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???????: ab initio???????????  

Full Text Available 05000 05300 05301 ab initio??????????? Unveil, Exonomy, GlimmerM, Genscan?????? ??????? ????? ???ab initio??????????????????? ??????????????????? ????????? ???????????????????????? Gli

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???????: ab initio???????????  

Full Text Available 05000 05300 05301 ab initio??????????? DAGGER, GENSCAN, HMMgene, Genie, VEIL, MORGAN, ????????? Gene recognition based on DAG shortest paths. Chuang JS, Roth D. Bioinformatics. 2001;17 ???(BG570)??????????????????????? ?????Burset/Guigo?????BG570???????? (BG570)????????????????????????? ??????????????????????????

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Ab initio Ehrenfest dynamics.  

Science.gov (United States)

We present an ab initio direct Ehrenfest dynamics scheme using a three time-step integrator. The three different time steps are implemented with nuclear velocity Verlet, nuclear-position-coupled midpoint Fock integrator, and time-dependent Hartree-Fock with a modified midpoint and unitary transformation algorithm. The computational cost of the ab initio direct Ehrenfest dynamics presented here is found to be only a factor of 2-4 larger than that of Born-Oppenheimer (BO) dynamics. As an example, we compute the vibration of the NaCl molecule and the intramolecular torsional motion of H2C=NH2+ by Ehrenfest dynamics compared with BO dynamics. For the vibration of NaCl with an initial kinetic energy of 1.16 eV, Ehrenfest dynamics converges to BO dynamics with the same vibrational frequency. The intramolecular rotation of H2C=NH2+ produces significant electronic excitation in the Ehrenfest trajectory. The amount of nonadiabaticity, suggested by the amplitude of the coherent progression of the excited and ground electronic states, is observed to be directly related to the strength of the electron-nuclear coupling. Such nonadiabaticity is seen to have a significant effect on the dynamics compared with the adiabatic approximation. PMID:16164281

Li, Xiaosong; Tully, John C; Schlegel, H Bernhard; Frisch, Michael J

2005-08-22

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Ab Initio.  

Science.gov (United States)

Hot carrier thermalization is a major source of efficiency loss in solar cells. Because of the subpicosecond time scale and complex physics involved, a microscopic characterization of hot carriers is challenging even for the simplest materials. We develop and apply an ab initio approach based on density functional theory and many-body perturbation theory to investigate hot carriers in semiconductors. Our calculations include electron-electron and electron-phonon interactions, and require no experimental input other than the structure of the material. We apply our approach to study the relaxation time and mean free path of hot carriers in Si, and map the band and k dependence of these quantities. We demonstrate that a hot carrier distribution characteristic of Si under solar illumination thermalizes within 350 fs, in excellent agreement with pump-probe experiments. Our work sheds light on the subpicosecond time scale after sunlight absorption in Si, and constitutes a first step towards ab initio quantification of hot carrier dynamics in materials. PMID:25014830

Bernardi, Marco; Vigil-Fowler, Derek; Lischner, Johannes; Neaton, Jeffrey B; Louie, Steven G

2014-06-27

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FiD: a software for ab initio structural identification of product ions from tandem mass spectrometric data.  

Science.gov (United States)

We present FiD (Fragment iDentificator), a software tool for the structural identification of product ions produced with tandem mass spectrometric measurement of low molecular weight organic compounds. Tandem mass spectrometry (MS/MS) has proven to be an indispensable tool in modern, cell-wide metabolomics and fluxomics studies. In such studies, the structural information of the MS(n) product ions is usually needed in the downstream analysis of the measurement data. The manual identification of the structures of MS(n) product ions is, however, a nontrivial task requiring expertise, and calls for computer assistance. Commercial software tools, such as Mass Frontier and ACD/MS Fragmenter, rely on fragmentation rule databases for the identification of MS(n) product ions. FiD, on the other hand, conducts a combinatorial search over all possible fragmentation paths and outputs a ranked list of alternative structures. This gives the user an advantage in situations where the MS/MS data of compounds with less well-known fragmentation mechanisms are processed. FiD software implements two fragmentation models, the single-step model that ignores intermediate fragmentation states and the multi-step model, which allows for complex fragmentation pathways. The software works for MS/MS data produced both in positive- and negative-ion modes. The software has an easy-to-use graphical interface with built-in visualization capabilities for structures of product ions and fragmentation pathways. In our experiments involving amino acids and sugar-phosphates, often found, e.g., in the central carbon metabolism of yeasts, FiD software correctly predicted the structures of product ions on average in 85% of the cases. The FiD software is free for academic use and is available for download from www.cs.helsinki.fi/group/sysfys/software/fragid. PMID:18763276

Heinonen, Markus; Rantanen, Ari; Mielikäinen, Taneli; Kokkonen, Juha; Kiuru, Jari; Ketola, Raimo A; Rousu, Juho

2008-10-01

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Ab initio calculations of dilithiopropenes  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Ab initio molecular orbital calculations with the 3-21G basis set show the most stable dilithiopropene structure to be the di-? lithium-bridged structure VI of 1,3-dilithiopropene. This structure is most simply regarded as an ion triplet of two lithium cations and a propenylidene dianion.

Kost, Daniel; Klein, Joseph; Streitwieser, Andrew; Schriver, George W.

1982-01-01

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AB-Initio Total Energy Calculations on the AGND Compound  

International Nuclear Information System (INIS)

In this study we present the results of the structural, thermodynamical, elastic, and electronic properties of the hypothetical Neodymium Silver (AgNd) compound by performing ab initio total energy calculations within the generalized gradient approximation (GGA) in VASP package. The some basic physical properties, such as lattice constant, bulk modulus, second-order elastic constants (Cij), the electronic band structures, and phonon frequencies are calculated and compared with the available experimental and other theoretical values. In order to gain further information, we have, also, predicted the Young's modulus, Poison's ratio, Anisotropy factor, sound velocities, and Debye temperature, and the reasonable values are found

2008-08-25

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Ab initio random structure searching  

Science.gov (United States)

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.

Pickard, Chris J.; Needs, R. J.

2011-02-01

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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

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Ab-Initio Molecular Dynamics  

CERN Document Server

Computer simulations and molecular dynamics in particular, is a very powerful method to provide detailed and essentially exact informations of classical many-body problems. With the advent of \\textit{ab-initio} molecular dynamics, where the forces are computed on-the-fly by accurate electronic structure calculations, the scope of either method has been greatly extended. This new approach, which unifies Newton's and Schr\\"odinger's equations, allows for complex simulations without relying on any adjustable parameter. This review is intended to outline the basic principles as well as a survey of the field. Beginning with the derivation of Born-Oppenheimer molecular dynamics, the Car-Parrinello method as well as novel hybrid scheme that unifies best of either approach are discussed. The predictive power is demonstrated by a series of applications ranging from insulators to semiconductors and even metals in condensed phases.

Kühne, Thomas D

2012-01-01

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Modeling Brown Dwarfs using ab initio equation of state data  

Science.gov (United States)

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

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

2013-07-01

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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(H_2)_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

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Ab initio quantum chemistry: Methodology and applications  

Digital Repository Infrastructure Vision for European Research (DRIVER)

This Perspective provides an overview of state-of-the-art ab initio quantum chemical methodology and applications. The methods that are discussed include coupled cluster theory, localized second-order Moller–Plesset perturbation theory, multireference perturbation approaches, and density functional theory. The accuracy of each approach for key chemical properties is summarized, and the computational performance is analyzed, emphasizing significant advances in algorithms and implementation o...

Friesner, Richard A.

2005-01-01

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Ab initio torsional potentials in silole dimers  

International Nuclear Information System (INIS)

The potential barriers for the internal rotation of silole dimers are studied theoretically using the ab initio molecular orbital method at the RHF/6-31G** level of calculations. In 2,2'-bisilole, it is found that the anti-conformation is the most stable structure in the ground state and that the potential barrier height for rotation over the perpendicular conformation is 3.3 kcal/mol. 21 refs., 4 figs., 2 tabs

1996-01-05

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Ab initio torsional potentials in silole dimers  

Energy Technology Data Exchange (ETDEWEB)

The potential barriers for the internal rotation of silole dimers are studied theoretically using the ab initio molecular orbital method at the RHF/6-31G** level of calculations. In 2,2{prime}-bisilole, it is found that the anti-conformation is the most stable structure in the ground state and that the potential barrier height for rotation over the perpendicular conformation is 3.3 kcal/mol. 21 refs., 4 figs., 2 tabs.

Yamaguchi, Yoichi [Osaka R& D Laboratories, Konohana-ku (Japan); Yamabe, Tokio [Kyoto Univ., Sakyo-ku (Japan)

1996-01-05

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Germacrene D Cyclization: An Ab Initio Investigation  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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...

Setzer, William N.

2008-01-01

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Germacrene D Cyclization: An Ab Initio Investigation  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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 wel...

Setzer, William N.

2008-01-01

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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

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Ab Initio Path to Heavy Nuclei  

CERN Document Server

We present the first ab initio calculations of nuclear ground states up into the domain of heavy nuclei, spanning the range from 16-O to 132-Sn based on two- plus three-nucleon interactions derived within chiral effective field theory. We employ the similarity renormalization group for preparing the Hamiltonian and use coupled-cluster theory to solve the many-body problem for nuclei with closed sub-shells. Through an analysis of theoretical uncertainties resulting from various truncations in this framework, we identify and eliminate the technical hurdles that previously inhibited the step beyond medium-mass nuclei, allowing for reliable validations of nuclear Hamiltonians in the heavy regime. Following this path we show that chiral Hamiltonians qualitatively reproduce the systematics of nuclear ground-state energies up to the neutron-rich Sn isotopes.

Binder, Sven; Calci, Angelo; Roth, Robert

2013-01-01

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Time-reversible ab initio molecular dynamics  

Science.gov (United States)

Time-reversible ab initio molecular dynamics based on a lossless multichannel decomposition for the integration of the electronic degrees of freedom [Phys. Rev. Lett. 97, 123001 (2006)] is explored. The authors present a lossless time-reversible density matrix molecular dynamics scheme. This approach often allows for stable Hartree-Fock simulations using only one single self-consistent field cycle per time step. They also present a generalization, introducing an additional ``forcing'' term, that in a special case includes a hybrid Lagrangian, i.e., Car-Parrinello-type, method, which can systematically be constrained to the Born-Oppenheimer potential energy surface by using an increasing number of self-consistency cycles in the nuclear force calculations. Furthermore, in analog to the reversible and symplectic leapfrog or velocity Verlet schemes, where not only the position but also the velocity is propagated, the authors propose a Verlet-type density velocity formalism for time-reversible Born-Oppenheimer molecular dynamics.

Niklasson, Anders M. N.; Tymczak, C. J.; Challacombe, Matt

2007-04-01

 
 
 
 
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Ab-initio nanoplasmonics: atoms matter  

CERN Document Server

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

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

2014-01-01

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Ab initio study of high-pressure phase transitions in silicon and germanium  

CERN Multimedia

We have investigated the structural sequence of the high-pressure phases of silicon and germanium. We have focussed on the cd -> beta-tin -> Imma -> sh phase transitions. We have used the plane-wave pseudopotential approach to the density-functional theory implemented within the Vienna ab-initio simulation package (VASP). We have determined the equilibrium properties of each structure and the values of the critical parameters including a hysteresis effect at the phase transitions. The order of the phase transitions has been obtained from the pressure dependence of the enthalpy. Our calculations identify a first-order phase transition from the cd to the beta-tin and from the Imma to the sh phase, and they indicate the possibility of a second-order phase-transition from the beta-tin to the Imma phase. Finally, we have derived the enthalpy barriers between the phases.

Gaál-Nagy, K; Strauch, D; Gaal-Nagy, Katalin; Pavone, Pasquale; Strauch, Dieter

2003-01-01

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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.

24

Integrated design of Nb-based superalloys: Ab initio calculations, computational thermodynamics and kinetics, and experimental results  

International Nuclear Information System (INIS)

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

2007-06-01

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Ab initio atomistic simulation of metals and multicomponent alloys  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

Tian, Fuyang

2013-01-01

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Ab initio Lattice Dynamics : Hydrogen-dense and Other Materials  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

2009-01-01

27

Recent achievements in ab initio modelling of liquid water  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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 simulat...

Khaliullin, Rustam Z.; Ku?hne, Thomas D.

2013-01-01

28

Ab Initio Theory of Gate Induced Gaps in Graphene Bilayers  

CERN Document Server

We study the gate voltage induced gap that occurs in graphene bilayers using \\textit{ab initio} density functional theory. Our calculations confirm the qualitative picture suggested by phenomenological tight-binding and continuum models. We discuss enhanced screening of the external interlayer potential at small gate voltages, which is more pronounced in the \\textit{ab initio} calculations, and quantify the role of crystalline inhomogeneity.

Min, H; Banerjee, S K; MacDonald, A H; Min, Hongki; Banerjee, Sanjay K.

2006-01-01

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Ab initio molecular dynamics: Concepts, recent developments, and future trends  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The methodology of ab initio molecular dynamics, wherein finite-temperature dynamical trajectories are generated by using forces computed “on the fly” from electronic structure calculations, has had a profound influence in modern theoretical research. Ab initio molecular dynamics allows chemical processes in condensed phases to be studied in an accurate and unbiased manner, leading to new paradigms in the elucidation of microscopic mechanisms, rationalization of experimental data, and tes...

2005-01-01

30

Ab initio energy landscape of LiF clusters  

CERN Document Server

A global search for possible LiF cluster structures is performed, up to (LiF)8. The method is based on simulated annealing, where all the energies are evaluated on the ab initio level. In addition, the threshold algorithm is employed to determine the energy barriers for the transitions among these structures, for the cluster (LiF)4, again on the ab initio level; and the corresponding tree graph is obtained.

Doll, K; Jansen, M; 10.1063/1.3455708

2010-01-01

31

Ab initio thermodynamic study of defective strontium titanate  

Digital Repository Infrastructure Vision for European Research (DRIVER)

In the presented thesis the perfect and defective SrTiO3 bulk crystals and their (001) surfaces are considered on ab initio level. Since the experimental study of the complex defective systems is comparatively expensive and difficult, and the computer performance has been greatly increased in the last years, the ab initio modeling became very efficient tool to be applied in this field. Additionally, there is a significant industrial demand for the investigation and improvements of the perform...

2013-01-01

32

Ab initio calculations of elastic constants of plagioclase feldspars  

Science.gov (United States)

Plagioclase feldspars comprise a signification portion of the Earth's crust, thus their elastic properties are essential for understanding the Earth's seismic structure. However, the accuracy of existing elastic constants for plagioclase feldspars is uncertain. Alexandrov & Ryzhova (1962, Bull Acad Sci USSR Geol Ser, 10) and Ryzhova (1964, Bull Acad Sci USSR Geol Ser, 7) measured the elastic constants for a series of natural plagioclase feldspars but were unable to measure all crystallographic directions for the triclinic symmetry. In addition, the exact chemical composition, degree of twinning, and imperfections of their samples were not well characterized. More recent experiments on albite were performed by Brown et al. (2006, Phys Chem Minerals, 33) whose values vary considerably from the earlier measurements. We calculated elastic constants for three members in the plagioclase solid solution family in order to compare and improve upon elastic constants using density functional theory (DFT) as implemented in the Vienna Ab-initio Simulation Package (VASP) (Kresse and Hafner, 1993, Phys Rev B, 47). Starting from the experimentally determined crystal structures of low albite, labradorite, and anorthite, we relaxed the geometries at constant volume. Then we strained the unit cell, calculated the corresponding stresses, and derived elastic constants from the finite differences, Cij=(??i)/(??j) where indices are given in Voigt notation. Our calculated values for albite fall in between those of Ryzhova (1964) and Brown et al. (2006), but are more similar to Brown et al. (2006). Our labradorite results are similar to Alexandrov and Ryzhova (1962) and Ryzhova (1964), but more similar to the latter. Anorthite elastic constants have not yet been measured, but our calculated results for anorthite follow a trend of increasing C11 and C22 and decreasing C44 with increasing Ca content. P-wave velocities for albite are between 486-798 km/s while velocities for labradorite are 582-784 km/s, and for anorthite, 583-794 km/s, suggesting that seismic anisotropy decreases with Ca content. This study provides more reliable elastic constants for determining elastic properties of plagioclase-bearing rocks for seismic applications.

Kaercher, P. M.; Militzer, B.; Wenk, H.

2012-12-01

33

Ab initio non-adiabatic molecular dynamics.  

Science.gov (United States)

Adiabatic nuclear potential energy surfaces (PESs) defined via the Born-Oppenheimer (BO) approximation are a fundamental concept underlying chemical reactivity theory. For a wide range of excited-state phenomena such as radiationless decay, energy and charge transfer, and photochemical reactions, the BO approximation breaks down due to strong couplings between two or more BO PESs. Non-adiabatic molecular dynamics (NAMD) is the method of choice to model these processes. We review new developments in quantum-classical dynamics, analytical derivative methods, and time-dependent density functional theory (TDDFT) which have lead to a dramatic expansion of the scope of ab initio NAMD simulations for molecular systems in recent years. We focus on atom-centered Gaussian basis sets allowing highly efficient simulations for molecules and clusters, especially in conjunction with hybrid density functionals. Using analytical derivative techniques, forces and derivative couplings can be obtained with machine precision in a given basis set, which is crucial for accurate and stable dynamics. We illustrate the performance of surface-hopping TDDFT for photochemical reactions of the lowest singlet excited states of cyclohexadiene, several vitamin D derivatives, and a bicyclic cyclobutene. With few exceptions, the calculated quantum yields and excited state lifetimes agree qualitatively with experiment. For systems with ?50 atoms, the present Turbomole implementation allows NAMD simulations with 0.2-0.4 ns total simulation time using hybrid density functionals and polarized double zeta valence basis sets on medium-size compute clusters. We close by discussing open problems and future directions. PMID:24068257

Tapavicza, Enrico; Bellchambers, Gregory D; Vincent, Jordan C; Furche, Filipp

2013-11-14

34

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

35

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

36

Towards New Horizons in Ab Initio Nuclear Structure Theory  

Directory of Open Access Journals (Sweden)

Full Text Available We present a cross-section of recent advances in ab initio nuclear structure theory, which have changed the horizons of this field. Starting from chiral effective field theory to construct the nuclear Hamiltonian and the similarity renormalization group to further soften it, we address several many-body approaches that have seen major developments over the past few years. We show that the domain of ab initio nuclear structure theory has been pushed well beyond the p-shell and that quantitative QCD-based predictions are becoming possible all the way from the proton to the neutron drip line up into the medium-mass regime.

Roth Robert

2014-03-01

37

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

38

Structure prediction based on ab initio simulated annealing  

International Nuclear Information System (INIS)

The prediction of possible crystal structures, with the type of atoms as the only input, has become a fast growing field of research. The general approach consists of the global exploration of the energy landscape of the chemical system, with typical methods being simulated annealing or genetic algorithms. In the case of simulated annealing, combinations of model potentials and ab initio calculations for the energy evaluation are state of the art. Only very recently, the possibility of simulated annealing based on ab initio calculations at all stages of the calculations has become feasible. This article summarizes the recent developments in this area

2008-06-01

39

Structure prediction based on ab initio simulated annealing  

Energy Technology Data Exchange (ETDEWEB)

The prediction of possible crystal structures, with the type of atoms as the only input, has become a fast growing field of research. The general approach consists of the global exploration of the energy landscape of the chemical system, with typical methods being simulated annealing or genetic algorithms. In the case of simulated annealing, combinations of model potentials and ab initio calculations for the energy evaluation are state of the art. Only very recently, the possibility of simulated annealing based on ab initio calculations at all stages of the calculations has become feasible. This article summarizes the recent developments in this area.

Doll, K; Schoen, J C; Jansen, M [Max-Planck-Institute for Solid State Research, Heisenbergstr. 1, D-70569 Stuttgart (Germany)], E-mail: k.doll@fkf.mpg.de

2008-06-01

40

Toward the Ab-initio Description of Medium Mass Nuclei  

Digital Repository Infrastructure Vision for European Research (DRIVER)

As ab-initio calculations of atomic nuclei enter the A=40-100 mass range, a great challenge is how to approach the vast majority of open-shell (degenerate) isotopes. We add realistic three-nucleon interactions to the state of the art many-body Green's function theory of closed-shells, and find that physics of neutron driplines is reproduced with very good quality. Further, we introduce the Gorkov formalism to extend ab-initio theory to semi-magic, fully open-shell, isotopes....

Barbieri, C.; Cipollone, A.; Soma, V.; Duguet, T.; Navratil, P.

2012-01-01

 
 
 
 
41

Multiple time step integrators in ab initio molecular dynamics  

Science.gov (United States)

Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we present two schemes that enable efficient time-scale separation in ab initio calculations: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynamics. This permits computational speedups of up to 4.4x, compared to standard Born-Oppenheimer ab initio molecular dynamics with a 0.5 fs time step, while maintaining the same energy conservation and accuracy.

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

2014-02-01

42

Ab initio torsional potential and transition frequencies of acetaldehyde  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The torsional potential, the torsional transition frequencies, and the contortional parameter were obtained for acetaldehyde by high-level ab initio calculations. As such, the theoretically derived contortional parameter and transition frequencies were in excellent agreement with the corresponding experimental values. In fact, no previous theoretical calculation led to such a good agreement.

Csa?sza?r, A. G.; Szalay, Viktor; Senent Di?ez, Mari?a Luisa

2004-01-01

43

Structural, electronic and optical properties of cubic SrTiO3 and KTaO3: Ab initio and GW calculations  

International Nuclear Information System (INIS)

We present first-principles VASP calculations of the structural, electronic, vibrational, and optical properties of paraelectric SrTiO3 and KTaO3. The ab initio calculations are performed in the framework of density functional theory with different exchange-correlation potentials. Our calculated lattice parameters, elastic constants, and vibrational frequencies are found to be in good agreement with the available experimental values. Then, the bandstructures are calculated with the GW approximation, and the corresponding band gap is used to obtain the optical properties of SrTiO3 and KTaO3.

2012-07-01

44

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

45

Carrier Scattering Rates in Zincblende Structure Semiconductors derived from 14 × 14 k · p and ab initio Pseudopotential Methods  

Digital Repository Infrastructure Vision for European Research (DRIVER)

A set of programs for calculating carrier-phonon and carrier-alloy scat-tering rates have been constructed. Energy bands, gradients of the energy, second derivatives of the energy and eigenvectors of the carrier states were first calculated using a 14 × 14 kp-method. Scattering rates were then derived, based upon the calculations of the developed kp software. Furthermore, scattering rates have also been derived using band structures from the ab initio pseudopotential code ABINIT. A progr...

Karlsen, Bjørnar

2013-01-01

46

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

47

Ab Initio Calculations of Light-Ion 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, 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.

Navrátil, P.; Quaglioni, S.; Roth, R.; Horiuchi, W.

48

Ab initio calculations of light-ion fusion 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. Above all nuclear scattering and reactions, which require the solution of the many-body quantum-mechanical problem in the continuum, represent an extraordinary theoretical as well as computational challenge for ab initio approaches. The ab initio No-Core Shell Model/Resonating-Group Method (NCSM/RGM) [1, 2, 3, 4] complements a microscopic cluster technique with the use of realistic interactions, and a microscopic and consistent description of the nucleon clusters. This approach is capable of describing simultaneously both bound and scattering states in light nuclei. Recent applications to light nuclei scattering and fusion reactions relevant to energy production in stars and Earth based fusion facilities, such as the deuterium-3He fusion [4], are presented. Progress toward the inclusion of the three nucleon force into the formalism is outlined.

Hupin, G.; Quaglioni, S.; Navrátil, P.

2012-10-01

49

Ab initio calculations of light-ion fusion reactions  

International Nuclear Information System (INIS)

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. Above all nuclear scattering and reactions, which require the solution of the many-body quantum-mechanical problem in the continuum, represent an extraordinary theoretical as well as computational challenge for ab initio approaches. The ab initio No-Core Shell Model/Resonating-Group Method (NCSM/RGM) complements a microscopic cluster technique with the use of realistic interactions, and a microscopic and consistent description of the nucleon clusters. This approach is capable of describing simultaneously both bound and scattering states in light nuclei. Recent applications to light nuclei scattering and fusion reactions relevant to energy production in stars and Earth based fusion facilities, such as the deuterium-3He fusion, are presented. Progress toward the inclusion of the three nucleon force into the formalism is outlined.

2012-10-20

50

Multiple Time Step Integrators in Ab Initio Molecular Dynamics  

CERN Document Server

Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we show that such a timescale separation is possible using two different schemes: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynami...

Luehr, Nathan; Martinez, Todd J

2013-01-01

51

The density matrix renormalization group for ab initio quantum chemistry  

CERN Document Server

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

Wouters, Sebastian

2014-01-01

52

Ab initio and perturbation treatment studies in different dielectric media  

Science.gov (United States)

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

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

2009-02-01

53

Complementary approaches to the ab initio calculation of melting properties  

CERN Multimedia

Several research groups have recently reported {\\em ab initio} calculations of the melting properties of metals based on density functional theory, but there have been unexpectedly large disagreements between results obtained by different approaches. We analyze the relations between the two main approaches, based on calculation of the free energies of solid and liquid and on direct simulation of the two coexisting phases. Although both approaches rely on the use of classical reference systems consisting of parameterized empirical interaction models, we point out that in the free energy approach the final results are independent of the reference system, whereas in the current form of the coexistence approach they depend on it. We present a scheme for correcting the predictions of the coexistence approach for differences between the reference and {\\em ab initio} systems. To illustrate the practical operation of the scheme, we present calculations of the high-pressure melting properties of iron using the correct...

Alfe`, D; Price, G D

2001-01-01

54

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

55

Ab initio calculation of uranium plasma emission coefficients  

International Nuclear Information System (INIS)

Ab initio calculations of energy-level, oscillator-strength, and emission distributions have been made for transition arrays involving the ground and 31 excited configurations of singly, doubly, and triply ionized uranium (U II, U III, and U IV). The quantum-mechanical model was based on a modification of the Slater-Condon theory in the single-configuration approximation. Wavefunctions were developed from an approach resembling the Hartree-Fock method with relativistic corrections. Tables of atomic parameters and graphs of weighted oscillator strength vs. wavelength are presented for each ion. There is good shape correlation and order-of-magnitude agreement between the calculated and measured uranium plasma emission coefficients at similar temperature/pressure conditions. This comparison supports the hypothesis that major emission features of spectroscopically complex systems can be predicted or verified with an ab initio approach. (orig.)

1980-01-01

56

Ab initio modeling of TiO2 nanotubes  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

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

2010-01-01

57

Ab initio investigations on H bonded molecular clusters  

Digital Repository Infrastructure Vision for European Research (DRIVER)

In this work molecular clusters of phenol and 2-naphthol with water, and molecular aniline homoclusters were studied by means of ab initio electronic structure theory. These systems can be observed experimentally in supersonic beam experiments and measured mass-selectively by spectroscopic methods. Molecular clusters in such experimental setups serve as test beds to explore the intermolecular interactions, since they are vibrationally cold and isolated from environmental influences. The compl...

Schemmel, Dominik

2010-01-01

58

Ab Initio Modeling of Ecosystems with Artificial Life  

CERN Document Server

Artificial Life provides the opportunity to study the emergence and evolution of simple ecosystems in real time. We give an overview of the advantages and limitations of such an approach, as well as its relation to individual-based modeling techniques. The Digital Life system Avida is introduced and prospects for experiments with ab initio evolution (evolution "from scratch"), maintenance, as well as stability of ecosystems are discussed.

Adami, C

2002-01-01

59

Ab initio, density functional theory, and semi-empirical calculations.  

Science.gov (United States)

This chapter introduces the theory and applications of commonly used methods of electronic structure calculation, with particular emphasis on methods applicable for modelling biomolecular systems. This chapter is sectioned as follows. We start by presenting ab initio methods, followed by a treatment of density functional theory (DFT) and some recent advances in semi-empirical methods. Treatment of excited states as well as basis sets are also presented. PMID:23034743

Johansson, Mikael P; Kaila, Ville R I; Sundholm, Dage

2013-01-01

60

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 Rechnungen basieren auf der Dichte-Funktional-Theorie, die sehr gut für die Beschreibung der material-spezifischen Eigenschaften von DMS geeignet ist. Wir verwenden die Koringa-Kohn-Rostoker (KKR) Gre...

Belhadji, Brahim

2009-01-01

 
 
 
 
61

Matrix isolation and ab initio studies of oxalic acid  

International Nuclear Information System (INIS)

Rotamerization and UV photochemical decomposition of oxalic acid were studied in various matrices and ab initio calculations in this paper. Two conformers, cTc (2 intramolecular hydrogen bonds) and cTt (one intramolecular hydrogen bond) and their conversion energy from one form to the other were observed and studied. Full Xe arc irradiation decomposes matrix oxalic acid. For 6 oxalic acid conformers other spectra are calculated and assigned along with their potential energy distributions. 25 refs., 8 figs., 11 tabs

1992-06-25

62

Matrix isolation and ab initio studies of oxalic acid  

Energy Technology Data Exchange (ETDEWEB)

Rotamerization and UV photochemical decomposition of oxalic acid were studied in various matrices and ab initio calculations in this paper. Two conformers, cTc (2 intramolecular hydrogen bonds) and cTt (one intramolecular hydrogen bond) and their conversion energy from one form to the other were observed and studied. Full Xe arc irradiation decomposes matrix oxalic acid. For 6 oxalic acid conformers other spectra are calculated and assigned along with their potential energy distributions. 25 refs., 8 figs., 11 tabs.

Nieminen, J.; Raesaenen, M.; Murto, J. [Univ. of Helsinki (Finland)

1992-06-25

63

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 excited states requires to go beyond ground-state density-functional theory (DFT). In this work we review three theoretical frameworks beyond DFT: the first is time-dependent density-functional theory ...

Olevano, Valerio

2009-01-01

64

Ab initio Gutzwiller method: first application to plutonium  

International Nuclear Information System (INIS)

Using a density matrix approach to Gutzwiller method, we present a formalism to treat ab initio multiband tight-binding Hamiltonians including local Coulomb interaction in a solid, like, e.g., the degenerate Hubbard model. After minimization with respect to the variational parameters, the approximate ground state is obtained, providing the equilibrium properties of a material. Finally, the method is coupled to the so-called 'linearized muffin-tin orbitals' technique. The first application to Pu is presented

2005-04-30

65

Ab initio Interlayer Potentials For Metals and Alloys  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Many modern materials and material systems are layered. The properties related to layers are connected to interactions between atomic layers. In the present thesis, we introduce the interlayer potential (ILP), a novel model potential which fully describes the interaction between layers. The ILPs are different from the usual interatomic potentials which present interaction between atoms. We use the Chen-Möbius inversion method to extract the ILPs from ab initio total energy calculations. The ...

Tian, Fuyang

2012-01-01

66

Hydrogen Desorption from Mg Hydride: An Ab Initio Study  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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 temperature...

Simone Giusepponi; Massimo Celino

2012-01-01

67

Ab initio molecular dynamics simulations of Aluminum solvation  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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 ...

Lubin, M. I.; Bylaska, J. H.; Weare, J. H.

1999-01-01

68

Ab initio DFT - the seamless connection between WFT and DFT  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

2010-01-01

69

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

70

Ab Initio Theory of Light-ion 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. Above all nuclear scattering and reactions, which require the solution of the many-body quantum-mechanical problem in the continuum, represent a theoretical and computational challenge for ab initio approaches. After a brief overview of the field, we present a new ab initio many-body approach capable of describing simultaneously both bound and scattering states in light nuclei. By combining the resonating-group method (RGM) with the ab initio no-core shell model (NCSM), we complement a microscopic cluster technique with the use of realistic interactions and a microscopic and consistent description of the clusters. We show results for neutron and proton scattering on light nuclei, including p-7Be and n-8He. We also highlight the first results of the d-3He and d-3H fusion calculations obtained within this approach.

Navrátil, Petr; Quaglioni, Sofia; Roth, Robert

2011-09-01

71

Ab Initio Theory of Light-ion Reactions  

International Nuclear Information System (INIS)

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. Above all nuclear scattering and reactions, which require the solution of the many-body quantum-mechanical problem in the continuum, represent a theoretical and computational challenge for ab initio approaches. After a brief overview of the field, we present a new ab initio many-body approach capable of describing simultaneously both bound and scattering states in light nuclei. By combining the resonating-group method (RGM) with the ab initio no-core shell model (NCSM), we complement a microscopic cluster technique with the use of realistic interactions and a microscopic and consistent description of the clusters. We show results for neutron and proton scattering on light nuclei, including p-7Be and n-8He. We also highlight the first results of the d-3He and d-3H fusion calculations obtained within this approach.

2011-09-23

72

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

73

Acceleration of the Convergence in ab initio Atomic Relaxations  

Science.gov (United States)

Atomic relaxations is often required to accurately describe the properties of nanosystems. In ab initio calculations, a common practice is to use a standard search algorithm, such as BFGS (Broyden-Fletcher-Goldfarb-Shanno) or CG (conjugate gradient) method, which starts the atomic relaxations without any knowledge of the Hessian matrix of the system. For example, the initial Hessian in BFGS method is often set to identity, and there is no preconditioning to CG method. One way to accelerate the convergence of the atomic relaxations is to estimate an approximate Hessian matrix of the system and then use it as the initial Hessian in BFGS method or a preconditioner in CG method. Previous attempts to obtain the approximated Hessian were focused on the use of classical force field models which rely on the existence of good parameters. Here, we present an alternative method to estimate the Hessian matrix of a nanosystem. First, we decompose the system into motifs which consist of a few atoms, then calculate the Hessian matrix elements on different motif types from ab initio calculations for small prototype systems. Then we generate the Hessian Matrix of the whole system by putting together these motif Hessians. We have applied our motif-based Hessian matrix in ab initio atomic relaxations in several bulk (with/without impurity) and quantum dot systems, and have found a speed up factor of 2 to 4 depending on the system size.

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

2006-03-01

74

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

75

Towards hydrogen metallization: an Ab initio approach; Vers la metallisation de l`hydrogene: approche AB initio  

Energy Technology Data Exchange (ETDEWEB)

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(H{sub 2}){sub 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) 109 refs.

Bernard, St

1998-12-31

76

A homology/ab initio hybrid algorithm for sampling near-native protein conformations.  

Science.gov (United States)

One of the major challenges for protein tertiary structure prediction strategies is the quality of conformational sampling algorithms, which can effectively and readily search the protein fold space to generate near-native conformations. In an effort to advance the field by making the best use of available homology as well as fold recognition approaches along with ab initio folding methods, we have developed Bhageerath-H Strgen, a homology/ab initio hybrid algorithm for protein conformational sampling. The methodology is tested on the benchmark CASP9 dataset of 116 targets. In 93% of the cases, a structure with TM-score ? 0.5 is generated in the pool of decoys. Further, the performance of Bhageerath-H Strgen was seen to be efficient in comparison with different decoy generation methods. The algorithm is web enabled as Bhageerath-H Strgen web tool which is made freely accessible for protein decoy generation (http://www.scfbio-iitd.res.in/software/Bhageerath-HStrgen1.jsp). PMID:23728619

Dhingra, Priyanka; Jayaram, Bhyravabhotla

2013-08-15

77

SURPRISES: when ab initio meets statistics in extended systems  

International Nuclear Information System (INIS)

The surface photoelectron and inner shell electron spectroscopy (SURPRISES) program suite performs ab initio calculations of photoionization and non-radiative decay spectra in nanoclusters and solid state systems by using a space-energy similarity procedure to reproduce the band-like part of the spectra. This approach provides an extension of Fano resonant multichannel scattering theory dealing with the complexity arising from condensed matter calculations at a computational cost comparable to that of molecules. The bottleneck of electron spectroscopy ab initio calculations in condensed matter is the size of the Hilbert space where the wavefunctions are expanded and the increase in number of final decay states in comparison to that of atoms and molecules. In particular, the diagonalization of the interchannel interaction to take into account the correlation between the double ion and the escaping electron is impracticable when hole delocalization on valence bands and electronic excitations are included in the model. To overcome this problem SURPRISES uses a 'space-energy similarity' approach, which allows the spreading of the Auger probability over the bands without tuning semi-empirical parameters. Furthermore, a completely new feature in the landscape of ab initio resonant decay processes calculations is represented by including energy loss through a statistical approach. Using the calculated lineshape as electron source, a Monte Carlo routine simulates the effect of inelastic losses on the original lineshape. In this process, the computed spectrum can be directly compared with acquired experimental spectra, thus avoiding background subtraction, a procedure not free from uncertainty. The program can exploit the symmetry of the system under investigation to reduce the calculation scaling and may compute photoemission and Auger decay angular distribution patterns including energy loss for the electrons emitted in resonance-affected photoionization processes. In this paper, we present general methods, computational techniques and a number of numerical tests applied to the calculation of Si K-LL and O K-LL Auger spectra from different SiO2 nanoclusters.

2009-01-01

78

Ab initio simulations for material properties inside Jupiter  

Science.gov (United States)

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

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

2013-07-01

79

Ab initio study of small gallium phosphate clusters  

Science.gov (United States)

Ab initio calculations have been performed on gallium phosphate clusters: Ga(OH) 4-, P(OH) 4+, (HO) 3GaOP(OH) 3 and Ga 2P 2O 4)(OH) 8. The influences of the basis set and the level of theory on predicted configurations of the clusters are discussed. Calculated IR spectra have been analyzed and compared with experimental ones. The potential energy surface for the Ga?O interaction has been used to derive force-field parameters. The latter were applied in the molecular dynamics simulation of the berlinite and low-cristobalite modifications of GaPO 4.

Murashov, Vladimir

1995-04-01

80

Stabilization of planar hexacoordinate boron: ab initio study  

International Nuclear Information System (INIS)

Using ab initio (MP2 (full)/6-31 G**) and DFT (B3LYP/6-311 + + G**) potentiality of existence of a stable anion BB6 (NH2)2- with a plane hexacoordinated boron atom was predicted and influence of Li+ counter ion on its stability and structural characteristics was studied. Transfer from isolated anion to lithium salt involves inessential upsetting of planarity of the central hypercoordinated node. The B-Li bond length amounts to 2.17-2.33 A, according to different levels of the calculation, being within standard values of ordinary bonds

2001-08-01

 
 
 
 
81

A transferable ab initio based force field for aqueous ions.  

Science.gov (United States)

We present a new polarizable force field for aqueous ions (Li(+), Na(+), K(+), Rb(+), Cs(+), Mg(2 +), Ca(2 +), Sr(2 +), and Cl(-)) derived from condensed phase ab initio calculations. We use maximally localized Wannier functions together with a generalized force and dipole-matching procedure to determine the whole set of parameters. Experimental data are then used only for validation purposes and a good agreement is obtained for structural, dynamic, and thermodynamic properties. The same procedure applied to crystalline phases allows to parametrize the interaction between cations and the chloride anion. Finally, we illustrate the good transferability of the force field to other thermodynamic conditions by investigating concentrated solutions. PMID:22443777

Tazi, Sami; Molina, John J; Rotenberg, Benjamin; Turq, Pierre; Vuilleumier, Rodolphe; Salanne, Mathieu

2012-03-21

82

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

83

Ab initio molecular dynamics via density based energy functionals  

CERN Multimedia

The use of energy functionals based on density as the basic variable is advocated for ab initio molecular dynamics. It is demonstrated that the constraint of positivity of density can be incorporated easily by using square root density for minimization of the energy functional. An ad hoc prescription for including nonlocal pseudopotentials for plane wave based calculations is proposed and is shown to yield improved results. Applications are reported for equilibrium geometries of small finite systems, viz. dimers and trimers of simple metal atoms like Na and Mg, which represent a rather stringent test for approximate kinetic energy functionals involved in such calculations.

Shah, V; Kanhere, D G; Vaishali Shah; Dinesh Nehete

1994-01-01

84

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

85

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%

2005-04-01

86

Ab Initio study of neutron drops with chiral Hamiltonians  

CERN Document Server

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

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

2014-01-01

87

Ab initio investigation of lasing thresholds in photonic molecules  

CERN Document Server

We investigate lasing thresholds in a representative photonic molecule composed of two coupled active cylinders of slightly different radii. Specifically, we use the recently formulated steady-state ab initio laser theory (SALT) to assess the effect of the underlying gain transition on lasing frequencies and thresholds. We find that the order in which modes lase can be modified by choosing suitable combinations of the gain center frequency and linewidth, a result that cannot be obtained using the conventional approach of quasi-bound modes. The impact of the gain transition center on the lasing frequencies, the frequency pulling effect, is also quantified.

Gagnon, Denis; Déziel, Jean-Luc; Dubé, Louis J

2014-01-01

88

Ab initio Gutzwiller method: first application to plutonium  

Energy Technology Data Exchange (ETDEWEB)

Using a density matrix approach to Gutzwiller method, we present a formalism to treat ab initio multiband tight-binding Hamiltonians including local Coulomb interaction in a solid, like, e.g., the degenerate Hubbard model. After minimization with respect to the variational parameters, the approximate ground state is obtained, providing the equilibrium properties of a material. Finally, the method is coupled to the so-called 'linearized muffin-tin orbitals' technique. The first application to Pu is presented.

Julien, J.-P. [CNRS-LEPES, 25 Av. des Martyrs BP166, Grenoble Cedex 9 38042 (France)]. E-mail: jpjulien@grenoble.cnrs.fr; Bouchet, J. [Centre d' Etudes de Bruyeres-le-Chatel, Departement de Physique Theorique et Appliquees, 916 80 Bruyeres-le-Chatel (France)

2005-04-30

89

Ab initio calculations on hydrogen storage in porous carbons  

International Nuclear Information System (INIS)

We have investigated through ab initio computations the possible ways to achieve efficient hydrogen storage on carbons. Firstly, we have considered how the curvature of a carbon surface could affect the chemisorption of atomic H0 Secondly, we show that electron donor elements such as Li and K, used as dopants for the carbon substrate, strongly enhance the physi-sorption energy of H2, allowing in principle its storage in this type of material at room temperature under mild conditions of pressure. (authors)

2005-01-01

90

Ab initio calculation of the static structural properties of Be  

International Nuclear Information System (INIS)

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

1982-01-01

91

Raman intensities in polyphenyls: an ab-initio study  

International Nuclear Information System (INIS)

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

2002-09-23

92

Ab initio studies of transition-metal dihydrogen chemistry  

International Nuclear Information System (INIS)

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

1988-06-06

93

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

2002-05-16

94

Ab initio studies of electromechanical effects in carbon nanotubes  

Scientific Electronic Library Online (English)

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

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

95

Hydrogen diffusion in liquid aluminum from ab initio molecular dynamics  

Science.gov (United States)

Ab initio molecular dynamics simulations are used to describe the diffusion of hydrogen in liquid aluminum at different temperatures. Quasi-instantaneous jumps separating periods of localized vibrations around a mean position are found to characterize the hydrogen motion at the microscopic scale. The hydrogen motion is furthermore analyzed using the van Hove function. We highlight a non-Fickian behavior for the hydrogen diffusion due to a large spatial distribution of hydrogen jumps. We show that a generalized continuous time random walk (CTRW) model describes the experimental diffusion coefficients in a satisfactory manner. Finally, the impact of impurities and alloying elements on hydrogen diffusion in aluminum is discussed.

Jakse, N.; Pasturel, A.

2014-05-01

96

Three-cluster dynamics within an ab initio framework  

CERN Document Server

We introduce a fully antisymmetrized treatment of three-cluster dynamics within the ab initio framework of the no-core shell model/resonating-group method (NCSM/RGM). Energy-independent non-local interactions among the three nuclear fragments are obtained from realistic nucleon-nucleon interactions and consistent ab initio many-body wave functions of the clusters. The three-cluster Schr\\"odinger equation is solved with bound-state boundary conditions by means of the hyperspherical-harmonic method on a Lagrange mesh. We discuss the formalism in detail and give algebraic expressions for systems of two single nucleons plus a nucleus. Using a soft similarity-renormalization-group evolved chiral nucleon-nucleon potential, we apply the method to an $^4$He+$n+n$ description of $^6$He and compare the results to experiment and to a six-body diagonalization of the Hamiltonian performed within the harmonic-oscillator expansions of the NCSM. Differences between the two calculations provide a measure of core ($^4$He) pola...

Quaglioni, S; Navrátil, P

2013-01-01

97

Ab initio study of Cu diffusion in ?-cristobalite  

Science.gov (United States)

We have studied the geometries, formation energies, migration barriers and diffusion of a copper interstitial with different charge states with and without an external electric field in the ?-cristobalite crystalline form of SiO2 using ab initio computer simulation. The most stable state almost throughout the band gap is charge q = + 1. The height of the migration barrier depends slightly on the charge state and varies between 0.11 and 0.18 eV. However, the charge has a strong influence on the shape of the barrier, as metastable states exist in the middle of the diffusion path for Cu with q = + 1. The heights and shapes of barriers also depend on the density of SiO2, because volume expansion has a similar effect to increase the positive charge on Cu. Furthermore, diffusion coefficients have been deduced from our calculations according to transition-state theory and these calculations confirm the experimental result that oxidation of Cu is a necessary condition for diffusion. Our molecular dynamics simulations show a similar ion diffusion, and dependence on charge state. These simulations also confirm the fact that diffusion of ions can be directly simulated using ab initio molecular dynamics.

Zelený, M.; Hegedüs, J.; Foster, A. S.; Drabold, D. A.; Elliott, S. R.; Nieminen, R. M.

2012-11-01

98

Ab initio study of Cu diffusion in ?-cristobalite  

International Nuclear Information System (INIS)

We have studied the geometries, formation energies, migration barriers and diffusion of a copper interstitial with different charge states with and without an external electric field in the ?-cristobalite crystalline form of SiO2 using ab initio computer simulation. The most stable state almost throughout the band gap is charge q = + 1. The height of the migration barrier depends slightly on the charge state and varies between 0.11 and 0.18 eV. However, the charge has a strong influence on the shape of the barrier, as metastable states exist in the middle of the diffusion path for Cu with q = + 1. The heights and shapes of barriers also depend on the density of SiO2, because volume expansion has a similar effect to increase the positive charge on Cu. Furthermore, diffusion coefficients have been deduced from our calculations according to transition-state theory and these calculations confirm the experimental result that oxidation of Cu is a necessary condition for diffusion. Our molecular dynamics simulations show a similar ion diffusion, and dependence on charge state. These simulations also confirm the fact that diffusion of ions can be directly simulated using ab initio molecular dynamics. (paper)

2012-11-01

99

Semiconductor alloys for optoelectronic applications: ab initio modeling  

Science.gov (United States)

Semiconductor alloys, for example group III metal nitrides and phosphides, such as AxB1-xN or ANxP1-x (where A,B metal atoms: Al, In, Ga) have been materials of interest for optoelectronic applications (light emitting diodes, lasers, detectors) for more then two decades. The potential possibility of tuning (via variation of the composition) of the band-gap and the lattice constant make them particularly attractive. The idea of tuning the band-gap (from infrared to ultraviolet), although simple in principle, requires solving a variety of practical problems, like lattice constants misfit of parent compounds, associated with atom sizes, thermodynamically determined phase segregation, system stability, band-gap bowing, efficiency of radiative transitions etc. The ab initio modeling is of particular importance in the field, since it allows to predict in a purely theoretical way the physical limits for various properties. It also provides a hint in which direction, technologically and experimentally, to proceed. We present the basic ideas behind the ab initio modeling and, as an example, the calculation results of structural, elastic and the electronic properties of chosen alloys are presented.

Scharoch, Pawel; Winiarski, Maciej; Polak, Maciej

2013-10-01

100

Ab initio valence force field calculations for quartz  

Science.gov (United States)

We have derived valence force constants for the tetrahedral SiO4 unit and the inter-tetrahedral SiOSi linkage from previous ab initio molecular orbital calculations on H4SiO4 and H6Si2O7 using a split-valence polarized Gaussian basis set (6-31G*), and used these to calculate the infrared and Raman active vibrational modes of ?-quartz. The calculation gives frequencies approximately 15% greater than experiment, as expected from harmonic force constants obtained at this level of Hartree-Fock theory, but the calculation gives the correct distribution of modes within each frequency range. Calculated 28 30 Si and 16 18 O isotope shifts and pressure shifts to 6 GPa are also in reasonable agreement with experiment. We have also used our ab initio force field to calculate the vibrational spectrum for ?-quartz. The results suggest either that inclusion of a torsional force constant is important for determining the stability of this high temperature polymorph, or that the ?-quartz has a disordered structure with lower symmetry (P62) domains, as suggested by earlier diffraction studies.

McMillan, Paul F.; Hess, Anthony C.

1990-03-01

 
 
 
 
101

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

102

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

International Nuclear Information System (INIS)

The accuracy of ab initio density functional theory calculations depends crucially on the applied exchange-correlation functional. In recent years, a true zoo of functionals has emerged in particular in the quantum chemistry community. All these developments were aimed on an improved description of different properties of molecules, solids and surfaces. In the first part of this thesis we apply four different exchange-correlation functionals (LDA, PBE, PBEsol and HSE03) to two model perovskites, namely SrTiO3 and BaTiO3. We evaluate structural, electronic and phonon properties in the high temperature cubic as well as the tetragonal distorted phase with special attention on the zone-centred phonon mode. Our results show that the ferroelectric instability strongly depends on the volume and to a lesser extent on the applied functional. The second part of the thesis concentrates on the description of the polar oxygen terminated surface of ZnO. In the simple ionic picture the surface is electrostatically unstable due to a diverging electrostatic energy and has to adopt a modified surface structure to compensate for the polarity. In a close collaboration with experiment, a novel reconstruction is suggested. The remarkable observation is that the previously investigated oxygen terminated surface behaves very different than the zinc terminated surface. The difference is explained by the different bond preferences of Zn and O atoms: as a d-element Zn 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)

2010-01-01

103

Ab initio study of the structural, elastic, thermodynamic, electronic and vibration properties of TbMg intermetallic compound  

Science.gov (United States)

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

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

2014-07-01

104

Ab initio theory and calculations of X-ray spectra; Theorie et calculs ab initio des spectres de rayons X  

Energy Technology Data Exchange (ETDEWEB)

There has been dramatic progress in recent years both in the calculation and interpretation of various x-ray spectroscopies. However, current theoretical calculations often use a number of simplified models to account for many-body effects, in lieu of first principles calculations. In an effort to overcome these limitations we describe in this article a number of recent advances in theory and in theoretical codes which offer the prospect of parameter free calculations that include the dominant many-body effects. These advances are based on ab initio calculations of the dielectric and vibrational response of a system. Calculations of the dielectric function over a broad spectrum yield system dependent self-energies and mean-free paths, as well as intrinsic losses due to multielectron excitations. Calculations of the dynamical matrix yield vibrational damping in terms of multiple-scattering Debye-Waller factors. Our ab initio methods for determining these many-body effects have led to new, improved, and broadly applicable x-ray and electron spectroscopy codes. (authors)

Rehr, J.J.; Kas, J.J.; Prange, M.P.; Sorini, A.P.; Takimoto, Y.; Vila, F. [Washington Univ., Dept. of Physics, Seattle, WA (United States)

2009-07-15

105

Ab initio centroid path integral molecular dynamics: Application to vibrational dynamics of diatomic molecular systems  

Science.gov (United States)

An ab initio centroid molecular dynamics (CMD) method is developed by combining the CMD method with the ab initio molecular orbital method. The ab initio CMD method is applied to vibrational dynamics of diatomic molecules, H2 and HF. For the H2 molecule, the temperature dependence of the peak frequency of the vibrational spectral density is investigated. The results are compared with those obtained by the ab initio classical molecular dynamics method and exact quantum mechanical treatment. It is shown that the vibrational frequency obtained from the ab initio CMD approaches the exact first excitation frequency as the temperature lowers. For the HF molecule, the position autocorrelation function is also analyzed in detail. The present CMD method is shown to well reproduce the exact quantum result for the information on the vibrational properties of the system.

Ohta, Yasuhito; Ohta, Koji; Kinugawa, Kenichi

2004-01-01

106

Molecular structure and interactions of nucleic acid components in nanoparticles: ab initio calculations  

International Nuclear Information System (INIS)

Self-associates of nucleic acid components (stacking trimers and tetramers of the base pairs of nucleic acids) and short fragments of nucleic acids are nanoparticles (linear sizes of these particles are more than 10 A). Modern quantum-mechanical methods and softwares allow one to perform ab initio calculations of the systems consisting of 150-200 atoms with enough large basis sets (for example, 6-31G*). The aim of this work is to reveal the peculiarities of molecular and electronic structures, as well as the energy features of nanoparticles of nucleic acid components. We had carried out ab initio calculations of the molecular structure and interactions in the stacking dimer, trimer, and tetramer of nucleic base pairs and in the stacking (TpG)(ApC) dimer and (TpGpC) (ApCpG) trimer of nucleotides, which are small DNA fragments. The performed calculations of molecular structures of dimers and trimers of nucleotide pairs showed that the interplanar distance in the structures studied is equal to 3.2 A on average, and the helical angle in a trimer is approximately equal to 30o: The distance between phosphor atoms in neighboring chains is 13.1 A. For dimers and trimers under study, we calculated the horizontal interaction energies. The analysis of interplanar distances and angles between nucleic bases and their pairs in the calculated short oligomers of nucleic acid base pairs (stacking dimer, trimer, and tetramer) has been carried out. Studies of interactions in the calculated short oligomers showed a considerable role of the cross interaction in the stabilization of the structures. The contribution of cross interactions to the horizontal interactions grows with the length of an oligomer. Nanoparticle components get electric charges in nanoparticles. Longwave low-intensity bands can appear in the electron spectra of nanoparticles.

2012-07-01

107

NestedMICA as an ab initio protein motif discovery tool  

Directory of Open Access Journals (Sweden)

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

Down Thomas A

2008-01-01

108

Ab initio computation of neutron-rich oxygen isotopes  

International Nuclear Information System (INIS)

We compute the binding energy of neutron-rich oxygen isotopes and employ the coupled-cluster method and chiral nucleon-nucleon interactions at next-to-next-to-next-to-leading order with two different cutoffs. We obtain rather well-converged results in model spaces consisting of up to 21 oscillator shells. For interactions with a momentum cutoff of 500 MeV, we find that 28O is stable with respect to 24O, while calculations with a momentum cutoff of 600 MeV result in a slightly unbound 28O. The theoretical error estimates due to the omission of the three-nucleon forces and the truncation of excitations beyond three-particle-three-hole clusters indicate that the stability of 28O cannot be ruled out from ab initio calculations, and that three-nucleon forces and continuum effects play the dominant role in deciding this question.

2009-08-01

109

Ab initio Computation of Neutron-Rich Oxygen Isotopes  

Energy Technology Data Exchange (ETDEWEB)

We compute the binding energy of neutron-rich oxygen isotopes and employ the coupled-cluster method and chiral nucleon-nucleon interactions at next-to-next-to-next-to-leading order with two different cutoffs. We obtain rather well-converged results in model spaces consisting of up to 21 oscillator shells. For interactions with a momentum cutoff of 500 MeV, we find that ^{28}O is stable with respect to ^{24}O, while calculations with a momentum cutoff of 600 MeV result in a slightly unbound ^{28}O. The theoretical error estimates due to the omission of the three-nucleon forces and the truncation of excitations beyond three-particle three-hole clusters indicate that the stability of ^{28}O cannot be ruled out from ab-initio calculations, and that three-nucleon forces and continuum effects play the dominant role in deciding this question.

Hagen, Gaute [ORNL; Papenbrock, T. [University of Tennessee, Knoxville (UTK) & Oak Ridge National Laboratory (ORNL); Dean, David Jarvis [ORNL; Hjorth-Jensen, M. [University of Oslo, Norway; Velamur Asokan, B. [Oak Ridge National Laboratory (ORNL)

2009-01-01

110

Ab-initio computation of neutron-rich oxygen isotopes  

CERN Document Server

We compute the binding energy of neutron-rich oxygen isotopes and employ the coupled-cluster method and chiral nucleon-nucleon interactions at next-to-next-to-next-to-leading order with two different cutoffs. We obtain rather well-converged results in model spaces consisting of up to 21 oscillator shells. For interactions with a momentum cutoff of 500 MeV, we find that 28O is stable with respect to 24O, while calculations with a momentum cutoff of 600 MeV result in a slightly unbound 28O. The theoretical error estimates due to the omission of the three-nucleon forces and the truncation of excitations beyond three-particle-three-hole clusters indicate that the stability of 28O cannot be ruled out from ab-initio calculations, and that three-nucleon forces and continuum effects play the dominant role in deciding this question.

Hagen, G; Dean, D J; Hjorth-Jensen, M; Asokan, B Velamur

2009-01-01

111

Ab initio correlated calculations of rare-gas dimer quadrupoles  

Science.gov (United States)

This paper reports ab initio calculations of rare gas ( RG=Kr , Ar, Ne, and He) dimer quadrupoles at the second order of Møller-Plesset perturbation theory (MP2). The study reveals the crucial role of the dispersion contribution to the RG2 quadrupole in the neighborhood of the equilibrium dimer separation. The magnitude of the dispersion quadrupole is found to be much larger than that predicted by the approximate model of Hunt. As a result, the total MP2 quadrupole moment is significantly smaller than was assumed in virtually all previous related studies. An analytical model for the distance dependence of the RG2 quadrupole is proposed. The model is based on the effective-electron approach of Jansen, but replaces the original Gaussian approximation to the electron density in an RG atom by an exponential one. The role of the nonadditive contribution in RG3 quadrupoles is discussed.

Donchev, Alexander G.

2007-10-01

112

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

113

Thermochemical study of uranium by ab initio quantum chemical calculations  

Energy Technology Data Exchange (ETDEWEB)

Ab initio Hartree Fock (HF) theory and Density Functional theory (DFT) have been used to predict the Gibbs free energy of formation ({delta}G{sub f}{sup 0}) for uranium (VI) hydrolysis complexes. B3LYP is a better method to calculate the chemical properties of the complex and large molecules. The calculations were performed in the presence of solvent (water) by using the dielectric continuum modeling PCM method as well as the revised Born model. The pressure parameter p=1354atm was used to reproduce the entropy of ions in solution. The calculated energy demonstrates that PCM model is better than Born model in calculating the hydration energy. The primary hydration shell has been included in the calculation. It shows that the B3LYP calculated results inclusive of the primary hydration shell and the PCM hydration energy have reasonable agreement with experiments. (author)

Yang, Tianxiao; Tsushima, Satoru; Suzuki, Atsuyuki [Department of Quantum Engineering and Systems Science, School of Engineering, Univ. of Tokyo, Tokyo (Japan)

2001-03-01

114

Ab initio studies on complexes formed by melamine and cyclotrione  

Directory of Open Access Journals (Sweden)

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

LIANGIANG ZHU

2007-04-01

115

Ab initio molecular dynamics simulation of methanol adsorbed in chabazite  

Science.gov (United States)

Ab initio molecular dynamics simulations based on density functional theory together with a plane wave basis set and Vanderbilt pseudopotentials are performed to explore the potential energy surface of a methanol molecule interacting with the Brønsted site of zeolite chabazite. In agreement with a recent study a stationary point is located which corresponds to a chemisorbed methoxonium species. However, molecular dynamics simulations at 400 K show that configurations corresponding to this structure are of minor probability. Instead, the most stable structure is a physisorbed complex in which the strongly interacting Brønsted proton is significantly delocalized in the region between the methanol and the framework oxygen of the zeolite catalyst. A stationary point of the potential energy surface corresponding to such a structure proves to be more stable than the ion pair complex by about 18 kJ/mol.

Haase, Frank; Sauer, Joachim; Hutter, Jürg

1997-02-01

116

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 ZnTe(2) pyrite semiconductor compound proposed here are presented. The opto-electronic properties of these dichalcogenide compounds have been calculated using quasiparticle GW theory. Bandgaps, band structures and effective masses are proposed as well as absorption coefficients and refraction indices. The compounds are all indirect semiconductors with very flat conduction band dispersion and high absorption coefficients. The work functions and surface properties are predicted. The Te and Se based compounds could be of interest as absorber materials in photovoltaic applications. PMID:21937783

Olsson, P; Vidal, J; Lincot, D

2011-10-12

117

Small Au clusters oxidation: an ab initio study.  

Science.gov (United States)

We have performed ab initio calculations in the Density Functional Theory framework on unsupported small gold clusters with size ranging from three to seven atoms. In our calculations we have introduced a single O2 molecule on different places around the cluster surface, and in both parallel and perpendicular position with respect to the cluster surface. We have found that the oxygen molecule bonds in-plane with the bidimensional Au cluster when the number of Au atoms is even, and it will be adsorbed off-plane if the number of Au atoms is odd. The latter case, despite not presenting a true chemical bonding, has great stability due to spin pairing and electrostatic interactions, and the structures will be distorted respect to the geometry of their pure Au cluster equivalents. PMID:20355502

Botana, J; Pereiro, M; Baldomir, D; Serantes, D; Arias, J E

2010-04-01

118

Ab initio Potential Energy Surface for H-H2  

Science.gov (United States)

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

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

1993-01-01

119

Ab initio calculations of nuclear widths via an integral relation  

CERN Document Server

I describe the computation of energy widths of nuclear states using an integral over the interaction region of ab initio variational Monte Carlo wave functions, and I present calculated widths for many states. I begin by presenting relations that connect certain short-range integrals to widths. I then present predicted widths for 5 <= A <= 9 nuclei, and I compare them against measured widths. They match the data more closely and with less ambiguity than estimates based on spectroscopic factors. I consider the consequences of my results for identification of observed states in ^8B, ^9He, and ^9Li. I also examine failures of the method and conclude that they generally involve broad states and variational wave functions that are not strongly peaked in the interaction region. After examining bound-state overlap functions computed from a similar integral relation, I conclude that overlap calculations can diagnose cases in which computed widths should not be trusted.

Nollett, Kenneth M

2012-01-01

120

Ab initio design of laser pulse for controlling photochemical reactions  

International Nuclear Information System (INIS)

With high level ab initio description of molecule-field interaction, we have developed an optimal control algorithm for manipulating molecular transformation and quantum populations. High order molecule-field interactions are fully taken into account through the use of electric-nuclear Born-Oppenheimer (ENBO) approximation. The present algorithm is demonstrated on the control of molecular post-pulse (transient)alignment and orientation. High degrees of alignment and orientation are achieved in a vibrationally selective manner by optimized infrared laser pulses of duration on the order one rotational period of molecule. To reveal the control mechanism behind the complicated optimal pulses, an analytical pulse design method is developed within the ENBO approximation, which is based on a two-state treatment of the dynamics in a Floquet picture. This analytical method is also illustrated on the control of the alignment of homonuclear diatomics. (author)

2008-03-01

 
 
 
 
121

Improved Embedding Ab Initio Model Potentials for Embedded Cluster Calculations  

Science.gov (United States)

An improvement in the method of production of embedding ab initio model potentials (AIMP) for embedded cluster calculations in ionic solids is proposed and applied to the oxides CeAlO3, CeO2, and UO2. The improvement affects the calculation of one of the AIMP components, the Pauli repulsion operator, which prevents the cluster electrons from collapsing onto the occupied orbitals of the host in embedded cluster calculations and, so, their over occupancy. The linear constants involved in such operator are proposed to be obtained in embedded cluster calculations in the perfect host, with the requirement that local structures calculated with working embedded clusters of relatively small size agree with those calculated with reference embedded clusters of much larger size.

Pascual, José Luis; Barros, Noémi; Barandiarán, Zoila; Seijo, Luis

2009-06-01

122

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

CERN Multimedia

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

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

1999-01-01

123

Methane under pressure: dissociation reactions from ab initio simulation  

Science.gov (United States)

Using ab initio molecular dynamics [1], we have investigated the stability of methane under pressure up to ˜24 GPa and in the temperature range 2-4000 K, studied in recent diamond anvil cell experiments [2]. In particular, we have explored the possible formation of alkanes from methane dissociation. We have calculated structural and vibrational properties, and compared the relative stability of several hydrocarbons mixtures. Our results show that the temperature is the main driving force for methane dissociation, with pressure enhancing the formation of higher hydrocarbons, at temperatures where dissociation is observed. [1] Qbox code: http://eslab.ucsvais.edu [2] A. Kolesnikov, Kutcherov VG. and Goncharov AF. Nature Geoscience , (2009) 8 (566-570)

Hohl, Detlef; Spanu, Leonardo; Donadio, Davide; Schwegler, Eric; Gygi, Francois; Galli, Giulia

2010-03-01

124

Quantitative Verification of Ab Initio Self-consistent Laser Theory  

CERN Document Server

We generalize and test the recent "ab initio" self-consistent (AISC) time-independent semiclassical laser theory. This self-consistent formalism generates all the stationary lasing properties in the multimode regime (frequencies, thresholds, internal and external fields, output power and emission pattern) from simple inputs: the dielectric function of the passive cavity, the atomic transition frequency, and the transverse relaxation time of the lasing transition. We find that the theory gives excellent quantitative agreement with full time-dependent simulations of the Maxwell-Bloch equations after it has been generalized to drop the slowly-varying envelope approximation. The theory is infinite order in the non-linear hole-burning interaction; the widely used third order approximation is shown to fail badly.

Ge, Li; Stone, A Douglas; Türeci, Hakan E

2008-01-01

125

138 Electrical Impedance Spectroscopy of a Pig Odorant Binding Protein immobilized onto gold interdigited microelectrodes: an ab-initio study  

Science.gov (United States)

In this work, an ab-initio study of the electrical response to odorants of a self-assembled monolayer of a pig OBP immobilized onto a miniaturized Si-substrate equipped with gold interdigitated electrodes (IDE), was started. Electrical Impedance Spectroscopy (EIS) was used as electrical characterization technique and a dedicated experimental set-up was arranged in order to carry out EIS measurements in controlled environment. The EIS data was fitted by using a fitting software based on Levenberg-Marquardt (LEVM) algorithm to determine the equivalent circuit of the system.

Capone, S.; Francioso, L.; Siciliano, P.; Persaud, K.; Pisanelli, A. M.

2009-05-01

126

Ab initio study of alanine polypeptide chain twisting  

DEFF Research Database (Denmark)

We have investigated the potential energy surfaces for alanine chains consisting of three and six amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles ph$ and psi, which are widely used for the characterization of the polypeptide chains. These particular degrees of freedom are essential for the characterization of the proteins folding process. Calculations have been carried out within the ab initio theoretical framework based on the density functional theory and accounting for all the electrons in the system. We have determined stable conformations and calculated the energy barriers for transitions between them. Using a thermodynamic approach, we have estimated the times of characteristic transitions between these conformations. The results of our calculations have been compared with those obtained by other theoretical methods and with the available experimental data extracted from the Protein Data Base. This comparison demonstrates a reasonable correspondence of the most prominent minima on the calculated potential energy surfaces to the experimentally measured angles phi and psi for alanine chains appearing in native proteins. We have also investigated the influence of the secondary structure of polypeptide chains on the formation of the potential energy landscape. This analysis has been performed for the sheet and the helix conformations of chains of six amino acids.

Solov'yov, Ilia; Yakubovich, Alexander V.

2006-01-01

127

Valence quantum Monte Carlo with ab initio effective core potentials  

International Nuclear Information System (INIS)

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

128

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

129

Ab initio study of MgH2 formation  

International Nuclear Information System (INIS)

Even if there is considerable literature dealing with structure and properties of MgH2 compound there are still some uncertain details about nature of bonding governing its formation and decomposition. In order to better understand the processes essential for absorption and desorption of MgH2, ab initio DFT based calculations of rutile MgH2 compound, elemental hcp-Mg, and three different hypothetical hcp-Mg-derived hydrides are performed. Our findings show that all structures are unstable, and that MgH (Wurtzite) is a closest possible candidate for intermediate phase between the hcp-Mg and MgH2 at 1:1 stoichiometry. An alternative hydration pathway is suggested, including promotion of hcp-Mg to bcc-Mg and consecutive transformation to rutile MgH2 by means of hydrogen incorporation into Mg matrix. Rutile MgH2 calculations with various hydrogen vacancies concentration are performed. Calculation shows that at high hydrogen concentration close to 1:2, stable substoichiometric hydride is possible. Calculation also shows that high vacancy (low hydrogen) concentration favors bcc-Mg2H over rutile Mg2H structure.

2009-12-15

130

Towards highly accurate ab initio thermochemistry of larger systems: Benzene  

Science.gov (United States)

The high accuracy extrapolated ab initio thermochemistry (HEAT) protocol is applied to compute the total atomization energy (TAE) and the heat of formation of benzene. Large-scale coupled-cluster calculations with more than 1500 basis functions and 42 correlated electrons as well as zero-point energies based on full cubic and (semi)diagonal quartic force fields obtained with the coupled-cluster singles and doubles with perturbative treatment of the triples method and atomic natural orbital (ANO) triple- and quadruple-zeta basis sets are presented. The performance of modifications to the HEAT scheme and the scaling properties of its contributions with respect to the system size are investigated. A purely quantum-chemical TAE and associated conservative error bar of 5463.0 +/- 3.1 kJ mol-1 are obtained, while the corresponding 95% confidence interval, based on a statistical analysis of HEAT results for other and related molecules, is +/- 1.8 kJ mol-1. The heat of formation of benzene is determined to be 101.5 +/- 2.0 kJ mol-1 and 83.9 +/- 2.1 kJ mol-1 at 0 K and 298.15 K, respectively.

Harding, Michael E.; Vázquez, Juana; Gauss, Jürgen; Stanton, John F.; Kállay, Mihály

2011-07-01

131

Ab initio calculation of double ionization of atoms  

Energy Technology Data Exchange (ETDEWEB)

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

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

2013-02-15

132

Ab initio analysis of plasmon dispersion in sodium under pressure  

Science.gov (United States)

We present an ab initio study of the electronic response function of sodium in its five known metallic phases from 0 to 180 GPa at room temperature. The considered formalism is based on a interpolation scheme within time-dependent density functional theory that uses maximally localized Wannier functions, providing an accurate sampling of the reciprocal space. Besides showing an excellent agreement with inelastic x-ray scattering experiments [Phys. Rev. Lett. 107, 086402 (2011), 10.1103/PhysRevLett.107.086402, Proc. Natl. Acad. Sci. USA 108, 20434 (2011), 10.1073/pnas.1116930108], our calculations reveal that the drastic decrease of the optical reflectivity measured in the high pressure phases oP8 and tI19 [Proc. Natl. Acad. Sci. USA 106, 6525 (2009), 10.1073/pnas.0902062106] is associated with a new low-energy plasmon arising from collective interband excitations. Additionally, our calculations predict the existence of an anisotropic interband plasmon in the stability pressure range of fcc Na (65 to 105 GPa).

Ibañez-Azpiroz, Julen; Rousseau, Bruno; Eiguren, Asier; Bergara, Aitor

2014-02-01

133

Ab initio simulations on rutile-based titania nanowires  

International Nuclear Information System (INIS)

The rod symmetry groups for monoperiodic (1D) nanostructures have been applied for construction of models for bulk-like TiO2 nanowires (NWs) cut from a rutile-based 3D crystal along the chosen [001] and [110] directions of crystallographic axes. In this study, we have considered nanowires described by both the Ti-atom centered rotation axes as well as the hollow site centered axes passing through the interstitial positions between the Ti and O atoms closest to the axes. The most stable [001]-oriented TiO2 NWs with rhombic cross sections are found to display the energetically preferable {110} facets only while the nanowires with quasi-square sections across the [110] axis are formed by the alternating { 11-bar 0 } and {001} facets. For simulations on rutile-based nanowires possessing different diameters for each NW type, we have performed large-scale ab initio Density Functional Theory (DFT) and hybrid DFT-Hartree Fock (DFT-HF) calculations with total geometry optimization within the Generalized Gradient Approximation (GGA) in the form of the Perdew-Becke-Ernzenhof (PBE) exchange-correlation functionals (PBE and PBE0, respectively), using the formalism of linear combination of localized atomic functions (LCAO). We have simulated both structural and electronic properties of TiO2 NWs depending both on orientation and position of symmetry axes as well as on diameter and morphology of nanowires.

2012-08-20

134

An Ab Initio Based Potential Energy Surface for Water  

Science.gov (United States)

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

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

1996-01-01

135

Shock Wave Induced Melting of Tin: Ab-initio Study  

Science.gov (United States)

Two kinds of shock wave experiments [Mabire et al and Hu et al.] have been reported on the shock wave induced melting of tin. Measurement of particle velocity histories along with temperature employing radiation pyrometery suggested shock melting in tin to be at 50 GPa; whereas measurement of longitudinal sound velocity behind the shock front revealed the shock melting at lower pressure of 39 GPa. In the present study, we have carried out theoretical analysis to understand shock induced melting of tin. Employing ab-initio density functional method, we calculated 0 K isotherm and then constructed the shock Hugoniot by adding the thermal contributions to pressure. Our melting line, determined by employing the theoretically calculated volume dependent Gruneisen parameter in Lindeman melting rule, agrees well with that measured in diamond anvil cell experiments. The intersection of the melting line with Hugoniot in temperature versus pressure plot suggests melting of tin at 37 GPa supporting the experimental measurement of Hu et al. at 39 GPa.

Mukherjee, D.; Joshi, K. D.; Gupta, Satish C.

2011-07-01

136

Ab initio calculation of anisotropic interfacial excess free energies  

Science.gov (United States)

We describe a simple method to determine, from ab initio calculations, the complete orientation dependence of interfacial free energies in solid-state crystalline systems. We illustrate the method with an application to precipitates in the Al-Ti alloy system. The method combines the cluster expansion formalism in its most general form (to model the system's energetics) with the inversion of the well known Wulff construction (to recover interfacial energies from equilibrium precipitate shapes). Although the inverse Wulff construction only provides the relative magnitude of the various interfacial free energies, absolute free energies can be recovered from a calculation of a single, conveniently chosen, planar interface. The method is able to account for essentially all sources of entropy (arising from phonons, bulk point defects, as well as interface roughness) and is thus able to transparently handle both atomically smooth and rough interfaces. The approach expresses the resulting orientation dependence of the interfacial properties using symmetry adapted bases for general orientation dependent quantities. As a byproduct, this paper thus provides a simple and general method to generate such basis functions, which prove useful in a variety of other applications, for instance to represent the anisotropy of the so-called constituent strain elastic energy.

van de Walle, A.; Hong, Q.; Miljacic, L.; Gopal, C. Balaji; Demers, S.; Pomrehn, G.; Kowalski, A.; Tiwary, P.

2014-05-01

137

Improved ab initio effective core potentials for molecular calculations  

International Nuclear Information System (INIS)

We have investigated the sources of error in bond lengths and dissociation energies computed from ab initio effective potentials derived from Phillips--Kleinman type pseudo-orbitals. We propose an alternate pseudo-orbital, effective potential treatment with the primary objective of agreement with all-electron molecular calculations. This new treatment forces the pseudo-orbitals to match precisely the Hartree--Fock orbitals in the valence region and thereby eliminates the major cause of error in the earlier calculations. Effective core potentials derived from these revised pseudo-orbitals were used to compute potential energy curves for the ground states of F2, Cl2, and LiCl and the results are compared with previous all-electron and effective potential calculations. Our effective potentials yield dissociation energies and bond lengths which are in excellent agreement with the all-electron values. Furthermore, in contrast to other procedures, our revised effective potentials result in an excellent description of the inner repulsive walls of the dissociation curves

1979-12-01

138

Nature of magnetism in iron pnictides: an ab initio study  

International Nuclear Information System (INIS)

While it is commonly believed that magnetic-mediate pairing is the source of superconductivity in the iron-based superconductors, the nature of magnetism is still under debate. We apply ab initio molecular dynamics to investigate physical properties of LaOFePn, BaFe2Pn2 and LiFePn (Pn=As,Sb), so-called 1111, 122 and 111 compounds, respectively. We find that, with substitution of As by Sb, the stripe-type antiferromagnetic orderings are always enhanced. By calculating Pauli susceptibility, we attribute the enhancement of magnetization to the increase of instability at (?,?) when As is substituted by Sb. Furthermore, we study the magnetic and lattice properties of LaOFePn (Pn=P,As,Sb,Bi) as well as ScOFeP, ScOFeAs and YOFeP and argue that LaOFeSb would be a candidate for a superconductor with highest transition temperature among the investigated compounds. We further suggest that the absence of antiferromagnetic phase in LaOFeP and the presence in LaOFeAs are due to the competition of instability in Pauli susceptibility between (?,?) and (0,0) and therefore argue that superconductivity can only occur through doping in LaOFeSb.

2010-03-21

139

Ab initio modeling of the motional Stark effect on MAST  

International Nuclear Information System (INIS)

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

2008-10-01

140

Ab initio modeling of the motional Stark effect on MAST.  

Science.gov (United States)

A multichord motional Stark effect (MSE) system has recently been built on the MAST tokamak. In MAST the pi and sigma lines of the MSE spectrum overlap due to the low magnetic field typical for present day spherical tokamaks. Also, the field curvature results in a large change in the pitch angle over the observation volume. The measured polarization angle does not relate to one local pitch angle but to an integration over all pitch angles in the observation volume. The velocity distribution of the neutral beam further complicates the measurement. To take into account volume effects and velocity distribution, an ab initio code was written that simulates the MSE spectrum on MAST. The code is modular and can easily be adjusted for other tokamaks. The code returns the intensity, polarized fraction, and polarization angle as a function of wavelength. Results of the code are presented, showing the effect on depolarization and wavelength dependence of the polarization angle. The code is used to optimize the design and calibration of the MSE diagnostic. PMID:19044669

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

2008-10-01

 
 
 
 
141

Ab initio SCF calculations on hydrogen bonded cresol isomers  

Science.gov (United States)

Ab initio GAUSSIAN 80 calculations with two different basis sets (STO-3G and 4 31 G*) were performed on hydrogen bonded cresol isomers for comparison with experimental data from free jet fluorescence excitation spectroscopy. For m-cresol, the calculated barriers for hindered internal rotation of the OH-group and the CH3-group are in good agreement with experiment. The calculations show the trans-linear configuration of p-cresol· B-clusters ( B = H2O, CH3OH) to be more stable than the all-planar configuration. This agrees with CI calculations and microwave spectroscopic investigations of the water dimer. Calculations of both the intermolecular stretch and bend frequencies of p-cresol· B-clusters show little dependence on the all-planar or trans-linear configuration but a strong dependence on the choice of the basis set. With the minimal basis set STO-3G, the vibrational energies are generally too high. The agreement between the calculated vibrational frequencies from the 4 31 G* basis set and the experimental values is fair.

Pohl, M.; Kleinermanns, K.

1988-12-01

142

Ab-initio longitudinal response function of {sup 4}He  

Energy Technology Data Exchange (ETDEWEB)

We report on our recent ab-initio calculation of the inclusive longitudinal electron scattering off {sup 4}He with two- and three-nucleon forces. The full four-body continuum dynamics is considered exactly via the Lorentz integral transform method. We show results for various kinematics up to q=500 MeV/c and compare it with available experimental data. The great importance of the final state interaction is demonstrated. The plane wave impulse approximation particularly fails in the quasi-elastic peak at low energies. The effect of the three-nucleon force results in the reduction of the quasi-elastic peak by 10% for momentum transfers q between 300 and 500 MeV/c. A good agreement with experimental data is found in the peak region. Only at q=500 MeV/c some discrepancies between theory and experiment are present in the low- and high-energy range. Interestingly, the effect of the three-nucleon force increases significantly at lower q, up to about 40% at q=100 MeV/c. Our findings suggest that the longitudinal response function is an electromagnetic observable, where one can learn about the not yet well established three-nucleon force. Unfortunately, at low momentum transfer experimental data are still missing.

Bacca, Sonia [TRIUMF, Vancouver, B.C. (Canada); Barnea, Nir [Racah Institute of Physics, Hebrew University, Jerusalem (Israel); Leidemann, Winfried; Orlandini, Giuseppina [Dipartimento di Fisica, Universita di Trento (Italy); INFN, Trento (Italy)

2009-07-01

143

Ab-initio longitudinal response function of 4He  

International Nuclear Information System (INIS)

We report on our recent ab-initio calculation of the inclusive longitudinal electron scattering off 4He with two- and three-nucleon forces. The full four-body continuum dynamics is considered exactly via the Lorentz integral transform method. We show results for various kinematics up to q=500 MeV/c and compare it with available experimental data. The great importance of the final state interaction is demonstrated. The plane wave impulse approximation particularly fails in the quasi-elastic peak at low energies. The effect of the three-nucleon force results in the reduction of the quasi-elastic peak by 10% for momentum transfers q between 300 and 500 MeV/c. A good agreement with experimental data is found in the peak region. Only at q=500 MeV/c some discrepancies between theory and experiment are present in the low- and high-energy range. Interestingly, the effect of the three-nucleon force increases significantly at lower q, up to about 40% at q=100 MeV/c. Our findings suggest that the longitudinal response function is an electromagnetic observable, where one can learn about the not yet well established three-nucleon force. Unfortunately, at low momentum transfer experimental data are still missing.

2009-03-16

144

FTIR, Raman spectra and ab initio calculations of 2-mercaptobenzothiazole.  

Science.gov (United States)

FTIR and Raman spectra of a rubber vulcanization accelerator, 2-mercaptobenzothiazole (MBT), were recorded in the solid phase. The harmonic vibrational wavenumbers, for both the toutomeric forms of MBT, as well as for its dimeric complex, have been calculated, using ab initio RHF and density functional B3LYP methods invoking different basis sets upto RHF/6-31G** and B3LYP/6-31G** and the results were compared with the experimental values. Conformational studies have been also carried out regarding its toutomeric monomer forms and its dimer form. With all the basis sets the thione form of MBT (II) is predicted to be more stable than thiol form (I) and dimeric conformation (III) is predicted to be more stable with monomeric conformations (I) and (II). Vibrational assignments have been made, and it has been found that the calculated normal mode frequencies of dimeric conformation (III) are required for the analysis of IR and Raman bands of the MBT. The predicted shift in NH- stretching vibration towards the lower wave number side with the B3LYP/6-31G** calculations for the most stable dimer form (III), is in better agreement with experimental results. The intermolecular sulfur-nitrogen distance in N-H...S hydrogen bond was found to be 3.35 angstroms from these calculations, is also in agreement to the experimental value. PMID:16098806

Rai, Amareshwar K; Singh, Rachana; Singh, K N; Singh, V B

2006-02-01

145

Ab initio study of edge sites reactivity on pyrophyllite  

International Nuclear Information System (INIS)

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

2005-03-14

146

Ab initio study of edge sites reactivity on pyrophyllite  

Energy Technology Data Exchange (ETDEWEB)

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

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

2005-07-01

147

Experimental, ab initio and density functional theory studies on sulfadiazine  

Science.gov (United States)

In the present study, combined experimental and computational study on molecular vibrations of free sulfadiazine has been reported. The theoretically possible stable conformers of free sulfadiazine molecule in electronically ground state were searched by means of torsion potential energy surfaces scan studies through C1 sbnd C7 sbnd S8 sbnd N8, C7 sbnd S8 sbnd N9 sbnd C10 and S8 sbnd N9 sbnd C10 sbnd N11 dihedral angles, at both semi-empirical PM3 and B3LYP/3-21G levels of theory. The final geometrical parameters for the obtained stable conformers were determined by means of geometry optimization carried out at ab initio HF/6-31G++(d,p) and DFT/B3LYP/6-31G++(d,p) theory levels. The harmonic and anharmonic vibrational wavenumbers and IR intensities were calculated at the same theory levels used in geometry optimization. The modes of the fundamental vibrations were characterized depending on their the total energy distribution (TED%). In order to fit the calculated harmonic wavenumbers to experimental ones, dual scale factors were used. The experimental infrared and Raman spectra of sulfadiazine in solid phase have been measured and compared with the calculated vibrational spectra of each conformer.

Ogruc-Ildiz, Gulce; Akyuz, Sevim; Ozel, Aysen E.

2009-04-01

148

Accurate ab initio-based molecular potentials: from extrapolation methods to global modelling  

International Nuclear Information System (INIS)

Accurate molecular potentials are key in theoretical chemical physics and therefore demands for suitable modelling strategies remain pressing. In this combination of a review and new results, we shall address methods to: (i) extrapolate to the one-electron basis set limit, (ii) predict a higher-quality ab initio potential by electron correlation scaling and (iii) refine iteratively an ab initio-based potential through variational calculations to reach near spectroscopic accuracy

2007-09-01

149

Ab initio simulations of thermal decomposition and of electron transfer reactions in room temperature ionic liquids.  

Science.gov (United States)

Selected aspects of the ab initio modelling of room temperature ionic liquids are discussed in our contribution, focusing on thermal decomposition reactions, and on the determination of the electrochemical stability window of these compounds. In both cases, we emphasise the role of ab initio simulation methods, able to deal simultaneously with the ionic and electronic side of the systems and phenomena under investigation. PMID:22455031

Ballone, Pietro; Cortes-Huerto, Robinson

2012-01-01

150

Ab initio determination of heavy oxide perovskite related structures from precession electron diffraction data  

International Nuclear Information System (INIS)

Two complex perovskite-related structures were solved by ab initio from precession electron diffraction intensities. Structure models were firstly derived from HREM images and than have been confirmed independently using two and three-dimensional sets of precession intensities. Patterson techniques prove to be effective for ab initio structure resolution, specially in case of projections with no overlapping atoms. Quality of precession intensity data may be suitable enough to resolve unknown heavy oxide structures

2007-06-01

151

Ab initio determination of heavy oxide perovskite related structures from precession electron diffraction data  

Energy Technology Data Exchange (ETDEWEB)

Two complex perovskite-related structures were solved by ab initio from precession electron diffraction intensities. Structure models were firstly derived from HREM images and than have been confirmed independently using two and three-dimensional sets of precession intensities. Patterson techniques prove to be effective for ab initio structure resolution, specially in case of projections with no overlapping atoms. Quality of precession intensity data may be suitable enough to resolve unknown heavy oxide structures.

Boulahya, Khalid; Ruiz-Gonzalez, Luisa; Parras, Marina [Dpto. Quimica Inorganica, Facultad de Ciencias Quimicas, Universidad Complutense de Madrid, E28040 Madrid (Spain); Gonzalez-Calbet, Jose M. [Dpto. Quimica Inorganica, Facultad de Ciencias Quimicas, Universidad Complutense de Madrid, E28040 Madrid (Spain)], E-mail: jgcalbet@quim.ucm.es; Nickolsky, M.S. [NanoMEGAS, Boulevard Edmond Machtens 79, Brussels B-1080 (Belgium); Nicolopoulos, Stavros [Universidad Politecnica de Valencia/ITQ Avda de los Naranjos, Valencia 46022 (Spain); NanoMEGAS, Boulevard Edmond Machtens 79, Brussels B-1080 (Belgium)], E-mail: info@nanomegas.com

2007-06-15

152

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

An ab initio equation of motion method is introduced to calculate the temperature-dependent mean square vibrational amplitudes which appear in the Debye-Waller factors in x-ray absorption, x-ray scattering, and related spectra. The approach avoids explicit calculations of phonon-modes, and is based instead on calculations of the displacement-displacement time correlation function from ab initio density functional theory molecular dynamics simulations. The method also yields ...

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

2011-01-01

153

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

2012-01-01

154

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

155

Symplectic ab initio no-core shell model  

Scientific Electronic Library Online (English)

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

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

156

AN AB INITIO MODEL FOR COSMIC-RAY MODULATION  

Energy Technology Data Exchange (ETDEWEB)

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

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

2013-07-20

157

An ab initio study of plutonium oxides surfaces  

International Nuclear Information System (INIS)

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

2007-01-01

158

Ab Initio Study of Thermodynamic Properties of Lithium, Sodium, and Potassium Sulfates  

Science.gov (United States)

The thermodynamic parameters of lithium, sodium, and potassium single and double sulfate crystals are determined by the method of ab initio calculation of a linear combination of atomic orbitals in the gradient approximation of density functional theory using the software package CRYSTAL09 within the framework of the quasi-harmonic approximation of the Debye theory. It is demonstrated that the standard entropies and heat capacities as well as the temperature dependences are in satisfactory agreement with the available experimental data. The average frequency, Debye temperature, and thermal conductivity coefficient increase with external pressure, whereas the Gruneisen parameter decreases. The dependences of the potentials of free and internal energies on the temperature and volume are expressed through the Birch-Murnaghan equation of state and a square-law dependence on these parameters of their vibrational components. The thermodynamic parameters of lithium-potassium sulfate appear closer to potassium sulfate, whereas for sodium-potassium, they lie between the corresponding parameters for single compounds.

Zhuravlev, Yu. N.; Bugaeva, I. A.; Zhuravleva, L. V.

2013-11-01

159

Ab initio analysis of the BCN, NBC and CNB fragments formation  

Science.gov (United States)

The Laser Ablation technique applied to the synthesis of nano-structured materials produce unique compositions, with correspondingly unique physical and chemical properties. In order to do smart utilization of this method, fundamental understanding of the precursor formation and incorporation mechanisms for the growth of different materials is crucial. Particularly important is to know what fragments are formed during the ablation process, in order to understand its dynamic evolution and eventual incorporation in the synthesized material. In connection to the synthesis of Boron Carbonitride, we have focused our attention on the dynamic evolution of the primary reactions upon BCN ablation using the ab initio method (Gaussian-98 software pack). The results (including the formation energy, direct and inverse rate constants, etc.) were estimated by considering the elementary reactions as bimolecular reactions: reactions between atoms, and atoms with diatomic molecules. The temperature dependence of the dissociation rate constant of three-atomic fragments by different channels was also analyzed using the RRKM theory. It was found that BCN and NBC are the most thermodynamically stable fragments. This theoretical analysis helps understand the strong tendency for BCN to grow stoichiometrically under a variety of experimental conditions.

Jara, Robert; Makarov, Vladimir; Morell, Gerardo; Weiner, Brad

2006-03-01

160

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

 
 
 
 
161

Ab initio calculation of molecular energies including parity violating interactions  

International Nuclear Information System (INIS)

A new approach, RHF-CIS, based on the perturbation of the ground state RHF wave function by the CIS excitations, has been implemented for evaluation of energy of parity violating interaction in molecules, Epv. The earlier approach, RHF-SDE, was based on the perturbation of the RHF ground states by the single-determinant ''excitations'' (SDE). The results obtained show the dramatic difference between Epv values in the RHF-CIS framework and those in the RHF-SDE framework: the Epv values of the RHF-CIS formalism are more than one order of magnitude greater compared to the RHF-SDE formalism as well as the corresponding tensor components. The maximal total value obtained for hydrogen peroxide in the RHF-CIS framework is 3.661 X 10-19 EH (DZ** basis set) while the maximal Epv value for the RHF-SDE formalism is just 3.635 X 10-20 EH (TZ basis set). It is remarkable that both in the RFH-CIS and in the RHF-SDE approaches the diagonal tensor components of Epv strictly follow the geometry of a molecule and are always different from zero at chiral conformations. The zeros of the total Epv at chiral geometries are now found to be the results of the interplay between the diagonal tensor components values. We have carried out exhaustive analysis of the RHF-SDE formalism and found that it is not sufficiently accurate for studies of Epv. To this end, we have completely reproduced the previous work, which has been done in the RHF-SDE frame-work, and developed it further, studying how the RHF-SDE results vary when changing size and quality of basis sets. This last resource does not save the RHF-SDE formalism for evaluations of Epv from the general failure. Packages of FORTRAN routines called ENWEAK/RHFSDE-93 and ENWEAK/RHFCIS-94 have been developed which run on top of an ab initio MO package. We used 6-31G and 6-31G**, DZ and DZ**, TZ and TZ**, and (10s, 6p,**) basis sets. We will discuss the importance of the present results for possible measurement of the parity violating energy difference between enantiomers of chiral molecules. (author). Abstract only

1995-08-01

162

Ab initio and DFT studies of the vibrational spectra of benzofuran and some of its derivatives  

Science.gov (United States)

The vibrational spectra of benzofuran and some of its derivatives have been systematically investigated by ab initio and density functional B3LYP methods. The harmonic vibrational wavenumbers and intensity of vibrational bands were calculated at ab initio and DFT levels invoking different basis sets up to 6-311++g**. Vibrational assignments have been made and it has been found that the calculated DFT frequencies agree well in most cases with the observed frequencies for each molecule. Conformational studies have also been carried out and it is evident from ab initio calculations that 2(3H) benzofuranone is more stable than 3(2H) benzofuranone in support to our earlier semiempirical results.

Singh, V. B.

2006-12-01

163

Classical and ab initio molecular dynamic simulation of an amorphous silica surface  

CERN Document Server

We present the results of a classical molecular dynamic simulation as well as of an ab initio molecular dynamic simulation of an amorphous silica surface. In the case of the classical simulation we use the potential proposed by van Beest et al. (BKS) whereas the ab initio simulation is done with a Car-Parrinello method (CPMD). We find that the surfaces generated by BKS have a higher concentration of defects (e.g. concentration of two-membered rings) than those generated with CPMD. In addition also the distribution functions of the angles and of the distances are different for the short rings. Hence we conclude that whereas the BKS potential is able to reproduce correctly the surface on the length scale beyond approx 5 Angstroems, it is necessary to use an ab initio method to predict reliably the structure at small scales.

Mischler, C; Binder, K; Mischler, Claus; Kob, Walter; Binder, Kurt

2002-01-01

164

Multiobjective evolutionary algorithm with many tables for purely ab initio protein structure prediction.  

Science.gov (United States)

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

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

2013-07-30

165

Ab initio modelling of UN grain boundary interfaces  

International Nuclear Information System (INIS)

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

2012-08-20

166

Exploring the ab initio/classical free energy perturbation method: The hydration free energy of water  

International Nuclear Information System (INIS)

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

2000-08-15

167

Exploring the ab initio/classical free energy perturbation method: The hydration free energy of water  

Energy Technology Data Exchange (ETDEWEB)

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

Sakane, Shinichi [Department of Chemistry and Biochemistry, and Center for Molecular and Engineering Thermodynamics, University of Delaware, Newark, Delaware 19716 (United States); Yezdimer, Eric M. [Department of Chemistry and Biochemistry, and Center for Molecular and Engineering Thermodynamics, University of Delaware, Newark, Delaware 19716 (United States); Liu, Wenbin [Department of Chemistry and Biochemistry, and Center for Molecular and Engineering Thermodynamics, University of Delaware, Newark, Delaware 19716 (United States); Barriocanal, Jose A. [Department of Chemistry and Biochemistry, and Center for Molecular and Engineering Thermodynamics, University of Delaware, Newark, Delaware 19716 (United States); Doren, Douglas J. [Department of Chemistry and Biochemistry, and Center for Molecular and Engineering Thermodynamics, University of Delaware, Newark, Delaware 19716 (United States); Wood, Robert H. [Department of Chemistry and Biochemistry, and Center for Molecular and Engineering Thermodynamics, University of Delaware, Newark, Delaware 19716 (United States)

2000-08-15

168

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

2007-12-01

169

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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 t...

Lopuszynski, Michal; Majewski, Jacek A.

2007-01-01

170

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

171

Development of a computer program for the determination of force field parameters derived from ab initio pes  

International Nuclear Information System (INIS)

A computer program has been developed in our laboratories for the parameter determination using energy, gradient and hessian values obtained by ab initio calculations. The empirical potential is fitted to the ab initio PES. (AIP) copyright 1995 American Institute of Physics

1995-04-01

172

Iron under Earth’s core conditions: Liquid-state thermodynamics and high-pressure melting curve from ab initio calculations  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Ab initio techniques based on density functional theory in the projector-augmented-wave implementation are used to calculate the free energy and a range of other thermodynamic properties of liquid iron at high pressures and temperatures relevant to the Earth’s core. The ab initio free energy is obtained by using thermodynamic integration to calculate the change of free energy on going from a simple reference system to the ab initio system, with thermal averages computed by ab initio molecul...

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

2002-01-01

173

Unraveling the structure of the h-BN/Rh(111) nanomesh with ab initio calculations  

International Nuclear Information System (INIS)

The properties of a single layer of h-BN on top of a Rh(111) surface are discussed in terms of an ab initio generated force field approach as well as by direct ab initio density-functional theory (DFT) calculations. A single-layer model for the h-BN/Rh(111) nanomesh, in contrast to a previously considered (incomplete) double-layer model of h-BN, can explain the experimental data. The main focus of this work is to compare a force field approach described earlier in (Laskowski et al 2007 Phys. Rev. Lett. 98 106802) with direct ab initio calculations. The calculated geometry of the h-BN layer is very similar to the structure predicted by the force field approach. The ab initio calculated density of states projected on N-px,y of BN corresponding to 'low' and 'high' regions with respect to the Rh surface shows a 1 eV splitting and thus explains the observed ?-band splitting. Moreover, we find good agreement between calculated and experimental scanning tunneling microscope (STM) images of this system

2008-02-13

174

Unraveling the structure of the h-BN/Rh(111) nanomesh with ab initio calculations  

Science.gov (United States)

The properties of a single layer of h-BN on top of a Rh(111) surface are discussed in terms of an ab initio generated force field approach as well as by direct ab initio density-functional theory (DFT) calculations. A single-layer model for the h-BN/Rh(111) nanomesh, in contrast to a previously considered (incomplete) double-layer model of h-BN, can explain the experimental data. The main focus of this work is to compare a force field approach described earlier in (Laskowski et al 2007 Phys. Rev. Lett. 98 106802) with direct ab initio calculations. The calculated geometry of the h-BN layer is very similar to the structure predicted by the force field approach. The ab initio calculated density of states projected on N-px,y of BN corresponding to 'low' and 'high' regions with respect to the Rh surface shows a 1 eV splitting and thus explains the observed ?-band splitting. Moreover, we find good agreement between calculated and experimental scanning tunneling microscope (STM) images of this system.

Laskowski, R.; Blaha, P.

2008-02-01

175

Unraveling the structure of the h-BN/Rh(111) nanomesh with ab initio calculations  

Energy Technology Data Exchange (ETDEWEB)

The properties of a single layer of h-BN on top of a Rh(111) surface are discussed in terms of an ab initio generated force field approach as well as by direct ab initio density-functional theory (DFT) calculations. A single-layer model for the h-BN/Rh(111) nanomesh, in contrast to a previously considered (incomplete) double-layer model of h-BN, can explain the experimental data. The main focus of this work is to compare a force field approach described earlier in (Laskowski et al 2007 Phys. Rev. Lett. 98 106802) with direct ab initio calculations. The calculated geometry of the h-BN layer is very similar to the structure predicted by the force field approach. The ab initio calculated density of states projected on N-p{sub x,y} of BN corresponding to 'low' and 'high' regions with respect to the Rh surface shows a 1 eV splitting and thus explains the observed {sigma}-band splitting. Moreover, we find good agreement between calculated and experimental scanning tunneling microscope (STM) images of this system.

Laskowski, R; Blaha, P [Institute of Materials Chemistry, Vienna University of Technology, A-1060 Vienna (Austria)

2008-02-13

176

Conformational properties of molecules by ab initio quantum mechanical energy minimization.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The recent literature on the determination of minimum energy conformations by ab initio quantum mechanical techniques is reviewed. The availability of computer-coded analytical first and second derivatives of the Hartree-Fock energy makes possible calculations that will be of significant assistance in structure determination of molecules. A short review of recent progress in empirical energy minimization and molecular dynamics is provided.

1985-01-01

177

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

Science.gov (United States)

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

Halpern, Arthur M.

2011-01-01

178

Ab initio studies of elastic properties and electronic structures of C and BN nanotubes  

Science.gov (United States)

The elastic properties and electronic structures of single-walled nanotubes (SWNTs) are studied using the ab initio package CRYSTAL-03. It is found that the Young modulus correlates strongly with the tube's electronic structure. The study reveals that a semiconductor-metal transition can be induced by uniaxial stress for carbon nanotubes, whereas this transition is not observed for boron nitride nanotubes.

Peng, Yong-Jin; Zhang, Li-Yun; Jin, Qing-Hua; Li, Bao-Hui; Ding, Da-Tong

2006-06-01

179

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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, Ludger

2007-01-01

180

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

 
 
 
 
181

Vibrational Properties of Hexagonal Boron Nitride: Inelastic X-Ray Scattering and Ab Initio Calculations  

International Nuclear Information System (INIS)

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

2007-03-02

182

Ab initio calculation of the lifetimes of 4p and 3d levels of Ca"+  

International Nuclear Information System (INIS)

We have done an ab initio calculation based on the Brueckner approximation for the lifetimes of 4p"2P and 3d"2D levels of Ca"+. The results of the Brueckner approximation differ from experiment by 2.5%. With leading third-order corrections included, our results agree with the latest accurate experiment within a 1% difference

1995-03-01

183

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

DEFF Research Database (Denmark)

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

Castelli, Ivano E.

2012-01-01

184

The Raman Spectrum of Triclinic Albite: A Comparison Between Ab Initio Calculated and Measured Frequencies  

Science.gov (United States)

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

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

2014-06-01

185

Ab initio investigations of Mg diffusion in ZnMgO  

Energy Technology Data Exchange (ETDEWEB)

We present ab initio calculations of possible diffusion paths for a single Mg atom in a ZnMgO supercell. Simple models are selected for the diffusion paths. We further estimate the energetic barrier by assuming that thermal energy at room temperature and elevated temperature suffices to activate the diffusion within the structure.

Giar, Marcel; Heiliger, Christian [I. Physikalisches Institut, Justus-Liebig-Universitaet, D-35392 Giessen (Germany)

2011-07-01

186

Raman and infrared spectra of minerals from ab initio molecular dynamics simulations: The spodumene crystal  

Science.gov (United States)

Ab initio molecular dynamics simulations with the Car-Parrinello method have been performed on the spodumene crystal at standard conditions and high pressure. Starting from the computed trajectories, accurate Raman and infrared spectra have been obtained and compared with available experimental measurements in the low and high pressure phases. The structural and spectroscopic changes due to the pressure effects are discussed.

Pagliai, Marco; Muniz-Miranda, Maurizio; Cardini, Gianni; Schettino, Vincenzo

2011-05-01

187

Paramagnetic Moessbauer relaxation spectra by simple ab initio and stochastic models  

International Nuclear Information System (INIS)

The stochastic and ab initio (resolvent) methods for the calculation of Moessbauer relaxation spectra are shortly reviewed. The relaxation matrix based on a first order dynamical Hamiltonian is calculated and corresponding simulations are presented. The spin-phonon interaction spectral bath densities are calculated in the Debye approximation for the direct one and two phonon processes. Some least squares fits are presented. (orig.)

1994-02-01

188

An ab initio study of native defects in cubic SiC: vacancies and stacking faults  

Energy Technology Data Exchange (ETDEWEB)

We present results of ab initio calculations for the atomic geometry, the energetics, and the electronic structure of native defects in cubic SiC. The calculations are performed in the framework of the density-functional theory in its local version using a plane-wave-pseudopotential code. Vacancies and stacking faults are considered as examples. (orig.) 14 refs.

Zywietz, A.; Kaeckell, P.; Furthmueller, J.; Bechstedt, F. [Jena Univ. (Germany). Inst. fuer Festkoerpertheorie und Theoretische Optik

1998-06-01

189

Modeling 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 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) [French] Resume: Un verre de composition 67 % SiO{sub 2} - 12 % Al{sub 2}O{sub 3} - 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 AIO{sub 3} 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 H{sub 2}O. (auteur)

Ganster, P.

2004-10-21

190

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

2003-08-01

191

Ab initio calculations on hydrogen storage in porous carbons; Calculs ab initio pour le storage de l'hydrogene dans les carbones poreux  

Energy Technology Data Exchange (ETDEWEB)

We have investigated through ab initio computations the possible ways to achieve efficient hydrogen storage on carbons. Firstly, we have considered how the curvature of a carbon surface could affect the chemisorption of atomic H{sup 0} Secondly, we show that electron donor elements such as Li and K, used as dopants for the carbon substrate, strongly enhance the physi-sorption energy of H{sub 2}, allowing in principle its storage in this type of material at room temperature under mild conditions of pressure. (authors)

Maresca, O. [Universitat Autonoma de Barcelona, Unitat de Quimica Fisica, Catalonia (Spain); Marinelli, F. [Universite de Provence et CNRS, Lab. de Physique des Interactions Ioniques et Moleculaires, Centre Saint-Jerome, 13 - Marseille (France); Pellenq, R.J.M. [Centre de Recherches en Matiere Condensee et Nanosciences, CNRS, 13 - Marseille (France); Duclaux, L.; Azais, Ph.; Conard, J. [Orleans Univ. et CNRS, Centre de Recherches sur la Matiere Divisees, 45 (France)

2005-08-01

192

Vibrational properties of a sodium tetrasilicate glass: Ab initio versus Classical Force Fields  

CERN Document Server

We compare some vibrational properties of a sodium tetrasilicate (Na$_{2}$Si$_{4}$O$_{9}$) glass model generated by molecular dynamics simulations. The vibrational study has been carried out using a classical valence force fields approach as well as an {\\it ab initio} approach in the framework of the density functional theory. The total and partial vibrational densities of states (VDOS) are presented, and some characteristics of the vibrational modes (participation ratios, correlation lengths) are determined using both approaches. We find that the shapes of the two calculated VDOS as well as those of their corresponding partial VDOS are quite similar, especially for a low-frequency band below 550 cm${}^{-1}$. For the intermediate- and high-frequency ranges, we observe larger discrepencies between the two calculations. Polarized Raman spectra are also calculated from the {\\it ab initio} and the valence-force-field eigenvectors in the bond-polarizability approximation. We find an overall agreement between the c...

Ispas, S; De Wispelaere, S; Kob, W

2003-01-01

193

Optimized Unrestricted Kohn-Sham Potentials from Ab Initio Spin Densities  

CERN Document Server

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

Boguslawski, Katharina; Reiher, Markus

2012-01-01

194

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

195

An ab initio dynamics study of the CH3Cl + OH reaction  

International Nuclear Information System (INIS)

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

2005-06-06

196

{\\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

197

Knockout reactions from p-shell nuclei: tests of ab initio structure models.  

Science.gov (United States)

Absolute cross sections have been determined following single neutron knockout reactions from 10Be and 10C at intermediate energy. Nucleon density distributions and bound-state wave function overlaps obtained from both variational Monte Carlo (VMC) and no core shell model (NCSM) ab initio calculations have been incorporated into the theoretical description of knockout reactions. Comparison to experimental cross sections demonstrates that the VMC approach, with the inclusion of 3-body forces, provides the best overall agreement while the NCSM and conventional shell-model calculations both overpredict the cross sections by 20% to 30% for 10Be and by 40% to 50% for 10C, respectively. This study gains new insight into the importance of 3-body forces and continuum effects in light nuclei and provides a sensitive technique to assess the accuracy of ab initio calculations for describing these effects. PMID:21599362

Grinyer, G F; Bazin, D; Gade, A; Tostevin, J A; Adrich, P; Bowen, M D; Brown, B A; Campbell, C M; Cook, J M; Glasmacher, T; McDaniel, S; Navrátil, P; Obertelli, A; Quaglioni, S; Siwek, K; Terry, J R; Weisshaar, D; Wiringa, R B

2011-04-22

198

Knockout reactions from p-shell nuclei : tests of ab initio structure models.  

Energy Technology Data Exchange (ETDEWEB)

Absolute cross sections have been determined following single neutron knockout reactions from {sup 10}Be and {sup 10}C at intermediate energy. Nucleon density distributions and bound-state wave function overlaps obtained from both variational Monte Carlo (VMC) and no core shell model (NCSM) ab initio calculations have been incorporated into the theoretical description of knockout reactions. Comparison to experimental cross sections demonstrates that the VMC approach, with the inclusion of 3-body forces, provides the best overall agreement while the NCSM and conventional shell-model calculations both overpredict the cross sections by 20% to 30% for {sup 10}Be and by 40% to 50% for {sup 10}C, respectively. This study gains new insight into the importance of 3-body forces and continuum effects in light nuclei and provides a sensitive technique to assess the accuracy of ab initio calculations for describing these effects.

Grinyer, G. F.; Bazin, D.; Gade, A.; Tostevin, J. A.; Adrich, P.; Bowen, M. D.; Brown, B. A.; Campbell, C. M.; Cook, J. M.; Glasmacher, T.; McDaniel, S.; Navratil, P.; Obertelli, A.; Quaglioni, S.; Siwek, K.; Terry, J. R.; Weisshaar, D.; Wiringa, R. B. (Physics); (Michigan State Univ.); (Univ. of Surrey); (LLNL)

2011-04-22

199

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

Science.gov (United States)

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

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

1998-08-01

200

Low-temperature metallic liquid hydrogen: an ab-initio path-integral molecular dynamics perspective  

Science.gov (United States)

Experiments and computer simulations have shown that the melting temperature of solid hydrogen drops with pressure above about 65 GPa, suggesting that a low temperature liquid state might exist. It has also been suggested that this liquid state might be non-molecular and metallic, although evidence for such behaviour is lacking. Using a combination of ab initio path-integral molecular dynamics and the two-phase methods, we have simulated the melting of solid hydrogen under finite temperatures. We found an atomic solid phase from 500 to 800 GPa which melts at 200 K. Beyond this and up to pressures of 1,200 GPa a metallic atomic liquid is stable at temperatures as low as 50 K. The quantum motion of the protons is critical to the low melting temperature in this system as ab initio simulations with classical nuclei lead to a considerably higher melting temperature of ˜300 K across the entire pressure range considered.

Chen, Ji; Li, Xin-Zheng; Zhang, Qianfan; Probert, Matthew; Pickard, Chris; Needs, Richard; Michaelides, Angelos; Wang, Enge

2013-03-01

 
 
 
 
201

Ab initio heats of formation of medium-sized hydrocarbons. 11. The benzenoid aromatics  

Energy Technology Data Exchange (ETDEWEB)

Ab initio calculations have been performed at the SCF level in the STO-3G, 3-21G, and 6-31G* basis sets on a variety of benzenoid and nonbenzenoid aromatic hydrocarbons, ranging from benzene to coronene. It is shown that (1) the enthalpy changes for homodesmic reactions involving only benzenoid aromatics can be computed accurately in all three bases and (2) there exist group equivalents for each basis set that enable conversion of ab initio total SCF energies to accurate heats of formation. Several examples demonstrate the extension of the method to substituted benzenes. The implications of these results concerning the correlation energies of aromatic hydrocarbons and the relationship of finite planar aromatics to the infinite graphitic sheet are discussed.

Schulman, J.M.; Peck, R.C.; Disch, R.L. (City Univ. of New York, NY (USA) Queens College, Flushing, NY (USA))

1989-07-19

202

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

203

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

International Nuclear Information System (INIS)

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

2008-06-02

204

Ab-initio molecular dynamics simulations of liquid Hg-Pb alloys  

Science.gov (United States)

Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-Pb alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Three liquid Hg-Pb mixtures (Hg30Pb70, Hg50Pb50 and Hg90Pb10) at 600K are considered. The radial distribution function g(r) and structure factor S(q) of considered alloys are compared with respective experimental results for liquid Hg (l-Hg) and lead (l-Pb). The radial distribution function g(r) shows the presence of short range order in the systems considered. Smooth curves of Bhatia-Thornton partial structure factors factor shows the presence of liquid state in the considered three alloys. Among the all considered alloys, Hg50Pb50 alloy shows presence of more chemical ordering and presence of hetero-coordination.

Sharma, Nalini; Thakur, Anil; Ahluwalia, P. K.

2014-04-01

205

Implementation of a vector potential method in an ab initio Hartree-Fock code  

Science.gov (United States)

For extended systems exposed to an external, electrostatic field, the presence of the field leads to an extra term (Evec . Pvec ) to the Hamiltonian, where Evec is the field vector and Pvec is the polarization of the system of interest. In order to find out how a polymer chain responds to an external electric perturbation, a field with a charge and a current term for the polarization is added to an ab initio Hartree-Fock Hamiltonian. The polarization expression is taken from an efficient vector potential approach (VPA) [1] for calculating electronic and nuclear responses of infinite periodic systems to finite electric fields and is implemented in the ab initio LCAO-SCF algorithm [3], which computes band structure of regular or helical polymers, taking into account the one-dimensional translational symmetry. A smoothing procedure for numerical differentiation of the orbital coefficients is used in order to calculate self-consistently the charge flow contribution to the polarization.

Tevekeliyska, Violina; Springborg, Michael; Champagne, Benoît; Kirtman, Bernard

2012-12-01

206

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

2008-03-01

207

Implicit infinite lattice summations for real space ab initio correlation methods  

CERN Multimedia

We suggest a local wave function based ab initio correlation method for infinite periodic systems, which can describe both the near range as well as the long range correlation effects coherently in the same scheme. Specifically, this work introduces a formalism which allows to describe the long range polarization cloud around a quasi particle in a solid explicitly in the formalism of local wave function based ab initio descriptions. To this end we reformulate the infinite lattice summation underlying the quantum chemistry formula to second order in a closed analytic form employing the elliptic theta function of the third kind. All formulas and manipulations are developed explicitely in full detail and a first numeric example demonstrates the principle idea. Good results for the long range polarization effects in LiH and LiF are found in agreement with earlier estimates.

Albrecht, M

2005-01-01

208

Ultracold mixtures of metastable He and Rb: scattering lengths from ab initio calculations and thermalization measurements  

CERN Document Server

We have investigated the ultracold interspecies scattering properties of metastable triplet He and Rb. We performed state-of-the-art ab initio calculations of the relevant interaction potential, and measured the interspecies elastic cross section for an ultracold mixture of metastable triplet $^4$He and $^{87}$Rb at a temperature of 0.5 mK. Our combined theoretical and experimental study gives an interspecies scattering length $a_{4+87}=+17^{+1}_{-4}$ $a_0$, which prior to this work was unknown. More general, our work shows the possibility of obtaining accurate scattering lengths using ab initio calculations for a system containing a heavy, many-electron atom, such as Rb.

Knoop, S; K?dziera, D; Mentel, ?; Puchalski, M; Mishra, H P; Flores, A S; Vassen, W

2014-01-01

209

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

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

2010-01-01

210

Scaling factors for ab initio vibrational frequencies: comparison of uncertainty models for quantified prediction  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Bayesian Model Calibration is used to revisit the problem of scaling factor calibration for semi-empirical correction of ab initio calculations. A particular attention is devoted to uncertainty evaluation for scaling factors, and to their effect on prediction of observables involving scaled properties. We argue that linear models used for calibration of scaling factors are generally not statistically valid, in the sense that they are not able to fit calibration data within their uncertainty l...

Pernot, Pascal

2008-01-01

211

Ab-initio study on interaction of hydrogen isotopes with defects in lithium oxide  

International Nuclear Information System (INIS)

The interaction of hydrogen isotopes with defects in Li2O was studied by ab-initio quantum chemical calculation. Three kinds of F-centers and Li vacancy were considered. The relaxation of ions around the vacancy and the stable position of a proton were calculated when the vacancy was produced in the Li2O crystal. From the calculated energy and the electron density map for each configuration, effects of vacancies on the proton were discussed. (author)

2001-06-01

212

Ultralong Rydberg Cs$_2$ Molecules Investigated by Combined ab initio Calculations and Perturbation Theory  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

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

2012-01-01

213

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

International Nuclear Information System (INIS)

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

214

Ab-initio calculations of spin tunneling through an indirect barrier  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We use a fully relativistic layer Green's functions approach to investigate spin-dependent tunneling through a symmetric indirect band gap barrier like GaAs/AlAs/GaAs heterostructure along [100] direction. The method is based on Linear Muffin Tin Orbitals and it is within the Density Functional Theory (DFT) in the Local Density Approximation (LDA). We find that the results of our {\\it ab-initio} calculations are in good agreement with the predictions of our previous empirica...

Chantis, Athanasios N.; Sandu, Titus; Xu, Jialei L.

2009-01-01

215

Ab-initio calculation of Raman spectra of single-walled BN nanotubes  

Science.gov (United States)

Raman spectra of single-walled boron nitride (SW-BN) nanotubes (NTs) are calculated by the ab-initio Hartree-Fock (RHF) methods. Calibration procedure is proposed to fit calculated spectra to experimental frequency ?=1366 cm peculiar to hexagonal h-BN, that allows us to interpret unambiguously the experimental spectra of BN-NTs. Most intensive and high-frequency whispering mode ?=880 cm is shown to be peculiar to armchair (n,n) SW-BN-NT.

Pokropivny, V.; Kovrygin, S.; Gubanov, V.; Lohmus, R.; Lohmus, A.; Vesi, U.

2008-05-01

216

Raman spectroscopy, ab-initio model calculations, and conformational, equilibria in ionic liquids  

Digital Repository Infrastructure Vision for European Research (DRIVER)

A review of the recent developments in the study and understanding of room temperature ionic liquids are given. An intimate picture of how and why these liquids are not crystals at ambient conditions is attempted, based on evidence from crystallographical results combined with vibrational spectroscopy and ab-initio molecular orbital calculations. A discussion is given, based mainly on some recent FT- Raman spectroscopic results on the model ionic liquid system of 1-butyl-3-methyl-imidazolium ...

Berg, Rolf W.

2008-01-01

217

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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 w...

Shukla, Alok; Dolg, Michael; Stoll, Hermann

1998-01-01

218

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

219

On Possible Pitfalls in ab initio QM/MM Minimization Approaches For Studies of Enzymatic Reactions  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Reliable studies of enzymatic reactions by combined quantum mechanics /molecular mechanics (QM/MM) approaches, with an ab initio description of the quantum region, presents a major challenge to computational chemists. The main problem is the need for a very large computer time for the evaluation of the QM energy, which in turn makes it extremely challenging to perform proper configurational sampling. A seemingly reasonable alternative is to perform energy minimization studies of the type used...

Kla?hn, Marco; Braun-sand, Sonja; Rosta, Edina; Warshel, Arieh

2005-01-01

220

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

Recent developments in path integral methodology have significantly reduced the computational expense of including quantum mechanical effects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of these developments requires a considerable programming effort, which has hindered their adoption. Here we describe i-PI, an interface written in Python that has been designed to minimise the effort required to bring state-of-the-art path i...

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

2014-01-01

 
 
 
 
221

Ab-initio approach to effective single-particle energies in doubly closed shell nuclei  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The present work discusses, from an ab-initio standpoint, the definition, the meaning, and the usefulness of effective single-particle energies (ESPEs) in doubly closed shell nuclei. We perform coupled-cluster calculations to quantify to what extent selected closed-shell nuclei in the oxygen and calcium isotopic chains can effectively be mapped onto an effective independent-particle picture. To do so, we revisit in detail the notion of ESPEs in the context of strongly correl...

Duguet, T.; Hagen, G.

2011-01-01

222

Photoelectron spectra of aluminum cluster anions: Temperature effects and ab initio simulations  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

Akola, Jaakko; Manninen, Matti; Hakkinen, Hannu; Landman, Uzi; Li, Xi; Wang, Lai-sheng

1999-01-01

223

Photoelectron spectra of aluminum cluster anions Temperature effects and ab initio simulations  

CERN Document Server

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

Akola, J; Hakkinen, H; Landman, U; Li, X; Wang, L S; Akola, Jaakko; Manninen, Matti; Hakkinen, Hannu; Landman, Uzi; Li, Xi; Wang, Lai-Sheng

1999-01-01

224

An ab initio Monte Carlo study of structural and thermal properties of Li{sub 8}  

Energy Technology Data Exchange (ETDEWEB)

We have developed and implemented an ab initio Monte Carlo scheme to investigate structural and thermal properties of small lithium clusters. This scheme is a hybrid HF/DFT procedure, which uses the converged Hartree-Fock density to calculate the Lee-Yang-Parr (LYP) correlation correction to the energy at each Monte Carlo (MC) step. The j-walking version of the MC sampling is used. Results on structures and thermal properties of Li{sub 8} are presented and discussed.

Srinivas, S.; Jellinek, J. [Argonne National Lab., IL (United States); Fantucci, P. [Metallorganica e Analitica, Milano (Italy)

1997-12-31

225

Longitudinal spin-fluctuations and superconductivity in ferromagnetic ZrZn$_{2}$ from ab initio calculations  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The recent discovery of superconductivity coexisting with weak itinerant ferromagnetism in the $d$-electron intermetallic compound ZrZn$_{2}$ strongly suggests spin-fluctuation mediated superconductivity. {\\it Ab initio} electronic structure calculations of the Fermi surface and generalized susceptibilities are performed to investigate the viability of longitudinal spin-fluctuation-induced spin-triplet superconductivity in the ferromagnetic state. The critical temperature is...

Santi, G.; Dugdale, S. B.; Jarlborg, T.

2001-01-01

226

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

Recent developments in path integral methodology have significantly reduced the computational expense of including quantum mechanical effects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of these developments requires a considerable programming effort, which has hindered their adoption. Here we describe i-PI, an interface written in Python that has been designed to minimise the effort required to bring state-of-the-art path integral techniques...

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

2014-01-01

227

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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...

2009-01-01

228

Ab-initio study on interaction of hydrogen isotopes with charged defects in lithium oxide  

International Nuclear Information System (INIS)

The interaction of hydrogen isotopes with defects in Li2O was studied by ab-initio quantum chemical calculations. Three kinds of F-centers and the lithium vacancy were considered. The relaxation of ions around the vacancy and the stable position of a proton were calculated when the vacancy was produced in the Li2O crystal. From the obtained energies and the electronic charge density maps for each configuration, the effects of the vacancies on the proton were discussed

2002-12-01

229

Incorporating Ab Initio energy into threading approaches for protein structure prediction  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

2011-01-01

230

Ab initio electronic and optical spectra of free-base porphyrins: The role of electronic correlation  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We present a theoretical investigation of electronic and optical properties of free-base porphyrins based on density functional theory and many-body perturbation theory. The electronic levels of free-base porphine (H2P) and its phenyl derivative, free-base tetraphenylporphyrin (H2TPP) are calculated using the ab initio GW approximation for the self-energy. The approach is found to yield results that compare favorably with the available photoemission spectra. The excitonic nature of the optica...

Palummo, Maurizia; Hogan, Conor; Sottile, Francesco; Bagala?, Paolo; Rubio Secades, A?ngel

2009-01-01

231

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

2000-01-01

232

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

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

1990-01-01

233

Ab initio treatment of electron correlations in polymers: lithium hydride chain and beryllium hydride polymer  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Correlated {\\em ab initio} electronic structure calculations are reported for the polymers lithium hydride chain $[LiH]_{\\infty}$ and beryllium hydride $[Be_{2}H_{4}]_{\\infty}$. First, employing a Wannier-function-based approach, the systems are studied at the Hartree-Fock level, by considering chains simulating the infinite polymers. Subsequently, for the model system $[LiH]_{\\infty}$, the correlation effects are computed by considering virtual excitations from the occupied...

Abdurahman, Ayjamal; Shukla, Alok; Dolg, Michael

2000-01-01

234

Scaling factors for ab initio vibrational frequencies: comparison of uncertainty models for quantified prediction  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Bayesian Model Calibration is used to revisit the problem of scaling factor calibration for semi-empirical correction of ab initio calculations. A particular attention is devoted to uncertainty evaluation for scaling factors, and to their effect on prediction of observables involving scaled properties. We argue that linear models used for calibration of scaling factors are generally not statistically valid, in the sense that they are not able to fit calibration data within t...

Pernot, Pascal

2009-01-01

235

Ab-initio calculations of diffusion barriers of small vacancy clusters in silicon  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Esta tese apresenta os resultados de um programa de investigação sobre a difusão da lacuna, bi-lacuna e tri-lacuna em silício utilizando simulações numéricas pelo método da teoria do funcional da densidade. Este método está implementado na forma de um programa informático referido como AIMPRO (Ab Initio Modelling PROgram). Para o cálculo dos pontos cela dos mecanismos de difusão foi usado o método “Nudged Elastic Band”. As condições fronteira dos problemas foram i...

Markevich, Alexander

2009-01-01

236

Estudo ab-initio da a-alanina em meio aquoso  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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 poin...

1999-01-01

237

Ab initio strategy for muon site assignment in wide band gap fluorides  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We report on an ab initio strategy based on density functional theory to identify the muon sites. Two issues must be carefully addressed: muon delocalization about candidate interstitial sites and local structural relaxation of the atomic positions due to mu(+)-sample interaction. Here, we verify our strategy's validity focusing on two wide band gap materials, LiF and YF3, where both mu(+) delocalization and crystal lattice relaxation play an important role in determining the mu(+) stopp...

Bernardini, F.; Bonfa, P.; Massidda, S.; Renzi, R.

2013-01-01

238

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

239

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

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

2012-01-01

240

Hyperfine tensors of nitrogen-vacancy center in diamond from \\emph{ab initio} calculations  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We determine and analyze the charge and spin density distributions of nitrogen-vacancy (N-V) center in diamond for both the ground and excited states by \\emph{ab initio} supercell calculations. We show that the hyperfine tensor of $^{15}$N nuclear spin is negative and strongly anisotropic in the excited state, in contrast to previous models used extensively to explain electron spin resonance measurements. In addition, we detect a significant redistribution of the spin densit...

Gali, Adam

2009-01-01

 
 
 
 
241

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

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

2013-01-01

242

Hydrogen Desorption from Mg Hydride: An Ab Initio Study  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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 temperature...

Simone Giusepponi; Massimo Celino

2012-01-01

243

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

International Nuclear Information System (INIS)

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

2013-11-21

244

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

Energy Technology Data Exchange (ETDEWEB)

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

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

2013-11-21

245

Nonadiabatic ab initio molecular dynamics using linear-response time-dependent density functional theory  

Science.gov (United States)

We review our recent work on ab initio nonadiabatic molecular dynamics, based on linear-response timedependent density functional theory for the calculation of the nuclear forces, potential energy surfaces, and nonadiabatic couplings. Furthermore, we describe how nuclear quantum dynamics beyond the Born-Oppenheimer approximation can be performed using quantum trajectories. Finally, the coupling and control of an external electromagnetic field with mixed quantum/classical trajectory surface hopping is discussed.

Curchod, Basile F. E.; Penfold, Thomas J.; Rothlisberger, Ursula; Tavernelli, Ivano

2013-09-01

246

Cohesive properties of bcc and fcc rubidium from ab initio pseudopotentials  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Total-energy calculations have been performed for Rb at zero temperature using a self-consistent ab initio pseudopotential approach within a local-density-functional scheme. The energy difference between fcc and bcc Rb, and the energy barrier between these structures, are found to be extremely small near the equilibrium volume. Agreement of the calculated cohesive properties of bcc Rb with experimental values is good in view of the softness of the material. A transition from bcc to fcc has be...

1985-01-01

247

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 signals, and compared its performance with another popular protein motif finder, MEME. NestedMICA, an open source protein motif discovery tool written in Java, is driven by a Monte...

Do?ruel Mutlu; Down Thomas A; Jp, Hubbard Tim

2008-01-01

248

On limits of ab initio calculations of pairing gap in nuclei  

Energy Technology Data Exchange (ETDEWEB)

A brief review of recent microscopic calculations of nuclear pairing gap is given. A semi-microscopic model is suggested in which the ab initio effective pairing interaction is supplemented with a small phenomenological addendum. It involves a parameter which is universal for all medium and heavy nuclei. Calculations for several isotopic and isotonic chains of semi-magic nuclei confirm the relevance of the model.

Saperstein, E. E., E-mail: saper@mbslab.kiae.ru [Kurchatov Institute (Russian Federation); Baldo, M. [Sezione di Catania, INFN (Italy); Lombardo, U. [INFN-LNS and University of Catania (Italy); Pankratov, S. S.; Zverev, M. V. [Kurchatov Institute (Russian Federation)

2011-11-15

249

Steady state Ab-initio Theory of Lasers with Injected Signals  

CERN Document Server

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

250

Ab initio vibrational predissociation dynamics of He-I2(B) complex  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Three-dimensional quantum mechanical calculations on the vibrational predissociation dynamics of HeI2 B state complex are performed using a potential energy surface accurately fitted to unrestricted open-shell coupled cluster ab initio data, further enabling extrapolation for large I2 bond lengths. A Lanczos iterative method with an optimized complex absorbing potential is used to determine energies and lifetimes of the vibrationally predissociating He,I2(B,v') complex for v' ? 26 of I2 vib...

Valde?s, A?lvaro; Prosmiti, Rita; Villarreal, Pablo; Delgado Barrio, Gerardo; Lemoine, Didier; Lepetit, Bruno

2007-01-01

251

Ab-Initio Structural Study of SrMoO3 Perovskite  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The equilibrium crystal structure parameter and bulk modulus of the SrMoO3 perovskite has been calculated with ab-initio method based on density functional theory (DFT) using both local density approximation (LDA) and generalized gradient approximation (GGA). The corresponding total free energy along with its various components for SrMoO3 was obtained. The lattice parameter and bulk modulus calculated for SrMoO3

Avinash Daga; Smita Sharma

2012-01-01

252

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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 sy...

2006-01-01

253

Ab initio study of antiphase boundaries and stacking faults in L12 and DO22 compounds  

DEFF Research Database (Denmark)

We have performed ab initio calculations of the energies of antiphase boundaries as well as complex and superlattice intrinsic stacking faults in nine intermetallic compounds observed in the face-centered-cubic L1(2) and DO22 structures. The calculations were performed by means of a Green's function technique based on the linear-muffin-tin-orbitals method within the tight-binding and atomic-sphere approximations.

Rosengaard, N. M.; Skriver, Hans Lomholt

1994-01-01

254

Ab initio study of antiphase boundaries and stacking faults in L12 and DO22 compounds  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We have performed ab initio calculations of the energies of antiphase boundaries as well as complex and superlattice intrinsic stacking faults in nine intermetallic compounds observed in the face-centered-cubic L1(2) and DO22 structures. The calculations were performed by means of a Green's function technique based on the linear-muffin-tin-orbitals method within the tight-binding and atomic-sphere approximations.

Rosengaard, N. M.; Skriver, Hans Lomholt

2009-01-01

255

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

CERN Multimedia

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

Morillon, B; Carbonell, J

2013-01-01

256

Relativistic configuration interaction oscillator strengths calculations with ab initio screened model-potential wavefunctions  

Science.gov (United States)

The relativistic configuration-interaction (CI) method with numerical Dirac-Fock wavefunctions generated in the field of ab initio screened model potential is used to compute oscillator strengths for some spin-allowed and spin-forbidden ns2 1S0-nsnp 1P1, 3P1 transitions in light systems with two valence electrons: beryllium, magnesium and zinc. The present results are discussed and compared with other theoretical and experimental data available.

Glowacki, Leszek; Migdalek, Jacek

2006-04-01

257

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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-p...

1999-01-01

258

Ab-initio simulation and experimental validation of beta-titanium alloys  

Digital Repository Infrastructure Vision for European Research (DRIVER)

In this progress report we present a new approach to the ab-initio guided bottom up design of beta-Ti alloys for biomedical applications using a quantum mechanical simulation method in conjunction with experiments. Parameter-free density functional theory calculations are used to provide theoretical guidance in selecting and optimizing Ti-based alloys with respect to three constraints: (i) the use of non-toxic alloy elements; (ii) the stabilization of the body centered cubic...

Raabe, D.; Sander, B.; Friak, M.; Ma, D.; Neugebauer, J.

2008-01-01

259

Ab Initio structure prediction for Escherichia coli: towards genome-wide protein structure modeling and fold assignment  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Genome-wide protein structure prediction and structure-based function annotation have been a long-term goal in molecular biology but not yet become possible due to difficulties in modeling distant-homology targets. We developed a hybrid pipeline combining ab initio folding and template-based modeling for genome-wide structure prediction applied to the Escherichia coli genome. The pipeline was tested on 43 known sequences, where QUARK-based ab initio folding simulation generated models with TM...

Xu, Dong; Zhang, Yang

2013-01-01

260

Atomic-like shell models for alkali trimers derived from ab initio calculations  

International Nuclear Information System (INIS)

Full text: Alkali metal clusters have received great attention due to their role as bridge between atomic and solid state physics. Among the smallest clusters, the trimers are of special interest, since these systems provide complex spectra including Jahn-Teller distortions, yet the spectra are well defined and still accessible via ab initio calculations. The experimental spectra, as well as ab initio calculations, show a regular pattern of electronic states. High level ab initio calculations [CCSD(T), CASPT2] provide detailed information about the participating electronic orbitals, and allow us to rationalize the observed patterns in terms of simplified shell models. For the low-spin states of K3 the standard electron-droplet model offers a qualitative explanation. In this simplified picture the electronic states are interpreted as single electron excitations into delocalized molecular orbitals with typical atomic-like shape. For the description of the quartet manifolds of K3, K2Rb, KRb2 and Rb3 we utilize the eigenstates of a harmonic oscillator in a quantum-dot-like confining potential. (author)

2008-07-02

 
 
 
 
261

The Gamow Shell Model as a tool for ab-initio nuclear structure calculations  

Science.gov (United States)

No core Gamow shell model (NCGSM) is applied for the first time to study selected well-bound and unbound states of helium isotopes. This model, formulated in the rigged Hilbert space and using a complete Berggren ensemble, is appropriate for a description of bound states, resonances, and the many-body scattering states. The ``dimensional catastrophe'' in NCGSM when increasing the number of active particles is much more serious than in the No Core Shell Model (NCSM). This problem has been alleviated by the application of the Density Matrix Renormalization Group (DMRG) method, opening a possibility for the ab initio calculation of exotic states in hydrogen, helium and lithium chains of isotopes. The ab initio NCGSM calculations start from either bare interaction or various renormalized two-body interactions such as Vlow-k. The single-particle Berggren ensemble consisting of bound, resonance and non-resonant continuum states is generated by the corresponding Gamow-Hartree-Fock potential. To test the validity of our approach, we benchmarked the NCGSM results against Fadeev and Fadeev-Yakubovsky exact calculations for ^3H and ^4He nuclei. We also performed ab-initio NCGSM calculations for the unstable nucleus ^5He and determined the ground state energy and decay width, starting from a realistic N^3LO interaction.

Papadimitriou, George; Barrett, Bruce; Rotureau, Jimmy; Ploszajczak, Marek

2012-10-01

262

Ab initio and semiempirical study of structure and electronic spectra of hydroxy substituted naphthoquinones  

Science.gov (United States)

The geometries of hydroxy derivatives of 1,4-naphthoquinone (NQ), viz., 2-hydroxy-1,4-naphthoquinone (2HNQ), 5-hydroxy-1,4-naphthoquinone (5HNQ), and 5,8-dihydroxy-1,4-naphthoquinone (DHNQ), have been optimized using the semiempirical and ab initio theoretical methods. Semiempirical methods used for the optimization are Austin Model 1 (AM1) and Zerner's Intermediate Neglect of Differential Overlap/1(ZINDO/1). For ab initio calculations the 6-31G * basis set is used. The electronic spectra of 1,4-naphthoquinone and its hydroxy derivatives are calculated using the semiempirical Zerner's Intermediate Neglect of Differential Overlap/Spectroscopy (ZINDO/S) method employing the geometries optimized at AM1, ZINDO/1 and ab initio levels and compared with their electronic absorption spectra measured by us. For hydroxy substituted systems, such calculations for spectral assignments are made for the first time. It is found that though the predictions of the three theoretical methods for the geometries are similar, the predictions of the ZINDO/S method using the ZINDO/1 optimized geometries, are better for the transition wavelengths in the visible region of the hydroxy substituted naphthoquinones, especially for 5HNQ and DHNQ.

Khan, Mohd. Shahid; Khan, Zahid H.

2005-02-01

263

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

International Nuclear Information System (INIS)

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

1998-08-01

264

Modelling of nuclear glasses by classical and ab initio molecular dynamics  

International Nuclear Information System (INIS)

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

2004-01-01

265

Modeling of nuclear glasses by classical and ab initio molecular dynamics  

International Nuclear Information System (INIS)

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

2004-01-01

266

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

International Nuclear Information System (INIS)

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

2010-01-01

267

A web-deployed interface for performing ab initio molecular dynamics, optimization, and electronic structure in FIREBALL  

Science.gov (United States)

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

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

2009-03-01

268

Ab initio pair potential energy curve for the argon atom pair and thermophysical properties of the dilute argon gas. I. Argon-argon interatomic potential and rovibrational spectra  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Abstract An argon-argon interatomic potential energy curve was derived from quantum-mechanical ab initio calculations using basis sets of up to d-aug-cc-pV(6+d)Z quality supplemented with bond functions and ab initio methods up to CCSDT(Q). In addition, corrections for relativistic effects were determined. An analytical potential function was fitted to the ab initio values and utilized to compute the rovibrational spectrum. The quality of the interatomic potential function was test...

2009-01-01

269

Carbon dioxide hydrate phase equilibrium and cage occupancy calculations using ab initio intermolecular potentials.  

Science.gov (United States)

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

Velaga, Srinath C; Anderson, Brian J

2014-01-16

270

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

Energy Technology Data Exchange (ETDEWEB)

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

Steckel, Janice A. [U.S. DOE

2012-11-29

271

Improved parametric fits for the HeH2 ab initio energy surface  

International Nuclear Information System (INIS)

A brief history of the development of ab initio calculations for the HeH2 quasi-molecule energy surface, and the parametric fits to these ab initio calculations, is presented. The concept of 'physical reasonableness' of the parametric fit is discussed. Several new improved parametric fits for the energy surface, meeting these requirements, are then proposed. One fit extends the Russek-Garcia parametric fit for the deep repulsion region to include r-dependent parameters, resulting in a more physically reasonable fit with smaller average error. This improved surface fit is applied to quasi-elastic collisions of He on H2 in the impulse approximation. Previous classical calculations of the scaled inelastic vibrorotational excitation energy distributions are improved with this more accurate parametric fit of the energy surface and with the incorporation of quantum effects in vibrational excitation. It is shown that Sigmund's approach in developing his scaling law is incomplete in the contribution of the three-body interactions to vibrational excitation of the H2 molecule is concerned. The Sigmund theory is extended to take into account for r-dependency of three-body interactions. A parametric fit for the entire energy surface from essentially 0 ?R?? and 1.2?r?1.6 a.u., where R is the intermolecular spacing and r is the hydrogen bonding length, is also presented. This fit is physically reasonable in all asymptotic limits. This first, full surface parametric fit is based primarily upon a composite of ab initio studies by Russek and Garcia and Meyer, Hariharan and Kutzelnigg. Parametric fits for the H2(1s?g)2, H2+(1s?g), H2+(2p?u) and (LiH2)+ energy surfaces are also presented. The new parametric fits for H2, H2+(1s?g) are shown to be improvements over the well-known Morse potentials for these surfaces

1992-01-01

272

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

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

2005-01-01

273

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

274

Ab initio Path Integral Molecular Dynamics Based on Fragment Molecular Orbital Method  

Science.gov (United States)

We have developed an ab initio path integral molecular dynamics method based on the fragment molecular orbital method. This “FMO-PIMD” method can treat both nuclei and electrons quantum mechanically, and is useful to simulate large hydrogen-bonded systems with high accuracy. After a benchmark calculation for water monomer, water trimer and glycine pentamer have been studied using the FMO-PIMD method to investigate nuclear quantum effects on structure and molecular interactions. The applicability of the present approach is demonstrated through a number of test calculations.

Fujita, Takatoshi; Watanabe, Hirofumi; Tanaka, Shigenori

2009-10-01

275

Ab-initio study on interaction of hydrogen isotopes with charged defects in lithium oxide  

Energy Technology Data Exchange (ETDEWEB)

The interaction of hydrogen isotopes with defects in Li{sub 2}O was studied by ab-initio quantum chemical calculations. Three kinds of F-centers and the lithium vacancy were considered. The relaxation of ions around the vacancy and the stable position of a proton were calculated when the vacancy was produced in the Li{sub 2}O crystal. From the obtained energies and the electronic charge density maps for each configuration, the effects of the vacancies on the proton were discussed.

Tanigawa, Hisashi E-mail: hisashi@flanker.q.t.u-tokyo.ac.jp; Tanaka, Satoru

2002-12-01

276

Fundamental absorption frequency from quasi-classical direct ab initio molecular dynamics: diatomic molecule  

Energy Technology Data Exchange (ETDEWEB)

A new approach is proposed to extract the fundamental absorption frequency from classical molecular dynamics simulation in which the oscillator amplitude is specified by setting the total energy equal to the harmonic zero-point energy. This approach is applied to D2 molecule. The fundamental absorption frequency and the anharmonic constant of D2, obtained from the quasiclassical direct ab initio molecular dynamics simulation method with the full Configuration Interaction level of theory with the aug-cc-pVTZ basis set, compare well with the experimentally observed values.

Aida, Misako; Dupuis, Michel

2005-01-31

277

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

278

Ab initio calculations of Curie temperatures in GdX compounds  

Energy Technology Data Exchange (ETDEWEB)

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

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

2006-02-09

279

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

280

Conformer-selected photodissociation: Ab Initio Multiple Spawning Dynamics of Excited Propanal Cation  

Science.gov (United States)

Recent experiments have shown that pure cis and gauche propanal cations can be prepared using REMPI (Resonance Enhanced Multiphoton Ionization Spectroscopy). The H elimination pathway which results when these conformer-selected cations are photoexcited was found to depend on the conformer (cis vs. gauche). This dependence is very surprising since the interconversion barrier of the two conformers is small compared to the excited energy. We use the ab initio multiple spawning (AIMS) method developed in our group to model the conformer-specific photodissociation and to elucidate its origins.

Tao, Hongli; Martinez, Todd

2007-03-01

 
 
 
 
281

The ionization dynamics of SF6: a full dimensional direct ab initio dynamics study  

International Nuclear Information System (INIS)

The ionization dynamics of SF6, which plays an important role in plasma dry etching of semiconductors, has been investigated by means of full dimensional direct ab initio dynamics calculations. The SF6+ ion, formed by the vertical ionization of SF6, decomposes directly into SF5+ and F without complex formation. The dynamics calculations showed that 22% of the total available energy is partitioned into the relative translational mode between SF5+ and F. The mechanism of the ionization of SF6 and the etching of silicon by the F atom were discussed on the basis of the theoretical results. (author)

2000-05-14

282

Solvent effects on 2-methoxyethanol conformers: an ab initio DFT study using the SCI-PCModel  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The four stable conformers of 2-methoxyethanol, CH3O-CH2-CH2-OH (tgg', ggg', ttg and ttt) are studied by ab initio calculations using the SCRF theory and the SCI-PCModel to assess solvent effects on the structure and vibrational spectra of this compound. Full geometry optimizations were carried out at the B3LYP/6-311+G(3df,2df,2p)//B3LYP/6-31G(d) level, and normal mode calculations were performed within the harmonic approximation using the B3LYP/6-31G(d) derived force fields. The solvent, her...

Gil, Francisco P. S. C.; Teixeira-dias, J. J. C.

1999-01-01

283

Ab initio potentials of F+Li2 accessible at ultracold temperatures  

International Nuclear Information System (INIS)

Ab initio calculations for the strongly exoergic Li2+F harpoon reaction are presented using density-functional theory, complete active space self-consistent field, and multireference configuration interaction methods to argue that this reaction would be an ideal candidate for investigation with ultracold molecules. The lowest six states are calculated with the aug-correlation-consistent polarized valence triple-zeta basis set and at least two can be accessed by a ground rovibronic Li2 molecule with zero collision energy at all reaction geometries. The large reactive cross section (characteristic of harpoon reactions) and chemiluminescent products are additional attractive features of these reactions.

2010-09-01

284

Ab initio rovibronic states of the thioketenyl radical in its X2? electronic ground state.  

Science.gov (United States)

We present an ab initio study of the thioketenyl (HCCS) radical in its degenerate X(2)? electronic ground state. All rotational and vibrational degrees of freedom are taken into account including the electronic orbital and spin angular momenta. The structure of the rovibronic levels and the nature of the corresponding wave functions show resonances even at very low energies due to strong couplings between the bending, rotation, and spin terms in the Hamiltonian. Assignments from the dominant contributions of the eigenvectors are discussed in parallel with previously published data. The rotational structures for the first excited vibronic states are computed as well as transition intensities for the fundamental one. PMID:21456658

Jutier, Laurent; Dhont, Guillaume

2011-03-28

285

Large-scale ab initio nanostructure electronic structure calculations for energy applications  

International Nuclear Information System (INIS)

Nanostructures have often been used to construct third-generation solar cells and for solid state lighting. To fully explore the potential for such energy applications, we need to understand the electronic and optical properties of the corresponding nanosystems. These include the quantum confinement effects, the electron hole separations, the exciton binding energy, and optical absorption spectrums. In the past ten years, we have developed a systematic approach to study such properties of thousand atom nanostructures based on ab initio calculations and large -cale comutations. In this paper, we present a few examples using such an approach to study the nanostructure properties related to energy applications

2008-07-01

286

Ab initio calculations of the optical properties of ions in glass  

International Nuclear Information System (INIS)

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

1984-07-01

287

Ab initio quantum chemical calculation as a tool of evaluating diamagnetic susceptibility of magnetically levitating substances  

Energy Technology Data Exchange (ETDEWEB)

On magnetic force evaluation necessary for magnetically levitated diamagnetic substances, isotropic diamagnetic susceptibility estimation by the ab initio quantum chemical calculation using Gaussian03W was verified for more than 300 molecules in a viewpoint of the accuracy in the absolute value and the calculation level affording good cost performance. From comparison, the method of B3PW91 / 6-311+G(d,p) was found to give the adequate absolute value by the relation of (observed) = (1.03 {+-} 0.005) x (calculated) - (1.22 {+-} 0.60) x 10{sup -6} in a unit of cm{sup 3} mol{sup -1} and good cost performance.

Fujiwara, Y [Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526 (Japan); Tanimoto, Y [Faculty of Pharmacy, Osaka Ohtani University, Nishikiorikita, Tondabayashi 584-8540 (Japan)], E-mail: fuji0710@sci.hiroshima-u.ac.jp

2009-03-01

288

Ab initio quantum chemical calculation as a tool of evaluating diamagnetic susceptibility of magnetically levitating substances  

International Nuclear Information System (INIS)

On magnetic force evaluation necessary for magnetically levitated diamagnetic substances, isotropic diamagnetic susceptibility estimation by the ab initio quantum chemical calculation using Gaussian03W was verified for more than 300 molecules in a viewpoint of the accuracy in the absolute value and the calculation level affording good cost performance. From comparison, the method of B3PW91 / 6-311+G(d,p) was found to give the adequate absolute value by the relation of (observed) = (1.03 ± 0.005) x (calculated) - (1.22 ± 0.60) x 10-6 in a unit of cm3 mol-1 and good cost performance.

2009-03-01

289

A transferable ab-initio based force field for aqueous ions  

CERN Document Server

We present a new polarizable force field for aqueous ions (Li+, Na+, K+, Rb+, Cs+, Mg2+, Ca2+, Sr2+ and Cl-) derived from condensed phase ab-initio calculations. We use Maximally Localized Wannier Functions together with a generalized force and dipole-matching procedure to determine the whole set of parameters. Experimental data is then used only for validation purposes and a good agreement is obtained for structural, dynamic and thermodynamic properties. The same procedure applied to crystalline phases allows to parametrize the interaction between cations and the chloride anion. Finally, we illustrate the good transferability of the force field to other thermodynamic conditions by investigating concentrated solutions.

Tazi, Sami; Rotenberg, Benjamin; Turq, Pierre; Vuilleumier, Rodolphe; Salanne, Mathieu; 10.1063/1.3692965

2012-01-01

290

Ab initio calculation of the spectrum and structure of (16)O.  

Science.gov (United States)

We present ab initio lattice calculations of the low-energy even-parity states of 16O using chiral nuclear effective field theory. We find good agreement with the empirical energy spectrum, and with the electromagnetic properties and transition rates. For the ground state, we find that the nucleons are arranged in a tetrahedral configuration of alpha clusters. For the first excited spin-0 state, we find that the predominant structure is a square configuration of alpha clusters, with rotational excitations that include the first spin-2 state. PMID:24679283

Epelbaum, Evgeny; Krebs, Hermann; Lähde, Timo A; Lee, Dean; Meissner, Ulf-G; Rupak, Gautam

2014-03-14

291

Bond dissociation energies of organophosphorus compounds: an assessment of contemporary ab initio procedures  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Thermodynamic properties of phosphorus-containing compounds were investigated using high-level ab initio computations. An extended set of contemporary density functional theory (DFT) Procedures was assessed for their ability to accurately predict bond dissociation energies of a set of phosphoranyl radicals. The results of meta- and double-hybrids as well as more recent methods, in particular M05, M05-2X, M06, and M06-2X, were compared with benchmark G3(MP2)-RAD Values. Standard heals of forma...

Hemelsoet, Karen; Durme, Frederick; Speybroeck, Veronique; Reyniers, Marie-franc?oise; Waroquier, Michel

2010-01-01

292

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

International Nuclear Information System (INIS)

First principle ab initio molecular dynamics simulations of the Car-Parrinello type have proved to be of invaluable help in understanding the microscopic mechanisms of chemical bonding both in solid state physics and in structural biophysics. In this work we present as test cases the study of the Cu coordination mode in two especially important examples: Prion protein and ?-amyloids. Using medium size PC-clusters as well as larger parallel platforms, we are able to deal with systems comprising 300 to 500 atoms and 1000 to 1500 electrons for as long as 2-3 ps. We present structural results which confirm indications coming from NMR and XAS data

2007-12-26

293

Ab Initio Calculations of Singlet and Triplet Excited States of Chlorine Nitrate and Nitric Acid  

Science.gov (United States)

Ab initio calculations of vertical excitations to singlet and triplet excited states of chlorine nitrate and nitric acid are reported. The nature of the electronic transitions are examined by decomposing the difference density into the sum of detachment and attachment densities. Counterparts for the three lowest singlet excited states of nitric acid survive relatively unperturbed in chlorine nitrate, while other low-lying singlet states of chlorine nitrate appear to be directly dissociative in the ClO chromophore. These results suggest an assignment of the two main peaks in the experimental chlorine nitrate absorption spectrum. In addition, triplet vertical excitations and the lowest optimized triplet geometries of both molecules are studied.

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

1994-01-01

294

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

2013-06-01

295

Longitudinal Spin Fluctuations and Superconductivity in Ferromagnetic ZrZn2 from Ab Initio Calculations  

Science.gov (United States)

The recent discovery of superconductivity coexisting with weak itinerant ferromagnetism in the d-electron intermetallic compound ZrZn2 strongly suggests spin-fluctuation mediated superconductivity. Ab initio electronic structure calculations of the Fermi surface and generalized susceptibilities are performed to investigate the viability of longitudinal spin-fluctuation-induced spin-triplet superconductivity in the ferromagnetic state. The critical temperature is estimated to be of the order of 1 K. Additionally, it is shown that in spite of a strong electron-phonon coupling ( ?ph = 0.7), conventional s-wave superconductivity is inhibited by the presence of strong spin fluctuations.

Santi, G.; Dugdale, S. B.; Jarlborg, T.

2001-12-01

296

Trapping Behavior of He in Ti Revisited by ab initio Calculations  

Science.gov (United States)

We report a detailed ab initio study of the trapping behavior of interstitial helium atoms (IHAs) in hcp Ti. The tetrahedral interstitial site for one He is confirmed to be the most stable IHA configuration, but the most favorable interstitial site comprises two adjacent octahedral sites for two helium atoms. The octahedral IHA can trap another IHA regardless of the site where it is initially located, whereas the tetrahedral IHA cannot. Hybridization among the different states is responsible for the stable order, which has significant implications for He clustering and bubble nucleation that can affect material performance in future fusion reactors. These results provide the basis for the development of improved atomistic models.

Wan, Chu-Bin; Zhou, Xiao-Song; Li, Shi-Na; Zhang, Hui-Jun; Liang, Jian-Hua; Peng, Shu-Ming; Ju, Xin

2014-01-01

297

High-pressure behaviour of yugawaralite at different water content: an ab initio study  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

Arletti, Rossella

2005-01-01

298

Second generation wave-function thermostat for ab-initio molecular dynamics  

CERN Multimedia

A rigorous two-thermostat formulation for ab-initio molecular dynamics using the fictitious Lagrangian approach is presented. It integrates the concepts of mass renormalization and temperature control for the wave functions. The new thermostat adapts to the instantaneous kinetic energy of the nuclei and thus minimizes its influence on the dynamics. Deviations from the canonical ensemble, which are possible in the previous two-thermostat formulation, are avoided. The method uses a model for the effective mass of the wave functions, which is open to systematic improvement.

Blöchl, P E

2001-01-01

299

Vibrational energy levels for CH4 from an ab initio potential  

Science.gov (United States)

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

Schwenke, D. W.; Partridge, H.

2001-01-01

300

Electronic transport coefficients from ab initio simulations and application to dense liquid hydrogen  

CERN Document Server

Using Kubo's linear response theory, we derive expressions for the frequency-dependent electrical conductivity (Kubo-Greenwood formula), thermopower, and thermal conductivity in a strongly correlated electron system. These are evaluated within ab initio molecular dynamics simulations in order to study the thermoelectric transport coefficients in dense liquid hydrogen, especially near the nonmetal-to-metal transition region. We also observe significant deviations from the widely used Wiedemann-Franz law which is strictly valid only for degenerate systems and give an estimate for its valid scope of application towards lower densities.

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

2012-01-01

 
 
 
 
301

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

302

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

303

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

304

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

305

Massless Fermions in multilayer graphitic systems with misoriented layers: Ab initio calculations and experimental fingerprints  

International Nuclear Information System (INIS)

We examine how the misorientation of a few stacked graphene layers affects the electronic structure of carbon nanosystems. We present ab initio calculations on bilayer and trilayer systems to demonstrate that the massless fermion behavior typical of single-layered graphene is also found in incommensurate multilayered graphitic systems. We also investigate the consequences of this property on experimental fingerprints, such as Raman spectroscopy and scanning tunneling microscopy (STM). Our simulations reveal that STM images of turbostratic few-layer graphite are sensitive to the layer arrangement. We also predict that the resonant Raman signals of graphitic samples are more sensitive to the orientation of the layers than to their number

2007-11-01

306

Massless fermions in multilayer graphitic systems with misoriented layers: Ab initio calculations and experimental fingerprints  

Science.gov (United States)

We examine how the misorientation of a few stacked graphene layers affects the electronic structure of carbon nanosystems. We present ab initio calculations on bilayer and trilayer systems to demonstrate that the massless fermion behavior typical of single-layered graphene is also found in incommensurate multilayered graphitic systems. We also investigate the consequences of this property on experimental fingerprints, such as Raman spectroscopy and scanning tunneling microscopy (STM). Our simulations reveal that STM images of turbostratic few-layer graphite are sensitive to the layer arrangement. We also predict that the resonant Raman signals of graphitic samples are more sensitive to the orientation of the layers than to their number.

Latil, Sylvain; Meunier, Vincent; Henrard, Luc

2007-11-01

307

Thermochemistry of trans-diimide and 1,1-diazene. Ab initio studies  

International Nuclear Information System (INIS)

The thermochemistry of trans-diimide, 1,1-diazene, cis-diimide, and diazenyl radical has been obtained using ab initio generalized valence bond and configuration interaction methods. Thus N-H bond energies at 298 K were found to be trans-diimide, 71.5 kcal; 1,1-diazene, 43.0 kcal; diazenyl radical, -24.1 kcal. The results of this study are used to interpret conflicting experimental results and to predict the thermochemistry of substituted 1,1-diazenes

1980-06-04

308

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

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

2000-01-01

309

Electronic states of Zn2 - Ab initio calculations of a prototype for Hg2  

Science.gov (United States)

The electronic states of Zn2 are investigated by ab initio polarization configuration-interaction calculations. Molecular states dissociating to Zn(1S) + Zn(1S, 3P, 1P) and Zn(3P) + Zn(3P) are treated. Important effects from states arising from Zn(+)(25) + Zn(-)(2P) are found in the potential-energy curves and electronic-transition moments. A model calculation for Hg2 based on the Zn2 curves and including spin-orbit coupling leads to a new interpretation of the emission bands in Hg vapor.

Hay, P. J.; Dunning, T. H., Jr.; Raffenetti, R. C.

1976-01-01

310

Atomic structure evolution during solidification of liquid niobium from ab initio molecular dynamics simulations.  

Science.gov (United States)

Atomic structure transitions of liquid niobium during solidification, at different temperatures from 3200 to 1500 K, were studied by using ab initio molecular dynamics simulations. The local atomic structure variations with temperature are investigated by using the pair-correlation function, the structure factor, the bond-angle distribution function, the Honeycutt-Anderson index, Voronoi tessellation and the cluster alignment methods. Our results clearly show that, upon quenching, the icosahedral short-range order dominates in the stable liquid and supercooled liquid states before the system transforms to crystalline body-center cubic phase at a temperature of about 1830 K. PMID:24334654

Debela, T T; Wang, X D; Cao, Q P; Zhang, D X; Wang, S Y; Wang, C Z; Jiang, J Z

2014-02-01

311

Electrostatic control of photoisomerization in the photoactive yellow protein chromophore: Ab initio multiple spawning dynamics  

Science.gov (United States)

The excited state dynamics of an anionic model photoactive yellow protein (PYP) chromophore have been investigated using the ab initio multiple spawning (AIMS) method. We observe two isomerization products, differing in the bond about which isomerization takes place. We also carried out AIMS simulations including a single point charge to mimic the Arg52 residue which is present in the protein environment. We show that a single point charge is sufficient to change the photoproduct distribution such that isomerization is restricted to only one of the two bonds where isomerization is observed in the isolated chromophore. These results corroborate recent speculations concerning the role of Arg52 in the photocycle of PYP.

Ko, Chaehyuk; Virshup, Aaron M.; Martínez, Todd J.

2008-07-01

312

AB initio study of the rotational-torsional spectrum of methyl formate  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The molecular structure of methyl formate is determined from ab initio calculations. The molecule presents two conformers (cis and trans) with a 5.3 kcal mol-1 difference in energy. In the most stable cis conformer, the carbonyl group eclipses the methyl group. The internal rotation barriers are V3(cis) = 368 cm-1 and V3(trans) = 26 cm -1 for the methyl group and VCO = 4826 cm-1 for the CO group. The dependence of the spectroscopic parameters on the torsional motions is detailed. The rotation...

Senent Di?ez, Mari?a Luisa; Villa, M.; Mele?ndez, F. J.; Domi?nguez Go?mez, R.

2005-01-01

313

Ab initio lattice dynamics of CoH and NiH  

International Nuclear Information System (INIS)

Research highlights: ? First principles lattice dynamics for 3d-metals hydrides are performed. ? No phase transition in the hydrides under pressure is observed. ? Atomic bonding in CoH is stronger than that in NiH. - Abstract: Ground state parameters and lattice dynamics of CoH and NiH phases are studied by means of the state-of-the-art ab initio pseudopotentials methods. Calculated ground state parameters and phonon DOS are in rather good agreement with available experimental data. No phase transformation for CoH and NiH was found in a wide pressure and temperature range.

2011-09-01

314

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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 compoun...

Hakan Arslan; Öztekin Algül

2007-01-01

315

Atomic structure evolution during solidification of liquid niobium from ab initio molecular dynamics simulations  

Science.gov (United States)

Atomic structure transitions of liquid niobium during solidification, at different temperatures from 3200 to 1500 K, were studied by using ab initio molecular dynamics simulations. The local atomic structure variations with temperature are investigated by using the pair-correlation function, the structure factor, the bond-angle distribution function, the Honeycutt-Anderson index, Voronoi tessellation and the cluster alignment methods. Our results clearly show that, upon quenching, the icosahedral short-range order dominates in the stable liquid and supercooled liquid states before the system transforms to crystalline body-center cubic phase at a temperature of about 1830 K.

Debela, T. T.; Wang, X. D.; Cao, Q. P.; Zhang, D. X.; Wang, S. Y.; Wang, C. Z.; Jiang, J. Z.

2014-02-01

316

Elastic Properties of CaSiO3 Perovskite from ab initio Molecular Dynamics  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Ab initio molecular dynamics simulations were performed to investigate the elasticity of cubic CaSiO3 perovskite at high pressure and temperature. All three independent elastic constants for cubic CaSiO3 perovskite, C11, C12, and C44, were calculated from the computation of stress generated by small strains. The elastic constants were used to estimate the moduli and seismic wave velocities at the high pressure and high temperature characteristic of the Earth’s interior. The dependence of te...

Shigeaki Ono

2013-01-01

317

Ab initio predictions on the rotational spectra of carbon-chain carbene molecules  

Science.gov (United States)

We predict rotational constants for the carbon-chain molecules H2C=(C=)nC, n=3-8, using ab initio computations, observed values for the earlier members in the series, H2CCC and H2CCCC with n=1 and 2, and empirical geometry corrections derived from comparison of computation and experiment on related molecules. H2CCC and H2CCCC have already been observed by radioastronomy; higher members in the series, because of their large dipole moments, which we have calculated, are candidates for astronomical searches. Our predictions can guide searches and assist in both astronomical and laboratory detection.

Maluendes, S. A.; McLean, A. D.; Loew, G. H. (Principal Investigator)

1992-01-01

318

Spin-orbit interaction effects in zincblende semiconductors: Ab initio pseudopotential calculations  

International Nuclear Information System (INIS)

Ab initio band structure calculations have been performed for the spin-orbit interaction effects at the top of the valence bands for GaAs and InSb. Relativistic, norm-conserving pseudopotentials are used with no correction made for the gaps from the local density approximation. The spin-orbit splitting at ? and linear terms in the /rvec char/k dependence of the splitting are found to be in excellent agreement with existing experiments and previous theoretical results. The effective mass and the cubic splitting terms are also examined. 6 refs., 1 fig., 2 tabs

1988-08-01

319

Atomic ionization of germanium by neutrinos from an ab initio approach  

Science.gov (United States)

An ab initio calculation of atomic ionization of germanium by neutrinos was carried out in the framework of multiconfiguration relativistic random phase approximation and benchmarked by related atomic structure and photoabsorption data. This improves over the conventional approach based on scattering off free electrons whose validity at sub-keV energy transfer is questionable. Limits on neutrino magnetic moments are derived using reactor neutrino data taken with low threshold germanium detectors. Future applications of these atomic techniques will greatly reduce the atomic uncertainties in low-energy neutrino and dark matter detections.

Chen, Jiunn-Wei; Chi, Hsin-Chang; Huang, Keh-Ning; Liu, C.-P.; Shiao, Hao-Tse; Singh, Lakhwinder; Wong, Henry T.; Wu, Chih-Liang; Wu, Chih-Pan

2014-04-01

320

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

 
 
 
 
321

Ab initio studies of ionization potentials of hydrated hydroxide and hydronium  

CERN Document Server

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

322

Quantum calculations of vibrational energies of H3O2- on an ab initio potential.  

Science.gov (United States)

We report a full-dimensional potential energy surface for H3O2-, based on fitting 66,965 ab initio electronic energies. A major feature of this potential is a barrier of roughly 200 cm-1 to internal rotation of the two hydroxyl groups about a line connecting the two oxygen atoms and the bridging hydrogen atom. The potential is used in calculations of vibrational energies, performed with the "Reaction Path" version of the code "MULTIMODE". The results are compared to recent infrared messenger experiments and are used to propose interpretations of the experimental results. PMID:15099067

Huang, Xinchuan; Braams, Bastiaan J; Carter, Stuart; Bowman, Joel M

2004-04-28

323

The chemical shift of deprotonated water dimer: Ab initio path integral simulation  

Science.gov (United States)

The 1H NMR chemical shift in deprotonated water dimer H3O2- has been studied by ab initio path integral simulation. The simulation predicts that the isotropic shielding of hydrogen-bonded proton increases as a function of temperature by about 0.003 ppm/K. This change is about an order of magnitude larger than that of the nonhydrogen-bonded proton. It is concluded that this is caused by the significant difference in the quantum distribution of proton at high and low temperatures in the low barrier hydrogen bond.

Shiga, Motoyuki; Suzuki, Kimichi; Tachikawa, Masanori

2010-03-01

324

Investigation of metal-insulator like transition through the ab initio density matrix renormalization group approach  

CERN Document Server

We have studied the Metal-Insulator like Transition (MIT) in lithium and beryllium ring-shaped clusters through ab initio Density Matrix Renormalization Group (DMRG) method. Performing accurate calculations for different interatomic distances and using Quantum Information Theory (QIT) we investigated the changes occurring in the wavefunction between a metallic-like state and an insulating state built from free atoms. We also discuss entanglement and relevant excitations among the molecular orbitals in the Li and Be rings and show that the transition bond length can be detected using orbital entropy functions. Also, the effect of different orbital basis on the effectiveness of the DMRG procedure is analyzed comparing the convergence behavior.

Fertitta, E; Barcza, G; Legeza, Ö

2014-01-01

325

Benefits of Parallel I/O in Ab Initio Nuclear Physics Calculations, ICCS 2009 Proceedings  

Energy Technology Data Exchange (ETDEWEB)

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.

Laghave, Nikhil; Sosonkina, Masha; Maris, Pieter; Vary, James P.

2009-05-20

326

Does Al4H14— cluster anion exist? High-level ab initio study  

Digital Repository Infrastructure Vision for European Research (DRIVER)

A comprehensive ab initio investigation using coupled cluster theory with the aug-cc-pVnZ, n?=?D,T basis sets is carried out to identify distinct structures of the Al4H14— cluster anion and to evaluate its fragmentation stability. Both thermodynamic and mechanistic aspects of the fragmentation reactions are studied. The observation of this so far the most hydrogenated aluminum tetramer was reported in the recent mass spectrometry study of Li et al. (2010) J Chem Phys 132:241103–241104...

Moc, Jerzy

2012-01-01

327

Relativistic ab initio study of forbidden transitions of singly ionized Zinc using CCSD(T)  

CERN Document Server

In this work, the {\\it ab initio} calculations have been carried out to study the oscillator strengths corresponding to `forbidden transitions' of astrophysically important electromagnetic transitions of singly ionized zinc, Zn II. Many important electron correlations are considered to all-orders using the relativistic coupled-cluster theory. Calculated ionization potentials are compared with the experimental values, wherever available. To our knowledge, oscillator strengths of magnetic dipole and electric quardupole transitions are estimated for the first time. The transitions span in the range of ultraviolet, visible, and near infrared regions and are important for astrophysical observations.

Dixit, Gopal; Chaudhuri, R K; Majumder, Sonjoy

2007-01-01

328

Structure and dynamics of liquid AsSe4 from ab initio molecular dynamics simulation  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Structural and dynamical properties of AsSe4 liquids have been studied by ab initio molecular dynamics simulations as a function of temperature. Calculated neutron structure factors are in good agreement with experimental data. Results show the existence of a significant amount of As-As homopolar bonds and of SeI and AsIV units which are not part of the picture of the cross-linking As(Se1/2)3 pyramids usually proposed for the glassy state.

Bauchy, Mathieu

2014-01-01

329

Density functional theory and ab initio methods applied to the analysis of inelastic neutron scattering spectra  

International Nuclear Information System (INIS)

The INS spectra of several azines have been analyzed starting from force constant matrix calculated via ab initio and DFT methods. In order to reproduce both vibrational frequencies and intensities, the initial force constants must be fitted until the spectral profile is reproduced. We have checked the various ways which can be followed by the user in this kind of analysis. The choice between scaling or refinement-procedure of the force constants can make an important difference in the reproduction of the INS spectrum

1999-06-15

330

Ab initio modeling of the short-range order in Fe-N austenite  

International Nuclear Information System (INIS)

We have studied the atomic structure of nitrogenous austenite. A high-precision ab initio method is utilized for the calculation of the pair potentials of interatomic interactions N-N in FCC Fe lattice. These potentials are used for the Monte Carlo modeling of the short-range order in the Fe-N system. It is discovered that nitrogen atoms in the FCC Fe lattice might be partially ordered. In this case, the atomic structure of nitrogenous austenite is characterized by the presence of the Fe6N phase with the short-range order over the N atoms located in the third coordination sphere.

2012-01-01

331

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

CERN Multimedia

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

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

2011-01-01

332

An ab initio investigation of the structure, vibrational frequencies, and intensities of HO2 and HOCl  

Science.gov (United States)

The infrared spectral intensities for HOCl and HO2 have been calculated using a new ab initio technique. Theoretical results for the geometries, vibrational frequencies, and the dipole moments of these species are also reported. All of the calculations were performed at the SCF level using near Hartree-Fock quality basis sets. The results for the molecular geometries and the vibrational frequencies are in good agreement with available experimental data. It is believed that the computed intensities are accurate to at least 50%. The results should be helpful in attempts to determine the stratospheric abundance of HOCl and HO2 by in situ infrared spectroscopic measurements.

Komornicki, A.; Jaffe, R. L.

1979-01-01

333

Carbon Nanotube with Square Cross-section: An Ab Initio Investigation  

CERN Document Server

Recently, Lagos et al. (Nature Nanotechnology 4, 149 (2009)) reported the discovery of the smallest possible silver square cross-section nanotube. A natural question is whether similar carbon nanotubes can exist. In this work we report ab initio results for the structural, stability and electronic properties for such hypothetical structures. Our results show that stable (or at least metastable) structures are possible with metallic properties. They also show that these structures can be obtained by a direct interconversion from SWNT(2,2). Large finite cubane-like oligomers, topologically related to these new tubes were also investigated.

Autreto, P A S; Flores, M Z S; Galvao, D S; 10.1063/1.348323

2010-01-01

334

Ab-initio study of disorder broadening of core photoemission spectra in random metallic alloys  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Ab-initio results of the core-level shift and the distribution about the average for the 3d5/2 electrons of Ag, Pd and 2p3/2 of Cu are presented for the face-centered-cubic AgPd and CuPd random alloys. The complete screening model, which includes both initial and final states effects in the same scheme, has been used in the investigations. The alloys have been modeled with a supercell containing 256 atoms. Density-functional theory calculations are carried out using the locally self consiste...

Marten, Tobias

2004-01-01

335

Estudio ab initio de la estructura electrónica y conformacional de oligómeros de tiofeno  

Directory of Open Access Journals (Sweden)

Full Text Available En este trabajo se presentan los resultados obtenidos en el estudio ab-initio, a nivel RHF/6-31G(d, de la estructura electrónica y conformacional de oligómeros de tiofeno (n = 2 - 8. Para cada oligómero se determinó la geometría de mínima energía, la estructura electrónica, el potencial de ionización vertical y la energía de excitación. Debido a la longitud de los enlaces C - C (1.462 Å y C = C (1.352 Å, la estructura de los oligómeros se caracterizó como tipo bencenoide. Los resultados obtenidos permiten proponer como modelo representativo del comportamiento de los oligotiofenos al oligómero con 6 anillos.

Marco Antonio Mora

2000-01-01

336

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

2002-05-01

337

Simulations of vibrational spectra from classical trajectories: Calibration with ab initio force fields  

Science.gov (United States)

An algorithm allowing simulating vibrational spectra from classical time-dependent trajectories was applied for infrared absorption, vibrational circular dichroism, Raman, and Raman optical activity of model harmonic systems. The implementation of the theory within the TINKER molecular dynamics (MD) program package was tested with ab initio harmonic force fields in order to determine the feasibility for more extended MD simulations. The results suggest that sufficiently accurate frequencies can be simulated with integration time steps shorter than about 0.5 fs. For a given integration time step, lower vibrational frequencies (~0-2000 cm-1) could be reproduced with a higher accuracy than higher-frequency vibrational modes (e.g., O-H and C-H stretching). In principle, the algorithm also provides correct intensities for ideal systems. In applied simulations, however, the intensity profiles are affected by an unrealistic energy distribution between normal modes and a slow energy relaxation. Additionally, the energy fluctuations may cause weakening of the intensities on average. For ab initio force fields, these obstacles could be overcome by an arbitrary normal mode energy correction. For general MD simulations, averaging of many shorter MD trajectories started with randomly distributed atomic velocities provided the best spectral shapes. ?-pinene, D-gluconic acid, formaldehyde dimer, and the acetylprolineamide molecule were used in the tests.

Horní?ek, Jan; Kaprálová, Petra; Bou?, Petr

2007-08-01

338

Ab initio density matrix renormalization group study of magnetic coupling in dinuclear iron and chromium complexes.  

Science.gov (United States)

The applicability of ab initio multireference wavefunction-based methods to the study of magnetic complexes has been restricted by the quickly rising active-space requirements of oligonuclear systems and dinuclear complexes with S > 1 spin centers. Ab initio density matrix renormalization group (DMRG) methods built upon an efficient parameterization of the correlation network enable the use of much larger active spaces, and therefore may offer a way forward. Here, we apply DMRG-CASSCF to the dinuclear complexes [Fe2OCl6](2-) and [Cr2O(NH3)10](4+). After developing the methodology through systematic basis set and DMRG M testing, we explore the effects of extended active spaces that are beyond the limit of conventional methods. We find that DMRG-CASSCF with active spaces including the metal d orbitals, occupied bridging-ligand orbitals, and their virtual double shells already capture a major portion of the dynamic correlation effects, accurately reproducing the experimental magnetic coupling constant (J) of [Fe2OCl6](2-) with (16e,26o), and considerably improving the smaller active space results for [Cr2O(NH3)10](4+) with (12e,32o). For comparison, we perform conventional MRCI+Q calculations and find the J values to be consistent with those from DMRG-CASSCF. In contrast to previous studies, the higher spin states of the two systems show similar deviations from the Heisenberg spectrum, regardless of the computational method. PMID:24511936

Harris, Travis V; Kurashige, Yuki; Yanai, Takeshi; Morokuma, Keiji

2014-02-01

339

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

340

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

Energy Technology Data Exchange (ETDEWEB)

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

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

2010-11-01

 
 
 
 
341

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

342

Embedding parameters in ab initio theory to develop well-controlled approximations based on molecular similarity  

CERN Multimedia

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

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

2013-01-01

343

Ab-initio based growth simulations of III-nitride nanowires  

Energy Technology Data Exchange (ETDEWEB)

III-Nitride based nanowires (NWs) have recently emerged as potential candidates for novel nanodevice applications. A prerequisite for improved device features is to achieve a better understanding of the atomic scale mechanisms that control the growth of these nanostructures. A key step is a quantitative description of the adatom kinetics taking place on the top and the side facets. In a recent ab-initio study we have investigated the thermodynamics and adatom kinetics on the non-polar GaN surfaces. Computing the potential energy surfaces for Ga adatoms revealed a strong anisotropy for the diffusion barriers for both a- and m-plane non-polar surfaces. Based on this insight and using the ab-initio computed kinetic parameters we developed a mesoscale growth model. This model consistently incorporates temperature and realistic growth geometries and allows to numerically solve the surface diffusion problem. Based on these calculations we provide a detailed discussion on the dependence of the NW growth rate on temperature, geometry as well as on the substrate.

Lymperakis, Liverios; Neugebauer, Joerg [Computational Materials Design Department, Max-Planck-Institut fuer Eisenforschung, Duesseldorf (Germany)

2010-07-01

344

An examination of structural characteristics of phenylacetylene by vibronic and rovibronic simulations of ab initio data.  

Science.gov (United States)

The structural properties of phenylacetylene have been investigated in the S(0)((1)A(1)) neutral ground and S(1)((1)B(2)) and S(2)((1)A(1)) singlet excited states and the D(0)((2)B(1)) cationic state using both rovibronic and multidimensional Franck-Condon simulations from data determined via correlated ab initio methods. Results are compared to experimental and ab initio data reported in the literature. (10,10)-CASSCF and a hybrid CASSCF/SACCI frequency analysis using the cc-pVDZ Dunning basis set have been employed to produce vibronic simulations of REMPI/FES, dispersed fluorescence, TPES and MATI spectra. Calculated rotational constants are used where appropriate to compare to rotationally resolved experimental studies. Whilst the simulations are of generally good quality, it is apparent that the distortion of the ring along the long axis upon electronic excitation is underestimated, resulting in smaller predicted changes in ipso and para CCC bond angles and weaker activities in the 6a and 9a modes compared with experiment. Simulations of one-photon MATI spectra on the other hand, which do not rely on excited state methodologies, compare very well with experiment, suggesting that the neutral and cationic ground state geometries are quite accurate, as are the predicted changes in geometry accompanying ionisation. Simulated rotational and vibrational profiles, as well as other calculated physical data, show good agreement with the numerous experimental and computational studies of phenylacetylene in the literature. PMID:17925970

Pugliesi, Igor; Tonge, Nicola M; Hornsby, Karen E; Cockett, Martin C R; Watkins, Mark J

2007-10-28

345

FTIR and FTRaman spectra, assignments, ab initio HF and DFT analysis of 4-nitrotoluene  

Science.gov (United States)

In this work, the experimental and theoretical study on molecular structure and vibrational spectra of 4-nitrotoluene are studied. The FTIR and FTRaman experimental spectra of the molecule have been recorded in the range of 4000-100 cm -1. Making use of the recorded data, the complete vibrational assignments are made and analysis of the observed fundamental bands of molecule is carried out. The experimental determinations of vibrational frequencies are compared with those obtained theoretically from ab initio HF and DFT quantum mechanical calculations using HF/6-31G (d, p), B3LYP/6-31++G* (d, p) and B3LYP/6-311++G* (d, p) methods. The differences between the observed and scaled wave number values of most of the fundamentals are very small in B3LYP than HF. The geometries and normal modes of vibrations obtained from ab initio HF and B3LYP calculations are in good agreement with the experimentally observed data. Comparison of the simulated spectra provides important information about the ability of the computational method (B3LYP) to describe the vibrational modes. The vibrations of NO 2 and CH 3 groups coupled with skeletal vibrations are also investigated.

Ramalingam, S.; Periandy, S.; Govindarajan, M.; Mohan, S.

2010-04-01

346

Ab initio density matrix renormalization group study of magnetic coupling in dinuclear iron and chromium complexes  

Science.gov (United States)

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

Harris, Travis V.; Kurashige, Yuki; Yanai, Takeshi; Morokuma, Keiji

2014-02-01

347

Surface processes and phase transitions from ab initio atomistic thermodynamics and statistical mechanics  

Energy Technology Data Exchange (ETDEWEB)

Knowledge of the surface composition and atomic geometry is a prerequisite for understanding the physical and chemical properties of modern materials such as those used in, for example, heterogeneous catalysis, corrosion resistance, sensors, and fuel cells. To understand the function of surfaces under realistic conditions, it is crucial to take into account the influence of environmental gas at finite (possibly high) temperatures and pressures. Recent experimental and theoretical studies have shown that when transition metal surfaces are exposed to high oxygen pressures, thin oxide-like structures can form which may have little similarity to the bulk oxides, and thus possess unique chemical and physical properties. Given that technological oxidation catalysis typically involves oxygen-rich conditions, such structures may be present, and in fact be the active material for the reaction, as opposed to the traditionally believed pure metal. Using the approach of ab initio atomistic thermodynamics, free energy phase-diagrams for oxygen/transition metal systems in (T, p)-space ranging from ultra-high vacuum to technically relevant pressures, p, and temperatures, T, are discussed. In addition, results of ab initio statistical mechanical schemes, namely, the Lattice-gas Hamiltonian plus Monte Carlo (MC) simulations, are presented for oxygen/transition metal and alkali-atom/metal systems, where for the latter, the recently introduced 'Wang-Landau' algorithm is employed, which affords an accurate estimation of the density of (configurational) states, therefore allowing a direct determination of all major thermodynamic functions.

Stampfl, Catherine [School of Physics, The University of Sydney, Sydney 2006 (Australia)

2005-07-15

348

Ab initio study of free-radical polymerization: polyethylene propagation kinetics.  

Science.gov (United States)

The chain-length dependence of the propagation rate coefficient for the free-radical polymerization of ethylene was investigated on an ab initio basis. Polyethylene was chosen as a test system because of its structural simplicity. Ab initio density functional theory at the B3LYP/6-31g(d) level was applied to study the kinetics of a set of addition reactions of a systematically growing radical alkyl chain to ethylene. These reactions are propagation steps in the free-radical polymerization of ethylene. Special attention was paid to low normal modes corresponding to internal rotations (IR), since the latter are important for an accurate description of the partition functions. The effect of coupling of the IR modes is also discussed. A comparison is made with the propagation rate constant derived from experiment. The results indicate that the propagation rate coefficient has largely converged by the hexyl radical stage, though a weaker chain-length dependence of k(p) for longer chains was detected. PMID:16404764

Van Cauter, Karen; Van Speybroeck, Veronique; Vansteenkiste, Peter; Reyniers, Marie-Francoise; Waroquier, Michel

2006-01-16

349

Ab initio group contribution method for activation energies of hydrogen abstraction reactions.  

Science.gov (United States)

The group contribution method for activation energies is applied to hydrogen abstraction reactions. To this end an ab initio database was constructed, which consisted of activation energies calculated with the ab initio CBS-QB3 method for a limited set of well-chosen homologous reactions. CBS-QB3 is shown to predict reaction rate coefficients within a factor of 2-4 and Arrhenius activation energies within 3-5 kJ mol(-1) of experimental data. Activation energies in the set of homologous reactions vary over 156 kJ mol(-1) with the structure of the abstracting radical and over 94 kJ mol(-1) with the structure of the abstracted hydrocarbon. The parameters required for the group contribution method, the so-called standard activation group additivity values, were determined from this database. To test the accuracy of the group contribution method, a large set of 88 additional activation energies were calculated from first principles and compared with the predictions from the group contribution method. It was found that the group contribution method yields accurate activation energies for hydrogen-transfer reactions between hydrogen molecules, alkylic hydrocarbons, and vinylic hydrocarbons, with the largest deviations being less than 6 kJ mol(-1). For reactions between allylic and propargylic hydrocarbons, the transition state is believed to be stabilized by resonance effects, thus requiring the introduction of an appropriate correction term to obtain a reliable prediction of the activation energy for this subclass of hydrogen abstraction reactions. PMID:16323223

Saeys, Mark; Reyniers, Marie-Françoise; Van Speybroeck, Veronique; Waroquier, Michel; Marin, Guy B

2006-01-16

350

FTIR and FT-Raman spectra, assignments, ab initio HF and DFT analysis of xanthine  

Science.gov (United States)

The molecular vibrations of xanthine were investigated in polycrystalline sample, at room temperature by Fourier transform infrared (FTIR) and FT-Raman spectroscopies. The spectra of the molecule have been recorded in the regions 4000-50 cm -1 and 3500-100 cm -1, respectively. Theoretical information on the optimized geometry, harmonic vibrational frequencies, infrared and Raman intensities were obtained by means of ab initio Hartree-Fock (HF) and density functional theory (DFT) gradient calculations with complete relaxation in the potential energy surface using 6-311++G(d,p) basis set. The vibrational frequencies which were determined experimentally from the spectral data are compared with those obtained theoretically from ab initio and DFT calculations. A close agreement was achieved between the observed and calculated frequencies by refinement of the scale factors. The infrared and Raman spectra were also predicted from the calculated intensities. Thermodynamic properties like entropy, heat capacity, zero point energy have been calculated for the molecule. Unambiguous vibrational assignment of all the fundamentals was made using the potential energy distribution (PED).

Arivazhagan, M.; Jeyavijayan, S.

2011-06-01

351

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

Science.gov (United States)

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

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

1995-01-01

352

Ab initio Calculation of optical properties of II-VI semiconductor surfaces  

Science.gov (United States)

In this work we present some ab initio calculations of reflectance anisotropy spectra (RAS) of VI-II semiconductor surfaces having different surface reconstructions. We use an ab initio pseudopotential formalism in the framework of the density functional theory and within the local density approximation (DFT-LDA). We study the (001) polar surface of cadmium telluride (CdTe) and zinc telluride ZnTe with differents reconstructions. Also we obtain RAS using a microscopic formulation based on a semi-empirical tight binding (SETB) approach which includes spin-orbit (SO) interactions [1]. We show RAS of each surface reconstruction and compare both theoretical results with experimental results [2]. We find a good agreement between experimental and theoretical spectra. [3pt] [1] R.A. V'azquez-Nava, B.S. Mendoza and C. Castillo, Phys. Rev. B 70, 165306 (2004). [0pt] [2] R. E. Balderas-Navarro, K. Hingerl, W. Hilber, D. Stifter, A. Bonanni and H. Sitter, J. Vac. Sci. Technol. B 18, 2224 (2000).

Vazquez-Nava, R. A.; Arzate, Norberto; Mendoza, B. S.

2009-03-01

353

Quantum simulations and ab initio electronic structure studies of (H2O)-2  

International Nuclear Information System (INIS)

The energetics of the negatively charged water dimer (H2O)-2, is studied using quantum-simulation techniques and ab initio electronic structure calculations. Using the RWK2-M potentials for water and a pseudopotential for the interaction of an electron with a water molecule in the ground state, consisting of Coulomb, adiabatic polarization, exclusion, and exchange contributions, it was found via the quantum path-integral molecular dynamics and the coupled quantum-classical time-dependent self-consistent field methods that while the minimum energy of (H2O)-2 corresponds to a nuclear configuration similar to that found for the neutral (H2O)2 cluster, other nuclear configurations are also exhibited at finite temperature, characterized by a higher total molecular cluster dipole moment and a larger magnitude of the excess electron binding energy. Quantitative agreement is found between the results obtained by the quantum simulations, employing the excess electron--molecule pseudopotential, and those derived, for selected nuclear configurations, via ab initio calculations, employing the Gaussian 86 code with the basis set for the water molecules supplemented by a large diffuse set located at the midpoint of the two oxygens and in addition by a diffuse set for the excess electron

1989-12-15

354

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

Science.gov (United States)

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. PMID:22411565

Xu, Dong; Zhang, Yang

2012-07-01

355

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

356

Effect of spin-orbit coupling on an ab initio Gutzwiller approach for Pu  

International Nuclear Information System (INIS)

We present an improved version of our recently proposed ab initio Gutzwiller method to study solids with strong local Coulomb interactions as a correction to first principles DFT-LDA (density functional theory in the local density approximation). The variational (Rayleigh-Ritz) parameters are the probabilities of atomic configurations. The quasiparticle spectrum is obtained from the eigenvalues of an effective Hamiltonian with renormalized hopping and on-site terms. Our method includes both an ab initio, parameter free, realistic description of the energy bands, as well as strong correlation aspects of the coherent part of the spectrum. It can be considered as an improvement to the LDA + U method, which has the same starting Hamiltonian but where the interactions are calculated only at the mean-field level. Application to ?-plutonium is presented, with particular attention to possible scenarios to discriminate between localized and less localized states due to spin-orbit coupling. This provides new insight into the still controversial electronic structure of this element

2007-10-11

357

Effect of spin-orbit coupling on an ab initio Gutzwiller approach for Pu  

Energy Technology Data Exchange (ETDEWEB)

We present an improved version of our recently proposed ab initio Gutzwiller method to study solids with strong local Coulomb interactions as a correction to first principles DFT-LDA (density functional theory in the local density approximation). The variational (Rayleigh-Ritz) parameters are the probabilities of atomic configurations. The quasiparticle spectrum is obtained from the eigenvalues of an effective Hamiltonian with renormalized hopping and on-site terms. Our method includes both an ab initio, parameter free, realistic description of the energy bands, as well as strong correlation aspects of the coherent part of the spectrum. It can be considered as an improvement to the LDA + U method, which has the same starting Hamiltonian but where the interactions are calculated only at the mean-field level. Application to {delta}-plutonium is presented, with particular attention to possible scenarios to discriminate between localized and less localized states due to spin-orbit coupling. This provides new insight into the still controversial electronic structure of this element.

Julien, J.P. [Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States)], E-mail: jpjulien@grenoble.cnrs.fr; Albers, R.C. [Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Bouchet, J. [CEA-DAM, Departement de Physique Theorique et Appliquee, Bruyeres-le-Chatel (France)

2007-10-11

358

Estudio ab initio del mecanismo de la reacción HSO + O3  

Science.gov (United States)

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

Nebot Gil, I.

359

Liquid chloroform structure from computer simulation with a full ab initio intermolecular interaction potential.  

Science.gov (United States)

We have calculated the intermolecular interaction energies of the chloroform dimer in 12 orientations using the second-order Møller-Plesset perturbation theory. Single point energies of important geometries were calibrated by the coupled cluster with single and double and perturbative triple excitation method. Dunning's correlation consistent basis sets up to aug-cc-pVQZ have been employed in extrapolating the interaction energies to the complete basis set limit values. With the ab initio potential data we constructed a 5-site force field model for molecular dynamics simulations. We compared the simulation results with recent experiments and obtained quantitative agreements for the detailed atomwise radial distribution functions. Our results were also consistent with previous results using empirical force fields with polarization effects. Moreover, the calculated diffusion coefficients reproduced the experimental data over a wide range of thermodynamic conditions. To the best of our knowledge, this is the first ab initio force field which is capable of competing with existing empirical force fields for liquid chloroform. PMID:24320333

Yin, Chih-Chien; Li, Arvin Huang-Te; Chao, Sheng D

2013-11-21

360

Ab initio calculation of free energies and thermodynamic properties of fcc metals  

Energy Technology Data Exchange (ETDEWEB)

Phase diagrams are indispensable tools in predicting material evolution during its processing. Current approaches to obtain such phase diagrams (e.g. CALPHAD) are based on an extra- and/or interpolation of experimental data. A crucial issue hampering this approach is the lack/high cost of specific experimental data (e.g. for unstable/metastable phases). For such cases, the replacement of experimental data by ab initio calculations is desirable. The accuracy of density-functional based ab initio methods is, in principle, only limited by the exchange-correlation (XC) functional. We have therefore evaluated the accuracy of the most commonly used functionals (LDA, GGA) by calculating key thermodynamic properties for a large set of metals (Al, Pb, Cu, Ag, Au, Pd, Pt, Rh, Ir). Great care was taken to ensure that convergence errors due to supercell size, k-point sampling, and energy cutoff are small compared to the error in the XC-functional. Based on the volume and temperature dependence of free energies calculated in the quasiharmonic approximation, thermodynamic quantities such as the thermal expansion or the heat capacity have been derived. The comparison to experiment yields an excellent agreement. A detailed analysis shows that the LDA/GGA results can typically be considered as error bars allowing to estimate the accuracy of the calculation in the absence of experiments.

Grabowski, Blazej; Hickel, Tilmann; Neugebauer, Joerg [Max-Planck-Institut fuer Eisenforschung GmbH, Duesseldorf (Germany)

2007-07-01

 
 
 
 
361

Thermodynamic assessment of the Ho–Te system supported by ab initio calculations  

Energy Technology Data Exchange (ETDEWEB)

Highlights: ? We calculated enthalpies of formation of the HoTe and Ho{sub 2}Te{sub 5} compounds by using ab initio method. ? We modeled the Gibbs energy of the HoTe intermediate phase for the first time. ? The thermodynamic parameters of the all phases existing in the system were determined. ? The complete phase diagram of the system (Ho–Te) is calculated. -- Abstract: The phase diagram of the Ho–Te binary system has been assessed by using the CALPHAD (Calculation of Phase Diagrams) method on the basis of the experimental data of the phase equilibria and enthalpies of formation from ab initio electronic-structure calculations within the framework of density-functional theory. Reasonable models were constructed for all the phases of the system. The liquid phase was described as the substitutional solution model with excess energy expressed by Redlich–Kister polynomial. The compounds Ho{sub 2}Te{sub 5} and HoTe{sub 3} were expressed as stoichiometric phases. The (HoTe) phase was modeled by two-sublattices; (Ho,Va){sub 1}(Te){sub 1}. A consistent set of thermodynamic parameters has been derived, and calculated phase diagram was compared with the experimental data. A good agreement between the calculated results and experimental data was obtained.

Ghamri, H.; Belgacem-Bouzida, A. [Laboratoire d’étude Physico-Chimique des Matériaux, Département de Physique, Faculté des Sciences, Université de Batna, Rue Chahid Boukhlouf, 05000 Batna (Algeria); Djaballah, Y., E-mail: ydjaballah@yahoo.fr [Laboratoire d’étude Physico-Chimique des Matériaux, Département de Physique, Faculté des Sciences, Université de Batna, Rue Chahid Boukhlouf, 05000 Batna (Algeria); Hidoussi, A. [Laboratoire d’étude Physico-Chimique des Matériaux, Département de Physique, Faculté des Sciences, Université de Batna, Rue Chahid Boukhlouf, 05000 Batna (Algeria)

2013-03-05

362

Structure and Raman spectra in cryolitic melts: simulations with an ab initio interaction potential.  

Science.gov (United States)

The Raman spectra of cryolitic melts have been calculated from molecular dynamics computer simulations using a polarizable ionic potential obtained by force-fitting to ab initio electronic structure calculations. Simulations which made use of this ab initio derived polarizable interaction potential reproduced the structure and dynamical properties of crystalline cryolite, Na3AlF6, rather well. The transferability of the potential model from solid state to the molten state is tested by comparing results for the Raman spectra of melts of various compositions with those previously obtained with empirically developed potentials and with experimental data. The shapes of the spectra and their evolution with composition in the mixtures conform quite well to those seen experimentally, and we discuss the relationship between the bands seen in the spectra and the vibrational modes of the AlFn((3–n)) coordination complexes which are found in the NaF/AlF3 mixtures. The simulations thus enable a link between the structure of the melt as derived through Raman spectroscopy and through diffraction experiments. We report results for quantities which relate to the degree of cross-linking between these coordination complexes and the diffusive properties of ions. PMID:24432905

Cikit, Serpil; Akdeniz, Zehra; Madden, Paul A

2014-01-30

363

Evolved Chiral NN+3N Hamiltonians for Ab Initio Nuclear Structure Calculations  

CERN Document Server

We discuss the building blocks for a consistent inclusion of chiral three-nucleon (3N) interactions into ab initio nuclear structure calculations beyond the lower p-shell. We highlight important technical developments, such as the similarity renormalization group (SRG) evolution in the 3N sector, a JT-coupled storage scheme for 3N matrix elements with efficient on-the-fly decoupling, and the importance truncated no-core shell model with 3N interactions. Together, these developments make converged ab initio calculations with explicit 3N interactions possible also beyond the lower p-shell. We analyze in detail the impact of various truncations of the SRG-evolved Hamiltonian, in particular the truncation of the harmonic-oscillator model space used for solving the SRG flow equations and the omission of the induced beyond-3N contributions of the evolved Hamiltonian. Both truncations lead to sizable effects in the upper p-shell and beyond and we present options to remedy these truncation effects. The analysis of th...

Roth, Robert; Langhammer, Joachim; Binder, Sven

2013-01-01

364

Can an ab initio three-body virial equation describe the mercury gas phase?  

Science.gov (United States)

We report a sixth-order ab initio virial equation of state (EOS) for mercury. The virial coefficients were determined in the temperature range from 500 to 7750 K using a three-body approximation to the N-body interaction potential. The underlying two-body and three-body potentials were fitted to highly accurate Coupled-Cluster interaction energies of Hg2 (Pahl, E.; Figgen, D.; Thierfelder, C.; Peterson, K. A.; Calvo, F.; Schwerdtfeger, P. J. Chem. Phys. 2010, 132, 114301-1) and equilateral-triangular configurations of Hg3. We find the virial coefficients of order four and higher to be negative and to have large absolute values over the entire temperature range considered. The validity of our three-body, sixth-order EOS seems to be limited to small densities of about 1.5 g cm(-3) and somewhat higher densities at higher temperatures. Termwise analysis and comparison to experimental gas-phase data suggest a small convergence radius of the virial EOS itself as well as a failure of the three-body interaction model (i.e., poor convergence of the many-body expansion for mercury). We conjecture that the nth-order term of the virial EOS is to be evaluated from the full n-body interaction potential for a quantitative picture. Consequently, an ab initio three-body virial equation cannot describe the mercury gas phase. PMID:24547987

Wiebke, J; Wormit, M; Hellmann, R; Pahl, E; Schwerdtfeger, P

2014-03-27

365

Thermodynamic assessment of the Ho–Te system supported by ab initio calculations  

International Nuclear Information System (INIS)

Highlights: ? We calculated enthalpies of formation of the HoTe and Ho2Te5 compounds by using ab initio method. ? We modeled the Gibbs energy of the HoTe intermediate phase for the first time. ? The thermodynamic parameters of the all phases existing in the system were determined. ? The complete phase diagram of the system (Ho–Te) is calculated. -- Abstract: The phase diagram of the Ho–Te binary system has been assessed by using the CALPHAD (Calculation of Phase Diagrams) method on the basis of the experimental data of the phase equilibria and enthalpies of formation from ab initio electronic-structure calculations within the framework of density-functional theory. Reasonable models were constructed for all the phases of the system. The liquid phase was described as the substitutional solution model with excess energy expressed by Redlich–Kister polynomial. The compounds Ho2Te5 and HoTe3 were expressed as stoichiometric phases. The (HoTe) phase was modeled by two-sublattices; (Ho,Va)1(Te)1. A consistent set of thermodynamic parameters has been derived, and calculated phase diagram was compared with the experimental data. A good agreement between the calculated results and experimental data was obtained

2013-03-05

366

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

International Nuclear Information System (INIS)

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

2007-09-26

367

Ab initio and classical molecular dynamics studies of the structural and dynamical behavior of water near a hydrophobic graphene sheet.  

Science.gov (United States)

The behavior of water near a graphene sheet is investigated by means of ab initio and classical molecular dynamics simulations. The wetting of the graphene sheet by ab initio water and the relation of such behavior to the strength of classical dispersion interaction between surface atoms and water are explored. The first principles simulations reveal a layered solvation structure around the graphene sheet with a significant water density in the interfacial region implying no drying or cavitation effect. It is found that the ab initio results of water density at interfaces can be reproduced reasonably well by classical simulations with a tuned dispersion potential between the surface and water molecules. Calculations of vibrational power spectrum from ab initio simulations reveal a shift of the intramolecular stretch modes to higher frequencies for interfacial water molecules when compared with those of the second solvation later or bulk-like water due to the presence of free OH modes near the graphene sheet. Also, a weakening of the water-water hydrogen bonds in the vicinity of the graphene surface is found in our ab initio simulations as reflected in the shift of intermolecular vibrational modes to lower frequencies for interfacial water molecules. The first principles calculations also reveal that the residence and orientational dynamics of interfacial water are somewhat slower than those of the second layer or bulk-like molecules. However, the lateral diffusion and hydrogen bond relaxation of interfacial water molecules are found to occur at a somewhat faster rate than that of the bulk-like water molecules. The classical molecular dynamics simulations with tuned Lennard-Jones surface-water interaction are found to produce dynamical results that are qualitatively similar to those of ab initio molecular dynamics simulations. PMID:23742495

Rana, Malay Kumar; Chandra, Amalendu

2013-05-28

368

Metastable phases and spinodal decomposition in Ti1-xAl xN system studied by ab initio and thermodynamic modeling, a comparison with the TiN-Si3N4 system  

International Nuclear Information System (INIS)

The total energies and lattice constants of binary hcp- and fcc-TiN, AlN and ternary Ti0.5Al0.5N phases are calculated by ab initio method using the Vienna ab initio simulation package (VASP). The values of total energies are then used to calculate the lattice stabilities of binary hcp- and fcc-TiN, AlN and the interaction parameter of ternary Ti1-xAl xN phases on the basis of the semiempirical, thermodynamic sub-lattice model. Based on these data, the Gibbs free energy diagram of the immiscible quasi-binary TiN-AlN system are constructed in order to discuss the relative phase stability of the metastable ternary hcp- and fcc-Ti1-xAl xN phases over the entire range of compositions. The prediction is compared with the published results from PVD and CVD experiments. The calculated lattice energy and the constructed Gibbs free energy diagram show, in agreement with the experiments, that metastable fcc-Ti1-xAl xN coatings can easily undergo spinodal decomposition into coherent fcc-TiN and fcc-AlN, but there is a relatively large barrier for the formation of the stable hcp-AlN. A comparison with the TiN-Si3N4 system shows that, due to the much higher de-mixing energy of this system as compared to the TiN-AlN one, spinodal decomposition may occur in that system also for semicoherent TiN and Si3N4 phases

2007-03-15

369

Ab initio determination of mode coupling in HSSH - The torsional splitting in the first excited S-S stretching state  

Science.gov (United States)

A mechanism for the enhanced splitting detected in the millimeter-wave rotational spectra of the first excited S-S stretching state of HSSH (disulfane) has been studied. The mechanism, which involves a potential coupling between the first excited S-S stretching state and excited torsional states, has been investigated in part by the use of ab initio theory. Based on an ab initio potential surface, coupling matrix elements have been calculated, and the amount of splitting has then been estimated by second-order perturbation theory. The result, while not in quantitative agreement with the measured splitting, lends plausibility to the assumed mechanism.

Herbst, Eric; Winnewisser, G.; Yamada, K. M. T.; Defrees, D. J.; Mclean, A. D.

1989-01-01

370

Structural phase transitions in Ruddlesden-Popper phases of strontium titanate: Ab initio and modulated Ginzburg-Landau approaches  

Science.gov (United States)

We present a systematic ab initio study of antiferrodistortive (AFD) order in Ruddlesden-Popper (RP) phases of strontium titanate, Sr1+nTinO3n+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 AFD order of bulk SrTiO3 as ˜1/n2 . A Ginzburg-Landau Hamiltonian including interoctahedral interactions reproduces our ab initio results well, opening a pathway to understanding other nanostructured perovskite systems.

Lee, Jeehye; Arias, Tomás A.

2010-11-01

371

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

372

Ab-initio vibrational properties of transition metal chalcopyrite alloys determined as high-efficiency intermediate-band photovoltaic materials  

Digital Repository Infrastructure Vision for European Research (DRIVER)

In this work, we present frozen phonon and linear response ab-initio research into the vibrational properties of the CuGaS2 chalcopyrite and transition metal substituted (CuGaS2)M alloys. These systems are potential candidates for developing a novel solar-cell material with enhanced optoelectronic properties based in the implementation of the intermediate-band concept. We have previously carried out ab-initio calculations of the electronic properties of these kinds of chalcopyrite metal alloy...

2008-01-01

373

A theoretical-spectroscopy, ab-initio-based study of the electronic ground state of 121SbH3  

Digital Repository Infrastructure Vision for European Research (DRIVER)

For the stibine isotopologue (SbH3)-Sb-121, we report improved theoretical calculations of the vibrational energies below 8000 cm- and simulations of the rovibrational spectrum in the 0-8000 cm(-1) region. The calculations are based on a refined ab initio potential energy surface and on a new dipole moment surface obtained at the coupled cluster CCSD(T) level. The theoretical results are compared with the available experimental data in order to validate the ab initio surfaces and the TROVE co...

Yurchenko, Sergei N.; Carvajal Zaera, Miguel; Yachmenev, Andrey; Thiel, Walter; Jensen, Per

2010-01-01

374

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

International Nuclear Information System (INIS)

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

2011-07-28

375

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

Energy Technology Data Exchange (ETDEWEB)

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

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

2011-07-28

376

Impact and penetration studies: Simplified models and materials design from ab initio methods  

Science.gov (United States)

In recent impact and penetration mechanical tests, steel projectiles (AISI4340) were impacted into targets like concrete with striking velocities (1200 m/s to 1500 m/s). Results indicated a material removal from the nose of the projectile, phase changes of the projectile materials, a reduction in the length of the projectile, and a blunting of the nose shape. These observations cannot be explained by current theories and numerical integration code that are used to study impact and penetration mechanics. Thus, the objectives of the thesis research are to (a) formulate and characterize the mechanisms responsible for the material erosion of the impacting projectile and the mass loss from the nose region; and (b) to determine the physical properties of alloy steels that are important to penetration mechanics from ab initio methods. The results can be used to design new projectile materials that can provide the desired penetration characteristics. These objectives are accomplished by investigating two related problems. The first problem is to formulate simplified models that can explain the penetration mechanics. The new models include the varying cross-section nose, changes of yield stress behind the shock wave and high strain rate phase transitions. Nose erosion effects, and time-dependent penetration path can be determined by integrating ODEs. A cavity expansion theory model is used to obtain the target resistance that is responsible slowing and deforming the penetrating projectile. The second problem concerns the determination of the constitutive relations from ab initio methods. The equation of state (EOS) and magnetic moments for alloy steels are investigated by using a special quasirandom structure technique and ab initio methods. Specifically, EOS for an interstitial disordered alloy Fe1-x-yNixCy is developed. First, the EOS of iron and phase transition of iron are studied and validated. Second, Nickel is considered to investigate the substitutional disordered alloy Fe1-x-y NixCy. Third, Carbon is placed at an interstitial position in the substitutional disordered alloy. These investigations will form foundation for future work involving new projectile with steel nose and shank made of multifunctional structural energetic materials.

Jiang, Tianci

377

Ab initio study of perovskite type oxide materials for solid oxide fuel cells  

Science.gov (United States)

Perovskite type oxides form a family of materials of significant interest for cathodes and electrolytes of solid oxide fuel cells (SOFCs). These perovskites not only are active catalysts for surface oxygen reduction (OR) reactions but also allow incorporating the spilt oxygen monomers into their bulk, an unusual and poorly understood catalytic mechanism that couples surface and bulk properties. The OR mechanisms can be influenced strongly by defects in perovskite oxides, composition, and surface defect structures. This thesis work initiates a first step in developing a general strategy based on first-principles calculations for detailed control of oxygen vacancy content, transport rates of surface and bulk oxygen species, and surface/interfacial reaction kinetics. Ab initio density functional theory methods are used to model properties relevant for the OR reactions on SOFC cathodes. Three main research thrusts, which focus on bulk defect chemistry, surface defect structures and surface energetics, and surface catalytic properties, are carried to investigate different level of material chemistry for improved understanding of key physics/factors that govern SOFC cathode OR activity. In the study of bulk defect chemistry, an ab initio based defect model is developed for modeling defect chemistry of LaMnO 3 under SOFC conditions. The model suggests an important role for defect interactions, which are typically excluded in previous defect models. In the study of surface defect structures and surface energetics, it is shown that defect energies change dramatically (1˜2 eV lower) from bulk values near surfaces. Based on the existing bulk defect model with the calculated ab initio surface defect energetics, we predict the (001) MnO 2 surface oxygen vacancy concentration of (La0.9Sr0.1 )MnO3 is about 5˜6 order magnitude higher than that of the bulk under typical SOFC conditions. Finally, for surface catalytic properties, we show that area specific resistance, oxygen exchange rates, and key OR energetics of the SOFC cathode perovskites, can be described by a single descriptor, either the bulk O p-band or the bulk oxygen vacancy formation energy. These simple descriptors will further enable first-principles optimization/design of new SOFC cathodes.

Lee, Yueh-Lin

378

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.

Wiuf Carsten

2007-12-01

379

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

2012-05-01

380

Nuclear fuel behavior at an atomic scale: the contributions of the ab initio calculations and the synchrotron radiation  

International Nuclear Information System (INIS)

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.)

2000-01-01

 
 
 
 
381

X-RAY EMISSION PROCESSES FOR MOLECULES : AN AB INITIO STUDY FOR THE N2O MOLECULE  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The oxygen and nitrogen X-ray spectra for the N2O molecule have been calculated using an ab initio molecular orbital method at the relaxed Hartree Fock level. Transition rates include interatomic contributions. The central and terminal nitrogen atom spectra are separately identified. Comparison with the experimental spectrum reveals the extent of satellite contamination in the electron impact excited spectrum.

Larkins, F.; Phillips, R.

1987-01-01

382

Ab initio molecular orbital calculation considering the quantum mechanical effect of nuclei by path integral molecular dynamics  

Science.gov (United States)

We present an accurate calculational scheme for many-body systems composed of electrons and nuclei, by path integral molecular dynamics technique combined with the ab initio molecular orbital theory. Based upon the scheme, the simulation of a water molecule at room temperature is demonstrated, applying all-electron calculation at the Hartree-Fock level of theory.

Shiga, Motoyuki; Tachikawa, Masanori; Miura, Shinichi

2000-12-01

383

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

Science.gov (United States)

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 with 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 nonhomologous targets. Further developments of sensitive fold-recognition and ab initio folding methods are critical for solving these problems. PMID:23760925

Zhang, Yang

2014-02-01

384

A Photoelectron Spectroscopy and ab initio Study of B3- and B4- Anions and Their Neutrals  

International Nuclear Information System (INIS)

The two smallest boron clusters (B3 and B4) in their neutral and anionic forms were studied by photoelectron spectroscopy and ab initio calculations. Vibrationally resolved photoelectron spectra were observed for B3- at three photon energies (355, 266, and 193 nm) and the electron affinity of B3 was measured to be +0.02 eV

2003-11-06

385

The electronic structure of LaMO3 (M=Ti-Ni) compounds from an ab-initio approach  

International Nuclear Information System (INIS)

The results obtained from the ab-initio band structure calculations based on the linearized muffin tin orbital atomic sphere approximation for LaMO3 (M=Ti-Ni) in terms of a parametrized nearest-neighbour tight binding (TB) model are analysed and also extracted various interaction strengths

1996-12-27

386

Ab initio studies of structures and properties of small potassium clusters  

CERN Document Server

We have studied the structure and properties of potassium clusters containing even number of atoms ranging from 2 to 20 at the ab initio level. The geometry optimization calculations are performed using all-electron density functional theory with gradient corrected exchange-correlation functional. Using these optimized geometries we investigate the evolution of binding energy, ionization potential, and static polarizability with the increasing size of the clusters. The polarizabilities are calculated by employing Moller-Plesset perturbation theory and time dependent density functional theory. The polarizabilities of dimer and tetramer are also calculated by employing large basis set coupled cluster theory with single and double excitations and perturbative triple excitations. The time dependent density functional theory calculations of polarizabilities are carried out with two different exchange-correlation potentials: (i) an asymptotically correct model potential and (ii) within the local density approximati...

Banerjee, Arup; Chakrabarti, Aparna

2008-01-01

387

Ab Initio Calculations of the Electronic Structures and Biological Functions of Protein Molecules  

Science.gov (United States)

The self-consistent cluster-embedding (SCCE) calculation method reduces the computational effort from M3 to about M1 (M is the number of atoms in the system) with unchanged calculation precision. So the ab initio, all-electron calculation of the electronic structure and biological function of protein molecule becomes a reality, which will promote new proteomics considerably. The calculated results of two real protein molecules, the trypsin inhibitor from the seeds of squash Cucurbita maxima (CMTI-I, 436 atoms) and the Ascaris trypsin inhibitor (912 atoms, two three-dimensional structures), are presented. The reactive sites of the inhibitors are determined and explained. The precision of structure determination of inhibitors are tested theoretically.

Zheng, Haoping

2003-04-01

388

Cluster form factor calculation in the ab initio no-core shell model  

CERN Multimedia

We derive expressions for cluster overlap integrals or channel cluster form factors for ab initio no-core shell model (NCSM) wave functions. These are used to obtain the spectroscopic factors and can serve as a starting point for the description of low-energy nuclear reactions. We consider the composite system and the target nucleus to be described in the Slater determinant (SD) harmonic oscillator (HO) basis while the projectile eigenstate to be expanded in the Jacobi coordinate HO basis. This is the most practical case. The spurious center of mass components present in the SD bases are removed exactly. The calculated cluster overlap integrals are translationally invariant. As an illustration, we present results of cluster form factor calculations for , , , , , , , , and , with all the nuclei described by multi-hbar Omega NCSM wave functions.

Navrátil, P

2004-01-01

389

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

390

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

2008-02-01

391

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

CERN Multimedia

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.

Huke, A; Chun, S M; Biller, A; Heide, P

2008-01-01

392

1\\/2,1\\/2 Representation space An ab initio construct  

CERN Document Server

A careful ab initio construction of the finite-mass (1/2,1/2) representation space of the Lorentz group reveals it to be a spin-parity multiplet. In general, it does not lend itself to a single-spin interpretation. We find that (1/2,1/2) representation space for massive particles naturally bifurcates into a triplet and a singlet of opposite relative intrinsic parties. The text-book separation into spin one and spin zero states occurs only for certain limited kinematical settings. We construct a wave equation for the (1/2,1/2) multiplet, and show that the particles and antiparticles in this representation space do not carry a definite spin but only a definite relative intrinsic parity. In general, both spin one and spin zero are covariantly inseparable inhabitants of massive vector fields. This last observation suggests that scalar particles, such as the Higgs, may be intrinsic part of massive vector gauge fields.

Ahluwalia, D V

2001-01-01

393

Ab initio investigation of surface phonons on the (0 0 1) surface of ZrC  

International Nuclear Information System (INIS)

We presented an ab initio pseudopotential study within the generalized gradient density functional approximation of the structural and electronic properties of the ZrC(0 0 1) surface. The calculated structural parameters for the ZrC(0 0 1) surface accord very well with previous experimental findings. The ZrC(0 0 1) surface is metallic, because at least one surface state crosses the Fermi level in the gap region of the projected electronic spectrum. Using our atomic and electronic structures, surface phonon dispersion curves are calculated by employing a linear response approach on the density functional perturbation theory. The calculated phonon spectrum compares very well with the experimental data. The atomic displacement patterns of the zone-center and zone-edge phonon modes are presented and analyzed for the ZrC(0 0 1) surface, carefully. Using this analyzation, energy locations and polarization characteristics of Love, Wallis, Lucas, and Fuchs–Kliewer modes have been determined

2014-02-01

394

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

International Nuclear Information System (INIS)

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

2013-05-15

395

Identifying Stereoisomers by ab-initio Calculation of Secondary Isotope Shifts on NMR Chemical Shieldings  

Directory of Open Access Journals (Sweden)

Full Text Available We present ab-initio calculations of secondary isotope effects on NMR chemical shieldings. The change of the NMR chemical shift of a certain nucleus that is observed if another nucleus is replaced by a different isotope can be calculated by computing vibrational corrections on the NMR parameters using electronic structure methods. We demonstrate that the accuracy of the computational results is sufficient to even distinguish different conformers. For this purpose, benchmark calculations for fluoro(2-2Hethane in gauche and antiperiplanar conformation are carried out at the HF, MP2 and CCSD(T level of theory using basis sets ranging from double- to quadruple-zeta quality. The methodology is applied to the secondary isotope shifts for 2-fluoronorbornane in order to resolve an ambiguity in the literature on the assignment of endo- and exo-2-fluoronorbornanes with deuterium substituents in endo-3 and exo-3 positions, also yielding insight into mechanistic details of the corresponding synthesis.

Karl-Heinz Böhm

2014-04-01

396

Communication: Comparing ab initio methods of obtaining effective U parameters for closed-shell materials  

Science.gov (United States)

The density functional theory (DFT)+U method is an efficient and effective way to calculate the ground-state properties of strongly correlated transition metal compounds, with the effective U parameters typically determined empirically. Two ab initio methods have been developed to compute the U parameter based on either constrained DFT (CDFT) or unrestricted Hartree-Fock (UHF) theory. Previous studies have demonstrated the success of both methods in typical open-shell materials such as FeO and NiO. In this Communication we report numerical instability issues that arise for the CDFT method when applied to closed-shell transition metals, by using ZnO and Cu2O as examples. By contrast, the UHF method behaves much more robustly for both closed- and open-shell materials, making it more suitable for treating closed-shell transition metals, as well as main group elements.

Yu, Kuang; Carter, Emily A.

2014-03-01

397

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

398

Ab initio calculations of the electronic transport in MnAs nanoclusters  

Energy Technology Data Exchange (ETDEWEB)

Magnetic MnAs nanoclusters can be grown on a GaAs substrate in a controlled manner. Such structures can be used to construct planar magnetic devices for spintronic applications. We perform ab initio calculations by means of the non-equilibrium Keldysh formalism implemented in the Korringa-Kohn-Rostoker Green's function method. We study the spin-dependent transport of MnAs in the hexagonal NiAs structure along different crystallographic directions. Furthermore we discuss in detail the transport through interfaces formed by two MnAs clusters with different magnetic domains. We found a very large magnetoresistance ratio above 200% while the spin polarization is low, which is originated by the different Fermi surface topologies of the two spin channels.

Czerner, Michael; Simon, Andre; Heiliger, Christian [I. Physikalisches Institut, Justus Liebig University Giessen, D-35392 (Germany)

2010-07-01

399

Ab initio modeling of radiation damage in MgF2 crystals  

Science.gov (United States)

MgF2 with a rutile structure is important radiation-resistant material with numerous applications due to its transparency from vacuum ultraviolet to infrared range of photon energies. We present and discuss the results of calculations for basic radiation defects in this crystal. The study is based on the large scale ab initio DFT calculations using hybrid B3PW exchange–correlation functional and atomic basis set. We analyzed the electronic structure, atomic displacements, charge density distribution as well as defect formation energies using large supercells. We compared properties of close and well separated F?H (Frenkel) defect pairs as well as individual defects. We simulated also formation and energetic preference of inert F2 interstitial molecules as sinks of mobile interstitial fluorine atoms which is relevant for material radiation stability. We discussed also diffusion of the primary electronic defects—F centers.

Abuova, F. U.; ??t?min, E. A.; Lisitsyn, V. M.; ?kilbekov, A. T.; Piskunov, S.

2014-05-01

400

Ab-initio simulation of optical-field induced currents in dielectrics  

CERN Document Server

We theoretically investigate the generation of ultrafast currents in insulators induced by strong few-cycle laser pulses. Ab-initio simulations based on time-dependent density functional theory give insights into the atomic-scale properties of the induced current signifying a femtosecond-scale insulator-metal transition. We observe the transition from nonlinear polarization currents during the laser pulse at low intensities to tunneling-like excitation into the conduction band at higher laser intensities. At high intensities, the current persists after the conclusion of the laser pulse considered to be the precursor of the dielectric breakdown on the femtosecond scale. We show that the transferred charge sensitively depends on the orientation of the polarization axis relative to the crystal axis suggesting that the induced charge separation reflects the anisotropic electronic structure. We find good agreement with very recent experimental data on the intensity and carrier-envelope phase dependence [1].

Wachter, Georg; Burgdörfer, Joachim; Sato, Shunsuke A; Tong, Xiao-Min; Yabana, Kazuhiro

2014-01-01

 
 
 
 
401

Ab initio high-resolution single-particle 3D reconstructions: the symmetry adapted functions way.  

Science.gov (United States)

A protocol to attain high-resolution single-particle reconstructions is presented. The protocol is the concatenation of two procedures: one to obtain an ab initio low-resolution reconstruction, the other to determine a fixed point of the consecutive applications of fast projection matching and 3D reconstruction. It is a reciprocal space formulation where the Fourier coefficients of the 3D scattering density are expressed in terms of symmetry adapted functions and the 2D particle images are represented by their Fourier-Bessel transforms. The new protocol shows advantages in terms of speed and accuracy when compared to other methods currently in use. We illustrate its performance as applied to high-resolution cryo-electron micrographs of rotavirus. PMID:20599509

Estrozi, Leandro F; Navaza, Jorge

2010-12-01

402

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

2007-05-01

403

Bond orders from ab initio calculations and a test of the principle of bond order conservation  

Energy Technology Data Exchange (ETDEWEB)

Bond orders and valence indexes of atoms were calculated from ab initio wave functions using the definition suggested by Mayer. Changes of these quantities were investigated under conditions occurring in chemical reactions. Calculations were performed to reveal the dependence of bond orders on bond length. The results are compared with Pauling's bond order-bond length relation. Bond orders were also calculated in triatomic metathesis reactions. Bond orders are able to describe the similarity of the transition state of reactants or products. Along the minimum-energy path the principle of conservation of bond order is valid a good approximation. The obtained correlations are applied to a bond energy-bond order type model to estimate trends in reaction series.

Lendvay, G. (Central Research Institute for Chemistry, Budapest (Hungary))

1989-06-01

404

Ab-initio simulation of photoinduced transformation of small rings in amorphous silica  

CERN Document Server

We have studied the photoinduced transformation of small rings (3-membered) in amorphous silica by Car-Parrinello simulations. The process of ring opening leading to the formation of a couple of paramagnetic centers, namely an E' and a non-bridging-oxygen hole center (NBOHC), has been proposed experimentally to occur in silica exposed to F2 laser irradiation (at 7.9 eV). By using a new scheme for the simulation of rare events in ab-initio molecular dynamics (Iannuzzi, Laio and Parrinello, Phys. Rev. Lett. 90, 238303 (2003)), we have identified the transformation path for the opening of a 3-membered ring induced by a self-trapped triplet exciton, the migration of NBOHC and formation of a couple of stable E' and NBOHC paramagnetic defects.

Bernasconi, D D M

2004-01-01

405

Mapping enzymatic catalysis using the effective fragment molecular orbital method : towards all ab initio biochemistry  

DEFF Research Database (Denmark)

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 [Formula: see text] kcal mol(-1) for MP2/cc-pVDZ and [Formula: see text] for MP2/cc-pVTZ in an ONIOM approach using EFMO-RHF/6-31G(d) for the high and low layers, respectively.

Svendsen, Casper Steinmann; Fedorov, Dmitri G.

2013-01-01

406

Ab initio simulations of diluted magnetic semiconductors: cobalt-doped zinc oxide  

Energy Technology Data Exchange (ETDEWEB)

The structural and magnetic properties of diluted magnetic III-V and II-VI semiconductors (DMS) have been investigated using ab initio simulations techniques based on density functional theory and the generalized gradient approximation (GGA) for the exchange-correlation term. In order to achieve an agreement with spectroscopic data of the electronic structure, it is necessary to employ methods which go beyond the standard implementation of density funcional theory allowing for a better description of Coulomb correlations in the poorly screened rather open ionic structures of the materials. As an example, we give a detailed description of Co-doped ZnO in the wurtzite lattice. (copyright 2008 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

Nayak, Sanjeev K.; Hucht, Alfred; Buschmann, Stephan; Entel, Peter [Physics Department, University of Duisburg-Essen, Duisburg (Germany); Ogura, Masako; Akai, Hisazumi [Department of Physics, Osaka University, Toyonaka (Japan)

2008-08-15

407

An ab initio study of singlet and triplet Rydberg states of N2  

International Nuclear Information System (INIS)

Potential energy curves for electronically excited states of molecular nitrogen are calculated using three different ab initio procedures. The most comprehensive of these involves the use of scattering calculations, performed at negative energy using the UK molecular R-matrix method. Such calculations are used to characterize all the Rydberg states of N2 with n ? 6 and ? ? 4 as well as many higher states including some Rydberg states associated with the first excited A 2?u state of N2+. Many of these states are previously unknown. The calculations are performed at a dense grid of internuclear separations allowing the many avoided crossings present in the system to be mapped out in detail. Extensive comparisons are made with the previously available data for excited states of N2. (paper)

2013-07-01

408

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.

Shimojo F.

2011-05-01

409

Ab initio/DFT calculations of butyl ammonium salt of O,O'-dibornyl dithiophosphate.  

Science.gov (United States)

O,O'-dibornyl dithiophosphete has been synthesized by the reaction of P2S5 and borneol in toluene. Fourier Transform Infrared spectra (FT-IR) of the title compound are measured. The molecular geometry, vibrational frequencies, infrared intensities and NMR spectrum of the title compound in the ground state have been calculated by using the density functional theory (DFT) and ab initio Hartree-Fock (HF) methods with the basis set of 6-31G(d). The computed bond lengths and bond angles show the good agreement with the experimental data. Moreover, the vibrational frequencies are calculated and the scaled values have been compared with experimental FT-IR spectra. Assignments of the vibrational modes are made on the basis of total energy distribution (TED) calculated with scaled quantum mechanical (SQM) method. The observed and calculated FT-IR and NMR spectra are in good agreement with each other. PMID:24747929

Kart, H H; Ozdemir Kart, S; Karaku?, M; Kurt, M

2014-08-14

410

Electronic and optical properties of SrTiO3 under pressure effect: Ab initio study  

Science.gov (United States)

We present an investigation on hydrostatic pressure dependence of electronic and optical properties of the perovskite SrTiO3 in cubic and tetragonal structures, including band structure, density of states, dielectric function, refractive index, absorption coefficient, reflectivity and electron energy-loss function. Calculations are performed using ab initio pseudopotential density functional method with the generalized gradient approximation. The cubic structure is optimized at zero pressure while the tetragonal structure is optimized under its structural phase transition pressure, which is previously calculated to be 6.0 GPa. Comparison between electronic and optical properties of the considered structures has been done. We find that the electronic and optical properties of the cubic phase are quite different from those of the tetragonal one.

Khaber, L.; Beniaiche, A.; Hachemi, A.

2014-07-01

411

Ab initio molecular dynamics, iterative methods and multiscale approaches in electronic structure calculations  

International Nuclear Information System (INIS)

The field of computational materials physics has grown very quickly in the past decade, and it is now possible to simulate properties of complex materials completely from first principles. The presentation has mostly focused on first-principles dynamic simulations. Such simulations have been pioneered by Car and Parrinello, who introduced a method for performing realistic simulations within the context of density functional theory. The Car-Parrinello method and related plane wave approaches are reviewed in depth. The Car-Parrinello method was reviewed and illustrated with several applications: the dynamics of the C60 solid, diffusion across Si steps, and computing free energy differences. Alternative ab initio simulation schemes, which use preconditioned conjugate gradient techniques for energy minimization and dynamics were also discussed

1998-06-01

412

Experimental and ab initio study of Ta-doped ZnO semiconductor  

International Nuclear Information System (INIS)

In this work, we present ?–? Perturbed-Angular-Correlation results in polycrystalline ZnO semiconductor implanted with 181Hf(?181Ta) probes. Calculations in Ta-doped ZnO were carried out using the Full-Potential Augmented Plane Wave plus local orbital method in a supercell and varying self-consistently the charge state of the impurity. Ta is a triple donor impurity with respect to Zn2?+? in ZnO and thus it can loose 1, 2 or 3 donor electrons under certain circumstances. As expected, the comparison between the experimental Electric-Field-Gradient tensor results and our ab initio predictions shows that the Ta impurity is in an ionized charge state at room temperature.

2010-04-01

413

Infrared Spectra of Water and Simple Negative Ions from Ab-initio Simulations  

Science.gov (United States)

We report an analysis of the much debated infrared spectra (IR) of water, as obtained by ab-initio molecular dynamics simulations with the PBE and PBE0 energy functionals. We compare power spectra of bond-bond correlations, those of Wannier function centers and IR spectra. Such comparison allows us to identify signatures, in IR spectra, arising from ionic vibrations and signatures stemming from the liquid electronic structure. We then analyze the changes the latter undergo in the presence of simple negative ions such as chloride. Finally, we discuss differences between results obtained at the PBE and PBE0 level of theory. Our results contribute a fundamental step toward the understanding of structural and spectroscopic properties of water at interfaces and complex solutions. Work supported by DOE/SciDACDE-FC02-06ER25794 and NSF/OCI-0749217.

Zhang, Cui; Donadio, Davide; Galli, Giulia; Duchemin, Ivan; Gygi, Francois

2010-03-01

414

Glycine in aqueous solution: solvation shells, interfacial water, and vibrational spectroscopy from ab initio molecular dynamics  

Science.gov (United States)

An aqueous glycine solution is studied with ab initio molecular dynamics to investigate the structural aspects of the different solvation shells within the zwitterion and their impact on the infrared spectrum. The individual contributions to the total IR spectrum from glycine and solvation water are decomposed systematically using the standard schemes in terms of maximally localized Wannier orbitals to define approximate molecular dipole moments in solution. The IR spectra of the aqueous solution and of the solvated zwitterionic glycine molecule itself are compared to those stemming from neutral glycine in the gas phase and a virtual ``isolated'' zwitterionic glycine molecule vertically transferred from solution into vacuum. Furthermore, electronic polarization effects due to solute-solvent coupling are discussed in detail for the solute and for the interfacial solvent molecules based on dipole moment distribution functions.

Sun, Jian; Bousquet, David; Forbert, Harald; Marx, Dominik

2010-09-01

415

Carbide precipitation at a grain boundary in molybdenum - an ab-initio DFT study  

International Nuclear Information System (INIS)

Atomic-scale stages of the growth of an interfacial precipitate film of tetragonal molybdenum carbide at a 5 (310) [001] symmetrical tilt grain boundary in molybdenum were investigated by means of atomistic supercell calculations on the basis of ab-initio density functional theory (DFT). In this presentation, the structural development of the precipitate with increasing carbon concentration is analysed. The structurally optimised atomistic model for the fully developed precipitate is compared to experimental high-resolution images from transmission electron microscopy, and it allows to clarify some ambiguous features therein. An atomic-scale twinning mechanism in the MoC precipitate is proposed. Finally, the influence of the carbon concentration on the stability of the metal-carbide interface with respect to cleavage is discussed

2007-03-26

416

Ab initio pseudopotential calculations of total energies and forces for hydrogen in palladium  

Energy Technology Data Exchange (ETDEWEB)

Ground-state properties of palladium-hydrogen systems are investigated in the framework of density functional theory in the local-density approximation. Norm-conserving ab initio pseudopotentials are used to describe the interactions between electrons and ion cores. The crystalline wave functions and the charge densities of the valence electrons are represented by a mixed basis containing plane waves and additionally localized d-like functions for palladium and s-like functions for hydrogen. Total energies are calculated for Pd-H systems with different hydrogen concentrations using Pd{sub n}H supercells (n=1, 4, 8, 16, 32). We report on the cohesive properties as well as the diffusion potentials and vibrational energies for the interstitial hydrogen. Lattice relaxations are taken into account by calculating atomic forces according to the Hellmann-Feynman theorem and statically relaxing the atomic positions. (orig.).

Elsaesser, C.; Faehnle, M. (Max-Planck-Inst. fuer Metallforschung, Inst. fuer Physik, Stuttgart (Germany)); Ho, K.M.; Chan, C.T. (Ames Lab. and Dept. of Physics, Iowa State Univ., Ames, IA (USA))

1991-06-01

417

Ab initio pseudopotential calculations of total energies and forces for hydrogen in palladium  

International Nuclear Information System (INIS)

Ground-state properties of palladium-hydrogen systems are investigated in the framework of density functional theory in the local-density approximation. Norm-conserving ab initio pseudopotentials are used to describe the interactions between electrons and ion cores. The crystalline wave functions and the charge densities of the valence electrons are represented by a mixed basis containing plane waves and additionally localized d-like functions for palladium and s-like functions for hydrogen. Total energies are calculated for Pd-H systems with different hydrogen concentrations using PdnH supercells (n=1, 4, 8, 16, 32). We report on the cohesive properties as well as the diffusion potentials and vibrational energies for the interstitial hydrogen. Lattice relaxations are taken into account by calculating atomic forces according to the Hellmann-Feynman theorem and statically relaxing the atomic positions. (orig.)

1991-06-01

418

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

Science.gov (United States)

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 epsilon-FeSi and CsCl-type FeSi. Finally, an equation of state for Fe5Si3 and Ni2Si is reported.

Santamaría-Perez, D.; Errandonea, D.; Vegas, A.; Nuss, J.; Jansen, M.; Rodríguez-Hernández, P.; Muñoz, A.; Boehler, R.

2008-07-01

419

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

International Nuclear Information System (INIS)

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

420

Glycine in aqueous solution: solvation shells, interfacial water, and vibrational spectroscopy from ab initio molecular dynamics.  

Science.gov (United States)

An aqueous glycine solution is studied with ab initio molecular dynamics to investigate the structural aspects of the different solvation shells within the zwitterion and their impact on the infrared spectrum. The individual contributions to the total IR spectrum from glycine and solvation water are decomposed systematically using the standard schemes in terms of maximally localized Wannier orbitals to define approximate molecular dipole moments in solution. The IR spectra of the aqueous solution and of the solvated zwitterionic glycine molecule itself are compared to those stemming from neutral glycine in the gas phase and a virtual "isolated" zwitterionic glycine molecule vertically transferred from solution into vacuum. Furthermore, electronic polarization effects due to solute-solvent coupling are discussed in detail for the solute and for the interfacial solvent molecules based on dipole moment distribution functions. PMID:20866146

Sun, Jian; Bousquet, David; Forbert, Harald; Marx, Dominik

2010-09-21

 
 
 
 
421

A set of molecular models based on quantum mechanical ab initio calculations and thermodynamic data  

CERN Document Server

A parameterization strategy for molecular models on the basis of force fields is proposed, which allows a rapid development of models for small molecules by using results from quantum mechanical (QM) ab initio calculations and thermodynamic data. The geometry of the molecular models is specified according to the atom positions determined by QM energy minimization. The electrostatic interactions are modeled by reducing the electron density distribution to point dipoles and point quadrupoles located in the center of mass of the molecules. Dispersive and repulsive interactions are described by Lennard-Jones sites, for which the parameters are iteratively optimized to experimental vapor-liquid equilibrium (VLE) data, i.e. vapor pressure, saturated liquid density, and enthalpy of vaporization of the considered substance. The proposed modeling strategy was applied to a sample set of ten molecules from different substance classes. New molecular models are presented for iso-butane, cyclohexane, formaldehyde, dimethyl...

Eckl, Bernhard; Hasse, Hans

2009-01-01

422

Ab initio theory for current-induced molecular switching: Melamine on Cu(001)  

Science.gov (United States)

Melamine on Cu(001) is mechanically unstable under the current of a scanning tunneling microscope tip and can switch among configurations. However, these are not equally accessible, and the switching critical current depends on the bias polarity. In order to explain such rich phenomenology, we have developed a scheme to evaluate the evolution of the reaction paths and activation barriers as a function of bias, which is rooted in the nonequilibrium Green's function method implemented within density functional theory. This, combined with the calculation of the inelastic electron tunneling spectroscopy signal, allows us to identify the vibrational modes promoting the observed molecular conformational changes. Finally, once our ab initio results are used within a resonance model, we are able to explain the details of the switching behavior, such as its dependence on the bias polarity, and the noninteger power relation between the reaction rate constants and both the bias voltage and the electric current.

Ohto, Tatsuhiko; Rungger, Ivan; Yamashita, Koichi; Nakamura, Hisao; Sanvito, Stefano

2013-05-01

423

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

424

Atomic carbon chains as spin-transmitters: An ab initio transport study  

DEFF Research Database (Denmark)

An atomic carbon chain joining two graphene flakes was recently realized in a ground-breaking experiment by Jin et al. (Phys. Rev. Lett., 102 (2009) 205501). We present ab initio results for the electron transport properties of such chains and demonstrate complete spin-polarization of the transmission in large energy ranges. The effect is due to the spin-polarized zig-zag edge terminating each graphene flake causing a spin-splitting of the graphene pi(z) bands, and the chain states. Transmission occurs when the graphene p-states resonate with similar states in the strongly hybridized edges and chain. This effect should in general hold for any p-conjugated molecules bridging the zig-zag edges of graphene electrodes. The polarization of the transmission can be controlled by chemically or mechanically modifying the molecule, or by applying an electrical gate.

Fürst, Joachim Alexander; Brandbyge, Mads

2010-01-01

425

Ab initio calculation of resonant x-ray scattering in manganites  

International Nuclear Information System (INIS)

We study the origin of the resonant x-ray signal in manganites and generalize the resonant cross section to the band-structure framework. With ab initio LSDA and LSDA+U calculations we determine the resonant x-ray spectrum of LaMnO3. 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 MnO6 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

2001-02-01

426

Ab initio calculation of resonant X-ray scattering in Manganites  

CERN Document Server

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

427

Change in inertial confinement fusion implosions upon using an ab initio multiphase DT equation of state.  

Science.gov (United States)

Improving the description of the equation of state (EOS) of deuterium-tritium (DT) has recently been shown to change significantly the gain of an inertial confinement fusion target [S.?X. Hu et al., Phys. Rev. Lett. 104, 235003 (2010)]. Here we use an advanced multiphase EOS, based on ab initio calculations, to perform a full optimization of the laser pulse shape with hydrodynamic simulations starting from 19 K in DT ice. The thermonuclear gain is shown to be a robust estimate over possible uncertainties of the EOS. Two different target designs are discussed, for shock ignition and self-ignition. In the first case, the areal density and thermonuclear energy can be recovered by slightly increasing the laser energy. In the second case, a lower in-flight adiabat is needed, leading to a significant delay (3 ns) in the shock timing of the implosion. PMID:22026681

Caillabet, L; Canaud, B; Salin, G; Mazevet, S; Loubeyre, P

2011-09-01

428

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

International Nuclear Information System (INIS)

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

2007-05-01

429

A unified scheme for ab initio molecular orbital theory and path integral molecular dynamics  

Science.gov (United States)

We present a general approach for accurate calculation of chemical substances which treats both nuclei and electrons quantum mechanically, adopting ab initio molecular orbital theory for the electronic structure and path integral molecular dynamics for the nuclei. The present approach enables the evaluation of physical quantities dependent on the nuclear configuration as well as the electronic structure, within the framework of Born-Oppenheimer adiabatic approximation. As an application, we give the path integral formulation of electric response properties-dipole moment and polarizability, which characterize the changes both in electronic structure and nuclear configuration at a given temperature when uniform electrostatic field is present. We also demonstrate the calcula