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Sample records for ab initio atomic

  1. Ab initio calculation of double ionization of atoms

    SciTech Connect

    Serov, V. V.

    2013-02-15

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

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

    ERIC Educational Resources Information Center

    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…

  3. Comparison between ab initio and semiempirical net atomic charges of some nicotinic acetylcholine receptor agonists

    SciTech Connect

    Yadav, J.S.; Hermsmeier, M.; Gund, T. )

    1989-01-01

    We have calculated the net atomic charges and molecular electrostatic potentials of two potent nicotinic acetylcholine receptor agonists, isoarecolone and acetylpiperazine, by three different methods to see how well they correlate and if the simplest method gives the same predictive results. The calculational methods involved calculating net atomic charges by semiempirical (MNDO from MOPAC) and ab initio (Mulliken) and ab initio (potential derived) at STO-3G basis set level. Some deviations were observed when comparisons were made atom by atom, but when group comparisons were made, good correlations were observed. When these partial charges were used to calculate the respective molecular electrostatic potentials on the van der Waals surface, very good correlations were obtained. This study shows that for routine electrostatic calculations, semiempirical MNDO Calculations give similar results and thus lead to similar predictions.

  4. Periodic arrays of intercalated atoms in twisted bilayer graphene: An ab initio investigation

    NASA Astrophysics Data System (ADS)

    Miwa, R. H.; Venezuela, P.; Morell, Eric Suárez

    2015-09-01

    We have performed an ab initio investigation of transition metals (TMs =Mo ,Ru ,Co ,andPt ) embedded in twisted bilayer graphene (tBG) layers. Our total energy results reveal that, triggered by the misalignment between the graphene layers, Mo and Ru atoms may form a quasiperiodic (triangular) array of intercalated atoms. In contrast, the formation of those structures is not expected for the other TMs, the Co and Pt atoms. The net magnetic moment (m ) of Mo and Ru atoms may be quenched upon intercalation, depending on the stacking region (AA or AB). For instance, we find a magnetic moment of 0.3 μB(1.8 μB) for Ru atoms intercalated between the AA (AB) regions of the stacked twisted layers. Through simulated scanning tunneling microscopy (STM) images, we verify that the presence of intercalated TMs can be identified by the formation of bright (hexagonal) spots lying on the graphene surface.

  5. Peculiarities of geminal atom interaction in chloro-containing imidazoles using ab initio calculations

    NASA Astrophysics Data System (ADS)

    Feshin, V. P.; Feshina, E. V.

    2000-07-01

    The results of ab initio calculations at the RHF/6-31G ∗ level of 1-methyl-4-chloro- and -5-chloroimidazoles as well as of 1-methyl-4,5-dichloroimidazoles with total optimization of their geometry were presented. They were used for the interpretation of peculiarities of an influence of the "pyridine" and "pyrrole" N atoms on the electron distribution of the Cl atoms in these molecules and of their 35Cl NQR frequencies. These peculiarities are caused by the different space electron distribution of these N atoms that causes the different polarization of the geminal Cl atom p-electron shell.

  6. Ab initio theory of spin entanglement in atoms and molecules

    NASA Astrophysics Data System (ADS)

    Pittalis, S.; Troiani, F.; Rozzi, C. A.; Vignale, G.

    2015-02-01

    We investigate spin entanglement in many-electron systems within the framework of density functional theory. We show that the entanglement length, which is extracted from the spatial dependence of the local concurrence, is a sensitive indicator of atomic shells and reveals the character, covalent or metallic, of chemical bonds. These findings shed light on the remarkable success of modern density functionals, which tacitly employ the entanglement length as a variable. This opens the way to further research on entanglement-based functionals.

  7. Ab initio prediction of protein structure with both all-atom and simplified force fields

    NASA Astrophysics Data System (ADS)

    Scheraga, Harold

    2004-03-01

    Using only a physics-based ab initio method, and both all-atom (ECEPP/3) and simplified united-residue (UNRES) force fields, global optimization of both potential functions with Monte Carlo-plus-Minimization (MCM) and Conformational Space Annealing (CSA), respectively, provides predicted structures of proteins without use of knowledge-based information. The all-atom approach has been applied to the 46-residue protein A, and the UNRES approach has been applied to larger CASP targets. The predicted structures will be described.

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

    SciTech Connect

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

    2013-12-12

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

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

    NASA Astrophysics Data System (ADS)

    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.

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

    NASA Astrophysics Data System (ADS)

    You, Y.; Yan, M. F.

    2013-05-01

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

  11. Ab Initio Vibrational Levels For HO2 and Vibrational Splittings for Hydrogen Atom Transfer

    NASA Technical Reports Server (NTRS)

    Barclay, V. J.; Dateo, Christopher E.; Hamilton, I. P.; Arnold, James O. (Technical Monitor)

    1994-01-01

    We calculate vibrational levels and wave functions for HO2 using the recently reported ab initio potential energy surface of Walch and Duchovic. There is intramolecular hydrogen atom transfer when the hydrogen atom tunnels through a T-shaped saddle point separating two equivalent equilibrium geometries, and correspondingly, the energy levels are split. We focus on vibrational levels and wave functions with significant splitting. The first three vibrational levels with splitting greater than 2/cm are (15 0), (0 7 1) and (0 8 0) where V(sub 2) is the O-O-H bend quantum number. We discuss the dynamics of hydrogen atom transfer; in particular, the O-O distances at which hydrogen atom transfer is most probable for these vibrational levels. The material of the proposed presentation was reviewed and the technical content will not reveal any information not already in the public domain and will not give any foreign industry or government a competitive advantage.

  12. Evolution of atomic structure in Al75Cu25 liquid from experimental and ab initio molecular dynamics simulation studies.

    PubMed

    Xiong, L H; Yoo, H; Lou, H B; Wang, X D; Cao, Q P; Zhang, D X; Jiang, J Z; Xie, H L; Xiao, T Q; Jeon, S; Lee, G W

    2015-01-28

    X-ray diffraction and electrostatic levitation measurements, together with the ab initio molecular dynamics simulation of liquid Al(75)Cu(25) alloy have been performed from 800 to 1600 K. Experimental and ab initio molecular dynamics simulation results match well with each other. No abnormal changes were experimentally detected in the specific heat capacity over total hemispheric emissivity and density curves in the studied temperature range for a bulk liquid Al(75)Cu(25) alloy measured by the electrostatic levitation technique. The structure factors gained by the ab initio molecular dynamics simulation precisely coincide with the experimental data. The atomic structure analyzed by the Honeycutt-Andersen index and Voronoi tessellation methods shows that icosahedral-like atomic clusters prevail in the liquid Al(75)Cu(25) alloy and the atomic clusters evolve continuously. All results obtained here suggest that no liquid-liquid transition appears in the bulk liquid Al(75)Cu(25) alloy in the studied temperature range. PMID:25524926

  13. Evolution of local atomic structure during solidification of Al2Au liquid: An ab initio study

    SciTech Connect

    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.

  14. Ab initio calculations of vacancy interactions with solute atoms in bcc Fe

    NASA Astrophysics Data System (ADS)

    Vincent, E.; Becquart, C. S.; Domain, C.

    2005-01-01

    Solute Cu plays a major role in the embrittlement of reactor pressure vessel (RPV) steels under radiation. In RPV steels and dilute FeCu alloys, the tomographic atom probe has revealed the formation of Cu atmospheres under neutron flux. More recently the role of other solutes such as Ni, Mn and Si which are also within the atmospheres has been put forward. It is thus very important to characterise the interactions of these solutes with radiation-induced point defects in order to understand the elementary mechanisms behind the formation of these atmospheres. We have investigated by ab initio calculations based on the density functional theory the interactions of point defects in dilute FeX alloys (X = Cu, Mn, Ni or Si). The structure of X-vacancy complexes has been determined, as well as their binding energies. Their relative stability is discussed and compared to experimental results obtained with model alloys.

  15. Combined ab initio molecular dynamics and experimental studies of carbon atom addition to benzene.

    PubMed

    McKee, Michael L; Reisenauer, Hans Peter; Schreiner, Peter R

    2014-04-17

    Car-Parrinello molecular dynamics was used to explore the reactions between triplet and singlet carbon atoms with benzene. The computations reveal that, in the singlet C atom reaction, products are very exothermic where nearly every collision yields a product that is determined by the initial encounter geometry. The singlet C atom reaction does not follow the minimum energy path because the bimolecular reaction is controlled by dynamics (i.e., initial orientation of encounter). On the other hand, in a 10 K solid Ar matrix, ground state C((3)P) atoms do tend to follow RRKM kinetics. Thus, ab initio molecular dynamics (AIMD) results indicate that a significant fraction of C-H insertion occurs to form phenylcarbene whereas, in marked contrast to previous theoretical and experimental conclusions, the Ar matrix isolation studies indicate a large fraction of direct cycloheptatetraene formation, without the intermediacy of phenylcarbene. The AIMD calculations are more consistent with vaporized carbon atom experiments where labeling studies indicate the initial formation of phenylcarbene. This underlines that the availability of thermodynamic sinks can completely alter the observed reaction dynamics. PMID:24661002

  16. Ab-initio atomic level stresses in Cu-Zr systems

    NASA Astrophysics Data System (ADS)

    Ojha, Madhusudan; Nicholson, Don M.; Egami, Takeshi

    2014-03-01

    In our recent studies [D. M. Nicholson, Madhusudan Ojha and Takeshi Egami, J. Phys.: Condens. Matter 25 435505 (2013)] we have calculated ab-initio atomic level stresses in the simple B2 Cu-Zr system, Cu50Zr50 liquid and glass and have found tremendous atomic level stress in the B2 structure due to strong bonding between Cu and Zr and significantly smaller atomic level stresses in liquid and glass due to reduced chemical order. We have extended our studies to additional structures and stoichiometries. On the basis of these results we discuss the relationship between short-range order, bonding, electronic density of states and atomic level stress. We are searching for an explanation of the unique position of Zr as a promotor of glass forming ability. We report the differences in atomic level stress, bonding, and density of states when Ti, Y, and Nb replace Zr on fixed structures. The work at the University of Tennessee and Oak Ridge National Laboratory was supported by the U.S. Department of Energy, Office of Basic Energy Sciences, Materials Science and Engineering Division.

  17. Energetics, diffusion, and magnetic properties of cobalt atom in a monolayer graphene: An ab initio study

    SciTech Connect

    Raji, Abdulrafiu T.; Lombardi, Enrico B.

    2015-09-21

    We use ab initio methods to study the binding, diffusion, and magnetic properties of cobalt atom embedded in graphene vacancies. We investigate the diffusion of Co-monovacancy (Co-MV) and Co-divacancy (Co-DV) defect complexes, and determine the minimum energy path (MEP), as well as the activation energy barrier of migration. We obtained similar activation energy barriers, of ∼5.8 eV, for Co-MV and Co-DV diffusion, respectively. Our calculations also suggest that, at electron–irradiation energy of 200 keV as used in a related experiment, the maximum energy transfer to the Co atom, of approximately 9.0 eV is sufficiently high to break metal-carbon bonding. The incident electron energy is also high enough to displace graphene's carbon atoms from their lattice positions. The breaking of metal-carbon bonding and the displacement of graphene atoms may act to facilitate the migration of Co. We conclude therefore that the detrapping and diffusion of cobalt as observed experimentally is likely to be radiation-induced, similar to what has been observed for Au and Fe in electron-irradiated graphene. Furthermore, we show that Co migration in graphene is such that its magnetic moment varies along the diffusion path. The magnetic moment of Co is consistently higher in Co-DV diffusion when compared to that of Co-MV diffusion.

  18. Ab initio calculations of self-interstitial interaction and migration with solute atoms in bcc Fe

    NASA Astrophysics Data System (ADS)

    Vincent, E.; Becquart, C. S.; Domain, C.

    2006-12-01

    The embrittlement of pressure vessel steels under radiation has been long ago correlated with the presence of solute Cu. Indeed the atom probe and the small angle neutron scattering, principally, have revealed the formation of Cu clusters under neutron flux in reactor pressure vessel (RPV) steels and dilute FeCu alloys. Other solutes such as Ni, Mn and Si which are also found within the clusters, are now suspected to contribute to the embrittlement. The interactions of these solutes with radiation induced point defects need thus to be characterized properly in order to understand the elementary mechanisms behind the formation of these clusters. We have investigated by ab initio calculations based on the density functional theory the interactions of self-interstitials with solute atoms in dilute FeX alloys (X = Cu, Mn, Ni or Si). Different possible configurations of solute-dumbbell complexes have been studied. Their binding energies are discussed, as well as their relative stability. The migration of dumbbells with a solute atom in their vicinity was also investigated. All these results are compared to some experimental ones obtained on dilute FeX model alloys. Our results indicate that for Mn solute atoms, diffusion via an interstitial mechanism is very likely.

  19. Ab initio thermodynamic evaluation of Pd atom interaction with CeO(2) surfaces.

    PubMed

    Mayernick, Adam D; Janik, Michael J

    2009-08-28

    Palladium supported on ceria is an effective catalytic material for three-way automotive catalysis, catalytic combustion, and solid-oxide fuel cell (SOFC) anodes. The morphology, oxidation state, and particle size of Pd on ceria affect catalytic activity and are a function of experimental conditions. This work utilizes ab initio thermodynamics using density functional theory (DFT) (DFT+U) methods to evaluate the stability of Pd atoms, PdO(x) species, and small Pd particles in varying configurations on CeO(2) (111), (110), and (100) single crystal surfaces. Over specific oxygen partial pressure and temperature ranges, palladium incorporation to form a mixed surface oxide is thermodynamically favorable versus other single Pd atom states on each ceria surface. For example, Pd atoms may incorporate into Ce fluorite lattice positions in a Pd(4+) oxidation state on the CeO(2) (111) surface. The ceria support shifts the transition between formal Pd oxidation states (Pd(0), Pd(2+), Pd(4+)) relative to bulk palladium and stabilizes certain oxidized palladium species on each surface. We show that temperature, oxygen pressure, and cell potential in a SOFC can influence the stable states of palladium supported on ceria surfaces, providing insight into structural stability during catalytic operation. PMID:19725615

  20. Ab initio kinetics studies of hydrogen atom abstraction from methyl propanoate.

    PubMed

    Tan, Ting; Yang, Xueliang; Ju, Yiguang; Carter, Emily A

    2016-02-14

    The kinetics of hydrogen abstraction by five radicals (H, CH3, O((3)P), OH, and HO2) from a biodiesel surrogate, methyl propanoate (MP), is theoretically investigated. We employ high-level ab initio quantum chemistry methods, coupled-cluster singles and doubles with perturbative triples correction (CCSD(T)) and multi-reference singles and doubles configuration interaction (MRSDCI) with the Davidson-Silver (DS) correction, and obtain chemically accurate reaction energetics. Overall, MRSDCI + DS predicts comparable energetics to CCSD(T) for MP + H/CH3/O/OH. The rate constants are computed using transition state theory (TST-Rice-Ramsperger-Kassel-Marcus theory) in conjunction with the separable-hindered-rotor approximation, variable reaction coordinate TST, and the multi-structure all-structure (MS-AS) approach. A simplified method, semi-multi-structure, is also employed for MP + OH/HO2, and the rate coefficients with this less expensive method are in good agreement with the results obtained with the MS-AS method. The fitted modified Arrhenius expressions are provided over a temperature range of 250 to 2000 K. The predicted rate coefficients for MP + OH agree remarkably well with experimental data over a wide temperature range. Branching ratio analysis of all the studied reactions shows that abstractions of the secondary H atoms within MP are expected to dominate the consumption of fuel at low temperatures, and the contributions of abstractions from the two methyl groups increase with temperature for all abstracting radicals. PMID:26796249

  1. Study of atomic structure of liquid Hg-In alloys using ab-initio molecular dynamics

    SciTech Connect

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

    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.

  2. Ab Initio Many-Electron Calculation of Hyperfast Time-Resolved Coherent Excitation and Decay Of Polyelectronic Atoms

    SciTech Connect

    Nicolaides, Cleanthes A.; Mercouris, Theodoros; Komninos, Yannis

    2007-11-29

    The theoretical quantitative understanding of time-resolved processes of coherent excitation and decay in polyelectronic atoms, induced by hypershort electromagnetic pulses, is a prerequisite for their possible control. We review key elements of an approach to the ab initio determination of perturbative as well as of nonperturbative solutions of the time-dependent Schroedinger equation describing such processes. The essential element of this approach is the development of formalism and methods that utilize physically relevant state-specific wavefunctions of stationary states of the discrete and the continuous spectrum.

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

    SciTech Connect

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

    2007-05-28

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

  4. Ab initio atomic recombination reaction energetics on model heat shield surfaces

    NASA Technical Reports Server (NTRS)

    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.

  5. Atomic and Electronic Structures of C_60+BN Nanopeapods from ab initio Pseudopotential Calculations

    NASA Astrophysics Data System (ADS)

    Trave, Andrea; Ribeiro, Filipe; Louie, Steven G.; Cohen, Marvin L.

    2004-03-01

    Nanopeapods are structures of nanometric size consisting of an external carbon nanotube encapsulating a chain or complex array of fullerenes. Recent calculations and experiments have proven that nanopeapods can be obtained assembling fullerenes within boron nitride nanotubes, creating novel materials of possible interest for electronic transport applications. To improve the understanding of the properties of these composite systems, as compared to empty nanotubes and carbon nanopeapods, ab-initio total energy calculations have been performed within the pseudopotential Density Functional Theory in local density approximation. Results of these calculations on the energetics and geometrical deformations involved in the encapsulation will be presented, followed by a discussion of the consequences on the electronic structures of these systems, with particular focus on aspects relevant to electronic transport phenomena. This work is supported by NFS (Grant DMR00-87088) and DOE (Contract DE-AC03-76SF00098), using computational resources at NERSC and NPACI.

  6. Atomic Spectral Methods for Ab Initio Molecular Electronic Energy Surfaces: Transitioning From Small-Molecule to Biomolecular-Suitable Approaches.

    PubMed

    Mills, Jeffrey D; Ben-Nun, Michal; Rollin, Kyle; Bromley, Michael W J; Li, Jiabo; Hinde, Robert J; Winstead, Carl L; Sheehy, Jeffrey A; Boatz, Jerry A; Langhoff, Peter W

    2016-08-25

    Continuing attention has addressed incorportation of the electronically dynamical attributes of biomolecules in the largely static first-generation molecular-mechanical force fields commonly employed in molecular-dynamics simulations. We describe here a universal quantum-mechanical approach to calculations of the electronic energy surfaces of both small molecules and large aggregates on a common basis which can include such electronic attributes, and which also seems well-suited to adaptation in ab initio molecular-dynamics applications. In contrast to the more familiar orbital-product-based methodologies employed in traditional small-molecule computational quantum chemistry, the present approach is based on an "ex-post-facto" method in which Hamiltonian matrices are evaluated prior to wave function antisymmetrization, implemented here in the support of a Hilbert space of orthonormal products of many-electron atomic spectral eigenstates familiar from the van der Waals theory of long-range interactions. The general theory in its various forms incorporates the early semiempirical atoms- and diatomics-in-molecules approaches of Moffitt, Ellison, Tully, Kuntz, and others in a comprehensive mathematical setting, and generalizes the developments of Eisenschitz, London, Claverie, and others addressing electron permutation symmetry adaptation issues, completing these early attempts to treat van der Waals and chemical forces on a common basis. Exact expressions are obtained for molecular Hamiltonian matrices and for associated energy eigenvalues as sums of separate atomic and interaction-energy terms, similar in this respect to the forms of classical force fields. The latter representation is seen to also provide a long-missing general definition of the energies of individual atoms and of their interactions within molecules and matter free from subjective additional constraints. A computer code suite is described for calculations of the many-electron atomic eigenspectra and

  7. Ab initio no core full configuration approach for light nuclei

    NASA Astrophysics Data System (ADS)

    Kim, Youngman; Shin, Ik Jae; Maris, Pieter; Vary, James P.; Forssén, Christian; Rotureau, Jimmy

    2014-07-01

    Comprehensive understanding of the structure and reactions of light nuclei poses theoretical and computational challenges. Still, a number of ab initio approaches have been developed to calculate the properties of atomic nuclei using fundamental interactions among nucleons. Among them, we work with the ab initio no core full configuration (NCFC) method and ab initio no core Gamow Shell Model (GSM). We first review these approaches and present some recent results.

  8. Ab initio no core full configuration approach for light nuclei

    NASA Astrophysics Data System (ADS)

    Kim, Youngman; Shin, Ik Jae; Maris, Pieter; Vary, James P.; Forssén, Christian; Rotureau, Jimmy

    2015-10-01

    Comprehensive understanding of the structure and reactions of light nuclei poses theoretical and computational challenges. Still, a number of ab initio approaches have been developed to calculate the properties of atomic nuclei using fundamental interactions among nucleons. Among them, we work with the ab initio no core full configuration (NCFC) method and ab initio no core Gamow Shell Model (GSM). We first review these approaches and present some recent results.

  9. Ab initio interaction potentials and scattering lengths for ultracold mixtures of metastable helium and alkali-metal atoms

    NASA Astrophysics Data System (ADS)

    Kedziera, Dariusz; Mentel, Łukasz; Żuchowski, Piotr S.; Knoop, Steven

    2015-06-01

    We have obtained accurate ab initio +4Σ quartet potentials for the diatomic metastable triplet helium+alkali-metal (Li, Na, K, Rb) systems, using all-electron restricted open-shell coupled cluster singles and doubles with noniterative triples corrections CCSD(T) calculations and accurate calculations of the long-range C6 coefficients. These potentials provide accurate ab initio quartet scattering lengths, which for these many-electron systems is possible, because of the small reduced masses and shallow potentials that result in a small amount of bound states. Our results are relevant for ultracold metastable triplet helium+alkali-metal mixture experiments.

  10. Ab Initio Study of Polonium

    SciTech Connect

    Zabidi, Noriza Ahmad; Kassim, Hasan Abu; Shrivastava, Keshav N.

    2008-05-20

    Polonium is the only element with a simple cubic (sc) crystal structure. Atoms in solid polonium sit at the corners of a simple cubic unit cell and no where else. Polonium has a valence electron configuration 6s{sup 2}6p{sup 4} (Z = 84). The low temperature {alpha}-phase transforms into the rhombohedral (trigonal) {beta} structure at {approx}348 K. The sc {alpha}-Po unit cell constant is a = 3.345 A. The beta form of polonium ({beta}-Po) has the lattice parameters, a{sub R} = 3.359 A and a rhombohedral angle 98 deg. 13'. We have performed an ab initio electronic structure calculation by using the density functional theory. We have performed the calculation with and without spin-orbit (SO) coupling by using both the LDA and the GGA for the exchange-correlations. The k-points in a simple cubic BZ are determined by R (0.5, 0.5, 0.5), {gamma} (0, 0, 0), X (0.5, 0, 0), M (0.5, 0.5, 0) and {gamma} (0, 0, 0). Other directions of k-points are {gamma} (0, 0, 0), X (0.5, 0, 0), R (0.5, 0.5, 0.5) and {gamma} (0, 0, 0). The SO splittings of p states at the {gamma} point in the GGA+SO scheme for {alpha}-Po are 0.04 eV and 0.02 eV while for the {beta}-Po these are 0.03 eV and 0.97 eV. We have also calculated the vibrational spectra for the unit cells in both the structures. We find that exchanging of a Po atom by Pb atom produces several more bands and destabilizes the {beta} phase.

  11. Ab initio calculation of Hubbard parameters for Rydberg-dressed atoms in a one-dimensional optical lattice

    NASA Astrophysics Data System (ADS)

    Chougale, Yashwant; Nath, Rejish

    2016-07-01

    We obtain ab initio the Hubbard parameters for Rydberg-dressed atoms in a one-dimensional (1D) sinusoidal optical lattice on the basis of maximally-localized Wannier states. Finite range, soft-core interatomic interactions become the trait of Rydberg admixed atoms, which can be extended over many neighboring lattice sites. In contrast to dipolar gases, where the interactions follow an inverse cubic law, the key feature of Rydberg-dressed interactions is the possibility of making neighboring couplings to the same magnitude as that of the onsite ones. The maximally-localized Wannier functions (MLWFs) are typically calculated via a spread-minimization procedure (Marzari N and Vanderbilt D 1997 Phys. Rev. B 56 12847) and are always found to be real functions apart from a trivial global phase when an isolated set of Bloch bands are considered. For an isolated single Bloch band, the above procedure reduces to a simple quasi-momentum-dependent unitary phase transformation. Here, instead of minimizing the spread, we employ a diagonal phase transformation which eliminates the imaginary part of the Wannier functions. The resulting Wannier states are found to be maximally localized and in exact agreement with those obtained via a spread-minimization procedure. Using these findings, we calculate the Hubbard couplings from the Rydberg admixed interactions, including dominant density-assisted tunneling (DAT) coefficients. Finally, we provide realistic lattice parameters for the state-of-the-art experimental Rydberg-dressed rubidium setup.

  12. Ab initio molecular dynamics calculations on scattering of hyperthermal H atoms from Cu(111) and Au(111)

    SciTech Connect

    Kroes, Geert-Jan Pavanello, Michele; Blanco-Rey, María; Alducin, Maite

    2014-08-07

    Energy loss from the translational motion of an atom or molecule impinging on a metal surface to the surface may determine whether the incident particle can trap on the surface, and whether it has enough energy left to react with another molecule present at the surface. Although this is relevant to heterogeneous catalysis, the relative extent to which energy loss of hot atoms takes place to phonons or electron-hole pair (ehp) excitation, and its dependence on the system's parameters, remain largely unknown. We address these questions for two systems that present an extreme case of the mass ratio of the incident atom to the surface atom, i.e., H + Cu(111) and H + Au(111), by presenting adiabatic ab initio molecular dynamics (AIMD) predictions of the energy loss and angular distributions for an incidence energy of 5 eV. The results are compared to the results of AIMDEFp calculations modeling energy loss to ehp excitation using an electronic friction (“EF”) model applied to the AIMD trajectories, so that the energy loss to the electrons is calculated “post” (“p”) the computation of the AIMD trajectory. The AIMD calculations predict average energy losses of 0.38 eV for Cu(111) and 0.13-0.14 eV for Au(111) for H-atoms that scatter from these surfaces without penetrating the surface. These energies closely correspond with energy losses predicted with Baule models, which is suggestive of structure scattering. The predicted adiabatic integral energy loss spectra (integrated over all final scattering angles) all display a lowest energy peak at an energy corresponding to approximately 80% of the average adiabatic energy loss for non-penetrative scattering. In the adiabatic limit, this suggests a way of determining the approximate average energy loss of non-penetratively scattered H-atoms from the integral energy loss spectrum of all scattered H-atoms. The AIMDEFp calculations predict that in each case the lowest energy loss peak should show additional energy loss

  13. Ab initio molecular dynamics calculations on scattering of hyperthermal H atoms from Cu(111) and Au(111)

    NASA Astrophysics Data System (ADS)

    Kroes, Geert-Jan; Pavanello, Michele; Blanco-Rey, María; Alducin, Maite; Auerbach, Daniel J.

    2014-08-01

    Energy loss from the translational motion of an atom or molecule impinging on a metal surface to the surface may determine whether the incident particle can trap on the surface, and whether it has enough energy left to react with another molecule present at the surface. Although this is relevant to heterogeneous catalysis, the relative extent to which energy loss of hot atoms takes place to phonons or electron-hole pair (ehp) excitation, and its dependence on the system's parameters, remain largely unknown. We address these questions for two systems that present an extreme case of the mass ratio of the incident atom to the surface atom, i.e., H + Cu(111) and H + Au(111), by presenting adiabatic ab initio molecular dynamics (AIMD) predictions of the energy loss and angular distributions for an incidence energy of 5 eV. The results are compared to the results of AIMDEFp calculations modeling energy loss to ehp excitation using an electronic friction ("EF") model applied to the AIMD trajectories, so that the energy loss to the electrons is calculated "post" ("p") the computation of the AIMD trajectory. The AIMD calculations predict average energy losses of 0.38 eV for Cu(111) and 0.13-0.14 eV for Au(111) for H-atoms that scatter from these surfaces without penetrating the surface. These energies closely correspond with energy losses predicted with Baule models, which is suggestive of structure scattering. The predicted adiabatic integral energy loss spectra (integrated over all final scattering angles) all display a lowest energy peak at an energy corresponding to approximately 80% of the average adiabatic energy loss for non-penetrative scattering. In the adiabatic limit, this suggests a way of determining the approximate average energy loss of non-penetratively scattered H-atoms from the integral energy loss spectrum of all scattered H-atoms. The AIMDEFp calculations predict that in each case the lowest energy loss peak should show additional energy loss in the

  14. Hydrogenated caged clusters of Si, Ge, and Sn and their endohedral doping with atoms: Ab initio calculations

    NASA Astrophysics Data System (ADS)

    Kumar, Vijay; Kawazoe, Yoshiyuki

    2007-04-01

    We report results of an ab initio study on the stability of hydrogenated empty cages XnHn with X=Si , Ge, and Sn, and n=8 , 10, 12, 14, 16, 18, 20, 24, and 28. All these cages have large highest-occupied-lowest-unoccupied molecular orbital (HOMO-LUMO) gaps. The HOMO-LUMO gap for Ge cages is found to be even larger than the values for Si cages, though in bulk Ge has a smaller band gap than Si. Cages with n=16 and 20 are found to be particularly stable in the form of fullerene structures. The bonding in the dodecahedral X20H20 cage is very close to sp3 type and it leads to the highest stability of this cage with perfect icosahedral symmetry. Endohedral doping of the empty cages such as SinHn (n=10-28) , with different guest atoms shows that doping can be used to manipulate the HOMO-LUMO gap with the possibility of varying their optical properties as well as to prepare species with large magnetic moments. Depending upon the guest atom, the character of the HOMO and the LUMO states and their origins either from the cage or the guest atom changes. This could lead to their applications in sensors. In contrast to the metal-encapsulated silicon-caged clusters, the embedding energy of the guest atom in the hydrogenated silicon fullerenes is small in most cases due to the weak interactions with the cage and therefore these slaved guest atoms can keep their atomic properties to a large extent. We find that atoms with closed electronic shell configurations such as Ca, Ba,… generally occupy the center of the cage. However, Be and other open electronic shell atoms tend to drift towards the wall of the cage. Doping of halogens such as iodine and alkalis such as Na can be used to produce, respectively hole and electron doping while transition-metal atoms such as V, Cr, Mn, and Fe are shown to produce atomiclike magnetic moments in many cases. In most of these cases the HOMO-LUMO gap becomes small because the guest atom orbital(s) are only partially occupied. However, for Ni and

  15. Ab initio vel ex eventu. II

    NASA Astrophysics Data System (ADS)

    Thiessen, P. A.; Treder, H.-J.

    Jedes initium wird durch experimenta crucis zum eventus. Jedes theoretisch interpretierbare ex-eventu-Resultat führt auf ein neues Initium. Gerade dies ist die gemeinsame Aussage von Atomistik, Quantenmechanik und Relativitätstheorie.Translated AbstractAb initio vel ex eventu. IIEvery initium becomes an eventus by experimenta crucis. Every theoretically interpretable ex-eventu result leads to a new initium. Right this is the joint assertion of atomism, quantum mechanics, and relativity.

  16. Hyper-Rayleigh light-scattering spectra determined by ab initio collisional hyperpolarizabilities of He-Ne atomic pairs

    SciTech Connect

    Glaz, W.; Bancewicz, T.; Godet, J.-L.; Maroulis, G.; Haskopoulos, A.

    2006-04-15

    The collision-induced (CI) first hyperpolarizability tensor for the He-Ne pair composed of the lightest noble gas elements has been obtained on the grounds of an ab initio method as a function of the interatomic distance R. Collision-induced hyper-Rayleigh (CIHR) spectra scattered in mixtures of such atoms at temperatures of 95 and 295 K are computed in absolute units both quantum mechanically and classically for the frequency shifts up to 1000 cm{sup -1}. The spectral features of the CIHR profiles due to the vector b{sub 1} and septor b{sub 3} parts of the hyperpolarizability tensor are discussed. The quantum character of computed spectra, especially significant at lower temperatures, has been found out. The integrated intensities of the spectra have been evaluated and used as a criterion of the reliability of the computed profiles. The frequency-dependent depolarization ratio of the CIHR spectra was evaluated and discussed. The properties of the resulting HR profiles have been compared with the depolarized CI Rayleigh spectrum of the He-Ne pair.

  17. Ab initio study of semiconductor atoms impurities in zigzag edge (10,0) carbon nanotubes

    SciTech Connect

    Muttaqien, Fahdzi Suprijadi

    2015-04-16

    The substitutional impurities in zigzag edge (10,0) carbon nanotubes have been studied by using first principles calculations. Silicon (Si), gallium (Ga), and arsenic (As) atom have been chosen as semiconductor based-atom for replacing carbon atoms in CNT’s surface. The silicon atom changes the energy gap of pristine zigzag (10,0) CNT, it is 0.19 eV more narrow than that of pristine CNT. Geometrically, the silicon atom creates sp{sup 3} bond with three adjacent carbon atoms, where the tetrahedral form of its sp{sup 3} bond is consisted of free unoccupied state. The silicon atom does not induce magnetism to zigzag CNT. Due to gallium (Ga) and arsenic (As) atom substitution, the zigzag CNT becomes metallic and has magnetic moment of 1 µ{sub B}. The valance and conduction band are crossed each other, then the energy gap is vanished. The electronic properties of GaAs-doped CNT are dominantly affected by gallium atom and its magnetic properties are dominantly affected by arsenic atom. These results prove that the CNT with desired properties can be obtained with substitutional impurities without any giving structural defect.

  18. Ab initio infrared and Raman spectra

    NASA Technical Reports Server (NTRS)

    Fredkin, D. R.; White, S. R.; Wilson, K. R.; Komornicki, A.

    1983-01-01

    It is pointed out that with increased computer power and improved computational techniques, such as the gradients developed in recent years, it is becoming practical to compute spectra ab initio, from the fundamental constants of nature, for systems of increasing complexity. The present investigation has the objective to explore several possible ab initio approaches to spectra, giving particular attention to infrared and nonresonance Raman. Two approaches are discussed. The sequential approach, in which first the electronic part and then later the nuclear part of the Born-Oppenheimer approximation is solved, is appropriate for small systems. The simultaneous approach, in which the electronic and nuclear parts are solved at the same time, is more appropriate for many-atom systems. A review of the newer quantum gradient techniques is provided, and the infrared and Raman spectral band contours for the water molecule are computed.

  19. Ab initio study of molecular and atomic oxygen on GeTe(111) surfaces

    SciTech Connect

    Deringer, Volker L.; Dronskowski, Richard

    2014-11-07

    Oxidation of the phase-change material germanium telluride (GeTe) is an atomic-scale process of fundamental importance, as it is detrimental to the stability of GeTe-based data-storage devices. Here, we present comprehensive density-functional theory simulations of molecular and atomic oxygen in contact with GeTe(111) surfaces. Molecular O{sub 2} is predicted to readily adsorb on the Ge-terminated (111) surface; the pristine Te-terminated counterpart, by contrast, appears quite inert. The coverage-dependent adsorption of O atoms is then investigated, and based on these data, a surface phase diagram for GeTe(111)/O is constructed. These results afford a detailed, atom-resolved picture of the initial surface oxidation of GeTe, and they harmonize well with a previous X-ray photoelectron spectroscopy study on this very topic.

  20. Ab initio infrared and Raman spectra

    NASA Astrophysics Data System (ADS)

    Fredkin, Donald R.; Komornicki, Andrew; White, Steven R.; Wilson, Kent R.

    1983-06-01

    We discuss several ways in which molecular absorption and scattering spectra can be computed ab initio, from the fundamental constants of nature. These methods can be divided into two general categories. In the first, or sequential, type of approach, one first solves the electronic part of the Schrödinger equation in the Born-Oppenheimer approximation, mapping out the potential energy, dipole moment vector (for infrared absorption) and polarizability tensor (for Raman scattering) as functions of nuclear coordinates. Having completed the electronic part of the calculation, one then solves the nuclear part of the problem either classically or quantum mechanically. As an example of the sequential ab initio approach, the infrared and Raman rotational and vibrational-rotational spectral band contours for the water molecule are computed in the simplest rigid rotor, normal mode approximation. Quantum techniques are used to calculate the necessary potential energy, dipole moment, and polarizability information at the equilibrium geometry. A new quick, accurate, and easy to program classical technique involving no reference to Euler angles or special functions is developed to compute the infrared and Raman band contours for any rigid rotor, including asymmetric tops. A second, or simultaneous, type of ab initio approach is suggested for large systems, particularly those for which normal mode analysis is inappropriate, such as liquids, clusters, or floppy molecules. Then the curse of dimensionality prevents mapping out in advance the complete potential, dipole moment, and polarizability functions over the whole space of nuclear positions of all atoms, and a solution in which the electronic and nuclear parts of the Born-Oppenheimer approximation are simultaneously solved is needed. A quantum force classical trajectory (QFCT) molecular dynamic method, based on linear response theory, is described, in which the forces, dipole moment, and polarizability are computed quantum

  1. AB INITIO AND CALPHAD THERMODYNAMICS OF MATERIALS

    SciTech Connect

    Turchi, P A

    2004-04-14

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

  2. Ab initio studies of atomic properties and experimental behavior of element 119 and its lighter homologs.

    PubMed

    Borschevsky, A; Pershina, V; Eliav, E; Kaldor, U

    2013-03-28

    Static dipole polarizabilities of element 119 and its singly charged cation are calculated, along with those of its lighter homologs, Cs and Fr. Relativity is treated within the 4-component Dirac-Coulomb formalism and electron correlation is included by the single reference coupled cluster approach with single, double, and perturbative triple excitations (CCSD(T)). Very good agreement with available experimental values is obtained for Cs, lending credence to the predictions for Fr and element 119. The atomic properties in group-1 are largely determined by the valence ns orbital, which experiences relativistic stabilization and contraction in the heavier elements. As a result, element 119 is predicted to have a relatively low polarizability (169.7 a.u.), comparable to that of Na. The adsorption enthalpy of element 119 on Teflon, which is important for possible future experimental studies of this element, is estimated as 17.6 kJ/mol, the lowest among the atoms considered here. PMID:23556718

  3. Ab initio studies of atomic properties and experimental behavior of element 119 and its lighter homologs

    NASA Astrophysics Data System (ADS)

    Borschevsky, A.; Pershina, V.; Eliav, E.; Kaldor, U.

    2013-03-01

    Static dipole polarizabilities of element 119 and its singly charged cation are calculated, along with those of its lighter homologs, Cs and Fr. Relativity is treated within the 4-component Dirac-Coulomb formalism and electron correlation is included by the single reference coupled cluster approach with single, double, and perturbative triple excitations (CCSD(T)). Very good agreement with available experimental values is obtained for Cs, lending credence to the predictions for Fr and element 119. The atomic properties in group-1 are largely determined by the valence ns orbital, which experiences relativistic stabilization and contraction in the heavier elements. As a result, element 119 is predicted to have a relatively low polarizability (169.7 a.u.), comparable to that of Na. The adsorption enthalpy of element 119 on Teflon, which is important for possible future experimental studies of this element, is estimated as 17.6 kJ/mol, the lowest among the atoms considered here.

  4. Ab initio study of Ga-GaN system: Transition from adsorbed metal atoms to a metal–semiconductor junction

    SciTech Connect

    Witczak, Przemysław; Kempisty, Pawel; Strak, Pawel

    2015-11-15

    Ab initio studies of a GaN(0001)-Ga system with various thicknesses of a metallic Ga layer were undertaken. The studied systems extend from a GaN(0001) surface with a fractional coverage of gallium atoms to a Ga-GaN metal–semiconductor (m–s) contact. Electronic properties of the system are simulated using density functional theory calculations for different doping of the bulk semiconductor. It is shown that during transition from a bare GaN(0001) surface to a m–s heterostructure, the Fermi level stays pinned at a Ga-broken bond highly dispersive surface state to Ga–Ga states at the m–s interface. Adsorption of gallium leads to an energy gain of about 4 eV for a clean GaN(0001) surface and the energy decreases to 3.2 eV for a thickly Ga-covered surface. The transition to the m–s interface is observed. For a thick Ga overlayer such interface corresponds to a Schottky contact with a barrier equal to 0.9 and 0.6 eV for n- and p-type, respectively. Bond polarization-related dipole layer occurring due to an electron transfer to the metal leads to a potential energy jump of 1.5 eV, independent on the semiconductor doping. Additionally high electron density in the Ga–Ga bond region leads to an energy barrier about 1.2 eV high and 4 Å wide. This feature may adversely affect the conductivity of the n-type m–s system.

  5. Ab initio simulations of subatomic resolution images in noncontact atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Kim, Minjung; Chelikowsky, James R.

    2015-03-01

    Direct imaging of polycyclic aromatic molecules with a subatomic resolution has recently been achieved with noncontact atomic force microscopy (nc-AFM). Specifically, nc-AFM employing a CO functionalized tip has provided details of the chemical bond in aromatic molecules, including the discrimination of bond order. However, the underlying physics of such high resolution imaging remains problematic. By employing new, efficient algorithms based on real space pseudopotentials, we calculate the forces between the nc-AFM tip and specimen. We simulate images of planar organic molecules with two different approaches: 1) with a chemically inert tip and 2) with a CO functionalized tip. We find dramatic differences in the resulting images, which are consistent with recent experimental work. Our work is supported by the DOE under DOE/DE-FG02-06ER46286 and by the Welch Foundation under Grant F-1837. Computational resources were provided by NERSC and XSEDE.

  6. Ab initio study of the adsorption, diffusion, and intercalation of alkali metal atoms on the (0001) surface of the topological insulator Bi2Se3

    NASA Astrophysics Data System (ADS)

    Ryabishchenkova, A. G.; Otrokov, M. M.; Kuznetsov, V. M.; Chulkov, E. V.

    2015-09-01

    Ab initio study of the adsorption, diffusion, and intercalation of alkali metal adatoms on the (0001) step surface of the topological insulator Bi2Se3 has been performed for the case of low coverage. The calculations of the activation energies of diffusion of adatoms on the surface and in van der Waals gaps near steps, as well as the estimate of diffusion lengths, have shown that efficient intercalation through steps is possible only for Li and Na. Data obtained for K, Rb, and Cs atoms indicate that their thermal desorption at high temperatures can occur before intercalation. The results have been discussed in the context of existing experimental data.

  7. Collective rotation from ab initio theory

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

    Through ab initio approaches in nuclear theory, we may now seek to quantitatively understand the wealth of nuclear collective phenomena starting from the underlying internucleon interactions. No-core configuration interaction (NCCI) calculations for p-shell nuclei give rise to rotational bands, as evidenced by rotational patterns for excitation energies, electromagnetic moments and electromagnetic transitions. In this review, NCCI calculations of 7-9Be are used to illustrate and explore ab initio rotational structure, and the resulting predictions for rotational band properties are compared with experiment. We highlight the robustness of ab initio rotational predictions across different choices for the internucleon interaction.

  8. Motif based Hessian matrixfor ab initio geometry optimization ofnanostructures

    SciTech Connect

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

    2006-04-05

    A simple method to estimate the atomic degree Hessian matrixof a nanosystem is presented. The estimated Hessian matrix, based on themotif decomposition of the nanosystem, can be used to accelerate abinitio atomic relaxations with speedups of 2 to 4 depending on the sizeof the system. In addition, the programing implementation for using thismethod in a standard ab initio package is trivial.

  9. A package for the ab-initio calculation of one- and two-photon cross sections of two-electron atoms, using a CI B-splines method

    NASA Astrophysics Data System (ADS)

    Nikolopoulos, L. A. A.

    2003-02-01

    A package is presented for the fully ab-initio calculation of one- and two-photon ionization cross sections for two-electron atomic systems (H -, He, Mg, Ca, …) under strong laser fields, within lowest-order perturbation theory (LOPT) and in the dipole approximation. The atomic structure is obtained through configuration interaction (CI) of antisymmetrized two-electron states expanded in a B-spline finite basis. The formulation of the theory and the relevant codes presented here represent the accumulation of work over the last ten years [1-11,13-15]. Extensions to more than two-photon ionization is straightforward. Calculation is possible for both the length and velocity form of the laser-atom interaction operator. The package is mainly, written in standard FORTRAN language and uses the publicly available libraries SLATEC, LAPACK and BLAS.

  10. Ab initio nuclear structure theory

    NASA Astrophysics Data System (ADS)

    Negoita, Gianina Alina

    Ab initio no core methods have become major tools for understanding the properties of light nuclei based on realistic nucleon-nucleon (NN) and three-nucleon (NNN) interactions. A brief description is provided for the inter-nucleon interactions that fit two-body scattering and bound state data, as well as NNN interactions. Major new progress, including the goal of applying these interactions to solve for properties of nuclei, is limited by convergence issues. That is, with the goal of obtaining high precision solutions of the nuclear many-body Hamiltonian with no core methods (all nucleons treated on the same footing), one needs to proceed to very large basis spaces to achieve a convergence pattern suitable for extrapolation to the exact result. This thesis investigates (1) the similarity renormalization group (SRG) approach to soften the interaction, while preserving its phase shift properties, and (2) adoption of a realistic basis space using Woods-Saxon (WS) single-particle wavefunctions. Both have their advantages and limitations, discussed here. For (1), SRG was demonstrated by applying it to a realistic NN interaction, JISP16, in a harmonic oscillator (HO) representation. The degree of interaction softening achieved through a regulator parameter is examined. For (2), new results are obtained with the realistic JISP16 NN interaction in ab initio calculations of light nuclei 4He, 6He and 12C, using a WS basis optimized to minimize the ground-state energy within the truncated no core shell model. These are numerically-intensive many-body calculations. Finally, to gain insight into the potential for no core investigations of heavier nuclei, an initial investigation was obtained for the odd mass A = 47 - 49 region nuclei straddling 48Ca. The motivation for selecting these nuclei stems from the aim of preparing for nuclear double beta-decay studies of 48Ca. In these heavier systems, phenomenological additions to the realistic NN interaction determined by previous

  11. Ab initio non-relativistic spin dynamics

    SciTech Connect

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

    2014-12-07

    Many magnetic materials do not conform to the (anti-)ferromagnetic paradigm where all electronic spins are aligned to a global magnetization axis. Unfortunately, most electronic structure methods cannot describe such materials with noncollinear electron spin on account of formally requiring spin alignment. To overcome this limitation, it is necessary to generalize electronic structure methods and allow each electron spin to rotate freely. Here, we report the development of an ab initio time-dependent non-relativistic two-component spinor (TDN2C), which is a generalization of the time-dependent Hartree-Fock equations. Propagating the TDN2C equations in the time domain allows for the first-principles description of spin dynamics. A numerical tool based on the Hirshfeld partitioning scheme is developed to analyze the time-dependent spin magnetization. In this work, we also introduce the coupling between electron spin and a homogenous magnetic field into the TDN2C framework to simulate the response of the electronic spin degrees of freedom to an external magnetic field. This is illustrated for several model systems, including the spin-frustrated Li{sub 3} molecule. Exact agreement is found between numerical and analytic results for Larmor precession of hydrogen and lithium atoms. The TDN2C method paves the way for the ab initio description of molecular spin transport and spintronics in the time domain.

  12. Ab initio non-relativistic spin dynamics

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

    Many magnetic materials do not conform to the (anti-)ferromagnetic paradigm where all electronic spins are aligned to a global magnetization axis. Unfortunately, most electronic structure methods cannot describe such materials with noncollinear electron spin on account of formally requiring spin alignment. To overcome this limitation, it is necessary to generalize electronic structure methods and allow each electron spin to rotate freely. Here, we report the development of an ab initio time-dependent non-relativistic two-component spinor (TDN2C), which is a generalization of the time-dependent Hartree-Fock equations. Propagating the TDN2C equations in the time domain allows for the first-principles description of spin dynamics. A numerical tool based on the Hirshfeld partitioning scheme is developed to analyze the time-dependent spin magnetization. In this work, we also introduce the coupling between electron spin and a homogenous magnetic field into the TDN2C framework to simulate the response of the electronic spin degrees of freedom to an external magnetic field. This is illustrated for several model systems, including the spin-frustrated Li3 molecule. Exact agreement is found between numerical and analytic results for Larmor precession of hydrogen and lithium atoms. The TDN2C method paves the way for the ab initio description of molecular spin transport and spintronics in the time domain.

  13. Ab initio phonon limited transport

    NASA Astrophysics Data System (ADS)

    Verstraete, Matthieu

    We revisit the thermoelectric (TE) transport properties of two champion materials, PbTe and SnSe, using fully first principles methods. In both cases the performance of the material is due to subtle combinations of structural effects, scattering, and phase space reduction. In PbTe anharmonic effects are completely opposite to the predicted quasiharmonic evolution of phonon frequencies and to frequently (and incorrectly) cited extrapolations of experiments. This stabilizes the material at high T, but also tends to enhance its thermal conductivity, in a non linear manner, above 600 Kelvin. This explains why PbTe is in practice limited to room temperature applications. SnSe has recently been shown to be the most efficient TE material in bulk form. This is mainly due to a strongly enhanced carrier concentration and electrical conductivity, after going through a phase transition from 600 to 800 K. We calculate the transport coefficients as well as the defect concentrations ab initio, showing excellent agreement with experiment, and elucidating the origin of the double phase transition as well as the new charge carriers. AH Romero, EKU Gross, MJ Verstraete, and O Hellman PRB 91, 214310 (2015) O. Hellman, IA Abrikosov, and SI Simak, PRB 84 180301 (2011)

  14. Interaction-induced dipoles of hydrogen molecules colliding with helium atoms: a new ab initio dipole surface for high-temperature applications.

    PubMed

    Li, Xiaoping; Mandal, Anirban; Miliordos, Evangelos; Hunt, Katharine L C

    2012-01-28

    We report new ab initio results for the interaction-induced dipole moments Δμ of hydrogen molecules colliding with helium atoms. These results are needed in order to calculate collision-induced absorption spectra at high temperatures; applications include modeling the radiative profiles of very cool white dwarf stars, with temperatures from 3500 K to 9000 K. We have evaluated the dipoles based on finite-field calculations, with coupled cluster methods in MOLPRO 2006 and aug-cc-pV5Z (spdfg) basis sets for both the H and He centers. We have obtained values of Δμ for eight H(2) bond lengths ranging from 0.942 a.u. to 2.801 a.u., for 15 intermolecular separations R ranging from 2.0 a.u. to 10.0 a.u., and for 19 different relative orientations. In general, our values agree well with earlier ab initio results, for the geometrical configurations that are treated in common, but we have determined more points on the collision-induced dipole surface by an order of magnitude. These results make it possible to calculate transition probabilities for molecules in excited vibrational states, overtones, and rotational transitions with ΔJ > 4. We have cast our results in the symmetry-adapted form needed for absorption line shape calculations, by expressing Δμ as a series in the spherical harmonics of the orientation angles of the intermolecular vector and of a unit vector along the H(2) bond axis. The expansion coefficients depend on the H(2) bond length and the intermolecular distance R. For large separations R, we show that the ab initio values of the leading coefficients converge to the predictions from perturbation theory, including both classical multipole polarization and dispersion effects. PMID:22299884

  15. Ensemble v-representable ab initio density-functional calculation of energy and spin in atoms: A test of exchange-correlation approximations

    SciTech Connect

    Kraisler, Eli; Makov, Guy; Kelson, Itzhak

    2010-10-15

    The total energies and the spin states for atoms and their first ions with Z=1-86 are calculated within the the local spin-density approximation (LSDA) and the generalized-gradient approximation (GGA) to the exchange-correlation (xc) energy in density-functional theory. Atoms and ions for which the ground-state density is not pure-state v-representable are treated as ensemble v-representable with fractional occupations of the Kohn-Sham system. A recently developed algorithm which searches over ensemble v-representable densities [E. Kraisler et al., Phys. Rev. A 80, 032115 (2009)] is employed in calculations. It is found that for many atoms, the ionization energies obtained with the GGA are only modestly improved with respect to experimental data, as compared to the LSDA. However, even in those groups of atoms where the improvement is systematic, there remains a non-negligible difference with respect to the experiment. The ab initio electronic configuration in the Kohn-Sham reference system does not always equal the configuration obtained from the spectroscopic term within the independent-electron approximation. It was shown that use of the latter configuration can prevent the energy-minimization process from converging to the global minimum, e.g., in lanthanides. The spin values calculated ab initio fit the experiment for most atoms and are almost unaffected by the choice of the xc functional. Among the systems with incorrectly obtained spin, there exist some cases (e.g., V, Pt) for which the result is found to be stable with respect to small variations in the xc approximation. These findings suggest a necessity for a significant modification of the exchange-correlation functional, probably of a nonlocal nature, to accurately describe such systems.

  16. Atomic kinetic Monte Carlo model based on ab initio data: Simulation of microstructural evolution under irradiation of dilute Fe CuNiMnSi alloys

    NASA Astrophysics Data System (ADS)

    Vincent, E.; Becquart, C. S.; Domain, C.

    2007-02-01

    The embrittlement of pressure vessel steels under radiation has been long ago correlated with the presence of Cu solutes. Other solutes such as Ni, Mn and Si are now suspected to contribute also to the embrittlement. The interactions of these solutes with radiation induced point defects thus need to be characterized properly in order to understand the elementary mechanisms behind the formation of the clusters formed upon radiation. Ab initio calculations based on the density functional theory have been performed to determine the interactions of point defects with solute atoms in dilute FeX alloys (X = Cu, Mn, Ni or Si) in order to build a database used to parameterise an atomic kinetic Monte Carlo model. Some results of irradiation damage in dilute Fe-CuNiMnSi alloys obtained with this model are presented.

  17. Ab Initio Modeling of Molecular Radiation

    NASA Technical Reports Server (NTRS)

    Jaffe, Richard; Schwenke, David

    2014-01-01

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

  18. Ab initio study of the adsorption, diffusion, and intercalation of alkali metal atoms on the (0001) surface of the topological insulator Bi2 Se3

    NASA Astrophysics Data System (ADS)

    Otrokov, Mikhail; Ryabishchenkova, Anastasia; Gosalvez, Miguel Angel; Kuznetsov, Vladimir; Chulkov, Evgueni

    We present the results of an ab initio study of the adsorption, diffusion, and intercalation of alkali metal adatoms on the (0001) stepped surface of the topological insulator Bi2Se3 for the case of low coverage. The calculations of the activation energies of the adatoms diffusion on the surface and in the van der Waals gaps near the steps, as well as the estimation of diffusion lengths, show that efficient intercalation through the steps is possible only for Li and Na. Data obtained for K, Rb, and Cs atoms indicate that their thermal desorption at high temperatures can start before intercalation. These results are discussed in the context of the experimental data available.

  19. An ab initio study of the ionization potentials and f-f spectroscopy of europium atoms and ions.

    SciTech Connect

    Naleway, C.; Seth, M.; Shepard, R.; Wagner, A. F.; Tilson, J. L.; Ermler, W. C.; Brozell, S. R.; Stevens Inst. of Tech.; Ohio State Univ.

    2002-04-01

    The first three ionization potentials of europium and the f-f spectroscopy of the two lowest multiplets of Eu+3 have been calculated using ab initio spin-orbit configuration interaction techniques. To accomplish this, a new averaged relativistic effective core potential has been developed which leaves only the 5s, 5p, and 4f in the valence space. A series of configuration interaction calculations were carried out up through single and partial double excitations with a double-zeta quality basis set. The computed ionization values have an absolute error of about 0.1 eV from the experimental values. The computed f-f spectroscopy for the lowest {sup 7}F multiplet of Eu{sup +3} has a RMS error with experiment of about 100 cm-1. The computed f-f spectroscopy for the first excited {sup 5}D multiplet has a higher RMS error of about 350 cm{sup -1}. The computed center of gravity separation between the {sup 5}D-{sup 7}F multiplet is underestimated by 750 cm{sup -1}. Comparisons between non-spin-orbit and spin-orbit configuration interaction calculations for the separations of the centers of gravity of multiplets are very favorable up through single and double excitations with differences of a tenth of an eV or less. The spin-orbit configuration interaction calculations are among the largest ever performed for lanthanides, with expansion lengths in excess of 1.9 million double-group-adapted functions. The calculations were achieved by application of a new parallel spin-orbit configuration interaction component in the COLUMBUS Program System.

  20. Ab initio alpha-alpha scattering

    NASA Astrophysics Data System (ADS)

    Elhatisari, Serdar; Lee, Dean; Rupak, Gautam; Epelbaum, Evgeny; Krebs, Hermann; Lähde, Timo A.; Luu, Thomas; Meißner, Ulf-G.

    2015-12-01

    Processes such as the scattering of alpha particles (4He), the triple-alpha reaction, and alpha capture play a major role in stellar nucleosynthesis. In particular, alpha capture on carbon determines the ratio of carbon to oxygen during helium burning, and affects subsequent carbon, neon, oxygen, and silicon burning stages. It also substantially affects models of thermonuclear type Ia supernovae, owing to carbon detonation in accreting carbon-oxygen white-dwarf stars. In these reactions, the accurate calculation of the elastic scattering of alpha particles and alpha-like nuclei—nuclei with even and equal numbers of protons and neutrons—is important for understanding background and resonant scattering contributions. First-principles calculations of processes involving alpha particles and alpha-like nuclei have so far been impractical, owing to the exponential growth of the number of computational operations with the number of particles. Here we describe an ab initio calculation of alpha-alpha scattering that uses lattice Monte Carlo simulations. We use lattice effective field theory to describe the low-energy interactions of protons and neutrons, and apply a technique called the ‘adiabatic projection method’ to reduce the eight-body system to a two-cluster system. We take advantage of the computational efficiency and the more favourable scaling with system size of auxiliary-field Monte Carlo simulations to compute an ab initio effective Hamiltonian for the two clusters. We find promising agreement between lattice results and experimental phase shifts for s-wave and d-wave scattering. The approximately quadratic scaling of computational operations with particle number suggests that it should be possible to compute alpha scattering and capture on carbon and oxygen in the near future. The methods described here can be applied to ultracold atomic few-body systems as well as to hadronic systems using lattice quantum chromodynamics to describe the interactions of

  1. Ab initio alpha-alpha scattering.

    PubMed

    Elhatisari, Serdar; Lee, Dean; Rupak, Gautam; Epelbaum, Evgeny; Krebs, Hermann; Lähde, Timo A; Luu, Thomas; Meißner, Ulf-G

    2015-12-01

    Processes such as the scattering of alpha particles ((4)He), the triple-alpha reaction, and alpha capture play a major role in stellar nucleosynthesis. In particular, alpha capture on carbon determines the ratio of carbon to oxygen during helium burning, and affects subsequent carbon, neon, oxygen, and silicon burning stages. It also substantially affects models of thermonuclear type Ia supernovae, owing to carbon detonation in accreting carbon-oxygen white-dwarf stars. In these reactions, the accurate calculation of the elastic scattering of alpha particles and alpha-like nuclei--nuclei with even and equal numbers of protons and neutrons--is important for understanding background and resonant scattering contributions. First-principles calculations of processes involving alpha particles and alpha-like nuclei have so far been impractical, owing to the exponential growth of the number of computational operations with the number of particles. Here we describe an ab initio calculation of alpha-alpha scattering that uses lattice Monte Carlo simulations. We use lattice effective field theory to describe the low-energy interactions of protons and neutrons, and apply a technique called the 'adiabatic projection method' to reduce the eight-body system to a two-cluster system. We take advantage of the computational efficiency and the more favourable scaling with system size of auxiliary-field Monte Carlo simulations to compute an ab initio effective Hamiltonian for the two clusters. We find promising agreement between lattice results and experimental phase shifts for s-wave and d-wave scattering. The approximately quadratic scaling of computational operations with particle number suggests that it should be possible to compute alpha scattering and capture on carbon and oxygen in the near future. The methods described here can be applied to ultracold atomic few-body systems as well as to hadronic systems using lattice quantum chromodynamics to describe the interactions of

  2. Phonocatalysis. An ab initio simulation experiment

    NASA Astrophysics Data System (ADS)

    Kim, Kwangnam; Kaviany, Massoud

    2016-06-01

    Using simulations, we postulate and show that heterocatalysis on large-bandgap semiconductors can be controlled by substrate phonons, i.e., phonocatalysis. With ab initio calculations, including molecular dynamic simulations, the chemisorbed dissociation of XeF6 on h-BN surface leads to formation of XeF4 and two surface F/h-BN bonds. The reaction pathway and energies are evaluated, and the sorption and reaction emitted/absorbed phonons are identified through spectral analysis of the surface atomic motion. Due to large bandgap, the atomic vibration (phonon) energy transfer channels dominate and among them is the match between the F/h-BN covalent bond stretching and the optical phonons. We show that the chemisorbed dissociation (the pathway activation ascent) requires absorption of large-energy optical phonons. Then using progressively heavier isotopes of B and N atoms, we show that limiting these high-energy optical phonons inhibits the chemisorbed dissociation, i.e., controllable phonocatalysis.

  3. Solute interaction with point defects in α Fe during thermal ageing: A combined ab initio and atomic kinetic Monte Carlo approach

    NASA Astrophysics Data System (ADS)

    Vincent, E.; Becquart, C. S.; Domain, C.

    2006-06-01

    Solute Cu plays a major role in the embrittlement of reactor pressure vessel (RPV) steels under radiation. In RPV steels and dilute FeCu alloys, characterization techniques such as the tomographic atom probe (TAP), or the small angle neutron scattering (SANS) have revealed the formation of solute rich clusters (with Cu, Ni, Mn and Si) under neutron flux. It is thus very important to characterize the interactions of these solutes with radiation-induced point defects in order to understand the elementary mechanisms behind the formation of these clusters. Ab initio calculations based on the density functional theory have been made in order to build a database used to parameterise an atomic kinetic Monte Carlo model. The interactions of point defects and solute atoms in dilute FeX alloys (X = Cu, Mn, Ni or Si) have been evaluated for different configurations of small solute clusters and solute-vacancy complexes. First results obtained with the kinetic Monte Carlo model will be presented and compared to some experimental observations.

  4. Collective rotation from ab initio theory

    NASA Astrophysics Data System (ADS)

    Caprio, Mark A.; Maris, Pieter; Vary, James P.

    2015-10-01

    The challenge of ab initio nuclear theory is to quantitatively predict the complex and highly-correlated behavior of the nuclear many-body system, starting from the underlying internucleon interactions. We may now seek to understand the wealth of nuclear collective phenomena through ab initio approaches. No-core configuration interaction (NCCI) calculations for p-shell nuclei give rise to rotational bands, as evidenced by rotational patterns for excitation energies, electromagnetic moments, and electromagnetic transitions. In this talk, the intrinsic structure of these bands is discussed, and the predicted rotational bands are compared to experiment. Supported by the US DOE under Award Nos. DE-FG02-95ER-40934, DESC0008485 (SciDAC/NUCLEI), and DE-FG02-87ER40371 and the US NSF under Award No. 0904782. Computational resources provided by NERSC (US DOE Contract No. DE-AC02-05CH11231).

  5. Ab initio Bogoliubov coupled cluster theory

    NASA Astrophysics Data System (ADS)

    Signoracci, Angelo; Hagen, Gaute; Duguet, Thomas

    2014-09-01

    Coupled cluster (CC) theory has become a standard method in nuclear theory for realistic ab initio calculations of medium mass nuclei, but remains limited by its requirement of a Slater determinant reference state which reasonably approximates the nuclear system of interest. Extensions of the method, such as equation-of-motion CC, permit the calculation of nuclei with one or two nucleons added or removed from a doubly magic core, yet still only a few dozen nuclei are accessible with modern computational restrictions. In order to extend the applicability of ab initio methods to open-shell systems, the superfluid nature of nuclei must be taken into account. By utilizing Bogoliubov algebra and employing spontaneous symmetry breaking with respect to particle number conservation, superfluid systems can be treated by a single reference state. An ab initio theory to include correlations on top of a Bogoliubov reference state has been developed in the guise of standard CC theory. The formalism and first results of this Bogoliubov coupled cluster theory will be presented to demonstrate the applicability of the method.

  6. Ab-initio calculations on melting of thorium

    NASA Astrophysics Data System (ADS)

    Mukherjee, D.; Sahoo, B. D.; Joshi, K. D.; Kaushik, T. C.; Gupta, Satish C.

    2016-05-01

    Ab-initio molecular dynamics study has been performed on face centered cubic structured thorium to determine its melting temperature at room pressure. The ion-electron interaction potential energy calculated as a function of temperature for three volumes (a0)3 and (1.02a0)3 and (1.04a0)3 increases gradually with temperature and undergoes a sharp jump at ~2200 K, ~2100 K and ~1800 K, respectively. Here, a0 = 5.043 Å is the equilibrium lattice parameter at 0 K obtained from ab-initio calculations. These jumps in interaction energy are treated as due to the onset of melting and corresponding temperatures as melting point. The melting point of 2100 K is close to the experimental value of 2023K. Further, the same has been verified by plotting the atomic arrangement evolved at various temperatures and corresponding pair correlation functions.

  7. Spin-orbit decomposition of ab initio nuclear wave functions

    NASA Astrophysics Data System (ADS)

    Johnson, Calvin W.

    2015-03-01

    Although the modern shell-model picture of atomic nuclei is built from single-particle orbits with good total angular momentum j , leading to j -j coupling, decades ago phenomenological models suggested that a simpler picture for 0 p -shell nuclides can be realized via coupling of the total spin S and total orbital angular momentum L . I revisit this idea with large-basis, no-core shell-model calculations using modern ab initio two-body interactions and dissect the resulting wave functions into their component L - and S -components. Remarkably, there is broad agreement with calculations using the phenomenological Cohen-Kurath forces, despite a gap of nearly 50 years and six orders of magnitude in basis dimensions. I suggest that L -S decomposition may be a useful tool for analyzing ab initio wave functions of light nuclei, for example, in the case of rotational bands.

  8. IR and Raman spectra, ab initio and density functional computations of the vibrational spectra, molecular geometries and atomic charges of uracil and 5-aminouracil.

    PubMed

    Singh, J S

    2014-09-15

    Infrared (IR) and Raman spectra of uracil and 5-aminouracil have been recorded and analyzed between the region 200-4000 cm(-1). The optimized molecular geometries, atomic polar tensor (APT) charges and vibrational characteristics have been studied theoretically using restricted Hartree-Fock (RHF) and density functional theory (DFT) methods. Using the Becke's exchange in conjunction with Lee-Yang-Parr's correlation functional and Becke's three-parameter hybrid method (B3LYP), the ab initio and DFT calculations were carried out to study the optimized molecular fundamental vibrational frequencies for uracil and 5-aminouracil by employing Gaussian-03 program. The fundamental vibrational frequencies along with their corresponding intensities in IR and Raman activities and depolarization ratios of the Raman lines have also been calculated using the RHF and DFT methods employing different basis sets. In quantum chemical calculations, the most of B3LYP/6-311++G** vibrational frequencies are in the excellent agreement with available experimental assignments and helped in the reassignments of some fundamental vibrational modes. On the basis of calculated results, the assignments of some missing frequencies in the experimental study are proposed. Assuming under the Cs point group for both molecules, the distribution of normal mode of vibrations between the two species as planar (a') and non-planar (a″) are given by 25a'+11a″, of which 30 modes (21a'+9a″) correspond to the uracil moiety and 6 modes (4a'+2a″) to the NH2 group. Kekule ring stretching mode is found to be comparatively higher frequency magnitude than the mode of uracil due to the involvement of hydrogen bonding of amino group. But, the ring breathing is found to be lower frequency magnitude compared to those for uracil which could be due to mass effect of the NH2 group in place of the hydrogen atom. All other bands have also been assigned different fundamentals/overtones/combinations. PMID:24793482

  9. Ab initio chemical kinetic study for reactions of H atoms with SiH(4) and Si(2)H(6): comparison of theory and experiment.

    PubMed

    Wu, S Y; Raghunath, P; Wu, J S; Lin, M C

    2010-01-14

    The reactions of hydrogen atom with silane and disilane are relevant to the understanding of catalytic chemical vapor deposition (Cat-CVD) and plasma enhanced chemical vapor deposition (PECVD) processes. In the present study, these reactions have been investigated by means of ab initio molecular-orbital and transition-state theory calculations. In both reactions, the most favorable pathway was found to be the H abstraction leading to the formation of SiH(3) and Si(2)H(5) products, with 5.1 and 4.0 kca/mol barriers, respectively. For H + Si(2)H(6), another possible reaction pathway giving SiH(3) + SiH(4) may take place with two different mechanisms with 4.3 and 6.7 kcal/mol barriers for H-atom attacking side-way and end-on, respectively. To validate the calculated energies of the reactions, two isodesmic reactions, SiH(3)+CH(4)-->SiH(4)+CH(3) and Si(2)H(5)+C(2)H(6)-->Si(2)H(6)+C(2)H(5) were employed; the predicted heats of the formation for SiH(3) (49.0 kcal/mol) and Si(2)H(5) (58.6 kcal/mol) were found to agree well with the experimental data. Finally, rate constants for both H-abstraction reactions predicted in the range of 290-2500 K agree well with experimental data. The result also shows that H+Si(2)H(6) producing H(2)+Si(2)H(5) is more favorable than SiH(3)+SiH(4.). PMID:19938820

  10. Atomic and electronic structure of hydrogen on ZnO (1bar 100) surface: ab initio hybrid calculations

    NASA Astrophysics Data System (ADS)

    Usseinov, A. B.; Kotomin, E. A.; Zhukovskii, Yu F.; Purans, J.; Sorokin, A. V.; Akilbekov, A. T.

    2013-12-01

    Hydrogen atoms unavoidably incorporated into ZnO during growth of bulk samples and thin films considerably affect their electrical conductivity. The results of first principles hybrid LCAO calculations are discussed for hydrogen atoms in the bulk and on the non-polar ZnO (1bar 100) surface. The incorporation energy, the atomic relaxation, the electronic density redistribution and the electronic structure modifications are compared for the surface adsorption and bulk interstitial H positions. It is shown that hydrogen has a strong binding with the surface O ions (2.7 eV) whereas its incorporation into bulk is energetically unfavorable. Surface hydrogen atoms are very shallow donors, thus, contributing to the electronic conductivity.

  11. Ab initio Study of He Stability in hcp-Ti

    SciTech Connect

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

    2010-12-20

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

  12. FT-IR and Raman spectra, ab initio and density functional computations of the vibrational spectra, molecular geometries and atomic charges of uracil and 5-methyluracil (thymine)

    NASA Astrophysics Data System (ADS)

    Singh, J. S.

    2015-02-01

    FT-IR (400-4000 cm-1) and Raman spectra (200-4000 cm-1) of uracil and 5-methyluracil (thymine) have been recorded and analyzed. The optimized molecular geometries, atomic polar tensor (APT) charges and vibrational characteristics have been studied theoretically using restricted Hartree-Fock (RHF) and density functional theory (DFT) methods. Using the Becke's exchange in conjunction with Lee-Yang-Parr's correlation functional and Becke's three-parameter hybrid method (B3LYP), the ab initio and DFT calculations were carried out to study the optimized molecular fundamental vibrational frequencies for uracil and 5-methyluracil (thymine) by employing Gaussian-03 program. The fundamental vibrational frequencies along with their corresponding intensities in IR and Raman activities and depolarization ratios of the Raman lines have also been calculated using the RHF and DFT methods employing different basis sets. In quantum chemical calculations, most of the B3LYP/6-311++G∗∗ vibrational frequencies are in excellent agreement with the available experimental assignments and helped to propose in the reassignments of some missing frequencies in experimental study. Assuming under the Cs point group for both molecules, the distribution of normal mode of vibrations between the two species as planar (a‧) and non-planar (a″) for all 39 normal vibrational modes of 5-methyluracil are given by 26a‧ + 13a″, of which 30 modes (21a‧ + 9a″) correspond to the uracil moiety and 9 modes (5a‧ + 4a″) to the CH3 group. Consistent assignments have been made for the internal modes of CH3 group, especially for the anti-symmetric CH3 stretching and bending modes. A possible explanation could be the planarity of pyrimidine ring and non-planarity at carbon site of methyl group which might cause the splitting of frequencies including three components due to the substitution of CH3 group at the site of C5 atom on pyrimidine ring of uracil. The three non-equivalent CH bonds of CH3

  13. FT-IR and Raman spectra, ab initio and density functional computations of the vibrational spectra, molecular geometries and atomic charges of uracil and 5-methyluracil (thymine).

    PubMed

    Singh, J S

    2015-02-25

    FT-IR (400-4000 cm(-1)) and Raman spectra (200-4000 cm(-1)) of uracil and 5-methyluracil (thymine) have been recorded and analyzed. The optimized molecular geometries, atomic polar tensor (APT) charges and vibrational characteristics have been studied theoretically using restricted Hartree-Fock (RHF) and density functional theory (DFT) methods. Using the Becke's exchange in conjunction with Lee-Yang-Parr's correlation functional and Becke's three-parameter hybrid method (B3LYP), the ab initio and DFT calculations were carried out to study the optimized molecular fundamental vibrational frequencies for uracil and 5-methyluracil (thymine) by employing Gaussian-03 program. The fundamental vibrational frequencies along with their corresponding intensities in IR and Raman activities and depolarization ratios of the Raman lines have also been calculated using the RHF and DFT methods employing different basis sets. In quantum chemical calculations, most of the B3LYP/6-311++G(∗∗) vibrational frequencies are in excellent agreement with the available experimental assignments and helped to propose in the reassignments of some missing frequencies in experimental study. Assuming under the Cs point group for both molecules, the distribution of normal mode of vibrations between the two species as planar (a') and non-planar (a″) for all 39 normal vibrational modes of 5-methyluracil are given by 26a'+13a″, of which 30 modes (21a'+9a″) correspond to the uracil moiety and 9 modes (5a'+4a″) to the CH3 group. Consistent assignments have been made for the internal modes of CH3 group, especially for the anti-symmetric CH3 stretching and bending modes. A possible explanation could be the planarity of pyrimidine ring and non-planarity at carbon site of methyl group which might cause the splitting of frequencies including three components due to the substitution of CH3 group at the site of C5 atom on pyrimidine ring of uracil. The three non-equivalent CH bonds of CH3 group are

  14. Introduction of a fully relativistic capable basis set in the ab initio orthogonalized linear combination of atomic orbitals method

    NASA Astrophysics Data System (ADS)

    Thomas, Patrick Ryan

    Large simulation cell sizes, relativistic effects, and the need to correctly model excited state properties are major impediments to the accurate prediction of the optical properties of candidate materials for solid-state laser crystal and luminescent applications. To overcome these challenges, new methods must be created to improve the electron orbital wavefunction and interactions. In this work, a method has been developed to create new analytical four-component, fully-relativistic and single-component scalar relativistic descriptions of the atomic orbital wave functions from Grasp2K numerically represented atomic orbitals. In addition, adapted theory for the calculation of the relativistic kinetic energy contribution to Hamiltonian which bypasses directly solving the Dirac equation has been explicated. The orbital description improvements are tested against YAG, YBCO, SnO2 and BiF3. The improvements to the basis set reflect an improvement in both computational speed and accuracy.

  15. Ab initio calculations of external-field shifts of the 661-nm quadrupolar clock transition in neutral Ag atoms

    SciTech Connect

    Topcu, Suat; Nasser, Jamil; Daku, Latevi Max Lawson; Fritzsche, Stephan

    2006-04-15

    Frequency shifts of the Ag I 4d{sup 10}5s {sup 2}S{sub 1/2}(F=0,M{sub F}=0) to 4d{sup 9}5s{sup 2} {sup 2}D{sub 5/2}(F{sup '}=2,M{sub F{sup '}}=0) electric-quadrupole transition at 330.6 nm due to external fields are calculated using multiconfigurational self-consistent field methods. As this forbidden transition is free from first order Doppler and Zeeman effects, it is under investigation for the realization of an atomic optical clock. The calculated perturbations are the light shift, the blackbody frequency shift, and the quadratic Zeeman shift. Results show that a total uncertainty of 10{sup -18} could be reach without confining the atoms in a Lamb-Dicke regime in an optical lattice.

  16. Ab initio melting curve of osmium

    NASA Astrophysics Data System (ADS)

    Burakovsky, L.; Burakovsky, N.; Preston, D. L.

    2015-11-01

    The melting curve of osmium up to a pressure P of 500 GPa is obtained from an extensive suite of ab initio quantum molecular dynamics (QMD) simulations using the Z method. The ab initio P =0 melting point of Os is 3370 ±75 K; this range encompasses all of the available data in the literature and corroborates the conclusion of J. W. Arblaster [Platinum Metals Rev. 49, 166 (2005)], 10.1595/147106705X70264 that the melting temperature of pure Os is 3400 ±50 K and that the 3300 K typically quoted in the literature is the melting point of impure Os. The T =0 equation of state (EOS) of Os and the P dependence of the optimized c /a ratio for the hexagonal unit cell, both to pressures ˜900 GPa, are obtained in the ab initio approach as validation of its use. Although excellent agreement with the available experimental data (P ≲80 GPa) is found, it is the third-order Birch-Murnaghan EOS with B0'=5 rather than the more widely accepted B0'=4 that describes the QMD data to higher pressures, in agreement with the more recent experimental EOS by Godwal et al. The theoretical melting curve of Os obtained earlier by Joshi et al. is shown to be inconsistent with our QMD results, and the possible reason for this discrepancy is suggested. Regularities in the melting curves of Os and five other third-row transition metals (Ta, W, Re, Pt, Au) could be used to estimate the currently unknown melting curves of Hf and Ir.

  17. Heavy atom nitroxyl radicals. I: An ab initio study of the ground and lower electronic excited states of the H2As=O free radical

    NASA Astrophysics Data System (ADS)

    Tarroni, Riccardo; Clouthier, Dennis J.

    2009-09-01

    A series of ab initio calculations have been undertaken to predict the spectroscopic properties of the ground and first two excited states of the recently discovered arsenyl (H2AsO) free radical. This 13 valence electron species can be viewed as similar to the formaldehyde radical anion with a ground state electron configuration of ⋯(π)2(n)2(π∗)1. The arsenyl radical is nonplanar (pyramidal) in the ground state with a 59° out-of-plane angle and a 1.67 Å AsO bond length. It has a low-lying n-π ∗(Ã A2″) excited state (Te˜5000 cm-1) which has a much larger out-of-plane angle (86°) and longer AsO bond length (1.81 Å). The π-π ∗(B˜ A2') excited state at ˜20 500 cm-1 is less pyramidal (out-of-plane angle=70°) and has a somewhat shorter AsO bond (1.77 Å). Similar trends are found for the H2PO and H2NO free radicals, although the latter has a planar ground state, due to sp2 hybridization of the N atom, and a very long B˜ state AsO bond length. The geometric variations of the ground and excited states of the H2EO (E=N, P, As) radicals, as well as the ground states of the corresponding anions and cations, can be readily rationalized from the Walsh diagram of the anion. The variations in the E-O bond length are a result of changes in both the orbital occupancy and pyramidalization of the molecule. The results of the present work have been employed in the analysis of the B˜ A2'-X˜ A2' electronic band system of the H2AsO free radical as reported in the companion paper.

  18. Ab initio quantum chemistry: Methodology and applications

    PubMed Central

    Friesner, Richard A.

    2005-01-01

    This Perspective provides an overview of state-of-the-art ab initio quantum chemical methodology and applications. The methods that are discussed include coupled cluster theory, localized second-order Moller–Plesset perturbation theory, multireference perturbation approaches, and density functional theory. The accuracy of each approach for key chemical properties is summarized, and the computational performance is analyzed, emphasizing significant advances in algorithms and implementation over the past decade. Incorporation of a condensed-phase environment by means of mixed quantum mechanical/molecular mechanics or self-consistent reaction field techniques, is presented. A wide range of illustrative applications, focusing on materials science and biology, are discussed briefly. PMID:15870212

  19. Ab Initio Study of Defect Properties in YPO4

    SciTech Connect

    Gao, Fei; Xiao, Haiyan Y.; Zhou, Yungang; Devanathan, Ramaswami; Hu, Shenyang Y.; Li, Yulan; Sun, Xin; Khaleel, Mohammad A.

    2012-03-01

    Ab initio methods based on density functional theory have been used to calculate the formation energies of intrinsic defects, including vacancies, interstitials, antisites and Frenkel pairs in YPO4 under the O-rich and Y2O3-rich, and the O-rich and Y-rich conditions. The larger size of the yttrium atom may give rise to higher formation energy of the phosphorus antisite defect. In general, the formation energies of anion interstitials are much smaller than those of cation interstitials for both conditions considered. It is of greatly interest to find that the relative stabilities among the same types of interstitials are independent of the reference states. The most stable configuration for oxygen interstitials is an O-O split interstitial near the Ta site, while the most stable configuration for cation interstitials is a tetrahedral interstitial near the Ta site. The cation split interstitials are unfavorable in YPO4, with much higher formation energies. Furthermore, the properties of Frenkel pairs are compared with those calculated using empirical potentials. The results reveal that both ab initio and empirical potential calculations show a similar trend in the formation energies of Frenkel pairs, but the formation energies obtained by empirical potentials are much larger than those calculated by ab initio method.

  20. He-atom scattering from MgO(100): calculating diffraction peak intensities with a semi ab initio potential.

    PubMed

    Martinez-Casado, R; Mallia, G; Usvyat, D; Maschio, L; Casassa, S; Schütz, M; Harrison, N M

    2011-08-28

    An efficient model describing the He-atom scattering process is presented. The He-surface interaction potential is calculated from first principles by exploiting second-order Rayleigh-Schrödinger many-body perturbation theory and fitted by using a variety of pairwise interaction potentials. The attractive part of the fitted analytical form has been upscaled to compensate the underestimation of the well depth for this system in the perturbation theory description. The improved potential has been introduced in the close-coupling method to calculate the diffraction pattern. Quantitative agreement between the computed and observed binding energy and diffraction intensities for the He-MgO(100) system is achieved. It is expected that the utility of He scattering for probing dynamical processes at surfaces will be significantly enhanced by this quantitative description. PMID:21748190

  1. Computational modeling of alloys at the atomic scale: from ab initio and thermodynamics to radiation-induced heterogeneous precipitation

    SciTech Connect

    Caro, A; Caro, M; Klaver, P; Sadigh, B; Lopasso, E M; Srivilliputhur, S G

    2007-02-02

    We describe the path we are following in the development of a computational approach to simulate radiation damage in FeCr ferritic steels. In these alloys magnetism introduces an anomaly in the heat of formation of the solid solution that has implications on the way excess Cr precipitates in the {alpha}{prime} phase in presence of heterogeneities. These complexities represent a challenge for atomistic (empirical) approaches that we address: (i) by proposing a modified many body potential, (ii) by using a thermodynamic package that determines free energy and phase diagrams, and (iii) by using a displacement Monte Carlo code in the transmutation ensemble that can deal with millions of atoms in parallel computational environments. This approach predicts that grain boundaries, dislocations and free surfaces are not preferential sites for precipitation of {alpha}{prime}.

  2. A study of small systems containing H and O atoms using nonlocal functionals: Comparison with ab initio and experiment

    SciTech Connect

    Seminario, J.M.

    1994-12-31

    Structures and energies have been calculated for HO, H{sub 2}O, O{sub 2}, HO{sub 2}, H{sub 2}O{sub 2}, and O{sub 3} molecules using the nonlocal functionals PW 86, PW 91, B-P86, and B-LYP with the goal of obtaining their atomization energies. Results were compared with those form highly correlated methods and experiment. It was found that all nonlocal functionals perform similarly to or better than correlated methods MP4 and QCI (using relatively equivalent basis sets). All nonlocal energies were self-consistently calculated using the optimized geometries for each functional. None of the results contain any empirical correction except those inherent to some of the functionals. Increasing the size of the basis set when using the nonlocal functionals does not lead to any significant improvement of the energies and surprisingly it worsens the results for one of the functionals.

  3. High accuracy ab initio studies of electron-densities for the ground state of Be-like atomic systems.

    PubMed

    Komasa, J; Słupski, R; Jankowski, K; Wasilewski, J; Teale, A M

    2013-04-28

    Benchmark results for electron densities in the ground states of Li(-), Be, C(2+), Ne(6+), and Ar(14+) have been generated from very accurate variational wave functions represented in terms of extensive basis sets of exponentially correlated Gaussian functions. For Ne(6+), and Ar(14+), the upper bounds to the energies improve over previous results known from the literature. For the remaining systems our bounds are from 0.1 to 1.1 μhartree higher than the most accurate ones. We present in graphical and, partially, numerical form results both for the radial electron densities and for the difference radial density distributions (DRD) (defined with respect to the Hartree-Fock radial density) that highlight the impact of correlation effects on electron densities. Next, we have employed these DRD distributions in studies of the performance of several broadly used orbital-based quantum-chemical methods in accounting for correlation effects on the density. Our computed benchmark densities for Be have been also applied for testing the possibility of using the mathematically strict result concerning exact atomic electron densities, obtained by Ahlrichs et al. [Phys. Rev. A 23, 2106 (1981)], for the determination of the reliability range of computed densities in the long-range asymptotic region. The results obtained for Be are encouraging. PMID:23635137

  4. High accuracy ab initio studies of electron-densities for the ground state of Be-like atomic systems

    NASA Astrophysics Data System (ADS)

    Komasa, J.; Słupski, R.; Jankowski, K.; Wasilewski, J.; Teale, A. M.

    2013-04-01

    Benchmark results for electron densities in the ground states of Li-, Be, C2+, Ne6+, and Ar14+ have been generated from very accurate variational wave functions represented in terms of extensive basis sets of exponentially correlated Gaussian functions. For Ne6+, and Ar14+, the upper bounds to the energies improve over previous results known from the literature. For the remaining systems our bounds are from 0.1 to 1.1 μhartree higher than the most accurate ones. We present in graphical and, partially, numerical form results both for the radial electron densities and for the difference radial density distributions (DRD) (defined with respect to the Hartree-Fock radial density) that highlight the impact of correlation effects on electron densities. Next, we have employed these DRD distributions in studies of the performance of several broadly used orbital-based quantum-chemical methods in accounting for correlation effects on the density. Our computed benchmark densities for Be have been also applied for testing the possibility of using the mathematically strict result concerning exact atomic electron densities, obtained by Ahlrichs et al. [Phys. Rev. A 23, 2106 (1981), 10.1103/PhysRevA.23.2106], for the determination of the reliability range of computed densities in the long-range asymptotic region. The results obtained for Be are encouraging.

  5. Ab Initio Neutron Drops with Chiral Hamiltonians

    NASA Astrophysics Data System (ADS)

    Potter, Hugh; Maris, Pieter; Vary, James

    2015-04-01

    Ab initio calculations for neutron drops are of interest for insights into neutron-rich nuclei and neutron star matter, and for examining the neutron-only sector of nucleon-nucleon and 3-nucleon interactions. I present ab initio results calculated using the no-core shell model with 2- and 3-body chiral Hamiltonians for neutron drops up to 20 neutrons confined in a 10 MeV harmonic trap. I discuss ground state energies, internal energies, radii, and evidence for pairing. In addition, excitation energies can be used to investigate the spin-orbit splittings in the p-shell and sd -shell. Prior Green's Function Monte Carlo calculations using the Argonne v8' potential with added 3-nucleon forces serve as a comparison. Supported by DOE Grants DESC0008485 (SciDAC/NUCLEI), DE-FG02-87ER40371, and NSF Grant 0904782; computational resources provided by the Oak Ridge Leadership Computing Facility (DOE Office of Science Contract DE-AC05-00OR22725) under an INCITE award.

  6. Ab Initio No-Core Shell Model

    SciTech Connect

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

    2011-04-11

    A long-standing goal of nuclear theory is to determine the properties of atomic nuclei based on the fundamental interactions among the protons and neutrons (i.e., nucleons). By adopting nucleon-nucleon (NN), three-nucleon (NNN) and higher-nucleon interactions determined from either meson-exchange theory or QCD, with couplings fixed by few-body systems, we preserve the predictive power of nuclear theory. This foundation enables tests of nature's fundamental symmetries and offers new vistas for the full range of complex nuclear phenomena. Basic questions that drive our quest for a microscopic predictive theory of nuclear phenomena include: (1) What controls nuclear saturation; (2) How the nuclear shell model emerges from the underlying theory; (3) What are the properties of nuclei with extreme neutron/proton ratios; (4) Can we predict useful cross sections that cannot be measured; (5) Can nuclei provide precision tests of the fundamental laws of nature; and (6) Under what conditions do we need QCD to describe nuclear structure, among others. Along with other ab initio nuclear theory groups, we have pursued these questions with meson-theoretical NN interactions, such as CD-Bonn and Argonne V18, that were tuned to provide high-quality descriptions of the NN scattering phase shifts and deuteron properties. We then add meson-theoretic NNN interactions such as the Tucson-Melbourne or Urbana IX interactions. More recently, we have adopted realistic NN and NNN interactions with ties to QCD. Chiral perturbation theory within effective field theory ({chi}EFT) provides us with a promising bridge between QCD and hadronic systems. In this approach one works consistently with systems of increasing nucleon number and makes use of the explicit and spontaneous breaking of chiral symmetry to expand the strong interaction in terms of a dimensionless constant, the ratio of a generic small momentum divided by the chiral symmetry breaking scale taken to be about 1 GeV/c. The resulting NN

  7. State-of-the-art ab initio potential energy curve for the krypton atom pair and thermophysical properties of dilute krypton gas.

    PubMed

    Jäger, Benjamin; Hellmann, Robert; Bich, Eckard; Vogel, Eckhard

    2016-03-21

    A new reference krypton-krypton interatomic potential energy curve was developed by means of quantum-chemical ab initio calculations for 36 interatomic separations. Highly accurate values for the interaction energies at the complete basis set limit were obtained using the coupled-cluster method with single, double, and perturbative triple excitations as well as t-aug-cc-pV5Z and t-aug-cc-pV6Z basis sets including mid-bond functions, with the 6Z basis set being newly constructed for this study. Higher orders of coupled-cluster terms were considered in a successive scheme up to full quadruple excitations. Core-core and core-valence correlation effects were included. Furthermore, relativistic effects were studied not only at a scalar relativistic level using second-order direct perturbation theory, but also utilizing full four-component and Gaunt-effect computations. An analytical pair potential function was fitted to the interaction energies, which is characterized by a depth of 200.88 K with an estimated standard uncertainty of 0.51 K. Thermophysical properties of low-density krypton were calculated for temperatures up to 5000 K. Second and third virial coefficients were obtained from statistical thermodynamics. Viscosity and thermal conductivity as well as the self-diffusion coefficient were computed using the kinetic theory of gases. The theoretical results are compared with experimental data and with results for other pair potential functions from the literature, especially with those calculated from the recently developed ab initio potential of Waldrop et al. [J. Chem. Phys. 142, 204307 (2015)]. Highly accurate experimental viscosity data indicate that both the present ab initio pair potential and the one of Waldrop et al. can be regarded as reference potentials, even though the quantum-chemical methods and basis sets differ. However, the uncertainties of the present potential and of the derived properties are estimated to be considerably lower. PMID:27004873

  8. State-of-the-art ab initio potential energy curve for the krypton atom pair and thermophysical properties of dilute krypton gas

    NASA Astrophysics Data System (ADS)

    Jäger, Benjamin; Hellmann, Robert; Bich, Eckard; Vogel, Eckhard

    2016-03-01

    A new reference krypton-krypton interatomic potential energy curve was developed by means of quantum-chemical ab initio calculations for 36 interatomic separations. Highly accurate values for the interaction energies at the complete basis set limit were obtained using the coupled-cluster method with single, double, and perturbative triple excitations as well as t-aug-cc-pV5Z and t-aug-cc-pV6Z basis sets including mid-bond functions, with the 6Z basis set being newly constructed for this study. Higher orders of coupled-cluster terms were considered in a successive scheme up to full quadruple excitations. Core-core and core-valence correlation effects were included. Furthermore, relativistic effects were studied not only at a scalar relativistic level using second-order direct perturbation theory, but also utilizing full four-component and Gaunt-effect computations. An analytical pair potential function was fitted to the interaction energies, which is characterized by a depth of 200.88 K with an estimated standard uncertainty of 0.51 K. Thermophysical properties of low-density krypton were calculated for temperatures up to 5000 K. Second and third virial coefficients were obtained from statistical thermodynamics. Viscosity and thermal conductivity as well as the self-diffusion coefficient were computed using the kinetic theory of gases. The theoretical results are compared with experimental data and with results for other pair potential functions from the literature, especially with those calculated from the recently developed ab initio potential of Waldrop et al. [J. Chem. Phys. 142, 204307 (2015)]. Highly accurate experimental viscosity data indicate that both the present ab initio pair potential and the one of Waldrop et al. can be regarded as reference potentials, even though the quantum-chemical methods and basis sets differ. However, the uncertainties of the present potential and of the derived properties are estimated to be considerably lower.

  9. Towards Accurate Ab Initio Predictions of the Spectrum of Methane

    NASA Technical Reports Server (NTRS)

    Schwenke, David W.; Kwak, Dochan (Technical Monitor)

    2001-01-01

    We have carried out extensive ab initio calculations of the electronic structure of methane, and these results are used to compute vibrational energy levels. We include basis set extrapolations, core-valence correlation, relativistic effects, and Born- Oppenheimer breakdown terms in our calculations. Our ab initio predictions of the lowest lying levels are superb.

  10. Ab initio electronic properties of dual phosphorus monolayers in silicon

    PubMed Central

    2014-01-01

    In the midst of the epitaxial circuitry revolution in silicon technology, we look ahead to the next paradigm shift: effective use of the third dimension - in particular, its combination with epitaxial technology. We perform ab initio calculations of atomically thin epitaxial bilayers in silicon, investigating the fundamental electronic properties of monolayer pairs. Quantitative band splittings and the electronic density are presented, along with effects of the layers’ relative alignment and comments on disordered systems, and for the first time, the effective electronic widths of such device components are calculated. PMID:25246862

  11. Ab initio study of hydrogen on beryllium surfaces

    NASA Astrophysics Data System (ADS)

    Bachurin, D. V.; Vladimirov, P. V.

    2015-11-01

    Static ab initio calculations were performed for five principal hexagonal close-packed beryllium surfaces: basal, prismatic (type I and II) and pyramidal (type I and II). The basal plane was found to be the most energetically favorable, while the energies of the prismatic (type I) and pyramidal (type I) planes were slightly higher followed by the type II planes. Beryllium is known to show extreme interlayer distance relaxation near the surface. Up to five outermost atomic layers were involved in surface relaxation. The presence of hydrogen on the beryllium surfaces led to a noticeable reduction of the surface energy.

  12. Guiding ab initio calculations by alchemical derivatives.

    PubMed

    to Baben, M; Achenbach, J O; von Lilienfeld, O A

    2016-03-14

    We assess the concept of alchemical transformations for predicting how a further and not-tested change in composition would change materials properties. This might help to guide ab initio calculations through multidimensional property-composition spaces. Equilibrium volumes, bulk moduli, and relative lattice stability of fcc and bcc 4d transition metals Zr, Nb, Mo, Tc, Ru, Rh, Pd, and Ag are calculated using density functional theory. Alchemical derivatives predict qualitative trends in lattice stability while equilibrium volumes and bulk moduli are predicted with less than 9% and 28% deviation, respectively. Predicted changes in equilibrium volume and bulk moduli for binary and ternary mixtures of Rh-Pd-Ag are in qualitative agreement even for predicted bulk modulus changes as large as +100% or -50%. Based on these results, it is suggested that alchemical transformations could be meaningful for enhanced sampling in the context of virtual high-throughput materials screening projects. PMID:26979677

  13. Ab initio determination of light hadron masses.

    PubMed

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

    2008-11-21

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

  14. Discovering chemistry with an ab initio nanoreactor

    DOE PAGESBeta

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

    2014-11-02

    Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provides detailed physical insight. While theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor – a highly accelerated, first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor we show new pathways for glycine synthesis frommore » primitive compounds proposed to exist on the early Earth, providing new insight into the classic Urey-Miller experiment. Ultimately, these results highlight the emergence of theoretical and computational chemistry as a tool for discovery in addition to its traditional role of interpreting experimental findings.« less

  15. Ab initio molar volumes and Gaussian radii.

    PubMed

    Parsons, Drew F; Ninham, Barry W

    2009-02-12

    Ab initio molar volumes are calculated and used to derive radii for ions and neutral molecules using a spatially diffuse model of the electron distribution with Gaussian spread. The Gaussian radii obtained can be used for computation of nonelectrostatic ion-ion dispersion forces that underlie Hofmeister specific ion effects. Equivalent hard-sphere radii are also derived, and these are in reasonable agreement with crystalline ionic radii. The Born electrostatic self-energy is derived for a Gaussian model of the electronic charge distribution. It is shown that the ionic volumes used in electrostatic calculations of strongly hydrated cosmotropic ions ought best to include the first hydration shell. Ionic volumes for weakly hydrated chaotropic metal cations should exclude electron overlap (in electrostatic calculations). Spherical radii are calculated as well as nonisotropic ellipsoidal radii for nonspherical ions, via their nonisotropic static polarizability tensors. PMID:19140766

  16. Discovering chemistry with an ab initio nanoreactor

    NASA Astrophysics Data System (ADS)

    Martinez, Todd

    Traditional approaches for modeling chemical reaction networks such as those involved in combustion have focused on identifying individual reactions and using theoretical approaches to explore the underlying mechanisms. Recent advances involving graphical processing units (GPUs), commodity products developed for the videogaming industry, have made it possible to consider a distinct approach wherein one attempts to discover chemical reactions and mechanisms. We provide a brief summary of these developments and then discuss the concept behind the ``ab initio nanoreactor'' which explores the space of possible chemical reactions and molecular species for a given stoichiometry. The nanoreactor concept is exemplified with an example to the Urey-Miller reaction network which has been previously advanced as a potential model for prebiotic chemistry. We briefly discuss some of the future directions envisioned for the development of this nanoreactor concept.

  17. Discovering chemistry with an ab initio nanoreactor

    PubMed Central

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

    2014-01-01

    Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provides detailed physical insight. While theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor – a highly accelerated, first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, providing new insight into the classic Urey-Miller experiment. These results highlight the emergence of theoretical and computational chemistry as a tool for discovery in addition to its traditional role of interpreting experimental findings. PMID:25411881

  18. Guiding ab initio calculations by alchemical derivatives

    NASA Astrophysics Data System (ADS)

    to Baben, M.; Achenbach, J. O.; von Lilienfeld, O. A.

    2016-03-01

    We assess the concept of alchemical transformations for predicting how a further and not-tested change in composition would change materials properties. This might help to guide ab initio calculations through multidimensional property-composition spaces. Equilibrium volumes, bulk moduli, and relative lattice stability of fcc and bcc 4d transition metals Zr, Nb, Mo, Tc, Ru, Rh, Pd, and Ag are calculated using density functional theory. Alchemical derivatives predict qualitative trends in lattice stability while equilibrium volumes and bulk moduli are predicted with less than 9% and 28% deviation, respectively. Predicted changes in equilibrium volume and bulk moduli for binary and ternary mixtures of Rh-Pd-Ag are in qualitative agreement even for predicted bulk modulus changes as large as +100% or -50%. Based on these results, it is suggested that alchemical transformations could be meaningful for enhanced sampling in the context of virtual high-throughput materials screening projects.

  19. Discovering chemistry with an ab initio nanoreactor.

    PubMed

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

    2014-12-01

    Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provide detailed physical insight. Although theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor--a highly accelerated first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor, we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, which provide new insight into the classic Urey-Miller experiment. These results highlight the emergence of theoretical and computational chemistry as a tool for discovery, in addition to its traditional role of interpreting experimental findings. PMID:25411881

  20. Discovering chemistry with an ab initio nanoreactor

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

    Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provide detailed physical insight. Although theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor—a highly accelerated first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor, we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, which provide new insight into the classic Urey-Miller experiment. These results highlight the emergence of theoretical and computational chemistry as a tool for discovery, in addition to its traditional role of interpreting experimental findings.

  1. Discovering chemistry with an ab initio nanoreactor

    SciTech Connect

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

    2014-11-02

    Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provides detailed physical insight. While theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor – a highly accelerated, first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, providing new insight into the classic Urey-Miller experiment. Ultimately, these results highlight the emergence of theoretical and computational chemistry as a tool for discovery in addition to its traditional role of interpreting experimental findings.

  2. Ab Initio Calculation of the Hoyle State

    SciTech Connect

    Epelbaum, Evgeny; Krebs, Hermann; Lee, Dean; Meissner, Ulf-G.

    2011-05-13

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

  3. Ab initio dynamics of the cytochrome P450 hydroxylation reaction

    PubMed Central

    Elenewski, Justin E.; Hackett, John C

    2015-01-01

    The iron(IV)-oxo porphyrin π-cation radical known as Compound I is the primary oxidant within the cytochromes P450, allowing these enzymes to affect the substrate hydroxylation. In the course of this reaction, a hydrogen atom is abstracted from the substrate to generate hydroxyiron(IV) porphyrin and a substrate-centered radical. The hydroxy radical then rebounds from the iron to the substrate, yielding the hydroxylated product. While Compound I has succumbed to theoretical and spectroscopic characterization, the associated hydroxyiron species is elusive as a consequence of its very short lifetime, for which there are no quantitative estimates. To ascertain the physical mechanism underlying substrate hydroxylation and probe this timescale, ab initio molecular dynamics simulations and free energy calculations are performed for a model of Compound I catalysis. Semiclassical estimates based on these calculations reveal the hydrogen atom abstraction step to be extremely fast, kinetically comparable to enzymes such as carbonic anhydrase. Using an ensemble of ab initio simulations, the resultant hydroxyiron species is found to have a similarly short lifetime, ranging between 300 fs and 3600 fs, putatively depending on the enzyme active site architecture. The addition of tunneling corrections to these rates suggests a strong contribution from nuclear quantum effects, which should accelerate every step of substrate hydroxylation by an order of magnitude. These observations have strong implications for the detection of individual hydroxylation intermediates during P450 catalysis. PMID:25681906

  4. Ab initio dynamics of the cytochrome P450 hydroxylation reaction

    NASA Astrophysics Data System (ADS)

    Elenewski, Justin E.; Hackett, John C.

    2015-02-01

    The iron(IV)-oxo porphyrin π-cation radical known as Compound I is the primary oxidant within the cytochromes P450, allowing these enzymes to affect the substrate hydroxylation. In the course of this reaction, a hydrogen atom is abstracted from the substrate to generate hydroxyiron(IV) porphyrin and a substrate-centered radical. The hydroxy radical then rebounds from the iron to the substrate, yielding the hydroxylated product. While Compound I has succumbed to theoretical and spectroscopic characterization, the associated hydroxyiron species is elusive as a consequence of its very short lifetime, for which there are no quantitative estimates. To ascertain the physical mechanism underlying substrate hydroxylation and probe this timescale, ab initio molecular dynamics simulations and free energy calculations are performed for a model of Compound I catalysis. Semiclassical estimates based on these calculations reveal the hydrogen atom abstraction step to be extremely fast, kinetically comparable to enzymes such as carbonic anhydrase. Using an ensemble of ab initio simulations, the resultant hydroxyiron species is found to have a similarly short lifetime, ranging between 300 fs and 3600 fs, putatively depending on the enzyme active site architecture. The addition of tunneling corrections to these rates suggests a strong contribution from nuclear quantum effects, which should accelerate every step of substrate hydroxylation by an order of magnitude. These observations have strong implications for the detection of individual hydroxylation intermediates during P450 catalysis.

  5. Ab initio dynamics of the cytochrome P450 hydroxylation reaction

    SciTech Connect

    Elenewski, Justin E.; Hackett, John C

    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.

  6. Ab initio tight-binding Hamiltonian for transition metal dichalcogenides

    NASA Astrophysics Data System (ADS)

    Fang, Shiang; Kuate Defo, Rodrick; Shirodkar, Sharmila N.; Lieu, Simon; Tritsaris, Georgios A.; Kaxiras, Efthimios

    2015-11-01

    We present an accurate ab initio tight-binding Hamiltonian for the transition metal dichalcogenides, MoS2, MoSe2, WS2, WSe2, with a minimal basis (the d orbitals for the metal atoms and p orbitals for the chalcogen atoms) based on a transformation of the Kohn-Sham density functional theory Hamiltonian to a basis of maximally localized Wannier functions. The truncated tight-binding Hamiltonian, with only on-site, first, and partial second neighbor interactions, including spin-orbit coupling, provides a simple physical picture and the symmetry of the main band-structure features. Interlayer interactions between adjacent layers are modeled by transferable hopping terms between the chalcogen p orbitals. The full-range tight-binding Hamiltonian can be reduced to hybrid-orbital k .p effective Hamiltonians near the band extrema that capture important low-energy excitations. These ab initio Hamiltonians can serve as the starting point for applications to interacting many-body physics including optical transitions and Berry curvature of bands, of which we give some examples.

  7. Macromolecular ab initio phasing enforcing secondary and tertiary structure

    PubMed Central

    Millán, Claudia; Sammito, Massimo; Usón, Isabel

    2015-01-01

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

  8. Ab initio derivation of model energy density functionals

    NASA Astrophysics Data System (ADS)

    Dobaczewski, Jacek

    2016-08-01

    I propose a simple and manageable method that allows for deriving coupling constants of model energy density functionals (EDFs) directly from ab initio calculations performed for finite fermion systems. A proof-of-principle application allows for linking properties of finite nuclei, determined by using the nuclear nonlocal Gogny functional, to the coupling constants of the quasilocal Skyrme functional. The method does not rely on properties of infinite fermion systems but on the ab initio calculations in finite systems. It also allows for quantifying merits of different model EDFs in describing the ab initio results.

  9. Ab initio and sup 17 O NMR study of aromatic compounds with dicoordinate oxygen atoms. (1) Methoxy- and (methylenedioxy)benzene derivatives

    SciTech Connect

    Biekofsky, R.R.; Pomilio, A.B.; Contreras, R.H. ); Orendt, A.M.; Facelli, J.C. )

    1990-09-20

    {sup 17}O NMR data at natural abundance in toluene-d{sub 8} at 74{degree}C were obtained for aromatic compounds containing methoxy and methylenedioxy groups as side-chains substituents. {sup 17}O chemical shifts of this series of compounds are significantly influenced by both electronic and steric effects. Ortho electronic and steric substituent chemical shift effects for methoxy and methylenedioxy groups were estimated. Ab initio calculations at the 4-31G level were used to determine geometries of the compounds to gain insight into the structural aspects of these compounds. A correlation between the calculated bond orders, P{sub C{sub Ar}P{minus}O}, and the {sup 17}O chemical shift was found.

  10. Ab initio molecular dynamics with simultaneous electron and phonon excitations: Application to the relaxation of hot atoms and molecules on metal surfaces

    NASA Astrophysics Data System (ADS)

    Novko, D.; Blanco-Rey, M.; Juaristi, J. I.; Alducin, M.

    2015-11-01

    The relaxation dynamics of hot H, N, and N2 on Pd(100), Ag(111), and Fe(110), respectively, is studied by means of ab initio molecular dynamics with electronic friction. This method is adapted here to account for the electron density changes caused by lattice vibrations, thus treating on an equal footing both electron-hole (e -h ) pair and phonon excitations. We find that even if the latter increasingly dominate the heavier is the hot species, the contribution of e -h pairs is by no means negligible in these cases because it gains relevance at the last stage of the relaxation process. The quantitative details of energy dissipation depend on the interplay of the potential energy surface, electronic structure, and kinetic factors.

  11. Ab initio pair potential energy curve for the argon atom pair and thermophysical properties for the dilute argon gas. II. Thermophysical properties for low-density argon

    NASA Astrophysics Data System (ADS)

    Vogel, Eckhard; Jäger, Benjamin; Hellmann, Robert; Bich, Eckard

    2010-12-01

    A recent argon-argon interatomic potential energy curve determined from quantum-mechanical ab initio calculations and described with an analytical representation [B. Jäger, R. Hellmann, E. Bich, and E. Vogel, Mol. Phys. 107, 2181 (2009); 108, 105 (2010)] was used to calculate the most important thermophysical properties of argon governed by two-body interactions. Second pressure, acoustic, and dielectric virial coefficients as well as viscosity and thermal conductivity in the limit of zero density were computed for natural argon from 83 to 10,000 K. The calculated values for the different thermophysical properties are compared with available experimental data and values computed for other argon-argon potentials. This extensive analysis shows that the proposed potential is superior to all previous ones and that the calculated thermophysical property values are accurate enough to be applied as standard values for the complete temperature range of the calculations.

  12. Atomic packing and diffusion in Fe{sub 85}Si{sub 2}B{sub 9}P{sub 4} amorphous alloy analyzed by ab initio molecular dynamics simulation

    SciTech Connect

    Wang, Yaocen; Takeuchi, Akira; Makino, Akihiro; Liang, Yunye; Kawazoe, Yoshiyuki

    2015-05-07

    In the work reported in this paper, ab initio molecular dynamics simulation was performed on Fe{sub 85}Si{sub 2}B{sub 9}P{sub 4} amorphous alloy. Preferred atomic environment of the elements was analyzed with Voronoi polyhedrons. It showed that B and P atoms prefer less neighbors compared with Fe and Si, making them structurally incompatible with Fe rich structure and repulsive to the formation of α-Fe. However, due to the low bonding energy of B and P caused by low coordination number, the diffusion rates of them were considerably large, resulting in the requirement of fast annealing for achieving optimum nano-crystallization for its soft magnetic property. The simulation work also indicates that diffusion rate in amorphous alloy is largely determined by bonding energy rather than atomic size.

  13. CO Oxidation on supported single Pt atoms - Experimental and Ab Initio density functional studies of CO interaction with Pt atom on theta-alumina(010) surface

    SciTech Connect

    Narula, Chaitanya Kumar; Debusk, Melanie Moses; Yoon, Mina; Allard Jr, Lawrence Frederick; Mullins, David R; Wu, Zili; Yang, Xiaofan; Veith, Gabriel M; Stocks, George Malcolm

    2013-01-01

    Although there are only a few known examples of supported single atoms, they are unique because they bridge the gap between homogenous and heterogeneous catalysis. The metal center is single supported atoms can be isoelectronic with their homogenous catalyst counterpart and may allow mechanistic pathways normally seen in homogenous catalysts. Here, we report CO oxidation activity of mono-disperse single Pt atoms supported on an inert substrate, -alumina (Al2O3), in the presence of stoichiometric oxygen. Since CO oxidation on single Pt atoms cannot occur via a conventional Langmuir-Hinshelwood scheme (L-H scheme) which requires at least one Pt-Pt bond, we have carried out a first principles density functional theoretical study of a proposed pathway which is a variation on the conventional L-H scheme and is inspired by organometallic chemistry of platinum. We find that a single supported Pt atom prefers to bond to O2 over CO. The CO then bonds with the oxygenated Pt atom and forms a carbonate which dissociates to liberate CO2, leaving an oxygen atom on Pt. A subsequent reaction with another CO molecule regenerates the single atom catalyst. An in-situ diffuse reflectance infrared study of CO adsorption on the catalyst s supported single atoms has been carried out to infer information on CO absorption modes and compare the observed spectra with calculated ones for intermediates in the proposed CO oxidation pathway. Our results clearly show that supported Pt single atoms are catalytically active and that this catalytic activity can occur without involving the substrate. Characterization by electron microscopy and X-ray absorption studies of the mono-disperse Pt/ -Al2O3, synthesized by solution methods, are also presented.

  14. Ab Initio: And a New Era of Airline Pilot Training.

    ERIC Educational Resources Information Center

    Gesell, Laurence E.

    1995-01-01

    Expansion of air transportation and decreasing numbers seeking pilot training point to a shortage of qualified pilots. Ab initio training, in which candidates with no flight time are trained to air transport proficiency, could resolve the problem. (SK)

  15. Ab initio two-component Ehrenfest dynamics

    NASA Astrophysics Data System (ADS)

    Ding, Feizhi; Goings, Joshua J.; Liu, Hongbin; Lingerfelt, David B.; Li, Xiaosong

    2015-09-01

    We present an ab initio two-component Ehrenfest-based mixed quantum/classical molecular dynamics method to describe the effect of nuclear motion on the electron spin dynamics (and vice versa) in molecular systems. The two-component time-dependent non-collinear density functional theory is used for the propagation of spin-polarized electrons while the nuclei are treated classically. We use a three-time-step algorithm for the numerical integration of the coupled equations of motion, namely, the velocity Verlet for nuclear motion, the nuclear-position-dependent midpoint Fock update, and the modified midpoint and unitary transformation method for electronic propagation. As a test case, the method is applied to the dissociation of H2 and O2. In contrast to conventional Ehrenfest dynamics, this two-component approach provides a first principles description of the dynamics of non-collinear (e.g., spin-frustrated) magnetic materials, as well as the proper description of spin-state crossover, spin-rotation, and spin-flip dynamics by relaxing the constraint on spin configuration. This method also holds potential for applications to spin transport in molecular or even nanoscale magnetic devices.

  16. Ab Initio Studies of Calcium Carbonate Hydration.

    PubMed

    Lopez-Berganza, Josue A; Diao, Yijue; Pamidighantam, Sudhakar; Espinosa-Marzal, Rosa M

    2015-11-25

    Ab initio simulations of large hydrated calcium carbonate clusters are challenging due to the existence of multiple local energy minima. Extensive conformational searches around hydrated calcium carbonate clusters (CaCO3·nH2O for n = 1-18) were performed to find low-energy hydration structures using an efficient combination of Monte Carlo searches, density-functional tight binding (DFTB+) method, and density-functional theory (DFT) at the B3LYP level, or Møller-Plesset perturbation theory at the MP2 level. This multilevel optimization yields several low-energy structures for hydrated calcium carbonate. Structural and energetics analysis of the hydration of these clusters revealed a first hydration shell composed of 12 water molecules. Bond-length and charge densities were also determined for different cluster sizes. The solvation of calcium carbonate in bulk water was investigated by placing the explicitly solvated CaCO3·nH2O clusters in a polarizable continuum model (PCM). The findings of this study provide new insights into the energetics and structure of hydrated calcium carbonate and contribute to the understanding of mechanisms where calcium carbonate formation or dissolution is of relevance. PMID:26505205

  17. Ab initio two-component Ehrenfest dynamics

    SciTech Connect

    Ding, Feizhi; Goings, Joshua J.; Liu, Hongbin; Lingerfelt, David B.; Li, Xiaosong

    2015-09-21

    We present an ab initio two-component Ehrenfest-based mixed quantum/classical molecular dynamics method to describe the effect of nuclear motion on the electron spin dynamics (and vice versa) in molecular systems. The two-component time-dependent non-collinear density functional theory is used for the propagation of spin-polarized electrons while the nuclei are treated classically. We use a three-time-step algorithm for the numerical integration of the coupled equations of motion, namely, the velocity Verlet for nuclear motion, the nuclear-position-dependent midpoint Fock update, and the modified midpoint and unitary transformation method for electronic propagation. As a test case, the method is applied to the dissociation of H{sub 2} and O{sub 2}. In contrast to conventional Ehrenfest dynamics, this two-component approach provides a first principles description of the dynamics of non-collinear (e.g., spin-frustrated) magnetic materials, as well as the proper description of spin-state crossover, spin-rotation, and spin-flip dynamics by relaxing the constraint on spin configuration. This method also holds potential for applications to spin transport in molecular or even nanoscale magnetic devices.

  18. An ab initio-based Er–He interatomic potential in hcp Er

    SciTech Connect

    Yang, Li; ye, Yeting; Fan, K. M.; Shen, Huahai; Peng, Shuming; Long, XG; Zhou, X. S.; Zu, Xiaotao; Gao, Fei

    2014-09-01

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

  19. Ab Initio Atom-Atom Potentials Using CamCASP: Theory and Application to Many-Body Models for the Pyridine Dimer.

    PubMed

    Misquitta, Alston J; Stone, Anthony J

    2016-09-13

    Creating accurate, analytic atom-atom potentials for small organic molecules from first principles can be a time-consuming and computationally intensive task, particularly if we also require them to include explicit polarization terms, which are essential in many systems. We describe how the CamCASP suite of programs can be used to generate such potentials using some of the most accurate electronic structure methods currently applicable. We derive the long-range terms from monomer properties and determine the short-range anisotropy parameters by a novel and robust method based on the iterated stockholder atom approach. Using these techniques, we develop distributed multipole models for the electrostatic, polarization, and dispersion interactions in the pyridine dimer and develop a series of many-body potentials for the pyridine system. Even the simplest of these potentials exhibits root mean square errors of only about 0.6 kJ mol(-1) for the low-energy pyridine dimers, significantly surpassing the best empirical potentials. Our best model is shown to support eight stable minima, four of which have not been reported before in the literature. Further, the functional form can be made systematically more elaborate so as to improve the accuracy without a significant increase in the human-time spent in their generation. We investigate the effects of anisotropy, rank of multipoles, and choice of polarizability and dispersion models. PMID:27467814

  20. Skutterudites under pressure: An ab initio study

    SciTech Connect

    Ram, Swetarekha; Kanchana, V.; Valsakumar, M. C.

    2014-03-07

    Ab initio results on the band structure, density of states, and Fermi surface (FS) properties of LaRu{sub 4}X{sub 12} (X = P, As, Sb) are presented at ambient pressure as well as under compression. The analysis of density of states reveals the major contribution at the Fermi level to be mainly from the Ru-d and X-p states. We have a complicated Fermi surface with both electron and hole characters for all the three compounds which is derived mainly from the Ru-d and X-p states. There is also a simpler FS with hole character derived from the P-p{sub z} orbital for LaRu{sub 4}P{sub 12} and Ru-d{sub z{sup 2}} orbital in the case of As and Sb containing compounds. More interestingly, Fermi surface nesting feature is observed only in the case of the LaRu{sub 4}P{sub 12}. Under compression, we observe the topology of the complicated FS sheet of LaRu{sub 4}As{sub 12} to change around V/V{sub 0} = 0.85, leading to a behaviour similar to that of a multiband superconductor, and in addition, we have two more hole pockets centered around Γ at V/V{sub 0} = 0.8 for the same compound. Apart from this, we find the hole pocket to vanish at V/V{sub 0} = 0.8 in the case of LaRu{sub 4}Sb{sub 12} and the opening of the complicated FS sheet gets reduced. The de Haas van Alphen calculation shows the number of extremal orbits in the complicated sheet to change in As and Sb containing compounds under compression, where we also observe the FS topology to change.

  1. Ab initio engineering of materials with stacked hexagonal tin frameworks.

    PubMed

    Shao, Junping; Beaufils, Clément; Kolmogorov, Aleksey N

    2016-01-01

    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. PMID:27387140

  2. Reactive Monte Carlo sampling with an ab initio potential

    NASA Astrophysics Data System (ADS)

    Leiding, Jeff; Coe, Joshua D.

    2016-05-01

    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 NH3 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.

  3. Ab initio engineering of materials with stacked hexagonal tin frameworks

    PubMed Central

    Shao, Junping; Beaufils, Clément; Kolmogorov, Aleksey N.

    2016-01-01

    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. PMID:27387140

  4. Ab initio calculations of grain boundaries in bcc metals

    NASA Astrophysics Data System (ADS)

    Scheiber, Daniel; Pippan, Reinhard; Puschnig, Peter; Romaner, Lorenz

    2016-03-01

    In this study, we compute grain boundary (GB) properties for a large set of GBs in bcc transition metals with a special focus on W, Mo and Fe using ab initio density functional theory (DFT) and semi-empirical second nearest neighbour modified embedded atom method (2NN-MEAM) potentials. The GB properties include GB energies, surface energies, GB excess volume and work of separation, which we analyse and then compare to experimental data. We find that the used 2NN-MEAM potentials can predict general trends of GB properties, but do not always reproduce the GB ground state structure and energy found with DFT. In particular, our results explain the experimental finding that W and Mo prefer intergranular fracture, while other bcc metals prefer transgranular cleavage.

  5. Ab initio engineering of materials with stacked hexagonal tin frameworks

    NASA Astrophysics Data System (ADS)

    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.

  6. Ab initio correlated calculations of rare-gas dimer quadrupoles

    NASA Astrophysics Data System (ADS)

    Donchev, Alexander G.

    2007-10-01

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

  7. Are polynuclear superhalogens without halogen atoms probable? A high-level ab initio case study on triple-bridged binuclear anions with cyanide ligands

    SciTech Connect

    Yin, Bing Wen, Zhen-Yi; Li, Teng; Li, Jin-Feng; Yu, Yang; Li, Jian-Li; Jiang, Zhen-Yi

    2014-03-07

    The first theoretical exploration of superhalogen properties of polynuclear structures based on pseudohalogen ligand is reported here via a case study on eight triply-bridged [Mg{sub 2}(CN){sub 5}]{sup −} clusters. From our high-level ab initio results, all these clusters are superhalogens due to their high vertical electron detachment energies (VDE), of which the largest value is 8.67 eV at coupled-cluster single double triple (CCSD(T)) level. Although outer valence Green's function results are consistent with CCSD(T) in most cases, it overestimates the VDEs of three anions dramatically by more than 1 eV. Therefore, the combined usage of several theoretical methods is important for the accuracy of purely theoretical prediction of superhalogen properties of new structures. Spatial distribution of the extra electron of high-VDE anions here indicates two features: remarkable aggregation on bridging CN units and non-negligible distribution on every CN unit. These two features lower the potential and kinetic energies of the extra electron respectively and thus lead to high VDE. Besides superhalogen properties, the structures, relative stabilities and thermodynamic stabilities with respect to detachment of CN{sup −1} were also investigated for these anions. The collection of these results indicates that polynuclear structures based on pseudohalogen ligand are promising candidates for new superhalogens with enhanced properties.

  8. On the isotropic Raman spectrum of Ar{sub 2} and how to benchmark ab initio calculations of small atomic clusters: Paradox lost

    SciTech Connect

    Chrysos, Michael Rachet, Florent; Dixneuf, Sophie

    2015-07-14

    This is the long-overdue answer to the discrepancies observed between theory and experiment in Ar{sub 2} regarding both the isotropic Raman spectrum and the second refractivity virial coefficient, B{sub R} [Gaye et al., Phys. Rev. A 55, 3484 (1997)]. At the origin of this progress is the advent (posterior to 1997) of advanced computational methods for weakly interconnected neutral species at close separations. Here, we report agreement between the previously taken Raman measurements and quantum lineshapes now computed with the employ of large-scale CCSD or smartly constructed MP2 induced-polarizability data. By using these measurements as a benchmark tool, we assess the degree of performance of various other ab initio computed data for the mean polarizability α, and we show that an excellent agreement with the most recently measured value of B{sub R} is reached. We propose an even more refined model for α, which is solution of the inverse-scattering problem and whose lineshape matches exactly the measured spectrum over the entire frequency-shift range probed.

  9. 4He Thermophysical Properties: New Ab Initio Calculations

    PubMed Central

    Hurly, John J.; Mehl, James B.

    2007-01-01

    Since 2000, atomic physicists have reduced the uncertainty of the helium-helium “ab initio” potential; for example, from approximately 0.6 % to 0.1 % at 4 bohr, and from 0.8 % to 0.1 % at 5.6 bohr. These results led us to: (1) construct a new inter-atomic potential ϕ07, (2) recalculate values of the second virial coefficient, the viscosity, and the thermal conductivity of 4He from 1 K to 10,000 K, and (3), analyze the uncertainties of the thermophysical properties that propagate from the uncertainty of ϕ07 and from the Born-Oppenheimer approximation of the electron-nucleon quantum mechanical system. We correct minor errors in a previous publication [J. J. Hurly and M. R. Moldover, J. Res. Nat. Inst. Standards Technol. 105, 667 (2000)] and compare our results with selected data published after 2000. The ab initio results tabulated here can serve as standards for the measurement of thermophysical properties. PMID:27110456

  10. Ab Initio Studies of Stratospheric Ozone Depletion Chemistry

    NASA Technical Reports Server (NTRS)

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

    1995-01-01

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

  11. THERMODYNAMICS OF MATERIALS: FROM AB INITIO TO PHENOMENOLOGY

    SciTech Connect

    Turchi, P A

    2004-09-24

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

  12. Ab initio study of the adsorption, diffusion, and intercalation of alkali metal atoms on the (0001) surface of the topological insulator Bi{sub 2}Se{sub 3}

    SciTech Connect

    Ryabishchenkova, A. G. Otrokov, M. M.; Kuznetsov, V. M.; Chulkov, E. V.

    2015-09-15

    Ab initio study of the adsorption, diffusion, and intercalation of alkali metal adatoms on the (0001) step surface of the topological insulator Bi{sub 2}Se{sub 3} has been performed for the case of low coverage. The calculations of the activation energies of diffusion of adatoms on the surface and in van der Waals gaps near steps, as well as the estimate of diffusion lengths, have shown that efficient intercalation through steps is possible only for Li and Na. Data obtained for K, Rb, and Cs atoms indicate that their thermal desorption at high temperatures can occur before intercalation. The results have been discussed in the context of existing experimental data.

  13. Titanium atoms dimerization phenomenon and magnetic properties of titanium-antisite (TiO) and chromium doped rutile TiO2, ab-initio calculation

    NASA Astrophysics Data System (ADS)

    Zarhri, Z.; Ziat, Y.; El Rhazouani, O.; Benyoussef, A.; Elkenz, A.

    2016-07-01

    The ab-initio calculations based on the Korringa Kohn Rostoker approximation approach combined with coherent potential approximation (KKR-CPA), were used to study the magnetic properties of the titanium anti-site (TiO) and chromium (Cr) doped TiO2. In the considered systems, we used different concentrations for TiO defect and Cr doping. In TiO2(0.98)(TiO)0.02, the obtained results indicate that TiO is a donor having half-metal behavior. TiO[3d] band is located at the Fermi level, although isn't 100% polarized, the ferromagnetic (FM) state is verified as being more stable than disordered local moment (DLM) state. For Ti0.98Cr0.02O2 the Cr doping introduced new states which give the material half-metallic feature. The majority spin of Cr impurities are located at the Fermi level and the conduction electrons around the Fermi level are 100% spin polarized. This indicates the stability of (FM) state. Moreover, in Ti0.98Cr0.02O2(0.98)(TiO)0.02, the top of the valence band is shifted to lower energy compared to pure TiO2, and the n-type of TiO2 is verified. The majority spin of Cr[3d] are located at 0.025 Ry close to the Fermi level. The predicted Curie temperatures (Tc) were calculated using the mean field approximation (MFA) and we predicted that TiO defect in Cr doped TiO2 makes Tc higher. This kind of defect makes the material useful for spinotronics's applications and devices.

  14. Combined crossed molecular beam and ab initio investigation of the multichannel reaction of boron monoxide (BO; X2Σ+) with Propylene (CH3CHCH2; X1A'): competing atomic hydrogen and methyl loss pathways.

    PubMed

    Maity, Surajit; Dangi, Beni B; Parker, Dorian S N; Kaiser, Ralf I; An, Yi; Sun, Bing-Jian; Chang, A H H

    2014-10-16

    The reaction dynamics of boron monoxide ((11)BO; X(2)Σ(+)) with propylene (CH(3)CHCH(2); X(1)A') were investigated under single collision conditions at a collision energy of 22.5 ± 1.3 kJ mol(-1). The crossed molecular beam investigation combined with ab initio electronic structure and statistical (RRKM) calculations reveals that the reaction follows indirect scattering dynamics and proceeds via the barrierless addition of boron monoxide radical with its radical center located at the boron atom. This addition takes place to either the terminal carbon atom (C1) and/or the central carbon atom (C2) of propylene reactant forming (11)BOC(3)H(6) intermediate(s). The long-lived (11)BOC(3)H(6) doublet intermediate(s) underwent unimolecular decomposition involving at least three competing reaction mechanisms via an atomic hydrogen loss from the vinyl group, an atomic hydrogen loss from the methyl group, and a methyl group elimination to form cis-/trans-1-propenyl-oxo-borane (CH(3)CHCH(11)BO), 3-propenyl-oxo-borane (CH(2)CHCH(2)(11)BO), and ethenyl-oxo-borane (CH(2)CH(11)BO), respectively. Utilizing partially deuterated propylene (CD(3)CHCH(2) and CH(3)CDCD(2)), we reveal that the loss of a vinyl hydrogen atom is the dominant hydrogen elimination pathway (85 ± 10%) forming cis-/trans-1-propenyl-oxo-borane, compared to the loss of a methyl hydrogen atom (15 ± 10%) leading to 3-propenyl-oxo-borane. The branching ratios for an atomic hydrogen loss from the vinyl group, an atomic hydrogen loss from the methyl group, and a methyl group loss are experimentally derived to be 26 ± 8%:5 ± 3%:69 ± 15%, respectively; these data correlate nicely with the branching ratios calculated via RRKM theory of 19%:5%:75%, respectively. PMID:25238644

  15. Ab initio simulation of transport phenomena in rarefied gases.

    PubMed

    Sharipov, Felix; Strapasson, José L

    2012-09-01

    Ab initio potentials are implemented into the direct simulation Monte Carlo (DSMC) method. Such an implementation allows us to model transport phenomena in rarefied gases without any fitting parameter of intermolecular collisions usually extracted from experimental data. Applying the method proposed by Sharipov and Strapasson [Phys. Fluids 24, 011703 (2012)], the use of ab initio potentials in the DSMC requires the same computational efforts as the widely used potentials such as hard spheres, variable hard sphere, variable soft spheres, etc. At the same time, the ab initio potentials provide more reliable results than any other one. As an example, the transport coefficients of a binary mixture He-Ar, viz., viscosity, thermal conductivity, and thermal diffusion factor, have been calculated for several values of the mole fraction. PMID:23030889

  16. Ab initio investigation of grain boundary cohesion in Al alloys

    NASA Astrophysics Data System (ADS)

    Zhang, Shengjun; Kontsevoi, Oleg Y.; Freeman, A. J.; Olson, G. B.

    2010-03-01

    Strength and hardness of aluminum alloys can be substantially increased by alloying with Mg, Zn, Cu, Si, and other elements. The main drawback of Al alloys is their susceptibility to stress corrosion cracking, which is caused by alloying impurities segregated at grain boundaries. We investigated the embrittling and cohesion-enhancing effects of impurities on a σ5(012)[100] grain boundary in Al by means of the full-potential linearized augmented plane-wave (FLAPW) method within the framework of the Rice-Wang thermodynamic model and within the ab initio tensile test approach. We calculated segregation energies, analyzed local atomic configurations, electronic structures and spatial charge density distributions around segregated impurities, and identified the roles of atomic size and the bonding behavior of the impurity with the surrounding Al atoms. The results show that He, H and Na are strong embrittlers, Zn is a weak embrittler, while Sc, B, Cu and Mg are cohesion enhancers. We further evaluated the effect of co-alloying with two or more elements on grain boundary strength. This work provides a fundamental basis for the design of high strength Al alloys.

  17. Ab initio study of the bonding in diatomic nickel

    SciTech Connect

    Noell, J.O.; Newton, M.D.; Hay, P.J.; Martin, R.L.; Bobrowicz, F.W.

    1980-09-01

    Hartree--Fock, GVB, and configuration interaction calculations were performed for diatomic nickel using an ab initio effective core potential. A basis set specifically optimized for the /sup 3/D state of atomic nickel is found to be far superior to the more common basis obtained from the /sup 3/F atomic state. Correlation effects are found to be significant in determining the bond energy. In particular, the two electrons of the s--s bond must be appropriately correlated. In addition, correlation effects which one would interpret as being principally intra-atomic in character are found to have a marked effect on the molecular properties. The theoretically predicted bond dissociation energy (D/sub e/) of 43.4 kcal/mol is significantly lower than the experimental estimate of 55 +- 5 kcal/mol. However, molecular partition functions calculated using the present results indicate that the experimental value should be revised downward to a value of approx.46 +- 5 kcal/mol, in good agreement with our calculations. An interatomic distance of 4.27 bohr is computed and compared with experimental estimates. Spectroscopic parameters for dipole-allowed transitions from the ground state were determined from SCF and GVB calculations and discussed in relation to the experimentally observed visible and ultraviolet spectra attributed to Ni/sub 2/.

  18. Ab initio simulations on rutile-based titania nanowires

    NASA Astrophysics Data System (ADS)

    Zhukovskii, Yu F.; Evarestov, R. A.

    2012-08-01

    The rod symmetry groups for monoperiodic (1D) nanostructures have been applied for construction of models for bulk-like TiO2 nanowires (NWs) cut from a rutile-based 3D crystal along the chosen [001] and [110] directions of crystallographic axes. In this study, we have considered nanowires described by both the Ti-atom centered rotation axes as well as the hollow site centered axes passing through the interstitial positions between the Ti and O atoms closest to the axes. The most stable [001]-oriented TiO2 NWs with rhombic cross sections are found to display the energetically preferable {110} facets only while the nanowires with quasi-square sections across the [110] axis are formed by the alternating { 1bar 10 } and {001} facets. For simulations on rutile-based nanowires possessing different diameters for each NW type, we have performed large-scale ab initio Density Functional Theory (DFT) and hybrid DFT-Hartree Fock (DFT-HF) calculations with total geometry optimization within the Generalized Gradient Approximation (GGA) in the form of the Perdew-Becke-Ernzenhof (PBE) exchange-correlation functionals (PBE and PBE0, respectively), using the formalism of linear combination of localized atomic functions (LCAO). We have simulated both structural and electronic properties of TiO2 NWs depending both on orientation and position of symmetry axes as well as on diameter and morphology of nanowires.

  19. Atomic arrangement and electron band structure of Si(1 1 1)-ß-√3 x √3-Bi reconstruction modified by alkali-metal adsorption: ab initio study.

    PubMed

    Eremeev, S V; Chukurov, E N; Gruznev, D V; Zotov, A V; Saranin, A A

    2015-08-01

    Using ab initio calculations, atomic structure and electronic properties of Si(1 1 1)[Formula: see text]-Bi surface modified by adsorption of 1/3 monolayer of alkali metals, Li, Na, K, Rb and Cs, have been explored. Upon adsorption of all metals, a similar atomic structure develops at the surface where twisted chained Bi trimers are arranged into a honeycomb network and alkali metal atoms occupy the [Formula: see text] sites in the center of each honeycomb unit. Among other structural characteristics, the greatest variation concerns the relative heights at which alkali metals reside with respect to Bi-trimer layer. Except for Li, the other metals reside higher than Bi layer and their heights increase with atomic number. All adsorbed surface structures display similar electron band structures of which the most essential feature is metallic surface-state band with a giant spin splitting. This electronic property allows one to consider the Si(1 1 1)[Formula: see text]-Bi surfaces modified by alkali metal adsorption as a set of material systems showing promise for spintronic applications. PMID:26151642

  20. Ab initio computations of photodissociation products of CFC alternatives

    SciTech Connect

    Tai, S.; Illinger, K.H.; Kenny, J.E.

    1995-12-31

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

  1. Ab Initio Structure Analysis Using Laboratory Powder Diffraction Data

    NASA Astrophysics Data System (ADS)

    Sasaki, Akito

    Today, laboratory X-ray diffractometers are seeing increasingly wide use in the ab initio crystal structure analysis of organic powder samples. This is because optics and optical devices have been improved, making it possible to obtain precise integrated intensities of reflections in high 2-theta ranges. Another reason is that one can use direct-space methods, which do not require “high-resolution diffraction data”, much more easily than before. Described here are some key points to remember when performig ab initio crystal structure analysis using powder diffraction data from organic compounds.

  2. Ab initio simulation of gap discrete breathers in strained graphene

    NASA Astrophysics Data System (ADS)

    Lobzenko, I. P.; Chechin, G. M.; Bezuglova, G. S.; Baimova, Yu. A.; Korznikova, E. A.; Dmitriev, S. V.

    2016-03-01

    The methods of the density functional theory were used for the first time for the simulation of discrete breathers in graphene. It is demonstrated that breathers can exist with frequencies lying in the gap of the phonon spectrum, induced by uniaxial tension of a monolayer graphene sheet in the "zigzag" direction (axis X), polarized in the "armchair" direction (axis Y). The found gap breathers are highly localized dynamic objects, the core of which is formed by two adjacent carbon atoms located on the Y axis. The atoms surrounding the core vibrate at much lower amplitudes along both the axes ( X and Y). The dependence of the frequency of these breathers on amplitude is found, which shows a soft type of nonlinearity. No breathers of this type were detected in the gap induced by stretching along the Y axis. It is shown that the breather vibrations may be approximated by the Morse oscillators, the parameters of which are determined from ab initio calculations. The results are of fundamental importance, as molecular dynamics calculations based on empirical potentials cannot serve as a reliable proof of the existence of breathers in crystals.

  3. Towards SiC Surface Functionalization: An Ab Initio Study

    SciTech Connect

    Cicero, G; Catellani, A

    2005-01-28

    We present a microscopic model of the interaction and adsorption mechanism of simple organic molecules on SiC surfaces as obtained from ab initio molecular dynamics simulations. Our results open the way to functionalization of silicon carbide, a leading candidate material for bio-compatible devices.

  4. Ab initio pseudopotential band calculation of organic conductors

    SciTech Connect

    Ishibashi, Shoji; Kohyama, Masanori

    1999-12-01

    The authors have calculated the band structures of organic conductors TTF-TCNQ and {beta}-(BEDT-TTF){sub 2}I{sub 3} using the ab initio plane-wave pseudopotential method within the local-density approximation (LDA). The Fermi-surface shape and the origin of bands near the Fermi level are investigated for each compound.

  5. Multiple time step integrators in ab initio molecular dynamics

    SciTech Connect

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

    2014-02-28

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

  6. Dialkylimidazolium chloroaluminates: Ab initio calculations, Raman and neutron scattering measurements

    SciTech Connect

    Takahasi, S. ); Curtiss, L.A.; Gosztola, D.; Koura, N. ); Loong, C.K.; Saboungi, M.L. . Materials Science Div.)

    1993-04-01

    The Raman and neutron scattering spectra of 46 mol% AlCl[sub 3] -54 mol% 1-ethyl-3-methyl imidazolium chloride (EMIC) and 67 mol% AlCl[sub 3] - 33 mol% EMIC melts are presented. Ab initio molecular orbital calculations have been carried out on structures of chloroaluminate anion and EMI cation and the interaction between anion and cation.

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

    NASA Astrophysics Data System (ADS)

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

    2013-10-01

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

  8. On the elimination of the electronic structure bottleneck in on the fly nonadiabatic dynamics for small to moderate sized (10-15 atom) molecules using fit diabatic representations based solely on ab initio electronic structure data: The photodissociation of phenol

    NASA Astrophysics Data System (ADS)

    Zhu, Xiaolei; Yarkony, David R.

    2016-01-01

    In this work, we demonstrate that for moderate sized systems, here a system with 13 atoms, global coupled potential energy surfaces defined for several electronic states over a wide energy range and for distinct regions of nuclear coordinate space characterized by distinct electron configurations, can be constructed with precise energetics and an excellent description of non-adiabatic interactions in all regions. This is accomplished using a recently reported algorithm for constructing quasi-diabatic representations, Hd, of adiabatic electronic states coupled by conical intersections. In this work, the algorithm is used to construct an Hd to describe the photodissociation of phenol from its first and second excited electronic states. The representation treats all 33 internal degrees of freedom in an even handed manner. The ab initio adiabatic electronic structure data used to construct the fit are obtained exclusively from multireference configuration interaction with single and double excitation wave functions comprised of 88 × 106 configuration state functions, at geometries determined by quasi-classical trajectories. Since the algorithm uses energy gradients and derivative couplings in addition to electronic energies to construct Hd, data at only 7379 nuclear configurations are required to construct a representation, which describes all nuclear configurations involved in H atom photodissociation to produce the phenoxyl radical in its ground or first excited electronic state, with a mean unsigned energy error of 202.9 cm-1 for electronic energies <60 000 cm-1.

  9. Ab initio studies of niobium defects in uranium

    SciTech Connect

    Xiang, S; Huang, H; Hsiung, L

    2007-06-01

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

  10. Volumic omit maps in ab initio dual-space phasing.

    PubMed

    Oszlányi, Gábor; Sütő, András

    2016-07-01

    Alternating-projection-type dual-space algorithms have a clear construction, but are susceptible to stagnation and, thus, inefficient for solving the phase problem ab initio. To improve this behaviour new omit maps are introduced, which are real-space perturbations applied periodically during the iteration process. The omit maps are called volumic, because they delete some predetermined subvolume of the unit cell without searching for atomic regions or analysing the electron density in any other way. The basic algorithms of positivity, histogram matching and low-density elimination are tested by their solution statistics. It is concluded that, while all these algorithms based on weak constraints are practically useless in their pure forms, appropriate volumic omit maps can transform them to practically useful methods. In addition, the efficiency of the already useful reflector-type charge-flipping algorithm can be further improved. It is important that these results are obtained by using non-sharpened structure factors and without any weighting scheme or reciprocal-space perturbation. The mathematical background of volumic omit maps and their expected applications are also discussed. PMID:27357850

  11. Ab Initio Simulation of the Photoelectron Spectrum for Methoxy Radical

    NASA Astrophysics Data System (ADS)

    Cheng, Lan; Weichman, Marissa L.; Kim, Jongjin B.; Ichino, Takatoshi; Neumark, Daniel; Stanton, John F.

    2015-06-01

    A theoretical simulation of the photoelectron spectrum for the ground state of methoxy radical is reported based on the quasidiabatic model Hamiltonian originally proposed by Köppel, Domcke, and Cederbaum. The parameters in the model Hamiltonian have been obtained from ab initio coupled-cluster calculations. The linear and quadratic force constants have been calculated using equation-of-motion coupled-cluster ionization potential method with the singles, doubles, and triples (EOMIP-CCSDT) truncation scheme together with atomic natural orbital basis sets of triple-zeta quality (ANO1). The cubic and quartic force constants have been obtained from EOMIP-CCSD calculations with ANO basis sets of double-zeta quality (ANO0), and the spin-orbit coupling constant has been computed at the EOMIP-CCSD/pCVTZ level. The nuclear Schroedinger equation has been solved using the Lanzcos algorithm to obtain vibronic energy levels as well as the corresponding intensities. The simulated spectrum compares favorably with the recent high-resolution slow electron velocity-map imaging experiment for vibronic levels up to 2000 cm-1.

  12. Ab initio study of MoS2 nanotube bundles

    NASA Astrophysics Data System (ADS)

    Verstraete, Matthieu; Charlier, Jean-Christophe

    2003-07-01

    Recently, the synthesis of a new phase of MoS2I1/3 stoichiometry was reported [M. Remskar, A. Mrzel, Z. Skraba, A. Jesih, M. Ceh, J. Demšar, P. Stadelmann, F. Lévy, and D. Mihailovic, Science 292, 479 (2001)]. Electron microscope images and diffraction data were interpreted to indicate bundles of sub-nanometer-diameter single-wall MoS2 nanotubes. After experimental characterization, the structure was attributed to an assembly of “armchair” nanotubes with interstitial iodine. Using first-principles total-energy calculations, bundles of MoS2 nanotubes with different topologies and stoichiometries are investigated. All of the systems are strongly metallic. Configurations with “zigzag” structures are found to be more stable energetically than the “armchair” ones, though all of the structures have similar stabilities. After relaxation, there remain several candidates which give a lattice parameter in relative agreement with experiment. Further, spin-polarized calculations indicate that a structure with armchair tubes iodine atoms in their center acquires a very large spontaneous magnetic moment of 12μB, while the other structures are nonmagnetic. Our ab initio calculations show that in most of the other structures, the tubes are very strongly bound together, and that the compounds should be considered as a crystal, rather than as a bundle of tubes in the habitual sense.

  13. Ab initio calculation of infrared intensities for hydrogen peroxide

    NASA Technical Reports Server (NTRS)

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

    1982-01-01

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

  14. Amide N-oxides: an ab initio molecular orbital study

    NASA Astrophysics Data System (ADS)

    Greenberg, Arthur; DuBois, Thomas D.

    2001-06-01

    There are no known examples of amide N-oxides. The present study employs ab initio molecular orbital calculations at the 6-3G ∗ level to explore potential target molecules in this class. Bridgehead bicyclic lactams appear to be attractive targets for oxidation to form the corresponding N-oxides because they have reduced (or zero) amide resonance energy. The amide N-oxide linkage is predicted to have a ca. 9-10 kcal/mol rotational barrier due to eclipsing of nonbonded oxygen atoms in the transition state. The linkage has a nearly flat conformational ( ΦON-CO) profile in the range 120-240° and this suggests that a very sterically hindered acyclic amide N-oxide may be a practical synthetic target. The oxidation of strained amides is calculated to be highly exothermic if dimethyldioxirane is employed. This reagent is predicted to react appreciably exothermically with normal, stable amides such as N, N-dimethylacetamide, thus offering the potential for generating and studying such relatively unstable amide N-oxides at low temperatures.

  15. Specific interactions between DNA and regulatory protein controlled by ligand-binding: Ab initio molecular simulation

    SciTech Connect

    Matsushita, Y. Murakawa, T. Shimamura, K. Oishi, M. Ohyama, T. Kurita, N.

    2015-02-27

    The catabolite activator protein (CAP) is one of the regulatory proteins controlling the transcription mechanism of gene. Biochemical experiments elucidated that the complex of CAP with cyclic AMP (cAMP) is indispensable for controlling the mechanism, while previous molecular simulations for the monomer of CAP+cAMP complex revealed the specific interactions between CAP and cAMP. However, the effect of cAMP-binding to CAP on the specific interactions between CAP and DNA is not elucidated at atomic and electronic levels. We here considered the ternary complex of CAP, cAMP and DNA in solvating water molecules and investigated the specific interactions between them at atomic and electronic levels using ab initio molecular simulations based on classical molecular dynamics and ab initio fragment molecular orbital methods. The results highlight the important amino acid residues of CAP for the interactions between CAP and cAMP and between CAP and DNA.

  16. Ab initio quantum transport calculations using plane waves

    NASA Astrophysics Data System (ADS)

    Garcia-Lekue, A.; Vergniory, M. G.; Jiang, X. W.; Wang, L. W.

    2015-08-01

    We present an ab initio method to calculate elastic quantum transport at the nanoscale. The method is based on a combination of density functional theory using plane wave nonlocal pseudopotentials and the use of auxiliary periodic boundary conditions to obtain the scattering states. The method can be applied to any applied bias voltage and the charge density and potential profile can either be calculated self-consistently, or using an approximated self-consistent field (SCF) approach. Based on the scattering states one can straightforwardly calculate the transmission coefficients and the corresponding electronic current. The overall scheme allows us to obtain accurate and numerically stable solutions for the elastic transport, with a computational time similar to that of a ground state calculation. This method is particularly suitable for calculations of tunneling currents through vacuum, that some of the nonequilibrium Greens function (NEGF) approaches based on atomic basis sets might have difficulty to deal with. Several examples are provided using this method from electron tunneling, to molecular electronics, to electronic devices: (i) On a Au nanojunction, the tunneling current dependence on the electrode-electrode distance is investigated. (ii) The tunneling through field emission resonances (FERs) is studied via an accurate description of the surface vacuum states. (iii) Based on quantum transport calculations, we have designed a molecular conformational switch, which can turn on and off a molecular junction by applying a perpendicular electric field. (iv) Finally, we have used the method to simulate tunnel field-effect transistors (TFETs) based on two-dimensional transition-metal dichalcogenides (TMDCs), where we have studied the performance and scaling limits of such nanodevices and proposed atomic doping to enhance the transistor performance.

  17. Ab initio molecular dynamics: concepts, recent developments, and future trends.

    PubMed

    Iftimie, Radu; Minary, Peter; Tuckerman, Mark E

    2005-05-10

    The methodology of ab initio molecular dynamics, wherein finite-temperature dynamical trajectories are generated by using forces computed "on the fly" from electronic structure calculations, has had a profound influence in modern theoretical research. Ab initio molecular dynamics allows chemical processes in condensed phases to be studied in an accurate and unbiased manner, leading to new paradigms in the elucidation of microscopic mechanisms, rationalization of experimental data, and testable predictions of new phenomena. The purpose of this work is to give a brief introduction to the technique and to review several important recent developments in the field. Several illustrative examples showing the power of the technique have been chosen. Perspectives on future directions in the field also will be given. PMID:15870204

  18. Recent progress in ab initio density matrix renormalization group methodology

    NASA Astrophysics Data System (ADS)

    Hachmann, Johannes; Dorando, Jonathan J.; Kin-Lic Chan, Garnet

    2008-03-01

    We present some recent developments in the ab initio density matrix renormalization group (DMRG) method for quantum chemical problems, in particular our local, quadratic scaling algorithm [1] for low dimensional systems. This method is particularly suited for the description of strong nondynamic correlation, and allows us to compute numerically exact (FCI) correlated energies for large active spaces, up to one order of magnitude larger then can be done by conventional CASCI techniques. Other features of this method are its inherent multireference nature, compactness, variational results, size-consistency and size-extensivity. In addition we will review the problems (predominantly organic electronic materials) on which we applied the ab initio DMRG: 1) metal-insulator transition in hydrogen chains [1] 2) all-trans polyacetylene [1] 3) acenes [2] 4) polydiacetylenes [3]. References [1] Hachmann, Cardoen, Chan, JCP 125 (2006), 144101. [2] Hachmann, Dorando, Avil'es, Chan, JCP 127 (2007), 134309. [3] unpublished.

  19. Understanding phonon transport in thermoelectric materials using ab initio approaches

    NASA Astrophysics Data System (ADS)

    Broido, David

    Good thermoelectric materials have low phonon thermal conductivity, kph. Accurate theories to describe kph are important components in developing predictive models of thermoelectric efficiency that can help guide synthesis and measurement efforts. We have developed ab initio approaches to calculate kph, in which phonon modes and phonon scattering rates are computed using interatomic force constants determined from density functional theory, and a full solution of the Boltzmann transport equation for phonons is implemented. A recent approach to calculate interatomic force constants using ab initio molecular dynamics has yielded a good description of the thermal properties of Bi2Te3. But, the complexity of new promising candidate thermoelectric materials introduces computational challenges in assessing their thermal properties. An example is germanane, a germanium based hydrogen-terminated layered semiconductor, which we will discuss in this talk.

  20. Ab Initio Calculations Of Light-Ion Reactions

    SciTech Connect

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

    2012-03-12

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

  1. Exploring complex chemical reactions by ab-initio simulation

    NASA Astrophysics Data System (ADS)

    Parrinello, Michele

    1998-03-01

    Recent progress in the ab-initio molecular dynamics method and the power of parallel computing, allow the detailed study of complex chemical reaction of great industrial relevance. We illustrate this unprecedented capability by investigating the second generation Ziegler-Natta catalytic process. In this inhomogeneous catalyst, a polymerization reaction is induced by TiCl4 molecules deposited on an MgCl2 solid support. A density functional based ab-initio molecular dynamics calculation conducted with a minimum of initial assumption allows to understand the nature of the catalytic center and to determine the reaction path with the associated free energy barrier. Furthermore our calculation can explain in a nontrivial way the stereo-selectivity of the process.

  2. Ab Initio Electronic Relaxation Times and Transport in Noble Metals

    NASA Astrophysics Data System (ADS)

    Mustafa, Jamal I.; Bernardi, Marco; Neaton, Jeffrey B.; Louie, Steven G.

    Relaxation times employed to study electron transport in metals are typically assumed to be constants and obtained empirically using the Drude model. Here, we employ ab initio calculations to compute the electron-phonon relaxation times of Cu, Ag, and Au, and find that they vary significantly on the Fermi surface, spanning ~15 -45 fs. We compute room temperature resistivities in excellent agreement with experiment by combining GW bandstructures, Wannier-interpolated band velocities, and ab initio relaxation times. Our calculations are compared to other approximations used for the relaxation times. Additionally, an importance sampling scheme is introduced to speed up the convergence of resistivity and transport calculations by sampling directly points on the Fermi surface. This work was supported by NSF Grant No. DMR15-1508412 and U.S. DOE under Contract No. DE-AC02-05CH11231. Computational resources have been provided by DOE at LBNL's NERSC facility.

  3. Ab initio Monte Carlo investigation of small lithium clusters.

    SciTech Connect

    Srinivas, S.

    1999-06-16

    Structural and thermal properties of small lithium clusters are studied using ab initio-based Monte Carlo simulations. The ab initio scheme uses a Hartree-Fock/density functional treatment of the electronic structure combined with a jump-walking Monte Carlo sampling of nuclear configurations. Structural forms of Li{sub 8} and Li{sub 9}{sup +} clusters are obtained and their thermal properties analyzed in terms of probability distributions of the cluster potential energy, average potential energy and configurational heat capacity all considered as a function of the cluster temperature. Details of the gradual evolution with temperature of the structural forms sampled are examined. Temperatures characterizing the onset of structural changes and isomer coexistence are identified for both clusters.

  4. Towards AB Initio Calculation of the Circular Dichroism of Peptides

    NASA Astrophysics Data System (ADS)

    Molteni, E.; Onida, G.; Tiana, G.

    2012-08-01

    In this work we plan to use ab initio spectroscopy calculations to compute circular dichroism (CD) spectra of peptides. CD provides information on protein secondary structure content; peptides, instead, remain difficult to address, due to their tendency to adopt multiple conformations in equilibrium. Therefore peptides are an interesting test-case for ab initio calculation of CD spectra. As a first application, we focus on the (83-92) fragment of HIV-1 protease, which is known to be involved in the folding and dimerization of this protein. As a preliminary step, we performed classical molecular dynamics (MD) simulations, in order to obtain a set of representative conformers of the peptide. Then, on some of the obtained conformations, we calculated absorption spectra at the independent particle, RPA and TDLDA levels, showing the presence of charge transfer excitations, and their influence on spectral features.

  5. FT-IR and Raman spectra, ab initio and density functional computations of the vibrational spectra, molecular geometries and atomic charges of uracil and 5-halogenated uracils (5-X-uracils; X=F, Cl, Br, I).

    PubMed

    Singh, J S

    2014-01-01

    Raman (200-4000 cm(-1)) and FT-IR (400-4000 cm(-1)) spectra of uracil and 5-halogenated uracils (5-X-uracils; X=F, Cl, Br, I) have been recorded and analyzed in the range 200-4000 cm(-1). The optimized molecular geometries, atomic polar tensor (APT) charges and vibrational characteristics have been studied theoretically using restricted Hartree-Fock (RHF) and density functional theory (DFT) methods. Ab initio and DFT calculations [using Becke's exchange in conjunction with Lee-Yang-Parr's correlation functional and Becke's three-parameter hybrid method (B3LYP)] were carried out to study the optimized molecular fundamental vibrational frequencies for uracil and 5-halogenated uracils by employing Gaussian-03 program. Gauss View software was used to make the vibrational analysis. Raman and IR spectra have been computed theoretically for the uracil and 5-halogenated molecules. The fundamental vibrational frequencies along with their corresponding intensities in IR and Raman activities and depolarization ratios of the Raman lines have also been calculated using the RHF and DFT methods employing different basis sets. Quantum chemical calculations helped in the reassignments of some fundamental vibrational modes. Most of the B3LYP/6-311++G(**) vibrational frequencies are in excellent agreement with available experimental assignments. The ring breathing and kekule stretching modes are found to lower magnitudes compared to those for uracil which could be due to mass effect of halogen atom in place of the hydrogen atom. The C-X (X=F, Cl, Br, I) stretching frequency is distinctly separated from the CH/NH ring stretching frequencies on the pyrimidine ring. All other bands have also been assigned different fundamentals/overtones/combinations. PMID:24036044

  6. FT-IR and Raman spectra, ab initio and density functional computations of the vibrational spectra, molecular geometries and atomic charges of uracil and 5-halogenated uracils (5-X-uracils; X = F, Cl, Br, I)

    NASA Astrophysics Data System (ADS)

    Singh, J. S.

    2014-01-01

    Raman (200-4000 cm-1) and FT-IR (400-4000 cm-1) spectra of uracil and 5-halogenated uracils (5-X-uracils; X = F, Cl, Br, I) have been recorded and analyzed in the range 200-4000 cm-1. The optimized molecular geometries, atomic polar tensor (APT) charges and vibrational characteristics have been studied theoretically using restricted Hartree-Fock (RHF) and density functional theory (DFT) methods. Ab initio and DFT calculations [using Becke's exchange in conjunction with Lee-Yang-Parr's correlation functional and Becke's three-parameter hybrid method (B3LYP)] were carried out to study the optimized molecular fundamental vibrational frequencies for uracil and 5-halogenated uracils by employing Gaussian-03 program. Gauss View software was used to make the vibrational analysis. Raman and IR spectra have been computed theoretically for the uracil and 5-halogenated molecules. The fundamental vibrational frequencies along with their corresponding intensities in IR and Raman activities and depolarization ratios of the Raman lines have also been calculated using the RHF and DFT methods employing different basis sets. Quantum chemical calculations helped in the reassignments of some fundamental vibrational modes. Most of the B3LYP/6-311++G∗∗ vibrational frequencies are in excellent agreement with available experimental assignments. The ring breathing and kekule stretching modes are found to lower magnitudes compared to those for uracil which could be due to mass effect of halogen atom in place of the hydrogen atom. The C-X (X = F, Cl, Br, I) stretching frequency is distinctly separated from the CH/NH ring stretching frequencies on the pyrimidine ring. All other bands have also been assigned different fundamentals/overtones/combinations.

  7. GAUSSIAN 76: An ab initio Molecular Orbital Program

    DOE R&D Accomplishments Database

    Binkley, J. S.; Whiteside, R.; Hariharan, P. C.; Seeger, R.; Hehre, W. J.; Lathan, W. A.; Newton, M. D.; Ditchfield, R.; Pople, J. A.

    1978-01-01

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

  8. Thermochemical data for CVD modeling from ab initio calculations

    SciTech Connect

    Ho, P.; Melius, C.F.

    1993-12-31

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

  9. The study of molecular spectroscopy by ab initio methods

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.

    1991-01-01

    This review illustrates the potential of theory for solving spectroscopic problems. The accuracy of approximate techniques for including electron correlation have been calibrated by comparison with full configuration-interaction calculations. Examples of the application of ab initio calculations to vibrational, rotational, and electronic spectroscopy are given. It is shown that the state-averaged, complete active space self-consistent field, multireference configuration-interaction procedure provides a good approach for treating several electronic states accurately in a common molecular orbital basis.

  10. Ab initio molecular dynamics simulation study of successive hydrogenation reactions of carbon monoxide producing methanol

    NASA Astrophysics Data System (ADS)

    Pham, Thi Nu; Ono, Shota; Ohno, Kaoru

    2016-04-01

    Doing ab initio molecular dynamics simulations, we demonstrate a possibility of hydrogenation of carbon monoxide producing methanol step by step. At first, the hydrogen atom reacts with the carbon monoxide molecule at the excited state forming the formyl radical. Formaldehyde was formed after adding one more hydrogen atom to the system. Finally, absorption of two hydrogen atoms to formaldehyde produces methanol molecule. This study is performed by using the all-electron mixed basis approach based on the time dependent density functional theory within the adiabatic local density approximation for an electronic ground-state configuration and the one-shot GW approximation for an electronic excited state configuration.

  11. Ab Initio Nuclear Structure and Reaction Calculations for Rare Isotopes

    SciTech Connect

    Draayer, Jerry P.

    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).

  12. Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics

    SciTech Connect

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

    2014-08-07

    We present a new algorithm for ab initio quantum nonadiabatic molecular dynamics that combines the best features of ab initio Multiple Spawning (AIMS) and Multiconfigurational Ehrenfest (MCE) methods. In this new method, ab initio multiple cloning (AIMC), the individual trajectory basis functions (TBFs) follow Ehrenfest equations of motion (as in MCE). However, the basis set is expanded (as in AIMS) when these TBFs become sufficiently mixed, preventing prolonged evolution on an averaged potential energy surface. We refer to the expansion of the basis set as “cloning,” in analogy to the “spawning” procedure in AIMS. This synthesis of AIMS and MCE allows us to leverage the benefits of mean-field evolution during periods of strong nonadiabatic coupling while simultaneously avoiding mean-field artifacts in Ehrenfest dynamics. We explore the use of time-displaced basis sets, “trains,” as a means of expanding the basis set for little cost. We also introduce a new bra-ket averaged Taylor expansion (BAT) to approximate the necessary potential energy and nonadiabatic coupling matrix elements. The BAT approximation avoids the necessity of computing electronic structure information at intermediate points between TBFs, as is usually done in saddle-point approximations used in AIMS. The efficiency of AIMC is demonstrated on the nonradiative decay of the first excited state of ethylene. The AIMC method has been implemented within the AIMS-MOLPRO package, which was extended to include Ehrenfest basis functions.

  13. Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics

    NASA Astrophysics Data System (ADS)

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

    2014-08-01

    We present a new algorithm for ab initio quantum nonadiabatic molecular dynamics that combines the best features of ab initio Multiple Spawning (AIMS) and Multiconfigurational Ehrenfest (MCE) methods. In this new method, ab initio multiple cloning (AIMC), the individual trajectory basis functions (TBFs) follow Ehrenfest equations of motion (as in MCE). However, the basis set is expanded (as in AIMS) when these TBFs become sufficiently mixed, preventing prolonged evolution on an averaged potential energy surface. We refer to the expansion of the basis set as "cloning," in analogy to the "spawning" procedure in AIMS. This synthesis of AIMS and MCE allows us to leverage the benefits of mean-field evolution during periods of strong nonadiabatic coupling while simultaneously avoiding mean-field artifacts in Ehrenfest dynamics. We explore the use of time-displaced basis sets, "trains," as a means of expanding the basis set for little cost. We also introduce a new bra-ket averaged Taylor expansion (BAT) to approximate the necessary potential energy and nonadiabatic coupling matrix elements. The BAT approximation avoids the necessity of computing electronic structure information at intermediate points between TBFs, as is usually done in saddle-point approximations used in AIMS. The efficiency of AIMC is demonstrated on the nonradiative decay of the first excited state of ethylene. The AIMC method has been implemented within the AIMS-MOLPRO package, which was extended to include Ehrenfest basis functions.

  14. Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics.

    PubMed

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

    2014-08-01

    We present a new algorithm for ab initio quantum nonadiabatic molecular dynamics that combines the best features of ab initio Multiple Spawning (AIMS) and Multiconfigurational Ehrenfest (MCE) methods. In this new method, ab initio multiple cloning (AIMC), the individual trajectory basis functions (TBFs) follow Ehrenfest equations of motion (as in MCE). However, the basis set is expanded (as in AIMS) when these TBFs become sufficiently mixed, preventing prolonged evolution on an averaged potential energy surface. We refer to the expansion of the basis set as "cloning," in analogy to the "spawning" procedure in AIMS. This synthesis of AIMS and MCE allows us to leverage the benefits of mean-field evolution during periods of strong nonadiabatic coupling while simultaneously avoiding mean-field artifacts in Ehrenfest dynamics. We explore the use of time-displaced basis sets, "trains," as a means of expanding the basis set for little cost. We also introduce a new bra-ket averaged Taylor expansion (BAT) to approximate the necessary potential energy and nonadiabatic coupling matrix elements. The BAT approximation avoids the necessity of computing electronic structure information at intermediate points between TBFs, as is usually done in saddle-point approximations used in AIMS. The efficiency of AIMC is demonstrated on the nonradiative decay of the first excited state of ethylene. The AIMC method has been implemented within the AIMS-MOLPRO package, which was extended to include Ehrenfest basis functions. PMID:25106573

  15. A Complete and Accurate Ab Initio Repeat Finding Algorithm.

    PubMed

    Lian, Shuaibin; Chen, Xinwu; Wang, Peng; Zhang, Xiaoli; Dai, Xianhua

    2016-03-01

    It has become clear that repetitive sequences have played multiple roles in eukaryotic genome evolution including increasing genetic diversity through mutation, changes in gene expression and facilitating generation of novel genes. However, identification of repetitive elements can be difficult in the ab initio manner. Currently, some classical ab initio tools of finding repeats have already presented and compared. The completeness and accuracy of detecting repeats of them are little pool. To this end, we proposed a new ab initio repeat finding tool, named HashRepeatFinder, which is based on hash index and word counting. Furthermore, we assessed the performances of HashRepeatFinder with other two famous tools, such as RepeatScout and Repeatfinder, in human genome data hg19. The results indicated the following three conclusions: (1) The completeness of HashRepeatFinder is the best one among these three compared tools in almost all chromosomes, especially in chr9 (8 times of RepeatScout, 10 times of Repeatfinder); (2) in terms of detecting large repeats, HashRepeatFinder also performed best in all chromosomes, especially in chr3 (24 times of RepeatScout and 250 times of Repeatfinder) and chr19 (12 times of RepeatScout and 60 times of Repeatfinder); (3) in terms of accuracy, HashRepeatFinder can merge the abundant repeats with high accuracy. PMID:26272474

  16. Ab initio calculations of reactions with light nuclei

    NASA Astrophysics Data System (ADS)

    Quaglioni, Sofia; Hupin, Guillaume; Calci, Angelo; Navrátil, Petr; Roth, Robert

    2016-03-01

    An ab initio (i.e., from first principles) theoretical framework capable of providing a unified description of the structure and low-energy reaction properties of light nuclei is desirable to further our understanding of the fundamental interactions among nucleons, and provide accurate predictions of crucial reaction rates for nuclear astrophysics, fusion-energy research, and other applications. In this contribution we review ab initio calculations for nucleon and deuterium scattering on light nuclei starting from chiral two- and three-body Hamiltonians, obtained within the framework of the ab initio no-core shell model with continuum. This is a unified approach to nuclear bound and scattering states, in which square-integrable energy eigenstates of the A-nucleon system are coupled to (A-a)+a target-plus-projectile wave functions in the spirit of the resonating group method to obtain an efficient description of the many-body nuclear dynamics both at short and medium distances and at long ranges.

  17. Self-trapping of carbon atoms in α'-Fe during the martensitic transformation: A qualitative picture from ab initio calculations

    NASA Astrophysics Data System (ADS)

    Ruban, A. V.

    2014-10-01

    Strain-induced and chemical interactions of interstitial carbon atoms in bcc or α-Fe are obtained in first-principles calculations. Subsequent Monte Carlo simulations show that at low temperatures, carbon atoms prefer to occupy at least two different octahedral sublattices, which is due to quite strong attractive interactions of carbon atoms at the corresponding coordination shells. The direct total-energy calculations of one of the obtained ordered structures with composition Fe16C2, show that it is more stable than the predicted earlier structure with the same composition but carbon atoms occupying only one octahedral sublattice. This indicates that the long-existing thermodynamic mean-field theory of ordering of carbon in α-Fe assuming strong preference of carbon atoms to occupy only one octahedral sublattice is deficient. It is shown that the presence of carbon atoms only at one octahedral sublattice in the experimentally observed martensitic phase, α'-Fe, is a self-trapping effect. It occurs during a displacive martensitic transformation from γ- to α-Fe, which kinematically transfers the carbon atoms from a single fcc octahedral sublattice to one of three octahedral sublattices, where they appear to be locked by a consequent tetragonal distortion minimizing elastic energy of the phase. The latter creates a strong preference for carbon atoms to be only at one already occupied octahedral sublattice preventing them from further distribution over the other sublattices.

  18. Ab initio calculation of diffusion barriers for Cu adatom hopping on Cu(1 0 0) surface and evolution of atomic configurations

    NASA Astrophysics Data System (ADS)

    Zhang, Wei; Gan, Jie; Li, Qian; Gao, Kun; Sun, Jian; Xu, Ning; Ying, Zhifeng; Wu, Jiada

    2011-06-01

    The self-diffusion dynamics of Cu adatoms on Cu(1 0 0) surface has been studied based on the calculation of the energy barriers for various hopping events using lattice-gas based approach and a modified model. To simplify the description of the interactions and the calculation of the energy barrier, a three-tier hierarchy of description of atomic configurations was conceived in which the active adatom and its nearest atoms were chosen to constitute basic configuration and taken as a whole to study many-body interactions of the atoms in various atomic configurations, whereas the impacts of the next nearest atoms on the diffusion of the active adatom were considered as multi-site interactions. Besides the simple hopping of single adatoms, the movements of dimers and trimers as the results of multiple hopping events have also been examined. Taking into account the hopping events of all adatoms, the stability of atomic configurations has been examined and the evolution of atomic configurations has also been analyzed.

  19. Electronic properties of liquid Hg-In alloys : Ab-initio molecular dynamics study

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

    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 (Hg10In90, Hg30In70,. Hg50In50, Hg70In30, and Hg90Pb10) 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.

  20. Ultracold mixtures of metastable He and Rb: Scattering lengths from ab initio calculations and thermalization measurements

    NASA Astrophysics Data System (ADS)

    Knoop, S.; Żuchowski, P. S.; KÈ©dziera, D.; Mentel, Ł.; Puchalski, M.; Mishra, H. P.; Flores, A. S.; Vassen, W.

    2014-08-01

    We have investigated the ultracold interspecies scattering properties of metastable triplet He and Rb. We performed state-of-the-art ab initio calculations of the relevant interaction potential, and measured the interspecies elastic cross section for an ultracold mixture of metastable triplet He4 and Rb87 in a quadrupole magnetic trap at a temperature of 0.5 mK. Our combined theoretical and experimental study gives an interspecies scattering length a4+87=+17-4+1a0, which prior to this work was unknown. More general, our work shows the possibility of obtaining accurate scattering lengths using ab initio calculations for a system containing a heavy, many-electron atom, such as Rb.

  1. Ethanol decomposition on transition metal nanoparticles during carbon nanotube growth: ab initio molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Shibuta, Yasushi; Shimamura, Kohei; Oguri, Tomoya; Arifin, Rizal; Shimojo, Fuyuki; Yamaguchi, Shu

    2015-03-01

    The growth mechanism of carbon nanotubes (CNT) has been widely discussed both from experimental and computational studies. Regarding the computational studies, most of the studies focuses on the aggregation of isolate carbon atoms on the catalytic metal nanoparticle, whereas the initial dissociation of carbon source molecules should affect the yield and quality of the products. On the other hand, we have studied the dissociation process of carbon source molecules on the metal surface by the ab initio molecular dynamics simulation. In the study, we investigate the ethanol dissociation on Pt and Ni clusters by ab initio MD simulations to discuss the initial stage of CNT growth by alcohol CVD technique. Part of this research is supported by the Grant-in-Aid for Young Scientists (a) (No. 24686026) from MEXT, Japan.

  2. Internal dynamics in azetidine: A microwave and ab initio study

    NASA Astrophysics Data System (ADS)

    López, Juan C.; Blanco, Susana; Lesarri, Alberto; Alonso, José L.

    2001-02-01

    The internal dynamics of interconversion between equivalent conformations due to the coupling between ring puckering and NH inversion in azetidine has been investigated by rotational spectroscopy and ab initio computations. Analysis of the rotational spectra in the 8-220 GHz region has been completed for the ground state and first four excited states of the ring-puckering vibration. Rotational transitions exhibit a characteristic doubling originated by tunneling between equivalent conformations through a C2v barrier, which is related to symmetric (A1) and antisymmetric (B1) inversion states. Additionally, nuclear quadrupole hyperfine structure arising from the N nucleus could be resolved for low-J transitions. Accurate rotational and centrifugal distortion parameters together with the energy difference between inversion states derived from μc-type inversion transitions have been derived for each ring-puckering state using a two-state Hamiltonian. An effective monodimensional reduced potential function for the ring-puckering vibration V(X)=10.82(X4+14.29X-8.93X2-0.28X3) has been found consistent with the observed experimental variation of the rotational and centrifugal distortion constants with ring-puckering. This asymmetric single minimum potential function supports the existence of only one stable equatorial form. The barrier to interconversion between equivalent equatorial conformers, related to the C2v conformation of azetidine in which the ring atoms and the NH group are coplanar, has been estimated to range between 1900 and 2600 cm-1. The strong dependence of the dipole moment and quadrupole coupling constants with ring-puckering vibrational state evidence structural changes that occur along the ring-puckering coordinate.

  3. Chiroptical properties of unsubstituted carbohydrates: Ab initio and semiempirical studies

    NASA Astrophysics Data System (ADS)

    Parra C., Alejandro

    Ab initio calculations support assignment of the vacuum ultraviolet circular dichroism (CD) of simple saccharides to 11A 1 --> 21B1 and 11A 1 --> 11A2 transitions centered on the oxygen atoms of the acetal group treated as two weakly coupled ether chromophores. The calculations are consistent with assignments previously made on the basis of a deconvolution of CD spectra. Estimates of the oxygen centered contributions to magnetic transition dipole moments were made. Semiempirical calculations were performed to model the NaD molar optical rotation of 1,6- and 3,6- anhydrosugars. For 1,6-anhydrosugars, current parameters produce reasonable agreement with experimental values. For 3,6-anhydrosugars, modifications to the ether parameters had to be introduced. The most relevant included a reorientation of the bond-centered s-->s* transition dipole charges in the ether chromophore to a C2v orientation, and a shift from prolate polarizability ellipsoids to general ellipsoids. These changes result in good agreement with experimental Na D molar rotations for 3,6-anhydrosugars. A low energy CD band arises in 3,6- and 1,6-anhydrosugars when agreement with the experimental NaD molar rotations is achieved. It is proposed that this band is a real feature in the spectrum. The origin of the band is primarily the interaction between b1 symmetry- oriented transition dipoles in the COC groups with other transition dipoles in the molecule. Comparison with experimental spectra leads to an assignment of this band to 11A1 --> 21B1 transitions centered on the COC groups.

  4. Interstitial Zn atoms do the trick in thermoelectric zinc antimonide, Zn4Sb3: a combined maximum entropy method X-ray electron density and ab initio electronic structure study.

    PubMed

    Cargnoni, Fausto; Nishibori, Eiji; Rabiller, Philippe; Bertini, Luca; Snyder, G Jeffrey; Christensen, Mogens; Gatti, Carlo; Iversen, Bo Brummerstadt

    2004-08-20

    The experimental electron density of the high-performance thermoelectric material Zn4Sb3 has been determined by maximum entropy (MEM) analysis of short-wavelength synchrotron powder diffraction data. These data are found to be more accurate than conventional single-crystal data due to the reduction of common systematic errors, such as absorption, extinction and anomalous scattering. Analysis of the MEM electron density directly reveals interstitial Zn atoms and a partially occupied main Zn site. Two types of Sb atoms are observed: a free spherical ion (Sb3-) and Sb2(4-) dimers. Analysis of the MEM electron density also reveals possible Sb disorder along the c axis. The disorder, defects and vacancies are all features that contribute to the drastic reduction of the thermal conductivity of the material. Topological analysis of the thermally smeared MEM density has been carried out. Starting with the X-ray structure ab initio computational methods have been used to deconvolute structural information from the space-time data averaging inherent to the XRD experiment. The analysis reveals how interstitial Zn atoms and vacancies affect the electronic structure and transport properties of beta-Zn4Sb3. The structure consists of an ideal A12Sb10 framework in which point defects are distributed. We propose that the material is a 0.184:0.420:0.396 mixture of A12Sb10, A11BCSb10 and A10BCDSb10 cells, in which A, B, C and D are the four Zn sites in the X-ray structure. Given the similar density of states (DOS) of the A12Sb10, A11BCSb10 and A10BCDSb10 cells, one may electronically model the defective stoichiometry of the real system either by n-doping the 12-Zn atom cell or by p-doping the two 13-Zn atom cells. This leads to similar calculated Seebeck coefficients for the A12Sb10, A11BCSb10 and A10BCDSb10 cells (115.0, 123.0 and 110.3 microV K(-1) at T=670 K). The model system is therefore a p-doped semiconductor as found experimentally. The effect is dramatic if these cells are

  5. Migration of Single Iridium Atoms and Tri-iridium Clusters on MgO Surfaces. Aberration-Corrected STEM Imaging and ab-initio Calculations

    SciTech Connect

    Han, Chang W.; Iddir, Hakim; Uzun, Alper; Curtiss, Larry A.; Browning, Nigel D.; Gates, Bruce C.; Ortalan, Volkan

    2015-11-06

    To address the challenge of fast, direct atomic-scale visualization of the diffusion of atoms and clusters on surfaces, we used aberration-corrected scanning transmission electron microscopy (STEM) with high scan speeds (as little as ~0.1 s per frame) to visualize the diffusion of (1) a heavy atom (Ir) on the surface of a support consisting of light atoms, MgO(100), and (2) an Ir3 cluster on MgO(110). Sequential Z-contrast images elucidate the diffusion mechanisms, including the hopping of Ir1 and the rotational migration of Ir3 as two Ir atoms remain anchored to the surface. Density functional theory (DFT) calculations provided estimates of the diffusion energy barriers and binding energies of the iridium species to the surfaces. The results show how the combination of fast-scan STEM and DFT calculations allow real-time visualization and fundamental understanding of surface diffusion phenomena pertaining to supported catalysts and other materials.

  6. Efficient Use of an Adapting Database of Ab Initio Calculations To Generate Accurate Newtonian Dynamics.

    PubMed

    Shaughnessy, M C; Jones, R E

    2016-02-01

    We develop and demonstrate a method to efficiently use density functional calculations to drive classical dynamics of complex atomic and molecular systems. The method has the potential to scale to systems and time scales unreachable with current ab initio molecular dynamics schemes. It relies on an adapting dataset of independently computed Hellmann-Feynman forces for atomic configurations endowed with a distance metric. The metric on configurations enables fast database lookup and robust interpolation of the stored forces. We discuss mechanisms for the database to adapt to the needs of the evolving dynamics, while maintaining accuracy, and other extensions of the basic algorithm. PMID:26669825

  7. An Ab Initio Full Potential Fully Relativistic Study of Atomic Carbon, Nitrogen, and Oxygen Chemisorption on the (111) Surface of δ-Pu

    NASA Astrophysics Data System (ADS)

    Atta-Fynn, Raymond; Ray, Asok

    2006-10-01

    Fully-relativistic full potential density functional calculations have been performed to investigate atomic carbon, nitrogen, and oxygen chemisorption on the (111) surface of δ-Pu using the all-electron linearized augmented plane wave plus local orbitals code WIEN2k and the generalized gradient approximation to density functional theory. The surface was modeled by a three-layer periodic slab separated by 60 Bohr vacuum with two atoms per surface unit cell. The hollow fcc adsorption site was found to be the most preferred site with chemisorption energies of 6.539 eV, 6.714 eV, and 8.2 eV for the C, N, and O adatoms, respectively. The respective distances of the C, N, and O adatoms from the surface were found to be 1.16 å, 1.08 å, and 1.25 å. Analysis of the partial charges inside the atomic spheres, charge density distributions, and the local density of states indicate hybridizations between Pu 5f and the 2p states of the adatoms.

  8. A study ab-initio of relative stability and electronic properties of substitutions of C by B and N atoms in the w-BN compound

    NASA Astrophysics Data System (ADS)

    Casiano Jimenéz, G.; Ortega López, C.; Espitia, M. J.

    2016-02-01

    In this work we study relative stability, structural and electronic properties of pure BN and with substitutions of carbon by boron and nitrogen atoms, e.i. for B0.9375C0.0625N and BC0.0625N0.9375, respectively. Using first-principles calculations in the Density Functional Theory (DFT), we found that it is more energetically favourable that the carbon atoms occupy the positions of the boron atoms (C by B). It was found that the new compounds BC0.0625N0.9375 (C by N) and B0.9375C0.0625N (C by B) have high bulk modulus, so they are very rigid. This property makes them good candidates for applications in hard coatings or devices for high power and temperatures. The density of state calculations shows that compound has metallic behaviour due to the hybridization of the orbitals C-2p and N-2p that cross the Fermi level.

  9. Cold collisions of polyatomic molecular radicals with S-state atoms in a magnetic field: an ab initio study of He + CH2(X) collisions.

    PubMed

    Tscherbul, T V; Grinev, T A; Yu, H-G; Dalgarno, A; Kłos, Jacek; Ma, Lifang; Alexander, Millard H

    2012-09-14

    We develop a rigorous quantum mechanical theory for collisions of polyatomic molecular radicals with S-state atoms in the presence of an external magnetic field. The theory is based on a fully uncoupled space-fixed basis set representation of the multichannel scattering wave function. Explicit expressions are presented for the matrix elements of the scattering Hamiltonian for spin-1/2 and spin-1 polyatomic molecular radicals interacting with structureless targets. The theory is applied to calculate the cross sections and thermal rate constants for spin relaxation in low-temperature collisions of the prototypical organic molecule methylene [CH(2)(X(3)B(1))] with He atoms. To this end, two accurate three-dimensional potential energy surfaces (PESs) of the He-CH(2)(X(3)B(1)) complex are developed using the state-of-the-art coupled-cluster method including single and double excitations along with a perturbative correction for triple excitations and large basis sets. Both PESs exhibit shallow minima and are weakly anisotropic. Our calculations show that spin relaxation in collisions of CH(2), CHD, and CD(2) molecules with He atoms occurs at a much slower rate than elastic scattering over a large range of temperatures (1 μK-1 K) and magnetic fields (0.01-1 T), suggesting excellent prospects for cryogenic helium buffer-gas cooling of ground-state ortho-CH(2)(X(3)B(1)) molecules in a magnetic trap. Furthermore, we find that ortho-CH(2) undergoes collision-induced spin relaxation much more slowly than para-CH(2), which indicates that magnetic trapping can be used to separate nuclear spin isomers of open-shell polyatomic molecules. PMID:22979854

  10. Cold collisions of polyatomic molecular radicals with S-state atoms in a magnetic field: An ab initio study of He + CH2(X~) collisions

    NASA Astrophysics Data System (ADS)

    Tscherbul, T. V.; Grinev, T. A.; Yu, H.-G.; Dalgarno, A.; Kłos, Jacek; Ma, Lifang; Alexander, Millard H.

    2012-09-01

    We develop a rigorous quantum mechanical theory for collisions of polyatomic molecular radicals with S-state atoms in the presence of an external magnetic field. The theory is based on a fully uncoupled space-fixed basis set representation of the multichannel scattering wave function. Explicit expressions are presented for the matrix elements of the scattering Hamiltonian for spin-1/2 and spin-1 polyatomic molecular radicals interacting with structureless targets. The theory is applied to calculate the cross sections and thermal rate constants for spin relaxation in low-temperature collisions of the prototypical organic molecule methylene [CH_2(tilde{X}^3B_1)] with He atoms. To this end, two accurate three-dimensional potential energy surfaces (PESs) of the He-CH_2(tilde{X}^3B_1) complex are developed using the state-of-the-art coupled-cluster method including single and double excitations along with a perturbative correction for triple excitations and large basis sets. Both PESs exhibit shallow minima and are weakly anisotropic. Our calculations show that spin relaxation in collisions of CH2, CHD, and CD2 molecules with He atoms occurs at a much slower rate than elastic scattering over a large range of temperatures (1 μK-1 K) and magnetic fields (0.01-1 T), suggesting excellent prospects for cryogenic helium buffer-gas cooling of ground-state ortho-CH_2(tilde{X}^3B_1) molecules in a magnetic trap. Furthermore, we find that ortho-CH2 undergoes collision-induced spin relaxation much more slowly than para-CH2, which indicates that magnetic trapping can be used to separate nuclear spin isomers of open-shell polyatomic molecules.

  11. {ital Ab initio} full charge-density study of the atomic volume of {alpha}-phase Fr, Ra, Ac, Th, Pa, U, Np, and Pu

    SciTech Connect

    Vitos, L.; Kollar, J.; Skriver, H.L.

    1997-02-01

    We have used a full charge-density technique based on the linear muffin-tin orbitals method in first-principles calculations of the atomic volumes of the light actinides including Fr, Ra, and Ac in their low-temperature crystallographic phases. The good agreement between the theoretical and experimental values along the series support the picture of itinerant 5f electronic states in Th to Pu. The increased deviation between theory and experiment found in Np and Pu may be an indication of correlation effects not included in the local density approximation. {copyright} {ital 1997} {ital The American Physical Society}

  12. New Variational Method for the Ab Initio Study in Valence Coordinates of the Renner-Teller Effect in Tetra-Atomic Systems.

    PubMed

    Jutier, Laurent; Léonard, Céline

    2010-05-11

    A new variational methodology for the treatment of the Renner-Teller effect in tetra-atomic molecules has been developed in valence coordinates. The kinetic-energy operator of Bramley et al. [Mol. Phys. 1991, 73, 1183] for any sequentially bonded four-atom molecule, A-B-C-D, in the singlet nondegenerate electronic state has been adapted to the Renner-Teller and spin couplings by modifying the expression of the nuclear angular momentum. The total Schrödinger equation is solved by diagonalizing the Hamiltonian matrix in a three-step contraction scheme. The main advantage of this new theoretical development is the possibility of studying different isotopomers using the same potential-energy surfaces. This procedure has been tested on HCCH(+) and its deuterated derivatives DCCD(+) and DCCH(+). The calculated rovibronic band origins were compared with previous data deduced from the Jacobi coordinates methodology, dimensionality reduced variational treatment, and photoelectron spectra with a good global agreement. Rotational structures for these systems are also tackled. PMID:26615691

  13. Ab Initio Computation of the Energies of Circular Quantum Dots

    SciTech Connect

    Lohne, M. Pedersen; Hagen, Gaute; Hjorth-Jensen, M.; Kvaal, S.; Pederiva, F.

    2011-01-01

    We perform coupled-cluster and diffusion Monte Carlo calculations of the energies of circular quantum dots up to 20 electrons. The coupled-cluster calculations include triples corrections and a renormalized Coulomb interaction defined for a given number of low-lying oscillator shells. Using such a renormalized Coulomb interaction brings the coupled-cluster calculations with triples correlations in excellent agreement with the diffusion Monte Carlo calculations. This opens up perspectives for doing ab initio calculations for much larger systems of electrons.

  14. The implementation of ab initio quantum chemistry calculations on transporters.

    PubMed

    Cooper, M D; Hillier, I H

    1991-06-01

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

  15. Ab initio vibrational and dielectric properties of Y V O

    NASA Astrophysics Data System (ADS)

    Vali, R.

    2009-10-01

    For the yttrium orthovanadate Y V O with a tetragonal zircon-type structure, the first complete set of Raman-active and IR-active phonon modes has been calculated using ab initio density functional perturbation theory. The calculated IR reflectivity spectra are in good agreement with available experimental data. We report the calculated frequencies of three Raman-active modes that could not be detected experimentally and a new assignment of the experimental Raman data. The contributions of each IR-active phonon modes to static dielectric tensor have been determined.

  16. Potential Dependence of Electrochemical Barriers from ab Initio Calculations.

    PubMed

    Chan, Karen; Nørskov, Jens K

    2016-05-01

    We present a simple and computationally efficient method to determine the potential dependence of the activation energies for proton-electron transfer from a single ab initio barrier calculation. We show that the potential dependence of the activation energy is given by the partial charge transferred at the transition state. The method is evaluated against the potential dependence determined explicitly through multiple calculations at varying potential. We show that the transfer coefficient is given by the charge transferred from the initial to transition state, which has significant implications for electrochemical kinetics. PMID:27088442

  17. Ab-Initio Shell Model with a Core

    SciTech Connect

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

    2008-06-04

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

  18. Ab Initio Calculations Applied to Problems in Metal Ion Chemistry

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Partridge, Harry; Arnold, James O. (Technical Monitor)

    1994-01-01

    Electronic structure calculations can provide accurate spectroscopic data (such as molecular structures) vibrational frequencies, binding energies, etc.) that have been very useful in explaining trends in experimental data and in identifying incorrect experimental measurements. In addition, ab initio calculations. have given considerable insight into the many interactions that make the chemistry of transition metal systems so diverse. In this review we focus on cases where calculations and experiment have been used to solve interesting chemical problems involving metal ions. The examples include cases where theory was used to differentiate between disparate experimental values and cases where theory was used to explain unexpected experimental results.

  19. An improved ab initio structure for fluorine peroxide (FOOF)

    NASA Astrophysics Data System (ADS)

    Mack, Hans-Georg; Oberhammer, Heinz

    1988-03-01

    Ab initio calculations with the 6-31G* and Dunning (9s5p/4s2p) basis sets augmented with p and d functions at various levels of theory (RHF, MP2, MP3, and MP4) were carried out on F 2O 2. The best result was obtained at the MP2 level with the Dunning basis plus one set of d functions on fluorine and two sets of d functions on oxygen. These calculations reproduce the experimental bond lengths to within 0.01 Å and the angles to within the experimental uncertainties.

  20. Ab initio study of neutron drops with chiral Hamiltonians

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  1. Ab-initio study of transition metal hydrides

    SciTech Connect

    Sharma, Ramesh; Shukla, Seema Dwivedi, Shalini Sharma, Yamini

    2014-04-24

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

  2. Accelerating ab initio path integral molecular dynamics with multilevel sampling of potential surface

    NASA Astrophysics Data System (ADS)

    Geng, Hua Y.

    2015-02-01

    A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics (AI-PIMD) simulation, without compromising the overall accuracy. To validate the method, the internal energy and free energy of an Einstein crystal are calculated and compared with the analytical solutions. As a preliminary application, we assess the performance of the method in a realistic model-the FCC phase of dense atomic hydrogen, in which the calculated result shows that the acceleration rate is about 3 to 4-fold for a two-level implementation, and can be increased up to 10 times if extrapolation is used. With only 16 beads used for the ab initio potential sampling, this method gives a well converged internal energy. The residual error in pressure is just about 3 GPa, whereas it is about 20 GPa for a plain AI-PIMD calculation with the same number of beads. The vibrational free energy of the FCC phase of dense hydrogen at 300 K is also calculated with an AI-PIMD thermodynamic integration method, which gives a result of about 0.51 eV/proton at a density of rs = 0.912.

  3. Accelerating ab initio path integral molecular dynamics with multilevel sampling of potential surface

    SciTech Connect

    Geng, Hua Y.

    2015-02-15

    A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics (AI-PIMD) simulation, without compromising the overall accuracy. To validate the method, the internal energy and free energy of an Einstein crystal are calculated and compared with the analytical solutions. As a preliminary application, we assess the performance of the method in a realistic model—the FCC phase of dense atomic hydrogen, in which the calculated result shows that the acceleration rate is about 3 to 4-fold for a two-level implementation, and can be increased up to 10 times if extrapolation is used. With only 16 beads used for the ab initio potential sampling, this method gives a well converged internal energy. The residual error in pressure is just about 3 GPa, whereas it is about 20 GPa for a plain AI-PIMD calculation with the same number of beads. The vibrational free energy of the FCC phase of dense hydrogen at 300 K is also calculated with an AI-PIMD thermodynamic integration method, which gives a result of about 0.51 eV/proton at a density of r{sub s}=0.912.

  4. In pursuit of the ab initio limit for conformational energy prototypes

    NASA Astrophysics Data System (ADS)

    Császár, Attila G.; Allen, Wesley D.; Schaefer, Henry F.

    1998-06-01

    The convergence of ab initio predictions to the one- and n-particle limits has been systematically explored for several conformational energy prototypes: the inversion barriers of ammonia, water, and isocyanic acid, the torsional barrier of ethane, the E/Z rotamer separation of formic acid, and the barrier to linearity of silicon dicarbide. Explicit ab initio results were obtained with atomic-orbital basis sets as large as [7s6p5d4f3g2h1i/6s5p4d3f2g1h] and electron correlation treatments as extensive as fifth-order Møller-Plesset perturbation theory (MP5), the full coupled-cluster method through triple excitations (CCSDT), and Brueckner doubles theory including perturbational corrections for both triple and quadruple excitations [BD(TQ)]. Subsequently, basis set and electron correlation extrapolation schemes were invoked to gauge any further variations in arriving at the ab initio limit. Physical effects which are tacitly neglected in most theoretical work have also been quantified by computations of non-Born-Oppenheimer (BODC), relativistic, and core correlation shifts of relative energies. Instructive conclusions are drawn for the pursuit of spectroscopic accuracy in theoretical conformational analyses, and precise predictions for the key energetic quantities of the molecular prototypes are advanced.

  5. Electron transfer modifies chemical properties of C70 fullerene surface: An ab initio molecular dynamics study of C70O3 molozonides doped with light atoms

    NASA Astrophysics Data System (ADS)

    Bil, Andrzej; Hutter, Jürg; Morrison, Carole A.

    2014-06-01

    Light metal atoms such as Li, K (electronic state 2S1/2) or Ca (1S0) encapsulated in a C70 cage considerably modifies the chemical properties of the fullerene surface due to metal-to-cage electron transfer. H-doped and anion ozonide systems were also considered to validate the electron transfer hypothesis. The relative stabilities of the eight isomers of the C70O3 molozonide series at room temperature depend on the identity of the endohedral guest, as was the preferred channel for thermal decomposition. No electron transfer was observed for the complex N@C70 where the fullerene acts as an inert container for the 4S3/2 radical.

  6. Ab initio study of intrinsic, H and He point defects in hcp-Er

    SciTech Connect

    Yang, Li; Peng, SM; Long, XG; Gao, Fei; Heinisch, Howard L.; Kurtz, Richard J.; Zu, Xiaotao T.

    2010-03-01

    Ab initio calculations based on density functional theory have been performed to determine the properties of self-interstitial atoms (SIAs), vacancies, and single H and He atoms in hcp-Er. The results show that the most stable configuration for an SIA is a basal octahedral (BO) configuration, while the octahedral (O), basal split (BS) and crowdion (C) interstitial configurations are less stable, followed by the split <0001> dumbbell and tetrahedral configurations. For both H and He defects, the formation energy of an interstitial atom is less than that of a substitutional atom in hcp-Er. Furthermore, the tetrahedral interstitial position is more stable than an octahedral position for both He and H interstitials. The hybridization of the He and H defects with Er atoms has been used to explain the relative stabilities of these defects in hcp-Er.

  7. Ab initio study of hot electrons in GaAs.

    PubMed

    Bernardi, Marco; Vigil-Fowler, Derek; Ong, Chin Shen; Neaton, Jeffrey B; Louie, Steven G

    2015-04-28

    Hot carrier dynamics critically impacts the performance of electronic, optoelectronic, photovoltaic, and plasmonic devices. Hot carriers lose energy over nanometer lengths and picosecond timescales and thus are challenging to study experimentally, whereas calculations of hot carrier dynamics are cumbersome and dominated by empirical approaches. In this work, we present ab initio calculations of hot electrons in gallium arsenide (GaAs) using density functional theory and many-body perturbation theory. Our computed electron-phonon relaxation times at the onset of the Γ, L, and X valleys are in excellent agreement with ultrafast optical experiments and show that the ultrafast (tens of femtoseconds) hot electron decay times observed experimentally arise from electron-phonon scattering. This result is an important advance to resolve a controversy on hot electron cooling in GaAs. We further find that, contrary to common notions, all optical and acoustic modes contribute substantially to electron-phonon scattering, with a dominant contribution from transverse acoustic modes. This work provides definitive microscopic insight into hot electrons in GaAs and enables accurate ab initio computation of hot carriers in advanced materials. PMID:25870287

  8. Three-cluster dynamics within an ab initio framework

    DOE PAGESBeta

    Quaglioni, Sofia; Romero-Redondo, Carolina; Navratil, Petr

    2013-09-26

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

  9. Oxidation of GaN: An ab initio thermodynamic approach

    NASA Astrophysics Data System (ADS)

    Jackson, Adam J.; Walsh, Aron

    2013-10-01

    GaN is a wide-band-gap semiconductor used in high-efficiency light-emitting diodes and solar cells. The solid is produced industrially at high chemical purities by deposition from a vapor phase, and oxygen may be included at this stage. Oxidation represents a potential path for tuning its properties without introducing more exotic elements or extreme processing conditions. In this work, ab initio computational methods are used to examine the energy potentials and electronic properties of different extents of oxidation in GaN. Solid-state vibrational properties of Ga, GaN, Ga2O3, and a single substitutional oxygen defect have been studied using the harmonic approximation with supercells. A thermodynamic model is outlined which combines the results of ab initio calculations with data from experimental literature. This model allows free energies to be predicted for arbitrary reaction conditions within a wide process envelope. It is shown that complete oxidation is favorable for all industrially relevant conditions, while the formation of defects can be opposed by the use of high temperatures and a high N2:O2 ratio.

  10. Ab initio thermodynamic model for magnesium carbonates and hydrates.

    PubMed

    Chaka, Anne M; Felmy, Andrew R

    2014-09-01

    An ab initio thermodynamic framework for predicting properties of hydrated magnesium carbonate minerals has been developed using density-functional theory linked to macroscopic thermodynamics through the experimental chemical potentials for MgO, water, and CO2. Including semiempirical dispersion via the Grimme method and small corrections to the generalized gradient approximation of Perdew, Burke, and Ernzerhof for the heat of formation yields a model with quantitative agreement for the benchmark minerals brucite, magnesite, nesquehonite, and hydromagnesite. The model shows how small differences in experimental conditions determine whether nesquehonite, hydromagnesite, or magnesite is the result of laboratory synthesis from carbonation of brucite, and what transformations are expected to occur on geological time scales. Because of the reliance on parameter-free first-principles methods, the model is reliably extensible to experimental conditions not readily accessible to experiment and to any mineral composition for which the structure is known or can be hypothesized, including structures containing defects, substitutions, or transitional structures during solid state transformations induced by temperature changes or processes such as water, CO2, or O2 diffusion. Demonstrated applications of the ab initio thermodynamic framework include an independent means to evaluate differences in thermodynamic data for lansfordite, predicting the properties of Mg analogues of Ca-based hydrated carbonates monohydrocalcite and ikaite, which have not been observed in nature, and an estimation of the thermodynamics of barringtonite from the stoichiometry and a single experimental observation. PMID:24679248

  11. Ab Initio Thermodynamic Model for Magnesium Carbonates and Hydrates

    SciTech Connect

    Chaka, Anne M.; Felmy, Andrew R.

    2014-03-28

    An ab initio thermodynamic framework for predicting properties of hydrated magnesium carbonate minerals has been developed using density-functional theory linked to macroscopic thermodynamics through the experimental chemical potentials for MgO, water, and CO2. Including semiempirical dispersion via the Grimme method and small corrections to the generalized gradient approximation of Perdew, Burke, and Ernzerhof for the heat of formation yields a model with quantitative agreement for the benchmark minerals brucite, magnesite, nesquehonite, and hydromagnesite. The model shows how small differences in experimental conditions determine whether nesquehonite, hydromagnesite, or magnesite is the result of laboratory synthesis from carbonation of brucite, and what transformations are expected to occur on geological time scales. Because of the reliance on parameter-free first principles methods, the model is reliably extensible to experimental conditions not readily accessible to experiment and to any mineral composition for which the structure is known or can be hypothesized, including structures containing defects, substitutions, or transitional structures during solid state transformations induced by temperature changes or processes such as water, CO2, or O2 diffusion. Demonstrated applications of the ab initio thermodynamic framework include an independent means to evaluate differences in thermodynamic data for lansfordite, predicting the properties of Mg analogs of Ca-based hydrated carbonates monohydrocalcite and ikaite which have not been observed in nature, and an estimation of the thermodynamics of barringtonite from the stoichiometry and a single experimental observation.

  12. Ab initio prediction of the critical thickness of a precipitate

    NASA Astrophysics Data System (ADS)

    Sampath, S.; Janisch, R.

    2013-09-01

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

  13. AB INITIO SIMULATIONS FOR MATERIAL PROPERTIES ALONG THE JUPITER ADIABAT

    SciTech Connect

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

    2012-09-15

    We determine basic thermodynamic and transport properties of hydrogen-helium-water mixtures for the extreme conditions along Jupiter's adiabat via ab initio simulations, which are compiled in an accurate and consistent data set. In particular, we calculate the electrical and thermal conductivity, the shear and longitudinal viscosity, and diffusion coefficients of the nuclei. We present results for associated quantities like the magnetic and thermal diffusivity and the kinematic shear viscosity along an adiabat that is taken from a state-of-the-art interior structure model. Furthermore, the heat capacities, the thermal expansion coefficient, the isothermal compressibility, the Grueneisen parameter, and the speed of sound are calculated. We find that the onset of dissociation and ionization of hydrogen at about 0.9 Jupiter radii marks a region where the material properties change drastically. In the deep interior, where the electrons are degenerate, many of the material properties remain relatively constant. Our ab initio data will serve as a robust foundation for applications that require accurate knowledge of the material properties in Jupiter's interior, e.g., models for the dynamo generation.

  14. Entropy of Liquid Water from Ab Initio Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Spanu, Leonardo; Zhang, Cui; Galli, Giulia

    2012-02-01

    The debate on the structural properties of water has been mostly based on the calculation of pair correlation functions. However, the simulation of thermodynamic and spectroscopic quantities may be of great relevance for the characterization of liquid water properties. We have computed the entropy of liquid water using a two-phase thermodynamic model and trajectories generated by ab initio molecular dynamics simulations [1]. In an attempt to better understand the performance of several density functionals in simulating liquid water, we have performed ab initio molecular dynamics using semilocal, hybrid [2] and van der Waals density functionals [3]. We show that in all cases, at the experimental equilibrium density and at temperatures in the vicinity of 300 K, the computed entropies are underestimated, with respect to experiment, and the liquid exhibits a degree of tetrahedral order higher than in experiments. We also discuss computational strategies to simulate spectroscopic properties of water, including infrared and Raman spectra.[4pt] [1] C.Zhang, L.Spanu and G.Galli, J.Phys.Chem. B 2011 (in press)[0pt] [2] C.Zhang, D.Donadio, F.Gygi and G.Galli, J. Chem. Theory Comput. 7, 1443 (2011)[0pt] [3] C.Zhang, J.Wu, G.Galli and F.Gygi, J. Chem. Theory Comput. 7, 3061 (2011)

  15. Unified ab initio approaches to nuclear structure and reactions

    NASA Astrophysics Data System (ADS)

    Navrátil, Petr; Quaglioni, Sofia; Hupin, Guillaume; Romero-Redondo, Carolina; Calci, Angelo

    2016-05-01

    The description of nuclei starting from the constituent nucleons and the realistic interactions among them has been a long-standing goal in nuclear physics. In addition to the complex nature of the nuclear forces, with two-, three- and possibly higher many-nucleon components, one faces the quantum-mechanical many-nucleon problem governed by an interplay between bound and continuum states. In recent years, significant progress has been made in ab initio nuclear structure and reaction calculations based on input from QCD-employing Hamiltonians constructed within chiral effective field theory. After a brief overview of the field, we focus on ab initio many-body approaches—built upon the no-core shell model—that are capable of simultaneously describing both bound and scattering nuclear states, and present results for resonances in light nuclei, reactions important for astrophysics and fusion research. In particular, we review recent calculations of resonances in the 6He halo nucleus, of five- and six-nucleon scattering, and an investigation of the role of chiral three-nucleon interactions in the structure of 9Be. Further, we discuss applications to the 7Be {({{p}},γ )}8{{B}} radiative capture. Finally, we highlight our efforts to describe transfer reactions including the 3H{({{d}},{{n}})}4He fusion.

  16. On the feasibility of ab initio electronic structure calculations for Cu using a single s orbital basis

    SciTech Connect

    Hegde, Ganesh Bowen, R. Chris

    2015-10-15

    The accuracy of a single s-orbital representation of Cu towards enabling multi-thousand atom ab initio calculations of electronic structure is evaluated in this work. If an electrostatic compensation charge of 0.3 electron per atom is used in this basis representation, the electronic transmission in bulk and nanocrystalline Cu can be made to compare accurately to that obtained with a Double Zeta Polarized basis set. The use of this representation is analogous to the use of single band effective mass representation for semiconductor electronic structure. With a basis of just one s-orbital per Cu atom, the representation is extremely computationally efficient and can be used to provide much needed ab initio insight into electronic transport in nanocrystalline Cu interconnects at realistic dimensions of several thousand atoms.

  17. Development of Novel Analytical Method for Ab Initio Powder Structural Analysis

    NASA Astrophysics Data System (ADS)

    Sakata, Makoto; Nishibori, Eiji; Sawa, Hiroshi

    Genetic Algorithm (GA) applied to ab initio structure determination from synchrotron powder diffraction is described. It seems to have an advantage over other real space methods for ab initio structure determination because of the existence of schema theorem. As an example, the case of Prednisolone Succinate is shown in some detail. Future development of GA in crystallography is briefly described.

  18. Ab initio study of nitrogen-multisubstituted neutral and positively charged C{sub 20} fullerene

    SciTech Connect

    Rani, Anita; Kumar, Ranjan

    2014-04-24

    Ab initio investigation of structural and electronic properties of Nitrogen doped fullerenes, obtained from C{sub 20} by replacing up to 10 C atoms with N atoms, are studied by means of first principals density functional theory calculations using numerical orbitals as basis sets. We have obtained the ground state structures for C{sub 20−n}N{sub n} for n=1-10. While substituting nitrogen atoms, we cannot substitute more than 9 nitrogen atoms. Nitrogen doping in C20 shows a significant change in density of states. For a better comparison with experimental measurements, we have also considered some positively charged ions and report the differences between properties of these ions and the corresponding neutral molecules.

  19. Ab initio study of beryllium-decorated fullerenes for hydrogen storage

    NASA Astrophysics Data System (ADS)

    Lee, Hoonkyung; Huang, Bing; Duan, Wenhui; Ihm, Jisoon

    2010-04-01

    We have found that a beryllium (Be) atom on nanostructured materials with H2 molecules generates a Kubas-like dihydrogen complex [Lee, Huang, Duan, and Ihm, Appl. Phys. Lett. 96, 143120 (2010)]. Here, we investigate the feasibility of Be-decorated fullerenes for hydrogen storage using ab initio calculations. We find that the aggregation of Be atoms on pristine fullerenes is energetically preferred, resulting in the dissociation of the dihydrogen. In contrast, for boron (B)-doped fullerenes, Be atoms prefer to be individually attached to B sites of the fullerenes, and a maximum of one H2 molecule binds to each Be atom in a form of dihydrogen with a binding energy of ˜0.3 eV. Our results show that individual dispersed Be-decorated B-doped fullerenes can serve as a room-temperature hydrogen storage medium.

  20. Site occupancy trend of Co in Ni2MnIn: Ab initio approach

    NASA Astrophysics Data System (ADS)

    Pal, Soumyadipta; Mahadevan, Priya; Biswas, C.

    2015-06-01

    The trend of site occupation of Co at Ni sites of Ni2MnIn system is studied in austenitic phase having L21 structure by ab initio density functional theory (DFT) calculation. The Co atoms prefer to be at Ni sites rather than Mn site and are ferromagetically coupled with Ni and Mn. The ground state has tetragonal structure for Ni1.5Co0.5MnIn and Ni1.25Co0.75MnIn. The Co tends to form cluster.

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

    NASA Astrophysics Data System (ADS)

    Eberhard, Bernd; Haider, Ferdinand

    2013-07-01

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

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

    PubMed

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

    2004-04-15

    An all-atom force field for 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) is presented. The classical intermolecular interaction potential for TATB is based on single-point energies determined from high-level ab initio calculations of TATB dimers. The newly developed potential function is used to examine bulk crystalline TATB via molecular dynamics simulations. The isobaric thermal expansion and isothermal compression under hydrostatic pressures obtained from the molecular dynamics simulations are in good agreement with experiment. The calculated volume-temperature expansion is almost one dimensional along the c crystallographic axis, whereas under compression, all three unit cell axes participate, albeit unequally. PMID:15267608

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

    SciTech Connect

    Minicozzi, V.; Rossi, G. C.; Stellato, F.; Morante, S.

    2007-12-26

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

  4. Improving Li2O2 conductivity via polaron preemption: An ab initio study of Si doping

    NASA Astrophysics Data System (ADS)

    Timoshevskii, Vladimir; Feng, Zimin; Bevan, Kirk H.; Goodenough, John; Zaghib, Karim

    2013-08-01

    We report on ab initio electronic structure simulations of Li2O2, where 1.6% of lithium atoms are substituted by silicon. It is demonstrated that this leads to the formation of conducting impurity states in the band gap of Li2O2. We show that these states originate from the antibonding orbitals of the oxygen pairs and are remarkably stable against possible polaron formation (upon electron injection). Through this polaron preemption mechanism, the proposed compound is expected to show significantly higher electronic mobility than stoichiometric Li2O2, which could have significant applications in lithium-air batteries.

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

    PubMed

    Rana, Malay Kumar; Chandra, Amalendu

    2013-05-28

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

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

    NASA Technical Reports Server (NTRS)

    Good, Brian S.

    2003-01-01

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

  7. Quantum calculations of the IR spectrum of liquid water using ab initio and model potential and dipole moment surfaces and comparison with experiment

    SciTech Connect

    Liu, Hanchao; Wang, Yimin; Bowman, Joel M.

    2015-05-21

    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{sub 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{sup −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.

  8. Quantum calculations of the IR spectrum of liquid water using ab initio and model potential and dipole moment surfaces and comparison with experiment

    NASA Astrophysics Data System (ADS)

    Liu, Hanchao; Wang, Yimin; Bowman, Joel M.

    2015-05-01

    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 H2O 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.

  9. Magnetic interactions in equi-atomic rare-earth intermetallic alloys RScGe (R = Ce, Pr, Nd and Gd) studied by time differential perturbed angular correlation spectroscopy and ab initio calculations

    NASA Astrophysics Data System (ADS)

    Mishra, S N

    2009-03-01

    Applying the time differential perturbed angular correlation (TDPAC) technique we have measured electric and magnetic hyperfine fields of the 111Cd impurity in equi-atomic rare-earth intermetallic alloys RScGe (R = Ce, Pr and Gd) showing antiferro- and ferromagnetism with unusually high ordering temperatures. The Cd nuclei occupying the Sc site show high magnetic hyperfine fields with saturation values Bhf(0) = 21 kG, 45 kG and 189 kG in CeScGe, PrScGe and GdScGe, respectively. By comparing the results with the hyperfine field data of Cd in rare-earth metals and estimations from the RKKY model, we find evidence for the presence of additional spin density at the probe nucleus, possibly due to spin polarization of Sc d band electrons. The principal electric field gradient component Vzz in CeScGe, PrScGe and GdScGe has been determined to be 5.3 × 1021 V m-2, 5.5 × 1021 V m-2 and 5.6 × 1021 V m-2, respectively. Supplementing the experimental measurements, we have carried out ab initio calculations for pure and Cd-doped RScGe compounds with R = Ce, Pr, Nd and Gd using the full potential linearized augmented plane wave (FLAPW) method based on density functional theory (DFT). From the total energies calculated with and without spin polarization we find ferrimagnetic ground states for CeScGe and PrScGe while NdScGe and GdScGe are ferromagnetic. In addition, we find a sizable magnetic moment at the Sc site, increasing from ≈0.10 μB in CeScGe to ≈0.3 μB in GdScGe, confirming the spin polarization of Sc d band electrons. The calculated electric field gradient and magnetic hyperfine fields of the Cd impurity closely agree with the experimental values. We believe spin polarization of Sc 3d band electrons, strongly hybridized with spin polarized 5d band electrons of the rare-earth, enables a long range Ruderman-Kittel-Kasuya-Yosida (RKKY) interaction between RE 4f moments which in turn leads to high magnetic ordering temperatures in RScGe compounds.

  10. Magnetic interactions in equi-atomic rare-earth intermetallic alloys RScGe (R = Ce, Pr, Nd and Gd) studied by time differential perturbed angular correlation spectroscopy and ab initio calculations.

    PubMed

    Mishra, S N

    2009-03-18

    Applying the time differential perturbed angular correlation (TDPAC) technique we have measured electric and magnetic hyperfine fields of the (111)Cd impurity in equi-atomic rare-earth intermetallic alloys RScGe (R = Ce, Pr and Gd) showing antiferro- and ferromagnetism with unusually high ordering temperatures. The Cd nuclei occupying the Sc site show high magnetic hyperfine fields with saturation values B(hf)(0) = 21 kG, 45 kG and 189 kG in CeScGe, PrScGe and GdScGe, respectively. By comparing the results with the hyperfine field data of Cd in rare-earth metals and estimations from the RKKY model, we find evidence for the presence of additional spin density at the probe nucleus, possibly due to spin polarization of Sc d band electrons. The principal electric field gradient component V(zz) in CeScGe, PrScGe and GdScGe has been determined to be 5.3 × 10(21) V m(-2), 5.5 × 10(21) V m(-2) and 5.6 × 10(21) V m(-2), respectively. Supplementing the experimental measurements, we have carried out ab initio calculations for pure and Cd-doped RScGe compounds with R = Ce, Pr, Nd and Gd using the full potential linearized augmented plane wave (FLAPW) method based on density functional theory (DFT). From the total energies calculated with and without spin polarization we find ferrimagnetic ground states for CeScGe and PrScGe while NdScGe and GdScGe are ferromagnetic. In addition, we find a sizable magnetic moment at the Sc site, increasing from ≈0.10 μ(B) in CeScGe to ≈0.3 μ(B) in GdScGe, confirming the spin polarization of Sc d band electrons. The calculated electric field gradient and magnetic hyperfine fields of the Cd impurity closely agree with the experimental values. We believe spin polarization of Sc 3d band electrons, strongly hybridized with spin polarized 5d band electrons of the rare-earth, enables a long range Ruderman-Kittel-Kasuya-Yosida (RKKY) interaction between RE 4f moments which in turn leads to high magnetic ordering temperatures in

  11. A general method for constructing multidimensional molecular potential energy surfaces from {ital ab} {ital initio} calculations

    SciTech Connect

    Ho, T.; Rabitz, H.

    1996-02-01

    A general interpolation method for constructing smooth molecular potential energy surfaces (PES{close_quote}s) from {ital ab} {ital initio} data are proposed within the framework of the reproducing kernel Hilbert space and the inverse problem theory. The general expression for an {ital a} {ital posteriori} error bound of the constructed PES is derived. It is shown that the method yields globally smooth potential energy surfaces that are continuous and possess derivatives up to second order or higher. Moreover, the method is amenable to correct symmetry properties and asymptotic behavior of the molecular system. Finally, the method is generic and can be easily extended from low dimensional problems involving two and three atoms to high dimensional problems involving four or more atoms. Basic properties of the method are illustrated by the construction of a one-dimensional potential energy curve of the He{endash}He van der Waals dimer using the exact quantum Monte Carlo calculations of Anderson {ital et} {ital al}. [J. Chem. Phys. {bold 99}, 345 (1993)], a two-dimensional potential energy surface of the HeCO van der Waals molecule using recent {ital ab} {ital initio} calculations by Tao {ital et} {ital al}. [J. Chem. Phys. {bold 101}, 8680 (1994)], and a three-dimensional potential energy surface of the H{sup +}{sub 3} molecular ion using highly accurate {ital ab} {ital initio} calculations of R{umlt o}hse {ital et} {ital al}. [J. Chem. Phys. {bold 101}, 2231 (1994)]. In the first two cases the constructed potentials clearly exhibit the correct asymptotic forms, while in the last case the constructed potential energy surface is in excellent agreement with that constructed by R{umlt o}hse {ital et} {ital al}. using a low order polynomial fitting procedure. {copyright} {ital 1996 American Institute of Physics.}

  12. The ab-initio density matrix renormalization group in practice

    SciTech Connect

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

    2015-01-21

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

  13. Ab Initio Calculations of Excited Carrier Dynamics in Gallium Nitride

    NASA Astrophysics Data System (ADS)

    Jhalani, Vatsal; Bernardi, Marco

    Bulk wurtzite GaN is the primary material for blue light-emission technology. The radiative processes in GaN are regulated by the dynamics of excited (or so-called ``hot'') carriers, through microscopic processes not yet completely understood. We present ab initio calculations of electron-phonon (e-ph) scattering rates for hot carriers in GaN. Our work combines density functional theory to compute the electronic states, and density functional perturbation theory to obtain the phonon dispersions and e-ph coupling matrix elements. These quantities are interpolated on fine Brillouin zone grids with maximally localized Wannier functions, to converge the e-ph scattering rates within 5 eV of the band edges. We resolve the contribution of the different phonon modes to the total scattering rate, and study the impact on the relaxation times of the long-range Fröhlich interaction due to the longitudinal-optical phonon modes.

  14. Highly anisotropic thermal conductivity of arsenene: An ab initio study

    NASA Astrophysics Data System (ADS)

    Zeraati, Majid; Vaez Allaei, S. Mehdi; Abdolhosseini Sarsari, I.; Pourfath, Mahdi; Donadio, Davide

    2016-02-01

    Elemental two-dimensional (2D) materials exhibit intriguing heat transport and phononic properties. Here we have investigated the lattice thermal conductivity of newly proposed arsenene, the 2D honeycomb structure of arsenic, using ab initio calculations. Solving the Boltzmann transport equation for phonons, we predict a highly anisotropic thermal conductivity of 30.4 and 7.8 W/mK along the zigzag and armchair directions, respectively, at room temperature. Our calculations reveal that phonons with mean free paths between 20 nm and 1 μ m provide the main contribution to the large thermal conductivity in the zigzag direction; mean free paths of phonons contributing to heat transport in the armchair directions range between 20 and 100 nm. The obtained anisotropic thermal conductivity and feasibility of synthesis, in addition to high electron mobility reported elsewhere, make arsenene a promising material for nanoelectronic applications and thermal management.

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

    PubMed

    Olsson, P; Vidal, J; Lincot, D

    2011-10-12

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

  16. Ab initio study of guanine damage by hydroxyl radical.

    PubMed

    Chaban, Galina M; Wang, Dunyou; Huo, Winifred M

    2015-01-15

    Multiconfigurational ab initio methods are used in this study to examine two initial reactions that take place during the OH radical attack of the DNA base guanine: a ring opening reaction and a hydrogen transfer reaction. The same reactions are also studied in the presence of a single water molecule. The ring opening reaction has a moderate barrier height of ∼20-25 kcal/mol that is relatively insensitive to the presence of water. The barrier of the H-transfer reaction, on the other hand, is lowered from ∼50 to ∼22 kcal/mol when one water molecule is added, thus becoming comparable to the barrier height of the ring opening reaction. PMID:25517252

  17. Vibrational and ab initio molecular dynamics studies of bradykinin

    NASA Astrophysics Data System (ADS)

    Święch, Dominika; Kubisiak, Piotr; Andrzejak, Marcin; Borowski, Piotr; Proniewicz, Edyta

    2016-07-01

    In this study, the comprehensive theoretical and experimental investigations of Raman (RS) and infrared absorption (IR) spectra of bradykinin (BK) are presented. The ab initio Born-Oppenheimer molecular dynamics (BOMD) calculations, in the presence of water molecules that form the first coordination sphere, were used for conformational analysis of the BK structure. Based on the Density Functional Theory (DFT) calculations at the B3LYP/6-311G(d) level the vibrational spectra were interpreted. The calculated frequencies were scaled by means of the effective scaling frequency factor (ESFF) method. The theoretical data, which confirm the compact structure of BK in the presence of the water molecules revealed the remarkable effect of the intermolecular hydrogen bonding on the BK structural properties.

  18. Ab initio water pair potential with flexible monomers.

    PubMed

    Jankowski, Piotr; Murdachaew, Garold; Bukowski, Robert; Akin-Ojo, Omololu; Leforestier, Claude; Szalewicz, Krzysztof

    2015-03-26

    A potential energy surface for the water dimer with explicit dependence on monomer coordinates is presented. The surface was fitted to a set of previously published interaction energies computed on a grid of over a quarter million points in the 12-dimensional configurational space using symmetry-adapted perturbation theory and coupled-cluster methods. The present fit removes small errors in published fits, and its accuracy is critically evaluated. The minimum and saddle-point structures of the potential surface were found to be very close to predictions from direct ab initio optimizations. The computed second virial coefficients agreed well with experimental values. At low temperatures, the effects of monomer flexibility in the virial coefficients were found to be much smaller than the quantum effects. PMID:25687650

  19. Efficient Ab initio Modeling of Random Multicomponent Alloys

    NASA Astrophysics Data System (ADS)

    Jiang, Chao; Uberuaga, Blas P.

    2016-03-01

    We present in this Letter a novel small set of ordered structures (SSOS) method that allows extremely efficient ab initio modeling of random multicomponent alloys. Using inverse II-III spinel oxides and equiatomic quinary bcc (so-called high entropy) alloys as examples, we demonstrate that a SSOS can achieve the same accuracy as a large supercell or a well-converged cluster expansion, but with significantly reduced computational cost. In particular, because of this efficiency, a large number of quinary alloy compositions can be quickly screened, leading to the identification of several new possible high-entropy alloy chemistries. The SSOS method developed here can be broadly useful for the rapid computational design of multicomponent materials, especially those with a large number of alloying elements, a challenging problem for other approaches.

  20. Ab initio H2O in realistic hydrophilic confinement.

    PubMed

    Allolio, Christoph; Klameth, Felix; Vogel, Michael; Sebastiani, Daniel

    2014-12-15

    A protocol for the ab initio construction of a realistic cylindrical pore in amorphous silica, serving as a geometric nanoscale confinement for liquids and solutions, is presented. Upon filling the pore with liquid water at different densities, the structure and dynamics of the liquid inside the confinement can be characterized. At high density, the pore introduces long-range oscillations into the water density profile, which makes the water structure unlike that of the bulk across the entire pore. The tetrahedral structure of water is also affected up to the second solvation shell of the pore wall. Furthermore, the effects of the confinement on hydrogen bonding and diffusion, resulting in a weakening and distortion of the water structure at the pore walls and a slowdown in diffusion, are characterized. PMID:25208765

  1. High-throughput ab-initio dilute solute diffusion database

    PubMed Central

    Wu, Henry; Mayeshiba, Tam; Morgan, Dane

    2016-01-01

    We demonstrate automated generation of diffusion databases from high-throughput density functional theory (DFT) calculations. A total of more than 230 dilute solute diffusion systems in Mg, Al, Cu, Ni, Pd, and Pt host lattices have been determined using multi-frequency diffusion models. We apply a correction method for solute diffusion in alloys using experimental and simulated values of host self-diffusivity. We find good agreement with experimental solute diffusion data, obtaining a weighted activation barrier RMS error of 0.176 eV when excluding magnetic solutes in non-magnetic alloys. The compiled database is the largest collection of consistently calculated ab-initio solute diffusion data in the world. PMID:27434308

  2. Ab initio calculation of the shock Hugoniot of bulk silicon

    NASA Astrophysics Data System (ADS)

    Strickson, Oliver; Artacho, Emilio

    2016-03-01

    We describe how ab initio molecular dynamics can be used to determine the Hugoniot locus (states accessible by a shock wave) for materials with a number of stable phases, and with an approximate treatment of plasticity and yield, without having to simulate these phenomena directly. We consider the case of bulk silicon, with forces from density-functional theory, up to 70 GPa. The fact that shock waves can split into multiple waves due to phase transitions or yielding is taken into account here by specifying the strength of any preceding waves explicitly based on their yield strain. Points corresponding to uniaxial elastic compression along three crystal axes and a number of postshock phases are given, including a plastically yielded state, approximated by an isotropic stress configuration following an elastic wave of predetermined strength. The results compare well to existing experimental data for shocked silicon.

  3. Interatomic Coulombic decay widths of helium trimer: Ab initio calculations

    SciTech Connect

    Kolorenč, Přemysl; Sisourat, Nicolas

    2015-12-14

    We report on an extensive study of interatomic Coulombic decay (ICD) widths in helium trimer computed using a fully ab initio method based on the Fano theory of resonances. Algebraic diagrammatic construction for one-particle Green’s function is utilized for the solution of the many-electron problem. An advanced and universal approach to partitioning of the configuration space into discrete states and continuum subspaces is described and employed. Total decay widths are presented for all ICD-active states of the trimer characterized by one-site ionization and additional excitation of an electron into the second shell. Selected partial decay widths are analyzed in detail, showing how three-body effects can qualitatively change the character of certain relaxation transitions. Previously unreported type of three-electron decay processes is identified in one class of the metastable states.

  4. Interatomic Coulombic decay widths of helium trimer: Ab initio calculations.

    PubMed

    Kolorenč, Přemysl; Sisourat, Nicolas

    2015-12-14

    We report on an extensive study of interatomic Coulombic decay (ICD) widths in helium trimer computed using a fully ab initio method based on the Fano theory of resonances. Algebraic diagrammatic construction for one-particle Green's function is utilized for the solution of the many-electron problem. An advanced and universal approach to partitioning of the configuration space into discrete states and continuum subspaces is described and employed. Total decay widths are presented for all ICD-active states of the trimer characterized by one-site ionization and additional excitation of an electron into the second shell. Selected partial decay widths are analyzed in detail, showing how three-body effects can qualitatively change the character of certain relaxation transitions. Previously unreported type of three-electron decay processes is identified in one class of the metastable states. PMID:26671378

  5. Ab initio calculation of thermodynamic properties of silicon

    NASA Astrophysics Data System (ADS)

    Wei, Siqing; Li, Changlin; Chou, M. Y.

    1994-11-01

    We present a fully ab initio calculation of the thermodynamic properties for silicon within the quasiharmonic approximation, making use of volume-dependent phonon frequencies obtained from pseudopotential local-density calculations. The temperature dependence of the thermal-expansion coefficient, specific heat (at constant volume), and other related quantities are studied. We confirm that the thermal-expansion coefficient behaves differently in three temperature regions: positive for temperature below 15 K, negative between 15 and 125 K, and positive again above 125 K. This finding agrees with experiment. The abnormal (negative) thermal-expansion coefficient at low temperatures is explained through a detailed study of mode Grüneisen parameters. Both specific-heat and thermal-expansion-coefficient values calculated are in excellent agreement with experiment up to a few hundred kelvin.

  6. XMVB: a program for ab initio nonorthogonal valence bond computations.

    PubMed

    Song, Lingchun; Mo, Yirong; Zhang, Qianer; Wu, Wei

    2005-04-15

    An ab initio nonorthogonal valence bond program, called XMVB, is described in this article. The XMVB package uses Heitler-London-Slater-Pauling (HLSP) functions as state functions, and calculations can be performed with either all independent state functions for a molecule or preferably a few selected important state functions. Both our proposed paired-permanent-determinant approach and conventional Slater determinant expansion algorithm are implemented for the evaluation of the Hamiltonian and overlap matrix elements among VB functions. XMVB contains the capabilities of valence bond self-consistent field (VBSCF), breathing orbital valence bond (BOVB), and valence bond configuration interaction (VBCI) computations. The VB orbitals, used to construct VB functions, can be defined flexibly in the calculations depending on particular applications and focused problems, and they may be strictly localized, delocalized, or bonded-distorted (semidelocalized). The parallel version of XMVB based on MPI (Message Passing Interface) is also available. PMID:15704237

  7. Ab initio theory of NMR chemical shifts in solids

    SciTech Connect

    Louie, S.G. |

    1997-12-31

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

  8. Ab initio Potential Energy Surface for H-H2

    NASA Technical Reports Server (NTRS)

    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.

  9. Transport coefficients in diamond from ab-initio calculations

    NASA Astrophysics Data System (ADS)

    Löfâs, Henrik; Grigoriev, Anton; Isberg, Jan; Ahuja, Rajeev

    2013-03-01

    By combining the Boltzmann transport equation with ab-initio electronic structure calculations, we obtain transport coefficients for boron-doped diamond. We find the temperature dependence of the resistivity and the hall coefficients in good agreement with experimental measurements. Doping in the samples is treated via the rigid band approximation and scattering is treated in the relaxation time approximation. In contrast to previous results, the acoustic phonon scattering is the dominating scattering mechanism for the considered doping range. At room temperature, we find the thermopower, S, in the range 1-1.6 mV/K and the power factor, S2σ, in the range 0.004-0.16 μW /cm K2.

  10. Ab initio potential energy surface and rovibrational states of HBO

    NASA Astrophysics Data System (ADS)

    Ha, Tae-Kyu; Makarewicz, Jan

    1999-01-01

    The potential energy surface describing the large-amplitude motion of H around the BO core in the HBO molecule has been determined from ab initio calculations. This surface has been sampled by a set of 170 grid points from a two-dimensional space defined by the stretching and the bending coordinates of the H nucleus. At each grid point, the BO bond length has been optimized using the second-order Møller-Plesset perturbation theory with the basis set aug-cc-pVTZ. The surface has a local minimum for the linear as well as the bent configuration of HBO. A low energy barrier to the linear configuration BOH causes a large-amplitude motion and a strong rovibrational interaction in the molecule. Its rovibrational dynamics is different from the dynamics in bent or quasilinear triatomic molecules.

  11. Ab initio electronic stopping power of protons in bulk materials

    NASA Astrophysics Data System (ADS)

    Shukri, Abdullah Atef; Bruneval, Fabien; Reining, Lucia

    2016-01-01

    The electronic stopping power is a crucial quantity for ion irradiation: it governs the deposited heat, the damage profile, and the implantation depth. Whereas experimental data are readily available for elemental solids, the data are much more scarce for compounds. Here we develop a fully ab initio computational scheme based on linear response time-dependent density-functional theory to predict the random electronic stopping power (RESP) of materials without any empirical fitting. We show that the calculated RESP compares well with experimental data, when at full convergence, with the inclusion of the core states and of the exchange correlation. We evaluate the unexpectedly limited magnitude of the nonlinear terms in the RESP by comparing with other approaches based on the time propagation of time-dependent density-functional theory. Finally, we check the validity of a few empirical rules of thumbs that are commonly used to estimate the electronic stopping power.

  12. Isofulminic acid, HONC: Ab initio theory and microwave spectroscopy.

    PubMed

    Mladenović, Mirjana; Lewerenz, Marius; McCarthy, Michael C; Thaddeus, Patrick

    2009-11-01

    Isofulminic acid, HONC, the most energetic stable isomer of isocyanic acid HNCO, higher in energy by 84 kcal/mol, has been detected spectroscopically by rotational spectroscopy supported by coupled cluster electronic structure calculations. The fundamental rotational transitions of the normal, carbon-13, oxygen-18, and deuterium isotopic species have been detected in the centimeter band in a molecular beam by Fourier transform microwave spectroscopy, and rotational constants and nitrogen and deuterium quadrupole coupling constants have been derived. The measured constants agree well with those predicted by ab initio calculations. A number of other electronic and spectroscopic parameters of isofulminic acid, including the dipole moment, vibrational frequencies, infrared intensities, and centrifugal distortion constants have been calculated at a high level of theory. Isofulminic acid is a good candidate for astronomical detection with radio telescopes because it is highly polar and its more stable isomers (HNCO, HOCN, and HCNO) have all been identified in space. PMID:19895013

  13. Ab initio study of helium behavior in titanium tritides

    SciTech Connect

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

    2013-03-01

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

  14. High-throughput ab-initio dilute solute diffusion database.

    PubMed

    Wu, Henry; Mayeshiba, Tam; Morgan, Dane

    2016-01-01

    We demonstrate automated generation of diffusion databases from high-throughput density functional theory (DFT) calculations. A total of more than 230 dilute solute diffusion systems in Mg, Al, Cu, Ni, Pd, and Pt host lattices have been determined using multi-frequency diffusion models. We apply a correction method for solute diffusion in alloys using experimental and simulated values of host self-diffusivity. We find good agreement with experimental solute diffusion data, obtaining a weighted activation barrier RMS error of 0.176 eV when excluding magnetic solutes in non-magnetic alloys. The compiled database is the largest collection of consistently calculated ab-initio solute diffusion data in the world. PMID:27434308

  15. Ab initio quantum dynamics using coupled-cluster.

    PubMed

    Kvaal, Simen

    2012-05-21

    The curse of dimensionality (COD) limits the current state-of-the-art ab initio propagation methods for non-relativistic quantum mechanics to relatively few particles. For stationary structure calculations, the coupled-cluster (CC) method overcomes the COD in the sense that the method scales polynomially with the number of particles while still being size-consistent and extensive. We generalize the CC method to the time domain while allowing the single-particle functions to vary in an adaptive fashion as well, thereby creating a highly flexible, polynomially scaling approximation to the time-dependent Schrödinger equation. The method inherits size-consistency and extensivity from the CC method. The method is dubbed orbital-adaptive time-dependent coupled-cluster, and is a hierarchy of approximations to the now standard multi-configurational time-dependent Hartree method for fermions. A numerical experiment is also given. PMID:22612082

  16. Efficient Ab initio Modeling of Random Multicomponent Alloys.

    PubMed

    Jiang, Chao; Uberuaga, Blas P

    2016-03-11

    We present in this Letter a novel small set of ordered structures (SSOS) method that allows extremely efficient ab initio modeling of random multicomponent alloys. Using inverse II-III spinel oxides and equiatomic quinary bcc (so-called high entropy) alloys as examples, we demonstrate that a SSOS can achieve the same accuracy as a large supercell or a well-converged cluster expansion, but with significantly reduced computational cost. In particular, because of this efficiency, a large number of quinary alloy compositions can be quickly screened, leading to the identification of several new possible high-entropy alloy chemistries. The SSOS method developed here can be broadly useful for the rapid computational design of multicomponent materials, especially those with a large number of alloying elements, a challenging problem for other approaches. PMID:27015491

  17. Ab Initio Screening of CO2-philic Groups.

    PubMed

    Tian, Ziqi; Saito, Tomonori; Jiang, De-En

    2015-04-23

    Ab initio calculations were used to identify CO2-philic groups. Over 55 neutral molecules were screened for CO2 affinity via binding energetics. It is found that poly(ethylene oxide)s (PEO) oligomers with more than three repeating units are good CO2-binding groups, consistent with the high-performance of PEO-based materials for CO2/N2 separation. More interestingly, two triazole groups linked with a methylene chain are also excellent for CO2 binding with a favorable interaction of more than 28 kJ/mol, indicating that polymers or covalent-organic frameworks (COFs) with triazoles may be utilized for CO2 capture. This work provides a useful guide to introduce promising organic groups into polymeric membranes and COFs for CO2/N2 separation media. PMID:25825811

  18. Ab initio methods for nuclear properties - a computational physics approach

    NASA Astrophysics Data System (ADS)

    Maris, Pieter

    2011-04-01

    A microscopic theory for the structure and reactions of light nuclei poses formidable challenges for high-performance computing. Several ab-initio methods have now emerged that provide nearly exact solutions for some nuclear properties. The ab-initio no-core full configuration (NCFC) approach is based on basis space expansion methods and uses Slater determinants of single-nucleon basis functions to express the nuclear wave function. In this approach, the quantum many-particle problem becomes a large sparse matrix eigenvalue problem. The eigenvalues of this matrix give us the binding energies, and the corresponding eigenvectors the nuclear wave functions. These wave functions can be employed to evaluate experimental quantities. In order to reach numerical convergence for fundamental problems of interest, the matrix dimension often exceeds 1 billion, and the number of nonzero matrix elements may saturate available storage on present-day leadership class facilities. I discuss different strategies for distributing and solving this large sparse matrix on current multicore computer architectures, including methods to deal with with memory bottleneck. Several of these strategies have been implemented in the code MFDn, which is a parallel fortran code for nuclear structure calculations. I will show scaling behavior and compare the performance of the pure MPI version with the hybrid MPI/OpenMP code on Cray XT4 and XT5 platforms. For large core counts (typically 5,000 and above), the hybrid version is more efficient than pure MPI. With this code, we have been able to predict properties of the unstable nucleus 14F, which have since been confirmed by experiments. I will also give an overview of other recent results for nuclei in the A = 6 to 16 range with 2- and 3-body interactions. Supported in part by US DOE Grant DE-FC02-09ER41582.

  19. Threshold displacement energy in GaN; Ab initio molecular dynamics study

    SciTech Connect

    Xiao, H. Y.; Gao, Fei; Zu, Xiaotao T.; Weber, William J.

    2009-06-25

    Large-scale ab initio molecular dynamics method has been used to determine the threshold displacement energies, Ed, along five specific directions and to determine the defect configurations created during low energy events. The Ed shows a significant dependence on direction. The minimum Ed is determined to be 39 eV along the <-1010> direction for a gallium atom and 17.0 eV along the <-1010> direction for a nitrogen atom, which are in reasonable agreement with the experimental measurements. The average Ed values determined are 73.2 and 32.4 eV for gallium and nitrogen atoms, respectively. The N defects created at low energy events along different crystallographic directions have a similar configuration (a N-N dumbbell configuration), but various configurations for Ga defects are formed in GaN.

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

    NASA Astrophysics Data System (ADS)

    Zheng, Haoping

    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 precise calculations. Thus the ab initio, all-electron calculation of the electronic structure and biological function of protein molecule has become 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), will be presented in this paper. The reactive sites of the inhibitors are determined and explained. The accuracy of structure determination of the inhibitors are tested theoretically.

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

    NASA Astrophysics Data System (ADS)

    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.

  2. Ab initio study of He point defects in fcc Au-Ag alloys

    SciTech Connect

    Zhu, Zi Qiang; Yang, Li; Nie, JL; Peng, SM; Long, XG; Zhou, X. S.; Zu, Xiaotao; Gao, Fei

    2013-04-25

    The relative stabilities of He defects in two fcc Au-Ag alloys (Au3Ag2 and AuAg) are investigated using ab initio method based on density functional theory. The results show that the stabilities of He defects in the two alloys mainly depend on the atomic arrangements of the nearest neighboring host metals. A He interstitial prefers to stay at a site with more Ag neighboring atoms, while the favorable substitutional site has more Au neighboring atoms in Au-Ag alloys. Moreover, the substitutional He defects are the most stable configurations in both the alloys, and the octahedral He interstitials are energetically more favorable than the tetrahedral interstitials. It is of interest to note that the properties of He defects slightly depend on the mass-density of Au-Ag alloys. The results also demonstrate that the relative stabilities of He defects are primarily attributed to the hybridization between metals d states and He p states.

  3. Boron and nitrogen impurities in SiC nanoribbons: an ab initio investigation

    NASA Astrophysics Data System (ADS)

    Costa, C. D.; Morbec, J. M.

    2011-05-01

    Using ab initio calculations based on density-functional theory we have performed a theoretical investigation of substitutional boron and nitrogen impurities in silicon carbide (SiC) nanoribbons. We have considered hydrogen terminated SiC ribbons with zigzag and armchair edges. In both systems we verify that the boron and nitrogen atoms energetically prefer to be localized at the edges of the nanoribbons. However, while boron preferentially substitutes a silicon atom, nitrogen prefers to occupy a carbon site. In addition, our electronic-structure calculations indicate that (i) substitutional boron and nitrogen impurities do not affect the semiconducting character of the armchair SiC nanoribbons, and (ii) the half-metallic behavior of the zigzag nanoribbons is maintained in the presence of substitutional boron impurities. In contrast, nitrogen atoms occupying edge carbon sites transform half-metallic zigzag nanoribbons into metallic systems.

  4. Boron and nitrogen impurities in SiC nanoribbons: an ab initio investigation.

    PubMed

    Costa, C D; Morbec, J M

    2011-05-25

    Using ab initio calculations based on density-functional theory we have performed a theoretical investigation of substitutional boron and nitrogen impurities in silicon carbide (SiC) nanoribbons. We have considered hydrogen terminated SiC ribbons with zigzag and armchair edges. In both systems we verify that the boron and nitrogen atoms energetically prefer to be localized at the edges of the nanoribbons. However, while boron preferentially substitutes a silicon atom, nitrogen prefers to occupy a carbon site. In addition, our electronic-structure calculations indicate that (i) substitutional boron and nitrogen impurities do not affect the semiconducting character of the armchair SiC nanoribbons, and (ii) the half-metallic behavior of the zigzag nanoribbons is maintained in the presence of substitutional boron impurities. In contrast, nitrogen atoms occupying edge carbon sites transform half-metallic zigzag nanoribbons into metallic systems. PMID:21540516

  5. Ab initio molecular dynamic study of solid-state transitions of ammonium nitrate

    NASA Astrophysics Data System (ADS)

    Yu, Hongyu; Duan, Defang; Liu, Hanyu; Yang, Ting; Tian, Fubo; Bao, Kuo; Li, Da; Zhao, Zhonglong; Liu, Bingbing; Cui, Tian

    2016-01-01

    High-pressure polymorphism and phase transitions have wide ranging consequences on the basic properties of ammonium nitrate. However, the phase diagram of ammonium nitrate at high pressure and high temperature is still under debate. This study systematically investigates the phase transitions and structural properties of ammonium nitrate at a pressure range of 5-60 GPa and temperature range of 250-400 K by ab initio molecular dynamics simulations. Two new phases are identified: one corresponds to the experimentally observed phase IV’ and the other is named AN-X. Simultaneously, the lattice strains play a significant role in the formation and stabilization of phase IV’, providing a reasonable explanation for experimental observation of phase IV-IV’ transition which only appears under nonhydrostatic pressure. In addition, 12 O atoms neighboring the NH (N atom in ammonium cation) atom are selected as reference system to clearly display the tanglesome rotation of ammonium cation.

  6. Ab initio molecular dynamic study of solid-state transitions of ammonium nitrate

    PubMed Central

    Yu, Hongyu; Duan, Defang; Liu, Hanyu; Yang, Ting; Tian, Fubo; Bao, Kuo; Li, Da; Zhao, Zhonglong; Liu, Bingbing; Cui, Tian

    2016-01-01

    High-pressure polymorphism and phase transitions have wide ranging consequences on the basic properties of ammonium nitrate. However, the phase diagram of ammonium nitrate at high pressure and high temperature is still under debate. This study systematically investigates the phase transitions and structural properties of ammonium nitrate at a pressure range of 5–60 GPa and temperature range of 250–400 K by ab initio molecular dynamics simulations. Two new phases are identified: one corresponds to the experimentally observed phase IV’ and the other is named AN-X. Simultaneously, the lattice strains play a significant role in the formation and stabilization of phase IV’, providing a reasonable explanation for experimental observation of phase IV-IV’ transition which only appears under nonhydrostatic pressure. In addition, 12 O atoms neighboring the NH (N atom in ammonium cation) atom are selected as reference system to clearly display the tanglesome rotation of ammonium cation. PMID:26754622

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

    NASA Technical Reports Server (NTRS)

    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.

  8. Recent progress with large-scale ab initio calculations: the CONQUEST code

    NASA Astrophysics Data System (ADS)

    Bowler, D. R.; Choudhury, R.; Gillan, M. J.; Miyazaki, T.

    While the success of density functional theory (DFT) has led to its use in a wide variety of fields such as physics, chemistry, materials science and biochemistry, it has long been recognised that conventional methods are very inefficient for large complex systems, because the memory requirements scale as N 2 and the cpu requirements as N 3 (where N is the number of atoms). The principles necessary to develop methods with linear scaling of the cpu and memory requirements with system size (O(N ) methods) have been established for more than ten years, but only recently have practical codes showing this scaling for DFT started to appear. We report recent progress in the development of the Conquest code, which performs O(N ) DFT calculations on parallel computers, and has a demonstrated ability to handle systems of over 10000 atoms. The code can be run at different levels of precision, ranging from empirical tight-binding, through ab initio tight-binding, to full ab initio , and techniques for calculating ionic forces in a consistent way at all levels of precision will be presented. Illustrations are given of practical Conquest calculations in the strained Ge/Si(001) system.

  9. Experimental and ab initio infrared study of chi-, kappa- and alpha-aluminas formed from gibbsite

    SciTech Connect

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

    2010-04-15

    chi-, kappa- and alpha-alumina phases formed by dehydration of micro-grained gibbsite between 773 and 1573 K are studied using infrared spectroscopy (IR). The structural transitions evidenced by X-ray diffraction (XRD) were interpreted by comparing IR measurements with ab initio simulations (except for the chi form whose complexity does not allow a reliable simulation). For each phase, IR spectrum presents specific bands corresponding to transverse optical (TO) modes of Al-O stretching and bending under 900 cm{sup -1}. The very complex chi phase, obtained at 773 K, provides a distinctive XRD pattern in contrast with the IR absorbance appearing as a broad structure extending between 200 and 900 cm{sup -1} resembling the equivalent spectra for gamma-alumina phase. kappa-alumina is forming at 1173 K and its rich IR spectrum is in good qualitative agreement with ab initio simulations. This complexity reflects the large number of atoms in the kappa-alumina unit cell and the wide range of internuclear distances as well as the various coordinances of both Al and O atoms. Ab initio simulations suggest that this form of transition alumina demonstrates a strong departure from the simple pattern observed for other transition alumina. At 1573 K, the stable alpha-ALPHAl{sub 2}OMICRON{sub 3} develops. Its IR spectra extends in a narrower energy range as compared to transition alumina and presents characteristics features similar to model alpha-ALPHAl{sub 2}OMICRON{sub 3}. Ab initio calculations show again a very good general agreement with the observed IR spectra for this phase. In addition, for both kappa- and alpha-ALPHAl{sub 2}OMICRON{sub 3}, extra modes, measured at high energy (above 790 cm{sup -1} for kappa and above 650 cm{sup -1} for alpha), can originate from either remnant chi-alumina or from surface modes. - Graphical abstract: Infrared spectra of the sequence Gibbsite ->chi->kappa->alpha-Al{sub 2}O{sub 3} obtained from 24 h calcinations of Gibbsite at 773 K, 1173 K

  10. Operator evolution for ab initio theory of light nuclei

    NASA Astrophysics Data System (ADS)

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

    2014-09-01

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

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

    NASA Technical Reports Server (NTRS)

    Good, Brian S.

    2004-01-01

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

  12. Ab initio calculation and anharmonic force field of hypochlorous acid, HOCl

    NASA Astrophysics Data System (ADS)

    Halonen, L.; Ha, T.-K.

    1988-03-01

    Ab initio calculations on HOCl have been performed at the third-order Møller-Plesset perturbation theory level to determine the equilibrium structure and the anharmonic force field. An empirical anharmonic force field based on the ab initio results is obtained using available experimental vibration-rotation data. Four of the six harmonic and six of the ten cubic force constants have been determined experimentally, the remaining values being fixed at the ab initio values. A good fit to the experimental vibration-rotation data of four isotopic species is obtained.

  13. Ab initio Ti-Zr-Ni phase diagram predicts stability of icosahedral TiZrNi quasicrystals

    NASA Astrophysics Data System (ADS)

    Hennig, R. G.; Carlsson, A. E.; Kelton, K. F.; Henley, C. L.

    2005-04-01

    The ab initio phase diagram determines the energetic stability of the icosahedral TiZrNi quasicrystal. The complete ab initio zero-temperature ternary phase diagram is constructed from the calculated energies of the elemental, binary and ternary Ti-Zr-Ni phases. For this, the icosahedral i -TiZrNi quasicrystal is approximated by periodic structures of up to 123 atoms/unit cell, based on a decorated-tiling model [R. G. Hennig, K. F. Kelton, A. E. Carlsson, and C. L. Henley, Phys. Rev. B 67, 134202 (2003)]. The approximant structures containing the 45-atom Bergman cluster are nearly degenerate in energy, and are all energetically stable against the competing phases. It is concluded that i -TiZrNi is a ground-state quasicrystal, as it is experimentally the low-temperature phase for its composition.

  14. Ab-initio study of pressure effects and hydrogen impurity in HgO

    NASA Astrophysics Data System (ADS)

    Choi, Minseok; Park, Chul-Hong

    2016-06-01

    Through ab-initio pseudopotential calculations, we investigated the deformation potential of HgO semiconductors and the structural stabilities of various crystal structures under pressure. We also investigated the microscopic structure of the hydrogen (H) impurity in HgO. Especially the state of hydrogen atoms captured by an acceptor-like Hg-vacancy (V Hg ) is focused on. The location of H is found to be very different from the original Hg-site, forming a strong H-O bond. The capture two H atoms by V Hg is found to be energetically favorable: the binding energy for one H and the second H are 1.01 eV and 0.07 eV, respectively.

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

    NASA Astrophysics Data System (ADS)

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

    2013-03-01

    The structure of liquid Pb on an ideal Si(001) surface was studied experimentally a decade ago by means of x-ray diffraction and the results were interpreted in terms of the presence of fivefold symmetry Pb structures captured transiently by the potential created by the unreconstructed Si(001) surface. We critically analyze this interpretation in the light of the results obtained in an extensive ab initio molecular dynamics study of a system comprising 314 Pb atoms and 175 Si atoms setup in 7 (001) ideal layers (a total number of 1956 valence electrons) in a slab geometry. The structure found for the first Pb layer is very different from that of bulk Pb, mostly consisting in one-dimensional lines. However, we do observe the possibility of forming transient structures, in particular icosahedral caps. Supported by FIS2008-02490/FIS, FIS2008-04894/FIS, GR120, INCITE09E2R206033ES and INCITE08PXIB206107PR.

  16. Decarboxylation of furfural on Pd(111): Ab initio molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

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

    2013-03-01

    Furfural conversion over metal catalysts plays an important role in the studies of biomass-derived feedstocks. We report ab initio molecular dynamics simulations for the decarboxylation process of furfural on the palladium surface at finite temperatures. We observed and analyzed the atomic-scale dynamics of furfural on the Pd(111) surface and the fluctuations of the bondlengths between the atoms in furfural. We found that the dominant bonding structure is the parallel structure in which the furfural plane, while slightly distorted, is parallel to the Pd surface. Analysis of the bondlength fluctuations indicates that the C-H bond is the aldehyde group of a furfural molecule is likely to be broken first, while the C =O bond has a tendency to be isolated as CO. Our results show that the reaction of decarbonylation dominates, consistent with the experimental measurements. Supported by DOE (DE-SC0004600). Simulations and calculations were performed on XSEDE's and NERSC's supercomputers.

  17. Ab initio perspective on the Mollwo-Ivey relation for F centers in alkali halides

    NASA Astrophysics Data System (ADS)

    Tiwald, Paul; Karsai, Ferenc; Laskowski, Robert; Gräfe, Stefanie; Blaha, Peter; Burgdörfer, Joachim; Wirtz, Ludger

    2015-10-01

    We revisit the well-known Mollwo-Ivey relation that describes the "universal" dependence of the absorption energies of F-type color centers on the lattice constant a of alkali-halide crystals, Eabs∝a-n. We perform both state-of-the-art ab initio quantum chemistry and post-DFT calculations of F-center absorption spectra. By "tuning" independently the lattice constant and the atomic species we show that the scaling with the lattice constant alone (keeping the elements fixed) would yield n =2 in agreement with the "particle-in-the-box" model. Keeping the lattice constant fixed and changing the atomic species enables us to quantify the ion-size effects which are shown to be responsible for the exponent n ≈1.8 .

  18. Dissociation dynamics of ethylene molecules on a Ni cluster using ab initio molecular dynamics simulations.

    PubMed

    Shimamura, K; Shibuta, Y; Ohmura, S; Arifin, R; Shimojo, F

    2016-04-13

    The atomistic mechanism of dissociative adsorption of ethylene molecules on a Ni cluster is investigated by ab initio molecular-dynamics simulations. The activation free energy to dehydrogenate an ethylene molecule on the Ni cluster and the corresponding reaction rate is estimated. A remarkable finding is that the adsorption energy of ethylene molecules on the Ni cluster is considerably larger than the activation free energy, which explains why the actual reaction rate is faster than the value estimated based on only the activation free energy. It is also found from the dynamic simulations that hydrogen molecules and an ethane molecule are formed from the dissociated hydrogen atoms, whereas some exist as single atoms on the surface or in the interior of the Ni cluster. On the other hand, the dissociation of the C-C bonds of ethylene molecules is not observed. On the basis of these simulation results, the nature of the initial stage of carbon nanotube growth is discussed. PMID:26953616

  19. Dissociation dynamics of ethylene molecules on a Ni cluster using ab initio molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Shimamura, K.; Shibuta, Y.; Ohmura, S.; Arifin, R.; Shimojo, F.

    2016-04-01

    The atomistic mechanism of dissociative adsorption of ethylene molecules on a Ni cluster is investigated by ab initio molecular-dynamics simulations. The activation free energy to dehydrogenate an ethylene molecule on the Ni cluster and the corresponding reaction rate is estimated. A remarkable finding is that the adsorption energy of ethylene molecules on the Ni cluster is considerably larger than the activation free energy, which explains why the actual reaction rate is faster than the value estimated based on only the activation free energy. It is also found from the dynamic simulations that hydrogen molecules and an ethane molecule are formed from the dissociated hydrogen atoms, whereas some exist as single atoms on the surface or in the interior of the Ni cluster. On the other hand, the dissociation of the C-C bonds of ethylene molecules is not observed. On the basis of these simulation results, the nature of the initial stage of carbon nanotube growth is discussed.

  20. Ab Initio Study of BiFeO3: Thermodynamic Stability Conditions.

    PubMed

    Heifets, E; Kotomin, E A; Bagaturyants, A A; Maier, J

    2015-07-16

    BiFeO3 is investigated intensively, mainly as a multiferroic material. In this paper, the state-of-the-art ab initio hybrid functional approach with atomic basis sets was employed for a study of the stability range of BiFeO3 with respect to its decomposition into binary oxides and elementary metals, as a function of temperature and oxygen partial pressure. The calculated atomic and electronic structure of BiFeO3 was compared with previous LDA+U calculations using plane-wave basis sets. Based on performed calculations, the phase diagram was constructed, which allows us to predict the stability region of stoichiometric BiFeO3. PMID:26266871

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

    PubMed

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

    2014-09-16

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

  2. Towards an ab initio description of correlated materials

    NASA Astrophysics Data System (ADS)

    Yee, Chuck-Hou

    Strongly-correlated materials are a rich playground for physical phenomena, exhibiting complex phase diagrams with many competing orders. Ab initio insights into materials combined with physical ideas provide the ability to identify the organizing principles driving the correlated electronic behavior and pursue first-principles design of new compounds. Realistic modeling of correlated materials is an active area of research, especially with the recent merger of density functional theory (DFT) with dynamical mean-field theory (DMFT). This thesis is structured in two parts. The first describes the methods and algorithmic developments which drive advances in DFT+DMFT. In Ch. 2 and 3, we provide an overview of the two foundational theories, DMFT and DFT. In the second half of Ch. 3, we describe some of the principles guiding the combination of the two theories to form DFT+DMFT. In Ch. 4, we describe the algorithm lying at the heart of modern DFT+DMFT implementations, the hybridization expansion formulation of continuous-time quantum monte carlo (CTQMC) for the general Anderson impurity problem, as well as a fast rejection algorithm for speeding-up the local trace evaluation. The final chapter in the methods section describes an algorithm for direct sampling of the partition function, and thus the free energy and entropy, of simple Anderson impurity models within CTQMC. The second part of the thesis is a collection of applications of our ab initio approach to key correlated materials. We first apply our method to plutonium binary alloys (Ch. 6), which when supplemented with slave-boson mean-field theory, allows us to understand the observed photoemission spectra. Ch. 7 describes the computation of spectra and optical conductivity for rare-earth nickelates grown as epitaxial thin films. In the final two chapters, we turn our attention to the high-temperature superconductors. In the first, we show that the charge-transfer energy is a key chemical variable which controls

  3. Ab Initio Studies of Halogen and Nitrogen Oxide Species of Interest in Stratospheric Chemistry

    NASA Technical Reports Server (NTRS)

    Lee, Timothy J.; Langhoff, Stephen R. (Technical Monitor)

    1995-01-01

    The ability of modern state-of-the art ab initio quantum chemical techniques to characterize reliably the gas-phase molecular structure, vibrational spectrum, electronic spectrum, and thermal stability of fluorine, chlorine, bromine and nitrogen oxide species will be demonstrated by presentation of some example studies. The ab initio results are shown to be in excellent agreement with the available experimental data, and where the experimental data are either not known or are inconclusive, the theoretical results are shown to fill in the gaps and to resolve experimental controversies. In addition, ab initio studies in which the electronic spectra and the characterization of excited electronic states of halogen oxide species will also be presented. Again where available, the ab initio results are compared to experimental observations, and are used to aid in the interpretation of experimental studies.

  4. Ab Initio Values of the Thermophysical Properties of Helium as Standards

    PubMed Central

    Hurly, John J.; Moldover, Michael R.

    2000-01-01

    Recent quantum mechanical calculations of the interaction energy of pairs of helium atoms are accurate and some include reliable estimates of their uncertainty. We combined these ab initio results with earlier published results to obtain a helium-helium interatomic potential that includes relativistic retardation effects over all ranges of interaction. From this potential, we calculated the thermophysical properties of helium, i.e., the second virial coefficients, the dilute-gas viscosities, and the dilute-gas thermal conductivities of 3He, 4He, and their equimolar mixture from 1 K to 104 K. We also calculated the diffusion and thermal diffusion coefficients of mixtures of 3He and 4He. For the pure fluids, the uncertainties of the calculated values are dominated by the uncertainties of the potential; for the mixtures, the uncertainties of the transport properties also include contributions from approximations in the transport theory. In all cases, the uncertainties are smaller than the corresponding experimental uncertainties; therefore, we recommend the ab initio results be used as standards for calibrating instruments relying on these thermophysical properties. We present the calculated thermophysical properties in easy-to-use tabular form.

  5. Ab initio calculations of the optical properties of crystalline and liquid InSb

    NASA Astrophysics Data System (ADS)

    Sano, Haruyuki; Mizutani, Goro

    2015-11-01

    Ab initio calculations of the electronic and optical properties of InSb were performed for both the crystalline and liquid states. Two sets of atomic structure models for liquid InSb at 900 K were obtained by ab initio molecular dynamics simulations. To reduce the effect of structural peculiarities in the liquid models, an averaging of the two sets of the calculated electronic and optical properties corresponding to the two liquid models was performed. The calculated results indicate that, owing to the phase transition from crystal to liquid, the density of states around the Fermi level increases. As a result, the energy band gap opening near the Fermi level disappears. Consequently, the optical properties change from semiconductor to metallic behavior. Namely, owing to the melting of InSb, the interband transition peaks disappear and a Drude-like dispersion is observed in the optical dielectric functions. The optical absorption at a photon energy of 3.06 eV, which is used in Blu-ray Disc systems, increases owing to the melting of InSb. This increase in optical absorption is proposed to result from the increased optical transitions below 2 eV.

  6. Ab initio calculation of oxygen self-diffusion coefficient in uranium dioxide UO2

    NASA Astrophysics Data System (ADS)

    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).

  7. Accelerating Ab Initio Path Integral Simulations via Imaginary Multiple-Timestepping.

    PubMed

    Cheng, Xiaolu; Herr, Jonathan D; Steele, Ryan P

    2016-04-12

    This work investigates the use of multiple-timestep schemes in imaginary time for computationally efficient ab initio equilibrium path integral simulations of quantum molecular motion. In the simplest formulation, only every n(th) path integral replica is computed at the target level of electronic structure theory, whereas the remaining low-level replicas still account for nuclear motion quantum effects with a more computationally economical theory. Motivated by recent developments for multiple-timestep techniques in real-time classical molecular dynamics, both 1-electron (atomic-orbital basis set) and 2-electron (electron correlation) truncations are shown to be effective. Structural distributions and thermodynamic averages are tested for representative analytic potentials and ab initio molecular examples. Target quantum chemistry methods include density functional theory and second-order Møller-Plesset perturbation theory, although any level of theory is formally amenable to this framework. For a standard two-level splitting, computational speedups of 1.6-4.0x are observed when using a 4-fold reduction in time slices; an 8-fold reduction is feasible in some cases. Multitiered options further reduce computational requirements and suggest that quantum mechanical motion could potentially be obtained at a cost not significantly different from the cost of classical simulations. PMID:26966920

  8. Ab initio study of weakly bound halogen complexes: RX⋯PH3.

    PubMed

    Georg, Herbert C; Fileti, Eudes E; Malaspina, Thaciana

    2013-01-01

    Ab initio calculations were employed to study the role of ipso carbon hybridization in halogenated compounds RX (R=methyl, phenyl, acetyl, H and X=F, Cl, Br and I) and its interaction with a phosphorus atom, as occurs in the halogen bonded complex type RX⋯PH3. The analysis was performed using ab initio MP2, MP4 and CCSD(T) methods. Systematic energy analysis found that the interaction energies are in the range -4.14 to -11.92 kJ mol(-1) (at MP2 level without ZPE correction). Effects of electronic correlation levels were evaluated at MP4 and CCSD(T) levels and a reduction of up to 27% in interaction energy obtained in MP2 was observed. Analysis of the electrostatic maps confirms that the PhCl⋯PH3 and all MeX⋯PH3 complexes are unstable. NBO analysis suggested that the charge transfer between the moieties is bigger when using iodine than bromine and chlorine. The electrical properties of these complexes (dipole and polarizability) were determined and the most important observed aspect was the systematic increase at the dipole polarizability, given by the interaction polarizability. This increase is in the range of 0.7-6.7 u.a. (about 3-7%). PMID:22895850

  9. Quantum supercharger library: hyper-parallel integral derivatives algorithms for ab initio QM/MM dynamics.

    PubMed

    Renison, C Alicia; Fernandes, Kyle D; Naidoo, Kevin J

    2015-07-01

    This article describes an extension of the quantum supercharger library (QSL) to perform quantum mechanical (QM) gradient and optimization calculations as well as hybrid QM and molecular mechanical (QM/MM) molecular dynamics simulations. The integral derivatives are, after the two-electron integrals, the most computationally expensive part of the aforementioned calculations/simulations. Algorithms are presented for accelerating the one- and two-electron integral derivatives on a graphical processing unit (GPU). It is shown that a Hartree-Fock ab initio gradient calculation is up to 9.3X faster on a single GPU compared with a single central processing unit running an optimized serial version of GAMESS-UK, which uses the efficient Schlegel method for s- and l-orbitals. Benchmark QM and QM/MM molecular dynamics simulations are performed on cellobiose in vacuo and in a 39 Å water sphere (45 QM atoms and 24843 point charges, respectively) using the 6-31G basis set. The QSL can perform 9.7 ps/day of ab initio QM dynamics and 6.4 ps/day of QM/MM dynamics on a single GPU in full double precision. © 2015 Wiley Periodicals, Inc. PMID:25975864

  10. Hydrogen Bonds in Crystalline Imidazoles Studied by 15N NMR and ab initio MO Calculations

    NASA Astrophysics Data System (ADS)

    Ueda, Takahiro; Nagatomo, Shigenori; Masui, Hirotsugu; Nakamura, Nobuo; Hayashi, Shigenobu

    1999-07-01

    Intermolecular hydrogen bonds of the type N-H...N in crystals of imidazole and its 4-substituted and 4,5-disubstituted derivatives were studied by 15N CP/MAS NMR and an ab initio molecular orbital (MO) calculation. In the 15N CP/MAS NMR spectrum of each of the imidazole derivatives, two peaks due to the two different functional groups, >NH and =N-, were observed. The value of the 15N isotropic chemical shift for each nitrogen atom depends on both the length of the intermolecular hydrogen bond and the kind of the substituent or substituents. It was found that the difference between the experimen-tal chemical shifts of >NH and =N-varies predominantly with the hydrogen bond length but does not show any systematic dependence on the kind of substituent. The ab initio MO calculations suggest that the hydrogen bond formation influences the 15N isotropic chemical shift predominantly, and that the difference between the 15N isotropic chemical shift of >NH and =N-varies linearly with the hydrogen bond length.

  11. An hybrid computing approach to accelerating the multiple scattering theory based ab initio methods

    NASA Astrophysics Data System (ADS)

    Wang, Yang; Stocks, G. Malcolm

    2014-03-01

    The multiple scattering theory method, also known as the Korringa-Kohn-Rostoker (KKR) method, is considered an elegant approach to the ab initio electronic structure calculation for solids. Its convenience in accessing the one-electron Green function has led to the development of locally-self consistent multiple scattering (LSMS) method, a linear scaling ab initio method that allows for the electronic structure calculation for complex structures requiring tens of thousands of atoms in unit cell. It is one of the few applications that demonstrated petascale computing capability. In this presentation, we discuss our recent efforts in developing a hybrid computing approach for accelerating the full potential electronic structure calculation. Specifically, in the framework of our existing LSMS code in FORTRAN 90/95, we explore the many core resources on GPGPU accelerators by implementing the compute intensive functions (for the calculation of multiple scattering matrices and the single site solutions) in CUDA, and move the computational tasks to the GPGPUs if they are found available. We explain in details our approach to the CUDA programming and the code structure, and show the speed-up of the new hybrid code by comparing its performances on CPU/GPGPU and on CPU only. The work was supported in part by the Center for Defect Physics, a DOE-BES Energy Frontier Research Center.

  12. Ab initio calculations of the optical properties of crystalline and liquid InSb

    SciTech Connect

    Sano, Haruyuki; Mizutani, Goro

    2015-11-15

    Ab initio calculations of the electronic and optical properties of InSb were performed for both the crystalline and liquid states. Two sets of atomic structure models for liquid InSb at 900 K were obtained by ab initio molecular dynamics simulations. To reduce the effect of structural peculiarities in the liquid models, an averaging of the two sets of the calculated electronic and optical properties corresponding to the two liquid models was performed. The calculated results indicate that, owing to the phase transition from crystal to liquid, the density of states around the Fermi level increases. As a result, the energy band gap opening near the Fermi level disappears. Consequently, the optical properties change from semiconductor to metallic behavior. Namely, owing to the melting of InSb, the interband transition peaks disappear and a Drude-like dispersion is observed in the optical dielectric functions. The optical absorption at a photon energy of 3.06 eV, which is used in Blu-ray Disc systems, increases owing to the melting of InSb. This increase in optical absorption is proposed to result from the increased optical transitions below 2 eV.

  13. Full-dimensional (15-dimensional) ab initio analytical potential energy surface for the H7+ cluster

    NASA Astrophysics Data System (ADS)

    Barragán, Patricia; Prosmiti, Rita; Wang, Yimin; Bowman, Joel M.

    2012-06-01

    Full-dimensional ab initio potential energy surface is constructed for the H_7^+ cluster. The surface is a fit to roughly 160 000 interaction energies obtained with second-order MöllerPlesset perturbation theory and the cc-pVQZ basis set, using the invariant polynomial method [B. J. Braams and J. M. Bowman, Int. Rev. Phys. Chem. 28, 577 (2009), 10.1080/01442350903234923]. We employ permutationally invariant basis functions in Morse-type variables for all the internuclear distances to incorporate permutational symmetry with respect to interchange of H atoms into the representation of the surface. We describe how different configurations are selected in order to create the database of the interaction energies for the linear least squares fitting procedure. The root-mean-square error of the fit is 170 cm-1 for the entire data set. The surface dissociates correctly to the H_5^+ + H2 fragments. A detailed analysis of its topology, as well as comparison with additional ab initio calculations, including harmonic frequencies, verify the quality and accuracy of the parameterized potential. This is the first attempt to present an analytical representation of the 15-dimensional surface of the H_7^+ cluster for carrying out dynamics studies.

  14. Emergent properties of nuclei from ab initio coupled-cluster calculations

    NASA Astrophysics Data System (ADS)

    Hagen, G.; Hjorth-Jensen, M.; Jansen, G. R.; Papenbrock, T.

    2016-06-01

    Emergent properties such as nuclear saturation and deformation, and the effects on shell structure due to the proximity of the scattering continuum and particle decay channels are fascinating phenomena in atomic nuclei. In recent years, ab initio approaches to nuclei have taken the first steps towards tackling the computational challenge of describing these phenomena from Hamiltonians with microscopic degrees of freedom. This endeavor is now possible due to ideas from effective field theories, novel optimization strategies for nuclear interactions, ab initio methods exhibiting a soft scaling with mass number, and ever-increasing computational power. This paper reviews some of the recent accomplishments. We also present new results. The recently optimized chiral interaction NNLO{}{{sat}} is shown to provide an accurate description of both charge radii and binding energies in selected light- and medium-mass nuclei up to 56Ni. We derive an efficient scheme for including continuum effects in coupled-cluster computations of nuclei based on chiral nucleon–nucleon and three-nucleon forces, and present new results for unbound states in the neutron-rich isotopes of oxygen and calcium. The coupling to the continuum impacts the energies of the {J}π =1/{2}-,3/{2}-,7/{2}-,3/{2}+ states in {}{17,23,25}O, and—contrary to naive shell-model expectations—the level ordering of the {J}π =3/{2}+,5/{2}+,9/{2}+ states in {}{53,55,61}Ca. ).

  15. A new ab initio potential energy surface for the Ne-H 2 interaction

    NASA Astrophysics Data System (ADS)

    Lique, François

    2009-03-01

    A new accurate three-dimensional potential energy surface for the Ne-H 2 system, which explicitly takes into account the r-dependence of the H 2 vibration, was determined from ab initio calculations. It was obtained with the single and double excitation coupled-cluster method with noniterative perturbational treatment of triple excitation [CCSD(T)]. Calculations was been performed using the augmented correlation-consistent polarized quintuple zeta basis set (aug-cc-pV5Z) for the three atoms. We checked the accuracy of the present ab initio calculations. We have determined, using the new Ne-H 2 potential energy surface, differential cross-sections for the rotational excitation of the H 2 and D 2 molecules in collision with Ne and we have compared them with experimental results of Faubel et al. [M. Faubel, F.A. Gianturco, F. Ragnetti, L.Y. Rusin, F. Sondermann, U. Tappe, J.P. Toennies, J. Chem. Phys. 101 (1994) 8800]. The overall agreement confirms that the new potential energy surface can be used for the simulation of molecular collisions and/or molecular spectroscopy of the van der Waals complex Ne-H 2.

  16. Melting curves of metals by ab initio calculations

    NASA Astrophysics Data System (ADS)

    Minakov, Dmitry; Levashov, Pavel

    2015-06-01

    In this work we used several ab initio approaches to reproduce melting curves and discussed their abilities, advantages and drawbacks. We used quasiharmonic appoximation and Lindemann criterion to build melting curves in wide region of pressures. This approach allows to calculate the total free energy of electrons and phonons, so it is possible to obtain all thermodynamic properties in the crystalline state. We also used quantum molecular dynamics simulations to investigate melting at various pressures. We explored the size-effect of the heat until it melts (HUM) method in detail. Special attention was paid to resolve the boundaries of the melting region on density. All calculations were performed for aluminum, copper and gold. Results were in good agreement with available experimental data. Also we studied the influence of electronic temperature on melting curves. It turned out that the melting temperature increased with the rise of electron temperature at normal density and had non-monotonic behavior at higher densities. This work is supported by the Ministry of Education and Science of the Russian Federation (Project No. 3.522.2014/K).

  17. Ab initio study of optical excitations in VO2

    NASA Astrophysics Data System (ADS)

    Coulter, John; Gali, Adam; Manousakis, Efstratios

    2014-03-01

    Motivated by recent experimental efforts to fabricate p-n junctions from transition metal oxides (TMOs) and a recent theoretical study claiming TMOs to be good absorbers and promising materials for efficient carrier multiplication, we study the optical properties of a prototypical TMO, the insulator M1 phase of vanadium dioxide (VO2), by ab initio methods. We applied the Bethe-Salpeter equations (BSE) to calculate the optical properties, starting from self-consistent GW quasi-particle energy levels and states. In contrast to expectations, the exciton binding energy obtained by BSE is in good agreement with the experiment. We find that the electron-electron interaction is very strong which makes this material promising for efficient carrier multiplication that might lead to an enhanced efficiency in photo-voltaics applications. To illustrate this more quantitatively, we calculated the impact ionization rate within the independent quasiparticle approximation, and find that the rate is significantly higher than silicon in the region of highest solar intensity, due to the strong multiple carrier excitations.

  18. Ab initio studies of phoshorene island single electron transistor.

    PubMed

    Ray, S J; Venkata Kamalakar, M; Chowdhury, R

    2016-05-18

    Phosphorene is a newly unveiled two-dimensional crystal with immense potential for nanoelectronic and optoelectronic applications. Its unique electronic structure and two dimensionality also present opportunities for single electron devices. Here we report the behaviour of a single electron transistor (SET) made of a phosphorene island, explored for the first time using ab initio calculations. We find that the band gap and the charging energy decrease monotonically with increasing layer numbers due to weak quantum confinement. When compared to two other novel 2D crystals such as graphene and MoS2, our investigation reveals larger adsorption energies of gas molecules on phosphorene, which indicates better a sensing ability. The calculated charge stability diagrams show distinct changes in the presence of an individual molecule which can be applied to detect the presence of different molecules with sensitivity at a single molecular level. The higher charging energies of the molecules within the SET display operational viability at room temperature, which is promising for possible ultra sensitive detection applications. PMID:27093536

  19. Ab initio studies of phosphorene island single electron transistor

    NASA Astrophysics Data System (ADS)

    Ray, S. J.; Venkata Kamalakar, M.; Chowdhury, R.

    2016-05-01

    Phosphorene is a newly unveiled two-dimensional crystal with immense potential for nanoelectronic and optoelectronic applications. Its unique electronic structure and two dimensionality also present opportunities for single electron devices. Here we report the behaviour of a single electron transistor (SET) made of a phosphorene island, explored for the first time using ab initio calculations. We find that the band gap and the charging energy decrease monotonically with increasing layer numbers due to weak quantum confinement. When compared to two other novel 2D crystals such as graphene and MoS2, our investigation reveals larger adsorption energies of gas molecules on phosphorene, which indicates better a sensing ability. The calculated charge stability diagrams show distinct changes in the presence of an individual molecule which can be applied to detect the presence of different molecules with sensitivity at a single molecular level. The higher charging energies of the molecules within the SET display operational viability at room temperature, which is promising for possible ultra sensitive detection applications.

  20. An Ab Initio Based Potential Energy Surface for Water

    NASA Technical Reports Server (NTRS)

    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.

  1. Ab initio description of the exotic unbound 7He nucleus

    DOE PAGESBeta

    Baroni, Simone; Navratil, Petr; Quaglioni, Sofia

    2013-01-11

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

  2. Exploring the free energy surface using ab initio molecular dynamics.

    PubMed

    Samanta, Amit; Morales, Miguel A; Schwegler, Eric

    2016-04-28

    Efficient exploration of configuration space and identification of metastable structures in condensed phase systems are challenging from both computational and algorithmic perspectives. In this regard, schemes that utilize a set of pre-defined order parameters to sample the relevant parts of the configuration space [L. Maragliano and E. Vanden-Eijnden, Chem. Phys. Lett. 426, 168 (2006); J. B. Abrams and M. E. Tuckerman, J. Phys. Chem. B 112, 15742 (2008)] have proved useful. Here, we demonstrate how these order-parameter aided temperature accelerated sampling schemes can be used within the Born-Oppenheimer and the Car-Parrinello frameworks of ab initio molecular dynamics to efficiently and systematically explore free energy surfaces, and search for metastable states and reaction pathways. We have used these methods to identify the metastable structures and reaction pathways in SiO2 and Ti. In addition, we have used the string method [W. E, W. Ren, and E. Vanden-Eijnden, Phys. Rev. B 66, 052301 (2002); L. Maragliano et al., J. Chem. Phys. 125, 024106 (2006)] within the density functional theory to study the melting pathways in the high pressure cotunnite phase of SiO2 and the hexagonal closed packed to face centered cubic phase transition in Ti. PMID:27131525

  3. TOPICAL REVIEW: Ab initio symplectic no-core shell model

    NASA Astrophysics Data System (ADS)

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

    2008-12-01

    The no-core shell model (NCSM) is a prominent ab initio method that yields a good description of the low-lying states in few-nucleon systems as well as in more complex p-shell nuclei. Nevertheless, its applicability is limited by the rapid growth of the many-body basis with larger model spaces and increasing number of nucleons. The symplectic no-core shell model (Sp-NCSM) aspires to extend the scope of the NCSM beyond the p-shell region by augmenting the conventional spherical harmonic oscillator basis with the physically relevant symplectic \\SpR{3} symmetry-adapted configurations of the symplectic shell model that describe naturally the monopole-quadrupole vibrational and rotational modes, and also partially incorporate α-cluster correlations. In this review, the models underpinning the Sp-NCSM approach, namely, the NCSM, the Elliott SU(3) model and the symplectic shell model, are discussed. Following this, a prescription for constructing translationally invariant symplectic configurations in the spherical harmonic oscillator basis is given. This prescription is utilized to unveil the extent to which symplectic configurations enter into low-lying states in 12C and 16O nuclei calculated within the framework of the NCSM with the JISP16 realistic nucleon-nucleon interaction. The outcomes of this proof-of-principle study are presented in detail.

  4. Microsolvation of methyl hydrogen peroxide: Ab initio quantum chemical approach

    NASA Astrophysics Data System (ADS)

    Kulkarni, Anant D.; Rai, Dhurba; Bartolotti, Libero J.; Pathak, Rajeev K.

    2009-08-01

    Methyl hydrogen peroxide (MHP), one of the simplest organic hydroperoxides, is a strong oxidant, with enhanced activity in aqueous ambience. The present study investigates, at the molecular level, the role of hydrogen bonding that is conducive to cluster formation of MHP with water molecules from its peroxide end, with the methyl group remaining hydrophobic for up to five water molecules. Ab initio quantum chemical computations on MHP⋯(H2O)n, [n =1-5] are performed at second order Møller-Plesset (MP2) perturbation theory employing the basis sets 6-31G(d,p) and 6-311++G(2d,2p) to study the cluster formation of MHP with water molecules from its peroxide end and hydrophobic hydration due to the methyl group. Successive addition of water molecules alters the hydrogen bonding pattern, which leads to changes in overall cluster geometry and in turn to IR vibrational frequency shifts. Molecular co-operativity in these clusters is gauged directly through a detailed many-body interaction energy analysis. Molecular electrostatic potential maps are shown to have a bearing on predicting further growth of these clusters, which is duly corroborated through sample calculations for MHP⋯(H2O)8. Further, a continuum solvation model calculation for energetically stable clusters suggests that this study should serve as a precursor for pathways to aqueous solvation of MHP.

  5. Ab initio modelling of methane hydrate thermophysical properties.

    PubMed

    Jendi, Z M; Servio, P; Rey, A D

    2016-04-21

    The key thermophysical properties of methane hydrate were determined using ab initio modelling. Using density functional theory, the second-order elastic constants, heat capacity, compressibility, and thermal expansion coefficient were calculated. A wide and relevant range of pressure-temperature conditions were considered, and the structures were assessed for stability using the mean square displacement and radial distribution functions. Methane hydrate was found to be elastically isotropic with a linear dependence of the bulk modulus on pressure. Equally significant, multi-body interactions were found to be important in hydrates, and water-water interactions appear to strongly influence compressibility like in ice Ih. While the heat capacity of hydrate was found to be higher than that of ice, the thermal expansion coefficient was significantly lower, most likely due to the lower rigidity of hydrates. The mean square displacement gave important insight into stability, heat capacity, and elastic moduli, and the radial distribution functions further confirmed stability. The presented results provide a much needed atomistic thermoelastic characterization of methane hydrates and are essential input for the large-scale applications of hydrate detection and production. PMID:27019976

  6. Engineering Room-temperature Superconductors Via ab-initio Calculations

    NASA Astrophysics Data System (ADS)

    Gulian, Mamikon; Melkonyan, Gurgen; Gulian, Armen

    The BCS, or bosonic model of superconductivity, as Little and Ginzburg have first argued, can bring in superconductivity at room temperatures in the case of high-enough frequency of bosonic mode. It was further elucidated by Kirzhnitset al., that the condition for existence of high-temperature superconductivity is closely related to negative values of the real part of the dielectric function at finite values of the reciprocal lattice vectors. In view of these findings, the task is to calculate the dielectric function for real materials. Then the poles of this function will indicate the existence of bosonic excitations which can serve as a "glue" for Cooper pairing, and if the frequency is high enough, and the dielectric matrix is simultaneously negative, this material is a good candidate for very high-Tc superconductivity. Thus, our approach is to elaborate a methodology of ab-initio calculation of the dielectric function of various materials, and then point out appropriate candidates. We used the powerful codes (TDDF with the DP package in conjunction with ABINIT) for computing dielectric responses at finite values of the wave vectors in the reciprocal lattice space. Though our report is concerned with the particular problem of superconductivity, the application range of the data processing methodology is much wider. The ability to compute the dielectric function of existing and still non-existing (though being predicted!) materials will have many more repercussions not only in fundamental sciences but also in technology and industry.

  7. Ab initio simulations of pseudomorphic silicene and germanene bidimensional heterostructures

    NASA Astrophysics Data System (ADS)

    Debernardi, Alberto; Marchetti, Luigi

    2016-06-01

    Among the novel two-dimensional (2D) materials, silicene and germanene, which are two honeycomb crystal structures composed of a monolayer of Si and Ge, respectively, have attracted the attention of material scientists because they combine the advantages of the new 2D ultimate-scaled electronics with their compatibility with industrial processes presently based on Si and Ge. We envisage pseudomorphic lateral heterostructures based on ribbons of silicene and germanene, which are the 2D analogs of conventional 3D Si/Ge superlattices and quantum wells. In spite of the considerable lattice mismatch (˜4 % ) between free-standing silicene and germanene, our ab initio simulations predict that, considering striped 2D lateral heterostructures made by alternating silicene and germanene ribbons of constant width, the silicene/germanene junction remains pseudomorphic—i.e., it maintains lattice-matched edges—up to critical ribbon widths that can reach some tens of nanometers. Such critical widths are one order of magnitude larger than the critical thickness measured in 3D pseudomorphic Si/Ge heterostructures and the resolution of state-of-the-art lithography, thus enabling the possibility of lithography patterned silicene/germanene junctions. We computed how the strain produced by the pseudomorphic growth modifies the crystal structure and electronic bands of the ribbons, providing a mechanism for band-structure engineering. Our results pave the way for lithography patterned lateral heterostructures that can serve as the building blocks of novel 2D electronics.

  8. Ab Initio Investigation of NH_3-O_2 Exciplex

    NASA Astrophysics Data System (ADS)

    Haupert, L. M.; Simpson, G.; Slipchenko, L. V.

    2010-06-01

    In their recent investigation of fluorescence from poly(amido amine) (PAMAM) dendrimers, Chu and Imae suggested an exciplex composed of tertiary amine and oxygen molecules might be responsible for fluorescence in PAMAM dendrimers. In this work, we present an ab initio investigation of the electronic structure of a possible ammonia-oxygen exciplex model system using equation-of-motion coupled cluster techniques. Geometry optimization of the triplet ground state produced a weakly bound state with an equilibrium separation of ˜ 3.5 Å, and an excited state geometry scan revealed a bound, excited triplet state with an equilibrium separation of 2.02 Å, consistent with results of earlier PM3 work by Juranic et al. The energy gap between the triplet ground state and first triplet excited state of the exciplex at 2.02 Å is 412.8 nm, lending support to the exciplex hypothesis. C.-C. Chu, and T. Imae, Macromol. Rapid. Commun., 30, 89-93 (2009). I. Juranic, H. S. Rzepa, and Y. MinYan, J. Chem. Soc. Perkin Trans., 2 (1990)

  9. Exploring the free energy surface using ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Samanta, Amit; Morales, Miguel A.; Schwegler, Eric

    2016-04-01

    Efficient exploration of configuration space and identification of metastable structures in condensed phase systems are challenging from both computational and algorithmic perspectives. In this regard, schemes that utilize a set of pre-defined order parameters to sample the relevant parts of the configuration space [L. Maragliano and E. Vanden-Eijnden, Chem. Phys. Lett. 426, 168 (2006); J. B. Abrams and M. E. Tuckerman, J. Phys. Chem. B 112, 15742 (2008)] have proved useful. Here, we demonstrate how these order-parameter aided temperature accelerated sampling schemes can be used within the Born-Oppenheimer and the Car-Parrinello frameworks of ab initio molecular dynamics to efficiently and systematically explore free energy surfaces, and search for metastable states and reaction pathways. We have used these methods to identify the metastable structures and reaction pathways in SiO2 and Ti. In addition, we have used the string method [W. E, W. Ren, and E. Vanden-Eijnden, Phys. Rev. B 66, 052301 (2002); L. Maragliano et al., J. Chem. Phys. 125, 024106 (2006)] within the density functional theory to study the melting pathways in the high pressure cotunnite phase of SiO2 and the hexagonal closed packed to face centered cubic phase transition in Ti.

  10. Accurate ab initio vibrational energies of methyl chloride

    SciTech Connect

    Owens, Alec; Yurchenko, Sergei N.; Yachmenev, Andrey; Tennyson, Jonathan; Thiel, Walter

    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.

  11. Ab Initio Potential Energy Surface for H-H2

    NASA Technical Reports Server (NTRS)

    Patridge, 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 +/- 3 micro E(h). Large basis sets have also been applied to reexamine the accuracy of theoretical repulsive potential energy surfaces (25-70 kcal/mol above the H-H2 asymptote) at small interatomic separations; the Boothroyd, Keogh, Martin, and Peterson (BKMP) potential energy surface is found to agree with results of the present calculations within the expected uncertainty (+/- 1 kcal/mol) of the fit. 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(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.

  12. Ab initio description of p-shell hypernuclei.

    PubMed

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

    2014-11-01

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

  13. Ab initio SCF calculations on hydrogen bonded cresol isomers

    NASA Astrophysics Data System (ADS)

    Pohl, M.; Kleinermanns, K.

    1988-12-01

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

  14. Predicting lattice thermal conductivity with help from ab initio methods

    NASA Astrophysics Data System (ADS)

    Broido, David

    2015-03-01

    The lattice thermal conductivity is a fundamental transport parameter that determines the utility a material for specific thermal management applications. Materials with low thermal conductivity find applicability in thermoelectric cooling and energy harvesting. High thermal conductivity materials are urgently needed to help address the ever-growing heat dissipation problem in microelectronic devices. Predictive computational approaches can provide critical guidance in the search and development of new materials for such applications. Ab initio methods for calculating lattice thermal conductivity have demonstrated predictive capability, but while they are becoming increasingly efficient, they are still computationally expensive particularly for complex crystals with large unit cells . In this talk, I will review our work on first principles phonon transport for which the intrinsic lattice thermal conductivity is limited only by phonon-phonon scattering arising from anharmonicity. I will examine use of the phase space for anharmonic phonon scattering and the Grüneisen parameters as measures of the thermal conductivities for a range of materials and compare these to the widely used guidelines stemming from the theory of Liebfried and Schölmann. This research was supported primarily by the NSF under Grant CBET-1402949, and by the S3TEC, an Energy Frontier Research Center funded by the US DOE, office of Basic Energy Sciences under Award No. DE-SC0001299.

  15. Ab initio simulations of peptide-mineral interactions

    NASA Astrophysics Data System (ADS)

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

    We performed Car-Parrinello Molecular Dynamics (CPMD) simulations of two amino acids, aspartic acid (Asp) and phophoserine (pSer), on a calcium oxalate monohydrate (COM) surface as a model of the interactions of phosphoproteins with biominerals. In our earlier work using in vitro experiments and classical Molecular Dynamics (MD) simulations we have demonstrated the importance of phosphorylation of serine on the interactions of osteopontin (OPN) with COM. We used configurations from our previous classical MD simulations as a starting point for the ab initio simulations. In the case of Asp we found that the α-carboxyl and amine groups form temporary close contacts with the surface. For the dipeptide Asp-pSer the carboxyl groups form permanent close contacts with the surface and the distances of its other functional groups do not vary much. We show how the interaction of carboxyl groups with COM crystal is established and confirm the importance of phosphorylation in mediating the interactions between COM surfaces and OPN.

  16. Ab initio study of the phenol-water cation radical

    NASA Astrophysics Data System (ADS)

    Hobza, Pavel; Burcl, Rudolf; Špirko, Vladimír; Dopfer, Otto; Müller-Dethlefs, Klaus; Schlag, Edward W.

    1994-07-01

    The phenol-water cation radical has been investigated by ab initio theory using the spin-restricted open-shell Hartree-Fock and spin-restricted open-shell second-order Møller-Plesset theories with 3-21G*(O) and 6-31G* basis sets. The full geometrical optimization was performed for several hydrogen-bonded structures and one hemibonded structure. Clearly, the most stable structure has been found for Cs symmetry with the linear hydrogen bond between the proton of the OH group of the phenol cation radical and the oxygen of the water, and the water hydrogens pointing away from the phenyl ring. For this structure harmonic (and for some intermolecular modes anharmonic) vibrational frequencies have been computed for various isotopic complexes. The computed shifts of phenol-localized intramolecular modes on complexation and on deuteration as well as the calculated intermolecular frequencies of the different isotopic complexes allow for an assignment of vibrational frequencies observed in the experimental zero-kinetic-energy (ZEKE) photoelectron spectra. Five out of a possible six intermolecular vibrations and several intramolecular modes have been assigned, including the 18b vibration which shows a strong blue shift in frequency upon complexation. Structure and properties of the phenol-water cation radical are compared with those of the corresponding neutral complex.

  17. An efficient approach to ab initio Monte Carlo simulation

    SciTech Connect

    Leiding, Jeff; Coe, Joshua D.

    2014-01-21

    We present a Nested Markov chain Monte Carlo (NMC) scheme for building equilibrium averages based on accurate potentials such as density functional theory. Metropolis sampling of a reference system, defined by an inexpensive but approximate potential, was used to substantially decorrelate configurations at which the potential of interest was evaluated, thereby dramatically reducing the number needed to build ensemble averages at a given level of precision. The efficiency of this procedure was maximized on-the-fly through variation of the reference system thermodynamic state (characterized here by its inverse temperature β{sup 0}), which was otherwise unconstrained. Local density approximation results are presented for shocked states of argon at pressures from 4 to 60 GPa, where—depending on the quality of the reference system potential—acceptance probabilities were enhanced by factors of 1.2–28 relative to unoptimized NMC. The optimization procedure compensated strongly for reference potential shortcomings, as evidenced by significantly higher speedups when using a reference potential of lower quality. The efficiency of optimized NMC is shown to be competitive with that of standard ab initio molecular dynamics in the canonical ensemble.

  18. Accurate ab initio vibrational energies of methyl chloride.

    PubMed

    Owens, Alec; Yurchenko, Sergei N; Yachmenev, Andrey; Tennyson, Jonathan; Thiel, Walter

    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, CH3 (35)Cl and CH3 (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 3Z. 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 CH3Cl without empirical refinement of the respective PESs. PMID:26133427

  19. Accurate ab initio vibrational energies of methyl chloride

    NASA Astrophysics Data System (ADS)

    Owens, Alec; Yurchenko, Sergei N.; Yachmenev, Andrey; Tennyson, Jonathan; Thiel, Walter

    2015-06-01

    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, CH335Cl and CH337Cl. 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 3Z. 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 CH3Cl without empirical refinement of the respective PESs.

  20. Ab initio effective interactions for s d -shell valence nucleons

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

    We perform ab initio no-core shell-model calculations for A =18 and 19 nuclei in a 4 ℏ Ω , or Nmax=4 , model space by using the effective JISP16 and chiral N3LO nucleon-nucleon potentials and transform the many-body effective Hamiltonians into the 0 ℏ Ω model space to construct the A -body effective Hamiltonians in the s d shell. We separate the A -body effective Hamiltonians with A =18 and A =19 into inert core, one-, and two-body components. Then we use these core, one-, and two-body components to perform standard shell-model calculations for the A =18 and A =19 systems with valence nucleons restricted to the s d shell. Finally, we compare the standard shell-model results in the 0 ℏ Ω model space with the exact no-core shell-model results in the 4 ℏ Ω model space for the A =18 and A =19 systems and find good agreement.

  1. Lead-Chalcogenides Under Pressure: Ab-Initio Study

    NASA Astrophysics Data System (ADS)

    Gupta, Dinesh C.; Hamid, Idris

    ab-initio calculations using fully relativistic pseudo-potential have been performed to investigate the high pressure phase transition, elastic and electronic properties of lead-chalcogenides including the less known lead polonium. The calculated ground state parameters, for the rock-salt structure show good agreement with the experimental data. The enthalpy calculations show that these materials undergo a first-order phase transition from rock-salt to CsCl structure at 19.4, 15.5, 11.5 and 7.3 GPa for PbS, PbSe, PbTe and PbPo, respectively. Present calculations successfully predicted the location of the band gap at L-point of Brillouin zone as well as the value of the band gap in every case at ambient pressure. It is observed that unlike other lead-chalcogenides, PbPo is semi-metal at ambient pressure. The pressure variation of the energy gap indicates that these materials metalized under high pressures. For this purpose, the electronic structure of these materials has also been computed in parent as well as in high pressure phase.

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

    PubMed

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

    2006-02-01

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

  3. Ab initio molecular dynamics calculations of ion hydration free energies

    SciTech Connect

    Leung, Kevin; Rempe, Susan B.; Lilienfeld, O. Anatole von

    2009-05-28

    We apply ab initio molecular dynamics (AIMD) methods in conjunction with the thermodynamic integration or '{lambda}-path' technique to compute the intrinsic hydration free energies of Li{sup +}, Cl{sup -}, and Ag{sup +} ions. Using the Perdew-Burke-Ernzerhof functional, adapting methods developed for classical force field applications, and with consistent assumptions about surface potential ({phi}) contributions, we obtain absolute AIMD hydration free energies ({Delta}G{sub hyd}) within a few kcal/mol, or better than 4%, of Tissandier et al.'s [J. Phys. Chem. A 102, 7787 (1998)] experimental values augmented with the SPC/E water model {phi} predictions. The sums of Li{sup +}/Cl{sup -} and Ag{sup +}/Cl{sup -} AIMD {Delta}G{sub hyd}, which are not affected by surface potentials, are within 2.6% and 1.2 % of experimental values, respectively. We also report the free energy changes associated with the transition metal ion redox reaction Ag{sup +}+Ni{sup +}{yields}Ag+Ni{sup 2+} in water. The predictions for this reaction suggest that existing estimates of {Delta}G{sub hyd} for unstable radiolysis intermediates such as Ni{sup +} may need to be extensively revised.

  4. Ab initio study of ice catalyzation of HOCl + HCl reaction

    SciTech Connect

    Zhou, Y.F.; Liu, C.B.

    2000-06-15

    The observations by Farman et al. revealed remarkable depletions in the total atmospheric ozone content in Antarctica. The observed total ozone decreased smoothing during the spring season from about 1975. Satellite observations have proved Antarctic ozone depletions over a very extended region, in general agreement with the local ground-based data of Farman et al. It was suggested that heterogeneous reactions occurring on particles in polar stratospheric clouds (PSCs) play a central role in the depletion of stratospheric ozone. Experiments proved that the reaction of HOCl + HCl was very slow in the gas phase, but on ice surface it was rapid. In this work the ice catalysis of HOCl + HCl reaction was investigated by using ab initio molecular orbital theory. The authors applied the Hartree-Fock self-consistent field and the second-order Moeller-Plesset perturbation theory with the basis sets of 6-31G* to the model system. The complexes and transition state were obtained along the reaction with and without the presence of ice surface. By comparing the results, a possible catalyzation mechanism of ice on the reaction is proposed.

  5. Ab initio Raman spectroscopy of water under extreme conditions

    NASA Astrophysics Data System (ADS)

    Rozsa, Viktor; Pan, Ding; Wan, Quan; Galli, Giulia

    Water exhibits one of the most complex phase diagrams of any binary compound. Despite extensive studies, the melting lines of high-pressure ice phases remain very controversial, with reports differing by hundreds of Kelvin. The boundary between ice VII and liquid phase is particularly disputed, with recent work exploring plasticity and amorphization mediating the transition. Raman measurements are often used to fingerprint melting, yet their interpretation is difficult without atomistic modeling. Here, we report a study of high P/T water where we computed Raman spectra using a method combining ab initio molecular dynamics and density functional perturbation theory, as implemented in the Qbox code. Spectra were computed for the liquid at 10 and 20 GPa, both at 1000 K, and for solid ice VII (20 GPa, 500 K). Decomposing the spectra into inter and intra molecular contributions provided insight into the dynamics of the hydrogen-bonded network at extreme conditions. The relevance of our simulation results for models of water in Earth, Uranus, and Neptune will be discussed, and an interpretation of existing experiments at high pressure will be presented.

  6. Ab initio modeling of the motional Stark effect on MAST

    SciTech Connect

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

    2008-10-15

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

  7. A combined photoelectron spectroscopy and ab initio study of the quasi-planar B24- cluster

    NASA Astrophysics Data System (ADS)

    Popov, Ivan A.; Piazza, Zachary A.; Li, Wei-Li; Wang, Lai-Sheng; Boldyrev, Alexander I.

    2013-10-01

    The structure and chemical bonding of the 24-atom boron cluster are investigated using photoelectron spectroscopy and ab initio calculations. The joint experimental and theoretical investigation shows that B24- possesses a quasi-planar structure containing fifteen outer and nine inner atoms with six of the inner atoms forming a filled pentagonal moiety. The central atom of the pentagonal moiety is puckered out of plane by 0.9 Å, reminiscent of the six-atom pentagonal caps of the well-known B12 icosahedral unit. The next closest isomer at the ROCCSD(T) level of theory has a tubular double-ring structure. Comparison of the simulated spectra with the experimental data shows that the global minimum quasi-planar B24- isomer is the major contributor to the observed photoelectron spectrum, while the tubular isomer has no contribution to the experiment. Chemical bonding analyses reveal that the periphery of the quasi-planar B24 constitutes 15 classical 2c-2e B-B σ-bonds, whereas delocalized σ- and π-bonds are found in the interior of the cluster with one unique 6c-2e π-bond responsible for bonding in the B-centered pentagon. The current work suggests that the 24-atom boron cluster continues to be quasi-2D, albeit the tendency to form filled pentagonal units, characteristic of 3D cage-like structures of bulk boron, is observed.

  8. Ab initio molecular dynamics studies of the structure and dynamics of molten SexTe1-x alloys

    NASA Astrophysics Data System (ADS)

    Lomba, E.; Katcho, N. A.; Otero-Díaz, L. C.

    2005-10-01

    We calculate the microscopic structure and dynamics of molten SexTe1-x alloys ( x=0.3 , 0.5, 0.7) at 748 K by means of ab initio molecular dynamics. We present results for the static and dynamic structure factors, diffusion coefficients, and frequency spectra, in addition to the electronic density of states. Both the results for the structural and dynamic properties are in relatively good agreement with the available experimental data, despite the known shortcomings of ab initio techniques for the limiting case x=0 . The results also indicate that, as expected, the increase in the number of Te atoms augments the metallic character of the sample in close connection with a corresponding disruption of the Se chain network that dominates the structure of the condensed phases of pure selenium.

  9. Ab initio cluster study of crystalline NaF

    SciTech Connect

    Temple, D.K.

    1992-01-01

    A highly-accurate ab initio cluster model of crystalline NaF has been constructed to explore the limits of cluster methods in the treatment of ionic solids. The focus of this model was the characterization of the lattice environment and its influence on the easily-polarizable fluorine anion. The model consisted of a central all-electron fluorine anion coordinated by pseudopotentials, to represent the nearest-neighbor sodium cations, and a finite array of point charges chosen to generate the correct crystal field from the surrounding infinite ionic lattice. The wavefunction and properties of the anion were calculated using the restricted Hartree-Fock and configuration interaction techniques from quantum chemistry. An extensive analysis of basis set incompleteness errors in the anion wavefunction was performed. Important features were identified in the embedded anion, such as its distortion under the influence of the lattice compressions, its stabilization from the Madelung potential, and its changes in size due to electron correlations. Bulk properties of the rocksalt-structure (B1) NaF crystal were derived from the total mode energies, calculated as a function of the crystal volume. The properties included the zero-pressure lattice constant, cohesive energy, and bulk modulus, and the pressure-volume equation-of-state. A series of test calculations explored the relationships, and their underlying physical mechanisms, between the features of the embedded anion and the bulk properties of the crystal. These features often produced opposing changes in the properties, demonstrating the importance of a thorough and systematic treatment of the embedded anion. The most thorough test calculation gave bulk properties that were within 1% of experiment. Using an embedded anion model for the high-pressure cesium-chloride (B2) phase of NaF, the B1-to-B2 structural transition was correctly predicted at 25 GPa, in excellent agreement with the experimental values of 23 to 27 GPa.

  10. Cosmic-Ray Modulation: an Ab Initio Approach

    NASA Astrophysics Data System (ADS)

    Engelbrecht, N. E.; Burger, R. A.

    2014-10-01

    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.

  11. Efficient conformational space exploration in ab initio protein folding simulation.

    PubMed

    Ullah, Ahammed; Ahmed, Nasif; Pappu, Subrata Dey; Shatabda, Swakkhar; Ullah, A Z M Dayem; Rahman, M Sohel

    2015-08-01

    Ab initio protein folding simulation largely depends on knowledge-based energy functions that are derived from known protein structures using statistical methods. These knowledge-based energy functions provide us with a good approximation of real protein energetics. However, these energy functions are not very informative for search algorithms and fail to distinguish the types of amino acid interactions that contribute largely to the energy function from those that do not. As a result, search algorithms frequently get trapped into the local minima. On the other hand, the hydrophobic-polar (HP) model considers hydrophobic interactions only. The simplified nature of HP energy function makes it limited only to a low-resolution model. In this paper, we present a strategy to derive a non-uniform scaled version of the real 20×20 pairwise energy function. The non-uniform scaling helps tackle the difficulty faced by a real energy function, whereas the integration of 20×20 pairwise information overcomes the limitations faced by the HP energy function. Here, we have applied a derived energy function with a genetic algorithm on discrete lattices. On a standard set of benchmark protein sequences, our approach significantly outperforms the state-of-the-art methods for similar models. Our approach has been able to explore regions of the conformational space which all the previous methods have failed to explore. Effectiveness of the derived energy function is presented by showing qualitative differences and similarities of the sampled structures to the native structures. Number of objective function evaluation in a single run of the algorithm is used as a comparison metric to demonstrate efficiency. PMID:26361554

  12. AN AB INITIO MODEL FOR COSMIC-RAY MODULATION

    SciTech Connect

    Engelbrecht, N. E.; Burger, R. A.

    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.

  13. Efficient conformational space exploration in ab initio protein folding simulation

    PubMed Central

    Ullah, Ahammed; Ahmed, Nasif; Pappu, Subrata Dey; Shatabda, Swakkhar; Ullah, A. Z. M. Dayem; Rahman, M. Sohel

    2015-01-01

    Ab initio protein folding simulation largely depends on knowledge-based energy functions that are derived from known protein structures using statistical methods. These knowledge-based energy functions provide us with a good approximation of real protein energetics. However, these energy functions are not very informative for search algorithms and fail to distinguish the types of amino acid interactions that contribute largely to the energy function from those that do not. As a result, search algorithms frequently get trapped into the local minima. On the other hand, the hydrophobic–polar (HP) model considers hydrophobic interactions only. The simplified nature of HP energy function makes it limited only to a low-resolution model. In this paper, we present a strategy to derive a non-uniform scaled version of the real 20×20 pairwise energy function. The non-uniform scaling helps tackle the difficulty faced by a real energy function, whereas the integration of 20×20 pairwise information overcomes the limitations faced by the HP energy function. Here, we have applied a derived energy function with a genetic algorithm on discrete lattices. On a standard set of benchmark protein sequences, our approach significantly outperforms the state-of-the-art methods for similar models. Our approach has been able to explore regions of the conformational space which all the previous methods have failed to explore. Effectiveness of the derived energy function is presented by showing qualitative differences and similarities of the sampled structures to the native structures. Number of objective function evaluation in a single run of the algorithm is used as a comparison metric to demonstrate efficiency. PMID:26361554

  14. Ab initio no-core shell model with continuum

    NASA Astrophysics Data System (ADS)

    Navratil, Petr

    2008-04-01

    The ab initio no-core shell model (NCSM) is a many-body approach to nuclear structure of light nuclei. The NCSM adopts an effective interaction theory to transform fundamental inter-nucleon interactions into effective interactions for a specified nucleus in a selected harmonic oscillator basis space [1]. The method is capable of predicting nuclear structure from inter-nucleon forces derived from quantum chromodynamics by means of chiral effective field theory [2]. NCSM extensions to the microscopic description of nuclear reactions are now under development. In my talk, I will first discuss our recent calculations of the ^4He total photo-absorption cross section using two- and three-nucleon interactions from chiral effective field theory [3]. I will then outline our effort to augment the NCSM by the resonating group method (RGM) technique to develop a new method capable of describing simultaneously both bound states and nuclear reactions on light nuclei [4]. This approach, which preserves translational symmetry and the Pauli principle, will allow us to calculate cross sections of reactions important for astrophysics and describe weakly-bound systems from first principles. I will present our first phase shift results for neutron scattering off ^3H, ^4He and ^7Li and proton scattering off ^3He, ^4He and ^7Be using realistic nucleon-nucleon potentials. 3mm [1] P. Navr'atil, J. P. Vary and B. R. Barrett, Phys. Rev. C 62, 054311 (2000). [2] P. Navr'atil and V. G. Gueorguiev and J. P. Vary, W. E. Ormand and A. Nogga, Phys. Rev. Lett. 99, 042501 (2007). [3] S. Quaglioni and P. Navr'atil, Phys. Lett. B 652, 370 (2007). [4] S. Quaglioni and P. Navr'atil, arXiv:0712.0855.

  15. Ab-initio calculations of electronic, transport, and structural properties of boron phosphide

    SciTech Connect

    Ejembi, J. I.; Nwigboji, I. H.; Franklin, L.; Malozovsky, Y.; Zhao, G. L.; Bagayoko, D.

    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.

  16. Ab initio based investigation of interstitial interactions and Snoek relaxation in Nb-O

    NASA Astrophysics Data System (ADS)

    Dmitriev, V. V.; Blanter, M. S.; Ruban, A. V.; Johansson, B.

    2012-02-01

    Chemical and strain-induced effective pair interactions of interstitial oxygen atoms in bcc Nb have been determined in supercell first-principles calculations using Vienna ab initio simulation package (VASP). The strain-induced interactions are in reasonable agreement with those obtained earlier within a phenomenological microscopic Krivoglaz-Kanzaki-Khachaturyan model (KKKM). At the same time, the chemical interactions, which have been considered to be small in earlier theoretical considerations, turned out to be dominating at the first several coordination shells. The obtained interactions have been used in calculations of the concentration- and temperature-dependence of the internal friction Snoek peak. The theoretical results are found to be in good agreement with the existing experimental data.

  17. Ab initio calculations on magnetism induced by composite defects in magnesium oxide

    SciTech Connect

    Zhang, Yao-Fang; Feng, Min; Shao, Bin; Lu, Yuan; Zuo, Xu; Liu, Hong

    2014-05-07

    The local magnetic state induced by the composite defects, composed of an oxygen vacancy and a nitrogen substituting oxygen, in magnesium oxide has been studied by using ab initio calculation based on density functional theory. The calculated results show that local magnetic moment can be induced by the composite defects around the oxygen vacancy, when the exchange split of the oxygen vacancy is enhanced either by the hybridization between the N-p and nearest neighbor O-p orbitals or by applying on-site Coulomb repulsion (U) and exchange interaction (J). We show that the magnetic state induced by the composite defect is energetically more stable than the non-magnetic state. In addition, we show that the U and J applied on the p-orbitals of N and O atoms may significantly impact the calculated magnetic state of the composite defect, resulting in magnetic state for a configuration that is non-magnetic by generalized gradient approximation.

  18. Stress reduction of Cu-doped diamond-like carbon films from ab initio calculations

    SciTech Connect

    Li, Xiaowei; Ke, Peiling; Wang, Aiying

    2015-01-15

    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.

  19. Pressure effect on elastic anisotropy of crystals from ab initio simulations: the case of silicate garnets.

    PubMed

    Mahmoud, A; Erba, A; Doll, K; Dovesi, R

    2014-06-21

    A general methodology has been devised and implemented into the solid-state ab initio quantum-mechanical Crystal program for studying the evolution under geophysical pressure of the elastic anisotropy of crystalline materials. This scheme, which fully exploits both translational and point symmetry of the crystal, is developed within the formal frame of one-electron Hamiltonians and atom-centered basis functions. Six silicate garnet end-members, among the most important rock-forming minerals of the Earth's mantle, are considered, whose elastic anisotropy is fully characterized under high hydrostatic compressions, up to 60 GPa. The pressure dependence of azimuthal anisotropy and shear-wave birefringence of seismic wave velocities for these minerals are accurately simulated and compared with available single-crystal measurements. PMID:24952556

  20. Experimental and ab initio investigations of microscopic properties of laser-shocked Ge-doped ablator

    NASA Astrophysics Data System (ADS)

    Huser, G.; Recoules, V.; Ozaki, N.; Sano, T.; Sakawa, Y.; Salin, G.; Albertazzi, B.; Miyanishi, K.; Kodama, R.

    2015-12-01

    Plastic materials (CH) doped with mid-Z elements are used as ablators in inertial confinement fusion (ICF) capsules and in their surrogates. Hugoniot equation of state (EOS) and electronic properties of CH doped with germanium (at 2.5% and 13% dopant fractions) are investigated experimentally up to 7 Mbar using velocity and reflectivity measurements of shock fronts on the GEKKO laser at Osaka University. Reflectivity and temperature measurements were updated using a quartz standard. Shocked quartz reflectivity was measured at 532 and 1064 nm. Theoretical investigation of shock pressure and reflectivity was then carried out by ab initio simulations using the quantum molecular dynamics (QMD) code abinit and compared with tabulated average atom EOS models. We find that shock states calculated by QMD are in better agreement with experimental data than EOS models because of a more accurate description of ionic structure. We finally discuss electronic properties by comparing reflectivity data to a semiconductor gap closure model and to QMD simulations.

  1. Polymerization transition in liquid AsS under pressure: An ab initio molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Ohmura, Satoshi; Shimojo, Fuyuki

    2011-12-01

    We study the pressure dependence of the structural and electronic properties of liquid AsS by ab initio molecular dynamics simulations. We confirm that liquid AsS consists of As4S4 molecules at ambient pressure, as in the crystalline state. With increasing pressure, a structural transition from molecular to polymeric liquid occurs near 2 GPa, which is eventually followed by metallization. The pressure dependence of the density and diffusion coefficients changes qualitatively with this transition. We find that, during metallization in the polymeric phase at higher pressures, the remnants of covalent interactions between atoms play an important role in the dynamics, i.e., the As-S bond length becomes longer with increasing pressure and the diffusion coefficients have a local maximum near 5 GPa. When the pressure approaches about 15 GPa, the covalent nature of the liquid becomes quite weak. These results explain recent experiments on the pressure dependence of the viscosity.

  2. HEAT: High accuracy extrapolated ab initio thermochemistry. III. Additional improvements and overview.

    SciTech Connect

    Harding, M. E.; Vazquez, J.; Ruscic, B.; Wilson, A. K.; Gauss, J.; Stanton, J. F.; Chemical Sciences and Engineering Division; Univ. t Mainz; The Univ. of Texas; Univ. of North Texas

    2008-01-01

    Effects of increased basis-set size as well as a correlated treatment of the diagonal Born-Oppenheimer approximation are studied within the context of the high-accuracy extrapolated ab initio thermochemistry (HEAT) theoretical model chemistry. It is found that the addition of these ostensible improvements does little to increase the overall accuracy of HEAT for the determination of molecular atomization energies. Fortuitous cancellation of high-level effects is shown to give the overall HEAT strategy an accuracy that is, in fact, higher than most of its individual components. In addition, the issue of core-valence electron correlation separation is explored; it is found that approximate additive treatments of the two effects have limitations that are significant in the realm of <1 kJ mol{sup -1} theoretical thermochemistry.

  3. Ab initio calculations of the reaction pathways for methane decomposition over the Cu (111) surface

    NASA Astrophysics Data System (ADS)

    Gajewski, Grzegorz; Pao, Chun-Wei

    2011-08-01

    Growth of large-area, few-layer graphene has been reported recently through the catalytic decomposition of methane (CH4) over a Cu surface at high temperature. In this study, we used ab initio calculations to investigate the minimum energy pathways of successive dehydrogenation reactions of CH4 over the Cu (111) surface. The geometries and energies of all the reaction intermediates and transition states were identified using the climbing image nudged elastic band method. The activation barriers for CH4 decomposition over this Cu surface are much lower than those in the gas phase; furthermore, analysis of electron density differences revealed significant degrees of charge transfer between the adsorbates and the Cu atoms along the reaction path; these features reveal the role of Cu as the catalytic material for graphene growth. All the dehydrogenation reactions are endothermic, except for carbon dimer (C2) formation, which is, therefore, the most critical step for subsequent graphene growth, in particular, on Cu (111) surface.

  4. Ab-initio study on crystal structure of α-RuCl3

    NASA Astrophysics Data System (ADS)

    Kee, Hae-Young; Kim, Heung-Sik

    α -RuCl3 was recently proposed as a candidate system for materialization of Kitaev model, but precise structural information of the compound has remained elusive. For the clarification of the full three-dimensional crystal structure of α-RuCl3, we performed ab-initio electronic structure calculations including effects of spin-orbit coupling (SOC) and electron correlations. We found that SOC prevents dimerization between Ru atoms, and keeps the system close to honeycomb lattice. The ground state crystal structure has monoclinic C 2 / m -type layer stacking, but trigonal P31 12 -and orthorhombic Cmc21 -type stacking orders are comparable to the C 2 / m structure in energy, so that stacking faults can be easily introduced. The electronic structure and the jeff=1/2 pseudospin exchange interactions and possible magnetic states in α-RuCl3 will be presented.

  5. Ab-initio Calculations of Electronic Properties of Boron Phosphide (BP)

    NASA Astrophysics Data System (ADS)

    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.

  6. Mapping Enzymatic Catalysis Using the Effective Fragment Molecular Orbital Method: Towards all ab initio Biochemistry

    PubMed Central

    Steinmann, Casper; Fedorov, Dmitri G.; Jensen, Jan H.

    2013-01-01

    We extend the Effective Fragment Molecular Orbital (EFMO) method to the frozen domain approach where only the geometry of an active part is optimized, while the many-body polarization effects are considered for the whole system. The new approach efficiently mapped out the entire reaction path of chorismate mutase in less than four days using 80 cores on 20 nodes, where the whole system containing 2398 atoms is treated in the ab initio fashion without using any force fields. The reaction path is constructed automatically with the only assumption of defining the reaction coordinate a priori. We determine the reaction barrier of chorismate mutase to be kcal mol−1 for MP2/cc-pVDZ and for MP2/cc-pVTZ in an ONIOM approach using EFMO-RHF/6-31G(d) for the high and low layers, respectively. PMID:23593259

  7. Ab-initio study of magnetism behavior in TiO2 semiconductor with structural defects

    NASA Astrophysics Data System (ADS)

    Zarhri, Z.; Houmad, M.; Ziat, Y.; El Rhazouani, O.; Slassi, A.; Benyoussef, A.; El Kenz, A.

    2016-05-01

    Magnetic, electronic and structural properties of titanium dioxide material with different structural defects are studied using the first-principles ab-initio calculations and the Korringa-Kohn-Rostoker method (KKR) combined with the coherent potential approximation (CPA) method in connection with the local density approximation (LDA). We investigated all structural defects in rutile TiO2 such as Titanium interstitial (Tii), Titanium anti-sites (Tio), Titanium vacancies (VTi), Oxygen interstitial (Oi), Oxygen anti-sites (OTi) and oxygen vacancies (Vo). Mechanisms of hybridization and interaction between magnetic atoms are investigated. The transition temperature is computed using the Mean Field Approximation (MFA).Magnetic stability energy of ferromagnetic and disordered local moment states is calculated to determine the most stable state. Titanium anti-sites have a half-metallic aspect. We also studied the change type caused by structural defects in this material.

  8. Pressure effect on elastic anisotropy of crystals from ab initio simulations: The case of silicate garnets

    SciTech Connect

    Mahmoud, A.; Erba, A. Dovesi, R.; Doll, K.

    2014-06-21

    A general methodology has been devised and implemented into the solid-state ab initio quantum-mechanical CRYSTAL program for studying the evolution under geophysical pressure of the elastic anisotropy of crystalline materials. This scheme, which fully exploits both translational and point symmetry of the crystal, is developed within the formal frame of one-electron Hamiltonians and atom-centered basis functions. Six silicate garnet end-members, among the most important rock-forming minerals of the Earth's mantle, are considered, whose elastic anisotropy is fully characterized under high hydrostatic compressions, up to 60 GPa. The pressure dependence of azimuthal anisotropy and shear-wave birefringence of seismic wave velocities for these minerals are accurately simulated and compared with available single-crystal measurements.

  9. reaxFF Reactive Force Field for Disulfide Mechanochemistry, Fitted to Multireference ab Initio Data.

    PubMed

    Müller, Julian; Hartke, Bernd

    2016-08-01

    Mechanochemistry, in particular in the form of single-molecule atomic force microscopy experiments, is difficult to model theoretically, for two reasons: Covalent bond breaking is not captured accurately by single-determinant, single-reference quantum chemistry methods, and experimental times of milliseconds or longer are hard to simulate with any approach. Reactive force fields have the potential to alleviate both problems, as demonstrated in this work: Using nondeterministic global parameter optimization by evolutionary algorithms, we have fitted a reaxFF force field to high-level multireference ab initio data for disulfides. The resulting force field can be used to reliably model large, multifunctional mechanochemistry units with disulfide bonds as designed breaking points. Explorative calculations show that a significant part of the time scale gap between AFM experiments and dynamical simulations can be bridged with this approach. PMID:27415976

  10. An investigation of ab initio shell-model interactions derived by no-core shell model

    NASA Astrophysics Data System (ADS)

    Wang, XiaoBao; Dong, GuoXiang; Li, QingFeng; Shen, CaiWan; Yu, ShaoYing

    2016-09-01

    The microscopic shell-model effective interactions are mainly based on the many-body perturbation theory (MBPT), the first work of which can be traced to Brown and Kuo's first attempt in 1966, derived from the Hamada-Johnston nucleon-nucleon potential. However, the convergence of the MBPT is still unclear. On the other hand, ab initio theories, such as Green's function Monte Carlo (GFMC), no-core shell model (NCSM), and coupled-cluster theory with single and double excitations (CCSD), have made many progress in recent years. However, due to the increasing demanding of computing resources, these ab initio applications are usually limited to nuclei with mass up to A = 16. Recently, people have realized the ab initio construction of valence-space effective interactions, which is obtained through a second-time renormalization, or to be more exactly, projecting the full-manybody Hamiltonian into core, one-body, and two-body cluster parts. In this paper, we present the investigation of such ab initio shell-model interactions, by the recent derived sd-shell effective interactions based on effective J-matrix Inverse Scattering Potential (JISP) and chiral effective-field theory (EFT) through NCSM. In this work, we have seen the similarity between the ab initio shellmodel interactions and the interactions obtained by MBPT or by empirical fitting. Without the inclusion of three-body (3-bd) force, the ab initio shell-model interactions still share similar defects with the microscopic interactions by MBPT, i.e., T = 1 channel is more attractive while T = 0 channel is more repulsive than empirical interactions. The progress to include more many-body correlations and 3-bd force is still badly needed, to see whether such efforts of ab initio shell-model interactions can reach similar precision as the interactions fitted to experimental data.

  11. Ab initio study of stability and migration of H and He in hcp-Sc

    SciTech Connect

    Yang, Li; Peng, SM; Long, XG; Gao, Fei; Heinisch, Howard L.; Kurtz, Richard J.; Zu, Xiaotao T.

    2011-01-05

    Ab initio calculations based on density functional theory have been performed to determine the relative stabilities and migration of H and He atoms in hcp-Sc. The results show that the formation energy of an interstitial H or He atom is smaller than that of a corresponding substitutional atom. The tetrahedral (T) interstitial position is more stable than an octahedral (O) position for both He and H interstitials. The nudged elastic band method has been used to study the migration of interstitial H and He atomss in hcp-Sc. It is found that the migration energy barriers for H interstitials in hcp-Sc are significantly different from those for He interstitials, but that their migration mechanisms are similar. In addition, the formation energies of five different configurations of a He-He pair were determined, revealing that the most stable configuration consists of two He atoms located at the second-neighbor tetrahedral interstitial sites along the c axis. The formation and relative stabilities of some small He clusters have also been investigated.

  12. Ab Initio Molecular Dynamics Simulations and GIPAW NMR Calculations of a Lithium Borate Glass Melt.

    PubMed

    Ohkubo, Takahiro; Tsuchida, Eiji; Takahashi, Takafumi; Iwadate, Yasuhiko

    2016-04-14

    The atomic structure of a molten 0.3Li2O-0.7B2O3 glass at 1250 K was investigated using ab initio molecular dynamics (AIMD) simulations. The gauge including projector augmented wave (GIPAW) method was then employed for computing the chemical shift and quadrupolar coupling constant of (11)B, (17)O, and (7)Li from 764 AIMD derived structures. The chemical shift and quadrupolar coupling constant distributions were directly estimated from the dynamical structure of the molten glass. (11)B NMR parameters of well-known structural units such as the three-coordinated ring, nonring, and four-coordinated tetrahedron were found to be in good agreement with the experimental results. In this study, more detailed classification of B units was presented based on the number of O species bonded to the B atoms. This highlights the limitations of (11)B NMR sensitivity for resolving (11)B local environment using the experimentally obtained spectra only. The (17)O NMR parameter distributions can theoretically resolve the bridging and nonbridging O atoms with different structural units such as nonring, single boroxol ring, and double boroxol ring. Slight but clear differences in the number of bridging O atoms surrounding Li that have not been reported experimentally were observed in the theoretically obtained (7)Li NMR parameters. PMID:27010637

  13. A new Fe–He interatomic potential based on ab initio calculations in α-Fe

    SciTech Connect

    Gao, Fei; Deng, Huiqiu; Heinisch, Howard L.; Kurtz, Richard J.

    2011-11-01

    A new interatomic potential for Fe−He interactions has been developed by fitting to the results obtained from ab initio calculations. Based on the electronic hybridization between Fe d-electrons and He s-electrons, an s-band model, along with a repulsive pair potential, has been developed to describe the Fe−He interaction. The atomic configurations and formation energies of single He defects and small interstitial He clusters are utilized in the fitting process. The binding properties and relative stabilities of the He-vacancy and interstitial He clusters are studied. The present Fe−He potential is also applied to study the emission of self-interstitial atoms from small He clusters in alpha-Fe matrices. It is found that the di-He cluster dissociates when the temperature is higher than 400K, but the larger He clusters can create an interstitial Fe atom. The temperature for kicking out an interstitial Fe atom is found to decrease with increasing size of the He clusters.

  14. Switchable magnetic moment in cobalt-doped graphene bilayer on Cu(111): An ab initio study

    NASA Astrophysics Data System (ADS)

    Souza, Everson S.; Scopel, Wanderlã L.; Miwa, R. H.

    2016-06-01

    In this work, we have performed an ab initio theoretical investigation of substitutional cobalt atoms in the graphene bilayer supported on the Cu(111) surface (Co/GBL/Cu). Initially, we examined the separated systems, namely, graphene bilayer adsorbed on Cu(111) (GBL/Cu) and a free standing Co-doped GBL (Co/GBL). In the former system, the GBL becomes n -type doped, where we map the net electronic charge density distribution along the GBL-Cu(111) interface. The substitutional Co atom in Co/GBL lies between the graphene layers, and present a net magnetic moment mostly due to the unpaired Co-3 dz2 electrons. In Co/GBL/Cu, we found that the Cu(111) substrate rules (i) the energetic stability, and (ii) the magnetic properties of substitutional Co atoms in the graphene bilayer. In (i), the substitutional Co atom becomes energetically more stable lying on the GBL surface, and in (ii), the magnetic moment of Co/GBL has been quenched due to the Cu(111) → Co/GBL electronic charge transfer. We verify that such a charge transfer can be tuned upon the application of an external electric field, and thus mediated by a suitable change on the electronic occupation of the Co-dz2 orbitals, we found a way to switch-on and -off the magnetization of the Co-doped GBL adsorbed on the Cu(111) surface.

  15. Revealing halogen bonding interactions with anomeric systems: an ab initio quantum chemical studies.

    PubMed

    Lo, Rabindranath; Ganguly, Bishwajit

    2015-02-01

    A computational study has been performed using MP2 and CCSD(T) methods on a series of O⋯X (X=Br, Cl and I) halogen bonds to evaluate the strength and characteristic of such highly directional noncovalent interactions. The study has been carried out on a series of dimeric complexes formed between interhalogen compounds (such as BrF, BrCl and BrI) and oxygen containing electron donor molecule. The existence and consequences of the anomeric effect of the electron donor molecule has also been investigated through an exploration of halogen bonding interactions in this halogen bonded complexes. The ab initio quantum chemical calculations have been employed to study both the nature and directionality of the halogen molecules toward the sp(3) oxygen atom in anomeric systems. The presence of anomeric nO→σ*CN interaction involves a dominant role for the availability of the axial and equatorial lone pairs of donor O atom to participate with interhalogen compounds in the halogen-bonded complexes. The energy difference between the axial and equatorial conformers with interhalogen compounds reaches up to 4.60 kJ/mol, which however depends upon the interacting halogen atoms and its attaching atoms. The energy decomposition analysis further suggests that the total halogen bond interaction energies are mainly contributed by the attractive electrostatic and dispersion components. The role of substituents attached with the halogen atoms has also been evaluated in this study. With the increase of halogen atom size and the positive nature of σ-hole, the halogen atom interacted more with the electron donor atom and the electrostatic contribution to the total interaction energy enhances appreciably. Further, noncovalent interaction (NCI) studies have been carried out to locate the noncovalent halogen bonding interactions in real space. PMID:25522359

  16. An ab initio study of relationships between bond lengths and the harmonic and anharmonic cross-coupling constants involving the double bonds in hetero-atom substituted conjugated dienes

    NASA Astrophysics Data System (ADS)

    Bock, Charles W.; Trachtman, Mendel; George, Philip

    1982-12-01

    The lengths of the terminal double bonds and the central CC single bond, and the cross-coupling constant involving the double bonds, calculated ab initio using the unscaled 4-31G basis set, are reported for 15 planar conformers of conjugated dienes containing the OCC'C″ grouping, 9 planar conformers containing the OCC'N grouping, and 6 planar conformers containing the OCC'O'grouping. The larger values for the CC bond length tend to be associated with the smaller values for the double-bond lengths, and vice versa. A linear relationship holds fairly well between rcc and the sum of the double-bond lengths. The sign of the cross-coupling constant is the same for each type of conjugated diene, negative for foc.c'c″ and foc.c'N' but positive for foc.c'o'. The values of foc.c'c″ and f oc.c'N are larger the smaller rcc' in accord with a linear relationship. For all three types of diene the values for pairs of cis and trans conformers do not differ very much, the ratio fcis/ ftrans being a little greater than 1 in ten cases and a little less than 1 in six cases. This lack of any marked difference between cis and trans conformers suggests that the coupling between the double bonds occurs in the main via the bonded framework of the molecule, and that "through-space" interactions, which would be a special feature of cis conformers, are of relatively little importance.

  17. Ab Initio and Analytic Intermolecular Potentials for Ar–CH3OH

    SciTech Connect

    Tasic, Uros; Alexeev, Yuri; Vayner, Grigoriy; Crawford, T Daniel; Windus, Theresa L.; Hase, William L.

    2006-09-20

    Ab initio calculations at the CCSD(T)/aug-cc-pVTZ level of theory were used to characterize the Ar–CH₃y6tOH intermolecular potential energy surface (PES). Potential energy curves were calculated for four different Ar + CH₃OH orientations and used to derive an analytic function for the intermolecular PES. A sum of Ar–C, Ar–O, Ar–H(C), and Ar–H(O) two-body potentials gives an excellent fit to these potential energy curves up to 100 kcal mol¯¹, and adding an additional r¯¹n term to the Buckingham two-body potential results in only a minor improvement in the fit. Three Ar–CH₃OH van der Waals minima were found from the CCSD(T)/aug-cc-pVTZ//MP2/aug-cc-pVTZ calculations. The structure of the global minimum is in overall good agreement with experiment (X.-C. Tan, L. Sun and R. L. Kuczkowski, J. Mol. Spectrosc., 1995, 171, 248). It is T-shaped with the hydroxyl H-atom syn with respect to Ar. Extrapolated to the complete basis set (CBS) limit, the global minimum has a well depth of 0.72 kcal mol¯¹ with basis set superposition error (BSSE) correction. The aug-cc-pVTZ basis set gives a well depth only 0.10 kcal mol¯¹ smaller than this value. The well depths of the other two minima are within 0.16 kcal mol¯¹ of the global minimum. The analytic Ar–CH₃OH intermolecular potential also identifies these three minima as the only van der Waals minima and the structures predicted by the analytic potential are similar to the ab initio structures. The analytic potential identifies the same global minimum and the predicted well depths for the minima are within 0.05 kcal mol¯1 of the ab initio values. Combining this Ar–CH₃OH intermolecular potential with a potential for a OH-terminated alkylthiolate self-assembled monolayer surface (i.e., HO-SAM) provides a potential to model Ar + HO-SAM collisions.

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

    PubMed

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

    2005-04-22

    The X2Pi g-2Sigma g+, X2Pi g-2Delta g, X2Pi g-2Sigma u+, X2Pi g-2Pi u transitions on CuCl2 have been studied using several exchange-correlation functionals from the various types of density functional theory (DFT) approaches like local density approximation (LDA), generalized gradient approximation (GGA), hybrid and meta-GGA. The results are compared with the experience and with those coming from the most sophisticated nondynamic and dynamic electronic correlation treatments using the same relativistic effective core potentials and especially developed basis sets to study the electronic structure of the five lowest states and the corresponding vertical and adiabatic transition energies. The calculated transition energies for three of the hybrid functionals (B3LYP, B97-2, and PBE0) are in very good agreement with the benchmark ab initio results and experimental figures. All of the other functionals largely overestimate the X2Pi g-2Sigma g+ and X2Pi g-2Delta g transition energies, many of them even placing the 2Delta g ligand field state above the charge transfer 2Pi u and 2Sigma u+ states. The relative weight of the Hartree-Fock exchange in the definition of the functional used appears to play a key role in the accurate description of the LambdaSSigma density defined by the orientation of the 3d hole (sigma, pi, or delta) on Cu in the field of both chlorine atoms, but no simple connection of this weight with the quality of the spectra has been found. Mulliken charges and spin densities are carefully analyzed; a possible link between the extent of spin density on the metal for the X2Pi g state and the performance of the various functionals was observed, suggesting that those that lead to the largest values (close to 0.65) are the ones that best reproduce these four transitions. Most functionals lead to a remarkably low ionicity for the three ligand field states even for the best performing functionals, compared to the complete active space (SCF) (21, 14) ab initio

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

    NASA Astrophysics Data System (ADS)

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

    2005-04-01

    The XΠg2-Σg +2, XΠg2-Δg2, XΠg2-Σu +2, XΠg2-Πu2 transitions on CuCl2 have been studied using several exchange-correlation functionals from the various types of density functional theory (DFT) approaches like local density approximation (LDA), generalized gradient approximation (GGA), hybrid and meta-GGA. The results are compared with the experience and with those coming from the most sophisticated nondynamic and dynamic electronic correlation treatments using the same relativistic effective core potentials and especially developed basis sets to study the electronic structure of the five lowest states and the corresponding vertical and adiabatic transition energies. The calculated transition energies for three of the hybrid functionals (B3LYP, B97-2, and PBE0) are in very good agreement with the benchmark ab initio results and experimental figures. All of the other functionals largely overestimate the XΠg2-Σg +2 and XΠg2-Δg2 transition energies, many of them even placing the Δg2 ligand field state above the charge transfer Πu2 and Σu +2 states. The relative weight of the Hartree-Fock exchange in the definition of the functional used appears to play a key role in the accurate description of the ΛSΣ density defined by the orientation of the 3d hole (σ, π, or δ) on Cu in the field of both chlorine atoms, but no simple connection of this weight with the quality of the spectra has been found. Mulliken charges and spin densities are carefully analyzed; a possible link between the extent of spin density on the metal for the XΠg2 state and the performance of the various functionals was observed, suggesting that those that lead to the largest values (close to 0.65) are the ones that best reproduce these four transitions. Most functionals lead to a remarkably low ionicity for the three ligand field states even for the best performing functionals, compared to the complete active space (SCF) (21, 14) ab initio values. These findings show that not only large

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

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

    Recent developments in path integral methodology have significantly reduced the computational expense of including quantum mechanical effects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of these developments requires a considerable programming effort, which has hindered their adoption. Here we describe i-PI, an interface written in Python that has been designed to minimise the effort required to bring state-of-the-art path integral techniques to an electronic structure program. While it is best suited to first principles calculations and path integral molecular dynamics, i-PI can also be used to perform classical molecular dynamics simulations, and can just as easily be interfaced with an empirical forcefield code. To give just one example of the many potential applications of the interface, we use it in conjunction with the CP2K electronic structure package to showcase the importance of nuclear quantum effects in high-pressure water. Catalogue identifier: AERN_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AERN_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 138626 No. of bytes in distributed program, including test data, etc.: 3128618 Distribution format: tar.gz Programming language: Python. Computer: Multiple architectures. Operating system: Linux, Mac OSX, Windows. RAM: Less than 256 Mb Classification: 7.7. External routines: NumPy Nature of problem: Bringing the latest developments in the modelling of nuclear quantum effects with path integral molecular dynamics to ab initio electronic structure programs with minimal implementational effort. Solution method: State-of-the-art path integral molecular dynamics techniques are implemented in a Python interface. Any electronic structure code can be patched to receive the atomic

  1. Ab initio study of the electrostatic multipole nature of torsional potentials in CH3SSCH3, CH3SSH, and HOOH

    NASA Technical Reports Server (NTRS)

    Sokalski, W. A.; Lai, J.; Luo, N.; Sun, S.; Shibata, M.; Ornstein, R.; Rein, R.

    1991-01-01

    The origin of torsional potentials in H3CSSCH3, H3CSSH, and HOOH and the anisotropy of the local charge distribution has been analyzed in terms of atomic multipoles calculated from the ab initio LCAO-MO-SCF wave function in the 6-31G* basis set. The results indicate that for longer -S-S-bonds the major contribution to these torsional barriers are electrostatic interactions of the atomic multipoles located on two atoms forming the rotated bond. This finding demonstrates the important role of electrostatic 1-2 interatomic interactions, usually neglected in conformational studies. It also opens the possibility to derive directly from accurate ab initio wave functions a simple nonempirical torsional potential involving atomic multipoles of two bonded atoms defining the torsional angle. For shorter -O-O- bonds, use of more precise models and inclusion of 1-3 interactions seems to be necessary.

  2. Ab initio study of the electrostatic multipole nature of torsional potentials in CH3SSCH3, CH3SSH, and HOOH.

    PubMed

    Sokalski, W A; Lai, J; Luo, N; Sun, S; Shibata, M; Ornstein, R; Rein, R

    1991-01-01

    The origin of torsional potentials in H3CSSCH3, H3CSSH, and HOOH and the anisotropy of the local charge distribution has been analyzed in terms of atomic multipoles calculated from the ab initio LCAO-MO-SCF wave function in the 6-31G* basis set. The results indicate that for longer -S-S-bonds the major contribution to these torsional barriers are electrostatic interactions of the atomic multipoles located on two atoms forming the rotated bond. This finding demonstrates the important role of electrostatic 1-2 interatomic interactions, usually neglected in conformational studies. It also opens the possibility to derive directly from accurate ab initio wave functions a simple nonempirical torsional potential involving atomic multipoles of two bonded atoms defining the torsional angle. For shorter -O-O- bonds, use of more precise models and inclusion of 1-3 interactions seems to be necessary. PMID:11538107

  3. Ab initio quantum chemical investigation of arsenic sulfide molecular diversity from As4S6 and As4

    NASA Astrophysics Data System (ADS)

    Kyono, Atsushi

    2013-10-01

    The structural diversity of arsenic sulfide molecules in compositions between As4S6 and As4 was investigated using ab initio quantum chemical calculations. The As4S6 molecule consists of four trigonal pyramid coordinations of As atoms bonding to three S atoms. In the As4S5 composition, only one type of molecular configuration corresponds to an uzonite-type molecule. In the As4S4 composition, two molecular configurations exist with realgar-type and pararealgar-type molecules. Three molecular configurations are in the As4S3 composition. The first configuration comprises trigonal pyramidal As atom coordinations of two types: bonding to two S atoms and one As atom, and bonding to one S atom and two As atoms. The second is the molecular configuration of dimorphite. The third comprises trigonal pyramidal As atom coordinations of two types: bonding to three As atoms, and bonding to one As atom and two S atoms. The As4S2 composition allows molecular configurations of two types. One is comprised of trigonal pyramidal As atom configurations of one type bonding to two As atoms and one S atom. The other comprises trigonal pyramidal As atom coordinations of three types: bonding to two S atoms and one As atoms, bonding to one S atom and two As atoms, and bonding to three As atoms. The As4S molecule has trigonal pyramidal As atom coordinations of two types: bonding to one S atom and two As atoms, and bonding to three As atoms. The As4S composition permits only one molecular configuration, which suggests that the mineral duranusite comprises the As4S molecular geometry. In all, ten molecular configurations are predicted in the molecular hierarchy of the arsenic sulfide binary system. The simulated Raman spectral profiles are helpful in searching for undiscovered arsenic sulfide minerals.

  4. Emergent properties of nuclei from ab initio coupled-cluster calculations

    DOE PAGESBeta

    Hagen, G.; Hjorth-Jensen, M.; Jansen, G. R.; Papenbrock, T.

    2016-05-17

    Emergent properties such as nuclear saturation and deformation, and the effects on shell structure due to the proximity of the scattering continuum and particle decay channels are fascinating phenomena in atomic nuclei. In recent years, ab initio approaches to nuclei have taken the first steps towards tackling the computational challenge of describing these phenomena from Hamiltonians with microscopic degrees of freedom. Our endeavor is now possible due to ideas from effective field theories, novel optimization strategies for nuclear interactions, ab initio methods exhibiting a soft scaling with mass number, and ever-increasing computational power. We review some of the recent accomplishments. We also present new results. The recently optimized chiral interaction NNLOmore » $${}_{{\\rm{sat}}}$$ is shown to provide an accurate description of both charge radii and binding energies in selected light- and medium-mass nuclei up to 56Ni. We derive an efficient scheme for including continuum effects in coupled-cluster computations of nuclei based on chiral nucleon–nucleon and three-nucleon forces, and present new results for unbound states in the neutron-rich isotopes of oxygen and calcium. Finally, the coupling to the continuum impacts the energies of the $${J}^{\\pi }=1/{2}^{-},3/{2}^{-},7/{2}^{-},3/{2}^{+}$$ states in $${}^{\\mathrm{17,23,25}}$$O, and—contrary to naive shell-model expectations—the level ordering of the $${J}^{\\pi }=3/{2}^{+},5/{2}^{+},9/{2}^{+}$$ states in $${}^{\\mathrm{53,55,61}}$$Ca.« less

  5. Far infrared spectra, conformational equilibria, vibrational assignments, ab initio calculations and structural parameters for 2-bromoethanol

    NASA Astrophysics Data System (ADS)

    Durig, J. R.; Shen, S.; Guirgis, G. A.

    2001-01-01

    The far infrared spectrum from 370 to 50 cm -1 of gaseous 2-bromoethanol, BrCH 2CH 2OH, was recorded at a resolution of 0.10 cm -1. The fundamental O-H torsion of the more stable gauche ( Gg') conformer, where the capital G refers to internal rotation around the C-C bond and the lower case g to the internal rotation around the C-O bond, was observed as a series of Q-branch transitions beginning at 340 cm -1. The corresponding O-H torsional modes were observed for two of the other high energy conformers, Tg (285 cm -1) and Tt (234 cm -1). The heavy atom asymmetric torsion (rotation around C-C bond) for the Gg' conformer has been observed at 140 cm -1. Variable temperature (-63 to -100°C) studies of the infrared spectra (4000-400 cm -1) of the sample dissolved in liquid xenon have been recorded. From these data the enthalpy differences have been determined to be 411±40 cm -1 (4.92±0.48 kJ/mol) for the Gg'/ Tt and 315±40 cm -1 (3.76±0.48 kJ/mol) for the Gg'/ Tg, with the Gg' conformer the most stable form. Additionally, the infrared spectrum of the gas, and Raman spectrum of the liquid phase are reported. The structural parameters, conformational stabilities, barriers to internal rotation and fundamental frequencies have been obtained from ab initio calculations utilizing different basis sets at the restricted Hartree-Fock or with full electron correlation by the perturbation method to second order. The theoretical results are compared to the experimental results when appropriate. Combining the ab initio calculations with the microwave rotational constants, r0 adjusted parameters have been obtained for the three 2-haloethanols (F, Cl and Br) for the Gg' conformers.

  6. Efficient ab initio free energy calculations by classically assisted trajectory sampling

    NASA Astrophysics Data System (ADS)

    Wilson, Hugh F.

    2015-12-01

    A method for efficiently performing ab initio free energy calculations based on coupling constant thermodynamic integration is demonstrated. By the use of Boltzmann-weighted sums over states generated from a classical ensemble, the free energy difference between the classical and ab initio ensembles is readily available without the need for time-consuming integration over molecular dynamics trajectories. Convergence and errors in this scheme are discussed and characterised in terms of a quantity representing the degree of misfit between the classical and ab initio systems. Smaller but still substantial efficiency gains over molecular dynamics are also demonstrated for the calculation of average properties such as pressure and total energy for systems in equilibrium.

  7. Ab Initio and Phenomenological Modeling of the Phonon Spectrum of Superhard cp-BC2N

    NASA Astrophysics Data System (ADS)

    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.

  8. Electron Transport through Polyene Junctions in between Carbon Nanotubes: an Ab Initio Realization

    NASA Astrophysics Data System (ADS)

    Chen, Yiing-Rei; Chen, Kai-Yu; Dou, Kun-Peng; Tai, Jung-Shen; Lee, Hsin-Han; Kaun, Chao-Cheng

    With both ab initio and tight-binding model calculations, we study a system of polyene bridged armchair carbon nanotube electrodes, considering one-polyene and two-polyene cases, to address aspects of quantum transport through junctions with multiple conjugated molecules. The ab initio results of the two-polyene cases not only show the interference effect in transmission, but also the sensitive dependence of such effect on the combination of relative contact sites, which agrees nicely with the tight-binding model. Moreover, we show that the discrepancy mainly brought by ab initio relaxation provides an insight into the influence upon transmission spectra, from the junction's geometry, bonding and effective potential. This work was supported by the Ministry of Science and Technology of the Republic of China under Grant Nos. 99-2112-M-003-012-MY2 and 103-2622-E-002-031, and the National Center for Theoretical Sciences of Taiwan.

  9. Exploring the speed and performance of molecular replacement with AMPLE using QUARK ab initio protein models

    SciTech Connect

    Keegan, Ronan M.; Bibby, Jaclyn; Thomas, Jens; Xu, Dong; Zhang, Yang; Mayans, Olga; Winn, Martyn D.; Rigden, Daniel J.

    2015-02-01

    Two ab initio modelling programs solve complementary sets of targets, enhancing the success of AMPLE with small proteins. AMPLE clusters and truncates ab initio protein structure predictions, producing search models for molecular replacement. Here, an interesting degree of complementarity is shown between targets solved using the different ab initio modelling programs QUARK and ROSETTA. Search models derived from either program collectively solve almost all of the all-helical targets in the test set. Initial solutions produced by Phaser after only 5 min perform surprisingly well, improving the prospects for in situ structure solution by AMPLE during synchrotron visits. Taken together, the results show the potential for AMPLE to run more quickly and successfully solve more targets than previously suspected.

  10. An Efficient Time-Stepping Scheme for Ab Initio Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Tsuchida, Eiji

    2016-08-01

    In ab initio molecular dynamics simulations of real-world problems, the simple Verlet method is still widely used for integrating the equations of motion, while more efficient algorithms are routinely used in classical molecular dynamics. We show that if the Verlet method is used in conjunction with pre- and postprocessing, the accuracy of the time integration is significantly improved with only a small computational overhead. We also propose several extensions of the algorithm required for use in ab initio molecular dynamics. The validity of the processed Verlet method is demonstrated in several examples including ab initio molecular dynamics simulations of liquid water. The structural properties obtained from the processed Verlet method are found to be sufficiently accurate even for large time steps close to the stability limit. This approach results in a 2× performance gain over the standard Verlet method for a given accuracy. We also show how to generate a canonical ensemble within this approach.

  11. An ab initio molecular dynamics study on hydrogen bonds between water molecules

    NASA Astrophysics Data System (ADS)

    Pan, Zhang; Chen, Jing; Lü, Gang; Geng, Yi-Zhao; Zhang, Hui; Ji, Qing

    2012-04-01

    The quantitative estimation of the total interaction energy of a molecular system containing hydrogen bonds (H bonds) depends largely on how to identify H bonding. The conventional geometric criteria of H bonding are simple and convenient in application, but a certain amount of non-H bonding cases are also identified as H bonding. In order to investigate the wrong identification, we carry out a systematic calculation on the interaction energy of two water molecules at various orientation angles and distances using ab initio molecular dynamics method with the dispersion correction for the Becke-Lee-Yang-Parr (BLYP) functionals. It is shown that, at many orientation angles and distances, the interaction energies of the two water molecules exceed the energy criterion of the H bond, but they are still identified as H-bonded by the conventional "distance-angle" criteria. It is found that in these non-H bonding cases the wrong identification is mainly caused by short-range interaction between the two neighbouring water molecules. We thus propose that, in addition to the conventional distance and angle criteria of H bonding, the distance dHṡṡṡH between the two neighbouring hydrogen atoms of the two water molecules should also be taken as a criterion, and the distance rOṡṡṡH between the hydrogen atom of the H-bond donor molecule and the oxygen atom of the acceptor molecule should be restricted by a lower limit. When dHṡṡṡH and rOṡṡṡH are small (e.g., dHṡṡṡH < 2.0 Å and rOṡṡṡH < 1.62 Å), the repulsion between the two neighbouring atoms increases the total energy of the two water molecules dramatically and apparently weakens the binding of the water dimer. A statistical analysis and comparison of the numbers of the H bonds identified by using different criteria have been conducted on a Car-Parrinello ab initio molecular dynamics simulation with dispersion correction for a system of 64 water molecules at near-ambient temperature. They

  12. Ab Initio Molecular Dynamics of Dimerization and Clustering in Alkali Metal Vapors.

    PubMed

    Chaban, Vitaly V; Prezhdo, Oleg V

    2016-06-30

    Alkali metals are known to form dimers, trimers, and tetramers in their vapors. The mechanism and regularities of this phenomenon characterize the chemical behavior of the first group elements. We report ab initio molecular dynamics (AIMD) simulations of the alkali metal vapors and characterize their structural properties, including radial distribution functions and atomic cluster size distributions. AIMD confirms formation of Men, where n ranges from 2 to 4. High pressure sharply favors larger structures, whereas high temperature decreases their fraction. Heavier alkali metals maintain somewhat larger fractions of Me2, Me3, and Me4, relative to isolated atoms. A single atom is the most frequently observed structure in vapors, irrespective of the element and temperature. Due to technical difficulties of working with high temperatures and pressures in experiments, AIMD is the most affordable method of research. It provides valuable understanding of the chemical behavior of Li, Na, K, Rb, and Cs, which can lead to development of new chemical reactions involving these metals. PMID:27294399

  13. Molecular dynamics modeling using ab initio interatomic potentials for thermal properties of Ni-rich alloys

    SciTech Connect

    Mei, J.; Cooper, B.R.; Hao, Y.G.; Scoy, F.L. Van

    1994-12-31

    Molecular dynamics simulations have been performed to study thermal expansions of Ni-rich (fcc structure) Ni/Cr alloys (which serve as the basis for practical superalloy systems). This has been done using ab initio interatomic potentials with no experimental input. The coefficient of thermal expansion (CTE) as a function of temperature has been calculated. By admixing Re and Me atoms into fee Ni and the fee alloy system Ni/Cr, additive effects on the thermal expansion have been predicted. While addition of Cr lowers the CTE of Ni, and moderate addition of Mo lowers the CTE of Ni over a wide temperature range, moderate addition of Re raises the CTE of both Ni and Ni/Cr alloys over a significant temperature range. An explanation for the contrasting effect of additive Re on the CTE, based on a one-dimensional atomic chain model, is that the trade-off, between atomic volume effects increasing the CTE over that of pure Ni and pair-potential effects (exemplified by the Grueneisen parameter) decreasing the CTE from that of pure nickel, changes for Re compared to Cr and Mo.

  14. Surface electron density models for accurate ab initio molecular dynamics with electronic friction

    NASA Astrophysics Data System (ADS)

    Novko, D.; Blanco-Rey, M.; Alducin, M.; Juaristi, J. I.

    2016-06-01

    Ab initio molecular dynamics with electronic friction (AIMDEF) is a valuable methodology to study the interaction of atomic particles with metal surfaces. This method, in which the effect of low-energy electron-hole (e-h) pair excitations is treated within the local density friction approximation (LDFA) [Juaristi et al., Phys. Rev. Lett. 100, 116102 (2008), 10.1103/PhysRevLett.100.116102], can provide an accurate description of both e-h pair and phonon excitations. In practice, its applicability becomes a complicated task in those situations of substantial surface atoms displacements because the LDFA requires the knowledge at each integration step of the bare surface electron density. In this work, we propose three different methods of calculating on-the-fly the electron density of the distorted surface and we discuss their suitability under typical surface distortions. The investigated methods are used in AIMDEF simulations for three illustrative adsorption cases, namely, dissociated H2 on Pd(100), N on Ag(111), and N2 on Fe(110). Our AIMDEF calculations performed with the three approaches highlight the importance of going beyond the frozen surface density to accurately describe the energy released into e-h pair excitations in case of large surface atom displacements.

  15. Ab initio calculations of the forbidden Bragg reflections energy spectra in wurtzites versus temperature.

    PubMed

    Oreshko, A P; Ovchinnikova, E N; Beutier, G; Collins, S P; Nisbet, G; Kolchinskaya, A M; Dmitrienko, V E

    2012-06-20

    Thermal-motion induced (TMI) scattering is caused by the influence of atomic displacements on electronic states in crystals and strongly depends on temperature. It corresponds to dipole-dipole resonant x-ray scattering, but is usually accompanied by dipole-quadrupole scattering. The phenomenological theory supposes the dipole-quadrupole term to be temperature independent (TI). As a result, the transformation of the energy spectra with temperature observed experimentally in ZnO and GaN corresponds to the interference between the TMI and TI terms. In the present paper the direct confirmation of this theoretical prediction is given. Ab initio molecular dynamics was used to simulate the sets of atomic sites at various temperatures followed by quantum mechanical calculation of resonant Bragg reflection energy spectra. The results of simulation are in excellent coincidence with experimental energy spectra of forbidden reflections and confirm the earlier phenomenological conjecture about the interference between the TI dipole-quadrupole and TMI dipole-dipole contributions to the resonant atomic factor. PMID:22627099

  16. Nonlocal torque operators in ab initio theory of the Gilbert damping in random ferromagnetic alloys

    NASA Astrophysics Data System (ADS)

    Turek, I.; Kudrnovský, J.; Drchal, V.

    2015-12-01

    We present an ab initio theory of the Gilbert damping in substitutionally disordered ferromagnetic alloys. The theory rests on introduced nonlocal torques which replace traditional local torque operators in the well-known torque-correlation formula and which can be formulated within the atomic-sphere approximation. The formalism is sketched in a simple tight-binding model and worked out in detail in the relativistic tight-binding linear muffin-tin orbital method and the coherent potential approximation (CPA). The resulting nonlocal torques are represented by nonrandom, non-site-diagonal, and spin-independent matrices, which simplifies the configuration averaging. The CPA-vertex corrections play a crucial role for the internal consistency of the theory and for its exact equivalence to other first-principles approaches based on the random local torques. This equivalence is also illustrated by the calculated Gilbert damping parameters for binary NiFe and FeCo random alloys, for pure iron with a model atomic-level disorder, and for stoichiometric FePt alloys with a varying degree of L 10 atomic long-range order.

  17. Heats of Segregation of BCC Binaries from Ab Initio and Quantum Approximate Calculations

    NASA Technical Reports Server (NTRS)

    Good, Brian S.

    2003-01-01

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

  18. Comparison of DFT and ab initio QM/MM methods for modelling reaction in chorismate synthase

    NASA Astrophysics Data System (ADS)

    Lawan, Narin; Ranaghan, Kara E.; Manby, Frederick R.; Mulholland, Adrian J.

    2014-07-01

    Quantum mechanics/molecular mechanics (QM/MM) methods are a popular tool in the investigation of enzyme reactions. Here, we compare B3LYP density functional theory (DFT) and ab initio QM/MM methods for modelling the conversion of 5-enolpyruvylshikimate-3-phosphate to chorismate in chorismate synthase. Good agreement with experimental data is only obtained at the SCS-MP2/CHARMM27 level for a reaction mechanism in which phosphate elimination precedes proton transfer. B3LYP predicts reaction energetics that are qualitatively wrong, stressing the need for ab initio QM/MM methods, and caution in interpretation of DFT results for this enzyme.

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

    SciTech Connect

    Sakane, Shinichi; Yezdimer, Eric M.; Liu, Wenbin; Barriocanal, Jose A.; Doren, Douglas J.; Wood, Robert H.

    2000-08-15

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

  20. Ab-initio based calculations of vacancy formation and clustering energies including lattice relaxation in Fe{sub 3}Al

    SciTech Connect

    Muratov, L.S.; Cooper, B.R.; Wills, J.M.

    1999-03-01

    Vacancy formation and clustering significantly affect structural properties of transition-metal aluminides. Ab-initio quantum mechanical total-energy calculations using a full-potential linear combination of muffin-tin orbitals (LMTO) technique provide a convenient method of studying relevant characteristics such as changes in density of states, and charge redistribution around defects. Augmented with Hellmann-Feymann forces, LMTO allows calculations of relaxation geometries and relaxation energies. The authors have performed such calculations for vacancies and antisite substitutional point defects in Fe{sub 3}Al with DO{sub 3} crystallographic structure. There are two limiting factors complicating calculations of defect formation energies directly from ab-initio calculations. The first is that a single defect, due to the lattice periodicity necessitated by the use of ab-initio total energy techniques, cannot be considered as an isolated defect, even in the maximum computable simulation cell. Unlike previous calculations, which did not find a dependency on the size of the simulation cell, the calculations have shown a significant difference in results for 32- and 16- atom cells. This difference provides information about vacancy clustering since it can be explained by a relatively small attractive interaction energy {approximately} 0.2 eV between two vacancies located in adjacent simulation cells and separated by the lattice constant distance (5.52 {angstrom}). By comparing the internal energies for two configurations of 30 atom cells (32 atom--2 vacancies), the authors were able to estimate that the attractive interaction between two vacancies could reach 1.2 eV. The second complication is the fact that chemical potentials of elements cannot be directly extracted from the total energy calculations for the compound. To deal with this problem, they considered two possible approximations and compared results, which were found to be quite similar for iron vacancies.

  1. Ab initio simulations of the structure, energetics and mobility of radiation-induced point defects in bcc Nb

    NASA Astrophysics Data System (ADS)

    Cerdeira, M. A.; Palacios, S. L.; González, C.; Fernández-Pello, D.; Iglesias, R.

    2016-09-01

    The formation, binding and migration energetics of helium clusters inside a niobium crystal have been analysed via ab initio simulations. The effect of placing several He atoms within an n-vacancy previously formed or as interstitials inside the initial perfect bulk matrix has been studied. DFT-based results show that He atoms prefer to aggregate forming small clusters at n-vacancy sites rather than at interstitial positions in the perfect crystal. The minimum formation energy is found when NHe is equal to the number of vacancies, n. It follows that vacancies act as almost perfect traps for He atoms, as is well known for other metals. The migration barriers of He atoms inside vacancies increase considerably when compared to what happens for vacancies alone. A secondary consequence is that the full set of energies obtained will be highly relevant as an input for new approaches to KMC simulations of defects in Nb.

  2. Relating Ab Initio Mechanical Behavior of Intergranular Glassy Films in Γ-Si3N4 to Continuum Scales

    NASA Astrophysics Data System (ADS)

    Ouyang, L.; Chen, J.; Ching, W.; Misra, A.

    2006-05-01

    Nanometer thin intergranular glassy films (IGFs) form in polycrystalline ceramics during sintering at high temperatures. The structure and properties of these IGFs are significantly changed by doping with rare earth elements. We have performed highly accurate large-scale ab initio calculations of the mechanical properties of both undoped and Yittria doped (Y-IGF) model by theoretical uniaxial tensile experiments. Uniaxial strain was applied by incrementally stretching the super cell in one direction, while the other two dimensions were kept constant. At each strain, all atoms in the model were fully relaxed using Vienna Ab initio Simulation Package VASP. The relaxed model at a given strain serves as the starting position for the next increment of strain. This process is carried on until the total energy (TE) and stress data show that the "sample" is fully fractured. Interesting differences are seen between the stress-strain response of undoped and Y-doped models. For the undoped model, the stress-strain behavior indicates that the initial atomic structure of the IGF is such that there is negligible coupling between the x- and the y-z directions. However, once the behavior becomes non- linear the lateral stresses increase, indicating that the atomic structure evolves with loading [1]. To relate the ab initio calculations to the continuum scales we analyze the atomic-scale deformation field under this uniaxial loading [1]. The applied strain in the x-direction is mostly accommodated by the IGF part of the model and the crystalline part experiences almost negligible strain. As the overall strain on the sample is incrementally increased, the local strain field evolves such that locations proximal to the softer spots attract higher strains. As the load progresses, the strain concentration spots coalesce and eventually form persistent strain localization zone across the IGF. The deformation pattern obtained through ab initio calculations indicates that it is possible to

  3. Combined electron beam imaging and ab initio modeling of T{sub 1} precipitates in Al-Li-Cu alloys

    SciTech Connect

    Dwyer, C.; Weyland, M.; Chang, L. Y.; Muddle, B. C.

    2011-05-16

    Among the many considerable challenges faced in developing a rational basis for advanced alloy design, establishing accurate atomistic models is one of the most fundamental. Here we demonstrate how advanced imaging techniques in a double-aberration-corrected transmission electron microscope, combined with ab initio modeling, have been used to determine the atomic structure of embedded 1 nm thick T{sub 1} precipitates in precipitation-hardened Al-Li-Cu aerospace alloys. The results provide an accurate determination of the controversial T{sub 1} structure, and demonstrate how next-generation techniques permit the characterization of embedded nanostructures in alloys and other nanostructured materials.

  4. Ab initio molecular treatment for charge transfer by P{sup 3+} ions on hydrogen and helium

    SciTech Connect

    Moussa, A.; Zaidi, A.; Lahmar, S.; Bacchus-Montabonel, M.-C.

    2010-02-15

    A theoretical treatment of charge-transfer processes induced by collision of phosphorus P{sup 3+}(3s{sup 2}){sup 1}S ions on atomic hydrogen and helium has been carried out using ab initio potential-energy curves and couplings at the multireference configuration interaction level of theory. The cross sections calculated by means of semiclassical collision methods show the existence of a significant charge transfer in the 0.1-700-keV laboratory energy range. Radial and rotational coupling interactions were analyzed for both collision systems.

  5. Ab initio search for novel bipolar magnetic semiconductors: Layered YZnAsO doped with Fe and Mn

    NASA Astrophysics Data System (ADS)

    Bannikov, V. V.; Ivanovskii, A. L.

    2013-02-01

    Very recently, the newest class of spintronic materials, where reversible spin polarization can be controlled by applying gate voltage: so-called bipolar magnetic semiconductors (Xingxing Li et al., arXiv:1208.1355) was proposed. In this work, a novel way to creation of bipolar magnetic semiconductors by doping of non-magnetic semiconducting 1111 phases with magnetic d n < 10 atoms is discussed using ab initio calculations of layered YZnAsO doped with Fe and Mn. In addition, more complex materials with several spectral intervals with opposite 100% spin polarization where multiple gate-controlled spin-polarization can be expected are proposed.

  6. Solving local structure around dopants in metal nanoparticles with ab initio modeling of X-ray absorption near edge structure

    DOE PAGESBeta

    Timoshenko, J.; Shivhare, A.; Scott, R. W.; Lu, D.; Frenkel, A. I.

    2016-06-30

    We adopted ab-initio X-ray Absorption Near Edge Structure (XANES) modelling for structural refinement of local environments around metal impurities in a large variety of materials. Our method enables both direct modelling, where the candidate structures are known, and the inverse modelling, where the unknown structural motifs are deciphered from the experimental spectra. We present also estimates of systematic errors, and their influence on the stability and accuracy of the obtained results. We illustrate our approach by following the evolution of local environment of palladium atoms in palladium-doped gold thiolate clusters upon chemical and thermal treatments.

  7. Theoretical design of a novel copper doped gold cluster supported on graphene utilizing ab initio molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Koizumi, Kenichi; Nobusada, Katsuyuki; Boero, Mauro

    2015-12-01

    Ab initio molecular dynamics simulations have been used to inspect the adsorption of O2 to a small gold-copper alloy cluster supported on graphene. The exposed Cu atom in this cluster acts as a crucial attractive site for the approaching of O2 and consequently widens the reaction channel for the adsorption process. Conversely, a pure Au cluster on the same graphene support is inactive for the O2 adsorption because the corresponding reaction channel for the adsorption is very narrow. These results clearly indicate that doping a different metal to the Au cluster is a way to enhance the oxygen adsorption and to promote catalytic reactions.

  8. Ab initio molecular dynamics simulation of structural transformation in zinc blende GaN under high pressure

    SciTech Connect

    Xiao, Hai Yan; Gao, Fei; Zu, Xiaotao T.; Weber, William J.

    2010-02-04

    High-pressure induced zinc blende to rocksalt phase transition in GaN has been investigated by ab initio molecular dynamics method to characterize the transformation mechanism at the atomic level. It was shown that at 100 GPa GaN passes through tetragonal and monoclinic states before rocksalt structure is formed. The transformation mechanism is consistent with that for other zinc blende semiconductors obtained from the same method. Detailed structural analysis showed that there is no bond breaking involved in the phase transition.

  9. Ab-initio investigation of spin-dependent transport properties in Fe-doped armchair graphyne nanoribbons

    NASA Astrophysics Data System (ADS)

    GolafroozShahri, S.; Roknabadi, M. R.; Shahtahmasebi, N.; Behdani, M.

    2016-12-01

    An ab-initio study on the spin-polarized transport properties of H-passivated Fe-doped graphyne nanoribbons is presented. All the calculations were based on density functional theory (DFT). Doping single magnetic atom on graphyne nanoribbons leads to metallicity which can significantly improve the conductivity. The currents are not degenerate for both up and down spin electrons and they are considerably spin-polarized. Therefore a relatively good spin-filtering can be expected. For configurations with geometric symmetry spin-rectifying is also observed. Therefore they can be applied as a dual spin-filter or a dual spin-diode in spintronic equipment.

  10. Ab initio molecular dynamics simulations of low energy recoil events in ceramics

    SciTech Connect

    Gao, Fei; Xiao, Haiyan Y.; Weber, William J.

    2011-07-15

    The recent progress in the use of large-scale ab initio molecular dynamics (AIMD) to investigate low energy recoil events and determine threshold displacement energies, Ed, in ceramics is reviewed. In general, Ed shows a significant dependence on recoil direction and atom. In 3C-SiC, the minimum Ed for both C and Si atoms is found along the <100> direction, with a value of 20 and 49 eV, respectively. The results demonstrate that significant charge transfer occurs during the dynamics process, and defects can enhance charge transfer to surrounding atoms, which provides important insights into the formation of charged defects. It is found that the C vacancy is a positively charged defect, whereas the Si vacancy is in its neutral state. The minimum Ed in GaN is determined to be 17 and 39 eV for N and Ga atoms, respectively, both along the direction. The average Ed for N atoms (32.4 eV) is smaller than that for Ga atoms (73.2 eV). It is of interest to note that the N defects created along different crystallographic directions have a similar configuration (a N-N dumbbell configuration), but various configurations for Ga defects are formed. In Y2Ti2O7 prochlore, the minimum Ed for Y atoms is determined to be 27 eV for a recoil along the <100> direction, 31.5 eV for Ti atoms along the <100> direction, 14.5 eV for O48f atoms along the <110> direction and 13 eV for O8b atoms along the <111> direction. The average Ed values determined are 32.7, 34.2, 14.2 and 16.1 eV for yttrium, titanium, O48f and O8b atoms, respectively. Cation interstitials at vacant 8a sites, which are generally occupied by oxygen anions, and at the bridge sites between two neighboring cations along the <010> direction are observed after low energy recoil events.

  11. Ab initio molecular dynamics simulations of low energy recoil events in ceramics

    SciTech Connect

    Gao, Fei; Xiao, Haiyan; Weber, William J

    2011-01-01

    The recent progress in the use of large-scale ab initio molecular dynamics (AIMD) to investigate low energy recoil events and determine threshold displacement energies, Ed, in ceramics is reviewed. In general, Ed shows a significant dependence on recoil direction and atom. In SiC, the minimum Ed for both C and Si atoms is found along the <100> direction, with a value of 20 and 49 eV, respectively. The results demonstrate that significant charge transfer occurs during the dynamics process, and defects can enhance charge transfer to surrounding atoms, which provides important insights into the formation of charged defects. It is found that the C vacancy is a positively charged defect, whereas the Si vacancy is in its neutral state. The minimum Ed in GaN is determined to be 17 and 39 eV for N and Ga atoms, respectively, both along the direction. The average Ed for N atoms (32.4 eV) is smaller than that for Ga atoms (73.2 eV). It is of interest to note that the N defects created along different crystallographic directions have a similar configuration (a N-N dumbbell configuration), but various configurations for Ga defects are formed. In Y2Ti2O7 prochlore, the minimum Ed for Y atoms is determined to be 27 eV for a recoil along the <100> direction, 31.5 eV for Ti atoms along the <100> direction, 14.5 eV for O48f atoms along the <110> direction and 13 eV for O8b atoms along the <111> direction. The average Ed values determined are 32.7, 34.2, 14.2 and 16.1 eV for yttrium, titanium, O48f and O8b atoms, respectively. Cation interstitials at vacant 8a sites, which are generally occupied by oxygen anions, and at the bridge sites between two neighboring cations along the <010> direction are observed after low energy recoil events.

  12. Development and application of ab initio QM/MM methods for mechanistic simulation of reactions in solution and in enzymes

    PubMed Central

    Hu, Hao; Yang, Weitao

    2013-01-01

    Determining the free energies and mechanisms of chemical reactions in solution and enzymes is a major challenge. For such complex reaction processes, combined quantum mechanics/molecular mechanics (QM/MM) method is the most effective simulation method to provide an accurate and efficient theoretical description of the molecular system. The computational costs of ab initio QM methods, however, have limited the application of ab initio QM/MM methods. Recent advances in ab initio QM/MM methods allowed the accurate simulation of the free energies for reactions in solution and in enzymes and thus paved the way for broader application of the ab initio QM/MM methods. We review here the theoretical developments and applications of the ab initio QM/MM methods, focusing on the determination of reaction path and the free energies of the reaction processes in solution and enzymes. PMID:24146439

  13. Structural stability of nitrogen-doped ultrathin single-walled boron nanotubes: an ab initio study

    NASA Astrophysics Data System (ADS)

    Jain, Sandeep Kumar; Srivastava, Pankaj

    2012-09-01

    Ab initio calculations have been performed for determining structural stabilities of nitrogen-doped ultrathin single-walled boron nanotube. We have considered ultrathin boron nanotubes of diameters <0.5 nm, which include mainly three conformations of BNTs viz. zigzag (5,0), armchair (3,3) and chiral (4,2) with diameters 4.60, 4.78 and 4.87 Å, respectively. It has been investigated that α-BNTs are highly stable, while hexagonal BNTs are found to be least stable. In view of increasing structural stability of hexagonal BNTs, substitutional doping of foreign atoms, i.e. nitrogen is chosen. The nitrogen atoms substitute the host atoms at the middle of the tubes. The substitution doping is made with all the three conformations. The structural stabilities of BNTs have been investigated by using density functional theory (DFT). Subsequently, the cohesive energy is calculated, which directly measures the structural stability. The cohesive energy of BNTs has been calculated for different nitrogen concentrations. We found that the structures get energetically more stable with increasing nitrogen concentration. Moreover, it is also revealed that all the three BNTs are almost equally stable for single-atom doping, while the armchair BNT (3,3) is highly stable followed by zigzag (5,0) and chiral (4,2) BNTs for two- and three-atom doping. The structural stability is an important factor for realization of any physical device. Thus, these BNTs can be used for field emission, semiconducting and highly conducting devices at nanoscale.

  14. Ab initio studies on the adsorption and implantation of Al and Fe to nitride materials

    NASA Astrophysics Data System (ADS)

    Riedl, H.; Zálešák, J.; Arndt, M.; Polcik, P.; Holec, D.; Mayrhofer, P. H.

    2015-09-01

    The formation of transfer material products on coated cutting and forming tools is a major failure mechanism leading to various sorts of wear. To describe the atomistic processes behind the formation of transfer materials, we use ab initio to study the adsorption energy as well as the implantation barrier of Al and Fe atoms for (001)-oriented surfaces of TiN, Ti0.50Al0.50N, Ti0.90Si0.10N, CrN, and Cr0.90Si0.10N. The interactions between additional atoms and nitride-surfaces are described for pure adhesion, considering no additional stresses, and for the implantation barrier. The latter, we simplified to the stress required to implant Al and Fe into sub-surface regions of the nitride material. The adsorption energies exhibit pronounced extrema at high-symmetry positions and are generally highest at nitrogen sites. Here, the binary nitrides are comparable to their ternary counterparts and the average adhesive energy is higher (more negative) on CrN than TiN based systems. Contrary, the implantation barrier for Al and Fe atoms is higher for the ternary systems Ti0.50Al0.50N, Ti0.90Si0.10N, and Cr0.90Si0.10N than for their binary counterparts TiN and CrN. Based on our results, we can conclude that TiN based systems outperform CrN based systems with respect to pure adhesion, while the Si-containing ternaries exhibit higher implantation barriers for Al and Fe atoms. The data obtained are important to understand the atomistic interaction of metal atoms with nitride-based materials, which is valid not just for machining operations but also for any combination such as interfaces between coatings and substrates or multilayer and phase arrangements themselves.

  15. Effect of electric field on the mechanical properties of bilayer boron nitride with AB stacking order: An ab initio study

    NASA Astrophysics Data System (ADS)

    Ansari, R.; Faghihnasiri, M.; Malakpour, S.; Sahmani, S.

    2015-07-01

    In the current investigation, ab initio calculations are performed to explore the influence of electric field on the mechanical properties of bilayer boron nitride with AB stacking order (AB-2LBN). To accomplish this, density functional theory (DFT) within the framework of generalized gradient approximation (GGA) is implemented. It is demonstrated that the electric field has significant effects on Young's modulus and Poisson's ratio of AB-2LBN when its magnitude is small. With increasing the magnitude of electric field, these effects diminish so that the mechanical properties with and without considering the electric field become approximately identical. Also, it is shown that the equilibrium strain energy decreases linearly by increasing the magnitude of applied electric field.

  16. How Is Acetylcholinesterase Phosphonylated by Soman? An Ab Initio QM/MM Molecular Dynamics Study

    PubMed Central

    2015-01-01

    Acetylcholinesterase (AChE) is a crucial enzyme in the cholinergic nerve system that hydrolyzes acetylcholine (ACh) and terminates synaptic signals by reducing the effective concentration of ACh in the synaptic clefts. Organophosphate compounds irreversibly inhibit AChEs, leading to irreparable damage to nerve cells. By employing Born–Oppenheimer ab initio QM/MM molecular dynamics simulations with umbrella sampling, a state-of-the-art approach to simulate enzyme reactions, we have characterized the covalent inhibition mechanism between AChE and the nerve toxin soman and determined its free energy profile for the first time. Our results indicate that phosphonylation of the catalytic serine by soman employs an addition–elimination mechanism, which is highly associative and stepwise: in the initial addition step, which is also rate-limiting, His440 acts as a general base to facilitate the nucleophilic attack of Ser200 on the soman’s phosphorus atom to form a trigonal bipyrimidal pentacovalent intermediate; in the subsequent elimination step, Try121 of the catalytic gorge stabilizes the leaving fluorine atom prior to its dissociation from the active site. Together with our previous characterization of the aging mechanism of soman inhibited AChE, our simulations have revealed detailed molecular mechanistic insights into the damaging function of the nerve agent soman. PMID:24786171

  17. A modified W-W interatomic potential based on ab initio calculations

    NASA Astrophysics Data System (ADS)

    Wang, J.; Zhou, Y. L.; Li, M.; Hou, Q.

    2014-01-01

    In this paper we have developed a Finnis-Sinclair-type interatomic potential for W-W interactions that is based on ab initio calculations. The modified potential is able to reproduce the correct formation energies of self-interstitial atom (SIA) defects in tungsten, offering a significant improvement over the Ackland-Thetford tungsten potential. Using the modified potential, the thermal expansion is calculated in a temperature range from 0 to 3500 K. The results are in reasonable agreement with the experimental data, thus overcoming the shortcomings of the negative thermal expansion using the Derlet-Nguyen-Manh-Dudarev tungsten potential. The W-W potential presented here is also applied to study in detail the diffusion of SIAs in tungsten. We reveal that the initial SIA initiates a sequence of tungsten atom displacements and replacements in the <1 1 1> direction. An Arrhenius fit to the diffusion data at temperatures below 550 K indicates a migration energy of 0.022 eV, which is in reasonable agreement with the experimental data.

  18. Beyond Born-Mayer: Improved Models for Short-Range Repulsion in ab Initio Force Fields.

    PubMed

    Van Vleet, Mary J; Misquitta, Alston J; Stone, Anthony J; Schmidt, J R

    2016-08-01

    Short-range repulsion within intermolecular force fields is conventionally described by either Lennard-Jones (A/r(12)) or Born-Mayer (A exp(-Br)) forms. Despite their widespread use, these simple functional forms are often unable to describe the interaction energy accurately over a broad range of intermolecular distances, thus creating challenges in the development of ab initio force fields and potentially leading to decreased accuracy and transferability. Herein, we derive a novel short-range functional form based on a simple Slater-like model of overlapping atomic densities and an iterated stockholder atom (ISA) partitioning of the molecular electron density. We demonstrate that this Slater-ISA methodology yields a more accurate, transferable, and robust description of the short-range interactions at minimal additional computational cost compared to standard Lennard-Jones or Born-Mayer approaches. Finally, we show how this methodology can be adapted to yield the standard Born-Mayer functional form while still retaining many of the advantages of the Slater-ISA approach. PMID:27337546

  19. Adsorption of DNA/RNA nucleobases on hexagonal boron nitride sheet: an ab initio study.

    PubMed

    Lin, Qing; Zou, Xiaolong; Zhou, Gang; Liu, Rui; Wu, Jian; Li, Jia; Duan, Wenhui

    2011-07-14

    Our ab initio calculations indicate that the interaction of deoxyribonucleic/ribonucleic acid (DNA/RNA) nucleobases [guanine (G), adenine (A), thymine (T), cytosine (C), and uracil (U)] with the hexagonal boron nitride (h-BN) sheet, a polar but chemically inert surface, is governed by mutual polarization. Unlike the case of graphene, all nucleobases exhibit the same stacking arrangement on the h-BN sheet due to polarization effects: the anions (N and O atoms) of nucleobases prefer to stay on top of cations (B) of the substrate as far as possible, regardless of the biological properties of nucleobases. The adsorption energies, ranging from 0.5 eV to 0.69 eV, increase in the order of U, C, T, A and G, which can be attributed to different side groups or atoms of nucleobases. The fundamental nature of DNA/RNA nucleobases and h-BN sheet remains unchanged upon adsorption, suggesting that the h-BN sheet is a promising template for DNA/RNA-related research, such as self-assembly. PMID:21637870

  20. Ab initio molecular dynamics of the reaction of quercetin with superoxide radical

    NASA Astrophysics Data System (ADS)

    Lespade, Laure

    2016-08-01

    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.

  1. Beyond Born-Mayer: Improved models for short-range repulsion in ab initio force fields

    DOE PAGESBeta

    Van Vleet, Mary J.; Misquitta, Alston J.; Stone, Anthony J.; Schmidt, Jordan R.

    2016-06-23

    Short-range repulsion within inter-molecular force fields is conventionally described by either Lennard-Jones or Born-Mayer forms. Despite their widespread use, these simple functional forms are often unable to describe the interaction energy accurately over a broad range of inter-molecular distances, thus creating challenges in the development of ab initio force fields and potentially leading to decreased accuracy and transferability. Herein, we derive a novel short-range functional form based on a simple Slater-like model of overlapping atomic densities and an iterated stockholder atom (ISA) partitioning of the molecular electron density. We demonstrate that this Slater-ISA methodology yields a more accurate, transferable, andmore » robust description of the short-range interactions at minimal additional computational cost compared to standard Lennard-Jones or Born-Mayer approaches. Lastly, we show how this methodology can be adapted to yield the standard Born-Mayer functional form while still retaining many of the advantages of the Slater-ISA approach.« less

  2. Amorphous Ge quantum dots embedded in crystalline Si: ab initio results.

    PubMed

    Laubscher, M; Küfner, S; Kroll, P; Bechstedt, F

    2015-10-14

    We study amorphous Ge quantum dots embedded in a crystalline Si matrix through structure modeling and simulation using ab initio density functional theory including spin-orbit interaction and quasiparticle effects. Three models are generated by replacing a spherical region within diamond Si by Ge atoms and creating a disordered bond network with appropriate density inside the Ge quantum dot. After total-energy optimisations of the atomic geometry we compute the electronic and optical properties. We find three major effects: (i) the resulting nanostructures adopt a type-I heterostructure character; (ii) the lowest optical transitions occur only within the Ge quantum dots, and do not involve or cross the Ge-Si interface. (iii) for larger amorphous Ge quantum dots, with diameters of about 2.0 and 2.7 nm, absorption peaks appear in the mid-infrared spectral region. These are promising candidates for intense luminescence at photon energies below the gap energy of bulk Ge. PMID:26402441

  3. Electromechanical effects in carbon nanotubes: Ab initio and analytical tight-binding calculations

    NASA Astrophysics Data System (ADS)

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

    2003-04-01

    We perform ab initio calculations of charged graphene and single-wall carbon nanotubes (CNTs). A wealth of electromechanical behaviors is obtained. (1) Both nanotubes and graphene expand upon electron injection. (2) Upon hole injection, metallic nanotubes and graphene display a nonmonotonic behavior. Upon increasing hole densities, the lattice constant initially contracts, reaches a minimum, and then starts to expand. The hole densities at minimum lattice constants are 0.3 |e|/atom for graphene and between 0.1 and 0.3|e|/atom for the metallic nanotubes studied. (3) Semiconducting CNT’s with small diameters (d≲20 Å) always expand upon hole injection. (4) Semiconducting CNT’s with large diameters (d≳20 Å) display a behavior intermediate between those of metallic and large-gap CNT’s. (5) The strain versus extra charge displays a linear plus power-law behavior, with characteristic exponents for graphene, metallic, and semiconducting CNT’s. All these features are physically understood within a simple tight-binding total-energy model.

  4. Raman spectroscopic features of the neutral vacancy in diamond from ab initio quantum-mechanical calculations.

    PubMed

    Baima, Jacopo; Zelferino, Alessandro; Olivero, Paolo; Erba, Alessandro; Dovesi, Roberto

    2016-01-21

    Quantum-mechanical ab initio calculations are performed to elucidate the vibrational spectroscopic features of a common irradiation-induced defect in diamond, i.e. the neutral vacancy. Raman spectra are computed analytically through a Coupled-Perturbed-Hartree-Fock/Kohn-Sham approach as a function of both different defect spin states and defect concentration. The experimental Raman features of defective diamond located in the 400-1300 cm(-1) spectral range, i.e. below the first-order line of pristine diamond at 1332 cm(-1), are well reproduced, thus corroborating the picture according to which, at low damage densities, this spectral region is mostly affected by non-graphitic sp(3) defects. No peaks above 1332 cm(-1) are found, thus ruling out previous tentative assignments of different spectral features (at 1450 and 1490 cm(-1)) to the neutral vacancy. The perturbation introduced by the vacancy to the thermal nuclear motion of carbon atoms in the defective lattice is discussed in terms of atomic anisotropic displacement parameters (ADPs), computed from converged lattice dynamics calculations. PMID:26686374

  5. The vibration properties of the (n,0) boron nitride nanotubes from ab initio quantum chemical simulations

    NASA Astrophysics Data System (ADS)

    Erba, A.; Ferrabone, M.; Baima, J.; Orlando, R.; Rérat, M.; Dovesi, R.

    2013-02-01

    The vibration spectrum of single-walled zigzag boron nitride (BN) nanotubes is simulated with an ab initio periodic quantum chemical method. The trend towards the hexagonal monolayer (h-BN) in the limit of large tube radius R is explored for a variety of properties related to the vibrational spectrum: vibration frequencies, infrared intensities, oscillator strengths, and vibration contributions to the polarizability tensor. The (n,0) family is investigated in the range from n = 6 (24 atoms in the unit cell and tube radius R = 2.5 Å) to n = 60 (240 atoms in the cell and R = 24.0 Å). Simulations are performed using the CRYSTAL program which fully exploits the rich symmetry of this class of one-dimensional periodic systems: 4n symmetry operators for the general (n,0) tube. Three sets of infrared active phonon bands are found in the spectrum. The first one lies in the 0-600 cm-1 range and goes regularly to zero when R increases; the connection between these normal modes and the elastic and piezoelectric constants of h-BN is discussed. The second (600-800 cm-1) and third (1300-1600 cm-1) sets tend regularly, but with quite different speed, to the optical modes of the h-BN layer. The vibrational contribution of these modes to the two components (parallel and perpendicular) of the polarizability tensor is also discussed.

  6. Ab initio study of biphenyl chemisorption on Si(001): Configurational stability

    NASA Astrophysics Data System (ADS)

    Mamatkulov, M.; Stauffer, L.; Minot, C.; Sonnet, Ph.

    2006-01-01

    We present an ab initio energetical and structural study of the configurational stability of the biphenyl molecule adsorbed on the Si(001) surface. A number of models in biphenyl tight-bridge, butterfly, twisted, and tilted configurations are considered. For an undissociated biphenyl adsorption, the tight-bridge configuration is found to be the most stable one, slightly favored over the butterfly configuration. The effect on the stability of various parameters is investigated. The position with respect to the surface of the first phenyl ring atom (C1) on which the second ring is bound plays a determinant role. The tilted dimer under the second ring mainly acts in the biphenyl butterfly and tilted configurations, and a second ring location above a silicon down-atom favors stability. The effect of the second ring height above the surface is also discussed. Our results allow us to classify these different contributions by decreasing importance. By the hypothesis of a dissociative biphenyl adsorption, the calculated adsorption energies are clearly lower than in the corresponding undissociated model and the dissociated butterfly configuration is largely favored. Comparing our results to the experimental data, we propose some interpretations relative to the weakly and strongly chemisorbed biphenyl molecule observed in the scanning tunneling microscopy experiments.

  7. Ab initio density-functional calculations in materials science: from quasicrystals over microporous catalysts to spintronics.

    PubMed

    Hafner, Jürgen

    2010-09-29

    During the last 20 years computer simulations based on a quantum-mechanical description of the interactions between electrons and atomic nuclei have developed an increasingly important impact on materials science, not only in promoting a deeper understanding of the fundamental physical phenomena, but also enabling the computer-assisted design of materials for future technologies. The backbone of atomic-scale computational materials science is density-functional theory (DFT) which allows us to cast the intractable complexity of electron-electron interactions into the form of an effective single-particle equation determined by the exchange-correlation functional. Progress in DFT-based calculations of the properties of materials and of simulations of processes in materials depends on: (1) the development of improved exchange-correlation functionals and advanced post-DFT methods and their implementation in highly efficient computer codes, (2) the development of methods allowing us to bridge the gaps in the temperature, pressure, time and length scales between the ab initio calculations and real-world experiments and (3) the extension of the functionality of these codes, permitting us to treat additional properties and new processes. In this paper we discuss the current status of techniques for performing quantum-based simulations on materials and present some illustrative examples of applications to complex quasiperiodic alloys, cluster-support interactions in microporous acid catalysts and magnetic nanostructures. PMID:21386539

  8. Microstructure from joint analysis of experimental data and ab initio interactions: Hydrogenated amorphous silicon

    SciTech Connect

    Biswas, Parthapratim; Drabold, D. A.; Atta-Fynn, Raymond

    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.

  9. Ab initio study of hydrogen-halo rotation in ammonia borane

    NASA Astrophysics Data System (ADS)

    Welchman, Evan; Thonhauser, T.

    2014-03-01

    The van der Waals crystal ammonia borane NH3BH3 is a promising hydrogen-storage material due to its large gravimetric storage density. In an isolated molecule, the H atoms reside in halos about either end of a central B-N backbone with three-fold rotational symmetry. However, in the solid phase at ambient temperature and pressure, experiments reveal a tetragonal unit cell with a four-fold rotational symmetry about the same axis, creating a geometric incompatibility. Using ab initio calculations at the DFT level (with vdW-DF to capture crucial van der Waals interactions), we elucidate this incompatibility by simulating the behavior of the hydrogen-halos and their substituent H atoms. We use Car-Parrinello molecular dynamics at several different temperatures to simulate behavior in the solid and NEB calculations to find barriers to rotation in solid and gas phase. We find that at room temperature the halos can rotate several degrees per fs and that the four-fold symmetry thus results from a time average. We further show that in the solid phase the complex network of dihydrogen bonds affects the torsional barrier for the halos, and thus their rate of rotation in the solid phase, contributing to the experimentally observed positional uncertainty. Supported by NSF DMR-1145968.

  10. Microwave and ab initio studies of the Xe-CH4 van der Waals complex

    NASA Astrophysics Data System (ADS)

    Wen, Qing; Jäger, Wolfgang

    2006-01-01

    An ab initio potential-energy surface of the Xe-CH4 van der Waals complex was constructed at the coupled cluster level of theory with single, double, and perturbatively included triple excitations. The recently developed small-core pseudopotential and augmented correlation-consistent polarized valence quadruple-zeta basis set was used for the xenon atom and Dunning's augmented correlation-consistent polarized valence triple-zeta basis set for the other atoms. The basis sets were supplemented with bond functions. Dipole moments were also calculated at various configurations. Rotational spectra of the Xe-CH4 van der Waals complex were recorded using a pulsed-nozzle Fourier transform microwave spectrometer. The isotopomers studied include those of CH4,CH134,CD4,CH3D, and CHD3 with the five most abundant Xe isotopes. Transitions within three internal rotor states, namely, the j =0,K=0;j=1,K=0; and j =2,K=1 states, were observed and assigned. Nuclear quadrupole hyperfine structures due to the presence of Xe131(I=3/2) were detected and analyzed. It was found that the j =1,K=0 state is perturbed by a Coriolis interaction with a nearby j =1,K=1 state. For isotopomers containing CH3D and CHD3, the j =2 states are no longer metastable and could not be observed. The spectroscopic results were used to derive structural and dynamical information of the Xe-CH4 complex.

  11. Ab initio construction of interatomic potentials for uranium dioxide across all interatomic distances

    SciTech Connect

    Tiwary, P.; Walle, A. van de; Groenbech-Jensen, N.

    2009-11-01

    We provide a methodology for generating interatomic potentials for use in classical molecular-dynamics simulations of atomistic phenomena occurring at energy scales ranging from lattice vibrations to crystal defects to high-energy collisions. A rigorous method to objectively determine the shape of an interatomic potential over all length scales is introduced by building upon a charged-ion generalization of the well-known Ziegler-Biersack-Littmark universal potential that provides the short- and long-range limiting behavior of the potential. At intermediate ranges the potential is smoothly adjusted by fitting to ab initio data. Our formalism provides a complete description of the interatomic potentials that can be used at any energy scale, and thus, eliminates the inherent ambiguity of splining different potentials generated to study different kinds of atomic-materials behavior. We exemplify the method by developing rigid-ion potentials for uranium dioxide interactions under conditions ranging from thermodynamic equilibrium to very high atomic-energy collisions relevant for fission events.

  12. Ab initio electronic structure study for TTF-TCNQ under uniaxial compression

    NASA Astrophysics Data System (ADS)

    Ishibashi, Shoji; Hashimoto, Tamotsu; Kohyama, Masanori; Terakura, Kiyoyuki

    2004-04-01

    We have investigated the electronic structure of TTF-TCNQ under uniaxial compression with ab initio plane-wave pseudopotential calculations within the local-density approximation and generalized gradient approximation. Depending on the compression direction, the constituent molecules are deformed in different ways. Along with these structural deformations, quasi-one-dimensional Fermi surfaces show dramatic changes in their shapes and sizes.

  13. Ab Initio Studies of Chlorine Oxide and Nitrogen Oxide Species of Interest in Stratospheric Chemistry

    NASA Technical Reports Server (NTRS)

    Lee, Timothy J.; Langhoff, Stephen R. (Technical Monitor)

    1995-01-01

    The ability of modern state-of-the art ab initio quantum chemical techniques to characterize reliably the gas-phase molecular structure, vibrational spectrum, electronic spectrum, and thermal stability of chlorine oxide and nitrogen oxide species will be demonstrated by presentation of some example studies. In particular the geometrical structures, vibrational spectra, and heats of formation Of ClNO2, CisClONO, and trans-ClONO are shown to be in excellent agreement with the available experimental data, and where the experimental data are either not known or are inconclusive, the ab initio results are shown to fill in the gaps and to resolve the experimental controversy. In addition, ab initio studies in which the electronic spectra and the characterization of excited electronic states of ClONO2, HONO2, ClOOC17 ClOOH, and HOOH will also be presented. Again where available, the ab initio results are compared to experimental observations, and are used to aid in the interpretation of the experimental studies.

  14. Matrix product operators, matrix product states, and ab initio density matrix renormalization group algorithms

    NASA Astrophysics Data System (ADS)

    Chan, Garnet Kin-Lic; Keselman, Anna; Nakatani, Naoki; Li, Zhendong; White, Steven R.

    2016-07-01

    Current descriptions of the ab initio density matrix renormalization group (DMRG) algorithm use two superficially different languages: an older language of the renormalization group and renormalized operators, and a more recent language of matrix product states and matrix product operators. The same algorithm can appear dramatically different when written in the two different vocabularies. In this work, we carefully describe the translation between the two languages in several contexts. First, we describe how to efficiently implement the ab initio DMRG sweep using a matrix product operator based code, and the equivalence to the original renormalized operator implementation. Next we describe how to implement the general matrix product operator/matrix product state algebra within a pure renormalized operator-based DMRG code. Finally, we discuss two improvements of the ab initio DMRG sweep algorithm motivated by matrix product operator language: Hamiltonian compression, and a sum over operators representation that allows for perfect computational parallelism. The connections and correspondences described here serve to link the future developments with the past and are important in the efficient implementation of continuing advances in ab initio DMRG and related algorithms.

  15. Matrix product operators, matrix product states, and ab initio density matrix renormalization group algorithms.

    PubMed

    Chan, Garnet Kin-Lic; Keselman, Anna; Nakatani, Naoki; Li, Zhendong; White, Steven R

    2016-07-01

    Current descriptions of the ab initio density matrix renormalization group (DMRG) algorithm use two superficially different languages: an older language of the renormalization group and renormalized operators, and a more recent language of matrix product states and matrix product operators. The same algorithm can appear dramatically different when written in the two different vocabularies. In this work, we carefully describe the translation between the two languages in several contexts. First, we describe how to efficiently implement the ab initio DMRG sweep using a matrix product operator based code, and the equivalence to the original renormalized operator implementation. Next we describe how to implement the general matrix product operator/matrix product state algebra within a pure renormalized operator-based DMRG code. Finally, we discuss two improvements of the ab initio DMRG sweep algorithm motivated by matrix product operator language: Hamiltonian compression, and a sum over operators representation that allows for perfect computational parallelism. The connections and correspondences described here serve to link the future developments with the past and are important in the efficient implementation of continuing advances in ab initio DMRG and related algorithms. PMID:27394094

  16. Predicting materials for solar energy conversion: ab-initio spectroscopy of heterogeneous interfaces

    NASA Astrophysics Data System (ADS)

    Galli, Giulia

    We will discuss some progress in predicting materials for solar energy conversion using ab initio calculations, in particular we will focus on heterogeneous interfaces between photo-electrodes and water and between nanocomposites. We will also address the problem of building much needed tighter connections between computational and laboratory experiments.

  17. CVRQD ab initio ground-state adiabatic potential energy surfaces for the water molecule.

    PubMed

    Barletta, Paolo; Shirin, Sergei V; Zobov, Nikolai F; Polyansky, Oleg L; Tennyson, Jonathan; Valeev, Edward F; Császár, Attila G

    2006-11-28

    The high accuracy ab initio adiabatic potential energy surfaces (PESs) of the ground electronic state of the water molecule, determined originally by Polyansky et al. [Science 299, 539 (2003)] and called CVRQD, are extended and carefully characterized and analyzed. The CVRQD potential energy surfaces are obtained from extrapolation to the complete basis set of nearly full configuration interaction valence-only electronic structure computations, augmented by core, relativistic, quantum electrodynamics, and diagonal Born-Oppenheimer corrections. We also report ab initio calculations of several quantities characterizing the CVRQD PESs, including equilibrium and vibrationally averaged (0 K) structures, harmonic and anharmonic force fields, harmonic vibrational frequencies, vibrational fundamentals, and zero-point energies. They can be considered as the best ab initio estimates of these quantities available today. Results of first-principles computations on the rovibrational energy levels of several isotopologues of the water molecule are also presented, based on the CVRQD PESs and the use of variational nuclear motion calculations employing an exact kinetic energy operator given in orthogonal internal coordinates. The variational nuclear motion calculations also include a simplified treatment of nonadiabatic effects. This sophisticated procedure to compute rovibrational energy levels reproduces all the known rovibrational levels of the water isotopologues considered, H(2) (16)O, H(2) (17)O, H(2) (18)O, and D(2) (16)O, to better than 1 cm(-1) on average. Finally, prospects for further improvement of the ground-state adiabatic ab initio PESs of water are discussed. PMID:17144700

  18. Ab initio charge-carrier mobility model for amorphous molecular semiconductors

    NASA Astrophysics Data System (ADS)

    Massé, Andrea; Friederich, Pascal; Symalla, Franz; Liu, Feilong; Nitsche, Robert; Coehoorn, Reinder; Wenzel, Wolfgang; Bobbert, Peter A.

    2016-05-01

    Accurate charge-carrier mobility models of amorphous organic molecular semiconductors are essential to describe the electrical properties of devices based on these materials. The disordered nature of these semiconductors leads to percolative charge transport with a large characteristic length scale, posing a challenge to the development of such models from ab initio simulations. Here, we develop an ab initio mobility model using a four-step procedure. First, the amorphous morphology together with its energy disorder and intermolecular charge-transfer integrals are obtained from ab initio simulations in a small box. Next, the ab initio information is used to set up a stochastic model for the morphology and transfer integrals. This stochastic model is then employed to generate a large simulation box with modeled morphology and transfer integrals, which can fully capture the percolative charge transport. Finally, the charge-carrier mobility in this simulation box is calculated by solving a master equation, yielding a mobility function depending on temperature, carrier concentration, and electric field. We demonstrate the procedure for hole transport in two important molecular semiconductors, α -NPD and TCTA. In contrast to a previous study, we conclude that spatial correlations in the energy disorder are unimportant for α -NPD. We apply our mobility model to two types of hole-only α -NPD devices and find that the experimental temperature-dependent current density-voltage characteristics of all devices can be well described by only slightly decreasing the simulated energy disorder strength.

  19. Ab initio global optimization of the structures of Si{sub n}H, n=4-10, using parallel genetic algorithms

    SciTech Connect

    Ona, Ofelia; Facelli, Julio C.; Bazterra, Victor E.; Caputo, Maria C.; Ferraro, Marta B.

    2005-11-15

    The results of ab initio global optimizations of the structures of Si{sub n}H, n=4-10, atomic clusters using a parallel genetic algorithm are presented. Driving the global search with the parallel implementation of the genetic algorithm are presented and using the density functional theory as implemented in the Carr-Parinello molecular dynamics code to calculate atomic cluster energies and perform the local optimization of their structures, we have been able to demonstrate that it is possible to perform global optimizations of the structure of atomic clusters using ab initio methods. The results show that this approach is able to find many structures that were not previously reported in the literature. Moreover, in most cases the new structures have considerable lower energies than those previously known. The results clearly demonstrate that these calculations are now possible and in spite of their larger computational demands provide more reliable results.

  20. Ab initio study of the H + HONO reaction: Direct abstraction versus indirect exchange processes

    SciTech Connect

    Hsu, C.C.; Lin, M.C.; Mebel, A.M.; Melius, C.F.

    1997-01-02

    The mechanism of the H + HONO reaction (for which no experimental data are available) has been elucidated by ab initio molecular orbital calculations using modified G2 and BAC-MP4 methods. These results indicate that the reaction occurs predominantly by two indirect metathetical processes. One produces OH + HNO and H{sub 2}O + NO from the decomposition of vibrationally excited hydroxyl nitroxide, HN(O)OH, formed by H atom addition to the N atom of HONO. The other produces H{sub 2}O + NO from the decomposition of vibrationally excited dihydroxylamino radical, N(OH){sub 2}, formed by H atom addition to the terminal O atom. These indirect displacement processes are much more efficient than the commonly assumed, direct H-abstraction reaction producing H{sub 2} + NO{sub 2}. A transition-state theory calculation for the direct abstraction reaction and RRKM calculations for the two indirect displacement processes give rise to the following rate constants, in units of cm{sup 3} molecule{sup -1} s{sup -1} for the 300-3500 K temperature range under atmospheric conditions: k{sub H(2)} = 3.33 x 10{sup -16}T{sup 1.55} exp(-3328.5/T), k{sub OH} = 9.36 x 10{sup -14}T{sup 0.86} exp(-2500.8/T), k{sub H(2)O} = 1.35 x 10{sup -17}T{sup 1.89} exp-(-1935.7/T), where the rate constant for H{sub 2}O production represents the sum from both indirect displacement reactions. 32 refs., 3 figs., 7 tabs.

  1. Ab initio analysis on the interaction of CO2 binding to peracetated D-glucopyranose.

    PubMed

    Honghong, Chang; Congcong, Yang; Xing, Li; Wenlong, Wei; Xianyong, Pang; Yan, Qiao

    2014-06-01

    CO2-philes can be utilized as additives, surfactants, and a potential phase-change physical solvent or absorbent for CO2, so the design and synthesis of CO2-philes typically non-fluorous compounds is important to develop more application areas of CO2. Researchers have recently reported that peracetated D-glucopyranose has high solubility in CO2. In order to study the interaction properties between sugar acetates with CO2, 1,2-di-O-acetyl-α-D-glucopyranose and 1,2-di-O-acetyl-β-D-glucopyranose were decided as substrates after initial chemical stimulations with peracetated D-glucopyranose, and the complex model was one CO2 molecule combined with one sugar substrate (1:1). Ab initio calculations of these two systems were accomplished including geometry optimizations with HF/3-21G, B3LYP/6-31+G**, and single point energies calibration with MP2/aug-cc-pVDZ. The results indicated that hydrogen atoms can interact with CO2 by C-H··O hydrogen bond, but the dominant ones are the interactions of oxygen atoms in substrates with a CO2 molecule. It was also found that the binding energies increased when more oxygen atoms of substrate interacted with CO2, but were not affected by their chemical environment. The interaction of sugar substrate with CO2 is distance related, and should be an electrostatic interaction not only Lewis acid-Lewis base and hydrogen bond interactions. Therefore, it can be expected that one CO2-phile could interact with more CO2 molecules if more acetate-like groups or oxygen atoms were introduced into the molecular structure based on all these results, and this can be a guideline for design CO2-philes. PMID:24844392

  2. Investigation of polarization effects in the gramicidin A channel from ab initio molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Timko, Jeff; Kuyucak, Serdar

    2012-11-01

    Polarization is an important component of molecular interactions and is expected to play a particularly significant role in inhomogeneous environments such as pores and interfaces. Here we investigate the effects of polarization in the gramicidin A ion channel by performing quantum mechanics/molecular mechanics molecular dynamics (MD) simulations and comparing the results with those obtained from classical MD simulations with non-polarizable force fields. We consider the dipole moments of backbone carbonyl groups and channel water molecules as well as a number of structural quantities of interest. The ab initio results show that the dipole moments of the carbonyl groups and water molecules are highly sensitive to the hydrogen bonds (H-bonds) they participate in. In the absence of a K+ ion, water molecules in the channel are quite mobile, making the H-bond network highly dynamic. A central K+ ion acts as an anchor for the channel waters, stabilizing the H-bond network and thereby increasing their average dipole moments. In contrast, the K+ ion has little effect on the dipole moments of the neighboring carbonyl groups. The weakness of the ion-peptide interactions helps to explain the near diffusion-rate conductance of K+ ions through the channel. We also address the sampling issue in relatively short ab initio MD simulations. Results obtained from a continuous 20 ps ab initio MD simulation are compared with those generated by sampling ten windows from a much longer classical MD simulation and running each window for 2 ps with ab initio MD. Both methods yield similar results for a number of quantities of interest, indicating that fluctuations are fast enough to justify the short ab initio MD simulations.

  3. High adsorption capacity of heavy metals on two-dimensional MXenes: an ab initio study with molecular dynamics simulation.

    PubMed

    Guo, Xun; Zhang, Xitong; Zhao, Shijun; Huang, Qing; Xue, Jianming

    2016-01-01

    Density functional theory (DFT) calculation is employed to study the adsorption properties of Pb and Cu on recently synthesized two-dimensional materials MXenes, including Ti3C2, V2C1 and Ti2C1. The influence of surface decoration with functional groups such as H, OH and F have also been investigated. Most of these studied MXenes exhibit excellent capability to adsorb Pb and Cu, especially the adsorption capacity of Pb on Ti2C1 is as high as 2560 mg g(-1). Both the binding energies and the adsorption capacities are sensitive to the functional groups attached to the MXenes' surface. Ab initio molecular dynamics (ab-init MD) simulation confirms that Ti2C1 remains stable at room temperature after adsorbing Pb atoms. Our calculations imply that these newly emerging two-dimensional MXenes are promising candidates for wastewater treatment and ion separation. PMID:26602974

  4. Defect-Enhanced Charge Transfer by Ion-Solid Interactions in SiC using Large-Scale Ab Initio Molecular Dynamics Simulations

    SciTech Connect

    Gao, Fei; Xiao, H. Y.; Zu, Xiaotao T.; Posselt, Matthias; Weber, William J.

    2009-07-10

    Large-scale ab initio molecular dynamics simulations of ion-solid interactions in SiC reveal that significant charge-transfer occurs between atoms and defects can enhance charge transfer to surrounding atoms. The results demonstrate that charge transfer to and from recoiling atoms can alter the energy barriers and dynamics for stable defect formation. The present simulations illustrate in detail the dynamic processes for charged defect formation. The averaged values of displacement threshold energies along four main crystallographic directions are smaller than those determined by empirical potentials due to charge transfer effects on recoil atoms.

  5. Defect-Enhanced Charge Transfer by Ion-Solid Interactions in SiC using Large-Scale Ab Initio Molecular Dynamics Simulations

    SciTech Connect

    Gao Fei; Weber, William J.; Xiao Haiyan; Zu Xiaotao; Posselt, Matthias

    2009-07-10

    Large-scale ab initio molecular dynamics simulations of ion-solid interactions in SiC reveal that significant charge transfer occurs between atoms, and defects can enhance charge transfer to surrounding atoms. The results demonstrate that charge transfer to and from recoiling atoms can alter the energy barriers and dynamics for stable defect formation. The present simulations illustrate in detail the dynamic processes for charged defect formation. The averaged values of displacement threshold energies along four main crystallographic directions are smaller than those determined by empirical potentials due to charge-transfer effects on recoil atoms.

  6. Probing the Si(001) surface with a Si tip: An ab initio study

    NASA Astrophysics Data System (ADS)

    Kantorovich, Lev; Hobbs, Chris

    2006-06-01

    Topographic noncontact atomic force microscopy (NC-AFM) images of the p(2×1) and c(4×2) reconstructions of the Si(001) surface are simulated for the cases of weak and strong tip-surface interactions and various temperatures using ab initio density functional theory. In the simulations the surface is imaged by a sharp silicon tip with a single dangling bond at its apex. At a very close approach to the surface, the tip flips a surface dimer when positioned close to its lower atom. The energy barriers for an individual flipped surface dimer to regain its initial configuration are calculated to be ˜0.1eV , implying that the surface should be able to “heal” itself at all but extremely low temperatures during one oscillation cycle of the cantilever. Thus, at small enough temperatures, T⩽70K , and large frequency shifts, the imaging process is dominated by tip induced dimer flip events resulting in a permanent deformation of the surface and an apparent p(2×1) symmetric phase to be observed. No dissipation is expected as the tip oscillations are conservative at these conditions. At intermediate temperatures, 70K⩽T⩽200K , the flipped dimers are able to return to the ground state during each tip oscillation, resulting in continuous healing of the surface and thus large dissipation is expected. At T⩾200K dimers flip back and forth easily resulting in an apparent symmetric p(2×1) phase and noticeable dissipation. At small frequency shifts the dimers do not flip, still the upper dimer atoms are imaged as bright so that surface reconstruction can easily be determined. The possibility of manipulating the orientation of dimers at low temperatures and large frequency shifts by means of preprogrammed scan directions, is also discussed.

  7. Ab initio lattice dynamical studies of silicon clathrate frameworks and their negative thermal expansion

    NASA Astrophysics Data System (ADS)

    Härkönen, Ville J.; Karttunen, Antti J.

    2014-01-01

    The thermal and lattice dynamical properties of seven silicon clathrate framework structures are investigated with ab initio density functional methods (frameworks I, II, IV, V, VII, VIII, and H). The negative thermal expansion (NTE) phenomenon is investigated by means of quasiharmonic approximation and applying it to equal time displacement correlation functions. The thermal properties of the studied clathrate frameworks, excluding the VII framework, resemble those of the crystalline silicon diamond structure. The clathrate framework VII was found to have an anomalous NTE temperature range up to 300 K and it is suitable for further studies of the mechanisms of NTE. Investigation of the displacement correlation functions revealed that in NTE, the volume derivatives of the mean square displacements and mean square relative displacements of atoms behave similarly to the vibrational entropy volume derivatives and consequently to the coefficients of thermal expansion as a function of temperature. All studied clathrate frameworks, excluding the VII framework, possess a phonon band gap or even two in the case of framework V.

  8. Ab-initio Electronic, Transport and Related Properties of Zinc Blende Boron Arsenide (zb-BAs)

    NASA Astrophysics Data System (ADS)

    Nwigboji, Ifeanyi H.; Malozovsky, Yuriy; Bagayoko, Diola

    We present results from ab-initio, self-consistent density functional theory (DFT) calculations of electronic, transport, and bulk properties of zinc blende boron arsenide (zb-BAs). We utilized a local density approximation (LDA) potential and the linear combination of atomic orbital (LCAO) formalism. Our computational technique follows the Bagayoko, Zhao, and Williams method, as enhanced by Ekuma and Franklin. Our results include electronic energy bands, densities of states, and effective masses. We explain the agreement between these findings, including the indirect band gap, and available, corresponding, experimental ones. This work confirms the capability of DFT to describe accurately properties of materials, provided the computations adhere to the conditions of validity of DFT [AIP Advances, 4, 127104 (2014)]. 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.

  9. Ab-Initio Calculations of Electronic Properties and Quantum Transport in U-Shaped Graphene Nanoribbons

    NASA Astrophysics Data System (ADS)

    Cuong, Nguyen Tien; Mizuta, Hiroshi; Cong, Bach Thanh; Otsuka, Nobuo; Chi, Dam Hieu

    2012-09-01

    Graphene is a promising candidate as a material used in nano-scale devices because of recent developments in advanced experimental techniques. Motivated by recent successful fabrications of U-shaped graphene channel transistors by using the gallium focused ion beam technology, we have performed ab-initio calculations to investigate the electronic properties and quantum transport in U-shaped graphene nanoribbons. The electronic properties are calculated using a numerical atomic orbital basis set in the framework of the density functional theory. The transport properties are investigated using the non-equilibrium Green's function method. The transmission spectra of U-shaped graphenes are analyzed in order to reveal the quantum transport of the systems. We found that the graphene nanoribbons tend to open a band gap when U-shaped structures are formed in both armchair and zigzag cases. The geometrical structures of U-shaped GNRs had enormous influences on the electron transport around the Fermi energy due to the formation of quasi-bound states at zigzag edges. The obtained results have provided valuable information for designing potential nano-scale devices based on graphenes.

  10. Born-Oppenheimer Ab Initio QM/MM Molecular Dynamics Simulations of Enzyme Reactions.

    PubMed

    Zhou, Y; Wang, S; Li, Y; Zhang, Y

    2016-01-01

    There are two key requirements for reliably simulating enzyme reactions: one is a reasonably accurate potential energy surface to describe the bond-forming/breaking process as well as to adequately model the heterogeneous enzyme environment; the other is to perform extensive sampling since an enzyme system consists of at least thousands of atoms and its energy landscape is very complex. One attractive approach to meet both daunting tasks is Born-Oppenheimer ab initio QM/MM molecular dynamics (aiQM/MM-MD) simulation with umbrella sampling. In this chapter, we describe our recently developed pseudobond Q-Chem-Amber interface, which employs a combined electrostatic-mechanical embedding scheme with periodic boundary condition and the particle mesh Ewald method for long-range electrostatics interactions. In our implementation, Q-Chem and the sander module of Amber are combined at the source code level without using system calls, and all necessary data communications between QM and MM calculations are achieved via computer memory. We demonstrate the applicability of this pseudobond Q-Chem-Amber interface by presenting two examples, one reaction in aqueous solution and one enzyme reaction. Finally, we describe our established aiQM/MM-MD enzyme simulation protocol, which has been successfully applied to study more than a dozen enzymes. PMID:27498636

  11. Surface magnetism of the carbon foam: An ab-initio theoretical study

    SciTech Connect

    Yu, Guodong; Jiang, Liwei; Zheng, Yisong

    2014-08-11

    By means of ab-initio calculations, we study the surface magnetism of carbon foam, a carbon allotrope constructed by both the sp{sup 2} and sp{sup 3} hybridized carbon atoms. It is found that the sp{sup 3}-terminated surface and sp{sup 2}-terminated surface with hydrogen saturation (sp{sup 2}H) have the antiferromagnetic and ferromagnetic ground states, respectively. And the corresponding phase transition temperatures of these two surfaces are estimated to exceed 100 K. In addition, the magnetic moment of the sp{sup 2}H surface can be effectively modulated by strain. More interestingly, at the level of generalized gradient approximation, as the lattice are stretched, a bulk bandgap will open. And in such a bandgap, the sp{sup 2}H surface states can form spin polarized Dirac cones at K(K′) point. Thus, in the vicinity of the Fermi level, only the electron with a specific spin behaves like a Dirac Fermion.

  12. Ab initio study of the unusual thermal transport properties of boron arsenide and related materials

    NASA Astrophysics Data System (ADS)

    Broido, D. A.; Lindsay, L.; Reinecke, T. L.

    2013-12-01

    Recently, using a first principles approach, we predicted that zinc blende boron arsenide (BAs) will have an ultrahigh lattice thermal conductivity, κ, of over 2000 Wm-1K-1 at room temperature (RT), comparable to that of diamond. Here, we provide a detailed ab initio examination of phonon thermal transport in boron arsenide, contrasting its unconventional behavior with that of other related materials, including the zinc blende crystals boron nitride (BN), boron phosphide, boron antimonide, and gallium nitride (GaN). The unusual vibrational properties of BAs contribute to its weak phonon-phonon scattering and phonon-isotope scattering, which are responsible for its exceptionally high κ. The thermal conductivity of BAs has contributions from phonons with anomalously large mean free paths (˜2 μm), two to three times those of diamond and BN. This makes κ in BAs sensitive to phonon scattering from crystal boundaries. An order of magnitude smaller RT thermal conductivity in a similar material, zinc blende GaN, is connected to more separated acoustic phonon branches, larger anharmonic force constants, and a large isotope mixture on the heavy rather than the light constituent atom. The striking difference in κ for BAs and GaN demonstrates the importance of using a microscopic first principles thermal transport approach for calculating κ. BAs also has an advantageous RT coefficient of thermal expansion, which, combined with the high κ value, suggests that it is a promising material for use in thermal management applications.

  13. Ab initio study of the effect of vacancies on the thermal conductivity of boron arsenide

    NASA Astrophysics Data System (ADS)

    Protik, Nakib Haider; Carrete, Jesús; Katcho, Nebil A.; Mingo, Natalio; Broido, David

    2016-07-01

    Using a first principles theoretical approach, we show that vacancies give anomalously strong suppression of the lattice thermal conductivity κ of cubic Boron arsenide (BAs), which has recently been predicted to have an exceptionally high κ . This effect is tied to the unusually large phonon lifetimes in BAs and results in a stronger reduction in the BAs κ than occurs in diamond. The large changes in bonding around vacancies cannot be accurately captured using standard perturbative methods and are instead treated here using an ab initio Green function approach. As and B vacancies are found to have similar effects on κ . In contrast, we show that commonly used mass disorder models for vacancies fail for large mass ratio compounds such as BAs, incorrectly predicting much stronger (weaker) phonon scattering when the vacancy is on the heavy (light) atom site. The quantitative treatment given here contributes to fundamental understanding of the effect of point defects on thermal transport in solids and provides guidance to synthesis efforts to grow high quality BAs.

  14. Experimental and ab initio investigations of microscopic properties of laser-shocked Ge-doped ablator.

    PubMed

    Huser, G; Recoules, V; Ozaki, N; Sano, T; Sakawa, Y; Salin, G; Albertazzi, B; Miyanishi, K; Kodama, R

    2015-12-01

    Plastic materials (CH) doped with mid-Z elements are used as ablators in inertial confinement fusion (ICF) capsules and in their surrogates. Hugoniot equation of state (EOS) and electronic properties of CH doped with germanium (at 2.5% and 13% dopant fractions) are investigated experimentally up to 7 Mbar using velocity and reflectivity measurements of shock fronts on the GEKKO laser at Osaka University. Reflectivity and temperature measurements were updated using a quartz standard. Shocked quartz reflectivity was measured at 532 and 1064 nm. Theoretical investigation of shock pressure and reflectivity was then carried out by ab initio simulations using the quantum molecular dynamics (QMD) code abinit and compared with tabulated average atom EOS models. We find that shock states calculated by QMD are in better agreement with experimental data than EOS models because of a more accurate description of ionic structure. We finally discuss electronic properties by comparing reflectivity data to a semiconductor gap closure model and to QMD simulations. PMID:26764839

  15. Ab initio calculations of phonon properties and spectra in condensed matter

    NASA Astrophysics Data System (ADS)

    Story, Shauna M.

    Phonons, the quantization of atomic vibrations, are important in studying many solid state properties, ranging from Raman, infrared, and neutron scattering to thermal expansion, specific heat, and heat conductivity to electrical resistivity and superconductivity. Generally, modeling the interatomic forces and vibrational modes of a given system require costly computer simulations, though once calculated, they provide the means to a wide variety of phonon properties. Our goal is to enable easy access to these phonon properties and to do this, we have developed a framework for easily automating the workflows involved in interfacing a phonon mode calculation with the analysis tools for determining such physical properties. This was originally implemented with the AI2PS (ab initio to phonon spectra) tool, meant solely for the calculation of vibrational properties. It has since greatly expanded in scope and capabilities to a general scientific workflow tool called Corvus, which was started with the eventual goal of collecting all our various scientific workflow efforts---phonon properties, optical properties, and so on---into a single hub. We present here both the evolution of AI2PS into the Corvus project and the phonon properties simulated, including Debye--Waller factors, phonon contributions the electron self--energy and spectral function, vibrational free energy, thermal expansion, and heat capacity.

  16. Ab initio guided design of bcc Mg-Li alloys for ultra light-weight applications

    NASA Astrophysics Data System (ADS)

    Friák, Martin; Counts, William Art; Raabe, Dierk; Neugebauer, Jörg

    2009-03-01

    Ab initio calculations are becoming increasingly useful to engineers interested in designing new alloys because these calculations are able to accurately predict basic material properties only knowing the atomic composition of the material. In this paper, fundamental physical properties (like formation energies and elastic constants) of 11 bcc Mg-Li compounds are calculated using density-functional theory (DFT) and compared with available experimental data. These DFT-determined properties are in turn used to calculate engineering parameters like (i) specific Young's modulus (Y/ρ) or (ii) bulk over shear modulus ratio (B/G) differentiating between brittle and ductile behavior. The engineering parameters are then used to identify alloys that have optimal mechanical properties needed for a light weight structural material. It was found that the stiffest bcc magnesium-lithium alloys contain about 70 at.% Mg while the most ductile alloys have 0-20 at.% Mg. The specific modulus for alloys with 70 at.% Mg is equal to that of Al-Mg alloys. An Ashby map containing Y/ρ vs. B/G shows that it is not possible to increase both Y/ρ and B/G by changing only the composition or local order of a binary alloy (W. A. Counts, M. Fri'ak, D. Raabe and J. Neugebauer, Acta Mater 57 (2009) 69-76).

  17. Engineering materials-design parameters of the Mg-Li Alloy System from ab initio calculations

    NASA Astrophysics Data System (ADS)

    Counts, William; Friak, Martin; Raabe, Dierk; Neugebauer, Jorg

    2008-03-01

    Ab initio calculations are becoming increasingly useful to engineers interested in designing new alloys because these calculations are able to accurately predict basic material properties only knowing the atomic composition of the material. Fundamental physical properties (like formation energy and elastic constants) of 11 bcc magnesium-lithium alloys were calculated using density-functional theory (DFT) and compared with available experimental data. These DFT determined properties were in turn used to calculate engineering parameters like the bulk modulus/shear modulus (B/G) and Young's modulus/density (E/ρ). From these engineering parameters, alloys with optimal mechanical properties need for a light weight structural material were identified. It was found that the stiffest bcc magnesium-lithium alloys contain about 70 at.% magnesium while the most ductile alloys have 0-20 at.% magnesium. In addition, the specific modulus for alloys with 70 at.% magnesium was found to be equal to that of aluminum-magnesium alloys and slightly lower than that of aluminum-lithium alloys.

  18. How fragility makes phase-change data storage robust: insights from ab initio simulations

    PubMed Central

    Zhang, Wei; Ronneberger, Ider; Zalden, Peter; Xu, Ming; Salinga, Martin; Wuttig, Matthias; Mazzarello, Riccardo

    2014-01-01

    Phase-change materials are technologically important due to their manifold applications in data storage. Here we report on ab initio molecular dynamics simulations of crystallization of the phase change material Ag4In3Sb67Te26 (AIST). We show that, at high temperature, the observed crystal growth mechanisms and crystallization speed are in good agreement with experimental data. We provide an in-depth understanding of the crystallization mechanisms at the atomic level. At temperatures below 550 K, the computed growth velocities are much higher than those obtained from time-resolved reflectivity measurements, due to large deviations in the diffusion coefficients. As a consequence of the high fragility of AIST, experimental diffusivities display a dramatic increase in activation energies and prefactors at temperatures below 550 K. This property is essential to ensure fast crystallization at high temperature and a stable amorphous state at low temperature. On the other hand, no such change in the temperature dependence of the diffusivity is observed in our simulations, down to 450 K. We also attribute this different behavior to the fragility of the system, in combination with the very fast quenching times employed in the simulations. PMID:25284316

  19. Interplay of force constants in the lattice dynamics of disordered alloys: An ab initio study

    NASA Astrophysics Data System (ADS)

    Chouhan, Rajiv K.; Alam, Aftab; Ghosh, Subhradip; Mookerjee, Abhijit

    2014-02-01

    A reliable prediction of interatomic force constants in disordered alloys is an outstanding problem. This is due to the need for a proper treatment of multisite (at least pair) correlation within a random environment. The situation becomes even more challenging for systems with a large difference in atomic size and mass. We propose a systematic density functional theory (DFT) based study to predict the ab initio force constants in random alloys. The method is based on a combination of special quasirandom structures and the augmented space recursion to calculate phonon spectra, density of states (DOS), etc. The bcc TaW and fcc NiPt alloys are considered as the two distinct test cases. The Ta-Ta (W-W) bond distance in the alloy is predicted to be smaller (larger) than those in pure Ta (W), which, in turn, yields stiffer (softer) force constants for Ta (W). Pt-Pt force constants in the alloy, however, are predicted to be softer compared to Ni-Ni, due to the large bond distance of the former. Our calculated force constants, phonon spectra, and DOS are compared with experiments and other theoretical results, wherever available. A correct trend of the present results for the two alloys paves a path for future studies in more complex alloy systems.

  20. Ab initio study of basal slip in Nb(2)AlC.

    PubMed

    Music, Denis; Sun, Zhimei; Voevodin, Andrey A; Schneider, Jochen M

    2006-05-01

    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. PMID:21690790

  1. Yttrium aluminium garnet under pressure: Structural, elastic, and vibrational properties from ab initio studies

    SciTech Connect

    Monteseguro, V.; Rodríguez-Hernández, P.; Muñoz, A.

    2015-12-28

    The structural, elastic, and vibrational properties of yttrium aluminum garnet Y{sub 3}Al{sub 5}O{sub 12} are studied under high pressure by ab initio calculations in the framework of the density functional theory. The calculated ground state properties are in good agreement with the available experimental data. Pressure dependences of bond length and bulk moduli of the constituent polyhedra are reported. The evolution of the elastic constants and the major elastic properties, Young and shear modulus, Poisson's ratios, and Zener anisotropy ratio, are described. The mechanical stability is analyzed, on the light of “Born generalized stability criteria,” showing that the garnet is mechanically unstable above 116 GPa. Symmetries, frequencies, and pressure coefficients of the Raman-active modes are discussed on the basis of the calculated total and partial phonon density of states, which reflect the dynamical contribution of each atom. The relations between the phonon modes of Y{sub 3}Al{sub 5}O{sub 12} and the internal and external molecular modes of the different polyhedra are discussed. Infrared-active modes, as well as the silent modes, and their pressure dependence are also investigated. No dynamical instabilities were found below 116 GPa.

  2. Disulfuric acid dissociated by two water molecules: ab initio and density functional theory calculations.

    PubMed

    Kim, Seong Kyu; Lee, Han Myoung; Kim, Kwang S

    2015-11-21

    We have studied geometries, energies and vibrational spectra of disulfuric acid (H2S2O7) and its anion (HS2O7(-)) hydrated by a few water molecules, using density functional theory (M062X) and ab initio theory (SCS-MP2 and CCSD(T)). The most noteworthy result is found in H2S2O7(H2O)2 in which the lowest energy conformer shows deprotonated H2S2O7. Thus, H2S2O7 requires only two water molecules, the fewest number of water molecules for deprotonation among various hydrated monomeric acids reported so far. Even the second deprotonation of the first deprotonated species HS2O7(-) needs only four water molecules. The deprotonation is supported by vibration spectra, in which acid O-H stretching peaks disappear and specific three O-H stretching peaks for H3O(+) (eigen structure) appear. We have also kept track of variations in several geometrical parameters, atomic charges, and hybrid orbital characters upon addition of water. As the number of water molecules added increases, the S-O bond weakens in the case of H2S2O7, but strengthens in the case of HS2O7(-). It implies that the decomposition leading to H2SO4 and SO3 hardly occurs prior to the 2nd deprotonation at low temperatures. PMID:26400266

  3. Determination of a silane intermolecular force field potential model from an ab initio calculation

    SciTech Connect

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

    2010-12-15

    Intermolecular interaction potentials of the silane dimer in 12 orientations have been calculated by using the Hartree-Fock (HF) self-consistent theory and the second-order Moeller-Plesset (MP2) perturbation theory. We employed basis sets from Pople's medium-size basis sets [up to 6-311++G(3df, 3pd)] and Dunning's correlation consistent basis sets (up to the triply augmented correlation-consistent polarized valence quadruple-zeta basis set). We found that the minimum energy orientations were the G and H conformers. We have suggested that the Si-H attractions, the central silicon atom size, and electronegativity play essential roles in weakly binding of a silane dimer. The calculated MP2 potential data were employed to parametrize a five-site force field for molecular simulations. The Si-Si, Si-H, and H-H interaction parameters in a pairwise-additive, site-site potential model for silane molecules were regressed from the ab initio energies.

  4. Microwave Spectra and AB Initio Studies of the Ne-Acetone Complex

    NASA Astrophysics Data System (ADS)

    Gao, Jiao; Thomas, Javix; Xu, Yunjie; Jäger, Wolfgang

    2015-06-01

    Microwave spectra of the neon-acetone van der Waals complex were measured using a cavity-based molecular beam Fourier-transform microwave spectrometer in the region from 5 to 18 GHz. Both 20Ne and 22Ne containing isotopologues were studied and both c- and weaker a-type rotational transitions were observed. The transitions are split into multiplets due to the internal rotation of two methyl groups in acetone. Electronic structure calculations were done at the MP2 level of theory with the 6-311++g (2d, p) basis set for all atoms and the internal rotation barrier height of the methyl groups was determined to be about 2.8 kJ/mol. The ab initio rotational constants were the basis for our spectroscopic searches, but the multiplet structures and floppiness of the complex made the quantum number assignment very difficult. The assignment was finally achieved with the aid of constructing closed frequency loops and predicting internal rotation splittings using the XIAM code. Analyses of the spectra yielded rotational and centrifugal distortion constants, as well as internal rotation parameters, which were interpreted in terms of structure and internal dynamics of the complex. H. Hartwig and H. Dreizler, Z. Naturforsch. A 51, 923 (1996).

  5. Ab-initio Calculation of Optoelectronic and Structural Properties of Cubic Lithium Oxide (Li2O)

    NASA Astrophysics Data System (ADS)

    Ziegler, Joshua; Polin, Daniel; Malozovsky, Yuriy; Bagayoko, Diola

    Using the Bagayoko, Zhao, and Williams (BZW) method, as enhanced by Ekuma and Franklin (BZW-EF), we performed ab-initio, density functional theory (DFT) calculations of optoelectronic, transport, and bulk properties of Li2S. In so doing, we avoid ``band gap'' and problems plaguing many DET calculations [AIP Advances 4, 127104 (2014)]. We employed a local density approximation (LDA) potential and the linear combination of atomic orbitals (LCAO). With the BZW-EF method, our results possess the full, physical content of DFT and agree with available, corresponding experimental ones. In particular, we found a room temperature indirect band gap of 6.659 eV that compares favorably with experimental values ranging from 5 to 7.99 eV. We also calculated total and partial density of states (DOS and PDOS), effective masses of charge carriers, the equilibrium lattice constant, and the bulk modulus. 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 Nos. DE-NA0001861 and DE- NA0002630), LaSPACE, and LONI-SUBR.

  6. Parametrization and Validation of Coarse Grained Force-Fields Derived from ab Initio Calculations.

    PubMed

    Prampolini, Giacomo

    2006-05-01

    A novel multisite interaction potential, suitable for computer simulations of complex materials as liquid crystals or polymers, is proposed and parametrized. Its validation is achieved through Monte Carlo numerical experiments at constant temperature and pressure, performed on the p-n-phenyls series and a typical mesogenic molecule (5CB). The model is constructed by connecting an array of anisotropic Gay-Berne sites and a collection of isotropic Lennard-Jones sites. The former mimics the rigid planar six-membered rings of the molecule, while the latter represents the flexible chain, if present. Such intermolecular potential, coupled with an intramolecular part to account for molecular flexibility, is parametrized from ab initio information only, obtained through the recently proposed Fragmentation-Reconstruction Method (FRM). Computer simulations are performed on all systems by exploring phase behavior at several temperatures and by comparing the resulting thermodynamic and structural properties with the relevant experimental data. Despite the simplicity of the present models, the good agreement with the experimental measures suggests the possibility of adopting such hybrid potentials for those systems with a large number of atoms, where high computational cost does not allow the use of more accurate atomistic potentials. PMID:26626663

  7. Ab initio calculations of magnetic properties of the interstitially doped YFe11Mo compound

    NASA Astrophysics Data System (ADS)

    Kokorina, E. E.; Medvedev, M. V.; Nekrasov, I. A.

    2016-02-01

    The recent increase in the number of studies of RFe11- x M x compounds is related to their promising application as permanent magnets. However, the insufficiently high value of the Curie temperature T C of these compounds is a barrier to their widespread use. The increase in the Curie temperature of these compounds is achieved by doping with the light nonmetallic atoms such as hydrogen, nitrogen, and carbon. In this paper, it is shown numerically that this doping leads to drastic changes of the electronic band dispersions in a wide energy region around the Fermi level. This in turn changes values of the magnetic moments of ions and Heisenberg exchange interaction parameters. The values of ab initio calculated magnetic moments and direct exchange interaction parameters make it possible to calculate the Curie temperatures for both parent and nitrogen-doped compounds within the mean-field approach to the Heisenberg model in the sample of YFe11Mo, a typical representative of the R(Fe,M)12L class. Theoretical values of T C obtained for YFe11Mo and YFe11MoN (514 and 723 K respectively) are consistent with experimental ones (472 and 664 K) with an accuracy of 10%. Also, the calculated increase in T C upon nitrogenization (about 200 K) is in good agreement with the experimental data.

  8. Two Dimensional Epitaxial Water Adlayer on Mica with Graphene Coating: An ab Initio Molecular Dynamics Study.

    PubMed

    Li, Hui; Zeng, Xiao Cheng

    2012-09-11

    Motivated by a recent atomic-force-microscopy (AFM) study of water adlayers on mica by Heath and co-workers (Graphene Visualizes the First Water Adlayers on Mica at Ambient Conditions. Science2010, 329, 1188), we performed an ab initio molecular dynamics study of structural and dynamic properties of monolayer, bilayer, and trilayer water adlayers on the muscovite mica (001) surface with and without a graphene coating. We find that in the first epitaxial water adlayer, water molecules that form strong hydrogen bonds with the oxygen on the mica surface show little motions, thereby solid-like, while those "bridging" water molecules on top of the first water adlayer exhibit "itinerant" behavior, thereby liquid-like. Overall, the Born-Oppenheim molecular dynamics (BOMD) simulations (based on the BLYP-D functional) show that the first water adlayer on mica exhibits a unique hybrid solid-liquid-like behavior with a very low diffusion coefficient at ambient conditions. In particular, no dangling hydrogen bonds are found in the first water adlayer on mica. Moreover, the bilayer and trilayer water adlayers show slightly higher structural stability than the first water adlayer. A graphene coating on the water adlayer further enhances stability of the water adlayers. Most importantly, the bilayer water adlayer on mica with the graphene coating becomes fully solid-like, the structure of which is the same as the bilayer slice of ice-Ih with a thickness of 7.4 Å, consistent with the AFM measurement. PMID:26605715

  9. Ab initio Structure Determination of Mg10Ir19B16

    SciTech Connect

    Xu, Qiang; Klimczuk, T.; Gortenmulder, T.; Jansen, J.; McGuire, Michael A; Cava, R. J.; Zandbergen, H

    2009-01-01

    The ab initio structure determination of a novel unconventional noncentro-symmetric superconductor Mg{sub 10}Ir{sub 19}B{sub 16} (T{sub c} = 5 K) has been performed using a method that involves a combination of experimental data and calculations. Electron diffraction, X-ray powder diffraction, phase estimation routines, quantum mechanical calculations, high-resolution electron microscopy, and structural chemistry arguments are used. With the strengths of different methods used to eliminate the ambiguities encountered in others, the complete structure, including a very light B atom, has been determined with a high accuracy from impure polycrystalline powder samples, which suggests that the type of analysis described may be used to successfully address other similar intractable problems. The solved structure of Mg{sub 10}Ir{sub 19}B{sub 16} shows a complex nature that irregular coordination environments preclude a conversional description of compact packing of coordination polyhedra; however, it can be easier understood as ordered in an onion-skin-like series of nested polyhedra.

  10. Direct molecular simulation of nitrogen dissociation based on an ab initio potential energy surface

    SciTech Connect

    Valentini, Paolo Schwartzentruber, Thomas E. Bender, Jason D. Nompelis, Ioannis Candler, Graham V.

    2015-08-15

    The direct molecular simulation (DMS) approach is used to predict the internal energy relaxation and dissociation dynamics of high-temperature nitrogen. An ab initio potential energy surface (PES) is used to calculate the dynamics of two interacting nitrogen molecules by providing forces between the four atoms. In the near-equilibrium limit, it is shown that DMS reproduces the results obtained from well-established quasiclassical trajectory (QCT) analysis, verifying the validity of the approach. DMS is used to predict the vibrational relaxation time constant for N{sub 2}–N{sub 2} collisions and its temperature dependence, which are in close agreement with existing experiments and theory. Using both QCT and DMS with the same PES, we find that dissociation significantly depletes the upper vibrational energy levels. As a result, across a wide temperature range, the dissociation rate is found to be approximately 4–5 times lower compared to the rates computed using QCT with Boltzmann energy distributions. DMS calculations predict a quasi-steady-state distribution of rotational and vibrational energies in which the rate of depletion of high-energy states due to dissociation is balanced by their rate of repopulation due to collisional processes. The DMS approach simulates the evolution of internal energy distributions and their coupling to dissociation without the need to precompute rates or cross sections for all possible energy transitions. These benchmark results could be used to develop new computational fluid dynamics models for high-enthalpy flow applications.

  11. Ab initio calculations of the reaction pathways for methane decomposition over the Cu (111) surface.

    PubMed

    Gajewski, Grzegorz; Pao, Chun-Wei

    2011-08-14

    Growth of large-area, few-layer graphene has been reported recently through the catalytic decomposition of methane (CH(4)) over a Cu surface at high temperature. In this study, we used ab initio calculations to investigate the minimum energy pathways of successive dehydrogenation reactions of CH(4) over the Cu (111) surface. The geometries and energies of all the reaction intermediates and transition states were identified using the climbing image nudged elastic band method. The activation barriers for CH(4) decomposition over this Cu surface are much lower than those in the gas phase; furthermore, analysis of electron density differences revealed significant degrees of charge transfer between the adsorbates and the Cu atoms along the reaction path; these features reveal the role of Cu as the catalytic material for graphene growth. All the dehydrogenation reactions are endothermic, except for carbon dimer (C(2)) formation, which is, therefore, the most critical step for subsequent graphene growth, in particular, on Cu (111) surface. PMID:21842949

  12. Why does bromine square palladium off? An ab initio study of brominated palladium and its nanomorphology.

    PubMed

    Yoo, Su-Hyun; Lee, Ji-Hwan; Delley, Bernard; Soon, Aloysius

    2014-09-14

    A first-principles description and prediction of brominated nanocrystals of Pd is presented. In particular, we conducted an extensive study of the adsorption behaviour of Br on various Pd surfaces (including both low and high Miller-index surfaces) as a function of its surface coverage. By coupling our calculated surface energies with ab initio (electrochemical) thermodynamics and the Gibbs-Wulff shape model, we find that the relative stability of the Pd surfaces is strongly modified by Br, allowing high Miller-index surfaces of Pd (namely the (210) surface) to become competitively favourable at moderate concentrations of Br. We also show that Pd nanoparticles assume a cube-like crystal shape at high concentrations of Br, exposing mainly the (100) facets with a Br surface coverage of 0.5 ML. This not only confirms and explains recent solution synthesis results, but also provides a quantitative atomic picture of the exposed surface facets, which is crucial in understanding the local surface chemistry of shape-controlled nanoparticles for better nanocatalyst design. PMID:25075669

  13. Generation of amorphous porous PdH: an ab initio approach

    NASA Astrophysics Data System (ADS)

    Rodriguez, Isaias; Valladares, Renela; Valladares, Ariel A.; Valladares, Alexander

    2014-03-01

    The hydrogen bubble template (HBT) method has been employed to generate amorphous porous structures in platinum, nickel, copper and gold. We used our ab initio approach to generate amorphous porous Pd50H50 ; Pd45H55 ; Pd40H60 , using an approach similar to the HBT method which keeps the interatomic distances the same as in the pure crystalline Pd, swapping palladium by hydrogen in a substitutional way, thus reducing the density and making the initial supercell metastable. We applied this HBT-like method to an initial 108-atom crystalline face-centered cubic palladium supercell, with an initial density of 12 . 02 g / cm3 . After the substitution we got three supercells: a crystalline supercell: Pd54H54, with a density of 6 . 056g/cm3 ; a supercell: Pd49H59, with a density of 5 . 506g/cm3 ; and a supercell: Pd43H65, with a density of 4 . 846g/cm3 . After the hydrogen insertion an MD process at 1000 K was applied, and the resulting structures finally relaxed. Pores appeared along well-defined spatial directions. We characterized the structures by means of the pair distribution function (PDF) and the bond-angle distribution. Our results will be discussed in the light of possible structures of amorphous porous palladium hydride. Supported by CONACYT and DGAPA, UNAM.

  14. Ab initio molecular dynamics simulations of threshold displacement energies in SrTiO3

    SciTech Connect

    Liu, Bin; Xiao, Haiyan; Zhang, Yanwen; Aidhy, Dilpuneet S; Weber, William J

    2013-01-01

    Ab initio molecular dynamics simulations have been carried out to study low-energy recoil events in SrTiO3. The threshold displacement energies are shown to be strongly dependent on both the orientation and the corresponding atomic arrangement. The minimum threshold displacement energies are 13 eV for an O recoil along the <100> O-O chain, 25 eV for a Sr recoil along the <100> Sr-Sr chain and 38 eV for a Ti recoil along the <110> Ti-Ti chain. The weighted average threshold displacement energies along the primary crystallographic directions are 35.7, 53.5 and > 64.9 eV for O, Sr and Ti, respectively. The interstitial configurations produced by the recoil events are <100> and <111> split-interstitials for O and Sr, respectively, together with a Ti interstitial occupying a distorted bridge position between two Sr sites. It is found that the recoil events in SrTiO3 are partial- charge transfer assisted processes, and the partial- charge transfer plays an important role in these recoil events.

  15. Regioselective synthesis and ab initio calculations of fused heterocycles thermally and under microwave irradiation

    NASA Astrophysics Data System (ADS)

    Salem, Mostafa E.; Ahmed, Ashour A.; Shaaban, Mohamed R.; Shibl, Mohamed F.; Farag, Ahmad M.

    2015-09-01

    Pyrazolo[1,5-a]pyrimidine, triazolo[1,5-a]pyrimidine, and pyrimido[1,2-a]benzimidazole, pyrido[1,2-a]benzimidazole ring systems incorporating phenylsulfonyl moiety were synthesized via the reaction of 3-(N,N-dimethylamino)-1-(thiophen-2-yl)-2-(phenylsulfonyl)prop-2-en-1-one derivatives with the appropriate aminoazoles as 1,3-binucleophiles and 1H-benzimidazol-2-ylacetonitrile using conventional methods as well as microwave irradiation. The regioselectivity of the cyclocondensation reactions was confirmed both experimentally by alternative synthesis of reaction products and theoretically using ab initio quantum chemical calculations namely the Density Functional Theory (DFT). The theoretical work was carried out using the Becke, three parameter, Lee-Yang-Parr hybrid functional (B3LYP) combined with the 6-311++G(d,p) basis set. It was found that the final cyclocondensation reaction product depends mainly on the initial addition to the activated double bond by the nitrogen atom of the 1,3-binucleophiles that has the higher electron density.

  16. Low-energy states of manganese-oxo corrole and corrolazine: multiconfiguration reference ab initio calculations.

    PubMed

    Zhao, Hailiang; Pierloot, Kristine; Langner, Ernie H G; Swarts, Jannie C; Conradie, Jeanet; Ghosh, Abhik

    2012-04-01

    Manganese(V)-oxo corrole and corrolazine have been studied with ab initio multiconfiguration reference methods (CASPT2 and RASPT2) and large atomic natural orbital (ANO) basis sets. The calculations confirm the expected singlet d(δ)(2) ground states for both complexes and rule out excited states within 0.5 eV of the ground states. The lowest excited states are a pair of Mn(V) triplet states with d(δ)(1)d(π)(1) configurations 0.5-0.75 eV above the ground state. Manganese(IV)-oxo macrocycle radical states are much higher in energy, ≥1.0 eV relative to the ground state. The macrocyclic ligands in the ground states of the complexes are thus unambiguously 'innocent'. The approximate similarity of the spin state energetics of the corrole and corrolazine complexes suggests that the latter macrocycle on its own does not afford any special stabilization for the Mn(V)O center. The remarkable stability of an Mn(V)O octaarylcorrolazine thus appears to be ascribable to the steric protection afforded by the β-aryl groups. PMID:22432719

  17. Ab initio no core configuration interaction calculations in the natural orbital basis

    NASA Astrophysics Data System (ADS)

    Constantinou, Chrysovalantis; Caprio, Mark A.; Vary, James P.; Maris, Pieter

    2015-10-01

    The natural orbital basis has been successfully used in the past in atomic and molecular structure calculations. The natural orbitals used in those calculations are calculated by diagonalizing the electron one-body density matrix. Here we develop natural orbitals for nuclear no-core configuration interaction (NCCI) calculations. A NCCI calculation using an initial single particle basis, such as the harmonic oscillator basis, must first be performed in order to obtain a one-body density matrix. The eigenvectors of the one-body density matrix are the natural orbitals, and the corresponding eigenvalues are the occupations of these natural orbitals in the nuclear wave function. According to these occupancies, the most important natural orbitals, in the sense of the most occupied, can then be selected and used in a NCCI calculation. We discuss ab initio nuclear NCCI calculations for light nuclei and assess their ability to provide faster convergence. Supported by the US DOE (under Grants DE-FG02-95ER-40934, DESC0008485 SciDAC/NUCLEI, and DE-FG02-87ER40371), and the US NSF (under Grant 0904782). Computational resources provided by NERSC (supported by US DOE Contract DE-AC02-05CH11231), and NDCRC.

  18. The vibrational behavior of silica clusters at the glass transition: Ab initio calculations and thermodynamic implications.

    PubMed

    Ottonello, G; Zuccolini, M Vetuschi; Belmonte, D

    2010-09-14

    We present the results of a computational investigation with ab initio procedures of the structure-energy and vibrational properties of silica clusters in a dielectric continuum with dielectric constant ε=3.8, through density functional theory/B3LYP gas phase calculations coupled with a polarized continuum model approach [integral equation formalism applied to a polarized continuum (IEFPCM)] and those of the periodical structure D(6h) which leads to the α-cristobalite polymorph of silica when subjected to symmetry operations with the same functional within the linear combination of atomic orbitals (LCAO) approximation and in the framework of Bloch's theorem. Based on the computed energies and vibrational features, an aggregate of the D(6h) network and the monomer locally ordered in the short-medium range and both present in the glass in a mutual arrangement lacking of spatial continuity reproduces satisfactorily the experimentally observed low T heat capacity and the deviation from the Debye T(3) law. Above T(g), the experimental heat capacity of the liquid is perfectly reproduced summing to the internal modes the translational and rotational contributions to the bulk heat capacity and subtracting the (acoustic) terms arising from coherent motion (no longer existent). PMID:20849179

  19. Ab-Initio Calculations of Electronic Properties of InP and GaP

    NASA Astrophysics Data System (ADS)

    Malozovsky, Y.; Franklin, L.; Ekuma, E. C.; Zhao, G. L.; Bagayoko, D.

    2013-06-01

    We present results from ab-initio, self-consistent local density approximation (LDA) calculations of electronic and related properties of zinc blende indium phosphide (InP) and gallium phosphide (GaP). We employed a 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). This method searches for the optimal basis set that yields the minima of the occupied energies. This search entails increases of the size of the basis set and the related modifications of angular symmetry and of radial orbitals. Our calculated, direct band gap of 1.398 eV (1.40 eV), at the Γ point, is in excellent agreement with experimental values, for InP, and our preliminary result for the indirect gap of GaP is 2.135 eV, from the Γ to X high symmetry points. We have also calculated electron and hole effective masses for both InP and GaP. These calculated properties also agree with experimental findings. We conclude that the BZW-EF method could be employed in calculations of electronic properties of high-Tc superconducting materials to explain their complex properties.

  20. Ab-Initio Computations of Electronic and Related Properties of cubic Lithium Selenide (Li2Se)

    NASA Astrophysics Data System (ADS)

    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.

  1. Ab-initio Calculations of Accurate Electronic Properties of ZnS

    NASA Astrophysics Data System (ADS)

    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.

  2. Ab-initio Calculations of Electronic Properties of InP and GaP

    NASA Astrophysics Data System (ADS)

    Malozovsky, Yuriy; Franklin, Lashounda; Ekuma, Chinedu; Zhao, Guang-Lin; Bagayoko, Diola

    2013-03-01

    We present results from ab-initio, self consistent local density approximation (LDA) calculations of electronic and related properties of zinc blende indium and gallium phosphides (InP & GaP) 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). This method searches for the optimal basis set that yields the minima of the occupied energies. This search entails methodically increasing the size of the basis set, up to the optimal one, and the accompanying enrichment of angular symmetry and of radial orbitals. Our calculated, direct band gap of 1.398 eV (1.40 eV) for InP, at the Γ point, is in excellent agreement with experimental values. We discuss our preliminary results for the indirect band gap, from Γ to X, of GaP. We also report calculated electron and hole effective masses for both InP and GaP and the total (DOS) and partial (pDOS) densities of states. This work was funded in part by the National Science Foundation and the Louisiana Board of Regents, through LASiGMA and LS-LAMP, [EPS-1003897, No. NSF (2010-15)-RII-SUBR, and HRD-1002541] and by the Louisiana Optical Network Initiative (LONI) at SUBR.

  3. Ab-initio Calculations of Accurate Electronic Properties of Wurzite AlN

    NASA Astrophysics Data System (ADS)

    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).

  4. Ab initio prediction of electronic, transport and bulk properties of Li2S

    NASA Astrophysics Data System (ADS)

    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.

  5. Ab initio parameterization of YFF1, a universal force field for drug-design applications.

    PubMed

    Yakovenko, Olexandr Ya; Li, Yvonne Y; Oliferenko, Alexander A; Vashchenko, Ganna M; Bdzhola, Volodymyr G; Jones, Steven J M

    2012-02-01

    The YFF1 is a new universal molecular mechanic force field designed for drug discovery purposes. The electrostatic part of YFF1 has already been parameterized to reproduce ab initio calculated dipole and quadrupole moments. Now we report a parameterization of the van der Waals interactions (vdW) for the same atom types that were previously defined. The 6-12 Lennard-Jones potential terms were parameterized against homodimerization energies calculated at the MP2/6-31 G level of theory. The Boys-Bernardi counterpoise correction was employed to account for the basis-set superposition error. As a source of structural information we used about 2,400 neutral compounds from the ZINC2007 database. About 6,600 homodimeric configurations were generated from this dataset. A special "closure" procedure was designed to accelerate the parameters fitting. As a result, dimerization energies of small organic compounds are reproduced with an average unsigned error of 1.1 kcal mol(-1). Although the primary goal of this work was to parameterize nonbonded interactions, bonded parameters were also derived, by fitting to PM6 semiempirically optimized geometries of approximately 20,000 compounds. PMID:21562826

  6. Periodic Trends in Lanthanide Compounds through the Eyes of Multireference ab Initio Theory.

    PubMed

    Aravena, Daniel; Atanasov, Mihail; Neese, Frank

    2016-05-01

    Regularities among electronic configurations for common oxidation states in lanthanide complexes and the low involvement of f orbitals in bonding result in the appearance of several periodic trends along the lanthanide series. These trends can be observed on relatively different properties, such as bonding distances or ionization potentials. Well-known concepts like the lanthanide contraction, the double-double (tetrad) effect, and the similar chemistry along the lanthanide series stem from these regularities. Periodic trends on structural and spectroscopic properties are examined through complete active space self-consistent field (CASSCF) followed by second-order N-electron valence perturbation theory (NEVPT2) including both scalar relativistic and spin-orbit coupling effects. Energies and wave functions from electronic structure calculations are further analyzed in terms of ab initio ligand field theory (AILFT), which allows one to rigorously extract angular overlap model ligand field, Racah, and spin-orbit coupling parameters directly from high-level ab initio calculations. We investigated the elpasolite Cs2NaLn(III)Cl6 (Ln(III) = Ce-Nd, Sm-Eu, Tb-Yb) crystals because these compounds have been synthesized for most Ln(III) ions. Cs2NaLn(III)Cl6 elpasolites have been also thoroughly characterized with respect to their spectroscopic properties, providing an exceptionally vast and systematic experimental database allowing one to analyze the periodic trends across the lanthanide series. Particular attention was devoted to the apparent discrepancy in metal-ligand covalency trends between theory and spectroscopy described in the literature. Consistent with earlier studies, natural population analysis indicates an increase in covalency along the series, while a decrease in both the nephelauxetic (Racah) and relativistic nephelauxetic (spin-orbit coupling) reduction with increasing atomic number is calculated. These apparently conflicting results are discussed on the

  7. Large scale ab initio calculations of extended defects in materials: screw dislocations in bcc metals

    NASA Astrophysics Data System (ADS)

    Dézerald, Lucile; Ventelon, Lisa; Willaime, François; Clouet, Emmanuel; Rodney, David

    2014-06-01

    Ab initio methods, based on the Density Functional Theory (DFT), have been extensively used to study point defects and defect clusters in materials. Present HPC resources and DFT codes now allow similar investigations to be performed on dislocations. The study of these extended defects requires not only larger simulation cells but also a higher accuracy because the energy differences, which are involved, are rather small, typically 50-to-100 meV for supercells containing 50-to-500 atoms. The topology of the Peierls potential of screw dislocations with 1/2 <111>Burgers vector, i.e. the 2D energy landscape seen by these dislocations, is being completely revisited by DFT calculations. From results obtained in all body-centered cubic (bcc) transition metals, except Cr (V, Nb, Ta, Mo, W and Fe), using the PWSCF code, which is part of the Quantum-Espresso package, we concluded that the 2D Peierls potentials have two common features: the single-hump shape of the barrier between two minima of the potential, and the presence of a maximum - and not a minimum as predicted by most empirical potentials - around the split core. In iron, the topology of the Peierls potential is reversed compared to the classical sinusoidal picture: the location of the saddle point and the maximum are indeed inverted with unexpected flat regions. The first results obtained within the framework of the PRACE project, DIMAIM (DIslocations in Metals using Ab Initio Methods), started at the beginning of 2013, will also be presented. In particular, in order to address the twinning-antitwinning asymmetry often observed in bcc metals and regarded as the major contribution to the breakdown of Schmid's law, we have determined the crystal orientation dependence of the Peierls stress, i.e. the critical stress required for dislocation motion. These computationally most expensive simulations were performed on the PRACE Tier-0 system at Barcelona Supercomputing Center (Marenostrum III). The scalability results

  8. Theoretical determination of molecular structure and conformation. Part X. Geometry and puckering potential of azetidine, (CH 2) 3NH, combination of electron diffraction and ab initio studies

    NASA Astrophysics Data System (ADS)

    Cremer, Dieter; Dorofeeva, Olga V.; Mastryukov, Vladimir S.

    1981-09-01

    Restricted Hartree—Fock calculations on 21 planar and puckered conformers of azetidine have been done employing a split valence basis augmented by d functions. Complete geometry optimizations have been performed for eight conformers. In this way the puckering potential of azetidine is explored over the range -40° < ø (puckering angle) < 40°, for both sp3 and sp2 hybridization of the nitrogen atom. In its equatorial form, azetidine is slightly more puckered than cyclobutane. This is because of a decrease of van der Waals' repulsion between H atoms. Charge effects lead to destabilization of the axial forms. There is only moderate coupling between puckering and methylene group rocking. Previously published electron diffraction (ED) data are reinvestigated using vibrational corrections and information from the ab initio calculations. On the basis of this MO constrained ED (MOCED) analysis a puckering angle φ = 35.1(1.8)° is found. Observed rg and re bond distances are compared with ab initio values.

  9. Serious Gaming for Test & Evaluation of Clean-Slate (Ab Initio) National Airspace System (NAS) Designs

    NASA Technical Reports Server (NTRS)

    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

  10. Widely tunable band gaps of graphdiyne: an ab initio study.

    PubMed

    Koo, Jahyun; Park, Minwoo; Hwang, Seunghyun; Huang, Bing; Jang, Byungryul; Kwon, Yongkyung; Lee, Hoonkyung

    2014-05-21

    Functionalization of graphdiyne, a two-dimensional atomic layer of sp-sp(2) hybrid carbon networks, was investigated through first-principles calculations. Hydrogen or halogen atoms preferentially adsorb on sp-bonded carbon atoms rather than on sp(2)-bonded carbon atoms, forming sp(2)- or sp(3)-hybridization. The energy band gap of graphdiyne is increased from ~0.5 eV to ~5.2 eV through the hydrogenation or halogenation. Unlike graphene, segregation of adsorbing atoms is energetically unfavourable. Our results show that hydrogenation or halogenation can be utilized for modifying the electronic properties of graphdiyne for applications to nano-electronics and -photonics. PMID:24691588

  11. Ab initio kinetics and thermal decomposition mechanism of mononitrobiuret and 1,5-dinitrobiuret.

    PubMed

    Sun, Hongyan; Vaghjiani, Ghanshyam L

    2015-05-28

    Mononitrobiuret (MNB) and 1,5-dinitrobiuret (DNB) are tetrazole-free, nitrogen-rich, energetic compounds. For the first time, a comprehensive ab initio kinetics study on the thermal decomposition mechanisms of MNB and DNB is reported here. In particular, the intramolecular interactions of amine H-atom with electronegative nitro O-atom and carbonyl O-atom have been analyzed for biuret, MNB, and DNB at the M06-2X/aug-cc-pVTZ level of theory. The results show that the MNB and DNB molecules are stabilized through six-member-ring moieties via intramolecular H-bonding with interatomic distances between 1.8 and 2.0 Å, due to electrostatic as well as polarization and dispersion interactions. Furthermore, it was found that the stable molecules in the solid state have the smallest dipole moment amongst all the conformers in the nitrobiuret series of compounds, thus revealing a simple way for evaluating reactivity of fuel conformers. The potential energy surface for thermal decomposition of MNB was characterized by spin restricted coupled cluster theory at the RCCSD(T)/cc-pV∞ Z//M06-2X/aug-cc-pVTZ level. It was found that the thermal decomposition of MNB is initiated by the elimination of HNCO and HNN(O)OH intermediates. Intramolecular transfer of a H-atom, respectively, from the terminal NH2 group to the adjacent carbonyl O-atom via a six-member-ring transition state eliminates HNCO with an energy barrier of 35 kcal/mol and from the central NH group to the adjacent nitro O-atom eliminates HNN(O)OH with an energy barrier of 34 kcal/mol. Elimination of HNN(O)OH is also the primary process involved in the thermal decomposition of DNB, which processes C2v symmetry. The rate coefficients for the primary decomposition channels for MNB and DNB were quantified as functions of temperature and pressure. In addition, the thermal decomposition of HNN(O)OH was analyzed via Rice-Ramsperger-Kassel-Marcus/multi-well master equation simulations, the results of which reveal the formation

  12. Ab initio kinetics and thermal decomposition mechanism of mononitrobiuret and 1,5-dinitrobiuret

    NASA Astrophysics Data System (ADS)

    Sun, Hongyan; Vaghjiani, Ghanshyam L.

    2015-05-01

    Mononitrobiuret (MNB) and 1,5-dinitrobiuret (DNB) are tetrazole-free, nitrogen-rich, energetic compounds. For the first time, a comprehensive ab initio kinetics study on the thermal decomposition mechanisms of MNB and DNB is reported here. In particular, the intramolecular interactions of amine H-atom with electronegative nitro O-atom and carbonyl O-atom have been analyzed for biuret, MNB, and DNB at the M06-2X/aug-cc-pVTZ level of theory. The results show that the MNB and DNB molecules are stabilized through six-member-ring moieties via intramolecular H-bonding with interatomic distances between 1.8 and 2.0 Å, due to electrostatic as well as polarization and dispersion interactions. Furthermore, it was found that the stable molecules in the solid state have the smallest dipole moment amongst all the conformers in the nitrobiuret series of compounds, thus revealing a simple way for evaluating reactivity of fuel conformers. The potential energy surface for thermal decomposition of MNB was characterized by spin restricted coupled cluster theory at the RCCSD(T)/cc-pV∞ Z//M06-2X/aug-cc-pVTZ level. It was found that the thermal decomposition of MNB is initiated by the elimination of HNCO and HNN(O)OH intermediates. Intramolecular transfer of a H-atom, respectively, from the terminal NH2 group to the adjacent carbonyl O-atom via a six-member-ring transition state eliminates HNCO with an energy barrier of 35 kcal/mol and from the central NH group to the adjacent nitro O-atom eliminates HNN(O)OH with an energy barrier of 34 kcal/mol. Elimination of HNN(O)OH is also the primary process involved in the thermal decomposition of DNB, which processes C2v symmetry. The rate coefficients for the primary decomposition channels for MNB and DNB were quantified as functions of temperature and pressure. In addition, the thermal decomposition of HNN(O)OH was analyzed via Rice-Ramsperger-Kassel-Marcus/multi-well master equation simulations, the results of which reveal the formation

  13. Ab Initio Kinetics and Thermal Decomposition Mechanism of Mononitrobiuret and 1,5- Dinitrobiuret

    SciTech Connect

    Sun, Hongyan; Vaghjiani, Ghanshyam G.

    2015-05-26

    Mononitrobiuret (MNB) and 1,5-dinitrobiuret (DNB) are tetrazole-free, nitrogen-rich, energetic compounds. For the first time, a comprehensive ab initio kinetics study on the thermal decomposition mechanisms of MNB and DNB is reported here. In particular, the intramolecular interactions of amine H-atom with electronegative nitro O-atom and carbonyl O-atom have been analyzed for biuret, MNB, and DNB at the M06-2X/aug-cc-pVTZ level of theory. The results show that the MNB and DNB molecules are stabilized through six-member-ring moieties via intramolecular H-bonding with interatomic distances between 1.8 and 2.0 Å, due to electrostatic as well as polarization and dispersion interactions. Furthermore, it was found that the stable molecules in the solid state have the smallest dipole moment amongst all the conformers in the nitrobiuret series of compounds, thus revealing a simple way for evaluating reactivity of fuel conformers. The potential energy surface for thermal decomposition of MNB was characterized by spin restricted coupled cluster theory at the RCCSD(T)/cc-pV∞ Z//M06-2X/aug-cc-pVTZ level. It was found that the thermal decomposition of MNB is initiated by the elimination of HNCO and HNN(O)OH intermediates. Intramolecular transfer of a H-atom, respectively, from the terminal NH2 group to the adjacent carbonyl O-atom via a six-member-ring transition state eliminates HNCO with an energy barrier of 35 kcal/mol and from the central NH group to the adjacent nitro O-atom eliminates HNN(O)OH with an energy barrier of 34 kcal/mol. Elimination of HNN(O)OH is also the primary process involved in the thermal decomposition of DNB, which processes C2v symmetry. The rate coefficients for the primary decomposition channels for MNB and DNB were quantified as functions of temperature and pressure. In addition, the thermal decomposition of HNN(O)OH was analyzed via Rice–Ramsperger–Kassel–Marcus/multi-well master equation simulations, the results of which reveal the

  14. An ab initio study of oxygen on strained graphene.

    PubMed

    Nguyen, Manh-Thuong

    2013-10-01

    Graphene under strain exhibits new fascinating properties. In this work, I show that lattice strain introduced by uniform expansion of unit cells can strongly modify the chemical properties of graphene. By employing density functional theory calculations I found that strain enhances the bonding between atomic oxygen and graphene. Strain also increases the diffusion energy barrier of atomic oxygen on graphene; however, it reduces the activation energy for oxygen migrating through the graphene sheet. Strong stability enhancement of atomic oxygen on graphene induced by strain would also change molecular oxygen dissociation reactions from endothermic to exothermic. PMID:23945352

  15. Ab initio refinement of the thermal equation of state for bcc tantalum: the effect of bonding on anharmonicity.

    PubMed

    Liu, Zhong-Li; Cai, Ling-Cang; Chen, Xiang-Rong; Wu, Qiang; Jing, Fu-Qian

    2009-03-01

    We report a detailed ab initio study for body-centered-cubic (bcc) Ta within the framework of the quasiharmonic approximation (QHA) to refine its thermal equation of state and thermodynamic properties. Based on the excellent agreement of our calculated phonon dispersion curve with experiment, the accurate thermal equations of state and thermodynamic properties are well reproduced. The thermal equation of state (EOS) and EOS parameters are considerably improved in our work compared with previous results by others. Furthermore, at high temperatures, the excellent agreement of our obtained thermal expansion and Hugoniot curves with experiments greatly verifies the validity of the quasiharmonic approximation at higher temperatures. It is known that pressure suppresses the vibrations of atoms from their equilibrium positions, i.e. the bondings among atoms are strengthened by pressure; for the same temperature, anharmonicity becomes less important at high pressure. Thus the highest valid temperature of the QHA can be reasonably extended to the larger range. PMID:21817394

  16. An ab initio study of the size-dependent mechanical behavior of single-walled AlN nanotubes

    NASA Astrophysics Data System (ADS)

    Hao, Jun-Hua; Wang, Yu-Fang; Yin, Yu-Hua; Jiang, Run; Wang, Yun-Feng; Jin, Qing-Hua

    2015-07-01

    Employing ab initio electronic structure calculations combined with the linear combination of atomic orbitals (LCAO) we have investigated a size dependence of mechanical behavior in single-walled AlN nanotubes with armchair and zigzag forms. A simple procedure of nanotubes construction based on the wurtzite (0 0 1) slab with monolayer rolling and subsequent cylindrical coordinate system introduction is suggested. The present calculations indicate that the Young's modulus and electronic band gap of these tubes are increased monotonically as the radius increases, but decreases with the Al-N bond length. In addition, the amount of charge transfer calculated by the Mulliken's population analysis is introduced to explain clearly the strength of bonding between Al and N atoms in single-walled AlN nanotubes.

  17. Ab initio structural and electronic analysis of CH3SH self-assembled on a Cu(110) substrate

    NASA Astrophysics Data System (ADS)

    D'Agostino, S.; Chiodo, L.; Della Sala, F.; Cingolani, R.; Rinaldi, R.

    2007-05-01

    Ab initio Density Functional Theory calculations are here reported to characterize the adsorption of methanethiol at the Cu(110) surface. Theoretical results suggest that the binding of the adsorbate to the substrate is rather weak and the molecular geometry is correspondingly almost unaffected by the adsorption. Otherwise, when CH3SH deprotonates producing methanethiolate, a stronger chemical bond is realized between the sulfur atom of CH3S radical and Cu surface atoms. A detailed study of structural and electronic properties of methanethiolate on Cu(110) for a p(2×2) and a c(2×2) overlayer structure has been carried out. We find that, in the most stable configuration, the molecule adsorbs in the shortbridge site. The chemical bond arises due to a strong hybridization among p orbitals of sulfur and d states from the substrate, as it is deduced by an analysis of partial densities of states and charge densities.

  18. π-Hydrogen Bonding of Aromatics on the Surface of Aerosols: Insights from Ab Initio and Molecular Dynamics Simulation.

    PubMed

    Feng, Ya-Juan; Huang, Teng; Wang, Chao; Liu, Yi-Rong; Jiang, Shuai; Miao, Shou-Kui; Chen, Jiao; Huang, Wei

    2016-07-14

    Molecular level insight into the interaction between volatile organic compounds (VOCs) and aerosols is crucial for improvement of atmospheric chemistry models. In this paper, the interaction between adsorbed toluene, one of the most significant VOCs in the urban atmosphere, and the aqueous surface of aerosols was studied by means of combined molecular dynamics simulations and ab initio quantum chemistry calculations. It is revealed that toluene can be stably adsorbed on the surface of aqueous droplets via hydroxyl-π hydrogen bonding between the H atoms of the water molecules and the C atoms in the aromatic ring. Further, significant modifications on the electrostatic potential map and frontier molecular orbital are induced by the solvation effect of surface water molecules, which would affect the reactivity and pathway of the atmospheric photooxidation of toluene. This study demonstrates that the surface interactions should be taken into consideration in the atmospheric chemical models on oxidation of aromatics. PMID:27280740

  19. The role of metals in amyloid aggregation - Experiments and ab initio simulations

    NASA Astrophysics Data System (ADS)

    Minicozzi, V.; Morante, S.; Rossi, G. C.; Stellato, F.; Christian, N.; Jansen, K.

    With a combination of modern spectroscopic techniques and numerical first principle simulations it is possible to investigate the physico-chemical basis of the beta-amyloid aggregation phenomenon, which is suspected to be at the basis of the development of the Alzheimer disease. On the experimental side, in fact, X-ray absorption spectroscopy can be successfully used to determine the atomic structure around the metal binding site in samples where beta-amyloid peptides are complexed with either Cu2+ or Zn2+ ions. Exploiting spectroscopic information obtained on a selected set of fragments of the natural Abeta-peptide, the residues that along the sequence are coordinated to the metal are identified. Although copper data can be consistently interpreted assuming that oligopeptides encompassing the minimal 1-16 amino acidic sequence display a metal coordination mode which involves three Histidines (His6, His13, and His14), in complexes with zinc a four Histidines coordination mode is seen to be preferred. Lacking a fourth Histidine in the Abeta1-16 fragment, this geometrical arrangement hints to a Zn2+ promoted inter-peptide aggregation mode. On the theoretical side, first principle ab initio molecular dynamics simulations of the Car-Parrinello type, which have proved to be of invaluable help in understanding the microscopic mechanisms of chemical bonding both in solid-state physics and structural biophysics, have been employed in an effort to give a microscopic basis and find a phenomenological interpretation of the body of available experimental data on Abeta-peptides-metal complexes. Using medium size PC-clusters as well as larger parallel platforms, it is possible to deal with systems comprising 300-500 atoms and 1,000-2,000 electrons for simulation times as long as 2-3 ps. We present structural results that nicely compare with NMR and XAS data.

  20. The ab initio calculation of molecular electric, magnetic and geometric properties.

    PubMed

    Bast, Radovan; Ekström, Ulf; Gao, Bin; Helgaker, Trygve; Ruud, Kenneth; Thorvaldsen, Andreas J

    2011-02-21

    We give an account of some recent advances in the development of ab initio methods for the calculation of molecular response properties, involving electric, magnetic, and geometric perturbations. Particular attention is given to properties in which the basis functions depend explicitly both on time and on the applied perturbations such as perturbations involving nuclear displacements or external magnetic fields when London atomic orbitals are used. We summarize a general framework based on the quasienergy for the calculation of arbitrary-order molecular properties using the elements of the density matrix in the atomic-orbital basis as the basic variables. We demonstrate that the necessary perturbed density matrices of arbitrary order can be determined from a set of linear equations that have the same formal structure as the set of linear equations encountered when determining the linear response equations (or time-dependent self-consistent-field equations). Additional components needed to calculate properties involving perturbation-dependent basis sets are flexible one- and two-electron integral techniques for geometric or magnetic-field differentiated integrals; in Kohn-Sham density-functional theory (KS-DFT), we also need to calculate derivatives of the exchange-correlation functional. We describe a recent proposal for evaluating these contributions based on automatic differentiation. Within this framework, it is now possible to calculate any molecular property for an arbitrary self-consistent-field reference state, including two- and four-component relativistic self-consistent-field wave functions. Examples of calculations that can be performed with this formulation are presented. PMID:21180690

  1. {ital Ab} {ital initio} studies of CN adsorbed on Ni(111)

    SciTech Connect

    Yang, H.; Caves, T.C.; Whitten, J.L.

    1995-11-15

    The adsorption of cyanide (CN) on Ni(111) is treated using an {ital ab} {ital initio} embedding theory. The Ni(111) surface is modeled as a three-layer, 28-atom cluster with the Ni atoms fixed at bulk lattice sites. The present calculations show that CN is able to bind to the surface either via the carbon, or nitrogen, or in a side-on geometry with very small differences in total energy ({approx}0.1 eV). Adsorption energies at threefold, bridge and atop sites are comparable, with the fcc threefold site more favorable over other adsorption sites by {approx}0.1 eV. At the fcc threefold site, adsorption energies and C--N stretching frequencies are 5.0 eV and 2150 cm{sup {minus}1} for the {eta}{sup 1}-cyanide-N, 4.9 eV and 1970 cm{sup {minus}1} for the {eta}{sup 1}-cyanide-C, and 4.9 eV and 1840 cm{sup {minus}1} for the {eta}{sup 2}-cyanide-C,N, respectively. Dipole moment calculations show that the bonding of CN to the Ni surface is largely ionic, while {eta}{sup 2}-cyanide-C,N has more covalent character. Calculated energy barriers in going from {eta}{sup 1}-cyanide-C to {eta}{sup 2}-cyanide-C,N, and from {eta}{sup 2}-cyanide-C,N to {eta}{sup 1}-cyanide-N are around 0.1 eV. Thus although CN is strongly bound to the surface (at {approx}5 eV), within an energy range of {approx}0.2 eV, the molecule is free to rotate to other geometries. During this rotation there are large changes in the dipole moment. {copyright} {ital 1995} {ital American} {ital Institute} {ital of} {ital Physics}.

  2. High-resolution infrared spectroscopy and ab initio studies of the cyclopropane-carbon dioxide interaction.

    PubMed

    Su, Zheng; Tam, Wai Shun; Xu, Yunjie

    2006-01-14

    A jet-cooled high-resolution infrared spectrum of the cyclopropane-carbon dioxide complex was detected for the first time, using a rapid scan infrared spectrometer with an astigmatic multipass sample cell. The spectrum was recorded in the vicinity of the CO2 asymmetric stretching band (nu3) and exhibits a b-dipole selection rule. Altogether, over 200 lines were observed, assigned, and fitted to Watson's S-reduction Hamiltonian. Rotational and quartic distortion constants were obtained. The band origin was located at 2347.6263(2) cm(-1), redshifted by 1.5230(2) cm(-1) from the corresponding frequency of the CO2 monomer. The experimentally determined structure shows that CO2 lies next to a C-C bond edge and is perpendicular to the C3 ring, indicating that the interaction is characterized by the bonding between the carbon atom of CO2 and the pseudo-pi system of cyclopropane. The intermolecular distance between the carbon atom of CO2 and the center of mass of cyclopropane was determined to be 3.667(2) A. Complete ab initio geometry optimizations and harmonic frequency calculations were carried out at the level of second-order Moller-Plesset perturbation theory with four different basis sets: cc-pVDZ, 6-311++G(d,p), aug-cc-pVDZ, and aug-cc-pVTZ. The lowest-energy structure identified with the three larger basis sets is in accord with the experimental finding. In addition, a transition state was identified and the tunneling barrier height was computed. PMID:16422587

  3. Melting of sodium under high pressure. An ab-initio study

    SciTech Connect

    González, D. J.; González, L. E.

    2015-08-17

    We report ab-initio molecular dynamics simulations of dense liquid/solid sodium for a pressure range from 0 to 100 GPa. The simulations have been performed with the orbital free ab-initio molecular dynamics method which, by using the electron density as the basic variable, allows to perform simulations with large samples and for long runs. The calculated melting curve shows a maximum at a pressure ≈ 30 GPa and it is followed by a long, steep decrease. These features are in good agreement with the experimental data. For various pressures along the melting curve, we have calculated several liquid static properties (pair distribution functions, static structure factors and short-range order parameters) in order to analyze the structural effects of pressure.

  4. Ab initio calculations on the magnetic properties of transition metal complexes

    SciTech Connect

    Bodenstein, Tilmann; Fink, Karin

    2015-12-31

    We present a protocol for the ab initio determination of the magnetic properties of mono- and polynuclear transition metal compounds. First, we obtain the low lying electronic states by multireference methods. Then, we include spin-orbit coupling and an external magnetic field for the determination of zero-field splitting and g-tensors. For the polynuclear complexes the magnetic exchange coupling constants are determined by a modified complete active space self consistent field method. Based on the results of the ab initio calculations, magnetic data such as magnetic susceptibility or magnetization are simulated and compared to experimental data. The results obtained for the polynuclear complexes are further analysed by calculations on model complexes where part of the magnetic centers are substituted by diamagnetic ions. The methods are applied to different Co and Ni containing transition metal complexes.

  5. Polysiloxanes: ab initio force field and structural, conformational and thermophysical properties

    NASA Astrophysics Data System (ADS)

    Sun, Huai; Rigby, David

    1997-07-01

    Various levels of ab initio calculation have been performed to determine the optimum strategy for parameterization of the valence parameters of a CFF-type force field for siloxanes and polysiloxanes. Electrostatic nonbond parameters have been determined using scaled electrostatic potential (ESP) charges adjusted for known systematic differences between ab initio and experimental data, while van der Waals nonbond parameters have been determined using a classical approach involving fitting to experimental liquid density and cohesive energy density data measured at atmospheric pressure and a single temperature for a set of four small molecules. Simulations have been performed on molecular crystals, liquids and isolated molecules, yielding results which agree favorably with available experimental data. Properties calculated include unit cell parameters and crystal densities, liquid densities from 303-473 K and 0-1800 bar, dependence of oligomer density and solubility parameters on chain length and temperature, gas-phase geometries and vibrational frequencies, and gas and liquid-phase conformational behavior.

  6. Ab initio molecular dynamics simulation of liquid water by quantum Monte Carlo

    SciTech Connect

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

    2015-04-14

    Although liquid water is ubiquitous in chemical reactions at roots of life and climate on the earth, the prediction of its properties by high-level ab initio molecular dynamics simulations still represents a formidable task for quantum chemistry. In this article, we present a room temperature simulation of liquid water based on the potential energy surface obtained by a many-body wave function through quantum Monte Carlo (QMC) methods. The simulated properties are in good agreement with recent neutron scattering and X-ray experiments, particularly concerning the position of the oxygen-oxygen peak in the radial distribution function, at variance of previous density functional theory attempts. Given the excellent performances of QMC on large scale supercomputers, this work opens new perspectives for predictive and reliable ab initio simulations of complex chemical systems.

  7. B28: the smallest all-boron cage from an ab initio global search

    NASA Astrophysics Data System (ADS)

    Zhao, Jijun; Huang, Xiaoming; Shi, Ruili; Liu, Hongsheng; Su, Yan; King, R. Bruce

    2015-09-01

    Our ab initio global searches reveal the lowest-energy cage for B28, which is built from two B12 units and prevails over the competing structural isomers such as planar, bowl, and tube. This smallest boron cage extends the scope of all-boron fullerene and provides a new structural motif of boron clusters and nanostructures.Our ab initio global searches reveal the lowest-energy cage for B28, which is built from two B12 units and prevails over the competing structural isomers such as planar, bowl, and tube. This smallest boron cage extends the scope of all-boron fullerene and provides a new structural motif of boron clusters and nanostructures. Electronic supplementary information (ESI) available: Planar isomer structures of B28 and spatial distributions of front molecular orbitals. See DOI: 10.1039/c5nr04034e

  8. Ab initio investigation of light-induced relativistic spin-flip effects in magneto-optics

    NASA Astrophysics Data System (ADS)

    Mondal, Ritwik; Berritta, Marco; Carva, Karel; Oppeneer, Peter M.

    2015-05-01

    Excitation of a metallic ferromagnet such as Ni with an intensive femtosecond laser pulse causes an ultrafast demagnetization within approximately 300 fs. It was proposed that the ultrafast demagnetization measured in femtosecond magneto-optical experiments could be due to relativistic light-induced processes. We perform an ab initio investigation of the influence of relativistic effects on the magneto-optical response of Ni. To this end, first, we develop a response theory formulation of the additional appearing ultrarelativistic terms in the Foldy-Wouthuysen transformed Dirac Hamiltonian due to the electromagnetic field, and second, we compute the influence of relativistic light-induced spin-flip transitions on the magneto-optics. Our ab initio calculations of relativistic spin-flip optical excitations predict that these can give only a very small contribution (≤0.1 %) to the laser-induced magnetization change in Ni.

  9. DFT and ab initio quantum chemical studies on p-cyanobenzoic acid

    NASA Astrophysics Data System (ADS)

    Arjunan, V.; Rani, T.; Varalakshmy, L.; Mohan, S.; Tedlamelekot, F.

    2011-05-01

    The Fourier transform infrared (FTIR) and FT-Raman spectra of p-cyanobenzoic acid (CBA) have been recorded in the range 4000-400 and 4000-100 cm -1, respectively. The complete vibrational assignment and analysis of the fundamental modes of the compound were carried out using the observed FTIR and FT-Raman data. The vibrational frequencies determined experimentally were compared with theoretical wavenumbers obtained from ab initio HF and DFT-B3LYP gradient calculations employing 6-31G**, 6-311++G** and cc-pVTZ basis sets for the optimised geometry of the compound. The geometry and normal modes of vibration obtained from the HF and DFT methods are in good agreement with the experimental data. The normal coordinate analysis was also carried out with ab initio force fields utilising Wilson's FG matrix method. The interactions of cyano and carboxylic acid groups with the skeletal vibrational modes were investigated.

  10. Ab Initio Many-Body Calculations Of Nucleon-Nucleus Scattering

    SciTech Connect

    Quaglioni, S; Navratil, P

    2008-12-17

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

  11. Hyperfine Parameters for Aluminum Hydride: An ab Initio Molecular Orbital Study

    NASA Astrophysics Data System (ADS)

    Gee, Myrlene; Wasylishen, Roderick E.

    2001-06-01

    An extensive ab initio molecular orbital study of the 27Al nuclear spin-rotation and nuclear quadrupolar coupling constants in aluminum hydride, AlH, has been performed. The 27Al nuclear spin-rotation constant (C⊥), 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.

  12. Ab initio NMR Confirmed Evolutionary Structure Prediction for Organic Molecular Crystals

    NASA Astrophysics Data System (ADS)

    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.

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

    SciTech Connect

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

    2011-04-22

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

  14. Knockout Reactions from p-Shell Nuclei: Tests of Ab Initio Structure Models

    SciTech Connect

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

    2011-04-22

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

  15. Properties of metals during the heating by intense laser irradiation using ab initio simulations

    NASA Astrophysics Data System (ADS)

    Holst, Bastian; Recoules, Vanina; Torrent, Marc; Mazevet, Stephane

    2011-10-01

    Ultrashort laser pulses irradiating a target heat the electrons to very high temperatures. In contrast, the ionic lattice is unaffected on the time scale of the laser pulse since the heat capacity of electrons is much smaller than that of the lattice. This non-equilibrium system can be described as a composition of two subsystems: one consisting of hot electrons and the other of an ionic lattice at low temperature. We studied the effect of this intense electronic excitations on the optical properties of gold using ab initio simulations. We additionally use ab initio linear response to compute the phonon spectrum and the electron-phonon coupling constant within Density Functional Theory for several electronic temperatures of few eV. LULI, Ecole Polytechnique, CNRS, CEA, UPMC, 91128 Palaiseau, France.

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

    SciTech Connect

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

    2004-11-30

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

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

    NASA Astrophysics Data System (ADS)

    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

  18. Large-scale ab initio configuration interaction calculations for light nuclei

    NASA Astrophysics Data System (ADS)

    Maris, Pieter; Metin Aktulga, H.; Caprio, Mark A.; Çatalyürek, Ümit V.; Ng, Esmond G.; Oryspayev, Dossay; Potter, Hugh; Saule, Erik; Sosonkina, Masha; Vary, James P.; Yang, Chao; Zhou, Zheng

    2012-12-01

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

  19. Explicit Polarization (X-Pol) Potential Using ab Initio Molecular Orbital Theory and Density Functional Theory†

    PubMed Central

    Song, Lingchun; Han, Jaebeom; Lin, Yen-lin; Xie, Wangshen; Gao, Jiali

    2010-01-01

    The explicit polarization (X-Pol) method has been examined using ab initio molecular orbital theory and density functional theory. The X-Pol potential was designed to provide a novel theoretical framework for developing next-generation force fields for biomolecular simulations. Importantly, the X-Pol potential is a general method, which can be employed with any level of electronic structure theory. The present study illustrates the implementation of the X-Pol method using ab initio Hartree—Fock theory and hybrid density functional theory. The computational results are illustrated by considering a set of bimolecular complexes of small organic molecules and ions with water. The computed interaction energies and hydrogen bond geometries are in good accord with CCSD(T) calculations and B3LYP/aug-cc-pVDZ optimizations. PMID:19618944

  20. Ab initio calculation of valley splitting in monolayer δ-doped phosphorus in silicon.

    PubMed

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

    2013-01-01

    : The differences in energy between electronic bands due to valley splitting are of paramount importance in interpreting transport spectroscopy experiments on state-of-the-art quantum devices defined by scanning tunnelling microscope lithography. Using vasp, we develop a plane-wave density functional theory description of systems which is size limited due to computational tractability. Nonetheless, we provide valuable data for the benchmarking of empirical modelling techniques more capable of extending this discussion to confined disordered systems or actual devices. We then develop a less resource-intensive alternative via localised basis functions in siesta, retaining the physics of the plane-wave description, and extend this model beyond the capability of plane-wave methods to determine the ab initio valley splitting of well-isolated δ-layers. In obtaining an agreement between plane-wave and localised methods, we show that valley splitting has been overestimated in previous ab initio calculations by more than 50%. PMID:23445785