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1

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

UK PubMed Central (United Kingdom)

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.

Elmlund D; Elmlund H

2012-12-01

2

PRAP: An ab initio Software Package for Automated Genome Wide Analysis of DNA Repeats for Prokaryotes.  

UK PubMed Central (United Kingdom)

MOTIVATION: Prokaryotic genome annotation has been focused mainly on identifying all genes and their protein functions. However, less than 30% of the prokaryotic genomes submitted to GenBank contain partial repeat features of specific types and none of the genomes contain complete repeat annotations. Deciphering all repeats in DNA sequences is an important and open task in genome annotation and bioinformatics. Hence, there is an immediate need of a tool capable of identifying full spectrum repeats in the whole genome. RESULTS: We report the PRAP (Prokaryotic Repeats Annotation Program) software package to automate the analysis of repeats in both finished and draft genomes. It is aimed at identifying full spectrum repeats at the scale of the prokaryotic genome. Compared to the major existing repeat finding tools, PRAP exhibits competitive or better results. The results are consistent with manually curated and experimental data. Repeats can be identified and grouped into families to define their relevant types. The final output is parsed into the EMBL/GenBank feature table format for reading and displaying in Artemis, where it can be combined or compared with other genome data. It is currently the most complete repeat finder for prokaryotes and is a valuable tool for genome annotation. AVAILABILITY: https://sites.google.com/site/prapsoftware/ CONTACT: hsuehc@ntu.edu.tw SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Chen GL; Chang YJ; Hsueh CH

2013-08-01

3

Ab initio molecular dynamics.  

Science.gov (United States)

In this chapter, an introduction to ab initio molecular dynamics (AIMD) has been given. Many of the basic concepts, like the Hellman-Feynman forces, the difference between the Car-Parrinello molecular dynamics and AIMD, have been explained. Also a very versatile AIMD code, the CP2K, has been introduced. On the application, the emphasis was on the aqueous systems and chemical reactions. The biochemical applications have not been discussed in depth. PMID:23034744

Laasonen, Kari

2013-01-01

4

Ab initio molecular dynamics.  

UK PubMed Central (United Kingdom)

In this chapter, an introduction to ab initio molecular dynamics (AIMD) has been given. Many of the basic concepts, like the Hellman-Feynman forces, the difference between the Car-Parrinello molecular dynamics and AIMD, have been explained. Also a very versatile AIMD code, the CP2K, has been introduced. On the application, the emphasis was on the aqueous systems and chemical reactions. The biochemical applications have not been discussed in depth.

Laasonen K

2013-01-01

5

The MSRC Ab Initio Methods Benchmark Suite: A measurement of hardware and software performance in the area of electronic structure methods  

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

6

Ab-initio calculations and phase diagram assessments of An-Al systems (An = U, Np, Pu)  

Energy Technology Data Exchange (ETDEWEB)

The enthalpies of formation of binary intermetallic compounds AnAl{sub n}(n=2,3,4,An=U,Np,Pu) were assessed from first principle calculations of total energies performed using full potential APW + lo technique within density functional theory (WIEN2k). The substantial contribution to entropies, S{sub 298}{sup o}, arising from lattice vibrations was calculated by direct method within harmonic crystal approximation (Phonon software + VASP for obtaining Hellmann-Feynman forces). The electronic heat capacity and the corresponding contribution to entropy were estimated from the density of states at Fermi level obtained from electronic structure calculations. The phase diagrams of the relevant systems An-Al were calculated based on the thermodynamic data assessed from ab-initio calculations, known equilibrium and calorimetry data by employing the FactSage program.

Sedmidubsky, D., E-mail: sedmidub@vscht.c [European Commission, Joint Research Centre, Institute for Transuranium Elements, Post Box 2340, D-76125 Karlsruhe (Germany); Institute of Chemical Technology, Technicka 5, 166 28 Prague (Czech Republic); Konings, R.J.M.; Soucek, P. [European Commission, Joint Research Centre, Institute for Transuranium Elements, Post Box 2340, D-76125 Karlsruhe (Germany)

2010-02-15

7

Ab-initio calculations and phase diagram assessments of An-Al systems (An = U, Np, Pu)  

International Nuclear Information System (INIS)

[en] The enthalpies of formation of binary intermetallic compounds AnAln(n=2,3,4,An=U,Np,Pu) were assessed from first principle calculations of total energies performed using full potential APW + lo technique within density functional theory (WIEN2k). The substantial contribution to entropies, S298o, arising from lattice vibrations was calculated by direct method within harmonic crystal approximation (Phonon software + VASP for obtaining Hellmann-Feynman forces). The electronic heat capacity and the corresponding contribution to entropy were estimated from the density of states at Fermi level obtained from electronic structure calculations. The phase diagrams of the relevant systems An-Al were calculated based on the thermodynamic data assessed from ab-initio calculations, known equilibrium and calorimetry data by employing the FactSage program.

2010-01-01

8

AB INITIO AND CALPHAD THERMODYNAMICS OF MATERIALS  

Energy Technology Data Exchange (ETDEWEB)

Ab initio electronic structure methods can supplement CALPHAD in two major ways for subsequent applications to stability in complex alloys. The first one is rather immediate and concerns the direct input of ab initio energetics in CALPHAD databases. The other way, more involved, is the assessment of ab initio thermodynamics {acute a} la CALPHAD. It will be shown how these results can be used within CALPHAD to predict the equilibrium properties of multi-component alloys.

Turchi, P A

2004-04-14

9

Ab initio random structure searching  

International Nuclear Information System (INIS)

It is essential to know the arrangement of the atoms in a material in order to compute and understand its properties. Searching for stable structures of materials using first-principles electronic structure methods, such as density-functional-theory (DFT), is a rapidly growing field. Here we describe our simple, elegant and powerful approach to searching for structures with DFT, which we call ab initio random structure searching (AIRSS). Applications to discovering the structures of solids, point defects, surfaces, and clusters are reviewed. New results for iron clusters on graphene, silicon clusters, polymeric nitrogen, hydrogen-rich lithium hydrides, and boron are presented. (topical review)

2011-02-09

10

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

11

Ab initio no core shell model  

Science.gov (United States)

Motivated by limitations of the Bloch-Horowitz-Brandow perturbative approach to nuclear structure we have developed the non-perturbative ab initio no core shell model (NCSM) capable of solving the properties of nuclei exactly for arbitrary nucleon-nucleon (NN) and NN+ three-nucleon (NNN) interactions with exact preservation of all symmetries. We present the complete ab initio NCSM formalism and review highlights obtained with it since its inception. These highlights include the first ab initio nuclear-structure calculations utilizing chiral NNN interactions, which predict the correct low-lying spectrum for 10B and explain the anomalous long 14C ?-decay lifetime. We also obtain the small quadrupole moment of 6Li. In addition to explaining long-standing nuclear structure anomalies, the ab initio NCSM provides a predictive framework for observables that are not yet measured or are not directly measurable. For example, reactions between short-lived systems and reaction rates near zero energy are relevant to fusion research but may not be known from experiment with sufficient precision. We, therefore, discuss, in detail, the extension of the ab initio NCSM to nuclear reactions and sketch a number of promising future directions for research emerging from the NCSM foundation, including a microscopic non-perturbative framework for the theory with a core. Having a parameter-free approach, we can construct systems with a core, which will provide an ab initio pathway to heavier nuclei.

Barrett, Bruce R.; Navrátil, Petr; Vary, James P.

2013-03-01

12

Ab Initio Study of Polonium  

International Nuclear Information System (INIS)

[en] 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

2008-05-20

13

Ab initio conformational study of caffeic acid  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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 conformatio...

VanBesien, E.; Marques, M. P. M.

14

Ab initio study of incommensurately modulated crystals  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We present an ab initio study of the average structure of some incommensurately (IC) modulated materials: K2SeO4, Mo2S3, AuTe2 (calaverite) and Pb2MgTeO6 (elpasolite structure). All the calculations are done using the local density approximation (LDA) and/or the general gradient approximation (GGA) ...

Caracas, R.; Gonze, Xavier

15

Ab initio calculations of free-energy reaction barriers  

International Nuclear Information System (INIS)

The theoretical description of chemical reactions was until recently limited to a 'static' approach in which important parameters such as the rate constant are deduced from the local topology of the potential energy surface close to minima and saddle points. Such an approach has, however, serious limitations. The growing computational power allows us now to use advanced simulation techniques to determine entropic effects accurately for medium-sized systems at ab initio level. Recently, we have implemented free-energy simulation techniques based on molecular dynamics, in particular on the blue-moon ensemble technique and on metadynamics, in the popular DFT code VASP. In the thermodynamic integration (blue-moon ensemble) technique, the free-energy profile is calculated as the path integral over the restoring forces along a parametrized reaction coordinate. In metadynamics, an image of the free-energy surface is constructed on the fly during the simulation by adding small repulsive Gaussian-shaped hills to the Lagrangian driving the dynamics. The two methods are tested on a simple chemical reaction-the nucleophilic substitution of methyl chloride by a chlorine anion.

2008-02-13

16

Towards hydrogen metallization: an Ab initio approach  

International Nuclear Information System (INIS)

The quest for metallic hydrogen is a major goal for both theoretical and experimental condensed matter physics. Hydrogen and deuterium have been compressed up to 200 GPa in diamond anvil cells, without any clear evidence for a metallic behaviour. Loubeyere has recently suggested that hydrogen could metallize, at pressures within experimental range, in a new Van der Waals compound: Ar(H2)2 which is characterized at ambient pressure by an open and anisotropic sublattice of hydrogen molecules, stabilized by an argon skeleton. This thesis deals with a detailed ab initio investigation, by Car-Parrinello molecular dynamics methods, of the evolution under pressure of this compound. In a last chapter, we go to much higher pressures and temperatures, in order to compare orbital and orbital free ab initio methods for the dense hydrogen plasma. (author)

1998-01-01

17

Ab Initio Calculations on Uracil-Water  

Energy Technology Data Exchange (ETDEWEB)

The potential energy surface for the interaction of uracil with one water molecule is investigated using ab initio techniques. The structures of four cyclic minima, as well as two transition-state structures, have been determined using second-order Moller-Plesset perturbation theory (MP2) and the interaction-optimized DZPi basis set. At the optimized geometries, the counterpoise-corrected interaction energies have also been computed with a slightly larger basis set containing bond functions, labeled ESPB.

Mourik, Van Tonja; Price, Sarah L.; Clary, David C.

1999-03-18

18

Ab initio simulation of magnetic tunnel junctions  

Energy Technology Data Exchange (ETDEWEB)

In this paper, we present the mathematical and implementation details of an ab initio method for calculating spin-polarized quantum transport properties of atomic scale spintronic devices under external bias potential. The method is based on carrying out density functional theory (DFT) within the Keldysh non-equilibrium Green's function (NEGF) formalism to calculate the self-consistent spin densities. We apply this method to investigate nonlinear and non-equilibrium spin-polarized transport in a Fe/MgO/Fe trilayer structure as a function of external bias voltage.

Waldron, Derek; Liu Lei; Guo Hong [Centre for the Physics of Materials and Department of Physics, McGill University, Montreal, PQ, H3A 2T8 (Canada)

2007-10-24

19

Ab initio mass tensor molecular dynamics  

CERN Multimedia

Mass tensor molecular dynamics was first introduced by Bennett [J. Comput. Phys. 19, 267 (1975)] for efficient sampling of phase space through the use of generalized atomic masses. Here, we show how to apply this method to ab initio molecular dynamics simulations with minimal computational overhead. Test calculations on liquid water show a threefold reduction in computational effort without making the fixed geometry approximation. We also present a simple recipe for estimating the optimal atomic masses using only the first derivatives of the potential energy.

Tsuchida, Eiji

2010-01-01

20

Ab initio simulation of magnetic tunnel junctions.  

UK PubMed Central (United Kingdom)

In this paper, we present the mathematical and implementation details of an ab initio method for calculating spin-polarized quantum transport properties of atomic scale spintronic devices under external bias potential. The method is based on carrying out density functional theory (DFT) within the Keldysh non-equilibrium Green's function (NEGF) formalism to calculate the self-consistent spin densities. We apply this method to investigate nonlinear and non-equilibrium spin-polarized transport in a Fe/MgO/Fe trilayer structure as a function of external bias voltage.

Waldron D; Liu L; Guo H

2007-10-01

 
 
 
 
21

Ab initio simulation of magnetic tunnel junctions.  

Science.gov (United States)

In this paper, we present the mathematical and implementation details of an ab initio method for calculating spin-polarized quantum transport properties of atomic scale spintronic devices under external bias potential. The method is based on carrying out density functional theory (DFT) within the Keldysh non-equilibrium Green's function (NEGF) formalism to calculate the self-consistent spin densities. We apply this method to investigate nonlinear and non-equilibrium spin-polarized transport in a Fe/MgO/Fe trilayer structure as a function of external bias voltage. PMID:21730459

Waldron, Derek; Liu, Lei; Guo, Hong

2007-09-21

22

Germacrene D Cyclization: An Ab Initio Investigation  

Directory of Open Access Journals (Sweden)

Full Text Available Essential oils that contain large concentrations of germacrene D are typically accompanied by cadinane sesquiterpenoids. The acid-catalyzed cyclization of germacrene D to give cadinane and selinane sesquiterpenes has been computationally investigated using both density functional (B3LYP/6-31G*) and post Hartree-Fock (MP2/6-31G**) ab initio methods. The calculated energies are in general agreement with experimentally observed product distributions, both from acid-catalyzed cyclizations as well as distribution of the compounds in essential oils.

William N. Setzer

2008-01-01

23

Ab initio calculation of the Hoyle state.  

UK PubMed Central (United Kingdom)

The Hoyle state plays a crucial role in the helium burning of stars heavier than our Sun and in the production of carbon and other elements necessary for life. This excited state of the carbon-12 nucleus was postulated by Hoyle as a necessary ingredient for the fusion of three alpha particles to produce carbon at stellar temperatures. Although the Hoyle state was seen experimentally more than a half century ago nuclear theorists have not yet uncovered the nature of this state from first principles. In this Letter we report the first ab initio calculation of the low-lying states of carbon-12 using supercomputer lattice simulations and a theoretical framework known as effective field theory. In addition to the ground state and excited spin-2 state, we find a resonance at -85(3)??MeV with all of the properties of the Hoyle state and in agreement with the experimentally observed energy.

Epelbaum E; Krebs H; Lee D; Meissner UG

2011-05-01

24

Giant magnetoresistance An ab-initio description  

CERN Multimedia

A new theoretical concept to study the microscopic origin of Giant Magnetoresistance (GMR) from first principles is presented. The method is based on ab-initio electronic structure calculations within the spin density functional theory using a Screened KORRINGA-KOHNROSTOKER method. Scattering at impurity atoms in the multilayers is described by means of a GREEN's-function method. The scattering potentials are calculated self-consistently. The transport properties are treated quasi-classically solving the BOLTZMANN equation including the electronic structure of the layered system and the anisotropic scattering. The solution of the BOLTZMANN equation is performed iteratively taking into account both scattering out and scattering in terms (vertex corrections). The method is applied to Co/Cu and Fe/Cr multilayers. Trends of scattering cross sections, residual resistivities and GMR ratios are discussed for various transition metal impurities at different positions in the Co/Cu or Fe/Cr multilayers. Furthermore the...

Binder, J

2000-01-01

25

Ab initio study of solution energy and diffusion of caesium in uranium dioxide  

Energy Technology Data Exchange (ETDEWEB)

The behaviour of caesium in nuclear fuels is investigated using density functional theory (DFT). In a first step, the incorporation and solution energies of Cs in pre-existing trap sites of UO{sub 2} (vacancies, interstitials, U-O di-vacancy and Schottky trio defects) are calculated using the projector-augmented-wave (PAW) derived pseudopotentials as implemented in the Vienna ab initio simulation package (VASP). Correlation effects are taken into account within the DFT + U approach. The solubility of caesium is found to be very low, in agreement with experimental data. The migration of Cs is found to be highly anisotropic, it is controlled by uranium diffusion with an Arrhenius activation energy of 4.8 eV in hyperstoichiometric UO{sub 2+x}, in good agreement with experimental values.

Gupta, F. [IRSN, DPAM, SEMIC, LETR, 13115 Saint Paul Lez Durance (France); Pasturel, A. [CNRS, Laboratoire de Physique et Modelisation des Milieux Condenses, Maison des Magisteres, 25 Avenue des Martyrs BP166, 38042 Grenoble (France); Brillant, G. [IRSN, DPAM, SEMIC, LETR, 13115 Saint Paul Lez Durance (France)], E-mail: guillaume.brillant@irsn.fr

2009-03-31

26

Cálculos ab initio con correlación electrónica  

Science.gov (United States)

Estamos entrando en una era donde la ortogonalidad entre las investigaciones de carácter experimental y de naturaleza teórica se irá difuminando progresivamente y la problemática a resolver quedará en escena como el único actor principal de la obra. Como premisa para una cooperación teórico-experimental de igual a igual, la metodología químico-cuántica utilizada debe ser capaz de ofrecer resultados de carácter predictivo. Sin duda, esta madurez en la metodología químico-cuántica ya la hemos alcanzado hace algunos años, tal y como muestra entre otras muchas, la labor que nuestro grupo ha realizado en el transcurso de la última década, dentro del campo de la Espectroscopía Teórica. Los estudios realizados comprenden una amplia gama de sistemas, variando tanto en tamaño como en complejidad, abordando problemáticas espectroscópicas consideradas tradicionalmente como especialmente controvertidas. Nuestra contribución científica más relevante reside en el carácter cuantitativo de las asignaciones espectroscópicas que hemos propuesto en base a resultados ab initio. Recordemos que en los años noventa los resultados ab initio solían presentar para las energías de excitación de sistemas de tamaño molecular moderado, como el benceno, errores de más de 1 eV. En comparación con el éxito relativo de los métodos semiempíricos, la frustración de la metodología ab initio quedaba todavía más patente. Los estudios que hemos presentado representan una comprensión profunda de los espectros electrónicos en sistemas orgánicos claves, mostrando el camino a seguir para obtener asignaciones espectroscópicas precisas (entre 0.1-0.2 eV). La naturaleza del método CASPT2 junto al diseño de estrategias computacionales nos ha permitido alcanzar el carácter cuantitativo con el que se caracterizan nuestras contribuciones[1,2]. Por todo ello, algunos de los trabajos publicados se consideran clásicos dentro del campo, pues en cierto modo definen el campo, y se reflejan en libros publicados recientemente. En la conferencia se analizarán ciertos pormenores de las investigaciones realizadas. El tipo de aplicaciones llevadas a cabo hasta la fecha se ilustrará mediante el estudio teórico del espectro electrónico de ciclooctatetraeno. Dando un paso más en la evolución de nuestra investigación, pretendemos en la actualidad describir, desde un formalismo teórico y al mismo nivel de exigencia, los mecanismos subyacentes que tienen lugar en las reacciones biológicas fototoinducidas, es decir, reacciones que se inician mediante la absorción de luz[3]. Como muestra de la caracterización de los procesos fotofísicos y fotoquímicos en fotobiología teórica, hemos elegido la descripción de la conversión interna ultrarrápida que tiene lugar en los cromóforos del ADN. Los estados excitados de las moléculas de los ácidos nucleicos presentan tiempos de vida media que se encuentran en el rango de sub-picosegundos, sugiriendo la presencia de un canal ultrarrápido de conversión interna, lo que normalmente se asocia en la fotoquímica contemporánea a una intersección cónica entre el estado excitado y el fundamental[4]. De esta forma nuestro ADN previene de forma eficaz posibles reacciones en el estado excitado y se revela como un excelente protector solar.

Merchán Bonete, M.

27

Ab initio density determination of subducting basalt  

Science.gov (United States)

High pressure and temperature experiments on glasses of compositions representative of mid-ocean ridge basalt (MORB) have demonstrated that, at temperatures and pressures corresponding to areas just below the transition zone, the basaltic portion of a subducting slab partitions into four or five phases: stishovite, Mg-perovskite, Ca-perovskite, and an aluminous, sodic phase with the Ca-ferrite structure, and possibly a new hexagonal aluminous phase (NAL). While thermoelastic properties of the first three phases have been well constrained throughout the mantle using various experimental and computational methods, resolution of the structures and thermoelastic properties of the Ca-ferrite and NAL minerals have been complicated by their complex solid solutions. Determination of the density profiles of these phases is important in understanding the buoyancy of subducting MORB as it approaches the transition zone. We present a computational structure determination using USPEX (Universal Structure Predictor: Evolutionary Xtallography) for end members of the Ca-ferrite and NAL phases. Thermoelastic parameters from ab initio Molecular Dynamics (MD) are then used to create density profiles for both minerals.

Thompson, M.; Weidner, D.

2009-12-01

28

An ab initio approach to organic photovoltaics  

Science.gov (United States)

Within the recent years, we have witnessed continual improvements in the Power Conversion Efficiencies (PCE) of organic photovoltaic devices. These improvements have been achieved by the discovery of new polymers which are being syntesised and their performance assessed experimentally. Scharber has introduced a simple model which determines the desired properties of polymers in order to achieve high PCE. An appealing alternative to the lengthy process of polymer synthesis consists in using ab initio calculations in order to predict the electronic structure of polymer candidates and evaluate the relevant properties in the determination of their PCE. In this work, Density Functional Theory (DFT) is being used to compute the optical band gap and HOMO / LUMO levels which, in conjunction with Scharber's model, allows to predict the efficiency of various polymer - fullerene blends. In order to assess the quality of such calculations and the validity of the model, we first compare the predictions with experimental device performances. We find that the model offers an indication as to what one should expect in terms of the maximum efficiency attainable experimentally. Lastly, we present new unsynthesised polymers which have shown promising results within this framework.

Gosselin, Vincent; Bérubé, Nicolas; Gaudreau, Josiane; Côté, Michel

2013-03-01

29

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; M.E. Fuentes; F. Espinosa; M. García; E. Macías; A. Durán; J. Siqueiros; L. Fuentes

2007-01-01

30

Ab Initio No-Core Shell Model  

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

31

Classical and ab initio preparation of organometallic model structures  

CERN Document Server

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

32

Ab Initio Simulation of Materials under Extreme Conditions  

Energy Technology Data Exchange (ETDEWEB)

The study of materials properties under extreme conditions has made considerable progress over the past decade due to both improvements in experimental techniques and advanced modeling methods. The availability of accurate models is crucial in order to analyze experimental 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 due to their ability to predict materials properties without the need for any experimental input. Ab initio simulations also allow for an exploration of materials properties in conditions that are unachievable using controlled experiments--such as e.g. the conditions prevailing in the core of large planets. In that limit, they constitute the only quantitative model of condensed matter available today. In this article, 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.

Gygi, F; Galli, G

2005-08-11

33

Real-world predictions from ab initio molecular dynamics simulations.  

UK PubMed Central (United Kingdom)

In this review we present the techniques of ab initio molecular dynamics simulation improved to its current stage where the analysis of existing processes and the prediction of further chemical features and real-world processes are feasible. For this reason we describe the relevant developments in ab initio molecular dynamics leading to this stage. Among them, parallel implementations, different basis set functions, density functionals, and van der Waals corrections are reported. The chemical features accessible through AIMD are discussed. These are IR, NMR, as well as EXAFS spectra, sampling methods like metadynamics and others, Wannier functions, dipole moments of molecules in condensed phase, and many other properties. Electrochemical reactions investigated by ab initio molecular dynamics methods in solution, on surfaces as well as complex interfaces, are also presented.

Kirchner B; di Dio PJ; Hutter J

2012-01-01

34

Real-world predictions from ab initio molecular dynamics simulations.  

Science.gov (United States)

In this review we present the techniques of ab initio molecular dynamics simulation improved to its current stage where the analysis of existing processes and the prediction of further chemical features and real-world processes are feasible. For this reason we describe the relevant developments in ab initio molecular dynamics leading to this stage. Among them, parallel implementations, different basis set functions, density functionals, and van der Waals corrections are reported. The chemical features accessible through AIMD are discussed. These are IR, NMR, as well as EXAFS spectra, sampling methods like metadynamics and others, Wannier functions, dipole moments of molecules in condensed phase, and many other properties. Electrochemical reactions investigated by ab initio molecular dynamics methods in solution, on surfaces as well as complex interfaces, are also presented. PMID:21842358

Kirchner, Barbara; di Dio, Philipp J; Hutter, Jürg

2012-01-01

35

Recent achievements in ab initio modelling of liquid water  

CERN Multimedia

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

36

Electron attachment to uracil. Theoretical ab initio study  

Energy Technology Data Exchange (ETDEWEB)

Ab initio calculations indicate that the uracil molecule can bind an electron and form a stable dipole-bound anion. The adiabatic electron affinity of this process is estimated to be only 0.003 15 hartree (0.086 eV). This study shows that the crucial factor which allows one to determine the electron efficiency of a polar molecule such as uracil in an ab initio calculation is a proper selection of the basis set. Without very diffused orbitals located on the positive side of the molecular dipole, the stable electronic states of the anion can be completely missed. 8 refs., 1 fig., 1 tab.

Oyler, N.A.; Adamowicz, L. (Univ. of Arizona, Tucson, AZ (United States))

1993-10-21

37

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

38

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.

M. Gautam; S. Tenguria; G. Misra

2011-01-01

39

Ab initio computations of photodissociation products of CFC alternatives  

Energy Technology Data Exchange (ETDEWEB)

Ab initio computations, have already been used to examine the energetics of the photodissociation of stratospheric chlorofluorocarbons. Our awn research has investigated the ab initio computation of vibrational frequencies and infrared intensities of CF{sub 3}CH{sub 2}F, CF{sub 3}CF{sub 2}H, and CF{sub 3}CH{sub 3}; continuing research will attempt to expand these computations to the energetics of the photodissociation of these molecules, since sane of the most common types of chlorofluorocarbon substitutes are hydrofluoroethanes.

Tai, S.; Illinger, K.H.; Kenny, J.E. [Tufts Univ., Medford, MA (United States)

1995-12-31

40

Ab initio structure determination using nano electron diffraction  

Digital Repository Infrastructure Vision for European Research (DRIVER)

This thesis is the summary of the development of electron diffraction into a mature method for ab initio structure determination. The progress is illustrated with the structure determination of some complicated unknown inorganic materials. The main step forwards is that it is now possible to apply e...

Xu, Q.

 
 
 
 
41

Ab initio study of structural and electronic properties of beryllium  

Energy Technology Data Exchange (ETDEWEB)

An ab initio calculation of the structural and electronic properties of beryllium is presented. The calculational method used is the self-consistent pseudopotential approach within the local-density-functional scheme. The calculated lattice constants, cohesive energy, bulk modulus, Poisson's ratio, electronic band structure, density of states, and charge density are all in good agreement with the experimental measurements.

Chou, M.Y.; Lam, P.K.; Cohen, M.L.

1983-10-15

42

Ab initio calculations in three-body cluster systems  

International Nuclear Information System (INIS)

In this work we briefly outline the extension of the ab initio no-core shell model/Resonating group method (NCSM/RGM) to three-body cluster states. We present the results for 6He ground state within a 4He+n+n cluster basis under this approach.

2013-06-10

43

Ab-initio calculations for dilute magnetic semiconductors  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Der Schwerpunkt dieser Arbeit sind ab-initio Rechnungen zu der elektronischen Struktur und den magnetischen Eigenschaften von verdünnten magnetischen Halbleitern (DMS). Ein besonderes Ziel ist es, die komplexen Austausch-Wechselwirkungen, die in diesen Systemen auftreten, zu verstehen. Unsere Rechnu...

Belhadji, Brahim

44

Ab initio rotation–vibration spectra of HCN and HNC  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We have calculated an ab initio HCN/HNC linelist for all transitions up to J=25 and 18 000 cm?1 above the zero point energy. This linelist contains more than 200 million lines each with frequencies and transition dipoles. The linelist has been calculated using our semi-global HCN/HNC VQZANO+PES and ...

Harris, G.J.; Polyansky, O.L.; Tennyson, J.

45

Ab initio calculations in three-body cluster systems  

Energy Technology Data Exchange (ETDEWEB)

In this work we briefly outline the extension of the ab initio no-core shell model/Resonating group method (NCSM/RGM) to three-body cluster states. We present the results for {sup 6}He ground state within a {sup 4}He+n+n cluster basis under this approach.

Romero-Redondo, C. [4004 Wesbrook Mall, Vancouver, British Columbia, V6T 2A3 (Canada); Navratil, P. [4004 Wesbrook Mall, Vancouver, British Columbia, V6T 2A3, Canada and Lawrence Livermore National Laboratory, P.O. Box 808, L-414, Livermore, CA 94551 (United States); Quaglioni, S. [Lawrence Livermore National Laboratory, P.O. Box 808, L-414, Livermore, CA 94551 (United States)

2013-06-10

46

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

47

Electronic excitations, spectroscopy and quantum transport from ab initio theory  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Spectroscopy and quantum transport constitute powerful ways to study the physics of matter and to access the electronic and atomic structure. Excitations, in turn determined by the electronic and atomic structure, lie at the origin of spectroscopy and quantum transport. Ab initio calculation of exci...

Olevano, Valerio

48

Ab initio simulation of dislocation cores in metals; Simulation ab initio des coeurs de dislocation dans les metaux  

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

49

Speed-up of ab initio hybrid Monte Carlo and ab initio path integral hybrid Monte Carlo simulations by using an auxiliary potential energy surface  

International Nuclear Information System (INIS)

[en] Efficiency of the ab initio hybrid Monte Carlo and ab initio path integral hybrid Monte Carlo methods is enhanced by employing an auxiliary potential energy surface that is used to update the system configuration via molecular dynamics scheme. As a simple illustration of this method, a dual-level approach is introduced where potential energy gradients are evaluated by computationally less expensive ab initio electronic structure methods. (author)

2009-01-01

50

Ab-initio modelling of defect properties in B2 NiAl  

Energy Technology Data Exchange (ETDEWEB)

The strongly ordering B2 phase of the intermetallic compound NiAl is known to be stable for a broad concentration range off its stoichiometry. Evidently this is due to the existence of constitutional defects. Experimental studies hav e shown that the dominant defect types in Al rich and Al poor parts of the B2 ph ase are Ni vacancies and Ni antisites (Ni atoms on the Al sublattice) respectively. We elucidate the ordering and ground state properties of defects in B2 NiAl on the basis of ab-initio calculations. We have applied the Cluster-Expansion (CE) formalism with Density Functional Theory (DFT) and the nudged elastic band method (as implemented within the computer code VASP) supplying the required input energies, as well as activation barriers for defect diffusion. Consistent with the existence of vacancies a full description of defects in NiAl bulk is only possible if vacancies are included by treating them as a third independent component within the CE formalism. One possible choice for a complete orthonormal basis set of point functions, required in such a ternary CE, are the first two Chebychev polynomials which were chosen in this case.

Lerch, Daniel; Doessel, Kerrin; Mueller, Stefan; Heinz, Klaus [Festkoerperphysik, Universitaet Erlangen-Nuernberg, Staudtstr. 7, D- 91058 Erlangen (Germany)

2007-07-01

51

Ab initio investigation of oxygen reduction on palladium and palladium-copper alloys as catalyst  

Energy Technology Data Exchange (ETDEWEB)

Platinum and other noble metals with their alloys are usually the favored electrocatalysts for the oxygen reduction reaction (ORR) in acid medium. By using the first principal calculations with palladium (Pd) copper (Cu) alloys, this study investigated the electronic reason which could explain the higher electro-activity of the alloys compared to a single metal. Based on calculations of Pt and PtCr{sub 3} for the ORR, the Ab initio program calculation VASP was used in order to determine the electronic point and the reasons why PdCu alloys show higher activity compared to palladium (Pd). ORR reaction presents many intermediate reactants that could be considered in this model. The adsorption energy analysis of these species on Pd, PdCu, Pd{sub 3}Cu and PdCu{sub 3} were presented and the reversible potential reduction of these species were discussed. The effect related to the adsorption of these intermediates was presented to the reversible potential. The reversible potential gap caused and used by the catalyst may be the first explanation on the difference in electro activity. In addition, the link between electrochemical parameter was shown to be the current exchange density and electronic parameter for an alloy. It was concluded that there is synergetic effect related to atomic composition of the alloys on the ORR. 3 refs., 1 tab., 4 figs.

Fouda-Onana, F.; Savadogo, O. [Ecole Polytechnique, Montreal, PQ (Canada). Laboratoire de nouveaux materiaux pour les systemes electrochimiques et energetiques

2006-07-01

52

Ab initio study of C14 laves phases in Fe-based systems  

Directory of Open Access Journals (Sweden)

Full Text Available Structural properties and energetics of Fe-based C14 Laves phases at various compositions (i.e. Fe2Fe, Fe2X, X2Fe, X2X, where X stands for Si, Cr, Mo, W, Ta) were investigated using the pseudopotential VASP (Vienna Ab initio Simulation Package) code employing the PAW-PBE (Projector Augmented Wave - Perdew Burke-Ernzerhof) pseudopotentials. Full relaxation was performed for all structures studied including the reference states of elemental constituents and the equilibrium structure parameters as well as bulk moduli were found. The structure parameters of experimentally found structures were very well reproduced by our calculations. It was also found that the lattice parameters and volumes of the unit cell decrease with increasing molar fraction of iron. Thermodynamic analysis shows that the Fe2X configurations of Laves phases are more stable than the X2Fe ones. Some of the X2Fe configurations are even unstable with respect to the weighted average of the Laves phases of elemental constituents. Our calculations predict the stability of Fe2Ta. On the other hand, Fe2Mo and Fe2W are slightly unstable (3.19 and 0.68 kJ.mol-1, respectively) and hypothetical structures Fe2Cr and Fe2Si are found unstable as well.

Pavlu J.; Šob M.

2012-01-01

53

Augmented wave ab initio EFG calculations: some methodological warnings  

International Nuclear Information System (INIS)

We discuss some accuracy aspects inherent to ab initio electronic structure calculations in the understanding of nuclear quadrupole interactions. We use the projector augmented wave method to study the electric-field gradient (EFG) at both Sn and O sites in the prototype cases SnO and SnO2. The term ab initio is used in the standard context of the also called first principles methods in the framework of the Density Functional Theory. As the main contributions of EFG calculations to problems in condensed matter physics are related to structural characterizations on the atomic scale, we discuss the 'state of the art' on theoretical EFG calculations and make a brief critical review on the subject, calling attention to some fundamental theoretical aspects.

2007-02-01

54

Ab Initio Calculations Of Light-Ion Reactions  

Energy Technology Data Exchange (ETDEWEB)

The exact treatment of nuclei starting from the constituent nucleons and the fundamental interactions among them has been a long-standing goal in nuclear physics. In addition to the complex nature of nuclear forces, one faces the quantum-mechanical many-nucleon problem governed by an interplay between bound and continuum states. In recent years, significant progress has been made in ab initio nuclear structure and reaction calculations based on input from QCD employing Hamiltonians constructed within chiral effective field theory. In this contribution, we present one of such promising techniques capable of describing simultaneously both bound and scattering states in light nuclei. By combining the resonating-group method (RGM) with the ab initio no-core shell model (NCSM), we complement a microscopic cluster approach with the use of realistic interactions and a microscopic and consistent description of the clusters. We discuss applications to light nuclei scattering, radiative capture and fusion reactions.

Navratil, P; Quaglioni, S; Roth, R; Horiuchi, W

2012-03-12

55

Serine Proteases an Ab Initio Molecular Dynamics Study  

CERN Document Server

In serine proteases (SP's), the H-bond between His-57 and Asp-102, and that between Gly-193 and the transition state intermediate play a crucial role for enzymatic function. To shed light on the nature of these interactions, we have carried out ab initio molecular dynamics simulations on complexes representing adducts between the reaction intermediate and elastase (one protein belonging to the SP family). Our calculations indicate the presence of a low--barrier H-bond between His-57 and Asp-102, in complete agreement with NMR experiments on enzyme--transition state analog complexes. Comparison with an ab initio molecular dynamics simulation on a model of the substrate--enzyme adduct indicates that the Gly-193--induced strong stabilization of the intermediate is accomplished by charge/dipole interactions and not by H-bonding as previously suggested. Inclusion of the protein electric field in the calculations does not affect significantly the charge distribution.

De Santis, L

1999-01-01

56

TiAl doping by vanadium: ab initio study  

International Nuclear Information System (INIS)

[en] Tetragonality degree in TiAl and vanadium doping effect on it were studied using the methods of calculation based on approximation of coherent potential and ab initio pseudopotentials. It is shown that vanadium substitution for Ti sublattice atoms entails increase in tetragonality degree but with substitution of the atoms in aluminium sublattice the tetragonality of the TiAl:V alloy decreases and at the content of vanadium about 8 at. % the lattice becomes actually cubical. In its turn, it may result in increase in TiAl ductility, the alloy being brittle at low temperatures[ru] ??????? ???????????????? ? TiAl ? ??????? ?? ??? ??????????? ???????? ??????????? ? ??????????? ??????? ???????, ?????????? ?? ??????????? ???????????? ?????????? ? ab initio ?????????????????. ????????, ??? ????????? ?????? ?????????? Ti ???????? ???????? ? ????? ??????? ????????????????, ?? ??? ????????? ?????? ? ??????????? ?????????? ???????????????? ?????? TiAl:V ??????????? ? ??? ?????????? ??????? ????? 8 ??. % ??????? ?????????? ??????????? ??????????. ??? ? ???? ??????? ????? ???????? ? ????????? ???????????? TiAl, ???????? ??? ?????? ????????????

2004-01-01

57

Ab initio calculations on porphyrins in the condensed phase  

Energy Technology Data Exchange (ETDEWEB)

Porphyrins are a promising class of materials for optical limiting applications, and in the condensed phase solvent effects have been shown to be significant. The authors report results with a method designed to simulate the effects of discrete solvent molecules, namely the effective fragment potential (EFP) approach which has been implemented for use in ab initio calculations. Further, a simulated annealing (SA) method has been implemented with the EFP solvation model in an attempt to solve the problem of multiple minima in clusters of molecules. The results with this method indicate some success on models of aqueous formamide and aqueous glutamic acid. Ab initio calculations can now be carried out on porphyrins, and the solvation methods are being updated for their use on these systems.

Day, P.N.; Wang, Z.; Pachter, R.

1998-07-01

58

Thermochemical data for CVD modeling from ab initio calculations  

Energy Technology Data Exchange (ETDEWEB)

Ab initio electronic-structure calculations are combined with empirical bond-additivity corrections to yield thermochemical properties of gas-phase molecules. A self-consistent set of heats of formation for molecules in the Si-H, Si-H-Cl, Si-H-F, Si-N-H and Si-N-H-F systems is presented, along with preliminary values for some Si-O-C-H species.

Ho, P. [Sandia National Labs., Albuquerque, NM (United States); Melius, C.F. [Sandia National Labs., Livermore, CA (United States)

1993-12-31

59

Ab initio studies of electromechanical effects in carbon nanotubes  

Scientific Electronic Library Online (English)

Full Text Available 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.

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

2002-06-01

60

GAUSSIAN 76: an ab initio molecular orbital program  

International Nuclear Information System (INIS)

[en] Gaussian 76 is a general-purpose computer program for ab initio Hartree-Fock molecular orbital calculations. It can handle basis sets involving s, p and d-type gaussian functions. Certain standard sets (STO-3G, 4-31G, 6-31G*, etc.) are stored internally for easy use. Closed shell (RHF) or unrestricted open shell (UHF) wave functions can be obtained. Facilities are provided for geometry optimization to potential minima and for limited potential surface scans

 
 
 
 
61

Application of ab initio methods to secondary lithium batteries  

Energy Technology Data Exchange (ETDEWEB)

Ab initio methods have started to be widely used in materials science for the prediction of properties of metals, alloys and compounds. These methods basically require only the atomic numbers of the constituent species. Such methods not only provide one with predictions of some of the properties of the material (even before synthesizing it) but also help one in understanding the phenomena that control those properties. The use of ab initio methods in the field of electrochemistry is, however, quite recent and rare. In this study, the authors demonstrate how ab initio methods can be used to investigate the properties of secondary lithium batteries. Particular examples will be given in predicting average insertion voltages in spinel Li-Mn and Li-Co oxides and in layered LiMO{sub 2} (M = Ti, V, Mn, Fe, Co and Al) compounds. Additionally, the stability of these compounds to metal reduction and structural stability of LiCoO{sub 2} upon lithium removal is investigated. They find that the oxygen anion plays an active role in the electrochemical intercalation of lithium. The amount of electron transfer to oxygen occurring upon lithium intercalation correlates strongly with the cell voltages. The more electron transfer to oxygen occurs, the higher lithium intercalation potential is obtained.

Aydinol, M.K.; Van Der Ven, A.; Ceder, G.

1998-07-01

62

Ab initio theories of nuclear structure and reactions  

Science.gov (United States)

The exact treatment of nuclei starting from the constituent nucleons and the fundamental interactions among them has been a long-standing goal in nuclear physics. In addition to the complex nature of nuclear forces with two-nucleon, three-nucleon and possibly even four-nucleon components, one faces the quantum-mechanical many-nucleon problem governed by an interplay between bound and continuum states. In recent years, significant progress has been made in ab initio nuclear structure and reaction calculations based on input from QCD employing Hamiltonians constructed within chiral effective field theory. I will discuss recent breakthroughs that allow for ab initio calculations for ground states and spectroscopy of nuclei throughout the p- and sd-shell and beyond with two- and three-nucleon interactions. I will highlight results obtained within the NCSM, CCM, QMC, and nuclear lattice EFT. I will also present new ab initio many-body approaches capable of describing both bound and scattering states in light nuclei simultaneously and discuss results for reactions important for astrophysics, such as ^7Be(p,?)^8B radiative capture, and for ^3H(d,n)^4He fusion.

Navratil, Petr

2012-10-01

63

Ab Initio Studies of Electronic Excitations in Real Solids  

CERN Multimedia

The first part of this article centers on the fact that key features of the dynamical response of weakly-correlated materials (the alkalis, Al), have been found experimentally to differ qualitatively from simple-model behavior. In the absence of ab initio theory, the surprises embodied in the experimental data were imputed to effects of dynamical correlations. We summarize results of ab initio investigations of linear response, performed within time-dependent density-functional theory (TDDFT), in which the unexpected features of the observed spectra are shown to be due to band-structure effects. Contrary to conventional wisdom, the response cannot be understood "universally," in terms of a simple scaling with the density, on going from metal to metal (e.g., through the alkali series) --even the shape of the dispersion curve for the plasmon energy is system-specific. The second part of this article starts out with the observation that a similar ab initio study of systems with more complex electronic structures...

Eguiluz, A G; Eguiluz, Adolfo G.; Ku, Wei

1999-01-01

64

Ab initio nuclear structure - the large sparse matrix eigenvalue problem  

International Nuclear Information System (INIS)

[en] The structure and reactions of light nuclei represent fundamental and formidable challenges for microscopic theory based on realistic strong interaction potentials. Several ab initio methods have now emerged that provide nearly exact solutions for some nuclear properties. The 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 1010 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 this large sparse matrix eigenvalue problem. We also outline the challenges that lie ahead for achieving further breakthroughs in fundamental nuclear theory using these ab initio approaches.

2009-07-01

65

Ab initio molecular dynamics simulations of Aluminum solvation  

CERN Multimedia

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

66

An ab initio study of the Rubidium clusters  

International Nuclear Information System (INIS)

Full text.Accurate calculations based on ab initio quantum mechanical method were carried out for small rubidium clusters Rbn (n=1-5) to determine their electronic and geometric structure. The detailed electronic structures of these clusters are studied. Stabilities from the point of view of binding and fragmentation energies are discussed. The LANL2DZ basis set is used for the optimization of molecular geometries. Geometries were optimized by minimizing the total energy within the KS (Kohn-Sham) formalism using the analytical technique. All computation were done by using Molpro program

2002-01-01

67

Ab initio computational study of 2-thioureidobenzoxazole molecule  

Science.gov (United States)

We have undertaken an ab initio computational study of 2-thioureidobenzoxazole based on the method of numeric localized atomic orbitals, pseudopotentials and DFT using SIESTA code. Electron Density of States, HOMOLUMO gap, formation energy, bond lengths and bond angles have been calculated. The bond lengths and bond angles are in close agreement with the experimental results reported earlier. It is also observed that the molecule is non magnetic and may behave as semiconductor as the HOMO-LUMO gap is 2.75827 eV.

Aditya, Pusala; Muthukumar, V. Sai; Sharma, Jyoti Dhar; Sundaresan, C. N.

2013-06-01

68

Ab initio thermodynamics of metals: Pt and Ru  

International Nuclear Information System (INIS)

We present ab initio calculation of thermodynamic properties of platinum and ruthenium. We show that the method based on quasiharmonic approximation and density-functional perturbation theory can be used to predict precisely thermodynamic properties of metals, from cubic metal Pt to hexagonal metal Ru. The former is so heavy that the spin-orbital coupling should be considered; the latter has anisotropic thermal expansion. Our results for the properties such as thermal expansion and heat capacities are in good agreement with available experimental data in a wide range of temperature.

2007-05-31

69

Shallow impurity level calculations in semiconductors using ab initio methods.  

Science.gov (United States)

An ab initio method is presented to calculate shallow impurity levels in bulk semiconductors. This method combines the GW calculation for the treatment of the central-cell potential with a potential patching method for large systems (with 64,000 atoms) to describe the impurity state wave functions. The calculated acceptor levels in Si, GaAs, and an isovalent bound state of GaP are in excellent agreement with experiments with a root-mean-square error of 8.4 meV. PMID:23679628

Zhang, Gaigong; Canning, Andrew; Grønbech-Jensen, Niels; Derenzo, Stephen; Wang, Lin-Wang

2013-04-19

70

Ab initio calculation of the static structural properties of Be  

Energy Technology Data Exchange (ETDEWEB)

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.

Chou, M.Y.; Lam, P.K.; Cohen, M.L. (California Univ., Berkeley (USA). Dept. of Physics; California Univ., Berkeley (USA). Lawrence Berkeley Lab.)

1982-06-01

71

Hydrogen Desorption from Mg Hydride: An Ab Initio Study  

Directory of Open Access Journals (Sweden)

Full Text Available Hydrogen desorption from hydride matrix is still an open field of research. By means of accurate first-principle molecular dynamics (MD) simulations an Mg–MgH2 interface is selected, studied and characterized. Electronic structure calculations are used to determine the equilibrium properties and the behavior of the surfaces in terms of structural deformations and total energy considerations. Furthermore, extensive ab-initio molecular dynamics simulations are performed at several temperatures to characterize the desorption process at the interface. The numerical model successfully reproduces the experimental desorption temperature for the hydride.

Simone Giusepponi; Massimo Celino

2012-01-01

72

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

73

Ab-Initio Shell Model with a Core  

Energy Technology Data Exchange (ETDEWEB)

We construct effective 2- and 3-body Hamiltonians for the p-shell by performing 12{h_bar}{Omega} ab initio no-core shell model (NCSM) calculations for A=6 and 7 nuclei and explicitly projecting the many-body Hamiltonians onto the 0{h_bar}{Omega} space. We then separate these effective Hamiltonians into 0-, 1- and 2-body contributions (also 3-body for A=7) and analyze the systematic behavior of these different parts as a function of the mass number A and size of the NCSM basis space. The role of effective 3- and higher-body interactions for A > 6 is investigated and discussed.

Lisetskiy, A F; Barrett, B R; Kruse, M; Navratil, P; Stetcu, I; Vary, J P

2008-06-04

74

Ab initio and classical molecular dynamics studies of electrode reactions  

International Nuclear Information System (INIS)

[en] A brief overview is given of some recent applications from our group of classical molecular dynamics (MD) and ab initio molecular dynamics (AIMD) simulations to the study of electrode reactions. Classical MD simulations are used to study solvent reorganization in outer-sphere electron transfer (ET) reactions, the first step in the oxygen reduction reaction, and ion transfer. AIMD simulations are used to study the structure of a water-vapor interface, and the mobility of solvated OH species on a Rh(111) surface by a proton transfer reaction between surface-bonded OH and a neighboring water molecule

2003-11-15

75

Ab initio and classical molecular dynamics studies of electrode reactions  

Energy Technology Data Exchange (ETDEWEB)

A brief overview is given of some recent applications from our group of classical molecular dynamics (MD) and ab initio molecular dynamics (AIMD) simulations to the study of electrode reactions. Classical MD simulations are used to study solvent reorganization in outer-sphere electron transfer (ET) reactions, the first step in the oxygen reduction reaction, and ion transfer. AIMD simulations are used to study the structure of a water-vapor interface, and the mobility of solvated OH species on a Rh(111) surface by a proton transfer reaction between surface-bonded OH and a neighboring water molecule.

Hartnig, Christoph; Vassilev, Peter; Koper, Marc T.M

2003-11-15

76

Ab initio electronic structure of rare earth orthoferrites  

International Nuclear Information System (INIS)

Ab initio FP-APW+lo calculations were performed for the rare earth orthoferrites RFeO3 with R=La, Nd, Sm, Gd, Dy, Lu using the well-known WIEN2k package. Ferromagnetic and antiferromagnetic alignments between the iron moments were studied using the GGA (PBE) functional for the exchange-correlation energy. Antiferromagnetic structures are energetically favoured in all cases. Except for SmFeO3, all antiferromagnetic configurations are insulators, while the ferromagnetic ones give metals except for LaFeO3 and LuFeO3. Hyperfine fields at the iron sites agree with experiment to within 25%.

2005-01-01

77

Ab initio electronic structure of rare earth orthoferrites  

Energy Technology Data Exchange (ETDEWEB)

Ab initio FP-APW+lo calculations were performed for the rare earth orthoferrites RFeO{sub 3} with R=La, Nd, Sm, Gd, Dy, Lu using the well-known WIEN2k package. Ferromagnetic and antiferromagnetic alignments between the iron moments were studied using the GGA (PBE) functional for the exchange-correlation energy. Antiferromagnetic structures are energetically favoured in all cases. Except for SmFeO{sub 3}, all antiferromagnetic configurations are insulators, while the ferromagnetic ones give metals except for LaFeO{sub 3} and LuFeO{sub 3}. Hyperfine fields at the iron sites agree with experiment to within 25%.

Iglesias, M. [Dpto. Fisica Aplicada, Fac. Fisica, Universidade Santiago de Compostela, E-15782, Santiago de Compostela (Spain)]. E-mail: famoises@usc.es; Rodriguez, A. [Dpto. Fisica Aplicada, Fac. Fisica, Universidade Santiago de Compostela, E-15782, Santiago de Compostela (Spain); Blaha, P. [Technical University of Vienna, Getreidemarkt 9/165, A-1060 Vienna (Austria); Pardo, V. [Dpto. Fisica Aplicada, Fac. Fisica, Universidade Santiago de Compostela, E-15782, Santiago de Compostela (Spain); Baldomir, D. [Dpto. Fisica Aplicada, Fac. Fisica, Universidade Santiago de Compostela, E-15782, Santiago de Compostela (Spain); Pereiro, M. [Dpto. Fisica Aplicada, Fac. Fisica, Universidade Santiago de Compostela, E-15782, Santiago de Compostela (Spain); Botana, J. [Dpto. Fisica Aplicada, Fac. Fisica, Universidade Santiago de Compostela, E-15782, Santiago de Compostela (Spain); Arias, J.E. [Inst. Investigacions Tecnoloxicas, Universidade Santiago de Compostela, E-15782, Santiago de Compostela (Spain); Schwarz, K. [Technical University of Vienna, Getreidemarkt 9/165, A-1060 Vienna (Austria)

2005-04-15

78

Ab-initio Study of Small Silver Nanoclusters  

International Nuclear Information System (INIS)

We explore the lowest energy structures and investigate the structural and electronic properties of small AgN (N = 1-10) clusters by employing an ab-initio self-consistent density functional method in the local density approximation. The calculation of binding energy, bond length and the energy difference of HOMO-LUMO states have been carried out in a large energy interval for different isomeric forms of Ag clusters. The cluster binding energies increases rapidly with cluster size, which is consistent with the size dependence properties of clusters but our values are slightly higher than the other calculations.

2004-01-01

79

Ab initio simulation of high-temperature liquid selenium  

CERN Document Server

Ab initio molecular dynamics simulation is used to investigate the structure and dynamics of liquid Se at temperatures of 870 and 1370~K. The calculated static structure factor is in excellent agreement with experimental data. The calculated radial distribution function gives a mean coordination number close to 2, but we find a significant fraction of one-fold and three-fold atoms, particularly at 1370~K, so that the chain structure is considerably disrupted. The self-diffusion coefficient has values ($\\sim 1 \\times 10^{-8}$~m~s$^{-1}$) typical of liquid metals.

Kirchhoff, F; Holender, J M

1995-01-01

80

Ab initio absorption spectra and optical gaps in nanocrystalline silicon.  

UK PubMed Central (United Kingdom)

The optical absorption spectra of Si(n)H(m) nanoclusters up to approximately 250 atoms are computed using a linear response theory within the time-dependent local density approximation (TDLDA). The TDLDA formalism allows the electronic screening and correlation effects, which determine exciton binding energies, to be naturally incorporated within an ab initio framework. We find the calculated excitation energies and optical absorption gaps to be in good agreement with experiment in the limit of both small and large clusters. The TDLDA absorption spectra exhibit substantial blueshifts with respect to the spectra obtained within the time-independent local density approximation.

Vasiliev I; O?üt S; Chelikowsky JR

2001-02-01

 
 
 
 
81

Ab Initio and Ab Exitu No-Core Shell Model  

Energy Technology Data Exchange (ETDEWEB)

We outline two complementary approaches based on the no core shell model (NCSM) and present recent results. In the ab initio approach, nuclear properties are evaluated with two-nucleon (NN) and three-nucleon interactions (TNI) derived within effective field theory (EFT) based on chiral perturbation theory (ChPT). Fitting two available parameters of the TNI generates good descriptions of light nuclei. In a second effort, an ab exitu approach, results are obtained with a realistic NN interaction derived by inverse scattering theory with off-shell properties tuned to fit light nuclei. Both approaches produce good results for observables sensitive to spin-orbit properties.

Vary, J P; Navratil, P; Gueorguiev, V G; Ormand, W E; Nogga, A; Maris, P; Shirokov, A

2007-10-02

82

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

International Nuclear Information System (INIS)

[en] 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 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)[de] Die Genauigkeit von ab-initio Dichtefunktional Rechnungen haengt entscheidend von den verwendeten Austausch-Korrelations Funktionalen ab. In letzter Zeit hat sich hierbei, vor allem in der Quantenchemie, ein regelrechter Funktional-Zoo herausgebildet. All diese Entwicklungen haben zum Ziel, die Beschreibung der physikalischen Eigenschaften von Molekuelen, Festkoerpern und Oberflaechen zu verbessern. Im ersten Teil dieser Dissertation werden vier verschiedene Austausch-Korrelations Funktionale (LDA, PBE, PBEsol, HSE03) an zwei Perovskiten, SrTiO3 und BaTiO3, getestet. Dabei werden strukturelle, elektronische und phononische Eigenschaften in der kubischen und tetragonal verzerrten Phase berechnet, mit besonderer Augenmerk auf die zonen-zentrierte Phononenmode. Unsere Ergebnisse zeigen, dass die ferroelektrische Instabilitaet stark vom Volumen, jedoch kaum vom verwendeten Funktional abhaengt. Der zweite Teil dieser Arbeit ist der Beschreibung polarer Oberflaechen, insbesondere jener von ZnO, gewidmet. Im Rahmen einer einfachen ionischen Beschreibung erweisen sich beide Oberflaechen als instabil, aufgrund der divergierenden elektrostatischen Energie. Die Oberflaechen muessen daher eine modifizierte Oberflaechenstruktur annehmen. Wir schlagen in enger Anlehnung an experimentelle Befunde ein neues Modell vor. Dabei stellt sich heraus, dass sich die Sauerstoff begrenzte Oberflaeche anders verhaelt als die Zink begrenzte Oberflaeche. Dieser Unterschied kann durch das verschiedene Bindungsverhalten der Zink- und der Sauerstoffatome erklaert werden: die d-Elektronen im Zink sind flexibler als die p-Elektronen im Sauerstoff. Der letzte Teil dieser Dissertation beschaeftigt sich mit der Implementierung eines lokalen Basissatzes in VASP. Alle fuer die PAW-Methode notwendigen Formeln werden abgeleitet. Der lokale Basissatz wird nach sphaerischen Besselfunktionen entwickelt. Besonderes Augenmerk wird auf den Erhalt der Translationsinvarianz des Hamiltonoperators gelegt. Der Basissatz wird dahingehend optimiert, dass dieses Ziel erreicht wird. Dies wird anha

2010-01-01

83

TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders.  

UK PubMed Central (United Kingdom)

UNLABELLED: We describe two new Generalized Hidden Markov Model implementations for ab initio eukaryotic gene prediction. The C/C++ source code for both is available as open source and is highly reusable due to their modular and extensible architectures. Unlike most of the currently available gene-finders, the programs are re-trainable by the end user. They are also re-configurable and include several types of probabilistic submodels which can be independently combined, such as Maximal Dependence Decomposition trees and interpolated Markov models. Both programs have been used at TIGR for the annotation of the Aspergillus fumigatus and Toxoplasma gondii genomes. AVAILABILITY: Source code and documentation are available under the open source Artistic License from http://www.tigr.org/software/pirate

Majoros WH; Pertea M; Salzberg SL

2004-11-01

84

Ab initio investigation of the oxygen reduction reaction (ORR) on palladiumiron catalysts  

Energy Technology Data Exchange (ETDEWEB)

The Density Functional Theory (DFT) in a Vienna Ab initio Simulation Package (VASP) was used to perform theoretical calculations of the adsorption and activation energies of the species involved in the limiting path of the oxygen reduction reaction (ORR) on platinum (Pt) and palladium (Pd) alloys. Recent calculations have shown that the ORR may proceed through the successive electroreductions of Pt-O2 to Pt-OOH, Pt-OOH to Pt-(OH)2, Pt-(OH)2 to Pt-OH and Pt-OH to Pt-OH2 rather than through the oxide pathway involving the successive electro-reductions of Pt-O2 to Pt-OOH, Pt-OOH to Pt-O, Pt-O to Pt-OH and Pt-OH to Pt-OH2. This study calculated the total energy of each of the intermediates, namely (MO2); (M-OOH); (M-O); (M-(OH)2); and, (M-OH2 ), where M is Pt, Pd and iron (Fe). The adsorption energy analysis of these species on Pd, Pd-Fe, Pd{sub 3}Fe and PdFe{sub 3} was presented according to calculation results. The relationship between the reversible potential values of these species and their associated adsorption was also determined. The correlations between these theoretical catalyst values and the difference in electro-catalytic activity were investigated with reference to changes in electronic intrinsic parameters of the alloys and surface properties. These parameters were used to interpret basic conditions of electro-catalysis of the oxygen reduction reaction.

Savadogo, O.; Fouda-Onama, F. [Ecole Polytechnique, Montreal, PQ (Canada). Laboratoire de nouveaux materiaux pour les systemes electrochimiques et energetiques

2006-07-01

85

Ab initio reaction paths and direct dynamics calculations  

Energy Technology Data Exchange (ETDEWEB)

A detailed study of methods for generating the minimum energy path of a chemical reaction using ab initio electronic structure calculations is presented; the convergence with respect to step size of the geometry and energy along this path is studied with several algorithms. The investigations are extended to the calculation of chemical reaction rate coefficients by interfacing the polyrate code for variational transition-state theory and semiclassical tunneling calculations with a locally modified Gaussian 82 electronic structure package that now contains reaction path following capabilities at both the Hartree-Fock and perturbation theory levels. This combined package is used to study the kinetics of the abstraction reaction CH{sub 3} + H{sub 2} {yields} CH{sub 4} + H, which is considered as a prototype organic reaction. They report calculations of reaction rates based on electronic structure theory and generalized transition-state theory, including a multidimensional tunneling correction, without performing an analytic fit to the potential surface. The calculation of dynamical processes directly from ab initio electronic structure input without the intermediary of a potential surface fit is called direct dynamics, and this paper demonstrates the feasibility of this approach for bimolecular reactions.

Baldridge, K.K.; Gordon, M.S. (North Dakota State Univ., Fargo (USA)); Steckler, R.; Truhlar, D.G. (Univ. of Minnesota, Minneapolis (USA))

1989-06-29

86

Ab Initio Studies of Liquid and Amorphous Ge  

CERN Multimedia

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 boundary conditions, and calculate averages over runs of up to 16 ps. The calculated liquid S(k,omega) agrees qualitatively with that obtained by Hosokawa et al, using inelastic X-ray scattering. In a-Ge, we find that the calculated S(k,omega) is in qualitative agreement with that obtained experimentally by Maley et al. Our results suggest that the ab initio approach is sufficient to allow approximate calculations of S(k,omega) in both liquid and amorphous materials.

Chai, J D

2004-01-01

87

Ab Initio and Analytic Intermolecular Potentials for Ar-CF?  

Energy Technology Data Exchange (ETDEWEB)

Ab initio calculations at the CCSD(T) level of theory are performed to characterize the Ar ? CF ? intermolecular potential. Extensive calculations, with and without a correction for basis set superposition error (BSSE), are performed with the cc-pVTZ basis set. Additional calculations are performed with other correlation consistent (cc) basis sets to extrapolate the Ar---CF?potential energy minimum to the complete basis set (CBS) limit. Both the size of the basis set and BSSE have substantial effects on the Ar + CF? potential. Calculations with the cc-pVTZ basis set and without a BSSE correction, appear to give a good representation of the potential at the CBS limit and with a BSSE correction. In addition, MP2 theory is found to give potential energies in very good agreement with those determined by the much higher level CCSD(T) theory. Two analytic potential energy functions were determined for Ar ? CF?by fitting the cc-pVTZ calculations both with and without a BSSE correction. These analytic functions were written as a sum of two body potentials and excellent fits to the ab initio potentials were obtained by representing each two body interaction as a Buckingham potential.

Vayner, Grigoriy; Alexeev, Yuri; Wang, Jiangping; Windus, Theresa L.; Hase, William L.

2006-03-09

88

Toward optimal fragment generations for ab initio protein structure assembly.  

UK PubMed Central (United Kingdom)

Fragment assembly using structural motifs excised from other solved proteins has shown to be an efficient method for ab initio protein-structure prediction. However, how to construct accurate fragments, how to derive optimal restraints from fragments, and what the best fragment length is are the basic issues yet to be systematically examined. In this work, we developed a gapless-threading method to generate position-specific structure fragments. Distance profiles and torsion angle pairs are then derived from the fragments by statistical consistency analysis, which achieved comparable accuracy with the machine-learning-based methods although the fragments were taken from unrelated proteins. When measured by both accuracies of the derived distance profiles and torsion angle pairs, we come to a consistent conclusion that the optimal fragment length for structural assembly is around 10, and at least 100 fragments at each location are needed to achieve optimal structure assembly. The distant profiles and torsion angle pairs as derived by the fragments have been successfully used in QUARK for ab initio protein structure assembly and are provided by the QUARK online server at http://zhanglab.ccmb. med.umich.edu/QUARK/.

Xu D; Zhang Y

2013-02-01

89

Summation of Parquet diagrams as an ab initio method in nuclear structure calculations  

International Nuclear Information System (INIS)

Research highlights: ? We present a Green's function based approach for doing ab initio nuclear structure calculations. ? In particular the sum the subset of so-called Parquet diagrams. ? Applying the theory to a simple but realistic model, results in good agreement with other ab initio methods. ? This opens up for ab initio calculations for medium-heavy nuclei. - Abstract: In this work we discuss the summation of the Parquet class of diagrams within Green's function theory as a possible framework for ab initio nuclear structure calculations. The theory is presented and some numerical details are discussed, in particular the approximations employed. We apply the Parquet method to a simple model, and compare our results with those from an exact solution. The main conclusion is that even at the level of approximation presented here, the results shows good agreement with other comparable ab initio approaches.

2011-01-01

90

Atmospheric oxidation of trichloroethylene: an ab initio study.  

UK PubMed Central (United Kingdom)

The atmospheric oxidation of trichloroethylene has previously been studied experimentally. Phosgene is thought to be the dominant product, although the mechanism of production is not well understood. Additionally, studies omitting a chlorine scavenger show the production of dichloroacetyl chloride. This influence of the chlorine atom on the trichloroethylene oxidation is not well understood. Using ab initio methods, this study presents a comprehensive computational study of both the hydroxyl radical and chlorine atom initiated atmospheric oxidation mechanisms of trichloroethylene (C(2)HCl(3)). Potential energy surfaces, including activation energies and enthalpies, are determined. The results from this study, in connection with experimental work, confirm the influence of the Cl-initiated oxidation in determining the product profile of the trichloroethylene oxidation. These products include dichloroacetyl chloride [Cl(2)CHC(O)Cl], formyl chloride [CH(O)Cl], phosgene [C(O)Cl(2)], and regeneration of the chlorine atom.

Christiansen CJ; Francisco JS

2010-09-01

91

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 (d)method. 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; QIWEN TENG; SHI WU

2007-01-01

92

Ab initio description of the exotic unbound 7He nucleus.  

UK PubMed Central (United Kingdom)

The neutron-rich unbound 7He nucleus has been the subject of many experimental investigations. While the ground-state 3/2- resonance is well established, there is a controversy concerning the excited 1/2- resonance reported in some experiments as low lying and narrow (E(R)?1??MeV, ??1??MeV) while in others as very broad and located at a higher energy. This issue cannot be addressed by ab initio theoretical calculations based on traditional bound-state methods. We introduce a new unified approach to nuclear bound and continuum states based on the coupling of the no-core shell model, a bound-state technique, with the no-core shell model combined with the resonating-group method, a nuclear scattering technique. Our calculations describe the ground-state resonance in agreement with experiment and, at the same time, predict a broad 1/2- resonance above 2 MeV.

Baroni S; Navrátil P; Quaglioni S

2013-01-01

93

Ab initio theory of NMR chemical shifts in solids  

Energy Technology Data Exchange (ETDEWEB)

A new formalism for ab initio calculation of the orbital magnetic susceptibility and the NMR chemical shifts in solids and liquids is presented. The 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. The formalism is based on the density functional theory in the local density approximation and makes use of a generalized f-sum rule to eliminate the divergent terms that plagued previous theories. Calculations have been successfully carried out for the diamagnetic susceptibility of a number of insulators and for the NMR chemical shifts of a variety of systems including free molecules, ionic crystals, hydrogen-bonded materials and amorphous carbon.

Louie, S.G. [Univ. of California, Berkeley, CA (United States)]|[Lawrence Berkeley National Lab., CA (United States)

1997-12-31

94

Electron transport through heterocyclic molecule: ab initio molecular orbital theory  

Energy Technology Data Exchange (ETDEWEB)

We have calculated the electron transport properties of molecule wires by an ab initio molecule orbital theory on the basis of the first-principles density functional theory (DFT) and the non-equilibrium Green function (NEGF) technique. The wires are made of heterocyclic molecule (furan, thiophene, and pyrrole, shown in first figure), in contact with the atomic scale Au electrodes. The results of our calculation reveal: (1) the furan has a much high conductance in contrast to the others and (2) the heteroatom can significantly affect the transport property by changing electronic structure of the heterocyclic molecule. We find the step-like I-V feature qualitative agreement with the experimental findings.

Cheng, W.W.; Liao, Y.X.; Chen, H.; Note, R.; Mizuseki, H.; Kawazoe, Y

2004-06-14

95

Ab initio theory of spin-transfer torques  

Energy Technology Data Exchange (ETDEWEB)

We develop an ab initio material-specific theory of current induced magnetization switching. The formulation is based on non-equilibrium Green's functions (NEGF) formalism applied to the so-called spin-mixing conductance, i.e., the linear response of the spin torque exerted on a magnetic layer to a spin accumulation in an adjacent non-magnetic layer. The numerical implementation employs the local spin density approximation (LSDA) and the linear muffin-tin orbital (LMTO) method. Possible substitutional disorder is treated using the coherent potential approximation (CPA) that allows for evaluation of the coherent (ballistic) and incoherent (diffusive) parts of the spin-mixing conductance. The developed scheme is applied to a few selected magnetic layers including systems containing diluted magnetic semiconductors and Heusler alloys. Their halfmetallic character leads to enhanced spin-mixing conductances with respect to charge conductances.

Carva, Karel [Charles University, Faculty of Mathematics and Physics, Department of Condensed Matter Physics, Ke Karlovu 5, CZ-12116 Prague 2 (Czech Republic)]. E-mail: carva@karlov.mff.cuni.cz; Turek, Ilja [Institute of Physics of Materials, Academy of Sciences of the Czech Republic, Zizkova 22, CZ-61662 Brno (Czech Republic)

2007-09-15

96

Ab initio theory of spin-transfer torques  

International Nuclear Information System (INIS)

We develop an ab initio material-specific theory of current induced magnetization switching. The formulation is based on non-equilibrium Green's functions (NEGF) formalism applied to the so-called spin-mixing conductance, i.e., the linear response of the spin torque exerted on a magnetic layer to a spin accumulation in an adjacent non-magnetic layer. The numerical implementation employs the local spin density approximation (LSDA) and the linear muffin-tin orbital (LMTO) method. Possible substitutional disorder is treated using the coherent potential approximation (CPA) that allows for evaluation of the coherent (ballistic) and incoherent (diffusive) parts of the spin-mixing conductance. The developed scheme is applied to a few selected magnetic layers including systems containing diluted magnetic semiconductors and Heusler alloys. Their halfmetallic character leads to enhanced spin-mixing conductances with respect to charge conductances.

2007-01-01

97

Equations of state of heavy metals: ab initio approaches  

International Nuclear Information System (INIS)

[en] The determination of equations of states of heavy metals through ab initio calculation, i.e. without any adjustable parameter, allows to access to pressure and temperature thermodynamic conditions sometimes inaccessible to experiment. To perform such calculations, density functional theory (DFT) is a good starting point: when electronic densities are homogeneous enough, the local density approximation (LDA) remarkably accounts for thermodynamic properties of heavy metals, such as tantalum, or the light actinides, as well for static properties - equilibrium volume, elastic constants - as for dynamical quantities like phonon spectra. For heavier elements, like neptunium or plutonium, relativistic effects and strong electronic interactions must be taken into account, which requires more sophisticated theoretical approaches. (authors)

2005-01-01

98

Ab initio methods for electron-molecule collisions  

Energy Technology Data Exchange (ETDEWEB)

This review concentrates on the recent advances in treating the electronic aspect of the electron-molecule interaction and leaves to other articles the description of the rotational and vibrational motions. Those methods which give the most complete treatment of the direct, exchange, and correlation effects are focused on. Such full treatments are generally necessary at energies below a few Rydbergs (approx. = 60 eV). This choice unfortunately necessitates omission of those active and vital areas devoted to the development of model potentials and approximate scattering formulations. The ab initio and model approaches complement each other and are both extremely important to the full explication of the electron-scattering process. Due to the rapid developments of recent years, the approaches that provide the fullest treatment are concentrated on. 81 refs.

Collins, L.A.; Schneider, B.I.

1987-01-01

99

A hydronitrogen solid: high pressure ab initio evolutionary structure searches  

Energy Technology Data Exchange (ETDEWEB)

High pressure ab initio evolutionary structure searches resulted in a hydronitrogen solid with a composition of (NH){sub 4}. The structure searches also provided two molecular isomers, ammonium azide (AA) and trans-tetrazene (TTZ) which were previously discovered experimentally and can be taken as molecular precursors for high pressure synthesis of the hydronitrogen solid. The computed pressure versus enthalpy diagram showed that the transformation pressure to the hydronitrogen solid is 36 GPa from AA and 75 GPa from TTZ. Its metastability was analyzed by the phonon dispersion spectrum and room-temperature vibrational density of state together with the transformation energy barrier back to molecular phases at 298 K. The predicted energy barrier of 0.21 eV/atom means that the proposed hydronitrogen solid should be very stable at ambient conditions. (fast track communication)

Hu Anguang; Zhang Fan, E-mail: Anguang.Hu@drdc-rddc.gc.ca [Defence Research and Development Canada-Suffield, PO Box 4000 Stn Main, Medicine Hat, AB, T1A 8K6 (Canada)

2011-01-19

100

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

 
 
 
 
101

An Efficient Approach to Ab Initio Monte Carlo Simulation  

CERN Multimedia

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

102

Self-vacancies in Gallium Arsenide: an ab initio calculation  

CERN Document Server

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

103

Symplectic ab initio no-core shell model  

Energy Technology Data Exchange (ETDEWEB)

The present study confirms the significance of the symplectic Sp(3,R) symmetry in nuclear dynamics as unveiled, for the first time, by examinations of realistic nucleon-nucleon interactions as well as of eigenstates calculated in the framework of the ab initio No-Core Shell Model (NCSM). The results reveal that the NCSM wave functions for light nuclei highly overlap (at the {approx} 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 JISP 16 and CD-Bonn realistic nucleon-nucleon interactions, which points to a more fundamental origin of the symplectic symmetry. (Author)

Draayer, J. P.; Dytrych, T.; Sviratcheva, K. D.; Bahri, C. [Department of Physics and Astronomy, Lousiana State University, Baton Rouge, 70803 Lousiana (United States); Vary, J. P. [Department of Physics and Astronomy, Iowa State University, Ames, 50011 Iowa (United States)

2008-12-15

104

Ab initio study of II-(VI)2 dichalcogenides  

Science.gov (United States)

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 ZnTe2 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.

Olsson, P.; Vidal, J.; Lincot, D.

2011-10-01

105

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

UK PubMed Central (United Kingdom)

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.

Olsson P; Vidal J; Lincot D

2011-10-01

106

Ab-initio melting curve and principal Hugoniot of tantalum  

International Nuclear Information System (INIS)

[en] We report first principles calculations of the melting curve and principal Hugoniot (P - V curve) of body centered cubic (bcc) tantalum in the pressure range 0-300 GPa. A description of lattice dynamics and thermal properties of bcc Ta using finite temperature density functional theory (DFT) is presented. The approach works within the projector augmented wave (PAW) implementation of DFT and explicitly treats in valence the 5p, 6s and 5d electrons. The principal Hugoniot (P - V curve), obtained using the Rankine-Hugoniot equation, is investigated using the generalized gradient approximations (GGA). Very good agreement with the shock experiments is obtained with GGA in all the range of pressure. We also report the temperature-pressure relation on the shock Hugoniot and the full ab-initio melting curve of Ta

2008-01-01

107

Ab initio study on the photochemical isomerization of furan derivatives  

UK PubMed Central (United Kingdom)

The photochemical isomerization reactions of furan, 2-methylfuran, 2-trimethylsilylfuran, and furan-2-carbonitrile were studied using ab initio methods. The results are in agreement with the previously reported data obtained through semiempirical methods. In particular, the sensitized irradiation of furan derivatives populates the first excited triplet state of the furan, and this triplet state can evolve only through O-Ca cleavage. The selection of the bond to be broken can depend on energetic factors (furan-2-carbonitrile) or on kinetic factors (2-methylfuran, 2-trimethylsilylfuran). The direct irradiation of furan derivatives populates the singlet excited state and leads to a conversion into the Dewar isomer or into the corresponding triplet state through the usual intersystem crossing procedure. The efficiency of these processes determines the presence or the absence of isomerized furan derivatives in the reaction mixtures.

D'Auria M

2000-04-01

108

Ab initio pseudopotential calculations of carbon impurities in Si  

Energy Technology Data Exchange (ETDEWEB)

Ab initio planewave pseudopotential method is used to study carbon diffusion and pairing in crystalline silicon. The calculation is performed with a 40 Ry planewave cutoff and 2x2x2 special k-point sampling with a supercell of 64 atoms. It is found that substitutional carbon attracts interstitial Si forming a <001> C interstitial with a large binding energy of 1.45 eV. The interstitial carbon is mobile and can migrate with a migration energy of 0.5 eV. The interstitial carbon can bind further to another substitutional carbon forming a substitutional carbon-interstitutional carbon pair with a binding energy of 1.0 eV. This model is used to understand the effect of high C concentration on the transient enhanced diffusion in Si.

Zhu, J.; Diaz de la Rubia, T.; Mailhiot, C. [Lawrence Livermore National Lab., CA (United States)

1997-11-01

109

Ab initio interatomic potentials of cubic boron nitride  

Energy Technology Data Exchange (ETDEWEB)

Chen's lattice inversion method is extended to calculate the interatomic potentials of the zinc-blende-type binary compounds with a virtual lattice technique, which proposes a scheme to obtain non-empirical interatomic potentials from first principle calculations. In this paper, the interatomic pair potentials PHI{sub N-N}, PHI{sub B-B} and PHI{sub B-N} are obtained from the ab initio cohesive energy curves relevant to the three distinct BN structures. The modified Stillinger-Weber (MSW) three-body potentials are determined by the dependence of the total energy on the lattice distortion. Based on the calculated interatomic potentials, the structural properties and lattice dynamics of cubic boron nitride (c-BN) have been evaluated.

Liu Ying; Kang Yanmei; Chen Nanxian

2003-02-03

110

Ab initio calculations for the photoelectron spectra of vanadium clusters.  

UK PubMed Central (United Kingdom)

We report ab initio calculations for the electronic and structural properties of V(n), V(n) (-), and V(n) (+) clusters up to n=8. We performed the calculations using a real-space pseudopotential method based on the local spin density approximation for exchange and correlation. This method assumes no explicit basis. Wave functions are evaluated on a uniform grid; only one parameter, the grid spacing, is used to control convergence of the electronic properties. Charged states are easily handled in real space, in contrast to methods based on supercells where Coulombic divergences require special handling. For each size and charge state, we find the lowest energy structure. Our results for the photoelectron spectra, using the optimized structure, agree well with those obtained by experiment. We also obtain satisfactory agreement with the measured ionization potential and electron affinity, and compare our results to calculations using an explicit basis.

Li S; Alemany MM; Chelikowsky JR

2004-09-01

111

Ab Initio Calculations of Co Shielding in Model Complexes  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract: Recent ab initio calculations of cobalt NMR shielding show that DFT-GIAO calculations using hybrid functionals are found to reproduce experimental values well. This method is used to calculate the variation of the cobalt NMR shielding tensor of sqaure pyramidal nitrosyl complexes with respect to the CoNO geometry and to differing basal ligands. The isotropic shielding is shown to have a large negative derivative with respect to CoX distance where X is a ligating atom.; the derivative with respect to NO distance is smaller but still significant. The zz component where z is along the CoN(NO) bond is more sensitive to the basal ligands but the other two principal components are sensitive to the CoNO geometry.

Elaine A. Moore

2002-01-01

112

Ab-Initio No-Core Shell Model  

Energy Technology Data Exchange (ETDEWEB)

We discuss the no-core shell model approach, an ab initio method with effective Hamiltonians derived from realistic nucleon-nucleon (NN) potentials as a function of the finite harmonic-oscillator (HO) basis space. We present results for three and four nucleon systems in model spaces that include up to 50{Dirac_h}{Omega} and 18{bar h}{Omega} HO excitations, respectively. For these light systems we are in agreement with results obtained by other exact methods. Also, we calculate the properties of {sup 6}Li and {sup 6}He in model spaces up to 10{Dirac_h}{Omega}, and of {sup 12}C for model spaces up to 6{Dirac_h}{Omega}.

Barrett, B R; Navratil, P; Vary, J P; Ormand, W E

2001-03-02

113

Ab initio calculation of formation enthalpies of ZrAl{sub 3} and HfAl{sub 3} compounds; Calcul ab initio des enthalpies de formation des composes ZrAl{sub 3} et HfAl{sub 3}  

Energy Technology Data Exchange (ETDEWEB)

The relative stabilities of L1{sub 2}, D0{sub 22}, and D0{sub 23} structures in ZrAl{sub 3} and HfAl{sub 3} compounds are investigated employing the Vienna ab initio simulation package (VASP). In ZrAl{sub 3} and HfAl{sub 3} compounds, the energetic effects related to the tetragonal distortion are important and lead to the stabilization of the D0{sub 22} and D0{sub 23} structures with respect to the L1{sub 2} structure. The effect of the cell internal displacements of the atoms in the D0{sub 23} structure is studied. In the case of the HfAl{sub 3} compound, the D0{sub 23} structure appears as the most stable structure after this last stage of relaxations. In the case of ZrAl{sub 3} compound, the D0{sub 23} structure is the most stable structure in both distorted and fully relaxed stages of the relaxation. The results are discussed in the framework of an antiphase boundary model. (orig.)

Colinet, C. [ENSEEG, Saint-Martin-d' Heres (France). Lab. de Thermodynamique et Physico-Chimie Metallurgiques; Pasturel, A. [ENSEEG, Saint-Martin-d' Heres (France). Lab. de Thermodynamique et Physico-Chimie Metallurgiques; Lab. de Physique et Modelisation des Milieux Condenses, CNRS, Grenoble (France)

2001-12-01

114

Raman spectra of BN-nanotubes: Ab-initio and bond-polarizability model calculations  

CERN Document Server

We present it ab-initio calculations of the non-resonant Raman spectra of zigzag and armchair BN nanotubes. In comparison, we implement a generalized bond-polarizability model where the parameters are extracted from first-principles calculations of the polarizability tensor of a BN sheet. For light-polarization along the tube-axis, the agreement between model and it ab-initio spectra is almost perfect. For perpendicular polarization, depolarization effects have to be included in the model in order to reproduce the it ab-initio Raman intensities.

Wirtz, L; Mauri, F; Rubio, A; Wirtz, Ludger; Lazzeri, Michele; Mauri, Francesco; Rubio, Angel

2005-01-01

115

NestedMICA as an ab initio protein motif discovery tool  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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 fi...

Do?ruel Mutlu; Down Thomas A; Hubbard Tim JP

116

Iron-chromium alloys and surfaces: from ab initio calculations to segregation isotherms  

International Nuclear Information System (INIS)

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)

2011-01-01

117

On-the-fly ab initio molecular dynamics with multiconfigurational Ehrenfest method.  

UK PubMed Central (United Kingdom)

In this article we report the formalism and first implementation of the ab initio multiconfigurational Ehrenfest (AI-MCE) method for simulation of ultrafast nonadiabatic dynamics, which uses the MOLPRO electronic structure program to calculate the potential energy surfaces on the fly. The approach is tested on the benchmark of the excited ??? state dynamics of ethylene producing the dynamics which agree with previous simulations by ab initio multiple spawning technique. The AI-MCE seems to be robust, stable and efficient.

Saita K; Shalashilin DV

2012-12-01

118

On-the-fly ab initio molecular dynamics with multiconfigurational Ehrenfest method  

Science.gov (United States)

In this article we report the formalism and first implementation of the ab initio multiconfigurational Ehrenfest (AI-MCE) method for simulation of ultrafast nonadiabatic dynamics, which uses the MOLPRO electronic structure program to calculate the potential energy surfaces on the fly. The approach is tested on the benchmark of the excited ??* state dynamics of ethylene producing the dynamics which agree with previous simulations by ab initio multiple spawning technique. The AI-MCE seems to be robust, stable and efficient.

Saita, Kenichiro; Shalashilin, Dmitrii V.

2012-12-01

119

An ab initio non-equilibrium Green's function approach to charge transport: dithiolethine  

CERN Multimedia

We present a novel ab initio non-equilibrium approach to calculate the current across a molecular junction. The method rests on a wave function based full ab initio description of the central region of the junction combined with a tight binding approximation for the electrodes in the frame of the Keldysh Green's function formalism. Our procedure is demonstrated for a dithiolethine molecule between silver electrodes. The main conducting channel is identified and the full current-voltage characteristic is calculated.

Schnurpfeil, A; Albrecht, M; Schnurpfeil, Alexander; Song, Bo; Albrecht, Martin

2005-01-01

120

Pt-induced nanowires on Ge(001): Ab initio study  

Science.gov (United States)

Using ab initio density-functional theory together with a semilocal approximation for exchange and correlation we study structural, energetical, and electronic properties for a variety of reconstruction models of the Ge(001)4×2 surface with a Pt coverage of 0.25 monolayer. The band-structure calculations are partially performed including spin-orbit interaction. Starting from the idea that the self-organization of the nanowire arrays is driven by the minimization of the total energy of the system, we investigate more than 20 possible overlayer structures, among them dimerized top Pt chains. The comparison of the surface energies, however, shows a clear preference of the formation of Pt-Ge bonds over Pt-Pt bonds. The most favorable surface structure contains fourfold-coordinated Pt atoms embedded in Ge atoms. The seemingly dimerized top chains are formed by edges of Ge tetramers parallel to Ge dimers in trenches two atomic layers below. Incorporation of Pt atoms in the surface Ge layer within the tetramer-dimer-chain model gives rise to the biggest energy gain. Its band structure describes an indirect semiconductor with almost vanishing gap. The role of the Pt 5d states and top-ridge Ge orbitals as well as of spin-orbit interaction is emphasized for the wire conductivity. The results are discussed in light of recent experimental scanning-tunneling microscopy studies.

Stekolnikov, A. A.; Furthmüller, J.; Bechstedt, F.

2008-10-01

 
 
 
 
121

Ab initio studies of niobium defects in uranium  

Energy Technology Data Exchange (ETDEWEB)

Uranium (U), with the addition of small amount of niobium (Nb), is stainless. The Nb is fully miscible with the high temperature phase of U and tends to segregate upon cooling below 647 C. The starting point of segregation is the configuration of Nb substitutional or interstitial defects. Using density-functional-theory based ab initio calculations, the authors find that the formation energy of a single vacancy is 1.08 eV, that of Nb substitution is 0.59 eV, that of Nb interstitial at octahedral site is 1.58 eV, and that of Nb interstitial at tetrahedral site is 2.35 eV; all with reference to a reservoir of {gamma} phase U and pure Nb. The formation energy of Nb defects correlates with the local perturbation of electron distribution; higher formation energy to larger perturbation. Based on this study, Nb atoms thermodynamically prefer to occupy substitutional sites in {gamma} phase U, and they prefer to be in individual substitutional defects than clusters.

Xiang, S; Huang, H; Hsiung, L

2007-06-01

122

Ab-initio calculations for dilute magnetic semiconductors  

Energy Technology Data Exchange (ETDEWEB)

This thesis focusses on ab-initio calculations for the electronic structure and the magnetic properties of dilute magnetic semiconductors (DMS). In particular we aim at the understanding of the complex exchange interactions in these systems. Our calculations are based on density functional theory, being ideally suited for a description of the material specific properties of the considered DMS. Moreover we use the KKR Green function method in connection with the coherent potential approximation (CPA), which allows to include the random substitutional disorder in a mean field-like approximation for the electronic structure. Finally we calculate the exchange coupling constants J{sub ij} between two impurities in a CPA medium by using the Lichtenstein formula and from this calculate the Curie temperature by a numerically exact Monte Carlo method. Based on this analysis we found and investigated four different exchange mechanisms being of importance in DMS systems: Double exchange, p-d exchange, antiferromagnetic superexchanges, and ferromagnetic superexchange. A second topic we have investigated in this thesis is the pressure dependence of the exchange interactions and the Curie temperatures in (Ga,Mn)As and (In,Mn)As, using the LDA and the LDA+U approximations. Exact calculations of T{sub C} by Monte Carlo simulations show a somehow different behavior. (orig.)

Belhadji, Brahim

2008-03-03

123

Atmospheric oxidation of tetrachloroethylene: an ab initio study.  

UK PubMed Central (United Kingdom)

A number of experimental studies have been conducted to determine the atmospheric oxidation of tetrachloroethylene, many indicating phosgene as the major product. Although various mechanisms have been suggested, the mechanism of phosgene production is unclear. Additionally, confusion has arisen over the role chlorine atoms may play in the oxidation of tetrachloroethylene and the products produced. To clarify these points, this study presents a comprehensive computational study of both the hydroxyl radical and the chlorine atom initiated atmospheric oxidation mechanism of tetrachloroethylene. The energetics for the oxidation of tetrachloroethylene (C(2)Cl(4)) are computed using ab initio methods. Potential energy surfaces of the reaction pathways are determined from the computations. This study clarifies the involvement of the Cl-initiated reaction pathways in the oxidation of tetrachloroethylene. Results from this work suggest that the final products are primarily from the Cl-initiated oxidation and include: trichloroacetyl chloride [ClC(O)CCl(3)], phosgene [C(O)Cl(2)], and regeneration of the initiating chlorine atom.

Christiansen CJ; Francisco JS

2010-09-01

124

Ab initio lattice dynamics of MnO.  

UK PubMed Central (United Kingdom)

Vibrational dynamics of the MnO lattice has been studied using density functional theory combined with the direct method. Considerations have been limited to the harmonic approximation. Ab initio calculated Hellmann-Feynman forces were used to obtain density of states and the dispersion relations of phonons in the MnO crystal. Corrections for the local Coulomb interactions were applied. The Hubbard energies were varied from 1 to 7.9 eV. Increased Hubbard terms give a significant increase in the on-site force constants of cations, while the force constants on anions are affected indirectly. The density of phonon states and the dispersion curves are shifted to higher frequencies with the increasing Hubbard energies. The on-site Coulomb interactions influence mainly the optical phonon vibrations. The higher Hubbard terms lower the mean-squared vibrations of both cations and anions. The lattice contribution to the heat capacity experiences small changes upon variation of Coulomb repulsion. Results of the calculations are compared to the existing experimental data.

Wdowik UD; Legut D

2009-07-01

125

Illustrative direct ab initio calculations of surface Raman spectra.  

UK PubMed Central (United Kingdom)

Illustrative ab initio calculations of Raman spectra of pyridine (Pyr) and pyridine in metal-molecule complexes with silver (Ag+-Pyr, Ag5+-Pyr) have been undertaken. The Raman spectra were computed numerically in the standard Placzek approximation with the additional feature of a static external electric field, F, perturbation to the system Hamiltonian. F was allowed to change the system equilibrium geometry and symmetry as well as the polarisability, resulting in shifted vibration frequencies and changed Raman intensities. All calculations were done on a Hartree-Fock (HF) level using the 6-31+G* or the Sadlej p-VTZ basis sets for Pyr, and the Stevens Krauss (SBKJC) VDZ ECP basis set for Ag. Raman enhancement factors over 5 orders of magnitude were obtained. The enhancement was analyzed as being due to polarization and charge transfer induced by the metal-molecule contact in the absence of F and in the presence of a strong F as due to increased polarisability derivatives along the surface normal. The use of the present method to qualitatively and quantitatively predict surface Raman spectra is discussed.

Johansson P

2005-02-01

126

Illustrative direct ab initio calculations of surface Raman spectra.  

Science.gov (United States)

Illustrative ab initio calculations of Raman spectra of pyridine (Pyr) and pyridine in metal-molecule complexes with silver (Ag+-Pyr, Ag5+-Pyr) have been undertaken. The Raman spectra were computed numerically in the standard Placzek approximation with the additional feature of a static external electric field, F, perturbation to the system Hamiltonian. F was allowed to change the system equilibrium geometry and symmetry as well as the polarisability, resulting in shifted vibration frequencies and changed Raman intensities. All calculations were done on a Hartree-Fock (HF) level using the 6-31+G* or the Sadlej p-VTZ basis sets for Pyr, and the Stevens Krauss (SBKJC) VDZ ECP basis set for Ag. Raman enhancement factors over 5 orders of magnitude were obtained. The enhancement was analyzed as being due to polarization and charge transfer induced by the metal-molecule contact in the absence of F and in the presence of a strong F as due to increased polarisability derivatives along the surface normal. The use of the present method to qualitatively and quantitatively predict surface Raman spectra is discussed. PMID:19785132

Johansson, Patrik

2005-02-01

127

Ab initio evaluations of the He solubility in liquid Li  

International Nuclear Information System (INIS)

Modified embedding atom methods (MEAM) are developed to have predictions of the partial molar heat of solution (-Hs) by direct simulation of metal cohesion, He-metal and He-He interaction. Transitions from crystalline Li to configurations, having the liquid Li structure's factors (h-bar (q)), are simulated ab initio. Once h-bar (q) reproduced, He atoms are added, one by one, to the Li system. Parallel lines for each case, with slopes clearly independent on the number of He atoms in the system, are obtained for energy versus pressure at given temperatures. Average differences between two adjacent parallels at zero pressure, once kinetic energy of the system discounted, represents the energy gained by an He atom when added to the Li system, related to the solution energy -Hs. The molar excess entropy of gas in solution (S-bar lex) is previously evaluated following diverse fundamental approaches: a 'thermodynamic liquid-hole' (TL-H) model for alkali liquids and a statistical-mechanics (Neff and McQuarrie's) model (SMM). Between 600 and 900 deg. C, a typical range of interest for the use of Li in fusion technology, the computed values for the (He) Henry's constant in Li range from 8x10-14 to 10-13 at. fr. Pa-1

2005-01-01

128

Ab initio molecular dynamics calculations of ion hydration free energies  

International Nuclear Information System (INIS)

We apply ab initio molecular dynamics (AIMD) methods in conjunction with the thermodynamic integration or '?-path' technique to compute the intrinsic hydration free energies of Li+, Cl-, and Ag+ ions. Using the Perdew-Burke-Ernzerhof functional, adapting methods developed for classical force field applications, and with consistent assumptions about surface potential (?) contributions, we obtain absolute AIMD hydration free energies (?Ghyd) within a few kcal/mol, or better than 4%, of Tissandier et al.'s [J. Phys. Chem. A 102, 7787 (1998)] experimental values augmented with the SPC/E water model ? predictions. The sums of Li+/Cl- and Ag+/Cl- AIMD ?Ghyd, which are not affected by surface potentials, are within 2.6% and 1.2 % of experimental values, respectively. We also report the free energy changes associated with the transition metal ion redox reaction Ag++Ni+?Ag+Ni2+ in water. The predictions for this reaction suggest that existing estimates of ?Ghyd for unstable radiolysis intermediates such as Ni+ may need to be extensively revised.

2009-05-28

129

Ab initio Green's function formalism for band structures  

CERN Multimedia

Using the Green's function formalism, an ab initio method for band structures of crystals is derived starting from the Hartree-Fock approximation. It is based on the algebraic diagrammatic construction scheme for the self-energy in terms of crystal orbitals (CO-ADC). In this approach, the poles of the Green's function are determined by solving a suitable Hermitian eigenvalue problem. The method is not only applicable to the outer valence and conduction bands, it is also stable for inner valence bands where strong electron correlations are effective. The key to the proposed scheme is to evaluate the self-energy in terms of Wannier orbitals before transforming it to a crystal momentum representation. Exploiting that electron correlations are mainly local, one can truncate the lattice summations by an appropriate configuration selection scheme. This yields a flat configuration space, i.e., its size scales only linearly with the number of atoms per unit cell for large systems and, under certain conditions, the co...

Buth, C; Albrecht, M; Fulde, P; Buth, Christian; Birkenheuer, Uwe; Albrecht, Martin; Fulde, Peter

2004-01-01

130

Ab initio molecular dynamics calculations of ion hydration free energies  

CERN Multimedia

We apply ab initio molecular dynamics (AIMD) methods in conjunction with the thermodynamic integration or "lambda-path" technique to compute the intrinsic hydration free energies of Li+, Cl-, and Ag+ ions. Using the Perdew-Burke-Ernzerhof functional, adapting methods developed for classical force field applications, and with consistent assumptions about surface potential (phi) contributions, we obtain absolute AIMD hydration free energies (Delta G(hyd)) within a few kcal/mol, or better than 4%, of Tissandier 's [J. Phys. Chem. A 102, 7787 (1998)] experimental values augmented with the SPC/E water model phi predictions. The sums of Li+/Cl- and Ag+/Cl- AIMD Delta G(hyd), which are not affected by surface potentials, are within 2.6% and 1.2 % of experimental values, respectively. We also report the free energy changes associated with the transition metal ion redox reaction Ag++Ni+-> Ag+Ni2+ in water. The predictions for this reaction suggest that existing estimates of Delta G(hyd) for unstable radiolysis interme...

Leung, Kevin; von Lilienfeld, Anatole O; 10.1063/1.3137054

2010-01-01

131

Ab initio spectroscopy and thermochemistry of the BN molecule  

Energy Technology Data Exchange (ETDEWEB)

The lowest {sup 1}{Sigma}{sup +} and {sup 3}PI states of the BN molecule have been studied using the quadratic configuration interaction method and (spdf) basis sets. The lowest {sup 1}{Sigma}{sup +} and {sup 3}PI states lie extremely closely (T{sub e} {approx equal} 100 cm{sup -1}) together; it is not clear which is the ground state. The very small separation should form a useful benchmark for basis sets and electron correlation methods. The dissociation energy D{sub 0} is computed to be 103.9+-2 kcal/mol. A self-consistent set of spectroscopic constants is derived from a combination of ab initio and experimental data. JANAF-style thermodynamic functions in the range 100-6000 K, including anharmonic, rovibrational coupling, centrifugal stretching, and spin-orbit coupling effects are computed using direct numerical summation over the 25 lowest electronic states. A modified procedure for the latter is outlined that reduces computer time by one or two orders of magnitude without compromise in accuracy. (orig.).

Martin, J.M.L. (Limburgs Universitair Centrum, Diepenbeek (Belgium). Dept. SBM Universitaire Instelling Antwerpen, Wilrijk (Belgium). Inst. for Materials Science); Francois, J.P. (Limburgs Universitair Centrum, Diepenbeek (Belgium). Dept. SBM); Gijbels, R. (Universitaire Instelling Antwerpen, Wilrijk (Belgium). Inst. for Materials Science)

1991-07-01

132

Ab initio construction of all-atom loop conformations.  

UK PubMed Central (United Kingdom)

In this study, a new ab initio method named CLOOP has been developed to build all-atom loop conformations. In this method, a loop main-chain conformation is generated by sampling main-chain dihedral angles from a restrained varphi/psi set, and the side-chain conformations are built randomly. The CHARMM all-atom force field was used to evaluate the loop conformations. Soft core potentials were used to treat the non-bond interactions, and a designed energy-minimization technique was used to close and optimize the loop conformations. It is shown that the two strategies improve the computational efficiency and the loop-closure rate substantially compared to normal minimization methods. CLOOP was used to construct the conformations of 4-, 8-, and 12-residue loops in Fiser's test set. The average main-chain root-mean-square deviations obtained in 1,000 trials for the 10 different loops of each size are 0.33, 1.27, and 2.77 A, respectively. CLOOP can build all-atom loop conformations with a sampling accuracy comparable with previous loop main-chain construction algorithms. [Figure: see text].

Jiang H; Blouin C

2006-01-01

133

Ab initio construction of all-atom loop conformations.  

Science.gov (United States)

In this study, a new ab initio method named CLOOP has been developed to build all-atom loop conformations. In this method, a loop main-chain conformation is generated by sampling main-chain dihedral angles from a restrained varphi/psi set, and the side-chain conformations are built randomly. The CHARMM all-atom force field was used to evaluate the loop conformations. Soft core potentials were used to treat the non-bond interactions, and a designed energy-minimization technique was used to close and optimize the loop conformations. It is shown that the two strategies improve the computational efficiency and the loop-closure rate substantially compared to normal minimization methods. CLOOP was used to construct the conformations of 4-, 8-, and 12-residue loops in Fiser's test set. The average main-chain root-mean-square deviations obtained in 1,000 trials for the 10 different loops of each size are 0.33, 1.27, and 2.77 A, respectively. CLOOP can build all-atom loop conformations with a sampling accuracy comparable with previous loop main-chain construction algorithms. [Figure: see text]. PMID:16247602

Jiang, Haiyan; Blouin, Christian

2005-10-25

134

Valence quantum Monte Carlo with ab initio effective core potentials  

Energy Technology Data Exchange (ETDEWEB)

Effective-core potentials (ECP's) obtained from ab initio methods are implemented in molecular quantum Monte Carlo (QMC). The theory is presented, and applied to the calculation of electron affinities (EA) of Li and Na, the ionization potential (IP) of Mg, the binding energies (D/sub e/) of NaH and Na/sub 2/, and the potential energy curve of Na/sub 2/. In all cases ECP--QMC results are found to be as accurate as previous all-electron results. In particular, the calculated quantities (vs experimental values) are (in eV): EA(Li) = 0.611 +- 0.020 (0.620), EA(Na) = 0.555 +- 0.021 (0.546), IP(Mg) = 7.637 +- 0.026 (7.646), D/sub e/ (NaH) = 1.954 +- 0.073 (1.971), and D/sub e/ (Na/sub 2/) = 0.746 +- 0.020 (0.747). In addition, the statistical precision obtained surpasses that which can be readily achieved in all-electron QMC calculations on these systems.

Hammond, B.L.; Reynolds, P.J.; Lester W.A. Jr.

1987-07-15

135

Valence quantum Monte Carlo with ab initio effective core potentials  

International Nuclear Information System (INIS)

[en] Effective-core potentials (ECP's) obtained from ab initio methods are implemented in molecular quantum Monte Carlo (QMC). The theory is presented, and applied to the calculation of electron affinities (EA) of Li and Na, the ionization potential (IP) of Mg, the binding energies (D/sub e/) of NaH and Na2, and the potential energy curve of Na2. In all cases ECP--QMC results are found to be as accurate as previous all-electron results. In particular, the calculated quantities (vs experimental values) are (in eV): EA(Li) = 0.611 +- 0.020 (0.620), EA(Na) = 0.555 +- 0.021 (0.546), IP(Mg) = 7.637 +- 0.026 (7.646), D/sub e/ (NaH) = 1.954 +- 0.073 (1.971), and D/sub e/ (Na2) = 0.746 +- 0.020 (0.747). In addition, the statistical precision obtained surpasses that which can be readily achieved in all-electron QMC calculations on these systems

1987-07-15

136

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

CERN Multimedia

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

137

An ab initio study of plutonium oxides surfaces  

International Nuclear Information System (INIS)

[en] 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)

2007-01-01

138

Symplectic ab initio no-core shell model  

Scientific Electronic Library Online (English)

Full Text Available 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 cua (more) l 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 results reveal that the NCSM wave functions for light nuclei highly overlap (at the 90% level) with only a few of the most (more) 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.

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

2008-12-01

139

Ab initio treatment of charge exchange in H+ + CH collisions  

International Nuclear Information System (INIS)

Compete text of publication follows. Proton collision with the CH radical is interesting as a benchmark system to check approximations that can be applied to collisions with larger molecules, which are relevant in radiation damage of biological systems. The aim of the present work was to check the validity of several approximations. In particular calculation at the Franck-Condon (FC) level was compared with more accurate calculations that employ the sudden approximation for rotation and vibration. We also discussed the extension of the calculation to energies below 50 eV. The ab initio study of ion-molecule collisions at low and intermediate energies is carried out by employing a molecular expansion. This method requires the calculation of potential energy surfaces and dynamical couplings of the supermolecule formed during the collision, which was carried out by means of quantum chemistry techniques implemented in MOLPRO. We have calculated total charge transfer cross sections with a fixed molecular orientation (? = 60 deg)1 and a 2-state basis (32A', 42A'). The eikonal calculation included both radial and rotational couplings, while only the radial coupling was included in the quantum mechanical calculation. Our results point out that the eikonal treatment is appropriate in the energy of this work. Besides, the approximation of neglecting the rotational coupling does not significantly modifies the total cross section. While the change of the cross section with p is relatively small for v > 0.1 a.u. (E ? 250 eV), at lower velocities the energy difference becomes critical and we obtain very large cross sections for p 3+, might be a consequence of the neglect of a vibronic resonant mechanism similar to that found in Ref. [5]. In practice, the extension of the present calculation to E

2010-01-01

140

Ab initio investigations of zinc chalcogenides semiconductor alloys  

Energy Technology Data Exchange (ETDEWEB)

The present work performs self-consistent ab initio full potential-linearized augmented plane wave method to study the structural, electronic and thermodynamic properties of ZnS{sub x}Se{sub 1-x}, ZnS{sub x}Te{sub 1-x} and ZnSe{sub x}Te{sub 1-x} semiconductor alloys. The ground-state properties were determined for the bulk materials (ZnS, ZnSe, and ZnTe) and for their alloys in cubic phase at various concentrations (x=0.25, 0.5 and 0.75). A marginal deviation of the lattice parameter from Vegard's law was observed for ZnS{sub x}Se{sub 1-x} and ZnSe{sub x}Te{sub 1-x} alloys, while the lattice bowing of ZnS{sub x}Te{sub 1-x} alloy was found to be significant. This is mainly because of the large mismatch of the lattice parameters of the binary compounds ZnS and ZnTe. A large deviation of the bulk modulus from linear concentration dependence was observed for all the three alloys. We have also investigated the effect of composition on bonding properties and correlated it to the charge-exchange effect in the optical bowing. Using the approach of Zunger et al. [21], the microscopic origins of the gap bowing were explained. The disorder parameter (gap bowing) for the alloys of interest was found to be mainly caused by the structural relaxation contributions. The charge-exchange contributions for all the three alloys were also found to be significant. The calculated phase diagram showed a broad miscibility gap for all the alloys of interest with a high critical temperature.

El Haj Hassan, F. [Universite Libanaise, Faculte des sciences (I), Laboratoire de Physique de Materiaux, Elhadath, Beirut (Lebanon)]. E-mail: hassan.f@ul.edu.lb; Amrani, B. [Departement de Physique, Universite de Mascara, Mascara 29000 (Algeria); Bahsoun, F. [Universite Libanaise, Faculte des sciences (I), Laboratoire de Physique de Materiaux, Elhadath, Beirut (Lebanon)

2007-04-01

 
 
 
 
141

PSI3: an open-source Ab Initio electronic structure package.  

UK PubMed Central (United Kingdom)

PSI3 is a program system and development platform for ab initio molecular electronic structure computations. The package includes mature programming interfaces for parsing user input, accessing commonly used data such as basis-set information or molecular orbital coefficients, and retrieving and storing binary data (with no software limitations on file sizes or file-system-sizes), especially multi-index quantities such as electron repulsion integrals. This platform is useful for the rapid implementation of both standard quantum chemical methods, as well as the development of new models. Features that have already been implemented include Hartree-Fock, multiconfigurational self-consistent-field, second-order Møller-Plesset perturbation theory, coupled cluster, and configuration interaction wave functions. Distinctive capabilities include the ability to employ Gaussian basis functions with arbitrary angular momentum levels; linear R12 second-order perturbation theory; coupled cluster frequency-dependent response properties, including dipole polarizabilities and optical rotation; and diagonal Born-Oppenheimer corrections with correlated wave functions. This article describes the programming infrastructure and main features of the package. PSI3 is available free of charge through the open-source, GNU General Public License.

Crawford TD; Sherrill CD; Valeev EF; Fermann JT; King RA; Leininger ML; Brown ST; Janssen CL; Seidl ET; Kenny JP; Allen WD

2007-07-01

142

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

143

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 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.

2008-04-16

144

Computer modeling of natural silicate melts: what can we learn from ab initio simulations  

CERN Multimedia

The structural and dynamical properties of four silicate liquids (silica, rhyolite, a model basalt and enstatite) are evaluated by ab initio molecular dynamics simulation using the density functional theory and are compared with classical simulations using a simple empirical force field. For a given composition, the structural parameters of the simulated melt vary little between the two calculations (ab initio versus empirical) and are in satisfactory agreement with structure data available in the literature. In contrast, ionic diffusivities and atomic vibration motions are found to be more sensitive to the details of the interactions. Furthermore, it is pointed out that the electronic polarization, as evaluated by the ab initio calculation, contributes significantly to the intensity of the infrared absorption spectra of molten silicates, a spectral feature which cannot be reproduced using nonpolarizable force field. However the vibration modes of TO4 species and some structural details are not accurately rep...

Vuilleumier, R; Guillot, B

2009-01-01

145

Shear stiffness in nanolaminar Ti3SiC2 challenges ab initio calculations  

International Nuclear Information System (INIS)

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. (fast track communication)

2010-04-28

146

Ab Initio Nuclear Structure Theory with Chiral NN+3N Interactions  

Science.gov (United States)

Low-energy nuclear theory has entered an era of ab initionuclear structure and reaction calculations based on QCD. One of the most promising paths from QCD to nuclear observables employs Hamiltonians constructed within chiral effective field theory as starting point for precise ab initio studies. However, the full inclusion of chiral two- plus three-nucleon (NN+3N) interactions in exact and approximate many-body calculations poses a formidable challenge. We discuss recent breakthroughs that allow for ab initio calculations for ground states and spectra of nuclei throughout the p- and the lower sd-shell with full 3N interactions using consistent Similarity Renormalization Group (SRG) transformations and the Importance Truncated No-Core Shell Model (IT-NCSM). Moreover, we discuss extensions of these ab initio calculations to heavy nuclei within coupled cluster theory using a normal ordering approximation of the 3N interaction.

Roth, R.; Langhammer, J.; Calci, A.; S. B.; Navrátil, P.

147

Shear stiffness in nanolaminar Ti3SiC2 challenges ab initio calculations.  

Science.gov (United States)

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

2010-03-30

148

Microwave rotational spectrum and ab initio equilibrium structure of fumaric acid: Anharmonicity bridging the molecular characterizations  

Science.gov (United States)

Accurate rotational constants of fumaric acid are obtained by supersonic-jet Fourier transform microwave spectroscopy. Comparison with high-level ab initio structure calculations, requires anharmonicity effects in the vibrational ground-state to be calculated. Fumaric Acid is observed by supersonic jet expansion microwave spectroscopy. Spectroscopic constants and electric dipole moments are obtained at high accuracy. Spectroscopic and ab initio data agree on a low-energy s-cis,s-trans conformer. Experiment and theory are compatible when anharmonic effects are taken into account.

Vogt, Natalja; Rajappan Nair, K. P.; Vogt, Jürgen; Grabow, Jens-Uwe

2011-07-01

149

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; Bertran Celso Aparecido

2002-01-01

150

Ab initio studies of the structural and electronic properties of solid cubane  

International Nuclear Information System (INIS)

[en] In this paper, we report ab initio calculation of the structural and electronic properties of solid cubane (s-C8H8) in the local-density approximation. By using an ab initio constant pressure extended molecular dynamics method with variable cell shape proposed by Wentzcovitch, Martins, and Price, we compute a lattice parameter a and a bond angle ? for the rhombohedral Bravais lattice and compare it with experimental x-ray data. We obtain bond lengths for the mononuclear C8H8 unit of basis atoms, as well as a density of states and heat of formation. copyright 1998 The American Physical Society

1998-01-01

151

Ab initio study of collective excitations in a disparate mass molten salt.  

UK PubMed Central (United Kingdom)

Ab initio molecular dynamics simulations and the approach of generalized collective modes are applied for calculations of spectra of longitudinal and transverse collective excitations in molten LiBr. Dispersion and damping of low- and high-frequency branches of collective excitations as well as wave-number dependent relaxing modes were calculated. The main mode contributions to partial, total, and concentration dynamic structure factors were estimated in a wide region of wave numbers. A role of polarization effects is discussed from comparison of mode contributions to concentration dynamic structure factors calculated for molten LiBr from ab initio and classical rigid ion simulations.

Bryk T; Klevets I

2012-12-01

152

Microscopic properties of liquid water from combined ab initio molecular dynamics and energy decomposition studies.  

UK PubMed Central (United Kingdom)

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 RZ; Kühne TD

2013-08-01

153

Physical Origin of Satellites in Photoemission of Doped Graphene: An Ab Initio GW Plus Cumulant Study  

Science.gov (United States)

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).

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

2013-04-01

154

Microscopic properties of liquid water from combined ab initio molecular dynamics and energy decomposition studies.  

Science.gov (United States)

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. PMID:23928575

Khaliullin, Rustam Z; Kühne, Thomas D

2013-08-09

155

Ab initio Molecular Dynamics Simulations of Water Under Static and Shock Compressed Conditions  

Energy Technology Data Exchange (ETDEWEB)

We report herein a series of ab initio simulations of water under both static and shocked conditions. We have calculated the coherent x-ray scattering intensity of several phases of water under high pressure, using ab initio Density Functional Theory (DFT). We provide new atomic scattering form factors for water at extreme conditions, which take into account frequently neglected changes in ionic charge and electron delocalization. We have also simulated liquid water undergoing shock loading of velocities from 5-11 km/s using the Multi-Scale Shock Technique (MSST). We show that Density Functional Theory (DFT) molecular dynamics results compare extremely well to experiments on the water shock Hugoniot.

Goldman, N; Fried, L E; Mundy, C J; Kuo, I W; Curioni, A; Reed, E

2007-07-25

156

Molecular conformations of nitramine explosives MM3 and ab initio studies  

Energy Technology Data Exchange (ETDEWEB)

With our group`s continuing interest in structure-reactivity relationships in explosives, molecular mechanics (MM3) parameters for nitramines have been carefully examined. Molecular properties of various nitramines including. RDX and HMX, namely geometries, rotational barriers, charge distributions, and molecular electrostatic potentials have been investigated by using MM3 and ab initio calculations. Based on MN3 and ab initio structural informations, we have attempted to fit the experimental densities and impact sensitivities, which are of importance to understand the performance of new explosive molecules.

Cho, S.G.; Kwon, I.B.; Lim, O.K. [Agency for Defense Development, Taejon (Korea, Republic of)

1995-12-01

157

Energy partitioning on intermolecular interactions: ab initio Monte Carlo study of water dimer  

Directory of Open Access Journals (Sweden)

Full Text Available Ab initio Monte Carlo computations were carried out on H2O dimer system. By introducing the energy partitioning scheme that we have developed recently, ab initio calculated H2O-H2O interaction can be analyzed from the viewpoint of atom-atom interaction. The electronic polarization caused by the interaction and its temperature dependence are also discussed. To our best knowledge, this is the first report on the thermal distribution of electronic distortion energy assigned to a molecule.

T.Amano; H.Sato; S.Sakaki

2007-01-01

158

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

159

Microscopic properties of liquid water from combined ab initio molecular dynamics and energy decomposition studies.  

UK PubMed Central (United Kingdom)

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 RZ; Kühne TD

2013-10-01

160

Modelling of nuclear glasses by classical and ab initio molecular dynamics; Modelisation de verres intervenant dans le conditionnement des dechets radioactifs par dynamiques moleculaires classique et ab initio  

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

 
 
 
 
161

The core stimulon of Corynebacterium pseudotuberculosis strain 1002 identified using ab initio methodologies.  

UK PubMed Central (United Kingdom)

Corynebacterium pseudotuberculosis is a bacterium which causes diseases such as caseous lymphadenitis in small ruminants, resulting in large-scale economic losses for agribusiness worldwide. Consequently, this bacterium including its transcriptional profile analysis has been the focus of various studies. Identification of the transcripts that appear under conditions that simulate the environment encountered by this bacterial species in the host is of great importance in discovering new targets for the production of more efficient vaccines. We sequenced the cDNA of Corynebacterium pseudotuberculosis strain 1002, using the SOLiD V3 system, under the following conditions: osmotic stress (2 M), acidity (pH), heat shock (50 °C) and control condition (N). To identify the transcripts shared among the stimulons and integrate this information with the results from BLAST and BLAST2GO, we developed the software CoreStImulon (CSI) which allows the user to individually distinguish the genes in terms of their participation in biological processes, their function and cellular location. In the biosynthetic processes, eleven genes represented in the core stimulon and twenty genes in the control were observed. This validates the hypothesis that the organisms strategy for surviving in a hostile environment is through growth reduction. The oxidation reduction process, response to stress process, and cell adhesion are controlled by genes that contribute to bacterial cell maintenance under stress conditions; these could be involved in their pathogenicity. The methodology for identification of transcripts obtained by ab initio assembly and shared among the stimulons permitted candidates selection for vaccine studies. CSI is available at https://sourceforge.net/projects/corestimulon/.

Pinto AC; Ramos RT; Silva WM; Rocha FS; Barbosa S; Miyoshi A; Schneider MP; Silva A; Azevedo V

2012-07-01

162

Vibrational properties of hexagonal boron nitride: inelastic X-ray scattering and ab initio calculations.  

UK PubMed Central (United Kingdom)

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 T; Kanda H; Rubio A; Wirtz L

2007-03-01

163

Vibrational properties of hexagonal boron nitride: inelastic X-ray scattering and ab initio calculations.  

Science.gov (United States)

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. PMID:17359168

Serrano, J; Bosak, A; Arenal, R; Krisch, M; Watanabe, K; Taniguchi, T; Kanda, H; Rubio, A; Wirtz, L

2007-03-01

164

Ab initio study of spin-dependent transport in carbon nanotubes with iron and vanadium adatoms  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We present an ab initio study of spin-dependent transport in armchair carbon nanotubes with transition metal adsorbates: iron or vanadium. The method based on density functional theory and nonequilibrium Green's functions is used to compute the electronic structure and zero-bias conductance. The pre...

Fürst, Joachim Alexander; Brandbyge, Mads; Jauho, Antti-Pekka; Stokbro, Kurt

165

Comparison between classical potentials and ab initio for silicon under large shear  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The homogeneous shear of the {111} planes along the direction of bulk silicon has been investigated using ab initio techniques, to better understand the strain properties of both shuffle and glide set planes. Similar calculations have been done with three empirical potentials, Stillinger-Weber...

Godet, Julien; Pizzagalli, Laurent; Brochard, Sandrine; Beauchamp, Pierre

166

Ab initio valence-bond cluster model for ionic solids: Alkaline-earth oxides  

Digital Repository Infrastructure Vision for European Research (DRIVER)

A linear M-O-M (M=metal, O=oxygen) cluster embedded in a Madelung field, and also including the quantum effects of the neighboring ions, is used to represent the alkaline-earth oxides. For this model an ab initio wave function is constructed as a linear combination of Slater determinants written in ...

Lorda Donat, Amparo; Illas i Riera, Francesc; Rubio Martínez, Jaime; Torrance, J. B.

167

Review on DFT and ab initio Calculations of Scalar Coupling Constants  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract: The present review summarizes the information available on the ab initio calculations of spin-spin nuclear coupling constants through hydrogen bonds or in van der Waals complexes. It also reports the sources of experimental data on nhJXY scalar couplings.

Ibon Alkorta; José Elguero

2003-01-01

168

Combining instanton theory and ab initio data to model tunneling dynamics  

Energy Technology Data Exchange (ETDEWEB)

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.

Smedarchina, Z. [Inst. of Organic Chemistry, Sofia (Bulgaria); Siebrand, W.; Zgierski, M.Z. [NRCC Ottawa (Canada); Zerbetto, F. [Univ. of Bologna (Italy)

1996-12-31

169

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

170

Ab initio treatment of proton collisions with water and water dimer  

International Nuclear Information System (INIS)

Charge transfer and ionization in collisions of H''+ with H2O and (H2O)2 is obtained by using simple ab initio methods based on one-electron wave functions and multi-center pseudo-potentials and independent particle model treatments.

2009-11-01

171

Graphene on the C-terminated SiC (000 ?1) surface: An ab initio study  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The atomic and electronic structures of a graphene layer on top of the (2 × 2) reconstruction of the SiC (000 ?1) surface are studied from ab initio calculations. At variance with the (0001) face, no C bufferlayer is found here. Si adatoms passivate the substrate surface so that the very first C lay...

Magaud, Laurence; Hiebel, Fanny; Varchon, François; Mallet, Pierre; Veuillen, Jean-Yves

172

Ab initio calculations of elastic properties of Ru1-xNixAl superalloys  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Ab initio total energy calculations based on the exact muffin-tin orbitals method, combined with the coherent potential approximation, have been used to study the thermodynamical and elastic properties of substitutional refractory Ru1-xNixAl alloys. We have found that the elastic constants C- and C-...

Bleskov, I D; Smirnova, E A; Vekilov, Yu Kh; Korzhavyi, P A; Johansson, B; Katsnelson, M; Vitos, L; Abrikosov, Igor

173

Opacity data for HCN and HNC from a new ab initio line list  

Digital Repository Infrastructure Vision for European Research (DRIVER)

A new extensive ab initio rotation-vibration HCN/HNC line list is presented. The line list contains rotation-vibration energy levels, line frequencies, and line strengths for transitions between states with energy less than 18,000 cm-1 and with J?60. This line list greatly improves the quality and r...

Harris, G.J.; Polyansky, O.L.; Tennyson, J.

174

Ab initio melting curve of copper by the phase coexistence approach.  

UK PubMed Central (United Kingdom)

Ab initio calculations of the melting properties of copper in the pressure range 0-100 GPa are reported. The ab initio total energies and ionic forces of systems representing solid and liquid copper are calculated using the projector augmented wave implementation of density functional theory with the generalized gradient approximation for exchange-correlation energy. An initial approximation to the melting curve is obtained using an empirical reference system based on the embedded-atom model, points on the curve being determined by simulations in which solid and liquid coexist. The approximate melting curve so obtained is corrected using calculated free energy differences between the reference and ab initio system. It is shown that for system-size errors to be rendered negligible in this scheme, careful tuning of the reference system to reproduce ab initio energies is essential. The final melting curve is in satisfactory agreement with extrapolated experimental data available up to 20 GPa, and supports the validity of previous calculations of the melting curve up to 100 GPa.

Vocadlo L; Alfè D; Price GD; Gillan MJ

2004-02-01

175

NestedMICA as an ab initio protein motif discovery tool  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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 ...

Dogruel, Mutlu; Down, Thomas A; Hubbard, Tim J P

176

Mechanisms for catalytic carbon nanofiber growth studied by ab initio density functional theory calculations  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Mechanisms and energetics of graphene growth catalyzed by nickel nanoclusters were studied using ab initio density functional theory calculations. It is demonstrated that nickel step-edge sites act as the preferential growth centers for graphene layers on the nickel surface. Carbon is transported fr...

Abild-Pedersen, Frank; Nørskov, Jens Kehlet; Rostrup-Nielsen, Jens; Sehested, Jens; Helveg, Stig

177

AB initio investigation of infrared optic phonon modes splitting in TiSe crystal  

International Nuclear Information System (INIS)

The calculation technique of a splitting of infrared optical optical phonon frequencies on longitudinal and transverse modes is described. The analysis of splitting at the Brillouin zone center and influence of these splitting on phonon spectrum is carried out on the base of TiSe phonon spectrum derived from ab initio calculations, performed earlier in other papers

2011-01-01

178

Experimental and ab initio DFT calculated Raman Spectrum of Sudan I, a Red Dye  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The red dye Sudan I was investigated by Raman spectroscopy using different excitation wavelengths (1064, 532 and 244 nm). A calculation of the Raman spectrum based on quantum mechanical ab initio density functional theory (DFT) was made using the RB3LYP method with the 3-21G and 6-311+G(d,p) basis s...

Kunov-Kruse, Andreas Jonas; Kristensen, Steffen Buus; Liu, Chuan; Berg, Rolf W.

179

Ab initio investigation of the static polarizability of planar and twisted infinite polythiophene chains  

Energy Technology Data Exchange (ETDEWEB)

In this paper, the authors investigate the electronic structure and the static longitudinal polarizability of regular finite and infinite chains of polythiophene at the ab initio Hartree-Fock level. The effects of the inclusion of polarization functions in the basis set and the influence of introducing a torsional twist between adjacent rings are considered.

Mosley, D.H.; Fripiat, J.G.; Champagne, B. [Facultes Universitaires Notre-Dame de la Paix, Namur (Belgium)

1994-12-31

180

Ab initio calculation atomics ground state wave function for interactions Ion- Atom  

International Nuclear Information System (INIS)

Ab initio calculation atomics ground state wave function for interactions Ion- Atom Atomic wave function expressed in a Slater - type basis obtained within Roothaan- Hartree - Fock for the ground state of the atoms He through B. The total energy is given for each atom.

2007-01-01

 
 
 
 
181

Cálculo ab initio de intensidades Raman dinâmicas utilizando a teoria da resposta linear Ab initio calculation of dynamic Raman intensities using the linear response theory  

Directory of Open Access Journals (Sweden)

Full Text Available 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

2003-01-01

182

Ab initio calculations of mechanical, thermodynamic and electronic structure properties of mullite, iota-alumina and boron carbide  

Science.gov (United States)

The alumino-silicate solid solution series (Al 4+2xSi2-2 xO10-x) is an important class of ceramics. Except for the end member (x=0), Al2 SiO5 the crystal structures of the other phases, called mullite, have partially occupied sites. Stoichiometric supercell models for the four mullite phases 3Al2O 3 · 2SiO2 · 2Al 2O3 · SiO2, 4 Al2O3· SiO 2, 9Al2O3 · SiO2, and iota-Al2 O3 (iota-alumina) are constructed starting from experimentally reported crystal structures. A large number of models were built for each phase and relaxed using the Vienna ab initio simulation package (VASP) program. The model with the lowest total energy for a given x was chosen as the representative structure for that phase. Electronic structure and mechanical properties of mullite phases were studied via first-principles calculations. Of the various phases of transition alumina, iota-Al 2O3 is the least well known. In addition structural details have not, until now, been available. It is the end member of the aluminosilicate solid solution series with x=1. Based on a high alumina content mullite phase, a structural model for iota- Al2O3 is constructed. The simulated x-ray diffraction (XRD) pattern of this model agrees well with a measured XRD pattern. The iota-Al2 O3 is a highly disordered ultra-low-density phase of alumina with a theoretical density of 2854kg/m3. Using this theoretically constructed model, elastic, thermodynamic, electronic, and spectroscopic properties of iota-Al2 O3 have been calculated and compared it with those of alpha- Al2O3 and gamma- Al2O3. Boron carbide (B4C) undergoes an amorphization under high velocity impacts. The mechanism of amorphization is not clear. Ab initio methods are used to carry out large-scale uniaxial compression simulations on two polytypes of stoichiometric boron carbide (B4C), B 11C-CBC, and B12- CCC where B11C or B12 is the 12-atom icosahedron and CBC or CCC is the three-atom chain. The simulations were performed on large supercells of 180 atoms. Simulated results indicate bending of the three-atom chain leads to the amorphization of the B 11C-CBC (B12-CCC ) at a uniaxial strain s=0.23 (0.22) and with a maximum stress of 168 (151) GPa. The mechanism of amorphization is analyzed with radial pair distribution function (RPDF), total density of states (TDOS), and the distribution of effective charges on atoms.

Aryal, Sita Ram

183

Iron-chromium alloys and surfaces: from ab initio calculations to segregation isotherms; L'alliage fer-chrome et ses surfaces: des calculs ab initio aux isothermes de segregation  

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

184

Electronic structure of the Ca3Co4O9 compound from ab initio local interactions  

Science.gov (United States)

We used fully correlated ab initio calculations to determine the effective parameters of Hubbard and t-J models for the thermoelectric misfit compound Ca3Co4O9. As for the NaxCoO2 family, the Fermi level orbitals are the a1g orbitals of the cobalt atoms; the eg' being always lower in energy by more than 240 meV. The electron correlation is found very large U/t˜26 as well as the parameters fluctuations as a function of the structural modulation. The main consequences are a partial a1g electrons localization and a fluctuation of the in-plane magnetic exchange from antiferromagnetic to ferromagnetic. The behavior of the Seebeck coefficient and the figure of merit are discussed in view of the ab initio results, as well as the 496 K phase transition.

Soret, Julien; Lepetit, Marie-Bernadette

2012-04-01

185

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.

2008-05-23

186

Like-charge guanidinium pairing from molecular dynamics and ab initio calculations.  

Science.gov (United States)

Pairing of guanidinium moieties in water is explored by molecular dynamics simulations of short arginine-rich peptides and ab initio calculations of a pair of guanidinium ions in water clusters of increasing size. Molecular dynamics simulations show that, in an aqueous environment, the diarginine guanidinium like-charged ion pairing is sterically hindered, whereas in the Arg-Ala-Arg tripeptide, this pairing is significant. This result is supported by the survey of protein structure databases, where it is found that stacked arginine pairs in dipeptide fragments exist solely as being imposed by the protein structure. In contrast, when two arginines are separated by a single amino acid, their guanidinium groups can freely approach each other and they frequently form stacked pairs. Molecular dynamics simulations results are also supported by ab initio calculations, which show stabilization of stacked guanidinium pairs in sufficiently large water clusters. PMID:21721561

Vazdar, Mario; Vym?tal, Ji?i; Heyda, Jan; Vondrášek, Ji?i; Jungwirth, Pavel

2011-07-01

187

Ab initio calculations of third-order elastic constants and related properties for selected semiconductors  

CERN Multimedia

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

188

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

CERN Multimedia

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

189

Molecular dynamics simulation of liquid carbon tetrachloride using ab initio force field  

Science.gov (United States)

Intermolecular interaction potentials of the carbon tetrachloride dimer in 12 orientations have been calculated using the Hartree-Fock self-consistent theory and the second-order Møller-Plesset (MP2) perturbation theory. We have employed basis sets from Pople's medium size basis sets [up to 6-311++G(3df,3pd)] to Dunning's correlation consistent basis sets (up to aug-cc-pVQZ). The calculated MP2 potential data were employed to parametrize a four-site force field for molecular simulations. We performed molecular dynamics simulations using the ab initio force field and compared the simulation results to experiments. Quantitative agreements for the atomwise radial distribution functions, the self-diffusion coefficients, and the neutron and x-ray diffraction scattering functions over a wide range of experimental conditions can be obtained, thus validating the ab initio force field without using experimental data a priori.

Li, Arvin Huang-Te; Huang, Shou-Cheng; Chao, Sheng D.

2010-01-01

190

Ab initio potential energy surfaces for NH-NH with analytical long range  

CERN Multimedia

We present four-dimensional ab initio potential energy surfaces for the three spin states of the NH-NH complex. The potentials are partially based on the work of Dhont et al. [J. Chem. Phys. 123, 184302 (2005)]. The surface for the quintet state is obtained at the RCCSD(T)/aug-cc-pVTZ level of theory and the energy diferences with the singlet and triplet states are calculated at the CASPTn/aug-cc-pVTZ (n = 2; 3) level of theory. The ab initio potentials are fitted to coupled spherical harmonics in the angular coordinates, and the long range is further expanded as a power series in 1/R. The RCCSD(T) potential is corrected for a size-consistency error prior to fitting. The long-range coeficients obtained from the fit are found to be in good agreement with perturbation theory calculations.

Janssen, Liesbeth M C; van der Avoird, Ad; Zuchowski, Piotr S \\; Podeszwa, Rafal

2009-01-01

191

Interatomic potentials for Al and Ni from experimental data and ab initio calculations  

Energy Technology Data Exchange (ETDEWEB)

New embedded-atom potentials for Al and Ni have been developed by fitting to both experimental data and the results of ab initio calculations. The ab initio data were obtained in the form of energies of different alternative computer-generated crystalline structures of these metals. The potentials accurately reproduce basic equilibrium properties of Al and Ni such as the elastic constants, phonon dispersion curves, vacancy formation and migration energies, stacking fault energies, and surface energies. The equilibrium energies of various alternative structures not included in the fitting database are calculated with these potentials. The results are compared with predictions of total-energy tight-binding calculations for the same structures. The embedded-atom potentials correctly reproduce the structural stability trends, which suggests that they are transferable to different local environments encountered in atomistic simulations of lattice defects.

Mishin, Y.; Farkas, D.; Miehl, M.J.; Papaconstantopoulos, D.A.

1999-07-01

192

Point defect modeling in materials: Coupling ab initio and elasticity approaches  

Science.gov (United States)

Modeling point defects at an atomic scale requires careful treatment of the long-range atomic relaxations. This elastic field can strongly affect point defect properties calculated in atomistic simulations because of the finite size of the system under study. This is an important restriction for ab initio methods which are limited to a few hundred atoms. We propose an original approach coupling ab initio calculations and linear elasticity theory to obtain the properties of an isolated point defect for reduced supercell sizes. The reliability and benefit of our approach are demonstrated for three problematic cases: the self-interstitial in zirconium, clusters of self-interstitials in iron, and the neutral vacancy in silicon.

Varvenne, Céline; Bruneval, Fabien; Marinica, Mihai-Cosmin; Clouet, Emmanuel

2013-10-01

193

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

Science.gov (United States)

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

194

Microscopic dynamics in liquid binary alloys: orbital-free ab-initio molecular dynamics studies  

Directory of Open Access Journals (Sweden)

Full Text Available We report an ab-initio molecular dynamics study on the collective excitations in several s-p bonded liquid binary alloys. Results are reported for the Li-Na, Li-Mg, K-Cs and Li-Ba liquid alloys at different concentrations, which display mass ratios ranging from ?3 for Li-Na to ?20 for Li-Ba, and varying ordering tendencies, ranging from strong homocoordinating in Li-Na to mildly heterocoordinating for one concentration of Li-Ba. The study has been carried out using the orbital free ab-initio molecular dynamics method, combined with local ionic pseudopotentials constructed within the same framework. We analyze the dependence of the collective modes on the concentration and the mass ratio of the alloy, finding a common behaviour for all systems notwithstanding the different ordering tendencies.

D.J.González; L.E.González

2008-01-01

195

Ab initio many-body treatment of the electronic structure of metals  

Energy Technology Data Exchange (ETDEWEB)

We propose a method for an ab initio determination of the second-quantized Hamiltonian describing the electronic properties of a certain material. A standard band structure calculation yields the Bloch functions, from which the static susceptibility and dielectric function can be calculated within the random phase approximation and maximally localized Wannier functions can be obtained. Within this Wannier basis all relevant one-particle and screened Coulomb matrix elements are calculated. This yields a multi-band Hubbard Hamiltonian with ab initio parameters to which established methods of many-body theory can be applied. For the simple metal Li an extended, four-band Hubbard model is obtained and a weak-coupling approximation for the self energy is justified.

Peschel, O. [Department of Physics, University of Bremen, P.O. Box 330 440, D-28334 Bremen (Germany)]. E-mail: opeschel@itp.uni-bremen.de; Czycholl, G. [Department of Physics, University of Bremen, P.O. Box 330 440, D-28334 Bremen (Germany); Schnell, I. [Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)

2006-05-01

196

Ab initio determination of an extended Heisenberg Hamiltonian in CuO2 layers  

CERN Multimedia

Accurate ab initio calculations on embedded Cu_4O_{12} square clusters, fragments of the La_2CuO_4 lattice, confirm a value of the nearest neighbor antiferromagnetic coupling (J=124 meV) previously obtained from ab initio calculations on bicentric clusters and in good agreement with experiment. These calculations predict non negligible antiferromagnetic second-neighbor interaction (J'=6.5 meV) and four-spin cyclic exchange (K=14 meV), which may affect the thermodynamic and spectroscopic properties of these materials. The dependence of the magnetic coupling on local lattice distortions has also been investigated. Among them the best candidate to induce a spin-phonon effect seems to be the movement of the Cu atoms, changing the Cu-Cu distance, for which the variation of the nearest neighbor magnetic coupling with the Cu-O distance is {\\Delta J}/{\\Delta d_{Cu-O}}\\sim 1700 cm^{-1} A^{-1}.

Calzado, C J; Calzado, Carmen J.; Malrieu, Jean-Paul

2000-01-01

197

Ab initio simulations and neutron scattering studies of structure and dynamics in PdH  

CERN Multimedia

The work presented in this PhD thesis is concerned with the interpretation of the neutron scattering measurements from the palladium hydrogen system by means of ab initio electronic structure calculations. The motivation of performing such calculations was due to recent neutron scattering studies on this system that showed a strong directional dependence to the dynamical structure factor together with a complex dependence on energy. Here we attempt to describe the origin of these features by ab initio simulations of the dynamical structure factor. The method assumes an adiabatic separation of the motion of the proton and palladium atoms. The proton wave functions are calculated by a direct solution of the associated single-particle Schroedinger equation using a plane wave basis set method and a mapping of the adiabatic surface. The Fourier components of the adiabatic potential are obtained from LDA pseudopotential calculations. Using Fermi's golden rule within the Born approximation we were then able to calcu...

Totolici, I E

2001-01-01

198

Large-scale ab initio configuration interaction calculations for light nuclei  

International Nuclear Information System (INIS)

[en] In ab-initio Configuration Interaction calculations, the nuclear wavefunction is expanded in Slater determinants of single-nucleon wavefunctions and the many-body Schrodinger equation becomes a large sparse matrix problem. The challenge is to reach numerical convergence to within quantified numerical uncertainties for physical observables using finite truncations of the infinite-dimensional basis space. We discuss strategies for constructing and solving the resulting large sparse matrix eigenvalue problems on current multicore computer architectures. Several of these strategies have been implemented in the code MFDn, a hybrid MPI/OpenMP Fortran code for ab-initio nuclear structure calculations that can scale to 100,000 cores and more. Finally, we will conclude with some recent results for 12C including emerging collective phenomena such as rotational band structures using SRG evolved chiral N3LO interactions.

2012-12-18

199

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

CERN Document Server

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

200

Ab initio calculations of potential energy curves of Hg/sub 2/ and TlHg  

Energy Technology Data Exchange (ETDEWEB)

Potential energy curves for electronic states of Hg/sub 2/ and TlHg are presented and analyzed. They are derived using large scale configuration interaction procedures for the valence electrons, with the core electrons represented by ab initio relativistic effective potentials. The effect of spin-orbit coupling are investigated for the low-lying excimer states. It is determined that neither system possesses strongly bound electronic states for which transitions to the repulsive ground states are optically allowed.

Celestino, K.C.; Ermler, W.C.

1984-08-15

 
 
 
 
201

Pair potentials for alumina from ab initio results on the Al2O3 molecule  

International Nuclear Information System (INIS)

We use results from an ab initio investigation by Chang et al. on energetically low-lying stationary points of the Al2O3 molecule to determine interionic potentials for the Al-O, O-O and Al-Al pairs. Our results are discussed in the perspective of previous studies of the condensed phases of alumina, with special regard to the structure of its molten state. (author)

2000-01-01

202

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

CERN Multimedia

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

203

Ab initio study of the double row model of the Si(553)-Au reconstruction  

CERN Multimedia

Using x-ray diffraction Ghose et al. [Surf. Sci. {\\bf 581} (2005) 199] have recently produced a structural model for the quantum-wire surface Si(553)-Au. This model presents two parallel gold wires located at the step edge. Thus, the structure and the gold coverage are quite different from previous proposals. We present here an ab initio study using density functional theory of the stability, electronic band structure and scanning tunneling microscopy images of this model.

Riikonen, S; Riikonen, Sampsa; Sanchez-Portal, Daniel

2005-01-01

204

Steady-State Ab Initio Laser Theory for N-level Lasers  

CERN Multimedia

We show that Steady-state Ab initio Laser Theory (SALT) can be applied to find the stationary multimode lasing properties of an N-level laser. This is achieved by mapping the N-level rate equations to an effective two-level model of the type solved by the SALT algorithm. This mapping yields excellent agreement with more computationally demanding N-level time domain solutions for the steady state.

Cerjan, Alexander; Ge, Li; Stone, A Douglas

2011-01-01

205

Steady state Ab-initio Theory of Lasers with Injected Signals  

CERN Multimedia

We present an ab-initio treatment of steady-state lasing with injected signals that treats both multimode lasing and spatial hole burning, and describes the transition to injection locking or partial locking in the multimode case. The theory shows that spatial hole burning causes a shift in the frequency of free-running laser modes away from the injection frequency, in contrast to standard approaches.

Cerjan, Alexander

2013-01-01

206

Ab initio properties of MgAlk (Alk = Li, Na, K, Rb, Cs)  

Science.gov (United States)

High level ab initio calculations are performed on the ground electronic state of diatomic molecules MgAlk (Alk = Li, Na, K, Rb, Cs). Potential energy curves and dipole moment functions are determined making use of the single-reference unrestricted and restricted coupled-cluster methods with large basis sets. Basic spectroscopic properties of the ground electronic states are derived from ro-vibrational bound state calculations.

Augustovi?ová, L.; Soldán, P.

2012-02-01

207

Association and dissociation mechanisms for BnOm. Ab-initio molecular orbital method  

International Nuclear Information System (INIS)

[en] We have discussed the collision induced dissociation (CID) and association (CIA) of low-Z clusters. The cross sections of CID and CIA had been measured for cationic boron clusters, Bn+ (n=1-13), on colliding with O2 beam at very low energy below 10 eV. We perform theoretical calculations using ab initio Molecular Orbital method and investigate the reaction path, whether CIA or CID is preferred. (author)

2007-01-01

208

High-pressure ion-thermal properties of metals from ab initio interatomic potentials  

Energy Technology Data Exchange (ETDEWEB)

It has recently become possible for the first time to calculate ab initio two-ion and three-ion interatomic potentials in d-electron transition metals. The nature of these potentials for the 3d series metals is discussed. In the case of copper, where three-ion contributions may be neglected, application is made to the ion-thermal component of the equation of state and to the calculation of melting on the shock Hugoniot. 13 refs., 3 figs.

Moriarty, J.A.

1985-06-01

209

The Projector Augmented Wave Method ab-initio molecular dynamics with full wave functions  

CERN Document Server

A brief introduction to the projector augmented wave method is given and recent developments are reviewed. The projector augmented wave method is an all-electron method for efficient ab-initio molecular dynamics simulations with the full wave functions. It extends and combines the traditions of existing augmented wave methods and the pseudopotential approach. Without sacrificing efficiency, the PAW method avoids transferability problems of the pseudopotential approach and it has been valuable to predict properties that depend on the full wave functions.

Blöchl, P E; Schimpl, J; Bl\\"ochl, Peter E.; Schimpl, Johannes

2002-01-01

210

High-pressure ion-thermal properties of metals from ab initio interatomic potentials  

International Nuclear Information System (INIS)

It has recently become possible for the first time to calculate ab initio two-ion and three-ion interatomic potentials in d-electron transition metals. The nature of these potentials for the 3d series metals is discussed. In the case of copper, where three-ion contributions may be neglected, application is made to the ion-thermal component of the equation of state and to the calculation of melting on the shock Hugoniot. 13 refs., 3 figs

1985-01-01

211

Ab initio study of optical absorption spectra of semiconductors and conjugated polymers  

International Nuclear Information System (INIS)

[en] The effects of electron-hole interaction on the optical properties of a variety of materials have been calculated using an ab initio method based on solving the Bethe-Salpeter equation. Results on selected semiconductors, insulators, and semiconducting polymers are presented. In the cases of alpha-quartz (SiO2) and poly-phenylene-vinylene, resonant excitonic states qualitatively alter the absorption spectra

2000-07-31

212

Dynamics of (H-, D2) collision on a new ab initio potential energy surface. CP-24  

International Nuclear Information System (INIS)

[en] Collisions of positive, neutral and negatively charged hydrogen atoms with hydrogen molecules constitute an important subject from a fundamental point of view. The exchange reaction H-+ D2(v = 0, j = 0) ? HD +D- in three dimensions has been studied in the collision energy range 0.3 - 3 eV, using time-dependent quantum mechanical wave packet method under centrifugal sudden approximation on a new ab initio potential energy surface

2004-01-01

213

Transformation of ab initio force fields in calculations of molecular vibrations using regundand vibrational coordinates  

International Nuclear Information System (INIS)

A technique was suggested to transform ab initio molecular force fields calculated using a set of independent vibrational coordinates into a form corresponding to a complete set of regundand coordinates and reflecting the molecular symmetry. Conditions necessary for the appropriate transformations to be possible are formulated. The possibility of transforming the force field for the simplest fragment containing regundand coordinates was demonstrated using ethylene as an example. (authors)

2011-01-01

214

Ab initio molecular dynamics simulation of hydrogen fluoride at several thermodynamic states  

DEFF Research Database (Denmark)

Liquid hydrogen fluoride is a simple but interesting system for studies of the influence of hydrogen bonds on physical properties. We have performed ab initio molecular dynamics simulations of HF at several thermodynamic states, where we examine the microscopic structure of the liquid as well as its static and dynamic properties. The results obtained show good agreement with well established data, and, moreover, we were able to show significant changes within the structure depending on the system's temperature and density.

Kreitmeir, M.; Bertagnolli, H.

2003-01-01

215

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.

1988-01-01

216

Ab initio study of the electronic spectrum of BeO  

Directory of Open Access Journals (Sweden)

Full Text Available Low-lying singlet and triplet electronic states of the BeO molecule are calculated by means of the quantum chemical ab initio method. It was found that all states in the energy range from 0 to 50000 cm-1 are of valence character. Particular attention was paid to the investigation of the dissociative behavior of the states considered. The vibrational structure of the AIP<-XIS and BIS+<-XIS+ spectral systems was calculated.

IVANA ADAMOVIC; MAJA PARAC; MICHAEL HANRATH; MILJENKO PERIC

1999-01-01

217

Ab initio molecular dynamics study of supercritical carbon dioxide including dispersion corrections.  

UK PubMed Central (United Kingdom)

Density functional theory based ab initio molecular dynamics simulations with explicit inclusion of empirical van der Waals (vdW) corrections of supercritical carbon dioxide have been performed. Significant changes in the intermolecular pair correlation functions of the fluid modeled with the added vdW interactions are observed, particularly at lower densities. The closest neighbor to a molecule is seen to be oriented in a distorted T-shaped geometry, consistent with earlier experiments and simulations.

Balasubramanian S; Kohlmeyer A; Klein ML

2009-10-01

218

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

CERN Document Server

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

219

A molecular mechanics valence force field for sulfonamides derived by ab initio methods  

Energy Technology Data Exchange (ETDEWEB)

Molecular mechanics valence force field parameters for the sulfonamide group, SO[sub 2]NH, have been derived from ab initio calculations at the RHF/6-31G* level of theory. The force field parameters were designed to be used in conjunction with existing parameters from the MM2/MMP2 force field. The new parameters are demonstrated to accurately reproduce the ab initio optimized geometries of four molecules that contain the sulfonamide group. The strategy used in force field parametrization is discussed. The conformational flexibility of the sulfonamide group has been investigated. Calculations at the RHF/6-31G* level reveal the existence of two stable conformers and that interconversion is achieved by nitrogen inversion rather than rotation about the S-N bond. The energetic effects of expanding the basis set to 6-31G** and of including MP2 and MP3 corrections for electron correlation are discussed. The geometries and Mulliken charges for the ab initio optimized structures are also reported.

Nicholas, J.B.; Burke, B.J.; Hopfinger, A.J. (Univ. of Illinois, Chicago (United States)); Vance, R.; Martin, E. (DowElanco, Walnut Creek, CA (United States))

1991-11-28

220

An accurate ab initio HOCl potential energy surface, vibrational and rotational calculations, and comparison with experiment  

International Nuclear Information System (INIS)

[en] Accurate ab initio multireference configuration interaction (CI) calculations with large correlation-consistent basis sets are performed for HOCl. After extrapolation to the complete basis set limit, the ab initio data are precisely fit to give a semiglobal three-dimensional potential energy surface to describe HOCl?Cl+OH from high overtone excitation of the OH-stretch. The average absolute deviation between the ab initio and fitted energies is 4.2thinspcm-1 for energies up to 60 kcal/mol relative to the HOCl minimum. Vibrational energies of HOCl including the six overtones of the OH-stretch are computed using a vibrational-Cl method on the fitted potential and also on a slightly adjusted potential. Near-spectroscopic accuracy is obtained using the adjusted potential; the average absolute deviation between theory and experiment for 19 experimentally reported states is 4.8thinspcm-1. Very good agreement with experiment is also obtained for numerous rotational energies for the ground vibrational state, the ClO-stretch fundamental, and the fifth overtone of the OH-stretch. copyright 1998 American Institute of Physics

1998-01-01

 
 
 
 
221

Theoretical study of silicon carbide under irradiation at the nano scale: classical and ab initio modelling  

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)

2006-01-01

222

Modelling of nuclear glasses by classical and ab initio molecular dynamics  

International Nuclear Information System (INIS)

[en] 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)

2004-01-01

223

Elucidation of the physicomechanical and ab initio quantum energy transitions of a crosslinked PLGA scaffold.  

UK PubMed Central (United Kingdom)

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.

Sibambo SR; Pillay V; Choonara YE; Khan RA; Sweet JL

2007-09-01

224

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

International Nuclear Information System (INIS)

[en] 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)

2010-01-01

225

Poisoning of Hydrogen Dissociation at Pd(100) by Adsorbed Sulfur Studied by ab initio Quantum Dynamics and ab initio Molecular Dynamics  

CERN Multimedia

We report calculations of the dissociative adsorption of H_2 at Pd (100) covered with 1/4 monolayer of sulfur using quantum dynamics as well as molecular dynamics and taking all six degrees of freedom of the two H atoms fully into account. The ab initio potential-energy surface (PES) is found to be very strongly corrugated. In particular we discuss the influence of tunneling, zero-point vibrations, localization of the nuclei's wave function when narrow valleys of the PES are passed, steering of the approaching H_2 molecules towards low energy barrier configurations, and the time scales of the center of mass motion and the other degrees of freedom. Several ``established'' concepts, which were derived from low-dimensional dynamical studies, are shown to be not valid.

Gross, A; Scheffler, M; Gross, Axel; Wei, Ching-Ming; Scheffler, Matthias

1998-01-01

226

Estudo ab-initio da a-alanina em meio aquoso Ab-initio study of a-alanine in aqueous medium  

Directory of Open Access Journals (Sweden)

Full Text Available 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/6-31G* level but it is not when diffuse functions and electron correlation are included. This results shows that the Z form does not exist in the gas phase. The inclusion of solvent effects changed significantly the results obtained in gas phase, therefore this inclusion make the Z form a stationary point within all level of theory, and the relative energy depends dramatically on the level of calculation.

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

1999-01-01

227

Combinatorial screening of polymer precursors for preparation of benzo[?] pyrene imprinted polymer: an ab initio computational approach.  

UK PubMed Central (United Kingdom)

A combinatorial screening procedure was used for the selection of polymer precursors in the preparation of molecularly imprinted polymer (MIP), which is useful in the detection of the air pollution marker molecule benzo[a]pyrene (BAP). Molecular imprinting is a technique for the preparation of polymer materials with specific molecular recognition receptors. The preparation of imprinted polymers requires polymer precursors such as functional monomer, cross-linking monomer, solvent, an initiator of polymerization and thermal or UV radiation. A virtual library of functional monomers was prepared based on interaction binding scores computed using HyperChem Release 8.0 software. Initially, the possible minimum energy conformation of the monomers and BAP were optimized using the semi-empirical (PM3) quantum method. The binding energy between the functional monomer and the template (BAP) was computed using the Hartree-Fock (HF) method with 6-31 G basis set, which is an ab initio approach based on Moller-Plesset second order perturbation theory (MP2). From the computations, methacrylic acid (MAA) and ethylene glycol dimethacrylate (EGDMA) were selected for preparation of BAP imprinted polymer. The larger interaction energy (?E) represents possibility of more affinity binding sites formation in the polymer, which provides high binding capacity. The theoretical predictions were complimented through adsorption experiments. There is a good agreement between experimental binding results and theoretical computations, which provides further evidence of the validity of the usefulness of computational screening procedures in the selection of appropriate MIP precursors in an experiment-free way.

Khan MS; Wate PS; Krupadam RJ

2012-05-01

228

Modeling of nuclear glasses by classical and ab initio molecular dynamics  

International Nuclear Information System (INIS)

[en] 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)[fr] Resume: Un verre de composition 67 % SiO2 - 12 % Al2O3 - 21 % CaO, choisi comme modele simplifie des pellicules d'alteration, est modelise par les methodes de dynamique moleculaire (DM) classique et ab initio. L'etude des effets de taille, en DM classique, montre que les systemes de 100 atomes presentent un caractere plus ordonne par rapport a des systemes de plus grande taille. L'effet observe est principalement lie a l'utilisation de termes de potentiels 3-corps. Non observable sur les facteurs de structure neutronique, le facteur calcule a partir d'une structure modelisee est en bonne adequation avec une mesure experimentale et valide le modele classique. Les structures modelisees presentent un exces d'atomes d'oxygenes non pontants qui peuvent etre compenses par des atomes d'oxygene tricoordonnes. L'exclusion non totale des atomes aluminium est aussi mis en evidence. La poursuite de la dynamique en DM ab initio de systemes de 100 et 200 atomes fabrique en DM classique permet d'affiner localement les structures (distances interatomiques, angles). Une description plus realiste des vibrations est obtenue. La modelisation de films minces en DM classique montre une zone enrichie en calcium en sub-surface ou l'on observe une depolymerisation du reseau vitreux. L'aluminium s'etend le plus en surface et s'y trouve tricoordonne. La distribution atomique des films et les entites AIO3 sont confirmes par un ajustement en DM ab initio. En DM classique, les atomes d'aluminium produisent un fort champ electrique au dessus de la surface et ils constituent, avec les sites NBO-Ca, des zones reactives avec H2O. (auteur)

2004-01-01

229

An Ab Initio Approach Towards Engineering Fischer-Tropsch Surface Chemistry  

Energy Technology Data Exchange (ETDEWEB)

One of the greatest societal challenges over the next decade is the production of cheap, renewable energy for the 10 billion people that inhabit the earth. This will require the development of various different energy sources potentially including fuels derived from methane, coal, and biomass and alternatives sources such as solar, wind and nuclear energy. One approach will be to synthesize gasoline and other fuels from simpler hydrocarbons such as CO derived from methane or other U.S. based sources such as coal. Syngas (CO and H{sub 2}) can be readily converted into higher molecular weight hydrocarbons through Fischer-Tropsch synthesis. Fischer-Tropsch synthesis involves the initiation or activation of CO and H{sub 2} bonds, the subsequent propagation steps including hydrogenation and carbon-carbon coupling, followed by chain termination reactions. Commercially viable catalysts include supported Co and Co-alloys. Over the first two years of this project we have used ab initio methods to determine the adsorption energies for all reactants, intermediates, and products along with the overall reaction energies and their corresponding activation barriers over the Co(0001) surface. Over the third year of the project we developed and advanced an ab initio-based kinetic Monte Carlo simulation code to simulate Fischer Tropsch synthesis. This report details our work over the last year which has focused on the derivation of kinetic parameters for the elementary steps involved in FT synthesis from ab initio density functional theoretical calculations and the application of the kinetic Monte Carlo algorithm to simulate the initial rates of reaction for FT over the ideal Co(0001) surface. The results from our simulations over Co(0001) indicate the importance of stepped surfaces for the activation of adsorbed CO. In addition, they demonstrate that the dominant CH{sub x}* surface intermediate under steady state conditions is CH*. This strongly suggests that hydrocarbon coupling occurs through reaction with the adsorbed CH*.

Matthew Neurock; David A. Walthall

2006-05-07

230

Time-domain ab initio studies of excitation dynamics in semiconductor quantum dots  

Science.gov (United States)

Solar energy applications require understanding of dynamical response of novel materials on nanometer scale. Our state-of-the-art non-adiabatic molecular dynamics techniques, implemented within time-dependent density functional theory, allow us to model such response at the atomistic level and in real time. The talk will focus on single and multiple exciton generation, relaxation, annihilation and dephasing in semiconductor quantum dots.[4pt] References:[0pt] [1] O. V. Prezhdo, "Multiple excitons and electron-phonon bottleneck in semiconductor quantum dots: Insights from ab initio studies", Chem. Phys. Lett. -- Frontier Article, 460, 1 (2008) [0pt] [2] O. V. Prezhdo "Photoinduced dynamics in semiconductor quantum-dots: insights from time-domain ab initio studies", Acc. Chem. Res., 42, 2005 (2009) [0pt] [3] A. B. Madrid, H.-D. Kim, O. V. Prezhdo, "Phonon-induced dephasing of excitons in silicon quantum dots: multiple exciton generation, fission and luminescence", ACS-Nano, 3, 2487 (2009) [0pt] [4] C. M. Isborn, O. V. Prezhdo, "Quantum dot charging quenches multiple exciton generation: first-principles calculations on small PbSe clusters", J. Phys. Chem. C, 113, 12617 (2009) [0pt] [5] S. V. Kilina, D. S. Kilin, O. V. Prezhdo, "Breaking the phonon bottleneck in PbSe and CdSe quantum dots: time-domain density functional theory of charge carrier relaxation", ACS-Nano, 3, 93 (2009). [0pt] [6] S. A. Fischer, A. B. Madrid, C. M. Isborn, O. V. Prezhdo, "Multiple exciton generation in small Si clusters: A high-level, ab initio study", J. Phys. Chem. Lett., 1, 232 (2010).

Prezhdo, Oleg

2011-03-01

231

Ab initio intermolecular potential energy surfaces of the water-rare gas atom complexes.  

Science.gov (United States)

Highly accurate analytical intermolecular potential energy surfaces (PESs) of the complexes composed of the water molecule and the rare gas (Rg) atom are presented for Rg=He, Ne, Ar, and Kr. These PESs were scanned using the supermolecule coupled cluster singles and doubles including connected triples method [CCSD(T)]. Efficient basis sets including the bond functions (3s3p2d1f1g) enabled the calculation of more than 430 single-point interaction energies for each complex. These energies were utilized to construct the analytical many-body representations of the PESs. They were refined using the interaction energies evaluated at the complete basis set limit in the PES stationary points. In addition, the corrections from the core correlation were calculated for the complexes including He, Ne, and Ar. The many-body PES of XeH(2)O was built using the ab initio energy values reported by Wen and Jager [J. Phys. Chem. A 110, 7560 (2006)]. The clear regularities of the equilibrium structure and the potential barriers were found in the RgH(2)O series. A comparison of the ab initio and experimental PESs of ArH(2)O [R. C. Cohen and R. J. Saykally, J. Chem. Phys. 98, 6007 (1993)] reveals their close similarity, except for the potential barriers corresponding to the planar saddle points. Their energetic order is different in both PESs. This suggests that an alternative PES with the reversed barriers, consistent with the ab initio ones, could be derived from the experimental data. PMID:19045406

Makarewicz, Jan

2008-11-14

232

Rotationally invariant ab initio evaluation of Coulomb and exchange parameters for DFT+U calculations.  

UK PubMed Central (United Kingdom)

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.

Mosey NJ; Liao P; Carter EA

2008-07-01

233

Understanding solvation in hydrofluoroalkanes: ab initio calculations and chemical force microscopy.  

UK PubMed Central (United Kingdom)

Understanding solvation in hydrofluoroalkane (HFA) propellants is of great importance for the development of novel pressurized metered-dose inhaler (pMDI) formulations. HFA-based pMDIs are not only the most widely used inhalation therapy devices for treating lung diseases, but they also hold promise as vehicles for the systemic delivery of biomolecules to and through the lungs. In this work we propose a combined microscopic experimental and computational approach to quantitatively relate the chemistry of moieties to their HFA-philicity. Binding energy calculations are used to determine the degree of interaction between a propellant HFA and candidate fragments. We define a new quantity, the enhancement factor E, which also takes into account fragment-fragment interactions. This quantity is expected to correlate well with the solubility and the ability of the moieties of interest to impart stability to colloidal dispersions in HFAs. We use a methyl-based (CH) segment and its fluorinated analog (CF) to test our approach. CH is an important baseline case since it represents the tails of surfactants in FDA-approved pMDIs. CF was chosen due to the improved solubility and ability of this chemistry to stabilize aqueous dispersions in HFAs. Adhesion force from Chemical Force Microscopy (CFM) is used as an experimental analog to the binding energy calculations. The force of interaction between a chemically modified AFM tip and substrate is measured in a model HFA, which is a liquid at ambient conditions. Silanes with the same chemistry as the fragments used in the ab initio calculations allow for direct comparison between the two techniques. The CFM results provide an absolute scale for HFA-philicity. Single molecule (pair) forces calculated from the CFM experiments are shown to be in very good agreement to the E determined from the ab initio calculations. The ab initio calculations and CFM are corroborated by previous experimental studies where propellants HFAs are seen to better solvate the CF functionality.

Wu L; Peguin RP; da Rocha SR

2007-07-01

234

Cobalt-doped ZnO nanocrystals: quantum confinement and surface effects from ab initio methods.  

UK PubMed Central (United Kingdom)

Cobalt-doped ZnO nanocrystals were studied through ab initio methods based on the Density Functional Theory. Both quantum confinement and surface effects were explicitly taken into account. When only quantum confinement effects are considered, Co atoms interact through a superexchange mechanism, stabilizing an antiferromagnetic ground state. Usually, this is the case for high quality nanoparticles with perfect surface saturation. When the surfaces were considered, a strong hybridization between the Co atoms and surfaces was observed, strongly changing their electronic and magnetic properties. Our results indicated that the surfaces might qualitatively change the properties of impurities in semiconductor nanocrystals.

Schoenhalz AL; Dalpian GM

2013-10-01

235

Cobalt-doped ZnO nanocrystals: quantum confinement and surface effects from ab initio methods.  

Science.gov (United States)

Cobalt-doped ZnO nanocrystals were studied through ab initio methods based on the Density Functional Theory. Both quantum confinement and surface effects were explicitly taken into account. When only quantum confinement effects are considered, Co atoms interact through a superexchange mechanism, stabilizing an antiferromagnetic ground state. Usually, this is the case for high quality nanoparticles with perfect surface saturation. When the surfaces were considered, a strong hybridization between the Co atoms and surfaces was observed, strongly changing their electronic and magnetic properties. Our results indicated that the surfaces might qualitatively change the properties of impurities in semiconductor nanocrystals. PMID:23942732

Schoenhalz, Aline L; Dalpian, Gustavo M

2013-08-13

236

Ab initio studies of ionization potentials of hydrated hydroxide and hydronium  

CERN Multimedia

The ionization potential distributions of hydrated hydroxide and hydronium are computed with many-body approach for electron excitations with configurations generated by {\\it ab initio} molecular dynamics. The experimental features are well reproduced and found to be closely related to the molecular excitations. In the stable configurations, the ionization potential is mainly perturbed by water molecules within the first solvation shell. On the other hand, electron excitation is delocalized on both proton receiving and donating complex during proton transfer, which shifts the excitation energies and broadens the spectra for both hydrated ions.

Swartz, Charles W

2013-01-01

237

Finite-temperature exchange-correlation functional in an ab initio molecular dynamics code  

Science.gov (United States)

We study the role of finite-temperature exchange-correlation functional in an ab initio molecular dynamics code using a variational approach to describe the electronic and ionic structures. We use the method proposed by Perrot and Dharma-wardana [Phys. Rev. B 62, 16536, 2000] to take into account the finite-temperature effect in the exchange-correlation functional. We find small influence of finite-temperature exchange-correlation functional compared to zero-temperature exchange-correlation functional for aluminum in the warm dense matter regime.

Faussurier, Gérald; Silvestrelli, Pier Luigi; Blancard, Christophe

2009-06-01

238

From empirical to ab initio: transferable potentials in the atomistic simulation of amorphous carbons  

International Nuclear Information System (INIS)

Full text: Silicon is often described as the prototype covalent material, and when it comes to developing atomistic models this situation is well described by the sentiment that 'everything works for silicon'. The same cannot be said for carbon though, where the interaction potential has always proved problematical, be it with empirical, tight-binding or ab initio methods. Thus far the most decisive contributions to understanding amorphous carbon networks have come from ab initio simulations using the Car-Parrinello method, where the fully quantum treatment of the valence electrons has provided unexpected insight into the local structure. However such first principles calculations are restricted spatially and temporally to systems with approximately 100 atoms and times of order one picosecond. There is therefore demand for less expensive techniques capable of resolving important questions whose solution can only to found with larger simulations running for longer times. In the case of tetrahedral amorphous carbon, such issues include the release of compressive stress through annealing, the origin of graphitic surface layers and the nature of the film growth process and thermal spike. Against this background tight-binding molecular dynamics has emerged as a popular alternative to first principles methods, and our group has an ongoing program to understand film growth using one of the efficient variants of tight-binding. Another direction of research is a new empirical potential based on the Environment Dependent Interaction Potential (EDIP) recently developed for silicon. The EDIP approach represents a promising direction for empirical potentials through its use of ab initio data to motivate the functional form as well as the more conventional parametrisation. By inverting ab initio cohesive energy curves the authors of EDIP arrived at a pair potential expression which reduces to the well-known Stillinger-Weber form at integer coordination, while providing interpolation and extrapolation to situations where the coordination was either fractional or beyond the fitting data set. The application of EDIP to carbon has thus far been quite encouraging, in particular the two-body pair potential which exhibits a remarkably good degree of transferability to coordinations two and six, despite being fitted to only the graphene and diamond structures. Current development work is concentrating on the c-axis ?-repulsion and dihedral rotation penalties which are absent from the original EDIP. Preliminary molecular dynamics simulations using this modified EDIP provide a visual and intuitive demonstration of why these effects are so important when modelling amorphous carbons

2000-01-01

239

Ab initio study of reactions between halogen atoms and various fuel molecules by Gaussian-2 theory.  

UK PubMed Central (United Kingdom)

Ab initio calculations by using Gaussian-2 theory have been carried out for the reactions between halogen atoms and various fuel molecules, i.e. fluorine, chlorine, and bromine atoms vs. hydrogen, methane, ethane, ethylene, acetylene, ammonia, silane, dichlorosilane and phosphine. The activation energy for the reaction between a halogen atom and a fuel molecule seems to indicate whether the reaction between the fuel gas and the corresponding halogen gas occurs spontaneously when they are brought into contact to each other at room temperature.

Kondo S; Tokuhashi K; Takahashi A; Kaise M

2000-12-01

240

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

CERN Document Server

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

 
 
 
 
241

Matrix IR spectrum and ab initio SCF calculations of molecular SiS sub 2  

Energy Technology Data Exchange (ETDEWEB)

In solid argon molecular SiS{sub 2} is generated by a reaction of SiS with S atoms. The antisymmetric stretching vibration {nu}{sub as}(SiS) is observed at 918 cm{sup {minus}1}. Bonding and structure (force constants from experimentally observed frequencies and results from ab initio SCF calculations) of SiS{sub 2} are compared with that of the similar molecules: CO, CS, CO{sub 2}, COS, CS{sub 2}, SiO, SiS, SiO{sub 2}, and SiOS.

Schnoeckel, H.; Koeppe, R. (Universitaet Muenster (West Germany))

1989-06-21

242

High capacity reversible hydrogen storage by metallo-carbohedrenes: An ab initio molecular dynamics simulation study  

Science.gov (United States)

Here, we report a hydrogen storage material based on partially hydrogenated metallo-carbohedrene (Ti8C12H12) cluster using an ab-initio molecular dynamics simulation study. The effective storage capacity of the partially hydrogenated metallo-carbohedrene with reversible adsorption-desorption behavior is estimated to be 10.96 wt. % albeit total hydrogen loading capacity of 15.06 wt. % for an isolated Ti8C12 cluster. On the basis of the results, it is inferred that the partially hydrogenated metallocarbohedrenes are very promising high capacity reversible hydrogen storage materials.

Banerjee, S.; Pillai, C. G. S.; Majumder, C.

2013-02-01

243

Temperature dependent mechanical properties of Mo–Si–B compounds via ab initio molecular dynamics  

Directory of Open Access Journals (Sweden)

Full Text Available A new method was proposed to obtain high temperature mechanical properties with a combination of ab initio molecular dynamics and stress-strain analyses. It was applied to compounds in the Mo–Si–B ternary system, namely, T1 (Mo5Si3) and T2 (Mo5SiB2) phases. The calculated coefficient of thermal expansion, thermal expansion anisotropy, and elastic constants agree well with those from the available experiments. The method enables us to theoretically access these properties up to 2000 K.

C. C. Dharmawardhana; R. Sakidja; S. Aryal; W. Y. Ching

2013-01-01

244

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.

2006-02-09

245

Ab initio investigation of phonon modes in the MgAl2O4 spinel  

International Nuclear Information System (INIS)

Ab initio infrared and Raman phonon modes in the normal cubic MgAl2O4 spinel are calculated at the first Brillouin zone centre using density functional theory with plane-wave basis and norm-conserving pseudopotentials. Good agreement with available experimental infrared and Raman spectra is found for both natural and synthetic spinel. A new set of infrared measurements on synthetic spinels shows extra vibrational infrared modes which are not predicted by calculations on normal spinel. The ionic character of spinels is illustrated by comparison between calculated and experimental Born effective charges. (author)

2002-05-03

246

Ab initio calculation of the ground-state properties of CoSi{sub 2}  

Energy Technology Data Exchange (ETDEWEB)

We have investigated the structural and electronic properties of CoSi{sub 2} by using a generalized gradient approximation of the density functional theory and ab initio pseudopotentials. The calculated lattice constant and electronic band structure have been used in the application of a linear response approach based on density functional perturbation theory for phonon studies. The structural results are in good agreement with previous works. The calculated phonon spectra are in good agreement with available experimental data. A detailed discussion of atomic displacement pattern is provided corresponding to the two sets of LO and TO phonon modes.

Ugur, G [Gazi Ueniversitesi Fen-Edebiyat Fakueltesi Fizik Boeluemue, 06500, Ankara (Turkey); Soyalp, F [Gazi Ueniversitesi Fen-Edebiyat Fakueltesi Fizik Boeluemue, 06500, Ankara (Turkey); Tuetuencue, H M [Sakarya Ueniversitesi Fen-Edebiyat Fakueltesi Fizik Boeluemue, 54100, Adapazari (Turkey); Duman, S [Sakarya Ueniversitesi Fen-Edebiyat Fakueltesi Fizik Boeluemue, 54100, Adapazari (Turkey); Srivastava, G P [University of Exeter, School of Physics, Stocker Road, Exeter EX4 4QL (United Kingdom)

2005-11-09

247

Ab initio calculation of the ground-state properties of CoSi2  

International Nuclear Information System (INIS)

We have investigated the structural and electronic properties of CoSi2 by using a generalized gradient approximation of the density functional theory and ab initio pseudopotentials. The calculated lattice constant and electronic band structure have been used in the application of a linear response approach based on density functional perturbation theory for phonon studies. The structural results are in good agreement with previous works. The calculated phonon spectra are in good agreement with available experimental data. A detailed discussion of atomic displacement pattern is provided corresponding to the two sets of LO and TO phonon modes.

2005-11-09

248

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

UK PubMed Central (United Kingdom)

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, Li(18)OH, and (6)LiOH isotopologues were predicted to near "spectroscopic" accuracy.

Koput J

2013-06-01

249

Ab initio calculations of potential energy surface for the FB + H2 -> FBH2 reaction  

International Nuclear Information System (INIS)

[en] Ab initio calculations of potential energy surface (PES) of the reaction FB + H2 -> FBH2, as well as energies of singlet-triplet transitions in BH and BF molecules, have been made. The results of PES calculations for the given reaction are compared with the previously calculated in the same approximation PES for the reaction HB + H2 -> BH3. Proportionality of the height of activation barriers of both reactions to the energies of BH and BF molecules has been revealed. 8 refs., 3 figs., 3 tabs

1995-01-01

250

Ab initio investigation of mechanical behaviour of MgB{sub 2} superconductor under pressure  

Energy Technology Data Exchange (ETDEWEB)

We present ab initio calculations of a set of physical properties for the newly discovered MgB{sub 2} superconductor. The zero pressure bulk modulus, the pressure derivative of the bulk modulus and their in- and out-of-plane linear values are evaluated. An analysis of the calculated parameters reveals the diversity in bonding interactions. The diboride is characterized by a moderately sizable anisotropy of compressibilites, which is smaller than for cuprates, but larger than for other related diborides. The anisotropic compression is expected to induce different pressure effects on different phonon modes and also to influence the electronic structure at the Fermi energy. (author). Letter-to-the-editor.

Islam, A.K.M.A.; Islam, F.N.; Kabir, S. [Department of Physics, Rajshahi University, Rajshahi (Bangladesh)

2001-07-09

251

Ab-initio Study of Known and Hypothetical Metal-Organic Frameworks  

Science.gov (United States)

Rosi et al. [1] have found that microporous Metal-Organic Frameworks (MOF) materials are candidates for hydrogen storage applications. In particular, MOF-5 was found to adsorb hydrogen up to 4.5 weight percent at 78 kelvin and 1.0 weight percent at room temperature and pressure of 20 bar. We use ab-initio techniques to investigate hydrogen adsorption, stability, and the electronic properties of known and hypothetical Metal-Organic Frameworks. [1] N.L. Rosi, J. Eckert, M. Eddaoudi, D.T. Vodak, J. Kim, M. O'Keeffe, and O.M. Yaghi

Fuentes-Cabrera, Miguel; Nicholson, Don M.

2004-03-01

252

Synthesis and ab initio calculations of nanolaminated (Cr,Mn)2AlC compounds  

Science.gov (United States)

We present an ab initio theoretical analysis of the temperature-dependent stability of inherently nanolaminated (Cr1-xMnx)2AlC. The results indicate energetic stability over the composition range x = 0.0 to 0.5 for temperatures ?600 K. Corresponding thin film compounds were grown by magnetron sputtering from four elemental targets. X-ray diffraction in combination with analytical transmission electron microscopy, including electron energy-loss spectroscopy and energy dispersive x-ray spectroscopy analysis, revealed that the films were epitaxial (0001)-oriented single-crystals with x up to 0.16.

Mockute, Aurelija; Dahlqvist, Martin; Emmerlich, Jens; Hultman, Lars; Schneider, Jochen M.; Persson, Per O. Å.; Rosen, Johanna

2013-03-01

253

Synthesis and Ab Initio/DFT Studies on 2-(4-methoxyphenyl)benzo[d]thiazole  

Directory of Open Access Journals (Sweden)

Full Text Available 2-aminothiophenol and 4-methoxybenzaldehyde were cyclized under microwaveirridation and solvent free conditions to synthesize 2-(4-methoxyphenyl)benzo[d]thiazole.The molecular structure and vibrational frequencies of the title compound in the groundstate have been investigated with ab initio (HF) and density functional theory methods(BLYP, B3LYP, B3PW91 and mPW1PW91) implementing the standard 6-311G(d,p) basisset. Comparison of the observed fundamental vibrational frequencies of title compound andcalculated results by HF and DFT methods indicate that B3LYP is superior to the scaledHF approach for molecular problems.

Hakan Arslan; Öztekin Algül

2007-01-01

254

Ab initio simulations of nitrogen evolution in quenched C Nx and SiBCN amorphous materials  

Science.gov (United States)

We report ab initio molecular dynamics simulations of the preparation of CNx , BCN, and SiBCN materials formed by energetic-ion-assisted deposition techniques. We focus on the formation of N2 molecules during liquid-quench simulations and investigate how density, temperature, and quench rate affect the number of N2 molecules formed in the network. We find that higher material density and shorter cooling times lead to reduced N2 formation and thus higher nitrogen incorporation into the structure. These results suggest a modification of common physical vapor deposition techniques to enhance N content in materials such as CNx .

Houska, J.; Bilek, M. M. M.; Warschkow, O.; McKenzie, D. R.; Vlcek, J.

2005-08-01

255

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

CERN Document Server

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

256

An exact ab initio theory of quantum transport using TDDFT and nonequilibrium Green's functions  

International Nuclear Information System (INIS)

We present an exact ab initio theory for describing the motion of interacting electrons through nanoscopic constrictions. Our theory is based on time-dependent density functional theory (TDDFT) and nonequilibrium Green functions. We consider the system electrode-device-electrode initially contacted and in equilibrium, therefore the scheme is thermodynamically consistent. Besides the steady-state responses one can also calculate physical dynamical responses. We show that the steady-state current results from a dephasing mechanism provided the electrodes are macroscopic and the device is finite. In the d.c. case, we obtain a Landauer-like formula when the effective potential of TDDFT is uniform deep inside the electrodes.

2006-04-01

257

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

258

Ab initio molecular dynamics simulation on the formation process of He@C?? synthesized by explosion.  

UK PubMed Central (United Kingdom)

The applications of endohedral non-metallic fullerenes are limited by their low production rate. Recently, an explosive method developed in our group shows promise to prepare He@C?? at fairly high yield, but the mechanism of He inserting into C?? cage at explosive conditions was not clear. Here, ab initio molecular dynamics analysis has been used to simulate the collision between C?? molecules at high-temperature and high-pressure induced by explosion. The results show that defects formed on the fullerene cage by collidsion can effectively decrease the reaction barrier for the insertion of He into C??, and the self-healing capability of the defects was also observed.

Li JY; Liu LM; Jin B; Liang H; Yu HJ; Zhang HC; Chu SJ; Peng RF

2013-04-01

259

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

260

Ab initio investigation of mechanical behaviour of MgB2 superconductor under pressure  

International Nuclear Information System (INIS)

We present ab initio calculations of a set of physical properties for the newly discovered MgB2 superconductor. The zero pressure bulk modulus, the pressure derivative of the bulk modulus and their in- and out-of-plane linear values are evaluated. An analysis of the calculated parameters reveals the diversity in bonding interactions. The diboride is characterized by a moderately sizable anisotropy of compressibilites, which is smaller than for cuprates, but larger than for other related diborides. The anisotropic compression is expected to induce different pressure effects on different phonon modes and also to influence the electronic structure at the Fermi energy. (author). Letter-to-the-editor

2001-07-09

 
 
 
 
261

Ab Initio Calculation of Spin Gap Behavior in $CaV_{4}O_{9}$  

CERN Multimedia

Second neighbor dominated exchange coupling in CaV4O9 has been obtained from ab initio density functional (DF) calculations. A DF-based self-consistent atomic deformation model reveals that the nearest neighbor coupling is small due to strong cancellation among the various superexchange processes. Exact diagonalization of the predicted Heisenberg model yields spin-gap behavior in good agreement with experiment. The model is refined by fitting to the experimental susceptibility. The resulting model agrees very well with the experimental susceptibility and triplet dispersion.

Hellberg, C S; Boyer, L L; Stokes, H T; Mehl, M J; Stokes, Harold T.; Mehl, Michael J.

1999-01-01

262

Ab initio many-body calculations of the 4He photo-absorption cross section  

CERN Document Server

A major goal of nuclear theory is to make quantitative calculations of low-energy nuclear observables starting from microscopic internucleon forces. Computationally, this is complicated by the large model spaces needed to reach convergence in many-body approaches, such as the no-core shell model (NCSM). In recent years, the similarity renormalization group (SRG) has provided a powerful and versatile means to soften interactions for ab initio structure calculations, thus leading to convergence within smaller model spaces. Here we compute the 4He total photo absorption cross section and study, for the first time, the consistency of the SRG approach in a continuum observable.

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

2013-01-01

263

{ital Ab Initio} Molecular Dynamics Studies of Off-Center Displacements in CuCl  

Energy Technology Data Exchange (ETDEWEB)

The unusual properties of CuCl have previously been interpreted using models that focus either on anharmonicity or off-center displacements from the zinc blende structure. We use {ital ab initio} molecular dynamics to show that both are important in determining the behavior of CuCl. At low temperatures, most of the Cu ions are located in off-center sites along the (111) directions. The lattice undergoes a gradual transition from static to dynamic disorder with rising temperature. Increasing pressure favors the zinc blende structure, in agreement with recent Raman experiments. {copyright} {ital 1999} {ital The American Physical Society }

Bickham, S.R.; Kress, J.D.; Collins, L.A. [Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Stumpf, R. [Computational Materials Group, Motorola, Los Alamos, New Mexico 87545 (United States)

1999-07-01

264

Ab initio theoretical study of the structures of thymine glycol and dihydrothymine  

International Nuclear Information System (INIS)

The structures of all diastereoisomers of 5,6-dihydroxy-5,6-dihydrothymine (thymine glycol) and 5,6-dihydrothymine, two important DNA lesions, have been optimized with ab initio quantum chemical methods at a 6-31G level of calculations. The methyl group on C5 of thymine glycol shows a strong preference for a pseudo axial orientation. In contrast, in 5,6-dihydrothymine a pseudo equatorial methyl is preferred. Consequently, the thymine glycol lesion is much more bulky than 5,6-dihydrothymine. This observation may explain the different biological consequences observed for the two lesions. (author).

1993-01-01

265

Analysis of Borderline Substitution/Electron Transfer Pathways from Direct ab initio MD Simulations  

Energy Technology Data Exchange (ETDEWEB)

Ab initio molecular dynamics simulations were carried out for the borderline reaction pathways in the reaction of CH2O?- with CH3Cl. The simulations reveal distinctive features of three types of mechanisms passing through the SN2-like transition state (TS): (i) a direct formation of SN2 products, (ii) a direct formation of ET products, and (iii) a 2-step formation of ET products via the SN2 valley. The direct formation of the ET product through the SN2-like TS appears to be more favorable at higher temperatures. The 2-step process depends on the amount of energy that goes into the C-C stretching mode.

Yamataka, H (Osaka University, Japan); Aida, M A.(Department of Chemistry, Graduate School of Science, Hiroshima University); Dupuis, Michel (BATTELLE (PACIFIC NW LAB))

2001-12-01

266

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

Science.gov (United States)

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

267

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; P. Srivastava

2013-01-01

268

Ab Initio post-Hartree-Fock studies on molecular structure and vibrational IR spectrum of formaldehyde  

International Nuclear Information System (INIS)

High-level ab initio studies using the 6-311G(3d/f, 2p) basis set with electron correlation included at the second-order Moller Plesset perturbation theory are reported. At this level, full geometry optimization was performed, followed by calculation of the vibrational IR spectrum. Predicted molecular parameters (bond lengths, bond angles, dipole moment, rotational constants) and vibrational IR spectra (harmonic wave numbers, absolute intensities) of formaldehyde and its deuterated species agree very well with the experimental data.

1992-01-01

269

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.

2004-01-01

270

Ab initio modelling of calcium phosphate clusters and their vibrational spectra  

Directory of Open Access Journals (Sweden)

Full Text Available Calcium phosphate and hydroxylcalcium phosphate clusters that model amorphous phase elementary unit cells as well as their vibrational spectra were calculated by ab initio quantum chemical method using GAMESS code. Normal coordinate analysis was accomplished for phosphate anion, tricalcium phosphate and hydroxylapatite. Calculated IR-spectra and spectra of inelastic neutron scattering were defined in comparison with experimental data. It was shown that within the suggested approach, vibrational spectroscopy appears to be a reliable method of verifying the quantum chemical calculated structure versus the experimental data.

I.E.Boldeskul; L.F.Sukhodub; A.N.Kalinkevich; V.D.Khavryutchenko

2006-01-01

271

Ab initio simulation of vacancy processes in Ni{sub 3}Al  

Energy Technology Data Exchange (ETDEWEB)

Properties of point defects such as antisites and vacancies in Ni{sub 3}Al are studied by means of ab initio calculations for supercells. Temperature dependent quantities such as defect formation energies are derived by means of a grandcanonical ensemble. Stimulated by experiments of residual resistivities suggesting an outstanding large activation energy of 4.6 eV due to Al vacancies, several models for point like defects are treated in combination with calculated migration barriers for nearest neighbor jumps and also the six-jump model.

Schweiger, H.; Moroni, E.; Wolf, W.; Pueschl, W.; Pfeiler, W.; Podloucky, R.

1999-07-01

272

Ab-initio calculations for the structural properties of Zr-Nb alloys  

Directory of Open Access Journals (Sweden)

Full Text Available Ab-initio calculations for the structural properties of Zr-Nb alloys at different values of the niobium concentration are done at zero temperature. Different cases for Zr-Nb alloys with unit cells having BCC and HCP structures are considered. Optimal values of the lattice constants are obtained. Critical value for the niobium concentration corresponding to the structural transformation HCP ? BCC at zero temperature is defined. Electronic densities of states for two different structures with niobium concentrations 12.5% and 25% having HCP and BCC structures, accordingly, are studied.

V.O. Kharchenko; D.O. Kharchenko

2013-01-01

273

Ab initio based force field and molecular dynamics simulations of crystalline TATB  

Science.gov (United States)

An all-atom force field for 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) is presented. The classical intermolecular interaction potential for TATB is based on single-point energies determined from high-level ab initio calculations of TATB dimers. The newly developed potential function is used to examine bulk crystalline TATB via molecular dynamics simulations. The isobaric thermal expansion and isothermal compression under hydrostatic pressures obtained from the molecular dynamics simulations are in good agreement with experiment. The calculated volume-temperature expansion is almost one dimensional along the c crystallographic axis, whereas under compression, all three unit cell axes participate, albeit unequally.

Gee, Richard H.; Roszak, Szczepan; Balasubramanian, Krishnan; Fried, Laurence E.

2004-04-01

274

Ab initio based force field and molecular dynamics simulations of crystalline TATB.  

UK PubMed Central (United Kingdom)

An all-atom force field for 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) is presented. The classical intermolecular interaction potential for TATB is based on single-point energies determined from high-level ab initio calculations of TATB dimers. The newly developed potential function is used to examine bulk crystalline TATB via molecular dynamics simulations. The isobaric thermal expansion and isothermal compression under hydrostatic pressures obtained from the molecular dynamics simulations are in good agreement with experiment. The calculated volume-temperature expansion is almost one dimensional along the c crystallographic axis, whereas under compression, all three unit cell axes participate, albeit unequally.

Gee RH; Roszak S; Balasubramanian K; Fried LE

2004-04-01

275

Electronic transport properties of fullerene functionalized carbon nanotubes: Ab initio and tight-binding calculations  

DEFF Research Database (Denmark)

Fullerene functionalized carbon nanotubes-NanoBuds-form a novel class of hybrid carbon materials, which possesses many advantageous properties as compared to the pristine components. Here, we report a theoretical study of the electronic transport properties of these compounds. We use both ab initio techniques and tight-binding calculations to illustrate these materials' transmission properties and give physical arguments to interpret the numerical results. Specifically, above the Fermi energy we find a strong reduction in electron transmission due to localized states in certain regions of the structure while below the Fermi energy all considered structures exhibit a high-transmission energy band with a geometry-dependent width.

Fürst, Joachim Alexander; Hashemi, J.

2009-01-01

276

Semiempirical and Ab Initio calculation of the molecular structures of substituted N-Benzoylimidazoles  

Directory of Open Access Journals (Sweden)

Full Text Available Possible reasons of low reactivities of some N-(2-X-benzoyl) imidazoles utilising ab initio Hartree-Fock calculations have been studied in imidazole-catalyzed hydrolysis. The elucidation of its molecular structures display that the inhibition of resonance, between the carbonyl group and the aromatic moiety, due to steric effects are very much important than that a possible stabilization of the reactant state by a donor-acceptor effects interaction between the orto nitro group of benzene ring and the imidazole ring.

Paulo Meneghelli

2001-01-01

277

An ab initio and density functional theory study of radical-clock reactions.  

UK PubMed Central (United Kingdom)

Density functional theory (DFT) and ab initio (CBS-RAD) calculations have been used to investigate a series of "radical clock" reactions. The calculated activation energies suggest that the barriers for these radical rearrangements are determined almost exclusively by the enthalpy effect with no evidence of significant polar effects. The ring-closure reactions to cyclopentylmethyl radical derivatives and the ring opening of cyclopropylmethyl radicals give different correlations between the calculated heat of reaction and barrier, but the two types of reaction are internally consistent.

Jäger CM; Hennemann M; Miesza?a A; Clark T

2008-02-01

278

Graph theory meets ab initio molecular dynamics: atomic structures and transformations at the nanoscale.  

UK PubMed Central (United Kingdom)

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 F; Andreoni W

2011-08-01

279

Graph Theory Meets Ab Initio Molecular Dynamics: Atomic Structures and Transformations at the Nanoscale  

Science.gov (United States)

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

280

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

Scientific Electronic Library Online (English)

Full Text Available 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. This 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.

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

1999-12-01

 
 
 
 
281

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

Directory of Open Access Journals (Sweden)

Full Text Available 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. This 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.

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

1999-01-01

282

Linear scaling Krylov subspace method for large scale {\\it ab initio} electronic structure calculations of metals  

CERN Document Server

An efficient and robust linear scaling method is presented for large scale {\\it ab initio} electronic structure calculations of a wide variety of materials including metals. The detailed short range and the effective long range contributions to the electronic structure are taken into account by solving an embedded cluster defined in a Krylov subspace, which provides rapid convergence for not only insulators but also metals. As an illustration of the method, we present a large scale calculation based on density functional theory for a palladium cluster with a single iron impurity.

Ozaki, T

2005-01-01

283

A Wannier-function-based $ab initio$ Hartree-Fock study of polyethylene  

CERN Multimedia

In the present letter, we report the extension of our Wannier-function-based ab initio Hartree-Fock approach---meant originally for three-dimensional crystalline insulators---to deal with quasi-one-dimensional periodic systems such as polymers. The system studied is all-transoid polyethylene, and results on optimized lattice parameters, cohesive energy and the band structure utilizing 6-31G** basis sets are presented. Our results are also shown to be in excellent agreement with those obtained with traditional Bloch-orbital-based approaches.

Shukla, A; Stoll, H; Shukla, Alok; Dolg, Michael; Stoll, Hermann

1998-01-01

284

Benefits of Parallel I/O in Ab Initio Nuclear Physics Calculations  

International Nuclear Information System (INIS)

[en] Many modern scientific applications rely on highly parallel calculations, which scale to 10's of thousands processors. However, most applications do not concentrate on parallelizing input/output operations. In particular, sequential I/O has been identified as a bottleneck for the highly scalable MFDn (Many Fermion Dynamics for nuclear structure) code performing ab initio nuclear structure calculations. In this paper, we develop interfaces and parallel I/O procedures to use a well-known parallel I/O library in MFDn. As a result, we gain efficient input/output of large datasets along with their portability and ease of use in the downstream processing.

2009-01-01

285

Ab initio theory of NMR chemical shifts in solids and liquids  

CERN Multimedia

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

286

Ab initio determination of exchange integrals and Néel temperature in the chain cuprates  

CERN Multimedia

We report ab initio quantum chemical cluster calculations of the chain (J_a) and the largest interchain (J_b) Heisenberg exchange of the chain cuprates Ca_2CuO_3 and Sr_2CuO_3. We find that J_a is comparable to the in-plane J in layered cuprates and J_a/J_b ~250-400. Using recent theory we obtain close agreement with experiment for the staggered moments and the critical temperatures. This implies that T_N does not depend on the third parameter J_c 2D cross-over.

Van Oosten, A B

1998-01-01

287

Ab initio investigation of VOSeO3, a spin gap system with coupled spin dimers  

CERN Multimedia

Motivated by an early experimental study of VOSeO3, which suggested that it is a quasi-2D system of weakly coupled spin dimers with a small spin gap, we have investigated the electronic structure of this material via density-functional calculations. These ab initio results indicate that the system is better thought of as an alternating spin-1/2 chain with moderate interchain interactions, an analog of (VO)2P2O7. The potential interest of this system for studies in high magnetic field given the presumably small value of the spin gap is emphasized.

Valenti, R; Mila, F; Valenti, Roser

2003-01-01

288

Estudo da geometria da uréia por métodos ab initio e simulação computacional de líquidos Studies of urea geometry by means of ab initio methods and computer simulations of liquids  

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.

José Jair Vianna Cirino; Celso Aparecido Bertran

2002-01-01

289

FREE ENERGIES OF CHEMICAL REACTIONS IN SOLUTION AND IN ENZYMES WITH AB INITIO QM/MM METHODS  

Science.gov (United States)

Combined QM/MM methods provide an accurate and efficient energetic description of complex chemical and biological systems, leading to significant advances in the understanding of chemical reactions in solution and in enzymes. Progress in QM/MM methodology and application will be reviewed, with a focus on ab initio QM based approaches. Ab initio QM/MM methods capitalize on the accuracy and reliability of the associated quantum mechanical approaches, however at a much higher computational cost compared with semiempirical quantum mechanical approaches. Thus reaction path and activation free energy calculations based on ab initio QM/MM methods encounter unique challenges in simulation timescales and phase space sampling. Recent developments overcoming these challenges and enabling accurate free energy determination for reaction processes in solution and enzymes will be featured in this review, along with applications.

Hu, Hao; Yang, Weitao

2013-01-01

290

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

Science.gov (United States)

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

291

Ab initio quantum chemistry in parallel-portable tools and applications  

Energy Technology Data Exchange (ETDEWEB)

In common with many of the computational sciences, ab initio chemistry faces computational constraints to which a partial solution is offered by the prospect of highly parallel computers. Ab initio codes are large and complex (O(10{sup 5}) lines of FORTRAN), representing a significant investment of communal effort. The often conflicting requirements of portability and efficiency have been successfully resolved on vector computers by reliance on matrix oriented kernels. This proves inadequate even upon closely-coupled shared-memory parallel machines. We examine the algorithms employed during a typical sequence of calculations. Then we investigate how efficient portable parallel implementations may be derived, including the complex multi-reference singles and doubles configuration interaction algorithm. A portable toolkit, modeled after the Intel iPSC and the ANL-ACRF PARMACS, is developed, using shared memory and TCP/IP sockets. The toolkit is used as an initial platform for programs portable between LANS, Crays and true distributed-memory MIMD machines. Timings are presented. 53 refs., 4 tabs.

Harrison, R.J.; Shepard, R. (Argonne National Lab., IL (United States)); Kendall, R.A. (Battelle Pacific Northwest Lab., Richland, WA (United States))

1991-01-01

292

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

International Nuclear Information System (INIS)

[en] 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.

2012-07-01

293

Ab initio investigation on a promising transparent conductive oxide, Nb:SnO{sub 2}  

Energy Technology Data Exchange (ETDEWEB)

The effects of Nb dopant on the lattice structure, thermal, electronic, and optical properties of rutile-phased SnO{sub 2} were investigated via ab initio calculations. The corresponding effects of Sb and Ta dopants were also studied for comparison. Results indicated that after SnO{sub 2} 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 E{sub f} 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:SnO{sub 2} is expected to be comparable with or even better than Ta:SnO{sub 2}. - Highlights: Black-Right-Pointing-Pointer In this study we model rutile-phased Nb:SnO{sub 2} with ab initio methods. Black-Right-Pointing-Pointer Nb dopants cause the variations in lattice structure and thermal stability. Black-Right-Pointing-Pointer Bands around E{sub f} enhance the conductivity and infrared electron excitation. Black-Right-Pointing-Pointer Band gaps and selection rule restrict the electron excitation in visible region.

Zhang Guanglei [School of Materials Science and Engineering, Shijiazhuang Tiedao University, Shijiazhuang, Hebei Province, 050043 (China); State Key Laboratory of Metastable Materials Science and Technology (Yanshan University) 066004 Qinhuangdao (China); Qin Guoqiang, E-mail: sjzqgq@126.com [School of Materials Science and Engineering, Shijiazhuang Tiedao University, Shijiazhuang, Hebei Province, 050043 (China) and State Key Laboratory of Metastable Materials Science and Technology, Yanshan University, 066004 Qinhuangdao (China); Yu Gang [School of Materials Science and Engineering, Shijiazhuang Tiedao University, Shijiazhuang, Hebei Province, 050043 (China); Hu Qianku [State Key Laboratory of Metastable Materials Science and Technology, Yanshan University, 066004 Qinhuangdao (China); School of Material Science and Engineering, Henan Polytechnic University, Jiaozuo, Henan Province, 454010 (China); Fu Hua; Shao Changtao [School of Materials Science and Engineering, Shijiazhuang Tiedao University, Shijiazhuang, Hebei Province, 050043 (China)

2012-07-01

294

An Ab Initio Approach Towards Engineering Fischer-Tropsch Surface Chemistry  

Energy Technology Data Exchange (ETDEWEB)

As petroleum prices continue to rise and the United States seeks to reduce its dependency on foreign oil, there is a renewed interest in the research and development of more efficient and alternative energy sources, such as fuel cells. One approach is to utilize processes that can produce long-chain hydrocarbons from other sources. One such reaction is Fischer-Tropsch synthesis. Fischer-Tropsch synthesis is a process by which syngas (CO and H{sub 2}) is converted to higher molecular weight hydrocarbons. The reaction involves a complex set of bond-breaking and bond-making reactions, such as CO and H{sub 2} activation, hydrocarbon hydrogenation reactions, and hydrocarbon coupling reactions. This report details our initial construction of an ab initio based kinetic Monte Carlo code that can be used to begin to simulate Fischer-Tropsch synthesis over model Co(0001) surfaces. The code is based on a stochastic kinetic formalism that allows us to explicitly track the transformation of all reactants, intermediates and products. The intrinsic kinetics for the simulations were derived from the ab initio results that we reported in previous year summaries.

Matthew Neurock

2005-06-13

295

Ab initio study of the high-temperature phase transition in crystalline GeO2.  

UK PubMed Central (United Kingdom)

Germanium dioxide (GeO2 ) takes two forms at ambient pressure: a thermodynamically stable rutile-type structure and a high-temperature quartz-type polymorph. Here, we investigate the phase stability at finite temperatures by ab initio phonon and thermochemical computations. We use gradient-corrected density-functional theory (PBE-GGA) and pay particular attention to the modeling of the "semicore" germanium 3d orbitals (ascribing them either to the core or to the valence region). The phase transition is predicted correctly in both cases, and computed heat capacities and entropies are in excellent agreement with thermochemical database values. Nonetheless, the computed formation energies of ?-quartz-type GeO2 (and, consequently, the predicted transition temperatures) differ significantly depending on theoretical method. Remarkably, the simpler and cheaper computational approach produces seemingly better results, not worse. In our opinion, GeO2 is a nice test case that illustrates both possibilities and limitations of modern ab initio thermochemistry. © 2013 Wiley Periodicals, Inc.

Deringer VL; Lumeij M; Stoffel RP; Dronskowski R

2013-10-01

296

Ab initio study of the high-temperature phase transition in crystalline GeO2.  

Science.gov (United States)

Germanium dioxide (GeO2 ) takes two forms at ambient pressure: a thermodynamically stable rutile-type structure and a high-temperature quartz-type polymorph. Here, we investigate the phase stability at finite temperatures by ab initio phonon and thermochemical computations. We use gradient-corrected density-functional theory (PBE-GGA) and pay particular attention to the modeling of the "semicore" germanium 3d orbitals (ascribing them either to the core or to the valence region). The phase transition is predicted correctly in both cases, and computed heat capacities and entropies are in excellent agreement with thermochemical database values. Nonetheless, the computed formation energies of ?-quartz-type GeO2 (and, consequently, the predicted transition temperatures) differ significantly depending on theoretical method. Remarkably, the simpler and cheaper computational approach produces seemingly better results, not worse. In our opinion, GeO2 is a nice test case that illustrates both possibilities and limitations of modern ab initio thermochemistry. © 2013 Wiley Periodicals, Inc. PMID:23873721

Deringer, Volker L; Lumeij, Marck; Stoffel, Ralf P; Dronskowski, Richard

2013-07-19

297

Optimized unrestricted Kohn-Sham potentials from ab initio spin densities.  

UK PubMed Central (United Kingdom)

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 (KS) 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 unrestricted KS-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 [Ch. R. Jacob, J. Chem. Phys. 135, 244102 (2011)] can provide such spin potentials accurately. This is demonstrated for two test cases, the lithium atom and the dioxygen molecule, and target (spin) densities from full configuration interaction and complete active space self-consistent field calculations, respectively.

Boguslawski K; Jacob CR; Reiher M

2013-01-01

298

Ab initio design of potent anti-MRSA peptides based on database filtering technology.  

UK PubMed Central (United Kingdom)

To meet the challenge of antibiotic resistance worldwide, a new generation of antimicrobials must be developed. This communication demonstrates ab initio design of potent peptides against methicillin-resistant Staphylococcus aureus (MRSA). Our idea is that the peptide is very likely to be active when the most probable parameters are utilized in each step of the design. We derived the most probable parameters (e.g., amino acid composition, peptide hydrophobic content, and net charge) from the antimicrobial peptide database by developing a database filtering technology (DFT). Different from classic cationic antimicrobial peptides usually with high cationicity, DFTamP1, the first anti-MRSA peptide designed using this technology, is a short peptide with high hydrophobicity but low cationicity. Such a molecular design made the peptide highly potent. Indeed, the peptide caused bacterial surface damage and killed community-associated MRSA USA300 in 60 min. Structural determination of DFTamP1 by NMR spectroscopy revealed a broad hydrophobic surface, providing a basis for its potency against MRSA known to deploy positively charged moieties on the surface as a mechanism for resistance. Our ab initio design combined with database screening led to yet another peptide with enhanced potency. Because of the simple composition, short length, stability to proteases, and membrane targeting, the designed peptides are attractive leads for developing novel anti-MRSA therapeutics. Our database-derived design concept can be applied to the design of peptide mimicries to combat MRSA as well.

Mishra B; Wang G

2012-08-01

299

Ab initio prediction of the critical thickness of a precipitate.  

Science.gov (United States)

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

2013-07-29

300

A high-level ab initio study of the N2 + N2 reaction channel.  

Science.gov (United States)

A new six-dimensional (6D) global potential energy surface (PES) is proposed for the full range description of the interaction of the N2(1?g+)+N2(1?g+) system governing collisional processes, including N atom exchange. The related potential energy values were determined using high-level ab initio methods. The calculations were performed at a coupled-cluster with single and double and perturbative triple excitations level of theory in order to have a first full range picture of the PES. Subsequently, in order to accurately describe the stretching of the bonds of the two interacting N2 molecules by releasing the constraints of being considered as rigid rotors, for the same molecular geometries higher level of theory multi reference calculations were performed. Out of the calculated values a 6D 4-atoms global PES was produced for use in dynamical calculations. The ab initio calculations were made possible by the combined use of High Throughput Computing and High Performance Computing techniques within the frame of a computing grid empowered molecular simulator. © 2013 Wiley Periodicals, Inc. PMID:24037708

Pacifici, Leonardo; Verdicchio, Marco; Lago, Noelia Faginas; Lombardi, Andrea; Costantini, Alessandro

2013-08-26

 
 
 
 
301

Ab initio study of the SeS local oscillator in zinc sulfide  

Science.gov (United States)

A method is presented to calculate the energy and symmetry of local vibrational modes (LVM's) at point defects in semiconductors from first principles. The force constants for the disturbed and undisturbed systems are calculated using a variant of the direct approach. The ab initio results are used as input parameters for a cluster simulation with up to 489 vibrating atoms, which accounts for hybridization effects between the LVM and the host lattice modes. The method is applied to the LVM of ZnS:SeS, which shows a pronounced fine structure due to both host and ligand induced isotope effects. The energy of the main peak, which represents the most abundant Selen isotope 80Se, is calculated as 229.6 cm-1. This agrees very well with the result of 229.2 cm-1 from Fourier transform infrared experiments found in the literature. It is shown that the ab initio result improves the understanding of the LVM, when compared to the previously used ad hoc model, especially in the low-energy region.

Petzke, K.

1999-11-01

302

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.

2004-08-02

303

Ab initio calculations on halogen-bonded complexes and comparison with density functional methods.  

Science.gov (United States)

A systematic theoretical investigation on a series of dimeric complexes formed between some halocarbon molecules and electron donors has been carried out by employing both ab initio and density functional methods. Full geometry optimizations are performed at the Moller-Plesset second-order perturbation (MP2) level of theory with the Dunning's correlation-consistent basis set, aug-cc-pVDZ. Binding energies are extrapolated to the complete basis set (CBS) limit by means of two most commonly used extrapolation methods and the aug-cc-pVXZ (X = D, T, Q) basis sets series. The coupled cluster with single, double, and noniterative triple excitations [CCSD(T)] correction term, determined as a difference between CCSD(T) and MP2 binding energies, is estimated with the aug-cc-pVDZ basis set. In general, the inclusion of higher-order electron correlation effects leads to a repulsive correction with respect to those predicted at the MP2 level. The calculations described herein have shown that the CCSD(T) CBS limits yield binding energies with a range of -0.89 to -4.38 kcal/mol for the halogen-bonded complexes under study. The performance of several density functional theory (DFT) methods has been evaluated comparing the results with those obtained from MP2 and CCSD(T). It is shown that PBEKCIS, B97-1, and MPWLYP functionals provide accuracies close to the computationally very expensive ab initio methods. PMID:18727160

Lu, Yun-Xiang; Zou, Jian-Wei; Fan, Ji-Cai; Zhao, Wen-Na; Jiang, Yong-Jun; Yu, Qing-Sen

2009-04-15

304

Ab initio calculations on halogen-bonded complexes and comparison with density functional methods.  

UK PubMed Central (United Kingdom)

A systematic theoretical investigation on a series of dimeric complexes formed between some halocarbon molecules and electron donors has been carried out by employing both ab initio and density functional methods. Full geometry optimizations are performed at the Moller-Plesset second-order perturbation (MP2) level of theory with the Dunning's correlation-consistent basis set, aug-cc-pVDZ. Binding energies are extrapolated to the complete basis set (CBS) limit by means of two most commonly used extrapolation methods and the aug-cc-pVXZ (X = D, T, Q) basis sets series. The coupled cluster with single, double, and noniterative triple excitations [CCSD(T)] correction term, determined as a difference between CCSD(T) and MP2 binding energies, is estimated with the aug-cc-pVDZ basis set. In general, the inclusion of higher-order electron correlation effects leads to a repulsive correction with respect to those predicted at the MP2 level. The calculations described herein have shown that the CCSD(T) CBS limits yield binding energies with a range of -0.89 to -4.38 kcal/mol for the halogen-bonded complexes under study. The performance of several density functional theory (DFT) methods has been evaluated comparing the results with those obtained from MP2 and CCSD(T). It is shown that PBEKCIS, B97-1, and MPWLYP functionals provide accuracies close to the computationally very expensive ab initio methods.

Lu YX; Zou JW; Fan JC; Zhao WN; Jiang YJ; Yu QS

2009-04-01

305

Ab initio study of structural and electronic properties of CunatC60  

Science.gov (United States)

Ab initio investigation of structural and electronic properties of copper doped endohedral fullerene has been performed using numerical atomic orbital density functional theory. We have obtained the ground state structures for CunatC60 (n=1-10). Which shows that C60 molecule can accommodate maximum of nine copper atoms, for n > 9 the cage eventually break. Encapsulated large number of copper atoms leads to deformation of cage with diameter varies from 7.00A? to 8.38A?. Binding energy/Cu atom is found to increase till n = 4 and after that it decreases with the number of Cu atoms with a sudden increase for n=10 and electronic affinity increases till n=2 then decreases uniformly till up to n=7 with a further sharp decrease for n=10. Ionization potential and Homo-Lumo gap shows a oscillatory nature. The results obtained are consistent with available theoretical and experimental results. The ab-initio calculations were performed using SIESTA code with generalized gradient approximation (GGA).

Dhiman, Shobhna; Kumar, Ranjan; Dharamvir, Keya

2013-06-01

306

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

International Nuclear Information System (INIS)

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. (comment)

2011-07-06

307

From ab initio quantum chemistry to molecular dynamics: The delicate case of hydrogen bonding in ammonia  

CERN Multimedia

The ammonia dimer (NH3)2 has been investigated using high--level ab initio quantum chemistry methods and density functional theory (DFT). The structure and energetics of important isomers is obtained to unprecedented accuracy without resorting to experiment. The global minimum of eclipsed C_s symmetry is characterized by a significantly bent hydrogen bond which deviates from linearity by about 20 degrees. In addition, the so-called cyclic C_{2h} structure is extremely close in energy on an overall flat potential energy surface. It is demonstrated that none of the currently available (GGA, meta--GGA, and hybrid) density functionals satisfactorily describe the structure and relative energies of this nonlinear hydrogen bond. We present a novel density functional, HCTH/407+, designed to describe this sort of hydrogen bond quantitatively on the level of the dimer, contrary to e.g. the widely used BLYP functional. This improved functional is employed in Car-Parrinello ab initio molecular dynamics simulations of liq...

Boese, A D; Martin, J M L; Marx, D; Chandra, Amalendu; Martin, Jan M.L.; Marx, Dominik

2003-01-01

308

Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field.  

UK PubMed Central (United Kingdom)

Ab initio protein folding is one of the major unsolved problems in computational biology owing to the difficulties in force field design and conformational search. We developed a novel program, QUARK, for template-free protein structure prediction. Query sequences are first broken into fragments of 1-20 residues where multiple fragment structures are retrieved at each position from unrelated experimental structures. Full-length structure models are then assembled from fragments using replica-exchange Monte Carlo simulations, which are guided by a composite knowledge-based force field. A number of novel energy terms and Monte Carlo movements are introduced and the particular contributions to enhancing the efficiency of both force field and search engine are analyzed in detail. QUARK prediction procedure is depicted and tested on the structure modeling of 145 nonhomologous proteins. Although no global templates are used and all fragments from experimental structures with template modeling score >0.5 are excluded, QUARK can successfully construct 3D models of correct folds in one-third cases of short proteins up to 100 residues. In the ninth community-wide Critical Assessment of protein Structure Prediction experiment, QUARK server outperformed the second and third best servers by 18 and 47% based on the cumulative Z-score of global distance test-total scores in the FM category. Although ab initio protein folding remains a significant challenge, these data demonstrate new progress toward the solution of the most important problem in the field.

Xu D; Zhang Y

2012-07-01

309

Ab initio calculations and interatomic potentials for iron and iron alloys: Achievements within the Perfect Project  

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.

2010-11-01

310

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

Science.gov (United States)

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

311

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

UK PubMed Central (United Kingdom)

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/Å 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/Å), a 15%-20% fraction of molecules are instantaneously dissociated and the resulting ionic flow yields a conductance of about 7.8???-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 neurobiology, electrochemistry, and hydrogen economy.

Saitta AM; Saija F; Giaquinta PV

2012-05-01

312

Liquid properties of dimethyl ether from molecular dynamics simulations using ab initio force fields.  

Science.gov (United States)

We have used molecular dynamic simulations to study the structural and dynamical properties of liquid dimethyl ether (DME) with a newly constructed ab initio force field in this article. The ab initio potential energy data were calculated at the second order Møller-Plesset (MP2) perturbation theory with Dunning's correlation consistent basis sets (up to aug-cc-pVQZ). We considered 17 configurations of the DME dime for the orientation sampling. The calculated MP2 potential data were used to construct a 3-site united atom force field model. The simulation results are compared with those using the empirical force field of Jorgensen and Ibrahim (Jorgensen and Ibrahim, J Am Chem Soc 1981, 103, 3976) and with available experimental measurements. We obtain quantitative agreements for the atom-wise radial distribution functions, the self-diffusion coefficients, and the shear viscosities over a wide range of experimental conditions. This force field thus provides a suitable starting point to predict liquid properties of DME from first principles intermolecular interactions with no empirical data input a priori. PMID:22278976

Wang, Shi-Bao; Li, Arvin Huang-Te; Chao, Sheng D

2012-01-25

313

Liquid properties of dimethyl ether from molecular dynamics simulations using ab initio force fields.  

UK PubMed Central (United Kingdom)

We have used molecular dynamic simulations to study the structural and dynamical properties of liquid dimethyl ether (DME) with a newly constructed ab initio force field in this article. The ab initio potential energy data were calculated at the second order Møller-Plesset (MP2) perturbation theory with Dunning's correlation consistent basis sets (up to aug-cc-pVQZ). We considered 17 configurations of the DME dime for the orientation sampling. The calculated MP2 potential data were used to construct a 3-site united atom force field model. The simulation results are compared with those using the empirical force field of Jorgensen and Ibrahim (Jorgensen and Ibrahim, J Am Chem Soc 1981, 103, 3976) and with available experimental measurements. We obtain quantitative agreements for the atom-wise radial distribution functions, the self-diffusion coefficients, and the shear viscosities over a wide range of experimental conditions. This force field thus provides a suitable starting point to predict liquid properties of DME from first principles intermolecular interactions with no empirical data input a priori.

Wang SB; Li AH; Chao SD

2012-04-01

314

Ab initio calculation of double-resonant Raman spectra for bilayer graphene  

Science.gov (United States)

The discovery that the application of an external electric field induces a band gap opening in bilayer graphene attracted a lot of interest on this system, due to important applications in nanoelectronics [1]. Raman spectroscopy is one of the most important experimental techniques for the characterisation of carbon based materials, providing informations on carriers concentration [2], disorder [3], number of layers on multi-layers graphene systems [4], and phonon properties. Most of the theoretical studies on multi-layers graphene are performed using a Tight Binding (TB) model, and full calculation of Raman matrix elements to obtain frequencies, intensities and linewidths of Raman bands has not been performed up to now. The developpement of a fully ab initio theoretical tool to compute Raman spectra is therefore higly desirable and particularly relevant for systems where a simple TB parametrization of the electronic structure and of the electron-phonon interaction is not available. In this talk I will discuss a recently developped methodology to compute fully ab initio double-resonant Raman spectra and I will present results for bilayer graphene.[4pt] [1] Ohta et al, Science 313, 951 (2006), [2] Malard et al, PRL 101, 257410 (2008), [3] Lucchese et al, Carbon 48, 1592 (2010), [4] Ferrari et al, PRL 97, 187401 (2006)

Gava, Paola; Calandra, Matteo; Lazzeri, Michele; Mauri, Francesco

2011-03-01

315

Structural phase transitions in Ruddlesden-Popper phases of strontium titanate: {\\em ab initio} and inhomogeneous Ginzburg-Landau approaches  

CERN Multimedia

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

316

Nuclear quantum effect on intramolecular hydrogen bond of hydrogen maleate anion: An ab initio path integral molecular dynamics study  

Science.gov (United States)

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

317

Multi-scale modeling of materials: from ab-initio calculations to kinetic simulations; Modelisation multiechelle des materiaux de l'ab-initio a la cinetique  

Energy Technology Data Exchange (ETDEWEB)

Ab-initio calculation methods, for the purposes of computing electronic structures, have made it possible, since the early nineties, to simulate the properties of perfect crystalline materials (materials free of any defect). By improving such methods, and with the increasing power of supercomputers, it has now become feasible to simulate the properties of elementary defects, which may seldom be accessed directly through experiments. This has opened up a vast, fruitful field of multi-scale simulations, where such data yield the basis for realistic simulations of the kinetics of materials evolution. The kinetic Monte-Carlo method thus provides the means to model phenomena acting at the scale of a second, or even of a year. In the issue of self-diffusion in silicon, multi-scale simulation has been successful in predicting an asymmetrical behaviour: a speeding up of vacancy diffusion under compression and a tailing off under tension, and conversely, a speeding up of interstitial diffusion under tension and a falling off under compression. Multi-scale modeling has also been successful in simulating irradiation defects in iron. (A.C.)

Willaime, F. [Division de l' energie nucleaire, CEA Centre de Saclay, 91191 Gif-sur-Yvette (France); Deutsch, T.; Pochet, P. [INAC, Direction des sciences de la matiere, CEA Centre de Grenoble, 38054 Grenoble Cedex 9 (France)

2010-07-01

318

Nuclear fuel behavior at an atomic scale: the contributions of the ab initio calculations and the synchrotron radiation; Comportement du combustible nucleaire a l'echelle atomique: les apports des calculs ab initio et du rayonnement synchrotron  

Energy Technology Data Exchange (ETDEWEB)

This paper presents fundamental researches based on the electronic structure calculations and X absorption spectroscopy, allowing the knowledge on nuclear fuels at an atomic scale. They bring a better understanding of these material behavior to accurate the macroscopic simulation. The calculation methods, the experimental techniques of validation and the ab initio calculations results are detailed. (A.L.B.)

Petit, T.; Ripert, M.; Martin, P.; Crocombette, J.P.; Jollet, F.; Blanc, P.; Grandjean, S.; Beres, A.; Den Auwer, C

2000-07-01

319

Ab initio identification of human microRNAs based on structure motifs  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background MicroRNAs (miRNAs) are short, non-coding RNA molecules that are directly involved in post-transcriptional regulation of gene expression. The mature miRNA sequence binds to more or less specific target sites on the mRNA. Both their small size and sequence specificity make the detection of completely new miRNAs a challenging task. This cannot be based on sequence information alone, but requires structure information about the miRNA precursor. Unlike comparative genomics approaches, ab initio approaches are able to discover species-specific miRNAs without known sequence homology. Results MiRPred is a novel method for ab initio prediction of miRNAs by genome scanning that only relies on (predicted) secondary structure to distinguish miRNA precursors from other similar-sized segments of the human genome. We apply a machine learning technique, called linear genetic programming, to develop special classifier programs which include multiple regular expressions (motifs) matched against the secondary structure sequence. Special attention is paid to scanning issues. The classifiers are trained on fixed-length sequences as these occur when shifting a window in regular steps over a genome region. Various statistical and empirical evidence is collected to validate the correctness of and increase confidence in the predicted structures. Among other things, we propose a new criterion to select miRNA candidates with a higher stability of folding that is based on the number of matching windows around their genome location. An ensemble of 16 motif-based classifiers achieves 99.9 percent specificity with sensitivity remaining on an acceptable high level when requiring all classifiers to agree on a positive decision. A low false positive rate is considered more important than a low false negative rate, when searching larger genome regions for unknown miRNAs. 117 new miRNAs have been predicted close to known miRNAs on human chromosome 19. All candidate structures match the free energy distribution of miRNA precursors which is significantly shifted towards lower free energies. We employed a human EST library and found that around 75 percent of the candidate sequences are likely to be transcribed, with around 35 percent located in introns. Conclusion Our motif finding method is at least competitive to state-of-the-art feature-based methods for ab initio miRNA discovery. In doing so, it requires less previous knowledge about miRNA precursor structures while programs and motifs allow a more straightforward interpretation and extraction of the acquired knowledge.

Brameier Markus; Wiuf Carsten

2007-01-01

320

Combinatorial screening of polymer precursors for preparation of benzo[?] pyrene imprinted polymer: an ab initio computational approach.  

Science.gov (United States)

A combinatorial screening procedure was used for the selection of polymer precursors in the preparation of molecularly imprinted polymer (MIP), which is useful in the detection of the air pollution marker molecule benzo[a]pyrene (BAP). Molecular imprinting is a technique for the preparation of polymer materials with specific molecular recognition receptors. The preparation of imprinted polymers requires polymer precursors such as functional monomer, cross-linking monomer, solvent, an initiator of polymerization and thermal or UV radiation. A virtual library of functional monomers was prepared based on interaction binding scores computed using HyperChem Release 8.0 software. Initially, the possible minimum energy conformation of the monomers and BAP were optimized using the semi-empirical (PM3) quantum method. The binding energy between the functional monomer and the template (BAP) was computed using the Hartree-Fock (HF) method with 6-31 G basis set, which is an ab initio approach based on Moller-Plesset second order perturbation theory (MP2). From the computations, methacrylic acid (MAA) and ethylene glycol dimethacrylate (EGDMA) were selected for preparation of BAP imprinted polymer. The larger interaction energy (?E) represents possibility of more affinity binding sites formation in the polymer, which provides high binding capacity. The theoretical predictions were complimented through adsorption experiments. There is a good agreement between experimental binding results and theoretical computations, which provides further evidence of the validity of the usefulness of computational screening procedures in the selection of appropriate MIP precursors in an experiment-free way. PMID:21877152

Khan, Muntazir S; Wate, Prateek S; Krupadam, Reddithota J

2011-08-30

 
 
 
 
321

Interplay of I-TASSER and QUARK for template-based and ab initio protein structure prediction in CASP10.  

UK PubMed Central (United Kingdom)

We develop and test a new pipeline in CASP10 to predict protein structures based on an interplay of I-TASSER and QUARK for both free-modeling (FM) and template-based modeling (TBM) targets. The most noteworthy observation is that sorting through the threading template pool using the QUARK-based ab initio models as probes allows the detection of distant-homology templates which might be ignored by the traditional sequence profile-based threading alignment algorithms. Further template assembly refinement by I-TASSER resulted in successful folding of two medium-sized FM targets with >150 residues. For TBM, the multiple threading alignments from LOMETS are, for the first time, incorporated into the ab initio QUARK simulations, which were further refined by I-TASSER assembly refinement. Compared to the traditional threading assembly refinement procedures, the inclusion of the threading-constrained ab initio folding models can consistently improve the quality of the full-length models as assessed by the GDT-HA and hydrogen-bonding scores. Despite the success, significant challenges still exist in domain boundary prediction and consistent folding of medium-size proteins (especially beta-proteins) for non-homologous targets. Further developments of sensitive fold-recognition and ab initio folding methods are critical for solving these problems. © Proteins 2013;. © 2013 Wiley Periodicals, Inc.

Zhang Y

2013-06-01

322

Ab initio molecular dynamics study of proton transfer in a polyglycine analog of the ion channel gramicidin A.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Proton transfer in biological systems is thought to often proceed through hydrogen-bonded chains of water molecules. The ion channel, gramicidin A (gA), houses within its helical structure just such a chain. Using the density functional theory based ab initio molecular dynamics Car-Parrinello method...

Sagnella, D E; Laasonen, K; Klein, M L

323

Ab initio calculation of the 66 low-lying electronic states of HeH+: adiabatic and diabatic representations  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We present an ab initio study of the HeH + molecule. Using the quantum chemistry package MOLPRO and a large adapted basis set, we have calculated the adiabatic potential energy curves of the first 20 1 ? +, 19 3 ? +, 12 1 ?, 9 3 ?, 4 1 ? and 2 3 ? electronic states of the ion in CASSCF and ...

324

Ab initio structure solution of decagonal quasicrystals by iterative dual space methods: Performance tests on synthetic and experimental data  

International Nuclear Information System (INIS)

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.

2010-04-01

325

Anisotropy of orbital moments and magnetic dipole term Tz in CrO2. An ab initio study  

Digital Repository Infrastructure Vision for European Research (DRIVER)

peer-reviewed , A systematic study is performed by the ab initio density-functional theory of the anisotropy of the orbital moments (lz) and the magnetic dipole term (Tz) in bulk CrO2. Two different band-structure techniques are used (full potential linearized-augmented-plane-wave method and linear-muf...

EDERER, CLAUDE

326

Anisotropy of orbital moments and magnetic dipole term Tz in CrO2. An ab initio study  

Digital Repository Infrastructure Vision for European Research (DRIVER)

A systematic study is performed by the ab initio density-functional theory of the anisotropy of the orbital moments (lz) and the magnetic dipole term (Tz) in bulk CrO2. Two different band-structure techniques are used (full potential linearized-augmented-plane-wave method and linear-muffin-tin-orbit...

EDERER, CLAUDE

327

Structural and magnetic ground-state properties of gamma-FeMn alloys from ab initio calculations  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The magnetic properties of fcc-FeMn alloys, especially at the Fe(0.5)Mn(0.5) composition, have been the subject of intense experimental and theoretical investigations for several decades. We carry out an ab initio theoretical study of this system, including simultaneous optimization of structural an...

Ekholm, Marcus; Abrikosov, Igor

328

Efficient evaluation of the accuracy of molecular quantum dynamics on an approximate analytical or interpolated ab initio potential energy surface  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Ab initio electronic structure methods have reached a satisfactory accuracy for the calculation of static properties, but remain too expensive for quantum dynamical calculations. Recently, an efficient semiclassical method was proposed to evaluate the accuracy of quantum dynamics on an approximate p...

Zimmermann, Tomas; Ruppen, Julien; Li, Baiqing; Vanicek, Jiri

329

A new ab initio potential energy surface for the NeCO complex with the vibrational coordinate dependence  

Digital Repository Infrastructure Vision for European Research (DRIVER)

A new high quality three-dimensional potential energy surface for the Ne–CO van der Waals complex is developed using the CCSD(T) method and avqz/avqz+33221 basis set. The ab initio calculation is performed in a total of 1365 configurations with supermolecule method. There is a single global minimum ...

Wang, Zhongquan; Feng, Eryin; Yu, Haijun; Zhang, Chunzao; Du, Jianming

330

Proton Transfer Studied Using a Combined Ab Initio Reactive Potential Energy Surface with Quantum Path Integral Methodology  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The rates of intramolecular proton transfer are calculated on a full-dimensional reactive electronic potential energy surface that incorporates high-level ab initio calculations along the reaction path and by using classical transition state theory, path-integral quantum transition state theory, and...

Wong, Kim; Sonnenberg, Jason; Paesani, Francesco; Yamamoto, Takeshi; Vanicek, Jiri; Zhang, Wei; Schlegel, Bernhard

331

Ab initio Hartree-Fock with electronic correlation study of the electronic properties of MgB2  

CERN Multimedia

We performed all-electron ab initio self-consistent field Hartree-Fock linear combination of atomic orbital, in which electronic correlation using density functional were included to perform electronic calculations in MgB2 new superconductor. Superconductivity in this compound was correlated with existence of Px,y band holes at Gamma point.

Reyes-Serrato, A; Reyes-Serrato, Armando; Galvan, Donald H.

2001-01-01

332

Proposal for an inhibitor of Alzheimer's disease blocking aggregation of amyloid-? peptides: ab initio molecular simulations  

Science.gov (United States)

Aggregation of amyloid-? (A?) peptides is believed to play a key role in the mechanism of molecular pathogenesis of Alzheimer's disease (AD). To inhibit the aggregation and prevent AD, numerous compounds have been synthesized. A previous experimental study elucidated that a triazine derivative AA3E2 has anti-amyloidogenic ability, while a triazine derivative AA3D2 having a different substituent has no inhibitory effect. However, the reason for this remarkable difference in the ability cannot be explained by the chemical structures of these derivatives. In the present study, we present stable structures of the solvated complexes with A? and AA3E2/AA3D2 obtained by classical molecular mechanics method. The specific interactions between A? and AA3E2/AA3D2 in the complexes are investigated by ab initio fragment molecular orbital calculations. Based on the results obtained, we attempt to propose new potent inhibitors for the A? aggregation.

Okamoto, A.; Nomura, K.; Yano, A.; Higai, S.; Kondo, T.; Kamba, S.; Kurita, N.

2013-04-01

333

Ab initio study of isomerism in molecular ions Li2AB+ with 10 valence electrons  

International Nuclear Information System (INIS)

Ab initio calculations of surfaces of Li2AB+ molecular ion potential energy with biatomic anions AB- with 10 valence electrons have been made in the framework of approximations MP2/6-31G1/HF/6-31G*+ZPE(HF/6-31G*) and MP4SDTQ/631G*//MP2/6-31G*+ZPE(MP2/6-31G*). Influence of electron correlation on the accuracy of calculations of their structural and vibrational characteristics is studied. The following most favourable structures have been found: linear for Li2BO+, Li2CN+, and bent one for Li2BS+, with cations coordinated at different anion atoms; onium one for AlOLi2+, AlSLi2+, SiNLi2+ and SiPLi2+ with both cations at electronegative atom of anion

1997-01-01

334

Investigation of the liquid Pb/Si(001) interface from ab initio molecular-dynamics calculations  

Science.gov (United States)

The structure of liquid Pb on an ideal Si(001) surface was studied experimentally a decade ago by means of x-ray diffraction and the results were interpreted in terms of the presence of fivefold symmetry Pb structures captured transiently by the potential created by the unreconstructed Si(001) surface. We critically analyze this interpretation in the light of the results obtained in an extensive ab initio molecular dynamics study of a system comprising 314 Pb atoms and 175 Si atoms setup in 7 (001) ideal layers (a total number of 1956 valence electrons) in a slab geometry. The structure found for the first Pb layer is very different from that of bulk Pb, mostly consisting in one-dimensional lines. However, we do observe the possibility of forming transient structures, in particular icosahedral caps.

Gonzalez, D. J.; Souto, J.; Alemany, M. M. G.; Longo, R. C.; Gallego, L. J.; Gonzalez, L. E.

2013-03-01

335

Ab initio potential energy and dipole moment surfaces of the F(-)(H2O) complex.  

Science.gov (United States)

We present full-dimensional, ab initio potential energy and dipole moment surfaces for the F(-)(H2O) complex. The potential surface is a permutationally invariant fit to 16,114 coupled-cluster single double (triple)/aVTZ energies, while the dipole surface is a covariant fit to 11,395 CCSD(T)/aVTZ dipole moments. Vibrational self-consistent field/vibrational configuration interaction (VSCF/VCI) calculations of energies and the IR-spectrum are presented both for F(-)(H2O) and for the deuterated analog, F(-)(D2O). A one-dimensional calculation of the splitting of the ground state, due to equivalent double-well global minima, is also reported. PMID:23756053

Kamarchik, Eugene; Toffoli, Daniele; Christiansen, Ove; Bowman, Joel M

2013-04-30

336

Ab initio construction of the 2-point velocity difference PDF for incompressible Navier-Stokes fluids  

Science.gov (United States)

Characterizing hydrodynamic turbulence in terms of the so-called 2-point velocity difference statistics is a basic aspect of fluid dynamics, both from the theoretical and experimental viewpoints. The issue concerns in particular the first-principle construction of the corresponding 2-point velocity difference probability density function (PDF) as well as the transport equation which determines its time evolution. The goal of this paper is to point out that the problem can be solved by suitably prescribing the ensemble-averaging operator to be employed in the statistical description of fluids. As a result, qualitative properties of the 2-point PDF which are usually ascribed to the occurrence of turbulence are shown to follow from the ab initio approach presented here and to characterize both deterministic and stochastic fluid descriptions.

Tessarotto, Massimo; Cremaschini, Claudio

2013-08-01

337

Global ab initio ground-state potential energy surface of N4.  

Science.gov (United States)

We present a global ground-state potential energy surface for N4 suitable for treating high-energy vibrational-rotational energy transfer and collision-induced dissociation in N2-N2 collisions. To obtain the surface, complete active space second-order perturbation theory calculations were performed for the ground singlet state with an active space of 12 electrons in 12 orbitals and the maug-cc-pVTZ triple zeta basis set. About 17,000 ab initio data points have been calculated for the N4 system, distributed along nine series of N2 + N2 geometries and three series of N3 + N geometries. The six-dimensional ground-state potential energy surface is fitted using least-squares fits to the many-body component of the electronic energies based on permutationally invariant polynomials in bond order variables. PMID:23901982

Paukku, Yuliya; Yang, Ke R; Varga, Zoltan; Truhlar, Donald G

2013-07-28

338

Ab initio study on the reaction between uranium and O2  

International Nuclear Information System (INIS)

[en] Optimized geometries, total energies and electronic structures of some gaseous atoms and molecules of uranium-oxygen system are calculated with harmonic vibration analysis using ab initio method. The potential energy surfaces (PESs) of the uranium oxidation process are also constructed. The calculated optimized geometries, infrared vibrational frequencies and the first ionized potential energies are in well accordance with available experimental data. Although U6p, U7s and U6d valence orbital electrons take part in the formation of U-O bond, the U5f electrons play an dominant role in this process and because the energies of U5f, U6d, U7s and Uds atomic orbitals are close to each other, these orbitals may hybrid and interact with O2p orbital, simultaneously, to form molecular orbitals of uranium oxides. The PESs show that different reaction modes result in different product geometries

2001-01-01

339

Ab initio simulations on the behavior of small ion clouds in the WITCH Penning trap system  

Energy Technology Data Exchange (ETDEWEB)

Various ab initio simulations on the behavior of ion clouds consisting of a small number of positively charged ions stored in the WITCH double Penning trap system are described. A general description of the simulation code used is presented and the expected behavior of the particles in the first of the two Penning traps is discussed. Special attention is paid to the influence of this behavior on the operation of the experimental setup. The effect of electric excitations on the ion motions is described in detail. Also the transfer of the ions between the two traps and consequences for their motion in the second Penning trap are addressed. Scaled Coulomb force simulations are used to estimate the size of the ion cloud inside the Penning traps for larger numbers of particles.

Coeck, S. [K.U.Leuven, Instituut voor Kern- en Stralingsfysica, Celestijnenlaan 200D, B-3001 Leuven (Belgium)]. E-mail: sam.coeck@fys.kuleuven.be; Delaure, B. [K.U.Leuven, Instituut voor Kern- en Stralingsfysica, Celestijnenlaan 200D, B-3001 Leuven (Belgium); Herbane, M. [K.U.Leuven, Instituut voor Kern- en Stralingsfysica, Celestijnenlaan 200D, B-3001 Leuven (Belgium); Kozlov, V.Yu. [K.U.Leuven, Instituut voor Kern- en Stralingsfysica, Celestijnenlaan 200D, B-3001 Leuven (Belgium); Kraev, I.S. [K.U.Leuven, Instituut voor Kern- en Stralingsfysica, Celestijnenlaan 200D, B-3001 Leuven (Belgium); Tandecki, M. [K.U.Leuven, Instituut voor Kern- en Stralingsfysica, Celestijnenlaan 200D, B-3001 Leuven (Belgium); Wauters, F. [K.U.Leuven, Instituut voor Kern- en Stralingsfysica, Celestijnenlaan 200D, B-3001 Leuven (Belgium); Beck, M. [Westfaelische Wilhelms-Universitaet Muenster, Institut fuer Kernphysik, Wilhelm-Klemm Str. 9, D-48149 Muenster (Germany); Delahaye, P. [CERN, Physics Department, CH-1211 Geneva 23 (Switzerland); Herlert, A. [CERN, Physics Department, CH-1211 Geneva 23 (Switzerland); Sturm, S. [CERN, Physics Department, CH-1211 Geneva 23 (Switzerland); Severijns, N. [K.U.Leuven, Instituut voor Kern- en Stralingsfysica, Celestijnenlaan 200D, B-3001 Leuven (Belgium)

2007-05-01

340

The ideal strength of gold under uniaxial stress: an ab initio study  

Energy Technology Data Exchange (ETDEWEB)

We employ an ab initio calculation based on density functional theory to investigate the ideal strength of face-centered cubic crystal Au under uniaxial stress along the [100] direction. We show that the stability of the perfect Au crystal under tensile stress is determined by the tetragonal shear stiffness modulus, with an ideal tensile strength of 4.2 GPa and the corresponding Lagrangian tensile strain of {approx} 0.07. The potential bifurcation from the primary uniaxial loading path is along the tetragonal shear. Under compressive stress, there is a stress-free body-centered cubic phase, which is unstable and ready to transform to a stress-free body-centered tetragonal phase with lower internal energy. The stable region is from - 1.6 to 4.2 GPa in the ideal strength, or from - 0.07 to 0.07 in the Lagrangian strain.

Wang Hao; Li Mo, E-mail: mo.li@mse.gatech.ed [School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30332 (United States)

2010-07-28

 
 
 
 
341

The equilibrium morphology of WC particles - A combined ab initio and experimental study  

International Nuclear Information System (INIS)

We report an ab initio density functional theory study, complemented by parallel experimental work, of the equilibrium shape of WC particles. The equilibrium shape is simulated under the condition of little or no liquid-phase sintering. The effects of the carbon-rich and carbon-deficient conditions and the adsorption of Co and Ni atoms on the surface of WC particles are investigated. The equilibrium shape of WC particles is found to be a truncated triangular prism under both carbon-rich and carbon-deficient conditions. The adsorption of Co and Ni on the WC surface can promote the formation of either truncated triangular prisms or near-hexagonal prisms, depending on their specific combination with the carbon chemical potential. Under all the conditions investigated, the equilibrium shapes of WC crystals can be described as 'bulky' rather than 'plate-like'. The findings in this study are consistent with the experimental observations.

2011-01-01

342

Ab initio calculations of the electronic and optical properties of germanium selenide  

International Nuclear Information System (INIS)

We have performed an ab initio calculation of the germanium selenide electronic structure, adopting the LDA and GGA approximations for the exchange-correlation potential within the DFT. These calculations have been carried out with and without the inclusion of the spin-orbit interaction. The subtle changes it produces in the band structure, the density of states and the optical properties have been discussed. Also, we propose the s-Ge state contribution at the edge of the valence band as having an important role. Based on our electronic structure, we discuss germanium selenide experimental core spectra and optical properties. We found excellent agreement between our results and available experimental core spectra data, and our calculated optical functions of GeSe explain the origin of the optical transitions, comparing them satisfactorily against existing experimental data.

2007-05-08

343

Ab Initio Linear Scaling Response Theory: Electric Polarizability by Perturbed Projection  

Science.gov (United States)

A linear scaling method for calculation of the static ab initio response within self-consistent field theory is developed and applied to the calculation of the static electric polarizability. The method is based on the density matrix perturbation theory [Niklasson and Challacombe, preceding Letter, Phys. Rev. Lett.PRLTAO0031-9007 92, 193001 (2004)], obtaining response functions directly via a perturbative approach to spectral projection. The accuracy and efficiency of the linear scaling method is demonstrated for a series of three-dimensional water clusters at the RHF/6-31G** level of theory. The locality of the response under a global electric field perturbation is numerically demonstrated by the approximate exponential decay of derivative density matrix elements.

Weber, Valéry; Niklasson, Anders M.; Challacombe, Matt

2004-05-01

344

The accuracy of ab initio molecular geometries for systems containing second-row atoms  

Science.gov (United States)

The performance of the standard hierarchy of ab initio models-that is, Hartree-Fock theory, second-order Møller-Plesset theory, coupled-cluster singles-and-doubles theory, and coupled-cluster singles-doubles-approximate-triples theory-in combination with correlation-consistent basis sets is investigated for equilibrium geometries of molecules containing second-row elements. From an analysis on a collection of 31 molecules (yielding statistical samples of 41 bond distances and 13 bond angles), the statistical errors (mean deviation, mean absolute deviation, standard deviation, and maximum absolute deviation) are established at each level of theory. The importance of core correlation is examined by comparing calculations in the frozen-core approximation with calculations where all electrons are correlated.

Coriani, Sonia; Marchesan, Domenico; Gauss, Jürgen; Hättig, Christof; Helgaker, Trygve; Jørgensen, Poul

2005-11-01

345

Ab initio study of mirages and magnetic interactions in quantum corrals  

CERN Multimedia

The state of the art ab initio calculations of quantum mirages,the spin-polarization of surface-state electrons and the exchange interaction between magnetic adatoms in Cu and Co corrals on Cu(111) are presented. We find that the spin-polarization of the surface-state electrons caused by magnetic adatoms can be projected to a remote location and can be strongly enhanced in corrals compared to an open surface.Our studies give a clear evidence that quantum corrals could permit to tailor the exchange interaction between magnetic adatoms at large separations. The spin-polarization of surface-state electrons at the empty focus in the Co corral used in the experimental setup of Manoharan et al., (Nature 403, 512 (2000)) is revealed.

Stepanyuk, V S; Hergert, W; Bruno, P

2005-01-01

346

The multiferroic phase of DyFeO{sub 3}: an ab initio study  

Energy Technology Data Exchange (ETDEWEB)

By performing accurate ab initio density functional theory (DFT) calculations, we study the role of 4f electrons in stabilizing the magnetic-field-induced ferroelectric state of DyFeO{sub 3}. We confirm that the ferroelectric polarization is driven by an exchange-strictive mechanism, working between adjacent spin-polarized Fe and Dy layers, as suggested by Y Tokunaga (2008 Phys. Rev. Lett. 101 097205). A careful electronic structure analysis suggests that coupling between Dy and Fe spin sublattices is mediated by Dy-d and O-2p hybridization. Our results are robust with respect to the different computational schemes used for d and f localized states, such as the DFT+U method, the Heyd-Scuseria-Ernzerhof (HSE) hybrid functional and the GW approach. Our findings indicate that the interaction between the f and d sublattices might be used to tailor the ferroelectric and magnetic properties of multiferroic compounds.

Stroppa, Alessandro [CNISM, L' Aquila (Italy); Marsman, Martijn; Kresse, Georg [Faculty of Physics and Center for Computational Materials Science, University of Vienna, Sensengasse 8/12, A-1090 Wien (Austria); Picozzi, Silvia, E-mail: astroppa@aquila.infn.i [CNR-SPIN, L' Aquila (Italy)

2010-09-15

347

Interactions of foreign interstitial and substitutional atoms in bcc iron from ab initio calculations  

Science.gov (United States)

C and N atoms are the most frequent foreign interstitial atoms (FIAs), and often incorporated into the surface layers of steels to enhance their properties by thermochemical treatments. Al, Si, Ti, V, Cr, Mn, Co, Ni, Cu, Nb and Mo are the most common alloying elements in steels, also can be called foreign substitutional atoms (FSAs). The FIA and FSA interactions play an important role in the diffusion of C and N atoms, and the microstructures and mechanical properties of surface modified layers. Ab initio calculations based on the density functional theory are carried out to investigate FIA interactions with FSA in ferromagnetic bcc iron. The FIA-FSA interactions are analyzed systematically from five aspects, including interaction energies, density of states (DOS), bond populations, electron density difference maps and local magnetic moments.

You, Y.; Yan, M. F.

2013-05-01

348

Collective proton dynamics at highly charged interfaces studied by ab initio metadynamics.  

UK PubMed Central (United Kingdom)

Surface proton conduction is of utmost importance in biology, materials science, and electrochemistry; yet experimental findings of ultrafast proton transport at densely packed arrays of anionic surface groups have remained controversial and unexplained. We present an ab initio molecular dynamics study of proton dynamics at sulfonic-acid terminated surface groups. Results furnish a highly efficient collective mechanism of hydronium ion translocations at a critical surface group separation of ~6.5 Å. Orientational fluctuations of SG trigger hydrogen bond breaking that sets off the hydronium ion motion. The activation free energy of this process is 0.3 eV (±0.1 eV). The soliton-like nature of this mechanism is owed to the trigonal symmetry of sulfonate anions and exceptionally strong interfacial hydrogen bonding. These insights should stimulate surface conductance studies at SG monolayers with sulfonic acid groups, and they bolster efforts in designing proton conducting polymers conducive to fuel cell operation above ~100 °C.

Vartak S; Roudgar A; Golovnev A; Eikerling M

2013-01-01

349

Cu-based organometallic systems: an ab initio study of the electronic and magnetic properties  

CERN Multimedia

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

350

Raman and ab initio studies of simple and binary 1-alkyl-3-methylimidazolium ionic liquids  

DEFF Research Database (Denmark)

Raman spectra of the ionic liquids, 1-butyl-3-methylimidazolium hexafluorophosphate ([C(4)mim][PF6]), 1-hexyl-3-methylimidazolium chloride ([C(6)mim]Cl), and 1-hexyl-3-methylimidazolium hexafluorophosphate ([C(6)mim][PF6]), and binary mixtures thereof, have been assigned using ab initio MP2 calculations. The previously reported anti and gauche forms of the [C(4)mim](+) cation have been observed, and this study reveals this to be a general feature of the long-chain I-alkyl derivatives. Analysis of mixtures Of [C(6)mim]Cl and [C(6)mim][PF6] has provided information on the nature of the hydrogen bonding between the imidazolium headgroup and the anions, and the invariance of the essentially 50:50 mixture of the predominant conformers informs on the nature of glass formation in these systems.

Berg, R.W.; Deetlefs, M.

2005-01-01

351

Ab initio investigation of electronic properties of the magnesium hydride molecular ion.  

UK PubMed Central (United Kingdom)

In this work, adiabatic potential energy curves, spectroscopic constants, dipole moments, and vibrational levels for numerous electronic states of magnesium hydride molecular ion (MgH(+)) are computed. These properties are determined by the use of an ab initio method involving a nonempirical pseudopotential for the magnesium core (Mg), the core polarization potential (CPP), the l-dependent cutoff functions and the full valence configuration interaction (FCI). The molecular ion is thus treated as a two-electron system. Our calculations on the MgH(+) molecular ion extend previous theoretical works to numerous electronic excited states in the various symmetries. A good agreement with the available theoretical and experimental works is obtained for the spectroscopic constants, the adiabatic potential energy curves, and the dipole moments for the lowest states of MgH(+).

Khemiri N; Dardouri R; Oujia B; Gadéa FX

2013-09-01

352

Temperature influence on a molecular switching under electric field: quantum transport ab initio calculation  

Science.gov (United States)

A molecular transistor based on torsion-angle conformation change driven by gate electric field is designed and studied using ab initio calculations. This transistor consists of a SH-C6H2F(CH3)C6H2(CH3)F-SH molecule sandwiched between two Au(111) electrodes, where the interaction between the molecular dipole and a gate voltage induced electric field will cause the molecule to twist along its c-axis. This twist changes the quantum conductivity of the molecule. The effect of thermal fluctuation on the molecular conformation is studied, so is the ability of the transistor to shut off its current. The advantages and challenges of using such molecular conformation change as a mechanism for transistor gating are discussed

Vergniory, Maia; Grandino-Roldan, Jose; García-Lekue, Aran; Wang, Lin-Wang

2011-03-01

353

Ab initio molecular dynamics simulation on the formation process of He@C?? synthesized by explosion.  

Science.gov (United States)

The applications of endohedral non-metallic fullerenes are limited by their low production rate. Recently, an explosive method developed in our group shows promise to prepare He@C?? at fairly high yield, but the mechanism of He inserting into C?? cage at explosive conditions was not clear. Here, ab initio molecular dynamics analysis has been used to simulate the collision between C?? molecules at high-temperature and high-pressure induced by explosion. The results show that defects formed on the fullerene cage by collidsion can effectively decrease the reaction barrier for the insertion of He into C??, and the self-healing capability of the defects was also observed. PMID:23296568

Li, Jian-Ying; Liu, Li-Min; Jin, Bo; Liang, Hua; Yu, Hai-Jun; Zhang, Hong-Chang; Chu, Shi-Jin; Peng, Ru-Fang

2013-01-08

354

Dissipation of alignment in CO2 gas: A comparison between ab initio predictions and experiments.  

UK PubMed Central (United Kingdom)

We present comparisons between measurements and ab initio calculations of the dissipation of the nonadiabatic laser-induced alignment in pure CO2 and CO2-He gas mixtures. The experiments were made for pressures between 2 and 20 bars at 295 K by using short non-resonant linearly polarized laser pulses for alignment and probe. The calculations are carried, free of any adjusted parameter, using refined intermolecular potentials and a requantized Classical Molecular Dynamics Simulations approach presented previously but not yet confronted to experiments. The results demonstrate that the model accurately reproduces the decays with time of both the transient revivals and "permanent" component of the alignment. The significant differences observed between the behaviors resulting from CO2-CO2 and CO2-He collisions are also well predicted by the model.

Hartmann JM; Boulet C; Vieillard T; Chaussard F; Billard F; Faucher O; Lavorel B

2013-07-01

355

Ab initio study of dissociation reaction of ethylene molecules on Ni cluster  

Science.gov (United States)

The dissociation reaction of ethylene molecules on the Ni cluster surface is investigated by ab initio molecular dynamics simulations. We observe that hydrogen atoms are generated from ethylene molecules at a rate of about 20 ps?1. The activation energy for the dissociation of a hydrogen atom is estimated to be about 0.52 eV, which corresponds to a rate of only about 0.1 ps?1. We find that the adsorption energy of an ethylene molecule on the Ni cluster is more than 1.5 eV, which is three times greater than the activation energy for the hydrogen dissociation. It is, therefore, suggested that the adsorption energy is responsible for the increase of the rate of the dissociation reaction. Based on these results, we discuss the microscopic process of the reaction of ethylene molecules on the Ni cluster in detail.

Shimamura, K.; Oguri, T.; Shibuta, Y.; Ohmura, S.; Shimojo, F.; Yamaguchi, S.

2013-08-01

356

An ab initio variationally computed room-temperature line list for (32)S(16)O3.  

UK PubMed Central (United Kingdom)

Ab initio potential energy and dipole moment surfaces are computed for sulfur trioxide (SO3) at the CCSD(T)-F12b level of theory with appropriate triple-zeta basis sets. The analytical representations of these surfaces are used, with a slight correction, to compute pure rotational and rotation-vibration spectra of (32)S(16)O3 using the variational nuclear motion program TROVE. The calculations considered transitions in the region 0-4000 cm(-1) with rotational states up to J = 85. The resulting line list of 174,674,257 transitions is appropriate for modelling room temperature (32)S(16)O3 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 DS; Tennyson J; Yurchenko SN

2013-07-01

357

Ab initio calculation of linear and nonlinear optical properties of semiconductor structures  

Directory of Open Access Journals (Sweden)

Full Text Available The theoretical and numerical approaches are discussed for ab initio calculations of optical properties. The density functional theory (DFT) combined with the local-density approximation (LDA) allows the calculation of the geometry of crystalline solids and their surfaces with a precision of about one percent. The DFT-LDA band structure and single-electron states therefore provide a reasonable starting point for the calculation of linear and nonlinear susceptibilities within the independent-particle approximation. However, this approach has to be improved by taking into account many-body interactions: self-energy effects, local-field corrections, and electron-hole attraction. Three types of optical spectra are studied: the frequency-dependent dielectric function, the second-harmonic generation, and surface reflectance anisotropy spectra. The systems considered are two-atomic semiconductors, their polytypes and their surfaces.

Bechstedt F.; Adolph B.; Schmidt W. G.

1999-01-01

358

Ab initio-driven trajectory-based nuclear quantum dynamics in phase space  

Science.gov (United States)

We derive a Bohmian trajectory-based quantum dynamics approach for the calculation of adiabatic and nonadiabatic quantum effects in ab initio on-the-fly molecular dynamics simulations. The method is designed for calculations in the full, unconstrained, phase space of molecular systems described within density functional theory and time-dependent density functional theory. The problem of solving quantum hydrodynamic equations using trajectories in high dimensions is addressed using an expansion of the nuclear amplitude in atom centered Gaussians that are propagated along the quantum trajectories. In this work, we investigate the adiabatic limit of this theory, even though the full nonadiabatic case is derived. The method is first tested on the H2 molecule and then applied to the study of the proton transfer dynamics in the phase space of the molecular complex (H3N-H-NH3)+.

Tavernelli, Ivano

2013-04-01

359

Ab initio study and spectral simulation of the XA?XB photodetachment processe of dichlorocarbene anion  

Science.gov (United States)

Combining ab initio molecular orbital calculations with Franck-Condon analysis to simulate vibrationally resolved photoelectron spectra have been carried out on the CCl(XA)?CCl2-(XB) detachment process. By using CCSD/6-311+G(2d, p) values, the theoretical spectra obtained are in agreement with the observed one, and, the equilibrium geometry parameters, 1.890 ± 0.002 Å and 102.9 ± 0.3° of the XB state of CCl2- are acquired, by employing an iterative Franck-Condon (IF-C) analysis procedure. In addition, on different levels of theory, our best calculated electron affinity (EA) is in fair agreement with the experimental value.

Zhang, Jin; Wang, Gan; Zheng, Qinghua; Ma, Jianguo

2013-09-01

360

Infrared shifts of the water dimer from the fully flexible ab initio HBB2 potential.  

UK PubMed Central (United Kingdom)

We report calculations of the infrared shifts for the water dimer, as obtained from the recent ab initio fully flexible HBB2 potential of Bowman and co-workers. The rovibrational calculations, which formally are 12-dimensional plus overall rotation, were performed within the [6+6]d adiabatic separation which decouples the 'fast' intramolecular modes from the 'slow' intermolecular ones. Apart from this decoupling, each set of modes is treated in a fully variational approach. The intramolecular motion was described in terms of Radau coordinates, using the f-embedding formulation of Wei & Carrington, and neglecting the rovibrational Coriolis coupling terms. Within this adiabatic approximation, the intermolecular motion is handled in a similar way as for rigid monomers, except for the rotational constants B's, averaged over intramolecular modes that depend now on the intermolecular geometry. Comparison with experimental data shows an excellent overall agreement.

Leforestier C

2012-06-01

 
 
 
 
361

Ab initio molecular dynamics simulation of lithiation-induced phase-transition of crystalline silicon  

International Nuclear Information System (INIS)

Highlights: ? Crystalline silicon amorphizes at a ratio of 0.3 Li atoms per Si atom. ? The average number of Si atoms around Li significantly decreases upon amorphization. ? We suggest several representative local structures of Li–Si amorphous alloy. - Abstract: We have studied the lithiation-induced amorphization of crystalline silicon by using first-principles calculations. Ab initio simulations show that crystalline silicon amorphizes at a ratio of 0.3 Li atoms per Si atom. Upon amorphization, the tetrahedral Si network suddenly collapses and the average number of Si atoms around Li significantly decreases from 4.6 to 2.6. We suggest the presence of ring structures, made of pure Si atoms and composite Li–Si atoms, as representative local structures of Li–Si amorphous alloy.

2012-02-15

362

The Hubbard chain at finite temperatures ab initio calculations of Tomonaga-Luttinger liquid properties  

CERN Multimedia

We present a novel treatment of finite temperature properties of the one-dimensional Hubbard model. Our approach is based on a Trotter-Suzuki mapping utilizing Shastry's classical model and a subsequent investigation of the quantum transfer matrix. We derive non-linear integral equations for three auxiliary functions which have a clear physical interpretation of elementary excitations of spin type and charge excitations in lower and upper Hubbard bands. This allows for a transparent analytical study of certain limiting cases as well as for precise numerical investigations. We present data for the specific heat, magnetic and charge susceptibilities for various particle densities and coupling strengths U. The structure exposed by these curves is discussed in terms of the elementary charge and spin excitations. Special emphasis is placed on the study of the low-temperature behavior within our ab initio approach confirming the scaling predictions by Tomonaga-Luttinger liquid theory. In addition we make contact wi...

Jüttner, G; Suzuki, J

1997-01-01

363

The constrained space orbital variation analysis for periodic ab initio calculations  

Science.gov (United States)

The constrained space orbital variation (CSOV) method for the analysis of the interaction energy has been implemented in the periodic ab initio CRYSTAL03 code. The method allows for the partition of the energy of two interacting chemical entities, represented in turn by periodic models, into contributions which account for electrostatic effects, mutual polarization and charge transfer. The implementation permits one to carry out the analysis both at the Hartree-Fock and density functional theory levels, where in the latter the most popular exchange-correlation functionals can be used. As an illustrating example, the analysis of the interaction between CO and the MgO (001) surface has been considered. As expected by the almost fully ionic character of the support, our periodic CSOV results, in general agree with those previously obtained using the embedded cluster approach, showing the reliability of the present implementation.

Cruz Hernández, N.; Zicovich-Wilson, Claudio Marcelo; Fdez. Sanz, Javier

2006-05-01

364

The constrained space orbital variation analysis for periodic ab initio calculations  

International Nuclear Information System (INIS)

[en] The constrained space orbital variation (CSOV) method for the analysis of the interaction energy has been implemented in the periodic ab initio CRYSTAL03 code. The method allows for the partition of the energy of two interacting chemical entities, represented in turn by periodic models, into contributions which account for electrostatic effects, mutual polarization and charge transfer. The implementation permits one to carry out the analysis both at the Hartree-Fock and density functional theory levels, where in the latter the most popular exchange-correlation functionals can be used. As an illustrating example, the analysis of the interaction between CO and the MgO (001) surface has been considered. As expected by the almost fully ionic character of the support, our periodic CSOV results, in general agree with those previously obtained using the embedded cluster approach, showing the reliability of the present implementation

1001-01-00

365

Ab initio Molecular Dynamics Study of Glycine Intramolecular Proton Transfer in Water  

CERN Multimedia

We use ab initio molecular dynamics simulations to quantify structural and thermodynamic properties of a model proton transfer reaction that converts a neutral glycine molecule, stable in the gas phase, to the zwitterion that predominates in aqueous solution. We compute the potential of mean force associated with the direct intramolecular proton transfer event in glycine. Structural analyses show that the average hydration number Nw of glycine is not constant along the reaction coordinate, but rather progresses from Nw=5 in the neutral molecule to Nw=8 for the zwitterion. We report the free energy difference between the neutral and charged glycine molecules, and the free energy barrier to proton transfer. Finally, we identify approximations inherent in our method and estimate corresponding corrections to our reported thermodynamic predictions.

Leung, K; Leung, Kevin; Rempe, Susan B.

2005-01-01

366

When a proton attacks cellobiose in the gas phase: ab initio molecular dynamics simulations.  

UK PubMed Central (United Kingdom)

Investigations of reaction pathways between a proton and cellobiose (CB), a glucose disaccharide of importance, were carried out in cis and trans CB using Ab Initio Molecular Dynamics (AIMD) simulations starting from optimized configurations where the proton is initially placed near groups with affinity for it. Near and above 300 K, protonated CB (H(+)CB) undergoes several transient reactions including charge transfer to the sugar backbone, water formation and dehydration, ring breaking and glycosidic bond breaking events as well as mutarotation and ring puckering events, all on a 10 ps timescale. cis H(+)CB is energetically favoured over trans H(+)CB in vacuo, with an energy gap larger than for the neutral CB.

Pincu M; Brauer B; Gerber RB

2013-08-01

367

When a proton attacks cellobiose in the gas phase: ab initio molecular dynamics simulations.  

Science.gov (United States)

Investigations of reaction pathways between a proton and cellobiose (CB), a glucose disaccharide of importance, were carried out in cis and trans CB using Ab Initio Molecular Dynamics (AIMD) simulations starting from optimized configurations where the proton is initially placed near groups with affinity for it. Near and above 300 K, protonated CB (H(+)CB) undergoes several transient reactions including charge transfer to the sugar backbone, water formation and dehydration, ring breaking and glycosidic bond breaking events as well as mutarotation and ring puckering events, all on a 10 ps timescale. cis H(+)CB is energetically favoured over trans H(+)CB in vacuo, with an energy gap larger than for the neutral CB. PMID:23936906

Pincu, Madeleine; Brauer, Brina; Gerber, R Benny

2013-08-28

368

Thermodynamic assessment of the Am-Pu system with input from ab initio  

International Nuclear Information System (INIS)

[en] Highlights: ? The phase diagram of Am-Pu has been assessed with the CALPHAD methodology. ? Input energetics from electronic structure calculations guided the assessment. ? A minor modification of the thermodynamics explains the two known phase diagrams. ? The results provide guidance and motivate further experimental studies for validation. - Abstract: Based on the CALPHAD approach, thermodynamic properties and phase diagram of the Am-Pu system are assessed with input from results of ab initio electronic-structure calculations within the framework of density-functional theory. Despite the limited availability of experimental data on this binary system, thermodynamic assessment has been performed and two phase diagrams are proposed that make distinction at high temperature between the relative stability of the bcc phase and the liquid state. Our investigation provides guidance and motivates further experimental studies.

2011-01-01

369

Ab initio high-pressure thermodynamics of cationic disordered MgAl2O4 spinel  

International Nuclear Information System (INIS)

Ab initio calculations are performed in the framework of density functional theory and the local density approximation, to evaluate structural, thermodynamic and vibrational behaviour of MgAl2O4 spinel with cationic disorder under pressure. An effective thermodynamic model using both a regular solution and a quadratic form for the internal energy is parametrized to describe the non-convergent cationic disordering. The evolution of cationic disorder rate with temperature and isostatic pressure is deduced from this model. Relative density and heat capacity excess evolution are simulated as a function of cationic disorder. Infrared modes are calculated in the Brillouin zone centre for several disordered spinels. Good agreement is found with available experimental data

2003-10-22

370

Insights into H2 formation in space from ab initio molecular dynamics.  

UK PubMed Central (United Kingdom)

Hydrogen formation is a key process for the physics and the chemistry of interstellar clouds. Molecular hydrogen is believed to form on the carbonaceous surface of dust grains, and several mechanisms have been invoked to explain its abundance in different regions of space, from cold interstellar clouds to warm photon-dominated regions. Here, we investigate direct (Eley-Rideal) recombination including lattice dynamics, surface corrugation, and competing H-dimers formation by means of ab initio molecular dynamics. We find that Eley-Rideal reaction dominates at energies relevant for the interstellar medium and alone may explain observations if the possibility of facile sticking at special sites (edges, point defects, etc.) on the surface of the dust grains is taken into account.

Casolo S; Tantardini GF; Martinazzo R

2013-04-01

371

Ab initio study of a TiO2/LaAlO3 heterostructure  

International Nuclear Information System (INIS)

In this work we explore the origin of the ferromagnetism appearing when a TiO2 film is grown on another non-magnetic oxide as a substrate such as LaAlO3 (001), concentrating on the role played by the oxygen vacancies in this phenomenon. Using Density Functional Theory ab-initio methods, we study the free-standing anatase film as well as the interfaces with either the LaO or AlO2 planes of LaAlO3. Our results show that the interface LaO/TiO2 is favored against the AlO2/TiO2 one if no oxygen vacancies are present in the interface whereas the contrary happens when there are oxygen vacancies. In both cases, the cohesive energy is of the same order of magnitude but only at AlO2/TiO2 we found a magnetic solution.

2009-05-01

372

Spectroscopic and Ab-Initio Studies of ? -Type Hydrogen Bonding in Cyclic Alcohols and Amines  

Science.gov (United States)

Infrared and Raman spectroscopy have been used to investigate several molecules capable of intramolecular ?-type hydrogen bonding. Ab-initio calculations have been utilized to complement the experimental work. The cyclic alcohols, 3-cyclopenten-1-ol (3CYPO), 2-cyclopenten-1-ol, 2-cyclohexen-1-ol, and the cyclic amines, 3-cyclopenten-1-amine, 2-aminoindan, 2-cyclopenten-1-amine, 1-aminoindan, and 2-hydroxytetralin have been studied. 3CYPO can exist in four different conformational forms and all were observed in the infrared and Raman spectra. The conformer with the weak ?-type intramolecular hydrogen bonding is about 400 cm-1 (1.1 kcal/mole) lower in energy than the other three conformations to which the lowest energy form can interconvert through ring-puckering or internal rotation vibrations. The interconversions and relative energies of all the other molecules were also investigated. In each case the conformation with the lowest energy had a ?-type hydrogen bonding.

Ocola, Esther; Laane, Jaan

2011-10-01

373

Ab initio simulations of H2 in Li-doped carbon nanotube systems  

CERN Document Server

Because of their unique structure, it has been proposed that carbon nanotube ropes may well provide an ideal container for the storage of molecular hydrogen. Indeed, there has been some experimental evidence of enhanced hydrogen uptake in doped Li and other alkali metal systems [Chen et al, Science 285, 91 (1999)]. We have therefore addressed this issue of hydrogen storage in Li-doped graphite and carbon nanotube systems theoretically with ab initio simulations. Our results find no evidence for such enhanced storage, based on the induced structural changes. In addition, we have also investigated the diffusion barriers for hydrogen to enter into nanotube interiors, both in the presence and absence of topological defects. Even if nanotube interiors are made accessible, the hydrogen uptake remains modest, i.e., less than 3.5 wt%. Mechanically or chemically processing nanotubes is therefore not likely to lead to greatly increased hydrogen storage.

Sabir, A; Roland, C; Bernholc, J; Sabir, Abdenour; Lu, Wenchang; Roland, Christopher; Bernholc, Jerzy

2006-01-01

374

Phase diagram studies on iron and nickel silicides: high-pressure experiments and ab initio calculations  

International Nuclear Information System (INIS)

We performed high-pressure ADXRD studies on Fe5Si3 and Ni2Si up to 75 GPa. No evidence of the occurrence of a phase transition was observed in them. Fe5Si3 was found to compress isotropically, but an anisotropic compression was observed in Ni2Si. These results are supported by ab initio total-energy calculations, which for Fe5Si3 also predicted a transition at 283 GPa from the hexagonal P63/mcm phase to a cubic phase. High-pressure melting studies were conducted on FeSi up to 70 GPa. We found a change in the melting slope at 12 GPa, which is attributed to the intersection of the melting curve with the phase boundary between ?-FeSi and CsCl-type FeSi. Finally, an equation of state for Fe5Si3 and Ni2Si is reported.

2008-01-01

375

Ab initio study on the dynamics of furfural at the liquid-solid interfaces  

Science.gov (United States)

Catalytic biomass conversion sometimes occurs at the liquid-solid interfaces. We report ab initio molecular dynamics simulations at finite temperatures for the catalytic reactions involving furfural at the water-Pd and water-Cu interfaces. We found that, during the dynamic process, the furan ring of furfural prefers to be parallel to the Pd surface and the aldehyde group tends to be away from the Pd surface. On the other hand, at the water-Cu(111) interface, furfural prefers to be tilted to the Cu surface while the aldehyde group is bonded to the surface. In both cases, interaction of liquid water and furfural is identified. The difference of dynamic process of furfural at the two interfaces suggests different catalytic reaction mechanisms for the conversion of furfural, consistent with the experimental investigations.

Dang, Hongli; Xue, Wenhua; Shields, Darwin; Liu, Yingdi; Jentoft, Friederike; Resasco, Daniel; Wang, Sanwu

2013-03-01

376

Atomic diffusion in covalent liquids under pressure from ab initio molecular dynamics  

Directory of Open Access Journals (Sweden)

Full Text Available The microscopic mechanisms of atomic diffusion in liquid GeO2 and SrGeO3 are investigated by ab initio molecular-dynamics simulations. We clarify the differences of diffusion mechanism between liquid GeO2 and SrGeO3. In both liquids, non-bridging oxygen double bonded to only one germanate plays a key role in the atomic diffusion mechanism. It is found that, in liquid SrGeO3 which has non-bridging oxygen in the equilibrium state at ambient pressure, atomic diffusion is possible without generating overcoordinated atoms at ambient pressure, while the over coordinated atoms are always needed for the formation of non-bridging oxygens in liquid GeO2. When the pressure increases, only liquid GeO2 has a diffusion maximum, which is given by, the atomic diffusion with concerted reaction gives the dif fusion maximum.

Ohmura S.; Yoshimura R.; Shimojo F.

2011-01-01

377

New developments in the ab initio treatment of low energy electron collisions with molecules  

Energy Technology Data Exchange (ETDEWEB)

Although there has been substantial progress in the ab initio treatment of low energy electron scattering from small diatomic and polyatomic molecules in the last few years a number of problems still remain. Most current research has focused on the calculation of fixed nuclei scattering amplitudes in the static-exchange (SE) approximation. A few calculations have gone beyond this approximation to include electron correlation and/or vibrational and rotational effects, the latter often within the framework of model or parameterized potentials. In this article we review a number of developments which have occurred since the last electron molecule satellite meeting at Daresbury Laboratory in July 1987. Our primary objective shall be to point out the strengths and weaknesses of current computational capabilities and to describe a new approach to electron polyatomic collisions using the complex Kohn method. 30 refs., 1 fig.

Schneider, B.I.; Rescigno, T.N.; McCurdy, C.W.; Lengsfield, B.H. III

1989-01-01

378

Ellipsometry and ab initio approaches to the refractive index of porous silicon  

International Nuclear Information System (INIS)

[en] Spectroscopic ellipsometry is used to determine the complex refractive index (n-ik), porosity, and thickness of porous silicon (PSi) films. These films are obtained by anodizing p-type crystalline silicon in a hydrofluoric acid bath. After etching, PSi samples are heated to 750 deg. Cin a controlled oxygen environment. A detailed analysis of the ellipsometry data is performed in order to determine the complex refractive index of PSi thin film. This frequency dependence of n and k is compared with the results of ab initio quantum mechanical calculations carried out by means of CASTEP codes within the density functional theory. The theoretical results show a diminution of the lattice constant as the oxygen content grows, in contrast to the hydrogen-saturated surface case

2007-10-03

379

Physical Properties of the ZnxCd1-x Se Alloys: Ab-Initio Method  

Directory of Open Access Journals (Sweden)

Full Text Available The present work performs self-consistent ab initio full-potential linear muffin-tin orbital (FP-LMTO) method to study the structural and electronic properties of the ternary ZnxCd1-xSe alloy, based on density functional theory (DFT). In this approach, both the local density approximation (LDA) and the generalized gradient approximation (GGA) were used for the exchange-correlation potential calculation. The ground-state properties are determined for the bulk materials CdSe, ZnSe and their alloy in cubic phase. In particular, the lattice constant, bulk modulus, electronic band structures and effective mass. We mainly showed deviation of the lattice parameter and bulk modulus from Vegard’s law of our alloys. We also presented the microscopic origins of the gap bowing using the approach of Zunger et al. The results are compared with other theoretical calculations and experimental data and are in reasonable agreement.

Mohammed Ameri; Meriem Fodil; Fatma Z. Aoumeur-Benkabou; Zoubir Mahdjoub; Fatima Boufadi; Ali Bentouaf

2012-01-01

380

Performance of an ab initio equation of state for magnesium oxide  

International Nuclear Information System (INIS)

A thermodynamically complete ab initio equation of state (EOS) for MgO was obtained using electron density functional theory and the quasiharmonic phonon approximation, and adjusted to match the ambient density. This EOS was demonstrated to be consistent with isotherm, thermal expansivity, heat capacity and melting curve measured in static experiments, and reproduced density and temperature measurements under shock wave loading of bulk and porous periclase. The Grueneisen parameter of periclase at a given density was shown to be weakly dependent on temperature. The B1-B2 phase change was calculated to occur near 320 GPa on the principal Hugoniot. The melting locus of periclase, relevant to the Earth's lower mantle pressures, was predicted to be accessible by shock wave loading of porous periclase, which could also put pressure and temperature bounds on B1-B2 transitions.

2004-08-04

 
 
 
 
381

Ab-initio study of phase transition in SmAs under pressure  

Science.gov (United States)

The pressure induced structural phase transformation of SmAs have been investigated using ab initio full-potential linear augmented plane wave plus local orbitals (FP-APW+lo) approach. The generalized gradient approximation is used for the exchange-correlation functional energy optimization to calculate the total energy. At ambient conditions SmAs stabilize in NaCl structure and undergoes first-order structural transition from Fm-3m to P4/mmm phase at 32.51 GPa which is in good agreement with the experimental value 32.1 GPa. The equilibrium lattice constants, bulk modulus and its pressure derivative and equation of state have also been computed. They are also in good agreement with measured data.

Singh, Sanjay Kumar; Rana, Pooja; Gupta, Dinesh Chandra

2012-06-01

382

An ab initio potential energy surface for the reaction N+ + H2? NH+ + H  

International Nuclear Information System (INIS)

[en] Preliminary results of ab initio unrestricted Hartree-Fock calculations for the potential energy surface for the reaction N+ + H2?NH+ + H are reported. For the collinear approach of N+ to H2, the 3?- surface has no activation barrier and has a shallow well (ca.1eV). For perpendicular approach (Csub(2V)symmetry) the 3B2 states is of high energy, the 3A2 state has a shallow well but as the bond angle increases the 3B1 states decreases in energy to become the state of lowest energy. Neither the collinear nor the perpendicular approaches give adiabatic pathways to the deep potential well of 3B1 (HNH)+. (auth.)

1975-10-01

383

Conformational composition of neutral leucine. Matrix isolation infrared and ab initio study  

Science.gov (United States)

Low-temperature matrix-isolation FTIR spectroscopy and ab initio calculations are employed to determine conformational composition of neutral leucine. The presence of three leucine conformers in the matrices is revealed. This is in agreement with the results of a detailed study of the potential energy surface of leucine which demonstrates that only five out of 105 possible conformers should have populations in the matrices larger than 2% and only three conformers, which are the ones detected in the experiment, should have populations larger than 10%. UV irradiation of the matrix samples are used to separate bands of the different conformers. We also show that the populations of the leucine conformers in the gas phase at 440 K are significantly different from the ones in matrices. The population of the lowest energy conformer in the gas phase being approximately 23% in the gas phase increases to over 64% in matrices.

Stepanian, Stepan G.; Ivanov, Alexander Yu.; Adamowicz, Ludwik

2013-09-01

384

Quantum mechanical ab initio simulation of the electron screening effect in metal deuteride crystals  

Energy Technology Data Exchange (ETDEWEB)

In antecedent experiments the electron screening energies of the d+d reactions in metallic environments have been determined to be enhanced by an order of magnitude in comparison to the case of gaseous deuterium targets. The analytical models describing averaged material properties have not been able to explain the experimental results so far. Therefore, a first effort has been undertaken to simulate the dynamics of reacting deuterons in a metallic lattice by means of an ab initio Hartree-Fock calculation of the total electrostatic force between the lattice and the successively approaching deuterons via path integration. The calculations have been performed for Li and Ta, clearly showing a migration of electrons from host metallic to the deuterium atoms. However, in order to avoid more of the necessary simplifications in the model the utilization of a massive parallel supercomputer would be required. (orig.) 3.

Huke, A.; Chun, S.M.; Biller, A.; Heide, P. [Technische Universitaet Berlin, Institut fuer Optik und Atomare Physik, Berlin (Germany); Czerski, K. [Technische Universitaet Berlin, Institut fuer Optik und Atomare Physik, Berlin (Germany); University of Szczecin, Institute of Physics, Szczecin (Poland)

2008-02-15

385

Quantum mechanical ab initio simulation of the electron screening effect in metal deuteride crystals  

International Nuclear Information System (INIS)

In antecedent experiments the electron screening energies of the d+d reactions in metallic environments have been determined to be enhanced by an order of magnitude in comparison to the case of gaseous deuterium targets. The analytical models describing averaged material properties have not been able to explain the experimental results so far. Therefore, a first effort has been undertaken to simulate the dynamics of reacting deuterons in a metallic lattice by means of an ab initio Hartree-Fock calculation of the total electrostatic force between the lattice and the successively approaching deuterons via path integration. The calculations have been performed for Li and Ta, clearly showing a migration of electrons from host metallic to the deuterium atoms. However, in order to avoid more of the necessary simplifications in the model the utilization of a massive parallel supercomputer would be required. (orig.) 3

2008-01-01

386

Ab initio and density functional studies of hydrocarbon adsorption in zeolites.  

Energy Technology Data Exchange (ETDEWEB)

The adsorption energies of methane and ethane in zeolites are investigated with ab initio molecular orbital theory and density functional theory. In this work we have used zeolite cluster models containing two, three, and five tetrahedral (Si, Al) atoms and have found equilibrium structures for complexes of methane, ethane, and propane with an acid site. If a large enough cluster is used and correlation effects are included via perturbation theory, the calculated adsorption energy for ethane is about 5 kcal/mol compared with the experimental value of 7.5 kcal/mol. The B3LYP density functional method gives a much smaller binding of {approximately}1 kcal/mol for ethane. The reason for the failure of density fictional theory is unclear.

Curtiss, L. A.

1998-08-21

387

Ab initio simulation of the electronic structure of Ta2O5 crystal modifications  

Science.gov (United States)

Ab initio simulation of the electronic structure crystalline ? and ? phases of tantalum(V) oxide (Ta2O5), representing a promising dielectric material for microelectronics, has been carried out. Both ideal crystals and those with neutral oxygen vacancies in various coordination positions have been studied. The simulation has been performed using the density functional theory with hybrid functionals involving the Hartree-Fock exchange energy. This approach gives a correct description of the bandgap width: 4.1 eV for ?-Ta2O5 and 3.1 eV for ?-Ta2O5. The energy levels related to oxygen vacancies in various positions have been determined for the spectra of electron states in ?- and ?-Ta2O5 polymorphs. It is established that the presence of oxygen vacancies in Ta2O5 crystal modifications leads to the formation of characteristic absorption peaks in their electron energy loss spectra.

Perevalov, T. V.; Shaposhnikov, A. V.

2013-06-01

388

Organic peracids: a structural puzzle for 17O NMR and ab initio chemical shift calculations.  

UK PubMed Central (United Kingdom)

We have applied (17)O NMR spectroscopy to investigate the structure of the organic peracids formed by reaction of acetic acid (AA) or lactic acid (LA) with aqueous hydrogen peroxide (HP), which are used in several "green chemistry" applications. The interpretation of the experimental spectra has been supported by ab initio calculations of the (17)O chemical shifts for several possible species, using a continuum representation of the solvent. The combined use of these tools has also allowed us to discuss the decomposition mechanism of LA/HP solutions. The calculated electric field gradients for water, HP, and CO(2) (a decomposition product of LA) correlate well with the experimental (17)O line widths.

Castiglione F; Baggioli A; Citterio A; Mele A; Raos G

2012-02-01

389

Ab initio density functional theory investigation of Li-intercalated silicon carbide nanotube bundles  

Energy Technology Data Exchange (ETDEWEB)

We present the results of ab initio density functional theory calculations on the energetic, and geometric and electronic structure of Li-intercalated (6,6) silicon carbide nanotube (SiCNT) bundles. Our results show that intercalation of lithium leads to the significant changes in the geometrical structure. The most prominent effect of Li intercalation on the electronic band structure is a shift of the Fermi energy which occurs as a result of charge transfer from lithium to the SiCNTs. All the Li-intercalated (6,6) SiCNT bundles are predicted to be metallic representing a substantial change in electronic properties relative to the undoped bundle, which is a wide band gap semiconductor. Both inside of the nanotube and the interstitial space are susceptible for intercalation. The present calculations suggest that the SiCNT bundle is a promising candidate for the anode material in battery applications.

Moradian, Rostam [Physics Department, Faculty of Science, Razi University, Kermanshah (Iran, Islamic Republic of); Nano Science and Technology Research Center, Razi University, Kermanshah (Iran, Islamic Republic of); Computational Physical Science Research Laboratory, Department of Nano Science, Institute for Studies in Theoretical Physics and Mathematics (IPM), PO Box 19395-5531, Tehran (Iran, Islamic Republic of)], E-mail: moradian.rostam@gmail.com; Behzad, Somayeh; Chegel, Raad [Physics Department, Faculty of Science, Razi University, Kermanshah (Iran, Islamic Republic of)

2009-06-15

390

Ab initio density functional theory investigation of structural and electronic properties of silicon carbide nanotube bundles  

Energy Technology Data Exchange (ETDEWEB)

By using ab initio density functional theory the structural and electronic properties of isolated and bundled (8,0) and (6,6) silicon carbide nanotubes (SiCNTs) are investigated. Our results show that for such small diameter nanotubes the inter-tube interaction causes a very small radial deformation, while band splitting and reduction of the semiconducting energy band gap are significant. We compared the equilibrium interaction energy and inter-tube separation distance of (8,0) SiCNT bundle with (10,0) carbon nanotube (CNT) bundle where they have the same radius. We found that there is a larger inter-tube separation and weaker inter-tube interaction in the (8,0) SiCNT bundle with respect to (10,0) CNT bundle, although they have the same radius.

Moradian, Rostam [Physics Department, Faculty of Science, Razi University, Kermanshah (Iran, Islamic Republic of); Nano Science and Technology Research Center, Razi University, Kermanshah (Iran, Islamic Republic of); Department of Nano Science, Computational Physical Science Research Laboratory, Institute for Studies in Theoretical Physics and Mathematics (IPM), P.O. Box 19395-5531, Tehran (Iran, Islamic Republic of)], E-mail: moradian.rostam@gmail.com; Behzad, Somayeh; Chegel, Raad [Physics Department, Faculty of Science, Razi University, Kermanshah (Iran, Islamic Republic of)

2008-10-01

391

Ab initio calculations on excited molecular ions of ethylene and acetylene  

International Nuclear Information System (INIS)

[en] Ab initio calculations of the energy and wave functions for neutral molecules and excited molecular ions are used to interpret the EMS and PES spectra of acetylene and ethylene. The five satellite regions of acetylene are assigned to intensity borrowed from 2?g, 3?g and 2?u primary hole states by ion states with configurations (?u)-2 (2?g)1, (?u)-2 (3?g)-l (?g)2, and (?u)-l (3?g)-1 (?g)l. The Dyson orbitals for the satellite regions of acetylene and ethylene are shown to differ from the Dyson orbitals of the primary holes. The importance of choosing basis sets appropriate to the excited states of the ion is illustrated. 51 refs., 2 tabs., 7 figs

1996-01-01

392

Ab initio pseudopotential studies of equilibrium lattice structures and phonon modes of bulk BC3  

International Nuclear Information System (INIS)

[en] Different stacking arrangements of BC3 layered crystals are studied with the use of the ab initio pseudopotential density-functional method. The total energies, lattice constants, electron energy band structures and density of states, as well as phonon frequencies are calculated for the possible bulk BC3 structures obtained by full relaxations starting from different initial atomic configurations of ABAB (or ABCABC)... layer stacking. Two stable BC3 structures, one semiconductor and the other metal, are obtained, which have lower total energies compared with those of the structures proposed previously. Our calculations show that except for these two BC3 structures, all the structures we studied, including the BC3 structures proposed previously, have imaginary phonon frequencies corresponding to the relative, parallel motion of the adjacent BC3 layers, indicating the instability of the layer stacking in these structures

2002-09-30

393

Ab initio pseudopotential studies of equilibrium latticestructures and phonon modes of bulk BC3  

Energy Technology Data Exchange (ETDEWEB)

Different stacking arrangements of BC3 layered crystals are studied with the use of the ab initio pseudopotential density-functional method. The total energies, lattice constants, electron energy band structures and density of states, as well as phonon frequencies are calculated for the possible bulk BC3 structures obtained by full relaxations starting from different initial atomic configurations of ABAB (or ABCABC)... layer stacking. Two stable BC3 structures, one semiconductor and the other metal, are obtained, which have lower total energies compared with those of the structures proposed previously. Our calculations show that except for these two BC3 structures, all the structures we studied, including the BC3 structures proposed previously, have imaginary phonon frequencies corresponding to the relative, parallel motion of the adjacent BC3 layers, indicating the instability of the layer stacking in these structures.

Sun, Hong; Ribeiro, Filipe J.; Li, Je-Luen; Roundy, David; Cohen,Marvin L.; Louie, StevenG.

2002-09-30

394

Equation of state and phase diagram of ammonia at high pressures from ab initio simulations.  

UK PubMed Central (United Kingdom)

We present an equation of state as well as a phase diagram of ammonia at high pressures and high temperatures derived from ab initio molecular dynamics simulations. The predicted phases of ammonia are characterized by analyzing diffusion coefficients and structural properties. Both the phase diagram and the subsequently computed Hugoniot curves are compared to experimental results. Furthermore, we discuss two methods that allow us to take into account nuclear quantum effects, which are of considerable importance in molecular fluids. Our data cover pressures up to 330 GPa and a temperature range from 500 K to 10,000 K. This regime is of great interest for interior models of the giant planets Uranus and Neptune, which contain, besides water and methane, significant amounts of ammonia.

Bethkenhagen M; French M; Redmer R

2013-06-01

395

Equation of state and phase diagram of ammonia at high pressures from ab initio simulations.  

Science.gov (United States)

We present an equation of state as well as a phase diagram of ammonia at high pressures and high temperatures derived from ab initio molecular dynamics simulations. The predicted phases of ammonia are characterized by analyzing diffusion coefficients and structural properties. Both the phase diagram and the subsequently computed Hugoniot curves are compared to experimental results. Furthermore, we discuss two methods that allow us to take into account nuclear quantum effects, which are of considerable importance in molecular fluids. Our data cover pressures up to 330 GPa and a temperature range from 500 K to 10,000 K. This regime is of great interest for interior models of the giant planets Uranus and Neptune, which contain, besides water and methane, significant amounts of ammonia. PMID:23802968

Bethkenhagen, Mandy; French, Martin; Redmer, Ronald

2013-06-21

396

Ab initio determination of excitation energies and magnetic couplings in correlated quasi-two-dimensional iridates  

Science.gov (United States)

To determine the strength of essential electronic and magnetic interactions in the iridates Sr2IrO4 and Ba2IrO4—potential platforms for high-temperature superconductivity—we use many-body techniques from wave-function-based electronic-structure theory. Multiplet physics, spin-orbit interactions, and Ir-O hybridization are all treated on equal footing, fully ab initio. Our calculations put the lowest d-d excitations of Sr2IrO4/Ba2IrO4 at 0.69/0.64 eV, substantially lower than in isostructural cuprates. Charge-transfer excitations start at 3.0/1.9 eV and the magnetic nearest-neighbor exchange coupling is 51/58 meV. Available experimental results are fully consistent with these values, which strongly constrains the parametrization of effective iridate Hamiltonians.

Katukuri, Vamshi M.; Stoll, Hermann; van den Brink, Jeroen; Hozoi, Liviu

2012-06-01

397

Ab initio study of the uranyl oxide hydrates: a proton transfer mediated by water  

International Nuclear Information System (INIS)

We present a first-principles study of the UO3?n(H2O) uranyl oxide hydrates, namely, schoepite (n = 2.25), metaschoepite (n = 2) and dehydrated metaschoepite (n = 1.75), which appear as the alteration U(VI) products of aqueous corrosion of nuclear fuel. For these compounds, the calculated enthalpy of formation is in good agreement with calorimetry and solubility measurements. We discuss the key electronic state factors behind the phase stability of uranyl oxide hydrates. An unexplored proton-transfer mechanism, which produces the H3O hydronium ions in UO3?nH2O, has been studied using ab initio molecular dynamics simulations at room temperature. For the hydronium ion, a very short lifetime of around 20 fs has been suggested.

2007-06-20

398

Prediction of toxicity of nitrobenzenes using ab initio and least squares support vector machines  

International Nuclear Information System (INIS)

A quantitative structure-property relationship (QSPR) study is suggested for the prediction of toxicity (IGC50) of nitrobenzenes. Ab initio theory was used to calculate some quantum chemical descriptors including electrostatic potentials and local charges at each atom, HOMO and LUMO energies, etc. Modeling of the IGC50 of nitrobenzenes as a function of molecular structures was established by means of the least squares support vector machines (LS-SVM). This model was applied for the prediction of the toxicity (IGC50) of nitrobenzenes, which were not in the modeling procedure. The resulted model showed high prediction ability with root mean square error of prediction of 0.0049 for LS-SVM. Results have shown that the introduction of LS-SVM for quantum chemical descriptors drastically enhances the ability of prediction in QSAR studies superior to multiple linear regression and partial least squares

2008-03-01

399

Ab initio modeling of the behavior of helium and xenon in actinide dioxide nuclear fuels  

Science.gov (United States)

By means of an ab initio plane wave pseudopotential method, the behavior of helium in UO2, PuO2, AmO2 and (Am0.5Pu0.5)O2 and of xenon in UO2 is studied. We first show that a pseudopotential approach in the generalized gradient approximation (GGA) can satisfactorily describe the cohesive properties of these actinide dioxides. We then calculate the formation energies of point defects (vacancies and interstitials), as well as the incorporation and solution energies of helium in UO2, PuO2, AmO2 and (Am0.5Pu0.5)O2, and of xenon in UO2. The results are discussed according to the incorporation site of the gas atom in the fluorite lattice and according to the dioxide stoichiometry.

Freyss, M.; Vergnet, N.; Petit, T.

2006-06-01

400

Parametrizing a polarizable force field from ab initio data. I. The fluctuating point charge model  

Science.gov (United States)

We have developed a polarizable force field for peptides, using all-atom OPLS (OPLS-AA) nonelectrostatic terms and electrostatics based on a fluctuating charge model and fit to ab initio calculations of polarization responses. We discuss the fitting procedure, and specific techniques we have developed that are necessary in order to obtain an accurate, stable model. Our model is comparable to the best existing molecular mechanics force fields in reproducing quantum-chemical peptide energetics. It also accurately reproduces many-body effects in many cases. We believe that straightforward extensions of our linear-response electrostatic model will significantly improve the accuracy for those cases that the present model does not adequately address.

Banks, Jay L.; Kaminski, George A.; Zhou, Ruhong; Mainz, Daniel T.; Berne, B. J.; Friesner, Richard A.

1999-01-01

 
 
 
 
401

Proposal for an inhibitor of Alzheimer's disease blocking aggregation of amyloid-? peptides: ab initio molecular simulations  

International Nuclear Information System (INIS)

Aggregation of amyloid-? (A?) peptides is believed to play a key role in the mechanism of molecular pathogenesis of Alzheimer's disease (AD). To inhibit the aggregation and prevent AD, numerous compounds have been synthesized. A previous experimental study elucidated that a triazine derivative AA3E2 has anti-amyloidogenic ability, while a triazine derivative AA3D2 having a different substituent has no inhibitory effect. However, the reason for this remarkable difference in the ability cannot be explained by the chemical structures of these derivatives. In the present study, we present stable structures of the solvated complexes with A? and AA3E2/AA3D2 obtained by classical molecular mechanics method. The specific interactions between A? and AA3E2/AA3D2 in the complexes are investigated by ab initio fragment molecular orbital calculations. Based on the results obtained, we attempt to propose new potent inhibitors for the A? aggregation.

2013-04-12

402

New amorphous forms of solid CO2 from ab initio molecular dynamics  

CERN Multimedia

By employing ab initio molecular dynamics simulations at constant pressure, we investigated behavior of amorphous carbon dioxide between 0-100 GPa and 200-500 K and found several new amorphous forms. We focused on evolution of the high-pressure tetrahedral amorphous form known as a-carbonia on its way down to zero pressure, where it eventually converts into a molecular amorphous solid. During decompression, two nonmolecular amorphous forms with different proportion of three and four-coordinated carbons and two mixed molecular-nonmolecular forms were observed. Transformation from a-carbonia to the molecular state appears to proceed discontinuously via several intermediate stages. This suggests that solid CO2 might belong to the group of materials exhibiting polyamorphism. We also studied relations of the amorphous forms to their crystalline counterparts. The predominantly four-coordinated a-carbonia is related to phase V according to their structural properties, while existence of the mixed forms may reflect h...

Plašienka, Dušan

2013-01-01

403

Double-bound electron attachment to uracil-water complexes. Theoretical ab initio study  

Energy Technology Data Exchange (ETDEWEB)

Ab initio calculations performed in this work found positive electron affinities for all three possible doubly H-bonded complexes of the uracil molecule with a simple water molecule. In all cases the excess electron is bound by the dipole field of the complex. No conventional stable `valence` anionic states were found with the theoretical procedure used in this work (SCF + second-order perturbation theory corrections for the electron correlation effects). The attachment of the excess electron lowers the relative energy differences between the three complexes, making their coexistence more probable. Structural changes in the uracil-water complex upon attachment of an electron were also found. The anion`s equilibrium geometry had noticeably shortened hydrogen-bond lengths and a shifted orientation of the water molecule with respect to the uracil molecule compared to the neutral system. 30 refs., 2 figs., 2 tabs.

Smets, J.; McCarthy, W.J.; Adamowicz, L. [Univ. of Arizona, Tucson, AZ (United States)

1996-08-29

404

Binary nature of monolayer boron sheets from ab initio global searches.  

UK PubMed Central (United Kingdom)

Boron could be the next element after carbon to form two-dimensional monolayer structures. Using the ab initio global searches, we found all low-lying monolayer boron sheets with 1-4 hexagonal holes in each unit cell. The two most stable boron sheets are composed of two kinds of elementary units with isolated-hexagon and twin-hexagon holes, respectively, so that the boron sheets are binary structures in nature. Detailed structural analyses indicate that there exist two types of close-lying stable monolayer boron sheets, revealing the polymorphism of boron sheet. These binary monolayer boron sheets are expected to serve as precursors to build various boron nanotubes, boron fullerenes, and other boron-based low-dimensional nanomaterials.

Lu H; Mu Y; Bai H; Chen Q; Li SD

2013-01-01

405

Ab initio structural and electronic properties of hydrogenated silicon nanoclusters in the ground and excited state  

International Nuclear Information System (INIS)

[en] Electronic and structural properties of small hydrogenated silicon nanoclusters as a function of dimension are calculated from ab initio technique. The effects induced by the creation of an electron-hole pair are discussed in detail, showing the strong interplay between the structural and optical properties of the system. The distortion induced on the structure after an electronic excitation of the cluster is analyzed together with the role of the symmetry constraint during the relaxation. We point out how the overall effect is that of significantly changing the electronic spectrum if no symmetry constraint is imposed to the system. Such distortion can account for the Stokes shift and provides a possible structural model to be linked to the four-level scheme invoked in the literature to explain recent results for the optical gain in silicon nanoclusters. Finally, formation energies for clusters with increasing dimension are calculated and their relative stability discussed

2004-04-15

406

Ab initio conformational study of the CO...H2 Van der Waals dimer  

International Nuclear Information System (INIS)

Quantum chemical fully ab initio conformational calculations were performed for the weakly bound van der Waals CO...H2 dimer in the framework of the supermolecule approach. The counterpoise-corrected interaction energies, computed through fourth-order MBPT using the basis sets described recently by Sadlej, were in excellent agreement with results obtained with larger basis sets constructured to give accurate values for the electric moments and polarizabilities of CO and H2. The relative stability of the configurations studied here was collinear structures > parallel structure > T-shaped structures. The collinear and parallel structures represent the most stable group of configurations. The present calculations show that they have values of De between 5.89 and 10.66 meV. The T-shaped structures represent relatively less stable configurations with values of D3 between 0.84 and 2.92 meV. 52 refs., 5 figs., 1 tab.

1995-01-01

407

Dissipation of alignment in CO2 gas: A comparison between ab initio predictions and experiments  

Science.gov (United States)

We present comparisons between measurements and ab initio calculations of the dissipation of the nonadiabatic laser-induced alignment in pure CO2 and CO2-He gas mixtures. The experiments were made for pressures between 2 and 20 bars at 295 K by using short non-resonant linearly polarized laser pulses for alignment and probe. The calculations are carried, free of any adjusted parameter, using refined intermolecular potentials and a requantized Classical Molecular Dynamics Simulations approach presented previously but not yet confronted to experiments. The results demonstrate that the model accurately reproduces the decays with time of both the transient revivals and ``permanent'' component of the alignment. The significant differences observed between the behaviors resulting from CO2-CO2 and CO2-He collisions are also well predicted by the model.

Hartmann, J.-M.; Boulet, C.; Vieillard, T.; Chaussard, F.; Billard, F.; Faucher, O.; Lavorel, B.

2013-07-01

408

Tight-binding model for carbon nanotubes from ab initio calculations  

International Nuclear Information System (INIS)

[en] Here we present a parametrized tight-binding (TB) model to calculate the band structure of single-wall carbon nanotubes (SWNTs). On the basis of ab initio calculations we fit the band structure of nanotubes of different radii with results obtained with an orthogonal TB model to third neighbors, which includes the effects of orbital hybridization by means of a reduced set of parameters. The functional form for the dependence of these parameters on the radius of the tubes can be used to interpolate appropriate TB parameters for different SWNTs and to study the effects of curvature on their electronic properties. Additionally, we have shown that the model gives an appropriate description of the optical spectra of SWNTs, which can be useful for a proper assignation of SWNTs' specific chirality from optical absorption experiments.

2010-07-14

409

Ln3+(NO3)n complexes studied using ab-initio quantum chemical calculations  

International Nuclear Information System (INIS)

[en] The structures and interaction energies of Ln3+(NO3-)n complexes have been studied using ab initio Hartree-Fock method for La3+, Eu3+ and Lu3+ cations with one to three nitrates in gas phase. The interaction energy between one cation and one bidentate nitrate is 20 to 30 kCal/mol greater than that with one monodentate nitrate. This value is quite lower than the interaction between a cation and one water molecule (about 90 kCal/mol), which could come and complete the hydration sphere of the cation when nitrate's coordination-type moves from bidentate to monodentate. The first studies on these systems with five water molecules in the hydration sphere show changes in the coordination type of nitrates or moves of water molecules in the second sphere. (authors)

2000-01-01

410

Ab initio based rate theory model of radiation induced amorphization in ?-SiC  

International Nuclear Information System (INIS)

[en] An ab initio informed rate theory framework for a multicomponent system is developed and used to model radiation induced amorphization in ?-SiC. Based on the published modeling and experimental studies we propose three possible energy landscapes (ELs) for defect recombination in SiC. We demonstrate that defect ELs have a dramatic effect on the shape of the dose to amorphization vs. temperature curve and on the critical temperature to amorphization Tcr. In the no-barrier EL model, Tcr is correlated with the mobility of silicon interstitials, while in the recombination and trapping models Tcr is governed by the rate of defect recombination. We conclude that both the defect migration barrier and the defect recombination barrier are key parameters to consider when modeling radiation resistance of SiC, and possibly of other multi-component covalent materials.

2011-07-31

411

Ab initio study of nitrogen antisites in GaN and AlN  

Energy Technology Data Exchange (ETDEWEB)

The authors present results of an ab initio study of the nitrogen antisite defect in GaN and AlN. The authors show that the neutral antisite in zinc-blende structure exhibits metastable behavior similar to the arsenic antisite in GaAs, but in the wurtzite structure the phenomenon does not exist. A new discovery is that the negative charge states of the nitrogen antisite are stabilized by the large band gap. In the negative charge states a large spontaneous Jahn-Teller displacement of the nitrogen antisite is observed in the [111] direction, both in the zinc-blende and in the wurtzite phase. The authors discuss the possible connection between the nitrogen antisite and the yellow luminescence commonly observed in GaN.

Mattila, T.; Nieminen, R.M. [Helsinki Univ. of Technology, Espoo (Finland). Lab. of Physics; Seitsonen, A.P. [Max-Planck-Gesesslschaft, Dahlem (Germany). Lab. of Physics

1996-12-31

412

Ab initio investigation of the switching behavior of the dithiole-benzene nano-molecular wire  

International Nuclear Information System (INIS)

We report a first-principle study of electrical transport and switching behavior in a single molecular conductor consisting of a dithiole-benzene sandwiched between two Au( 100) electrodes. Ab initio total energy calculations reveal dithiole-benzene molecules on a gold surface, contacted by a monoatomic gold scanning tunneling microscope tip to have two classes of low energy conformations with differing symmetries. Lateral motion of the tip or excitation of the molecule cause it 10 change from one conformation class to the other and to switch between a strongly and a weakly conducting state. Thus, surprisingly. despite their apparent simplicity, these Au-dithiole-benzene -Au nano wires are shown to be electrically bi-stable switches, the smallest two-terminal molecular switches to date. The projected density of states and transmission coefficients are analyzed, and it suggests that the variation of the coupling between the molecule and the electrodes with external bias leads to switching behavior.

2008-01-01

413

Melting curve and Hugoniot of molybdenum up to 400 GPa by ab initio simulations  

International Nuclear Information System (INIS)

[en] We report ab initio calculations of the melting curve and Hugoniot of molybdenum for the pressure range 0 - 400 GPa, using density functional theory (DFT) in the projector augmented wave (PAW) implementation. We use the 'reference coexistence' technique to overcome uncertainties inherent in earlier DFT calculations of the melting curve of Mo. Our calculated melting curve agrees well with experiment at ambient pressure and is consistent with shock data at high pressure, but does not agree with the high pressure melting curve from static compression experiments. Our calculated P(V) and T(P) Hugoniot relations agree well with shock measurements. We use calculations of phonon dispersion relations as a function of pressure to eliminate some possible interpretations of the solid-solid phase transition observed in shock experiments on Mo

2008-01-01

414

High-Level Ab-Initio Calculation on the NiO? System  

Energy Technology Data Exchange (ETDEWEB)

Several high-level ab-initio methods were employed in studies of the narrow singlet-triplet separation of the cyclic dorm of the nickel dioxide (NiO?). It is shown that the complete visions of the locally renormalized couples cluster method with singles, doubles, and noniterative triples (LR-CCSD(T)) approach, in contrast to the standard CCSD(T) method, provides results in concert with predictions of the density functional theory (DFT) and internally contracted multi-reference configuration interaction method (IIC-MCRCI), which favor the triplet state to be the lowest one. Relevant discussion of several aspects related to underlying CCSD calculations, indicate that the dominate roll of singly excited amplitudes violates the paradigm about the leading role to two-body effect in description of the correlation energy. These results are compared with the results of the second order Generalized Van Vleck Perturbation Theory (GVVPPT2) approach which supports the CCSD(T) predictions.

Song, Jie; Apra, Edoardo; Khait, Yuri; Hoffmann, Mark R.; Kowalski, Karol

2006-09-20

415

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

CERN Multimedia

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 strongly to a single H2O molecule in liquid water. The Mn in Mn(III)P is on average coplanar with the porphine plane and forms a stable complex with two H2O molecules. The residence times of these water molecules exceed 15 ps. The DFT+U method correctly predicts that water displaces NO from Mn(III)P-NO, but yields an ambiguous spin state for the MnP(II)-NO complex.

Leung, K; Leung, Kevin; Medforth, Craig J.

2007-01-01

416

Ab initio calculations of various protonation sites in perfluorodiethyl ether: Models for high temperature lubricant decomposition?  

Energy Technology Data Exchange (ETDEWEB)

Although perfluoropolyether (PFPE) lubricants have found successful application in spacecraft mechanisms and computer hard drives, there eventual breakdown is irksome, and the mechanism of decomposition is the subject of much scrutiny. However, very little notice is taken of the monomer ethers on which the polymer lubricants are based. Recently, concerted studies of the Lewis base properties of various fluorinated ethers have been performed, both from an experimental and a theoretical viewpoint. As an extension of the theoretical work, this study presents ab initio theoretical consideration of the multiple potential basic sites within perfluorodiethyl ether, (CF{sub 3}CF{sub 2}){sub 2}O, by way of the proton affinity of the molecule at various possible protonation sites (i.e., oxygen and fluorine atoms). The results indicate that although protonation at the oxygen is more energetically favored, protonation at the fluorine is not much higher in energy and provides for formation of an excellent leaving group, HF.

Ball, D.W. [Cleveland State Univ., OH (United States). Dept. of Chemistry

1995-04-01

417

Towards a frequency independent incremental ab initio scheme for the self energy  

CERN Document Server

The frequency dependence of the self energy of a general many--body problem is identified as a main obstacle in correlation calculations based on local approaches. A frequency independent formulation is proposed instead and proven to yield exactly the same numerical results as the original common scheme. Our approach is embedded in a general local-orbital based ab initio frame to obtain the Green's function for large heterogenous systems. First a Green's function formalism is introduced. Then the self energy is constructed from an incremental scheme. Subsequently we apply the proposed frequency independent formulation. The theory is applied to para-ditholbenzene as a realistic system and the numerical accuracy of the correlation contributions obtained from our frequency independent access are carefully tested against the exact frequency dependent results. Perfect agreement is reached and a speed--up of a factor 50 is established for the incremental scheme.

Albrecht, M

2004-01-01

418

Ab-initio density functional study of defect-free and defective CdO  

Energy Technology Data Exchange (ETDEWEB)

Ab-initio density functional calculation of the structural, electronic, dynamical and dielectric properties of CdO has been performed. The effect of the oxygen substitution by fluorine and vacancy formation on the lattice constant has also been investigated. In the first case the lattice constant increases whereas in the second one, a decrease is observed. This result is in good agreement with the experimental results. The DFT band gap decrease with the increase of the lattice constant indicating that the experimentally observed increase of the band gap when doping with fluorine is related with the Burstein-Moss effect rather than with the lattice constant change. (copyright 2005 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

Ferro, R.; Rodriguez, J.A. [Fac. of Physics, University of Havana, San Lazaro y L, 10400 Vedado, C. Havana (Cuba); Verstraete, M.; Solomko, V.; Bertrand, P. [Fac. of Appl. Science, Univ. Catholic of Louvain, Place Croix du Sud 1, 1348, Louvain-la-Neuve (Belgium)

2005-08-01

419

An ab initio study on the structure and energetics of the ClO hydrates  

Science.gov (United States)

The hydrates of chlorine monoxide, ClO · (H 2O) n, n = 1-6, have been studied by means of DFT (B3LYP) method along with aug-cc-pVTZ basis set. Ab initio (MP2 and CCSD(T)) methods and extension of the basis sets up to quintuple- ? have been done for monohydrates in order to test the methodology. Two rather different intermolecular interactions have been found, namely: conventional hydrogen bonds and OCl⋯O associations. Here it is demonstrated that both types of interactions participate in the formation of hydrates; the OCl⋯O association however produces always the most stable conformations. Equilibrium geometries and relative energies have been calculated and compared with those obtained by other authors. Calculated binding energies indicate that the ClO radical plays an important role in the stabilization of these small clusters, yielding strong interactions with the water molecules.

Gálvez, Oscar; Gómez, Pedro C.

2007-11-01

420

Global ab initio ground-state potential energy surface of N4.  

UK PubMed Central (United Kingdom)

We present a global ground-state potential energy surface for N4 suitable for treating high-energy vibrational-rotational energy transfer and collision-induced dissociation in N2-N2 collisions. To obtain the surface, complete active space second-order perturbation theory calculations were performed for the ground singlet state with an active space of 12 electrons in 12 orbitals and the maug-cc-pVTZ triple zeta basis set. About 17?000 ab initio data points have been calculated for the N4 system, distributed along nine series of N2 + N2 geometries and three series of N3 + N geometries. The six-dimensional ground-state potential energy surface is fitted using least-squares fits to the many-body component of the electronic energies based on permutationally invariant polynomials in bond order variables.

Paukku Y; Yang KR; Varga Z; Truhlar DG

2013-07-01

 
 
 
 
421

Structural phase transition of CdTe: an ab initio study.  

UK PubMed Central (United Kingdom)

A constant pressure ab initio MD technique and density functional theory with a generalized gradient approximation (GGA) was used to study the pressure-induced phase transition in zinc-blende CdTe. We found that CdTe undergoes a structural first-order phase transition to [Formula: see text] (binary ?-tin) tetragonal structure in the constant pressure molecular dynamics simulation at 20 GPa. When the pressure was increased to 50 GPa, the phase of tetragonal structure converted to a new Imm2 orthorhombic structure. These phase transformations were also calculated by using the enthalpy calculations. Transition phases, lattice parameters and bulk properties we attained are comparable with experimental and theoretical data.

Alptekin S

2013-01-01

422

Ab initio local-spin-density study of oscillatory exchange coupling in Fe/Au multilayers  

International Nuclear Information System (INIS)

[en] Fully self-consistent ab initio local-spin-density calculations of the interlayer exchange coupling (IEC) in Fe/Au multilayers have been performed. The thickness of the ferromagnetic body-centred cubic Fe layers has been kept fixed at five monolayers (ML), the thickness of the face-centred cubic Au spacer layers has been varied between 2 and 30 ML. Agreement of the calculated and observed oscillation periods of the interlayer exchange coupling has been obtained. To verify the Rudermann-Kittel-Kasuya-Yoshida and quantum-well (QW) pictures for the IEC, detailed investigations of the Fermi surface of Au and of the modulation of the Bloch states in the spacer layer by means of QW oscillations have been performed. (author)

2002-05-06

423

Ab initio local-spin-density study of oscillatory exchange coupling in Fe/Au multilayers  

Energy Technology Data Exchange (ETDEWEB)

Fully self-consistent ab initio local-spin-density calculations of the interlayer exchange coupling (IEC) in Fe/Au multilayers have been performed. The thickness of the ferromagnetic body-centred cubic Fe layers has been kept fixed at five monolayers (ML), the thickness of the face-centred cubic Au spacer layers has been varied between 2 and 30 ML. Agreement of the calculated and observed oscillation periods of the interlayer exchange coupling has been obtained. To verify the Rudermann-Kittel-Kasuya-Yoshida and quantum-well (QW) pictures for the IEC, detailed investigations of the Fermi surface of Au and of the modulation of the Bloch states in the spacer layer by means of QW oscillations have been performed. (author)

Hafner, R.; Spisak, D.; Lorenz, R.; Hafner, J. [Institut fuer Materialphysik and Centre for Computational Materials Science, Universitaet Wien, Vienna (Austria)

2002-05-06

424

Mapping Enzymatic Catalysis using the Effective Fragment Molecular Orbital Method: Towards all ab initio Biochemistry  

CERN Multimedia

We extend the Effective Fragment Molecular Orbital (EFMO) method to the frozen domain approach where only the geometry of an active part is optimized, while the many-body polarization effects are considered for the whole system. The new approach efficiently mapped out the entire reaction path of chorismate mutase in less than four days using 80 cores on 20 nodes, where the whole system containing 2398 atoms is treated in the ab initio fashion without using any force fields. The reaction path is constructed automatically with the only assumption of defining the reaction coordinate a priori. We determine the reaction barrier of chorismate mutase to be $18.3\\pm 3.6$ kcal mol$^{-1}$ using ONIOM with MP2/cc-pVDZ and EFMO/6-31G(d) for the high and low layers, respectively.

Steinmann, Casper; Jensen, Jan H

2012-01-01

425

Electronic and magnetic structures and conductivity of strontium ferrite: An Ab Initio LSDA + U approach  

International Nuclear Information System (INIS)

Using the first-principle nonempirical linear muffin-tin orbital method in the tight-binding approximation (TB-LMTO) to the LSDA + U approximation, the electronic and magnetic structures and defect formation in strontium ferrite Sr3Fe2O6 are studied. It is found that Sr3Fe2O6 is a G type antiferromagnetic with the semiconductor electronic structure. The calculated band gap of 1.82 eV agrees well with experimental value (?2 eV). The ferrite spectrum corresponds to that of a semiconductor with a band gap of charge transfer. Based on ab initio LSDA + U calculations, various types and configurations of defects in the oxygen sublattice (oxygen vacancies, anti-Frenkel defects) are studied and a model for ionic transport in Sr3Fe2O6 is proposed

2007-01-01

426

Ab initio study of the electronic structure and elastic properties of Al5C3N  

Science.gov (United States)

We investigate the electronic structure, chemical bonding and elastic properties of the hexagonal aluminum carbonitride, Al5C3N, by ab initio calculations. Al5C3N is a semiconductor with a narrow indirect gap of 0.81 eV. The valence bands below the Fermi level (EF) originate from the hybridized Al p—C p and Al p—N p states. The calculated bulk and Young's moduli are 201 GPa and 292 GPa, which are slightly lower than those of Ti3SiC2. The values of the bulk-to-shear-modulus and bulk-modulus-to-c44 are 1.73 and 1.97, respectively, which are higher than those of Ti2AlC and Ti2AlN, indicating that Al5C3N is a ductile ceramic.

Xu, Xue-Wen; Hu, Long; Yu, Xiao; Lu, Zun-Ming; Fan, Ying; Li, Yang-Xian; Tang, Cheng-Chun

2011-12-01

427

Spin-transfer mechanism of ferromagnetism in polymerized fullerenes: $Ab initio$ calculations  

CERN Multimedia

A mechanism of the high temperature ferromagnetism in polymerized fullerenes is suggested. It is assumed that some of the C$_{60}$ molecules in the crystal become magnetically active due to spin and charge transfer from paramagnetic impurities (atoms or groups), such as hydrogen, fluorine, hydroxyl group OH, amino group NH$_2$, or methyl group CH$_3$, dispersed in the fullerene matrix. The exchange interaction between the spins localized on the magnetically active fullerenes is evaluated using \\textit{ab initio} calculations. The nearest neighbour and next nearest neighbour exchange interaction is found to be in the range $0.1\\div 0.3 $ eV, that is, high enough to account for the room temperature ferromagnetism.

Kvyatkovskii, O E; Shelankov, A L; Makarova, T L

2005-01-01

428

A correlation study of quinoline derivatives and their pharmaceutical behavior by ab initio calculated NQR parameters.  

UK PubMed Central (United Kingdom)

In this paper, ab initio calculated NQR parameters for some quinoline-containing derivatives are presented. The calculations are carried out in a search for the relationships between the charge distribution of these compounds and their ability to interact with haematin. On the basis of NQR parameters, pi-electron density on the nitrogen atom of the quinoline ring plays a dominant role in determining the ability of quinolines to interact with haematin. This point was confirmed with investigation of Fe+3 cation-pi quinoline ring interactions in 2- and 4-aminoquinoline. However, our results do not show any preference for those carbon atoms of the quinoline ring which previous reports have noted. In order to calculate the NQR parameters, the electric field gradient (EFG) should be evaluated at the site of a quadrupolar nucleus in each compound. EFGs are calculated by the Gaussian 98 program using the B3LYP/6-31 G* level of theory.

Rafiee MA; Hadipour NL; Naderi-manesh H

2004-03-01

429

A correlation study of quinoline derivatives and their pharmaceutical behavior by ab initio calculated NQR parameters.  

Science.gov (United States)

In this paper, ab initio calculated NQR parameters for some quinoline-containing derivatives are presented. The calculations are carried out in a search for the relationships between the charge distribution of these compounds and their ability to interact with haematin. On the basis of NQR parameters, pi-electron density on the nitrogen atom of the quinoline ring plays a dominant role in determining the ability of quinolines to interact with haematin. This point was confirmed with investigation of Fe+3 cation-pi quinoline ring interactions in 2- and 4-aminoquinoline. However, our results do not show any preference for those carbon atoms of the quinoline ring which previous reports have noted. In order to calculate the NQR parameters, the electric field gradient (EFG) should be evaluated at the site of a quadrupolar nucleus in each compound. EFGs are calculated by the Gaussian 98 program using the B3LYP/6-31 G* level of theory. PMID:15368921

Rafiee, Marjan A; Hadipour, Nasser L; Naderi-manesh, Hossein

2004-03-01

430

Ab-Initio Calculation of the Metal-Insulator Transition in Lithium rings  

CERN Multimedia

We study how the Mott metal-insulator transition (MIT) is affected when we have to deal with electrons with different angular momentum quantum numbers. For that purpose we apply ab-initio quantum-chemical methods to lithium rings in order to investigate the analogue of a MIT. By changing the interatomic distance we analyse the character of the many-body wavefunction and discuss the importance of the $s-p$ orbital quasi-degeneracy within the metallic regime. The charge gap (ionization potential minus electron affinity) shows a minimum and the static electric dipole polarizability has a pronounced maximum at a lattice constant where the character of the wavefunction changes from significant $p$ to essentially $s$-type. In addition, we examine rings with bond alternation in order to answer the question under which conditions a Peierls distortion occurs.

Paulus, B; Fulde, P; Stoll, H; Paulus, Beate; Rosciszewski, Krzysztof; Fulde, Peter; Stoll, Hermann

2003-01-01

431

Ab initio MO analysis of interaction paths between radicals in ferromagnetic organic systems.  

UK PubMed Central (United Kingdom)

Interaction path analyses for pi-conjugated organic systems were performed at the ab initio molecular orbital level to examine the relationship between inter-radical interactions and the high-spin stability of the system. It was found that the high-spin stability results from through-bond interactions between radicals, not from through-space interactions, in relation to the stabilization of a low-spin state due to the effects of electron correlation. L(ij)(min) value for estimating the mixing of nonbonding molecular orbitals well predicted the relationship between the through-bond interactions and the high-spin stability. Furthermore, molecular orbital calculations revealed that the all-trans type interaction path between radicals produces long-range exchange interactions, and the additivity of high-spin stability is observed by keeping short-range through-bond interaction paths.

Orimoto Y; Imai T; Naka K; Aoki Y

2006-05-01

432

Ab initio based rate theory model of radiation induced amorphization in {beta}-SiC  

Energy Technology Data Exchange (ETDEWEB)

An ab initio informed rate theory framework for a multicomponent system is developed and used to model radiation induced amorphization in {beta}-SiC. Based on the published modeling and experimental studies we propose three possible energy landscapes (ELs) for defect recombination in SiC. We demonstrate that defect ELs have a dramatic effect on the shape of the dose to amorphization vs. temperature curve and on the critical temperature to amorphization T{sub cr}. In the no-barrier EL model, T{sub cr} is correlated with the mobility of silicon interstitials, while in the recombination and trapping models T{sub cr} is governed by the rate of defect recombination. We conclude that both the defect migration barrier and the defect recombination barrier are key parameters to consider when modeling radiation resistance of SiC, and possibly of other multi-component covalent materials.

Swaminathan, Narasimhan, E-mail: swaminathan2@wisc.edu [Materials Science and Engineering Department, University of Wisconsin, Madison (United States); Morgan, Dane, E-mail: ddmorgan@wisc.edu [Materials Science and Engineering Department, University of Wisconsin, Madison (United States); Material Science Program, University of Wisconsin, Madison (United States); Szlufarska, Izabela, E-mail: szlufarska@wisc.edu [Materials Science and Engineering Department, University of Wisconsin, Madison (United States); Material Science Program, University of Wisconsin, Madison (United States)

2011-07-31

433

Ab initio GW electron-electron interaction effects in Quantum Transport  

CERN Multimedia

We present an ab initio approach to electronic transport in nanoscale systems which includes electronic correlations through the GW approximation. With respect to Landauer approaches based on density-functional theory (DFT), we introduce a physical quasiparticle electronic-structure into a non-equilibrium Green's function theory framework. We use an equilibrium non-selfconsistent $G^0W^0$ self-energy considering both full non-hermiticity and dynamical effects. The method is applied to a real system, a gold mono-atomic chain. With respect to DFT results, the conductance profile is modified and reduced by to the introduction of diffusion and loss-of-coherence effects. The linear response conductance characteristic appear to be in agreement with experimental results.

Darancet, P; Mayou, D; Olevano, V; Darancet, Pierre; Ferretti, Andrea; Mayou, Didier; Olevano, Valerio

2006-01-01

434

{\\it Ab initio} Simulation of Silver Transport in Ge_xSe_1-x: Ag  

CERN Multimedia

In this paper, we present models of Ge-Se glasses heavily doped with Ag obtained from {\\it ab initio} simulation and study the dynamics of the network with an emphasis on the motion of Ag$^+$ ions. The models are analyzed with partial pair correlation functions, static structure factors and novel wavelet techniques. The electronic properties are characterized by the electronic density of states and analysis of specific electronic eigenstates. As Ag content increases, the optical band gap increases. Ag diffusion is observed directly from thermal simulation. The most diffusive Ag$^+$ ions move preferentially through low density regions of the network and the existence of well-defined trapping centers is confirmed. Preliminary information about temperature dependence of trapping and release is provided.

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

2005-01-01

435

Estudo ab-initio da a-alanina em meio aquoso  

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Full Text Available 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/6-31G* level but it is not when diffuse functions and electron correlation are included. This results shows that the Z form does not exist in the gas phase. The inclusion of solvent effects changed significantly the results obtained in gas phase, therefore this inclusion make the Z form a stationary point within all level of theory, and the relative energy depends dramatically on the level of calculation.

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

1999-01-01

436

Ab initio calculation of resonant X-ray scattering in Manganites  

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We study the origin of the resonant x-ray signal in manganites and generalize the resonant cross-section to the band structure framework. With {\\it ab initio} LSDA and LSDA+U calculations we determine the resonant x-ray spectrum of LaMnO$_3$. The calculated spectrum and azimuthal angle dependence at the Mn $K$-edge reproduce the measured data without adjustable parameters. The intensity of this signal is directly related to the orthorhombicity of the lattice. We also predict a resonant x-ray signal at the La $L$-edge, caused by the tilting of the MnO$_6$ octahedra. This shows that the resonant x-ray signal in the hard x-ray regime can be understood in terms of the band structure of a material and is sensitive to the fine details of crystal structure.

Benedetti, P; Pavarini, E; Vigliante, A; Wochner, P; Benedetti, Patrizia; Brink, Jeroen van den; Pavarini, Eva; Vigliante, Assunta; Wochner, Peter

2001-01-01

437

Ab Initio Atomic Simulations of Antisite Pair Recovery in Cubic Silicon Carbide  

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The thermal stability of an antisite pair in 3C-SiC is studied using ab initio molecular dynamics within the framework of density functional theory. The lifetime of the antisite pair configuration is calculated for temperatures between 1800 and 2250 K, and the effective activation energy for antisite pair recombination is determined to be 2.52 eV. The recombination energy path and static energy barrier are also calculated using the nudged elastic band method, along with the dimer method to accurately locate the transition states. The consistency of the results suggests that the antisite pair cannot be correlated with the DI photoluminescence center, as proposed by previously theoretical interpretations. An extended exchange mechanism is found for the antisite pair recombination, and this may be a dominant mechanism for antisite pair recombination and diffusion of impurities in compound semiconductors.

Gao, Fei; Du, Jincheng; Bylaska, Eric J.; Posselt, Matthias; Weber, William J.

2007-05-28

438

A wave function based ab initio non-equilibrium Green's function approach to charge transport  

CERN Multimedia

We present a novel ab initio non-equilibrium approach to calculate the current across a molecular junction. The method rests on a wave function based description of the central region of the junction combined with a tight binding approximation for the electrodes in the frame of the Keldysh Green's function formalism. In addition we present an extension so as to include effects of the two-particle propagator. Our procedure is demonstrated for a dithiolbenzene molecule between silver electrodes. The full current-voltage characteristic is calculated. Specific conclusions for the contribution of correlation and two-particle effe