xN alloys over the whole composition range from pure InN to pure GaN. The computed values are generally in reasonably good agreement with the existing experimental data for both parent compounds InN and GaN and provide predictions for GaxIn1-xN in the composition range 0-1 (0< x<1). The compositional dependence of the elastic constants, Born effective charge, high-frequency dielectric constant and vibration modes was investigated

435

Ab initio theoretical study of the small fullerenes C20 to C36

International Nuclear Information System (INIS)

Ab initio self-consistent field (SCF) Hartree-Fock calculations with complete geometry optimization are reported for all the isomers of the small fullerenes in the range C20-C36. The comparison between the energies of the different isomers of each fullerene shows the destabilizing effect of geometrical configurations containing two, three and four adjacent pentagons. However, no relation between molecular symmetry and stability can be established. In order to understand the sudden end of the C2 loss process at C32+ during the photofragmentation experiment of the carbon clusters (see O'Brien, Heath, Curl and Smalley, J. Chem. Phys. 88, 220 (1988)), the authors have also investigated possible reaction paths, in the present case Stone-Wales rotations between the isomers of each Cn, and C2 losses from Cn to Cn-2. A recently proposed hybrid of Hartree-Fock and density functional theory is also used to study these small fullerenes

436

The density functional theory (DFT)+U method is an efficient and effective way to calculate the ground-state properties of strongly correlated transition metal compounds, with the effective U parameters typically determined empirically. Two ab initio methods have been developed to compute the U parameter based on either constrained DFT (CDFT) or unrestricted Hartree-Fock (UHF) theory. Previous studies have demonstrated the success of both methods in typical open-shell materials such as FeO and NiO. In this Communication we report numerical instability issues that arise for the CDFT method when applied to closed-shell transition metals, by using ZnO and Cu2O as examples. By contrast, the UHF method behaves much more robustly for both closed- and open-shell materials, making it more suitable for treating closed-shell transition metals, as well as main group elements. PMID:24697417

Yu, Kuang; Carter, Emily A

2014-03-28

437

Ab initio modelling of the behaviour of helium in americium and plutonium oxides

International Nuclear Information System (INIS)

By means of an ab initio plane wave pseudo potential method, plutonium dioxide and americium dioxide are modelled, and the behaviour of helium in both these materials is studied. We first show that a pseudo potential approach in the Generalized Gradient Approximation (GGA) can satisfactorily describe the cohesive properties of PuO2 and AmO2. We then calculate the formation energies of point defects (vacancies and interstitials), as well as the incorporation and solution energies of helium in PuO2 and AmO2. The results are discussed according to the incorporation site of the gas atom in the lattice and to the stoichiometry of PuO2±x and AmO2±x. (authors)

438

An ab initio variationally computed room-temperature line list for SO3

{\\it Ab initio} potential energy and dipole moment surfaces are computed for sulfur trioxide (SO$_3$) at the CCSD(T)-F12b level of theory and appropriate triple-zeta basis sets. These surfaces are fitted and used, with a slight correction for the equilibrium S--O distance, to compute pure rotational and rotation-vibraton spectra of \\sothree\\ using the variational nuclear motion program TROVE. The calculations considered transitions in the region 0--4000 \\cm\\ with rotational states up to J=85. The resulting line list of 349~348~513 transitions is appropriate for modelling room temperature SO3 spectra. Good agreement is found with the observed infrared absorption spectra and the calculations are used to place the measured relative intensities on an absolute scale. A list of 10~878 experimental transitions is provided in a form suitable for inclusion in standard atmospheric and planetary spectroscopic databases.

Underwood, Daniel S; Yurchenko, Sergei N

2013-01-01

439

Ab initio study of multiferroic BiFeO3 (110) surfaces

The nature of multiferroic surfaces, more specifically, the energetic, ferroelectric, and noncollinear magnetic properties of BiFeO3 (110) surfaces, is investigated using ab initio (first-principles) calculations based on the fully unconstrained spin-density functional theory. As in the case of other perovskite oxides, the O-terminated surface is found to be energetically favorable. The spontaneous polarization and magnetic moment at the surface rotate in different ways from their counterparts in the bulk, which leads to a unique magnetoelectric response at the surface. The detailed lattice-distortion-mode (symmetry) analysis reveals that the rotation of the ferroelectric polarization results from the additional symmetry breaking due to the surface termination, whereas the rotation of the magnetic moment is predominantly caused by the magnetocrystalline anisotropy. Furthermore, we investigate the effect of epitaxial strain and find that the strain responses of both the polarization and the magnetic moment are markedly enhanced at the surfaces.

Shimada, Takahiro; Arisue, Kou; Wang, Jie; Kitamura, Takayuki

2014-06-01

440

An ab initio study of van der Waals potential energy parameters for silver clusters.

We employ ab initio calculations of van der Waals complexes to study the potential energy parameters (C(6) coefficients) of van der Waals interactions for modeling of the adsorption of silver clusters on the graphite surface. Electronic structure calculations of the (Ag(2))(2), Ag(2)-H(2), and Ag(2)-C(6)H(6) complexes are performed using a coupled-cluster approach that includes single, double, and perturbative triple excitations (CCSD(T)), Møller-Plesset second-order perturbation theory (MP2), and spin-component-scaled MP2 (SCS-MP2) methods. Using the atom pair approximation, the C(6) coefficients for silver-silver, silver-hydrogen, and silver-carbon atom systems are obtained after subtracting the energies of quadrupole-quadrupole interactions from the total electronic energy. PMID:21348479

Hänninen, Vesa; Korpinen, Markus; Ren, Qinghua; Hinde, Robert; Halonen, Lauri

2011-03-24

441

High-accuracy ab initio rotation-vibration transitions for water.

The spectrum of water vapor is of fundamental importance for a variety of processes, including the absorption and retention of sunlight in Earth's atmosphere. Therefore, there has long been an urgent need for a robust and accurate predictive model for this spectrum. In our work on the high-resolution spectrum of water, we report first-principles calculations that approach experimental accuracy. To achieve this, we performed exceptionally large electronic structure calculations and considered a variety of effects, including quantum electrodynamics, which have routinely been neglected in studies of small many-electron molecules. The high accuracy of the resulting ab initio procedure is demonstrated for the main isotopomers of water. PMID:12543967

Polyansky, Oleg L; Császár, Attila G; Shirin, Sergei V; Zobov, Nikolai F; Barletta, Paolo; Tennyson, Jonathan; Schwenke, David W; Knowles, Peter J

2003-01-24

442

Ab initio molecular dynamics study of the hydrogen diffusion in sodium and lithium hydrides

Light weight complex metal hydrides, sodium hydride (NaH), and lithium hydride (LiH) are the last step materials during hydrogen release process of alanates and borates, which are promising candidates for hydrogen storage. We report ab initio molecular dynamics (MD) calculations based on density functional theory to study the hydrogen-deuterium exchange in NaH and LiH. We predict the single hydrogen-deuterium exchange in NaH and LiH and calculate the self-diffusion constants, ?D?NaH?1.46×10-9 m2 s-1 of deuterium in NaH at 420 K and ?D?LiH?1.49×10-9 m2 s-1 of deuterium in LiH at 550 K, which are in good agreement with the experimental values.

Ramzan, M.; Ahuja, R.

2009-07-01

443

Ab initio study of energy characteristics and magnetic properties of point defects in GaAs

International Nuclear Information System (INIS)

Energy of formation of intrinsic point defects and energy of dissolving of transition metal impurities in gallium arsenide were determined on the basis of ab initio calculations with application of a method of the locally self-congruent Green function being a generalization of the coherent potential approximation. On the basis of the calculated energy values one makes a conclusion that AsGa antistructural defect is the most commonly occurring one in GaAs. The calculations have shown that the impurities of transition metals excluding Ni substitute preferentially for gallium nodes. One calculated magnetic moments of impurity atoms depending on chemical environment. Mn atoms are shown to have a tendency to form clusters in the compensated GaAs

444

Ab initio modeling of martensitic transformations (MT) in magnetic shape memory alloys

International Nuclear Information System (INIS)

The magnetic field-induced (MFI) changes of the electronic, magnetic and phonon properties of magnetic shape memory Heusler alloys Ni-Mn-Ga and Ni-Mn-In are discussed on the basis of first-principles calculations. Without an external magnetic field, the lattice instability to shear wave propagation in [110] direction shows up in the calculation as softening of the TA2? [110] (2?/a) mode at ??13. The ab initio modeling of magnetic field effects shows that the phase (austenite or martensite) is favored which has larger magnetization. This is in agreement with experiments on Ni-Mn-In, for which the martensitic transformation (MT) can be shifted by 40K to lower temperatures in an external field of 5T

445

Ab initio MRD CI calculations on the cesium hydride (CsH) molecule

International Nuclear Information System (INIS)

Ab initio multi-reference configuration interaction (MRD CI) calculations were carried out for the potential energy curves of the first 17 electronic states of the CsH molecule up to large bond distances (20 bohr). The 1?+ states were also calculated by means of relativistic all-electron SCF and CI using the spin-free no-pair operator with external field projectors. For the low-lying states, the spectroscopic parameters were determined. Dipole moments as well as the transition dipole moments: ?(X1?+?A1?+), ?(X1?+?B1?+), ?(A1?+?B1?+), were also calculated. Non-relativistic and relativistic results are compared. An analysis of the interactions in the 1,3?+ states is also proposed. (orig.)

446

Symmetry-adapted ab initio no-core shell model calculations for 12C

International Nuclear Information System (INIS)

Symmetry-adapted no-core shell-model calculations reveal dominant symmetry patterns in the structure of light nuclei, independent of whether the system Hamiltonian is phenomenological in nature or derived from realistic interactions. We show results of large-scale nuclear structure computations based on the ab initio symmetry-adapted no-core shell model that use only a fraction of the model space. In addition, the symmetry patterns unveiled in these results are employed to explore ultra-large model spaces for 12C. The outcome suggests a possible path forward for realizing collective theories that target correlated highly-deformed and alpha-cluster structures in terms of microscopic degrees of freedom that build forward from the nucleon-nucleon interaction itself.

447

Ab initio contribution to the study of complexes formed during dilute FeCu alloys radiation

Cu plays an important role in the embrittlement of pressure vessel steels under radiation and entities containing both Cu atoms and vacancies seem to appear as a consequence of displacement cascades. The characterisation of the stability as well as the migration of small Cu-vacancy complexes is thus necessary to understand and simulate the formation of these entities. For instance, cascade ageing studied by kinetic Monte Carlo or by rate theory models requires a good characterisation of such complexes which are parameters for these methods. We have investigated, by ab initio calculations based on the density functional theory, point defects and small defects in dilute FeCu alloys. The structure of small Cu clusters and Cu-vacancy complexes has been determined, as well as their formation and binding energies. Their relative stability is discussed. Vacancy migration energies in the presence of Cu atoms have been calculated and analysed. All the results are compared to the figures obtained with empirical interat...

Becquart, C S

2003-01-01

448

Ab-initio calculations of electronic, transport, and structural properties of boron phosphide

International Nuclear Information System (INIS)

We present results from ab-initio, self-consistent density functional theory calculations of electronic and related properties of zinc blende boron phosphide (zb-BP). We employed a local density approximation potential and implemented the linear combination of atomic orbitals formalism. This technique follows the Bagayoko, Zhao, and Williams method, as enhanced by the work of Ekuma and Franklin. The results include electronic energy bands, densities of states, and effective masses. The calculated band gap of 2.02?eV, for the room temperature lattice constant of a?=?4.5383?Å, is in excellent agreement with the experimental value of 2.02?±?0.05?eV. Our result for the bulk modulus, 155.7?GPa, agrees with experiment (152–155?GPa). Our predictions for the equilibrium lattice constant and the corresponding band gap, for very low temperatures, are 4.5269?Å and 2.01?eV, respectively.

449

Ab initio characterization of the Mg-HF van der Waals complex

The equilibrium structure and the three-dimensional potential energy surface of the Mg-HF van der Waals complex in its ground electronic state have been determined from accurate ab initio calculations using the coupled-cluster method, CCSD(T), in conjunction with the basis sets of triple- through quintuple-zeta quality. The core-electron correlation, high-order valence-electron correlation, and scalar relativistic effects were investigated. The Mg-HF complex was confirmed to be linear at equilibrium, with a vibrationless dissociation energy (into Mg and HF) De of 280 cm-1. The vibration-rotation energy levels of two isotopologues, M24g-HF and M24g-DF, were predicted using the variational method. The predicted spectroscopic constants can be useful in a further analysis of high-resolution vibration-rotation spectra of the Mg-HF complex.

Koput, Jacek; Makarewicz, Jan

2010-10-01

450

Ab initio determination of coarse-grained interactions in double-stranded DNA

We derive the coarse-grained interactions between DNA nucleotides from ab initio total-energy calculations based on density functional theory (DFT). The interactions take into account base and sequence specificity, and are decomposed into physically distinct contributions that include hydrogen bonding, stacking interactions, backbone, and backbone-base interactions. The interaction energies of each contribution are calculated from DFT for a wide range of configurations and are fitted by simple analytical expressions for use in the coarse-grained model, which reduces each nucleotide into two sites. This model is not derived from experimental data, yet it successfully reproduces the stable B-DNA structure and gives good predictions for the persistence length. It may be used to realistically probe dynamics of DNA strands in various environments at the ?s time scale and the ?m length scale.

Hsu, Chia Wei; Fyta, Maria; Lakatos, Greg; Melchionna, Simone; Kaxiras, Efthimios

2012-09-01

451

Ab initio spin-orbit calculations on the lowest states of the nickel dimer.

Potential energy curves of the lowest electronic states of the Ni(2) dimer are calculated near the equilibrium using the multireference ab initio methods including the spin-orbit interaction. Scalar-relativistic results fully confirm previous qualitative interpretations based on the correlation with atomic limits and the symmetry of vacancies in the atomic 3d(9) shells. Spin-orbit calculations firmly establish the symmetry of the ground state as 0(+)(g) and give the excitation energies 70 ± 30 cm(-1) and 200 ± 80 cm(-1) for the lowest 0(-)(u) and 5(u) states, respectively. The model electronic spectrum of the Ni(2) shows some trends that might be observed in matrix isolation far-infrared and electron spin resonance spectra. PMID:22697540

Cheskidov, Alexander V; Buchachenko, Alexei A; Bezrukov, Dmitry S

2012-06-01

452

Ab initio structure determination of lanthanum cyclo-tetratungstate {alpha}-La

Energy Technology Data Exchange (ETDEWEB)

Lanthanum tungstate {alpha}-La{sub 2}W{sub 2}O{sub 9} was successfully synthesized by the ceramic route. Its crystal structure was determined ab initio from neutron diffraction data (space group P{bar 1} No. 2; a = 7.2489(1) {angstrom}, b = 7.2878(1) {angstrom}, c = 7.0435(1) {angstrom}, {alpha} = 96.367(1){degree}, {beta} = 94.715(1){degree}, {gamma} = 70.286(1){degree}; Z = 2; reliability factors: R{sub p} = 6.0%, R{sub wp} = 6.9%, R{sub B} = 3.0%). The structure exhibits isolated [W{sub 4}O{sub 18}]{sup 12{minus}} groups in the form of rings involving [WO{sub 6}] octahedra alternating with [WO{sub 5}] trigonal bipyramids sharing corners. These rings are inserted in the 3D framework built by the 9- and 10-fold coordination polyhedra of the lanthanum atoms.

Laligant, Y.; Le Bail, A.; Goutenoire, F.

2001-06-01

453

We theoretically investigate the generation of ultrafast currents in insulators induced by strong few-cycle laser pulses. Ab initio simulations based on time-dependent density functional theory give insight into the atomic-scale properties of the induced current signifying a femtosecond-scale insulator-metal transition. We observe the transition from nonlinear polarization currents during the laser pulse at low intensities to tunnelinglike excitation into the conduction band at higher laser intensities. At high intensities, the current persists after the conclusion of the laser pulse considered to be the precursor of the dielectric breakdown on the femtosecond scale. We show that the transferred charge sensitively depends on the orientation of the polarization axis relative to the crystal axis, suggesting that the induced charge separation reflects the anisotropic electronic structure. We find good agreement with very recent experimental data on the intensity and carrier-envelope phase dependence [A. Schiffrin et al., Nature (London) 493, 70 (2013)].

Wachter, Georg; Lemell, Christoph; Burgdörfer, Joachim; Sato, Shunsuke A.; Tong, Xiao-Min; Yabana, Kazuhiro

2014-08-01

454

Ab initio study of the volume dependence of dynamical and thermodynamical properties of silicon

Motivated by the negative thermal expansion observed for silicon between 20 K and 120 K, we present first an ab initio study of the volume dependence of interatomic force constants, phonon frequencies of TA(X) and TA(L) modes, and of the associated mode Gruneisen parameters. The influence of successive nearest neighbors shells is analysed. Analytical formulas, taking into account interactions up to second nearest neighbors, are developped for phonon frequencies of TA(X) and TA(L) modes and the corresponding mode Gruneisen parameters. We also analyze the volume and pressure dependence of various thermodynamic properties (specific heat, bulk modulus, thermal expansion), and point out the effect of the negative mode Gruneisen parameters of the acoustic branches on these properties. Finally, we present the evolution of the mean square atomic displacement and of the atomic temperature factor with the temperature for different volumes, for which the anomalous effects are even greater.

Rignanese, G M; Gonze, X

1995-01-01

455

Quantum fluctuations and isotope effects in ab initio descriptions of water

International Nuclear Information System (INIS)

Isotope substitution is extensively used to investigate the microscopic behavior of hydrogen bonded systems such as liquid water. The changes in structure and stability of these systems upon isotope substitution arise entirely from the quantum mechanical nature of the nuclei. Here, we provide a fully ab initio determination of the isotope exchange free energy and fractionation ratio of hydrogen and deuterium in water treating exactly nuclear quantum effects and explicitly modeling the quantum nature of the electrons. This allows us to assess how quantum effects in water manifest as isotope effects, and unravel how the interplay between electronic exchange and correlation and nuclear quantum fluctuations determine the structure of the hydrogen bond in water

456

Cu-based organometallic systems: an ab initio study of the electronic and magnetic properties

Within a first principles framework, we study the electronic properties of the recently synthesized organometallic coordination polymer Cu(II)- 2,5-bis(pyrazol-1-yl)-1,4-dihydroxybenzene (CuCCP). Considering this system as a starting point, we present a way of designing reliable modified structures by using a combination of classical with quantum mechanical methods. In a next step, we analyze via ab initio calculations the effect of the proposed modifications on the electronic and magnetic properties of the original compound. For CuCCP we have performed two types of substitutions aimed at changing the intra- and inter-chain Cu-Cu interaction as well as the Cu coordination. This study shows that such a design procedure has important predictive power for possible interesting systems to be synthesized in the laboratory.

Salguero, L A; Valenti, R; Rahaman, B; Saha-Dasgupta, T; Buchsbaum, C; Schmidt, M U; Jeschke, Harald O.; Valenti, Roser; Rahaman, Badiur; Saha-Dasgupta, Tanusri; Buchsbaum, Christian; Schmidt, Martin U.

2006-01-01