Finite Elements in Ab Initio Electronic-Structure Calulations
Pask, J. E.; Sterne, P. A.
Over the course of the past two decades, the density functional theory (DFT) (see e.g., [1]) of Hohenberg, Kohn, and Sham has proven to be an accurate and reliable basis for the understanding and prediction of a wide range of materials properties from first principles (ab initio), with no experimental input or empirical parameters. However, the solution of the Kohn-Sham equations of DFT is a formidable task and this has limited the range of physical systems which can be investigated by such rigorous, quantum mechanical means. In order to extend the interpretive and predictive power of such quantum mechanical theories further into the domain of "real materials", involving nonstoichiometric deviations, defects, grain boundaries, surfaces, interfaces, and the like; robust and efficient methods for the solution of the associated quantum mechanical equations are critical. The finite-element (FE) method (see e.g., [2]) is a general method for the solution of partial differential and integral equations which has found wide application in diverse fields ranging from particle physics to civil engineering. Here, we discuss its application to large-scale ab initio electronic-structure calculations.
Quantum chemistry the development of ab initio methods in molecular electronic structure theory
Schaefer III, Henry F
2004-01-01
This guide is guaranteed to prove of keen interest to the broad spectrum of experimental chemists who use electronic structure theory to assist in the interpretation of their laboratory findings. A list of 150 landmark papers in ab initio molecular electronic structure methods, it features the first page of each paper (which usually encompasses the abstract and introduction). Its primary focus is methodology, rather than the examination of particular chemical problems, and the selected papers either present new and important methods or illustrate the effectiveness of existing methods in predi
Ab Initio Calculations of the Electronic Structures and Biological Functions of Protein Molecules
Zheng, Haoping
2003-04-01
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.
{ital Ab initio} electronic structure, magnetism, and magnetocrystalline anisotropy of UGa{sub 2}
Energy Technology Data Exchange (ETDEWEB)
Divis, M. [Department of Metal Physics, Charles University, Ke Karlovu 5, 121 16 Prague 2 (Czech Republic)]|[Max-Planck-Gesellschaft, Research Group ``Electron Systems,`` University of Technology, D-01062 Dresden (Germany); Richter, M.; Eschrig, H.; Steinbeck, L. [Max-Planck-Gesellschaft, Research Group ``Electron Systems,`` University of Technology, D-01062 Dresden (Germany)
1996-04-01
{ital Ab} {ital initio} electronic structure calculations for the intermetallic compound UGa{sub 2} were performed using an optimized linear combination of atomic orbitals method based on the local spin density approximation. Three separate calculations were done treating the uranium 5{ital f} states as band states and as localized states with occupation two and three, respectively. In the itinerant approach, spin and orbital moments, magnetocrystalline anisotropy, and the Sommerfeld constant were calculated and found to deviate significantly from the related experimental data. In the localized approach, crystal field parameters were obtained for the 5{ital f} states, which have been treated by self-interaction corrected local-density theory. This approach with 5{ital f}{sup 2} occupation is shown to provide reasonable results for the anisotropy of the susceptibility, for the field dependence of the magnetic moments, and for the Sommerfeld constant. {copyright} {ital 1996 The American Physical Society.}
Ab initio electronic structure calculations of solid, solution-processed metallotetrabenzoporphyrins
Shea, Patrick B.; Kanicki, Jerzy
2012-04-01
An ab initio study of the electronic structures of solid metallotetrabenzoporphyrins (MTBPs) utilized in organic transistors and photovoltaics is presented. Band structures, densities of states, and orbitals are calculated for H2, Cu, Ni, and Zn core substitutions of the unit cell of solid TBP, as deposited via soluble precursors that are thermally annealed to produce polycrystalline, semiconducting thin-films. While the unit cells of the studied MTBPs are nearly isomorphous, substitution of the core atoms alters the structure of the bands around the energy bandgap and the composition of the densities of states. Cu and Ni core substitutions introduce nearly dispersionless energy bands near the valence and conduction band edges, respectively, that form acceptor or deep generation/recombination states.
Directory of Open Access Journals (Sweden)
Salah Belaidi
2011-01-01
Full Text Available The geometric, electronic structure, effect of the substitution, and structure physical-chemistry relationship for oxazoles derivatives have been studied by ab initio and DFT theory. In the present work, the calculated values, namely, net charges, bond lengths, dipole moments, electron affinities, heats of formation, and QSAR properties are reported and discussed in terms of the reactivity of oxazole derivatives.
Giovannetti, G.; Brocks, G.; van den Brink, J.
2008-01-01
We investigate the effect that potassium intercalation has on the electronic structure of copper phthalocyanine (CuPc) molecular crystals by means of ab initio density functional calculations. Pristine CuPc (in its alpha and beta structures) is found to be an insulator containing local magnetic
Electronic Structure of Hydrogenated and Surface-Modified GaAs Nanocrystals: Ab Initio Calculations
Directory of Open Access Journals (Sweden)
Hamsa Naji Nasir
2012-01-01
Full Text Available Two methods are used to simulate electronic structure of gallium arsenide nanocrystals. The cluster full geometrical optimization procedure which is suitable for small nanocrystals and large unit cell that simulates specific parts of larger nanocrystals preferably core part as in the present work. Because of symmetry consideration, large unit cells can reach sizes that are beyond the capabilities of first method. The two methods use ab initio Hartree-Fock and density functional theory, respectively. The results show that both energy gap and lattice constant decrease in their value as the nanocrystals grow in size. The inclusion of surface part in the first method makes valence band width wider than in large unit cell method that simulates the core part only. This is attributed to the broken symmetry and surface passivating atoms that split surface degenerate states and adds new levels inside and around the valence band. Bond length and tetrahedral angle result from full geometrical optimization indicate good convergence to the ideal zincblende structure at the centre of hydrogenated nanocrystal. This convergence supports large unit cell methodology. Existence of oxygen atoms at nanocrystal surface melts down density of states and reduces energy gap.
Electronic structure and transport in graphene/haeckelite hybrids: an ab initio study
International Nuclear Information System (INIS)
Zhu, Zhen; Fthenakis, Zacharias G; Tománek, David
2015-01-01
We combine ab initio density functional theory (DFT) structural studies with DFT-based nonequilibrium Green's function calculations to investigate how the presence of non-hexagonal rings affects electronic transport in graphitic structures. We find that infinite monolayers, finite-width nanoribbons, and nanotubes formed of 5–8 haeckelite with only 5- and 8-membered rings are generally more conductive than their graphene-based counterparts. The presence of haeckelite defect lines in the perfect graphitic structure, a model of grain boundaries in CVD-grown graphene, increases the electronic conductivity and renders it highly anisotropic. (paper)
The role of ab initio electronic structure calculations in studies of the strength of materials
Czech Academy of Sciences Publication Activity Database
Šob, Mojmír; Friák, Martin; Legut, Dominik; Fiala, J.; Vitek, V.
387-389, - (2004), s. 148-157 ISSN 0032-3888. [International Conference on the Strength of Materials /13./. Budapest, 25.08.2003-30.08.2003] R&D Projects: GA AV ČR(CZ) IAA1041302; GA ČR(CZ) GA202/03/1351; GA MŠk(CZ) OC 523.90 Institutional research plan: CEZ:AV0Z2041904 Keywords : theoretical strength * ab initio calculations * metallic materials Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.224, year: 2004
Hoy, Erik P; Mazziotti, David A
2015-08-14
Tensor factorization of the 2-electron integral matrix is a well-known technique for reducing the computational scaling of ab initio electronic structure methods toward that of Hartree-Fock and density functional theories. The simplest factorization that maintains the positive semidefinite character of the 2-electron integral matrix is the Cholesky factorization. In this paper, we introduce a family of positive semidefinite factorizations that generalize the Cholesky factorization. Using an implementation of the factorization within the parametric 2-RDM method [D. A. Mazziotti, Phys. Rev. Lett. 101, 253002 (2008)], we study several inorganic molecules, alkane chains, and potential energy curves and find that this generalized factorization retains the accuracy and size extensivity of the Cholesky factorization, even in the presence of multi-reference correlation. The generalized family of positive semidefinite factorizations has potential applications to low-scaling ab initio electronic structure methods that treat electron correlation with a computational cost approaching that of the Hartree-Fock method or density functional theory.
International Nuclear Information System (INIS)
Bernholc, J.
1998-01-01
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 C 60 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
Roy, Soumendra K.; Jian, Tian; Lopez, Gary V.; Li, Wei-Li; Su, Jing; Bross, David H.; Peterson, Kirk A.; Wang, Lai-Sheng; Li, Jun
2016-02-01
The observation of the gaseous UFO- anion is reported, which is investigated using photoelectron spectroscopy and relativisitic ab initio calculations. Two strong photoelectron bands are observed at low binding energies due to electron detachment from the U-7sσ orbital. Numerous weak detachment bands are also observed due to the strongly correlated U-5f electrons. The electron affinity of UFO is measured to be 1.27(3) eV. High-level relativistic quantum chemical calculations have been carried out on the ground state and many low-lying excited states of UFO to help interpret the photoelectron spectra and understand the electronic structure of UFO. The ground state of UFO- is linear with an O-U-F structure and a 3H4 spectral term derived from a U 7sσ25fφ15fδ1 electron configuration, whereas the ground state of neutral UFO has a 4H7/2 spectral term with a U 7sσ15fφ15fδ1 electron configuration. Strong electron correlation effects are found in both the anionic and neutral electronic configurations. In the UFO neutral, a high density of electronic states with strong configuration mixing is observed in most of the scalar relativistic and spin-orbit coupled states. The strong electron correlation, state mixing, and spin-orbit coupling of the electronic states make the excited states of UFO very challenging for accurate quantum chemical calculations.
Energy Technology Data Exchange (ETDEWEB)
Tohme, Samir N.; Korek, Mahmoud, E-mail: mahmoud.korek@bau.edu.lb, E-mail: fkorek@yahoo.com; Awad, Ramadan [Faculty of Science, Beirut Arab University, P.O. Box 11-5020 Riad El Solh, Beirut 1107 2809 (Lebanon)
2015-03-21
Ab initio techniques have been applied to investigate the electronic structure of the LiYb molecule. The potential energy curves have been computed in the Born–Oppenheimer approximation for the ground and 29 low-lying doublet and quartet excited electronic states. Complete active space self-consistent field, multi-reference configuration interaction, and Rayleigh Schrödinger perturbation theory to second order calculations have been utilized to investigate these states. The spectroscopic constants, ω{sub e}, R{sub e}, B{sub e}, …, and the static dipole moment, μ, have been investigated by using the two different techniques of calculation with five different types of basis. The eigenvalues, E{sub v}, the rotational constant, B{sub v}, the centrifugal distortion constant, D{sub v}, and the abscissas of the turning points, R{sub min} and R{sub max}, have been calculated by using the canonical functions approach. The comparison between the values of the present work, calculated by different techniques, and those available in the literature for several electronic states shows a very good agreement. Twenty-one new electronic states have been studied here for the first time.
Energy Technology Data Exchange (ETDEWEB)
Olsson, Paer
2004-04-01
The efficiency of fast neutron reactors, such as for fusion, breeding and transmutation, depend strongly on the neutron radiation resistance of the materials used in the reactors. The binary Fe-Cr alloy, which has many attractive properties in this regard, is the base for the best steels of today which are, however, still not up to the required standards. Therefore, substantial effort has been devoted to finding new materials that can cope with the demands better. Experimental studies must be complemented with extensive theoretical modelling in order to understand the effects that different alloying elements has on the resistance properties of materials. To this end, the first steps of multi-scale modelling has been taken, starting out with ab initio calculations of the electronic structure of the complete concentration range range of the disordered binary Fe-C alloy. The mixing enthalpy of Fe-Cr has been quantitatively predicted and has, together with data from literature, been used in order to fit two sets of interatomic potentials for the purpose of simulating defect evolution with molecular dynamics and kinetic Monte-Carlo codes. These dedicated Fe-Cr alloy potentials are new and represent important additions to the pure element potentials that can be found in literature.
Relaxation and electronic structure of the V 2O 3(0001) surface: ab initio cluster model studies
Czekaj, I.; Hermann, K.; Witko, M.
2003-02-01
The electronic structure and geometric relaxation of the (0001) surface of rhombohedral vanadium sesquioxide, V 2O 3, is studied theoretically with large surface cluster models where ab initio density functional theory is used to characterize charging and bonding. Geometric relaxation in the topmost surface region, up to 5 layers, with its three different bulk terminations is determined by minimizing total energies of the clusters. This yields major relaxation effects depending on the termination. The oxygen layer termination OVV ' exhibits strong relaxation of sub-surface vanadium layers resulting in increased ionic charging at the surface (measured by corresponding atom charges). The metal layer termination VV 'O leads to inwards relaxation of the two topmost vanadium layers by over 40% resulting also in increased surface charging. Ionic charging at the surface is the smallest for the half metal layer V 'OV termination where only the topmost vanadium layer relaxes inwards by 30% in addition to some rearrangement of sub-surface vanadium. This termination is believed to be the most stable of the three relaxed bulk-type terminations based also on analogies with experiments for Cr 2O 3(0001). However, total density-of-states and atom-projected partial densities-of-states curves depend relatively little on surface termination to allow a clear discrimination which could assist an unambiguous experimental identification.
Energy Technology Data Exchange (ETDEWEB)
Hussain, Altaf, E-mail: altafiub@yahoo.com [Department of Physics, Islamia University of Bahawalpur, Punjab 63100 (Pakistan); Aryal, Sitaram; Rulis, Paul [Department of Physics, University of Missouri-Kansas City, MO 64110 (United States); Choudhry, M. Arshad [Department of Physics, Islamia University of Bahawalpur, Punjab 63100 (Pakistan); Chen, Jun [Institute of Applied Physics and Computational Mathematics, Beijing 10088 (China); Ching, W.Y. [Department of Physics, University of Missouri-Kansas City, MO 64110 (United States)
2011-04-28
The electronic structure and optical properties of the Ni{sub 3}Al intermetallic alloy are studied by the first-principles orthogonalized linear combination of atomic orbitals method. Disordered models at different temperatures were constructed using molecular dynamics and the Vienna ab initio simulation package. The average charge transfer from Al to Ni increases steadily with temperature until the liquid phase is reached. The localization index shows the presence of relatively localized states even above the Fermi level in the disordered models. The calculated optical conductivity of the ordered phase is rich in structures and in reasonable agreement with the experimental data. The spectra of the disordered Ni{sub 3}Al models show a single broadened peak at 4.96 eV in the 0 K model which shifts towards 6.62 eV at 1400 K and then down to 5.83 eV in the liquid phase. Other results on the band structure and density of states are also discussed.
International Nuclear Information System (INIS)
Olsson, Paer
2004-04-01
The efficiency of fast neutron reactors, such as for fusion, breeding and transmutation, depend strongly on the neutron radiation resistance of the materials used in the reactors. The binary Fe-Cr alloy, which has many attractive properties in this regard, is the base for the best steels of today which are, however, still not up to the required standards. Therefore, substantial effort has been devoted to finding new materials that can cope with the demands better. Experimental studies must be complemented with extensive theoretical modelling in order to understand the effects that different alloying elements has on the resistance properties of materials. To this end, the first steps of multi-scale modelling has been taken, starting out with ab initio calculations of the electronic structure of the complete concentration range range of the disordered binary Fe-C alloy. The mixing enthalpy of Fe-Cr has been quantitatively predicted and has, together with data from literature, been used in order to fit two sets of interatomic potentials for the purpose of simulating defect evolution with molecular dynamics and kinetic Monte-Carlo codes. These dedicated Fe-Cr alloy potentials are new and represent important additions to the pure element potentials that can be found in literature
International Nuclear Information System (INIS)
Minár, J.; Braun, J.; Ebert, H.
2013-01-01
Highlights: ► We compare spin-resolved ARPES data of ferromagnetic 3d transition metals to many-body LSDA + DMFT based spectroscopic calculations. ► We document LSDA + DMFT provides a detailed and reliable interpretation of the data. ► We demonstrate that local correlations are dominant in Ni, whereas non-local correlations are important in Fe and Co. ► We reproduce the 6 eV satellite structure in ferromagnetic Ni LDSDA + DMFT in combination with the one-step model of photoemission provides a more or less complete description of the electronic structure of Fe, Co and Ni. -- Abstract: Various technical developments enlarged the potential of angle-resolved photoemission spectroscopy (ARPES) tremendously during the last two decades. In particular improved momentum and energy resolution in combination with spin-resolution as well as the use of photon energies from few eV up to several keV makes ARPES a rather unique tool to investigate the electronic properties of solids and surfaces. Obviously, this rises the need for a corresponding theoretical formalism that allows to accompany experimental ARPES studies in an adequate way. As will be demonstrated by several examples this goal could be achieved by various recent developments on the basis of density functional theory (DFT) in combination with dynamical mean field theory (DMFT) and with the one-step model of photoemission (1SM). A concrete realization of electronic structure calculations in the framework of multiple scattering theory further more provides direct access to the spectral function of the initial states via the one-electron Green function. Based on this bare spectral function matrix-element and final-state effects as well as surface related features may be calculated in addition using the one-step formalism that offers the possibility to analyse corresponding angle-resolved photoemission experiments in a quantitative sense. The impact of chemical disorder can be handled by means of the coherent
Ab-initio calculations of electronic structure and optical properties of TiAl alloy
Energy Technology Data Exchange (ETDEWEB)
Hussain, Altaf [Department of Physics, The Islamia University of Bahawalpur, Bahawalpur 63120 (Pakistan); Sikandar Hayat, Sardar, E-mail: sikandariub@yahoo.co [Department of Physics, Hazara University, Mansehra 21300 (Pakistan); Choudhry, M.A. [Department of Physics, The Islamia University of Bahawalpur, Bahawalpur 63120 (Pakistan)
2011-05-01
The electronic structures and optical properties of TiAl intermetallic alloy system are studied by the first-principle orthogonalized linear combination of atomic orbitals method. Results on the band structure, total and partial density of states, localization index, effective atomic charges, and optical conductivity are presented and discussed in detail. Total density of states spectra reveal that (near the Fermi level) the majority of the contribution is from Ti-3d states. The effective charge calculations show an average charge transfer of 0.52 electrons from Ti to Al in primitive cell calculations of TiAl alloy. On the other hand, calculations using supercell approach reveal an average charge transfer of 0.48 electrons from Ti to Al. The localization index calculations, of primitive cell as well as of supercell, show the presence of relatively localized states even above the Fermi level for this alloy. The calculated optical conductivity spectra of TiAl alloy are rich in structures, showing the highest peak at 5.73 eV for supercell calculations. Calculations of the imaginary part of the linear dielectric function show a prominent peak at 5.71 eV and a plateau in the range 1.1-3.5 eV.
Keith, J. Brandon; Fennick, Jacob R.; Junkermeier, Chad E.; Nelson, Daniel R.; Lewis, James P.
2009-03-01
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
Roy, Soumendra K; Jian, Tian; Lopez, Gary V; Li, Wei-Li; Su, Jing; Bross, David H; Peterson, Kirk A; Wang, Lai-Sheng; Li, Jun
2016-02-28
The observation of the gaseous UFO(-) anion is reported, which is investigated using photoelectron spectroscopy and relativisitic ab initio calculations. Two strong photoelectron bands are observed at low binding energies due to electron detachment from the U-7sσ orbital. Numerous weak detachment bands are also observed due to the strongly correlated U-5f electrons. The electron affinity of UFO is measured to be 1.27(3) eV. High-level relativistic quantum chemical calculations have been carried out on the ground state and many low-lying excited states of UFO to help interpret the photoelectron spectra and understand the electronic structure of UFO. The ground state of UFO(-) is linear with an O-U-F structure and a (3)H4 spectral term derived from a U 7sσ(2)5fφ(1)5fδ(1) electron configuration, whereas the ground state of neutral UFO has a (4)H(7/2) spectral term with a U 7sσ(1)5fφ(1)5fδ(1) electron configuration. Strong electron correlation effects are found in both the anionic and neutral electronic configurations. In the UFO neutral, a high density of electronic states with strong configuration mixing is observed in most of the scalar relativistic and spin-orbit coupled states. The strong electron correlation, state mixing, and spin-orbit coupling of the electronic states make the excited states of UFO very challenging for accurate quantum chemical calculations.
Bylaska, Eric J; Glaesemann, Kurt R; Felmy, Andrew R; Vasiliu, Monica; Dixon, David A; Tratnyek, Paul G
2010-11-25
Electronic structure methods were used to calculate the gas and aqueous phase reaction energies for reductive dechlorination (i.e., hydrogenolysis), reductive β-elimination, dehydrochlorination, and nucleophilic substitution by OH− of 1,2,3-trichloropropane. The thermochemical properties ΔH(f)°(298.15 K), S°(298.15 K, 1 bar), and ΔG(S)(298.15 K, 1 bar) were calculated by using ab initio electronic structure calculations, isodesmic reactions schemes, gas-phase entropy estimates, and continuum solvation models for 1,2,3-trichloropropane and several likely degradation products: CH3−CHCl−CH2Cl, CH2Cl−CH2−CH2Cl, C•H2−CHCl−CH2Cl, CH2Cl−C•H−CH2Cl, CH2═CCl−CH2Cl, cis-CHCl═CH−CH2Cl, trans-CHCl═CH−CH2Cl, CH2═CH−CH2Cl, CH2Cl−CHCl−CH2OH, CH2Cl−CHOH−CH2Cl, CH2═CCl−CH2OH, CH2═COH−CH2Cl, cis-CHOH═CH−CH2Cl, trans-CHOH═CH−CH2Cl, CH(═O)−CH2−CH2Cl, and CH3−C(═O)−CH2Cl. On the basis of these thermochemical estimates, together with a Fe(II)/Fe(III) chemical equilibrium model for natural reducing environments, all of the reactions studied were predicted to be very favorable in the standard state and under a wide range of pH conditions. The most favorable reaction was reductive β-elimination (ΔG(rxn)° ≈ −32 kcal/mol), followed closely by reductive dechlorination (ΔG(rxn)° ≈ −27 kcal/mol), dehydrochlorination (ΔG(rxn)° ≈ −27 kcal/mol), and nucleophilic substitution by OH− (ΔG(rxn)° ≈ −25 kcal/mol). For both reduction reactions studied, it was found that the first electron-transfer step, yielding the intermediate C•H2−CHCl−CH2Cl and the CH2Cl−C•H−CH2Cl species, was not favorable in the standard state (ΔG(rxn)° ≈ +15 kcal/mol) and was predicted to occur only at relatively high pH values. This result suggests that reduction by natural attenuation is unlikely.
Aryal, Sita Ram
The alumino-silicate solid solution series (Al 4+2xSi2-2 xO10-x) is an important class of ceramics. Except for the end member (x=0), Al2 SiO5 the crystal structures of the other phases, called mullite, have partially occupied sites. Stoichiometric supercell models for the four mullite phases 3Al2O 3 · 2SiO2 · 2Al 2O3 · SiO2, 4 Al2O3· SiO 2, 9Al2O3 · SiO2, and iota-Al2 O3 (iota-alumina) are constructed starting from experimentally reported crystal structures. A large number of models were built for each phase and relaxed using the Vienna ab initio simulation package (VASP) program. The model with the lowest total energy for a given x was chosen as the representative structure for that phase. Electronic structure and mechanical properties of mullite phases were studied via first-principles calculations. Of the various phases of transition alumina, iota-Al 2O3 is the least well known. In addition structural details have not, until now, been available. It is the end member of the aluminosilicate solid solution series with x=1. Based on a high alumina content mullite phase, a structural model for iota- Al2O3 is constructed. The simulated x-ray diffraction (XRD) pattern of this model agrees well with a measured XRD pattern. The iota-Al2 O3 is a highly disordered ultra-low-density phase of alumina with a theoretical density of 2854kg/m3. Using this theoretically constructed model, elastic, thermodynamic, electronic, and spectroscopic properties of iota-Al2 O3 have been calculated and compared it with those of alpha- Al2O3 and gamma- Al2O3. Boron carbide (B4C) undergoes an amorphization under high velocity impacts. The mechanism of amorphization is not clear. Ab initio methods are used to carry out large-scale uniaxial compression simulations on two polytypes of stoichiometric boron carbide (B4C), B 11C-CBC, and B12- CCC where B11C or B12 is the 12-atom icosahedron and CBC or CCC is the three-atom chain. The simulations were performed on large supercells of 180 atoms
Bakkari, Karim; Fersi, Riadh; Kebir Hlil, El; Bessais, Lotfi; Thabet Mliki, Najeh
2018-03-01
First-principle calculations combining density functional theory and the full-potential linearized augmented plane wave (FP-LAPW) method are performed to investigate the electronic and magnetic structure of Pr2Co7 in its two polymorphic forms, (2:7 H) and (2:7 R), for the first time. This type of calculation was also performed for PrCo5 and PrCo2 intermetallics. We have computed the valence density of states separately for spin-up and spin-down states in order to investigate the electronic band structure. This is governed by the strong contribution of the partial DOS of 3d-Co bands compared to the partial DOS of the 4f-Pr bands. Such a high ferromagnetic state is discussed in terms of the strong spin polarization observed in the total DOS. The magnetic moments carried by the Co and Pr atoms located in several sites for all compounds are computed. These results mainly indicate that cobalt atoms make a dominant contribution to the magnetic moments. The notable difference in the atomic moments of Pr and Co atoms between different structural slabs is explained in terms of the magnetic characteristics of the PrCo2 and PrCo5 compounds and the local chemical environments of the Pr and Co atoms in different structural slabs of Pr2Co7. From spin-polarized calculations we have simulated the 3d and 4f band population to estimate the local magnetic moments. These results are in accordance with the magnetic moments calculated using the FP-LAPW method. In addition, the exchange interactions J ij are calculated and used as input for M(T) simulations. Involving the data obtained from the electronic structure calculations, the appropriate Padé Table is applied to simulate the magnetization M(T) and to estimate the mean-field Curie temperature. We report a fairly good agreement between the ab initio calculation of magnetization and Curie temperature with the experimental data.
Ab-initio study of the electronic structure of sup 1 sup 9 F implanted in GaAs and GaN crystals
Park, J H; Cho, H S; Shin, Y N
1998-01-01
We have studied the nuclear quadrupole interaction of a fluorine atom implanted in gallium arsenide and gallium nitride cluster models using the ab-initio Hartree-Fock theory. For the three possible fluorine sites in GaAs and GaN, we have determined the location of the implanted fluorine atom by using a self-consistent calculation, the electric field gradient at the implanted atom, and the electronic structure. Good agreement is found with experimental data wherever they are available. Predictions are made for the implanted fluorine site associated with the total energy and the electric field gradient which are expected to be measurable by a variety of experimental techniques.
Hughes, I. D.; Däne, M.; Ernst, A.; Hergert, W.; Lüders, M.; Staunton, J. B.; Szotek, Z.; Temmerman, W. M.
2008-06-01
We describe an ab initio theory of finite temperature magnetism in strongly-correlated electron systems. The formalism is based on spin density functional theory, with a self-interaction corrected local spin density approximation (SIC-LSDA). The self-interaction correction is implemented locally, within the Kohn-Korringa-Rostoker (KKR) multiple-scattering method. Thermally induced magnetic fluctuations are treated using a mean-field 'disordered local moment' (DLM) approach and at no stage is there a fitting to an effective Heisenberg model. We apply the theory to the 3d transition metal oxides, where our calculations reproduce the experimental ordering tendencies, as well as the qualitative trend in ordering temperatures. We find a large insulating gap in the paramagnetic state which hardly changes with the onset of magnetic order.
Faas, S.; Snijders, Jaap; van Lenthe, J.H.; HernandezLaguna, A; Maruani, J; McWeeny, R; Wilson, S
2000-01-01
In this paper we present the first application of the ZORA (Zeroth Order Regular Approximation of the Dirac Fock equation) formalism in Ab Initio electronic structure calculations. The ZORA method, which has been tested previously in the context of Density Functional Theory, has been implemented in
Buchachenko, Alexei A; Chałasiński, Grzegorz; Szcześniak, Małgorzata M
2010-01-14
A thorough ab initio study of the Mn(2) dimer in its lowest electronic states that correlate to the ground Mn((6)S)+Mn((6)S) dissociation limit is reported. Performance of multireference methods is examined in calculations of the fully spin-polarized S=5((11) summation operator(+) (u)) state against the recent accurate single-reference coupled cluster CCSD(T) results [A. A. Buchachenko, Chem. Phys. Lett. 459, 73 (2008)]. The detailed comparison reveals a serious disagreement between the multireference configuration interaction (MRCI) and related nonperturbative results on the one hand and the complete active space perturbation theory (CASPT) calculations on the other. A striking difference found in the CASPT results of the second and third orders indicates poor perturbation expansion convergence. It is shown that a similar problem has affected most of the previous calculations performed using CASPT2 and similar perturbative approximations. The composition of the active space in the reference multiconfigurational self-consistent field calculations, the core correlation contribution, and basis set saturation effects are also analyzed. The lower spin states, S=0-4, are investigated using the MRCI method. The results indicate a similar dispersion binding for all the spin states within the manifold related to the closed 4s shells, which appears to screen and suppress the spin coupling between the half-filled 3d atomic shells. On this premise, the full set of model potentials is built by combining the accurate reference CCSD(T) interaction potential for S=5 and the MRCI spin-exchange energies for the SHeisenberg model. The effective spin-coupling parameter J is estimated as -3.9 cm(-1), a value roughly 2.5 times smaller in magnitude than those measured in the inert gas cryogenic matrices. Compressing of the Mn(2) dimer in the matrix cage is suggested as the prime cause of this disagreement.
International Nuclear Information System (INIS)
Wang, Y.; Lu, Y.H.; Wang, X.D.; Cao, Q.P.; Zhang, D.X.; Jiang, J.Z.
2014-01-01
Highlights: • The SOC effect affects the cohesion energy of crystal phase. • The effect of SOC was reduced due to random local atomic structures in liquids. • The local geometrical structures also affect the melting points. • Both SOC effect and local atomic structures are important for melting point difference. - Abstract: The origin of different melting points between Al 2 Cu and Al 2 Au has been studied using ab initio molecular dynamics simulations. Cohesive energy, electronic structures and structure information of both crystal and liquid phases have been analyzed. It is found that spin orbital coupling (SOC) plays an important role on the cohesive energy of crystal phase, consistent with the different melting points of these two alloys. Whereas, it seems that SOC has no effect on the formation energy and structure of liquid phase. Possible mechanism of reduced SOC effect at liquid phase is proposed. Our results are helpful to understand the glass formation ability difference between Al 2 Cu and Al 2 Au
Staunton, J. B.; Ostanin, S.; Razee, S. S.; Gyorffy, B. L.; Szunyogh, L.; Ginatempo, B.; Bruno, Ezio
2004-12-01
Using a first-principles, relativistic electronic structure theory of finite temperature metallic magnetism, we investigate the variation of magnetic anisotropy K with magnetization M in metallic ferromagnets. We apply the theory to the high uniaxial K material, L10-ordered FePt, and find its magnetic easy axis perpendicular to the Fe/Pt layers for all M and K to be proportional to M2 for a broad range of values of M. For small M, near the Curie temperature, the calculations pick out the easy axis for the onset of magnetic order. Our abinitio results for this important magnetic material agree well with recent experimental measurements, whereas the single-ion anisotropy model fails to give the correct qualitative behavior.
Slassi, A.; Hammi, M.; El Rhazouani, O.
2017-07-01
The surface relaxations, surface energies and electronic structures of BaO- and SnO2-terminated BaSnO3 (001) surfaces have been studied by employing the first-principles density functional theory. For both terminations, we find that the upper-layer Ba and Sn atoms move inward, whereas upper-layer O atoms move outward from the surface. Moreover, the largest relaxations are occurred on the first-layer atoms of both terminations. The surface rumpling of BaO-terminated BaSnO3 (001) is slightly less than that of the SnO2-terminated BaSnO3 (001) surface. The surface energies show that both terminated surfaces are energetically stable and favorable. Finally, the surface band gap is slightly decreased for the BaO termination, while it is dramatically decreased for the SnO2 termination.
International Nuclear Information System (INIS)
Guo, G.Y.; Wang, Y.K.; Chen, Y.Y.
2004-01-01
We have carried out a theoretical study of the electronic structure and magnetic properties of both bulk and supercell slab CeCo 2 . The calculations are based on first-principles density functional theory with generalized gradient approximation (GGA) and also with the GGA+U scheme. Both GGA and GGA+U calculations predict bulk CeCo 2 to be nonmagnetic, in agreement with experiments. However, calculations for a supercell slab with a 14 A thickness, show that the system becomes ferrimagnetic. In particular, the local magnetic moments on all the Ce and Co atoms in the thin film are pronounced. This suggests that surface effect may play a significant role in the magnetism observed in nano-particle CeCo 2
Srinivasu, K; Chandrakumar, K R S; Ghosh, Swapan K
2010-11-25
Although the boron hydrides are well-known in the literature, the aluminum hydride chemistry is limited to very few systems such as AlH(3), its dimer, and its polymeric form. In view of the recent experimental studies on the possible existence of the aluminum hydrides, herein, we have undertaken a systematic study on the electronic structure and properties of these aluminum hydrides. Under this, we have studied different classes of hydrides, viz., closo (Al(n)H(n+2)), nido (Al(n)H(n+4)), and arachno (Al(n)H(n+6)), similar to the boranes. All the aluminum hydrides are found to have exceptionally large highest-occupied molecular orbital-lowest-unoccupied molecular orbital gaps, low electron affinities, large ionization potentials and also large enthalpy and free energy of atomization. In addition, most of the structures are also found to have high symmetries. These exceptional properties can be indicative of the pronounced stability, and hence, it is expected that other aluminum hydride complexes can indeed be observed experimentally.
International Nuclear Information System (INIS)
Kamiya, Toshio; Ueda, Kazushige; Hiramatsu, Hidenori; Kamioka, Hayato; Ohta, Hiromichi; Hirano, Masahiro; Hosono, Hideo
2005-01-01
Electronic structures of layered oxychalcogenides LaCuOCh (Ch=S, Se, Te) were studied using relativistic ab initio band calculations to understand their optical and electronic properties. Step-like structures terminated with one or two sharp peaks were observed in low-temperature (10 K) optical absorption spectra. Third optical nonlinearity measurements supported that the sharp peaks came from split excitonic levels. The ab initio calculations reproduced well these characteristic structures in the spectra and proved that the step-like optical absorption structures originated from two-dimensional nature of the electronic structures associated with the layered crystal structure of LaCuOCh. The split energies of the excitonic levels were quantitatively explained by spin-orbit interaction in the chalcogen ions
Energy Technology Data Exchange (ETDEWEB)
Pavloudis, Th. [Department of Physics, Aristotle University of Thessaloniki, GR-54124 Thessaloniki (Greece); Zervos, M. [Nanostructured Materials and Devices Laboratory, Department of Mechanical and Manufacturing Engineering, PO Box 20537, Nicosia 1678 (Cyprus); Komninou, Ph. [Department of Physics, Aristotle University of Thessaloniki, GR-54124 Thessaloniki (Greece); Kioseoglou, J., E-mail: sifisl@auth.gr [Department of Physics, Aristotle University of Thessaloniki, GR-54124 Thessaloniki (Greece)
2016-08-31
We carry out ab initio electronic structure calculations of (Si{sub x}Sn{sub 1−x}){sub 3}N{sub 4} using density functional theory with projector augmented-wave potentials under the generalized gradient approximation. We find that the energetically favorable structure of Sn{sub 3}N{sub 4} is the face-centered cubic spinel structure, followed by the hexagonal structure which has energy band gaps of 1.85 eV and 1.44 eV respectively. The (Si{sub x}Sn{sub 1−x}){sub 3}N{sub 4} ternary compound can exhibit both cubic and hexagonal crystal structures over the full range of x. However, the cubic structure is found to be energetically favorable for x < 0.3 above which the hexagonal structure of (Si{sub x}Sn{sub 1−x}){sub 3}N{sub 4} dominates. The energy band gap can be tuned continuously from 1.44 eV up to 5.8 eV in the case of the hexagonal crystal structure of (Si{sub x}Sn{sub 1−x}){sub 3}N{sub 4} and from 1.85 eV to 4.82 eV in the case of cubic (Si{sub x}Sn{sub 1−x}){sub 3}N{sub 4}. Nevertheless the energy gap of (Si{sub x}Sn{sub 1−x}){sub 3}N{sub 4} is direct only for x < 0.3 when it is cubic and for x < 0.5 when hexagonal. - Highlights: • (Si{sub x}Sn{sub 1−x}){sub 3}N{sub 4} exhibits both cubic and hexagonal crystal structures. • The cubic structure is favorable for x < 0.3 and the hexagonal structure for x > 0.3. • The bandgap of hexagonal (Si{sub x}Sn{sub 1−x}){sub 3}N{sub 4} may be tuned from 1.44 eV up to 5.8 eV. • The bandgap may be tuned from 1.85 eV to 4.82 eV for the cubic (Si{sub x}Sn{sub 1−x}){sub 3}N{sub 4}. • Bandgaps are direct for x < 0.3 (cubic) and for x < 0.5 3 (hexagonal (Si{sub x}Sn{sub 1−x}){sub 3}N{sub 4}).
Ab initio valence calculations in chemistry
Cook, D B
1974-01-01
Ab Initio Valence Calculations in Chemistry describes the theory and practice of ab initio valence calculations in chemistry and applies the ideas to a specific example, linear BeH2. Topics covered include the Schrödinger equation and the orbital approximation to atomic orbitals; molecular orbital and valence bond methods; practical molecular wave functions; and molecular integrals. Open shell systems, molecular symmetry, and localized descriptions of electronic structure are also discussed. This book is comprised of 13 chapters and begins by introducing the reader to the use of the Schrödinge
Hunca, Batu; Dharmawardhana, Chamila; Sakidja, Ridwan; Ching, Wai-Yim
2016-10-01
The thermomechanical properties and electronic structure of vitreloy (Z r41.2T i13.8C u12.5N i10B e22.5 ) are investigated using accurate ab initio molecular dynamic (AIMD) simulations and ab initio calculations. The structure of the model with 512 atoms is validated by comparison to the experimental data with calculated thermomechanical properties in good agreement with the existing measurements. Detailed calculation of the electronic structure and bonding at the density functional level is obtained. It is revealed that the traditional definition of bond length in metallic glasses has a limited interpretation, and any theory based on geometrical consideration of their values for discussion on the structural units in metallic glasses has similarly limited applications. On the other hand, we advocate the use of a quantum mechanical based metric, the total bond order density (TBOD), and their partial components or PBOD as valuable parameters to characterize the interatomic bonding in multicomponent glasses such as vitreloy.
DEFF Research Database (Denmark)
Shim, Irene; Baba, M. Sai; Gingerich, K.A.
2002-01-01
The low-lying states of the molecule Ge-2 and of the ion Ge-2(-) have been investigated by all electron ab initio multiconfiguration self-consistent field (CASSCF) and multi-reference configuration interaction (MRCI) calculations. The relativistic corrections for the Darwin contact term...... and for the mass-velocity term have been determined in perturbation calculations. Treatment of the spin-orbit coupling has been included. The ground state of Ge-2 is derived as 0(g)(+)((3)Sigma(g)(-)) with equilibrium distance 2.422 Angstrom, and vibrational frequency 270 cm(-1). The spectroscopic constants of 15...... excited states are presented. Thermal functions based on the theoretically determined molecular parameters were used to derive the thermodynamic properties of the Ge-2 molecule from new mass spectrometric equilibrium data. The literature value for the dissociation energy of Ge-2 has been re...
Suetin, D. V.; Shein, I. R.
2018-02-01
Ab initio calculations were used to study the properties of a series of hexagonal (Fe2N-like) subcarbides M2C, where M = Tc, Ru, Rh, Pd, Re, Os, Ir, and Pt, and to calculate their equilibrium structural parameters, electronic properties, phase stability, elastic constants, compression modulus, shear modulus, Young's modulus, compressibility, Pugh's indicator, Poisson ratio, elastic anisotropy indices, and also hardness, Debye temperature, sound velocity, and low-temperature heat capacity. It is found based on these results that all the subcarbides are mechanically stable; however, their formation energies E form are positive with respect to a mixture of d-metal and graphite. In addition, the calculation of the phonon spectra of these subcarbides shows the existence of negative modes, which indicates their dynamical instability. Thus, a successful synthesis of these subcarbides at normal conditions is highly improbable.
DEFF Research Database (Denmark)
Shim, Irene; Gingerich, K. A.
1984-01-01
In the present study we present all-electron ab initio Hartree–Fock (HF) and configuration interaction (CI) calculations of the 2Sigma+ ground state as well as of 16 excited states of the RhC molecule. The calculated spectroscopic constants of the lowest lying states are in good agreement...... with the experimental data. The chemical bond in the electronic ground state is mainly due to interaction of the 4d orbitals of Rh with the 2s and 2p orbitals of C. The bond is a triple bond composed of two pi bonds and one sigma bond. The 5s electron of Rh hardly participates in the bond formation. It is located...
International Nuclear Information System (INIS)
Nomura, Kenji; Ohta, Hiromichi; Hirano, Masahiro; Kamiya, Toshio; Uruga, Tomoya; Hosono, Hideo
2007-01-01
Ionic amorphous oxide semiconductors (IAOSs) are new materials for flexible thin film transistors that exhibit field-effect mobilities of ∼10 cm 2 V -1 s -1 [K. Nomura et al., Nature 488, 432 (2004)]. The local coordination structure in an IAOS, In-Ga-Zn-O (a-IGZO), was examined using extended x-ray absorption fine structure analysis combined with ab initio calculations. The short-range ordering and coordination structures in a-IGZO are similar to those in the corresponding crystalline phase, InGaZnO 4 , and edge-sharing structures consisting of In-O polyhedra remain in the amorphous structure. The In 3+ 5s orbitals form an extended state with a band effective mass of ∼0.2m e at the conduction band bottom
Kas, Milaim; Loreau, Jérôme; Liévin, Jacques; Vaeck, Nathalie
2017-05-21
We have performed a systematic ab initio study on alkali and alkaline earth hydroxide neutral (MOH) and anionic (MOH - ) species where M = Li, Na, K, Rb, Cs or Be, Mg, Ca, Sr, Ba. The CCSD(T) method with extended basis sets and Dirac-Fock relativistic effective core potentials for the heavier atoms has been used to study their equilibrium geometries, interaction energies, electron affinities, electric dipole moment, and potential energy surfaces. All neutral and anionic species exhibit a linear shape with the exception of BeOH, BeOH - , and MgOH - , for which the equilibrium structure is found to be bent. Our analysis shows that the alkaline earth hydroxide anions are valence-bound whereas the alkali hydroxide anions are dipole bound. In the context of sympathetic cooling of OH - by collision with ultracold alkali and alkaline earth atoms, we investigate the 2D MOH - potential energy surfaces and the associative detachment reaction M + OH→- MOH + e - , which is the only energetically allowed reactive channel in the cold regime. We discuss the implication for the sympathetic cooling of OH - and conclude that Li and K are the best candidates for an ultracold buffer gas.
Sambathkumar, K; Jeyavijayan, S; Arivazhagan, M
2015-08-05
Combined experimental and theoretical studies were conducted on the molecular structure and vibrational spectra of 4-AminoPhthalhydrazide (APH). The FT-IR and FT-Raman spectra of APH were recorded in the solid phase. The molecular geometry and vibrational frequencies of APH in the ground state have been calculated by using the ab initio HF (Hartree-Fock) and density functional methods (B3LYP) invoking 6-311+G(d,p) basis set. The optimized geometric bond lengths and bond angles obtained by HF and B3LYP method show best agreement with the experimental values. Comparison of the observed fundamental vibrational frequencies of APH with calculated results by HF and density functional methods indicates that B3LYP is superior to the scaled Hartree-Fock approach for molecular vibrational problems. The difference between the observed and scaled wave number values of most of the fundamentals is very small. A detailed interpretation of the NMR spectra of APH was also reported. The theoretical spectrograms for infrared and Raman spectra of the title molecule have been constructed. UV-vis spectrum of the compound was recorded and the electronic properties, such as HOMO and LUMO energies, were performed by time dependent density functional theory (TD-DFT) approach. Finally the calculations results were applied to simulated infrared and Raman spectra of the title compound which show good agreement with observed spectra. And the temperature dependence of the thermodynamic properties of constant pressure (Cp), entropy (S) and enthalpy change (ΔH0→T) for APH were also determined. Copyright © 2015 Elsevier B.V. All rights reserved.
Energy Technology Data Exchange (ETDEWEB)
Feller, D.F.
1993-07-01
This collection of benchmark timings represents a snapshot of the hardware and software capabilities available for ab initio quantum chemical calculations at Pacific Northwest Laboratory`s Molecular Science Research Center in late 1992 and early 1993. The ``snapshot`` nature of these results should not be underestimated, because of the speed with which both hardware and software are changing. Even during the brief period of this study, we were presented with newer, faster versions of several of the codes. However, the deadline for completing this edition of the benchmarks precluded updating all the relevant entries in the tables. As will be discussed below, a similar situation occurred with the hardware. The timing data included in this report are subject to all the normal failures, omissions, and errors that accompany any human activity. In an attempt to mimic the manner in which calculations are typically performed, we have run the calculations with the maximum number of defaults provided by each program and a near minimum amount of memory. This approach may not produce the fastest performance that a particular code can deliver. It is not known to what extent improved timings could be obtained for each code by varying the run parameters. If sufficient interest exists, it might be possible to compile a second list of timing data corresponding to the fastest observed performance from each application, using an unrestricted set of input parameters. Improvements in I/O might have been possible by fine tuning the Unix kernel, but we resisted the temptation to make changes to the operating system. Due to the large number of possible variations in levels of operating system, compilers, speed of disks and memory, versions of applications, etc., readers of this report may not be able to exactly reproduce the times indicated. Copies of the output files from individual runs are available if questions arise about a particular set of timings.
International Nuclear Information System (INIS)
Nahif, F; Music, D; Mráz, S; To Baben, M; Schneider, J M
2013-01-01
Using density functional theory, the effect of Si on the stability and electronic structure of γ- and α-Al 2 O 3 has been investigated. The concentration range from 0 to 5 at.% is probed and the additive is positioned at different substitutional sites in the γ-phase. The calculations for (Al,Si) 2 O 3 predict a trend towards spontaneous decomposition into α-/γ-Al 2 O 3 and SiO 2 . Therefore, the formation of the metastable γ-(Al,Si) 2 O 3 phase can only be expected during non-equilibrium processing where the decomposition is kinetically hindered. The Si-induced changes in stability of this metastable solid solution may be understood based on the electronic structure. As the Si concentration is increased, stiff silicon–oxygen bonds are formed giving rise to the observed stabilization of the γ-phase. (paper)
Energy Technology Data Exchange (ETDEWEB)
Wang, Y. [International Center for New-Structured Materials (ICNSM), Laboratory of New-Structured Materials, State Key Laboratory of Silicon Materials, and Department of Materials Science and Engineering, Zhejiang University, Hangzhou 310027 (China); Lu, Y.H., E-mail: luyh@zju.edu.cn [International Center for New-Structured Materials (ICNSM), Laboratory of New-Structured Materials, State Key Laboratory of Silicon Materials, and Department of Materials Science and Engineering, Zhejiang University, Hangzhou 310027 (China); Wang, X.D.; Cao, Q.P. [International Center for New-Structured Materials (ICNSM), Laboratory of New-Structured Materials, State Key Laboratory of Silicon Materials, and Department of Materials Science and Engineering, Zhejiang University, Hangzhou 310027 (China); Zhang, D.X. [State Key Laboratory of Modern Optical Instrumentation, Zhejiang University, Hangzhou 310027 (China); Jiang, J.Z., E-mail: jiangjz@zju.edu.cn [International Center for New-Structured Materials (ICNSM), Laboratory of New-Structured Materials, State Key Laboratory of Silicon Materials, and Department of Materials Science and Engineering, Zhejiang University, Hangzhou 310027 (China)
2014-11-15
Highlights: • The SOC effect affects the cohesion energy of crystal phase. • The effect of SOC was reduced due to random local atomic structures in liquids. • The local geometrical structures also affect the melting points. • Both SOC effect and local atomic structures are important for melting point difference. - Abstract: The origin of different melting points between Al{sub 2}Cu and Al{sub 2}Au has been studied using ab initio molecular dynamics simulations. Cohesive energy, electronic structures and structure information of both crystal and liquid phases have been analyzed. It is found that spin orbital coupling (SOC) plays an important role on the cohesive energy of crystal phase, consistent with the different melting points of these two alloys. Whereas, it seems that SOC has no effect on the formation energy and structure of liquid phase. Possible mechanism of reduced SOC effect at liquid phase is proposed. Our results are helpful to understand the glass formation ability difference between Al{sub 2}Cu and Al{sub 2}Au.
Indari, E. D.; Wungu, T. D. K.; Hidayat, R.
2017-07-01
Organic lead halide perovskite material based solar cells show impressive power conversion efficiencies, which can reach above 19 percent for perovskite solar cell with methyl-ammonium cations. These efficiencies are originated from efficient photoexcitation and charge carrier transport and not observed in conventional perovskite crystals. In this preliminary research work, we therefore performed Density Functional Theory (DFT) calculation of formamidinium lead iodide (FAPI), an alternative to methyl-ammonium lead iodide (MAPI), to predict their electronic structure and density of state (DOS). The calculation result at the most stable lattice parameters show a good agreement with the experiment results. The obtained band gap energy is 1.307 eV. The valence band is dominantly formed by the 5p orbitals of I- anions, while the conduction band is dominantly formed by the 6p orbitals of Pb2+ cations. The DOS of valence band of this perovskite seems smaller compared to the case of methyl-ammonium lead iodide perovskite, which then may explain the observation of smaller power conversion efficiencies in perovskite solar cells with this formamidinium cations.
Giant magnetoresistance An ab-initio description
Binder, J
2000-01-01
A new theoretical concept to study the microscopic origin of Giant Magnetoresistance (GMR) from first principles is presented. The method is based on ab-initio electronic structure calculations within the spin density functional theory using a Screened KORRINGA-KOHNROSTOKER method. Scattering at impurity atoms in the multilayers is described by means of a GREEN's-function method. The scattering potentials are calculated self-consistently. The transport properties are treated quasi-classically solving the BOLTZMANN equation including the electronic structure of the layered system and the anisotropic scattering. The solution of the BOLTZMANN equation is performed iteratively taking into account both scattering out and scattering in terms (vertex corrections). The method is applied to Co/Cu and Fe/Cr multilayers. Trends of scattering cross sections, residual resistivities and GMR ratios are discussed for various transition metal impurities at different positions in the Co/Cu or Fe/Cr multilayers. Furthermore the...
International Nuclear Information System (INIS)
Fuh, Huei-Ru; Liu, Yun-Ping; Chen, Shao-Hua; Wang, Yin-Kuo
2013-01-01
Highlights: ► Double perovskite. ► Compensated magnetism. ► First principle. - Abstract: We investigated possible candidates for a compensated half-metal (CHM) with a double perovskite structure A 2 CrRu(Os)O 6 (A = Si, Ge, Sn, and Pb). Electronic structures and magnetic properties were analyzed using the accurate full-potential linear augmented plane wave method within the generalized gradient approximation (GGA). The compensated magnetism can be divided into half-metallic antiferromagnets (HM-AF) and antiferromagnetic insulator (AF-Is) based on their zero magnetic moments. A 2 CrRuO 6 (A = Si, Ge, Sn, and Pb) is a potential candidate for HM-AF, and Sn 2 CrOsO 6 and Pb 2 CrOsO 6 can be classified as AF-Is. The HM-AF and AF-Is states are both attributed to the superexchange and generalized double exchange mechanism. When the GGA + U calculation is taken into account, all A 2 CrRu(Os)O 6 (A = Si, Ge, Sn, and Pb) states become unconventional AF-Is because the two AF state-coupled ions consisted of two different elements and the two spin-resolved densities of states were no longer the same. Further experimental confirmation will be done for the possible CHM of A 2 CrRuO 6 (A = Si, Ge, Sn, and Pb), Sn 2 CrOsO 6 , and Pb 2 CrOsO 6 .
AB INITIO calculations of magneto-optical effects
Czech Academy of Sciences Publication Activity Database
Kuneš, Jan; Oppeneer, P. M.
2002-01-01
Roč. 2, - (2002), s. 141-146 ISSN 1346-7948 R&D Projects: GA AV ČR IAA1010214 Institutional research plan: CEZ:AV0Z1010914 Keywords : electronic structure * ab initio calculation * polar magneto-optical Kerr effect * transitiom metal * uranium intermetallics * CrO 2 Subject RIV: BM - Solid Matter Physics ; Magnetism
Ab initio electronic stopping power in materials
International Nuclear Information System (INIS)
Shukri, Abdullah-Atef
2015-01-01
The average energy loss of an ion per unit path length when it is moving through the matter is named the stopping power. The knowledge of the stopping power is essential for a variety of contemporary applications which depend on the transport of ions in matter, especially ion beam analysis techniques and ion implantation. Most noticeably, the use of proton or heavier ion beams in radiotherapy requires the knowledge of the stopping power. Whereas experimental data are readily available for elemental solids, the data are much more scarce for compounds. The linear response dielectric formalism has been widely used in the past to study the electronic stopping power. In particular, the famous pioneering calculations due to Lindhard evaluate the electronic stopping power of a free electron gas. In this thesis, we develop a fully ab initio scheme based on linear response time-dependent density functional theory to predict the impact parameter averaged quantity named the random electronic stopping power (RESP) of materials without any empirical fitting. The purpose is to be capable of predicting the outcome of experiments without any knowledge of target material besides its crystallographic structure. Our developments have been done within the open source ab initio code named ABINIT, where two approximations are now available: the Random-Phase Approximation (RPA) and the Adiabatic Local Density Approximation (ALDA). Furthermore, a new method named 'extrapolation scheme' have been introduced to overcome the stringent convergence issues we have encountered. These convergence issues have prevented the previous studies in literature from offering a direct comparison to experiment. First of all, we demonstrate the importance of describing the realistic ab initio electronic structure by comparing with the historical Lindhard stopping power evaluation. Whereas the Lindhard stopping power provides a first order description that captures the general features of the
Topological Semimetals Studied by Ab Initio Calculations
Hirayama, Motoaki; Okugawa, Ryo; Murakami, Shuichi
2018-04-01
In topological semimetals such as Weyl, Dirac, and nodal-line semimetals, the band gap closes at points or along lines in k space which are not necessarily located at high-symmetry positions in the Brillouin zone. Therefore, it is not straightforward to find these topological semimetals by ab initio calculations because the band structure is usually calculated only along high-symmetry lines. In this paper, we review recent studies on topological semimetals by ab initio calculations. We explain theoretical frameworks which can be used for the search for topological semimetal materials, and some numerical methods used in the ab initio calculations.
Bicanonical ab Initio Molecular Dynamics for Open Systems.
Frenzel, Johannes; Meyer, Bernd; Marx, Dominik
2017-08-08
Performing ab initio molecular dynamics simulations of open systems, where the chemical potential rather than the number of both nuclei and electrons is fixed, still is a challenge. Here, drawing on bicanonical sampling ideas introduced two decades ago by Swope and Andersen [ J. Chem. Phys. 1995 , 102 , 2851 - 2863 ] to calculate chemical potentials of liquids and solids, an ab initio simulation technique is devised, which introduces a fictitious dynamics of two superimposed but otherwise independent periodic systems including full electronic structure, such that either the chemical potential or the average fractional particle number of a specific chemical species can be kept constant. As proof of concept, we demonstrate that solvation free energies can be computed from these bicanonical ab initio simulations upon directly superimposing pure bulk water and the respective aqueous solution being the two limiting systems. The method is useful in many circumstances, for instance for studying heterogeneous catalytic processes taking place on surfaces where the chemical potential of reactants rather than their number is controlled and opens a pathway toward ab initio simulations at constant electrochemical potential.
Energy Technology Data Exchange (ETDEWEB)
Neef, Matthias
2007-03-19
Aim of this thesis was to reach by a systematic study of different ab initio procedures an improved description of the electronic properties of FeSi and FeGe. Central result is the itinerant description of FeSi as a semiconductor in the neighbourhood of a ferromagnetic instability. The regardment of the nonlocal exchange in the effective one-particle approximation leads to a metastable magnetic state scarcely above the magnetic ground state. The application of the hybrid functional leads to a 1st order metal-isolator transition for large lattice parameters: FeSi transforms at increasement of the lattice parameter from an unmagnetic isolator to a magnetic metal. A similar behavior is found in the isostructural compound FeGe. The two systems FeSi and FeGe were systematically and detailedly analyzed by means of ab initio procedures. Thereby the structural, electronic, and magnetic properties were studied with DFT and HF calculations. Both calculations with spin polarization and without spin polarization were performed.
Augmented wave ab initio EFG calculations: some methodological warnings
International Nuclear Information System (INIS)
Errico, Leonardo A.; Renteria, Mario; Petrilli, Helena M.
2007-01-01
We discuss some accuracy aspects inherent to ab initio electronic structure calculations in the understanding of nuclear quadrupole interactions. We use the projector augmented wave method to study the electric-field gradient (EFG) at both Sn and O sites in the prototype cases SnO and SnO 2 . The term ab initio is used in the standard context of the also called first principles methods in the framework of the Density Functional Theory. As the main contributions of EFG calculations to problems in condensed matter physics are related to structural characterizations on the atomic scale, we discuss the 'state of the art' on theoretical EFG calculations and make a brief critical review on the subject, calling attention to some fundamental theoretical aspects
Augmented wave ab initio EFG calculations: some methodological warnings
Energy Technology Data Exchange (ETDEWEB)
Errico, Leonardo A. [Departamento de Fisica-IFLP (CONICET), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CC67 (1900) La Plata (Argentina); Renteria, Mario [Departamento de Fisica-IFLP (CONICET), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CC67 (1900) La Plata (Argentina); Petrilli, Helena M. [Instituto de Fisica-DFMT, Universidade de Sao Paulo, C.P. 66318, 05315-970 Sao Paulo, SP (Brazil)]. E-mail: hmpetril@macbeth.if.usp.br
2007-02-01
We discuss some accuracy aspects inherent to ab initio electronic structure calculations in the understanding of nuclear quadrupole interactions. We use the projector augmented wave method to study the electric-field gradient (EFG) at both Sn and O sites in the prototype cases SnO and SnO{sub 2}. The term ab initio is used in the standard context of the also called first principles methods in the framework of the Density Functional Theory. As the main contributions of EFG calculations to problems in condensed matter physics are related to structural characterizations on the atomic scale, we discuss the 'state of the art' on theoretical EFG calculations and make a brief critical review on the subject, calling attention to some fundamental theoretical aspects.
Pseudopotential for ab initio calculations of uranium compounds
Smirnov, G. S.; Pisarev, V. V.; Stegailov, V. V.
2018-01-01
The density functional theory (DFT) is a research tool of the highest importance for electronic structure calculations. It is often the only affordable method for ab initio calculations of complex materials. The pseudopotential approach allows reducing the total number of electrons in the model that speeds up calculations. However, there is a lack of pseudopotentials for heavy elements suitable for condensed matter DFT models. In this work, we present a pseudopotential for uranium developed in the Goedecker–Teter–Hutter form. Its accuracy is illustrated using several molecular and solid-state calculations.
Ab initio calculation of tensile strength in iron
Czech Academy of Sciences Publication Activity Database
Friák, Martin; Šob, Mojmír; Vitek, V.
2003-01-01
Roč. 83, 31-34 (2003), s. 3529-3537 ISSN 1478-6435. [Multiscale Materials Modelling: Working Theory for Industry /1./. London, 17.06.2002-20.06.2002] R&D Projects: GA AV ČR IAA1041302; GA ČR GA202/03/1351; GA MŠk OC 523.90 Institutional research plan: CEZ:AV0Z2041904 Keywords : ab initio calculations * electronic structure * theoretical tensile strength Subject RIV: BM - Solid Matter Physics ; Magnetism
Stretching siloxanes: An ab initio molecular dynamics study
Lupton, E. M.; Nonnenberg, C.; Frank, I.; Achenbach, F.; Weis, J.; Bräuchle, C.
2005-10-01
We present an ab initio molecular dynamics study of siloxane elastomers placed under tensile stress for comparison with single molecule AFM experiments. Of particular interest is stress-induced chemical bond breaking in the high force regime, where a description of the molecular electronic structure is essential to determine the rupture mechanism. We predict an ionic mechanism for the bond breaking process with a rupture force of 4.4 nN for an isolated siloxane decamer pulled at a rate of 27.3 m/s and indicate lower values at experimental polymer lengths and pulling rates.
Ab Initio molecular dynamics with excited electrons
Alavi, A.; Kohanoff, J.; Parrinello, M.; Frenkel, D.
1994-01-01
A method to do ab initio molecular dynamics suitable for metallic and electronically hot systems is described. It is based on a density functional which is costationary with the finite-temperature functional of Mermin, with state being included with possibly fractional occupation numbers.
Ab initio theory of magnetic correlations in itinerant magnets
International Nuclear Information System (INIS)
Ling, M.F.
1997-01-01
One of the challenging problems in modern magnetism is the description of the paramagnetic state because at finite temperatures the effect of spin fluctuation plays a fundamental role in altering the electronic structure. In magnetic metals, the magnetic properties are linked to the underlying spin-polarised electronic structure in a highly complex manner. In recent years, first-principles electronic structure theories based on the spin density functional (SDF) theory have been able to provide a quantitative account of many ground-state magnetic properties. In this article, the effect of spin fluctuation on the spin-polarised electronic structure and thus the magnetic properties will be discussed and its incorporation into ab initio calculations explained. If the magnetic and compositional ordering energies of magnetic metallic alloys are close, the compositional and magnetic correlations can profoundly influence each other. A theoretical formalism for treating these correlations within the framework of a first-principle electronic structure theory will be elaborated and the application to a number of magnetic alloys discussed and compared with experiments. (author)
Towards hydrogen metallization: an Ab initio approach
International Nuclear Information System (INIS)
Bernard, St.
1998-01-01
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)
Thiessen, P. A.; Treder, H.-J.
Jedes initium wird durch experimenta crucis zum eventus. Jedes theoretisch interpretierbare ex-eventu-Resultat führt auf ein neues Initium. Gerade dies ist die gemeinsame Aussage von Atomistik, Quantenmechanik und Relativitätstheorie.Translated AbstractAb initio vel ex eventu. IIEvery initium becomes an eventus by experimenta crucis. Every theoretically interpretable ex-eventu result leads to a new initium. Right this is the joint assertion of atomism, quantum mechanics, and relativity.
Germacrene D Cyclization: An Ab Initio Investigation
Setzer, William N.
2008-01-01
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...
Highly scalable Ab initio genomic motif identification
Marchand, Benoit
2011-01-01
We present results of scaling an ab initio motif family identification system, Dragon Motif Finder (DMF), to 65,536 processor cores of IBM Blue Gene/P. DMF seeks groups of mutually similar polynucleotide patterns within a set of genomic sequences and builds various motif families from them. Such information is of relevance to many problems in life sciences. Prior attempts to scale such ab initio motif-finding algorithms achieved limited success. We solve the scalability issues using a combination of mixed-mode MPI-OpenMP parallel programming, master-slave work assignment, multi-level workload distribution, multi-level MPI collectives, and serial optimizations. While the scalability of our algorithm was excellent (94% parallel efficiency on 65,536 cores relative to 256 cores on a modest-size problem), the final speedup with respect to the original serial code exceeded 250,000 when serial optimizations are included. This enabled us to carry out many large-scale ab initio motiffinding simulations in a few hours while the original serial code would have needed decades of execution time. Copyright 2011 ACM.
Dispersion Interactions between Rare Gas Atoms: Testing the London Equation Using ab Initio Methods
Halpern, Arthur M.
2011-01-01
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…
Germacrene D cyclization: an Ab initio investigation.
Setzer, William N
2008-01-01
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.
Germacrene D Cyclization: An Ab Initio Investigation
Directory of Open Access Journals (Sweden)
William N. Setzer
2008-01-01
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.
Ab initio studies on proton affinities of substituted furans
International Nuclear Information System (INIS)
Lee, Gab Yong; Lee, Hyun Mee
1998-01-01
The geometry of furan, relevant to the binding of bis-furan lexitropsin that contains this ring to the base pair of minor groove of DNA, is optimized by semiempirical (MNDO) and ab initio (Hartree-Fock) methods. The proton affinity and electronic structure are evaluated at the 6-31G and 6-31G level of theory for the optimized geometry. The proton affinities are also studied for various substituted furans with the electron donating and -withdrawing groups to estimate the substituent effect on the proton affinity of furans. It has been found that the electron-donating substituents increase the proton affinity of of furan, whereas the electron-withdrawing substituents decrease it. This result can be explained with atomic charge and electron density at oxygen of substituted furans
Ab initio design of coherent thermal sources
Drevillon, Jérémie; Ben-Abdallah, Philippe
2007-12-01
Emission of thermal light from a hot body has been considered for a long time as broadband and quasi-isotropic. Today, we know that this paradigm is wrong and it has been shown that many micro- and nanostructured materials are able to radiate in narrow spectral bands and around specific directions of space. However, so far, only heuristic strategies based on trial and error have been followed for engineering such sources. Here, we present a general method for the ab initio design of coherent thermal sources by using only the first principles of optics. Our results pave the way toward the inverse design of new composite emitting structures for high performance applications in optics.
Ab-initio calculations for dilute magnetic semiconductors
Energy Technology Data Exchange (ETDEWEB)
Belhadji, Brahim
2008-03-03
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.)
Ab initio study of ideal tensile strength and mechanical stability of transition-metal disilicides
Czech Academy of Sciences Publication Activity Database
Friák, Martin; Šob, Mojmír; Vitek, V.
2003-01-01
Roč. 68, č. 18 (2003), s. 184101-1 - 181101-10 ISSN 0163-1829 R&D Projects: GA AV ČR IAA1041302; GA ČR GA202/03/1351; GA MŠk OC 523.90 Institutional research plan: CEZ:AV0Z2041904 Keywords : ab initio calculations * electronic structure * theoretical tensile strength Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 2.962, year: 2003
Ab initio calculations of ideal tensile strength and mechanical stability in copper
Czech Academy of Sciences Publication Activity Database
Černý, M.; Šob, Mojmír; Pokluda, J.; Šandera, P.
2004-01-01
Roč. 16, č. 7 (2004), s. 1045-1052 ISSN 0953-8984 R&D Projects: GA ČR GA202/03/1351; GA AV ČR IAA1041302 Grant - others:GA MŠk1(CZ) 262100002 Institutional research plan: CEZ:AV0Z2041904 Keywords : ab initio calculations * electronic structure * theoretical tensile strength Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 2.049, year: 2004
Electronic structure and conductivity of ferroelectric hexaferrite: AB INITIO calculations
Czech Academy of Sciences Publication Activity Database
Knížek, Karel; Novák, Pavel; Küpferling, M.
2006-01-01
Roč. 73, č. 15 (2006), 153103/1-153103/4 ISSN 1098-0121 R&D Projects: GA AV ČR(CZ) IAA1010214 EU Projects: European Commission(XE) HPRN-CT-2002-00293 - SCOOTMO Institutional research plan: CEZ:AV0Z10100521 Keywords : ferroelectric hexaferrite * conductivity * GGA+U method Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.107, year: 2006
Electronic Structure of Silicon Nanowires Matrix from Ab Initio Calculations.
Monastyrskii, Liubomyr S; Boyko, Yaroslav V; Sokolovskii, Bogdan S; Potashnyk, Vasylyna Ya
2016-12-01
An investigation of the model of porous silicon in the form of periodic set of silicon nanowires has been carried out. The electronic energy structure was studied using a first-principle band method-the method of pseudopotentials (ultrasoft potentials in the basis of plane waves) and linearized mode of the method of combined pseudopotentials. Due to the use of hybrid exchange-correlation potentials (B3LYP), the quantitative agreement of the calculated value of band gap in the bulk material with experimental data is achieved. The obtained results show that passivation of dangling bonds with hydrogen atoms leads to substantial transformation of electronic energy structure. At complete passivation of the dangling silicon bonds by hydrogen atoms, the band gap value takes the magnitude which substantially exceeds that for bulk silicon. The incomplete passivation gives rise to opposite effect when the band gap value decreases down the semimetallic range.
Realization of prediction of materials properties by ab initio ...
Indian Academy of Sciences (India)
Unknown
IMR), Tohoku University, Sendai 980-8577, Japan. Abstract. Ab initio treatment is becoming realistic to predict physical, chemical, and even mechanical pro- perties of academically and industrially interesting materials. There is, however, some ...
Ab initio adiabatic and quasidiabatic potential energy surfaces of H ...
Indian Academy of Sciences (India)
s12039-015-1022-8. Ab initio adiabatic and quasidiabatic potential energy surfaces of H. ++. CN system. BHARGAVA ANUSURI and SANJAY KUMAR. ∗. Department of Chemistry, Indian Institute of Technology Madras, Chennai 600 036, India.
Ab Initio Atomistic Thermodynamics for Surfaces: A Primer
National Research Council Canada - National Science Library
Rogal, Jutta; Reuter, Karsten
2006-01-01
.... These techniques are referred to as first-principles (or in latin: ab initio) to indicate that they do not rely on empirical or fitted parameters, which then makes them applicable for a wide range of realistic conditions...
Ab initio phonon scattering by dislocations
Wang, Tao; Carrete, Jesús; van Roekeghem, Ambroise; Mingo, Natalio; Madsen, Georg K. H.
2017-06-01
Heat management in thermoelectric and power devices as well as in random access memories poses a grand challenge and can make the difference between a working and an abandoned device design. Despite the prevalence of dislocations in all these technologies, the modeling of their thermal resistance is based on 50-year-old analytical approximations, whose simplicity was driven by practical limitations rather than physical insight. We introduce an efficient ab initio approach based on Green's functions computed by two-dimensional reciprocal space integration. By combining elasticity theory and density functional theory, we calculate the scattering strength of a 90∘ misfit edge dislocation in Si. Because of the breakdown of the Born approximation, earlier literature models fail, even qualitatively. We find that a dislocation density larger than 109cm-2 is necessary to substantially influence thermal conductivity at room temperature and above. We quantify how much of the reduction of thermal conductivity measured in nanograined samples can be explained by realistic dislocation concentrations.
Lifshitz invariants from ab initio lattice dynamics
Schiaffino, Andrea; Stengel, Massimiliano
The interaction between different order parameters is vital to explain the emergence of new functionalities (hybrid improper ferroelectricity, magnetoelectricity) in multiferroic systems. While considerable theoretical efforts have been directed in the past at studying couplings (e.g. trilinear or biquadratic) that occur in a homogeneous sample, recent research has revealed an increasing number of cases where the interesting physics emerges from inhomogeneities in some order parameter (e.g. flexoelectricity, domain walls), rather than the uniform bulk phase itself. These are usually described in phenomenological theories via symmetry-allowed gradient-mediated terms, the so-called Lifshitz invariants. Here I will present a general method to calculate such couplings ab initio, within the framework of density-functional perturbation theory. I will start with a brief overview on the most challenging aspects of these calculations, i.e. how to deal with the breakdown of the translational symmetry, and with the unusual electrostatic effects that occur in such a regime. Next, I will demonstrate this strategy in practice by presenting calculations of the most relevant gradient coefficients involving strain, octahedral tilts and polarization in ferroelastic SrTiO3. MINECO-Spain through Grants No. FIS2013-48668-C2-2-P and No. SEV-2015-0496, and by Generalitat de Catalunya (Grant No. 2014SRG301).
Ab initio modelling of transition metals in diamond
International Nuclear Information System (INIS)
Watkins, M; Mainwood, A
2003-01-01
Transition metals (TM) from the first transition series are commonly used as solvent catalysts in the synthesis of diamond by high pressure, high temperature processes. Ab initio calculations on these metals, in finite clusters of tetrahedrally coordinated carbon, enable us to investigate trends in their stability and properties. By carrying out systematic studies of interstitial, substitutional and semi-vacancy TM defects, we show that the electronic structure of the TMs is complicated by the presence of 'dangling bonds' when the TM disrupts the crystal lattice: interstitial defects conform to the Ludwig-Woodbury (LW) model, whilst substitutional and semi-vacancy defects move from approximating the LW model early in the transition series to approaching the vacancy model for the heavier metals. Multi-configurational self-consistent field methods allow genuine many-electron states to be modelled; for neutral interstitial, and all substitutional TMs, the crystal fields are found to exceed the exchange energies in strength. Consequently, low spin states are found for these defects. We find substitutional defects to be the most stable, but that semi-vacancy TMs are very similar in energy to the substitutional defects late in the transition series; interstitial defects are only metastable in diamond. Given appropriate charge compensators neutral and positively charged interstitial TM defects were stable, while negatively charged species appeared to be strongly disfavoured
Perovskite transparent conducting oxides: an ab initio study.
Dabaghmanesh, S; Saniz, R; Amini, M N; Lamoen, D; Partoens, B
2013-10-16
We present an ab initio study of the electronic structure and of the formation energies of various point defects in BaSnO3 and SrGeO3. We show that La and Y impurities substituting Ba or Sr are shallow donors with a preferred 1 + charge state. These defects have a low formation energy within all the suitable equilibrium growth conditions considered. Oxygen vacancies behave as shallow donors as well, preferring the 2 + charge state. Their formation energies, however, are higher in most growth conditions, indicating a limited contribution to conductivity. The calculated electron effective mass in BaSnO3, with a value of 0.21 m(e), and the very high mobility reported recently in La-doped BaSnO3 single-crystals, suggest that remarkably low scattering rates can be achieved in the latter. In the case of SrGeO3, our results point to carrier density and mobility values in the low range for typical polycrystalline TCOs, in line with experiment.
Energy Technology Data Exchange (ETDEWEB)
Barrett, Bruce R. [Univ. of Arizona, Tucson, AZ (United States); Navrátil, Petr [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Vary, James P. [Ames Lab. and Iowa State Univ., Ames, IA (United States)
2012-11-17
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
Ab initio simulation of transport phenomena in rarefied gases.
Sharipov, Felix; Strapasson, José L
2012-09-01
Ab initio potentials are implemented into the direct simulation Monte Carlo (DSMC) method. Such an implementation allows us to model transport phenomena in rarefied gases without any fitting parameter of intermolecular collisions usually extracted from experimental data. Applying the method proposed by Sharipov and Strapasson [Phys. Fluids 24, 011703 (2012)], the use of ab initio potentials in the DSMC requires the same computational efforts as the widely used potentials such as hard spheres, variable hard sphere, variable soft spheres, etc. At the same time, the ab initio potentials provide more reliable results than any other one. As an example, the transport coefficients of a binary mixture He-Ar, viz., viscosity, thermal conductivity, and thermal diffusion factor, have been calculated for several values of the mole fraction.
Use of ab initio quantum chemical methods in battery technology
Energy Technology Data Exchange (ETDEWEB)
Deiss, E. [Paul Scherrer Inst. (PSI), Villigen (Switzerland)
1997-06-01
Ab initio quantum chemistry can nowadays predict physical and chemical properties of molecules and solids. An attempt should be made to use this tool more widely for predicting technologically favourable materials. To demonstrate the use of ab initio quantum chemistry in battery technology, the theoretical energy density (energy per volume of active electrode material) and specific energy (energy per mass of active electrode material) of a rechargeable lithium-ion battery consisting of a graphite electrode and a nickel oxide electrode has been calculated with this method. (author) 1 fig., 1 tab., 7 refs.
Monte Carlo methods in AB initio quantum chemistry quantum Monte Carlo for molecules
Lester, William A; Reynolds, PJ
1994-01-01
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
Ab initio Disordered Local Moment Approach for a Doped Rare-Earth Magnet
Matsumoto, Munehisa; Banerjee, Rudra; Staunton, Julie B.
Following the finite-temperature ab initio calculation framework based on the relativistic disordered local moments [J. B. Staunton et al., Phys. Rev. Lett. 93, 257204 (2004); Phys. Rev. B 74, 144411 (2006)], we computationally demonstrate the possibility of doping-enhanced coercivity at high-temperatures, taking YCo5 as a working material in order to extract the 3d-electron part of the electronic structure of the rare-earth permanent magnets. Alkaline-earth dopants are shown to be the candidates to realize the proposed phenomenon.
All-electron ab initio investigations of the electronic states of the NiC molecule
DEFF Research Database (Denmark)
Shim, Irene; Gingerich, Karl. A.
1999-01-01
The low-lying electronic states of NiC are investigated by all-electron ab initio multi-configuration self-consistent-field (CASSCF) calculations including relativistic corrections. The electronic structure of NiC is interpreted as perturbed antiferromagnetic couplings of the localized angular...... with new experimental data by Brugh and Morse. D-e is determined as 2.76 eV, and D-0 as 2.70 eV. (C) 1999 Elsevier Science B.V. All rights reserved....
Ab initio study of spin-dependent transport in carbon nanotubes with iron and vanadium adatoms
DEFF Research Database (Denmark)
Fürst, Joachim Alexander; Brandbyge, Mads; Jauho, Antti-Pekka
2008-01-01
We present an ab initio study of spin-dependent transport in armchair carbon nanotubes with transition metal adsorbates: iron or vanadium. The method based on density functional theory and nonequilibrium Green's functions is used to compute the electronic structure and zero-bias conductance....... The presence of the adsorbate causes scattering of electrons of mainly one spin type. The scattering is shown to be due to a coupling of the two armchair band states to the metal 3d orbitals with matching symmetry, giving rise to Fano antiresonances appearing as dips in the transmission function. The spin type...
Ab initio structure determination via powder X-ray diffraction
Indian Academy of Sciences (India)
Although the method of structure completion when once the starting model is provided is facile through the Rietveld refinement technique, the structure solution ab initio os still not push-button technology. In this article a survey of the recent development in this area is provided with an illustration of the structure determination ...
Cyanogen Azide. Ionization Potentials and Ab Initio SCF MO Calculation
DEFF Research Database (Denmark)
Bak, Börge; Jansen, Peter; Stafast, Herbert
1975-01-01
The Ne(I) and He(I) photoelectron(PE) spectra of cyanogen azide, NCN3, have been recorded at high resolution. Their interpretation is achieved by comparison with the PE spectrum of HN3 and an ab initio LCGO SCF MO calculation. Deviations from Koopmans' theorem of quite different magnitudes...
Quantifying transition voltage spectroscopy of molecular junctions: Ab initio calculations
DEFF Research Database (Denmark)
Chen, Jingzhe; Markussen, Troels; Thygesen, Kristian Sommer
2010-01-01
Transition voltage spectroscopy (TVS) has recently been introduced as a spectroscopic tool for molecular junctions where it offers the possibility to probe molecular level energies at relatively low bias voltages. In this work we perform extensive ab initio calculations of the nonlinear current...
Projector augmented wave method: ab initio molecular dynamics ...
Indian Academy of Sciences (India)
Unknown
The projector augmented wave method is an all-electron method for efficient ab initio molecular dynamics simulations with full wave functions. .... In that case the muffin–tin approximation is used solely to define the basis set. ..... functions probe the local character of the auxiliary wave function in the atomic region. Examples ...
The Properties of Some Simple Covalent Hydrides: An Ab Initio ...
African Journals Online (AJOL)
Some properties of the monomeric binary hydrides of the elements of the first two rows of the periodic table have been determined using ab initio molecular orbital theory. The properties in question are the energetic, structural, electronic, topological and vibrational characteristics. In general, a gradual convergence towards ...
Hydrogen Bond Dynamics in Aqueous Solutions: Ab initio Molecular ...
Indian Academy of Sciences (India)
Rate equation for the decay of CHB(t) · Definition of Hydrogen Bonds · Results of Molecular Dynamics · Dynamics of anion-water and water-water hydrogen bonds · Structural relaxation of anion-water & water-water H-bonds · Ab initio Molecular Dynamics : · Slide 14 · Dynamics of hydrogen bonds : CPMD results · Slide 16.
Ab initio calculation of the structural, mechanical and ...
African Journals Online (AJOL)
An ab initio plane-wave Pseudopotential calculations using the density functional theory (DFT) implementing the generalised gradient approximation (GGA) to study the structural, elastic constants, phonon dispersion curves, density of state and thermal properties of BeS. Also we calculated the shear modulus, Young's ...
Early stage precipitation in aluminum alloys : An ab initio study
Zhang, X.
2017-01-01
Multiscale computational materials science has reached a stage where many complicated phenomena or properties that are of great importance to manufacturing can be predicted or explained. The word “ab initio study” becomes commonplace as the development of density functional theory has enabled the
Young Modulus of Crystalline Polyethylene from ab Initio Molecular Dynamics
Hageman, J.C.L.; Meier, Robert J.; Heinemann, M.; Groot, R.A. de
1997-01-01
The Young modulus for crystalline polyethylene is calculated using ab initio molecular dynamics based on density functional theory in the local density approximation (DFT-LDA). This modulus, which can be seen as the ultimate value for the Young modulus of polyethylene fibers, is found to be 334 GPa.
Ab initio molecular dynamics simulation of laser melting of silicon
Silvestrelli, P.-L.; Alavi, A.; Parrinello, M.; Frenkel, D.
1996-01-01
The method of ab initio molecular dynamics, based on finite temperature density functional theory, is used to simulate laser heating of crystal silicon. We have found that a high concentration of excited electrons dramatically weakens the covalent bond. As a result, the system undergoes a melting
Ab initio study of phase equilibria in TiCx
DEFF Research Database (Denmark)
Korzhavyi, P.A.; Pourovskii, L.V.; Hugosson, H.W.
2002-01-01
The phase diagram for the vacancy-ordered structures in the substoichiometric TiCx (x = 0.5-1.0) has been established from Monte Carlo simulations with the long-range pair and multisite effective interactions obtained from ab initio calculations. Three ordered superstructures of vacancies (Ti2C, ...
Ab initio calculations of mechanical properties: Methods and applications
Czech Academy of Sciences Publication Activity Database
Pokluda, J.; Černý, Miroslav; Šob, Mojmír; Umeno, Y.
2015-01-01
Roč. 73, AUG (2015), s. 127-158 ISSN 0079-6425 R&D Projects: GA ČR(CZ) GAP108/12/0311 Institutional support: RVO:68081723 Keywords : Ab initio methods * Elastic moduli * Intrinsic hardness * Stability analysis * Theoretical strength * Intrinsic brittleness/ductility Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 31.083, year: 2015
Realization of prediction of materials properties by ab initio ...
Indian Academy of Sciences (India)
Unknown
Ab initio treatment is becoming realistic to predict physical, chemical, and even mechanical pro- perties of academically and ... materials under very high pressure in earth by direct method, and prediction of wavelength of emitted light from Na clusters with GW .... observed band gap value for semiconductors. This big. Quasi- ...
Realization of prediction of materials properties by ab initio ...
Indian Academy of Sciences (India)
Ab initio treatment is becoming realistic to predict physical, chemical, and even mechanical properties of academically and industrially interesting materials. There is, however, some limitation in size and time of the system up to the order of several hundred atoms and ∼ 1 pico second, even if we use the fastest ...
Perspective: Ab initio force field methods derived from quantum mechanics
Xu, Peng; Guidez, Emilie B.; Bertoni, Colleen; Gordon, Mark S.
2018-03-01
It is often desirable to accurately and efficiently model the behavior of large molecular systems in the condensed phase (thousands to tens of thousands of atoms) over long time scales (from nanoseconds to milliseconds). In these cases, ab initio methods are difficult due to the increasing computational cost with the number of electrons. A more computationally attractive alternative is to perform the simulations at the atomic level using a parameterized function to model the electronic energy. Many empirical force fields have been developed for this purpose. However, the functions that are used to model interatomic and intermolecular interactions contain many fitted parameters obtained from selected model systems, and such classical force fields cannot properly simulate important electronic effects. Furthermore, while such force fields are computationally affordable, they are not reliable when applied to systems that differ significantly from those used in their parameterization. They also cannot provide the information necessary to analyze the interactions that occur in the system, making the systematic improvement of the functional forms that are used difficult. Ab initio force field methods aim to combine the merits of both types of methods. The ideal ab initio force fields are built on first principles and require no fitted parameters. Ab initio force field methods surveyed in this perspective are based on fragmentation approaches and intermolecular perturbation theory. This perspective summarizes their theoretical foundation, key components in their formulation, and discusses key aspects of these methods such as accuracy and formal computational cost. The ab initio force fields considered here were developed for different targets, and this perspective also aims to provide a balanced presentation of their strengths and shortcomings. Finally, this perspective suggests some future directions for this actively developing area.
Energy Technology Data Exchange (ETDEWEB)
Ventelon, L. [CEA Saclay, Dept. des Materiaux pour le Nucleaire (DEN/DANS/DMN/SRMP), 91 - Gif-sur-Yvette (France)
2008-07-01
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.)
Ab initio calculations of the concentration dependent band gap reduction in dilute nitrides
Rosenow, Phil; Bannow, Lars C.; Fischer, Eric W.; Stolz, Wolfgang; Volz, Kerstin; Koch, Stephan W.; Tonner, Ralf
2018-02-01
While being of persistent interest for the integration of lattice-matched laser devices with silicon circuits, the electronic structure of dilute nitride III/V-semiconductors has presented a challenge to ab initio computational approaches. The origin of the computational problems is the strong distortion exerted by the N atoms on most host materials. Here, these issues are resolved by combining density functional theory calculations based on the meta-GGA functional presented by Tran and Blaha (TB09) with a supercell approach for the dilute nitride Ga(NAs). Exploring the requirements posed to supercells, it is shown that the distortion field of a single N atom must be allowed to decrease so far that it does not overlap with its periodic images. This also prevents spurious electronic interactions between translational symmetric atoms, allowing us to compute band gaps in very good agreement with experimentally derived reference values. In addition to existing approaches, these results offer a promising ab initio avenue to the electronic structure of dilute nitride semiconductor compounds.
Ab Initio Studies of Metal Hexaboride Materials
Schmidt, Kevin M.
Metal hexaborides are refractory ceramics with several qualities relevant to materials design, such as low work functions, high hardness, low thermal expansion coefficients, and high melting points, among many other properties of interest for industrial applications. Thermal and mechanical stability is a common feature provided by the covalently-bonded network boron atoms, and electronic properties can vary significantly with the resident metal. While these materials are currently employed as electron emitters and abrasives, promising uses of these materials also include catalytic applications for chemical dissociation reactions of various molecules such as hydrogen, water and carbon monoxide, for example. However, these extensions require a thorough understanding of particular mechanical and electronic properties. This dissertation is a collection of studies focused on understanding the behavior of metal hexaboride materials using computational modeling methods to investigate materials properties of these from both classical and quantum mechanical points of view. Classical modeling is performed using molecular dynamics methods with interatomic potentials obtained from density functional theory (DFT) calculations. Atomic mean-square displacements from the quasi-harmonic approximation and lattice energetic data are produced with DFT for developing the potentials. A generalized method was also developed for the inversion of cohesive energy curves of crystalline materials; pairwise interatomic potentials are extracted using detailed geometrical descriptions of the atomic interactions and a list of atomic displacements and degeneracies. The surface structure of metal hexaborides is studied with DFT using several model geometries to describe the terminal cation layouts, and these provide a basis for further studies on metal hexaboride interactions with hydrogen. The surface electronic structure calculations show that segregated regions of metal and boron
Polariton Bose condensate in an open system: Ab initio approach
Elistratov, A. A.; Lozovik, Yu. E.
2018-01-01
In the framework of path-integral formalism and Keldysh technique for a nonequilibrium system we explore the kinetics of the polariton condensate in a quantum well embedded in an optical microcavity. We take into account pumping and leakage of excitons and photons. We make an ab initio derivation of the equations governing the dynamics of the condensates and reservoirs and show that the real open polariton system has a non-Markovian character at times comparable to the Rabi oscillation period.
i-PI: A Python interface for ab initio path integral molecular dynamics simulations
Ceriotti, Michele; More, Joshua; Manolopoulos, David E.
2014-03-01
Recent developments in path integral methodology have significantly reduced the computational expense of including quantum mechanical effects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of these developments requires a considerable programming effort, which has hindered their adoption. Here we describe i-PI, an interface written in Python that has been designed to minimise the effort required to bring state-of-the-art path integral techniques to an electronic structure program. While it is best suited to first principles calculations and path integral molecular dynamics, i-PI can also be used to perform classical molecular dynamics simulations, and can just as easily be interfaced with an empirical forcefield code. To give just one example of the many potential applications of the interface, we use it in conjunction with the CP2K electronic structure package to showcase the importance of nuclear quantum effects in high-pressure water. Catalogue identifier: AERN_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AERN_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 138626 No. of bytes in distributed program, including test data, etc.: 3128618 Distribution format: tar.gz Programming language: Python. Computer: Multiple architectures. Operating system: Linux, Mac OSX, Windows. RAM: Less than 256 Mb Classification: 7.7. External routines: NumPy Nature of problem: Bringing the latest developments in the modelling of nuclear quantum effects with path integral molecular dynamics to ab initio electronic structure programs with minimal implementational effort. Solution method: State-of-the-art path integral molecular dynamics techniques are implemented in a Python interface. Any electronic structure code can be patched to receive the atomic
Ab initio nuclear structure - the large sparse matrix eigenvalue problem
International Nuclear Information System (INIS)
Vary, James P; Maris, Pieter; Ng, Esmond; Yang, Chao; Sosonkina, Masha
2009-01-01
The structure and reactions of light nuclei represent fundamental and formidable challenges for microscopic theory based on realistic strong interaction potentials. Several ab initio methods have now emerged that provide nearly exact solutions for some nuclear properties. The ab initio no core shell model (NCSM) and the no core full configuration (NCFC) method, frame this quantum many-particle problem as a large sparse matrix eigenvalue problem where one evaluates the Hamiltonian matrix in a basis space consisting of many-fermion Slater determinants and then solves for a set of the lowest eigenvalues and their associated eigenvectors. The resulting eigenvectors are employed to evaluate a set of experimental quantities to test the underlying potential. For fundamental problems of interest, the matrix dimension often exceeds 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 this large sparse matrix eigenvalue problem. We also outline the challenges that lie ahead for achieving further breakthroughs in fundamental nuclear theory using these ab initio approaches.
Ab Initio Nuclear Structure and Reaction Calculations for Rare Isotopes
Energy Technology Data Exchange (ETDEWEB)
Draayer, Jerry P. [Louisiana State Univ., Baton Rouge, LA (United States)
2014-09-28
We have developed a novel ab initio symmetry-adapted no-core shell model (SA-NCSM), which has opened the intermediate-mass region for ab initio investigations, thereby providing an opportunity for first-principle symmetry-guided applications to nuclear structure and reactions for nuclear isotopes from the lightest p-shell systems to intermediate-mass nuclei. This includes short-lived proton-rich nuclei on the path of X-ray burst nucleosynthesis and rare neutron-rich isotopes to be produced by the Facility for Rare Isotope Beams (FRIB). We have provided ab initio descriptions of high accuracy for low-lying (including collectivity-driven) states of isotopes of Li, He, Be, C, O, Ne, Mg, Al, and Si, and studied related strong- and weak-interaction driven reactions that are important, in astrophysics, for further understanding stellar evolution, X-ray bursts and triggering of s, p, and rp processes, and in applied physics, for electron and neutrino-nucleus scattering experiments as well as for fusion ignition at the National Ignition Facility (NIF).
Linker, Gerrit-Jan; van Loosdrecht, Paul H. M.; van Duijnen, Piet; Broer, Ria
2010-01-01
We performed ab initio quantum chemical calculations for the geometrical and electronic structure of the EDO-TTF (ethylenedioxy-tetrathiafulvalene) molecule using HF, CASSCF and DFT methods. We compare these in vacuo results with the properties of the (EDO-TTF)(2)PF6 crystal at near room
Energy Technology Data Exchange (ETDEWEB)
Bernard, St
1998-12-31
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.
Sumner, Isaiah; Iyengar, Srinivasan S
2007-10-18
We have introduced a computational methodology to study vibrational spectroscopy in clusters inclusive of critical nuclear quantum effects. This approach is based on the recently developed quantum wavepacket ab initio molecular dynamics method that combines quantum wavepacket dynamics with ab initio molecular dynamics. The computational efficiency of the dynamical procedure is drastically improved (by several orders of magnitude) through the utilization of wavelet-based techniques combined with the previously introduced time-dependent deterministic sampling procedure measure to achieve stable, picosecond length, quantum-classical dynamics of electrons and nuclei in clusters. The dynamical information is employed to construct a novel cumulative flux/velocity correlation function, where the wavepacket flux from the quantized particle is combined with classical nuclear velocities to obtain the vibrational density of states. The approach is demonstrated by computing the vibrational density of states of [Cl-H-Cl]-, inclusive of critical quantum nuclear effects, and our results are in good agreement with experiment. A general hierarchical procedure is also provided, based on electronic structure harmonic frequencies, classical ab initio molecular dynamics, computation of nuclear quantum-mechanical eigenstates, and employing quantum wavepacket ab initio dynamics to understand vibrational spectroscopy in hydrogen-bonded clusters that display large degrees of anharmonicities.
Ab initio simulations and neutron scattering studies of structure and dynamics in PdH
International Nuclear Information System (INIS)
Totolici, I.E.
2001-07-01
The work presented in this PhD thesis is concerned with the interpretation of the neutron scattering measurements from the palladium hydrogen system by means of ab initio electronic structure calculations. The motivation of performing such calculations was due to recent neutron scattering studies on this system that showed a strong directional dependence to the dynamical structure factor together with a complex dependence on energy. Here we attempt to describe the origin of these features by ab initio simulations of the dynamical structure factor. The method assumes an adiabatic separation of the motion of the proton and palladium atoms. The proton wave functions are calculated by a direct solution of the associated single-particle Schroedinger equation using a plane wave basis set method and a mapping of the adiabatic surface. The Fourier components of the adiabatic potential are obtained from LDA pseudopotential calculations. Using Fermi's golden rule within the Born approximation we were then able to calculate the dynamical structure factor, S(Q,ω), for exciting the proton from its ground state to various excited states as a function of the magnitude and direction of the scattering wave vector. The results are in agreement with the inelastic neutron scattering spectra and allow us to identify the origin of previous inexplicable features, in particular the strong directional dependence to the experimental data. The method was extended to investigate the expansion of the equilibrium lattice constant as a function of the H isotope when the zero-point energy of the proton/deuterium is explicitly taken into account in the relaxation process. The results we obtained predicted a bigger lattice constant for the hydride, as expected. Furthermore, other complex ab initio calculations were carried out in order to describe the origin of the large optic dispersion, seen previously in the coherent neutron scattering data. Our calculated dispersion proved to be in good
Ab initio simulations for material properties inside Jupiter
French, Martin; Becker, Andreas; Lorenzen, Winfried; Nettelmann, Nadine; Bethkenhagen, Mandy; Wicht, Johannes; Redmer, Ronald
2013-07-01
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).
Ab-initio theory of scanning tunneling microscopy
di Ventra, M.; Pantelides, S. T.
1998-03-01
An ab-initio theory of the Scanning Tunneling Microscope (STM) has been developed by treating the sample and the tip as a single system. The theory combines density functional theory with the Kubo-Greenwood linear-response formalism for the conductivity( See, e.g., N.F. Mott in Conduction in Non-Crystalline Materials), (Oxford University Press, Oxford, 1987).. The current is computed by taking into account the atomic relaxations that occur on both the surface and the tip due to their mutal interactions. Illustrative examples will be presented for the case of a clean Al(110) surface and the same surface with a vacancy.
Iterative projection algorithms for ab initio phasing in virus crystallography.
Lo, Victor L; Kingston, Richard L; Millane, Rick P
2016-12-01
Iterative projection algorithms are proposed as a tool for ab initio phasing in virus crystallography. The good global convergence properties of these algorithms, coupled with the spherical shape and high structural redundancy of icosahedral viruses, allows high resolution phases to be determined with no initial phase information. This approach is demonstrated by determining the electron density of a virus crystal with 5-fold non-crystallographic symmetry, starting with only a spherical shell envelope. The electron density obtained is sufficiently accurate for model building. The results indicate that iterative projection algorithms should be routinely applicable in virus crystallography, without the need for ancillary phase information. Copyright © 2016 Elsevier Inc. All rights reserved.
Ab initio modeling of small proteins by iterative TASSER simulations
Directory of Open Access Journals (Sweden)
Zhang Yang
2007-05-01
Full Text Available Abstract Background Predicting 3-dimensional protein structures from amino-acid sequences is an important unsolved problem in computational structural biology. The problem becomes relatively easier if close homologous proteins have been solved, as high-resolution models can be built by aligning target sequences to the solved homologous structures. However, for sequences without similar folds in the Protein Data Bank (PDB library, the models have to be predicted from scratch. Progress in the ab initio structure modeling is slow. The aim of this study was to extend the TASSER (threading/assembly/refinement method for the ab initio modeling and examine systemically its ability to fold small single-domain proteins. Results We developed I-TASSER by iteratively implementing the TASSER method, which is used in the folding test of three benchmarks of small proteins. First, data on 16 small proteins (α-root mean square deviation (RMSD of 3.8Å, with 6 of them having a Cα-RMSD α-RMSD α-RMSD of the I-TASSER models was 3.9Å, whereas it was 5.9Å using TOUCHSTONE-II software. Finally, 20 non-homologous small proteins (α-RMSD of 3.9Å was obtained for the third benchmark, with seven cases having a Cα-RMSD Conclusion Our simulation results show that I-TASSER can consistently predict the correct folds and sometimes high-resolution models for small single-domain proteins. Compared with other ab initio modeling methods such as ROSETTA and TOUCHSTONE II, the average performance of I-TASSER is either much better or is similar within a lower computational time. These data, together with the significant performance of automated I-TASSER server (the Zhang-Server in the 'free modeling' section of the recent Critical Assessment of Structure Prediction (CASP7 experiment, demonstrate new progresses in automated ab initio model generation. The I-TASSER server is freely available for academic users http://zhang.bioinformatics.ku.edu/I-TASSER.
Hydrogen diffusion in liquid aluminum from ab initio molecular dynamics
Jakse, N.; Pasturel, A.
2014-05-01
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.
Tailoring magnetoresistance at the atomic level: An ab initio study
Tao, Kun
2012-01-05
The possibility of manipulating the tunneling magnetoresistance (TMR) of antiferromagnetic nanostructures is predicted in the framework of ab initio calculations. By the example of a junction composed of an antiferromagnetic dimer and a spin-polarized scanning tunneling microscopy tip we show that the TMR can be tuned and even reversed in sign by lateral and vertical movements of the tip. Moreover, our finite-bias calculations demonstrate that the magnitude and the sign of the TMR can also be tuned by an external voltage. © 2012 American Physical Society.
Energy Technology Data Exchange (ETDEWEB)
Borges, P. D., E-mail: pdborges@gmail.com, E-mail: lscolfaro@txstate.edu; Scolfaro, L., E-mail: pdborges@gmail.com, E-mail: lscolfaro@txstate.edu [Department of Physics, Texas State University, San Marcos, Texas 78666 (United States)
2014-12-14
The thermoelectric properties of indium nitride in the most stable wurtzite phase (w-InN) as a function of electron and hole concentrations and temperature were studied by solving the semiclassical Boltzmann transport equations in conjunction with ab initio electronic structure calculations, within Density Functional Theory. Based on maximally localized Wannier function basis set and the ab initio band energies, results for the Seebeck coefficient are presented and compared with available experimental data for n-type as well as p-type systems. Also, theoretical results for electric conductivity and power factor are presented. Most cases showed good agreement between the calculated properties and experimental data for w-InN unintentionally and p-type doped with magnesium. Our predictions for temperature and concentration dependences of electrical conductivity and power factor revealed a promising use of InN for intermediate and high temperature thermoelectric applications. The rigid band approach and constant scattering time approximation were utilized in the calculations.
High Accuracy ab Initio Calculations of Rotational-Vibrational Levels of the HCN/HNC System.
Makhnev, Vladimir Yu; Kyuberis, Aleksandra A; Zobov, Nikolai F; Lodi, Lorenzo; Tennyson, Jonathan; Polyansky, Oleg L
2018-02-08
Highly accurate ab initio calculations of vibrational and rotational-vibrational energy levels of the HCN/HNC (hydrogen cyanide/hydrogen isocyanide) isomerising system are presented for several isotopologues. All-electron multireference configuration interaction (MRCI) electronic structure calculations were performed using basis sets up to aug-cc-pCV6Z on a grid of 1541 geometries. The ab initio energies were used to produce an analytical potential energy surface (PES) describing the two minima simultaneously. An adiabatic Born-Oppenheimer diagonal correction (BODC) correction surface as well as a relativistic correction surface were also calculated. These surfaces were used to compute vibrational and rotational-vibrational energy levels up to 25 000 cm -1 which reproduce the extensive set of experimentally known HCN/HNC levels with a root-mean-square deviation σ = 1.5 cm -1 . We studied the effect of nonadiabatic effects by introducing opportune radial and angular corrections to the nuclear kinetic energy operator. Empirical determination of two nonadiabatic parameters results in observed energies up to 7000 cm -1 for four HCN isotopologues (HCN, DCN, H 13 CN, and HC 15 N) being reproduced with σ = 0.37 cm -1 . The height of the isomerization barrier, the isomerization energy and the dissociation energy were computed using a number of models; our best results are 16 809.4, 5312.8, and 43 729 cm -1 , respectively.
Thermodynamic assessment of the Ho–Te system supported by ab initio calculations
Energy Technology Data Exchange (ETDEWEB)
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
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.
Ab initio study on the reaction between uranium and O2
International Nuclear Information System (INIS)
Shuai Maobing; Zhao Pengji; Tian Anmin
2000-08-01
Optimized geometries, total energies and electronic structures of some gaseous atoms and molecules of uranium-oxygen system are calculated with harmonic vibration analysis using ab initio method. The potential energy surfaces (PESs) of the uranium oxidation process are also constructed. The calculated optimized geometries, infrared vibrational frequencies and the first ionized potential energies are in well accordance with available experimental data. Although U6p, U7s and U6d valence orbital electrons take part in the formation of U - O bond, the U5f electrons play an dominant role in this process and because the energies of U5f, U6d, U7s and Uds atomic orbitals are close to each other, these orbitals may hybrid and interact with O2p orbital, simultaneously, to form molecular orbitals of uranium oxides. The PESs show that different reaction modes result in different product geometries
Ab initio study of thermoelectric properties of doped SnO2 superlattices
International Nuclear Information System (INIS)
Borges, P.D.; Silva, D.E.S.; Castro, N.S.; Ferreira, C.R.; Pinto, F.G.; Tronto, J.; Scolfaro, L.
2015-01-01
Transparent conductive oxides, such as tin dioxide (SnO 2 ), have recently shown to be promising materials for thermoelectric applications. In this work we studied the thermoelectric properties of Fe-, Sb- and Zn-uniformly doping and co-doping SnO 2 , as well as of Sb and Zn planar (or delta)-doped layers in SnO 2 forming oxide superlattices (SLs). Based on the semiclassical Boltzmann transport equations (BTE) in conjunction with ab initio electronic structure calculations, the Seebeck coefficient (S) and figure of merit (ZT) are obtained for these systems, and are compared with available experimental data. The delta doping approach introduces a remarkable modification in the electronic structure of tin dioxide, when compared with the uniform doping, and colossal values for ZT are predicted for the delta-doped oxide SLs. This result is a consequence of the two-dimensional electronic confinement and the strong anisotropy introduced by the doped planes. In comparison with the uniformly doped systems, our predictions reveal a promising use of delta-doped SnO 2 SLs for enhanced S and ZT, which emerge as potential candidates for thermoelectric applications. - Graphical abstract: Band structure and Figure of merit for SnO2:Sb superlattice along Z direction, P. D. Borges, D. E. S. Silva, N. S. Castro, C. R. Ferreira, F. G. Pinto, J. Tronto and L. Scolfaro, Ab initio study of thermoelectric properties of doped SnO2 superlattices. - Highlights: • Thermoelectric properties of SnO 2 -based alloys and superlattices. • High figure of merit is predicted for planar-doped SnO 2 superlattices. • Nanotechnology has an important role for the development of thermoelectric devices.
Ab initio study of thermoelectric properties of doped SnO{sub 2} superlattices
Energy Technology Data Exchange (ETDEWEB)
Borges, P.D., E-mail: pdborges@gmail.com [Instituto de Ciências Exatas e Tecnológicas, Universidade Federal de Viçosa, 38810-000 Rio Paranaíba, MG (Brazil); Silva, D.E.S.; Castro, N.S.; Ferreira, C.R.; Pinto, F.G.; Tronto, J. [Instituto de Ciências Exatas e Tecnológicas, Universidade Federal de Viçosa, 38810-000 Rio Paranaíba, MG (Brazil); Scolfaro, L. [Department of Physics, Texas State University, 78666 San Marcos, TX (United States)
2015-11-15
Transparent conductive oxides, such as tin dioxide (SnO{sub 2}), have recently shown to be promising materials for thermoelectric applications. In this work we studied the thermoelectric properties of Fe-, Sb- and Zn-uniformly doping and co-doping SnO{sub 2}, as well as of Sb and Zn planar (or delta)-doped layers in SnO{sub 2} forming oxide superlattices (SLs). Based on the semiclassical Boltzmann transport equations (BTE) in conjunction with ab initio electronic structure calculations, the Seebeck coefficient (S) and figure of merit (ZT) are obtained for these systems, and are compared with available experimental data. The delta doping approach introduces a remarkable modification in the electronic structure of tin dioxide, when compared with the uniform doping, and colossal values for ZT are predicted for the delta-doped oxide SLs. This result is a consequence of the two-dimensional electronic confinement and the strong anisotropy introduced by the doped planes. In comparison with the uniformly doped systems, our predictions reveal a promising use of delta-doped SnO{sub 2} SLs for enhanced S and ZT, which emerge as potential candidates for thermoelectric applications. - Graphical abstract: Band structure and Figure of merit for SnO2:Sb superlattice along Z direction, P. D. Borges, D. E. S. Silva, N. S. Castro, C. R. Ferreira, F. G. Pinto, J. Tronto and L. Scolfaro, Ab initio study of thermoelectric properties of doped SnO2 superlattices. - Highlights: • Thermoelectric properties of SnO{sub 2}-based alloys and superlattices. • High figure of merit is predicted for planar-doped SnO{sub 2} superlattices. • Nanotechnology has an important role for the development of thermoelectric devices.
Ab initio dynamics of the cytochrome P450 hydroxylation reaction
Energy Technology Data Exchange (ETDEWEB)
Elenewski, Justin E.; Hackett, John C, E-mail: jchackett@vcu.edu [Department of Physiology and Biophysics and The Massey Cancer Center, School of Medicine, Virginia Commonwealth University, 401 College Street, Richmond, Virginia 23219-1540 (United States)
2015-02-14
The iron(IV)-oxo porphyrin π-cation radical known as Compound I is the primary oxidant within the cytochromes P450, allowing these enzymes to affect the substrate hydroxylation. In the course of this reaction, a hydrogen atom is abstracted from the substrate to generate hydroxyiron(IV) porphyrin and a substrate-centered radical. The hydroxy radical then rebounds from the iron to the substrate, yielding the hydroxylated product. While Compound I has succumbed to theoretical and spectroscopic characterization, the associated hydroxyiron species is elusive as a consequence of its very short lifetime, for which there are no quantitative estimates. To ascertain the physical mechanism underlying substrate hydroxylation and probe this timescale, ab initio molecular dynamics simulations and free energy calculations are performed for a model of Compound I catalysis. Semiclassical estimates based on these calculations reveal the hydrogen atom abstraction step to be extremely fast, kinetically comparable to enzymes such as carbonic anhydrase. Using an ensemble of ab initio simulations, the resultant hydroxyiron species is found to have a similarly short lifetime, ranging between 300 fs and 3600 fs, putatively depending on the enzyme active site architecture. The addition of tunneling corrections to these rates suggests a strong contribution from nuclear quantum effects, which should accelerate every step of substrate hydroxylation by an order of magnitude. These observations have strong implications for the detection of individual hydroxylation intermediates during P450 catalysis.
AB INITIO SIMULATIONS FOR MATERIAL PROPERTIES ALONG THE JUPITER ADIABAT
International Nuclear Information System (INIS)
French, Martin; Becker, Andreas; Lorenzen, Winfried; Nettelmann, Nadine; Bethkenhagen, Mandy; Redmer, Ronald; Wicht, Johannes
2012-01-01
We determine basic thermodynamic and transport properties of hydrogen-helium-water mixtures for the extreme conditions along Jupiter's adiabat via ab initio simulations, which are compiled in an accurate and consistent data set. In particular, we calculate the electrical and thermal conductivity, the shear and longitudinal viscosity, and diffusion coefficients of the nuclei. We present results for associated quantities like the magnetic and thermal diffusivity and the kinematic shear viscosity along an adiabat that is taken from a state-of-the-art interior structure model. Furthermore, the heat capacities, the thermal expansion coefficient, the isothermal compressibility, the Grüneisen parameter, and the speed of sound are calculated. We find that the onset of dissociation and ionization of hydrogen at about 0.9 Jupiter radii marks a region where the material properties change drastically. In the deep interior, where the electrons are degenerate, many of the material properties remain relatively constant. Our ab initio data will serve as a robust foundation for applications that require accurate knowledge of the material properties in Jupiter's interior, e.g., models for the dynamo generation.
Ab initio study of the low-lying electronic states of the CaO molecule
Energy Technology Data Exchange (ETDEWEB)
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
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
Embedded atom approach for gold–silicon system from ab initio
Indian Academy of Sciences (India)
In the present paper, an empirical embedded atom method (EAM) potential for gold–silicon (Au–Si) is developed by fitting to ab initio force (the 'force matching' method) and experimental data. The force database is generated within ab initio molecular dynamics (AIMD). The database includes liquid phase at various ...
Ab initio and Gordon--Kim intermolecular potentials for two nitrogen molecules
International Nuclear Information System (INIS)
Ree, F.H.; Winter, N.W.
1980-01-01
Both ab initio MO--LCAO--SCF and the electron-gas (or Gordon--Kim) methods have been used to compute the intermolecular potential (Phi) of N 2 molecules for seven different N 2 --N 2 orientations. The ab initio calculations were carried out using a [4s3p] contracted Gaussian basis set with and without 3d polarization functions. The larger basis set provides adequate results for Phi>0.002 hartree or intermolecular separations less than 6.5--7 bohr. We use a convenient analytic expression to represent the ab initio data in terms of the intermolecular distance and three angles defining the orientations of the two N 2 molecules. The Gordon--Kim method with Rae's self-exchange correction yields Phi, which agrees reasonably well over a large repulsive range. However, a detailed comparison of the electron kinetic energy contributions shows a large difference between the ab initio and the Gordon--Kim calculations. Using the ab initio data we derive an atom--atom potential of the two N 2 molecules. Although this expression does not accurately fit the data at some orientations, its spherical average agrees with the corresponding average of the ab initio Phi remarkably well. The spherically averaged ab initio Phi is also compared with the corresponding quantities derived from experimental considerations. The approach of the ab initio Phi to the classical quadrupole--quadrupole interaction at large intermolecular separation is also discussed
Embedded atom approach for gold–silicon system from ab initio ...
Indian Academy of Sciences (India)
In the present paper, an empirical embedded atom method (EAM) potential for gold–silicon (Au–Si) is developed by fitting to ab initio force (the 'force matching' method) and experimental data. The force database is generated within ab initio molecular dynamics (AIMD). The database includes liquid phase at various ...
Summation of Parquet diagrams as an ab initio method in nuclear structure calculations
International Nuclear Information System (INIS)
Bergli, Elise; Hjorth-Jensen, Morten
2011-01-01
Research highlights: → We present a Green's function based approach for doing ab initio nuclear structure calculations. → In particular the sum the subset of so-called Parquet diagrams. → Applying the theory to a simple but realistic model, results in good agreement with other ab initio methods. → This opens up for ab initio calculations for medium-heavy nuclei. - Abstract: In this work we discuss the summation of the Parquet class of diagrams within Green's function theory as a possible framework for ab initio nuclear structure calculations. The theory is presented and some numerical details are discussed, in particular the approximations employed. We apply the Parquet method to a simple model, and compare our results with those from an exact solution. The main conclusion is that even at the level of approximation presented here, the results shows good agreement with other comparable ab initio approaches.
Ab initio and kinetic modeling studies of formic acid oxidation
DEFF Research Database (Denmark)
Marshall, Paul; Glarborg, Peter
2015-01-01
A detailed chemical kinetic model for oxidation of formic acid (HOCHO) in flames has been developed, based on theoretical work and data from literature. Ab initio calculations were used to obtain rate coefficients for reactions of HOCHO with H, O, and HO2. Modeling predictions with the mechanism...... have been compared to the experimental results of de Wilde and van Tiggelen (1968) who measured the laminar burning velocities for HOCHO flames over a range of stoichiometries and dilution ratios. The modeling predictions are generally satisfactory. The governing reaction mechanisms are outlined based...... on calculations with the kinetic model. Formic acid is consumed mainly by reaction with OH, yielding OCHO, which dissociates rapidly to CO2 + H, and HOCO, which may dissociate to CO + OH or CO2 + H, or react with H, OH, or O2 to form more stable products. The branching fraction of the HOCHO + OH reaction, as well...
Symplectic ab initio no-core shell model
Energy Technology Data Exchange (ETDEWEB)
Draayer, J. P.; Dytrych, T.; Sviratcheva, K. D.; Bahri, C. [Department of Physics and Astronomy, Lousiana State University, Baton Rouge, 70803 Lousiana (United States); Vary, J. P. [Department of Physics and Astronomy, Iowa State University, Ames, 50011 Iowa (United States)
2008-12-15
The present study confirms the significance of the symplectic Sp(3,R) symmetry in nuclear dynamics as unveiled, for the first time, by examinations of realistic nucleon-nucleon interactions as well as of eigenstates calculated in the framework of the ab initio No-Core Shell Model (NCSM). The results reveal that the NCSM wave functions for light nuclei highly overlap (at the {approx} 90% level) with only a few of the most deformed Sp(3,R)-symmetric basis states. This points to the possibility of achieving convergence of higher-lying collective modes and reaching heavier nuclei by expanding the NCSM basis space beyond its current limits through Sp(3,R) basis states. Furthermore the symplectic symmetry is found to be favored by the JISP 16 and CD-Bonn realistic nucleon-nucleon interactions, which points to a more fundamental origin of the symplectic symmetry. (Author)
Molybdenum-titanium phase diagram evaluated from ab initio calculations
Barzilai, Shmuel; Toher, Cormac; Curtarolo, Stefano; Levy, Ohad
2017-07-01
The design of next generation β -type titanium implants requires detailed knowledge of the relevant stable and metastable phases at temperatures where metallurgical heat treatments can be performed. Recently, a standard specification for surgical implant applications was established for Mo-Ti alloys. However, the thermodynamic properties of this binary system are not well known and two conflicting descriptions of the β -phase stability have been presented in the literature. In this study, we use ab initio calculations to investigate the Mo-Ti phase diagram. These calculations predict that the β phase is stable over a wide concentration range, in qualitative agreement with one of the reported phase diagrams. In addition, they predict stoichiometric compounds, stable at temperatures below 300 ∘C , which have not yet been detected by experiments. The resulting solvus, which defines the transition to the β -phase solid solution, therefore occurs at lower temperatures and is more complex than previously anticipated.
Ab initio dynamical exchange interactions in frustrated antiferromagnets
Simoni, Jacopo; Stamenova, Maria; Sanvito, Stefano
2017-08-01
The ultrafast response to an optical pulse excitation of the spin-spin exchange interaction in transition metal antiferromagnets is studied within the framework of the time-dependent spin-density functional theory. We propose a formulation for the full dynamical exchange interaction, which is nonlocal in space, and it is derived starting from ab initio arguments. Then, we investigate the effect of the laser pulse on the onset of the dynamical process. It is found that we can distinguish two types of excitations, both activated immediately after the action of the laser pulse. While the first one can be associated to a Stoner-like excitation and involves the transfer of spin from one site to another, the second one is related to the ultrafast modification of a Heisenberg-like exchange interaction and can trigger the formation of spin waves in the first few hundred femtoseconds of the time evolution.
Ab initio Eliashberg Theory: Making Genuine Predictions of Superconducting Features
Sanna, Antonio; Flores-Livas, José A.; Davydov, Arkadiy; Profeta, Gianni; Dewhurst, Kay; Sharma, Sangeeta; Gross, E. K. U.
2018-04-01
We present an application of Eliashberg theory of superconductivity to study a set of novel superconducting systems with a wide range of structural and chemical properties. The set includes three intercalated group-IV honeycomb layered structures, SH3 at 200 GPa (the superconductor with the highest measured critical temperature), the similar system SeH3 at 150 GPa, and a lithium doped mono-layer of black phosphorus. The theoretical approach we adopt is a recently developed, fully ab initio Eliashberg approach that takes into account the Coulomb interaction in a full energy-resolved fashion avoiding any free parameters like μ*. This method provides reasonable estimations of superconducting properties, including TC and the excitation spectra of superconductors.
Ab initio electron propagator theory of molecular wires. I. Formalism.
Dahnovsky, Yu; Zakrzewski, V G; Kletsov, A; Ortiz, J V
2005-11-08
Ab initio electron propagator methodology may be applied to the calculation of electrical current through a molecular wire. A new theoretical approach is developed for the calculation of the retarded and advanced Green functions in terms of the electron propagator matrix for the bridge molecule. The calculation of the current requires integration in a complex half plane for a trace that involves terminal and Green's-function matrices. Because the Green's-function matrices have complex poles represented by matrices, a special scheme is developed to express these "matrix poles" in terms of ordinary poles. An expression for the current is derived for a terminal matrix of arbitrary rank. For a single terminal orbital, the analytical expression for the current is given in terms of pole strengths, poles, and terminal matrix elements of the electron propagator. It is shown that Dyson orbitals with high pole strengths and overlaps with terminal orbitals are most responsible for the conduction of electrical current.
Ab initio Potential Energy Surface for H-H2
Partridge, Harry; Bauschlicher, Charles W., Jr.; Stallcop, James R.; Levin, Eugene
1993-01-01
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.
Reactive Monte Carlo sampling with an ab initio potential
International Nuclear Information System (INIS)
Leiding, Jeff; Coe, Joshua D.
2016-01-01
We present the first application of reactive Monte Carlo in a first-principles context. The algorithm samples in a modified NVT ensemble in which the volume, temperature, and total number of atoms of a given type are held fixed, but molecular composition is allowed to evolve through stochastic variation of chemical connectivity. We discuss general features of the method, as well as techniques needed to enhance the efficiency of Boltzmann sampling. Finally, we compare the results of simulation of NH 3 to those of ab initio molecular dynamics (AIMD). We find that there are regions of state space for which RxMC sampling is much more efficient than AIMD due to the “rare-event” character of chemical reactions.
Thermal transport properties of antimonene: an ab initio study.
Wang, Shudong; Wang, Wenhua; Zhao, Guojun
2016-11-16
Searching for low thermal conductivity materials is crucial for thermoelectric devices. Here we report on the phonon transport properties of recently fabricated single layer antimony, antimonene [Ares, et al., Adv. Mater., 2016, 28, 6332]. Ab initio calculations in combination with the Boltzmann transport equation (BTE) for phonons show that antimonene has a low lattice thermal conductivity (15.1 W m -1 K -1 at 300 K), indicating its potential thermoelectric applications. The low lattice thermal conductivity is due to its small group velocity, low Debye temperature and large buckling height. We also investigate in detail the mode contributions to total thermal conductivity and find at low frequency that the longitudinal acoustic (LA) branch dominates the thermal conductivity. Moreover, we show that the lattice thermal conductivity of antimonene can further be reduced by minimizing the sample size. Our findings open the field for thermoelectric applications based on antimonene.
Ab initio engineering of materials with stacked hexagonal tin frameworks
Shao, Junping; Beaufils, Clément; Kolmogorov, Aleksey N.
2016-07-01
The group-IV tin has been hypothesized to possess intriguing electronic properties in an atom-thick hexagonal form. An attractive pathway of producing sizable 2D crystallites of tin is based on deintercalation of bulk compounds with suitable tin frameworks. Here, we have identified a new synthesizable metal distannide, NaSn2, with a 3D stacking of flat hexagonal layers and examined a known compound, BaSn2, with buckled hexagonal layers. Our ab initio results illustrate that despite being an exception to the 8-electron rule, NaSn2 should form under pressures easily achievable in multi-anvil cells and remain (meta)stable under ambient conditions. Based on calculated Z2 invariants, the predicted NaSn2 may display topologically non-trivial behavior and the known BaSn2 could be a strong topological insulator.
Quantum plasmonics: from jellium models to ab initio calculations
Directory of Open Access Journals (Sweden)
Varas Alejandro
2016-08-01
Full Text Available Light-matter interaction in plasmonic nanostructures is often treated within the realm of classical optics. However, recent experimental findings show the need to go beyond the classical models to explain and predict the plasmonic response at the nanoscale. A prototypical system is a nanoparticle dimer, extensively studied using both classical and quantum prescriptions. However, only very recently, fully ab initio time-dependent density functional theory (TDDFT calculations of the optical response of these dimers have been carried out. Here, we review the recent work on the impact of the atomic structure on the optical properties of such systems. We show that TDDFT can be an invaluable tool to simulate the time evolution of plasmonic modes, providing fundamental understanding into the underlying microscopical mechanisms.
Constructing ab initio and empirical potential energy surfaces for water
International Nuclear Information System (INIS)
Kain, Jacqueline Sophie
2001-01-01
The infrared spectrum of water is possibly one of the most well studied and yet portions of it are still poorly understood. Recently, significant advances have been made in assigning water spectra using variational nuclear calculations. The major factor determining the accuracy of ro-vibrational spectra of water is the accuracy of the underlying Potential Energy Surface. Even the most accurate ab initio Potential Energy Surface does not reproduce the Born-Oppenheimer surface to sufficient accuracy for spectroscopic studies. Furthermore, effects beyond this model such as the adiabatic correction, the relativistic correction and the non-adiabatic correction have to be considered. This thesis includes a discussion on how the relativistic correction was calculated, for the water molecule, from first-order perturbation theory. The relativistic correction improved vibrational stretching motion while making the prediction of the bending modes far worse. For rotational motion the relativistic effect had an increasing effect with increasing Ka. A further alteration to the ab initio calculations is introduced by adjusting the barrier to linearity in the water potential. This alteration to the barrier was considered in order to compensate for the lack of convergence of quantum chemical calculations of the Born-Oppenheimer surface. This barrier attempts to represent the change in the potential from linear to equilibrium. We show the improvements this has on the calculated energy levels by comparison with the HITRAN database. This then led the way to the improved spectroscopic potential presented here in this thesis. This new spectroscopic potential reduces the overall standard deviation significantly for vibrational and rotational energy levels. (author)
Ab initio molecular dynamics: basic concepts, current trends and novel applications
International Nuclear Information System (INIS)
Tuckerman, Mark E
2002-01-01
The field of ab initio molecular dynamics (AIMD), in which finite temperature molecular dynamics (MD) trajectories are generated with forces obtained from accurate 'on the fly' electronic structure calculations, is a rapidly evolving and growing technology that allows chemical processes in condensed phases to be studied in an accurate and unbiased way. This article is intended to present the basics of the AIMD method as well as to provide a broad survey of the state of the art of the field and showcase some of its capabilities. Beginning with a derivation of the method from the Born-Oppenheimer approximation, issues including the density functional representation of electronic structure, basis sets, calculation of observables and the Car-Parrinello extended Lagrangian algorithm are discussed. A number of example applications, including liquid structure and dynamics and aqueous proton transport, are presented in order to highlight some of the current capabilities of the approach. Finally, advanced topics such as inclusion of nuclear quantum effects, excited states and scaling issues are addressed. (topical review)
Rutigliano, M.; Zazza, C.; Sanna, N.; Pieretti, A.; Mancini, G.; Barone, V.; Cacciatore, M.
2009-10-01
The adsorption dynamics of atomic oxygen on a model β-cristobalite silica surface has been studied by combining ab initio electronic structure calculations with a molecular dynamics semiclassical approach. We have evaluated the interaction potential of atomic and molecular oxygen interacting with an active Si site of a model β-cristobalite surface by performing DFT electronic structure calculations. As expected, O is strongly chemisorbed, Eb = 5.57 eV, whereas molecular oxygen can be weakly adsorbed with a high-energy barrier to the adsorption state of ˜2 eV. The binding energies calculated for silica clusters of different sizes have revealed the local nature of the O,O2-silica interaction. Semiclassical collision dynamic calculations show that O is mainly adsorbed in single-bounce collisions, with a smaller probability for adsorption via a multicollision mechanism. The probability for adsorption/desorption (reflected) collisions at the three impact energies is small but not negligible at the higher energy considered in the trajectory calculations, about Pr = 0.2 at Ekin = 0.8 eV. The calculations give evidence of a complex multiphonon excitation-deexcitation mechanism underlying the dynamics of stable adsorption and inelastic reflection collisions.
Ab Initio Enhanced calphad Modeling of Actinide-Rich Nuclear Fuels
Energy Technology Data Exchange (ETDEWEB)
Morgan, Dane [Univ. of Wisconsin, Madison, WI (United States); Yang, Yong Austin [Univ. of Wisconsin, Madison, WI (United States)
2013-10-28
The process of fuel recycling is central to the Advanced Fuel Cycle Initiative (AFCI), where plutonium and the minor actinides (MA) Am, Np, and Cm are extracted from spent fuel and fabricated into new fuel for a fast reactor. Metallic alloys of U-Pu-Zr-MA are leading candidates for fast reactor fuels and are the current basis for fast spectrum metal fuels in a fully recycled closed fuel cycle. Safe and optimal use of these fuels will require knowledge of their multicomponent phase stability and thermodynamics (Gibbs free energies). In additional to their use as nuclear fuels, U-Pu-Zr-MA contain elements and alloy phases that pose fundamental questions about electronic structure and energetics at the forefront of modern many-body electron theory. This project will validate state-of-the-art electronic structure approaches for these alloys and use the resulting energetics to model U-Pu-Zr-MA phase stability. In order to keep the work scope practical, researchers will focus on only U-Pu-Zr-{Np,Am}, leaving Cm for later study. The overall objectives of this project are to: Provide a thermodynamic model for U-Pu-Zr-MA for improving and controlling reactor fuels; and, Develop and validate an ab initio approach for predicting actinide alloy energetics for thermodynamic modeling.
Devi, Assa Aravindh Sasikala
2014-05-01
Investigations on freestanding binary and ternary clusters of Fe (x) Co (y) Ir (z) (x + y + z = 5, 6) are carried out using ab initio density functional theory techniques. The geometry, chemical order, binding energy, magnetic moment and electronic structure of the clusters are analyzed for the entire range of composition. Composition dependent structural transition is observed in the five atom clusters, while octahedral geometry prevailed in clusters with six atoms. Both the clusters show increment in binding energy with the increase in number of heterogeneous bonds. Analysis based on the chemical order parameter indicates that clusters favor mixing rather than segregation. The clusters exhibit ferromagnetic ordering and the inter-dependence of optimal cluster geometry to the magnetic moments and electronic structure is observed.
International Nuclear Information System (INIS)
Rubin, Yu.V.; Belous, L.F.
2012-01-01
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 30 o : 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.
Ab initio Molecular Orbital Studies of the Vibrational Spectra of some ...
African Journals Online (AJOL)
Ab initio Molecular Orbital Studies of the Vibrational Spectra of some van der Waals Complexes. Part 4. Complexes of Sulphur Dioxide with Carbon Dioxide, Carbonyl Sulphide, Carbon Disulphide and Nitrous Oxide.
Ab initio study of gas phase and water-assisted tautomerization of ...
Indian Academy of Sciences (India)
WINTEC
Ab initio study of gas phase and water-assisted tautomerization of maleimide and formamide. 623. Figure 4. Keto to enol conversion of (a) maleimide and (b) formamide in gas phase. (c) maleimide and (d) forma- mide with water.
2017-03-24
NUMBER (Include area code) 24 March 2017 Briefing Charts 01 March 2017 - 31 March 2017 Ab initio Quantum Chemical and Experimental Reaction Kinetics...Laboratory AFRL/RQRS 1 Ara Road Edwards AFB, CA 93524 *Email: ghanshyam.vaghjiani@us.af.mil Ab initio Quantum Chemical and Experimental Reaction ...Clearance 17161 Zador et al., Prog. Energ. Combust. Sci., 37 371 (2011) Why Quantum Chemical Reaction Kinetics Studies? DISTRIBUTION A: Approved for
Ab initio transport across bismuth selenide surface barriers
Narayan, Awadhesh
2014-11-24
© 2014 American Physical Society. We investigate the effect of potential barriers in the form of step edges on the scattering properties of Bi2Se3(111) topological surface states by means of large-scale ab initio transport simulations. Our results demonstrate the suppression of perfect backscattering, while all other scattering processes, which do not entail a complete spin and momentum reversal, are allowed. Furthermore, we find that the spin of the surface state develops an out-of-plane component as it traverses the barrier. Our calculations reveal the existence of quasibound states in the vicinity of the surface barriers, which appear in the form of an enhanced density of states in the energy window corresponding to the topological state. For double barriers we demonstrate the formation of quantum well states. To complement our first-principles results we construct a two-dimensional low-energy effective model and illustrate its shortcomings. Our findings are discussed in the context of a number of recent experimental works.
Ab initio prediction of nano-structured materials using supercomputer
International Nuclear Information System (INIS)
Kumar, V.; Kawazoe, Y.
2003-01-01
Full text: Nano-structured materials are currently attracting great attention due to their promise in future nano-technologies. In the scale of a nanometer, properties of matter are sensitive to the atomic details that are often difficult to obtain from experiments. Impurities could change the properties very significantly. Predictive computer simulations based on ab initio methods are playing a very important role in not only supporting and explaining the experimental findings but also suggesting new possibilities. We shall present a brief overview of the current research done in our group using the supercomputing facilities of the IMR in designing and predicting nano-structured materials. These include the areas of molecular electronics, carbon fullerenes and nanotubes, super-structures on surfaces, multilayers, clusters and nanowires using calculational approaches such as all electron mixed basis, augmented plane wave, localized basis and pseudopotential plane wave methods. More accurate descriptions based on GW and QMC methods are also used. The possibilities of doing large scale calculations are also allowing the study of biological systems such as DNA. We shall discuss in more detail our recent predictions of novel metal encapsulated silicon fullerenes and nanotubes that offer new possibilities in developing silicon based technologies at the nano-scale
Ab Initio Liquid Water Dynamics in Aqueous TMAO Solution.
Usui, Kota; Hunger, Johannes; Sulpizi, Marialore; Ohto, Tatsuhiko; Bonn, Mischa; Nagata, Yuki
2015-08-20
Ab initio molecular dynamics (AIMD) simulations in trimethylamine N-oxide (TMAO)-D2O solution are employed to elucidate the effects of TMAO on the reorientational dynamics of D2O molecules. By decomposing the O-D groups of the D2O molecules into specific subensembles, we reveal that water reorientational dynamics are retarded considerably in the vicinity of the hydrophilic TMAO oxygen (O(TMAO)) atom, due to the O-D···O(TMAO) hydrogen-bond. We find that this reorientational motion is governed by two distinct mechanisms: The O-D group rotates (1) after breaking the O-D···O(TMAO) hydrogen-bond, or (2) together with the TMAO molecule while keeping this hydrogen-bond intact. While the orientational slow-down is prominent in the AIMD simulation, simulations based on force field models exhibit much faster dynamics. The simulated angle-resolved radial distribution functions illustrate that the O-D···O(TMAO) hydrogen-bond has a strong directionality through the sp(3) orbital configuration in the AIMD simulation, and this directionality is not properly accounted for in the force field simulation. These results imply that care must be taken when modeling negatively charged oxygen atoms as single point charges; force field models may not adequately describe the hydration configuration and dynamics.
Ab initio calculations of free-energy reaction barriers
International Nuclear Information System (INIS)
Bucko, T
2008-01-01
The theoretical description of chemical reactions was until recently limited to a 'static' approach in which important parameters such as the rate constant are deduced from the local topology of the potential energy surface close to minima and saddle points. Such an approach has, however, serious limitations. The growing computational power allows us now to use advanced simulation techniques to determine entropic effects accurately for medium-sized systems at ab initio level. Recently, we have implemented free-energy simulation techniques based on molecular dynamics, in particular on the blue-moon ensemble technique and on metadynamics, in the popular DFT code VASP. In the thermodynamic integration (blue-moon ensemble) technique, the free-energy profile is calculated as the path integral over the restoring forces along a parametrized reaction coordinate. In metadynamics, an image of the free-energy surface is constructed on the fly during the simulation by adding small repulsive Gaussian-shaped hills to the Lagrangian driving the dynamics. The two methods are tested on a simple chemical reaction-the nucleophilic substitution of methyl chloride by a chlorine anion
Development of materials science by Ab initio powder diffraction analysis
International Nuclear Information System (INIS)
Fujii, Kotaro
2015-01-01
Crystal structure is most important information to understand properties and behavior of target materials. Technique to analyze unknown crystal structures from powder diffraction data (ab initio powder diffraction analysis) enables us to reveal crystal structures of target materials even we cannot obtain a single crystal. In the present article, three examples are introduced to show the power of this technique in the field of materials sciences. The first example is dehydration/hydration of the pharmaceutically relevant material erythrocycin A. In this example, crystal structures of two anhydrous phases were determined from synchrotron X-ray powder diffraction data and their different dehydration/hydration properties were understood from the crystal structures. In the second example, a crystal structure of a three dimensional metal-organic-framework prepared by a mechanochemical reaction was determined from laboratory X-ray powder diffraction data and the reaction scheme has been revealed. In the third example, a crystal structure of a novel oxide-ion conductor of a new structure family was determined from synchrotron X-ray and neutron powder diffraction data which gave an important information to understand the mechanism of the oxide-ion conduction. (author)
An Ab Initio Based Potential Energy Surface for Water
Partridge, Harry; Schwenke, David W.; Langhoff, Stephen R. (Technical Monitor)
1996-01-01
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.
Accurate ab initio vibrational energies of methyl chloride
International Nuclear Information System (INIS)
Owens, Alec; Yurchenko, Sergei N.; Yachmenev, Andrey; Tennyson, Jonathan; Thiel, Walter
2015-01-01
Two new nine-dimensional potential energy surfaces (PESs) have been generated using high-level ab initio theory for the two main isotopologues of methyl chloride, CH 3 35 Cl and CH 3 37 Cl. The respective PESs, CBS-35 HL , and CBS-37 HL , are based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set (CBS) limit, and incorporate a range of higher-level (HL) additive energy corrections to account for core-valence electron correlation, higher-order coupled cluster terms, scalar relativistic effects, and diagonal Born-Oppenheimer corrections. Variational calculations of the vibrational energy levels were performed using the computer program TROVE, whose functionality has been extended to handle molecules of the form XY 3 Z. Fully converged energies were obtained by means of a complete vibrational basis set extrapolation. The CBS-35 HL and CBS-37 HL PESs reproduce the fundamental term values with root-mean-square errors of 0.75 and 1.00 cm −1 , respectively. An analysis of the combined effect of the HL corrections and CBS extrapolation on the vibrational wavenumbers indicates that both are needed to compute accurate theoretical results for methyl chloride. We believe that it would be extremely challenging to go beyond the accuracy currently achieved for CH 3 Cl without empirical refinement of the respective PESs
Accurate ab initio vibrational energies of methyl chloride
Energy Technology Data Exchange (ETDEWEB)
Owens, Alec, E-mail: owens@mpi-muelheim.mpg.de [Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr (Germany); Department of Physics and Astronomy, University College London, Gower Street, WC1E 6BT London (United Kingdom); Yurchenko, Sergei N.; Yachmenev, Andrey; Tennyson, Jonathan [Department of Physics and Astronomy, University College London, Gower Street, WC1E 6BT London (United Kingdom); Thiel, Walter [Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr (Germany)
2015-06-28
Two new nine-dimensional potential energy surfaces (PESs) have been generated using high-level ab initio theory for the two main isotopologues of methyl chloride, CH{sub 3}{sup 35}Cl and CH{sub 3}{sup 37}Cl. The respective PESs, CBS-35{sup HL}, and CBS-37{sup HL}, are based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set (CBS) limit, and incorporate a range of higher-level (HL) additive energy corrections to account for core-valence electron correlation, higher-order coupled cluster terms, scalar relativistic effects, and diagonal Born-Oppenheimer corrections. Variational calculations of the vibrational energy levels were performed using the computer program TROVE, whose functionality has been extended to handle molecules of the form XY {sub 3}Z. Fully converged energies were obtained by means of a complete vibrational basis set extrapolation. The CBS-35{sup HL} and CBS-37{sup HL} PESs reproduce the fundamental term values with root-mean-square errors of 0.75 and 1.00 cm{sup −1}, respectively. An analysis of the combined effect of the HL corrections and CBS extrapolation on the vibrational wavenumbers indicates that both are needed to compute accurate theoretical results for methyl chloride. We believe that it would be extremely challenging to go beyond the accuracy currently achieved for CH{sub 3}Cl without empirical refinement of the respective PESs.
Double-walled silicon nanotubes: an ab initio investigation
Lima, Matheus P.
2018-02-01
The synthesis of silicon nanotubes realized in the last decade demonstrates multi-walled tubular structures consisting of Si atoms in {{sp}}2 and the {{sp}}3 hybridizations. However, most of the theoretical models were elaborated taking as the starting point {{sp}}2 structures analogous to carbon nanotubes. These structures are unfavorable due to the natural tendency of the Si atoms to undergo {{sp}}3. In this work, through ab initio simulations based on density functional theory, we investigated double-walled silicon nanotubes proposing layered tubes possessing most of the Si atoms in an {{sp}}3 hybridization, and with few {{sp}}2 atoms localized at the outer wall. The lowest-energy structures have metallic behavior. Furthermore, the possibility to tune the band structure with the application of a strain was demonstrated, inducing a metal-semiconductor transition. Thus, the behavior of silicon nanotubes differs significantly from carbon nanotubes, and the main source of the differences is the distortions in the lattice associated with the tendency of Si to make four chemical bonds.
Efficient conformational space exploration in ab initio protein folding simulation.
Ullah, Ahammed; Ahmed, Nasif; Pappu, Subrata Dey; Shatabda, Swakkhar; Ullah, A Z M Dayem; Rahman, M Sohel
2015-08-01
Ab initio protein folding simulation largely depends on knowledge-based energy functions that are derived from known protein structures using statistical methods. These knowledge-based energy functions provide us with a good approximation of real protein energetics. However, these energy functions are not very informative for search algorithms and fail to distinguish the types of amino acid interactions that contribute largely to the energy function from those that do not. As a result, search algorithms frequently get trapped into the local minima. On the other hand, the hydrophobic-polar (HP) model considers hydrophobic interactions only. The simplified nature of HP energy function makes it limited only to a low-resolution model. In this paper, we present a strategy to derive a non-uniform scaled version of the real 20×20 pairwise energy function. The non-uniform scaling helps tackle the difficulty faced by a real energy function, whereas the integration of 20×20 pairwise information overcomes the limitations faced by the HP energy function. Here, we have applied a derived energy function with a genetic algorithm on discrete lattices. On a standard set of benchmark protein sequences, our approach significantly outperforms the state-of-the-art methods for similar models. Our approach has been able to explore regions of the conformational space which all the previous methods have failed to explore. Effectiveness of the derived energy function is presented by showing qualitative differences and similarities of the sampled structures to the native structures. Number of objective function evaluation in a single run of the algorithm is used as a comparison metric to demonstrate efficiency.
Machine Learning Force Field Parameters from Ab Initio Data
Energy Technology Data Exchange (ETDEWEB)
Li, Ying [Argonne; Li, Hui [Department; Pickard, Frank C. [Laboratory; Narayanan, Badri [Center; Sen, Fatih G. [Center; Chan, Maria K. Y. [Center; Computational; Sankaranarayanan, Subramanian K. R. S. [Center; Computational; Brooks, Bernard R. [Laboratory; Roux, Benoît [Department; Center; Computational
2017-08-11
Machine learning (ML) techniques with the genetic algorithm (GA) have been applied to determine a polarizable force field parameters using only ab initio data from quantum mechanics (QM) calculations of molecular clusters at the MP2/6-31G(d,p), DFMP2(fc)/jul-cc-pVDZ, and DFMP2(fc)/jul-cc-pVTZ levels to predict experimental condensed phase properties (i.e., density and heat of vaporization). The performance of this ML/GA approach is demonstrated on 4943 dimer electrostatic potentials and 1250 cluster interaction energies for methanol. Excellent agreement between the training data set from QM calculations and the optimized force field model was achieved. The results were further improved by introducing an offset factor during the machine learning process to compensate for the discrepancy between the QM calculated energy and the energy reproduced by optimized force field, while maintaining the local “shape” of the QM energy surface. Throughout the machine learning process, experimental observables were not involved in the objective function, but were only used for model validation. The best model, optimized from the QM data at the DFMP2(fc)/jul-cc-pVTZ level, appears to perform even better than the original AMOEBA force field (amoeba09.prm), which was optimized empirically to match liquid properties. The present effort shows the possibility of using machine learning techniques to develop descriptive polarizable force field using only QM data. The ML/GA strategy to optimize force fields parameters described here could easily be extended to other molecular systems.
Cosmic-ray modulation: an ab initio approach
International Nuclear Information System (INIS)
Engelbrecht, N.E.; Burger, R.A.
2014-01-01
A better understanding of cosmic-ray modulation in the heliosphere can only be gained through a proper understanding of the effects of turbulence on the diffusion and drift of cosmic rays. We present an ab initio model for cosmic-ray modulation, incorporating for the first time the results yielded by a two-component turbulence transport model. This model is solved for periods of minimum solar activity, utilizing boundary values chosen so that model results are in fair to good agreement with spacecraft observations of turbulence quantities, not only in the solar ecliptic plane but also along the out-of-ecliptic trajectory of the Ulysses spacecraft. These results are employed as inputs for modelled slab and 2D turbulence energy spectra. The latter spectrum is chosen based on physical considerations, with a drop-off at the very lowest wavenumbers commencing at the 2D outerscale. There currently exist no models or observations for this quantity, and it is the only free parameter in this study. The modelled turbulence 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 cosmic-ray drifts are modelled in a self-consistent way, employing a recently developed model for drift along the wavy current sheet. The resulting diffusion coefficients and drift expressions are applied to the study of galactic cosmic-ray protons and antiprotons using a three dimensional, steady-state cosmic-ray modulation code, and sample solutions in fair agreement with multiple spacecraft observations are presented. (author)
Cosmic-ray modulation: an ab initio approach
Energy Technology Data Exchange (ETDEWEB)
Engelbrecht, N.E.; Burger, R.A., E-mail: 12580996@nwu.ac.za [Center for Space Research, North-West University, Potchefstroom (South Africa)
2014-07-01
A better understanding of cosmic-ray modulation in the heliosphere can only be gained through a proper understanding of the effects of turbulence on the diffusion and drift of cosmic rays. We present an ab initio model for cosmic-ray modulation, incorporating for the first time the results yielded by a two-component turbulence transport model. This model is solved for periods of minimum solar activity, utilizing boundary values chosen so that model results are in fair to good agreement with spacecraft observations of turbulence quantities, not only in the solar ecliptic plane but also along the out-of-ecliptic trajectory of the Ulysses spacecraft. These results are employed as inputs for modelled slab and 2D turbulence energy spectra. The latter spectrum is chosen based on physical considerations, with a drop-off at the very lowest wavenumbers commencing at the 2D outerscale. There currently exist no models or observations for this quantity, and it is the only free parameter in this study. The modelled turbulence 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 cosmic-ray drifts are modelled in a self-consistent way, employing a recently developed model for drift along the wavy current sheet. The resulting diffusion coefficients and drift expressions are applied to the study of galactic cosmic-ray protons and antiprotons using a three dimensional, steady-state cosmic-ray modulation code, and sample solutions in fair agreement with multiple spacecraft observations are presented. (author)
AN AB INITIO MODEL FOR COSMIC-RAY MODULATION
Energy Technology Data Exchange (ETDEWEB)
Engelbrecht, N. E.; Burger, R. A. [Center for Space Research, North-West University, Potchefstroom 2520 (South Africa)
2013-07-20
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.
Lithium Insertion In Silicon Nanowires: An ab Initio Study
Zhang, Qianfan
2010-09-08
The ultrahigh specific lithium ion storage capacity of Si nanowires (SiNWs) has been demonstrated recently and has opened up exciting opportunities for energy storage. However, a systematic theoretical study on lithium insertion in SiNWs remains a challenge, and as a result, understanding of the fundamental interaction and microscopic dynamics during lithium insertion is still lacking. This paper focuses on the study of single Li atom insertion into SiNWs with different sizes and axis orientations by using full ab initio calculations. We show that the binding energy of interstitial Li increases as the SiNW diameter grows. The binding energies at different insertion sites, which can be classified as surface, intermediate, and core sites, are quite different. We find that surface sites are energetically the most favorable insertion positions and that intermediate sites are the most unfavorable insertion positions. Compared with the other growth directions, the [110] SiNWs with different diameters always present the highest binding energies on various insertion locations, which indicates that [110] SiNWs are more favorable by Li doping. Furthermore, we study Li diffusion inside SiNWs. The results show that the Li surface diffusion has a much higher chance to occur than the surface to core diffusion, which is consistent with the experimental observation that the Li insertion in SiNWs is layer by layer from surface to inner region. After overcoming a large barrier crossing surface-to-intermediate region, the diffusion toward center has a higher possibility to occur than the inverse process. © 2010 American Chemical Society.
Optical properties of highly compressed polystyrene: An ab initio study
Hu, S. X.; Collins, L. A.; Colgan, J. P.; Goncharov, V. N.; Kilcrease, D. P.
2017-10-01
Using all-electron density functional theory, we have performed an ab initio study on x-ray absorption spectra of highly compressed polystyrene (CH). We found that the K -edge shifts in strongly coupled, degenerate polystyrene cannot be explained by existing continuum-lowering models adopted in traditional plasma physics. To gain insights into the K -edge shift in warm, dense CH, we have developed a model designated as "single mixture in a box" (SMIAB), which incorporates both the lowering of the continuum and the rising of the Fermi surface resulting from high compression. This simple SMIAB model correctly predicts the K -edge shift of carbon in highly compressed CH in good agreement with results from quantum molecular dynamics (QMD) calculations. Traditional opacity models failed to give the proper K -edge shifts as the CH density increased. Based on QMD calculations, we have established a first-principles opacity table (FPOT) for CH in a wide range of densities and temperatures [ρ =0.1 -100 g /c m3 and T =2000 -1 000 000 K ]. The FPOT gives much higher Rosseland mean opacity compared to the cold-opacity-patched astrophysics opacity table for warm, dense CH and favorably compares to the newly improved Los Alamos atomic model for moderately compressed CH (ρCH≤10 g /c m3 ), but remains a factor of 2 to 3 higher at extremely high densities (ρCH≥50 g /c m3 ). We anticipate the established FPOT of CH will find important applications to reliable designs of high-energy-density experiments. Moreover, the understanding of K -edge shifting revealed in this study could provide guides for improving the traditional opacity models to properly handle the strongly coupled and degenerate conditions.
Ab initio study of charge, spin and orbital ordering in manganites
Tyer, R
2001-01-01
The subject of this thesis was the calculation of the electronic structure for the manganites LaMnO sub 3 and CaMnO sub 3. The implementation of the Self-Interaction Corrected Local Spin Density (SIC-LSD) formalism within the Tight Binding Linear Muffin-Tin Orbital method in conjunction with the Atomic Sphere Approximation was used for these calculations. The SIC-LSD total energy functional has been used to investigate the spin ordering and valency of CaMnO sub 3 and LaMnO sub 3. In order to assess the role of the structural distortion in LaMnO sub 3 , these calculations were performed for an idealised cubic structure as well as for the observed distorted orthorhombic structure. Orbital rotations of the localised (SIC corrected) states were implemented. These orbital rotations were then used to perform the first ab-initio investigation of orbital ordering in LaMnO sub 3. For the experimentally observed A-type antiferromagnetic ordering, the correct orbital structure of alternating manganese d sub 3 sub x sub ...
Synthesis, FTIR, FT-Raman, UV-visible, ab initio and DFT studies on benzohydrazide.
Arjunan, V; Rani, T; Mythili, C V; Mohan, S
2011-08-01
A systematic vibrational spectroscopic assignment and analysis of benzohydrazide (BH) has been carried out by using FTIR and FT-Raman spectral data. The vibrational analysis were aided by electronic structure calculations--ab initio (RHF) and hybrid density functional methods (B3LYP and B3PW91) performed with 6-31G(d,p) and 6-311++G(d,p) basis sets. Molecular equilibrium geometries, electronic energies, IR intensities, harmonic vibrational frequencies, depolarization ratios and Raman activities have been computed. Potential energy distribution (PED) and normal mode analysis have also been performed. The assignments proposed based on the experimental IR and Raman spectra have been reviewed and complete assignment of the observed spectra have been proposed. UV-visible spectrum of the compound was also recorded and the electronic properties, such as HOMO and LUMO energies and λ(max) were determined by time-dependent DFT (TD-DFT) method. The geometrical, thermodynamical parameters and absorption wavelengths were compared with the experimental data. The interactions of carbonyl and hydrazide groups on the benzene ring skeletal modes were investigated. Copyright © 2011 Elsevier B.V. All rights reserved.
Ab initio study of the EFG tensor at Cd impurities in Sc2O3 semiconductor
International Nuclear Information System (INIS)
Munoz, E.L.; Richard, D.; Errico, L.A.; Renteria, M.
2009-01-01
We present an ab initio study of diluted Cd impurities localized at both cation sites of the semiconductor Sc 2 O 3 . The electric-field-gradient (EFG) tensor at Cd impurities located at both cationic sites of the host structure was determined from the calculation of the electronic structure of the doped system. Calculations were performed with the full-potential augmented-plane wave plus local orbitals (APW+lo) method within the framework of the density functional theory. We studied the atomic structural relaxations and the perturbation of the electronic charge density induced by the impurities in the host system in a fully self-consistent way. We showed that the Cd impurity introduces an increase of 8% in the nearest oxygen neighbors bond-lengths, changing the EFG sign for probes located at the asymmetric cation site. The APW+lo predictions for the charged state of the Cd impurity were compared with EFG results existent in the literature, coming from time-differential γ-γ perturbed-angular-correlations experiments performed on 111 Cd-implanted Sc 2 O 3 powder samples. From the excellent agreement between theory and experiment, we can strongly suggest that the Cd acceptor impurities are ionized at room temperature. Finally, we showed that simple calculations like those performed within the point-charge model with antishielding factors do not correctly describe the problem of a Cd impurity in Sc 2 O 3 .
Chen, Chen; Arntsen, Christopher; Voth, Gregory A.
2017-10-01
Incorporation of quantum mechanical electronic structure data is necessary to properly capture the physics of many chemical processes. Proton hopping in water, which involves rearrangement of chemical and hydrogen bonds, is one such example of an inherently quantum mechanical process. Standard ab initio molecular dynamics (AIMD) methods, however, do not yet accurately predict the structure of water and are therefore less than optimal for developing force fields. We have instead utilized a recently developed method which minimally biases AIMD simulations to match limited experimental data to develop novel multiscale reactive molecular dynamics (MS-RMD) force fields by using relative entropy minimization. In this paper, we present two new MS-RMD models using such a parameterization: one which employs water with harmonic internal vibrations and another which uses anharmonic water. We show that the newly developed MS-RMD models very closely reproduce the solvation structure of the hydrated excess proton in the target AIMD data. We also find that the use of anharmonic water increases proton hopping, thereby increasing the proton diffusion constant.
Tunneling of electrons via rotor–stator molecular interfaces: Combined ab initio and model study
Energy Technology Data Exchange (ETDEWEB)
Petreska, Irina, E-mail: irina.petreska@pmf.ukim.mk [Institute of Physics, Faculty of Natural Sciences and Mathematics, Ss. Cyril and Methodius University, PO Box 162, 1000 Skopje, Former Yugolav Republic of Macedonia, The (Macedonia, The Former Yugoslav Republic of); Ohanesjan, Vladimir [Institute of Physics, Faculty of Natural Sciences and Mathematics, Ss. Cyril and Methodius University, PO Box 162, 1000 Skopje, Former Yugolav Republic of Macedonia, The (Macedonia, The Former Yugoslav Republic of); Pejov, Ljupčo [Institute of Chemistry, Department of Physical Chemistry, Ss. Cyril and Methodius University, Arhimedova 5, P.O. Box 162, 1000 Skopje, Former Yugolav Republic of Macedonia, The (Macedonia, The Former Yugoslav Republic of); Kocarev, Ljupčo [Macedonian Academy of Sciences and Arts, Krste Misirkov 2, PO Box 428, 1000 Skopje, Former Yugolav Republic of Macedonia, The (Macedonia, The Former Yugoslav Republic of); Faculty of Computer Science and Engineering, Ss. Cyril and Methodius University, Skopje, Former Yugolav Republic of Macedonia, The (Macedonia, The Former Yugoslav Republic of)
2016-07-01
Tunneling of electrons through rotor–stator anthracene aldehyde molecular interfaces is studied with a combined ab initio and model approach. Molecular electronic structure calculated from first principles is utilized to model different shapes of tunneling barriers. Together with a rectangular barrier, we also consider a sinusoidal shape that captures the effects of the molecular internal structure more realistically. Quasiclassical approach with the Simmons’ formula for current density is implemented. Special attention is paid on conformational dependence of the tunneling current. Our results confirm that the presence of the side aldehyde group enhances the interesting electronic properties of the pure anthracene molecule, making it a bistable system with geometry dependent transport properties. We also investigate the transition voltage and we show that conformation-dependent field emission could be observed in these molecular interfaces at realistically low voltages. The present study accompanies our previous work where we investigated the coherent transport via strongly coupled delocalized orbital by application of Non-equilibrium Green’s Function Formalism.
Ab initio study of effects of substitutional additives on the phase stability of γ-alumina
International Nuclear Information System (INIS)
Jiang Kaiyun; Music, Denis; Sarakinos, Kostas; Schneider, Jochen M
2010-01-01
Using ab initio calculations, we have evaluated two structural descriptions of γ-Al 2 O 3 , spinel and tetragonal hausmannite, and explored the relative stability of γ-Al 2 O 3 with respect to α-Al 2 O 3 with 2.5 at.% of Si, Cr, Ti, Sc, and Y additives to identify alloying element induced electronic structure changes that impede the γ to α transition. The total energy calculations indicate that Si stabilizes γ-Al 2 O 3 , while Cr stabilizes α-Al 2 O 3 . As Si is added, a bond length increase in α-Al 2 O 3 is observed, while strong and short Si-O bonds are formed in γ-Al 2 O 3 , consequently stabilizing this phase. On the other hand, Cr additions induce a smaller bond length increase in α-Al 2 O 3 than in γ-Al 2 O 3 , therefore stabilizing the α-phase. The bulk moduli of γ-Al 2 O 3 with these additives show no significant changes. The phase stability and elastic property data discussed here underline the application potential of Si alloyed γ-Al 2 O 3 for applications at elevated temperatures. Furthermore it is evident that the tetragonal hausmannite structure is a suitable description for γ-Al 2 O 3 .
Electronic and magnetic properties of α-MnO2 from ab initio calculations
Crespo, Y.; Seriani, N.
2013-10-01
α-MnO2, an active catalyst for oxygen reduction and evolution reactions, has been investigated using ab initio calculations with different exchange-correlation functionals: the generalized-gradient approximation in the version of Perdew, Burke, and Ernzerhof (PBE), PBE+U, and hybrid functionals. Both hybrid functionals and PBE+U (U≥2.0 eV) fail to capture the antiferromagnetic (AFM) ground state found experimentally, and a ferromagnetic configuration has the lowest energy. An AFM ground state is then recovered when using PBE or PBE+U (U≤1.6 eV). Interestingly, a reduction of the gap is observed at increasing values of the U parameter. We offer a qualitative explanation for the change in the calculated ground state employing the results for the electronic structure and physical arguments similar to those exposed in the Goodenough-Kanamori-Anderson rules. It is argued that the pz orbital of oxygen atoms with sp2 hybridization plays a fundamental role in the superexchange AFM interaction and in the reduction of the gap.
Adane, Legesse; Bharatam, Prasad V.
In several literature reports biuret and its sulfur analogs are reported to exist in their diketo form with general formula H2N bond CX bond NH bond CY bond NH2 (X = O, Y = O, biuret; X = Y = S, dithiobiuret; and X = O, Y = S, thiobiuret). On the other hand, recently reported results on the electronic structure of biguanide analogs (X = Y = NH)demonstrated that a form equivalent to diketo is not the preferred structure. Thus, a systematic ab initio study on the tautomeric preferences of biuret and its sulfur analogs (dithiobiuret and thiobiuret) has been carried out. The results indicate that an interplay of conjugative stabilization and intramolecular hydrogen bonding to play a role in tautomeric preferences. Energy and geometric parameters, natural bond orbital analyses have been employed to understand the chemistry of the title compounds. The results indicate that unlike biguanides, these compounds prefer diketo forms containing hydrogen on the bridging nitrogen (N4) and in a trans-arrangement (1a-4a). However, tautomerization of these keto forms to the corresponding enol isomers was also found to be highly probable.
Ab initio random structure search for 13-atom clusters of fcc elements
International Nuclear Information System (INIS)
Chou, J P; Hsing, C R; Wei, C M; Cheng, C; Chang, C M
2013-01-01
The 13-atom metal clusters of fcc elements (Al, Rh, Ir, Ni, Pd, Pt, Cu, Ag, Au) were studied by density functional theory calculations. The global minima were searched for by the ab initio random structure searching method. In addition to some new lowest-energy structures for Pd 13 and Au 13 , we found that the effective coordination numbers of the lowest-energy clusters would increase with the ratio of the dimer-to-bulk bond length. This correlation, together with the electronic structures of the lowest-energy clusters, divides the 13-atom clusters of these fcc elements into two groups (except for Au 13 , which prefers a two-dimensional structure due to the relativistic effect). Compact-like clusters that are composed exclusively of triangular motifs are preferred for elements without d-electrons (Al) or with (nearly) filled d-band electrons (Ni, Pd, Cu, Ag). Non-compact clusters composed mainly of square motifs connected by some triangular motifs (Rh, Ir, Pt) are favored for elements with unfilled d-band electrons. (paper)
Ab initio study of basal slip in Nb2AlC
International Nuclear Information System (INIS)
Music, Denis; Sun, Zhimei; Voevodin, Andrey A; Schneider, Jochen M
2006-01-01
Using ab initio calculations, we have studied shearing in Nb 2 AlC, where NbC and Al layers are interleaved. The stress-strain analysis of this deformation mode reveals Nb-Al bond breaking, while the Nb-C bond length decreases by 4.1%. Furthermore, there is no evidence for phase transformation during deformation. This is consistent with basal slip and may be understood on the basis of the electronic structure: bands below the Fermi level are responsible for the dd bonding between NbC basal planes and only a single band with a weak dd interaction is not resistant to shearing, while all other bands are unaffected. The Al-Nb bonding character can be described as mainly metallic with weak covalent-ionic contributions. Our study demonstrates that Al layers move with relative ease under shear strain. Phase conservation upon shearing is unusual for carbides and may be due to the layered nature of the phase studied. Here, we describe the electronic origin of basal slip in Nb 2 AlC, the atomic mechanism which enables reversible plasticity in this class of materials
Ab initio modelling of screw dislocations in body-centered cubic transition metals
International Nuclear Information System (INIS)
Dezerald, Lucile
2014-01-01
We performed electronic structure ab initio calculations based on density functional theory (DFT) to study the <111> screw dislocation properties in body-centered cubic transition metals (V, Nb, Ta, Mo, W and Fe). In all investigated elements, the nondegenerate easy core is the minimum energy configuration and the split core configuration has a high energy near or above that of the hard core, contrary to interatomic potential predictions. A strong group dependence of the core energy of the easy dislocation is also evidenced, related to the position of the Fermi level with respect to the minimum of the pseudo-gap of the electronic density of states. Our work also reveals an atypical behavior in Fe, with a low relative energy at the hard core position, close to that of the saddle configuration between easy cores, resulting in a flat Peierls potential around the hard core configuration, at variance with other elements. From these DFT calculations, the two-dimensional energetic landscape in the {111} plane (Peierls potential) is constructed and we investigated several properties of dislocation glide and in particular, the kink-pair formation enthalpy, as well as the dependence of the Peierls stress on crystal orientation. We proposed a simple modification to the Schmid law that takes account of the non-straight trajectory of the dislocation and that qualitatively explains why the twinning/anti-twinning asymmetry is less pronounced in Fe than in other body-centered cubic metals. (author) [fr
The role of metallic ions in nano-bio hybrid catalysts from ab initio first principles
Behera, Sushant; Deb, Pritam
We employ high-accuracy linear-scaling density functional theory calculations with a near-complete basis set and a minimal parameter implicit solvent model, within the self-consistent calculation, on silver ion assimilated on bacteriorhodopsin (bR) at specific binding sites. The geometry optimization indicates the formation of stable active sites at the interface of nano-bio hybrid and density of states reflects the metallic behavior of the active sites. Detailed kinetics of the catalytic reaction is revealed using ab initio electronic structure calculations. We observed that the metal ion incorporated active sites are more efficient in electrolytic splitting of water than pristine sites due to their less value of Gibbs free energy for hydrogen evolution reaction and strong synergistic effect. The volcano plot analysis and free energy diagram are considered to understan hydrogen evolution efficiency. Moreover, the essential role of metallic ion on catalytic efficiency is elucidated. DBT, Government of India, vide Grant No BT/357/NE/TBP/ 2012. DST, GoI for financial support under INSPIRE Fellowship(IF150325).
Indian Academy of Sciences (India)
Results of ab initio electronic structure calculations on the compound MgB2 using the FPLAPW method employing GGA for the exchange-correlation energy are presented. Total energy minimization enables us to estimate the equilibrium volume, / ratio and the bulk modulus, all of which are in excellent agreement with ...
Indian Academy of Sciences (India)
Abstract. Results of ab initio electronic structure calculations on the compound MgB2 using the. FPLAPW method employing GGA for the exchange-correlation energy are presented. Total energy minimization enables us to estimate the equilibrium volume, c/a ratio and the bulk modulus, all of which are in excellent ...
An ab initio study of plutonium oxides surfaces; Etude ab initio des surfaces d'oxydes de Pu
Energy Technology Data Exchange (ETDEWEB)
Jomard, G.; Bottin, F.; Amadon, B
2007-07-01
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)
Ab initio calculations of Gamow-Teller strengths in the s d shell
Saxena, Archana; Srivastava, Praveen C.; Suzuki, Toshio
2018-02-01
In the present work we perform a systematic shell-model study of Gamow-Teller transition-strength distributions in s d shell nuclei using ab initio effective interactions. The ab initio effective interactions are based on in-medium similarity renormalization-group and coupled-cluster effective interaction approaches. The aim of the present work is to test the predictive power of ab initio effective interactions by using the available experimental data of Gamow-Teller strength distributions in s d shell nuclei. We perform calculations for 20Ne→20F , 23Na→23Mg , 23Na→23Ne , 24Mg→24Na , 24Mg→24Al , 25Mg→25Al , 26Mg→26Na , 26Mg→26Al , 26Si→26Al , 27Al→27Si , 28Si→28P , 31P→31Si , and 32S→32P transitions. For comparison we also show the results obtained by using the phenomenological USDB Hamiltonian. The phenomenological USDB results of the Gamow-Teller (GT+ and GT-) strength distributions show reasonable agreements with the experimental data in comparison with the ab initio interactions. We also calculate the electron-capture reaction rates for 23Na(e-,ν )23Ne and 25Mg(e-,ν )25Na using ab initio and USDB interactions.
Lawson, John W.; Bauschlicher, Charles W.; Daw, Murray
2011-01-01
Refractory materials such as metallic borides, often considered as ultra high temperature ceramics (UHTC), are characterized by high melting point, high hardness, and good chemical inertness. These materials have many applications which require high temperature materials that can operate with no or limited oxidation. Ab initio, first principles methods are the most accurate modeling approaches available and represent a parameter free description of the material based on the quantum mechanical equations. Using these methods, many of the intrinsic properties of these material can be obtained. We performed ab initio calculations based on density functional theory for the UHTC materials ZrB2 and HfB2. Computational results are presented for structural information (lattice constants, bond lengths, etc), electronic structure (bonding motifs, densities of states, band structure, etc), thermal quantities (phonon spectra, phonon densities of states, specific heat), as well as information about point defects such as vacancy and antisite formation energies.
2018-01-01
We introduce a simple scheme to efficiently compute photon exchange-correlation contributions due to the coupling to transversal photons as formulated in the newly developed quantum-electrodynamical density-functional theory (QEDFT).1−5 Our construction employs the optimized-effective potential (OEP) approach by means of the Sternheimer equation to avoid the explicit calculation of unoccupied states. We demonstrate the efficiency of the scheme by applying it to an exactly solvable GaAs quantum ring model system, a single azulene molecule, and chains of sodium dimers, all located in optical cavities and described in full real space. While the first example is a two-dimensional system and allows to benchmark the employed approximations, the latter two examples demonstrate that the correlated electron-photon interaction appreciably distorts the ground-state electronic structure of a real molecule. By using this scheme, we not only construct typical electronic observables, such as the electronic ground-state density, but also illustrate how photon observables, such as the photon number, and mixed electron-photon observables, for example, electron–photon correlation functions, become accessible in a density-functional theory (DFT) framework. This work constitutes the first three-dimensional ab initio calculation within the new QEDFT formalism and thus opens up a new computational route for the ab initio study of correlated electron–photon systems in quantum cavities.
Odell, Anders
2011-10-03
The influence of the electrode\\'s Fermi surface on the transport properties of a photoswitching molecule is investigated with state-of-the-art ab initio transport methods. We report results for the conducting properties of the two forms of dithienylethene attached either to Ag or to nonmagnetic Ni leads. The I-V curves of the Ag/dithienylethene/Ag device are found to be very similar to those reported previously for Au. In contrast, when Ni is used as the electrode material the zero-bias transmission coefficient is profoundly different as a result of the role played by the Ni d bands in the bonding between the molecule and the electrodes. Intriguingly, despite these differences the overall conducting properties depend little on the electrode material. We thus conclude that electron transport in dithienylethene is, for the cases studied, mainly governed by the intrinsic electronic structure of the molecule. © 2011 American Physical Society.
Petit, L; Paudyal, D; Mudryk, Y; Gschneidner, K A; Pecharsky, V K; Lüders, M; Szotek, Z; Banerjee, R; Staunton, J B
2015-11-13
We explain a profound complexity of magnetic interactions of some technologically relevant gadolinium intermetallics using an ab initio electronic structure theory which includes disordered local moments and strong f-electron correlations. The theory correctly finds GdZn and GdCd to be simple ferromagnets and predicts a remarkably large increase of Curie temperature with a pressure of +1.5 K kbar(-1) for GdCd confirmed by our experimental measurements of +1.6 K kbar(-1). Moreover, we find the origin of a ferromagnetic-antiferromagnetic competition in GdMg manifested by noncollinear, canted magnetic order at low temperatures. Replacing 35% of the Mg atoms with Zn removes this transition, in excellent agreement with long-standing experimental data.
Petit, L.; Paudyal, D.; Mudryk, Y.; Gschneidner, K. A.; Pecharsky, V. K.; Lüders, M.; Szotek, Z.; Banerjee, R.; Staunton, J. B.
2015-11-01
We explain a profound complexity of magnetic interactions of some technologically relevant gadolinium intermetallics using an ab initio electronic structure theory which includes disordered local moments and strong f -electron correlations. The theory correctly finds GdZn and GdCd to be simple ferromagnets and predicts a remarkably large increase of Curie temperature with a pressure of +1.5 K kbar-1 for GdCd confirmed by our experimental measurements of +1.6 K kbar-1 . Moreover, we find the origin of a ferromagnetic-antiferromagnetic competition in GdMg manifested by noncollinear, canted magnetic order at low temperatures. Replacing 35% of the Mg atoms with Zn removes this transition, in excellent agreement with long-standing experimental data.
Černý, M.; Pokluda, J.; Šob, M.; Friák, M.; Šandera, P.
2003-01-01
Ab initio electronic structure calculations of the ideal strength of Fe, Co, Ni, and Cr under isotropic tension were performed using the linear muffin-tin orbital method in the atomic sphere approximation. Magnetic ordering was taken into account by means of a spin-polarized calculation. Two approximations for the exchange-correlation term were employed: namely, the local (spin) density approximation and the generalized gradient approximation. Computed values of equilibrium lattice parameters, bulk moduli, and magnetic moments were compared with available experimental data. The stability of the ground-state structure in the tensile region was assessed via comparison of its total energy and enthalpy with those of some other structures. No instabilities were found before reaching the inflection point on the total energy versus volume curve and the stress related to this point was therefore considered to be the ideal strength.
Ab Initio Description of Disordered Sr1−xKxFe2As2 Using the Coherent Potential Approximation
Pulikkotil, J. J.
2010-04-29
The electronic structure of disordered Sr1−xKxFe2As2 is studied by ab initio density functional theory. As no superstructure and/or atomic short range ordering is reported for Sr1−xKxFe2As2, the coherent potential approximation can be used to describe the effects of chemical disorder. We find clear deviations from the rigid band model characteristics. Nonmagnetic calculations show an enhancement of the density of states at the Fermi energy in the range 0.4≤x≤0.65, which coincides with the region where experiments observe an enhanced superconducting transition temperature, and antiferromagnetic calculations indicate a significant renormalization of states at Fermi energy. Analyzing the distribution of the Fe 3d states over the range 0≤x≤1 we propose an effective three band model.
Ab Initio Atomistic Thermodynamics for Surfaces: A Primer
National Research Council Canada - National Science Library
Rogal, Jutta; Reuter, Karsten
2006-01-01
.... Modern electronic structure theory methods like density-functional theory (DFT) have matured, allowing a description that is often already accurate enough to allow for a modeling with predictive character...
Ab Initio and Phenomenological Modeling of the Phonon Spectrum of Superhard cp-BC2N
Basalaev, Yu. M.; Kopytov, A. V.; Pavlova, T. Yu.; Poplavnoi, A. S.
2015-11-01
The phonon spectrum of hypothetical superhard cp-BC2N is calculated based on ab initio method of density functional in the center of the Brillouin zone and interpolated over the entire Brillouin zone using the Keating phenomenological model. The interaction parameters are determined by optimization of the IR- and Ramanactive frequencies for a phenomenological model by their comparison with the results of ab initio calculations. Numerical values of short-range interaction constants and charges are in agreement with the characteristics of the chemical bond calculated ab initio. These parameters have transparent physical meaning and chemical nature and can further be used for both qualitative estimations of any physical and physico-chemical quantities and quantitative calculations of the phonon spectra of a number of isostructural compounds. The Keating phenomenological model is used to study the genesis of the phonon spectrum from the spectra of sublattices.
Jung, Julie; Atanasov, Mihail; Neese, Frank
2017-08-07
Actinide chemistry is gaining increased focus in modern research, particularly in the fields of energy research and molecular magnetism. However, the structure-function and structure-property relationships of actinides have still not been studied as intensely as those for transition metals. In this work, we report a detailed ab initio study of the spectroscopic, magnetic, and bonding properties of the trivalent actinide free ions and their associated hexachloride complexes in octahedral symmetry. The electronic structures of these systems are examined using complete active-space self-consistent-field calculations followed by second-order N-electron valence perturbation theory, including both scalar relativistic and spin-orbit-coupling effects. The computed energies and wave functions are further analyzed by means of ab initio ligand-field theory (AILFT) and finally chemically interpreted by means of the angular overlap model (AOM). The derived Slater-Condon and spin-orbit parameters have allowed us to systematically rationalize the spectroscopic and magnetic properties of the investigated free ions and complexes along the entire actinide series. Overall, the AILFT- and AOM-derived parameters accurately reproduce the multireference electronic structure calculations. The small observed discrepancies with respect to experimentally derived ligand-field parameters are essentially due to an underestimation of the electronic correlation, which arises from both the constrained size of the active space (restricted to the f orbitals) and the limit of the perturbation approach to account for dynamical correlation. Our analysis also provides insight into the metal-ligand covalency trends along the series. Consistent with natural population analysis, the nephelauxetic (Slater-Condon parameters) and relativistic nephelauxetic (spin-orbit-coupling) reductions determined for these complexes indicate a decrease in the covalency along the series. These trends also hold, to varying
Lischner, Johannes; Vigil-Fowler, Derek; Louie, Steven G
2013-04-05
We calculate the photoemission spectra of suspended and epitaxial doped graphene using an ab initio cumulant expansion of the Green's function based on the GW self-energy. Our results are compared to experiment and to standard GW calculations. For doped graphene on a silicon carbide substrate, we find, in contrast to earlier calculations, that the spectral function from GW only does not reproduce experimental satellite properties. However, ab initio GW plus cumulant theory combined with an accurate description of the substrate screening results in good agreement with experiment, but gives no plasmaron (i.e., no extra well-defined excitation satisfying Dyson's equation).
Ab Initio Calculations of Deuterium Isotope Effects on Chemical Shifts of Salt-Bridged Lysines
DEFF Research Database (Denmark)
Ullah, Saif; Ishimoto, Takayoshi; Williamson, Mike P.
2011-01-01
Deuterium isotope effects measure the change in chemical shift on substitution of a proton by deuterium. They have been calculated by direct treatment of the H/D nuclear quantum effect using a multicomponent ab initio molecular orbital method based on a non-Born−Oppenheimer approximation. This me......Deuterium isotope effects measure the change in chemical shift on substitution of a proton by deuterium. They have been calculated by direct treatment of the H/D nuclear quantum effect using a multicomponent ab initio molecular orbital method based on a non-Born−Oppenheimer approximation...
Ab initio calculations versus polarized neutron diffraction for the spin density of free radicals
Ressouche, E
2003-01-01
The determination of the magnetization distribution using polarized neutron diffraction has played a key role during the last twenty years in the field of molecular magnetism. This distribution can also be obtained by first principle ab initio calculations. Such calculations always rely on approximations and the question that arises is to know whether the obtained results are reliable enough to represent accurately the properties of these molecules. The comparison between polarized neutron experimental results and ab initio calculations has turned to provide stringent tests for these methods. In the resent article a comparison between experimental and theoretical results is made and is illustrated by examples based on magnetic free radicals. (author)
Fishchuk, A.V.; Merritt, J.M.; Avoird, A. van der
2007-01-01
The three adiabatic potential surfaces of the Br(P-2)-HCN complex that correlate to the P-2 ground state of the Br atom were calculated ab initio. With the aid of a geometry-dependent diabatic mixing angle, also calculated ab initio, these adiabatic potential surfaces were transformed into a set of
Energy Technology Data Exchange (ETDEWEB)
Ganster, P
2004-10-15
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)
Electronic structure and tautomerism of aryl ketones
Energy Technology Data Exchange (ETDEWEB)
Novak, Igor, E-mail: inovak@csu.edu.au [Charles Sturt University, POB 883, Orange, NSW 2800 (Australia); Klasinc, Leo, E-mail: klasinc@irb.hr [Physical Chemistry Department, Ruđer Bošković Institute, HR-10002 Zagreb (Croatia); Šket, Boris, E-mail: Boris.Sket@fkkt.uni-lj.si [Faculty of Chemistry and Chemical Technology, University of Ljubljana, SI-1000 (Slovenia); McGlynn, S.P., E-mail: sean.mcglynn@chemgate.chem.lsu.edu [Louisiana State University, Baton Rouge, LA 70803 (United States)
2015-07-15
Graphical abstract: Photoelectron spectroscopy, tautomerism. - Highlights: • UV photoelectron spectroscopy of aryl ketones. • The relative stability of tautomers and their electronic structures. • The factors influencing tautomerism. - Abstract: The electronic structures of several aryl ketones (AK) and their α-halo derivatives have been studied by UV photoelectron spectroscopy (UPS). The relative stabilities of keto–enol tautomers have been determined using high-level ab initio calculations and the results were used in the analysis of UPS spectra. The main features of electronic structure and tautomerism of the AK derivatives are discussed.
Magnetic interactions and electronic structure of system: An ab-initio ...
Indian Academy of Sciences (India)
Tufan Roy
Corresponding author. E-mail: aparnachakrabarti@gmail.com. Published online 19 June 2017. Abstract. First-principles density functional theory-based calculations have been carried out to predict the effects of Mn replacement by Fe and Cr on electronic as well as magnetic properties of Pt2MnGa and Ni2MnGa. All the.
Ab-initio study of electronic structure and elastic properties of ZrC
Energy Technology Data Exchange (ETDEWEB)
Mund, H. S., E-mail: hmoond@gmail.com; Ahuja, B. L. [Department of Physics, University College of Science, M. L. Sukhadia University, Udaipur, Rajasthan313001 (India)
2016-05-23
The electronic and elastic properties of ZrC have been investigated using the linear combination of atomic orbitals method within the framework of density functional theory. Different exchange-correlation functionals are taken into account within generalized gradient approximation. We have computed energy bands, density of states, elastic constants, bulk modulus, shear modulus, Young’s modulus, Poisson’s ratio, lattice parameters and pressure derivative of the bulk modulus by calculating ground state energy of the rock salt structure type ZrC.
Magnetic interactions and electronic structure of system: An ab-initio ...
Indian Academy of Sciences (India)
Tufan Roy
2017-06-19
Jun 19, 2017 ... expansion up to lmax = 3 has been taken for each atom. 3. Results .... for the Mn atom. This large exchange splitting of Y atom for both the compounds leads to large partial magnetic moments on the Y atom (3.671μB for Mn in Pt2MnGa,. 3.025μB for ... for Pt-based systems, more localization of Mn-magnetic.
Ab initio theory of the electronic structure of nf-ions in solids and liquids
International Nuclear Information System (INIS)
Kulagin, N.
1998-01-01
Full text: In the books and papers we developed the self-consistent field theory of nl- ions in Me+n:[L]k- clusters, where k is number of ligands - L, by ion-ligands distance - R. The results which were obtained for all RE and AC ions for Me+n:[L]k, where L - F - , O -2 and so on ligands, are closely corresponded to experimental data. The expression for energy of the cluster may be write as: E = E 0 + kE 1 + k'(E z + E c + E e + E ex ), (Eq.1), where E 0 and E 1 are the energies of the free nl-ion and surrounding one; E z , E c and E e are the energy of electrons interaction with 'strange' nucleus, Coulomb electron-electron interaction and exchange one. E ex is the energy of the interaction of electrons and nucleus with external field. The equations for the radial one-electron wave functions of the ions in the cluster were obtained by minimizing the Eq. 1 for the radial orbitals of the central ion and ligand one. We have received the general system of equations of the self-consistent field for cluster in liquids and solid states. The results of calculations of the energy structure of clusters and values of the standard radial integrals (spectroscopy parameters) for Ac-ions in 1-2-3 superconductors and RE-ions in garnet crystals by different values of R are qualitatively and quantitatively correct. We've got the best results for pressure dependence of Nd ions spectra, change of optical and X-Ray spectra after irradiation of garnets. We explained the nature of anomalous in SrTiO 3 and separate lasers crystals by used of results of the calculations. In the framework of our approach we obtained the best accuracy for the energy of X- Ray lines for all nf- ions in solids and liquids
Laser cooling of BH and GaF: insights from an ab initio study.
Gao, Yu-feng; Gao, Tao
2015-04-28
The feasibility of laser cooling BH and GaF is investigated using ab initio quantum chemistry. The ground state X (1)Σ(+) and first two excited states (3)Π and (1)Π of BH and GaF are calculated using the multireference configuration interaction (MRCI) level of theory. For GaF, the spin-orbit coupling effect is also taken into account in the electronic structure calculations at the MRCI level. Calculated spectroscopic constants for BH and GaF show good agreement with available theoretical and experimental results. The highly diagonal Franck-Condon factors (BH: f00 = 0.9992, f11 = 0.9908, f22 = 0.9235; GaF: f00 = 0.997, f11 = 0.989, f22 = 0.958) for the (1)Π (v' = 0-2) → X (1)Σ(+) (v = 0-2) transitions in BH and GaF are determined, which are found to be in good agreement with the theoretical and experimental data. Radiative lifetime calculations of the (1)Π (v' = 0-2) state (BH: 131, 151, and 187 ns; GaF: 2.26, 2.36, and 2.48 ns) are found to be short enough for rapid laser cooling. The proposed laser cooling schemes that drive the (1)Π (v' = 0) → X (1)Σ(+) (v = 0) transition use just one laser wavelength λ00 (BH: 436 nm, GaF: 209 nm). Though the cooling wavelength of GaF is deep in the UVC, a frequency quadrupled Ti:sapphire laser (189-235 nm) could be capable of generating useful quantities of light at this wavelength. The present results indicate that BH and GaF are two good choices of molecules for laser cooling.
Ab initio study of effects of substitutional additives on the phase stability of {gamma}-alumina
Energy Technology Data Exchange (ETDEWEB)
Jiang Kaiyun; Music, Denis; Sarakinos, Kostas; Schneider, Jochen M, E-mail: jiang@mch.rwth-aachen.d [Materials Chemistry, RWTH Aachen University, Mies van der Rohe Strasse 10, D-52074 Aachen (Germany)
2010-12-22
Using ab initio calculations, we have evaluated two structural descriptions of {gamma}-Al{sub 2}O{sub 3}, spinel and tetragonal hausmannite, and explored the relative stability of {gamma}-Al{sub 2}O{sub 3} with respect to {alpha}-Al{sub 2}O{sub 3} with 2.5 at.% of Si, Cr, Ti, Sc, and Y additives to identify alloying element induced electronic structure changes that impede the {gamma} to {alpha} transition. The total energy calculations indicate that Si stabilizes {gamma}-Al{sub 2}O{sub 3}, while Cr stabilizes {alpha}-Al{sub 2}O{sub 3}. As Si is added, a bond length increase in {alpha}-Al{sub 2}O{sub 3} is observed, while strong and short Si-O bonds are formed in {gamma}-Al{sub 2}O{sub 3}, consequently stabilizing this phase. On the other hand, Cr additions induce a smaller bond length increase in {alpha}-Al{sub 2}O{sub 3} than in {gamma}-Al{sub 2}O{sub 3}, therefore stabilizing the {alpha}-phase. The bulk moduli of {gamma}-Al{sub 2}O{sub 3} with these additives show no significant changes. The phase stability and elastic property data discussed here underline the application potential of Si alloyed {gamma}-Al{sub 2}O{sub 3} for applications at elevated temperatures. Furthermore it is evident that the tetragonal hausmannite structure is a suitable description for {gamma}-Al{sub 2}O{sub 3}.
Schwenke, David W.; Jaffe, Richard L.; Chaban, Galina M.
2016-01-01
We have generated accurate global potential energy surfaces for CO+Ar and CO+O that correlate with atom-diatom pairs in their ground electronic states based on extensive ab initio electronic structure calculations and used these potentials in quasi-classical trajectory nuclear dynamics calculations to predict the thermal dissociation rate coefficients over 5000- 35000 K. Our results are not compatible with the 20-45 year old experimental results. For CO + Ar we obtain fairly good agreement with the experimental rate coefficients of Appleton et al. (1970) and Mick and Roth (1993), but our computed rate coefficients exhibit a stronger temperature dependence. For CO + O our dissociation rate coefficient is in close agreement with the value from the Park model, which is an empirical adjustment of older experimental results. However, we find the rate coefficient for CO + O is only 1.5 to 3.3 times larger than CO + Ar over the temperature range of the shock tube experiments (8000-15,000 K). The previously accepted value for this rate coefficient ratio is 15, independent of temperature. We also computed the rate coefficient for the CO + O ex- change reaction which forms C + O2. We find this reaction is much faster than previously believed and is the dominant process in the removal of CO at temperatures up to 16,000 K. As a result, the dissociation of CO is accomplished in two steps (react to form C+O2 and then O2 dissociates) that are endothermic by 6.1 and 5.1 eV, instead of one step that requires 11.2 eV to break the CO bond.
Linker, Gerrit-Jan; Loosdrecht, Paul H. M. van; Duijnen, Piet van; Broer, Ria
2010-03-01
We performed ab initio quantum chemical calculations for the geometrical and electronic structure of the EDO-TTF (ethylenedioxy-tetrathiafulvalene) molecule using HF, CASSCF and DFT methods. We compare these in vacuo results with the properties of the (EDO-TTF) 2PF 6 crystal at near room temperature. We demonstrate that, by bending and charging the molecule in vacuum, the deformation that is thought to be the origin of charge ordering in this material is an inherent property of the EDO-TTF molecule. We further show that deformations can be readily made at ambient temperatures.
Ultra strong polymer fibers : Ab initio calculations on polyethylene
Hageman, J.C.L.; Groot, R.A. de; Meier, Robert J.
1998-01-01
The Car-Parrinello technique is used to study the electronic structure of orthorhombic polyethylene as well as the elastic modulus. The theoretical band structure and density of states are in very good agreement with experiments. The best experimentally realized elastic modulus is better than 86% of
Ab initio study on the paths of oxygen abstraction of hydrogen trioxide
Indian Academy of Sciences (India)
Keywords. Ab initio calculations; atmospheric chemistry; hydrogen trioxide; acid rain. 1. Introduction. Processes such as volcanic eruptions, biogenic activi- ty, and the combustion of fossil fuels are resources for the emission of sulphur gases into the atmosphere. Sul- phur has been recognized as an important constituent of.
Ab initio Molecular Orbital Studies of the Vibrational Spectra of some ...
African Journals Online (AJOL)
NJD
2004-06-15
Jun 15, 2004 ... The binary complexes formed between sulphur dioxide, as electron donor, and the series carbon dioxide, carbonyl sulphide and carbon disulphide, as electron acceptors, have been studied by means of ab initio molecular orbital theory. The optimized structures, the interaction energies and the vibrational ...
DEFF Research Database (Denmark)
Andersen, Vinca Bonde; Berg, Rolf W.; Shim, Irene
2017-01-01
The iminodisulfonate, [N(SO3)2]3–, and phosphinodisulfonate, [P(SO3)2]3–, ions have been investigated by performing ab initio MP2/6-311+G**calculations. The nitrogen and phosphorus atoms as part of the ions are shown to be divalent with a negative charge and two lone pairs on the nitrogen and pho...
DEFF Research Database (Denmark)
Svendsen, Casper Steinmann; Jensen, Jan; Fedorov, Dmitri
2013-01-01
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...
Ab initio calculations of fundamental properties of SrTe1− xOx alloys
Indian Academy of Sciences (India)
Home; Journals; Bulletin of Materials Science; Volume 39; Issue 3. Ab initio ... Department of Physics, Faculty of Sciences, Badji Mokhtar University, P.O. Box 12, 23000 Annaba, Algeria; Laboratoire LPR, Département de Physique, Faculté des Sciences, Université Badji Mokhtar, Annaba, Algeria; Laboratoire de Physique et ...
Calibration of the isomer shift for iodine resonant transition by ab initio calculations
Czech Academy of Sciences Publication Activity Database
Wdowik, U. D.; Legut, Dominik; Ruebenbauer, K.
2010-01-01
Roč. 114, č. 26 (2010), s. 7146-7152 ISSN 1089-5639 Institutional research plan: CEZ:AV0Z20410507 Keywords : ab initio * isomer shift of iodine * calibration * I127 * I129 Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 2.732, year: 2010
DEFF Research Database (Denmark)
Cybulski, Hubert; Fernandez, Berta; Henriksen, Christian
2012-01-01
We evaluate the phenylacetylene-argon intermolecular potential energy surface by fitting a representative number of ab initio interaction energies to an analytic function. These energies are calculated at a grid of intermolecular geometries, using the CCSD(T) method and the aug-cc-pVDZ basis set ...... Institute of Physics. [http://dx.doi.org/10.1063/1.4742153]...
Czech Academy of Sciences Publication Activity Database
Ma, D.; Friák, Martin; von Pezold, J.; Raabe, D.; Neugebauer, J.
2015-01-01
Roč. 85, FEB (2015), s. 53-66 ISSN 1359-6454 Institutional support: RVO:68081723 Keywords : Solid-solution strengthening * DFT * Peierls–Nabarro model * Ab initio * Al alloys Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 5.058, year: 2015
High accuracy ab initio calculations on reactions of OH with 1-alkenes. The case of propene
Czech Academy of Sciences Publication Activity Database
Izsák, R.; Szöri, Milan; Knowles, P. J.; Viskolcz, B.
2009-01-01
Roč. 5, č. 9 (2009), s. 2313-2321 ISSN 1549-9618 Institutional research plan: CEZ:AV0Z40550506 Keywords : multireference ab initio calculations * OH-addition * H-abstraction by OH Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.804, year: 2009
Non-adiabatic collisions in H + O2 system: An ab initio study
Indian Academy of Sciences (India)
WINTEC
Abstract. An ab initio study on the low-lying potential energy surfaces of H+ + O2 system for different orientations (γ) of H+ have been undertaken employing the multi-reference configuration interaction. (MRCI) method and Dunning's cc-pVTZ basis set to examine their role in influencing the collision dyna- mics. Nonadiabatic ...
Understanding hydration of Zn(2+) in hydrothermal fluids with ab initio molecular dynamics
Liu, X.; Lu, X.; Wang, R.; Meijer, E.J.
2011-01-01
With ab initio molecular dynamics simulations, the free-energy profiles of hydrated Zn2+ are calculated for both gaseous and aqueous systems from ambient to supercritical conditions, and from the derived free-energy information, the speciation of hydrated Zn2+ has been revealed. It is shown that the
An Efficient Method for Electron-Atom Scattering Using Ab-initio Calculations
Energy Technology Data Exchange (ETDEWEB)
Xu, Yuan; Yang, Yonggang; Xiao, Liantuan; Jia, Suotang [Shanxi University, Taiyuan (China)
2017-02-15
We present an efficient method based on ab-initio calculations to investigate electron-atom scatterings. Those calculations profit from methods implemented in standard quantum chemistry programs. The new approach is applied to electron-helium scattering. The results are compared with experimental and other theoretical references to demonstrate the efficiency of our method.
Ab Initio Calculations and Raman and SERS Spectral Analyses of Amphetamine Species
DEFF Research Database (Denmark)
Berg, Rolf W.; Nørbygaard, Thomas; White, Peter C.
2011-01-01
. The spectra of amphetamine and amphetamine-H+ sampleswere obtained and assigned according to a comparison of the experimental spectra and the ab initio MO calculations, performed using the Gaussian 03W program (Gaussian, Inc., Pittsburgh, PA). The analyses were based on complete geometry minimization...
Ab initio and work function and surface energy anisotropy of LaB6
Uijttewaal, M. A.; de Wijs, G. A.; de Groot, R. A.
2006-01-01
Lanthanum hexaboride is one of the cathode materials most used in high-power electronics technology, but the many experimental results do not provide a consistent picture of the surface properties. Therefore, we report the first ab initio calculations of the work functions and surface energies of
New ab initio based pair potential for accurate simulation of phase transitions in ZnO
Wang, Shuaiwei; Fan, Zhaochuan; Koster, Rik S.; Fang, Changming; Van Huis, Marijn A.; Yalcin, Anil O.; Tichelaar, Frans D.; Zandbergen, Henny W.; Vlugt, Thijs J H
2014-01-01
A set of interatomic pair potentials is developed for ZnO based on the partially charged rigid ion model (PCRIM). The derivation of the potentials combines lattice inversion, empirical fitting, and ab initio energy surface fitting. We show that, despite the low number of parameters in this model
DEFF Research Database (Denmark)
Abild-Pedersen, Frank; Nørskov, Jens Kehlet; Rostrup-Nielsen, Jens
2006-01-01
Mechanisms and energetics of graphene growth catalyzed by nickel nanoclusters were studied using ab initio density functional theory calculations. It is demonstrated that nickel step-edge sites act as the preferential growth centers for graphene layers on the nickel surface. Carbon is transported...
Precise Ab-initio prediction of terahertz vibrational modes in crystalline systems
DEFF Research Database (Denmark)
Jepsen, Peter Uhd; Clark, Stewart J.
2007-01-01
We use a combination of experimental THz time-domain spectroscopy and ab-initio density functional perturbative theory to accurately predict the terahertz vibrational spectrum of molecules in the crystalline phase. Our calculations show that distinct vibrational modes found in solid-state materials...
Czech Academy of Sciences Publication Activity Database
Meliá, C.; Ferrer, S.; Řezáč, Jan; Parisel, O.; Reinaud, O.; Moliner, V.; de la Lande, A.
2013-01-01
Roč. 19, č. 51 (2013), s. 17328-17337 ISSN 0947-6539 Institutional support: RVO:61388963 Keywords : ab initio calculations * copper * electron transfer * enzymes * molecular dynamics * reaction mechanisms Subject RIV: CC - Organic Chemistry Impact factor: 5.696, year: 2013
Ab initio study of solute transition-metal interactions with point defects in bcc Fe
Olsson, P.; Klaver, T.P.C.; Domain, C.
2010-01-01
The properties of 3d, 4d, and 5d transition-metal elements in ?-Fe have been studied using ab initio density-functional theory. The intrinsic properties of the solutes have been characterized as well as their interaction with point defects. Vacancies and interstitials of (110) and (111) orientations
Ab initio Calculations of Charge Symmetry Breaking in the A=4 Hypernuclei
Czech Academy of Sciences Publication Activity Database
Gazda, Daniel; Gal, A.
2016-01-01
Roč. 116, č. 12 (2016), s. 122501 ISSN 0031-9007 R&D Projects: GA ČR(CZ) GA15-04301S Institutional support: RVO:61389005 Keywords : ab initio * shell model * four-body calculations Subject RIV: BE - Theoretical Physics Impact factor: 8.462, year: 2016
Ab initio Defect Energetics in LaBO3 Perovskite Solid Oxide Fuel Cell Materials
DEFF Research Database (Denmark)
Lee, Yueh-Lin; Morgan, Dane; Kleis, Jesper
2009-01-01
Perovskite materials of the form ABO3 are a promising family of compounds for use in solid oxide fuel cell (SOFC) cathodes. Study of the physics of these compounds under SOFC conditions with ab initio methods is particularly challenging due to high temperatures, exchange of oxygen with O2 gas...
Ab initio molecular dynamics simulation of hydrogen fluoride at several thermodynamic states
DEFF Research Database (Denmark)
Kreitmeir, M.; Bertagnolli, H.; Mortensen, Jens Jørgen
2003-01-01
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 ...
Gas phase ion chemistry of coumarins: ab initio calculations used to ...
African Journals Online (AJOL)
The gas phase ion chemistry of coumarins using electron ionization (EI), positive chemical ionization (PCI) and negative chemical ionization (NCI) in a time of flight and quadrupole mass spectrometer (qMS) coupled to a gas chromatograph is outlined. The observations in NCI mode were complimented with Ab initio ...
Ab initio prediction of vacancy properties in concentrated alloys : The case of fcc Cu-Ni
Zhang, X.; Sluiter, M.H.F.
2015-01-01
Vacancy properties in concentrated alloys continue to be of great interest because nowadays ab initio supercell simulations reach a scale where even defect properties in disordered alloys appear to be within reach. We show that vacancy properties cannot generally be extracted from supercell total
A fragment-based approach towards ab-initio treatment of polymeric ...
Indian Academy of Sciences (India)
Reshma S Pingale
2017-06-20
Jun 20, 2017 ... conquer'-type approach for the ab-initio studies of these polymeric systems. The method employs a fragmentation technique with independent fragment optimization for obtaining optimized geometries of the oligomers of various polymeric materials such as polyfuran, polypyrrole, polythiophene and other ...
Ab initio výpočty v chemii po 28 letech
Czech Academy of Sciences Publication Activity Database
Čársky, Petr; Urban, M.
2008-01-01
Roč. 102, č. 10 (2008), s. 865-872 ISSN 0009-2770 Institutional research plan: CEZ:AV0Z40400503 Keywords : quantum chemistry * ab-initio calculation Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 0.593, year: 2008
Ab initio study of gas phase and water-assisted tautomerization of ...
Indian Academy of Sciences (India)
WINTEC
Water-assisted tautomerization in maleimide and formamide showed that difference in energy barrier reduces to 2⋅83 kcal/mol from 10⋅41 kcal/mol (in gas phase) at B3LYP level, which resulted that maleimide readily undergoes tautomerization in water molecule. Keywords. Ab Initio calculations; maleimide; formamide; ...
Czech Academy of Sciences Publication Activity Database
Dračínský, Martin; Möller, H. M.; Exner, T. E.
2013-01-01
Roč. 9, č. 8 (2013), s. 3806-3815 ISSN 1549-9618 R&D Projects: GA ČR GA13-24880S Institutional support: RVO:61388963 Keywords : ab initio molecular dynamics * NMR spectroscopy * DFT calculations * hydration Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 5.310, year: 2013
Ab initio molecular dynamics approach to a quantitative description of ion pairing in water
Czech Academy of Sciences Publication Activity Database
Pluhařová, Eva; Maršálek, Ondřej; Schmidt, B.; Jungwirth, Pavel
2013-01-01
Roč. 4, č. 23 (2013), s. 4177-4181 ISSN 1948-7185 R&D Projects: GA ČR GBP208/12/G016 Institutional support: RVO:61388963 Keywords : ion pairing * charge transfer * water * ab initio molecular dynamics Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 6.687, year: 2013
Ab initio calculation atomics ground state wave function for interactions Ion- Atom
International Nuclear Information System (INIS)
Shojaee, F.; Bolori zadeh, M. A.
2007-01-01
Ab initio calculation atomics ground state wave function for interactions Ion- Atom Atomic wave function expressed in a Slater - type basis obtained within Roothaan- Hartree - Fock for the ground state of the atoms He through B. The total energy is given for each atom.
Mechanical properties of carbynes investigated by ab initio total-energy calculations
DEFF Research Database (Denmark)
Castelli, Ivano E.; Salvestrini, Paolo; Manini, Nicola
2012-01-01
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....
Sanz, Cristina; Lin, Hui-Ju; Lado, Beatriz; Stafford, Catherine A.; Bowden, Harriet W.
2016-01-01
The article summarizes results from two experimental studies (N = 23, N = 21) investigating the extent to which working memory capacity (WMC) intervenes in "ab initio" language development under two pedagogical conditions [± grammar lesson + input-based practice + explicit feedback]. The linguistic target is the use of morphosyntax to…
Ab initio and DFT study of Octanitrocubane. | Ejuh | Journal of the ...
African Journals Online (AJOL)
The molecular stability, structure, dipole moment, charge transfer, polarizability and energy of Octonitrocubane have been studied by using ab- initio Quantum Mechanical calculations. We have used the Restricted Hartree-Fock (RHF) and density functional Becke3LYP (B3LYP) theories by employing 6-31G, 6- 31++G** and ...
Czech Academy of Sciences Publication Activity Database
Sandlöbes, S.; Pei, Z.; Friák, Martin; Zhu, L.-F.; Wang, F.; Zaefferer, S.; Raabe, D.; Neugebauer, J.
2014-01-01
Roč. 70, MAY (2014), s. 92-104 ISSN 1359-6454 Grant - others:GA MŠk(CZ) LM2010005 Institutional support: RVO:68081723 Keywords : Magnesium * Rare-earth elements * Ductility * Modeling * Ab initio Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 4.465, year: 2014
Ab initio study of antiphase boundaries and stacking faults in L12 and DO22 compounds
DEFF Research Database (Denmark)
Rosengaard, N. M.; Skriver, Hans Lomholt
1994-01-01
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...
Ab initio study of the bcc-hcp transformation in iron
Czech Academy of Sciences Publication Activity Database
Friák, Martin; Šob, Mojmír
2008-01-01
Roč. 77, č. 17 (2008), 174117/1-174117/7 ISSN 1098-0121 R&D Projects: GA MŠk OC 147; GA AV ČR IAA1041302 Institutional research plan: CEZ:AV0Z20410507 Keywords : ab initio calculations * phase transformations * iron Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.322, year: 2008
Sprik, M.; Meijer, E.M.
1998-01-01
Ab initio molecular dynamics methods have been used to study the reaction mechanism of acidcatalyzed addition of water to formaldehyde in a model system of an aqueous solution of sulfuric acid. Using the method of constraints we find that an H
Ab initio theory of perpendicular transport in layered magnetic systems
Czech Academy of Sciences Publication Activity Database
Kudrnovský, Josef; Drchal, Václav; Turek, Ilja; Dederichs, P. H.; Weinberger, P.; Bruno, P.
2002-01-01
Roč. 240, - (2002), s. 177-179 ISSN 0304-8853 R&D Projects: GA AV ČR IAA1010829; GA ČR GA202/00/0122; GA MŠk OC P5.30; GA MŠk OC P3.40; GA MŠk OC P3.70 Institutional research plan: CEZ:AV0Z1010914 Keywords : magnetoresistance -theory * ferromagnetic multilayers * disorder-alloys * electronic structure Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.046, year: 2002
International Nuclear Information System (INIS)
Simpson, R.W.; Lane, N.F.; Chaney, R.C.
1978-01-01
The electronic structure for a Ni atom cluster embedded in bulk Ni by use of a spin-averaged local exchange SCF Ni crystal potential is calculated with an ab initio LCAO-Mo variational method. A single hydrogen impurity is added at the cluster center (fcc octahedral interstitial site) and the electronic structure computed iteratively until the change in electron density from the pure Ni cluster density is self-consistent. The H-Ni 6 self-consistent density change is compared to the charge density around a free hydrogen atom and to the initial-response density change in H-Ni 14 and H-Ni 38 clusters. 14 references
A Review of Solid-Solution Models of High-Entropy Alloys Based on Ab Initio Calculations
Directory of Open Access Journals (Sweden)
Fuyang Tian
2017-11-01
Full Text Available Similar to the importance of XRD in experiments, ab initio calculations, as a powerful tool, have been applied to predict the new potential materials and investigate the intrinsic properties of materials in theory. As a typical solid-solution material, the large degree of uncertainty of high-entropy alloys (HEAs results in the difficulty of ab initio calculations application to HEAs. The present review focuses on the available ab initio based solid-solution models (virtual lattice approximation, coherent potential approximation, special quasirandom structure, similar local atomic environment, maximum-entropy method, and hybrid Monte Carlo/molecular dynamics and their applications and limits in single phase HEAs.
Electronic structure and tautomerism of thioamides
Energy Technology Data Exchange (ETDEWEB)
Novak, Igor, E-mail: inovak@csu.edu.au [Charles Sturt University, POB 883, Orange, NSW 2800 (Australia); Klasinc, Leo, E-mail: klasinc@irb.hr [Physical Chemistry Department, Ruđer Bošković Institute, HR-10002 Zagreb (Croatia); McGlynn, Sean P., E-mail: sean.mcglynn@chemgate.chem.lsu.edu [Louisiana State University, Baton Rouge, LA 70803 (United States)
2016-05-15
Highlights: • Electronic structure of thioamide group and its relation to Lewis basicity. • Tautomerism of the (thio)amide groups. • Substituent effects on the electronic structure of (thio)amide group. - Abstract: The electronic structures of several thioamides have been studied by UV photoelectron spectroscopy (UPS). The relative stabilities of keto–enol tautomers have been determined using high-level ab initio calculations and the results were used in the analysis of UPS spectra. The main features of electronic structure and tautomerism of thioamide derivatives are discussed. The predominant tautomers in the gas phase are of keto–(thio)keto form. The addition of cyclohexanone moiety to the thioamide group enhances the Lewis base character of the sulfur atom. The addition of phenyl group to the (thio)amide group significantly affects its electronic structure.
International Nuclear Information System (INIS)
Orimoto, Yuuichi; Aoki, Yuriko
2016-01-01
An automated property optimization method was developed based on the ab initio O(N) elongation (ELG) method and applied to the optimization of nonlinear optical (NLO) properties in DNA as a first test. The ELG method mimics a polymerization reaction on a computer, and the reaction terminal of a starting cluster is attacked by monomers sequentially to elongate the electronic structure of the system by solving in each step a limited space including the terminal (localized molecular orbitals at the terminal) and monomer. The ELG-finite field (ELG-FF) method for calculating (hyper-)polarizabilities was used as the engine program of the optimization method, and it was found to show linear scaling efficiency while maintaining high computational accuracy for a random sequenced DNA model. Furthermore, the self-consistent field convergence was significantly improved by using the ELG-FF method compared with a conventional method, and it can lead to more feasible NLO property values in the FF treatment. The automated optimization method successfully chose an appropriate base pair from four base pairs (A, T, G, and C) for each elongation step according to an evaluation function. From test optimizations for the first order hyper-polarizability (β) in DNA, a substantial difference was observed depending on optimization conditions between “choose-maximum” (choose a base pair giving the maximum β for each step) and “choose-minimum” (choose a base pair giving the minimum β). In contrast, there was an ambiguous difference between these conditions for optimizing the second order hyper-polarizability (γ) because of the small absolute value of γ and the limitation of numerical differential calculations in the FF method. It can be concluded that the ab initio level property optimization method introduced here can be an effective step towards an advanced computer aided material design method as long as the numerical limitation of the FF method is taken into account.
Adsorption of ethanol on V2O5 (010) surface for gas-sensing applications: Ab initio investigation
International Nuclear Information System (INIS)
Qin, Yuxiang; Cui, Mengyang; Ye, Zhenhua
2016-01-01
Highlights: • Ethanol adsorbed on V 2 O 5 (010) surface was investigated by ab initio calculations. • Ethanol prefers to adsorb on “Hill”-like surface, rather than“Valley”-like region. • Surface O 1(H) site plays a key role to dominate the ethanol adsorption process. • Sensing mechanism is related with electronic structure and electron redistribution. • Gas sensitivity is reflected by quantitative electron population analysis. - Abstract: The adsorption of ethanol on V 2 O 5 (010) surface was investigated by means of density functional theory (DFT) with a combined generalized gradient approximation (GGA) plus Hubbard U approach to exploit the potential sensing applications. The adsorption configurations were first constructed by considering different orientations of ethanol molecule to V and O sites on the “Hill”- and “Valley”-like regions of corrugated (010) surface. It is found that ethanol molecule can adsorb on whole surface in multiple stable configurations. Nevertheless the molecular adsorption on the “Hill”-like surface is calculated to occur preferentially, and the single coordinated oxygen on “Hill”-like surface (O 1(H) ) acting as the most energetically favorable adsorption site shows the strongest adsorption ability to ethanol molecule. Surface adsorption of ethanol tunes the electronic structure of V 2 O 5 and cause an n-doping effect. As a consequence, the Fermi levels shift toward the conductive bond increasing the charge carrier concentration of electrons in adsorbed V 2 O 5 . The sensitive electronic structure and the multiple stable configurations to ethanol adsorption highlight the high adsorption activity and then the potential of V 2 O 5 (010) surface applied to high sensitive sensor for ethanol vapor detection. Further Mulliken population and Natural bond orbital (NBO) calculations quantify the electron transfer from the adsorbed ethanol to the surface, and correlates the adsorption ability of surface sites
Allen, B. Danette; Alexandrov, Natalia
2016-01-01
Incremental approaches to air transportation system development inherit current architectural constraints, which, in turn, place hard bounds on system capacity, efficiency of performance, and complexity. To enable airspace operations of the future, a clean-slate (ab initio) airspace design(s) must be considered. This ab initio National Airspace System (NAS) must be capable of accommodating increased traffic density, a broader diversity of aircraft, and on-demand mobility. System and subsystem designs should scale to accommodate the inevitable demand for airspace services that include large numbers of autonomous Unmanned Aerial Vehicles and a paradigm shift in general aviation (e.g., personal air vehicles) in addition to more traditional aerial vehicles such as commercial jetliners and weather balloons. The complex and adaptive nature of ab initio designs for the future NAS requires new approaches to validation, adding a significant physical experimentation component to analytical and simulation tools. In addition to software modeling and simulation, the ability to exercise system solutions in a flight environment will be an essential aspect of validation. The NASA Langley Research Center (LaRC) Autonomy Incubator seeks to develop a flight simulation infrastructure for ab initio modeling and simulation that assumes no specific NAS architecture and models vehicle-to-vehicle behavior to examine interactions and emergent behaviors among hundreds of intelligent aerial agents exhibiting collaborative, cooperative, coordinative, selfish, and malicious behaviors. The air transportation system of the future will be a complex adaptive system (CAS) characterized by complex and sometimes unpredictable (or unpredicted) behaviors that result from temporal and spatial interactions among large numbers of participants. A CAS not only evolves with a changing environment and adapts to it, it is closely coupled to all systems that constitute the environment. Thus, the ecosystem that
Amino acids interacting with defected carbon nanotubes: ab initio calculations
Directory of Open Access Journals (Sweden)
M. Darvish Ganji
2016-09-01
Full Text Available The adsorption of a number of amino acids on a defected single-walled carbon nanotube (SWCNT is investigated by using the density-functional theory (DFT calculations. The adsorption energies and equilibrium distances are calculated for various configurations such as amino acid attaching to defect sites heptagon, pentagon and hexagon in defective tube and also for several molecular orientations with respect to the nanotube surface. The results showed that amino acids prefer to be physisorbed on the outer surface of the defected nanotube with different interaction strength following the hierarchy histidine > glycine > phenylalanine > cysteine. Comparing these findings with those obtained for perfect SWCNTs reveals that the adsorption energy of the amino acids increase for adsorption onto defected CNTs. The adsorption nature has also been evaluated by means of electronics structures analysis within the Mulliken population and DOS spectra for the interacting entities.
Malshe, M.; Raff, L. M.; Hagan, M.; Bukkapatnam, S.; Komanduri, R.
2010-05-01
The variation in the fitting accuracy of neural networks (NNs) when used to fit databases comprising potential energies obtained from ab initio electronic structure calculations is investigated as a function of the number and nature of the elements employed in the input vector to the NN. Ab initio databases for H2O2, HONO, Si5, and H2CCHBr were employed in the investigations. These systems were chosen so as to include four-, five-, and six-body systems containing first, second, third, and fourth row elements with a wide variety of chemical bonding and whose conformations cover a wide range of structures that occur under high-energy machining conditions and in chemical reactions involving cis-trans isomerizations, six different types of two-center bond ruptures, and two different three-center dissociation reactions. The ab initio databases for these systems were obtained using density functional theory/B3LYP, MP2, and MP4 methods with extended basis sets. A total of 31 input vectors were investigated. In each case, the elements of the input vector were chosen from interatomic distances, inverse powers of the interatomic distance, three-body angles, and dihedral angles. Both redundant and nonredundant input vectors were investigated. The results show that among all the input vectors investigated, the set employed in the Z-matrix specification of the molecular configurations in the electronic structure calculations gave the lowest NN fitting accuracy for both Si5 and vinyl bromide. The underlying reason for this result appears to be the discontinuity present in the dihedral angle for planar geometries. The use of trigometric functions of the angles as input elements produced significantly improved fitting accuracy as this choice eliminates the discontinuity. The most accurate fitting was obtained when the elements of the input vector were taken to have the form Rij-n, where the Rij are the interatomic distances. When the Levenberg-Marquardt procedure was modified
Ab initio studies of equations of state and chemical reactions of reactive structural materials
Zaharieva, Roussislava
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
Computational prediction of muon stopping sites using ab initio random structure searching (AIRSS)
Liborio, Leandro; Sturniolo, Simone; Jochym, Dominik
2018-04-01
The stopping site of the muon in a muon-spin relaxation experiment is in general unknown. There are some techniques that can be used to guess the muon stopping site, but they often rely on approximations and are not generally applicable to all cases. In this work, we propose a purely theoretical method to predict muon stopping sites in crystalline materials from first principles. The method is based on a combination of ab initio calculations, random structure searching, and machine learning, and it has successfully predicted the MuT and MuBC stopping sites of muonium in Si, diamond, and Ge, as well as the muonium stopping site in LiF, without any recourse to experimental results. The method makes use of Soprano, a Python library developed to aid ab initio computational crystallography, that was publicly released and contains all the software tools necessary to reproduce our analysis.
Electronic properties of liquid Hg-In alloys : Ab-initio molecular dynamics study
International Nuclear Information System (INIS)
Sharma, Nalini; Ahluwalia, P. K.; Thakur, Anil
2016-01-01
Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-In alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Three liquid Hg-In alloys (Hg 10 In 90 , Hg 30 In 70,. Hg 50 In 50 , Hg 70 In 30 , and Hg 90 Pb 10 ) at 299 K are considered. The calculated results for liquid Hg (l-Hg) and lead (l-In) are also drawn. Along with the calculated results of considered five liquid alloys of Hg-In alloy. The results obtained from electronic properties namely total density of state and partial density of states help to find the local arrangement of Hg and In atoms and the presence of liquid state in the considered five alloys.
Ab initio Equation of State and Phase Diagram of MgO in the megabar regime
Soubiran, F.; Militzer, B.
2017-12-01
Accurate equations of state (EOS) and phase diagrams for silicate materials are a cornerstone of Earth, Super-Earth's and giant planet cores' models. While recent shock wave experiments have provided new data on the principal Hugoniot curve, accessing off-Hugoniot states is much more challenging. Ab initio computer simulations offer the possibility to complement the experiments in this regard. Here we report results of an extensive set of ab initio simulations of MgO in solid and liquid phases over a wide range of parameters relevant for Earth, Super-Earth's and giant planet's interiors. Using the thermodynamic integration technique, we derive a consistent EOS including free energy and entropy information. We will discuss the relative stability of different phases.
Study of atomic structure of liquid Hg-In alloys using ab-initio molecular dynamics
Energy Technology Data Exchange (ETDEWEB)
Sharma, Nalini; Ahluwalia, P. K. [Department of Physics, Himachal Pradesh University, Shimla(HP)-171005 (India); Thakur, Anil [Department of Physics, Govt. P. G. College Solan (HP)-173212 (India)
2015-05-15
Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-In alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Five liquid Hg-In mixtures (Hg{sub 10}In{sub 90}, Hg{sub 30}In{sub 70}, Hg{sub 50}In{sub 50}, Hg{sub 70}In{sub 30} and Hg{sub 90}In{sub 10}) at 299K 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 (l-In). 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 alloys.
Electronic properties of liquid Hg-In alloys : Ab-initio molecular dynamics study
Energy Technology Data Exchange (ETDEWEB)
Sharma, Nalini, E-mail: nalini-2808@yahoo.co.in; Ahluwalia, P. K. [Department of Physics, Himachal Pradesh University, Shimla-1771005 (India); Thakur, Anil [Department Of Physics, Govt. College Solan, Himachal Pradesh-173212 (India)
2016-05-23
Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-In alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Three liquid Hg-In alloys (Hg{sub 10}In{sub 90}, Hg{sub 30}In{sub 70,.} Hg{sub 50}In{sub 50}, Hg{sub 70}In{sub 30}, and Hg{sub 90}Pb{sub 10}) at 299 K are considered. The calculated results for liquid Hg (l-Hg) and lead (l-In) are also drawn. Along with the calculated results of considered five liquid alloys of Hg-In alloy. The results obtained from electronic properties namely total density of state and partial density of states help to find the local arrangement of Hg and In atoms and the presence of liquid state in the considered five alloys.
Hyperfine Parameters for Aluminum Hydride: An ab Initio Molecular Orbital Study.
Gee, Myrlene; Wasylishen, Roderick E.
2001-06-01
An extensive ab initio molecular orbital study of the (27)Al nuclear spin-rotation and nuclear quadrupolar coupling constants in aluminum hydride, AlH, has been performed. The (27)Al nuclear spin-rotation constant (C( perpendicular)), calculated to be approximately 300 kHz, was neglected in a previous analysis of the hyperfine structure in the microwave spectrum (M. Goto and S. Saito, Astrophys. J. 452, L147-148 (1995)). Unfortunately, the ab initio calculations do not provide a definitive value for the aluminum nuclear quadrupolar coupling constant, but suggest a value of -49+/-4 MHz. It is apparent that the microwave study of AlH should be repeated. Copyright 2001 Academic Press.
Low-temperature metallic liquid hydrogen: an ab-initio path-integral molecular dynamics perspective
Chen, Ji; Li, Xin-Zheng; Zhang, Qianfan; Probert, Matthew; Pickard, Chris; Needs, Richard; Michaelides, Angelos; Wang, Enge
2013-03-01
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.
Ab initio model of optical properties of two-temperature warm dense matter
International Nuclear Information System (INIS)
Holst, B.; Recoules, V.; Mazevet, S.; Torrent, M.
2014-01-01
We present a model to describe thermophysical and optical properties of two-temperature systems consisted of heated electrons and cold ions in a solid lattice that occur during ultrafast heating experiments. Our model is based on ab initio simulations within the framework of density functional theory. The optical properties are obtained by evaluating the Kubo-Greenwood formula. By applying the material parameters of our ab initio model to a two-temperature model we are able to describe the temperature relaxation process of femtosecond-laser-heated gold and its optical properties within the same theoretical framework. Recent time-resolved measurements of optical properties of ultrafast heated gold revealed the dynamics of the interaction between femtosecond laser pulses and solid state matter. Different scenarios obtained from simulations of our study are compared with experimental data. (authors)
Implementation of a vector potential method in an ab initio Hartree-Fock code
Tevekeliyska, Violina; Springborg, Michael; Champagne, Benoît; Kirtman, Bernard
2012-12-01
For extended systems exposed to an external, electrostatic field, the presence of the field leads to an extra term (E⃗. P⃗) to the Hamiltonian, where E⃗ is the field vector and P⃗ 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.
Nuclear quantum effects in ab initio dynamics: Theory and experiments for lithium imide
Ceriotti, Michele; Miceli, Giacomo; Pietropaolo, Antonino; Colognesi, Daniele; Nale, Angeloclaudio; Catti, Michele; Bernasconi, Marco; Parrinello, Michele
2010-11-01
Owing to their small mass, hydrogen atoms exhibit strong quantum behavior even at room temperature. Including these effects in first-principles calculations is challenging because of the huge computational effort required by conventional techniques. Here we present the first ab initio application of a recently developed stochastic scheme, which allows to approximate nuclear quantum effects inexpensively. The proton momentum distribution of lithium imide, a material of interest for hydrogen storage, was experimentally measured by inelastic neutron-scattering experiments and compared with the outcome of quantum thermostatted ab initio dynamics. We obtain favorable agreement between theory and experiments for this purely quantum-mechanical property, thereby demonstrating that it is possible to improve the modeling of complex hydrogen-containing materials without additional computational effort.
Computational prediction of muon stopping sites using ab initio random structure searching (AIRSS).
Liborio, Leandro; Sturniolo, Simone; Jochym, Dominik
2018-04-07
The stopping site of the muon in a muon-spin relaxation experiment is in general unknown. There are some techniques that can be used to guess the muon stopping site, but they often rely on approximations and are not generally applicable to all cases. In this work, we propose a purely theoretical method to predict muon stopping sites in crystalline materials from first principles. The method is based on a combination of ab initio calculations, random structure searching, and machine learning, and it has successfully predicted the Mu T and Mu BC stopping sites of muonium in Si, diamond, and Ge, as well as the muonium stopping site in LiF, without any recourse to experimental results. The method makes use of Soprano, a Python library developed to aid ab initio computational crystallography, that was publicly released and contains all the software tools necessary to reproduce our analysis.
Ab initio quantum-enhanced optical phase estimation using real-time feedback control
DEFF Research Database (Denmark)
Berni, Adriano; Gehring, Tobias; Nielsen, Bo Melholt
2015-01-01
as demonstrated in a variety of different optical systems(3-8). Most of these accounts, however, deal with the measurement of a very small shift of an already known phase, which is in stark contrast to ab initio phase estimation where the initial phase is unknown(9-12). Here, we report on the realization......Optical phase estimation is a vital measurement strategy that is used to perform accurate measurements of various physical quantities including length, velocity and displacements(1,2). The precision of such measurements can be greatly enhanced by the use of entangled or squeezed states of light...... of a quantum-enhanced and fully deterministic ab initio phase estimation protocol based on real-time feedback control. Using robust squeezed states of light combined with a real-time Bayesian adaptive estimation algorithm, we demonstrate deterministic phase estimation with a precision beyond the quantum shot...
Atomic carbon chains as spin-transmitters: An ab initio transport study
DEFF Research Database (Denmark)
Fürst, Joachim Alexander; Brandbyge, Mads; Jauho, Antti-Pekka
2010-01-01
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 transmi......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...... 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....
Ab initio NMR Confirmed Evolutionary Structure Prediction for Organic Molecular Crystals
Pham, Cong-Huy; Kucukbenli, Emine; de Gironcoli, Stefano
2015-03-01
Ab initio crystal structure prediction of even small organic compounds is extremely challenging due to polymorphism, molecular flexibility and difficulties in addressing the dispersion interaction from first principles. We recently implemented vdW-aware density functionals and demonstrated their success in energy ordering of aminoacid crystals. In this work we combine this development with the evolutionary structure prediction method to study cholesterol polymorphs. Cholesterol crystals have paramount importance in various diseases, from cancer to atherosclerosis. The structure of some polymorphs (e.g. ChM, ChAl, ChAh) have already been resolved while some others, which display distinct NMR spectra and are involved in disease formation, are yet to be determined. Here we thoroughly assess the applicability of evolutionary structure prediction to address such real world problems. We validate the newly predicted structures with ab initio NMR chemical shift data using secondary referencing for an improved comparison with experiments.
Approaches to ab initio molecular replacement of α-helical transmembrane proteins.
Thomas, Jens M H; Simkovic, Felix; Keegan, Ronan; Mayans, Olga; Zhang, Chengxin; Zhang, Yang; Rigden, Daniel J
2017-12-01
α-Helical transmembrane proteins are a ubiquitous and important class of proteins, but present difficulties for crystallographic structure solution. Here, the effectiveness of the AMPLE molecular replacement pipeline in solving α-helical transmembrane-protein structures is assessed using a small library of eight ideal helices, as well as search models derived from ab initio models generated both with and without evolutionary contact information. The ideal helices prove to be surprisingly effective at solving higher resolution structures, but ab initio-derived search models are able to solve structures that could not be solved with the ideal helices. The addition of evolutionary contact information results in a marked improvement in the modelling and makes additional solutions possible.
Energy Technology Data Exchange (ETDEWEB)
Halasyamani, Shiv [Univ. of Houston, TX (United States); Fennie, Craig [Cornell Univ., Ithaca, NY (United States)
2016-11-03
We have focused on the synthesis, characterization, and ab initio theory on multi-functional mixed-metal fluorides. With funding from the DOE, we have successfully synthesized and characterized a variety of mixed metal fluoride materials.
X-ray magnetic scattering in SDW Cr - ab initio study
International Nuclear Information System (INIS)
Takahashi, M.; Igarashi, J.-I.; Hirai, K.
2004-01-01
Full text: Resonant x-ray scattering at the K-edge of transition metal atom has attracted much attention as a powerful tool for obtaining information on magnetic or orbital properties of 3d electrons. Recently Mannix et al. performed the x-ray magnetic scattering experiment in SDW Chromium and observed the finite scattering intensity with resonant enhancement at Cr K-edge on the SDW magnetic spot (0, 0, 1 ±δ). Applying ab-initio band structure calculation based on the local spin density approximation, we analyze the scattering spectra and elucidate the mechanism of the resonant enhancement in connection with the electronic structure. We assumed the bcc structure with the lattice constant a = 5.45a 0 and the SDW wavelength λ SDW = 20a, which are nearly equilibrium value at the spin-flip temperature T SF = 122K. The K-edge x-ray absorption and scattering spectra are calculated using Fermi's golden rule. We evaluate the non-resonant scattering amplitude within the spherical and dipolar approximations for spin and orbital moment contributions, respectively. The calculated absorption spectra are in good agreement with the experiment. This may assure the validity of the calculation. We obtained finite scattering amplitude with resonant enhancement at the K-edge. The calculated photon energy dependence of the scattering intensity shows good agreement with the experiment. The contribution of the 3d and 4p orbital moments to the non-resonant scattering amplitude is negligible in consequence of the smallness of their values, which are l max d ∼ 0.006ℎ and l max p ∼ 0.00007ℎ. On the other hand, although the 3d and 4p orbital moments are infinitesimal, they play important role on the resonant enhancement, which occurs through the 1s - 4p dipole transition and reflects the 4p orbital polarization. The 4p orbital polarization is caused by the on-site spin-orbit interaction in 4p orbital itself and the hybridization of the 4p orbital with the 3d orbital at neighboring
Study of carvedilol by combined Raman spectroscopy and ab initio MO calculations
Marques, M. P. M.; Oliveira, P. J.; Moreno, A. J. M.; Carvalho, L. A. E. Batista de
2002-01-01
The novel cardioprotective drug carvedilol was studied by both Raman spectroscopy and ab initio molecular orbital methods (using the density functional theory approach). The spectra, acquired both for the solid samples and DMSO solutions as a function of pH, were assigned in view of the calculated wavenumbers and intensities, and also based on the experimental data obtained for individual compounds which comprise the molecule, namely carbazole and 1,2-dimethoxybenzene. The pH dependence of th...
Ab initio excited states calculations of Kr3+, probing semi-empirical modelling
Czech Academy of Sciences Publication Activity Database
Milko, Petr; Kalus, R.; Paidarová, Ivana; Hrušák, Jan; Gadéa, F. X.
-, 23 June (2009), s. 25 ISSN 1432-2234 R&D Projects: GA AV ČR IAA100400501 Institutional research plan: CEZ:AV0Z40400503 Keywords : cluster modelling * rare gas ions * ab initio potential energie * evaporation energies Subject RIV: CF - Physical ; Theoretical Chemistry http://www.springerlink.com/content/100493/?Content+Status=Accepted&sort=p_OnlineDate&sortorder=desc&v=condensed&o=20
Base pairing motifs involving 1,8-naphthyridine: an ab initio study
Czech Academy of Sciences Publication Activity Database
Czernek, Jiří
2006-01-01
Roč. 7, - (2006), s. 124-127. ISBN 90-6764-443-9. ISSN 1573-4196. [International Conference on Computational Methods in Sciences and Engineering. Chania, Crete, 27.10.2006-01.11.2006] R&D Projects: GA AV ČR KJB400500602; GA AV ČR 1ET400500402 Institutional research plan: CEZ:AV0Z40500505 Keywords : ab initio * electron correlation * MP2 Subject RIV: CD - Macromolecular Chemistry
Ab initio theory of the N2V defect in diamond for quantum memory implementation
Udvarhelyi, Péter; Thiering, Gergő; Londero, Elisa; Gali, Adam
2017-10-01
The N2V defect in diamond is characterized by means of ab initio methods relying on density functional theory calculated parameters of a Hubbard model Hamiltonian. It is shown that this approach appropriately describes the energy levels of correlated excited states induced by this defect. By determining its critical magneto-optical parameters, we propose to realize a long-living quantum memory by N2V defect, i.e., H 3 color center in diamond.
An ab initio study of core-valence correlation. [in atoms
Partridge, H.; Bauschlicher, C. W., Jr.; Walch, S. P.; Liu, B.
1983-01-01
Especially in the cases of the first two columns of the periodic table, the inclusion of core-valence correlation in ab initio CI calculations yields a contraction of the atomic valence shell and improves both calculated atomic ionization potentials and atomic energy separations. For the alkali dimers Na2, K2, and Rb2, the presently calculated bond lengths are in excellent agreement with experiments when core-valence is included. In addition, the valence dissociation energies are accurate.
Ab initio study of Co and Ni under uniaxial and biaxial loading and in epitaxial overlayers
Czech Academy of Sciences Publication Activity Database
Zelený, Martin; Legut, Dominik; Šob, Mojmír
2008-01-01
Roč. 78, č. 22 (2008), 224105/1-224105/11 ISSN 1098-0121 R&D Projects: GA ČR GD106/05/H008; GA AV ČR IAA1041302; GA MŠk OC 147 Institutional research plan: CEZ:AV0Z20410507 Keywords : ab initio calculations * epitaxial overlayers * uniaxial and biaxial loading Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.322, year: 2008
Ab initio study of phase transformations in transition-metal disilicides
Czech Academy of Sciences Publication Activity Database
Káňa, Tomáš; Šob, Mojmír; Vitek, V.
2011-01-01
Roč. 19, č. 7 (2011), s. 919-926 ISSN 0966-9795 R&D Projects: GA AV ČR IAA100100920; GA MŠk(CZ) OC10008 Institutional research plan: CEZ:AV0Z20410507 Keywords : silicides various * phase transformation * plastic deformation mechanisms * defects * dislocation geometry and arrangement * ab-initio calculations * aero-engine components Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.649, year: 2011
Czech Academy of Sciences Publication Activity Database
Hemzalová, P.; Friák, Martin; Šob, Mojmír; Ma, D.; Udyansky, A.; Raabe, D.; Neugebauer, J.
2013-01-01
Roč. 88, č. 17 (2013), Art. no. 174103 ISSN 1098-0121 R&D Projects: GA ČR(CZ) GAP108/12/0311; GA ČR GD106/09/H035; GA AV ČR IAA100100920 Institutional support: RVO:68081723 Keywords : nitrides * ab initio * thermodynamics * elasticity Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.664, year: 2013
Czech Academy of Sciences Publication Activity Database
Slavíček, Petr; Fárník, Michal
2011-01-01
Roč. 13, č. 26 (2011), s. 12123-12137 ISSN 1463-9076 R&D Projects: GA ČR GA203/09/0422; GA ČR GAP208/11/0161 Institutional research plan: CEZ:AV0Z40400503 Keywords : photochemistry * hydrogen bonded heterocycles * ab initio methods Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.573, year: 2011
DNA oligonucleotide-cis-platin Binding: Ab initio interpretation of the vibrational spectra
Czech Academy of Sciences Publication Activity Database
Andrushchenko, Valery; Wieser, H.; Bouř, Petr
2007-01-01
Roč. 111, č. 39 (2007), s. 9714-9723 ISSN 1089-5639 R&D Projects: GA AV ČR IAA400550702; GA ČR GA202/07/0732 Institutional research plan: CEZ:AV0Z40550506 Keywords : cis - platin * DNA * vibrational spektra * ab initio Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.918, year: 2007
Ab Initio theory of the Gilbert damping in random ferromagnetic alloys
Czech Academy of Sciences Publication Activity Database
Drchal, Václav; Turek, I.; Kudrnovský, Josef
2017-01-01
Roč. 30, č. 6 (2017), s. 1669-1672 ISSN 1557-1939 R&D Projects: GA ČR GA15-13436S Institutional support: RVO:68378271 Keywords : Gilbert damping * ferromagnetic alloys * ab initio * nonlocal torques Subject RIV: BM - Solid Matter Physics ; Magnetism OBOR OECD: Condensed matter physics (including formerly solid state physics, supercond.) Impact factor: 1.180, year: 2016
Approaches to ab initio molecular replacement of α-helical transmembrane proteins
Thomas, Jens M. H.; Simkovic, Felix; Keegan, Ronan; Mayans, Olga; Zhang, Chengxin; Zhang, Yang; Rigden, Daniel J.
2017-01-01
α-Helical transmembrane proteins are a ubiquitous and important class of proteins, but present difficulties for crystallographic structure solution. Here, the effectiveness of the AMPLE molecular replacement pipeline in solving α-helical transmembrane-protein structures is assessed using a small library of eight ideal helices, as well as search models derived from ab initio models generated both with and without evolutionary contact information. The ideal helices prove to be surprisingly effe...
Temperature dependence of magnetic anisotropy: An ab initio approach
Staunton, J. B.; Szunyogh, L.; Buruzs, A.; Gyorffy, B. L.; Ostanin, S.; Udvardi, L.
2006-10-01
We present a first-principles theory of the variation of magnetic anisotropy, K , with temperature, T , in metallic ferromagnets. It is based on relativistic electronic structure theory and calculation of magnetic torque. Thermally induced local moment magnetic fluctuations are described within the relativistic generalization of the disordered local moment theory from which the T dependence of the magnetization, m , is found. We apply the theory to a uniaxial magnetic material with tetragonal crystal symmetry, L10 -ordered FePd, and find its uniaxial K consistent with a magnetic easy axis perpendicular to the Fe/Pd layers for all m and proportional to m2 for a broad range of values of m . This is the same trend that we have previously found in L10 -ordered FePt and which agrees with experiment. We also study a magnetically soft cubic magnet, the Fe50Pt50 solid solution, and find that its small magnetic anisotropy constant K1 rapidly diminishes from 8μeV to zero. K1 evolves from being proportional to m7 at low T to m4 near the Curie temperature. The accounts of both the tetragonal and cubic itinerant electron magnets differ from those extracted from single ion anisotropy models and instead receive clear interpretations in terms of two ion anisotropic exchange.
Ab initio study of boron nitride lines on graphene
Mata-Carrizal, Berenice; Sanginés-Mendoza, Raúl; Martinez, Edgar
2013-03-01
Graphene has unusual electronic properties which make it a promising material for electronic devices. Neverthless, the absence of a band gap sets limitations on its practical applications. Thus, it is crucial to find methods to create and tune the band gap of systems based on graphene. In this way, we explore the modulation of the electronic properties of graphene through doping with boron nitride lines. In particular, we studied the electronic structure of graphene sheets doped with boron nitride lines armchair and zigzag type. The calculations were performed using the pseudopotential LCAO method with a Generalized Gradient Approximation (GGA) for the exchange-correlation energy functional. We found that both doping lines type induce a bandgap and that the energy gap increases as the length of doping lines increases. Accordingly to our DFT calculations, we found that the energy gap on graphene doped with armchair and zigzag lines is due to a two different mechanisms to drain charge from pi- to sigma- orbitals. Thus, we found that doping graphene with boron nitride lines is a useful way to induce and modulate the bandgap on graphene. This research was supported by Consejo Nacional de Ciencia y Tecnología (Conacyt) under Grant No. 133022.
Proper construction of ab initio global potential surfaces with accurate long-range interactions
International Nuclear Information System (INIS)
Ho, Tak-San; Rabitz, Herschel
2000-01-01
An efficient procedure based on the reproducing kernel Hilbert space interpolation method is presented for constructing intermolecular potential energy surfaces (PES) using not only calculated ab initio data but also a priori information on long-range interactions. Explicitly, use of the reciprocal power reproducing kernel on the semiinfinite interval [0,∞) yields a set of exact linear relations between dispersion (multipolar) coefficients and PES data points at finite internuclear separations. Consequently, given a combined set of ab initio data and the values of dispersion (multipolar) coefficients, the potential interpolation problem subject to long-range interaction constraints can be solved to render globally smooth, asymptotically accurate ab initio potential energy surfaces. Very good results have been obtained for the one-dimensional He-He potential curve and the two-dimensional Ne-CO PES. The construction of the Ne-CO PES was facilitated by invoking a new reproducing kernel for the angular coordinate based on the optimally stable and shape-preserving Bernstein basis functions. (c) 2000 American Institute of Physics
Legrain, Fleur; Carrete, Jesús; van Roekeghem, Ambroise; Madsen, Georg K H; Mingo, Natalio
2018-01-18
Machine learning (ML) is increasingly becoming a helpful tool in the search for novel functional compounds. Here we use classification via random forests to predict the stability of half-Heusler (HH) compounds, using only experimentally reported compounds as a training set. Cross-validation yields an excellent agreement between the fraction of compounds classified as stable and the actual fraction of truly stable compounds in the ICSD. The ML model is then employed to screen 71 178 different 1:1:1 compositions, yielding 481 likely stable candidates. The predicted stability of HH compounds from three previous high-throughput ab initio studies is critically analyzed from the perspective of the alternative ML approach. The incomplete consistency among the three separate ab initio studies and between them and the ML predictions suggests that additional factors beyond those considered by ab initio phase stability calculations might be determinant to the stability of the compounds. Such factors can include configurational entropies and quasiharmonic contributions.
Resolution of ab initio shapes determined from small-angle scattering
Directory of Open Access Journals (Sweden)
Anne T. Tuukkanen
2016-11-01
Full Text Available Spatial resolution is an important characteristic of structural models, and the authors of structures determined by X-ray crystallography or electron cryo-microscopy always provide the resolution upon publication and deposition. Small-angle scattering of X-rays or neutrons (SAS has recently become a mainstream structural method providing the overall three-dimensional structures of proteins, nucleic acids and complexes in solution. However, no quantitative resolution measure is available for SAS-derived models, which significantly hampers their validation and further use. Here, a method is derived for resolution assessment for ab initio shape reconstruction from scattering data. The inherent variability of the ab initio shapes is utilized and it is demonstrated how their average Fourier shell correlation function is related to the model resolution. The method is validated against simulated data for proteins with known high-resolution structures and its efficiency is demonstrated in applications to experimental data. It is proposed that henceforth the resolution be reported in publications and depositions of ab initio SAS models.
A molecular mechanics valence force field for sulfonamides derived by ab initio methods
Energy Technology Data Exchange (ETDEWEB)
Nicholas, J.B.; Burke, B.J.; Hopfinger, A.J. (Univ. of Illinois, Chicago (United States)); Vance, R.; Martin, E. (DowElanco, Walnut Creek, CA (United States))
1991-11-28
Molecular mechanics valence force field parameters for the sulfonamide group, SO[sub 2]NH, have been derived from ab initio calculations at the RHF/6-31G* level of theory. The force field parameters were designed to be used in conjunction with existing parameters from the MM2/MMP2 force field. The new parameters are demonstrated to accurately reproduce the ab initio optimized geometries of four molecules that contain the sulfonamide group. The strategy used in force field parametrization is discussed. The conformational flexibility of the sulfonamide group has been investigated. Calculations at the RHF/6-31G* level reveal the existence of two stable conformers and that interconversion is achieved by nitrogen inversion rather than rotation about the S-N bond. The energetic effects of expanding the basis set to 6-31G** and of including MP2 and MP3 corrections for electron correlation are discussed. The geometries and Mulliken charges for the ab initio optimized structures are also reported.
Electronic structure and superconductivity of MgB2
Indian Academy of Sciences (India)
Unknown
Abstract. Results of ab initio electronic structure calculations on the compound, MgB2, using the FPLAPW method employing GGA for the exchange–correlation energy are presented. Total energy minimization enables us to estimate the equilibrium volume, c/a ratio and the bulk modulus, all of which are in excellent.
Electronic structure and superconductivity of MgB 2
Indian Academy of Sciences (India)
Results of ab initio electronic structure calculations on the compound, MgB2, using the FPLAPW method employing GGA for the exchange–correlation energy are presented. Total energy minimization enables us to estimate the equilibrium volume, / ratio and the bulk modulus, all of which are in excellent agreement with ...
Electronic structure and superconductivity of MgB2
Indian Academy of Sciences (India)
Results of ab initio electronic structure calculations on the compound, MgB2, using the FPLAPW method employing GGA for the exchange–correlation energy are presented. Total energy minimization enables us to estimate the equilibrium volume, / ratio and the bulk modulus, all of which are in excellent agreement with ...
Iron -chromium alloys and free surfaces: from ab initio calculations to thermodynamic modeling
International Nuclear Information System (INIS)
Levesque, M.
2010-11-01
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
Mendive-Tapia, Eduardo; Staunton, Julie B.
2017-05-01
We describe a disordered local moment theory for long-period magnetic phases and investigate the temperature and magnetic field dependence of the magnetic states in the heavy rare earth elements (HREs), namely, paramagnetic, conical and helical antiferromagnetic (HAFM), fan, and ferromagnetic (FM) states. We obtain a generic HRE magnetic phase diagram which is consequent on the response of the common HRE valence electronic structure to f -electron magnetic moment ordering. The theory directly links the first-order HAFM-FM transition to the loss of Fermi surface nesting, induced by this magnetic ordering, as well as provides a template for analyzing the other phases and exposing where f -electron correlation effects are particularly intricate. Gadolinium, for a range of hexagonal, close-packed lattice constants c and a , is the prototype, described ab initio, and applications to other HREs are made straightforwardly by scaling the effective pair and quartic local moment interactions that emerge naturally from the theory with de Gennes factors and choosing appropriate lanthanide-contracted c and a values.
Ab initio study of the EFG tensor at Cd impurities in Sc{sub 2}O{sub 3} semiconductor
Energy Technology Data Exchange (ETDEWEB)
Munoz, E.L.; Richard, D. [Departamento de Fisica and IFLP (CONICET-UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CC 67, 1900 La Plata (Argentina); Errico, L.A. [Departamento de Fisica and IFLP (CONICET-UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CC 67, 1900 La Plata (Argentina); Universidad Nacional del Noroeste Bonaerense (UNNOBA), Monteagudo 2772, Pergamino, CP 2700 Buenos Aires (Argentina); Renteria, M., E-mail: renteria@fisica.unlp.edu.a [Departamento de Fisica and IFLP (CONICET-UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CC 67, 1900 La Plata (Argentina)
2009-10-01
We present an ab initio study of diluted Cd impurities localized at both cation sites of the semiconductor Sc{sub 2}O{sub 3}. The electric-field-gradient (EFG) tensor at Cd impurities located at both cationic sites of the host structure was determined from the calculation of the electronic structure of the doped system. Calculations were performed with the full-potential augmented-plane wave plus local orbitals (APW+lo) method within the framework of the density functional theory. We studied the atomic structural relaxations and the perturbation of the electronic charge density induced by the impurities in the host system in a fully self-consistent way. We showed that the Cd impurity introduces an increase of 8% in the nearest oxygen neighbors bond-lengths, changing the EFG sign for probes located at the asymmetric cation site. The APW+lo predictions for the charged state of the Cd impurity were compared with EFG results existent in the literature, coming from time-differential gamma-gamma perturbed-angular-correlations experiments performed on {sup 111}Cd-implanted Sc{sub 2}O{sub 3} powder samples. From the excellent agreement between theory and experiment, we can strongly suggest that the Cd acceptor impurities are ionized at room temperature. Finally, we showed that simple calculations like those performed within the point-charge model with antishielding factors do not correctly describe the problem of a Cd impurity in Sc{sub 2}O{sub 3}.
Bibby, Jaclyn; Keegan, Ronan M.; Mayans, Olga; Winn, Martyn D.; Rigden, Daniel J.
2012-01-01
Protein ab initio models predicted from sequence data alone can enable the elucidation of crystal structures by molecular replacement. However, the calculation of such ab initio models is typically computationally expensive. Here, a computational pipeline based on the clustering and truncation of cheaply obtained ab initio models for the preparation of structure ensembles is described. Clustering is used to select models and to quantitatively predict their local accuracy, allowing rational tr...
Efficient approach to compute melting properties fully from ab initio with application to Cu
Zhu, Li-Fang; Grabowski, Blazej; Neugebauer, Jörg
2017-12-01
Applying thermodynamic integration within an ab initio-based free-energy approach is a state-of-the-art method to calculate melting points of materials. However, the high computational cost and the reliance on a good reference system for calculating the liquid free energy have so far hindered a general application. To overcome these challenges, we propose the two-optimized references thermodynamic integration using Langevin dynamics (TOR-TILD) method in this work by extending the two-stage upsampled thermodynamic integration using Langevin dynamics (TU-TILD) method, which has been originally developed to obtain anharmonic free energies of solids, to the calculation of liquid free energies. The core idea of TOR-TILD is to fit two empirical potentials to the energies from density functional theory based molecular dynamics runs for the solid and the liquid phase and to use these potentials as reference systems for thermodynamic integration. Because the empirical potentials closely reproduce the ab initio system in the relevant part of the phase space the convergence of the thermodynamic integration is very rapid. Therefore, the proposed approach improves significantly the computational efficiency while preserving the required accuracy. As a test case, we apply TOR-TILD to fcc Cu computing not only the melting point but various other melting properties, such as the entropy and enthalpy of fusion and the volume change upon melting. The generalized gradient approximation (GGA) with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional and the local-density approximation (LDA) are used. Using both functionals gives a reliable ab initio confidence interval for the melting point, the enthalpy of fusion, and entropy of fusion.
Messina, Luca; Castin, Nicolas; Domain, Christophe; Olsson, Pär
2017-02-01
The quality of kinetic Monte Carlo (KMC) simulations of microstructure evolution in alloys relies on the parametrization of point-defect migration rates, which are complex functions of the local chemical composition and can be calculated accurately with ab initio methods. However, constructing reliable models that ensure the best possible transfer of physical information from ab initio to KMC is a challenging task. This work presents an innovative approach, where the transition rates are predicted by artificial neural networks trained on a database of 2000 migration barriers, obtained with density functional theory (DFT) in place of interatomic potentials. The method is tested on copper precipitation in thermally aged iron alloys, by means of a hybrid atomistic-object KMC model. For the object part of the model, the stability and mobility properties of copper-vacancy clusters are analyzed by means of independent atomistic KMC simulations, driven by the same neural networks. The cluster diffusion coefficients and mean free paths are found to increase with size, confirming the dominant role of coarsening of medium- and large-sized clusters in the precipitation kinetics. The evolution under thermal aging is in better agreement with experiments with respect to a previous interatomic-potential model, especially concerning the experiment time scales. However, the model underestimates the solubility of copper in iron due to the excessively high solution energy predicted by the chosen DFT method. Nevertheless, this work proves the capability of neural networks to transfer complex ab initio physical properties to higher-scale models, and facilitates the extension to systems with increasing chemical complexity, setting the ground for reliable microstructure evolution simulations in a wide range of alloys and applications.
Theoretical ab initio study of Xenon pentafluoride anion. Mechanism of Xenon pseudorotation
Fleurat-Lessard, Paul; Durupthy, Olivier; Volatron, François
2002-09-01
Ab initio calculations have been performed on XeF 5- anion at the MP2 and CCSD(T) levels with a large basis set. Four extrema have been optimized and characterized by frequencies analysis. We find the absolute minimum to be of D 5h symmetry in accordance with the experimental data; the theoretical vibrational spectrum of this minimum is in good agreement with the experimental one. Three other extrema are found to be higher in energy depending on the angular separation of the Xenon lone pairs as predicted by the VSEPR theory. Finally the characterized transition state has been found to belong to the Xenon pseudorotation pathway.
Orbital free ab initio study of static and dynamic properties of some liquid transition metals
Directory of Open Access Journals (Sweden)
Bhuiyan G. M.
2017-01-01
Full Text Available Several static and dynamic properties of liquid transition metals Cr, Mn and Co are studied for the first time using the orbital free ab-initio molecular dynamics simulation (OF-AIMD. This method is based on the density functional theory (DFT which accounts for the electronic energy of the system whereas the interionic forces are derived from the electronic energy via the Hellman-Feynman theorem. The external energy functional is treated with a local pseudopotential. Results are reported for static structure factors, isothermal compressibility, diffusion coeffcients, sound velocity and viscosity and comparison is performed with the available experimental data and other theoretical calculations.
Polarization and charge-transfer effects in aqueous solution via ab initio QM/MM simulations.
Mo, Yirong; Gao, Jiali
2006-02-23
Combined ab initio quantum mechanical and molecular mechanical (QM/MM) simulations coupled with the block-localized wave function energy decomposition (BLW-ED) method have been conducted to study the solvation of two prototypical ionic systems, acetate and methylammonium ions in aqueous solution. Calculations reveal that the electronic polarization between the targeted solutes and water is the primary many-body effect, whereas the charge-transfer term only makes a small fraction of the total solute-solvent interaction energy. In particular, the polarization effect is dominated by the solvent (water) polarization.
Ab initio study of small Au n Pd- (n=1-5) cluster anions
International Nuclear Information System (INIS)
Guo Jianjun; Shi Jian; Yang Jixian; Die Dong
2007-01-01
Ab initio method based on density-functional theory has been used to investigate the Au n Pd - (n=1-5) cluster anions. The possible stable geometrical configurations with their electronic states are determined, and the energy gaps between the HOMO and LUMO of the ground states are investigated. Our results show that the one excess electron is strong enough to modify the known growth pattern of the neutral Au n Pd clusters, and indicate that the larger is the Au n Pd cluster, the smaller are the distortions by the one excess electron
DEFF Research Database (Denmark)
Fürst, Joachim Alexander; Hashemi, J.; Markussen, Troels
2009-01-01
techniques and tight-binding calculations to illustrate these materials' transmission properties and give physical arguments to interpret the numerical results. Specifically, above the Fermi energy we find a strong reduction in electron transmission due to localized states in certain regions of the structure......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...
Jupiter models with improved ab initio hydrogen EOS (H-REOS.2)
Nettelmann, Nadine; Becker, Andreas; Holst, Bastian; Redmer, Ronald
2011-01-01
The amount and distribution of heavy elements in Jupiter gives indications on the process of its formation and evolution. Core mass and metallicity predictions however depend on the equations of state used, and on model assumptions. We present an improved ab initio hydrogen equation of state, H-REOS.2 and compute the internal structure and thermal evolution of Jupiter within the standard three-layer approach. The advance over our previous Jupiter models with H-REOS.1 by Nettelmann et al.(2008...
Heat capacities of xenotime-type ceramics: An accurate ab initio prediction
Ji, Yaqi; Beridze, George; Bosbach, Dirk; Kowalski, Piotr M.
2017-10-01
Because of ability to incorporate actinides into their structure, the lanthanide phosphate ceramics (LnPO4) are considered as potential matrices for the disposal of nuclear waste. Here we present highly reliable ab initio prediction of the variation of heat capacities and the standard entropies of these compounds in zircon structure along lanthanide series (Ln = Dy, …,Lu) and validate them against the existing experimental data. These data are helpful for assessment of thermodynamic parameters of these materials in the context of using them as matrices for immobilization of radionuclides for the purpose of nuclear waste management.
Ab initio phonon dispersions of face centered cubic Pb: effects of spin-orbit coupling
International Nuclear Information System (INIS)
Dal Corso, Andrea
2008-01-01
I present the ab initio phonon dispersions of face centered cubic Pb calculated within the framework of density functional perturbation theory, with plane waves and a fully relativistic ultrasoft pseudopotential which includes spin-orbit coupling effects. I find that, within the local density approximation, the theory gives phonon frequencies close to the experimental inelastic neutron scattering data. Many of the anomalies present in these dispersions are well reproduced by the fully relativistic pseudopotential theory and can be shown to appear only for small values of the smearing parameter that controls the sharpness of the Fermi surface.
Ramsdellite-structured LiTiO 2: A new phase predicted from ab initio calculations
Koudriachova, M. V.
2008-06-01
A new phase of highly lithiated titania with potential application as an anode in Li-rechargeable batteries is predicted on the basis of ab initio calculations. This phase has a composition LiTiO2 and may be accessed through electrochemical lithiation of ramsdellite-structured TiO2 at the lowest potential reported for titanium dioxide based materials. The potential remains constant over a wide range of Li-concentrations. The new phase is metastable with respect to a tetragonally distorted rock salt structure, which hitherto has been the only known polymorph of LiTiO2.
Vibrational energy levels for CH4 from an ab initio potential
Schwenke, D. W.; Partridge, H.
2001-01-01
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.
Ab initio R-matrix calculations of e+-molecule scattering
Danby, Grahame; Tennyson, Jonathan
1990-01-01
The adaptation of the molecular R-matrix method, originally developed for electron-molecule collision studies, to positron scattering is discussed. Ab initio R-matrix calculations are presented for collisions of low energy positrons with a number of diatomic systems including H2, HF and N2. Differential elastic cross sections for positron-H2 show a minimum at about 45 deg for collision energies between 0.3 and 0.5 Ryd. The calculations predict a bound state of positronHF. Calculations on inelastic processes in N2 and O2 are also discussed.
Phonon spectrum of lead oxychloride Pb3O2Cl2: Ab initio calculation and experiment
Zakir'yanov, D. O.; Chernyshev, V. A.; Zakir'yanova, I. D.
2016-02-01
IR and Raman spectra of Pb3O2Cl2 in the range of 50-600 cm-1 have been detected for the first time. Ab initio calculations of the crystal structure and the phonon spectrum of Pb3O2Cl2 in the framework of LCAO approach have been performed by the Hartree-Fock method and in the framework of the density functional theory with the use of hybrid functionals. The results of calculations have made it possible to interpret the experimental vibration spectra and reveal silent modes, which do not manifest themselves in these spectra but influence the optical properties of the crystal.
Testing the density matrix expansion against ab initio calculations of trapped neutron drops
Energy Technology Data Exchange (ETDEWEB)
Bogner, S. K. [Michigan State University, East Lansing; Hergert, H. [Michigan State University, East Lansing; Furnstahl, R. J. [Ohio State University; Kortelainen, Erno M [ORNL; Stoitsov, M. V. [University of Tennessee, Knoxville (UTK) & Oak Ridge National Laboratory (ORNL); Maris, Pieter [Iowa State University; Vary, J. P. [Iowa State University
2011-01-01
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.
Pagliai, Marco; Muniz-Miranda, Francesco; Cardini, Gianni; Righini, Roberto; Schettino, Vincenzo
2011-05-01
In order to extract spectroscopic information from trajectories obtained by classical or ab initio molecular dynamics simulations, usually Fourier transforms are employed. In recent years wavelet transforms have been shown to be a valid alternative tool to analyze time-series, due to their capability of localizing a signal both in time and frequency. In this article wavelet transforms are applied for the analysis of Car-Parrinello molecular dynamics simulations to the purpose of time-correlating structural and spectroscopic properties of methyl acetate dissolved in water and methanol. The results demonstrate the possibility of obtaining information that may be of valuable help in the interpretation of time-resolved spectroscopic data.
The role of Metals in Amyloid Aggregation: A Test Case for ab initio Simulations
International Nuclear Information System (INIS)
Minicozzi, V.; Rossi, G. C.; Stellato, F.; Morante, S.
2007-01-01
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 β-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
Ab initio Hartree-Fock study on surface desorption process in tritium release
International Nuclear Information System (INIS)
Taniguchi, M.; Tanaka, S.
1998-01-01
Dissociative adsorption of hydrogen on Li 2 O (110) surface has been investigated with ab initio Hartree-Fock quantum chemical calculation technique. Heat of adsorption and surface potential energy for H 2 dissociative adsorption were evaluated by calculating the total energy of the system. The calculated results on adsorption heat indicated that H 2 adsorption is endothermic. However, when an oxygen vacancy exists adjacent to the adsorption site, the heat of adsorption became less endothermic and the activation energy required to dissociate the H-H bonding was smaller than that for the terrace site. This is considered to be caused by the excess charge localized near the defect. (orig.)
Spin-orbit interaction effects in zincblende semiconductors: Ab initio pseudopotential calculations
International Nuclear Information System (INIS)
Li, Ming-Fu; Surh, M.P.; Louie, S.G.
1988-06-01
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 Γ 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
Simple synthesis, structure and ab initio study of 1,4-benzodiazepine-2,5-diones
Jadidi, Khosrow; Aryan, Reza; Mehrdad, Morteza; Lügger, Thomas; Ekkehardt Hahn, F.; Ng, Seik Weng
2004-04-01
A simple procedure for the synthesis of pyrido[2,1-c][1,4] benzodiazepine-6,12-dione ( 1) and 1,4-benzodiazepine-2,5-diones ( 2a- 2d), using microwave irradiation and/or conventional heating is reported. The configuration of 1 was determined by single-crystal X-ray diffraction. A detailed ab initio B3LYP/6-31G* calculation of structural parameters and substituent effects on ring inversion barriers (Δ G#) and also free energy differences (Δ G0) for benzodiazepines are reported.
First Benchmark of Relativistic Photoionization Theories against 3D ab initio Simulation.
Hafizi, B; Gordon, D F; Palastro, J P
2017-03-31
Photoelectron spectra and ionization rates encompassing relativistic intensities and hydrogenlike ions with relativistic binding energies are obtained using a quasiclassical S-matrix approach. These results, along with those based on the imaginary time method, are compared with three-dimensional, ½-period ab initio simulations for a wide range of ionization potentials and electric field amplitudes. Significant differences between the three results are demonstrated. Time-dependent simulations indicate that the peak ionization current can occur before the peak of the electric field.
Pietrucci, Fabio; Andreoni, Wanda
2011-08-01
Social permutation invariant coordinates are introduced describing the bond network around a given atom. They originate from the largest eigenvalue and the corresponding eigenvector of the contact matrix, are invariant under permutation of identical atoms, and bear a clear signature of an order-disorder transition. Once combined with ab initio metadynamics, these coordinates are shown to be a powerful tool for the discovery of low-energy isomers of molecules and nanoclusters as well as for a blind exploration of isomerization, association, and dissociation reactions.
Czech Academy of Sciences Publication Activity Database
Slavíček, Petr; Winter, B.; Faubel, M.; Bradforth, S. E.; Jungwirth, Pavel
2009-01-01
Roč. 131, č. 18 (2009), s. 6460-6467 ISSN 0002-7863 R&D Projects: GA MŠk LC512; GA ČR GA203/08/0114 Grant - others:GA ČR(CZ) GP203/07/P449 Institutional research plan: CEZ:AV0Z40550506; CEZ:AV0Z40400503 Keywords : DNA bases * photoelectron spectroscopy * ab initio calculations Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 8.580, year: 2009
Benefits of Parallel I/O in Ab Initio Nuclear Physics Calculations
International Nuclear Information System (INIS)
Laghave, Nikhil; Sosonkina, Masha; Maris, Pieter; Vary, James P.
2009-01-01
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.
Energy Technology Data Exchange (ETDEWEB)
Wang, Xue B.; Woo, Hin-koon; Wang, Lai S.; Minofar, Babak; Jungwirth, Pavel
2006-04-20
The electronic structure and electron affinity of the acetyloxyl radical (CH3COO) were investigated by low-temperature anion photoelectron spectroscopy and ab initio calculations. Photoelectron spectra of the acetate anion (CH3COO-) were obtained at two photon energies (355 and 266 nm) and under three different temperatures (300, 70, and 20 K) using a new low temperature ion-trap photoelectron spectroscopy apparatus. In contrast to a featureless spectrum at 300 K, a well-resolved vibrational progression corresponding to the OCO bending mode was observed at low temperatures in the 355 nm spectrum, yielding an accurate electron affinity for the acetyloxyl radical as 3.250 + 0.010 eV. This experimental result is supported by ab initio calculations, which also indicate three low-lying electronic states observed in the 266 nm spectrum. The calculations suggest a 19° decrease of the OCO angle upon detaching an electron from acetate, consistent with the vibrational progression observed experimentally.
Rezaee, Mohammadreza; Compton, Robert
2015-05-01
Collision induced dissociation (CID) and ab initio calculations were utilized to study a few derivatives of azobenzene molecule and their product ions. High level computational methods along with large basis set size yield values in close agreement with the experimental results. Möller-Plesset and coupled-cluster theory including perturbative triple excitations, CCSD(T), method were performed to obtain a high accuracy estimation of the bond dissociation energy value. The electron affinities have been studied experimentally using the photoelectron spectroscopy method as well as theoretically using ab inito calculations. For the trans-2,2',6,6' tetra-fluoro azobenzene the bond dissociation has been experimentally determined to be 1.88 eV and the vertical detachment energy is 1.78 eV.
International Nuclear Information System (INIS)
Errico, L.A.; Renteria, M.; Bibiloni, A.G.; Darriba, G.N.
2005-01-01
We report an ab initio study of the temperature dependence of the electric-field gradient (EFG) tensor at Cd impurities replacing cations in Lu 2 O 3 . Calculations were performed with the Full-Potential Linearized-Augmented Plane Wave method that allows us to treat the electronic structure and the processes induced by the impurity in the host-lattice without the use of external parameters. In this new insight, the EFG thermal dependence arises from the ionization of an impurity acceptor level introduced in the band-gap of Lu 2 O 3 by Cd impurities, in good agreement with a previously proposed two state model. (copyright 2005 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)
Energy Technology Data Exchange (ETDEWEB)
Errico, L.A.; Renteria, M.; Bibiloni, A.G.; Darriba, G.N. [Departamento de Fisica, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CC 67, 1900 La Plata (Argentina)
2005-08-01
We report an ab initio study of the temperature dependence of the electric-field gradient (EFG) tensor at Cd impurities replacing cations in Lu{sub 2}O{sub 3}. Calculations were performed with the Full-Potential Linearized-Augmented Plane Wave method that allows us to treat the electronic structure and the processes induced by the impurity in the host-lattice without the use of external parameters. In this new insight, the EFG thermal dependence arises from the ionization of an impurity acceptor level introduced in the band-gap of Lu{sub 2}O{sub 3} by Cd impurities, in good agreement with a previously proposed two state model. (copyright 2005 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)
Andrianov, A. Vl.; Savel'Eva, O. A.; Bauer, E.; Staunton, J. B.
2011-10-01
Ab initio electronic structure theory finds the type of magnetic order of the heavy rare earths to be correlated directly with the a and c lattice parameters of their hexagonal-close-packed crystal lattices. We refine our experimental data and obtain magnetic phase diagrams showing magnetic state and transition temperatures versus a and c for Tb and for the alloy Ho0.4Gd0.6. For both systems we mark out the boundaries in a and c space between incommensurate (helical) antiferromagnetic order and ferromagnetic states and find that these agree very well with the theoretical prediction as well as with each other. These data support the proposition of a universal “crystallomagnetic” phase diagram for the heavy rare earths.
Futera, Zdenek; English, Niall J.
2017-07-01
The response of water to externally applied electric fields is of central relevance in the modern world, where many extraneous electric fields are ubiquitous. Historically, the application of external fields in non-equilibrium molecular dynamics has been restricted, by and large, to relatively inexpensive, more or less sophisticated, empirical models. Here, we report long-time non-equilibrium ab initio molecular dynamics in both static and oscillating (time-dependent) external electric fields, therefore opening up a new vista in rigorous studies of electric-field effects on dynamical systems with the full arsenal of electronic-structure methods. In so doing, we apply this to liquid water with state-of-the-art non-local treatment of dispersion, and we compute a range of field effects on structural and dynamical properties, such as diffusivities and hydrogen-bond kinetics.
DEFF Research Database (Denmark)
Shim, Irene; Kingcade, Joseph E. , Jr.; Gingerich, Karl A.
1986-01-01
In the present work we present all-electron ab initio Hartree–Fock (HF) and configuration interaction (CI) calculations of six electronic states of the PdGe molecule. The molecule is predicted to have a 3Pi ground state and two low-lying excited states 3Sigma− and 1Sigma+. The electronic structure...... with a small charge transfer from the Pd to the Ge atom. The dissociation energy of the PdGe molecule has been determined from the mass spectrometric equilibrium data combined with the theoretical results as D00 =252.0±10.5 kJ mol−1. The Journal of Chemical Physics is copyrighted by The American Institute...
International Nuclear Information System (INIS)
Yamamoto, S.; Yamaguchi, K.; Nasu, K.
1990-01-01
Ab initio molecular-orbital calculations for CuO 6 clusters have been performed to elucidate the electronic structures of undoped and doped copper oxides, which are of current interest in relation to high-T c superconductivity. The electron correlation effects for these species are thoroughly investigated by the full-valence configuration-interaction method and the complete-active-space self-consistent-field method. The electron correlation effect is relatively simple for the A g state (σ hole), whereas pair excitations and spin-flip excitations give sizable contributions to the configuration-interaction wave function for the B state (in-plane π hole). Implications of these results are discussed in relation to the mechanisms of the high-T c superconductivity
Ab initio calculation of vibrational dipole moment matrix elements. Pt.1
International Nuclear Information System (INIS)
Cantarella, E.; Culot, F.; Lievin, J.
1992-01-01
This paper is the first part of a series devoted to the ab initio calculation of some vibrational properties helpful in the interpretation of high resolution spectroscopy, atmospherical and astrophysical data. An ab initio method of calculation of the vibrational transition energies and dipole moment matrix elements is described and analyzed. The main features of this method are the resolution of both electronic and vibrational problems by analytical variational techniques and the representation of the potential energy and dipole moment hypersurfaces as Taylor's series expansions in normal coordinates up to the fourth order. The dipole moment matrix elements are then evaluated by simple analytical formulae. In this first paper, some of the approximations inherent to the methodology are systematically analyzed on the basis of results obtained for diatomic molecules (BeH, HF, NH and NO) with a comparison to experimental and other theoretical results found in the literature. The dependence on the results of the effects of electrical and mechanical anharmonicities, electron correlation and basis set dependencies are investigated. The applicability of the method to small polyatomic systems is discussed in the second paper of this series, on the basis of test calculations on the water molecule
Experimental and ab initio investigations on textured Li–Mn–O spinel thin film cathodes
Energy Technology Data Exchange (ETDEWEB)
Fischer, J., E-mail: Julian.Fischer@kit.edu [Karlsruhe Institute of Technology (KIT), Institute for Applied Materials (IAM), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen (Germany); Music, D. [RWTH Aachen University, Materials Chemistry, Kopernikusstrasse 10, 52074 Aachen (Germany); Bergfeldt, T.; Ziebert, C.; Ulrich, S.; Seifert, H.J. [Karlsruhe Institute of Technology (KIT), Institute for Applied Materials (IAM), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen (Germany)
2014-12-01
This paper describes the tailored preparation of nearly identical lithium–manganese–oxide thin film cathodes with different global grain orientations. The thin films were synthesized by rf magnetron sputtering from a LiMn{sub 2}O{sub 4}-target in a pure argon plasma. Under appropriate processing conditions, thin films with a cubic spinel structure and a nearly similar density and surface topography but different grain orientation, i.e. (111)- and (440)-textured films, were achieved. The chemical composition was determined by inductively coupled plasma optical emission spectroscopy and carrier gas hot extraction. The constitution- and microstructure were evaluated by X-ray diffraction and Raman spectroscopy. The surface morphology and roughness were investigated by scanning electron and atomic force microscopy. The differently textured films represent an ideal model system for studying potential effects of grain orientation on the lithium ion diffusion and electrochemical behavior in LiMn{sub 2}O{sub 4}-based thin films. They are nearly identical in their chemical composition, atomic bonding behavior, surface-roughness, morphology and thickness. Our initial ab initio molecular dynamics data indicate that Li ion transport is faster in (111)-textured structure than in (440)-textured one. - Highlights: • Thin film model system of differently textured cubic Li–Mn–O spinels. • Investigation of the Li–Mn–O thin film mass density by X-ray reflectivity. • Ab initio molecular dynamics simulation on Li ion diffusion in LiMn{sub 2}O{sub 4}.
Ab initio determination of the nuclear quadrupole moments of 114In, 115In, and 117In
International Nuclear Information System (INIS)
Errico, Leonardo A.; Renteria, Mario
2006-01-01
We present here ab initio determinations of the nuclear-quadrupole moment Q of hyperfine-probe-nuclear states of three different In isotopes: the 5 + 192 keV excited state of 114 In (probe for nuclear quadrupole alignment spectroscopy), the 9/2 + ground state of 115 In (nuclear magnetic and nuclear quadrupole resonance probe), and the 3/2 + 659 keV excited state of 117 In (perturbed angular correlations probe). These nuclear-quadrupole moments were determined by comparing experimental nuclear-quadrupole frequencies to the electric field gradient tensor calculated with high accuracy at In sites in metallic indium within the density functional theory. These ab initio calculations were performed with the full-potential linearized augmented plane wave method. The results obtained for the quadrupole moments of 114 In [Q( 114 In)=-0.14(1) b] are in clear discrepancy with those reported in the literature [Q( 114 In)=+0.16(6) b and +0.739(12) b]. For 115 In and 117 In our results are in excellent agreement with the literature and in the last case Q( 117 In) is determined with more precision. In the case of Q( 117 In), its sign cannot be determined because standard γ-γ perturbed angular correlations experiments are not sensitive to the sign of the nuclear-quadrupole frequency
Yusuf, Muhammad; Roza, Destria; Nasution, Ahmad Kamil
2017-11-01
The computational calculation was performed on the acetalization of 2-hydroxybenzaldehyde by using ab initio method. Ab initio method is derived directly from theoretical principles with no inclusion of experimental data and this is an approximate quantum mechanical calculation. The aim of this research was to studies the acetalization of 2-hydroxybenzaldehyde mechanism using halogen acid catalysts. Computational calculation which was applied on the acetalization of 2-hydroxybenzaldehyde using halogen acid catalysts provided possible reaction steps. The first step was formation of a labile hemiacetal because it is essentially tetrahedral intermediates containing a leaving group. The second step was formation of a stable acetal. The results of computational calculation of acetalization of 2-hydroxybenzaldehyde provided possible energy change in the each step of the reaction process. A labile hemiacetal showed higher energy (481.04 kJ/mol) than 2-hydroxybenzaldehyde dimethyl acetal (65.32 kJ/mol) and 2-hydroxybenzaldehyde (0 kJ/mol) due to its instability. In general, acetalization of 2-hydroxybenzaldehyde reaction is a reversible reaction. The effect of Lewis acidity on halogen acid catalysts was also studied in this research. Based on the Mulliken charge on the H atom, it is found that HF has the highest Lewis acidity compared to other halogen acids with order HF> HCl> HBr> HI. As a result, HF was the efficient catalysts for acetalization of 2-Hydroxybenzaldehyde.
Ab initio molecular dynamics of the reaction of quercetin with superoxide radical
Energy Technology Data Exchange (ETDEWEB)
Lespade, Laure, E-mail: l.lespade@ism.u-bordeaux1.fr
2016-08-22
Highlights: • Ab initio molecular dynamics is performed to describe the reaction of quercetin and superoxide. • The reaction occurs near the sites 4′ and 7 when the system contains sufficiently water molecules. • The difference of reactivity of superoxide compared to commonly used radicals as DPPH{sup ·} or ABTS{sup ·+} is explained. - Abstract: Superoxide plays an important role in biology but in unregulated concentrations it is implicated in a lot of diseases such as cancer or atherosclerosis. Antioxidants like flavonoids are abundant in plant and are good scavengers of superoxide radical. The modeling of superoxide scavenging by flavonoids from the diet still remains a challenge. In this study, ab initio molecular dynamics of the reaction of the flavonoid quercetin toward superoxide radical has been carried out using Car–Parrinello density functional theory. The study has proven different reactant solvation by modifying the number of water molecules surrounding superoxide. The reaction consists in the gift of a hydrogen atom of one of the hydroxyl groups of quercetin to the radical. When it occurs, it is relatively fast, lower than 100 fs. Calculations show that it depends largely on the environment of the hydroxyl group giving its hydrogen atom, the geometry of the first water layer and the presence of a certain number of water molecules in the second layer, indicating a great influence of the solvent on the reactivity.
Ab initio results for intermediate-mass, open-shell nuclei
Baker, Robert B.; Dytrych, Tomas; Launey, Kristina D.; Draayer, Jerry P.
2017-01-01
A theoretical understanding of nuclei in the intermediate-mass region is vital to astrophysical models, especially for nucleosynthesis. Here, we employ the ab initio symmetry-adapted no-core shell model (SA-NCSM) in an effort to push first-principle calculations across the sd-shell region. The ab initio SA-NCSM's advantages come from its ability to control the growth of model spaces by including only physically relevant subspaces, which allows us to explore ultra-large model spaces beyond the reach of other methods. We report on calculations for 19Ne and 20Ne up through 13 harmonic oscillator shells using realistic interactions and discuss the underlying structure as well as implications for various astrophysical reactions. This work was supported by the U.S. NSF (OCI-0904874 and ACI -1516338) and the U.S. DOE (DE-SC0005248), and also benefitted from the Blue Waters sustained-petascale computing project and high performance computing resources provided by LSU.
Field theoretic approach to dynamical orbital localization in ab initio molecular dynamics
International Nuclear Information System (INIS)
Thomas, Jordan W.; Iftimie, Radu; Tuckerman, Mark E.
2004-01-01
Techniques from gauge-field theory are employed to derive an alternative formulation of the Car-Parrinello ab initio molecular-dynamics method that allows maximally localized Wannier orbitals to be generated dynamically as the calculation proceeds. In particular, the Car-Parrinello Lagrangian is mapped onto an SU(n) non-Abelian gauge-field theory and the fictitious kinetic energy in the Car-Parrinello Lagrangian is modified to yield a fully gauge-invariant form. The Dirac gauge-fixing method is then employed to derive a set of equations of motion that automatically maintain orbital locality by restricting the orbitals to remain in the 'Wannier gauge'. An approximate algorithm for integrating the equations of motion that is stable and maintains orbital locality is then developed based on the exact equations of motion. It is shown in a realistic application (64 water molecules plus one hydrogen-chloride molecule in a periodic box) that orbital locality can be maintained with only a modest increase in CPU time. The ability to keep orbitals localized in an ab initio molecular-dynamics calculation is a crucial ingredient in the development of emerging linear scaling approaches
Ab Initio Potential Energy Surfaces and the Calculation of Accurate Vibrational Frequencies
Lee, Timothy J.; Dateo, Christopher E.; Martin, Jan M. L.; Taylor, Peter R.; Langhoff, Stephen R. (Technical Monitor)
1995-01-01
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.
Ab initio calculation of oxygen self-diffusion coefficient in uranium dioxide UO2
Dorado, Boris; Garcia, Philippe; Torrent, Marc
Uranium dioxide UO2 is the most widely used nuclear fuel worldwide and its atomic transport properties are relevant to practically all engineering aspects of the material. Although transport properties have already been studied in UO2 by means of first-principles calculations, the ab initio determination of self-diffusion coefficients has up to now remained unreachable because the relevant computational tools were neither available or adapted. The present work reports our results related to the ab initio calculation of the oxygen self-diffusion coefficient in UO2. We first determine the Gibbs free energies of formation of oxygen charged defects by calculating both the electronic and vibrational (hence entropic) contributions. Then, we use the transition state theory in order to compute the effective jump frequency of the defects, which in turn provides us with the value of the pre-exponential factor. The results are compared to self-diffusion data obtained experimentally with a careful monitoring of the relevant thermodynamic conditions (oxygen partial pressure, temperature, impurity content).
Galler, Anna; Gunacker, Patrik; Tomczak, Jan; Thunström, Patrik; Held, Karsten
Recently, approaches such as the dynamical vertex approximation (D ΓA) or the dual-fermion method have been developed. These diagrammatic approaches are going beyond dynamical mean field theory (DMFT) by including nonlocal electronic correlations on all length scales as well as the local DMFT correlations. Here we present our efforts to extend the D ΓA methodology to ab-initio materials calculations (ab-initio D ΓA). Our approach is a unifying framework which includes both GW and DMFT-type of diagrams, but also important nonlocal correlations beyond, e.g. nonlocal spin fluctuations. In our multi-band implementation we are using a worm sampling technique within continuous-time quantum Monte Carlo in the hybridization expansion to obtain the DMFT vertex, from which we construct the reducible vertex function using the two particle-hole ladders. As a first application we show results for transition metal oxides. Support by the ERC project AbinitioDGA (306447) is acknowledged.
Chitnis, Abhishek; Chakraborty, B.; Tripathi, B. M.; Tyagi, A. K.; Garg, Nandini
2018-02-01
Lithium metatitanate (LTO) and lithium metazirconate (LZO) are lithium rich ceramics which can be used as tritium breeder materials for thermonuclear reactors. In-situ x-ray diffraction and ab-initio studies at high pressure show that LTO has a higher bulk modulus than that of LZO. In fact these studies indicate that they are the least compressible of the known lithium rich ceramics like Li2O or Li4SiO4, which are potential candidates for blanket materials. These studies show that the TiO6 octahedra are responsible for the higher bulk modulus of LTO when compared to that of LZO. It has also been shown that the compressibility and distortion of the softer LiO6 octahedra can be controlled by altering the stacking sequence of the more rigid covalently bonded octahedra. This knowledge can be used by chemists to design new lithium based ceramics with higher bulk modulus. It was observed that LTO was stable upto 34 GPa. Ab initio DFT calculations helped to understand the anisotropy in compressibility of both LZO and LTO. This study also shows, that even though the empirical potentials developed by Vijaykumar et al. successfully determine the ambient pressure structure of lithium metatitanate, they cannot be used at non ambient conditions like high pressure [1].
Ab initio molecular dynamics of the reaction of quercetin with superoxide radical
International Nuclear Information System (INIS)
Lespade, Laure
2016-01-01
Highlights: • Ab initio molecular dynamics is performed to describe the reaction of quercetin and superoxide. • The reaction occurs near the sites 4′ and 7 when the system contains sufficiently water molecules. • The difference of reactivity of superoxide compared to commonly used radicals as DPPH · or ABTS ·+ is explained. - Abstract: Superoxide plays an important role in biology but in unregulated concentrations it is implicated in a lot of diseases such as cancer or atherosclerosis. Antioxidants like flavonoids are abundant in plant and are good scavengers of superoxide radical. The modeling of superoxide scavenging by flavonoids from the diet still remains a challenge. In this study, ab initio molecular dynamics of the reaction of the flavonoid quercetin toward superoxide radical has been carried out using Car–Parrinello density functional theory. The study has proven different reactant solvation by modifying the number of water molecules surrounding superoxide. The reaction consists in the gift of a hydrogen atom of one of the hydroxyl groups of quercetin to the radical. When it occurs, it is relatively fast, lower than 100 fs. Calculations show that it depends largely on the environment of the hydroxyl group giving its hydrogen atom, the geometry of the first water layer and the presence of a certain number of water molecules in the second layer, indicating a great influence of the solvent on the reactivity.
Ab initio phonon point defect scattering and thermal transport in graphene
Polanco, Carlos A.; Lindsay, Lucas
2018-01-01
We study the scattering of phonons from point defects and their effect on lattice thermal conductivity κ using a parameter-free ab initio Green's function methodology. Specifically, we focus on the scattering of phonons by boron (B), nitrogen (N), and phosphorus substitutions as well as single- and double-carbon vacancies in graphene. We show that changes of the atomic structure and harmonic interatomic force constants locally near defects govern the strength and frequency trends of the scattering of out-of-plane acoustic (ZA) phonons, the dominant heat carriers in graphene. ZA scattering rates due to N substitutions are nearly an order of magnitude smaller than those for B defects despite having similar mass perturbations. Furthermore, ZA phonon scattering rates from N defects decrease with increasing frequency in the lower-frequency spectrum in stark contrast to expected trends from simple models. ZA phonon-vacancy scattering rates are found to have a significantly softer frequency dependence (˜ω0 ) in graphene than typically employed in phenomenological models. The rigorous Green's function calculations demonstrate that typical mass-defect models do not adequately describe ZA phonon-defect scattering rates. Our ab initio calculations capture well the trend of κ vs vacancy density from experiments, though not the magnitudes. This work elucidates important insights into phonon-defect scattering and thermal transport in graphene, and demonstrates the applicability of first-principles methods toward describing these properties in imperfect materials.
Phase diagrams from ab-initio calculations: Re-W and Fe-B
Energy Technology Data Exchange (ETDEWEB)
Hammerschmidt, Thomas; Bialon, Arthur; Palumbo, Mauro; Fries, Suzana G.; Drautz, Ralf [ICAMS, Ruhr-Universitaet Bochum (Germany)
2011-07-01
The CALPHAD (CaLculation of Phase Diagrams) method relies on Gibbs energy databases and is of limited predictive power in cases where only limited experimental data is available for constructing the Gibbs energy databases. This is problematic for, e.g., the calculation of the phase transformation kinetics within phase field simulations that not only require the thermodynamic equilibrium data but also information on metastable phases. Such information is difficult to obtain directly from experiment but ab-initio calculations may supplement experimental databases as they comprise metastable phases and arbitrary chemical compositions. We present simulations for two prototypical systems: Re-W and Fe-B. For both systems we calculate the heat of formation for an extensive set of structures using ab-initio calculations and employ the total energies in CALPHAD in order to determine the corresponding phase diagrams. We account for the configurational entropy within the Bragg-Williams approximation and neglect the phenomenological excess-term that is commonly used in CALPHAD as well as the contribution of phonons and electronic excitations to the free energy. According to our calculations the complex intermetallic phases in Re-W are stabilized by the configurational entropy. For Fe-B, we calculate metastable and stable phase diagrams including recently predicted new stable phases.
Yang, Jing; He, Bao-Ji; Jang, Richard; Zhang, Yang; Shen, Hong-Bin
2015-12-01
Cysteine-rich proteins cover many important families in nature but there are currently no methods specifically designed for modeling the structure of these proteins. The accuracy of disulfide connectivity pattern prediction, particularly for the proteins of higher-order connections, e.g., >3 bonds, is too low to effectively assist structure assembly simulations. We propose a new hierarchical order reduction protocol called Cyscon for disulfide-bonding prediction. The most confident disulfide bonds are first identified and bonding prediction is then focused on the remaining cysteine residues based on SVR training. Compared with purely machine learning-based approaches, Cyscon improved the average accuracy of connectivity pattern prediction by 21.9%. For proteins with more than 5 disulfide bonds, Cyscon improved the accuracy by 585% on the benchmark set of PDBCYS. When applied to 158 non-redundant cysteine-rich proteins, Cyscon predictions helped increase (or decrease) the TM-score (or RMSD) of the ab initio QUARK modeling by 12.1% (or 14.4%). This result demonstrates a new avenue to improve the ab initio structure modeling for cysteine-rich proteins. http://www.csbio.sjtu.edu.cn/bioinf/Cyscon/ zhng@umich.edu or hbshen@sjtu.edu.cn. Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
Ab Initio Simulations of Temperature Dependent Phase Stability and Martensitic Transitions in NiTi
Haskins, Justin B.; Thompson, Alexander E.; Lawson, John W.
2016-01-01
For NiTi based alloys, the shape memory effect is governed by a transition from a low-temperature martensite phase to a high-temperature austenite phase. Despite considerable experimental and computational work, basic questions regarding the stability of the phases and the martensitic phase transition remain unclear even for the simple case of binary, equiatomic NiTi. We perform ab initio molecular dynamics simulations to describe the temperature-dependent behavior of NiTi and resolve several of these outstanding issues. Structural correlation functions and finite temperature phonon spectra are evaluated to determine phase stability. In particular, we show that finite temperature, entropic effects stabilize the experimentally observed martensite (B19') and austenite (B2) phases while destabilizing the theoretically predicted (B33) phase. Free energy computations based on ab initio thermodynamic integration confirm these results and permit estimates of the transition temperature between the phases. In addition to the martensitic phase transition, we predict a new transition between the B33 and B19' phases. The role of defects in suppressing these phase transformations is discussed.
Ab initio quantum chemistry in parallel-portable tools and applications
International Nuclear Information System (INIS)
Harrison, R.J.; Shepard, R.; Kendall, R.A.
1991-01-01
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 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
Experimental and ab initio investigations on textured Li–Mn–O spinel thin film cathodes
International Nuclear Information System (INIS)
Fischer, J.; Music, D.; Bergfeldt, T.; Ziebert, C.; Ulrich, S.; Seifert, H.J.
2014-01-01
This paper describes the tailored preparation of nearly identical lithium–manganese–oxide thin film cathodes with different global grain orientations. The thin films were synthesized by rf magnetron sputtering from a LiMn 2 O 4 -target in a pure argon plasma. Under appropriate processing conditions, thin films with a cubic spinel structure and a nearly similar density and surface topography but different grain orientation, i.e. (111)- and (440)-textured films, were achieved. The chemical composition was determined by inductively coupled plasma optical emission spectroscopy and carrier gas hot extraction. The constitution- and microstructure were evaluated by X-ray diffraction and Raman spectroscopy. The surface morphology and roughness were investigated by scanning electron and atomic force microscopy. The differently textured films represent an ideal model system for studying potential effects of grain orientation on the lithium ion diffusion and electrochemical behavior in LiMn 2 O 4 -based thin films. They are nearly identical in their chemical composition, atomic bonding behavior, surface-roughness, morphology and thickness. Our initial ab initio molecular dynamics data indicate that Li ion transport is faster in (111)-textured structure than in (440)-textured one. - Highlights: • Thin film model system of differently textured cubic Li–Mn–O spinels. • Investigation of the Li–Mn–O thin film mass density by X-ray reflectivity. • Ab initio molecular dynamics simulation on Li ion diffusion in LiMn 2 O 4
Energy Technology Data Exchange (ETDEWEB)
Raybaud, P.
1998-10-28
Ab-initio calculations within the DFT and GGA have been carried out in an attempt to understand better which property sets the activity of transition metal sulfides (TMS) in the hydro-desulfurization reaction (HDS), a most important step in the refining of crude oil. A systematic study of the structural cohesive and electronic properties of more than thirty bulk TMS has allowed us to find a new simple relationship between the experimental catalytic activities known in HDS, and the properly defined sulfur-metal (S-M) bond energy. On this volcano curve reminiscent of the Sabatier principles, ionic metallic sulfides (as Ni{sub 3}S{sub 2}, Ci{sub 9}S{sub 8}) exhibit the weakest bonds whereas ion-covalent semi-conductors (as MoS{sub 2}) exhibit the strongest bonds: the highest activities correspond to intermediate bond strengths (RuS{sub 2}). Our study of the electronic structure of the MoS{sub 2} edge surfaces has revealed acceptor surface states localized on Coordinatively Unsaturated Mo ions and the significance of those states for the activation of hetero-aromatic molecules like thiophene. On such surfaces, the energetic profiles we establish for the thiophene HDS reaction point out the surface anionic vacancy regeneration steps as rate determining. We have calculated the optimal positions of Co (Ni) in decoration on the MoS{sub 2} edge planes, in excellent agreement with available EXAFS data on real catalysts. Introducing the promoter Co (Ni) induces a lower optimal sulfur coverage and a lower surface S-M bond strength in proportion of the Co (Ni) coverage, and lower for Ni than for Co. Simplified energy profiles for the thiophene HDS reactions on promoted (101-bar 0) surfaces show that the C-S scission step is likely to become rate determining. Our results show altogether that bulk and surface S-M strengths in TMS systems show similar trends, insofar as they are primarily determined by the local electronic structure. (author)
Xu, Dong
Accurate prediction of the vibrational spectra in polyatomic molecules and free radicals depends on obtaining high quality solutions to the vibrational Schrodinger equation. The quantum simple harmonic oscillator provides the traditional first approximation for modeling molecular vibrational states. Rarely does a vibrational analysis extend beyond this first approximation, and harmonic energy levels are routinely used to predict the infrared spectra and other dynamical properties of molecules. However, there are many large-amplitude molecular motions that are extremely anharmonic, including internal torsions about atom-atom single bonds, bending and stretching of weak bonds in van der Waals complexes, and isomerization along relocalization coordinates in free radicals. In these cases, the harmonic treatment provided by electronic structure quantum chemistry packages is completely inadequate. Furthermore, the anharmonicity often includes strong coupling among two or more distinct vibrational coordinates, necessitating a multi-dimensional analysis of the vibrational Schrodinger equation along the coupled coordinates. A novel ab initio solver package, FEMVib, is developed within the finite element method (FEM) framework. A mixed programming paradigm that combines C++, Fortran and Python is employed to take advantage of existing numerical libraries. FEMVib has been rigorously tested to resolve the eigenvalues and wavefunctions of hundreds of vibrational energy states to high accuracy and precision. It may be used to calculate the complete vibrational spectra of triatomic molecules or to approximate larger systems through a "relaxed" model that allows complete coupling of up to three selected vibrational coordinates. FEMVib provides physical chemists with a general, robust and accurate computational tool for molecular vibrational analysis.
Balabin, Roman M.
2009-10-01
High-level ab initio electronic structure calculations, including extrapolations to the complete basis set (CBS) limit, were performed, and highly precise relative energies of five-member N-heterocycles were determined. Nitrogen-containing heterocycles studied included tautomers of tetrazole (CH2N4) and triazoles (C2H3N3). Valence focal-point analysis of 1H-tetrazole, 2H-tetrazole, 5H-tetrazole, 1H-1,2,3-triazole, 2H-1,2,3-triazole, 1H-1,2,4-triazole, and 4H-1,2,4-triazole and a number of transition state (TS) calculations were performed, using energy values determined by CCSD(T)/aug-cc-pVTZ, MP3/aug-cc-pVQZ, and MP2/aug-cc-pV5Z. An accuracy of 0.10-0.25 kcal mol-1 (35-87 cm-1) was obtained for comparison of tautomer energy differences. Relative CCSD(T)/CBS energies of 2.07, 3.98, and 6.25 kcal mol-1 for 1H-tetrazole, 1H-1,2,3-triazole, and 4H-1,2,4-triazole, respectively, were calculated. Use of electron correlation methods resulted in markedly different convergence behaviors for triazole and tetrazole tautomers. Similarly, differences in convergence were observed for TSs with respect to corresponding minima structures. It was confirmed that the MP2 method predicts an acyclic structure for 5H-tetrazole. The same was not observed for the corresponding TS geometry. Comparison with density functional theory (B3LYP) and model chemistry methods (CBS-4M and CBS-QB3) is reported.
C and Si in the core - an experimental and ab initio approach
Vocadlo, L.; Alfe, D.; Wood, I. G.; Dobson, D.; Price, G. D.
2003-04-01
The fact that the core is largely composed of iron (Fe) was firmly established as a result of Birch's analysis of materials-density/sound-wave velocity systematics. Today we believe that the outer core is about 6 to 10% less dense than pure liquid Fe, while the solid inner core is a few percent less dense than pure Fe. From cosmochemical and other considerations, it is likely that the alloying elements in the core might include S, O, Si, H and C. It is also possible that the core contains minor amounts of other elements, such as Ni and K. Here we present our results from both experiments and ab initio computer calculations on Fe alloyed with C and Si at Earth's core conditions. Neutron diffraction experiments indicate that Fe3C will be non-magnetic at core conditions; ab initio calculations on the non-magnetic phase of Fe3C suggest that, at core P and T, its density and incompressibity are inconsistent with the observations from PREM. Calcuations on FeSi show that it adopts the CsCl structure at core pressures; this result has recently been validated by our high pressure experiments in which we were able to synthesise CsCl-FeSi. This is an extemely interesting result since CsCl-FeSi is iso-structural with bcc-Fe, and experiments have recently shown (Lin et al., 2002) that Si stabilises bcc-Fe with respect to hcp-Fe up to 80 GPa. Ab initio molecular dynamics simulations have been used to calculate the chemical potentials of Fe alloys. In order to match the density jump at the inner core boundary, we predict an inner core with 8 mol% S/Si and 0.3 mol% O, and an outer core containing 10 mol % S/Si and 8 mol % O. Finally we present preliminary results for the calculated high P/T elastic constants of iron alloys as a function of composition.
Improved parametric fits for the HeH2 ab initio energy surface
International Nuclear Information System (INIS)
Muchnick, P.
1992-01-01
A brief history of the development of ab initio calculations for the HeH 2 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 H 2 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 H 2 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 H 2 (1sσ g ) 2 , H 2 + (1sσ g ), H 2 + (2pσ u ) and (LiH 2 ) + energy surfaces are also presented. The new parametric fits for H 2 , H 2 + (1sσ g ) are shown to be improvements over the well-known Morse potentials for these surfaces
Ab initio study of perovskite type oxide materials for solid oxide fuel cells
Lee, Yueh-Lin
2011-12-01
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
Amel Laref; Abeer AlMudlej; Slimane Laref; Jun Tao Yang; Yong-Chen Xiong; Shi Jun Luo
2017-01-01
Ab-initio calculations are performed to examine the electronic structures and magnetic properties of spin-polarized Ga1?x Mn x P (x = 0.03, 0.25, 0.5, and 0.75) ternary alloys. In order to perceive viable half-metallic (HM) states and unprecedented diluted magnetic semiconductors (DMSs) such as spintronic materials, the full potential linearized augmented plane wave method is utilized within the generalized gradient approximation (GGA). In order to tackle the correlation effects on 3d states ...
DEFF Research Database (Denmark)
Berg, Rolf W.
The hydrogen bonding interactions in selected archetypal vapor molecules formed in the gas phase over protic ionic liquids are discussed, based on Raman spectroscopy assisted with ab initio molecular orbital DFT-type quantum mechanical calculations (B3LYP with 6-311+G(d,p) basis sets) on assumed...... Ionic Liquid, To be submitted for J. Phys. Chem. A (2009)....
DEFF Research Database (Denmark)
Pedersen, Kim Vestergaard; Christensen, Henrik; Shim, Irene
2004-01-01
Trichlorothioacetyl chloride 1, tetrachlorothiirane 2, and trichloroethenesulfenyl chloride 3 and the equilibria between them have been investigated by ab initio Hartree-Fock (HF), Møller-Plesset second order perturbation (MP2) calculations, and by Gaussian-3 theory, G3(MP2). The transition states...
Czech Academy of Sciences Publication Activity Database
Chocholoušová, Jana; Vacek, Jaroslav; Hobza, Pavel
2002-01-01
Roč. 4, - (2002), s. 2119-2122 ISSN 1463-9076 R&D Projects: GA MŠk LN00A032 Institutional research plan: CEZ:AV0Z4040901 Keywords : formic acid dimer * ab initio calculations * molecular dynamics simulations Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.838, year: 2002
Czech Academy of Sciences Publication Activity Database
Štrof, J.; Pavlů, Jana; Wdowik, U.; Buršík, Jiří; Šob, Mojmír; Vřešťál, Jan
2014-01-01
Roč. 44, MAR (2014), s. 62-69 ISSN 0364-5916 R&D Projects: GA MŠk(CZ) ED1.1.00/02.0068 Institutional support: RVO:68081723 Keywords : laves phases * V-Zr system * ab initio calculations Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.370, year: 2014
Knight, Chris; Maupin, C Mark; Izvekov, Sergei; Voth, Gregory A
2010-10-12
In this report, a general methodology is presented for the parametrization of a reactive force field using data from a condensed phase ab initio molecular dynamics (AIMD) simulation. This algorithm allows for the creation of an empirical reactive force field that accurately reproduces the underlying ab initio reactive surface while providing the ability to achieve long-time statistical sampling for large systems not possible with AIMD alone. In this work, a model for the hydrated excess proton is constructed where the hydronium cation and proton hopping portions of the model are statistically force-matched to the results of Car-Parrinello Molecular Dynamics (CPMD) simulations. The flexible nature of the algorithm also allows for the use of the more accurate classical simple point-charge flexible water (SPC/Fw) model to describe the water-water interactions while utilizing the ab initio data to create an overall multistate molecular dynamics (MS-MD) reactive model of the hydrated excess proton in water. The resulting empirical model for the system qualitatively reproduces thermodynamic and dynamic properties calculated from the ab initio simulation while being in good agreement with experimental results and previously developed multistate empirical valence bond (MS-EVB) models. The present methodology, therefore, bridges the AIMD technique with the MS-MD modeling of reactive events, while incorporating key strengths of both.
O'Connor, Joseph M; Baldridge, Kim K; Rodgers, Betsy L; Aubrey, Marissa; Holland, Ryan L; Kassel, W Scott; Rheingold, Arnold L
2010-08-18
The first demonstration of photochemical enediyne liberation from a metal complex has led to a new class of enediynes, the cyclopentadienidoenediynes, which are demonstrated to exist as air-stable solids with low ionization potentials and large dipole moments. NMR and IR spectroscopy, X-ray crystallography, and ab initio computations enable a comparison with the ubiquitous benzoenediynes.
Zhang, Yang
2014-02-01
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. Copyright © 2013 Wiley Periodicals, Inc.
Silvestrelli, P.-L.; Alavi, A.; Parrinello, M.; Frenkel, D.
1997-01-01
The method of ab initio molecular dynamics, based on finite-temperature density-functional theory, is used to simulate laser heating of crystalline silicon. We found that a high concentration of excited electrons dramatically weakens the covalent bonding. As a result the system undergoes a melting
Koten, G. van; Albrecht, M.A.; Gossage, R.A.; Frey, H.; Ehlers, A.W.; Baerends, E.J.; Merbach, A.E.
2001-01-01
The detailed mechanism of the reversible binding and fast exchange of SO2 on the organoplatinum(II) complex [PtI(NCN)], 1, has been studied experimentally in solution (C2F4Br2) using low-temperature NMR spectroscopy and theoretically by ab initio calculations. Direct bonding of SO2 and formation of
DEFF Research Database (Denmark)
Gorelik, Tatiana E; van de Streek, Jacco; Kilbinger, Andreas F M
2012-01-01
Ab-initio crystal structure analysis of organic materials from electron diffraction data is presented. The data were collected using the automated electron diffraction tomography (ADT) technique. The structure solution and refinement route is first validated on the basis of the known crystal stru...
Efficacy of the SU(3) scheme for ab initio large-scale calculations beyond the lightest nuclei
Czech Academy of Sciences Publication Activity Database
Dytrych, Tomáš; Maris, P.; Launey, K. D.; Draayer, J. P.; Vary, J. P.; Langr, D.; Saule, E.; Caprio, M. A.; Catalyurek, U.; Sosonkina, M.
2016-01-01
Roč. 207, OCT (2016), s. 202-210 ISSN 0010-4655 R&D Projects: GA ČR GA16-16772S Institutional support: RVO:61389005 Keywords : nuclear structure * Ab initio methods * Shell model * models based on group theory Subject RIV: BE - Theoretical Physics Impact factor: 3.936, year: 2016
Szekrényes, Zsolt; Kamarás, Katalin; Tarczay, György; Llanes-Pallás, Anna; Marangoni, Tomas; Prato, Maurizio; Bonifazi, Davide; Björk, Jonas; Hanke, Felix; Persson, Mats
2012-04-19
The thermal response of hydrogen bonds is a crucial aspect in the self-assembly of molecular nanostructures. To gain a detailed understanding of their response, we investigated infrared spectra of monomers and hydrogen-bonded dimers of two uracil-derivative molecules, supported by density functional theory calculations. Matrix isolation spectra of monomers, temperature dependence in the solid state, and ab initio molecular dynamics calculations give a comprehensive picture about the dimer structure and dynamics of such systems as well as a proper assignment of hydrogen-bond affected bands. The evolution of the hydrogen bond melting is followed by calculating the C═O···H-N distance distributions at different temperatures. The result of this calculation yields excellent agreement with the H-bond melting temperature observed by experiment.
Limitations of Ab Initio Predictions of Peptide Binding to MHC Class II Molecules
DEFF Research Database (Denmark)
Zhang, Hao; Lund, Ole; Nielsen, Morten
2010-01-01
Successful predictions of peptide MHC binding typically require a large set of binding data for the specific MHC molecule that is examined. Structure based prediction methods promise to circumvent this requirement by evaluating the physical contacts a peptide can make with an MHC molecule based...... on the highly conserved 3D structure of peptide:MHC complexes. While several such methods have been described before, most are not publicly available and have not been independently tested for their performance. We here implemented and evaluated three prediction methods for MHC class II molecules: statistical...... potentials derived from the analysis of known protein structures; energetic evaluation of different peptide snapshots in a molecular dynamics simulation; and direct analysis of contacts made in known 3D structures of peptide:MHC complexes. These methods are ab initio in that they require structural data...
Ab initio potential energy surfaces and quantum dynamics for polyatomic bimolecular reactions.
Fu, Bina; Zhang, Donghui
2018-03-26
There has been great progress in the development of potential energy surfaces (PESs) and quantum dynamics calculations in the gas phase. The establishment of fitting procedure for highly accurate PESs and new developments in quantum reactive scattering on reliable PESs allow accurate characterization of reaction dynamics beyond triatomic systems. This review will give the recent development in our group in constructing ab initio PESs based on the neural networks, and the time-dependent wave packet calculations for bimolecular reactions beyond three atoms. Bimolecular reactions of current interest to the community, namely, OH+H2, H+H2O, OH+CO, H+CH4 and Cl+CH4 are focused on. Quantum mechanical characterization of these reactions uncovers interesting dynamical phenomena with an unprecedented level of sophistication, and has greatly advanced our understanding of polyatomic reaction dynamics.
The constrained space orbital variation analysis for periodic ab initio calculations
International Nuclear Information System (INIS)
Cruz Hernandez, N.; Zicovich-Wilson, Claudio Marcelo; Fdez Sanz, Javier
2006-01-01
The constrained space orbital variation (CSOV) method for the analysis of the interaction energy has been implemented in the periodic ab initio CRYSTAL03 code. The method allows for the partition of the energy of two interacting chemical entities, represented in turn by periodic models, into contributions which account for electrostatic effects, mutual polarization and charge transfer. The implementation permits one to carry out the analysis both at the Hartree-Fock and density functional theory levels, where in the latter the most popular exchange-correlation functionals can be used. As an illustrating example, the analysis of the interaction between CO and the MgO (001) surface has been considered. As expected by the almost fully ionic character of the support, our periodic CSOV results, in general agree with those previously obtained using the embedded cluster approach, showing the reliability of the present implementation
Experimental and ab initio study of Ta-doped ZnO semiconductor
Energy Technology Data Exchange (ETDEWEB)
Munoz, E. L., E-mail: munoz@fisica.unlp.edu.ar; Richard, D., E-mail: richard@fisica.unlp.edu.ar [UNLP, Departamento de Fisica and Instituto de Fisica La Plata (IFLP, CCT La Plata, CONICET), Fac. de Ciencias Exactas (Argentina); Eversheim, P. D. [Universitaet Bonn, Helmholtz-Institut fuer Strahlen-und Kernphysik (H-ISKP) (Germany); Renteria, M., E-mail: renteria@fisica.unlp.edu.ar [UNLP, Departamento de Fisica and Instituto de Fisica La Plata (IFLP, CCT La Plata, CONICET), Fac. de Ciencias Exactas (Argentina)
2010-04-15
In this work, we present {gamma}-{gamma} Perturbed-Angular-Correlation results in polycrystalline ZnO semiconductor implanted with {sup 181}Hf({yields}{sup 181}Ta) 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 Zn{sup 2 + } 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.
Experimental and ab initio study of Ta-doped ZnO semiconductor
International Nuclear Information System (INIS)
Muñoz, E. L.; Richard, D.; Eversheim, P. D.; Rentería, M.
2010-01-01
In this work, we present γ–γ Perturbed-Angular-Correlation results in polycrystalline ZnO semiconductor implanted with 181 Hf(→ 181 Ta) 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 Zn 2 + 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.
Structural properties of iron nitride on Cu(100): An ab-initio molecular dynamics study
Heryadi, Dodi
2011-01-01
Due to their potential applications in magnetic storage devices, iron nitrides have been a subject of numerous experimental and theoretical investigations. Thin films of iron nitride have been successfully grown on different substrates. To study the structural properties of a single monolayer film of FeN we have performed an ab-initio molecular dynamics simulation of its formation on a Cu(100) substrate. The iron nitride layer formed in our simulation shows a p4gm(2x2) reconstructed surface, in agreement with experimental results. In addition to its structural properties, we are also able to determine the magnetization of this thin film. Our results show that one monolayer of iron nitride on Cu(100) is ferromagnetic with a magnetic moment of 1.67 μ B. © 2011 Materials Research Society.
Prediction of toxicity of nitrobenzenes using ab initio and least squares support vector machines
Energy Technology Data Exchange (ETDEWEB)
Niazi, Ali [Department of Chemistry, Faculty of Sciences, Azad University of Arak, Arak (Iran, Islamic Republic of)], E-mail: ali.niazi@gmail.com; Jameh-Bozorghi, Saeed; Nori-Shargh, Davood [Department of Chemistry, Faculty of Sciences, Azad University of Arak, Arak (Iran, Islamic Republic of)
2008-03-01
A quantitative structure-property relationship (QSPR) study is suggested for the prediction of toxicity (IGC{sub 50}) of nitrobenzenes. Ab initio theory was used to calculate some quantum chemical descriptors including electrostatic potentials and local charges at each atom, HOMO and LUMO energies, etc. Modeling of the IGC{sub 50} of nitrobenzenes as a function of molecular structures was established by means of the least squares support vector machines (LS-SVM). This model was applied for the prediction of the toxicity (IGC{sub 50}) of nitrobenzenes, which were not in the modeling procedure. The resulted model showed high prediction ability with root mean square error of prediction of 0.0049 for LS-SVM. Results have shown that the introduction of LS-SVM for quantum chemical descriptors drastically enhances the ability of prediction in QSAR studies superior to multiple linear regression and partial least squares.
Carbon diffusion in molten uranium: an ab initio molecular dynamics study
Garrett, Kerry E.; Abrecht, David G.; Kessler, Sean H.; Henson, Neil J.; Devanathan, Ram; Schwantes, Jon M.; Reilly, Dallas D.
2018-04-01
In this work we used ab initio molecular dynamics within the framework of density functional theory and the projector-augmented wave method to study carbon diffusion in liquid uranium at temperatures above 1600 K. The electronic interactions of carbon and uranium were described using the local density approximation (LDA). The self-diffusion of uranium based on this approach is compared with literature computational and experimental results for liquid uranium. The temperature dependence of carbon and uranium diffusion in the melt was evaluated by fitting the resulting diffusion coefficients to an Arrhenius relationship. We found that the LDA calculated activation energy for carbon was nearly twice that of uranium: 0.55 ± 0.03 eV for carbon compared to 0.32 ± 0.04 eV for uranium. Structural analysis of the liquid uranium-carbon system is also discussed.
Formation Dynamics of Potassium-Based Graphite Intercalation Compounds: An Ab Initio Study
Jiang, Xiankai; Song, Bo; Tománek, David
2018-04-01
This paper is a contribution to the Physical Review Applied collection in memory of Mildred S. Dresselhaus. We use ab initio molecular dynamics simulations to study the microscopic dynamics of potassium intercalation in graphite. Upon adsorbing on graphite from the vapor phase, K atoms transfer their valence charge to the substrate. K atoms adsorbed on the surface diffuse rapidly along the graphene basal plane and eventually enter the interlayer region following a "U -turn" across the edge, gaining additional energy. This process is promoted at higher coverages associated with higher K pressure, leading to the formation of a stable intercalation compound. We find that the functionalization of graphene edges is an essential prerequisite for intercalation since bare edges reconstruct and reconnect, closing off the entry channels for the atoms.
AB INITIO STUDY OF AMMONIA CLUSTERS: (NH3n (n = 2-6
Directory of Open Access Journals (Sweden)
Herudi Kandau
2010-06-01
Full Text Available Hydrogen bonded neutral clusters of ammonia, (NH3n (n = 2-6, have been theoretically investigated employing the D95++(d,p (and wherever necessary, higher basis sets at the Hartree-Fock (HF level as well as with second-order Møller-Plesset (MP2 perturbation theory. While the ammonia trimer and tetramer exhibit perfect molecular symmetries and are nonpolar, the pentamer and hexamer both optimize with slight deviations from perfect symmetries and are seen to posses marginal, but nonzero dipole moments. The (NH3n linear clusters are seen to be chemically softer than the corresponding cyclic ones. Keywords: ab initio calculation, ammonia clusters, Hartree-Fock, Møller-Plesset
Ab-initio study of NiGe/Ge Schottky contact
Vaidya, Dhirendra; Lodha, Saurabh; Ganguly, Swaroop
2017-04-01
Germanium is a promising material for next-generation electronic and photonic devices, and engineering ohmic contacts to it can be expected to be a key challenge therein. The sensitivity of the Schottky barrier height of the NiGe/Ge contact to the detailed interfacial structure is revealed using the ab-initio study of pseudo-epitaxial NiGe(001)/Ge(100) contact using the computationally efficient meta-generalized-gradient-approximation, which can overcome the well-known bandgap underestimation problem. The p-type Schottky barrier height for an atomically flat pseudo-epitaxial NiGe(001)/Ge(100) contact is calculated to be 260 meV, an overestimate of about 160 meV compared to experiments. However, the estimated modulation of this barrier height, by about 270 meV, due to interface morphology points to a possible explanation for this discrepancy and suggests ways to engineer the contact for lesser resistivity.
Chaban, Vitaly V; Prezhdo, Oleg V
2016-07-07
The Haber-Bosch process is the main industrial method for producing ammonia from diatomic nitrogen and hydrogen. We use a combination of ab initio thermochemical analysis and reactive molecular dynamics to demonstrate that a significant increase in the ammonia production yield can be achieved using hydroxylated graphene and related species. Exploiting the polarity difference between N2/H2 and NH3, as well as the universal proton acceptor behavior of NH3, we demonstrate a strong shift of the equilibrium of the Haber-Bosch process toward ammonia (ca. 50 kJ mol(-1) enthalpy gain and ca. 60-70 kJ mol(-1) free energy gain). The modified process is of significant importance to the chemical industry.
Progress towards an ab initio real-time treatment of warm dense matter
Baczewski, Andrew; Cangi, Attila; Hansen, Stephanie; Jensen, Daniel
2017-10-01
Time-dependent density functional theory (TDDFT) provides an accurate description of equilibrium properties of warm dense matter, such as the dynamic structure factor (Baczewski et al., Phys. Rev. Lett., 116(11), 2016). While non-equilibrium properties, such as stopping power, have also been demonstrated to be within the grasp of TDDFT, the ultrafast isochoric heating of condensed matter into the warm dense state, enabled by recent advances in XFELs, remains beyond its capabilities. In this talk, we will describe the successes of and continuing challenges for TDDFT for warm dense matter, and present progress towards a more complete ab initio treatment of isochoric x-ray heating. Sandia National Laboratories is a multi-mission laboratory managed and operated by National Technology and Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International, Inc., for the DOE's National Nuclear Security Administration under contract DE-NA0003525.
Magnetic properties of vanadium doped CdTe: Ab initio calculations
Energy Technology Data Exchange (ETDEWEB)
Goumrhar, F. [Laboratory of Physics of High Energy, Modeling & Simulations (LPHE-MS), Faculty of Sciences, Mohammed V University of Rabat, Av. Ibn Batouta, B.P. 1014 Rabat (Morocco); Bahmad, L., E-mail: bahmad@fsr.ac.ma [Laboratory of Magnetism and High Energy Physics (LMPHE-URAC12), Faculty of Sciences, Mohammed V University of Rabat, Av. Ibn Batouta, B.P. 1014 Rabat (Morocco); Mounkachi, O. [Material and Nanomaterial Center, MAScIR Fondation, Rabat (Morocco); Benyoussef, A. [Laboratory of Magnetism and High Energy Physics (LMPHE-URAC12), Faculty of Sciences, Mohammed V University of Rabat, Av. Ibn Batouta, B.P. 1014 Rabat (Morocco); Material and Nanomaterial Center, MAScIR Fondation, Rabat (Morocco); Hassan II Academy of Sciences and Technology, Rabat (Morocco)
2017-04-15
In this paper, we are applying the ab initio calculations to study the magnetic properties of vanadium doped CdTe. This study is based on the Korringa–Kohn–Rostoker method (KKR) combined with the coherent potential approximation (CPA), within the local density approximation (LDA). This method is called KKR-CPA-LDA. We have calculated and plotted the density of states (DOS) in the energy diagram for different concentrations of dopants. We have also investigated the magnetic and half-metallic properties of this compound and shown the mechanism of exchange interaction. Moreover, we have estimated the Curie temperature T{sub c} for different concentrations. Finally, we have shown how the crystal field and the exchange splittings vary as a function of the concentrations.
Estudo ab-initio da a-alanina em meio aquoso
Directory of Open Access Journals (Sweden)
Sambrano Júlio Ricardo
1999-01-01
Full Text Available Ab initio Hartree-Fock (HF, Density Functional (B3LYP and electron correlation (MP2 methods have been used to caracterize the aqueous medium intramolecular hydrogen bond in a-alanine. The 6-31G* and 6-31++G** were taken from Gaussian94 library. We were concerned on the structure of three conformers of a-alanine, in their neutral form plus on the structure of the zwitterionic form (Z. The Z structure is a stationary point at the HF/6-31G* level but it is not when diffuse functions and electron correlation are included. This results shows that the Z form does not exist in the gas phase. The inclusion of solvent effects changed significantly the results obtained in gas phase, therefore this inclusion make the Z form a stationary point within all level of theory, and the relative energy depends dramatically on the level of calculation.
Ab Initio Molecular Dynamics Studies of Pb m Sb n ( m + n ≤ 9) Alloy Clusters
Song, Bingyi; Xu, Baoqiang; Yang, Bin; Jiang, Wenlong; Chen, Xiumin; Xu, Na; Liu, Dachun; Dai, Yongnian
2017-10-01
Structure, stability, and dynamics of Pb m Sb n ( m + n ≤ 9) clusters were investigated using ab initio molecular dynamics. Size dependence of binding energies, the second-order energy difference of clusters, dissociation energy, HOMO-LUMO gaps, Mayer bond order, and the diffusion coefficient of Pb m Sb n clusters were discussed. Results suggest that Pb3Sb2, Pb4Sb2, and Pb5Sb4 ( n = 2 or 4) clusters have higher stability than other clusters, which is consistent with previous findings. In case of Pb-Sb alloy, the dynamics results show that Pb4Sb2 (Pb-22.71 wt pct Sb) can exist in gas phase at 1073 K (800 °C), which reasonably explains the azeotropic phenomenon, and the calculated values are in agreement with the experimental results (Pb-22 wt pct Sb).
Ab initio theory for current-induced molecular switching: Melamine on Cu(001)
Ohto, Tatsuhiko
2013-05-28
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. © 2013 American Physical Society.
Ab initio electron propagator theory of molecular wires. II. Multiorbital terminal description.
Dahnovsky, Yu; Ortiz, J V
2006-04-14
Correlated, ab initio electron propagator methodology may be applied to the calculation of electrical current through a molecular wire. A new theoretical formalism is developed for the calculation of retarded and advanced Green functions in terms of the electron propagator matrix for a bridge molecule. The calculation of the current requires integration in a complex half-plane for a trace that involves terminal and Green function matrices that may have any rank. Because the latter arrays have poles represented by matrices, an alternative expression is developed in terms of ordinary poles which are (n-1)-fold degenerate or nondegenerate. For an arbitrary number of terminal orbitals, the analytical expression for the current is given in terms of pole strengths, poles, and terminal matrix elements of the electron propagator, i.e., the parameters that are found in the output of numerical calculations.
Ab initio study of long-period superstructures in close-packed A3B compounds
DEFF Research Database (Denmark)
Rosengaard, N. M.; Skriver, Hans Lomholt
1994-01-01
We have performed ab initio calculations of the stability of one-dimensional long-period superstructures in Cu3Pd, Cu3Al, and Ag3Mg by means of an interface Green's function technique based on the linear-muffin-tin-orbitals method within the tight-binding and atomic-sphere approximations......-structure calculations of the structural energy differences for the two short-period superstructures DO22 and DO23. We find that at zero temperature the ground states of Cu3Pd, Cu3Al, and Ag3Mg are one-dimensional superstructures with antiphase boundary separations of 2-5 unit cells of the underlying L1(2) structure....
Ab-initio Hartree-Fock study of tritium desorption from Li{sub 2}O
Energy Technology Data Exchange (ETDEWEB)
Taniguchi, Masaki; Tanaka, Satoru [Tokyo Univ. (Japan). Faculty of Engineering
1998-03-01
Dissociative adsorption of hydrogen on Li{sub 2}O (110) surface has been investigated with ab-initio Hartree-Fock quantum chemical calculation technique. Heat of adsorption and potential energy surface for H{sub 2} dissociative adsorption was evaluated by calculating the total energy of the system. Calculation results on adsorption heat indicated that H{sub 2} adsorption is endothermic. However, when oxygen vacancy exists adjacent to the adsorption sites, heat of adsorption energy became less endothermic and the activation energy required to dissociate the H-H bonding was smaller than that for the terrace site. This is considered to be caused by the excess charge localized near the defect. (author)
Ab initio theory of the equation of state for compressed rare gas crystals
Pilipenko, E. A.; Troitskaya, E. P.; Gorbenko, Ie. Ie.
2018-01-01
Nonempirical equations of state of compressed rare gas crystals Ne, Ar, Kr, and Xe are studied on the basis of the earlier-obtained ab initio adiabatic potential. The paired and three-body short-range repulsive potentials are calculated by the Hartree-Fock method in the basis of localized functions with their exact mutual orthogonalization and do not contain experimentally determined parameters. The theory is compared with the experiment and results of calculations by other authors. Analysis of the proposed equations of state for large compressions has shown the importance of taking into account the three-body interaction and the terms of the higher order in the overlap integral in compressed neon and the sufficiency of the quadratic approximation in the orthogonalization of functions in heavy rare gas crystals.
Rotational Energy Transfer of N2 Determined Using a New Ab Initio Potential Energy Surface
Huo, Winifred M.; Stallcop, James R.; Partridge, Harry; Langhoff, Stephen R. (Technical Monitor)
1997-01-01
A new N2-N2 rigid-rotor surface has been determined using extensive Ab Initio quantum chemistry calculations together with recent experimental data for the second virial coefficient. Rotational energy transfer is studied using the new potential energy surface (PES) employing the close coupling method below 200 cm(exp -1) and coupled state approximation above that. Comparing with a previous calculation based on the PES of van der Avoird et al.,3 it is found that the new PES generally gives larger cross sections for large (delta)J transitions, but for small (delta)J transitions the cross sections are either comparable or smaller. Correlation between the differences in the cross sections and the two PES will be attempted. The computed cross sections will also be compared with available experimental data.
Ab initio potential energy surface and vibration-rotation energy levels of beryllium monohydroxide.
Koput, Jacek
2017-01-05
The accurate potential energy surface of beryllium monohydroxide, BeOH, in its ground electronic state X 2A' has been determined from ab initio calculations using the coupled-cluster approach in conjunction with the correlation-consistent core-valence basis sets up to septuple-zeta quality. The higher-order electron correlation, scalar relativistic, and adiabatic effects were taken into account. The BeOH molecule was confirmed to be bent at equilibrium, with the BeOH angle of 141.2° and the barrier to linearity of 129 cm -1 . The vibration-rotation energy levels of the BeOH and BeOD isotopologues were predicted using a variational approach and compared with recent experimental data. The results can be useful in a further analysis of high-resolution vibration-rotation spectra of these interesting species. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.
Ab initio potential energy surface and vibration-rotation energy levels of sulfur dioxide.
Koput, Jacek
2017-05-05
An accurate potential energy surface of sulfur dioxide, SO 2 , in its ground electronic state X∼ 1A1 has been determined from ab initio calculations using the coupled-cluster approach in conjunction with the correlation-consistent basis sets up to septuple-zeta quality. The results obtained with the conventional and explicitly correlated coupled-cluster methods are compared. The role of the core-electron correlation, higher-order valence-electron correlation, scalar relativistic, and adiabatic effects in determining the structure and dynamics of the SO 2 molecule is discussed. The vibration-rotation energy levels of the 32 SO 2 and 34 SO 2 isotopologues were predicted using a variational approach. It was shown that the inclusion of the aforementioned effects was mandatory to attain the "spectroscopic" accuracy. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.
The equilibrium morphology of WC particles - A combined ab initio and experimental study
International Nuclear Information System (INIS)
Zhong Yang; Zhu Hong; Shaw, Leon L.; Ramprasad, R.
2011-01-01
We report an ab initio density functional theory study, complemented by parallel experimental work, of the equilibrium shape of WC particles. The equilibrium shape is simulated under the condition of little or no liquid-phase sintering. The effects of the carbon-rich and carbon-deficient conditions and the adsorption of Co and Ni atoms on the surface of WC particles are investigated. The equilibrium shape of WC particles is found to be a truncated triangular prism under both carbon-rich and carbon-deficient conditions. The adsorption of Co and Ni on the WC surface can promote the formation of either truncated triangular prisms or near-hexagonal prisms, depending on their specific combination with the carbon chemical potential. Under all the conditions investigated, the equilibrium shapes of WC crystals can be described as 'bulky' rather than 'plate-like'. The findings in this study are consistent with the experimental observations.
An ab initio investigation of how residual resistivity can decrease when an alloy is deformed
Lowitzer, S.; Ködderitzsch, D.; Ebert, H.; Tulip, P. R.; Marmodoro, A.; Staunton, J. B.
2010-11-01
For a class of transition metal materials residual resistivity is observed to decrease when the materials are deformed and short-range order is removed. We investigate this counter-intuitive behavior with an ab initio theoretical study of the residual resistivity of several late transition metal-rich disordered alloys. The calculations are performed using the Korringa-Kohn-Rostoker (KKR) method applied to the Kubo-Greenwood formalism. The electronic effects arising from short-range ordering and clustering within the disorder are described using the non-local coherent-potential approximation (NL-CPA). We find a simple, general explanation of this K-state-like effect in terms of changes to the amplitude for d-electron hopping between majority late transition metal nearest-neighbor atoms at the Fermi energy.
Thakor, V.; Staunton, J. B.; Poulter, J.; Ostanin, S.; Ginatempo, B.; Bruno, Ezio
2003-05-01
We present ab initio calculations of the static paramagnetic spin susceptibility for hcp iron at finite temperatures and for a range of pressures. The dominant magnetic fluctuations in hcp Fe are found to be incommensurate antiferromagnetic, characterized by the wave vector qinc=(0.56,0.22,0). We show that qinc is linked to a Fermi-surface nesting feature. For the lowest pressure ˜16 GPa at which hcp Fe forms, we find that these modes become unstable below a Néel temperature (TN) of 69 K. TN rapidly diminishes with increasing pressure. We therefore predict that hcp Fe will be found to have an incommensurate spin-density-wave-ordered state over a small pressure range starting with the onset of hcp phase. We note the coincidence with the superconductivity recently found in this material.
Ab-initio calculations of electronic, transport, and structural properties of boron phosphide
Energy Technology Data Exchange (ETDEWEB)
Ejembi, J. I.; Nwigboji, I. H.; Franklin, L.; Malozovsky, Y.; Zhao, G. L.; Bagayoko, D., E-mail: diola-bagayoko@subr.edu [Department of Physics, Southern University and A and M College, Baton Rouge, Louisiana 70813 (United States)
2014-09-14
We present results from ab-initio, self-consistent density functional theory calculations of electronic and related properties of zinc blende boron phosphide (zb-BP). We employed a local density approximation potential and implemented the linear combination of atomic orbitals formalism. This technique follows the Bagayoko, Zhao, and Williams method, as enhanced by the work of Ekuma and Franklin. The results include electronic energy bands, densities of states, and effective masses. The calculated band gap of 2.02 eV, for the room temperature lattice constant of a=4.5383 Å, is in excellent agreement with the experimental value of 2.02±0.05 eV. Our result for the bulk modulus, 155.7 GPa, agrees with experiment (152–155 GPa). Our predictions for the equilibrium lattice constant and the corresponding band gap, for very low temperatures, are 4.5269 Å and 2.01 eV, respectively.
Ab-initio Calculations of Electronic Properties of Boron Phosphide (BP)
Ejembi, John; Franklin, Lashaunda; Malozovsky, Yuriy; Bagayoko, Diola
2014-03-01
We present results from ab-initio, self consistent local density approximation (LDA) calculations of electronic and related properties of zinc blende boron phosphide (BP). We employed a local density approximation (LDA) potential and implemented the linear combination of atomic orbitals (LCAO) formalism. This implementation followed the Bagayoko, Zhao, and Williams (BZW) method, as enhanced by Ekuma and Franklin (BZW-EF). We discuss our preliminary results for the indirect band gap, from Γ to X, of Boron Phosphide. We also report calculated electron and hole effective masses for Boron Phosphide and total (DOS) and partial (pDOS) density of states. Acknowledgments: This research is funded in part by the National Science Foundation (NSF) and the Louisiana Board of Regents, through LASiGMA [Award Nos. EPS- 1003897, NSF (2010-15)-RII-SUBR] and NSF HRD-1002541, the US Department of Energy - National, Nuclear Security Administration (NNSA) (Award No. DE-NA0001861), LaSPACE, and LONI-SUBR.
Evolution of local atomic structure during solidification of Al2Au liquid: An ab initio study
Energy Technology Data Exchange (ETDEWEB)
Xiong, L H; Lou, H B; Wang, X D; Debela, T T; Cao, Q P; Zhang, D X; Wang, S Y; Wang, C Z; Jiang, J Z
2014-04-01
The local atomic structure evolution in Al2Au alloy during solidification from 2000 K to 400 K was studied by ab initio molecular dynamics simulations and analyzed using the structure factor, pair correlation functions, bond angle distributions, the Honeycutt-Anderson (HA) index and Voronoi tessellation methods. It was found that the icosahedral-like clusters are negligible in the Al2Au stable liquid and supercooled liquid states, and the most abundant clusters are those having HA indices of 131 and 120 or Voronoi indices of < 0,4,4,0 >, < 0,3, 6,0 > and < 0,4,4,2 > with coordination numbers of 8, 9 and 10, respectively. These clusters are similar to the local atomic structures in the CaF2-type Al2Au crystal, revealing the existence of structure heredity between liquid and crystalline phase in Al2Au alloy. (C) 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.
Design of two-photon molecular tandem architectures for solar cells by ab initio theory
DEFF Research Database (Denmark)
Ørnsø, Kristian Baruël; García Lastra, Juan Maria; De La Torre, Gema
2015-01-01
An extensive database of spectroscopic properties of molecules from ab initio calculations is used to design molecular complexes for use in tandem solar cells that convert two photons into a single electron–hole pair, thereby increasing the output voltage while covering a wider spectral range...... of the structural and energetic properties of several thousand porphyrin dyes. The third design is a molecular analogy of the intermediate band solar cell, and involves a single dye molecule with strong intersystem crossing to ensure a long lifetime of the intermediate state. Based on the calculated energy levels...... and molecular orbitals, energy diagrams are presented for the individual steps in the operation of such tandem solar cells. We find that theoretical open circuit voltages of up to 1.8 V can be achieved using these tandem designs. Questions about the practical implementation of prototypical devices...
Solid-State Polymerization of Acetylene under Pressure: {ital Ab Initio} Simulation
Energy Technology Data Exchange (ETDEWEB)
Bernasconi, M.; Parrinello, M. [Max-Planck-Institut fuer Festkoerperforschung, Heisenbergstr.1, D-70569 Stuttgart (Germany); Bernasconi, M. [Istituto Nazionale Fisica della Materia and Dipartimento di Fisica, Universita di Milano, Via Celoria 16, 20133 Milano (Italy); Chiarotti, G.; Focher, P.; Tosatti, E. [Istituto Nazionale Fisica della Materia and International School for Advanced Studies, Via Beirut 4, I-34014 Trieste (Italy); Tosatti, E. [International Centre for Theoretical Physics (ICTP), P.O.Box 586, I-34014 Trieste (Italy)
1997-03-01
We have simulated by {ital ab initio} constant pressure molecular dynamics the solid-state polymerization of acetylene recently observed experimentally in the pressure range 3.5{endash}14 GPa. We have found a massive polymerization only at much higher pressure (25 GPa). However, we have also found that a triplet exciton self-trapped on a single, {ital cis}-bent molecule in crystalline acetylene is a very effective polymerization seed at lower pressure ({lt}9GPa), much closer to the experimental threshold. Therefore, we propose that the polymerization observed experimentally is possibly catalyzed by a similar seed. We predict that injection of triplet excitons would greatly enhance the polymerization rate. {copyright} {ital 1997} {ital The American Physical Society}
On-the-fly ab initio semiclassical dynamics for computing vibrationally resolved electronic spectra
Vanicek, Jiri; Wehrle, Marius; Sulc, Miroslav; Oberli, Solene; Laboratory of Theoretical Physical Chemistry Team
We combine the thawed Gaussian approximation (TGA) with an on-the-fly ab initio (OTF-AI) scheme to calculate the vibrationally resolved emission spectra of oligothiophenes with up to five rings as well as absorption and photoelectron spectra of ammonia. The efficiency of the OTF-AI-TGA permits treating all vibrational degrees of freedom on an equal footing even in pentathiophene with 105 vibrational degrees of freedom, thus obviating the need for the global harmonic approximation, popular for large systems. Besides reproducing almost perfectly the experimental emission spectra, in order to provide a deeper insight into the associated physical and chemical processes, we also develop a novel systematic approach to assess the importance and coupling between individual vibrational degrees of freedom during the dynamics. This allows us to explain how the vibrational line shapes of the oligothiophenes change with increasing number of rings. Swiss National Science Foundation Grant No. 200020 150098.
All Electron ab initio Investigations of the Electronic States of the MoN Molecule
DEFF Research Database (Denmark)
Shim, Irene; Gingerich, Karl A.
1999-01-01
The low lying electronic states of the molecule MoN have been investigated by performing all electron ab initio multi-configuration self-consistent-field (CASSCF) calculations. The relativistic corrections for the one electron Darwin contact term and the relativistic mass-velocity correction have...... been determined in perturbation calculations. The electronic ground state is confirmed as being 4 . The chemical bond of MoN has triple bond character due to the approximately fully occupied delocalized bonding and orbitals. The spectroscopic constants for the ground state and ten excited states have....... The spectroscopic constants for the 4 ground state have been determined as re = 1.636 Å and e = 1109 cm-1, and for the 4 state as re = 1.662 Å and e = 941 cm-1. The values for the ground state are in excellent agreement with available experimental data. The MoN molecule is polar with charge transfer from Mo to N...
Quantum mechanical ab initio simulation of the electron screening effect in metal deuteride crystals
Energy Technology Data Exchange (ETDEWEB)
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
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.
Raman Spectroscopy and Ab-Initio Model Calculations on Ionic Liquids
DEFF Research Database (Denmark)
Berg, Rolf W.
2007-01-01
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...... that the structural resolving power of Raman spectroscopy will be appreciated by the reader. It is of remarkable use on crystals of known different conformations and on the corresponding liquids, especially in combination with modern quantum mechanics calculations. It is hoped that these interdisciplinary methods...... 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-methylimidazolium ([C4mim][X]) salts. The rotational isomerism of the [C4mim]þ cation is described: the presence of anti...
Ab initio atomic recombination reaction energetics on model heat shield surfaces
Senese, Fredrick; Ake, Robert
1992-01-01
Ab initio quantum mechanical calculations on small hydration complexes involving the nitrate anion are reported. The self-consistent field method with accurate basis sets has been applied to compute completely optimized equilibrium geometries, vibrational frequencies, thermochemical parameters, and stable site labilities of complexes involving 1, 2, and 3 waters. The most stable geometries in the first hydration shell involve in-plane waters bridging pairs of nitrate oxygens with two equal and bent hydrogen bonds. A second extremely labile local minimum involves out-of-plane waters with a single hydrogen bond and lies about 2 kcal/mol higher. The potential in the region of the second minimum is extremely flat and qualitatively sensitive to changes in the basis set; it does not correspond to a true equilibrium structure.
International Nuclear Information System (INIS)
Degoli, Elena; Bisi, O.; Ossicini, Stefano; Cantele, G.; Ninno, D.; Luppi, Eleonora; Magri, Rita
2004-01-01
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
Ab initio 0 νββ matrix elements from the valence space IMSRG
Stroberg, Ragnar; Payne, Charlie; Holt, Jason
2017-09-01
Neutrinoless double beta decay poses two main challenges to nuclear theory: (1) The process has not been observed, and so there is no way to experimentally constrain an empirical effective operator for phenomenological approaches, as is done with e.g. the quenching of gA or effective charges for E2 transitions. This may be addressed by deriving the transition operator from chiral effective field theory, however this raises the second issue: (2) Nuclei of interest in searches for neutrinoless double beta decay, such as 76Ge and 136Xe, are difficult to treat with the ab initio many-body approaches needed to employ a transition operator derived from chiral effective field theory. I will discuss recent process towards overcoming these two difficulties by using the valence space in-medium similarity renormalization group approach.
Ab initio calculation of ICD widths in photoexcited HeNe
Energy Technology Data Exchange (ETDEWEB)
Jabbari, G.; Klaiman, S.; Chiang, Y.-C.; Gokhberg, K., E-mail: kirill@pci.uni-heidelberg.de [Theoretische Chemie, Physikalisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 229, D-69120 Heidelberg (Germany); Trinter, F.; Jahnke, T. [Institut für Kernphysik, Goethe-Universität Frankfurt, Max-von-Laue-Str. 1, D-60438 Frankfurt (Germany)
2014-06-14
Excitation of HeNe by synchrotron light just below the frequency of the 1s → 3p transition of isolated He has been recently shown to be followed by resonant interatomic Coulombic decay (ICD). The vibrationally resolved widths of the ICD states were extracted with high precision from the photoion spectra. In this paper, we report the results of ab initio calculations of these widths. We show that interaction between electronic states at about the equilibrium distance of HeNe makes dark states of He accessible for the photoexcitation and subsequent electronic decay. Moreover, the values of the calculated widths are shown to be strongly sensitive to the presence of the non-adiabatic coupling between the electronic states participating in the decay. Therefore, only by considering the complete manifold of interacting decaying electronic states a good agreement between the measured and computed ICD widths can be achieved.
Trends in magnetism of free Rh clusters via relativistic ab-initio calculations.
Šipr, O; Ebert, H; Minár, J
2015-02-11
A fully relativistic ab-initio study on free Rh clusters of 13-135 atoms is performed to identify general trends concerning their magnetism and to check whether concepts which proved to be useful in interpreting magnetism of 3d metals are applicable to magnetism of 4d systems. We found that there is no systematic relation between local magnetic moments and coordination numbers. On the other hand, the Stoner model appears well-suited both as a criterion for the onset of magnetism and as a guide for the dependence of local magnetic moments on the site-resolved density of states at the Fermi level. Large orbital magnetic moments antiparallel to spin magnetic moments were found for some sites. The intra-atomic magnetic dipole Tz term can be quite large at certain sites but as a whole it is unlikely to affect the interpretation of x-ray magnetic circular dichroism experiments based on the sum rules.
Study of the atomic rare gas behaviour by ab initio calculations
International Nuclear Information System (INIS)
Petit, Th.
2002-01-01
The atomic behaviour of helium and krypton in uranium dioxide has been studied using an ab initio simulation technique. Incorporation energies and solution energies of these two rare gases have been calculated. Krypton atoms are found to be insoluble in this nuclear fuel whatever the trap considered and their presence in the lattice induces swelling when they are located in interstitial sites or in oxygen vacancies. Due to its small atomic size, the predicted helium behaviour is very different. Indeed, helium is found to be soluble in stoichiometric and hyper-stoichiometric uranium dioxide in the presence of uranium vacancies or divacancies constituted by one uranium and one oxygen vacancy. Moreover helium atoms induce a lattice parameter contraction except in interstitial sites where a slight expansion is calculated. (author)
Prediction of toxicity of nitrobenzenes using ab initio and least squares support vector machines
International Nuclear Information System (INIS)
Niazi, Ali; Jameh-Bozorghi, Saeed; Nori-Shargh, Davood
2008-01-01
A quantitative structure-property relationship (QSPR) study is suggested for the prediction of toxicity (IGC 50 ) of nitrobenzenes. Ab initio theory was used to calculate some quantum chemical descriptors including electrostatic potentials and local charges at each atom, HOMO and LUMO energies, etc. Modeling of the IGC 50 of nitrobenzenes as a function of molecular structures was established by means of the least squares support vector machines (LS-SVM). This model was applied for the prediction of the toxicity (IGC 50 ) of nitrobenzenes, which were not in the modeling procedure. The resulted model showed high prediction ability with root mean square error of prediction of 0.0049 for LS-SVM. Results have shown that the introduction of LS-SVM for quantum chemical descriptors drastically enhances the ability of prediction in QSAR studies superior to multiple linear regression and partial least squares
All Electron ab initio Investigations of the Electronic States of the MoN Molecule
DEFF Research Database (Denmark)
Shim, Irene; Gingerich, Karl A.
1999-01-01
The low lying electronic states of the molecule MoN have been investigated by performing all electron ab initio multi-configuration self-consistent-field (CASSCF) calculations. The relativistic corrections for the one electron Darwin contact term and the relativistic mass-velocity correction have...... been derived. The excited doublet states, 2 , 2 , 2 , and 2 + are found to be lower lying than the 4 state that has been investigated experimentally. Elaborate multi configuration configuration interaction (MRCI) calculations have been carried out for the states 4 and 4 using various basis sets....... The spectroscopic constants for the 4 ground state have been determined as re = 1.636 Å and e = 1109 cm-1, and for the 4 state as re = 1.662 Å and e = 941 cm-1. The values for the ground state are in excellent agreement with available experimental data. The MoN molecule is polar with charge transfer from Mo to N...
Quantifying Ab Initio Equation of State Errors for Hydrogen-Helium Mixtures
Clay, Raymond; Morales, Miguel
2017-06-01
In order to produce predictive models of Jovian planets, an accurate equation of state for hydrogen-helium mixtures is needed over pressure and temperature ranges spanning multiple orders of magnitude. While extensive theoretical work has been done in this area, previous controversies regarding the equation of state of pure hydrogen have demonstrated exceptional sensitivity to approximations commonly employed in ab initio calculations. To this end, we present the results of our quantum Monte Carlo based benchmarking studies for several major classes of density functionals. Additionally, we expand upon our published results by considering the impact that ionic finite size effects and density functional errors translate to errors in the equation of state. Sandia National Laboratories is a multi-mission laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.
International Nuclear Information System (INIS)
Walker, I C; McEwen, I J; Holland, D M P; Shaw, D A; Guest, M F
2008-01-01
The absolute photoabsorption spectrum of ethylene oxide (C 2 H 4 O) has been measured between onset and 30 eV, using monochromated synchrotron radiation. Below the ionization threshold (10.56 eV) the spectrum is dominated by sharp peaks related to excitation of Rydberg series converging on the first ionization energy. Above the ionization threshold, valence-excited states, which give rise to broad bands, predominate. Underlying Rydberg states are signalled in weak vibrational structure on the valence bands. Ab initio multireference configuration interaction (MRDCI) calculations have been carried out to assist in assignment of the excited states, both valence and Rydberg. The lowest-lying valence state is electric-dipole forbidden; the first optically allowed valence state lies close to the ionization onset. The spectrum of the oxide is compared with those of cyclopropane (C 3 H 6 ) and ethylene sulphide (C 2 H 4 S)
Barbosa, Marcelo
A review about the nuclear properties, namely the nuclear moments (magnetic dipole moment and electric quadrupole moment) and their interaction with electromagnetic fields external to the nucleus (hyperfine interactions), as well as the angular distribution of radiation produced by $\\gamma$-decay, is presented. A detailed description about the theory of Perturbed Angular Correlations was done, including the comparison between $\\gamma-\\gamma$- correlations and $e^{-}- \\gamma$ correlations. For dynamic nuclear interactions, an introduction to the theory of stochastic states in PAC was performed. We focused on ab-initio implementation of observables for analyzing fluctuating quadrupole hyperfine interactions on time dependent perturbed angular correlations experiments. The development of computacional codes solving the full problem, adapted to fit data obtained on single crystals or polycrystals for two-state transient fields with any axial symmetry and orientation was the main purpose of this work. The final pa...
International Nuclear Information System (INIS)
Moradian, Rostam; Behzad, Somayeh; Chegel, Raad
2008-01-01
By using ab initio density functional theory the structural and electronic properties of isolated and bundled (8,0) and (6,6) silicon carbide nanotubes (SiCNTs) are investigated. Our results show that for such small diameter nanotubes the inter-tube interaction causes a very small radial deformation, while band splitting and reduction of the semiconducting energy band gap are significant. We compared the equilibrium interaction energy and inter-tube separation distance of (8,0) SiCNT bundle with (10,0) carbon nanotube (CNT) bundle where they have the same radius. We found that there is a larger inter-tube separation and weaker inter-tube interaction in the (8,0) SiCNT bundle with respect to (10,0) CNT bundle, although they have the same radius
Stress reduction of Cu-doped diamond-like carbon films from ab initio calculations
Directory of Open Access Journals (Sweden)
Xiaowei Li
2015-01-01
Full Text Available Structure and properties of Cu-doped diamond-like carbon films (DLC were investigated using ab initio calculations. The effect of Cu concentrations (1.56∼7.81 at.% on atomic bond structure was mainly analyzed to clarify the residual stress reduction mechanism. Results showed that with introducing Cu into DLC films, the residual compressive stress decreased firstly and then increased for each case with the obvious deterioration of mechanical properties, which was in agreement with the experimental results. Structural analysis revealed that the weak Cu-C bond and the relaxation of both the distorted bond angles and bond lengths accounted for the significant reduction of residual compressive stress, while at the higher Cu concentration the increase of residual stress attributed to the existence of distorted Cu-C structures and the increased fraction of distorted C-C bond lengths.
Ab Initio Molecular-Dynamics Simulation of Neuromorphic Computing in Phase-Change Memory Materials.
Skelton, Jonathan M; Loke, Desmond; Lee, Taehoon; Elliott, Stephen R
2015-07-08
We present an in silico study of the neuromorphic-computing behavior of the prototypical phase-change material, Ge2Sb2Te5, using ab initio molecular-dynamics simulations. Stepwise changes in structural order in response to temperature pulses of varying length and duration are observed, and a good reproduction of the spike-timing-dependent plasticity observed in nanoelectronic synapses is demonstrated. Short above-melting pulses lead to instantaneous loss of structural and chemical order, followed by delayed partial recovery upon structural relaxation. We also investigate the link between structural order and electrical and optical properties. These results pave the way toward a first-principles understanding of phase-change physics beyond binary switching.
NestedMICA as an ab initio protein motif discovery tool
Directory of Open Access Journals (Sweden)
Down Thomas A
2008-01-01
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/
Directory of Open Access Journals (Sweden)
Provero P
2005-05-01
Full Text Available Abstract Background Understanding transcriptional regulation of gene expression is one of the greatest challenges of modern molecular biology. A central role in this mechanism is played by transcription factors, which typically bind to specific, short DNA sequence motifs usually located in the upstream region of the regulated genes. We discuss here a simple and powerful approach for the ab initio identification of these cis-regulatory motifs. The method we present integrates several elements: human-mouse comparison, statistical analysis of genomic sequences and the concept of coregulation. We apply it to a complete scan of the human genome. Results By using the catalogue of conserved upstream sequences collected in the CORG database we construct sets of genes sharing the same overrepresented motif (short DNA sequence in their upstream regions both in human and in mouse. We perform this construction for all possible motifs from 5 to 8 nucleotides in length and then filter the resulting sets looking for two types of evidence of coregulation: first, we analyze the Gene Ontology annotation of the genes in the set, searching for statistically significant common annotations; second, we analyze the expression profiles of the genes in the set as measured by microarray experiments, searching for evidence of coexpression. The sets which pass one or both filters are conjectured to contain a significant fraction of coregulated genes, and the upstream motifs characterizing the sets are thus good candidates to be the binding sites of the TF's involved in such regulation. In this way we find various known motifs and also some new candidate binding sites. Conclusion We have discussed a new integrated algorithm for the "ab initio" identification of transcription factor binding sites in the human genome. The method is based on three ingredients: comparative genomics, overrepresentation, different types of coregulation. The method is applied to a full-scan of the
14N NQR lineshape in nanocrystals: An ab initio investigation of urea
Gregorovič, Alan
2017-05-01
14N nuclear quadrupole resonance (NQR) lineshapes mostly contain information of low interest, although in nanocrystals they may display some unexpected behaviour. In this work, we present an ab initio computational study of the 14N NQR lineshapes in urea nanocrystals as a function of the nanocrystal size and geometry, focusing on the surface induced broadening of the lineshapes. The lineshapes were obtained through a calculation of the electric field gradient for each nitrogen site in the nanocrystal separately, taking into account the individual crystal field by embedding the molecule of interest in a suitable lattice of point multipoles representing other urea molecules in the nanocrystal. The small influence of distant molecules is found with a series expansion, using the in-crystal Sternheimer shieldings which we also calculated ab initio. We have considered nanocrystals with two geometries: a sphere and a cube, with characteristic sizes between 5 and 100 nm. Our calculations suggest that there is a dramatic difference between the linewidths for the two geometries. For spheres, we find a steep drop in linewidths at ˜10 nm; at 5 nm the linewidth is ˜11 kHz, whereas for sizes above 20 nm the linewidth is practically negligible (<100 Hz). For cubes, on the other hand, we find a steady 1/size decrease, from 12 kHz at 10 nm to 1.2 kHz at 100 nm. This analysis is important for 14N NQR spectroscopy of crystalline pharmaceuticals, where nanoparticles are increasingly more often embedded in some sort of matrix. Although this is only a theoretical analysis, we believe that this work can serve as a guidance for the forthcoming experimental analysis.
Integration of QUARK and I-TASSER for Ab Initio Protein Structure Prediction in CASP11.
Zhang, Wenxuan; Yang, Jianyi; He, Baoji; Walker, Sara Elizabeth; Zhang, Hongjiu; Govindarajoo, Brandon; Virtanen, Jouko; Xue, Zhidong; Shen, Hong-Bin; Zhang, Yang
2016-09-01
We tested two pipelines developed for template-free protein structure prediction in the CASP11 experiment. First, the QUARK pipeline constructs structure models by reassembling fragments of continuously distributed lengths excised from unrelated proteins. Five free-modeling (FM) targets have the model successfully constructed by QUARK with a TM-score above 0.4, including the first model of T0837-D1, which has a TM-score = 0.736 and RMSD = 2.9 Å to the native. Detailed analysis showed that the success is partly attributed to the high-resolution contact map prediction derived from fragment-based distance-profiles, which are mainly located between regular secondary structure elements and loops/turns and help guide the orientation of secondary structure assembly. In the Zhang-Server pipeline, weakly scoring threading templates are re-ordered by the structural similarity to the ab initio folding models, which are then reassembled by I-TASSER based structure assembly simulations; 60% more domains with length up to 204 residues, compared to the QUARK pipeline, were successfully modeled by the I-TASSER pipeline with a TM-score above 0.4. The robustness of the I-TASSER pipeline can stem from the composite fragment-assembly simulations that combine structures from both ab initio folding and threading template refinements. Despite the promising cases, challenges still exist in long-range beta-strand folding, domain parsing, and the uncertainty of secondary structure prediction; the latter of which was found to affect nearly all aspects of FM structure predictions, from fragment identification, target classification, structure assembly, to final model selection. Significant efforts are needed to solve these problems before real progress on FM could be made. Proteins 2016; 84(Suppl 1):76-86. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.
Ab-initio electronic and magnetic properties of Fe-Al alloys
Directory of Open Access Journals (Sweden)
Apiñaniz, E.
2000-06-01
Full Text Available This work presents ab-initio self-consistent calculations performed with the TB-LMTO code to study the different phases of the Fe-Al phase diagram, corresponding to the ordered structures B2, DO3 and B32 and for Fe50Al50 and Fe3Al compositions. Both, unpolarized and spin-polarized calculations have been performed to deduce the energetic difference between the paramagnetic and ferromagnetic state of the corresponding structure. Calculations for the disordered structures have also been performed for the previously mentioned compositions. These results show that by disordering the alloy magnetism is enhanced and that the equilibrium lattice parameter increases.
En este trabajo se presentan cálculos autoconsistentes ab-initio realizados con el método TB-LMTO (Tight Binding Linear Muffin Tin Orbital con el fin de estudiar las diferentes estructuras que se presentan en el diagrama de fases de las aleaciones Fe-Al. Se han estudiado las estructuras ordenadas B2, DO3 y B32 para las siguientes concentraciones: Fe50Al50 y Fe3Al. Asimismo, se han realizado cálculos teniendo y sin tener en cuenta la polarización de spin con el fin de poder deducir la diferencia energética entre los estados ferromágneticos y paramágneticos de la misma estructura. Por otra parte se han realizado estos mismos cálculos para estructuras desordenadas y las mismas concentraciones. Los resultados muestran que mediante el desorden aumenta el magnetismo de estas aleaciones y crece el parámetro de red.
Yabana, Kazuhiro
2017-05-01
Ab-initio density functional theory (DFT) has been successful for calculations of ground state properties of various materials. Time-dependent density functional theory (TDDFT) is an extension of the DFT and can describe electron dynamics in molecules, nano-structures, and solids induced by optical electric fields. We have been developing a computational method to describe electron dynamics in a crystalline solid under an irradiation of an ultrashort laser pulse, solving the time-dependent Kohn-Sham equation in real time. The method can be used for an ab-initio description of light-matter interactions. We further couple the electron dynamics calculation with the macroscopic Maxwell equations in a multiscale implementation. It can describe laser pulse propagation in dielectrics and, in particular,the energy transfer from the laser pulse to electrons in dielectrics without any empirical parameters. We apply the method to analyze recent experiments utilizing attosecond spectroscopy methods. We show a few examples. One is for the ultrafast changes of dielectric properties of diamond during the irradiation of an intense few-cycle laser pulse. We mimic the pump-probe measurement employing the multiscale Maxwell + TDDFT simulation. We clarified that the dynamical Franz-Keldysh effect is responsible for the mechanism. The other is to identify the onset of the energy transfer from the laser pulse to SiO_2 when we increase the intensity of the laser pulse. We are currently extending the analysis to obtain a clear and intuitive understanding for the initial stage of laser damage processes.
Winter, Bernd; Weber, Ramona; Hertel, Ingolf V; Faubel, Manfred; Jungwirth, Pavel; Brown, Eric C; Bradforth, Stephen E
2005-05-18
Photoelectron spectroscopy combined with the liquid microjet technique enables the direct probing of the electronic structure of aqueous solutions. We report measured and calculated lowest vertical electron binding energies of aqueous alkali cations and halide anions. In some cases, ejection from deeper electronic levels of the solute could be observed. Electron binding energies of a given aqueous ion are found to be independent of the counterion and the salt concentration. The experimental results are complemented by ab initio calculations, at the MP2 and CCSD(T) level, of the ionization energies of these prototype ions in the aqueous phase. The solvent effect was accounted for in the electronic structure calculations in two ways. An explicit inclusion of discrete water molecules using a set of snapshots from an equilibrium classical molecular dynamics simulations and a fractional charge representation of solvent molecules give good results for halide ions. The electron binding energies of alkali cations computed with this approach tend to be overestimated. On the other hand, the polarizable continuum model, which strictly provides adiabatic binding energies, performs well for the alkali cations but fails for the halides. Photon energies in the experiment were in the EUV region (typically 100 eV) for which the technique is probing the top layers of the liquid sample. Hence, the reported energies of aqueous ions are closely connected with both structures and chemical reactivity at the liquid interface, for example, in atmospheric aerosol particles, as well as fundamental bulk solvation properties.
Energy Technology Data Exchange (ETDEWEB)
Xin, H. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Stanford Univ., Stanford, CA (United States); LaRue, J. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Oberg, H. [Stockholm Univ., Stockholm (Sweden); Beye, M. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Helmholtz Zentrum Berlin fur Materialien und Energie GmbH, Berlin (Germany); Dell' Angela, M. [Univ. of Hamburg and Center for Free Electron Laser Science, Hamburg (Germany); Turner, J. J. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Gladh, J. [Stockholm Univ., Stockholm (Sweden); Ng, M. L. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Sellberg, J. A. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Helmholtz Zentrum Berlin fur Materialien und Energie GmbH, Berlin (Germany); Kaya, S. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Mercurio, G. [Univ. of Hamburg and Center for Free Electron Laser Science, Hamburg (Germany); Hieke, F. [Univ. of Hamburg and Center for Free Electron Laser Science, Hamburg (Germany); Nordlund, D. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Schlotter, W. F. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Dakovski, G. L. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Minitti, M. P. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Fohlisch, A. [Helmholtz Zentrum Berlin fur Materialien und Energie GmbH, Berlin (Germany); Univ. Potsdam, Potsdam (Germany); Wolf, M. [Fritz-Haber Institute of the Max-Planck-Society, Berlin (Germany); Wurth, W. [Univ. of Hamburg and Center for Free Electron Laser Science, Hamburg (Germany); DESY Photon Science, Hamburg (Germany); Ogasawara, H. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Norskov, J. K. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Stanford Univ., Stanford, CA (United States); Ostrom, H. [Stockholm Univ., Stockholm (Sweden); Pettersson, L. G. M. [Stockholm Univ., Stockholm (Sweden); Nilsson, A. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Stockholm Univ., Stockholm (Sweden); Ablid-Pedersen, F. [SLAC National Accelerator Lab., Menlo Park, CA (United States)
2015-04-16
We show that coadsorbed oxygen atoms have a dramatic influence on the CO desorption dynamics from Ru(0001). In contrast to the precursor-mediated desorption mechanism on Ru(0001), the presence of surface oxygen modifies the electronic structure of Ru atoms such that CO desorption occurs predominantly via the direct pathway. This phenomenon is directly observed in an ultrafast pump-probe experiment using a soft x-ray free-electron laser to monitor the dynamic evolution of the valence electronic structure of the surface species. This is supported with the potential of mean force along the CO desorption path obtained from density-functional theory calculations. Charge density distribution and frozen-orbital analysis suggest that the oxygen-induced reduction of the Pauli repulsion, and consequent increase of the dative interaction between the CO 5σ and the charged Ru atom, is the electronic origin of the distinct desorption dynamics. Ab initio molecular dynamics simulations of CO desorption from Ru(0001) and oxygen-coadsorbed Ru(0001) provide further insights into the surface bond-breaking process.
Energy Technology Data Exchange (ETDEWEB)
Kordatos, Apostolis [National Center for Scientific Research “Demokritos”, Athens, 15310 (Greece); Kelaidis, Nikolaos, E-mail: n.kelaidis@inn.demokritos.gr [National Center for Scientific Research “Demokritos”, Athens, 15310 (Greece); Giamini, Sigiava Aminalragia [National Center for Scientific Research “Demokritos”, Athens, 15310 (Greece); University of Athens, Department of Physics, Section of Solid State Physics, Athens, 15684 Greece (Greece); Marquez-Velasco, Jose [National Center for Scientific Research “Demokritos”, Athens, 15310 (Greece); National Technical University of Athens, Department of Physics, Athens, 15784 Greece (Greece); Xenogiannopoulou, Evangelia; Tsipas, Polychronis; Kordas, George; Dimoulas, Athanasios [National Center for Scientific Research “Demokritos”, Athens, 15310 (Greece)
2016-04-30
Highlights: • Growth of non-defective few layer graphene on Rh(1 1 1) substrates using an ambient- pressure CVD method. • Control of graphene stacking order via the cool-down rate. • Graphene is grown with a mainly AB-stacking geometry on single-crystalline Rhodium for a slow cool-down rate and non-AB for a very fast cool-down. • Good epitaxial orientation of the surface is presented through the RHEED data and confirmed with ARPES characterization for the lower cool-down rate, where graphene's ΓK direction a perfectly aligned with the ΓK direction of the Rh(1 1 1) single crystal. - Abstract: Graphene synthesis on single crystal Rh(1 1 1) catalytic substrates is performed by Chemical Vapor Deposition (CVD) at 1000 °C and atmospheric pressure. Raman analysis shows full substrate coverage with few layer graphene. It is found that the cool-down rate strongly affects the graphene stacking order. When lowered, the percentage of AB (Bernal) -stacked regions increases, leading to an almost full AB stacking order. When increased, the percentage of AB-stacked graphene regions decreases to a point where almost a full non AB-stacked graphene is grown. For a slow cool-down rate, graphene with AB stacking order and good epitaxial orientation with the substrate is achieved. This is indicated mainly by Raman characterization and confirmed by Reflection high-energy electron diffraction (RHEED) imaging. Additional Scanning Tunneling Microscopy (STM) topography data confirm that the grown graphene is mainly an AB-stacked structure. The electronic structure of the graphene/Rh(1 1 1) system is examined by Angle resolved Photo-Emission Spectroscopy (ARPES), where σ and π bands of graphene, are observed. Graphene's ΓK direction is aligned with the ΓK direction of the substrate, indicating no significant contribution from rotated domains.
International Nuclear Information System (INIS)
Kordatos, Apostolis; Kelaidis, Nikolaos; Giamini, Sigiava Aminalragia; Marquez-Velasco, Jose; Xenogiannopoulou, Evangelia; Tsipas, Polychronis; Kordas, George; Dimoulas, Athanasios
2016-01-01
Highlights: • Growth of non-defective few layer graphene on Rh(1 1 1) substrates using an ambient- pressure CVD method. • Control of graphene stacking order via the cool-down rate. • Graphene is grown with a mainly AB-stacking geometry on single-crystalline Rhodium for a slow cool-down rate and non-AB for a very fast cool-down. • Good epitaxial orientation of the surface is presented through the RHEED data and confirmed with ARPES characterization for the lower cool-down rate, where graphene's ΓK direction a perfectly aligned with the ΓK direction of the Rh(1 1 1) single crystal. - Abstract: Graphene synthesis on single crystal Rh(1 1 1) catalytic substrates is performed by Chemical Vapor Deposition (CVD) at 1000 °C and atmospheric pressure. Raman analysis shows full substrate coverage with few layer graphene. It is found that the cool-down rate strongly affects the graphene stacking order. When lowered, the percentage of AB (Bernal) -stacked regions increases, leading to an almost full AB stacking order. When increased, the percentage of AB-stacked graphene regions decreases to a point where almost a full non AB-stacked graphene is grown. For a slow cool-down rate, graphene with AB stacking order and good epitaxial orientation with the substrate is achieved. This is indicated mainly by Raman characterization and confirmed by Reflection high-energy electron diffraction (RHEED) imaging. Additional Scanning Tunneling Microscopy (STM) topography data confirm that the grown graphene is mainly an AB-stacked structure. The electronic structure of the graphene/Rh(1 1 1) system is examined by Angle resolved Photo-Emission Spectroscopy (ARPES), where σ and π bands of graphene, are observed. Graphene's ΓK direction is aligned with the ΓK direction of the substrate, indicating no significant contribution from rotated domains.
International Nuclear Information System (INIS)
Liu, Hanchao; Wang, Yimin; Bowman, Joel M.
2015-01-01
The calculation and characterization of the IR spectrum of liquid water have remained a challenge for theory. In this paper, we address this challenge using a combination of ab initio approaches, namely, a quantum treatment of IR spectrum using the ab initio WHBB water potential energy surface and a refined ab initio dipole moment surface. The quantum treatment is based on the embedded local monomer method, in which the three intramolecular modes of each embedded H 2 O monomer are fully coupled and also coupled singly to each of six intermolecular modes. The new dipole moment surface consists of a previous spectroscopically accurate 1-body dipole moment surface and a newly fitted ab initio intrinsic 2-body dipole moment. A detailed analysis of the new dipole moment surface in terms of the coordinate dependence of the effective atomic charges is done along with tests of it for the water dimer and prism hexamer double-harmonic spectra against direct ab initio calculations. The liquid configurations are taken from previous molecular dynamics calculations of Skinner and co-workers, using the TIP4P plus E3B rigid monomer water potential. The IR spectrum of water at 300 K in the range of 0–4000 cm −1 is calculated and compared with experiment, using the ab initio WHBB potential and new ab initio dipole moment, the q-TIP4P/F potential, which has a fixed-charged description of the dipole moment, and the TTM3-F potential and dipole moment surfaces. The newly calculated ab initio spectrum is in very good agreement with experiment throughout the above spectral range, both in band positions and intensities. This contrasts to results with the other potentials and dipole moments, especially the fixed-charge q-TIP4P/F model, which gives unrealistic intensities. The calculated ab initio spectrum is analyzed by examining the contribution of various transitions to each band
Ab initio calculation of electronic structure and magnetic properties of R2Fe14BNx (R = Pr,Nd)
Tian, Guang; Zha, Liang; Yang, Wenyun; Qiao, Guanyi; Wang, Changsheng; Yang, Yingchang; Yang, Jinbo
2018-05-01
The site preference of N atom for R2Fe14BNx (R= Pr, Nd) and the interstitial nitrogen effect on the magnetic properties have been studied by the first-principles method. It was found that the nitrogen is more likely to occupy the 4e site for Pr2Fe14BNx compound, while 4f site for Nd2Fe14BNx. When N atoms entering some specific crystal sites (such as 2a and 4f), the total magnetic moments of these compounds are not reduced, but slightly increased. Although the doping of N may reduce the total magnetic moments of some R2Fe14B compounds in the cases of optimal occupancy, the volumetric effect caused by N doping can still change the electron density distributions of Fe near the Fermi level, improving the magnetic ordering temperature of such compounds.
Czech Academy of Sciences Publication Activity Database
Romanyuk, Olexandr; Supplie, O.; Susi, T.; May, M.M.; Hannappel, T.
2016-01-01
Roč. 94, č. 15 (2016), s. 1-9, č. článku 155309. ISSN 2469-9950 R&D Projects: GA ČR GF16-34856L Institutional support: RVO:68378271 Keywords : interface structure * GaP/Si heterointerface * interface electronic states * core- level shifts Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.836, year: 2016
Ab initio and homology based prediction of protein domains by recursive neural networks
Directory of Open Access Journals (Sweden)
Mooney Catherine
2009-06-01
Full Text Available Abstract Background Proteins, especially larger ones, are often composed of individual evolutionary units, domains, which have their own function and structural fold. Predicting domains is an important intermediate step in protein analyses, including the prediction of protein structures. Results We describe novel systems for the prediction of protein domain boundaries powered by Recursive Neural Networks. The systems rely on a combination of primary sequence and evolutionary information, predictions of structural features such as secondary structure, solvent accessibility and residue contact maps, and structural templates, both annotated for domains (from the SCOP dataset and unannotated (from the PDB. We gauge the contribution of contact maps, and PDB and SCOP templates independently and for different ranges of template quality. We find that accurately predicted contact maps are informative for the prediction of domain boundaries, while the same is not true for contact maps predicted ab initio. We also find that gap information from PDB templates is informative, but, not surprisingly, less than SCOP annotations. We test both systems trained on templates of all qualities, and systems trained only on templates of marginal similarity to the query (less than 25% sequence identity. While the first batch of systems produces near perfect predictions in the presence of fair to good templates, the second batch outperforms or match ab initio predictors down to essentially any level of template quality. We test all systems in 5-fold cross-validation on a large non-redundant set of multi-domain and single domain proteins. The final predictors are state-of-the-art, with a template-less prediction boundary recall of 50.8% (precision 38.7% within ± 20 residues and a single domain recall of 80.3% (precision 78.1%. The SCOP-based predictors achieve a boundary recall of 74% (precision 77.1% again within ± 20 residues, and classify single domain proteins as
High pressure behaviour of uranium dicarbide (UC{sub 2}): Ab-initio study
Energy Technology Data Exchange (ETDEWEB)
Sahoo, B. D., E-mail: bdsahoo@barc.gov.in; Mukherjee, D.; Joshi, K. D.; Kaushik, T. C. [Applied Physics Division, Bhabha Atomic Research Centre, Mumbai 400085 (India)
2016-08-28
The structural stability of uranium dicarbide has been examined under hydrostatic compression employing evolutionary structure search algorithm implemented in the universal structure predictor: evolutionary Xtallography (USPEX) code in conjunction with ab-initio electronic band structure calculation method. The ab-initio total energy calculations involved for this purpose have been carried out within both generalized gradient approximations (GGA) and GGA + U approximations. Our calculations under GGA approximation predict the high pressure structural sequence of tetragonal → monoclinic → orthorhombic for this material with transition pressures of ∼8 GPa and 42 GPa, respectively. The same transition sequence is predicted by calculations within GGA + U also with transition pressures placed at ∼24 GPa and ∼50 GPa, respectively. Further, on the basis of comparison of zero pressure equilibrium volume and equation of state with available experimental data, we find that GGA + U approximation with U = 2.5 eV describes this material better than the simple GGA approximation. The theoretically predicted high pressure structural phase transitions are in disagreement with the only high experimental study by Dancausse et al. [J. Alloys. Compd. 191, 309 (1993)] on this compound which reports a tetragonal to hexagonal phase transition at a pressure of ∼17.6 GPa. Interestingly, during lowest enthalpy structure search using USPEX, we do not see any hexagonal phase to be closer to the predicted monoclinic phase even within 0.2 eV/f. unit. More experiments with varying carbon contents in UC{sub 2} sample are required to resolve this discrepancy. The existence of these high pressure phases predicted by static lattice calculations has been further substantiated by analyzing the elastic and lattice dynamic stability of these structures in the pressure regimes of their structural stability. Additionally, various thermo-physical quantities such as
Bakowies, Dirk
2009-04-01
A theoretical composite approach, termed ATOMIC for Ab initio Thermochemistry using Optimal-balance Models with Isodesmic Corrections, is introduced for the calculation of molecular atomization energies and enthalpies of formation. Care is taken to achieve optimal balance in accuracy and cost between the various components contributing to high-level estimates of the fully correlated energy at the infinite-basis-set limit. To this end, the energy at the coupled-cluster level of theory including single, double, and quasiperturbational triple excitations is decomposed into Hartree-Fock, low-order correlation (MP2, CCSD), and connected-triples contributions and into valence-shell and core contributions. Statistical analyses for 73 representative neutral closed-shell molecules containing hydrogen and at least three first-row atoms (CNOF) are used to devise basis-set and extrapolation requirements for each of the eight components to maintain a given level of accuracy. Pople's concept of bond-separation reactions is implemented in an ab initio framework, providing for a complete set of high-level precomputed isodesmic corrections which can be used for any molecule for which a valence structure can be drawn. Use of these corrections is shown to lower basis-set requirements dramatically for each of the eight components of the composite model. A hierarchy of three levels is suggested for isodesmically corrected composite models which reproduce atomization energies at the reference level of theory to within 0.1 kcal/mol (A), 0.3 kcal/mol (B), and 1 kcal/mol (C). Large-scale statistical analysis shows that corrections beyond the CCSD(T) reference level of theory, including coupled-cluster theory with fully relaxed connected triple and quadruple excitations, first-order relativistic and diagonal Born-Oppenheimer corrections can normally be dealt with using a greatly simplified model that assumes thermoneutral bond-separation reactions and that reduces the estimate of these
Speciation of magnesium in monohydrocalcite: XANES, ab initio and geochemical modeling
Fukushi, Keisuke; Suzuki, Yuma; Kawano, Jun; Ohno, Takeshi; Ogawa, Masahiro; Yaji, Toyonari; Takahashi, Yoshio
2017-09-01
Monohydrocalcite (MHC: CaCO3·H2O), a rare carbonate mineral formed under surface conditions, is usually observed in nature as containing a variable amount of Mg, with a 0.007-0.45 Mg/Ca mole ratio. The variable Mg composition in MHC is anticipated as a promising proxy to assess paleo-hydrochemistry especially in saline lakes. Although the roles of Mg on the formation and stability of MHC have been studied intensively, the Mg speciation in MHC has remained unclear and controversial. This study examined Mg speciation in MHC using X-ray absorption near edge structure (XANES), ab initio molecular simulation, and geochemical modeling. Mg-XANES spectra of MHC with different Mg/Ca ratios prepared from mixing solutions of Na2CO3, CaCl2 and MgCl2 revealed that the Mg in MHC is a mixture of amorphous Mg carbonate (AMC) and other Mg containing phase. The contribution of AMC to total Mg is negatively correlated to the crystallinity of MHC. Results show that AMC might play a protective role in the crystallization and the transformation to stable calcium carbonates. Ab initio calculation of Mg2+ substitution into MHC showed that a limited amount of Mg2+ can be incorporated into the MHC structure. Six-fold coordination of Mg2+ is substituted for eight-fold coordination of Ca2+ in the MHC structure. The other type of Mg in MHC revealed from the XANES analyses most likely corresponds to the structural Mg in MHC. The contribution of the structural Mg is almost constant at 0.06 in Mg/Ca, representing the limit of solid solubility of Mg in MHC. The solubility products of the MHC with the limit of solid solubility of Mg and the AMC associated with MHC were estimated from the reacted solution compositions. Prediction of the Mg/Ca ratio as a function of the initial solution conditions using solubility reasonably reproduces the observed apparent Mg/Ca ratios in MHC from the present study and earlier studies. The apparent Mg/Ca ratio of MHC is useful to elucidate water chemistry
Ab initio STM and STS simulations on magnetic and nonmagnetic metallic surfaces
Energy Technology Data Exchange (ETDEWEB)
Dick, Alexey
2008-04-14
The aim of this work was to provide an in-depth understanding of a new generation of scan- ning tunneling microscopy experiments, performed employing different regimes of the STM: the spectroscopy-mode (the so-called Fourier Transformed STM, FT-STM), and the spin-sensitive mode (the so-called spin-polarized STM, SP-STM). In the present thesis ab initio tools are proposed that are based on DFT calculations to theoretically predict and analyze such types of the STM. The first part of this thesis focusses on the simulation of FT-STM, the mode that allows to probe local dispersion properties of the electrons at the surface. In order to provide the theoretical counterpart of the experimental FT-STM spectra we have introduced a new implicit approach that is derived from Tersoff-Hamann theory of the STM. The importance of an accurate description of surface wavefunctions at 5-15 A above the surface as well as the spurious quantum- size effects have been discussed in detail together with approaches to obtain converged FT-STM images. We applied our method to FT-STM experiments performed on Ag(110) surfaces. In the second part of the thesis we discuss the modeling of the spin-resolved STM, the mode that allows to characterize the magnetic structure of a surface. As a case system we studied here the magnetically-ordered transition-metal nitride surface Mn{sub 3}N{sub 2}(010). Because SP-STM experiments did not allow a conclusive understanding of the surface structure, we have first employed ab initio thermodynamics to figure out the most stable magnetic and atomic configuration of the surface that are consistent with experiments. To simulate SP-STM images on the most stable Mn{sub 3}N{sub 2}(010) surface we have employed the spin-generalized transfer-Hamiltonian formalism, assuming that the tip wavefunctions have dominant radial symmetry (s-like tip). (orig.)
Energy Technology Data Exchange (ETDEWEB)
Lucas, G
2006-10-15
The behaviour of silicon carbide under irradiation has been studied using classical and ab initio simulations, focusing on the nano scale elementary processes. First, we have been interested in the calculation of threshold displacement energies, which are difficult to determine both experimentally and theoretically, and also the associated Frenkel pairs. In the framework of this thesis, we have carried out simulations in classical and ab initio molecular dynamics. For the classical approach, two types of potentials have been used: the Tersoff potential, which led to non satisfactory results, and a new one which has been developed during this thesis. This potential allows a better modelling of SiC under irradiation than most of the empirical potentials available for SiC. It is based on the EDIP potential, initially developed to describe defects in silicon, that we have generalized to SiC. For the ab initio approach, the feasibility of the calculations has been validated and average energies of 19 eV for the C and 38 eV for the Si sublattices have been determined, close to the values empirically used in the fusion community. The results obtained with the new potential EDIP are globally in agreement with those values. Finally, the elementary processes involved in the crystal recovery have been studied by calculating the stability of the created Frenkel pairs and determining possible recombination mechanisms with the nudged elastic band method. (author)
Directory of Open Access Journals (Sweden)
Martin Alberto JM
2009-01-01
Full Text Available Abstract Background Prediction of protein structures from their sequences is still one of the open grand challenges of computational biology. Some approaches to protein structure prediction, especially ab initio ones, rely to some extent on the prediction of residue contact maps. Residue contact map predictions have been assessed at the CASP competition for several years now. Although it has been shown that exact contact maps generally yield correct three-dimensional structures, this is true only at a relatively low resolution (3–4 Å from the native structure. Another known weakness of contact maps is that they are generally predicted ab initio, that is not exploiting information about potential homologues of known structure. Results We introduce a new class of distance restraints for protein structures: multi-class distance maps. We show that Cα trace reconstructions based on 4-class native maps are significantly better than those from residue contact maps. We then build two predictors of 4-class maps based on recursive neural networks: one ab initio, or relying on the sequence and on evolutionary information; one template-based, or in which homology information to known structures is provided as a further input. We show that virtually any level of sequence similarity to structural templates (down to less than 10% yields more accurate 4-class maps than the ab initio predictor. We show that template-based predictions by recursive neural networks are consistently better than the best template and than a number of combinations of the best available templates. We also extract binary residue contact maps at an 8 Å threshold (as per CASP assessment from the 4-class predictors and show that the template-based version is also more accurate than the best template and consistently better than the ab initio one, down to very low levels of sequence identity to structural templates. Furthermore, we test both ab-initio and template-based 8
Efficacy of the SU(3) scheme for ab initio large-scale calculations beyond the lightest nuclei
Energy Technology Data Exchange (ETDEWEB)
Dytrych, T. [Academy of Sciences of the Czech Republic (ASCR), Prague (Czech Republic); Louisiana State Univ., Baton Rouge, LA (United States); Maris, Pieter [Iowa State Univ., Ames, IA (United States); Launey, K. D. [Louisiana State Univ., Baton Rouge, LA (United States); Draayer, J. P. [Louisiana State Univ., Baton Rouge, LA (United States); Vary, James [Iowa State Univ., Ames, IA (United States); Langr, D. [Czech Technical Univ., Prague (Czech Republic); Aerospace Research and Test Establishment, Prague (Czech Republic); Saule, E. [Univ. of North Carolina, Charlotte, NC (United States); Caprio, M. A. [Univ. of Notre Dame, IN (United States); Catalyurek, U. [The Ohio State Univ., Columbus, OH (United States). Dept. of Electrical and Computer Engineering; Sosonkina, M. [Old Dominion Univ., Norfolk, VA (United States)
2016-06-09
We report on the computational characteristics of ab initio nuclear structure calculations in a symmetry-adapted no-core shell model (SA-NCSM) framework. We examine the computational complexity of the current implementation of the SA-NCSM approach, dubbed LSU3shell, by analyzing ab initio results for ^{6}Li and ^{12}C in large harmonic oscillator model spaces and SU(3)-selected subspaces. We demonstrate LSU3shell's strong-scaling properties achieved with highly-parallel methods for computing the many-body matrix elements. Results compare favorably with complete model space calculations and signi cant memory savings are achieved in physically important applications. In particular, a well-chosen symmetry-adapted basis a ords memory savings in calculations of states with a fixed total angular momentum in large model spaces while exactly preserving translational invariance.
Driving nuclei with resonant electrons: Ab initio study of (e+H2) 2Σu+
International Nuclear Information System (INIS)
Robicheaux, F.
1991-01-01
We have calculated the cross sections for vibrational excitation and dissociative attachment in H 2 below 5 eV scattering energy. This completely ab initio calculation uses the frame-transformation method of Greene and Jungen [Adv. At. Mol. Phys. 21, 51 (1985)] for electron-vibronic coupling in resonant scattering from a neutral molecule. We found it necessary to modify their method to obtain good agreement with previous theory and experiment for v=0→v f with v f =1--3; for larger v f and for dissociative attachment we obtained good agreement with previous theory and qualitative agreement with experiment. The fixed-nuclei phase shifts were derived from a fully ab initio calculation in prolate spheroidal coordinates and then transformed to spherical l=1 phase shifts. The vibrational structure of H 2 - becomes evident for excitation from higher vibrational states of H 2 as well as for larger Δv's, confirming previous theory and experiment
Czech Academy of Sciences Publication Activity Database
Burda, J.; Lánská, Božena
2001-01-01
Roč. 74, č. 3 (2001), s. 569-577 ISSN 0141-3910 R&D Projects: GA AV ČR IAA4050702; GA AV ČR KSK2050602 Grant - others:GA UK(XC) 156/99/B Institutional research plan: CEZ:AV0Z4050913 Keywords : ab initio calculations * lactams * reaction mechanism Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 0.905, year: 2001
DEFF Research Database (Denmark)
Åstrand, P.-O.; Bak, K.L.; Sauer, S.P.A.
2001-01-01
The two lowest singlet excitation energies of 26 2-imidazolyl-2-thiazolylazo compounds have been investigated by ab initio methods within the second-order polarization propagator approximation (SOPPA). Various combinations of 4- and 5-substituents at both the imidazole and thiazole units have bee...... included in this study, the longest wavelength was calculated to be 1049 nm. (C) 2001 Elsevier Science B.V. All rights reserved....
X-ray spectroscopy at the Mn K edge in LaMnO3 : An ab initio study
Hozoi, L.; Vries, A.H. de; Broer, R.
2001-01-01
We present ab initio quantum chemical embedded cluster calculations of Mn core-valence and d-d transitions in LaMnO3. The results are also important for the analysis of recent x-ray absorption and x-ray scattering experiments at the Mn K edge in LaMnO3. We find that the first two peaks of the
Czech Academy of Sciences Publication Activity Database
Zeizinger, M.; Burda, J. V.; Šponer, Jiří; Kapsa, V.; Leszczynski, J.
2001-01-01
Roč. 105, č. 34 (2001), s. 8086-8092 ISSN 0305-4470 R&D Projects: GA AV ČR IAA4050702; GA MŠk LN00A032 Institutional research plan: CEZ:AV0Z4040901 Keywords : palladium square-planar complexes * platinum analogues * ab initio Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.542, year: 2001
Czech Academy of Sciences Publication Activity Database
Černý, Miroslav; Šešták, Petr; Řehák, Petr; Všianská, Monika; Šob, Mojmír
2016-01-01
Roč. 669, JUL (2016), s. 218-225 ISSN 0921-5093 R&D Projects: GA ČR(CZ) GA16-24711S; GA ČR(CZ) GAP108/12/0311; GA MŠk(CZ) LQ1601 Institutional support: RVO:68081723 Keywords : Theoretical strength * Computational tensile test * Grain boundary embrittlement * Ab initio calculations Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.094, year: 2016
International Nuclear Information System (INIS)
Pereiro, M.; Botana, J.; Baldomir, D.; Warda, K.; Wojtczak, L.; Man'kovsky, S.V.; Iglesias, M.; Pardo, V.; Arias, J.E.
2005-01-01
Ab initio full-potential linearized augmented-plane-wave (FP-LAPW) method combined with the semiclassical Boltzmann formalism was employed to calculate the giant magnetoresistance ratio in the trilayers nFe/3Cr/nFe (1=< n=<8). The present results emphasize the very important role of the ferromagnetic layer as well as the interfacial scattering and surface roughness on the giant magnetoresistance effect
Czech Academy of Sciences Publication Activity Database
Čurík, Roman; Šulc, M.
2010-01-01
Roč. 43, č. 17 (2010), s. 175205 ISSN 0953-4075 R&D Projects: GA MŠk(CZ) OC10046; GA MŠk OC09079; GA AV ČR KJB400400803; GA ČR GA202/08/0631 Institutional research plan: CEZ:AV0Z40400503 Keywords : Ab initio calculations * Commonly used * DFT potential Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.902, year: 2010
Czech Academy of Sciences Publication Activity Database
Čársky, Petr
2010-01-01
Roč. 43, č. 17 (2010), s. 175204 ISSN 0953-4075 R&D Projects: GA MŠk OC09079; GA MŠk(CZ) OC10046; GA ČR GA202/08/0631 Institutional research plan: CEZ:AV0Z40400503 Keywords : ab initio calculations * electron scattering * polyatomic molecules Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.902, year: 2010
Marques, Yuri Bento; de Paiva Oliveira, Alcione; Ribeiro Vasconcelos, Ana Tereza; Cerqueira, Fabio Ribeiro
2016-12-15
MicroRNAs (miRNAs) are key gene expression regulators in plants and animals. Therefore, miRNAs are involved in several biological processes, making the study of these molecules one of the most relevant topics of molecular biology nowadays. However, characterizing miRNAs in vivo is still a complex task. As a consequence, in silico methods have been developed to predict miRNA loci. A common ab initio strategy to find miRNAs in genomic data is to search for sequences that can fold into the typical hairpin structure of miRNA precursors (pre-miRNAs). The current ab initio approaches, however, have selectivity issues, i.e., a high number of false positives is reported, which can lead to laborious and costly attempts to provide biological validation. This study presents an extension of the ab initio method miRNAFold, with the aim of improving selectivity through machine learning techniques, namely, random forest combined with the SMOTE procedure that copes with imbalance datasets. By comparing our method, termed Mirnacle, with other important approaches in the literature, we demonstrate that Mirnacle substantially improves selectivity without compromising sensitivity. For the three datasets used in our experiments, our method achieved at least 97% of sensitivity and could deliver a two-fold, 20-fold, and 6-fold increase in selectivity, respectively, compared with the best results of current computational tools. The extension of miRNAFold by the introduction of machine learning techniques, significantly increases selectivity in pre-miRNA ab initio prediction, which optimally contributes to advanced studies on miRNAs, as the need of biological validations is diminished. Hopefully, new research, such as studies of severe diseases caused by miRNA malfunction, will benefit from the proposed computational tool.
Ab initio study of energetics and magnetism of sigma phase in Co–Mo and Fe–Mo systems
Czech Academy of Sciences Publication Activity Database
Pavlů, Jana; Vřešťál, Jan; Šob, Mojmír
2016-01-01
Roč. 24, č. 2 (2016), č. článku Art. Number 025009. ISSN 0965-0393 R&D Projects: GA ČR GA14-15576S Institutional support: RVO:68081723 Keywords : intermetallics * magnetic properties * phase stability * thermodynamic properties * site occupancy * ab-initio calculations Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.891, year: 2016
Experimental and ab initio studies on sub-lattice ordering and magnetism in Co2Fe(Ge1−xSix) alloys
International Nuclear Information System (INIS)
Deka, Bhargab; Kundu, Ashis; Ghosh, Subhradip; Srinivasan, A.
2015-01-01
Crystallographic and magnetic properties of bulk Co 2 Fe(Ge 1−x Si x ) alloys with 0 ≤ x ≤ 1, synthesized by arc melting method, have been studied. Co 2 FeSi alloy has been found to crystallize with L2 1 structure, but the super-lattice peaks are absent in the X-ray diffraction patterns of alloys containing high Ge concentration. Unit cell volume of this series of alloys decreased from 185.2 to 178.5 Å 3 as Si content was increased from 0 to 1.00. All alloy compositions exhibit ferromagnetic behavior with a high Curie temperature (T C ). T C showed a systematic variation with x. A comparison between the values of saturation magnetization (M s ) and effective moment per magnetic atom p c estimated from the temperature dependent susceptibility data above T C , shows that the alloys have half-metallic character. The alloy with x = 0 follows Slater-Pauling (S-P) rule with M s of 5.99μ B . However, M s for the alloy with x = 1.00 was found to be 5.42μ B , which is lower than the value of 6.0μ B predicted by S-P rule. Since atomic disorder is known to affect the M s and electronic structure of these alloys, ab initio calculations were carried out to explain the deviation in observed M s from S-P rule prediction and the half-metallic character of the alloys. Ab initio calculations reveal that alloys with L2 1 structure have M s value as predicted by S-P rule. However, introduction of 12.5% DO 3 disorder, which occurs due to swapping of Co and Fe atoms in the unit cell, decreases M s of alloys with x > 0 from the S-P prediction to values obtained experimentally. The results analyzed from the view point of electronic structure of the alloys in different ordered states bring out the influence of disorder on the observed magnetic properties of these technologically important alloys
Experimental and ab initio studies on sub-lattice ordering and magnetism in Co2Fe(Ge1-xSix) alloys
Deka, Bhargab; Kundu, Ashis; Ghosh, Subhradip; Srinivasan, A.
2015-10-01
Crystallographic and magnetic properties of bulk Co2Fe(Ge1-xSix) alloys with 0 ≤ x ≤ 1, synthesized by arc melting method, have been studied. Co2FeSi alloy has been found to crystallize with L21 structure, but the super-lattice peaks are absent in the X-ray diffraction patterns of alloys containing high Ge concentration. Unit cell volume of this series of alloys decreased from 185.2 to 178.5 Å3 as Si content was increased from 0 to 1.00. All alloy compositions exhibit ferromagnetic behavior with a high Curie temperature (TC). TC showed a systematic variation with x. A comparison between the values of saturation magnetization (Ms) and effective moment per magnetic atom pc estimated from the temperature dependent susceptibility data above TC, shows that the alloys have half-metallic character. The alloy with x = 0 follows Slater-Pauling (S-P) rule with Ms of 5.99μB. However, Ms for the alloy with x = 1.00 was found to be 5.42μB, which is lower than the value of 6.0μB predicted by S-P rule. Since atomic disorder is known to affect the Ms and electronic structure of these alloys, ab initio calculations were carried out to explain the deviation in observed Ms from S-P rule prediction and the half-metallic character of the alloys. Ab initio calculations reveal that alloys with L21 structure have Ms value as predicted by S-P rule. However, introduction of 12.5% DO3 disorder, which occurs due to swapping of Co and Fe atoms in the unit cell, decreases Ms of alloys with x > 0 from the S-P prediction to values obtained experimentally. The results analyzed from the view point of electronic structure of the alloys in different ordered states bring out the influence of disorder on the observed magnetic properties of these technologically important alloys.
Ab initio-based approach to structural change of compound semiconductor surfaces during MBE growth
Ito, Tomonori; Akiyama, Toru; Nakamura, Kohji
2009-01-01
Phase diagrams of GaAs and GaN surfaces are systematically investigated by using our ab initio-based approach in conjunction with molecular beam epitaxy (MBE). The phase diagrams are obtained as a function of growth parameters such as temperature and beam equivalent pressure (BEP). The versatility of our approach is exemplified by the phase diagram calculations for GaAs(0 0 1) surfaces, where the stable phases and those phase boundaries are successfully determined as functions of temperature and As 2 and As 4 BEPs. The initial growth processes are clarified by the phase diagram calculations for GaAs(1 1 1)B-(2×2). The calculated results demonstrate that the As-trimer desorption on the GaAs(1 1 1)B-(2×2) with Ga adatoms occurs beyond 500-700 K while the desorption without Ga adatoms does beyond 800-1000 K. This self-surfactant effect induced by Ga adsorption crucially affects the initial growth of GaAs on the GaAs(1 1 1)B-(2×2). Furthermore, the phase diagram calculations for GaN(0 0 0 1) suggests that Ga adsorption or desorption during GaN MBE growth can easily change the pseudo-(1×1) to the (2×2)-Ga via newly found (1×1) and vice versa. On the basis of this finding, the possibility of ghost island formation during MBE growth is discussed.
Barabash, Sergey V.; Pramanik, Dipankar
2015-03-01
Development of low-leakage dielectrics for semiconductor industry, together with many other areas of academic and industrial research, increasingly rely upon ab initio tunneling and transport calculations. Complex band structure (CBS) is a powerful formalism to establish the nature of tunneling modes, providing both a deeper understanding and a guided optimization of materials, with practical applications ranging from screening candidate dielectrics for lowest ``ultimate leakage'' to identifying charge-neutrality levels and Fermi level pinning. We demonstrate that CBS is prone to a particular type of spurious ``phantom'' solution, previously deemed true but irrelevant because of a very fast decay. We demonstrate that (i) in complex materials, phantom modes may exhibit very slow decay (appearing as leading tunneling terms implying qualitative and huge quantitative errors), (ii) the phantom modes are spurious, (iii) unlike the pseudopotential ``ghost'' states, phantoms are an apparently unavoidable artifact of large numerical basis sets, (iv) a presumed increase in computational accuracy increases the number of phantoms, effectively corrupting the CBS results despite the higher accuracy achieved in resolving the true CBS modes and the real band structure, and (v) the phantom modes cannot be easily separated from the true CBS modes. We discuss implications for direct transport calculations. The strategy for dealing with the phantom states is discussed in the context of optimizing high-quality high- κ dielectric materials for decreased tunneling leakage.
Ab-initio approach to the effect of Fe on the diffusion in hcp Zr
International Nuclear Information System (INIS)
Perez, Rodolfo Ariel; Weissmann, Mariana
2008-01-01
The role of Fe in the hcp Zr diffusion process is analyzed, given its ultra-fast diffusion (up to nine orders of magnitude higher than the self-diffusion in the temperature range 779-1128 K) and the enhancement observed in the self and substitutional diffusion induced by its unavoidable presence as impurity. Ab-initio calculations using SIESTA and WIEN2K codes were performed in order to find the actual Fe minimum energy configuration within the hcp Zr matrix and its interaction with vacancies. Several off-centre quasi-interstitial positions with energies similar to substitutional Fe were encountered. The comparison with diffusion coefficient measurements and Moessbauer experiments allows us to discard the substitutional position of the Fe atom as well as to affirm that its presence creates a considerable lattice distortion together with an increment in the number of vacancies. The above effects could be responsible for the enhancement in the self and substitutional diffusion, whereas the large amount of quasi-interstitial positions for Fe could be, at least partially, responsible for the ultra-fast Fe diffusion
Light focusing through a multiple scattering medium: ab initio computer simulation
Danko, Oleksandr; Danko, Volodymyr; Kovalenko, Andrey
2018-01-01
The present study considers ab initio computer simulation of the light focusing through a complex scattering medium. The focusing is performed by shaping the incident light beam in order to obtain a small focused spot on the opposite side of the scattering layer. MSTM software (Auburn University) is used to simulate the propagation of an arbitrary monochromatic Gaussian beam and obtain 2D distribution of the optical field in the selected plane of the investigated volume. Based on the set of incident and scattered fields, the pair of right and left eigen bases and corresponding singular values were calculated. The pair of right and left eigen modes together with the corresponding singular value constitute the transmittance eigen channel of the disordered media. Thus, the scattering process is described in three steps: 1) initial field decomposition in the right eigen basis; 2) scaling of decomposition coefficients for the corresponding singular values; 3) assembling of the scattered field as the composition of the weighted left eigen modes. Basis fields are represented as a linear combination of the original Gaussian beams and scattered fields. It was demonstrated that 60 independent control channels provide focusing the light into a spot with the minimal radius of approximately 0.4 μm at half maximum. The intensity enhancement in the focal plane was equal to 68 that coincided with theoretical prediction.
International Nuclear Information System (INIS)
Music, Denis; Schneider, Jochen M
2008-01-01
We have studied the correlation between chemical composition, structure, chemical bonding and elastic properties of amorphous B 6 O based solids using ab initio molecular dynamics. These solids are of different chemical compositions, but the elasticity data appear to be a function of density. This is in agreement with previous experimental observations. As the density increases from 1.64 to 2.38 g cm -3 , the elastic modulus increases from 74 to 253 GPa. This may be understood by analyzing the cohesive energy and the chemical bonding of these compounds. The cohesive energy decreases from -7.051 to -7.584 eV/atom in the elastic modulus range studied. On the basis of the electron density distributions, Mulliken analysis and radial distribution functions, icosahedral bonding is the dominating bonding type. C and N promote cross-linking of icosahedra and thus increase the density, while H hinders the cross-linking by forming OH groups. The presence of icosahedral bonding is independent of the density
Ab initio screening methodology applied to the search for new permanent magnetic materials
International Nuclear Information System (INIS)
Drebov, Nedko; Gumbsch, Peter; Elsässer, Christian; Martinez-Limia, Alberto; Kunz, Lothar; Gola, Adrien; Eckl, Thomas; Shigematsu, Takashi
2013-01-01
In this paper a computational high-throughput screening (HTS) approach to the search for alternative permanent magnetic materials is presented. Systems considered for a start are binary intermetallic compounds composed of rare-earth (RE) and transition metal (TM) elements. With the tight-binding-linear muffin-tin-orbital-atomic-sphere-approximation (TB-LMTO-ASA) method of density functional theory (DFT) a variety of RE–TM intermetallic phases is investigated and their magnetic properties are obtained at rather low computational costs. Next, interstitial elements such as boron, carbon and nitrogen in these phases are considered. For promising candidate phases with high and stable spontaneous ferromagnetic polarization, the calculated local magnetic moments and exchange coupling parameters, as obtained from TB-LMTO-ASA calculations, are then used for Monte Carlo simulations to identify candidates with sufficiently high Curie temperatures (T c ). Finally, magnetocrystalline anisotropy constants (K 1 ) of the most promising candidate phases are calculated with accurate, potential-shape-unrestricted DFT calculations using the Vienna ab initio simulation package. The computational HTS procedure is illustrated by results for a selection of hard-magnetic RE–TM phases like RETM 5 , RE 2 TM 17 and RE 2 TM 14 B. (paper)
ESTUDIO TEÓRICO DE LA MOLÉCULA DE HIDROGENO CALCULO AB-INITIO
Directory of Open Access Journals (Sweden)
N. Quitián
2010-09-01
Full Text Available Utilizando la técnica LCGO-SCF-MO (Combinación Lineal de los Orbitales Moleculares en Orbitales Gausianos, en el método del Campo Auto-Coherente, se determinaron las energías de orbital, la energía electrónica total, la energía de repulsión nuclear y la energía de Hartree-Fock de la molécula de hidrógeno en su estado fundamental, mediante un cálculo ab initio y utilizando una base de funciones gausianas. Los orbitales moleculares fueron desarrollados en términos de una función Is contraída por átomo de hidrógeno, obtenida por la minimización de los coeficientes y de los exponentes de los orbitales gausianos para el átomo aislado. Los resultados obtenidos nos permiten afirmar que la base molecular mejora sensiblemente los resultados, acercándose más al límite de Hartree-Fock.
Ab initio study of the Br(2P)-HBr van der Waals complex.
Toboła, R; Chałasiński, G; Kłos, J; Szcześniak, M M
2009-05-14
This study reports an ab initio characterization of a prereactive van der Waals complex between an open-shell atom Br((2)P) and a closed shell molecule HBr. The three adiabatic potential surfaces 1 (2)A('), 2 (2)A('), and 1 (2)A("), which result from the splitting of degenerate P state of Br are obtained from coupled cluster calculations. The coupling between same-symmetry states is calculated by multireference configuration-interaction method. A transformation to a diabatic representation and inclusion of the spin-orbit coupling effects on the interactions are also discussed. Bound states are calculated using an adiabatic bender model. The global minimum on the lowest adiabatic potential surface corresponds to a T-shaped geometry and has a well depth of D(e)=762.5 cm(-1) at R(e)=3.22 A. A secondary minimum occurs for a hydrogen-bonded geometry with D(e)=445.3 cm(-1) at R(e)=4.24 A. Upon inclusion of spin-orbit coupling the hydrogen-bonded minimum remains at the same depth, but the T-shaped minimum washes out to less than half of its spin-free value. The lowest bound state is localized in the linear minimum. The spin-orbit coupling plays a very important role in shaping of the potential energy surfaces of Br-HBr.
Berggren, Elisabet; White, Andrew; Ouedraogo, Gladys; Paini, Alicia; Richarz, Andrea-Nicole; Bois, Frederic Y; Exner, Thomas; Leite, Sofia; Grunsven, Leo A van; Worth, Andrew; Mahony, Catherine
2017-11-01
We describe and illustrate a workflow for chemical safety assessment that completely avoids animal testing. The workflow, which was developed within the SEURAT-1 initiative, is designed to be applicable to cosmetic ingredients as well as to other types of chemicals, e.g. active ingredients in plant protection products, biocides or pharmaceuticals. The aim of this work was to develop a workflow to assess chemical safety without relying on any animal testing, but instead constructing a hypothesis based on existing data, in silico modelling, biokinetic considerations and then by targeted non-animal testing. For illustrative purposes, we consider a hypothetical new ingredient x as a new component in a body lotion formulation. The workflow is divided into tiers in which points of departure are established through in vitro testing and in silico prediction, as the basis for estimating a safe external dose in a repeated use scenario. The workflow includes a series of possible exit (decision) points, with increasing levels of confidence, based on the sequential application of the Threshold of Toxicological (TTC) approach, read-across, followed by an "ab initio" assessment, in which chemical safety is determined entirely by new in vitro testing and in vitro to in vivo extrapolation by means of mathematical modelling. We believe that this workflow could be applied as a tool to inform targeted and toxicologically relevant in vitro testing, where necessary, and to gain confidence in safety decision making without the need for animal testing.
Ab initio ro-vibronic spectroscopy of SiCCl (X{sup ~2}Π)
Energy Technology Data Exchange (ETDEWEB)
Brites, Vincent [Université d’Evry Val d’Essonne, Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, LAMBE CNRS UMR 8587, Boulevard F. Mitterrand, 91025 Evry Cedex (France); Mitrushchenkov, Alexander O.; Léonard, Céline, E-mail: celine.leonard@u-pem.fr [Université Paris-Est, Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, 5 bd Descartes, 77454 Marne-la-Vallée (France); Peterson, Kirk A. [Department of Chemistry, Washington State University, Pullman, Washington 99164 (United States)
2014-07-21
The full dimensional potential energy surfaces of the {sup 2}A{sup ′} and {sup 2}A{sup ′′} electronic components of X{sup ~2}Π SiCCl have been computed using the explicitly correlated coupled cluster method, UCCSD(T)-F12b, combined with a composite approach taking into account basis set incompleteness, core-valence correlation, scalar relativity, and higher order excitations. The spin-orbit and dipole moment surfaces have also been computed ab initio. The ro-vibronic energy levels and absorption spectrum at 5 K have been determined from variational calculations. The influence of each correction on the fundamental frequencies is discussed. An assignment is proposed for bands observed in the LIF experiment of Smith et al. [J. Chem. Phys. 117, 6446 (2002)]. The overall agreement between the experimental and calculated ro-vibronic levels is better than 7 cm{sup −1} which is comparable with the 10–20 cm{sup −1} resolution of the emission spectrum.
Integration of ab-initio nuclear calculation with derivative free optimization technique
Energy Technology Data Exchange (ETDEWEB)
Sharda, Anurag [Iowa State Univ., Ames, IA (United States)
2008-01-01
Optimization techniques are finding their inroads into the field of nuclear physics calculations where the objective functions are very complex and computationally intensive. A vast space of parameters needs searching to obtain a good match between theoretical (computed) and experimental observables, such as energy levels and spectra. Manual calculation defies the scope of such complex calculation and are prone to error at the same time. This body of work attempts to formulate a design and implement it which would integrate the ab initio nuclear physics code MFDn and the VTDIRECT95 code. VTDIRECT95 is a Fortran95 suite of parallel code implementing the derivative-free optimization algorithm DIRECT. Proposed design is implemented for a serial and parallel version of the optimization technique. Experiment with the initial implementation of the design showing good matches for several single-nucleus cases are conducted. Determination and assignment of appropriate number of processors for parallel integration code is implemented to increase the efficiency and resource utilization in the case of multiple nuclei parameter search.
Set of molecular models based on quantum mechanical ab initio calculations and thermodynamic data.
Eckl, Bernhard; Vrabec, Jadran; Hasse, Hans
2008-10-09
A parametrization 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 ether, sulfur dioxide, dimethyl sulfide, thiophene, hydrogen cyanide, acetonitrile, and nitromethane. Most of the models are able to describe the experimental VLE data with deviations of a few percent.
Communication: A hydrogen-bonded difluorocarbene complex: Ab initio and matrix isolation study
Sosulin, Ilya S.; Shiryaeva, Ekaterina S.; Tyurin, Daniil A.; Feldman, Vladimir I.
2017-10-01
Structure and spectroscopic features of the CF2⋯HF complexes were studied by ab initio calculations at the CCSD(T) level and matrix isolation FTIR spectroscopy. The calculations predict three stable structures. The most energetically favorable structure corresponds to hydrogen bonding of HF to the lone pair of the C atom (the interaction energy of 3.58 kcal/mol), whereas two less stable structures are the H⋯F bonded complexes (the interaction energies of 0.30 and 0.24 kcal/mol). The former species was unambiguously characterized by the absorptions in the FTIR spectra observed after X-ray irradiation of fluoroform in a xenon matrix at 5 K. The corresponding features appear at 3471 (H-F stretching), 1270 (C-F symmetric stretching, shoulder), 1175 (antisymmetric C-F stretching), and 630 (libration) cm-1, in agreement with the computational predictions. To our knowledge, it is the first hydrogen-bonded complex of dihalocarbene. Possible weaker manifestations of the H⋯F bonded complexes were also found in the C-F stretching region; however, their assignment is tentative. The H⋯C bonded complex is protected from reaction yielding a fluoroform molecule by a remarkably high energy barrier (23.85 kcal/mol), so it may be involved in various chemical reactions.
Au55, a stable glassy cluster: results of ab initio calculations
Directory of Open Access Journals (Sweden)
Dieter Vollath
2017-10-01
Full Text Available Structure and properties of small nanoparticles are still under discussion. Moreover, some thermodynamic properties and the structural behavior still remain partially unknown. One of the best investigated nanoparticles is the Au55 cluster, which has been analyzed experimentally and theoretically. However, up to now, the results of these studies are still inconsistent. Consequently, we have carried out the present ab initio study of the Au55 cluster, using up-to-date computational concepts, in order to clarify these issues. Our calculations have confirmed the experimental result that the thermodynamically most stable structure is not crystalline, but it is glassy. The non-crystalline structure of this cluster was validated by comparison of the coordination numbers with those of a crystalline cluster. It was found that, in contrast to bulk materials, glass formation is connected to an energy release that is close to the melting enthalpy of bulk gold. Additionally, the surface energy of this cluster was calculated using two different theoretical approaches resulting in values close to the surface energy for bulk gold. It shall be emphasized that it is now possible to give a confidence interval for the value of the surface energy.
Černý, Jiří; Schneider, Bohdan; Biedermannová, Lada
2017-07-14
Water molecules represent an integral part of proteins and a key determinant of protein structure, dynamics and function. WatAA is a newly developed, web-based atlas of amino-acid hydration in proteins. The atlas provides information about the ordered first hydration shell of the most populated amino-acid conformers in proteins. The data presented in the atlas are drawn from two sources: experimental data and ab initio quantum-mechanics calculations. The experimental part is based on a data-mining study of a large set of high-resolution protein crystal structures. The crystal-derived data include 3D maps of water distribution around amino-acids and probability of occurrence of each of the identified hydration sites. The quantum mechanics calculations validate and extend this primary description by optimizing the water position for each hydration site, by providing hydrogen atom positions and by quantifying the interaction energy that stabilizes the water molecule at the particular hydration site position. The calculations show that the majority of experimentally derived hydration sites are positioned near local energy minima for water, and the calculated interaction energies help to assess the preference of water for the individual hydration sites. We propose that the atlas can be used to validate water placement in electron density maps in crystallographic refinement, to locate water molecules mediating protein-ligand interactions in drug design, and to prepare and evaluate molecular dynamics simulations. WatAA: Atlas of Protein Hydration is freely available without login at .
Shimamura, Kohei; Shimojo, Fuyuki; Nakano, Aiichiro; Tanaka, Shigenori
2016-12-01
NH3 is an essential molecule as a nitrogen source for prebiotic amino acid syntheses such as the Strecker reaction. Previous shock experiments demonstrated that meteorite impacts on ancient oceans would have provided a considerable amount of NH3 from atmospheric N2 and oceanic H2O through reduction by meteoritic iron. However, specific production mechanisms remain unclear, and impact velocities employed in the experiments were substantially lower than typical impact velocities of meteorites on the early Earth. Here, to investigate the issues from the atomistic viewpoint, we performed multi-scale shock technique-based ab initio molecular dynamics simulations. The results revealed a rapid production of NH3 within several picoseconds after the shock, indicating that shocks with greater impact velocities would provide further increase in the yield of NH3. Meanwhile, the picosecond-order production makes one expect that the important nitrogen source precursors of amino acids were obtained immediately after the impact. It was also observed that the reduction of N2 proceeded according to an associative mechanism, rather than a dissociative mechanism as in the Haber-Bosch process.
On-the-Fly ab Initio Semiclassical Calculation of Glycine Vibrational Spectrum.
Gabas, Fabio; Conte, Riccardo; Ceotto, Michele
2017-06-13
We present an on-the-fly ab initio semiclassical study of vibrational energy levels of glycine, calculated by Fourier transform of the wavepacket correlation function. It is based on a multiple coherent states approach integrated with monodromy matrix regularization for chaotic dynamics. All four lowest-energy glycine conformers are investigated by means of single-trajectory semiclassical spectra obtained upon classical evolution of on-the-fly trajectories with harmonic zero-point energy. For the most stable conformer I, direct dynamics trajectories are also run for each vibrational mode with energy equal to the first harmonic excitation. An analysis of trajectories evolved up to 50 000 atomic time units demonstrates that, in this time span, conformers II and III can be considered as isolated species, while conformers I and IV show a pretty facile interconversion. Therefore, previous perturbative studies based on the assumption of isolated conformers are often reliable but might be not completely appropriate in the case of conformer IV and conformer I for which interconversion occurs promptly.
Experimental and ab initio DFT calculated Raman Spectrum of Sudan I, a Red Dye
DEFF Research Database (Denmark)
Kunov-Kruse, Andreas Jonas; Kristensen, Steffen Buus; Liu, Chuan
2011-01-01
The red dye Sudan I was investigated by Raman spectroscopy using different excitation wavelengths (1064, 532 and 244 nm). A calculation of the Raman spectrum based on quantum mechanical ab initio density functional theory (DFT) was made using the RB3LYP method with the 3-21G and 6-311+G(d,p) basis...... of the Sudan I molecule was involved in the majority of the vibrations through N N and C–N stretching and various bending modes. Low-intensity bands in the lower wavenumber range (at about 721, 616, 463 and 218 cm−1) were selectively enhanced by the resonance Raman effect when using the 532 nm excitation line....... Comparison was made with other azo dyes in the literature on natural, abundant plant pigments. The results show that there is a possibility in foodstuff analysis to distinguish Sudan I from other dyes by using Raman spectroscopy with more than one laser wavelength for resonance enhancement of the different...
Ab initio electronic band structure calculation of InP in the wurtzite phase
Dacal, Luis C. O.; Cantarero, Andrés
2011-05-01
We present ab initio calculations of the InP band structure in the wurtzite phase and compare it with that of the zincblende phase. In both calculations, we use the full potential linearized augmented plane wave method as implemented in the WIEN2k code and the modified Becke-Johnson exchange potential, which provides an improved value of the bandgap. The structural optimization of the wurtizte InP gives a=0.4150 nm, c=0.6912 nm, and an internal parameter u=0.371, showing the existence of a spontaneous polarization along the growth axis. As compared to the ideal wurtzite structure (that with the lattice parameter derived from the zincblende structure calculations), the actual wurtzite structure is compressed (-1.3%) in plane and expanded (0.7%) along the c-direction. The value of the calculated band gaps agrees well with recent optical experiments. The calculations are also consistent with the optical transitions found using polarized light.
An ab initio study of the polytypism in InP
Dacal, Luis C. O.; Cantarero, A.
2016-09-01
The existence of polytypism in semiconductor nanostructures gives rise to the appearance of stacking faults which many times can be treated as quantum wells. In some cases, despite of a careful growth, the polytypism can be hardly avoided. In this work, we perform an ab initio study of zincblende stacking faults in a wurtzite InP system, using the supercell approach and taking the limit of low density of narrow stacking faults regions. Our results confirm the type II band alignment between the phases, producing a reliable qualitative description of the band gap evolution along the growth axis. These results show an spacial asymmetry in the zincblende quantum wells, that is expected due to the fact that the wurtzite stacking sequence (ABAB) is part of the zincblende one (ABCABC), but with an unexpected asymmetry between the valence and the conduction bands. We also present results for the complex dielectric function, clearly showing the influence of the stacking on the homostructure values and surprisingly proving that the correspondent bulk results can be used to reproduce the polytypism even in the limit we considered.
Conformational study of glyoxal bis(amidinohydrazone) by ab initio methods
Mannfors, B.; Koskinen, J. T.; Pietilä, L.-O.
1997-08-01
We report the first ab initio molecular orbital study on the ground state of the endiamine tautomer of glyoxal bis(amidinohydrazone) (or glyoxal bis(guanylhydrazone), GBG) free base. The calculations were performed at the following levels of theory: Hartree-Fock, second-order Møller-Plesset perturbation theory and density functional theory (B-LYP and B3-LYP) as implemented in the Gaussian 94 software. The standard basis set 6-31G(d) was found to be sufficient. The default fine grid of Gaussian 94 was used in the density functional calculations. Molecular properties, such as optimized structures, total energies and the electrostatic potential derived (CHELPG) atomic charges, were studied as functions of C-C and N-N conformations. The lowest energy conformation was found to be all- trans, in agreement with the experimental solid-state structure. The second conformer with respect to rotation around the central C-C bond was found to be the cis conformer with an MP2//HF energy of 4.67 kcal mol -1. For rotation around the N-N bond the energy increased monotonically from the trans conformation to the cis conformation, the cis energy being very high, 22.01 kcal mol -1 (MP2//HF). The atomic charges were shown to be conformation dependent, and the bond charge increments and especially the conformational changes of the bond charge increments were found to be easily transferable between structurally related systems.
Ab-initio study of the dielectric response of high-permittivity perovskites for energy storage
International Nuclear Information System (INIS)
Do-Amaral-De-Andrade-Sophia, Gustavo
2014-01-01
Many of materials based on transition metals have a wide range of applications, such as the storage of energy, due to their peculiar properties (high-dielectric constants, ferro-electricity,...). The knowledge of their bulk properties is essential in designing targeted devices with high performance. For instance, ABO 3 perovskites are peculiarly interesting for their atomic structural flexibility, allowing high number of atoms substitution and giving them specific chemical and electrical properties compared to the pure compounds. In this context, first principles calculations can be useful to understand the structural and electronic properties of these materials. The pressure-induced giant dielectric anomaly of ABO 3 perovskites has been investigated at the ab initio level. Its mechanism has been analyzed in terms of thermodynamic phase stability, structural and phonon contributions and Born effective charges. It is shown that the IR-active soft phonon is responsible for the anomaly. This mode always involves a displacement and a deformation of the oxygen octahedra, while the roles of A and B ions vary among the materials and between high- and low-pressure phase transitions. A sharp increase in the phonon amplitude near the phase transition gives rise to the dielectric anomaly. The use of hybrid functionals is required for agreement with experimental data. The calculations show that the dielectric anomaly in the pressure-induced phase transitions of these perovskites is a property of the bulk material. (author)
Direct molecular simulation of nitrogen dissociation based on an ab initio potential energy surface
International Nuclear Information System (INIS)
Valentini, Paolo; Schwartzentruber, Thomas E.; Bender, Jason D.; Nompelis, Ioannis; Candler, Graham V.
2015-01-01
The direct molecular simulation (DMS) approach is used to predict the internal energy relaxation and dissociation dynamics of high-temperature nitrogen. An ab initio potential energy surface (PES) is used to calculate the dynamics of two interacting nitrogen molecules by providing forces between the four atoms. In the near-equilibrium limit, it is shown that DMS reproduces the results obtained from well-established quasiclassical trajectory (QCT) analysis, verifying the validity of the approach. DMS is used to predict the vibrational relaxation time constant for N 2 –N 2 collisions and its temperature dependence, which are in close agreement with existing experiments and theory. Using both QCT and DMS with the same PES, we find that dissociation significantly depletes the upper vibrational energy levels. As a result, across a wide temperature range, the dissociation rate is found to be approximately 4–5 times lower compared to the rates computed using QCT with Boltzmann energy distributions. DMS calculations predict a quasi-steady-state distribution of rotational and vibrational energies in which the rate of depletion of high-energy states due to dissociation is balanced by their rate of repopulation due to collisional processes. The DMS approach simulates the evolution of internal energy distributions and their coupling to dissociation without the need to precompute rates or cross sections for all possible energy transitions. These benchmark results could be used to develop new computational fluid dynamics models for high-enthalpy flow applications
Ab initio calculation of the electronic absorption spectrum of liquid water
Energy Technology Data Exchange (ETDEWEB)
Martiniano, Hugo F. M. C.; Galamba, Nuno [Grupo de Física Matemática da Universidade de Lisboa, Av. Professor Gama Pinto 2, 1649-003 Lisboa (Portugal); Cabral, Benedito J. Costa, E-mail: ben@cii.fc.ul.pt [Grupo de Física Matemática da Universidade de Lisboa, Av. Professor Gama Pinto 2, 1649-003 Lisboa (Portugal); Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa (Portugal); Instituto de Física da Universidade de São Paulo, CP 66318, 05314-970 São Paulo, SP (Brazil)
2014-04-28
The electronic absorption spectrum of liquid water was investigated by coupling a one-body energy decomposition scheme to configurations generated by classical and Born-Oppenheimer Molecular Dynamics (BOMD). A Frenkel exciton Hamiltonian formalism was adopted and the excitation energies in the liquid phase were calculated with the equation of motion coupled cluster with single and double excitations method. Molecular dynamics configurations were generated by different approaches. Classical MD were carried out with the TIP4P-Ew and AMOEBA force fields. The BLYP and BLYP-D3 exchange-correlation functionals were used in BOMD. Theoretical and experimental results for the electronic absorption spectrum of liquid water are in good agreement. Emphasis is placed on the relationship between the structure of liquid water predicted by the different models and the electronic absorption spectrum. The theoretical gas to liquid phase blue-shift of the peak positions of the electronic absorption spectrum is in good agreement with experiment. The overall shift is determined by a competition between the O–H stretching of the water monomer in liquid water that leads to a red-shift and polarization effects that induce a blue-shift. The results illustrate the importance of coupling many-body energy decomposition schemes to molecular dynamics configurations to carry out ab initio calculations of the electronic properties in liquid phase.
Building the equation of state of TATB from ab initio simulations and DAC experiments
Pineau, Nicolas; Plisson, Thomas; Sollier, Arnaud
2017-06-01
Modelling equations of state for energetic molecular crystals in the full thermodynamic range of inert compression, prior to detonation, is a challenging issue. Indeed the unreacted regime under high pressure is difficult to explore experimentally, and although first principle calculations allow filling that gap, the need for experimental support is crucial in order to validate the chosen methodological approach, and in fine the simulation results. In this study we present our methodology for building ab initio based EOSs for molecular crystals, using van der Waals corrected DFT and Path Integral Molecular Dynamics (PIMD). Then we present recent experimental results on the isotropic compression of TATB using diamond anvil cells (DAC) and synchrotron radiation to reach pressures up to 65 GPa, beyond the current estimations for the von Neumann spike. The close agreement between the experimental and simulation data validates the methodology employed to obtain the cold curve of the explosive. The shock properties of inert TATB obtained with this EOS compare well to recent laser-driven shock compression experiments.
Ab initio study of interaction of helium with edge and screw dislocations in tungsten
International Nuclear Information System (INIS)
Bakaev, Alexander; Terentyev, Dmitry; Grigorev, Petr; Posselt, Matthias; Zhurkin, Evgeny E.
2017-01-01
Highlights: • Both screw (SD) and edge dislocations (ED) offer trapping sites for He in tungsten. • He atom is attracted to SD and ED with the interaction energy of ~1.3 and ~3.0 eV, respectively. • The attraction of He to dislocations can contribute to the nucleation of He clusters at high T. - Abstract: The interaction of a single He atom with edge and screw dislocations in tungsten has been studied using ab initio calculations. It was revealed that He is strongly attracted to the core of both dislocations with the interaction energy of −1.3 and −3.0 eV for screw and edge dislocations, respectively, which corresponds to the detrapping temperature in thermal desorption spectroscopy experiments of about 500 K and 1050 K, respectively. The lowest energy positions for He around the dislocation cores are identified and the atomic structures are rationalized on the basis of elasticity theory considerations. Both types of dislocations exhibit a higher binding energy for He as compared to the He-He binding (known as self-trapping) and are weaker traps as compared to a single vacancy. It is, thus, concluded that the strong attraction to dislocation lines can contribute to the nucleation of He clusters in the temperature range which already excludes He self-trapping.
Large scale ab initio molecular dynamics using the OpenAtom software
Ismail-Beigi, Sohrab; Mandal, Subhasish; Kim, Minjung; Mikida, Eric; Bohm, Eric; Jindal, Prateek; Jain, Nikhil; Kale, Laxmikant; Martyna, Glenn
First principles molecular dynamics approaches permit one to simulate dynamic and time-dependent phenomena in physics, chemistry, and materials science without the use of empirical potentials or ad hoc assumptions about the interatomic interactions since they describe electrons, nuclei and their interactions explicitly. We describe our collaborative efforts in developing and enhancing the OpenAtom open source ab initio density functional software package based on plane waves and pseudopotentials (http://charm.cs.uiuc.edu/OpenAtom/). OpenAtom takes advantage of the Charm++ parallel framework. We present parallel scaling results on a large metal organic framework (MOF) material of scientific and potential technological interest for hydrogen storage. In the process, we highlight the capabilities of the software which include molecular dynamics (Car-Parrinello or Born-Oppenheimer), k-points, spin, path integral beads for quantum nuclear effects, and parallel tempering for exploration of complex phase spaces. Particular efforts have been made to ensure that the different capabilities interoperate in various combinations with high performance and scaling. Comparison to other available open source software will also be assessed. This collaboration is supported NSF SI2-SSI Grant ACI-1339804.
Ab initio calculation of the electronic absorption spectrum of liquid water
International Nuclear Information System (INIS)
Martiniano, Hugo F. M. C.; Galamba, Nuno; Cabral, Benedito J. Costa
2014-01-01
The electronic absorption spectrum of liquid water was investigated by coupling a one-body energy decomposition scheme to configurations generated by classical and Born-Oppenheimer Molecular Dynamics (BOMD). A Frenkel exciton Hamiltonian formalism was adopted and the excitation energies in the liquid phase were calculated with the equation of motion coupled cluster with single and double excitations method. Molecular dynamics configurations were generated by different approaches. Classical MD were carried out with the TIP4P-Ew and AMOEBA force fields. The BLYP and BLYP-D3 exchange-correlation functionals were used in BOMD. Theoretical and experimental results for the electronic absorption spectrum of liquid water are in good agreement. Emphasis is placed on the relationship between the structure of liquid water predicted by the different models and the electronic absorption spectrum. The theoretical gas to liquid phase blue-shift of the peak positions of the electronic absorption spectrum is in good agreement with experiment. The overall shift is determined by a competition between the O–H stretching of the water monomer in liquid water that leads to a red-shift and polarization effects that induce a blue-shift. The results illustrate the importance of coupling many-body energy decomposition schemes to molecular dynamics configurations to carry out ab initio calculations of the electronic properties in liquid phase
360⁰ -View of Quantum Theory and Ab Initio Simulation at Extreme Conditions: 2014 Sanibel Symposium
Energy Technology Data Exchange (ETDEWEB)
Cheng, Hai-Ping [Univ. of Florida, Gainesville, FL (United States)
2016-09-02
The Sanibel Symposium 2014 was held February 16-21, 2014, at the King and Prince, St. Simons Island, GA. It was successful in bringing condensed-matter physicists and quantum chemists together productively to drive the emergence of those specialties. The Symposium had a significant role in preparing a whole generation of quantum theorists. The 54th Sanibel meeting looked to the future in two ways. We had 360⁰-View sessions to honor the exceptional contributions of Rodney Bartlett (70), Bill Butler (70), Yngve Öhrn (80), Fritz Schaefer (70), and Malcolm Stocks (70). The work of these five has greatly impacted several generations of quantum chemists and condensed matter physicists. The “360⁰” is the sum of their ages. More significantly, it symbolizes a panoramic view of critical developments and accomplishments in theoretical and computational chemistry and physics oriented toward the future. Thus, two of the eight 360⁰-View sessions focused specifically on younger scientists. The 360⁰-View program was the major component of the 2014 Sanibel meeting. Another four sessions included a sub-symposium on ab initio Simulations at Extreme Conditions, with focus on getting past the barriers of present-day Born-Oppenheimer molecular dynamics by advances in finite-temperature density functional theory, orbital-free DFT, and new all-numerical approaches.
Ab initio study of interaction of helium with edge and screw dislocations in tungsten
Energy Technology Data Exchange (ETDEWEB)
Bakaev, Alexander, E-mail: bakaev_vic@mail.ru [SCK-CEN, Nuclear Materials Science Institute, Boeretang 200, Mol 2400 (Belgium); Department of Experimental Nuclear Physics K-89, Institute of Physics, Nanotechnology and Telecommunications, Peter the Great St. Petersburg Polytechnic University, 29 Polytekhnicheskaya str., 195251 St. Petersburg (Russian Federation); Institute of Ion Beam Physics and Materials Research, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstrasse 400, 01328 Dresden (Germany); Terentyev, Dmitry [SCK-CEN, Nuclear Materials Science Institute, Boeretang 200, Mol 2400 (Belgium); Grigorev, Petr [SCK-CEN, Nuclear Materials Science Institute, Boeretang 200, Mol 2400 (Belgium); Department of Experimental Nuclear Physics K-89, Institute of Physics, Nanotechnology and Telecommunications, Peter the Great St. Petersburg Polytechnic University, 29 Polytekhnicheskaya str., 195251 St. Petersburg (Russian Federation); Ghent University, Applied Physics EA17 FUSION-DC, St. Pietersnieuwstraat, 41 B4, B-9000 Gent (Belgium); Posselt, Matthias [Institute of Ion Beam Physics and Materials Research, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstrasse 400, 01328 Dresden (Germany); Zhurkin, Evgeny E. [Department of Experimental Nuclear Physics K-89, Institute of Physics, Nanotechnology and Telecommunications, Peter the Great St. Petersburg Polytechnic University, 29 Polytekhnicheskaya str., 195251 St. Petersburg (Russian Federation)
2017-02-15
Highlights: • Both screw (SD) and edge dislocations (ED) offer trapping sites for He in tungsten. • He atom is attracted to SD and ED with the interaction energy of ~1.3 and ~3.0 eV, respectively. • The attraction of He to dislocations can contribute to the nucleation of He clusters at high T. - Abstract: The interaction of a single He atom with edge and screw dislocations in tungsten has been studied using ab initio calculations. It was revealed that He is strongly attracted to the core of both dislocations with the interaction energy of −1.3 and −3.0 eV for screw and edge dislocations, respectively, which corresponds to the detrapping temperature in thermal desorption spectroscopy experiments of about 500 K and 1050 K, respectively. The lowest energy positions for He around the dislocation cores are identified and the atomic structures are rationalized on the basis of elasticity theory considerations. Both types of dislocations exhibit a higher binding energy for He as compared to the He-He binding (known as self-trapping) and are weaker traps as compared to a single vacancy. It is, thus, concluded that the strong attraction to dislocation lines can contribute to the nucleation of He clusters in the temperature range which already excludes He self-trapping.
Energy Technology Data Exchange (ETDEWEB)
Walker, I C; McEwen, I J [School of Engineering and Physical Sciences, Heriot-Watt University, Riccarton, Edinburgh EH14 4AS (United Kingdom); Holland, D M P; Shaw, D A; Guest, M F [Daresbury Laboratory, Daresbury, Warrington, Cheshire WA4 4AD (United Kingdom)
2008-06-14
The absolute photoabsorption spectrum of ethylene oxide (C{sub 2}H{sub 4}O) has been measured between onset and 30 eV, using monochromated synchrotron radiation. Below the ionization threshold (10.56 eV) the spectrum is dominated by sharp peaks related to excitation of Rydberg series converging on the first ionization energy. Above the ionization threshold, valence-excited states, which give rise to broad bands, predominate. Underlying Rydberg states are signalled in weak vibrational structure on the valence bands. Ab initio multireference configuration interaction (MRDCI) calculations have been carried out to assist in assignment of the excited states, both valence and Rydberg. The lowest-lying valence state is electric-dipole forbidden; the first optically allowed valence state lies close to the ionization onset. The spectrum of the oxide is compared with those of cyclopropane (C{sub 3}H{sub 6}) and ethylene sulphide (C{sub 2}H{sub 4}S)
Characterization of Elastic Properties of Porous Graphene Using an Ab Initio Study
Directory of Open Access Journals (Sweden)
Reza Ansari
2016-12-01
Full Text Available Importance of covalent bonded two-dimensional monolayer nanostructures and also hydrocarbons is undeniably responsible for creation of new fascinating materials like polyphenylene polymer, a hydrocarbon super honeycomb network, so-called porous graphene. The mechanical properties of porous graphene such as its Young’s modulus, Poisson’s ratio and the bulk modulus as the determinative properties are calculated in this paper using ab initio calculations. To accomplish this aim, the density functional theory on the basis of generalized gradient approximation and the Perdew–Burke–Ernzerhof exchange correlation is employed. Density functional theory calculations are used to calculate strain energy of porous graphene with respect to applied strain. Selected numerical results are then presented to study the properties of porous graphene. Comparisons are made between the properties of porous graphene and those of other analogous nanostructures. The results demonstrated lower stiffness of porous graphene than those of graphene and graphyne, and higher stiffness than that of graphdyine and other graphyne families. Unlikely, Poisson’s ratio is observed to be more than that of graphene and also less than that of graphyne. It is further observed that the presence of porosity and also formation of C-H bond in the pore sites is responsible for these discrepancies. Porous graphene is found to behave as the isotropic material.
Room temperature linelists for CO2 asymmetric isotopologues with ab initio computed intensities
Zak, Emil J.; Tennyson, Jonathan; Polyansky, Oleg L.; Lodi, Lorenzo; Zobov, Nikolay F.; Tashkun, Sergei A.; Perevalov, Valery I.
2017-12-01
The present paper reports room temperature line lists for six asymmetric isotopologues of carbon dioxide: 16O12C18O (628), 16O12C17O (627), 16O13C18O (638),16O13C17O (637), 17O12C18O (728) and 17O13C18O (738), covering the range 0-8000 cm-1. Variational rotation-vibration wavefunctions and energy levels are computed using the DVR3D software suite and a high quality semi-empirical potential energy surface (PES), followed by computation of intensities using an ab initio dipole moment surface (DMS). A theoretical procedure for quantifying sensitivity of line intensities to minor distortions of the PES/DMS renders our theoretical model as critically evaluated. Several recent high quality measurements and theoretical approaches are discussed to provide a benchmark of our results against the most accurate available data. Indeed, the thesis of transferability of accuracy among different isotopologues with the use of mass-independent PES is supported by several examples. Thereby, we conclude that the majority of line intensities for strong bands are predicted with sub-percent accuracy. Accurate line positions are generated using an effective Hamiltonian, constructed from the latest experiments. This study completes the list of relevant isotopologues of carbon dioxide; these line lists are available to remote sensing studies and inclusion in databases.
Energy Technology Data Exchange (ETDEWEB)
Biswas, Parthapratim, E-mail: Partha.Biswas@usm.edu [Department of Physics and Astronomy, The University of Southern Mississippi, Hattiesburg, MS 39406 (United States); Department of Physics and Astronomy, Condensed Matter and Surface Science Program, Ohio University, Ohio 45701 (United States); Drabold, D. A., E-mail: drabold@ohio.edu [Department of Physics and Astronomy, Condensed Matter and Surface Science Program, Ohio University, Ohio 45701 (United States); Atta-Fynn, Raymond, E-mail: attafynn@uta.edu [Department of Physics, The University of Texas, Arlington, Texas 76019 (United States)
2014-12-28
A study of the formation of voids and molecular hydrogen in hydrogenated amorphous silicon is presented based upon a hybrid approach that involves inversion of experimental nuclear magnetic resonance data in conjunction with ab initio total-energy relaxations in an augmented solution space. The novelty of this approach is that the voids and molecular hydrogen appear naturally in the model networks unlike conventional approaches, where voids are created artificially by removing silicon atoms from the networks. Two representative models with 16 and 18 at. % of hydrogen are studied in this work. The result shows that the microstructure of the a-Si:H network consists of several microvoids and few molecular hydrogen for concentration above 15 at. % H. The microvoids are highly irregular in shape and size, and have a linear dimension of 5–7 Å. The internal surface of a microvoid is found to be decorated with 4–9 hydrogen atoms in the form of monohydride Si–H configurations as observed in nuclear magnetic resonance experiments. The microstructure consists of (0.9–1.4)% hydrogen molecules of total hydrogen in the networks. These observations are consistent with the outcome of infrared spectroscopy, nuclear magnetic resonance, and calorimetry experiments.
Varnali, Tereza; Edwards, Howell G M
2010-07-13
The recognition that scytonemin, the radiation protectant pigment produced by extremophilic cyanobacterial colonies in stressed terrestrial environments, is a key biomarker for extinct or extant life preserved in geological scenarios is critically important for the detection of life signatures by remote analytical instrumentation on planetary surfaces and subsurfaces. The ExoMars mission to seek life signatures on Mars is just one experiment that will rely upon the detection of molecules such as scytonemin in the Martian regolith. Following a detailed structural analysis of the parent scytonemin, we report here for the first time a similar analysis of several of its methoxy derivatives that have recently been extracted from stressed cyanobacteria. Ab initio calculations have been carried out to determine the most stable molecular configurations, and the implications of the structural changes imposed by the methoxy group additions on the spectral characteristics of the parent molecule are discussed. The calculated electronic absorption bands of the derivative molecules reveal that their capability of removing UVA wavelengths is removed while preserving the ability to absorb the shorter wavelength UVB and UVC radiation, in contrast to scytonemin itself. This is indicative of a special role for these molecules in the protective strategy of the cyanobacterial extremophiles.
Single-particle cryo-EM-Improved ab initio 3D reconstruction with SIMPLE/PRIME.
Reboul, Cyril F; Eager, Michael; Elmlund, Dominika; Elmlund, Hans
2018-01-01
Cryogenic electron microscopy (cryo-EM) and single-particle analysis now enables the determination of high-resolution structures of macromolecular assemblies that have resisted X-ray crystallography and other approaches. We developed the SIMPLE open-source image-processing suite for analysing cryo-EM images of single-particles. A core component of SIMPLE is the probabilistic PRIME algorithm for identifying clusters of images in 2D and determine relative orientations of single-particle projections in 3D. Here, we extend our previous work on PRIME and introduce new stochastic optimization algorithms that improve the robustness of the approach. Our refined method for identification of homogeneous subsets of images in accurate register substantially improves the resolution of the cluster centers and of the ab initio 3D reconstructions derived from them. We now obtain maps with a resolution better than 10 Å by exclusively processing cluster centers. Excellent parallel code performance on over-the-counter laptops and CPU workstations is demonstrated. © 2017 The Protein Society.
Ab initio excited states from the in-medium similarity renormalization group
Parzuchowski, N. M.; Morris, T. D.; Bogner, S. K.
2017-04-01
We present two new methods for performing ab initio calculations of excited states for closed-shell systems within the in-medium similarity renormalization group (IMSRG) framework. Both are based on combining the IMSRG with simple many-body methods commonly used to target excited states, such as the Tamm-Dancoff approximation (TDA) and equations-of-motion (EOM) techniques. In the first approach, a two-step sequential IMSRG transformation is used to drive the Hamiltonian to a form where a simple TDA calculation (i.e., diagonalization in the space of 1 p 1 h excitations) becomes exact for a subset of eigenvalues. In the second approach, EOM techniques are applied to the IMSRG ground-state-decoupled Hamiltonian to access excited states. We perform proof-of-principle calculations for parabolic quantum dots in two dimensions and the closed-shell nuclei 16O and 22O. We find that the TDA-IMSRG approach gives better accuracy than the EOM-IMSRG when calculations converge, but it is otherwise lacking the versatility and numerical stability of the latter. Our calculated spectra are in reasonable agreement with analogous EOM-coupled-cluster calculations. This work paves the way for more interesting applications of the EOM-IMSRG approach to calculations of consistently evolved observables such as electromagnetic strength functions and nuclear matrix elements, and extensions to nuclei within one or two nucleons of a closed shell by generalizing the EOM ladder operator to include particle-number nonconserving terms.
International Nuclear Information System (INIS)
LaBarge, M.S.; Hillig, K.W. II; Kuczkowski, R.L.; Cremer, D.
1986-01-01
The rotational spectra of six isotopic species of trans-difluoroethylene ozonide (trans-3,5-difluoro-1,2,4-trioxolane) were assigned. These included the parent species, the single- and double-substituted deuterium species, the double 18 O/sub p/, the triple 18 O, and and 13 C species. The spectrum consisted of b-type transitions with a 10:6 intensity alternation. The electric dipole moment was determined from Stark effect measurements to be μ/sub b/ = 0.994 (5) D. These results support an average structure having an O/sub p/-O/sub p/ twist ring conformation with C 2 symmetry and diaxial fluorine substituents. The shortening of the C-O/sub p/ bonds (1.368 A) relative to the C-O/sub c/ bonds (1.401 A) is very apparent in this member of the fluoroozonide series. Ab initio calculations were performed at the HG/6-31G/sup */ level and analyzed in terms of electron density distributions. Experimental and theoretical results are rationalized in terms of anomeric interactions with the peroxy oxygen atoms
Energy Technology Data Exchange (ETDEWEB)
Fischer, Sean A.; Apra, Edoardo; Govind, Niranjan; Hess, Wayne P.; El-Khoury, Patrick Z.
2017-02-03
Recent developments in nanophotonics have paved the way for achieving significant advances in the realm of single molecule chemical detection, imaging, and dynamics. In particular, surface-enhanced Raman scattering (SERS) is a powerful analytical technique that is now routinely used to identify the chemical identity of single molecules. Understanding how nanoscale physical and chemical processes affect single molecule SERS spectra and selection rules is a challenging task, and is still actively debated. Herein, we explore underappreciated chemical phenomena in ultrasensitive SERS. We observe a fluctuating excited electronic state manifold, governed by the conformational dynamics of a molecule (4,4’-dimercaptostilbene, DMS) interacting with a metallic cluster (Ag20). This affects our simulated single molecule SERS spectra; the time trajectories of a molecule interacting with its unique local environment dictates the relative intensities of the observable Raman-active vibrational states. Ab initio molecular dynamics of a model Ag20-DMS system are used to illustrate both concepts in light of recent experimental results.
Ab initio defect properties for modeling radiation-induced segregation in Fe-Ni-Cr alloys
International Nuclear Information System (INIS)
Tucker, J.D.; Allen, T.R.; Morgan, D.; Najafabadi, R.
2007-01-01
Radiation-induced segregation (RIS) has been studied with experimental and theoretical methods for over 30 years and many models have been built in an attempt to understand the mechanisms involved. Input parameters for these models are often not available experimentally, limiting the model's predictive capabilities. In an effort to obtain more accurate input parameters we have calculated formation and migration energies for both vacancies and interstitials using ab initio methods in face-centered cubic (fcc) Fe-Ni-Cr alloys, with an emphasis on Ni-based alloys with dilute concentrations of Cr and Fe. The data gives new insight into a number of properties including species dependence of migration barriers and binding energies for both vacancies and interstitials. We predict species dependent vacancy migration barriers for Cr (0.82 eV), Fe (0.95 eV), and Ni (1.08 eV) and interstitial migration barriers for Cr (0.08 eV), Fe (0.11 eV), and Ni (0.14 eV) in a Ni matrix. Significant binding between Cr and the interstitial dumbbell was also observed. Further work will build on this data to create a rate theory models for RIS. (author)
Buczek, P.; Borisov, V.; Bersier, C.; Ostanin, S.; Sandratskii, L.; Staunton, J. B.; Gross, E. K. U.; Mertig, I.; Ernst, A.
2012-02-01
et al. Motivated by a experimental reports on possible high temperature superconductivity in palladium hydride [Tripodi ,Physica C 388-389, 571 (2003)], we present a first principle study of spin fluctuations, electron-phonon coupling and critical temperature in PdHx, 0 <=x <=1. A prerequisite for any qualitative study of exchange-enhanced materials is the knowledge of spin flip fluctuation spectrum. It is generally believed [Berk & Schrieffer, Phys. Rev. Lett., 17, 433 (1966)] that the ferromagnetic-like paramagnons of Pd are destructive for the conventional, i.e. s-wave, superconductivity. We describe them using linear response time dependent density functional theory, recently implemented to study complex metals [Buczek ,Phys. Rev. Lett. 105, 097205 (2010)] . We find that hydrogenation suppresses the intense spin fluctuations of pure Pd, driving it away from a magnetic critical point. Under the assumption of s-wave pairing, this could lead to the formation of the superconducting state. The ab-initio estimated electron-phonon coupling is strong enough to support superconductivity. Please look for the complementary contribution of Christophe Bersier.
Ab-initio Calculations of Accurate Electronic Properties of ZnS
Khamala, Bethuel; Franklin, Loushanda; Malozovski, Yuriy; Stewart, Anthony; Bagayoko, Diola; Bagayoko Research Group Team
2014-03-01
We present the results from ab-initio, self consistent, local density approximation (LDA) calculations of the electronic and related properties of zinc-blende zinc sulphide (zb-ZnS). We employed the Ceperley and Alder LDA potential and the linear combination of atomic orbital (LCAO) formalism in our non-relativistic computations. The implementation of the LCAO formalism followed the Bagayoko, Zhao, and Williams method as enhanced by Ekuma and Franklin (BZW-EF). The BZW-EF method includes a methodical search for the optimal basis set that yields the minima of the occupied energies. This search entails increasing the size of the basis set and related modifications of angular symmetry and of radial orbitals. Our calculated, direct gap of 3.725 eV, at the Γ point, is in excellent agreement with experiment. We have also calculated the total (DOS) and partial (pDOS) densities of states, electron and hole effective masses and total energies that agree very well with available, corresponding experimental results. Acknowledgement: This research is funded in part by the National Science Foundation (NSF) and the Louisiana Board of Regents, through LASiGMA [Award Nos. EPS- 1003897, NSF (2010-15)-RII-SUBR] and NSF HRD-1002541, the US Department of Energy - National, Nuclear Security Administration (NNSA) (Award No. DE-NA0001861), LaSPACE, and LONI-SUBR.
Ab-initio Computation of the Electronic, transport, and Bulk Properties of Calcium Oxide.
Mbolle, Augustine; Banjara, Dipendra; Malozovsky, Yuriy; Franklin, Lashounda; Bagayoko, Diola
We report results from ab-initio, self-consistent, local Density approximation (LDA) calculations of electronic and related properties of calcium oxide (CaO) in the rock salt structure. We employed the Ceperley and Alder LDA potential and the linear combination of atomic orbitals (LCAO) formalism. Our calculations are non-relativistic. We implemented the LCAO formalism following the Bagayoko, Zhao, and Williams (BZW) method, as enhanced by Ekuma and Franklin (BZW-EF). The BZW-EF method involves a methodical search for the optimal basis set that yields the absolute minima of the occupied energies, as required by density functional theory (DFT). Our calculated, indirect band gap of 6.91eV, from towards the L point, is in excellent agreement with experimental value of 6.93-7.7eV, at room temperature (RT). We have also calculated the total (DOS) and partial (pDOS) densities of states as well as the bulk modulus. Our calculated bulk modulus is in excellent agreement with experiment. Work funded in part by the US Department of Energy (DOE), National Nuclear Security Administration (NNSA) (Award No.DE-NA0002630), the National Science Foundation (NSF) (Award No, 1503226), LaSPACE, and LONI-SUBR.
Ab-initio Calculations of Accurate Electronic Properties of Wurzite AlN
Nwigboji, Ifeanyi; Malozovsky, Yuriy; Bagayoko, Diola; Bagayoko Research Group Team
2014-03-01
We present results from ab-initio, self consistent local density approximation (LDA) calculations of electronic and related properties of wurtzite Aluminum Nitride (w-AlN). Our non-relativistic computations employed the Ceperley and Alder LDA potential and the linear combination of atomic orbital (LCAO) formalism. The implementation of the LCAO formalism followed the Bagayoko, Zhao, and Williams' method as enhanced by Ekuma and Franklin (BZW-EF). The BZW-EF method verifiably obtains the minima of the occupied energies; these minima provide the most variationally and physically valid density functional theory (DFT) description of the ground states of materials under study. Our preliminary results for w-AlN show that w-AlN has a direct band gap of 5.82 eV at the Γ point. The preliminary energy bands were obtained with a basis set comprising 48 functions. None of the several, larger basis sets tested to date led to occupied energies lower than those obtained with the above 48. While most previous LDA calculations are 2 eV smaller or more than the experimental value of 5.9 eV that is in excellent agreement with our finding, considering the typical experimental uncertainty of 0.2 eV for absorption measurements on AlN. We also discuss our calculated density of states (DOS) and partial densities of states (pDOS).
Ab initio prediction of electronic, transport and bulk properties of Li2S
Malozovsky, Yuriy; Franklin, Lashounda; Ekuma, Chinedu; Bagayoko, Diola
2015-08-01
In this paper, we present results from ab initio, self-consistent, local density approximation (LDA) calculations of electronic and related properties of cubic antifluorite (anti-CaF2) lithium sulfide (Li2S). Our nonrelativistic computations implemented the linear combination of atomic orbital (LCAO) formalism following the Bagayoko, Zhao and Williams method, as enhanced by Ekuma and Franklin (BZW-EF). Consequently, using several self-consistent calculations with increasing basis sets, we searched for the smallest basis set that yields the absolute minima of the occupied energies. The outcomes of the calculation with this basis set, called the optimal basis set, have the full physical content of density functional theory (DFT). Our calculated indirect band gap, from Γ to X, is 3.723 eV, for the low temperature experimental lattice constant of 5.689 Å. The predicted indirect band gap of 3.702 eV is obtained for the computationally determined equilibrium lattice constant of 5.651 Å. We have also calculated the total density of states (DOS) and partial densities of states (pDOS), electron and hole effective masses and the bulk modulus of Li2S. Due to a lack of experimental results, most of the calculated ones reported here are predictions for this material suspected of exhibiting a high temperature superconductivity similar to that of MgB2.
Ab-Initio Computations of Electronic and Related Properties of cubic Lithium Selenide (Li2Se)
Goita, Abdoulaye; Nwigboji, Ifeanyi H.; Malozovsky, Yuriy; Bagayoko, Diola
We present theoretical predictions, from ab-initio, self-consistent calculations, of electronic and related properties of cubic lithium selenide (Li2Se). We employed a local density approximation (LDA) potential and the linear combination of atomic orbitals (LCAO). We performed the computations following the Bagayoko, Zhao, and Williams (BZW) method, as enhanced by Ekuma and Franklin (BZW-EF). Our results include electronic energies, total and partial densities of states, effective masses, and the bulk modulus. The theoretical equilibrium lattice constant is 5.882 Å. We found cubic Li2Se to have a direct band gap of 4.363 eV (prediction), at Γ. This gap is 4.065 eV for a room temperature lattice constant of 6.017 Å. The calculated bulk modulus is 31.377 GPa. Acknowledgments: This work was funded in part by the National Science Foundation (NSF) and the Louisiana Board of Regents, through LASiGMA [Award Nos. EPS- 1003897, NSF (2010-15)-RII-SUBR] and NSF HRD-1002541, the US Department of Energy - National, Nuclear Security Administration (NNSA) (Award No. DE- NA0002630), LaSPACE, and LONI-SUBR.