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Sample records for ab initio atomic

  1. Ab initio molecular simulations with numeric atom-centered orbitals

    NASA Astrophysics Data System (ADS)

    Blum, Volker; Gehrke, Ralf; Hanke, Felix; Havu, Paula; Havu, Ville; Ren, Xinguo; Reuter, Karsten; Scheffler, Matthias

    2009-11-01

    We describe a complete set of algorithms for ab initio molecular simulations based on numerically tabulated atom-centered orbitals (NAOs) to capture a wide range of molecular and materials properties from quantum-mechanical first principles. The full algorithmic framework described here is embodied in the Fritz Haber Institute "ab initio molecular simulations" (FHI-aims) computer program package. Its comprehensive description should be relevant to any other first-principles implementation based on NAOs. The focus here is on density-functional theory (DFT) in the local and semilocal (generalized gradient) approximations, but an extension to hybrid functionals, Hartree-Fock theory, and MP2/GW electron self-energies for total energies and excited states is possible within the same underlying algorithms. An all-electron/full-potential treatment that is both computationally efficient and accurate is achieved for periodic and cluster geometries on equal footing, including relaxation and ab initio molecular dynamics. We demonstrate the construction of transferable, hierarchical basis sets, allowing the calculation to range from qualitative tight-binding like accuracy to meV-level total energy convergence with the basis set. Since all basis functions are strictly localized, the otherwise computationally dominant grid-based operations scale as O(N) with system size N. Together with a scalar-relativistic treatment, the basis sets provide access to all elements from light to heavy. Both low-communication parallelization of all real-space grid based algorithms and a ScaLapack-based, customized handling of the linear algebra for all matrix operations are possible, guaranteeing efficient scaling (CPU time and memory) up to massively parallel computer systems with thousands of CPUs.

  2. Ab initio quantum transport in atomic carbon chains

    NASA Astrophysics Data System (ADS)

    Botello-Méndez, Andrés R.; Charlier, Jean-Christophe; Banhart, Florian; NAPS Team; Carbyne Collaboration

    2015-03-01

    Carbyne, the sp-hybridized phase of carbon, is still a missing link in the family of carbon allotropes. Recently, detailed electrical measurements and first-principles electronic transport calculations have been performed on monoatomic carbon chains. When the 1D system is under strain, the current-voltage curves exhibit a semiconducting behavior, which corresponds to the polyyne structure of the atomic chain with alternating single and triple bonds. Conversely, when the chain is unstrained, the ohmic behavior is observed in agreement with the metallic cumulene structure with double bonds, confirming recent theoretical predictions, namely that a metal-insulator transition can be induced by adjusting the strain. The key role of the contacting leads is also scrutinized by ab initio quantum conductance calculations, explaining the rectifying behavior measured in monoatomic carbon chains in a non-symmetric contact configuration.

  3. ab initio MD simulations of geomaterials with ~1000 atoms

    NASA Astrophysics Data System (ADS)

    Martin, G. B.; Kirtman, B.; Spera, F. J.

    2009-12-01

    In the last two decades, ab initio studies of materials using Density Functional Theory (DFT) have increased exponentially in popularity. DFT codes are now used routinely to simulate properties of geomaterials--mainly silicates and geochemically important metals such as Fe. These materials are ubiquitous in the Earth’s mantle and core and in terrestrial exoplanets. Because of computational limitations, most First Principles Molecular Dynamics (FPMD) calculations are done on systems of only ~100 atoms for a few picoseconds. While this approach can be useful for calculating physical quantities related to crystal structure, vibrational frequency, and other lattice-scale properties (especially in crystals), it is statistically marginal for duplicating physical properties of the liquid state like transport and structure. In MD simulations in the NEV ensemble, temperature (T), and pressure (P) fluctuations scale as N-1/2; small particle number (N) systems are therefore characterized by greater statistical state point location uncertainty than large N systems. Previous studies have used codes such as VASP where CPU time increases with N2, making calculations with N much greater than 100 impractical. SIESTA (Soler, et al. 2002) is a DFT code that enables electronic structure and MD computations on larger systems (N~103) by making some approximations, such as localized numerical orbitals, that would be useful in modeling some properties of geomaterials. Here we test the applicability of SIESTA to simulate geosilicates, both hydrous and anhydrous, in the solid and liquid state. We have used SIESTA for lattice calculations of brucite, Mg(OH)2, that compare very well to experiment and calculations using CRYSTAL, another DFT code. Good agreement between more classical DFT calculations and SIESTA is needed to justify study of geosilicates using SIESTA across a range of pressures and temperatures relevant to the Earth’s interior. Thus, it is useful to adjust parameters in

  4. Ab initio simulation of atomic-scale imaging in noncontact atomic force microscopy.

    PubMed

    Caciuc, V; Hölscher, H

    2009-07-01

    In this paper, we summarize some results of our ab initio simulations aimed at investigating the mechanism of the NC-AFM image contrast on semiconductor and metallic surfaces. We start with an introduction into the basic ideas behind the ab initio simulation process of the NC-AFM experimental results. Our simulations reveal that the interaction of a clean silicon tip with a semiconductor surface like InAs(110) might lead to bond-formation and bond-breaking processes during the approach and retraction of the tip. This imaging mechanism is very similar to that observed on a metallic surface like Ag(110). Interestingly, a clean silicon tip can become contaminated with Ag surface atoms. On both types of surface we observe a significant energy dissipation which is caused by a hysteresis in the tip-sample force curves calculated on the approach and retraction path.

  5. Ab initio Kinetics of Methylamine Radical Thermal Decomposition and H-abstraction from Monomethylhydrazine by H Atom

    DTIC Science & Technology

    2014-08-01

    Technical Paper 3. DATES COVERED (From - To) December 2013- August 2014 4. TITLE AND SUBTITLE Ab initio Kinetics of Methylamine Radical Thermal...phase kinetics of H-abstraction reactions from CH3NHNH2 by H atoms was further investigated by ab initio second-order multireference perturbation...distribution unlimited Ab initio Kinetics of Methylamine Radical Thermal Decomposition and H-abstraction from Monomethylhydrazine by H Atom

  6. An efficient method for electron-atom scattering using ab-initio calculations

    NASA Astrophysics Data System (ADS)

    Xu, Yuan; Yang, Yonggang; Xiao, Liantuan; Jia, Suotang

    2017-02-01

    We present an efficient method based on ab-initio calculations to investigate electron-atom scatterings. Those calculations profit from methods implemented in standard quantum chemistry programs. The new approach is applied to electron-helium scattering. The results are compared with experimental and other theoretical references to demonstrate the efficiency of our method.

  7. 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…

  8. Conformational space of clindamycin studied by ab initio and full-atom molecular dynamics.

    PubMed

    Kulczycka-Mierzejewska, Katarzyna; Trylska, Joanna; Sadlej, Joanna

    2016-01-01

    Molecular dynamics (MD) simulations allow determining internal flexibility of molecules at atomic level. Using ab initio Born-Oppenheimer molecular dynamics (BOMD), one can simulate in a reasonable time frame small systems with hundreds of atoms, usually in vacuum. With quantum mechanics/molecular mechanics (QM/MM) or full-atom molecular dynamics (FAMD), the influence of the environment can also be simulated. Here, we compare three types of MD calculations: ab initio BOMD, hybrid QM/MM, and classical FAMD. As a model system, we use a small antibiotic molecule, clindamycin, which is one of the lincosamide antibiotics. Clindamycin acquires two energetically stable forms and we investigated the transition between these two experimentally known conformers. We performed 60-ps BOMD simulations in vacuum, 50-ps QM/MM, and 100-ns FAMD in explicit water. The transition between two antibiotic conformers was observed using both BOMD and FAMD methods but was not noted in the QM/MM simulations.

  9. Charge relaxation resistance at atomic scale: An ab initio calculation

    NASA Astrophysics Data System (ADS)

    Wang, Bin; Wang, Jian

    2008-06-01

    We report an investigation of ac quantum transport properties of a nanocapacitor from first principles. At low frequencies, the nanocapacitor is characterized by a static electrochemical capacitance Cμ and the charge relaxation resistance Rq . We carry out a first principle calculation within the nonequilibrium Green’s function formalism. In particular, we investigate charge relaxation resistance of a single carbon atom as well as two carbon atoms in a nanocapacitor made of a capped carbon nanotube (CNT) and an alkane chain connected to a bulk Si. The nature of charge relaxation resistance is predicted for this nanocapacitor. Specifically, we find that the charge relaxation resistance shows resonant behavior and it becomes sharper as the distance between plates of nanocapacitor increases. If there is only one transmission channel dominating the charge transport through the nanocapacitor, the charge relaxation resistance Rq is half of resistance quantum h/2e2 . This result shows that the theory of charge relaxation resistance applies at atomic scale.

  10. 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.

  11. 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.

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

    PubMed

    Pietrucci, Fabio; Andreoni, Wanda

    2011-08-19

    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.

  13. 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.

  14. 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.

  15. 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.

  16. Ab Initio Study on Atomic Structures and Physical Properties of CdSe Quantum Nanodots

    DTIC Science & Technology

    2009-11-25

    CdSe quantum dots , with magic number (( CdSe )13, ( CdSe )19, ( CdSe )33 and ( CdSe )34 ). Effects of organic ligand binding on the stability of CdSe as well...calculations of optical absorption spectra for CdSe quantum dots , with magic number (( CdSe )13, ( CdSe )19, ( CdSe )33 and ( CdSe )34 ), have been calculated in...1 AOARD-08-4037 Title of Proposed Project: Ab initio study on atomic structures and physical

  17. Ab-initio atomic level stresses in Cu-Zr crystal, liquid and glass phases

    NASA Astrophysics Data System (ADS)

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

    2013-03-01

    The Cu-Zr system provides interesting playground for the study of glass structure, stability, and formability and liquid dynamics. Glasses form over a wide range of concentrations while they compete against various intermetallic compounds. We have calculated from first-principles the atomic level stresses, a new tool to characterize materials, within the local approximation to Density Functional Theory (DFT) for Cu-Zr glasses and compounds from low temperature to 4500K. Comparisons between ordered crystalline compounds and liquids and glasses allow us to relate atomic level stress to relaxation of chemical short-range order and structural relaxation. The results are counter-intuitive at times; a smaller atom is under higher compressive pressure, whereas geometrically they should be under tension. Ab-initio calculations were done using Vienna Ab-initio Simulation Package (VASP) and Locally Self-consistent Multiple Scattering (LSMS) codes. 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.

  18. 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.

  19. 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.

  20. Ab initio calculation of the real contact area on the atomic scale

    NASA Astrophysics Data System (ADS)

    Wolloch, M.; Feldbauer, G.; Mohn, P.; Redinger, J.; Vernes, A.

    2015-05-01

    We present an approach to determine the onset of contact between a tip and a surface. The real contact area depending on the distance is calculated using Bader's quantum theory of atoms in molecules. The jump to contact, which is often observed in atomic force microscopy experiments, is used as an indicator for the initial point of contact, which in turn is defined by atomic relaxations and thus without the need of external parameters. Within our approach the contact area is estimated by evaluating the zero flux surfaces between the touching Bader atoms, where the necessary electronic density cutoff for the Bader partitioning is calculated to depend on the initial point of contact. Our proposed approach is therefore completely ab initio and we are able to define and calculate the real area of contact without imposing restrictions or free parameters. As a prototype system we choose a tip made of a ten-atom tungsten pyramid above a moiré layer of graphene on an fcc iridium (111) substrate. We find that the contact area depends exponentially on the effective distance between the tip apex and the surface atom directly below within the atomically relaxed nanosystem.

  1. Ab initio protein folding simulations using atomic burials as informational intermediates between sequence and structure.

    PubMed

    van der Linden, Marx Gomes; Ferreira, Diogo César; de Oliveira, Leandro Cristante; Onuchic, José N; de Araújo, Antônio F Pereira

    2014-07-01

    The three-dimensional structure of proteins is determined by their linear amino acid sequences but decipherment of the underlying protein folding code has remained elusive. Recent studies have suggested that burials, as expressed by atomic distances to the molecular center, are sufficiently informative for structural determination while potentially obtainable from sequences. Here we provide direct evidence for this distinctive role of burials in the folding code, demonstrating that burial propensities estimated from local sequence can indeed be used to fold globular proteins in ab initio simulations. We have used a statistical scheme based on a Hidden Markov Model (HMM) to classify all heavy atoms of a protein into a small number of burial atomic types depending on sequence context. Molecular dynamics simulations were then performed with a potential that forces all atoms of each type towards their predicted burial level, while simple geometric constraints were imposed on covalent structure and hydrogen bond formation. The correct folded conformation was obtained and distinguished in simulations that started from extended chains for a selection of structures comprising all three folding classes and high burial prediction quality. These results demonstrate that atomic burials can act as informational intermediates between sequence and structure, providing a new conceptual framework for improving structural prediction and understanding the fundamentals of protein folding.

  2. 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.

  3. Ab initio random structure search for 13-atom clusters of fcc elements.

    PubMed

    Chou, J P; Hsing, C R; Wei, C M; Cheng, C; Chang, C M

    2013-03-27

    The 13-atom metal clusters of fcc elements (Al, Rh, Ir, Ni, Pd, Pt, Cu, Ag, Au) were studied by density functional theory calculations. The global minima were searched for by the ab initio random structure searching method. In addition to some new lowest-energy structures for Pd13 and Au13, we found that the effective coordination numbers of the lowest-energy clusters would increase with the ratio of the dimer-to-bulk bond length. This correlation, together with the electronic structures of the lowest-energy clusters, divides the 13-atom clusters of these fcc elements into two groups (except for Au13, which prefers a two-dimensional structure due to the relativistic effect). Compact-like clusters that are composed exclusively of triangular motifs are preferred for elements without d-electrons (Al) or with (nearly) filled d-band electrons (Ni, Pd, Cu, Ag). Non-compact clusters composed mainly of square motifs connected by some triangular motifs (Rh, Ir, Pt) are favored for elements with unfilled d-band electrons.

  4. Multiple-Timestep ab Initio Molecular Dynamics Using an Atomic Basis Set Partitioning.

    PubMed

    Steele, Ryan P

    2015-12-17

    This work describes an approach to accelerate ab initio Born-Oppenheimer molecular dynamics (MD) simulations by exploiting the inherent timescale separation between contributions from different atom-centered Gaussian basis sets. Several MD steps are propagated with a cost-efficient, low-level basis set, after which a dynamical correction accounts for large basis set relaxation effects in a time-reversible fashion. This multiple-timestep scheme is shown to generate valid MD trajectories, on the basis of rigorous testing for water clusters, the methanol dimer, an alanine polypeptide, protonated hydrazine, and the oxidized water dimer. This new approach generates observables that are consistent with those of target basis set trajectories, including MD-based vibrational spectra. This protocol is shown to be valid for Hartree-Fock, density functional theory, and second-order Møller-Plesset perturbation theory approaches. Recommended pairings include 6-31G as a low-level basis set for 6-31G** or 6-311G**, as well as cc-pVDZ as the subset for accurate dynamics with aug-cc-pVTZ. Demonstrated cost savings include factors of 2.6-7.3 on the systems tested and are expected to remain valid across system sizes.

  5. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

    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. Five liquid Hg-In mixtures (Hg10In90, Hg30In70, Hg50In50, Hg70In30 and Hg90In10) 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.

  7. Atomic structure of amorphous Mg40Cu35Ti25 alloy: An ab initio molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Durandurdu, Murat

    2013-01-01

    Ab initio molecular dynamics simulations are carried out to model amorphous Mg40Cu35Ti25 and its local structural packing are investigated using a variety of analyzing techniques. Cu-atoms commonly form 12 fold coordinated clusters and some of which are perfect or defective types icosahedrons, implying an icosohedral short range order around Cu atoms. Mg and Ti atoms, on the other hand, favor to structure in higher coordinated polyhedrons. The coordination number of Ti atoms is slightly less than Mg atoms. The immiscibility effect between Ti and Mg is reflected by a low fraction of Mg-Ti bonding in the model. The atomic packing of Mg40Cu35Ti25 appears to be noticeably different from that of Mg-Cu-X (X=Y and Gd) metallic glasses even though all these materials exhibit primarily the same type of bonding natures.

  8. Ab initio effective core potentials for molecular calculations. Potentials for the transition metal atoms Sc to Hg

    SciTech Connect

    Hay, P.J.; Wadt, W.R.

    1985-01-01

    Ab initio effective core potentials (ECP's) have been generated to replace the Coulomb, exchange, and core-orthogonality effects of the chemically inert core electron in the transition metal atoms Sc to Hg. For the second and third transition series relative ECP's have been generated which also incorporate the mass--velocity and Darwin relativistic effects into the potential. The ab initio ECP's should facilitate valence electron calculations on molecules containing transition-metal atoms with accuracies approaching all-electron calculations at a fraction of the computational cost. Analytic fits to the potentials are presented for use in multicenter integral evaluation. Gaussian orbital valence basis sets are developed for the (3d,4s,4p), (4d,5s,5p), and (5d,6s,6p) orbitals of the first, second, and third transition series atoms, respectively. All-electron and valence-electron atomic excitation energies are also compared for the low-lying states of Sc--Hg, and the valence-electron calculations are found to reproduce the all-electron excitation energies (typically within a few tenths of an eV).

  9. Dual folding pathways of an α /β protein from all-atom ab initio folding simulations

    NASA Astrophysics Data System (ADS)

    Lei, Hongxing; Wang, Zhi-Xiang; Wu, Chun; Duan, Yong

    2009-10-01

    Successful ab initio folding of proteins with both α-helix and β-sheet requires a delicate balance among a variety of forces in the simulation model, which may explain that the successful folding of any α /β proteins to within experimental error has yet to be reported. Here we demonstrate that it is an achievable goal to fold α /β proteins with a force field emphasizing the balance between the two major secondary structures. Using our newly developed force field, we conducted extensive ab initio folding simulations on an α /β protein full sequence design (FSD) employing both conventional molecular dynamics and replica exchange molecular dynamics in combination with a generalized-Born solvation model. In these simulations, the folding of FSD to the native state with high population (>64.2%) and high fidelity (Cα-Root Mean Square Deviation of 1.29 Å for the most sampled conformation when compared to the experimental structure) was achieved. The folding of FSD was found to follow two pathways. In the major pathway, the folding started from the formation of the helix. In the minor pathway, however, folding of the β-hairpin started first. Further examination revealed that the helix initiated from the C-terminus and propagated toward the N-terminus. The formation of the hydrophobic contacts coincided with the global folding. Therefore the hydrophobic force does not appear to be the driving force of the folding of this protein.

  10. 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.

  11. 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.

  12. 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

  13. Ab initio studies of the nuclear magnetic resonance chemical shifts of a rare gas atom in a zeolite

    NASA Astrophysics Data System (ADS)

    Jameson, Cynthia J.; Lim, Hyung-Mi

    1995-09-01

    The intermolecular chemical shift of a rare gas atom inside a zeolite cavity is calculated by ab initio analytical derivative theory using gauge-including atomic orbitals (GIAO) at the Ar atom and the atoms of selected neutral clusters each of which is a 4-, 6-, or 8-ring fragment of the zeolite cage. The Si, Al, O atoms and the charge-balancing counterions (Na+, K+, Ca2+) of the clusters (from 24 to 52 atoms) are at coordinates taken from the refined single crystal x-ray structure of the NaA, KA, and CaA zeolites. Terminating OH groups place the H atom at an appropriate O-H distance along the bond to the next Si or Al atom in the crystal. The chemical shift of the Ar atom located at various positions relative to the cluster is calculated using Boys-Bernardi counterpoise correction at each position. The dependence of the rare gas atom chemical shift on the Al/Si ratio of the clusters is investigated. The resulting shielding values are fitted to a pairwise additive form to elicit effective individual Ar-O, Ar-Na, Ar-K, Ar-Ca intermolecular shielding functions of the form σ(39Ar, Ar...Ozeol)= a6r-6+a8r-8+a10r-10+a12r -12, where r is the distance between the Ar and the O atom. A similar form is used for the counterions. The dependence of the Ar shielding on the Al/Si ratio is established (the greater the Al content, the higher the Ar chemical shift), which is in agreement with the few experimental cases where the dependence of the 129Xe chemical shift on the Al/Si ratio of the zeolite has been observed.

  14. Ab initio studies on the structure of and atomic interactions in cellulose III(I) crystals.

    PubMed

    Ishikawa, Tetsuya; Hayakawa, Daichi; Miyamoto, Hitomi; Ozawa, Motoyasu; Ozawa, Tomonaga; Ueda, Kazuyoshi

    2015-11-19

    The crystal structure of cellulose III(I)was analyzed using first-principles density functional theory (DFT). The geometry was optimized using variable-cell relaxation, as implemented in Quantum ESPRESSO. The Perdew-Burke-Ernzerhof (PBE) functional with a correction term for long-range van der Waals interactions (PBE-D) reproduced the experimental structure well. By using the optimized crystal structure, the interactions existed among the cellulose chains in the crystal were precisely investigated using the NBO analysis. The results showed that the weak bonding nature of CH/O and the hydrogen bonding occur among glucose molecules in the optimized crystal structure. To investigate the strength of interaction, dimeric and trimeric glucose units were extracted from the crystal, and analyzed using MP2 ab initio counterpoise methods with BSSE correction. The results estimated the strength of the interactions. That is, the packed chains along with a-axis interacts with weak bonding nature of CH/O and dispersion interactions by -7.50 kcal/mol, and two hydrogen bonds of O2HO2…O6 and O6HO6…O2 connect the neighboring packed chains with -11.9 kcal/mol. Moreover, FMO4 calculation was also applied to the optimized crystal structure to estimate the strength of the interactions. These methods can well estimate the interactions existed in the crystal structure of cellulose III(I).

  15. Atomic properties of element 113 and its adsorption on inert surfaces from ab initio Dirac-Coulomb calculations.

    PubMed

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

    2008-12-25

    Fully relativistic ab initio Dirac-Coulomb Fock-space coupled cluster calculations were performed on Tl and element 113. The calculated polarizabilty of element 113, 29.85 au, is the smallest in group 13, except for B. The estimated atomic and van der Waals radii of element 113 are also the smallest among these elements. Using the calculated atomic properties and an adsorption model, adsorption enthalpies of elements Al through 113 on inert surfaces, such as Teflon and polyethylene, are predicted. The trends in the atomic properties and DeltaH(ads) in group 13 were found to reverse from In to element 113, reflecting the strong relativistic contraction and stabilization of the outer np(1/2) orbital, which are largest for element 113. The small values of DeltaH(ads) for element 113 on Teflon (14 kJ/mol) and polyethylene (16 kJ/mol) guarantee its transport from the target chamber to the chemistry set up, and the 6 kJ/mol difference relative to Tl values makes possible the separation and identification of the superheavy element on the inert surfaces.

  16. 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.

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

    PubMed

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

    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 in the

  18. 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

  19. 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.

  20. Ab initio Theory of Semiconductor Nanocrystals

    NASA Astrophysics Data System (ADS)

    Wang, Lin-Wang

    2007-03-01

    With blooming experimental synthesis of various nanostructures out of many semiconductor materials, there is an urgent need to calculate the electronic structures and optical properties of these nanosystems based on reliable ab initio methods. Unfortunately, due to the O(N^3) scaling of the conventional ab initio calculation methods based on the density functional theory (DFT), and the >1000 atom sizes of the most experimental nanosystems, the direct applications of these conventional ab intio methods are often difficult. Here we will present the calculated results using our O(N) scaling charge patching method (CPM) [1,2] to nanosystems up to 10,000 atoms. The CPM yields the charge density of a nanosystem by patching the charge motifs generated from small prototype systems. The CPM electron/hole eigen energies differ from the directly calculated results by only ˜10-20 meV. We will present the optical band gaps of quantum dots and wires, quantum rods, quantum dot/quantum well, and quantum dots doped with impurities. Besides good agreements with experimental measurements, we will demonstrate why it is important to perform ab initio calculations, in contrast with the continuum model k.p calculations. We will show the effects of surface polarization potentials and the internal electric fields. Finally, a linear scaling 3 dimensional fragment (LS3DF) method will be discussed. The LS3DF method can be used to calculate the total energy and atomic forces of a large nanosystem, with the results practically the same as the direct DFT method. Our work demonstrates that, with the help of supercomputers, it is now feasible to calculate the electronic structures and optical properties of >10,000 atom nanocrystals with ab initio accuracy. [1] L.W. Wang, Phys. Rev. Lett. 88, 256402 (2002). [2] J. Li, L.W. Wang, Phys. Rev. B 72, 125325 (2005).

  1. 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.

  2. 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.

  3. YinYang atom: a simple combined ab initio quantum mechanical molecular mechanical model.

    PubMed

    Shao, Yihan; Kong, Jing

    2007-05-10

    A simple interface is proposed for combined quantum mechanical (QM) molecular mechanical (MM) calculations for the systems where the QM and MM regions are connected through covalent bonds. Within this model, the atom that connects the two regions, called YinYang atom here, serves as an ordinary MM atom to other MM atoms and as a hydrogen-like atom to other QM atoms. Only one new empirical parameter is introduced to adjust the length of the connecting bond and is calibrated with the molecule propanol. This model is tested with the computation of equilibrium geometries and protonation energies for dozens of molecules. Special attention is paid on the influence of MM point charges on optimized geometry and protonation energy, and it is found that it is important to maintain local charge-neutrality in the MM region in order for the accurate calculation of the protonation and deprotonation energies. Overall the simple YinYang atom model yields comparable results to some other QM/MM models.

  4. 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.

  5. Site of metabolism prediction based on ab initio derived atom representations.

    PubMed

    Finkelmann, Arndt R; Göller, Andreas H; Schneider, Gisbert

    2017-03-21

    Machine learning models for site of metabolism (SoM) prediction offer the ability to identify metabolic soft spots in low molecular weight drug molecules at low computational cost and enable data-based reactivity prediction. SoM prediction is an atom classification problem. Successful construction of machine learning models requires atom representations that capture the reactivity-determining features of a potential reaction site. We have developed a descriptor scheme that characterizes an atom's steric and electronic environment and its relative location in the molecular structure. The partial charge distributions were obtained from fast quantum mechanical calculations. We successfully trained machine learning classifiers on curated cytochrome p450 metabolism data. The models based on the new atom descriptors showed sustained accuracy for retrospective analyses of metabolism optimization campaigns and lead optimization projects from Bayer Pharmaceuticals. The results obtained demonstrate the practicality of quantum-chemistry-supported machine learning models for hit-to-lead optimization.

  6. 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.

  7. 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.

  8. 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.

  9. Ab initio study of edge smoothing, atom attraction, and downward funneling in Ag/Ag(100)

    NASA Astrophysics Data System (ADS)

    Shim, Yunsic; Amar, Jacques G.

    2011-06-01

    The results of density-functional theory (DFT) calculations of the energy barriers for three low-barrier relaxation processes in Ag/Ag(100) growth—edge-zipping, atom attraction, and downward funneling—are presented and compared with embedded atom method (EAM) calculations. In general, we find good agreement between the DFT values for these processes and the values assumed in recent simulations of low-temperature Ag/Ag(100) growth [Shim and Amar, Phys. Rev. BPRBMDO1098-012110.1103/PhysRevB.81.045416 81, 045416 (2010)]. We also find reasonable agreement between our DFT results and the results of EAM calculations, although in a few specific cases there is a noticeable disagreement. In order to investigate the effects of long-range interactions, we have also carried out additional calculations for more complex configurations. While our EAM results indicate that long-range interactions such as “pinning” can significantly enhance the energy barriers for edge-zipping and atom attraction, these effects can be significantly weaker in our DFT calculations due to the redistribution of the electron density.

  10. 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.

  11. 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

  12. 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.

  13. Ab initio dynamical vertex approximation

    NASA Astrophysics Data System (ADS)

    Galler, Anna; Thunström, Patrik; Gunacker, Patrik; Tomczak, Jan M.; Held, Karsten

    2017-03-01

    Diagrammatic extensions of dynamical mean-field theory (DMFT) such as the dynamical vertex approximation (DΓ A) allow us to include nonlocal correlations beyond DMFT on all length scales and proved their worth for model calculations. Here, we develop and implement an Ab initio DΓ A approach (AbinitioDΓ A ) for electronic structure calculations of materials. The starting point is the two-particle irreducible vertex in the two particle-hole channels which is approximated by the bare nonlocal Coulomb interaction and all local vertex corrections. From this, we calculate the full nonlocal vertex and the nonlocal self-energy through the Bethe-Salpeter equation. The AbinitioDΓ A approach naturally generates all local DMFT correlations and all nonlocal G W contributions, but also further nonlocal correlations beyond: mixed terms of the former two and nonlocal spin fluctuations. We apply this new methodology to the prototypical correlated metal SrVO3.

  14. An ab initio study of the structure and atomic transport in bulk liquid Ag and its liquid-vapor interface

    NASA Astrophysics Data System (ADS)

    del Rio, Beatriz G.; González, David J.; González, Luis E.

    2016-10-01

    Several static and dynamic properties of bulk liquid Ag at a thermodynamic state near its triple point have been calculated by means of ab initio molecular dynamics simulations. The calculated static structure shows a very good agreement with the available experimental data. The dynamical structure reveals propagating excitations whose dispersion at long wavelengths is compatible with the experimental sound velocity. Results are also reported for other transport coefficients. Additional simulations have also been performed so as to study the structure of the free liquid surface. The calculated longitudinal ionic density profile shows an oscillatory behaviour, whose properties are analyzed through macroscopic and microscopic methods. The intrinsic X-ray reflectivity of the surface is predicted to show a layering peak associated to the interlayer distance.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. Local atomic and electronic structures in ferromagnetic topological insulator Cr-doped (BixSb1-x) 2Te3 studied by XAFS and ab initio calculations

    NASA Astrophysics Data System (ADS)

    Liu, Zhen; Wei, Xinyuan; Wang, Jiajia; Pan, Hong; Ji, Fuhao; Ye, Mao; Yang, Zhongqin; Qiao, Shan

    2015-09-01

    The local atomic and electronic structures around the dopants in Cr-doped (BixSb1 -x )2Te3 are studied by x-ray absorption fine structure (XAFS) measurements and first-principles calculations. Both Cr and Bi are confirmed substituting Sb sites (CrSb and BiSb). The six nearest Te atoms around Cr move towards Cr and shorten the Cr-Te bond lengths to 2.76 Å and 2.77 Å for x =0.1 and x =0.2 , respectively. Importantly, we reveal the hybridization between the Sb/Te p states and Cr d states by the presence of a pre-edge peak at Cr K -absorption edge, which is also supported by our ab initio calculations. These findings provide important clues to understand the mechanism of ferromagnetic order in this system with quantum anomalous Hall effect.

  20. 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)

  1. Folding processes of the B domain of protein A to the native state observed in all-atom ab initio folding simulations

    NASA Astrophysics Data System (ADS)

    Lei, Hongxing; Wu, Chun; Wang, Zhi-Xiang; Zhou, Yaoqi; Duan, Yong

    2008-06-01

    Reaching the native states of small proteins, a necessary step towards a comprehensive understanding of the folding mechanisms, has remained a tremendous challenge to ab initio protein folding simulations despite the extensive effort. In this work, the folding process of the B domain of protein A (BdpA) has been simulated by both conventional and replica exchange molecular dynamics using AMBER FF03 all-atom force field. Started from an extended chain, a total of 40 conventional (each to 1.0 μs) and two sets of replica exchange (each to 200.0 ns per replica) molecular dynamics simulations were performed with different generalized-Born solvation models and temperature control schemes. The improvements in both the force field and solvent model allowed successful simulations of the folding process to the native state as demonstrated by the 0.80 A˚ Cα root mean square deviation (RMSD) of the best folded structure. The most populated conformation was the native folded structure with a high population. This was a significant improvement over the 2.8 A˚ Cα RMSD of the best nativelike structures from previous ab initio folding studies on BdpA. To the best of our knowledge, our results demonstrate, for the first time, that ab initio simulations can reach the native state of BdpA. Consistent with experimental observations, including Φ-value analyses, formation of helix II/III hairpin was a crucial step that provides a template upon which helix I could form and the folding process could complete. Early formation of helix III was observed which is consistent with the experimental results of higher residual helical content of isolated helix III among the three helices. The calculated temperature-dependent profile and the melting temperature were in close agreement with the experimental results. The simulations further revealed that phenylalanine 31 may play critical to achieve the correct packing of the three helices which is consistent with the experimental observation

  2. Atomic and electronic structure of Pd{sub 40}Ni{sub 40}P{sub 20} bulk metallic glass from ab initio simulations

    SciTech Connect

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

    2011-10-01

    The atomic structure of Pd{sub 40}Ni{sub 40}P{sub 20} bulk metallic glass has been simulated using an ab initio molecular dynamics method with projector-augmented wave pseudopotentials for electron-ion interaction and generalized gradient approximation for exchange-correlation energy. The calculated extended x-ray absorption fine structure (EXAFS) spectra of Pd-K and Ni-K edges, the mass density, and the electronic structure agree remarkably well with the available experimental data and the EXAFS spectra measured at the SPring-8 synchrotron radiation facility. Our results show that the atomic structure can be described in terms of P-centered polyhedra. There are no two P atoms that are nearest neighbors at this composition, and this could be a reason for the observed optimal P concentration of about 20 at.%. The neighboring polyhedra share metal (M) atoms and form a polar covalently bonded random network of P-M-P favoring certain angles. The remaining M atoms act as metallic glue with a tendency of nanoscale clustering of Pd-Pd and Ni-Ni atoms.

  3. Modelling the local atomic structure of molybdenum in nuclear waste glasses with ab initio molecular dynamics simulations.

    PubMed

    Konstantinou, Konstantinos; Sushko, Peter V; Duffy, Dorothy M

    2016-09-21

    The nature of chemical bonding of molybdenum in high level nuclear waste glasses has been elucidated by ab initio molecular dynamics simulations. Two compositions, (SiO2)57.5-(B2O3)10-(Na2O)15-(CaO)15-(MoO3)2.5 and (SiO2)57.3-(B2O3)20-(Na2O)6.8-(Li2O)13.4-(MoO3)2.5, were considered in order to investigate the effect of ionic and covalent components on the glass structure and the formation of the crystallisation precursors (Na2MoO4 and CaMoO4). The coordination environments of Mo cations and the corresponding bond lengths calculated from our model are in excellent agreement with experimental observations. The analysis of the first coordination shell reveals two different types of molybdenum host matrix bonds in the lithium sodium borosilicate glass. Based on the structural data and the bond valence model, we demonstrate that the Mo cation can be found in a redox state and the molybdate tetrahedron can be connected with the borosilicate network in a way that inhibits the formation of crystalline molybdates. These results significantly extend our understanding of bonding in Mo-containing nuclear waste glasses and demonstrate that tailoring the glass composition to specific heavy metal constituents can facilitate incorporation of heavy metals at high concentrations.

  4. 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.

  5. The application of ab initio calculations to molecular spectroscopy

    NASA Technical Reports Server (NTRS)

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

    1989-01-01

    The state of the art in ab initio molecular structure calculations is reviewed, with an emphasis on recent developments such as full configuration-interaction benchmark calculations and atomic natural orbital basis sets. It is shown that new developments in methodology combined with improvements in computer hardware are leading to unprecedented accuracy in solving problems in spectroscopy.

  6. The application of ab initio calculations to molecular spectroscopy

    NASA Technical Reports Server (NTRS)

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

    1989-01-01

    The state of the art in ab initio molecular structure calculations is reviewed with an emphasis on recent developments, such as full configuration-interaction benchmark calculations and atomic natural orbital basis sets. It is found that new developments in methodology, combined with improvements in computer hardware, are leading to unprecedented accuracy in solving problems in spectroscopy.

  7. Adsorption of inert gases including element 118 on noble metal and inert surfaces from ab initio Dirac-Coulomb atomic calculations.

    PubMed

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

    2008-10-14

    The interaction of the inert gases Rn and element 118 with various surfaces has been studied on the basis of fully relativistic ab initio Dirac-Coulomb CCSD(T) calculations of atomic properties. The calculated polarizability of element 118, 46.3 a.u., is the largest in group 18, the ionization potential is the lowest at 8.91 eV, and the estimated atomic radius is the largest, 4.55 a.u. These extreme values reflect, in addition to the general trends in the Periodic Table, the relativistic expansion and destabilization of the outer valence 7p(3/2) orbital. Van der Waals coefficients C(3) and adsorption enthalpies DeltaH(ads) of Ne through element 118 on noble metals and inert surfaces, such as quartz, ice, Teflon, and graphite, were calculated in a physisorption model using the atomic properties obtained. The C(3) coefficients were shown to steadily increase in group 18, while the increase in DeltaH(ads) from Ne to Rn does not continue to element 118: The large atomic radius of the latter element is responsible for a decrease in the interaction energy. We therefore predict that experimental distinction between Rn and 118 by adsorption on these types of surfaces will not be feasible. A possible candidate for separating the two elements is charcoal; further study is needed to test this possibility.

  8. Ab initio alpha-alpha scattering.

    PubMed

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

    2015-12-03

    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

  9. 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

  10. Modelling the local atomic structure of molybdenum in nuclear waste glasses with ab initio molecular dynamics simulations

    SciTech Connect

    None, None

    2016-01-01

    The nature of chemical bonding of molybdenum in high level nuclear waste glasses has been elucidated by ab initio molecular dynamics simulations. Two compositions, (SiO2)57.5 – (B2O3)10 – (Na2O)15 – (CaO)15 – (MoO3)2.5 and (SiO2)57.3 – (B2O3)20 – (Na2O)6.8 – (Li2O)13.4 – (MoO3)2.5 , were considered in order to investigate the effect of ionic and covalent components on the glass structure and the formation of the crystallisation precursors (Na2MoO4 and CaMoO4). The coordination environments of Mo cations and the corresponding bond lengths calculated from our model are in excellent agreement with experimental observations. The analysis of the first coordination shell reveals two different types of molybdenum host matrix bonds in the lithium sodium borosilicate glass. Based on the structural data and the bond valence model, we demonstrate that the Mo cation can be found in a redox state and the molybdate tetrahedron can be connected with the borosilicate network in a way that inhibits the formation of crystalline molybdates. These results significantly extend our understanding of bonding in Mo-containing nuclear waste glasses and demonstrate that tailoring the glass composition to specific heavy metal constituents can facilitate incorporation of heavy metals at high concentrations. K.K. was supported through the Impact Studentship scheme at UCL co-funded by the IHI Corporation and UCL. P.V.S. thanks the Royal Society, which supported preliminary work on this project, and the Laboratory Directed Research and Development program at PNNL, a multiprogram national laboratory operated by Battelle for the U.S. Department of Energy. Via our membership of the UK's HEC Materials Chemistry Consortium, which is funded by EPSRC (EP/L000202), this work used the ARCHER UK National Supercomputing Service (http://www.archer.ac.uk).

  11. Curvy-steps approach to constraint-free extended-Lagrangian ab initio molecular dynamics, using atom-centered basis functions: convergence toward Born-Oppenheimer trajectories.

    PubMed

    Herbert, John M; Head-Gordon, Martin

    2004-12-15

    A dynamical extension of the "curvy-steps" approach to linear-scaling self-consistent field calculations is presented, which yields an extended-Lagrangian formulation of ab initio molecular dynamics. An exponential parametrization of the one-electron density matrix, expressed in terms of atom-centered Gaussian basis functions, facilitates propagation along the manifold of density matrices in a geometrically correct fashion that automatically enforces idempotency constraints. The extended Lagrangian itself is constraint free, thus neither density matrix purification nor expensive, iterative solution for Lagrange multipliers is required. Propagation is highly efficient, and time steps compare favorably to those used in Car-Parrinello molecular dynamics simulations. The behavior of the method, especially with regard to the maintenance of adiabatic decoupling of nuclei and electrons, is examined for a sequence of diatomic molecules, and comparison is made to trajectories propagated on the converged Born-Oppenheimer surface. Certain claims to the contrary notwithstanding, our results demonstrate that vibrational frequencies may depend on the value of the fictitious mass parameter, even in an atom-centered basis. Light-atom stretching frequencies can be significantly redshifted, even when the nuclear and electronic energy scales are well separated. With a sufficiently small fictitious mass and a short time step, accurate frequencies can be obtained; we characterize appropriate values of these parameters for a wide range of vibrational frequencies.

  12. Ab initio theory of many-body interaction and phonon frequencies of rare-gas crystals under pressure in the model of deformable atoms

    NASA Astrophysics Data System (ADS)

    Troitskaya, E. P.; Chabanenko, V. V.; Gorbenko, Ie. Ie.; Pilipenko, E. A.

    2015-01-01

    Ab initio calculations of phonon frequencies of compressed rare-gas crystals have been performed taking into account the many-body interaction in the model of deformable atoms. In the short-range repulsive potential, along with the previously considered three-body interaction associated with the overlap of the electron shells of atoms, the three-body forces generated by the mutual deformation of the electron shells of the nearest-neighbor atoms have been investigated in the dipole approximation. The relevant forces make no contribution to the elastic moduli but affect the equation for lattice vibrations. At high compressions, the softening of the longitudinal mode at the points L and X is observed for all the rare-gas crystals, whereas the transverse mode T 1 is softened in the direction Σ and at the point L for solid xenon. This effect is enhanced by the three-body forces. There is a good agreement between the theoretical phonon frequencies and the experimental values at zero pressure.

  13. Ab initio study of cyanoguanidine isomers

    NASA Astrophysics Data System (ADS)

    Arbuznikov, A. V.; Sheludyakova, L. A.; Burgina, E. B.

    1995-06-01

    An ab initio quantum chemical study of the geometric structure and stability of cyanoguanidine isomers was carried out at the Hartree-Fock and Møller-Plesset levels of theory. Two stable separable isomers ('cyanioime' and 'cyanoamine') are found. This gives evidence in favour of the vibrational spectroscopy data showing the existence of both isomers.

  14. Ab initio study of cyanoguanidine isomers

    NASA Astrophysics Data System (ADS)

    Arbuznikov, A. V.; Sheludyakova, L. A.; Burgina, E. B.

    1995-06-01

    An ab initio quantum chemical study of the geometric structure and stability of cyanoguanidine isomers was carried out at the Hartree-Fock and Møller-Plesset levels of theory. Two stable separable isomers (‘cyanioime' and ‘cyanoamine') are found. This gives evidence in favour of the vibrational spectroscopy data showing the existence of both isomers.

  15. All-atom ab initio native structure prediction of a mixed fold (1FME): a comparison of structural and folding characteristics of various beta beta alpha miniproteins.

    PubMed

    Kim, Eunae; Jang, Soonmin; Pak, Youngshang

    2009-11-21

    We performed an all-atom ab initio native structure prediction of 1FME, which is one of the computationally challenging mixed fold beta beta alpha miniproteins, by combining a novel conformational search algorithm (multiplexed Q-replica exchange molecular dynamics scheme) with a well-balanced all-atom force field employing a generalized Born implicit solvation model (param99MOD5/GBSA). The nativelike structure of 1FME was identified from the lowest free energy minimum state and in excellent agreement with the NMR structure. Based on the interpretation of the free energy landscape, the structural properties as well as the folding behaviors of 1FME were compared with other beta beta alpha miniproteins (1FSD, 1PSV, and BBA5) that we have previously studied with the same force field. Our simulation showed that the 28-residue beta beta alpha miniproteins (1FME, 1FSD, and 1PSV) share a common feature of the free energy topography and exhibit the three local minimum states on each computed free energy map, but the 23-residue miniprotein (BBA5) follows a downhill folding with a single minimum state. Also, the structure and stability changes resulting from the two point mutation (Gln1-->Glu1 and Ile7-->Tyr7) of 1FSD were investigated in details for direct comparison with the experiment. The comparison shows that upon mutation, the experimentally observed turn type switch from an irregular turn (1FSD) to type I(') turn (1FME) was well reproduced with the present simulation.

  16. Prediction of the adsorption behavior of elements 112 and 114 on inert surfaces from ab initio Dirac-Coulomb atomic calculations.

    PubMed

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

    2008-01-14

    The interaction of elements 112 and 114 with inert surfaces has been studied on the basis of fully relativistic ab initio Dirac-Coulomb CCSD(T) calculations of their atomic properties. The calculated polarizabilities of elements 112 and 114 are significantly lower than corresponding Hg and Pb values due to the relativistic contraction of the valence ns and np(12) orbitals, respectively, in the heavier elements. Due to the same reason, the estimated van der Waals radius of element 114 is smaller than that of Pb. The enthalpies of adsorption of Hg, Pb, and elements 112 and 114 on inert surfaces such as quartz, ice, and Teflon were predicted on the basis of these atomic calculations using a physisorption model. At the present level of accuracy, -DeltaH(ads) of element 112 on these surfaces is slightly (about 2 kJ/mol) larger than -DeltaH(ads)(Hg). The calculated -DeltaH(ads) of element 114 on quartz is about 7 kJ/mol and on Teflon is about 3 kJ/mol smaller than the respective values of -DeltaH(ads)(Pb). The trend of increasing -DeltaH(ads) in group 14 from C to Sn is thus reversed, giving decreasing values from Sn to Pb to element 114 due to the relativistic stabilization and contraction of the np(12) atomic orbitals. This is similar to trends shown by other atomic properties of these elements. The small difference in DeltaH(ads) of Pb and element 114 on inert surfaces obtained within a picture of physisorption contrasts with the large difference (more than 100 kJ/mol) in the chemical reactivity between these elements.

  17. Stoichiometric and sodium-doped titanium silicate molecular sieve containing atomically defined -OTiOTiO- chains: Quantum ab initio calculations, spectroscopic properties, and reactivity

    NASA Astrophysics Data System (ADS)

    Bordiga, S.; Turnes Palomino, G.; Zecchina, A.; Ranghino, G.; Giamello, E.; Lamberti, C.

    2000-02-01

    Ab initio calculations on a linear -OTiOTiO- chain embedded in an envelope of (SiO4) tetrahedra, mimicking the structure of Na2TiSi5O13 molecular sieve (ETS-10), confirm that the peculiar optical properties of the solid are associated with the presence of -OTiOTiO- linear chains behaving as quantum wires. The optical [in the UV-Vis (ultraviolet-range)] and the magnetic [(ESR) electron spin resonance] properties of these chains can be modified by adsorbing Na vapors. The sodium atoms diffusing into the channels undergo a ionization process with formation of Na+ (localized in the main channels) and Ti3+ (in the -OTiOTiO- chain, which so becomes a nonstoichiometric wire) characterized by Ti/Na ratios in the 2-4 range. Successive adsorption of oxygen at room temperature leads to the partial (Ti/Na˜2) or total (Ti/Na˜4) restoration of the chain stoichiometry and to the predominant formation of sodium oxide. The formation of a minor fraction of superoxide negative ions whose magnetic properties are revealed by ESR spectroscopy is also observed. Total restoration of the optical properties of the original samples is always obtained when the oxygen adsorption is made at 473 K. The sample keeps its structural integrity during the reduction and successive oxidation process.

  18. Ab initio calculations for industrial materials engineering: successes and challenges.

    PubMed

    Wimmer, Erich; Najafabadi, Reza; Young, George A; Ballard, Jake D; Angeliu, Thomas M; Vollmer, James; Chambers, James J; Niimi, Hiroaki; Shaw, Judy B; Freeman, Clive; Christensen, Mikael; Wolf, Walter; Saxe, Paul

    2010-09-29

    Computational materials science based on ab initio calculations has become an important partner to experiment. This is demonstrated here for the effect of impurities and alloying elements on the strength of a Zr twist grain boundary, the dissociative adsorption and diffusion of iodine on a zirconium surface, the diffusion of oxygen atoms in a Ni twist grain boundary and in bulk Ni, and the dependence of the work function of a TiN-HfO(2) junction on the replacement of N by O atoms. In all of these cases, computations provide atomic-scale understanding as well as quantitative materials property data of value to industrial research and development. There are two key challenges in applying ab initio calculations, namely a higher accuracy in the electronic energy and the efficient exploration of large parts of the configurational space. While progress in these areas is fueled by advances in computer hardware, innovative theoretical concepts combined with systematic large-scale computations will be needed to realize the full potential of ab initio calculations for industrial applications.

  19. Ab Initio Crystal Field for Lanthanides.

    PubMed

    Ungur, Liviu; Chibotaru, Liviu F

    2017-03-13

    An ab initio methodology for the first-principle derivation of crystal-field (CF) parameters for lanthanides is described. The methodology is applied to the analysis of CF parameters in [Tb(Pc)2 ](-) (Pc=phthalocyanine) and Dy4 K2 ([Dy(4) K(2) O(OtBu)(12) ]) complexes, and compared with often used approximate and model descriptions. It is found that the application of geometry symmetrization, and the use of electrostatic point-charge and phenomenological CF models, lead to unacceptably large deviations from predictions based on ab initio calculations for experimental geometry. It is shown how the predictions of standard CASSCF (Complete Active Space Self-Consistent Field) calculations (with 4f orbitals in the active space) can be systematically improved by including effects of dynamical electronic correlation (CASPT2 step) and by admixing electronic configurations of the 5d shell. This is exemplified for the well-studied Er-trensal complex (H3 trensal=2,2',2"-tris(salicylideneimido)trimethylamine). The electrostatic contributions to CF parameters in this complex, calculated with true charge distributions in the ligands, yield less than half of the total CF splitting, thus pointing to the dominant role of covalent effects. This analysis allows the conclusion that ab initio crystal field is an essential tool for the decent description of lanthanides.

  20. AB initio infrared and Raman spectra

    NASA Astrophysics Data System (ADS)

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

    1982-08-01

    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 Schroedinger 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 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.

  1. Ab Initio and Ab Exitu No-Core Shell Model

    SciTech Connect

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

    2007-10-02

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

  2. DFT and ab initio calculations on two reactions between hydrogen atoms and the fire suppressants 2-H heptafluoropropane and CF3Br.

    PubMed

    Lee, Edmond P F; Dyke, John M; Chow, Wan-Ki; Chau, Foo-Tim; Mok, Daniel K W

    2007-07-15

    Reaction enthalpies and barrier heights of the reactions CF3Br+H-->CF3+HBr {reaction (1)} and CF3CHFCF3+H-->CF3CFCF3+H2 {reaction (2)} have been calculated at the near state-of-the-art ab initio level, and also by employing the B3LYP, BH&HLYP, BB1K, MPW1K, MPWB1K and TPSS1KCIS functionals. In addition, the integrated molecular orbital+molecular orbital (IMOMO) method has been used to study reaction (2). The ab initio benchmark values of the reaction enthalpy (298 K) and barrier height (0 K) of reaction (2) are reported for the first time {-(0.7+/-0.7) and 13.3+/-0.5 kcal/mole respectively}. When density functional theory (DFT) results are compared with ab initio benchmarks for both reactions (1) and (2), the MPWB1K functional is found to have the best performance of the six functionals used. The IMOMO method with the RCCSD/aug-cc-pVTZ and/or RCCSD(T)/aug-cc-pVTZ levels, as the high levels of calculation on the model system, gives reaction enthalpies and barrier heights of reaction (2), which agree with ab initio benchmark values to within 1 kcal/mole. Computed key geometrical parameters and imaginary vibrational frequencies of the transition state structures of reactions (1) and (2) obtained at different levels of calculation are compared. The magnitudes of the computed imaginary vibrational frequencies of the transition states of both reactions considered are found to be very sensitive to the levels of calculation used to obtain them. The heat of formation (298 K) of CF3CFCF3 calculated at the near state-of-the-art level has a value of -(318+/-3) kcal/mole.

  3. Ab Initio Density Funcitonal Calculations of Adsorption of Transiton Metal Atoms on theta-Al2O3 (010) Surface

    SciTech Connect

    Narula, Chaitanya Kumar; Stocks, George Malcolm

    2012-01-01

    The catalytic properties of metal clusters and particles depend on their environment, however, little is known so far about the subnanometer metal particles, smallest being single atoms, supported on metal oxide substrates, especially, the systems that can be experimentally synthesized. Employing first principles density functional theory approach, we have studied single metal atoms, Ni, Pt, Pd, Cu, Au, and Ag, adsorbed on a -Al2O3 (010) surface. We find that metal adsorption on a dry alumina surface follows the binding strength order of Pd>Pt>Ni>Cu>Au>Ag. Interestingly, Ni, Pt, and Pd atoms, supported on alumina, exhibit no magnetization whereas Cu, Ag, and Au exhibit unpaired electrons. The bonding picture that emerges from this study shows that Ni, Pt, and Pd, are d10 species with d-s hybrid character that are able to interact with the 2p orbital of surface oxygen. The interaction of Group 11 (Cu, Ag, Au) atoms with 010 surface of -Al2O3 is superficially similar to that of Group 10 metals. Group 11 metals with filled d orbitals have low tendency for d-s hybridization due to larger energy gaps than Group 10 metals. As a result of the overlap with O 2p, the d orbital shifts to lower energy. The magnetization of Group 11 metals is primarily due to single electrons in s orbitals.

  4. 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.

  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-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

  6. 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.

  7. Ab initio and Atomic kinetic Monte Carlo modelling of segregation in concentrated FeCrNi alloys

    NASA Astrophysics Data System (ADS)

    Piochaud, J. B.; Becquart, C. S.; Domain, C.

    2014-06-01

    Internal structure of pressurised water reactors are made of austenitic materials. Under irradiation, the microstructure of these concentrated alloys evolves and solute segregation on grain boundaries or irradiation defects such as dislocation loops are observed to take place. In order to model and predict the microstructure evolution, a multiscale modelling approach needs to be developed, which starts at the atomic scale. Atomic Kinetic Monte Carlo (AKMC) modelling is the method we chose to provide an insight on defect mediated diffusion under irradiation. In that approach, we model the concentrated commercial steel as a FeCrNi alloy (γ-Fe70Cr20Ni10). As no reliable empirical potential exists at the moment to reproduce faithfully the phase diagram and the interactions of the elements and point defects, we have adjusted a pair interaction model on large amount of DFT calculations. The point defect properties in the Fe70Cr20Ni10, and more precisely, how their formation energy depends on the local environment will be presented and some AKMC results on thermal non equilibrium segregation and radiation induce segregation will be presented. The effect of Si on the segregation will also be discussed.

  8. Direct ab initio dynamics studies of the hydrogen abstraction reactions of hydrogen atom with n-propyl radical and isopropyl radical.

    PubMed

    Li, Qian Shu; Zhang, Yue; Zhang, Shaowen

    2005-02-01

    The kinetics of the hydrogen abstraction reactions of hydrogen atom with n-propyl radical and isopropyl radical were studied using the direct ab initio dynamics approach. BHandHLYP/cc-pVDZ method was employed to optimize the geometries of stationary points as well as the points on the minimum energy path (MEP). The energies of all the points for the two reactions were further refined at the QCISD(T)/cc-pVTZ level of theory. No barrier was found at the QCISD(T)/cc-pVTZ//BHandHLYP/cc-pVDZ level of theory for both reactions. The forward and reverse rate constants were evaluated with both canonical variational transition state theory (CVT) and microcanonical variational transition state theory (mu VT) in the temperature range of 300-2,500 K. The fitted three-parameter Arrhenius expression of the calculated CVT rate constants at the QCISD(T)/cc-pVTZ//BHandHLYP/cc-pVDZ level of theory are k(CVT) (n-C3H7) = 1.68 x 10(-14) T(0.84) e((319.5/T)) cm3 molecule(-1) s(-1) and k(CVT) (iso-C3H7)=4.99 x 10(-14) T(0.90) e((159.5/T)) cm3 molecule(-1) s(-1) for reactions of n-C3H7 + H and iso-C3H7 + H, respectively, which are in good agreement with available literature data. The variational effects were analysed.

  9. Ab initio investigation of potential energy curves of the 23 electronic states of IBr correlating to neutral (2)P atoms.

    PubMed

    Patchkovskii, Serguei

    2006-02-28

    Potential energy surfaces for all Born-Oppenheimer electronic states of IBr molecule correlating to the neutral (2)P ((2)P(3/2) and (2)P(1/2)) iodine and bromine are calculated for the first time. Electric dipole and polarizability curves (static and transition) are also determined. Calculations include scalar and spin-orbit relativistic effects within all-electron Douglas-Kroll two-component Hamiltonian. Electron correlation is treated with quasi-degenerate multi-reference second-order perturbation theory. Seven adiabatic electronic states (X (1)Sigma(+), A'(3)Pi(2), A (3)Pi(1), 1 (3)Pi(0-), B (3)Pi(0+), B'(3)Sigma, and 2 (3)Pi(0+)) exhibit significant covalent bonding, and can support vibrational states. Calculated spectroscopic parameters agree with experiment to better than 1000 cm(-1) (T(e)), 10 cm(-1) (omega(e)), and 0.05 Angstrom (r(e)). A new 1 (3)Pi(0-) state correlating to ground-state atoms is predicted at T(e) approximately 14 000 cm(-1), omega(e) approximately 80 cm(-1), and r(e) approximately 3.0 Angstrom. The second new state (2 (3)Pi(0+)) correlates to excited iodine atom, with T(e) approximately 20 000 cm(-1), omega(e) approximately 115 cm(-1), and r(e) approximately 3.3 Angstrom. Non-adiabatic coupling parameters are calculated for the four avoided crossings, which arise due to electronic spin-orbit interaction. Estimated parameters of the B (3)Pi(0+)/B'(3)Sigma crossing (R(c) approximately 3.32 Angstrom; V approximately 120 cm(-1)) agree with experimental values. The previously unsuspected 2 (3)Pi(0-)/1 (1)Sigma(-) crossing of two repulsive surfaces provides a new collisional deactivation channel for Br* atoms at relative velocities above 1000 m s(-1). Several repulsive states (including 1 (1)Pi(1) and 2 (3)Pi(1)) intersect the B/B' system near the avoided crossing point, and may affect dynamics of IBr in strong laser fields.

  10. 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.

  11. Ab initio calculations of the melting temperatures of refractory bcc metals.

    PubMed

    Wang, L G; van de Walle, A

    2012-01-28

    We present ab initio calculations of the melting temperatures for bcc metals Nb, Ta and W. The calculations combine phase coexistence molecular dynamics (MD) simulations using classical embedded-atom method potentials and ab initio density functional theory free energy corrections. The calculated melting temperatures for Nb, Ta and W are, respectively, within 3%, 4%, and 7% of the experimental values. We compare the melting temperatures to those obtained from direct ab initio molecular dynamics simulations and see if they are in excellent agreement with each other. The small remaining discrepancies with experiment are thus likely due to inherent limitations associated with exchange-correlation energy approximations within density-functional theory.

  12. Germacrene D Cyclization: An Ab Initio Investigation

    PubMed Central

    Setzer, William N.

    2008-01-01

    Essential oils that contain large concentrations of germacrene D are typically accompanied by cadinane sesquiterpenoids. The acid-catalyzed cyclization of germacrene D to give cadinane and selinane sesquiterpenes has been computationally investigated using both density functional (B3LYP/6-31G*) and post Hartree-Fock (MP2/6-31G* *) ab initio methods. The calculated energies are in general agreement with experimentally observed product distributions, both from acid-catalyzed cyclizations as well as distribution of the compounds in essential oils. PMID:19325722

  13. 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

  14. Molecular associations from ab initio pair potentials

    NASA Astrophysics Data System (ADS)

    Iglesias, E.; Sordo, T. L.; Sordo, J. A.

    1991-12-01

    A method of building up stable molecular associations by using pair potentials from ab initio calculations is presented. The Matsuoka-Clementi-Yoshimine potential has been chosen to emulate the water-water interactions while 1-6-12 potentials are used to compute both solute-solvent and solute-solute interactions. Parameters for neutral-amino-acid-water and neutral- amino-acid-neutral-amino-acid interactions are provided by the program. Supermolecules are constructed by minimization of the interaction energy of the molecules involved. Both steepest-decent and Fletcher-Powell algorithms are available to carry out such a minimization.

  15. Ab-initio phasing in protein crystallography

    NASA Astrophysics Data System (ADS)

    van der Plas, J. L.; Millane, Rick P.

    2000-11-01

    The central problem in the determination of protein structures form x-ray diffraction dada (x-ray crystallography) corresponds to a phase retrieval problem with undersampled amplitude data. Algorithms for this problem that have an increased radius of convergence have the potential for reducing the amount of experimental work, and cost, involved in determining protein structures. We describe such an algorithm. Application of the algorithm to a simulated crystallographic problem shows that it converges to the correct solution, with no initial phase information, where currently used algorithms fail. The results lend support to the possibility of ab initio phasing in protein crystallography.

  16. Ab-initio Studies Of Lithium Oxide

    NASA Astrophysics Data System (ADS)

    Gupta, M. K.; Goel, Prabhatasree; Mittal, R.; Chaplot, S. L.

    2010-12-01

    Lithium oxide is an important material because of its high thermal conductivity and superionic behavior at high temperature. It behaves like a superionic conductor above 1200 K. Phonon frequencies have been calculated using ab-initio method. The calculations of phonon dispersion relation near unit cell volume corresponding to the superionic transition indicate softening of zone boundary transverse acoustic phonon mode along (110). The instability of phonon mode could lead to the dynamical disorder of lithium sub lattice. Thermal expansion and equation of states are also computed. The results compare well with our previous semi-empirical potential calculations.

  17. 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.

  18. 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.

  19. Ab initio no core shell model

    SciTech Connect

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

    2012-11-17

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

  20. Ab initio based polarizable force field parametrization

    NASA Astrophysics Data System (ADS)

    Masia, Marco

    2008-05-01

    Experimental and simulation studies of anion-water systems have pointed out the importance of molecular polarization for many phenomena ranging from hydrogen-bond dynamics to water interfaces structure. The study of such systems at molecular level is usually made with classical molecular dynamics simulations. Structural and dynamical features are deeply influenced by molecular and ionic polarizability, which parametrization in classical force field has been an object of long-standing efforts. Although when classical models are compared to ab initio calculations at condensed phase, it is found that the water dipole moments are underestimated by ˜30%, while the anion shows an overpolarization at short distances. A model for chloride-water polarizable interaction is parametrized here, making use of Car-Parrinello simulations at condensed phase. The results hint to an innovative approach in polarizable force fields development, based on ab initio simulations, which do not suffer for the mentioned drawbacks. The method is general and can be applied to the modeling of different systems ranging from biomolecular to solid state simulations.

  1. Ab initio MCDHF calculations of electron-nucleus interactions

    NASA Astrophysics Data System (ADS)

    Bieroń, Jacek; Froese Fischer, Charlotte; Fritzsche, Stephan; Gaigalas, Gediminas; Grant, Ian P.; Indelicato, Paul; Jönsson, Per; Pyykkö, Pekka

    2015-05-01

    We present recent advances in the development of atomic ab initio multiconfiguration Dirac-Hartree-Fock theory, implemented in the GRASP relativistic atomic structure code. For neutral atoms, the deviations of properties calculated within the Dirac-Hartree-Fock (DHF) method (based on independent particle model of an atomic cloud) are usually dominated by electron correlation effects, i.e. the non-central interactions of individual electrons. We present the recent advances in accurate calculations of electron correlation effects in small, medium, and heavy neutral atoms. We describe methods of systematic development of multiconfiguration expansions leading to systematic, controlled improvement of the accuracy of the ab initio calculations. These methods originate from the concept of the complete active space (CAS) model within the DHF theory, which, at least in principle, permits fully relativistic calculations with full account of electron correlation effects. The calculations within the CAS model on currently available computer systems are feasible only for very light systems. For heavier atoms or ions with more than a few electrons, restrictions have to be imposed on the multiconfiguration expansions. We present methods and tools, which are designed to extend the numerical calculations in a controlled manner, where multiconfiguration expansions account for all leading electron correlation effects. We show examples of applications of the GRASP code to calculations of hyperfine structure constants, but the code may be used for calculations of arbitrary bound-state atomic properties. In recent years it has been applied to calculations of atomic and ionic spectra (transition energies and rates), to determinations of nuclear electromagnetic moments, as well as to calculations related to interactions of bound electrons with nuclear electromagnetic moments leading to violations of discrete symmetries.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. Discovering chemistry with an ab initio nanoreactor

    DOE PAGES

    Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; ...

    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

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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)

  16. 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.

  17. Ab initio phase diagram of iridium

    NASA Astrophysics Data System (ADS)

    Burakovsky, L.; Burakovsky, N.; Cawkwell, M. J.; Preston, D. L.; Errandonea, D.; Simak, S. I.

    2016-09-01

    The phase diagram of iridium is investigated using the Z methodology. The Z methodology is a technique for phase diagram studies that combines the direct Z method for the computation of melting curves and the inverse Z method for the calculation of solid-solid phase boundaries. In the direct Z method, the solid phases along the melting curve are determined by comparing the solid-liquid equilibrium boundaries of candidate crystal structures. The inverse Z method involves quenching the liquid into the most stable solid phase at various temperatures and pressures to locate a solid-solid boundary. Although excellent agreement with the available experimental data (to ≲65 GPa) is found for the equation of state (EOS) of Ir, it is the third-order Birch-Murnaghan EOS with B0'=5 rather than the more widely accepted B0'=4 that describes our ab initio data to higher pressure (P ) . Our results suggest the existence of a random-stacking hexagonal close-packed structure of iridium at high P . We offer an explanation for the 14-layer hexagonal structure observed in experiments by Cerenius and Dubrovinsky.

  18. Ab Initio Quantum Simulations of Liquid Water

    NASA Astrophysics Data System (ADS)

    Gergely, John; Ceperley, David; Gygi, Francois

    2007-03-01

    Some recent efforts at simulating liquid water have employed ``ab initio'' molecular dynamics (AIMD) methods with forces from a version of density functional theory (DFT) and, in some cases, imaginary-time path integrals (PI) to study quantum effects of the protons. Although AIMD methods have met with many successes, errors introduced by the approximations and choices of simulation parameters are not fully understood. We report on path integral Monte Carlo (PIMC) studies of liquid water using DFT energies that provide quantitative benchmarks for PI-AIMD work. Specifically, we present convergence studies of the path integrals and address whether the Trotter number can be reduced by improving the form of the (approximate) action. Also, we assess 1) whether typical AIMD simulations are sufficiently converged in simulation time, i.e., if there is reason to suspect that nonergodic behavior in PI-AIMD methods leads to poor convergence, and 2) the relative efficiency of the methods. E. Schwegler, J.C. Grossman, F. Gygi, G. Galli, J. Chem. Phys 121, 5400 (2004).

  19. Ab initio calculations of nitramine dimers

    NASA Astrophysics Data System (ADS)

    Koh-Fallet, Sharon; Schweigert, Igor

    2015-06-01

    Elevated temperatures and pressures are typically thought to have opposing effects on the reaction channels of nitramine decomposition. These high temperatures promote reactions with loose transition structures (positive activation entropies and volumes), such as N-N bond homolysis. Elevated pressures promote reactions with tight transition structures (negative activation entropies and volumes), such as intramolecular and intermolecular H transfer. However, no quantitative data exists regarding the range of temperatures and pressures at which these effects become pronounced. We are pursuing ab initio calculations of the corresponding unimolecular and bimolecular transition structures with the objective of estimating the relevant thermochemical parameters and quantifying the effects of elevated temperature and pressures on the corresponding rate constants. Here, we present density functional theory and complete active space calculations of gas-phase molecular dimers of nitramines as an intermediate step toward modeling transition structures directly in the condensed phase. This work was supported by the Naval Research Laboratory via the American Society for Engineering and Education and by the Office of Naval Research, both directly and through the Naval Research Laboratory.

  20. Ab-initio study of hexagonal apatites

    NASA Astrophysics Data System (ADS)

    Calderin, Lazaro; Stott, Malcom J.

    2001-03-01

    A silicon stabilized mixture of calcium phosphate phases has been recognized as playing an important role in actively resorbable coatings and in ceramics as bone materials. The nature of this material is being investigated using a variety of techniques including a combination of crystallographic analysis of measured x-ray diffraction spectra, and ab initio quantum mechanics simulations. We have used all-electron, density functional based calculations to investigate a group of hexagonal apatites. The fully relaxed crystallographic structures of hydroxyapatite, and related apatites have been obtained. We will present the results and discuss the nature of the bonding in these materials. The x-ray diffraction pattern and the infra-red spectra have also been obtained and will be compared with experiment. Acknowledgments:This work is part of a collaboration with the Applied Ceramics group of M.Sayer, and with Millenium Biologix Inc. Support of the NSERC of Canada through the award of a Co-operative R & D grant to the collaboration is acknowledged.

  1. 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.

  2. 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.

  3. On the isotropic Raman spectrum of Ar2 and how to benchmark ab initio calculations of small atomic clusters: Paradox lost

    NASA Astrophysics Data System (ADS)

    Chrysos, Michael; Dixneuf, Sophie; Rachet, Florent

    2015-07-01

    This is the long-overdue answer to the discrepancies observed between theory and experiment in Ar2 regarding both the isotropic Raman spectrum and the second refractivity virial coefficient, BR [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 BR 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.

  4. 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.

  5. 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

  6. Quantum plasmonics: from jellium models to ab initio calculations

    NASA Astrophysics Data System (ADS)

    Varas, Alejandro; García-González, Pablo; Feist, Johannes; García-Vidal, F. J.; Rubio, Angel

    2016-08-01

    Light-matter interaction in plasmonic nanostructures is often treated within the realm of classical optics. However, recent experimental findings show the need to go beyond the classical models to explain and predict the plasmonic response at the nanoscale. A prototypical system is a nanoparticle dimer, extensively studied using both classical and quantum prescriptions. However, only very recently, fully ab initio time-dependent density functional theory (TDDFT) calculations of the optical response of these dimers have been carried out. Here, we review the recent work on the impact of the atomic structure on the optical properties of such systems. We show that TDDFT can be an invaluable tool to simulate the time evolution of plasmonic modes, providing fundamental understanding into the underlying microscopical mechanisms.

  7. Reactive Monte Carlo sampling with an ab initio potential

    DOE PAGES

    Leiding, Jeff; Coe, Joshua D.

    2016-05-04

    Here, 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 also 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). Furthermore, we find that there are regions of state space formore » which RxMC sampling is much more efficient than AIMD due to the “rare-event” character of chemical reactions.« less

  8. 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.

  9. Ab Initio Study of KCl and NaCl Clusters

    NASA Astrophysics Data System (ADS)

    Brownrigg, Clifton; Hira, Ajit; Pacheco, Jose; Salazar, Justin

    2013-03-01

    We continue our interest in the theoretical study of molecular clusters to examine the chemical properties of small KnCln and NanCln clusters (n = 2 - 15). The potentially important role of these molecular species in biochemical and medicinal processes is well known. This work applies the hybrid ab initio methods of quantum chemistry to derive the different alkali-halide (MnHn) geometries. Of particular interest is the competition between hexagonal ring geometries and rock salt structures. Electronic energies, rotational constants, dipole moments, and vibrational frequencies for these geometries are calculated. Magic numbers for cluster stability are identified and are related to the property of cluster compactness. Mapping of the singlet, triplet, and quintet, potential energy surfaces is performed. Calculations have been performed to examine the interactions of these clusters with some atoms and molecules of biological interest, including O, O2, and Fe. The potential for design of new medicinal drugs is explored.

  10. 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.

  11. 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.

  12. Atomic arrangement and electron band structure of Si(1 1 1)-ß-\\sqrt{3}\\times \\sqrt{3} -Bi reconstruction modified by alkali-metal adsorption: ab initio study

    NASA Astrophysics Data System (ADS)

    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)\\sqrt{3}× \\sqrt{3} -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 {{T}4} 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)\\sqrt{3}× \\sqrt{3} -Bi surfaces modified by alkali metal adsorption as a set of material systems showing promise for spintronic applications.

  13. 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

    2015-08-05

    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.

  14. 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.

  15. 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.

  16. 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.

  17. Ab initio solution of macromolecular crystal structures without direct methods.

    PubMed

    McCoy, Airlie J; Oeffner, Robert D; Wrobel, Antoni G; Ojala, Juha R M; Tryggvason, Karl; Lohkamp, Bernhard; Read, Randy J

    2017-04-04

    The majority of macromolecular crystal structures are determined using the method of molecular replacement, in which known related structures are rotated and translated to provide an initial atomic model for the new structure. A theoretical understanding of the signal-to-noise ratio in likelihood-based molecular replacement searches has been developed to account for the influence of model quality and completeness, as well as the resolution of the diffraction data. Here we show that, contrary to current belief, molecular replacement need not be restricted to the use of models comprising a substantial fraction of the unknown structure. Instead, likelihood-based methods allow a continuum of applications depending predictably on the quality of the model and the resolution of the data. Unexpectedly, our understanding of the signal-to-noise ratio in molecular replacement leads to the finding that, with data to sufficiently high resolution, fragments as small as single atoms of elements usually found in proteins can yield ab initio solutions of macromolecular structures, including some that elude traditional direct methods.

  18. Ab-Initio Molecular Dynamics Simulation of Graphene Sheet

    NASA Astrophysics Data System (ADS)

    Kolev, S.; Balchev, I.; Cvetkov, K.; Tinchev, S.; Milenov, T.

    2017-01-01

    The study of graphene is important because it is a promising material for a variety of applications in the electronic industry. In the present work, the properties of а 2D periodic graphene sheet are studied with the use of ab initio molecular dynamics. DFT in the generalized gradient approximation is used in order to carry out the dynamical simulations. The PBE functional and DZVP-MOLOPT basis set are implemented in the CP2K/Quickstep package. A periodic box, consisting of 288 carbon atoms is chosen for the simulations. After geometry optimization it has dimensions 2964 x 2964 x 1500 pm and form angles of 90, 90, 60 degrees. The dynamical simulation is run for 1 ps in the NPT ensemble, at temperature T = 298.15 K. The radial distribution function shows a first peak at 142 pm, marking the bond length between carbon atoms. The density of states for the periodic systems is simulated as occupied orbitals represent the valence band and unoccupied ones the conduction band. The calculated bandgap, as expected is close to 0 eV.

  19. 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.

  20. The hydration structure of carbon monoxide by ab initio methods

    NASA Astrophysics Data System (ADS)

    Awoonor-Williams, Ernest; Rowley, Christopher N.

    2017-01-01

    The solvation of carbon monoxide (CO) in liquid water is important for understanding its toxicological effects and biochemical roles. In this paper, we use ab initio molecular dynamics (AIMD) and CCSD(T)-F12 calculations to assess the accuracy of the Straub and Karplus molecular mechanical (MM) model for CO(aq). The CCSD(T)-F12 CO-H2O potential energy surfaces show that the most stable structure corresponds to water donating a hydrogen bond to the C center. The MM-calculated surface incorrectly predicts that the O atom is a stronger hydrogen bond acceptor than the C atom. The AIMD simulations indicate that CO is solvated like a hydrophobic solute, with very limited hydrogen bonding with water. The MM model tends to overestimate the degree of hydrogen bonding and overestimates the atomic radius of the C atom. The calculated Gibbs energy of hydration using the TIP3P water model is in good agreement with the experiment (9.3 kJ mol-1 expt. vs 10.7 kJ mol-1 calc.). The calculated diffusivity of CO (aq) in TIP3P-model water was 5.1 ×10-5 cm2/s calc., more than double the experimental value of 2.3 ×10-5 cm2/s. The hydration energy calculated using the TIP4P-FB water model is in poorer agreement with the experiment (ΔG = 6.8 kJ/mol) but the diffusivity is in better agreement (D =2.5 ±0.1 ×10-5 cm2/s).

  1. 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

    SciTech Connect

    Zhu, Xiaolei Yarkony, David R.

    2016-01-14

    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, H{sup d}, of adiabatic electronic states coupled by conical intersections. In this work, the algorithm is used to construct an H{sup d} 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 × 10{sup 6} 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 H{sup d}, 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{sup −1} for electronic energies <60 000 cm{sup −1}.

  2. Study on structures and properties of ammonia clusters (NH3)n (n=1-5) and liquid ammonia in terms of ab initio method and atom-bond electronegativity equalization method ammonia-8P fluctuating charge potential model.

    PubMed

    Yu, Ling; Yang, Zhong-Zhi

    2010-05-07

    Structures, binding energies, and vibrational frequencies of (NH(3))(n) (n=2-5) isomers and dynamical properties of liquid ammonia have been explored using a transferable intermolecular potential eight point model including fluctuating charges and flexible body based on a combination of the atom-bond electronegativity equalization and molecular (ABEEM) mechanics (ABEEM ammonia-8P) in this paper. The important feature of this model is to divide the charge sites of one ammonia molecule into eight points region containing four atoms, three sigma bonds, and a lone pair, and allows the charges in system to fluctuate responding to the ambient environment. Due to the explicit descriptions of charges and special treatment of hydrogen bonds, the results of equilibrium geometries, dipole moments, cluster interaction energies, vibrational frequencies for the gas phase of small ammonia clusters, and radial distribution function for liquid ammonia calculated with the ABEEM ammonia-8P potential model are in good agreement with those measured by available experiments and those obtained from high level ab initio calculations. The properties of ammonia dimer are studied in detail involving the structure and one-dimensional, two-dimensional potential energy surface. As for interaction energies, the root mean square deviation is 0.27 kcal/mol, and the linear correlation coefficient reaches 0.994.

  3. Ab Initio Infrared and Raman Spectra.

    DTIC Science & Technology

    1982-08-01

    tions. For parameters not depending on momenta, a parallel ab fhti Monte Carlo approach would use electronic energies and other parameters of... Monte Carlo approach. Specifically, as one of us has suggested,t I classical molecular dynamics may be integrated with ab iniHo quan- tum force...alternative approach, for phenomena which are not explicitly time dependent, is a Monte Carlo procedure in which at each trial nuclear configuration

  4. 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.

  5. 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.

  6. 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.

  7. Ab-Initio Study of Incongruent Melting in Silicates

    NASA Astrophysics Data System (ADS)

    Pinilla, C.; Stixrude, L. P.

    2014-12-01

    Knowledge of the multi-component thermodynamics and phase equilibria of silicate melts at Earth's interior conditions are key to understand the chemical and thermal evolution of the planet. Yet they remain poorly constrained with a wide uncertainty on the eutectic composition and temperature. In this work we present results from ab-initio molecular dynamics in combination with the two-phase coexistance method to study properties of a system of MgSiO3 liquid coexisting with crystalline MgO at conditions of the deep lower mantle. During incongruent melting the crystal may either grow via partial freezing of the liquid or shrink via partial melting at a given temperature and pressure. The melting process can be studied using the two-phases method where liquid and solid are in contact at a given temperature and pressure and so under thermodynamic equilibrium. We characterise the composition and densities of the resultant solid and liquid phases, provide chemical potentials of the liquid phase and study the structural and dynamical properties of the melt. In addition, we discuss the performance of alternative computational methods applied to the study of incongruent melting in silicate systems where long simulation times and a large number of atoms are usually needed. Finally, we discuss the implication of our findings for the evolution of the Earth's interior.

  8. 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.

  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. 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.

  11. Ab initio calculations of correlated electron dynamics in ultrashort pulses

    NASA Astrophysics Data System (ADS)

    Feist, Johannes

    2010-03-01

    The availability of ultrashort and intense light pulses on the femtosecond and attosecond timescale promises to allow to directly probe and control electron dynamics on their natural timescale. A crucial ingredient to understanding the dynamics in many-electron systems is the influence of electron correlation, induced by the interelectronic repulsion. In order to study electron correlation in ultrafast processes, we have implemented an ab initio simulation of the two-electron dynamics in helium atoms. We solve the time-dependent Schr"odinger equation in its full dimensionality, with one temporal and five spatial degrees of freedom in linearly polarized laser fields. In our computational approach, the wave function is represented through a combination of time-dependent close coupling with the finite element discrete variable representation, while time propagation is performed using an Arnoldi-Lanczos approximation with adaptive step size. This approach is optimized to allow for efficient parallelization of the program and has been shown to scale linearly using up to 1800 processor cores for typical problem sizes. This has allowed us to perform highly accurate and well- converged computations for the interaction of ultrashort laser pulses with He. I will present some recent results on using attosecond and femtosecond pulses to probe and control the temporal structure of the ionization process. This work was performed in collaboration with Stefan Nagele, Renate Pazourek, Andreas Kaltenb"ack, Emil Persson, Barry I. Schneider, Lee A. Collins, and Joachim Burgd"orfer.

  12. Protons in polar media: An ab initio molecular dynamics study

    NASA Astrophysics Data System (ADS)

    von Rosenvinge, Tycho

    1998-10-01

    The hydrates of hydrogen chloride are ionic crystals that contain hydronium (H3O+). The hydronium in the monohydrate has been reported to be statistically disordered between two possible sites related by inversion symmetry. Ab initio molecular dynamics calculations are presented for the monohydrate, as well as the di-, and tri-hydrates, of hydrogen chloride using the density functional based Car-Parrinello technique. The simulations were carried out with the goal of investigating proton disorder in these crystals. The possible role of nuclear quantum effects has been explored via path integral molecular dynamic simulations. The present results suggest that the proposed disordered sites in the monohydrate are dynamically unstable and therefore unlikely to be responsible for the reported disorder. No useful information was obtained for the dihydrate because the large unit cell leads to difficulties in carrying out the simulations. Nuclear quantum effects are shown to be important for characterizing the proton distributions in the trihydrate. The structure and dynamical behavior of liquid HF with dissolved KF have been investigated using the Car- Parrinello ab initio molecular dynamics scheme. Specifically, a system with stoichiometry KFċ2HF was studied at temperatures of 400K and 1000K. This system, which was started from a phase separated mixture, rapidly formed into solvated potassium ions and HnFn+1/sp- polyfluoride anions with n = 1, 2, 3, and 4. The resulting polyfluoride anions were classified, and their structures and dynamical behavior were compared with the known structures and spectra of crystalline compounds KF/cdot xHF and with theoretical predictions of isolated gas phase species. The present study reveals dramatic frequency shifts in the H atom vibrational modes with variation in the HF coordination number of the polyfluoride anion. In particular the FH wagging motion red shifts while the FH stretch blue shifts as n increases. The present calculations

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

    NASA Astrophysics Data System (ADS)

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

    2015-02-01

    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.

  14. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-03-01

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

  16. 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

    2014-01-03

    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.

  17. Resonance and aromaticity: an ab initio valence bond approach.

    PubMed

    Rashid, Zahid; van Lenthe, Joop H; Havenith, Remco W A

    2012-05-17

    Resonance energy is one of the criteria to measure aromaticity. The effect of the use of different orbital models is investigated in the calculated resonance energies of cyclic conjugated hydrocarbons within the framework of the ab initio Valence Bond Self-Consistent Field (VBSCF) method. The VB wave function for each system was constructed using a linear combination of the VB structures (spin functions), which closely resemble the Kekulé valence structures, and two types of orbitals, that is, strictly atomic (local) and delocalized atomic (delocal) p-orbitals, were used to describe the π-system. It is found that the Pauling-Wheland's resonance energy with nonorthogonal structures decreases, while the same with orthogonalized structures and the total mean resonance energy (the sum of the weighted off-diagonal contributions in the Hamiltonian matrix of orthogonalized structures) increase when delocal orbitals are used as compared to local p-orbitals. Analysis of the interactions between the different structures of a system shows that the resonance in the 6π electrons conjugated circuits have the largest contributions to the resonance energy. The VBSCF calculations also show that the extra stability of phenanthrene, a kinked benzenoid, as compared to its linear counterpart, anthracene, is a consequence of the resonance in the π-system rather than the H-H interaction in the bay region as suggested previously. Finally, the empirical parameters for the resonance interactions between different 4n+2 or 4n π electrons conjugated circuits, used in Randić's conjugated circuits theory or Herdon's semi-emprical VB approach, are quantified. These parameters have to be scaled by the structure coefficients (weights) of the contributing structures.

  18. Separable metamaterials: analytical ab-initio homogenization and chirality

    NASA Astrophysics Data System (ADS)

    Ciattoni, Alessandro; Rago, Domenico; Rizza, Carlo

    2016-11-01

    We investigate the ab-initio homogenization of separable metamaterials with factorized dielectric permittivity profiles, which can be achieved through suitable grey-scale permittivity design techniques. Separability allows such metamaterials to be physically regarded as the superposition of three fictitious 1D generating media. We prove that, in the long-wavelength limit, separable metamaterials admit a simple and analytical description of their electromagnetic bi-anisotropic response, which can be reconstructed from the properties of the 1D generating media. Our approach provides a strategy that allows the full ab-initio and flexible design of a complex bianisotropic response by using the simple and well-known properties of 1D metamaterials.

  19. High Level Ab Initio Kinetics as a Tool for Astrochemistry

    NASA Astrophysics Data System (ADS)

    Klippenstein, Stephen

    2015-05-01

    We will survey the application of ab initio theoretical kinetics to reactions of importance to astrochemistry. Illustrative examples will be taken from our calculations for (i) interstellar chemistry, (ii) Titan's atmospheric chemistry, and (iii) the chemistry of extrasolar giant planets. The accuracy of various aspects of the calculations will be summarized including (i) the underlying ab initio electronic structure calculations, (ii) the treatment of the high pressure recombination process, and (iii) the treatment of the pressure dependence of the kinetics. The applications will consider the chemistry of phosphorous on giant planets, the kinetics of water dimerization, the chemistry of nitrogen on Titan's atmosphere, as well as various reactions of interstellar chemistry interest such as the recombination of OH with H, and O(3P) reacting with C2H5, CH2, and CCS. Chemical Sciences and Engineering Division.

  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. Ab initio theories for light nuclei and neutron stars

    NASA Astrophysics Data System (ADS)

    Gezerlis, Alexandros

    2016-09-01

    In this talk I will touch upon several features of modern ab initio low-energy nuclear theory. I will start by discussing what ``ab initio'' means in this context. Specifically, I will spend some time going over nucleon-nucleon and three-nucleon interactions and their connections with the underlying theory of Quantum Chromodynamics. I will then show how these interactions are used to describe light nuclei using essentially exact few-body methods. I will then discuss heavier systems, especially those of astrophysical relevance, as well as the methods used to tackle them. This work was supported by the Natural Sciences and Engineering Research Council (NSERC) of Canada and the Canada Foundation for Innovation (CFI).

  2. Ab Initio Atomistic Thermodynamics for Surfaces: A Primer

    DTIC Science & Technology

    2006-02-01

    Ab Initio Atomistic Thermodynamics for Surfaces: A Primer Jutta Rogal and Karsten Reuter Fritz - Haber -Institut der Max-Planck-Gesellschaft... Fritz - Haber -Institut der Max-Planck-Gesellschaft Faradayweg 4-6 D-14195 Berlin Germany 8. PERFORMING ORGANIZATION REPORT NUMBER 9. SPONSORING...of the Fritz - Haber -Institut, in particular Wei-Xue Li, Cathy Stampfl and Mira Todorova. Particular thanks go to Matthias Scheffler for his continued

  3. 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.

  4. 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.

  5. 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.

  6. An ab initio study on atomic and electronic structures of two-dimensional Al3Ti at Al/TiB2 interface

    NASA Astrophysics Data System (ADS)

    Men, H.

    2016-09-01

    The atomic and electronic structures of a two-dimentional (2D) Al3Ti layer at Al/TiB2 interface has been investigated using first-principle calculations. The result reveals the 2D-Al3Ti adopts the structure of bulk Al3Ti. There exists a strong Ti(3d)-Al(3p) hybridization between Ti and Al atoms of the 2D-Al3Ti, as well as between surface Ti atoms of TiB2 and Al atoms of 2D-Al3Ti. It leads to a stronger covalent Ti-Al bonding at the Al/2D-Al3Ti/TiB2 interface than at the Al/TiB2 interface, which is responsible for the stability of 2D-Al3Ti.

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

    PubMed

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

    2014-08-07

    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.

  8. 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).

  9. Diffusion in liquid Germanium using ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Kulkarni, R. V.; Aulbur, W. G.; Stroud, D.

    1996-03-01

    We describe the results of calculations of the self-diffusion constant of liquid Ge over a range of temperatures. The calculations are carried out using an ab initio molecular dynamics scheme which combines an LDA model for the electronic structure with the Bachelet-Hamann-Schlüter norm-conserving pseudopotentials^1. The energies associated with electronic degrees of freedom are minimized using the Williams-Soler algorithm, and ionic moves are carried out using the Verlet algorithm. We use an energy cutoff of 10 Ry, which is sufficient to give results for the lattice constant and bulk modulus of crystalline Ge to within 1% and 12% of experiment. The program output includes not only the self-diffusion constant but also the structure factor, electronic density of states, and low-frequency electrical conductivity. We will compare our results with other ab initio and semi-empirical calculations, and discuss extension to impurity diffusion. ^1 We use the ab initio molecular dynamics code fhi94md, developed at 1cm the Fritz-Haber Institute, Berlin. ^2 Work supported by NASA, Grant NAG3-1437.

  10. Ab initio molecular dynamics using hybrid density functionals.

    PubMed

    Guidon, Manuel; Schiffmann, Florian; Hutter, Jürg; VandeVondele, Joost

    2008-06-07

    Ab initio molecular dynamics simulations with hybrid density functionals have so far found little application due to their computational cost. In this work, an implementation of the Hartree-Fock exchange is presented that is specifically targeted at ab initio molecular dynamics simulations of medium sized systems. We demonstrate that our implementation, which is available as part of the CP2K/Quickstep program, is robust and efficient. Several prescreening techniques lead to a linear scaling cost for integral evaluation and storage. Integral compression techniques allow for in-core calculations on systems containing several thousand basis functions. The massively parallel implementation respects integral symmetry and scales up to hundreds of CPUs using a dynamic load balancing scheme. A time-reversible multiple time step scheme, exploiting the difference in computational efficiency between hybrid and local functionals, brings further time savings. With extensive simulations of liquid water, we demonstrate the ability to perform, for several tens of picoseconds, ab initio molecular dynamics based on hybrid functionals of systems in the condensed phase containing a few thousand Gaussian basis functions.

  11. Ab initio molecular dynamics using hybrid density functionals

    NASA Astrophysics Data System (ADS)

    Guidon, Manuel; Schiffmann, Florian; Hutter, Jürg; Vandevondele, Joost

    2008-06-01

    Ab initio molecular dynamics simulations with hybrid density functionals have so far found little application due to their computational cost. In this work, an implementation of the Hartree-Fock exchange is presented that is specifically targeted at ab initio molecular dynamics simulations of medium sized systems. We demonstrate that our implementation, which is available as part of the CP2K/Quickstep program, is robust and efficient. Several prescreening techniques lead to a linear scaling cost for integral evaluation and storage. Integral compression techniques allow for in-core calculations on systems containing several thousand basis functions. The massively parallel implementation respects integral symmetry and scales up to hundreds of CPUs using a dynamic load balancing scheme. A time-reversible multiple time step scheme, exploiting the difference in computational efficiency between hybrid and local functionals, brings further time savings. With extensive simulations of liquid water, we demonstrate the ability to perform, for several tens of picoseconds, ab initio molecular dynamics based on hybrid functionals of systems in the condensed phase containing a few thousand Gaussian basis functions.

  12. A highly accurate ab initio potential energy surface for methane

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

    A new nine-dimensional potential energy surface (PES) for methane has been generated using state-of-the-art ab initio theory. The PES is based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set limit and incorporates a range of higher-level additive energy corrections. These include core-valence electron correlation, higher-order coupled cluster terms beyond perturbative triples, scalar relativistic effects, and the diagonal Born-Oppenheimer correction. Sub-wavenumber accuracy is achieved for the majority of experimentally known vibrational energy levels with the four fundamentals of 12CH4 reproduced with a root-mean-square error of 0.70 cm-1. The computed ab initio equilibrium C-H bond length is in excellent agreement with previous values despite pure rotational energies displaying minor systematic errors as J (rotational excitation) increases. It is shown that these errors can be significantly reduced by adjusting the equilibrium geometry. The PES represents the most accurate ab initio surface to date and will serve as a good starting point for empirical refinement.

  13. Ab initio rotation-vibration spectra of HCN and HNC

    NASA Astrophysics Data System (ADS)

    Harris, Gregory J.; Polyansky, Oleg L.; Tennyson, Jonathan

    2002-03-01

    We have calculated an ab initio HCN/HNC linelist for all transitions up to J=25 and 18 000 cm -1 above the zero point energy. This linelist contains more than 200 million lines each with frequencies and transition dipoles. The linelist has been calculated using our semi-global HCN/HNC VQZANO+PES and dipole moment surface, which were reported in van Mourik et al. (J. Chem. Phys. 115 (2001) 3706). With this linelist we synthesise absorption spectra of HCN and HNC at 298 K and we present the band centre and band transition dipoles for the bands which are major features in these spectra. Several of the HCN bands and many of the HNC bands have not been previously studied. Our line intensities reproduce via fully ab initio methods the unusual intensity structure of the HCN CN stretch fundamental (00 01) for the first time and also the forbidden (02 20) HCN bending overtone. We also compare the J=1→0 pure rotational transition dipole in the HCN/HNC ground and vibrationally excited states with experimental and existing ab initio results.

  14. 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.

  15. Ab initio computational applications to complex biomolecular systems

    NASA Astrophysics Data System (ADS)

    Liang, Lei

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

  16. Ab Initio Studies of Surfaces and Interfaces

    NASA Astrophysics Data System (ADS)

    Garrity, Kevin F.

    2011-12-01

    Over the past 50 years, our ability to design and fabricate materials and devices with ever-smaller components has improved to the point that many technologies are crucially dependent on surfaces and interfaces. As this process continues, the atomic details of these surfaces and interfaces will take on increasing importance, both in understanding the behavior of existing structures as well as proposing and testing new materials and devices. First principles techniques are especially well-suited for exploring these systems, as they have the predictive capability required to understand the new phenomena which emerge at atomic length scales. In this work, we use first principles density functional theory to explore the properties of a variety of interesting surfaces and interfaces. First, we consider the thermodynamics and kinetics of Sr and La deposition on semiconductor surfaces, which is the first step in epitaxial oxide growth on semiconductors. Using this knowledge, we propose a method for growing LaAlO3 on epitaxially on Si. In addition, we explore the surface chemistry of a ferroelectric (PbTiO3) as a function a polarization in order to understand its applications to advanced catalysis. Finally, we investigate the coupling of phonons through an epitaxial interface between SrTiO3 and La 1-xSrxMnO 3, where an interfacial coupling of atomic motion is used to dynamically modulate the conductivity of a La1-xSr xMnO3 thin film.

  17. 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.

  18. 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.

  19. Developmental AB Initio Molecular Orbital Theory

    NASA Astrophysics Data System (ADS)

    Blurock, Edward (Ned) Samuel

    The frozen core approximation (FCA) was applied to the main group elements of the first four rows of the periodic table (i.e., through Iodine). For hydride bond lengths, the results of the FCA calculation were consistently closer to experiment. The FCA calculation assumes that the core space is complete and restricts its further optimization. The standard calculation does not have this restriction and further completion of the core space (during the optimization procedure) by valence orbitals on neighboring atoms produced shorter (compared to FCA and experiment) hydride bond lengths. A new set of two-electron integrals was developed combining the use of Rys quadrature and the axis-switch algorithm. The combined algorithm was found to be advantageous only under higher contraction. Also, it was determined that extension of the algorithm to higher angular momentum functions would yield improvement in only selected cases. The SYMGEN program, a symbolic algebra program written by the author, was used to generate and globally optimize the newly developed code. The SYMGEN program is a general program with potential uses in a variety of other coding and global optimization problems.

  20. 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.

  1. 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.

  2. {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}

  3. Ab initio analytical Raman intensities for periodic systems through a coupled perturbed Hartree-Fock/Kohn-Sham method in an atomic orbital basis. I. Theory.

    PubMed

    Maschio, Lorenzo; Kirtman, Bernard; Rérat, Michel; Orlando, Roberto; Dovesi, Roberto

    2013-10-28

    We present a fully analytical formulation for calculating Raman intensities of crystalline periodic systems using a local basis set. Numerical differentiation with respect to atomic coordinates and with respect to wavevectors is entirely avoided as is the determination of crystal orbital coefficient derivatives with respect to nuclear displacements. Instead, our method utilizes the orbital energy-weighted density matrix and is based on the self-consistent solution of first- and second-order Coupled Perturbed Hartree-Fock/Kohn-Sham equations for the electronic response to external electric fields at the equilibrium geometry. This method has also been implemented in the Crystal program, which uses a Gaussian type basis set.

  4. Molecular geometry and polarizability of small cadmium selenide clusters from all-electron ab initio and Density Functional Theory calculations.

    PubMed

    Karamanis, Panaghiotis; Maroulis, George; Pouchan, Claude

    2006-02-21

    We have calculated molecular geometries and electric polarizabilities for small cadmium selenide clusters. Our calculations were performed with conventional ab initio and density functional theory methods and Gaussian-type basis sets especially designed for (CdSe)(n). We find that the dipole polarizability per atom converges rapidly to the bulk value.

  5. Ab initio study of the optical properties of carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Chang, Eric

    2006-03-01

    We present an ab initio study of the optical properties of carbon nanotubes. We use state-of-the-art electronic structure methods based on many-body perturbation theory to compute the optical absorption and resonance Raman spectra of large tubes which have up to 200 atoms [1,2]. Our symmetry-based method makes the study of large tubes feasible within the many- body framework and also allows us to understand the symmetry properties of the excitons and selection rules. We include a study of the so-called dark excitons which are crucial for understanding luminescence efficiency in carbon nanotubes. The mechanism that explains the dark-bright splitting can be understood within our symmetry-based approach. Finally, we present an analysis of the two-photon spectra for several carbon nanotubes, a theoretical analysis which, in conjunction with combined one- and two-photon experiments, allows one to measure the binding energy of excitons. We find in all cases that the excitonic binding energy is large, ranging from 0.5 to 0.9 eV depending on the diameter of the tube, and that the excitonic wavefunction is Wannier-like and extended over many atoms. Our studies for the one- and two-photon absorption and resonance Raman spectra have been fruitful for understanding the corresponding experiments. In particular, our theoretical results are in good agreement with one- and two-photon absorption experiments [3-5]. The results for resonance Raman show that such a spectroscopic technique is a good alternative to optical absorption since it allows for the selection of tubes of a given diameter while probing the same excited states. 1. E.K. Chang, G. Bussi, A. Ruini, and E. Molinari, Phys. Rev. Lett. 92, 196401 (2004). 2. E.K. Chang, G. Bussi, A. Ruini, and E. Molinari, Phys. Rev. B 72, 195423 (2005). 3. M. Y. Sfeir et al., Science 306, 1540 (2004). 4. J. Maultzsch et al., to be published in Phys. Rev. B, see also cond-mat/0505150. 5. Z. M. Li et. al., Phys. Rev. Lett. 87, 127401 (2001).

  6. Theoretical study on isotope and temperature effect in hydronium ion using ab initio path integral simulation

    NASA Astrophysics Data System (ADS)

    Tachikawa, Masanori; Shiga, Motoyuki

    2004-09-01

    We have applied the ab initio path integral molecular dynamics simulation to study hydronium ion and its isotopes, which are the simplest systems for hydrated proton and deuteron. In this simulation, all the rotational and vibrational degrees of freedom are treated fully quantum mechanically, while the potential energies of the respective atomic configurations are calculated "on the fly" using ab initio quantum chemical approach. With the careful treatment of the ab initio electronic structure calculation by relevant choices in electron correlation level and basis set, this scheme is theoretically quite rigorous except for Born-Oppenheimer approximation. This accurate calculation allows a close insight into the structural shifts for the isotopes of hydronium ion by taking account of both quantum mechanical and thermal effects. In fact, the calculation is shown to be successful to quantitatively extract the geometrical isotope effect with respect to the Walden inversion. It is also shown that this leads to the isotope effect on the electronic structure as well as the thermochemical properties.

  7. 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.

  8. 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.

  9. 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.

  10. Ab Initio Study of Phase Equilibria in TiCx

    NASA Astrophysics Data System (ADS)

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

    2002-01-01

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

  11. Pseudorotation motion in tetrahydrofuran: an ab initio study.

    PubMed

    Rayón, Víctor M; Sordo, Jose A

    2005-05-22

    The use of different models based on experimental information about the observed level splitings, rotational constants, and far-infrared transition frequencies leads to different predictions on the equilibrium geometry for tetrahydrofuran. High-level ab initio calculations [coupled cluster singles, doubles (triples)/complete basis set (second order Moller-Plesset triple, quadrupole, quintuple)+zero-point energy(anharmonic)] suggest that the equilibrium conformation of tetrahydrofuran is an envelope C(s) structure. The theoretical geometrical parameters might be helpful to plan further microwave spectroscopic studies in order to get a physical interpretation of the measurements.

  12. Accelerating ab initio molecular dynamics simulations by linear prediction methods

    NASA Astrophysics Data System (ADS)

    Herr, Jonathan D.; Steele, Ryan P.

    2016-09-01

    Acceleration of ab initio molecular dynamics (AIMD) simulations can be reliably achieved by extrapolation of electronic data from previous timesteps. Existing techniques utilize polynomial least-squares regression to fit previous steps' Fock or density matrix elements. In this work, the recursive Burg 'linear prediction' technique is shown to be a viable alternative to polynomial regression, and the extrapolation-predicted Fock matrix elements were three orders of magnitude closer to converged elements. Accelerations of 1.8-3.4× were observed in test systems, and in all cases, linear prediction outperformed polynomial extrapolation. Importantly, these accelerations were achieved without reducing the MD integration timestep.

  13. Morphing ab initio potential energy curve of beryllium monohydride

    NASA Astrophysics Data System (ADS)

    Špirko, Vladimír

    2016-12-01

    Effective (mass-dependent) potential energy curves of the ground electronic states of 9BeH, 9BeD, and 9BeT are constructed by morphing a very accurate MR-ACPF ab initio potential of Koput (2011) within the framework of the reduced potential energy curve approach of Jenč (1983). The morphing is performed by fitting the RPC parameters to available experimental ro-vibrational data. The resulting potential energy curves provide a fairly quantitative reproduction of the fitted data. This allows for a reliable prediction of the so-far unobserved molecular states in terms of only a small number of fitting parameters.

  14. Ab initio evidence for nonthermal characteristics in ultrafast laser melting

    NASA Astrophysics Data System (ADS)

    Lian, Chao; Zhang, S. B.; Meng, Sheng

    2016-11-01

    Laser melting of semiconductors has been observed for almost 40 years; surprisingly, it is not well understood where most theoretical simulations show a laser-induced thermal process. Ab initio nonadiabatic simulations based on real-time time-dependent density functional theory reveal intrinsic nonthermal melting of silicon, at a temperature far below the thermal melting temperature of 1680 K. Both excitation threshold and time evolution of diffraction intensity agree well with experiment. Nonthermal melting is attributed to excitation-induced drastic changes in bonding electron density, and the subsequent decrease in the melting barrier, rather than lattice heating as previously assumed in the two-temperature models.

  15. Communication: Ab initio Joule-Thomson inversion data for argon

    NASA Astrophysics Data System (ADS)

    Wiebke, Jonas; Senn, Florian; Pahl, Elke; Schwerdtfeger, Peter

    2013-02-01

    The Joule-Thomson coefficient μH(P, T) is computed from the virial equation of state up to seventh-order for argon obtained from accurate ab initio data. Higher-order corrections become increasingly more important to fit the low-temperature and low-pressure regime and to avoid the early onset of divergence in the Joule-Thomson inversion curve. Good agreement with experiment is obtained for temperatures T > 250 K. The results also illustrate the limitations of the virial equation in regions close to the critical temperature.

  16. Ab initio quantum chemical study of electron transfer in carboranes

    NASA Astrophysics Data System (ADS)

    Pati, Ranjit; Pineda, Andrew C.; Pandey, Ravindra; Karna, Shashi P.

    2005-05-01

    The electron transfer (ET) properties of 10- and 12-vertex carboranes are investigated by the ab initio Hartree-Fock method within the Marcus-Hush (MH) two-state model and the Koopman theorem (KT) approach. The calculated value of the ET coupling matrix element, VAB, is consistently higher in the KT approach than in the MH two-state model. For the carborane molecules functionalized by -CH 2 groups at C-vertices, VAB strongly depends on the relative orientation of the planes containing the terminal -CH 2 groups. The predicted conformation dependence of VAB offers a molecular mechanism to control ET between two active centers in molecular systems.

  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 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.

  19. 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.

  20. Electric field response in bilayer graphene: Ab initio investigation

    NASA Astrophysics Data System (ADS)

    Mori, Yutaro; Minamitani, Emi; Ando, Yasunobu; Kasamatsu, Shusuke; Watanabe, Satoshi

    2016-11-01

    Stimulated by quantum capacitance measurements, we have investigated the electric properties of bilayer graphene (BLG) with carrier doping under an external electric field using ab initio calculations. We found that the relative permittivity of BLG depends weakly on the applied electric field, and that the BLG can be regarded as a dielectric material rather than a pair of metallic films. We also found that carrier doping affects the band gap of BLG under electric fields, although carrier doping has a much smaller effect on the band gap and density of states than the application of electric fields.

  1. Communication: Ab initio Joule-Thomson inversion data for argon.

    PubMed

    Wiebke, Jonas; Senn, Florian; Pahl, Elke; Schwerdtfeger, Peter

    2013-02-21

    The Joule-Thomson coefficient μ(H)(P, T) is computed from the virial equation of state up to seventh-order for argon obtained from accurate ab initio data. Higher-order corrections become increasingly more important to fit the low-temperature and low-pressure regime and to avoid the early onset of divergence in the Joule-Thomson inversion curve. Good agreement with experiment is obtained for temperatures T > 250 K. The results also illustrate the limitations of the virial equation in regions close to the critical temperature.

  2. First fully ab initio potential energy surface of methane with a spectroscopic accuracy

    NASA Astrophysics Data System (ADS)

    Nikitin, A. V.; Rey, M.; Tyuterev, Vl. G.

    2016-09-01

    Full 9-dimensional ab initio potential energy surfaces for the methane molecule are constructed using extended electronic structure coupled-cluster calculations with various series of basis sets following increasing X cardinal numbers: cc-pVXZ (X = 3, 4, 5, 6), aug-cc-ACVXZ (X = 3, 4, 5), and cc-pCVXZ-F12 (X = 3, 4). High-order dynamic electron correlations including triple and quadrupole excitations as well as relativistic and diagonal Born-Oppenheimer breakdown corrections were accounted for. Analytical potential functions are parametrized as non-polynomial expansions in internal coordinates in irreducible tensor representation. Vibrational energy levels are reported using global variational nuclear motion calculations with exact kinetic energy operator and a full account of the tetrahedral symmetry of CH4. Our best ab initio surface including above-mentioned contributions provides the rms (obs.-calc.) errors of less than 0.11 cm-1 for vibrational band centers below 4700 cm-1, and ˜0.3 cm-1 for all 229 assigned experimentally determined vibrational levels up to the Icosad range <7900 cm-1 without empirically adjusted parameters. These results improve the accuracy of ab initio methane vibrational predictions by more than an order of magnitude with respect to previous works. This is an unprecedented accuracy of first-principles calculations of a five-atomic molecule for such a large data set. New ab initio potential results in significantly better band center predictions even in comparison with best available empirically corrected potential energy surfaces. The issues related to the basis set extrapolation and an additivity of various corrections at this level of accuracy are discussed.

  3. 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.

  4. Three-cluster dynamics within an ab initio framework

    DOE PAGES

    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

  5. 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.

  6. Emission Spectroscopy and Ab Initio Calculations for TaN

    NASA Astrophysics Data System (ADS)

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

    2002-10-01

    The emission spectra of TaN have been investigated in the region 3000-35 000 cm -1 using a Fourier transform spectrometer. The spectra were observed in a tantalum hollow-cathode lamp by discharging a mixture of 1.5 Torr of Ne and about 6 mTorr of N 2. In addition to previously known bands, numerous additional bands were observed and assigned to a number of new transitions. The spectroscopic properties of the low-lying electronic states of TaN were also predicted by ab initio calculations. A 1Σ + state, with equilibrium constants of Be=0.457 852 1(48) cm -1, α e=0.002 235 9(67) cm -1, and Re=1.683 099 9(88) Å, has been identified as the ground state of TaN based on our experimental observations supported by the ab initio results. The first excited state has been identified as the a3Δ 1 spin component at 2827 cm -1 above the ground state. To higher energies, the states become difficult to assign because of their Hund's case (c) behavior and extensive interactions between the spin components of the electronic terms.

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

    PubMed

    Chaka, Anne M; Felmy, Andrew R

    2014-09-04

    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.

  8. Unified ab initio approaches to nuclear structure and reactions

    DOE PAGES

    Navratil, Petr; Quaglioni, Sofia; Hupin, Guillaume; ...

    2016-04-13

    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 7Bemore » $${({\\rm{p}},\\gamma )}^{8}{\\rm{B}}$$ radiative capture. Lastly, we highlight our efforts to describe transfer reactions including the 3H$${({\\rm{d}},{\\rm{n}})}^{4}$$He fusion.« less

  9. Implementation of renormalized excitonic method at ab initio level.

    PubMed

    Zhang, Hongjiang; Malrieu, Jean-Paul; Ma, Haibo; Ma, Jing

    2012-01-05

    The renormalized excitonic method [Hajj et al., Phys Rev B 2005, 72, 224412], in which the excited state of the whole system may be described as a linear combination of local excitations, has been implemented at ab initio level. Its performance is tested on the ionization potential and the energy gap between singlet ground state and lowest triplet for linear molecular hydrogen chains and more realistic systems, such as polyenes and polysilenes, using full configuration interaction (FCI) wave functions with a minimal basis set. The influence of different block sizes and the extent of interblock interactions are investigated. It has been demonstrated that satisfactory results can be obtained if the near degeneracies between the model space and the outer space are avoided and if interactions between the next-nearest neighbor blocks are considered. The method can be used with larger basis sets and other accurate enough ab initio evaluations (instead of FCI) of local excited states, from blocks, or from dimers or trimers of blocks. It provides a new possibility to accurately and economically describe the low-lying delocalized excited states of large systems, even inhomogeneous ones.

  10. 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.

  11. Ab initio study of hot electrons in GaAs

    PubMed Central

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

    2015-01-01

    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

  12. 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.

  13. 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.

  14. Ab initio studies of hyperconjugation effects on charge distribution in tetracyclododecane alcohols

    NASA Astrophysics Data System (ADS)

    Tostes, J. Glauco R.; Seidl, Peter Rudolf; Soto, M. M.; De M. Carneiro, J. W.; Lie, S. K.; Taft, C. A.; Brown, W.; Lester, W. A., Jr.

    1995-05-01

    Ab initio calculations using the STO-3G, 6-31G, and 6-31G ∗∗ basis sets are used to investigate charge distribution in tetracyclododecane alcohols. The calculated net atomic charges using fully optimized geometries indicate that certain carbon and hydrogen atoms in the proximity of a nonbonding oxygen lone pair are more negatively charged and the carbon-carbon and carbon-hydrogen bonds are longer. Analysis of these charges and bond lengths as well as atomic orbital populations suggests that the differences between charge distribution on carbon and hydrogen atoms adjacent to the hydroxyl group and their corresponding carbon-carbon and carbon-hydrogen bond lengths can be explained in terms of hyperconjugation.

  15. Ab initio research of energy loss for energetic protons in solid-density Be

    NASA Astrophysics Data System (ADS)

    He, Bin; Meng, Xu-Jun; Wang, Zhi-Gang; Wang, Jian-Guo

    2017-03-01

    Ab initio research of energy loss for energetic protons in solid-density Be is made based on the average atom model. Our results are found in good agreement with the recent experiment for both warm and cool matter. Our results are compared with the local density approximation model and the reason for their difference is also explored. The energy loss at smaller projectile energies is predicted by our model and local density approximation, which helps probe the higher reliability of the proving model and judge the existence of the non-Fermi-Dirac velocity distribution for free electrons exists in dense plasmas in future.

  16. 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.

  17. Structure of alcohol cluster ions in the gas phase, according to spectrometry and ab initio calculations

    NASA Astrophysics Data System (ADS)

    Krisilov, A. V.; Lantsuzskaya, E. V.; Levina, A. M.

    2017-01-01

    Reduced ion mobility and scattering cross sections are calculated from experimentally obtained spectra of the ion mobility of linear aliphatic alcohols with carbon atom numbers from 2 to 9. A linear increase in the scattering cross sections as the molecular weight grows is found. According to the results from experiments and quantum chemical calculations, alcohol cluster ions do not form a compact structure. Neither are dipole moments compensated for during dimerization, in contrast to the aldehydes and ketones described earlier. It was concluded from ab initio calculations that charge delocalization in monomeric and dimeric ions of alcohols increases the dipole moment many times over.

  18. Ab Initio Electronic Structure Calculations of Cytochrome P450 -- Ligand Interactions

    NASA Astrophysics Data System (ADS)

    Segall, M. D.; Payne, M. C.; Ellis, S. W.; Tucker, G. T.

    1997-03-01

    The Cytochrome P450 superfamily of enzymes are of great interest in pharmacology as they participate in an enormous range of physiological processes including drug deactivation and xenobiotic detoxification. We apply ab initio electronic structure calculations to model the interactions of the haem molecule at the P450 active site with substrate and inhibitor ligands. These calculations, based on density function theory, were performed with the CETEP code which uses a plane wave basis set and pseudopotentials to perform efficient LDA, GGA and spin dependent calculations. A change in the spin state of the haem iron atom is observed on binding of a substrate molecule, consistent with the accepted reaction mechanism.

  19. Assessing the Thermoelectric Properties of Sintered Compounds via High-Throughput Ab-Initio Calculations

    NASA Astrophysics Data System (ADS)

    Wang, Shidong; Wang, Zhao; Setyawan, Wahyu; Mingo, Natalio; Curtarolo, Stefano

    2011-10-01

    Several thousand compounds from the Inorganic Crystal Structure Database have been considered as nanograined, sintered-powder thermoelectrics with the high-throughput ab-initio AFLOW framework. Regression analysis unveils that the power factor is positively correlated with both the electronic band gap and the carrier effective mass, and that the probability of having large thermoelectric power factors increases with the increasing number of atoms per primitive cell. Avenues for further investigation are revealed by this work. These avenues include the role of experimental and theoretical databases in the development of novel materials.

  20. 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.

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

    PubMed

    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 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.

  2. 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.

  3. 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.

  4. 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.

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

    NASA Astrophysics Data System (ADS)

    Ohta, Yasuhito; Ohta, Koji; Kinugawa, Kenichi

    2004-01-01

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

  6. Ab initio study of magnetic single layer MPX3 metal-phosphorous-trichalcogenides

    NASA Astrophysics Data System (ADS)

    Chittari, Bheema Lingam; Hwang, Euyheon; Jung, Jeil; MacDonald, Allan H.

    We analyze the electronic structure of two dimensional (2D) MPX3 (M= V, Cr, Mn, Fe, Co, Ni, Cu, Zn, and X = S, Se, Te) transition metal thiophosphates, viewing them as single layer van der Waals materials that can exhibit magnetic order. Our ab initio calculations for MPX3 single layer compounds predict both semiconducting phases with variable band gap sizes and metallic phases, and an intimate interplay between magnetic order and the presence of a gap. A systematic trend of decreasing band gaps in antiferromagnetic states is observed as the chalcogen atoms S, Se, and Te change from smaller to larger atomic number, Ferromagnetic, antiferromagnetic, and nonmagnetic phases, and lattice constant changes accompanied by distortions in crystal symmetry, occur as the metal atom is varied. The sensitive interdependence between magnetic, structural, and electronic properties suggests the important potential of this class of 2D magnetic van der Waals materials for strain and field-effect carrier tunable spintronics.

  7. 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.

  8. 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

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. Ab initio electronic and lattice dynamical properties of cerium dihydride

    NASA Astrophysics Data System (ADS)

    Gurel, Tanju; Eryigit, Resul

    2007-03-01

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

  14. Approximate ab initio calculations of electronic structure of amorphous silicon

    NASA Astrophysics Data System (ADS)

    Durandurdu, M.; Drabold, D. A.; Mousseau, N.

    2000-12-01

    We report on ab initio calculations of electronic states of two large and realistic models of amorphous silicon generated using a modified version of the Wooten-Winer-Weaire algorithm and relaxed, in both cases, with a Keating and a modified Stillinger-Weber potentials. The models have no coordination defects and a very narrow bond-angle distribution. We compute the electronic density-of-states and pay particular attention to the nature of the band-tail states around the electronic gap. All models show a large and perfectly clean optical gap and realistic Urbach tails. Based on these results and the extended quasi-one-dimensional stringlike structures observed for certain eigenvalues in the band tails, we postulate that the generation of model a-Si without localized states might be achievable under certain circumstances.

  15. 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.

  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.

  17. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2011-10-01

    The structural stabilities of the (Zn,Cd)(S,Se,Te)2 dichalcogenides have been determined ab initio. These compounds are shown to be stable in the pyrite phase, in agreement with available experiments. Structural parameters for the ZnTe2 pyrite semiconductor compound proposed here are presented. The opto-electronic properties of these dichalcogenide compounds have been calculated using quasiparticle GW theory. Bandgaps, band structures and effective masses are proposed as well as absorption coefficients and refraction indices. The compounds are all indirect semiconductors with very flat conduction band dispersion and high absorption coefficients. The work functions and surface properties are predicted. The Te and Se based compounds could be of interest as absorber materials in photovoltaic applications.

  19. 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.

  20. 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].

  1. Ab initio electron propagator theory of molecular wires. I. Formalism.

    PubMed

    Dahnovsky, Yu; Zakrzewski, V G; Kletsov, A; Ortiz, J V

    2005-11-08

    Ab initio electron propagator methodology may be applied to the calculation of electrical current through a molecular wire. A new theoretical approach is developed for the calculation of the retarded and advanced Green functions in terms of the electron propagator matrix for the bridge molecule. The calculation of the current requires integration in a complex half plane for a trace that involves terminal and Green's-function matrices. Because the Green's-function matrices have complex poles represented by matrices, a special scheme is developed to express these "matrix poles" in terms of ordinary poles. An expression for the current is derived for a terminal matrix of arbitrary rank. For a single terminal orbital, the analytical expression for the current is given in terms of pole strengths, poles, and terminal matrix elements of the electron propagator. It is shown that Dyson orbitals with high pole strengths and overlaps with terminal orbitals are most responsible for the conduction of electrical current.

  2. Ab initio simulations of liquid carbon monoxide at high pressure

    NASA Astrophysics Data System (ADS)

    Leonhardi, Tanis C.; Militzer, Burkhard

    2017-03-01

    Carbon monoxide occurs as a volatile species in the interiors of terrestrial planets, and as a disequilibrium atmospheric constituent in the giant planets. It plays an important role during the accretionary stages of planet formation reacting with gases to form compounds such as CH4 and H2O. The structure of carbon monoxide is unknown over the majority of the temperature and pressure regime in giant planet interiors. Here we perform ab initio molecular dynamics simulations to characterize CO to 140 GPa and 5,000 K. We find that CO is stable as a molecular liquid at lower P-T conditions, as a polymeric liquid at higher P-T conditions found in ice giant interiors, and as a plasma at high-T.

  3. 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.

  4. An ab initio study on anionic aerogen bonds

    NASA Astrophysics Data System (ADS)

    Esrafili, Mehdi D.; Mohammadian-Sabet, Fariba

    2017-01-01

    An ab initio study is carried out to investigate the anionic aerogen bonds in complexes of KrO3, XeO3 and XeOF2 with F-, Cl-, Br-, CN-, NC-, N3-, SH-, SCN-, NCS-, OH- and OCH3- anions. All of the anionic aerogen bonds analyzed here have a partial covalent character. Charge transfer from the anion to the Kr-O or Xe-O σ∗ orbital stabilizes these complexes and leads to a sizable redshift in the corresponding stretching frequencies. The J(Kr-O) or J(Xe-O) spin-spin coupling constants can be regarded as a useful tool for the characterization of strength of the anionic aerogen-bonded complexes.

  5. Simple calculation of ab initio melting curves: Application to aluminum

    NASA Astrophysics Data System (ADS)

    Robert, Grégory; Legrand, Philippe; Arnault, Philippe; Desbiens, Nicolas; Clérouin, Jean

    2015-03-01

    We present a simple, fast, and promising method to compute the melting curves of materials with ab initio molecular dynamics. It is based on the two-phase thermodynamic model of Lin et al [J. Chem. Phys. 119, 11792 (2003), 10.1063/1.1624057] and its improved version given by Desjarlais [Phys. Rev. E 88, 062145 (2013), 10.1103/PhysRevE.88.062145]. In this model, the velocity autocorrelation function is utilized to calculate the contribution of the nuclei motion to the entropy of the solid and liquid phases. It is then possible to find the thermodynamic conditions of equal Gibbs free energy between these phases, defining the melting curve. The first benchmark on the face-centered cubic melting curve of aluminum from 0 to 300 GPa demonstrates how to obtain an accuracy of 5%-10%, comparable to the most sophisticated methods, for a much lower computational cost.

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

    NASA Astrophysics Data System (ADS)

    Wu, Henry; Mayeshiba, Tam; Morgan, Dane

    2016-07-01

    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.

  7. Ab-initio theory of spin fluctuations in magnets

    NASA Astrophysics Data System (ADS)

    Antropov, Vladimir; Ke, Liqin; van Schilfgaarde, Mark; Katsnelson, Mikhael

    2011-03-01

    We propose a framework for a true ab initio theory of magnetism, based on many-body perturbation theory (MPBT). It fits in naturally with methods based MPBT such as the GW approximation; but the approach can be implemented as an extension to any existing static method for electronic structure such as the local spin density approximation to density functional theory, to include spin fluctuations. Initially we calculated the spin fluctuation contributions using random phase approximation. The self consistency procedure similar to the one used in Moryia-Kawabata theory can be naturally implemented. The fluctuation dissipation theorem is used to calculate the reduction of the mean field magnetic moment in itinerant magnets. The applications of the technique includes traditional 3d ferromagnetic metals, their alloys and compounds and 5f systems.

  8. An Ab Initio Study of Alkali-C60 Complexes

    NASA Astrophysics Data System (ADS)

    Frick, Nathan; Hira, A. S.; Ray, A. K.

    2003-03-01

    We extend our previous work on fullerene-alkali complexes1-2 by presenting the results of an ab initio theoretical study of the alkali LiC60+, LiC60, NaC60+, NaC60, KC60+, and KC60 complexes. In the endohedral complexes for Li and Na, there is displacement of the adatom from the center. Of the ions, exohedral Li+ will sit closest to the cage, and among the neutrals, exohedral K remains closest. Bond lengths are consistently longer for the fivefold and threefold approaches. Adsorbates inside the fullerene donate negative charge to the carbons, but ions outside obtain a small amount, resulting in a polarization of the molecule. In the ion complexes, there is lowering of the orbital energy levels by 3 to 4 eV, resulting in an increase in the number of bound, but unoccupied, electronic orbitals. The HOMO-LUMO gap, of interest in superconductivity studies, is reduced by about 50 1. A.S. Hira and A.K. Ray, Phys. Rev. A 52, 141(1995); A 54, 2205(1996). 2. Ajit Hira and A. K. Ray, "An Initio Modeling of the Endohedral and Exohedral Complexes of C60Na2+ Complexes", Bull. Am. Phys. Soc. 47 (March 2002).

  9. 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.

  10. 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

  11. Ab initio study of He trapping, diffusion and clustering in Y2O3

    NASA Astrophysics Data System (ADS)

    Lai, Wensheng; Ou, Yidian; Lou, Xiaofeng; Wang, Fei

    2017-02-01

    Ab initio calculations have been performed to study the formation and migration energies of helium atoms and the stability of helium-vacancy clusters in a Y2O3 crystal. The calculated formation energies show that a helium atom is preferred to occupy an yttrium vacancy site with a large volume and low electron density. The migration energy of the helium atom by an interstitial mechanism is 0.31 eV. Calculations of the binding energies of an extra helium atom to the helium-vacancy clusters vary with the number of helium atoms in the clusters with a typical value of 0.4-0.7 eV. This turns negative when the He atoms reach saturation; that indicates that vacancy clusters can attract a limited number of helium atoms to form small stable helium-vacancy clusters. Our calculations suggest that the use of Y2O3 in oxide dispersion strengthened ferritic steels may reduce He gas bubble formation as it may act as sink for trapping helium atoms.

  12. 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.

  13. Ab initio path integral ring polymer molecular dynamics: Vibrational spectra of molecules

    NASA Astrophysics Data System (ADS)

    Shiga, Motoyuki; Nakayama, Akira

    2008-01-01

    The path integral ring polymer molecular dynamics method is combined with 'on-the-fly' ab initio electronic structure calculations and applied to vibrational spectra of small molecules, LiH and H 2O, at the room temperature. The results are compared with those of the numerically exact solution and ab initio path integral centroid molecular dynamics calculation. The peak positions in the calculated spectra are found to be reasonable, showing the red-shift due to potential anharmonicity. This unification enables the investigation of real-time quantum dynamics of chemically complex molecular systems on the ab initio Born-Oppenheimer potential energy surface.

  14. Ab initio research of stopping power for energetic ions in solids

    NASA Astrophysics Data System (ADS)

    He, Bin; Meng, Xu-Jun; Wang, Jian-Guo

    2017-03-01

    A new physical scenario is suggested to estimate the stopping power of energetic α particles in solid-density Be, Na, and Al at room temperature in an ab initio way based on the average atom model. In the scenario the stopping power is caused by the transition of free electrons to higher energy states and the ionization of bound electrons of the atom. Our results are found generally in good agreement with the recommended data in Al, Be and Na as well as the experimental data in Al. A comparison of energy loss with the recent experiment of protons in Be indicates that the scenario is more reasonable than the local density approximation in this case.

  15. Ab initio effective core potentials for molecular calculations. Potentials for main group elements Na to Bi

    SciTech Connect

    Wadt, W.R.; Hay, P.J.

    1985-01-01

    A consistent set of ab initio effective core potentials (ECP) has been generated for the main group elements from Na to Bi using the procedure originally developed by Kahn. The ECP's are derived from all-electron numerical Hartree--Fock atomic wave functions and fit to analytical representations for use in molecular calculations. For Rb to Bi the ECP's are generated from the relativistic Hartree--Fock atomic wave functions of Cowan which incorporate the Darwin and mass--velocity terms. Energy-optimized valence basis sets of (3s3p) primitive Gaussians are presented for use with the ECP's. Comparisons between all-electron and valence-electron ECP calculations are presented for NaF, NaCl, Cl/sub 2/, Cl/sub 2//sup -/, Br/sub 2/, Br/sub 2//sup -/, and Xe/sub 2//sup +/. The results show that the average errors introduced by the ECP's are generally only a few percent.

  16. Ab initio calculation of vibrational properties of a-Si:H with inner voids

    NASA Astrophysics Data System (ADS)

    Nakhmanson, S. M.; Drabold, D. A.

    1998-05-01

    We have performed an ab initio calculation of vibrational properties of hydrogenated amorphous silicon (a-Si:H) using a molecular dynamics method. A Wooten, Winer, Weaire (WWW) 216 atom model for pure amorphous silicon (a-Si) updated by Djordjevic, Thorpe and Wooten has been employed as a ``base'' for our a-Si:H models with voids that were made by removing a cluster of silicon atoms out of the bulk and terminating the resulting dangling bonds with hydrogens. Our calculation shows that the presence of voids leads to localized low energy (30-50 cm-1) states in vibrational spectrum of the system. The nature and localization properies of these states are carefully analysed by various visualization techniques. Web resources: http://www.phy.ohiou.edu/ ĩnakhmans/Professional/Bubbles/bubpr.htm

  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

    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.

  19. Trends in magnetism of free Rh clusters via relativistic ab-initio calculations.

    PubMed

    Šipr, O; Ebert, H; Minár, J

    2015-02-11

    A fully relativistic ab-initio study on free Rh clusters of 13-135 atoms is performed to identify general trends concerning their magnetism and to check whether concepts which proved to be useful in interpreting magnetism of 3d metals are applicable to magnetism of 4d systems. We found that there is no systematic relation between local magnetic moments and coordination numbers. On the other hand, the Stoner model appears well-suited both as a criterion for the onset of magnetism and as a guide for the dependence of local magnetic moments on the site-resolved density of states at the Fermi level. Large orbital magnetic moments antiparallel to spin magnetic moments were found for some sites. The intra-atomic magnetic dipole Tz term can be quite large at certain sites but as a whole it is unlikely to affect the interpretation of x-ray magnetic circular dichroism experiments based on the sum rules.

  20. Ab initio based polarizable force field generation and application to liquid silica and magnesia

    NASA Astrophysics Data System (ADS)

    Beck, Philipp; Brommer, Peter; Roth, Johannes; Trebin, Hans-Rainer

    2011-12-01

    We extend the program potfit, which generates effective atomic interaction potentials from ab initio data, to electrostatic interactions and induced dipoles. The potential parametrization algorithm uses the Wolf direct, pairwise summation method with spherical truncation. The polarizability of oxygen atoms is modeled with the Tangney-Scandolo interatomic force field approach. Due to the Wolf summation, the computational effort in simulation scales linearly in the number of particles, despite the presence of electrostatic interactions. Thus, this model allows to perform large-scale molecular dynamics simulations of metal oxides with realistic potentials. Details of the implementation are given, and the generation of potentials for SiO2 and MgO is demonstrated. The approach is validated by simulations of microstructural, thermodynamic, and vibrational properties of liquid silica and magnesia.

  1. Ab initio calculations on peptide-derived oxazoles and thiazoles: Improved molecular mechanics parameters for the AMBER* force field

    NASA Astrophysics Data System (ADS)

    Boden, Christopher D. J.; Pattenden, Gerald

    1999-03-01

    Ab initio calculations at the RHF/6-31G* and MP2/6- 31G*//RHF/6-31G* levels of theory are performed for 2-methyl-4-carboxamido-oxazoles and -thiazoles, including rotational profiles for the ring-carboxamide bond, which showed the expected conjugation and hydrogen bonding effects. On the basis of these data, newly optimised stretch, bend and torsional parameters for the AMBER* force field are derived, along with CHELPG-fitted partial atomic charges.

  2. Ab initio calculation of the potential bubble nucleus 34Si

    NASA Astrophysics Data System (ADS)

    Duguet, T.; Somà, V.; Lecluse, S.; Barbieri, C.; Navrátil, P.

    2017-03-01

    Background: The possibility that an unconventional depletion (referred to as a "bubble") occurs in the center of the charge density distribution of certain nuclei due to a purely quantum mechanical effect has attracted theoretical and experimental attention in recent years. Based on a mean-field rationale, a correlation between the occurrence of such a semibubble and an anomalously weak splitting between low angular-momentum spin-orbit partners has been further conjectured. Energy density functional and valence-space shell model calculations have been performed to identify and characterize the best candidates, among which 34Si appears as a particularly interesting case. While the experimental determination of the charge density distribution of the unstable 34Si is currently out of reach, (d ,p ) experiments on this nucleus have been performed recently to test the correlation between the presence of a bubble and an anomalously weak 1 /2--3 /2- splitting in the spectrum of 35Si as compared to 37S. Purpose: We study the potential bubble structure of 34Si on the basis of the state-of-the-art ab initio self-consistent Green's function many-body method. Methods: We perform the first ab initio calculations of 34Si and 36S. In addition to binding energies, the first observables of interest are the charge density distribution and the charge root-mean-square radius for which experimental data exist in 36S. The next observable of interest is the low-lying spectroscopy of 35Si and 37S obtained from (d ,p ) experiments along with the spectroscopy of 33Al and 35P obtained from knock-out experiments. The interpretation in terms of the evolution of the underlying shell structure is also provided. The study is repeated using several chiral effective field theory Hamiltonians as a way to test the robustness of the results with respect to input internucleon interactions. The convergence of the results with respect to the truncation of the many-body expansion, i.e., with respect to

  3. An analytical ab initio potential surface and the calculated tunneling energies for the HCl dimer

    NASA Astrophysics Data System (ADS)

    Bunker, P. R.; Epa, V. C.; Jensen, Per; Karpfen, Alfred

    1991-03-01

    The six-dimensional potential energy surface of the HCl dimer has been calculated ab initio at 1654 nuclear geometries [A. Karpfen, P. R. Bunker and P. Jensen, Chem. Phys., in press]. In the present paper we have fitted an analytical function to these points; the analytical function is similar to that used previously by us for the potential surface of the HF dimer. The fitted function has 38 adjustable parameters and the standard deviation of the weighted fit is 19.0 cm -1. We have determined the minimum energy path for the trans-bending tunneling motion on this surface, and have calculated the tunneling and K-rotation energies and wavefunctions. Around equilibrium the path is qualitatively similar to that for the HF dimer in that there are two equivalent hydrogen-bonded structures of Cs symmetry (which are approximately L-shaped with a "bound" and a "free" H-atom) that can tunnel through a C2 h saddle point (the "closed" C2 h saddle point). However, away from equilibrium the path is qualitatively different from that found for the HF dimer since the HCl dimer never becomes linear along the path; in fact it passes through a second C2 h saddle point (the "open" C2 h saddle point). As a result the A-rotational constant only varies slightly along the path, and this explains the experimental observation that the tunneling splitting varies little with K-type rotation for the HCl dimer, in contrast to the situation for the HF dimer. Quantitatively it is clear that errors in the ab initio calculation, errors in the fitting of an analytic function to the points, the correction to the path that is caused by the zero point motion in the other vibrations, and the coupling between the four low-frequency modes, will all be relatively more significant than they were for the HF dimer because the full six-dimensional potential is much flatter; the ab initio dissociation energy is only ˜600 cm -1, and the ab initio tunneling barrier is only ˜70 cm -1. Therefore, we modify the

  4. CO oxidation on supported single Pt atoms: experimental and ab initio density functional studies of CO interaction with Pt atom on θ-Al2O3(010) surface.

    PubMed

    Moses-DeBusk, Melanie; Yoon, Mina; Allard, Lawrence F; Mullins, David R; Wu, Zili; Yang, Xiaofan; Veith, Gabriel; Stocks, G Malcolm; Narula, Chaitanya K

    2013-08-28

    Although there are only a few known examples of supported single-atom catalysts, they are unique because they bridge the gap between homogeneous and heterogeneous catalysis. Here, we report the CO oxidation activity of monodisperse single Pt atoms supported on an inert substrate, θ-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 carried out a first-principles density functional theoretical study of a proposed pathway which is a variation on the conventional L-H scheme and inspired by the organometallic chemistry of platinum. We find that a single supported Pt atom prefers to bond to O2 over CO. CO then bonds with the oxygenated Pt atom and forms a carbonate which dissociates to liberate CO2, leaving an oxygen atom on Pt. Subsequent reaction with another CO molecule regenerates the single-atom catalyst. The energetics of the proposed mechanism suggests that the single Pt atoms will get covered with CO3 unless the temperature is raised to eliminate CO2. We find evidence for CO3 coverage at room temperature supporting the proposed mechanism in an in situ diffuse reflectance infrared study of CO adsorption on the catalyst's supported single atoms. Thus, 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 monodisperse Pt/θ-Al2O3 are also presented.

  5. Vibrational spectrum, ab initio calculations, conformational equilibria and torsional modes of 1,3-dichloropropane

    NASA Astrophysics Data System (ADS)

    Duffy, Daniel J.; Quenneville, Jason; Baumbaugh, T. M.; Kitchener, S. A.; McCormick, R. K.; Dormady, C. N.; Croce, T. A.; Navabi, A.; Stidham, Howard D.; Hsu, Shaw L.; Guirgis, Gamil A.; Deng, Shiping; Durig, James R.

    2004-02-01

    Ab initio calculations are reported for three of four possible conformers of 1,3-dichloropropane. The fourth conformer, with C s symmetry, has a predicted enthalpy difference of more than 1500 cm -1 from the most stable conformer from each calculation regardless of the basis set used, so there is little chance of observing it. Thus, there is no evidence in the infrared or Raman spectrum of the presence of a fourth conformer. The order of stability given by the ab initio calculations is C 2(GG)>C 1(AG)>C 2v(AA)>C s(GG'), where A indicates the anti form for one of the CH 2Cl groups and G indicates the gauche conformation for the other CH 2Cl group relative to the plane of the carbon atoms. Almost every band observed can be confidently assigned to one or another of the conformers. Many observed bands proved to be of a composite nature, with several nearly coincident vibrations of different conformers contributing to the band contour. Nonetheless, a complete assignment of fundamentals is possible for the most stable C 2 conformer, and 5 of the fundamentals of the C 2v conformer and 13 those of the C 1 conformer can be confidently assigned.

  6. Ab initio simulation of elastic and mechanical properties of Zn- and Mg-doped hydroxyapatite (HAP).

    PubMed

    Aryal, Sitaram; Matsunaga, Katsuyuki; Ching, Wai-Yim

    2015-07-01

    Hydroxyapatite (HAP) is an important bioceramic which constitutes the mineral components of bones and hard tissues in mammals. It is bioactive and used as bioceramic coatings for metallic implants and bone fillers. HAP readily absorbs a large amount of impurities. Knowledge on the elastic and mechanical properties of impurity-doped HAP is a subject of great importance to its potential for biomedical applications. Zn and Mg are the most common divalent cations HAP absorbs. Using density function theory based ab initio methods, we have carried out a large number of ab initio calculations to obtain the bulk elastic and mechanical properties of HAP with Zn or Mg doped in different concentration at the Ca1 and Ca2 sites using large 352-atom supercells. Detailed information on their dependece on the concetraion of the substitued impurity is obtained. Our results show that Mg enhances overall elastic and bulk mechanical properties whereas Zn tends to degrade except at low concentrations. At a higher concentration, the mechanical properties of Zn and Mg doped HAP also depend significantly on impurity distribution between the Ca1 and Ca2 sites. There is a strong evidence that Zn prefers Ca2 site for substituion whereas Mg has no such preference. These results imply that proper control of dopant concentration and their site preference must carefully considered in using doped HAP for specific biomedical applications.

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

    PubMed

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

    2015-07-05

    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.

  8. Quantum wave packet ab initio molecular dynamics: an approach to study quantum dynamics in large systems.

    PubMed

    Iyengar, Srinivasan S; Jakowski, Jacek

    2005-03-15

    A methodology to efficiently conduct simultaneous dynamics of electrons and nuclei is presented. The approach involves quantum wave packet dynamics using an accurate banded, sparse and Toeplitz representation for the discrete free propagator, in conjunction with ab initio molecular dynamics treatment of the electronic and classical nuclear degree of freedom. The latter may be achieved either by using atom-centered density-matrix propagation or by using Born-Oppenheimer dynamics. The two components of the methodology, namely, quantum dynamics and ab initio molecular dynamics, are harnessed together using a time-dependent self-consistent field-like coupling procedure. The quantum wave packet dynamics is made computationally robust by using adaptive grids to achieve optimized sampling. One notable feature of the approach is that important quantum dynamical effects including zero-point effects, tunneling, as well as over-barrier reflections are treated accurately. The electronic degrees of freedom are simultaneously handled at accurate levels of density functional theory, including hybrid or gradient corrected approximations. Benchmark calculations are provided for proton transfer systems and the dynamics results are compared with exact calculations to determine the accuracy of the approach.

  9. Ab initio study of the SeS local oscillator in zinc sulfide

    NASA Astrophysics Data System (ADS)

    Petzke, K.

    1999-11-01

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

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

    NASA Astrophysics Data System (ADS)

    Boguslawski, Katharina; Jacob, Christoph R.; Reiher, Markus

    2013-01-01

    The reconstruction of the exchange-correlation potential from accurate ab initio electron densities can provide insights into the limitations of the currently available approximate functionals and provide guidance for devising improved approximations for density-functional theory (DFT). For open-shell systems, the spin density is introduced as an additional fundamental variable in spin-DFT. Here, we consider the reconstruction of the corresponding unrestricted Kohn-Sham (KS) potentials from accurate ab initio spin densities. In particular, we investigate whether it is possible to reconstruct the spin exchange-correlation potential, which determines the spin density in unrestricted KS-DFT, despite the numerical difficulties inherent to the optimization of potentials with finite orbital basis sets. We find that the recently developed scheme for unambiguously singling out an optimal optimized potential [Ch. R. Jacob, J. Chem. Phys. 135, 244102 (2011), 10.1063/1.3670414] can provide such spin potentials accurately. This is demonstrated for two test cases, the lithium atom and the dioxygen molecule, and target (spin) densities from full configuration interaction and complete active space self-consistent field calculations, respectively.

  11. 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.

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

    SciTech Connect

    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 NNLO${}_{{\\rm{sat}}}$ 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.

  13. 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.

  14. 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.

  15. 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. ).

  16. 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%).

  17. Determination of structure and acidity scales in zeolite systems by ab initio and pseudopotential calculations

    SciTech Connect

    Kassab, E.; Seiti, K.; Allavena, M.

    1988-11-17

    SCF ab initio calculations at the 6-31G level have been used to investigate the structure of several aggregates simulating some of the proton donor sites within faujasite-type zeolites. The Si(OH)/sub 4/, H/sub 3/SiOHAlH/sub 3/, and (OH)/sub 3/SiOHAl(OH)/sub 3/ clusters have been successively examined. Deprotonation energies and charge distribution are determined at a higher level by using a 6-31G basis set augmented with polarization and diffuse functions. The results are compared with values obtained by using pseudopotential methods. The small differences between the two sets of results demonstrate that comparable accuracy should be expected from both procedures. Finally, deprotonation energies of (OH)/sub 3/T/sub 1/OHT/sub 2/(OH)/sub 3/ aggregates (T/sub 1/, T/sub 2/ = AlSi, BSi, GaSi; AlGe, BGe, GaGe) are calculated by using pseudopotential methods and compared with the results given by the semiempirical MNDO method. In some cases ab initio SCF calculations were also performed. The results confirm that the inclusion of boron atom lowers the acidity as already demonstrated by experimental investigation. The effects due to the inclusion of Ga are discussed and compared to available experimental data.

  18. Ab initio study of structural and magnetic properties of Si-doped Fe2P

    NASA Astrophysics Data System (ADS)

    Delczeg-Czirjak, E. K.; Delczeg, L.; Punkkinen, M. P. J.; Johansson, B.; Eriksson, O.; Vitos, L.

    2010-08-01

    Ab initio electronic-structure methods are used to study the properties of Fe2P1-xSix in ferromagnetic and paramagnetic states. The site preference and lattice relaxation are calculated with the projector augmented wave method as implemented in the Vienna ab initio simulation package. The paramagnetic state is modeled by the disordered local magnetic moment scheme, and the chemical and magnetic disorder is treated using the coherent potential approximation in combination with the exact muffin-tin orbital formalism. The calculated lattice parameters, atomic positions, and magnetic properties are in good agreement with the experimental and other theoretical results. In contrast to the observation, for the ferromagnetic state the body centered orthorhombic structure (bco, space group Imm2&barbelow; ) is predicted to have lower energy than the hexagonal structure (hex, space group P6¯2m ). The zero-point spin fluctuation energy difference is found to be large enough to stabilize the hex phase. For the paramagnetic state, the hex structure is calculated to be the stable phase and the computed total energy versus composition indicates a hex to bco crystallographic phase transition with increasing Si content. The phonon vibrational free energy, estimated from the theoretical equation of state, turns out to stabilize the hexagonal phase, whereas the electronic and magnetic entropies favor the low symmetry orthorhombic structure.

  19. 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.

  20. Ab initio electronic structure and optical conductivity of bismuth tellurohalides

    NASA Astrophysics Data System (ADS)

    Schwalbe, Sebastian; Wirnata, René; Starke, Ronald; Schober, Giulio A. H.; Kortus, Jens

    2016-11-01

    We investigate the electronic structure, dielectric, and optical properties of bismuth tellurohalides BiTe X (X =I , Cl, Br) by means of all-electron density functional theory. In particular, we present the ab initio conductivities and dielectric tensors calculated over a wide frequency range, and compare our results with the recent measurements by Akrap et al. [Phys. Rev. B 90, 035201 (2014), 10.1103/PhysRevB.90.035201], Makhnev et al. [Opt. Spectrosc. 117, 764 (2014), 10.1134/S0030400X14110125], and Rusinov et al. [JETP Lett. 101, 507 (2015), 10.1134/S0021364015080147]. We show how the low-frequency branch of the optical conductivity can be used to identify characteristic intra- and interband transitions between the Rashba spin-split bands in all three bismuth tellurohalides. We further calculate the refractive indices and dielectric constants, which in turn are systematically compared to previous predictions and measurements. We expect that our quantitative analysis will contribute to the general assessment of bulk Rashba materials for their potential use in spintronics devices.

  1. 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.

  2. 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.

  3. 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).

  4. Challenges for large scale ab initio Quantum Monte Carlo

    NASA Astrophysics Data System (ADS)

    Kent, Paul

    2015-03-01

    Ab initio Quantum Monte Carlo is an electronic structure method that is highly accurate, well suited to large scale computation, and potentially systematically improvable in accuracy. Due to increases in computer power, the method has been applied to systems where established electronic structure methods have difficulty reaching the accuracies desired to inform experiment without empiricism, a necessary step in the design of materials and a helpful step in the improvement of cheaper and less accurate methods. Recent applications include accurate phase diagrams of simple materials through to phenomena in transition metal oxides. Nevertheless there remain significant challenges to achieving a methodology that is robust and systematically improvable in practice, as well as capable of exploiting the latest generation of high-performance computers. In this talk I will describe the current state of the art, recent applications, and several significant challenges for continued improvement. Supported through the Predictive Theory and Modeling for Materials and Chemical Science program by the Office of Basic Energy Sciences (BES), Department of Energy (DOE).

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

    DOE PAGES

    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

  6. Ab Initio Study of Covalently Functionalized Graphene and Carbon Nanotubes

    NASA Astrophysics Data System (ADS)

    Jha, Sanjiv; Hammouri, Mahmoud; Vasiliev, Igor; Magedov, Igor; Frolova, Liliya; Kalugin, Nikolai

    2014-03-01

    The electronic and structural properties of carbon nanomaterials can be affected by chemical functionalization. We apply ab initio computational methods based on density functional theory to study the properties of graphene and single-walled carbon nanotubes functionalized with benzyne. Our calculations are carried out using the SIESTA electronic structure code combined with the generalized gradient approximation for the exchange correlation functional. The calculated binding energies, densities of states, and band structures of functionalized graphene and carbon nanotubes are analyzed in comparison with the available experimental data. The surfaces of carbon nanotubes are found to be significantly more reactive toward benzyne molecules than the surface of graphene. The strength of interaction between benzyne and carbon nanotubes is affected by the curvature of the nanotube sidewall. The binding energies of benzyne molecules attached to both semiconducting zigzag and metallic armchair nanotubes increase with decreasing the nanotube diameter. Supported by NSF CHE-1112388, NMSU GREG Award, NSF ECCS-0925988, NIH-5P20RR016480-12, and NIH- P20 GM103451.

  7. 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.

  8. Ab initio liquid water from PBE0 hybrid functional simulations

    NASA Astrophysics Data System (ADS)

    Li, Zhaofeng; Wu, Xifan; Car, Roberto

    2010-03-01

    For reasons of computational efficiency, so far most ab initio molecular dynamics simulations of liquid water have been based on semi-local density functional approximations, such as PBE and BLYP. These approaches yield a liquid structure that, albeit qualitatively correct, is overstructured compared to experiment, even after nuclear quantum effects have been taken into account.footnotetextJ. A. Morrone and R. Car, Phys. Rev. Lett. 101, 017801(2008) A major cause of this inaccuracy is the delocalization error associated to semi-local density functional approximations, which, as a consequence, overestimate slightly the hydrogen bond strength in the liquid. In this work we adopt the PBE0 hybrid functional approximation, which, by mixing a fraction of exact (Hartree-Fock) exchange, reduces significantly the delocalization error of semi-local functionals. Our approach is based on a numerically efficient order-N implementation of exact exchange.footnotetextX. Wu, A. Selloni, and R. Car, Phys. Rev. B 79, 085102(2009) We find that PBE0 systematically improves the agreement of the simulated liquid with experiment. Our conclusion is substantiated by the calculated radial distribution functions, H-bond statistics, and molecular dipole distribution.

  9. Ab initio predictions of the symmetry energy and recent constraints

    NASA Astrophysics Data System (ADS)

    Sammarruca, Francesca

    2017-01-01

    The symmetry energy plays a crucial role in the structure and the dynamics of neutron-rich systems, including the formation of neutron skins, the location of neutron drip lines, as well as intriguing correlations with the structure of compact stars. With experimental efforts in progress or being planned to shed light on the less known aspects of the nuclear chart, microscopic predictions based on ab initio approaches are very important. In recent years, chiral effective field theory has become popular because of its firm connection with quantum chromodynamics and its systematic approach to the development of nuclear forces. Predictions of the symmetry energy obtained from modern chiral interactions will be discussed in the light of recent empirical constraints extracted from heavy ion collisions at 400 MeV per nucleon at GSI. Applications of our equations of state to neutron-rich systems will also be discussed, with particular emphasis on neutron skins, which are sensitive to the density dependence of the symmetry energy.

  10. An efficient approach to ab initio Monte Carlo simulation.

    PubMed

    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(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.

  11. 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.

  12. 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.

  13. 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.

  14. Perovskite transparent conducting oxides: an ab initio study.

    PubMed

    Dabaghmanesh, S; Saniz, R; Amini, M N; Lamoen, D; Partoens, B

    2013-10-16

    We present an ab initio study of the electronic structure and of the formation energies of various point defects in BaSnO3 and SrGeO3. We show that La and Y impurities substituting Ba or Sr are shallow donors with a preferred 1 + charge state. These defects have a low formation energy within all the suitable equilibrium growth conditions considered. Oxygen vacancies behave as shallow donors as well, preferring the 2 + charge state. Their formation energies, however, are higher in most growth conditions, indicating a limited contribution to conductivity. The calculated electron effective mass in BaSnO3, with a value of 0.21 m(e), and the very high mobility reported recently in La-doped BaSnO3 single-crystals, suggest that remarkably low scattering rates can be achieved in the latter. In the case of SrGeO3, our results point to carrier density and mobility values in the low range for typical polycrystalline TCOs, in line with experiment.

  15. Ab initio calculations of nuclear reactions important for astrophysics

    NASA Astrophysics Data System (ADS)

    Navratil, Petr; Dohet-Eraly, Jeremy; Calci, Angelo; Horiuchi, Wataru; Hupin, Guillaume; Quaglioni, Sofia

    2016-09-01

    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. One of the newly developed approaches is the No-Core Shell Model with Continuum (NCSMC), capable of describing both bound and scattering states in light nuclei simultaneously. We will present NCSMC results for reactions important for astrophysics that are difficult to measure at relevant low energies, such as 3He(α,γ)7Be and 3H(α,γ)7Li and 11C(p,γ)12N radiative capture, as well as the 3H(d,n)4He fusion. We will also address prospects of calculating the 2H(α,γ)6Li capture reaction within the NCSMC formalism. Prepared in part by LLNL under Contract DE-AC52-07NA27344. Supported by the U.S. DOE, OS, NP, under Work Proposal No. SCW1158, and by the NSERC Grant No. SAPIN-2016-00033. TRIUMF receives funding from the NRC Canada.

  16. 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.

  17. 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.

  18. Electronic structure and conductivity of ferroelectric hexaferrite: Ab initio calculations

    NASA Astrophysics Data System (ADS)

    Knížek, K.; Novák, P.; Küpferling, M.

    2006-04-01

    Ba0.5Sr1.5Zn2Fe12O22 is a promising multiferroic compound in which the electric polarization is intimately connected to the magnetic state. In principle, ferroelectrity might exist above the room temperature, but the electrical conductivity that increases with increasing temperature limits it to temperatures below ≈130K . We present results of an ab initio electronic structure calculation of the (BaSr)Zn2Fe12O22 system. To improve the description of strongly correlated 3d electrons of iron, the GGA+U method is used. The results show that the electrical conductivity strongly depends on relative fractions of iron and zinc in the tetrahedral sublattice that belongs to the spinel block of the hexaferrite structure. If this sublattice is fully occupied by zinc, the system is an insulator with a gap of ≈1.5eV . If it is occupied equally by Fe and Zn the gap decreases by a factor of 2, and the system is metallic when this sublattice is filled by iron only.

  19. 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.

  20. Ab initio modeling of decomposition in iron based alloys

    NASA Astrophysics Data System (ADS)

    Gorbatov, O. I.; Gornostyrev, Yu. N.; Korzhavyi, P. A.; Ruban, A. V.

    2016-12-01

    This paper reviews recent progress in the field of ab initio based simulations of structure and properties of Fe-based alloys. We focus on thermodynamics of these alloys, their decomposition kinetics, and microstructure formation taking into account disorder of magnetic moments with temperature. We review modern theoretical tools which allow a consistent description of the electronic structure and energetics of random alloys with local magnetic moments that become totally or partially disordered when temperature increases. This approach gives a basis for an accurate finite-temperature description of alloys by calculating all the relevant contributions to the Gibbs energy from first-principles, including a configurational part as well as terms due to electronic, vibrational, and magnetic excitations. Applications of these theoretical approaches to the calculations of thermodynamics parameters at elevated temperatures (solution energies and effective interatomic interactions) are discussed including atomistic modeling of decomposition/clustering in Fe-based alloys. It provides a solid basis for understanding experimental data and for developing new steels for modern applications. The precipitation in Fe-Cu based alloys, the decomposition in Fe-Cr, and the short-range order formation in iron alloys with s-p elements are considered as examples.

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

    PubMed

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

    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(+), Cl(-), and Ag(+) ions. Using the Perdew-Burke-Ernzerhof functional, adapting methods developed for classical force field applications, and with consistent assumptions about surface potential (phi) contributions, we obtain absolute AIMD hydration free energies (DeltaG(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(+)/Cl(-) and Ag(+)/Cl(-) AIMD DeltaG(hyd), which are not affected by surface potentials, are within 2.6% and 1.2 % of experimental values, respectively. We also report the free energy changes associated with the transition metal ion redox reaction Ag(+)+Ni(+)-->Ag+Ni(2+) in water. The predictions for this reaction suggest that existing estimates of DeltaG(hyd) for unstable radiolysis intermediates such as Ni(+) may need to be extensively revised.

  2. 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.

  3. Ab initio Quantum Chemical Reaction Kinetics: Recent Applications in Combustion Chemistry (Briefing Charts)

    DTIC Science & Technology

    2015-06-28

    Charts 3. DATES COVERED (From - To) June 2015-June 2015 4. TITLE AND SUBTITLE AB INITIO QUANTUM CHEMICAL REACTION KINETICS: RECENT APPLICATIONS IN...Unlimited. 13. SUPPLEMENTARY NOTES Briefing Charts presented at 9th Int. Conf. Chemical Kinetics; Ghent, Belgium; 28 Jun 2015. PA#15351. 14. ABSTRACT...ghanshyam.vaghjiani@us.af.mil Ab initio Quantum Chemical Reaction Kinetics: Recent Applications in Combustion Chemistry Ghanshyam L. Vaghjiani* DISTRIBUTION A

  4. Experimental and ab initio study of the mechanical properties of hydroxyapatite

    NASA Astrophysics Data System (ADS)

    Snyders, R.; Music, D.; Sigumonrong, D.; Schelnberger, B.; Jensen, J.; Schneider, J. M.

    2007-05-01

    The authors have studied the elastic properties of radio frequency sputtered phase pure, stoichiometric, and dense hydroxyapatite films by nanoindentation. The measured elastic modulus values have been compared to ab initio calculated data. The calculation technique was based on the determination of all elastic constants. The calculated and measured elastic modulus values differ by ˜10%. The good agreement indicates that the elasticity of hydroxyapatite can be described using ab initio calculations, establishing the elastic modulus thereof.

  5. Ab-initio simulations of materials using VASP: Density-functional theory and beyond.

    PubMed

    Hafner, Jürgen

    2008-10-01

    During the past decade, computer simulations based on a quantum-mechanical description of the interactions between electrons and between electrons and atomic nuclei have developed an increasingly important impact on solid-state physics and chemistry and on materials science-promoting not only a deeper understanding, but also the possibility to contribute significantly to materials design for future technologies. This development is based on two important columns: (i) The improved description of electronic many-body effects within density-functional theory (DFT) and the upcoming post-DFT methods. (ii) The implementation of the new functionals and many-body techniques within highly efficient, stable, and versatile computer codes, which allow to exploit the potential of modern computer architectures. In this review, I discuss the implementation of various DFT functionals [local-density approximation (LDA), generalized gradient approximation (GGA), meta-GGA, hybrid functional mixing DFT, and exact (Hartree-Fock) exchange] and post-DFT approaches [DFT + U for strong electronic correlations in narrow bands, many-body perturbation theory (GW) for quasiparticle spectra, dynamical correlation effects via the adiabatic-connection fluctuation-dissipation theorem (AC-FDT)] in the Vienna ab initio simulation package VASP. VASP is a plane-wave all-electron code using the projector-augmented wave method to describe the electron-core interaction. The code uses fast iterative techniques for the diagonalization of the DFT Hamiltonian and allows to perform total-energy calculations and structural optimizations for systems with thousands of atoms and ab initio molecular dynamics simulations for ensembles with a few hundred atoms extending over several tens of ps. Applications in many different areas (structure and phase stability, mechanical and dynamical properties, liquids, glasses and quasicrystals, magnetism and magnetic nanostructures, semiconductors and insulators, surfaces

  6. Intramolecular SN2 reaction caused by photoionization of benzene chloride-NH3 complex: direct ab initio molecular dynamics study.

    PubMed

    Tachikawa, Hiroto

    2006-01-12

    Ionization processes of chlorobenzene-ammonia 1:1 complex (PhCl-NH3) have been investigated by means of full dimensional direct ab initio molecular dynamics (MD) method, static ab initio calculations, and density functional theory (DFT) calculations. The static ab initio and DFT calculations of neutral PhCl-NH3 complex showed that one of the hydrogen atoms of NH3 orients toward a carbon atom in the para-position of PhCl. The dynamics calculation for ionization of PhCl-NH3 indicated that two reaction channels are competitive with each other as product channels: one is an intramolecular SN2 reaction expressed by a reaction scheme [PhCl-NH3]+-->SN2 intermediate complex-->PhNH3++Cl, and the other is ortho-NH3 addition complex (ortho complex) in which NH3 attacks the ortho-carbon of PhCl+ and the trajectory leads to a bound complex expressed by (PhCl-NH3)+. The mechanism of the ionization of PhCl-NH3 is discussed on the basis of the theoretical results.

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

    PubMed

    Yang, L; Peng, S M; Long, X G; Gao, F; Heinisch, H L; Kurtz, R J; Zu, X T

    2011-01-26

    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 atoms 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 their migration mechanisms are similar. In addition, the formation energies of five different configurations of a H-H pair were determined, revealing that the most stable configuration consists of two H atoms located at the second-neighbor tetrahedral interstitial sites along the hexagonal direction. The formation and relative stabilities of some small He clusters have also been investigated.

  8. Ab initio study of the phononic origin of negative thermal expansion

    NASA Astrophysics Data System (ADS)

    Argaman, Uri; Eidelstein, Eitan; Levy, Ohad; Makov, Guy

    2016-11-01

    Negative thermal expansion is an uncommon phenomenon of theoretical interest. Multiple hypotheses regarding its microscopic origins have been suggested. In this paper, the thermal expansion of a representative semiconductor, Si, and a representative metal, Ti, are calculated ab initio using density-functional perturbation theory. The phonon modes' contributions to the thermal expansion are analyzed and the negative thermal expansion is shown to be dominated by negative mode Grüneisen parameters at specific points on the Brillouin zone boundaries. Thus, the elastic (Debye) theory for negative thermal expansion is shown to be irrelevant for these phenomena. The anomalous behavior of these modes in Ti is shown to be unaffected by an electronic topological transition as previously suggested, instead it arises from complex interplay of atomic displacements of the anomalous mode.

  9. Ab-initio study of quasi one-dimensional Br adsorption on Pt(110)

    NASA Astrophysics Data System (ADS)

    Franchini, Cesare; Redinger, Josef; Podloucky, Raimund

    2001-03-01

    Halogen atoms interact strongly with metal surfaces. For this reason they play an important role in many technologically important processes. The Pt(110) surface is known to reconstruct into an (1x2) structure of "missing-row" type (MR). Its strong anisotropic character can be used as template to prepare single crystal surfaces of Pt-Br-Pt chains, which exhibit quasi one-dimensional (1D) behavior. We present ab-initio investigations based on the Full-potential Linearized Augmented Plane Wave method (FLAPW), as implemented in the FLEUR package, and the Tersoff-Hamann model for simulating STM images. Structural and electronic properties of the Br/Pt(110) surface at half coverage and of the clean Pt(110) surface and its (1x2) MR reconstruction are studied in detail. Results are compared to available LEED and STM data.

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

    SciTech Connect

    Curtiss, L. A.

    1998-08-21

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

  11. Piezoelectricity in two-dimensional materials: Comparative study between lattice dynamics and ab initio calculations

    NASA Astrophysics Data System (ADS)

    Michel, K. H.; ćakır, D.; Sevik, C.; Peeters, F. M.

    2017-03-01

    The elastic constant C11 and piezoelectric stress constant e1 ,11 of two-dimensional (2D) dielectric materials comprising h-BN, 2 H -MoS2 , and other transition-metal dichalcogenides and dioxides are calculated using lattice dynamical theory. The results are compared with corresponding quantities obtained with ab initio calculations. We identify the difference between clamped-ion and relaxed-ion contributions with the dependence on inner strains which are due to the relative displacements of the ions in the unit cell. Lattice dynamics allows us to express the inner-strain contributions in terms of microscopic quantities such as effective ionic charges and optoacoustical couplings, which allows us to clarify differences in the piezoelectric behavior between h-BN and MoS2. Trends in the different microscopic quantities as functions of atomic composition are discussed.

  12. Ab-initio simulations on initial growth steps of high-K oxides on silicon

    NASA Astrophysics Data System (ADS)

    Bloechl, Peter E.

    2003-03-01

    One of the most acute challenges of semiconductor industry is the introduction of new so-called high-K gate oxides. Conventional SiO2 based gate oxides need to be replaced in order to avoid quantum mechanical leakage currents through ultrathin oxide layers. State of the art electronic structure calculations and ab-initio molecular dynamics simulations of the deposition of metals onto silicon and the formation of oxides have been performed. Atomic structure, chemical binding and electronic structure have been analyzed for a wide range of different adsorption structures of Zr, Hf, and Sr on silicon. Silicide formation and the step-wise formation of the oxides have been investigated. Particular emphasis will be given to the formation of the interface between SrTiO3 and silicon (001).

  13. Reactive Monte Carlo sampling with an ab initio potential

    SciTech Connect

    Leiding, Jeff; Coe, Joshua D.

    2016-05-04

    Here, 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 also 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). Furthermore, 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.

  14. Electronic and optical properties of K-doped ZnO: Ab initio study

    NASA Astrophysics Data System (ADS)

    Aimouch, D. E.; Meskine, S.; Hayn, R.; Zaoui, A.; Boukortt, A.

    2016-08-01

    We present the results of ab initio calculations of K-doped ZnO in the wurtzite structure using a supercell of 32 atoms and density functional theory. A complete analysis of its electronic, optical and magnetic properties is provided. The local spin density approximation (LSDA) has been used to analyze the density of states and to understand the K influence at different concentration values. The material is revealed to become a p-type doped semiconductor. The optical constant or refractive index, the dielectric function, and the absorption coefficient were determined and show a good agreement with available experimental data. Potassium doping leads to an absorption peak at about 380 nm. That peak might improve the absorption characteristics of ZnO for solar cell or optical applications.

  15. Ab initio molecular dynamics study on the excitation dynamics of psoralen compounds

    NASA Astrophysics Data System (ADS)

    Nakai, H.; Yamauchi, Y.; Nakata, A.; Baba, T.; Takahashi, H.

    2003-08-01

    Ab initio molecular dynamics (AIMD) simulations are performed for studying the S0→T1 excitation dynamics of psoralen compounds; namely, nonsubstituted psoralen, 5-methoxypsoralen (5-MOP), and 8-methoxypsoralen (8-MOP). The density functional theory calculations at the B3LYP/D95V level are used for evaluating the atomic forces in every AIMD step. The specific behavior of 8-MOP in the T1 state, which has been reported by the experimental study, is found to be due to a unique open-ring structure, which leads to a different spin distribution in comparison with the cases of psoralen and 5-MOP and further to a crossing between the S0 and T1 states.

  16. Ab-initio Study of the Diffusion Mechanisms of Gallium in a Silicon Matrix

    NASA Astrophysics Data System (ADS)

    Levasseur-Smith, Kevin; Mousseau, Normand

    2007-03-01

    We present the results of a study into the diffusion mechanisms of Ga defects in crystalline Si. The dominant neutral configurations for single and multi-atom defects are established by ab-initio calculations using the density functional theory in the LDA approximation, with a LCAO basis as implemented in the SIESTA package. We find formation energies of 0.7 eV and 2.9 eV, respectively, for the substitutional and tetrahedral interstitial defects, while the diatomic substitutional-tetrahedral complex has a formation energy of 2.2 eV. Subsequent calculations using this same DFT package in conjunction with the activation relaxation technique (ART nouveau) allow us to determine possible diffusion pathways as well as their corresponding saddle points and energy barriers.

  17. Ab initio electronic structure, magnetism, and magnetocrystalline anisotropy of UGa2

    NASA Astrophysics Data System (ADS)

    Diviš, Martin; Richter, Manuel; Eschrig, Helmut; Steinbeck, Lutz

    1996-04-01

    Ab initio electronic structure calculations for the intermetallic compound UGa2 were performed using an optimized linear combination of atomic orbitals method based on the local spin density approximation. Three separate calculations were done treating the uranium 5f states as band states and as localized states with occupation two and three, respectively. In the itinerant approach, spin and orbital moments, magnetocrystalline anisotropy, and the Sommerfeld constant were calculated and found to deviate significantly from the related experimental data. In the localized approach, crystal field parameters were obtained for the 5f states, which have been treated by self-interaction corrected local-density theory. This approach with 5f2 occupation is shown to provide reasonable results for the anisotropy of the susceptibility, for the field dependence of the magnetic moments, and for the Sommerfeld constant.

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

    PubMed

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

  19. Thermal transmission at Si/Ge interface: ab initio lattice dynamics calculation

    NASA Astrophysics Data System (ADS)

    Alkurdi, A.; Merabia, S.

    2017-01-01

    We perform lattice dynamics calculations (LD) on silicon/germanium interfaces using ab initio interatomic force constants to predict the interfacial phonon transmission as a function of both phonon frequency and the transmission angle. We carry out a spectral and angular analysis to quantify the contribution of each phonon mode in a given scattering direction. The effect of the interaction range was studied at this interface by taking account of more or less atom layers across the interface. Moreover, we were able to predict the thermal boundary conductance (TBC) as a function of the transmission angle and temperature as well. Our results show that, the thermal energy transmission is highly anisotropic while thermal energy reflection is almost isotropic. In addition, we found that it seems there is a global critical angle of transmission beyond which almost no thermal energy is transmitted. This can be used to device high pass phonon filter via changing the orientation of the interface.

  20. Ab Initio Simulation of Electrical Currents Induced by Ultrafast Laser Excitation of Dielectric Materials

    NASA Astrophysics Data System (ADS)

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

    2014-08-01

    We theoretically investigate the generation of ultrafast currents in insulators induced by strong few-cycle laser pulses. Ab initio simulations based on time-dependent density functional theory give insight into the atomic-scale properties of the induced current signifying a femtosecond-scale insulator-metal transition. We observe the transition from nonlinear polarization currents during the laser pulse at low intensities to tunnelinglike excitation into the conduction band at higher laser intensities. At high intensities, the current persists after the conclusion of the laser pulse considered to be the precursor of the dielectric breakdown on the femtosecond scale. We show that the transferred charge sensitively depends on the orientation of the polarization axis relative to the crystal axis, suggesting that the induced charge separation reflects the anisotropic electronic structure. We find good agreement with very recent experimental data on the intensity and carrier-envelope phase dependence [A. Schiffrin et al., Nature (London) 493, 70 (2013)].

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. Ab initio molecular dynamics of liquid hydrogen chloride

    NASA Astrophysics Data System (ADS)

    Dubois, Vincent; Pasquarello, Alfredo

    2005-03-01

    We carried out an ab initio molecular dynamics simulation of liquid hydrogen chloride (ℓ-HCl) at a temperature of 313 K. Comparison with inelastic neutron scattering data shows that the simulation achieves an overall good description of the structural correlations, improving significantly upon a description based on classical interaction potentials. Despite some minor differences between theory and experiment in the H-H partial structure factor, the simulation gives a description of the hydrogen bonding in impressive agreement with experiment, for both the amount and the bond-length distribution of the bonds. In the simulation, 40% of the molecules are nonbonded, while the hydrogen-bonded chains are short, principally consisting of dimers (25%) and trimers (15%). Neighboring molecules in the simulation are found to form L-shaped arrangements, like in the isolated (HCl)2 dimer and in crystalline phases of HCl. The time correlation of the molecular-axis orientation is found to be characterized by a very short decay time (0.13 ps), consistent with the short length of the hydrogen-bonded chains. Other dynamical properties investigated in this work include the diffusion coefficient and the vibrational density of states. We evaluated the molecular dipole of the HCl molecule in the liquid using a definition based on the coupling of rotational modes to an external electric field. The average dipole moment (1.53 D) derived in this way is found to be considerably larger than for the isolated molecule (1.11 D). Our results show that the dipole moment in ℓ-HCl undergoes large fluctuations, both in orientation and in modulus. Upon the onset of an external field, such dipole fluctuations concur to reduce the fluctuations of the dielectric response.

  6. 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

  7. Ab initio valence-space theory for exotic nuclei

    NASA Astrophysics Data System (ADS)

    Holt, Jason

    2015-10-01

    Recent advances in ab initio nuclear structure theory have led to groundbreaking predictions in the exotic medium-mass region, from the location of the neutron dripline to the emergence of new magic numbers far from stability. Playing a key role in this progress has been the development of sophisticated many-body techniques and chiral effective field theory, which provides a systematic basis for consistent many-nucleon forces and electroweak currents. Within the context of valence-space Hamiltonians derived from the nonperturbative in-medium similarity renormalization group (IM-SRG) approach, I will discuss the importance of 3N forces in understanding and making new discoveries in the exotic sd -shell region. Beginning in oxygen, we find that the effects of 3N forces are decisive in explaining why 24O is the last bound oxygen isotope, validating first predictions of this phenomenon from several years ago. Furthermore, 3N forces play a key role in reproducing spectroscopy, including signatures of doubly magic 22,24O, and physics beyond the dripline. Similar improvements are obtained in new spectroscopic predictions for exotic fluorine and neon isotopes, where agreement with recent experimental data is competitive with state-of-the-art phenomenology. Finally, I will discuss first applications of the IM-SRG to effective valence-space operators, such as radii and E 0 transitions, as well as extensions to general operators crucial for our future understanding of electroweak processes, such as neutrinoless double-beta decay. This work was supported by NSERC and the NRC Canada.

  8. 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.

  9. 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.

  10. Uniaxial phase transition in Si: Ab initio calculations

    NASA Astrophysics Data System (ADS)

    Cheng, C.

    2003-04-01

    Based on a previously proposed thermodynamic analysis, [C. Cheng, W. H. Huang, and H. J. Li, Phys. Rev. B 63, 153202 (2001)] we study the relative stabilities of five Si phases under uniaxial compression using ab initio methods. The five phases are diamond, βSn, simple-hexagonal (sh), simple-cubic, and hexagonal closed-packed structures. The possible phase-transition patterns were investigated by considering the phase transitions between any two chosen phases of the five phases. By analyzing the different contributions to the relative phase stability, we identified the most important factors in reducing the phase-transition pressures at uniaxial compression. We also show that it is possible to have phase transitions occur only when the phases are under uniaxial compression, in spite of no phase transition when under hydrostatic compression. Taking all five phases into consideration, the phase diagram at uniaxial compression was constructed for pressures up to 20 GPa. The stable phases were found to be diamond, βSn, and sh structures, i.e., the same as those when under hydrostatic condition. According to the phase diagram, direct phase transition from the diamond to the sh phase is possible if the applied uniaxial pressures, on increasing, satisfy the condition Px>Pz. Similarly, the sh-to-βSn transition on increasing pressures is also possible if the applied uniaxial pressures are varied from the condition of Px>Pz, on which the phase of sh is stable to the condition Px

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. Methods for Using Ab Initio Potential Energy Surfaces in Studies of Gas-Phase Reactions of Energetic Molecules

    DTIC Science & Technology

    2014-08-20

    Ab Initio Potential Energy Surfaces in Studies of Gas-Phase Reactions of Energetic Molecules The focus of this research was to apply efficient...methods for using ab initio potential energy surfaces (PESs) computed with high levels of quantum chemistry theory to predict chemical reaction properties...in non peer-reviewed journals: Methods for Using Ab Initio Potential Energy Surfaces in Studies of Gas-Phase Reactions of Energetic Molecules Report

  16. 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

  17. Ab initio calculations of the intermolecular chemical shift in nuclear magnetic resonance in the gas phase and for adsorbed species

    NASA Astrophysics Data System (ADS)

    Jameson, Cynthia J.; de Dios, Angel C.

    1992-07-01

    The chemical shifts observed in nuclear magnetic resonance experiments are the differences in shielding of the nuclear spin in different electronic environments. These are known to depend on intermolecular interactions as evidenced by density-dependent chemical shifts in the gas phase, gas-to-liquid shifts, and adsorption shifts on surfaces. We present the results of the first ab initio intermolecular chemical shielding function calculated for a pair of interacting atoms for a wide range of internuclear separations. We used the localized orbital local origin (LORG) approach of Hansen and Bouman and also investigated the second-order electron correlation contributions using second-order LORG (SOLO). The 39Ar shielding in Ar2 passes through zero at some very short distance, going through a minimum, and asymptotically approaches zero at larger separations. The 21Ne shielding function in Ne2 has a similar shape. The Drude model suggests a method of scaling that portion of the shielding function that is weighted most heavily by exp[-V(R)/kT]. The scaling factors, which have been verified in the comparison of 21Ne in Ne2 against 39Ar in Ar2 ab initio results, allows us to project out from the same 39Ar in Ar2 ab initio values the appropriate 129Xe shielding functions in the Xe-Ar, Xe-Kr, and Xe-Xe interacting pairs. These functions lead to temperature-dependent second virial coefficients of chemical shielding which agree with experiments in the gas phase. Ab initio calculations of 39Ar shielding in clusters of argon are used to model the observed 129Xe chemical shifts of Xe, Xe2,...,Xe8 trapped in the cages of zeolite NaA.

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

    DOE PAGES

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

    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

  19. Experimental and ab initio structural studies of liquid Zr[subscript 2]Ni

    SciTech Connect

    Hao, S.G.; Kramer, M.J.; Wang, C.Z.; Ho, K.M.; Nandi, S.; Kreyssig, A.; Goldman, A.I.; Wessels, V.; Sahu, K.K.; Kelton, K.F.; Hyers, R.W.; Canepari, S.M.; Rogers, J.R.

    2009-05-01

    High-energy x-ray diffraction and ab initio molecular-dynamics simulations demonstrate that the short-range order in the deeply undercooled Zr{sub 2}Ni liquid is quite nuanced. The second diffuse scattering peak in the total structure factory sharpens with supercooling, revealing a shoulder on the high-Q side that is often taken to be a hallmark of increasing icosahedral order. However, a Voronoi tessellation indicates that only approximately 3.5% of all the atoms are in an icosahedral or icosahedral-like environment. In contrast, a Honeycutt-Andersen analysis indicates that a much higher fraction of the atoms is in icosahedral (15%--18%) or distorted icosahedral (25%--28%) bond-pair environments. These results indicate that the liquid contains a large population of fragmented clusters with pentagonal and distorted pentagonal faces, but the fully developed icosahedral fragments are rare. Interestingly, in both cases, the ordering changes little over the 500 K of cooling. All metrics show that the nearest-neighbor atomic configurations of the most deeply supercooled simulated liquid (1173 K) differ topologically and chemically from those in the stable C16 compound, even though the partial pair distributions are similar. The most significant structural change upon decreasing the temperature from 1673 to 1173 K is an increase in the population of Zr in Ni-centered clusters. The structural differences between the liquid and the C16 increase the nucleation barrier, explaining glass formation in the rapidly quenched alloys.

  20. Well-characterized sequence features of eukaryote genomes and implications for ab initio gene prediction.

    PubMed

    Huang, Ying; Chen, Shi-Yi; Deng, Feilong

    2016-01-01

    In silico analysis of DNA sequences is an important area of computational biology in the post-genomic era. Over the past two decades, computational approaches for ab initio prediction of gene structure from genome sequence alone have largely facilitated our understanding on a variety of biological questions. Although the computational prediction of protein-coding genes has already been well-established, we are also facing challenges to robustly find the non-coding RNA genes, such as miRNA and lncRNA. Two main aspects of ab initio gene prediction include the computed values for describing sequence features and used algorithm for training the discriminant function, and by which different combinations are employed into various bioinformatic tools. Herein, we briefly review these well-characterized sequence features in eukaryote genomes and applications to ab initio gene prediction. The main purpose of this article is to provide an overview to beginners who aim to develop the related bioinformatic tools.

  1. 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.

  2. Ab initio calculation of (hyper)polarizabilities using a sum-over-states formalism.

    NASA Astrophysics Data System (ADS)

    Taylor, Caroline M.; Chaudhuri, Rajat K.; Potts, Davin M.; Freed, Karl F.

    2001-03-01

    Hyperpolarizabilities are relevant to a wide range of non-linear optical properties. Ab initio computations often require a high level of correlation for accurate determination of β and γ , and especially of thier frequency dependence. While sum-over-states methods are widely used within semi-empirical frameworks, they have not been employed with high level ab initio methods because of the computational costs associated with calculating a sufficient number of states. The effective valence shell Hamiltonian method (H^v) is a highly correlated, size-extensive, ab initio, multireference, perturbative (``perturb-then-diagonalize'') method. A single H^v calculation yields a large number of states, making it ideal for use with the sum-over-states fomalism for determination of molecular properties. The method has been used to calculate the (hyper)polarizabilities of small polyene systems.

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

    NASA Astrophysics Data System (ADS)

    Mischler, C.; Kob, W.; Binder, K.

    2002-08-01

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

  4. Ab Initio potential grid based docking: From High Performance Computing to In Silico Screening

    NASA Astrophysics Data System (ADS)

    de Jonge, Marc R.; Vinkers, H. Maarten; van Lenthe, Joop H.; Daeyaert, Frits; Bush, Ian J.; van Dam, Huub J. J.; Sherwood, Paul; Guest, Martyn F.

    2007-09-01

    We present a new and completely parallel method for protein ligand docking. The potential of the docking target structure is obtained directly from the electron density derived through an ab initio computation. A large subregion of the crystal structure of Isocitrate Lyase, was selected as docking target. To allow the full ab initio treatment of this region special care was taken to assign optimal basis functions. The electrostatic potential is tested by docking a small charged molecule (succinate) into the binding site. The ab initio grid yields a superior result by producing the best binding orientation and position, and by recognizing it as the best. In contrast the same docking procedure, but using a classical point-charge based potential, produces a number of additional incorrect binding poses, and does not recognize the correct pose as the best solution.

  5. Global exploration of the energy landscape of solids on the ab initio level.

    PubMed

    Doll, K; Schön, J C; Jansen, M

    2007-12-14

    Predicting which crystalline modifications can be present in a chemical system requires the global exploration of its energy landscape. Due to the large computational effort involved, in the past this search for sufficiently stable minima has been performed employing a variety of empirical potentials and cost functions followed by a local optimization on the ab initio level. However, this entails the risk of overlooking important modifications that are not modeled accurately using empirical potentials. In order to overcome this critical limitation, we develop an approach to employ ab initio energy functions during the global optimization phase of the structure prediction. As an example, we perform a global exploration of the landscape of LiF on the ab initio level and show that the relevant crystalline modifications are found during the search.

  6. Density-matrix based determination of low-energy model Hamiltonians from ab initio wavefunctions.

    PubMed

    Changlani, Hitesh J; Zheng, Huihuo; Wagner, Lucas K

    2015-09-14

    We propose a way of obtaining effective low energy Hubbard-like model Hamiltonians from ab initio quantum Monte Carlo calculations for molecular and extended systems. The Hamiltonian parameters are fit to best match the ab initio two-body density matrices and energies of the ground and excited states, and thus we refer to the method as ab initio density matrix based downfolding. For benzene (a finite system), we find good agreement with experimentally available energy gaps without using any experimental inputs. For graphene, a two dimensional solid (extended system) with periodic boundary conditions, we find the effective on-site Hubbard U(∗)/t to be 1.3 ± 0.2, comparable to a recent estimate based on the constrained random phase approximation. For molecules, such parameterizations enable calculation of excited states that are usually not accessible within ground state approaches. For solids, the effective Hamiltonian enables large-scale calculations using techniques designed for lattice models.

  7. 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.

  8. 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.

  9. Exploring the speed and performance of molecular replacement with AMPLE using QUARK ab initio protein models.

    PubMed

    Keegan, Ronan M; Bibby, Jaclyn; Thomas, Jens; Xu, Dong; Zhang, Yang; Mayans, Olga; Winn, Martyn D; Rigden, Daniel J

    2015-02-01

    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. 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.

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

    PubMed

    Bryk, Taras; Klevets, Ivan

    2012-12-14

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

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

    PubMed

    Khaliullin, Rustam Z; Kühne, Thomas D

    2013-10-14

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

  13. A density functional and ab initio investigation of the p-aminobenzoic acid molecule

    NASA Astrophysics Data System (ADS)

    Lago, A. F.; Dávalos, J. Z.; de Brito, A. Naves

    2007-08-01

    The p-aminobenzoic acid (C 7H 7NO 2) molecule has been investigated at different levels of theory. DFT methods (B3LYP and PBE1PBE), second order Møller-Plesset perturbation theory (MP2) and composite ab initio methods (G3MP2 and CBS) have been employed, in conjunction with large basis sets. Important informations on the electronic structure and thermochemistry of this molecule have been extracted, and the performance of the density functional and ab initio methods has been evaluated, based on the comparison of the calculated and the available experimental data.

  14. Ab initio approach to the development of interatomic potentials for the shell model of silica polymorphs

    NASA Astrophysics Data System (ADS)

    de Boer, K.; Jansen, A. P. J.; van Santen, R. A.

    1994-06-01

    We have developed a new method for deriving parameters for the shell model of silica polymorphs. All parameters for the shell model are derived in a self-consistent way from ab initio energy surfaces, polarizabilities and dipole moments of small clusters. This yields an ab initio partial charge shell model potential. The predictive power of our potential is demonstrated by presenting predictions for the structure of α-quartz, α-cristobalite, coesite, stishovite and the IR spectrum of α-quartz which are compared with experiment and predictions of the widely used potentials of Jackson and Catlow, and Kramer, Farragher, van Beest and van Santen.

  15. 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.

  16. Solving local structure around dopants in metal nanoparticles with ab initio modeling of X-ray absorption near edge structure

    DOE PAGES

    Timoshenko, J.; Shivhare, A.; Scott, R. W.; ...

    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.

  17. Solving local structure around dopants in metal nanoparticles with ab initio modeling of X-ray absorption near edge structure.

    PubMed

    Timoshenko, Janis; Shivhare, Atal; Scott, Robert W J; Lu, Deyu; Frenkel, Anatoly I

    2016-07-20

    We adopted ab initio X-ray absorption near edge structure (XANES) modeling for structural refinement of local environments around metal impurities in a large variety of materials. Our method enables both direct modeling, where the candidate structures are known, and the inverse modeling, 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 revealing the evolution of local environment of palladium atoms in palladium-doped gold thiolate clusters upon chemical and thermal treatments.

  18. Obtaining detailed structural information about supramolecular systems on surfaces by combining high-resolution force microscopy with ab initio calculations.

    PubMed

    Kawai, Shigeki; Sadeghi, Ali; Xu, Feng; Feng, Xu; Peng, Lifen; Lifen, Peng; Pawlak, Rémy; Glatzel, Thilo; Willand, Alexander; Orita, Akihiro; Otera, Junzo; Goedecker, Stefan; Meyer, Ernst

    2013-10-22

    State-of-the art experimental techniques such as scanning tunneling microscopy have great difficulties in extracting detailed structural information about molecules adsorbed on surfaces. By combining atomic force microscopy and Kelvin probe force microscopy with ab initio calculations, we demonstrate that we can obtain a wealth of detailed structural information about the molecule itself and its environment. Studying an FFPB molecule on a gold surface, we are able to determine its exact location on the surface, the nature of its bonding properties with neighboring molecules that lead to the growth of one-dimensional strips, and the internal torsions and bendings of the molecule.

  19. 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.

  20. 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

  1. Interatomic Coulombic decay in a He dimer: Ab initio potential-energy curves and decay widths

    SciTech Connect

    Kolorenc, Premysl; Kryzhevoi, Nikolai V.; Sisourat, Nicolas; Cederbaum, Lorenz S.

    2010-07-15

    The energy gained by either of the two helium atoms in a helium dimer through simultaneous ionization and excitation can be efficiently transferred to the other helium atom, which then ionizes. The respective relaxation process called interatomic Coulombic decay (ICD) is the subject of the present paper. Specifically, we are interested in ICD of the lowest of the ionized excited states, namely, the He{sup +}(n=2)He states, for which we calculated the relevant potential-energy curves and the interatomic decay widths. The full-configuration interaction method was used to obtain the potential-energy curves. The decay widths were computed by utilizing the Fano ansatz, Green's-function methods, and the Stieltjes imaging technique. The behavior of the decay widths with the interatomic distance is examined and is elucidated, whereby special emphasis is given to the asymptotically large interatomic separations. Our calculations show that the electronic ICD processes dominate over the radiative decay mechanisms over a wide range of interatomic distances. The ICD in the helium dimer has recently been measured by Havermeier et al. [Phys. Rev. Lett. 104, 133401 (2010)]. The impact of nuclear dynamics on the ICD process is extremely important and is discussed by Sisourat et al. [Nat. Phys. 6, 508 (2010)] based on the ab initio data computed in the present paper.

  2. Ab initio based State Specific Modeling of N2+O System

    NASA Astrophysics Data System (ADS)

    Luo, Han

    Nitrogen and atomic oxygen play an important role in high temperature gas systems. Their Zeldovich reaction product nitric oxide not only affects aerothermal loads and emissions of hypersonic vehicles, but also has the possibility to influence the efficiency of hypersonic propulsion. Atomic oxygen induced nitrogen dissociation is another reaction mechanism of the N2+O system. However, due to the difficulty of conducting ground tests, there are no experimental data for this reaction now. Thermo-chemical nonequilibrium could make the problem more difficult since experiments could only track macroscopic gas properties instead of internal energy distribution. On the other hand, current reaction and internal energy exchange models are able to reproduce equilibrium condition. Whether their predictions at nonequilibrium conditions are reliable is still questionable. The work in this thesis employs quasi-classical trajectory (QCT) method based on an ab-initio chemistry calculated potential energy surface for the N2+O system. Through QCT calculations of different initial condition, high fidelity cross sections and rates are obtained. The cross sections are further used to generate a ME-QCT-VT model for vibrational excitation/relaxation, a state-specific exchange (SSE) model and a state-specific dissociation (SSD) model. These models are verified by comparison with direct QCT calculated rates and other experimental data or models. Although there are no flowfield calculations in this work, the models are able to be applied easily in DSMC calculations.

  3. Ab initio study of interaction of helium with edge and screw dislocations in tungsten

    NASA Astrophysics Data System (ADS)

    Bakaev, Alexander; Terentyev, Dmitry; Grigorev, Petr; Posselt, Matthias; Zhurkin, Evgeny E.

    2017-02-01

    The interaction of a single He atom with edge and screw dislocations in tungsten has been studied using ab initio calculations. It was revealed that He is strongly attracted to the core of both dislocations with the interaction energy of -1.3 and -3.0 eV for screw and edge dislocations, respectively, which corresponds to the detrapping temperature in thermal desorption spectroscopy experiments of about 500 K and 1050 K, respectively. The lowest energy positions for He around the dislocation cores are identified and the atomic structures are rationalized on the basis of elasticity theory considerations. Both types of dislocations exhibit a higher binding energy for He as compared to the He-He binding (known as self-trapping) and are weaker traps as compared to a single vacancy. It is, thus, concluded that the strong attraction to dislocation lines can contribute to the nucleation of He clusters in the temperature range which already excludes He self-trapping.

  4. Ab initio transport calculations of molecular wires with electron-phonon couplings

    NASA Astrophysics Data System (ADS)

    Hirose, Kenji; Kobayashi, Nobuhiko

    2009-03-01

    Understanding of electron transport through nanostructures becomes important with the advancement of fabrication process to construct atomic-scale devices. Due to the drastic change of transport properties by contact conditions to electrodes in local electric fields, first-principles calculation approaches are indispensable to understand and characterize the transport properties of nanometer-scale molecular devices. Here we study the transport properties of molecular wires between metallic electrodes, especially focusing on the effects of contacts to electrodes and of the electron-phonon interactions. We use an ab initio calculation method based on the scattering waves, which are obtained by the recursion-transfer-matrix (RTM) method, combined with non-equilibrium Green's function (NEGF) method including the electron-phonon scatterings. We find that conductance shows exponential behaviors as a function of the length of molecular wires due to tunneling process determined by the HOMO-LUMO energy gap. From the voltage drop behaviors inside the molecular wires, we show that the contact resistances are dominant source for the bias drop and thus are related to local heating. We will present the electron-phonon coupling effects at contact on the inelastic scattering and discuss on the local heating and local temperature, comparing them with those of metallic atomic wires.

  5. Comparative study of crystallization process in metallic melts using ab initio molecular dynamics simulations.

    PubMed

    Debela, Tekalign T; Wang, X D; Cao, Q P; Zhang, D X; Jiang, J Z

    2017-03-14

    The crystallization process of liquid metals is studied using ab initio molecular dynamics simulations. The evolution of short-range order during quenching in Pb and Zn liquids is compared with body-centered cubic (bcc) Nb and V, and hexagonal closed-packed (hcp) Mg. We found that the fraction and type of the short-range order depends on the system under consideration, in which the icosahedral symmetry seems to dominate in the body-centered cubic metals. Although the local atomic structures in stable liquids are similar, liquid hcp-like Zn, bcc-like Nb and V can be deeply supercooled far below its melting point before crystallization while the supercooled temperature range in liquid Pb is limited. Further investigations into the nucleation process reveal the process of polymorph selection. In the body-centered cubic systems, the polymorph selection occurs in the supercooled state before the nucleation is initiated, while in the closed-packed systems it starts at the time of onset of crystallization. Atoms with bcc-like lattices in all studied supercooled liquids are always detected before the polymorph selection. It is also found that the bond orientational ordering is strongly correlated with the crystallization process in supercooled Zn and Pb liquids.

  6. Semiconductiong Properties of Clathrates Ba8@Ge43: ab initio Study

    NASA Astrophysics Data System (ADS)

    Eguchi, Haruki; Tsumuraya, Kazuo; Takenaka, Hiroyuki; Suzuki, Akihiko; Tanigaki, Katsumi

    2003-03-01

    The Si-clathrates have been usually synthesized when alkaline or alkaline-earth atoms are coexisted with the host Si atoms, which is also the case for the Ge-clathrates. The I-encapsulating Si-clathrates have been also synthesized recently. In the case of the hydrate clathrates, the formation has been controlled by both the sizes of the endohedral molecules and the hydrophobic interactions of the molecules in the water.[1] We study the mechanism of the clathrate formation through the binding nature of the Si-X and Ge-X dimers, where X is selected elements in the periodic table. We calculate the charge transfers (population analysis), the binding energies, and the bonding distances using the ab-initio molecular dynamics method with planewaves and pseudo-potentials. We discuss the mechanism of the formation of the Si-clathrates comparing with that of the hydrate clathrates and evaluate the stability of clathrates predicted by the present study. [1]E.Dendy Sloan,Jr, Clathrate Hydrates of Natural Gasses, Marcel Dekker, 1998.

  7. Ab Initio study of the diffusion mechanisms of gallium in a silicon matrix

    NASA Astrophysics Data System (ADS)

    Levasseur-Smith, K.; Mousseau, N.

    2008-07-01

    We present the results of a study into the diffusion mechanisms of Ga defects in crystalline Si using ab initio techniques. Five stable neutral configurations for single and multi-atom defects are identified by density-functional theory (DFT) calculations within the local density approximation and using a localized basis set as implemented in the SIESTA package. Formation energy (E_F) calculations on these stable structures show the most likely neutral single-atom defect to be the Ga substitutional, with an EF of 0.7 eV in good agreement with previous work. Charge state studies show the Ga tetrahedral interstitial defect to be in a +1 state for most doping conditions. They also indicate the possibility for a gallium substitutional-tetrahedral interstitial complex to act as a deactivating center for the Ga dopants except in n-doped regime, where the complex adopts a -1 charge state. Migration pathway calculations using SIESTA coupled with the activation relaxation technique (ART nouveau) allow us to determine possible migration paths from the stable configurations found, under various charge states. In general, diffusion barriers decrease as the charge state becomes more negative, suggesting that the presence of Si self-interstitials can enhance diffusion through the kicking out of substitutional Si and by adding negative charge carriers to the system. An overall picture of a possible Ga diffusion and complex formation mechanism is presented based on these results.

  8. Ab initio prediction of superdense tetragonal and monoclinic polymorphs of carbon

    SciTech Connect

    Li, Zhen -Zhen; Wang, Jian -Tao; Xu, Li -Fang; Chen, Changfeng

    2016-11-02

    The design and synthesis of three-dimensional denser carbons are one of the hot issues in condensed matter physics because of their fascinating properties. Here we identify by ab initio calculations several tetragonal and monoclinic polymorphs of carbon that adopt the t32, t32*, m32, and m32* structures in P4¯21c, P43212, P21/c, and C2 symmetry, respectively. These carbon polymorphs have large 32-atom unit cells in all-sp3 bonding networks comprising five- and six-membered rings that are dynamically stable, as verified by a phonon mode analysis. Electronic band structure calculations show that they are insulators with band gaps in the range of 5.19–5.41 eV, close to the calculated band gap of 5.34 eV for diamond. Remarkably, these carbon phases possess an extremely high atom number density exceeding that of diamond. Lastly, the present results establish different types of carbon phases and offer insights into their outstanding structural and electronic properties.

  9. Ab initio prediction of superdense tetragonal and monoclinic polymorphs of carbon

    DOE PAGES

    Li, Zhen -Zhen; Wang, Jian -Tao; Xu, Li -Fang; ...

    2016-11-02

    The design and synthesis of three-dimensional denser carbons are one of the hot issues in condensed matter physics because of their fascinating properties. Here we identify by ab initio calculations several tetragonal and monoclinic polymorphs of carbon that adopt the t32, t32*, m32, and m32* structures in P4¯21c, P43212, P21/c, and C2 symmetry, respectively. These carbon polymorphs have large 32-atom unit cells in all-sp3 bonding networks comprising five- and six-membered rings that are dynamically stable, as verified by a phonon mode analysis. Electronic band structure calculations show that they are insulators with band gaps in the range of 5.19–5.41 eV,more » close to the calculated band gap of 5.34 eV for diamond. Remarkably, these carbon phases possess an extremely high atom number density exceeding that of diamond. Lastly, the present results establish different types of carbon phases and offer insights into their outstanding structural and electronic properties.« less

  10. Ab initio density-functional calculations in materials science: from quasicrystals over microporous catalysts to spintronics

    NASA Astrophysics Data System (ADS)

    Hafner, Jürgen

    2010-09-01

    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.

  11. 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.

  12. Liquid boron: x-ray measurements and ab initio molecular dynamics simulations.

    SciTech Connect

    Price, D. L.; Alatas, A.; Hennet, L.; Jakse, N.; Krishnan, S.; Pasturel, A.; Pozdnyakova, I.; Saboungi, M. L.; Said, A.; Scheunemann, R.; Schirmacher, W.; Sinn, H.; Centre de Recherche sure les Conditions Extremes et Materiaux; Lab. de Physique ed Modelisantion des Milieux Condensees; KLA-Tencor; Containerless Research, Inc.; Univ. Munchen; DESY

    2009-01-01

    We report results of a comprehensive study of liquid boron with x-ray measurements of the atomic structure and dynamics coupled with ab initio molecular dynamics simulations. There is no evidence of survival into the liquid of the icosahedral arrangements that characterize the crystal structures of boron but many atoms appear to adopt a geometry corresponding to the pentagonal pyramids of the crystalline phases. Despite similarities in the melting behavior of boron and silicon, there is little evidence of a significant structural shift with temperature that might suggest an eventual liquid-liquid phase transition. Relatively poor agreement with the observed damping of the sound excitations is obtained with the simple form of mode-coupling theory that has proved successful with other monatomic liquids, indicating that higher-order correlation functions arising from directional bonding and short-lived local structures are playing a crucial role. The large ratio of the high frequency to the isothermal sound velocity indicates a much stronger viscoelastic stiffening than in other monatomic liquids.

  13. Ab initio prediction of superdense tetragonal and monoclinic polymorphs of carbon

    NASA Astrophysics Data System (ADS)

    Li, Zhen-Zhen; Wang, Jian-Tao; Xu, Li-Fang; Chen, Changfeng

    2016-11-01

    The design and synthesis of three-dimensional denser carbons are one of the hot issues in condensed matter physics because of their fascinating properties. Here we identify by ab initio calculations several tetragonal and monoclinic polymorphs of carbon that adopt the t 32 , t 32* , m 32 , and m 32* structures in P 4 ¯21c , P 43212 , P 21/c , and C 2 symmetry, respectively. These carbon polymorphs have large 32-atom unit cells in all-s p3 bonding networks comprising five- and six-membered rings that are dynamically stable, as verified by a phonon mode analysis. Electronic band structure calculations show that they are insulators with band gaps in the range of 5.19-5.41 eV, close to the calculated band gap of 5.34 eV for diamond. Remarkably, these carbon phases possess an extremely high atom number density exceeding that of diamond. The present results establish different types of carbon phases and offer insights into their outstanding structural and electronic properties.

  14. 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.

  15. Hydration of the cyanide ion: an ab initio quantum mechanical charge field molecular dynamics study.

    PubMed

    Moin, Syed Tarique; Hofer, Thomas S

    2014-12-21

    This paper presents an ab initio quantum mechanical charge field molecular dynamics simulation study of the cyanide anion (CN(-)) in aqueous solution where hydrogen bond formation plays a dominant role in the hydration process. Preferential orientation of water hydrogens compared to oxygen atoms was quantified in terms of radial, angular as well as coordination number distributions. All structural results indicate that the water hydrogens are attracted towards CN(-) atoms, thus contributing to the formation of the hydration layer. Moreover, a clear picture of the local arrangement of water molecules around the ellipsoidal CN(-) ion is provided via angular-radial distribution and spatial distribution functions. Apart from the structural analysis, the evaluation of water dynamics in terms of ligand mean residence times and H-bond correlation functions indicates the weak structure making capacity of the CN(-) ion. The similar values of H-bond lifetimes obtained for the NHwat and CHwat bonds indicate an isokinetic behaviour of these H-bonds, since there is a very small difference in the magnitude of the lifetimes. On the other hand, the H-bond lifetimes between water molecules of the hydration shell, and between solute and solvent evidence the slightly stable hydration of the CN(-). Overall, the H-bonding dominates in the hydration process of the cyanide anion enabling it to become soluble in the aqueous environment associated to chemical and biological processes.

  16. 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.

  17. Reaction mechanisms and kinetics of the iminovinylidene radical with NO: Ab initio study

    SciTech Connect

    Hsiao, Ming-Kai; Chung, Yi-Hua; Hung, Yu-Ming; Chen, Hui-Lung

    2014-05-28

    The nitric oxide (NO) is a notorious compound for polluting environment. Recent year, removing nitric oxide from the atmosphere becomes a focus of the investigation. In our work, we study the iminovinylidene (HNCC) radical reacted with NO molecule. The mechanism and kinetic for reaction of the HNCC radical with the NO molecule is investigated via considering the possible channels of the N and O atoms of NO attacking the N and C atoms of the HNCC based on the high level ab initio molecular orbital calculations in conjunction with variational TST and RRKM calculations. The species involved have been optimized at the B3LYP/6-311++G(3df,2p) level and their single-point energies are refined by the CCSD(T)/aug-cc-PVQZ//B3LYP/6-311++G(3df,2p) method. The calculated potential energy surfaces indicated that energetically the most favorable channel for the HNCC + NO reaction was predicted to be the formation of HNC+CNO (P8) product via the addition reaction of the C atom of HNCC radical and the N atom of NO with the head to head orientation. To rationalize the scenario of the calculated results, we also employ the Fukui functions and HSAB theory to seek for a possible explanation. In addition, the reaction rate constants were calculated using VariFlex code, and the results show that the total rate coefficient, k{sub total}, at Ar pressure 760 Torr can be represented with an equation: k{sub total} = 6.433 × 10{sup −11} T {sup 0.100} exp(0.275 kcal mol{sup −1}/RT) at T = 298–3000 K, in units of cm{sup 3} molecule{sup −1} s{sup −1}.

  18. Probing the Sub-cycle AC Stark Shift by means of Attosecond Pulses: An ab initio Study of Transient Absorption

    NASA Astrophysics Data System (ADS)

    Zhao, Di; Telnov, Dmitry A.; Chu, Shih-I.

    2012-06-01

    We report a first fully ab initio theoretical exploration of the sub-cycle dynamical AC Stark shift and broadening of He atoms driven by an attosecond pulse and IR pulse. Since the duration of the UV pulse is much shorter than that of the optical cycle of the IR dressing laser field, the sub-cycle dynamics of the dressed atoms can be unfolded by applying the attosecond pulse at different time delay. A nonperturbative method is developed to calculate the transient absorption spectrum without weak-field limitation. By solving the time-dependent Schr"odinger equation accurately by means of the time-dependent generalized pseudospectral method, we predict novel sub-cycle laser-induced time-dependent AC Stark shift and power broadening of He atoms whose dynamical features are in good agreement with the latest ongoing experiments at UCF. Detailed results will be presented. This work is partially supported by DOE and NSF.

  19. Ab initio path integral molecular dynamics simulation study on the dihydrogen bond of NH4+⋯BeH2

    NASA Astrophysics Data System (ADS)

    Hayashi, Aiko; Shiga, Motoyuki; Tachikawa, Masanori

    2005-07-01

    An ab initio path integral molecular dynamics simulation has been performed to study the quantum and thermal effects of a dihydrogen bonded cation, NH4+⋯BeH2. In this system, an attractive interaction exists between two neighboring hydrogen atoms as N δ- H δ+ ⋯H δ- Be δ+ involving large-amplitude of vibration. Some properties playing a key role for this dihydrogen bonded system, such as the bond length, bond angle, and distribution of atomic charges, are investigated in detail by comparing the results of path integral and classical molecular dynamics with those of the equilibrium structure. It was found that the atomic charges of H δ+ and H δ- are decreased and the dihydrogen H δ+ ⋯H δ- bond length is expanded as the thermal and zero-point quantum effects.

  20. 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.

  1. Ab initio molecular dynamics simulations of a binary system of ionic liquids.

    PubMed

    Brüssel, Marc; Brehm, Martin; Voigt, Thomas; Kirchner, Barbara

    2011-08-14

    This work presents first insights into the structural properties of a binary mixture of ionic liquids from the perspective of ab initio molecular dynamics simulations. Simulations were carried out for a one-to-one mixture of 1-ethyl-3-methyl-imidazolium thiocyanate and 1-ethyl-3-methyl-imidazolium chloride and compared to pure 1-ethyl-3-methyl-imidazolium thiocyanate.

  2. Computer simulation of acetonitrile and methanol with ab initio-based pair potentials

    NASA Astrophysics Data System (ADS)

    Hloucha, M.; Sum, A. K.; Sandler, S. I.

    2000-10-01

    This study address the adequacy of ab initio pair interaction energy potentials for the prediction of macroscopic properties. Recently, Bukowski et al. [J. Phys. Chem. A 103, 7322 (1999)] performed a comprehensive study of the potential energy surfaces for several pairs of molecules using symmetry-adapted perturbation theory. These ab initio energies were then fit to an appropriate site-site potential form. In an attempt to bridge the gap between ab initio interaction energy information and macroscopic properties prediction, we performed Gibbs ensemble Monte Carlo (GEMC) simulations using their developed pair potentials for acetonitrile and methanol. The simulations results show that the phase behavior of acetonitrile is well described by just the pair interaction potential. For methanol, on the other hand, pair interactions are insufficient to properly predict its vapor-liquid phase behavior, and its saturated liquid density. We also explored simplified forms for representing the ab initio interaction energies by refitting a selected range of the data to a site-site Lennard-Jones and to a modified Buckingham (exponential-6) potentials plus Coulombic interactions. These were also used in GEMC simulations in order to evaluate the quality and computational efficiency of these different potential forms. It was found that the phase behavior prediction for acetonitrile and methanol are highly dependent on the details of the interaction potentials developed.

  3. Ab initio prediction of vacancy properties in concentrated alloys: The case of fcc Cu-Ni

    NASA Astrophysics Data System (ADS)

    Zhang, Xi; Sluiter, Marcel H. F.

    2015-05-01

    Vacancy properties in concentrated alloys continue to be of great interest because nowadays ab initio supercell simulations reach a scale where even defect properties in disordered alloys appear to be within reach. We show that vacancy properties cannot generally be extracted from supercell total energies in a consistent manner without a statistical model. Essential features of such a model are knowledge of the chemical potential and imposition of invariants. In the present work, we derive the simplest model that satisfies these requirements and we compare it with models in the literature. As illustration we compute ab initio vacancy properties of fcc Cu-Ni alloys as a function of composition and temperature. Ab initio density functional calculations were performed for SQS supercells at various compositions with and without vacancies. Various methods of extracting alloy vacancy properties were examined. A ternary cluster expansion yielded effective cluster interactions (ECIs) for the Cu-Ni-Vac system. Composition and temperature dependent alloy vacancy concentrations were obtained using statistical thermodynamic models with the ab initio ECIs. An Arrhenius analysis showed that the heat of vacancy formation was well represented by a linear function of temperature. The positive slope of the temperature dependence implies a negative configurational entropy contribution to the vacancy formation free energy in the alloy. These findings can be understood by considering local coordination effects.

  4. 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

    2016-07-07

    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.

  5. Ab initio calculations on the inclusion complexation of cyclobis(paraquat- p-phenylene)

    NASA Astrophysics Data System (ADS)

    Zhang, Ke-Chun; Liu, Lei; Mu, Ting-Wei; Guo, Qing-Xiang

    2001-01-01

    Semiempirical PM3, ab initio HF/3-21g ∗, and DFT B3LYP/6-31g ∗ calculations in vacuum and in solution were performed on the inclusion complexation of cyclobis(paraquat- p-phenylene) with nine symmetric aromatic substrates. A good correlation was found between the theoretical stabilization energies and experimental free energy changes upon complexation.

  6. 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.

  7. An efficient and accurate molecular alignment and docking technique using ab initio quality scoring

    PubMed Central

    Füsti-Molnár, László; Merz, Kenneth M.

    2008-01-01

    An accurate and efficient molecular alignment technique is presented based on first principle electronic structure calculations. This new scheme maximizes quantum similarity matrices in the relative orientation of the molecules and uses Fourier transform techniques for two purposes. First, building up the numerical representation of true ab initio electronic densities and their Coulomb potentials is accelerated by the previously described Fourier transform Coulomb method. Second, the Fourier convolution technique is applied for accelerating optimizations in the translational coordinates. In order to avoid any interpolation error, the necessary analytical formulas are derived for the transformation of the ab initio wavefunctions in rotational coordinates. The results of our first implementation for a small test set are analyzed in detail and compared with published results of the literature. A new way of refinement of existing shape based alignments is also proposed by using Fourier convolutions of ab initio or other approximate electron densities. This new alignment technique is generally applicable for overlap, Coulomb, kinetic energy, etc., quantum similarity measures and can be extended to a genuine docking solution with ab initio scoring. PMID:18624561

  8. Ab-initio kinetics and thermodynamics studies of ammonia-borane for hydrogen storage

    NASA Astrophysics Data System (ADS)

    Miranda, Caetano R.; Ceder, Gerbrand

    2007-03-01

    Ammonia-borane (BH3NH3) is a promising chemical hydrogen storage material given its high gravimetry and volumetric properties. However, the ammonia-borane (AB) thermal hydrogen release is not very efficient, being mainly limited by the kinetics of hydrogenation. Using ab initio calculations, we have investigated the thermodynamics and kinetics of hydrogen release on AB by calculating the free energies of the H2 release reactions for different possible decomposition products. Our results indicate that AB regeneration through the ammonia-borane polymeric and borazine-cyclotriborazane cycles is very unlikely due to the strong exothermic character of the reactions. The kinetics of hydrogen release is further investigated with the recently developed metadynamics method. This method allows us to calculate the multidimensional free energy surface of hydrogen release on AB. Our simulations reveal the atomistic mechanism of hydrogenation and provide the free energies barriers and transition states involved in inter and intramolecule H2 release on AB.

  9. 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

    2016-01-07

    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.

  10. Investigation of Co-Doped ZnO Nanowires by X-ray Absorption Spectroscopy and Ab Initio Simulation

    NASA Astrophysics Data System (ADS)

    Chu, Manh Hung; Nguyen, Van Duy; Nguyen, Duc Hoa; Nguyen, Van Hieu

    2017-01-01

    The local structure of single room- and high-temperature Co-implanted ZnO nanowires with subsequent thermal annealing has been studied using hard-x-ray techniques in combination with ab initio Zn K-edge x-ray absorption near-edge structure (XANES) simulations. X-ray fluorescence data reveal a homogeneous distribution of Co atoms/ions with concentration of about 0.1 at.% to 0.3 at.% in the nanowires. XANES data indicate substitutional incorporation of Co2+ ions at Zn sites in both types of nanowire. Improved structural order around Co atoms is obtained in nanowires with high-temperature ion implantation followed by thermal annealing. The ab initio Zn K-edge simulations not only confirm recovery of implantation-induced damage in the ZnO host lattice by the thermal annealing process, but also assist in studying the effect of oxygen vacancies in the Zn K-edge XANES spectra. Microphotoluminescence data certify that high-temperature ion implantation with subsequent thermal annealing is an effective approach to achieve the strongest optical activation of Co ions and good energy transfer to Co ions from the ZnO host matrix.

  11. Systematic ab initio study of the electronic and magnetic properties of different pure and mixed iron systems

    SciTech Connect

    Izquierdo, J.; Vega, A.; Balbas, L. C.; Sanchez-Portal, Daniel; Junquera, Javier; Artacho, Emilio; Soler, Jose M.; Ordejon, Pablo

    2000-05-15

    We present a theoretical study of the electronic and magnetic properties of iron systems in different environments: pure iron systems [dimer, bcc bulk, (100) surface, and free-standing iron monolayer], and low-dimensional iron systems deposited on Ag (100) surface (monoatomic linear wires, iron monolayer, planar, and three-dimensional clusters). Electronic and magnetic properties have been calculated using a recently developed total-energy first-principles method based on density-functional theory with numerical atomic orbitals as a basis set for the description of valence electrons and nonlocal pseudopotentials for the atomic core. The Kohn-Sham equations are solved self-consistently within the generalized gradient approximation for the exchange-correlation potential. Tests on the pseudopotential, the basis set, grid spacing, and k sampling are carefully performed. This technique, which has been proved to be very efficient for large nonmagnetic systems, is applied in this paper to calculate electronic and magnetic properties of different iron nanostructures. The results compare well with previous ab initio all-electron calculations and with experimental data. The method predicts the correct trends in the magnetic moments of Fe systems for a great variety of environments and requires a smaller computational effort than other ab initio methods. (c) 2000 The American Physical Society.

  12. 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.

  13. 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.

  14. 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.

  15. Ab-initio study of free standing TiO2 clusters: Stability and magnetism

    NASA Astrophysics Data System (ADS)

    Rana, T. H.; Kumar, Pankaj; Solanki, A. K.; Skomski, R.; Kashyap, A.

    2013-05-01

    We report the structural behavior of nanoscale Titanium Dioxide (TiO2) clusters as well as their magnetic properties by varying the cluster size with the help of ground state geometries. The clusters of atomic scale rutile (TiO2)n, where n = 1-11, have been considered and geometrically stabilized through the Density Functional Theory as implemented in Vienna ab-initio Simulation Package. It is being observed that as the size of cluster increases from n = 2 to 11, the total energy decreases. The results of formation energy reveal the fact that as the cluster grows, it moves towards the stability and it is observed that n = 11 is the most stable structure. The stabilized clusters are different in geometries and co-ordination numbers. Finally, all the clusters have been investigated with self consistent treatment of spin orbit coupling for magnetism studies. The magnetic properties of free clusters depict oscillatory behavior for magnetic moment with respect to the cluster size.

  16. Ab initio study of the Br(2P)-HBr van der Waals complex.

    PubMed

    Toboła, R; Chałasiński, G; Kłos, J; Szcześniak, M M

    2009-05-14

    This study reports an ab initio characterization of a prereactive van der Waals complex between an open-shell atom Br((2)P) and a closed shell molecule HBr. The three adiabatic potential surfaces 1 (2)A('), 2 (2)A('), and 1 (2)A("), which result from the splitting of degenerate P state of Br are obtained from coupled cluster calculations. The coupling between same-symmetry states is calculated by multireference configuration-interaction method. A transformation to a diabatic representation and inclusion of the spin-orbit coupling effects on the interactions are also discussed. Bound states are calculated using an adiabatic bender model. The global minimum on the lowest adiabatic potential surface corresponds to a T-shaped geometry and has a well depth of D(e)=762.5 cm(-1) at R(e)=3.22 A. A secondary minimum occurs for a hydrogen-bonded geometry with D(e)=445.3 cm(-1) at R(e)=4.24 A. Upon inclusion of spin-orbit coupling the hydrogen-bonded minimum remains at the same depth, but the T-shaped minimum washes out to less than half of its spin-free value. The lowest bound state is localized in the linear minimum. The spin-orbit coupling plays a very important role in shaping of the potential energy surfaces of Br-HBr.

  17. A theoretical study of benzaldehyde derivatives as tyrosinase inhibitors using Ab initio calculated NQCC parameters

    PubMed Central

    Rafiee, Marjan; Javaheri, Masoumeh

    2015-01-01

    Tyrosinase is a multifunctional copper-containing enzyme. It can catalyze two distinct reactions of melanin synthesis and benzaldehyde derivatives, which are potential tyrosinase inhibitors. To find the relationships between charge distributions of benzaldehyde and their pharmaceutical behavior, the present study aimed at investigating nuclear quadrupole coupling constants of quadrupolare nuclei in the functional benzaldehyde group and calculating some its derivatives. In addition, the differences between the electronic structures of various derivatives of this depigmenting drug were examined. All ab initio calculations were carried out using Gaussian 03. The results predicted benzaldehyde derivatives to be bicentral inhibitors; nevertheless, the oxygen or hydrogen contents of the aldehyde group were not found to be the only active sites. Furthermore with the presence of the aldehyde group, the terminal methoxy group in C4 was found to contribute to tyrosinase inhibitory activities. In addition, an oxygen atom with high charge density in the side chain was found to play an important role in its inhibitory effect. PMID:27844007

  18. Spectroscopic fingerprints of toroidal nuclear quantum delocalization via ab initio path integral simulations.

    PubMed

    Schütt, Ole; Sebastiani, Daniel

    2013-04-05

    We investigate the quantum-mechanical delocalization of hydrogen in rotational symmetric molecular systems. To this purpose, we perform ab initio path integral molecular dynamics simulations of a methanol molecule to characterize the quantum properties of hydrogen atoms in a representative system by means of their real-space and momentum-space densities. In particular, we compute the spherically averaged momentum distribution n(k) and the pseudoangular momentum distribution n(kθ). We interpret our results by comparing them to path integral samplings of a bare proton in an ideal torus potential. We find that the hydroxyl hydrogen exhibits a toroidal delocalization, which leads to characteristic fingerprints in the line shapes of the momentum distributions. We can describe these specific spectroscopic patterns quantitatively and compute their onset as a function of temperature and potential energy landscape. The delocalization patterns in the projected momentum distribution provide a promising computational tool to address the intriguing phenomenon of quantum delocalization in condensed matter and its spectroscopic characterization. As the momentum distribution n(k) is also accessible through Nuclear Compton Scattering experiments, our results will help to interpret and understand future measurements more thoroughly.

  19. 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.

  20. High-level ab initio studies of hydrogen abstraction from prototype hydrocarbon systems.

    PubMed

    Temelso, Berhane; Sherrill, C David; Merkle, Ralph C; Freitas, Robert A

    2006-09-28

    Symmetric and nonsymmetric hydrogen abstraction reactions are studied using state-of-the-art ab initio electronic structure methods. Second-order Møller-Plesset perturbation theory (MP2) and the coupled-cluster singles, doubles, and perturbative triples [CCSD(T)] methods with large correlation consistent basis sets (cc-pVXZ, where X = D,T,Q) are used in determining the transition-state geometries, activation barriers, and thermodynamic properties of several representative hydrogen abstraction reactions. The importance of basis set, electron correlation, and choice of zeroth-order reference wave function in the accurate prediction of activation barriers and reaction enthalpies are also investigated. The ethynyl radical (*CCH), which has a very high affinity for hydrogen atoms, is studied as a prototype hydrogen abstraction agent. Our high-level quantum mechanical computations indicate that hydrogen abstraction using the ethynyl radical has an activation energy of less than 3 kcal mol(-1) for hydrogens bonded to an sp(2) or sp(3) carbon. These low activation barriers further corroborate previous studies suggesting that ethynyl-type radicals would make good tooltips for abstracting hydrogens from diamondoid surfaces during mechanosynthesis. Modeling the diamond C(111) surface with isobutane and treating the ethynyl radical as a tooltip, hydrogen abstraction in this reaction is predicted to be barrierless.

  1. Ab initio molecular dynamics simulations of low energy recoil events in MgO

    DOE PAGES

    Petersen, B. A.; Liu, B.; Weber, W. J.; ...

    2017-01-11

    In this paper, low-energy recoil events in MgO are studied using ab initio molecular dynamics simulations to reveal the dynamic displacement processes and final defect configurations. Threshold displacement energies, Ed, are obtained for Mg and O along three low-index crystallographic directions, [100], [110], and [111]. The minimum values for Ed are found along the [110] direction consisting of the same element, either Mg or O atoms. Minimum threshold values of 29.5 eV for Mg and 25.5 eV for O, respectively, are suggested from the calculations. For other directions, the threshold energies are considerably higher, 65.5 and 150.0 eV for Omore » along [111] and [100], and 122.5 eV for Mg along both [111] and [100] directions, respectively. These results show that the recoil events in MgO are partial-charge transfer assisted processes where the charge transfer plays an important role. Finally, there is a similar trend found in other oxide materials, where the threshold displacement energy correlates linearly with the peak partial-charge transfer, suggesting this behavior might be universal in ceramic oxides.« less

  2. Ab initio investigation into the stability and electronic properties of GaN-nanowires

    NASA Astrophysics Data System (ADS)

    Carter, D. J.; Gale, J. D.; Delley, B.; Stampfl, C.

    2006-03-01

    Recent reports of successful fabrication of high quality gallium nanostructures such as quantum dots, nanocrystallites and nanowires, eg. [1], open the door to their possible role as important nanoscale building blocks for future optoelectronic, high-temperature/power and spintronic device applications. In the present work we perform ab initio calculations, using the DMol^3 [2] and SIESTA [3] codes, for wurtzite GaN nanowires. We have examined nanowires in the [0001], [1010], and [1120] directions, and investigated the stability, electronic and atomic structures as a function of nanowire radius. We found that only nanowires in the [0001] direction are stable, and that wires in the other directions can be stabilised by saturating dangling bonds with hydrogen. We have also investigated the properties of key point defects and dopants. [1] J. C. Johnson, et al. Nature Materials 1, 106 (2002). [2] B. Delley, J. Chem. Phys. 92, 508 (1990); ibid 113, 7756 (2000). [3] J.M. Soler, et al. J. Phys.: Condens. Matter. 14, 2745 (2002).

  3. Ab initio Determination of Formation Energies and Charge Transfer Levels of Charged Ions in Water

    NASA Astrophysics Data System (ADS)

    Vatti, Anoop Kishore; Todorova, Mira; Neugebauer, Joerg

    The ability to describe the complex atomic and electronic structure of liquid water and hydrated ions on a microscopic level is a key requirement to understand and simulate electro-chemical and biological processes. Identifying theoretical concepts which enable us to achieve an accurate description in a computationally efficient way is thereby of central importance. Aiming to unravel the importance and influence of different contributions on the hydration energy of ions we perform extensive ab-initio molecular dynamics simulations for charged and neutral cations (Zn, Mg) and anions (Cl, Br, I) in water. The structural correlations and electronic properties of the studied ions are analysed and compared to experimental observations. Following an approach inspired by the defect chemistry in semiconductors and aligning the water band edges on an absolute scale allows us to benchmark the calculated formation energies, identify transition states and compare the results to experiment. Based on these results we discuss the performance of various DFT xc-functionals to predict charge transfer levels and photo-emission experiments.

  4. Electronic and magnetic properties of α-MnO2 from ab initio calculations

    NASA Astrophysics Data System (ADS)

    Crespo, Y.; Seriani, N.

    2013-10-01

    α-MnO2, an active catalyst for oxygen reduction and evolution reactions, has been investigated using ab initio calculations with different exchange-correlation functionals: the generalized-gradient approximation in the version of Perdew, Burke, and Ernzerhof (PBE), PBE+U, and hybrid functionals. Both hybrid functionals and PBE+U (U≥2.0 eV) fail to capture the antiferromagnetic (AFM) ground state found experimentally, and a ferromagnetic configuration has the lowest energy. An AFM ground state is then recovered when using PBE or PBE+U (U≤1.6 eV). Interestingly, a reduction of the gap is observed at increasing values of the U parameter. We offer a qualitative explanation for the change in the calculated ground state employing the results for the electronic structure and physical arguments similar to those exposed in the Goodenough-Kanamori-Anderson rules. It is argued that the pz orbital of oxygen atoms with sp2 hybridization plays a fundamental role in the superexchange AFM interaction and in the reduction of the gap.

  5. Valley Hall effect in silicene and hydrogenated silicene ruled by grain boundaries: An ab initio investigation

    NASA Astrophysics Data System (ADS)

    Miwa, R. H.; Kagimura, R.; Lima, Matheus P.; Fazzio, A.

    2015-05-01

    We have performed an ab initio theoretical study of the energetic stability and the electronic properties of pristine and hydrogen-adsorbed grain boundaries (GBs) in silicene. We find that GBs in silicene present lower formation energy when compared with their counterparts in graphene. Removing the inversion symmetry, by applying an external electric field perpendicular to the silicene sheet, we verify the formation of valley-indexed metallic states lying along the GBs, characterizing the quantum valley Hall effect (QVHE). Here, we find the maintenance of the QVHE upon the presence of disordered and asymmetric geometries along the GBs. Those metallic states are suppressed upon the adsorption of H adatoms along the GBs. The H adatoms promote an unbalance on the electronic occupation of the unsaturated π electrons beside the hydrogenated GB rows, giving rise to (i) a net magnetic moment on the Si atoms along the edge sites of the hydrogenated GBs and (ii) an electronic band structure characterized by spin-polarized valley states protected against backscattering processes.

  6. Ab initio calculation of optical constants from visible to x-ray energies

    NASA Astrophysics Data System (ADS)

    Prange, M. P.; Rivas, G.; Ankudinov, A. L.; Rehr, J. J.

    2004-03-01

    We present a semi-automated approach for ab initio calculations of optical constants of materials from the visible to the hard x-ray energies. The approach is based on a generalization of the real space Green's formalism implemented in the FEFF8 spectroscopy code to include optical spectra. The method includes self-consistent potentials, core-hole and self-energy effects, inelastic losses and a full- or high order multiple-scattering. The procedure is based on calculations of the imaginary part of the dielectric function ɛ2 summed over all edges, from which other optical constants are derived using Kramers-Kronig transforms and analytical relations. These constants include the complex index of refraction, the real part of the dielectric function, and energy loss spectra. In contrast to standard atomic tables, the calculations include solid-state corrections, such as fine structure, Debye-Waller factors, lifetime broadening, etc. Typical results for several materials are presented and compared with experiment.

  7. Ab initio Calculations of Relaxations and Miscibility in Pt(111)-Sn System

    NASA Astrophysics Data System (ADS)

    Fei, Weibin; Staikov, Pavlin; Rahman, Talat S.

    1997-03-01

    We will present first the studies of the structure, surface energy, surface stress and workfunction of clean Pt(111), using ab initio, norm-conserving, non-local and soft pseudopotentials with a plane wave basis. A preconditioned steepest descent method (N. Chetty, M. Weinert, T. S. Rahman, and J. W. Davenport, Phys. Rev. B 52) (1995) 6313. is used to solve iteratively Kohn-Sham equations for a given set of atomic positions. For Pt(111) we find an outward relaxation of 0.75% for the top layer and a surface energy 0.119 eV/Åin reasonable agreement with available experimental data and other theoretical calculations. We discuss the convergence of the results with the number of layers included in the supercell and k-point sampling. The local electronic densities of states are evaluated to examine the relative contributions of the s, p, and d orbitals. Next, the electronic structural properties are calculated in the presence of Sn as an impurity. The impact of Sn on the local density of states and the nature of the Pt-Sn bond is assessed.

  8. 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.

  9. 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.

  10. 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.

  11. 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).

  12. 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).

  13. Can DNA-binding proteins of replisome tautomerize nucleotide bases? Ab initio model study.

    PubMed

    Brovarets', Ol'ha O; Yurenko, Yevgen P; Dubey, Igor Ya; Hovorun, Dmytro M

    2012-01-01

    Ab initio quantum-chemical study of specific point contacts of replisome proteins with DNA modeled by acetic acid with canonical and mutagenic tautomers of DNA bases methylated at the glycosidic nitrogen atoms was performed in vacuo and continuum with a low dielectric constant (ϵ ∼ 4) corresponding to a hydrophobic interface of protein-nucleic acid interaction. All tautomerized complexes were found to be dynamically unstable, because the electronic energies of their back-reaction barriers do not exceed zero-point vibrational energies associated with the vibrational modes whose harmonic vibrational frequencies become imaginary in the transition states of the tautomerization reaction. Additionally, based on the physicochemical arguments, it was demonstrated that the effects of biomolecular environment cannot ensure dynamic stabilization. This result allows suggesting that hypothetically generated by DNA-binding proteins of replisome rare tautomers will have no impact on the total spontaneous mutation due to the low reverse barrier allowing a quick return to the canonical form.

  14. Ab initio study of He-He interactions in homogeneous electron gas

    NASA Astrophysics Data System (ADS)

    Wang, Jinlong; Niu, Liang-Liang; Zhang, Ying

    2017-02-01

    We have investigated the immersion energy of a single He and the He-He interactions in homogeneous electron gas using ab initio calculations. It is found that He dislikes electrons and He-He interact via the He induced Friedel oscillations of electron densities. A critical electron density at which the global binding energy extremum shifts from the first minimum to the second one is identified. We also discover that the He-He global binding energy minimum of ∼-0.09 eV is reached at an optimal electron density of 0.04 e/Å3, corresponding to an optimal He-He separation of ∼1.7 Å. Further, the He atoms are found to gain a trivial amount of 2s and 2p states from the free electrons, inducing a hybridization between the He s- and p-states. The present results can qualitatively interpret the well-known He self-trapping behavior in metals.

  15. 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.

  16. Superhard F-carbon predicted by ab initio particle-swarm optimization methodology.

    PubMed

    Tian, Fei; Dong, Xiao; Zhao, Zhisheng; He, Julong; Wang, Hui-Tian

    2012-04-25

    A simple (5 + 6 + 7)-sp(3) carbon (denoted as F-carbon) with eight atoms per unit cell predicted by a newly developed ab initio particle-swarm optimization methodology on crystal structure prediction is proposed. F-carbon can be seen as the reconstruction of AA-stacked or 3R-graphite, and is energetically more stable than 2H-graphite beyond 13.9 GPa. Band structure and hardness calculations indicate that F-carbon is a transparent superhard carbon with a gap of 4.55 eV at 15 GPa and a hardness of 93.9 GPa at zero pressure. Compared with the previously proposed Bct-, M- and W-carbons, the simulative x-ray diffraction pattern of F-carbon also well matches the superhard intermediate phase of the experimentally cold-compressed graphite. The possible transition route and energy barrier were observed using the variable cell nudged elastic band method. Our simulations show that the cold compression of graphite can produce some reversible metastable carbons (e.g. M- and F-carbons) with energy barriers close to diamond or lonsdaleite.

  17. 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.

  18. 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).

  19. 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.

  20. Nitrogen Molecule-Ethylene Sulfide Complex Investigated by Fourier Transform Microwave Spectroscopy and AB Initio Calculation

    NASA Astrophysics Data System (ADS)

    Iwano, Sakae; Kawashima, Yoshiyuki; Hirota, Eizi

    2016-06-01

    We have systematically investigated the van der Waals complexes consisting of the one from each of the two groups: (Rg, CO, N_2 or CO_2) and (dimethyl ether, dimethyl sulfide, ethylene oxide or ethylene sulfide), by using Fourier transform microwave spectroscopy supplemented by ab initio MO calculations, in order to understand the dynamical behavior of van der Waals complexes and to obtain information on the potential function to internal motions in complexes. Two examples of the N_2 complex were investigated: N_2-DME (dimethyl ether), for which we reported a preliminary result and N_2-EO (ethylene oxide). In the present study we focused attention to the N_2-ES (ethylene sulfide) complex. We have detected two sets of the {b}-type transitions for the 15N_2-ES in ortho and para states, and have analyzed them by using the asymmetric-rotor program of {A}-reduction. In contrast with the N_2-EO, for which each of the ortho and para states were found split into a strong/weak pair, only some transitions of the 15N_2-ES were accompanied by two or three components. The observed spectra of the 14N_2-ES were complicated because of hyperfine splittings due to the nuclear quadrupole coupling of the two nitrogen atoms. We concluded that the N_2 moiety was located in the plane perpendicular to the C-S-C plane and bisecting the CSC angle of the ES. Two isomers were expected to exist for 15NN-ES, one with 15N in the inner and the other in the outer position, and in fact two sets of the spectra were detected. We have carried out ab initio molecular orbital calculations at the level of MP2 with basis sets 6-311++G(d, p), aug-cc-pVDZ, and aug-cc-pVTZ, to complement the information on the intracomplex motions obtained from the observed rotational spectra. Y. Kawashima, A. Sato, Y. Orita, and E. Hirota, J. Phys. Chem. A, 2012 116, 1224 Y. Kawashima, Y. Tatamitani, Y. Morita, and E. Hirota, 61st International Symposium on Molecular Spectroscopy, TE10 (2006) Y. Kawashima and E. Hirota, J

  1. 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

  2. Mn doped InP nanowires: An ab initio study

    NASA Astrophysics Data System (ADS)

    Schmidt, Tome; Venezuela, Pedro; Arantes, Jeverson; Fazzio, Adalberto

    2006-03-01

    We investigated the electronic and magnetic properties of Mn doped InP nanowires. Our study was based on total energy density functional calculations. The Mn dopants were placed substitutionally in In atom sites. We have found that the most energetically favorable position for the Mn atom is near the surface. However, a small amount of Mn atoms will be located at ``bulk-like'' positions in the wire. When the Mn atoms are in ``bulk-like'' positions, the Mn-3d majority-spin-orbitals appear in two different regions of the valence band (VB): about 2.0 eV below the top of the VB and resonant with the top of the VB. In these cases there is also an empty orbital in the gap whit p-character. The total valence spin-densities (ρ- ρ), for a single Mn atom in any of the configurations studied here, show a strong localized magnetic moment around the Mn atom site. In order to study the magnetic coupling we also did calculations with two Mn atoms in each cell. For several configurations studied, we concluded that if both Mn atoms are in ``bulk-like'' positions the system presents ferromagnetic ordering. On the other hand, if at least one of the Mn atoms is located near the surface, there is no magnetic ordering or the system is antiferromagnetic.

  3. Error-estimation-guided rebuilding of de novo models increases the success rate of ab initio phasing.

    PubMed

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

    2012-11-01

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

  4. 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

  5. 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

  6. 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

  7. Hydrogen-hydrogen bonds in highly branched alkanes and in alkane complexes: A DFT, ab initio, QTAIM, and ELF study.

    PubMed

    Monteiro, Norberto K V; Firme, Caio L

    2014-03-06

    The hydrogen-hydrogen (H-H) bond or hydrogen-hydrogen bonding is formed by the interaction between a pair of identical or similar hydrogen atoms that are close to electrical neutrality and it yields a stabilizing contribution to the overall molecular energy. This work provides new, important information regarding hydrogen-hydrogen bonds. We report that stability of alkane complexes and boiling point of alkanes are directly related to H-H bond, which means that intermolecular interactions between alkane chains are directional H-H bond, not nondirectional induced dipole-induced dipole. Moreover, we show the existence of intramolecular H-H bonds in highly branched alkanes playing a secondary role in their increased stabilities in comparison with linear or less branched isomers. These results were accomplished by different approaches: density functional theory (DFT), ab initio, quantum theory of atoms in molecules (QTAIM), and electron localization function (ELF).

  8. Length dependence of the thermal conductance of alkane-based single-molecule junctions: An ab initio study

    NASA Astrophysics Data System (ADS)

    Klöckner, J. C.; Bürkle, M.; Cuevas, J. C.; Pauly, F.

    2016-11-01

    Motivated by recent experiments, we present here a systematic ab initio study of the length dependence of the thermal conductance of single-molecule junctions. We make use of a combination of density functional theory with nonequilibrium Green's function techniques to investigate the length dependence of the phonon transport in single-alkane chains, contacted with gold electrodes via both thiol and amine anchoring groups. Additionally, we study the effect of the substitution of the hydrogen atoms in the alkane chains by heavier fluorine atoms to form polytetrafluoroethylenes. Our results demonstrate that (i) the room-temperature thermal conductance is fairly length independent for chains with more than 5 methylene units and (ii) the efficiency of the thermal transport is strongly influenced by the strength of the phononic metal-molecule coupling. Our study sheds light on the phonon transport in molecular junctions, and it provides clear guidelines for the design of molecular junctions for thermal management.

  9. Self-Assembly and Dynamics of Organic 2D Molecular Sieves: Ab Initio and Molecular Dynamics Studies

    NASA Astrophysics Data System (ADS)

    St. John, Alexander; Wexler, Carlos

    2015-03-01

    Spontaneous molecular self-assembly is a promising route for bottom-up manufacturing of two-dimensional (2D) nanostructures with specific topologies on atomically flat surfaces. Of particular interest is the possibility of selective lock-and-key interaction of guest molecules inside cavities formed by complex self-assembled host structures. Our host structure is a monolayer consisting of interdigitated 1,3,5-tristyrylbenzene substituted by alkoxy peripheral chains containing n = 6, 8, 10, 12, or 14 carbon atoms (TSB3,5-C n) deposited on a highly ordered pyrolytic graphite (HOPG) surface. Using ab initio methods from quantum chemistry and molecular dynamics simulations, we construct and analyze the structure and functionality of the TSB3,5-C n monolayer as a molecular sieve. Supported by ACS-PRF 52696-ND5.

  10. 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.

  11. 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

  12. 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.

  13. {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}.

  14. Hydration of potassium iodide dimer studied by photoelectron spectroscopy and ab initio calculations

    NASA Astrophysics Data System (ADS)

    Li, Ren-Zhong; Zeng, Zhen; Hou, Gao-Lei; Xu, Hong-Guang; Zhao, Xiang; Gao, Yi Qin; Zheng, Wei-Jun

    2016-11-01

    We measured the photoelectron spectra of (KI)2-(H2O)n (n = 0-3) and conducted ab initio calculations on (KI)2-(H2O)n anions and their corresponding neutrals up to n = 6. Two types of spectral features are observed in the experimental spectra of (KI)2-(H2O) and (KI)2-(H2O)2, indicating that two types of isomers coexist, in which the high EBE feature corresponds to the hydrated chain-like (KI)2- while the low EBE feature corresponds to the hydrated pyramidal (KI)2-. In (KI)2-(H2O)3, the (KI)2- unit prefers a pyramidal configuration, and one of the K-I distances is elongated significantly, thus a K atom is firstly separated out from the (KI)2- unit. As for the neutrals, the bare (KI)2 has a rhombus structure, and the structures of (KI)2(H2O)n are evolved from the rhombus (KI)2 unit by the addition of H2O. When the number of water molecules reaches 4, the K-I distances have significant increment and one of the I atoms prefers to leave the (KI)2 unit. The comparison of (KI)2(H2O)n and (NaI)2(H2O)n indicates that it is slightly more difficult to pry apart (KI)2 than (NaI)2 via hydration, which is in agreement with the lower solubility of KI compared to that of NaI.

  15. 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.

  16. Ab initio studies on the adsorption and implantation of Al and Fe to nitride materials

    SciTech Connect

    Riedl, H.; Zálešák, J.; Arndt, M.; Polcik, P.; Holec, D.; Mayrhofer, P. H.

    2015-09-28

    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, Ti{sub 0.50}Al{sub 0.50}N, Ti{sub 0.90}Si{sub 0.10}N, CrN, and Cr{sub 0.90}Si{sub 0.10}N. 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 Ti{sub 0.50}Al{sub 0.50}N, Ti{sub 0.90}Si{sub 0.10}N, and Cr{sub 0.90}Si{sub 0.10}N 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.

  17. Verification of Anderson superexchange in MnO via magnetic pair distribution function analysis and ab initio theory

    DOE PAGES

    Benjamin A. Frandsen; Brunelli, Michela; Page, Katharine; ...

    2016-05-11

    Here, we present a temperature-dependent atomic and magnetic pair distribution function (PDF) analysis of neutron total scattering measurements of antiferromagnetic MnO, an archetypal strongly correlated transition-metal oxide. The known antiferromagnetic ground-state structure fits the low-temperature data closely with refined parameters that agree with conventional techniques, confirming the reliability of the newly developed magnetic PDF method. The measurements performed in the paramagnetic phase reveal significant short-range magnetic correlations on a ~1 nm length scale that differ substantially from the low-temperature long-range spin arrangement. Ab initio calculations using a self-interaction-corrected local spin density approximation of density functional theory predict magnetic interactions dominatedmore » by Anderson superexchange and reproduce the measured short-range magnetic correlations to a high degree of accuracy. Further calculations simulating an additional contribution from a direct exchange interaction show much worse agreement with the data. Furthermore, the Anderson superexchange model for MnO is thus verified by experimentation and confirmed by ab initio theory.« less

  18. Ab Initio Quality NMR Parameters in Solid-State Materials Using a High-Dimensional Neural-Network Representation.

    PubMed

    Cuny, Jérôme; Xie, Yu; Pickard, Chris J; Hassanali, Ali A

    2016-02-09

    Nuclear magnetic resonance (NMR) spectroscopy is one of the most powerful experimental tools to probe the local atomic order of a wide range of solid-state compounds. However, due to the complexity of the related spectra, in particular for amorphous materials, their interpretation in terms of structural information is often challenging. These difficulties can be overcome by combining molecular dynamics simulations to generate realistic structural models with an ab initio evaluation of the corresponding chemical shift and quadrupolar coupling tensors. However, due to computational constraints, this approach is limited to relatively small system sizes which, for amorphous materials, prevents an adequate statistical sampling of the distribution of the local environments that is required to quantitatively describe the system. In this work, we present an approach to efficiently and accurately predict the NMR parameters of very large systems. This is achieved by using a high-dimensional neural-network representation of NMR parameters that are calculated using an ab initio formalism. To illustrate the potential of this approach, we applied this neural-network NMR (NN-NMR) method on the (17)O and (29)Si quadrupolar coupling and chemical shift parameters of various crystalline silica polymorphs and silica glasses. This approach is, in principal, general and has the potential to be applied to predict the NMR properties of various materials.

  19. Verification of Anderson Superexchange in MnO via Magnetic Pair Distribution Function Analysis and ab initio Theory

    NASA Astrophysics Data System (ADS)

    Frandsen, Benjamin A.; Brunelli, Michela; Page, Katharine; Uemura, Yasutomo J.; Staunton, Julie B.; Billinge, Simon J. L.

    2016-05-01

    We present a temperature-dependent atomic and magnetic pair distribution function (PDF) analysis of neutron total scattering measurements of antiferromagnetic MnO, an archetypal strongly correlated transition-metal oxide. The known antiferromagnetic ground-state structure fits the low-temperature data closely with refined parameters that agree with conventional techniques, confirming the reliability of the newly developed magnetic PDF method. The measurements performed in the paramagnetic phase reveal significant short-range magnetic correlations on a ˜1 nm length scale that differ substantially from the low-temperature long-range spin arrangement. Ab initio calculations using a self-interaction-corrected local spin density approximation of density functional theory predict magnetic interactions dominated by Anderson superexchange and reproduce the measured short-range magnetic correlations to a high degree of accuracy. Further calculations simulating an additional contribution from a direct exchange interaction show much worse agreement with the data. The Anderson superexchange model for MnO is thus verified by experimentation and confirmed by ab initio theory.

  20. Phonon spectra of eulytite crystals Bi4M3O12 (M = Ge,Si): ab initio study

    NASA Astrophysics Data System (ADS)

    Avram, N. M.; Chernyshev, V. A.; Andreici, E.-L.; Petrov, V. P.; Petkova, P.

    2016-11-01

    In this paper we present the results of ab initio DFT calculation of phonon spectra for bismuth ortho-germanate Bi4Ge3O12 and bismuth ortho-silicate Bi4Si3O12 crystals, in the center of the first Brillouin zone. First, the geometry optimization was performed using the analytical energy gradients, with respect to atomic coordinates and unit cell parameters. Vibrational frequencies and normal modes were calculated within the harmonic approximation by diagonalizing the mass-weighted Hessian matrix. The IR and Raman spectra of both crystals were simulated with the periodic ab initio Crystal 09 code and B3LYP hybrid functional and the two sets of Transverse-Optical and Longitudinal-Optical frequencies are generated, together with their intensities. Also, the influence of isotopic substitution for Bi, Ge and O in phonon modes and the picture with values of frequencies shift in each mode by isotopic substitution were calculated. The obtained results are discussed and the comparision between the computed spectra and experimental data is quite satisfactory, which justifies the model and simulation scheme used for the title systems.

  1. Ab initio electronic structure of quasi-two-dimensional materials: A "native" Gaussian-plane wave approach.

    PubMed

    Trevisanutto, Paolo E; Vignale, Giovanni

    2016-05-28

    Ab initio electronic structure calculations of two-dimensional layered structures are typically performed using codes that were developed for three-dimensional structures, which are periodic in all three directions. The introduction of a periodicity in the third direction (perpendicular to the layer) is completely artificial and may lead in some cases to spurious results and to difficulties in treating the action of external fields. In this paper we develop a new approach, which is "native" to quasi-2D materials, making use of basis function that are periodic in the plane, but atomic-like in the perpendicular direction. We show how some of the basic tools of ab initio electronic structure theory - density functional theory, GW approximation and Bethe-Salpeter equation - are implemented in the new basis. We argue that the new approach will be preferable to the conventional one in treating the peculiarities of layered materials, including the long range of the unscreened Coulomb interaction in insulators, and the effects of strain, corrugations, and external fields.

  2. Neutrino-nucleus interaction: an ab-initio perspective

    NASA Astrophysics Data System (ADS)

    Lovato, Alessandro

    2017-01-01

    Understanding of the structure and of the electroweak interactions of atomic nuclei in terms of their individual constituents is an intriguing nuclear many-body problem. I will present how the Quantum Monte Carlo community is pursuing a consistent description of the structure of atomic nuclei and their interaction with electroweak probes, providing a reliable estimate of the theoretical uncertainty of the calculation. I will also present benchmark calculations between Quantum Monte Carlo and the spectral function approach. Testing the factorization ansatz is of crucial importance, as the latter allows to combine a fully relativistic description of the interaction vertex with an accurate treatment of nuclear dynamics.

  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. 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.

  6. Ab initio study of AlxMoNbTiV high-entropy alloys.

    PubMed

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

    2015-02-25

    The Al(x)MoNbTiV (x = 0-1.5) high-entropy alloys (HEAs) adopt a single solid-solution phase, having the body centered cubic (bcc) crystal structure. Here we employ the ab initio exact muffin-tin orbitals method in combination with the coherent potential approximation to investigate the equilibrium volume, elastic constants, and polycrystalline elastic moduli of Al(x)MoNbTiV HEAs. A comparison between the ab initio and experimental equilibrium volumes demonstrates the validity and accuracy of the present approach. Our results indicate that Al addition decreases the thermodynamic stability of the bcc structure with respect to face-centered cubic and hexagonal close packed lattices. For the elastically isotropic Al(0.4)MoNbTiV HEAs, the valence electron concentration (VEC) is about 4.82, which is slightly different from VEC ∼ 4.72 obtained for the isotropic Gum metals and refractory--HEAs.

  7. 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.

  8. Effects of Mg II and Ca II ionization on ab-initio solar chromosphere models

    NASA Technical Reports Server (NTRS)

    Rammacher, W.; Cuntz, M.

    1991-01-01

    Acoustically heated solar chromosphere models are computed considering radiation damping by (non-LTE) emission from H(-) and by Mg II and Ca II emission lines. The radiative transfer equations for the Mg II k and Ca II K emission lines are solved using the core-saturation method with complete redistribution. The Mg II k and Ca II K cooling rates are compared with the VAL model C. Several substantial improvements over the work of Ulmschneider et al. (1987) are included. It is found that the rapid temperature rises caused by the ionization of Mg II are not formed in the middle chromosphere, but occur at larger atmospheric heights. These models represent the temperature structure of the 'real' solar chromosphere much better. This result is a major precondition for the study of ab-initio models for solar flux tubes based on MHD wave propagation and also for ab-initio models for the solar transition layer.

  9. 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

  10. Ab initio electron mobility and polar phonon scattering in GaAs

    NASA Astrophysics Data System (ADS)

    Zhou, Jin-Jian; Bernardi, Marco

    2016-11-01

    In polar semiconductors and oxides, the long-range nature of the electron-phonon (e -ph ) interaction is a bottleneck to compute charge transport from first principles. Here, we develop an efficient ab initio scheme to compute and converge the e -ph relaxation times (RTs) and electron mobility in polar materials. We apply our approach to GaAs, where by using the Boltzmann equation with state-dependent RTs, we compute mobilities in excellent agreement with experiment at 250 -500 K . The e -ph RTs and the phonon contributions to intravalley and intervalley e -ph scattering are also analyzed. Our work enables efficient ab initio computations of transport and carrier dynamics in polar materials.

  11. Liquid Be, Ca and Ba. An orbital-free ab-initio molecular dynamics study

    SciTech Connect

    Rio, B. G. del; González, L. E.

    2015-08-17

    Several static and dynamic properties of liquid beryllium (l-Be), liquid calcium (l-Ca) and liquid barium (l-Ba) near their triple point have been evaluated by the orbital-free ab initio molecular dynamics method (OF-AIMD), where the interaction between valence electrons and ions is described by means of local pseudopotentials. These local pseudopotentials used were constructed through a force-matching process with those obtained from a Kohn-Sham ab initio molecular dynamics study (KS-AIMD) of a reduced system with non-local pseudopotentials. The calculated static structures show good agreement with the available experimental data, including an asymmetric second peak in the structure factor which has been linked to the existence of a marked icosahedral short-range order in the liquid. As for the dynamic properties, we obtain collective density excitations whose associated dispersion relations exhibit a positive dispersion.

  12. Ab initio calculation of valley splitting in monolayer δ-doped phosphorus in silicon

    PubMed Central

    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

  13. 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.

  14. Theoretical method for full ab initio calculation of DNA/RNA-ligand interaction energy

    NASA Astrophysics Data System (ADS)

    Chen, Xi H.; Zhang, John Z. H.

    2004-06-01

    In this paper, we further develop the molecular fractionation with conjugate caps (MFCC) scheme for quantum mechanical computation of DNA-ligand interaction energy. We study three oligonuclear acid interaction systems: dinucleotide dCG/water, trinucleotide dCGT/water, and a Watson-Crick paired DNA segment, dCGT/dGCA. Using the basic MFCC approach, the nucleotide chains are cut at each phosphate group and a pair of conjugate caps (concaps) are inserted. Five cap molecules have been tested among which the dimethyl phosphate anion is proposed to be the standard concap for application. For each system, one-dimensional interaction potential curves are computed using the MFCC method and the calculated interaction energies are found to be in excellent agreement with corresponding results obtained from the full system ab initio calculations. The current study extends the application of the MFCC method to ab initio calculations for DNA- or RNA-ligand interaction energies.

  15. Study of the betulin molecule in a water environment; ab initio and molecular simulation calculations.

    PubMed

    Pospíšil, Miroslav; Kovář, Petr; Vácha, Robert; Svoboda, Michal

    2012-01-01

    Ab initio and molecular simulation methods were used in calculations of the neutral individual betulin molecule, and molecular simulations were used to optimize the betulin molecule immersed in various amounts of water. Individual betulin was optimized in different force fields to find the one exhibiting best agreement with ab initio calculations obtained in the Gaussian03 program. Dihedral torsions of active groups of betulin were determined for both procedures, and related calculated structures were compared successfully. The selected force field was used for subsequent optimization of betulin in a water environment, and a conformational search was performed using quench molecular dynamics. The total energies of betulin and its interactions in water bulk were calculated, and the influence of water on betulin structure was investigated.

  16. 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

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

    PubMed

    Yang, Jianjun; Tse, John S

    2011-11-17

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

  18. The Pu-U-Am system: An ab initio informed CALPHAD thermodynamic study

    NASA Astrophysics Data System (ADS)

    Perron, A.; Turchi, P. E. A.; Landa, A.; Söderlind, P.; Ravat, B.; Oudot, B.; Delaunay, F.

    2015-03-01

    Phase diagram and thermodynamic properties of the Am-U system, that are experimentally unknown, are calculated using the CALPHAD method with input from ab initio electronic-structure calculations for the fcc and bcc phases. A strong tendency toward phase separation across the whole composition range is predicted. In addition, ab initio informed Pu-U and Am-Pu thermodynamic assessments are combined to build a Pu-U-Am thermodynamic database. Regarding the Pu-rich corner of the ternary system, predictions indicate that Am acts as a powerful δ-Pu (fcc) stabilizer. In the U-rich corner, similar predictions are made but to a lesser extent. In both cases, the bcc phase is destabilized and the fcc phase is enhanced. Finally, results and methodology are discussed and compared with previous assessments and guidelines are provided for further experimental studies.

  19. [Photoelectron Spectra of CCl2-: Ab Initio Calculation and Franck-Condon Analysis].

    PubMed

    Wu, Jun

    2015-12-01

    Geometry optimization and harmonic vibrational frequency calculations were performed on the X¹A₁ state of CCl₂ and X²B₁ state of CCl₂⁻ at the B3LYP, MP2, CCSD levels. Franck-Condon analysis and spectral simulations were carried out on the photoelectron band of CCl₂⁻ including Duschinsky effects. The simulated spectra obtained are in excellent agreement with the experiment. Note that Duschinsky effect between bending vibration and the symmetric stretch modes should be considered in the CCl₂ (X¹A₁)-CCl₂⁻ (X²B₁) photodetachment process. By combining ab initio calculations with Franck-Condon analyses, the assignment of spectrum observed is firmly established to the X¹A₁-X²B₁ photodetachment process of the CCl₂⁻ radical, and the recommended geometric parameters of which in the literature are confirmed again base on ab initio theory and IFCA process.

  20. Ab initio calculations on twisted graphene/hBN: Electronic structure and STM image simulation

    NASA Astrophysics Data System (ADS)

    Correa, J. D.; Cisternas, E.

    2016-09-01

    By performing ab initio calculations we obtained theoretical scanning tunneling microscopy (STM) images and studied the electronic properties of graphene on a hexagonal boron-nitrite (hBN) layer. Three different stack configurations and four twisted angles were considered. All calculations were performed using density functional theory, including van der Waals interactions as implemented in the SIESTA ab initio package. Our results show that the electronic structure of graphene is preserved, although some small changes are induced by the interaction with the hBN layer, particularly in the total density of states at 1.5 eV under the Fermi level. When layers present a twisted angle, the density of states shows several van Hove singularities under the Fermi level, which are associated to moiré patterns observed in theoretical STM images.

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

    NASA Astrophysics Data System (ADS)

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

    2014-04-01

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

  2. Ab initio molecular dynamics simulation of liquid water by quantum Monte Carlo.

    PubMed

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

    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.

  3. Structural properties of liquid N-methylacetamide via ab initio, path integral, and classical molecular dynamics

    NASA Astrophysics Data System (ADS)

    Whitfield, T. W.; Crain, J.; Martyna, G. J.

    2006-03-01

    In order to better understand the physical interactions that stabilize protein secondary structure, the neat liquid state of a peptidic fragment, N-methylacetamide (NMA), was studied using computer simulation. Three different descriptions of the molecular liquid were examined: an empirical force field treatment with classical nuclei, an empirical force field treatment with quantum mechanical nuclei, and an ab initio density functional theory (DFT) treatment. The DFT electronic structure was evaluated using the BLYP approximate functional and a plane wave basis set. The different physical effects probed by the three models, such as quantum dispersion, many-body polarization, and nontrivial charge distributions on the liquid properties, were compared. Much of the structural ordering in the liquid is characterized by hydrogen bonded chains of NMA molecules. Modest structural differences are present among the three models of liquid NMA. The average molecular dipole in the liquid under the ab initio treatment, however, is enhanced by 60% over the gas phase value.

  4. Controlling Magnetic and Ferroelectric Order Through Geometry: Synthesis, Ab Initio Theory, Characterization of New Multi-Ferric Fluoride Materials

    SciTech Connect

    Halasyamani, Shiv; Fennie, Craig

    2016-11-03

    We have focused on the synthesis, characterization, and ab initio theory on multi-functional mixed-metal fluorides. With funding from the DOE, we have successfully synthesized and characterized a variety of mixed metal fluoride materials.

  5. Steady-state ab initio laser theory for N-level lasers.

    PubMed

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

    2012-01-02

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

  6. Ab initio dipole moment and theoretical rovibrational intensities in the electronic ground state of PH 3

    NASA Astrophysics Data System (ADS)

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

    2006-09-01

    We report a six-dimensional CCSD(T)/aug-cc-pVTZ dipole moment surface for the electronic ground state of PH 3 computed ab initio on a large grid of 10 080 molecular geometries. Parameterized, analytical functions are fitted through the ab initio data, and the resulting dipole moment functions are used, together with a potential energy function determined by refining an existing ab initio surface in fittings to experimental wavenumber data, for simulating absorption spectra of the first three polyads of PH 3, i.e., ( ν2, ν4), ( ν1, ν3, 2 ν2, 2 ν4, ν2 + ν4), and ( ν1 + ν2, ν3 + ν2, ν1 + ν4, ν3 + ν4, 2 ν2 + ν4, ν2 + 2 ν4, 3 ν2, 3 ν4). The resulting theoretical transition moments show excellent agreement with experiment. A line-by-line comparison of the simulated intensities of the ν2/ ν4 band system with 955 experimental intensity values reported by Brown et al. [L.R. Brown, R.L. Sams, I. Kleiner, C. Cottaz, L. Sagui, J. Mol. Spectrosc. 215 (2002) 178-203] gives an average absolute percentage deviation of 8.7% (and a root-mean-square deviation of 0.94 cm -1 for the transition wavenumbers). This is very remarkable since the calculations rely entirely on ab initio dipole moment surfaces and do not involve any adjustment of these surfaces to reproduce the experimental intensities. Finally, we predict the line strengths for transitions between so-called cluster levels (near-degenerate levels formed at high rotational excitation) for J up to 60.

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

    SciTech Connect

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

    2013-11-21

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

  8. Ab initio equation of state of hydrogen for inertial fusion applications

    NASA Astrophysics Data System (ADS)

    Benedict, Lorin X.; Morales, Miguel A.; Schwegler, Eric; Tamblyn, Isaac; Bonev, Stanimir A.; Correa, Alfredo A.; Clark, Daniel S.; Haan, Steven W.; LLNL Collaboration

    2011-06-01

    We describe ab initio electronic structure calculations (DFT molecular dynamics and quantum Monte Carlo) of the equation of state of hydrogen in a regime relevant for ICF applications. We find the computed EOS to be quite close to that of the most recent SESAME table (constructed by G. Kerley, 2004). A simple density-dependent correction brings the recent SESAME EOS into nearly perfect agreement with ours in the chosen region. Simulations of ICF applications with this corrected SESAME table are discussed.

  9. Ab initio molecular dynamics study of liquid sodium and cesium up to critical point

    SciTech Connect

    Yuryev, Anatoly A.; Gelchinski, Boris R.

    2015-08-17

    Ab initio modeling of liquid metals Na and K is carried out using the program SIESTA. We have determined the parameters of the model (the optimal step, the number of particles, the initial state etc) and calculated a wide range of properties: the total energy, pair correlation function, coefficient of self-diffusion, heat capacity, statistics of Voronoi polyhedra, the density of electronic states up to the critical temperature.

  10. Ab initio molecular dynamics study of liquid sodium and cesium up to critical point

    NASA Astrophysics Data System (ADS)

    Yuryev, Anatoly A.; Gelchinski, Boris R.

    2015-08-01

    Ab initio modeling of liquid metals Na and K is carried out using the program SIESTA. We have determined the parameters of the model (the optimal step, the number of particles, the initial state etc) and calculated a wide range of properties: the total energy, pair correlation function, coefficient of self-diffusion, heat capacity, statistics of Voronoi polyhedra, the density of electronic states up to the critical temperature.

  11. Optical and other material properties of SiO2 from ab initio studies

    NASA Astrophysics Data System (ADS)

    Warmbier, Robert; Mohammed, Faris; Quandt, Alexander

    2014-07-01

    The optical properties of photonic devices largely depend on the dielectric properties of the underlying materials. We apply modern ab initio methods to study crystalline SiO2 phases, which serve as toy models for amorphous glass. We discuss the dielectric response from the infrared to the VIS/UV, which is crucial for glass based photonic applications. Low density silica, like cristobalite, may provide a good basis for high transmission optical devices.

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

    SciTech Connect

    Tiago, M.L.; Chang, Eric K.; Rohlfing, Michael; Louie, Steven G.

    2000-04-30

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

  13. Resolution of ab initio shapes determined from small-angle scattering.

    PubMed

    Tuukkanen, Anne T; Kleywegt, Gerard J; Svergun, Dmitri I

    2016-11-01

    Spatial resolution is an important characteristic of structural models, and the authors of structures determined by X-ray crystallography or electron cryo-microscopy always provide the resolution upon publication and deposition. Small-angle scattering of X-rays or neutrons (SAS) has recently become a mainstream structural method providing the overall three-dimensional structures of proteins, nucleic acids and complexes in solution. However, no quantitative resolution measure is available for SAS-derived models, which significantly hampers their validation and further use. Here, a method is derived for resolution assessment for ab initio shape reconstruction from scattering data. The inherent variability of the ab initio shapes is utilized and it is demonstrated how their average Fourier shell correlation function is related to the model resolution. The method is validated against simulated data for proteins with known high-resolution structures and its efficiency is demonstrated in applications to experimental data. It is proposed that henceforth the resolution be reported in publications and depositions of ab initio SAS models.

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

    PubMed

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

    2007-09-01

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

  15. Density-matrix based determination of low-energy model Hamiltonians from ab initio wavefunctions

    SciTech Connect

    Changlani, Hitesh J.; Zheng, Huihuo; Wagner, Lucas K.

    2015-09-14

    We propose a way of obtaining effective low energy Hubbard-like model Hamiltonians from ab initio quantum Monte Carlo calculations for molecular and extended systems. The Hamiltonian parameters are fit to best match the ab initio two-body density matrices and energies of the ground and excited states, and thus we refer to the method as ab initio density matrix based downfolding. For benzene (a finite system), we find good agreement with experimentally available energy gaps without using any experimental inputs. For graphene, a two dimensional solid (extended system) with periodic boundary conditions, we find the effective on-site Hubbard U{sup ∗}/t to be 1.3 ± 0.2, comparable to a recent estimate based on the constrained random phase approximation. For molecules, such parameterizations enable calculation of excited states that are usually not accessible within ground state approaches. For solids, the effective Hamiltonian enables large-scale calculations using techniques designed for lattice models.

  16. Ab Initio Prediction of Adsorption Isotherms for Small Molecules in Metal-Organic Frameworks.

    PubMed

    Kundu, Arpan; Piccini, GiovanniMaria; Sillar, Kaido; Sauer, Joachim

    2016-10-17

    For CO and N2 on Mg(2+) sites of the metal-organic framework CPO-27-Mg (Mg-MOF-74), ab initio calculations of Gibbs free energies of adsorption have been performed. Combined with the Bragg-Williams/Langmuir model and taking into account the experimental site availability (76.5%), we obtained adsorption isotherms in close agreement with those in experiment. The remaining deviations in the Gibbs free energy (about 1 kJ/mol) are significantly smaller than the "chemical accuracy" limit of about 4 kJ/mol. The presented approach uses (i) a DFT dispersion method (PBE+D2) to optimize the structure and to calculate anharmonic frequencies for vibrational partition functions and (ii) a "hybrid MP2:(PBE+D2)+ΔCCSD(T)" method to determine electronic energies. With the achieved accuracy (estimated uncertainty ±1.4 kJ/mol), the ab initio energies become useful benchmarks for assessing different DFT + dispersion methods (PBE+D2, B3LYP+D*, and vdW-D2), whereas the ab initio heats, entropies, and Gibbs free energies of adsorption are used to assess the reliability of experimental values derived from fitting isotherms or from variable-temperature IR studies.

  17. An ab initio calculation of the fundamental and overtone HCl stretching vibrations for the HCl dimer

    NASA Astrophysics Data System (ADS)

    Jensen, Per; Bunker, P. R.; Epa, V. C.; Karpfen, A.

    1992-02-01

    We have previously determined an analytical ab initio six-dimensional potential energy surface for the HCl dimer, and have used it to determine the minimum energy path for the trans-tunneling motion. In the present paper we refine this path by fitting to data. We calculate a further 178 ab initio points in order to determine the HCl stretching energies, and HCl stretching dipole moment functions, at eight positions along the minimum energy path. We use these ab initio results to compute the stretching wavenumbers and transition moments from the v1 = v2 = 0 state to all states of (HCl) 2 that have v1 + v2 ≤ 3, where v1 and v2 are the local mode quantum numbers for the HCl stretching vibrations. In doing this calculation we have assumed an adiabatic separation of the HCl stretching motion from the other vibrational motions in the dimer, and have used the semirigid bender Hamiltonian to average over the trans-tunneling motion. We obtain the fundamental "free-H" stretch v1 at 2877 cm -1 and the fundamental "bound-H" stretch v2 at 2861 cm -1; the experimental values are 2880 and 2854 cm -1, respectively.

  18. Thermal transport in nanocrystalline Si and SiGe by ab initio based Monte Carlo simulation

    NASA Astrophysics Data System (ADS)

    Yang, Lina; Minnich, Austin J.

    2017-03-01

    Nanocrystalline thermoelectric materials based on Si have long been of interest because Si is earth-abundant, inexpensive, and non-toxic. However, a poor understanding of phonon grain boundary scattering and its effect on thermal conductivity has impeded efforts to improve the thermoelectric figure of merit. Here, we report an ab-initio based computational study of thermal transport in nanocrystalline Si-based materials using a variance-reduced Monte Carlo method with the full phonon dispersion and intrinsic lifetimes from first-principles as input. By fitting the transmission profile of grain boundaries, we obtain excellent agreement with experimental thermal conductivity of nanocrystalline Si [Wang et al. Nano Letters 11, 2206 (2011)]. Based on these calculations, we examine phonon transport in nanocrystalline SiGe alloys with ab-initio electron-phonon scattering rates. Our calculations show that low energy phonons still transport substantial amounts of heat in these materials, despite scattering by electron-phonon interactions, due to the high transmission of phonons at grain boundaries, and thus improvements in ZT are still possible by disrupting these modes. This work demonstrates the important insights into phonon transport that can be obtained using ab-initio based Monte Carlo simulations in complex nanostructured materials.

  19. Resolution of ab initio shapes determined from small-angle scattering

    PubMed Central

    Tuukkanen, Anne T.; Kleywegt, Gerard J.; Svergun, Dmitri I.

    2016-01-01

    Spatial resolution is an important characteristic of structural models, and the authors of structures determined by X-ray crystallography or electron cryo-microscopy always provide the resolution upon publication and deposition. Small-angle scattering of X-rays or neutrons (SAS) has recently become a mainstream structural method providing the overall three-dimensional structures of proteins, nucleic acids and complexes in solution. However, no quantitative resolution measure is available for SAS-derived models, which significantly hampers their validation and further use. Here, a method is derived for resolution assessment for ab initio shape reconstruction from scattering data. The inherent variability of the ab initio shapes is utilized and it is demonstrated how their average Fourier shell correlation function is related to the model resolution. The method is validated against simulated data for proteins with known high-resolution structures and its efficiency is demonstrated in applications to experimental data. It is proposed that henceforth the resolution be reported in publications and depositions of ab initio SAS models. PMID:27840683

  20. Thermal transport in nanocrystalline Si and SiGe by ab initio based Monte Carlo simulation

    PubMed Central

    Yang, Lina; Minnich, Austin J.

    2017-01-01

    Nanocrystalline thermoelectric materials based on Si have long been of interest because Si is earth-abundant, inexpensive, and non-toxic. However, a poor understanding of phonon grain boundary scattering and its effect on thermal conductivity has impeded efforts to improve the thermoelectric figure of merit. Here, we report an ab-initio based computational study of thermal transport in nanocrystalline Si-based materials using a variance-reduced Monte Carlo method with the full phonon dispersion and intrinsic lifetimes from first-principles as input. By fitting the transmission profile of grain boundaries, we obtain excellent agreement with experimental thermal conductivity of nanocrystalline Si [Wang et al. Nano Letters 11, 2206 (2011)]. Based on these calculations, we examine phonon transport in nanocrystalline SiGe alloys with ab-initio electron-phonon scattering rates. Our calculations show that low energy phonons still transport substantial amounts of heat in these materials, despite scattering by electron-phonon interactions, due to the high transmission of phonons at grain boundaries, and thus improvements in ZT are still possible by disrupting these modes. This work demonstrates the important insights into phonon transport that can be obtained using ab-initio based Monte Carlo simulations in complex nanostructured materials. PMID:28290484

  1. Thermal transport in nanocrystalline Si and SiGe by ab initio based Monte Carlo simulation.

    PubMed

    Yang, Lina; Minnich, Austin J

    2017-03-14

    Nanocrystalline thermoelectric materials based on Si have long been of interest because Si is earth-abundant, inexpensive, and non-toxic. However, a poor understanding of phonon grain boundary scattering and its effect on thermal conductivity has impeded efforts to improve the thermoelectric figure of merit. Here, we report an ab-initio based computational study of thermal transport in nanocrystalline Si-based materials using a variance-reduced Monte Carlo method with the full phonon dispersion and intrinsic lifetimes from first-principles as input. By fitting the transmission profile of grain boundaries, we obtain excellent agreement with experimental thermal conductivity of nanocrystalline Si [Wang et al. Nano Letters 11, 2206 (2011)]. Based on these calculations, we examine phonon transport in nanocrystalline SiGe alloys with ab-initio electron-phonon scattering rates. Our calculations show that low energy phonons still transport substantial amounts of heat in these materials, despite scattering by electron-phonon interactions, due to the high transmission of phonons at grain boundaries, and thus improvements in ZT are still possible by disrupting these modes. This work demonstrates the important insights into phonon transport that can be obtained using ab-initio based Monte Carlo simulations in complex nanostructured materials.

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

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

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

  3. Ab initio molecular dynamics simulation of pressure-induced phase transformation in BeO

    SciTech Connect

    Xiao, Haiyan; Duan, G; Zu, X T; Weber, William J

    2011-01-01

    Ab initio molecular dynamics (MD) method has been used to study high pressure-induced phase transformation in BeO based on the local density approximation (LDA) and the generalized gradient approximation (GGA). Both methods show that the wurtzite (WZ) and zinc blende (ZB) BeO transforms to the rocksalt (RS) structure smoothly at high pressure. The transition pressures obtained from the LDA method are about 40 GPa larger than the GGA result for both WZ {yields} RS and ZB {yields} RS phase transformations, and the phase transformation mechanisms revealed by the LDA and GGA methods are different. For WZ {yields} RS phase transformations both mechanisms obtained from the LDA and GGA methods are not comparable to the previous ab initio MD simulations of WZ BeO at 700 GPa based on the GGA method. It is suggested that the phase transformation mechanisms of BeO revealed by the ab initio MD simulations are affected remarkably by the exchange-correlation functional employed and the way of applying pressure.

  4. Condensed-matter ab initio approach for strongly correlated electrons: Application to a quantum spin liquid candidate

    SciTech Connect

    Yamaji, Youhei

    2015-12-31

    Recently, condensed-matter ab initio approaches to strongly correlated electrons confined in crystalline solids have been developed and applied to transition-metal oxides and molecular conductors. In this paper, an ab initio scheme based on constrained random phase approximations and localized Wannier orbitals is applied to a spin liquid candidate Na{sub 2}IrO{sub 3} and is shown to reproduce experimentally observed specific heat.

  5. Electronic Structure of Silicon Nanowires Matrix from Ab Initio Calculations

    NASA Astrophysics Data System (ADS)

    Monastyrskii, Liubomyr S.; Boyko, Yaroslav V.; Sokolovskii, Bogdan S.; Potashnyk, Vasylyna Ya.

    2016-01-01

    An investigation of the model of porous silicon in the form of periodic set of silicon nanowires has been carried out. The electronic energy structure was studied using a first-principle band method—the method of pseudopotentials (ultrasoft potentials in the basis of plane waves) and linearized mode of the method of combined pseudopotentials. Due to the use of hybrid exchange-correlation potentials (B3LYP), the quantitative agreement of the calculated value of band gap in the bulk material with experimental data is achieved. The obtained results show that passivation of dangling bonds with hydrogen atoms leads to substantial transformation of electronic energy structure. At complete passivation of the dangling silicon bonds by hydrogen atoms, the band gap value takes the magnitude which substantially exceeds that for bulk silicon. The incomplete passivation gives rise to opposite effect when the band gap value decreases down the semimetallic range.

  6. Electronic Structure of Silicon Nanowires Matrix from Ab Initio Calculations.

    PubMed

    Monastyrskii, Liubomyr S; Boyko, Yaroslav V; Sokolovskii, Bogdan S; Potashnyk, Vasylyna Ya

    2016-12-01

    An investigation of the model of porous silicon in the form of periodic set of silicon nanowires has been carried out. The electronic energy structure was studied using a first-principle band method-the method of pseudopotentials (ultrasoft potentials in the basis of plane waves) and linearized mode of the method of combined pseudopotentials. Due to the use of hybrid exchange-correlation potentials (B3LYP), the quantitative agreement of the calculated value of band gap in the bulk material with experimental data is achieved. The obtained results show that passivation of dangling bonds with hydrogen atoms leads to substantial transformation of electronic energy structure. At complete passivation of the dangling silicon bonds by hydrogen atoms, the band gap value takes the magnitude which substantially exceeds that for bulk silicon. The incomplete passivation gives rise to opposite effect when the band gap value decreases down the semimetallic range.

  7. Ab-initio modeling of electromechanical coupling at Si surfaces

    SciTech Connect

    Hoppe, Sandra; Müller, Stefan; Michl, Anja; Weissmüller, Jörg

    2014-08-21

    The electromechanical coupling at the silicon (100) and (111) surfaces was studied via density functional theory by calculating the response of the ionization potential and the electron affinity to different types of strain. We find a branched strain response of those two quantities with different coupling coefficients for negative and positive strain values. This can be attributed to the reduced crystal symmetry due to anisotropic strain, which partially lifts the degeneracy of the valence and conduction bands. Only the Si(111) electron affinity exhibits a monotonously linear strain response, as the conduction band valleys remain degenerate under strain. The strain response of the surface dipole is linear and seems to be dominated by volume changes. Our results may help to understand the mechanisms behind electromechanical coupling at an atomic level in greater detail and for different electronic and atomic structures.

  8. Ab-Initio Study of the Group 2 Hydride Anions

    NASA Astrophysics Data System (ADS)

    Harris, Joe P.; Wright, Timothy G.; Manship, Daniel R.

    2013-06-01

    The beryllium hydride (BeH)- dimer has recently been shown to be surprisingly strongly bound, with an electronic structure which is highly dependent on internuclear separation. At the equilibrium distance, the negative charge is to be found on the beryllium atom, despite the higher electronegativity of the hydrogen. The current study expands this investigation to the other Group 2 hydrides, and attempts to explain these effects. M. Verdicchio, G. L. Bendazzoli, S. Evangelisti, T. Leininger J. Phys. Chem. A, 117, 192, (2013)

  9. Ab initio study of tungsten defects near the surface

    NASA Astrophysics Data System (ADS)

    Guerrero, C. L.; Gordillo, N.; Iglesias, R.; Perlado, J. M.; Gonzalez, C.

    2016-05-01

    A first principles analysis of the behaviour of point defects, namely, self-interstitial atoms, a single vacancy and light impurity atoms such as H and He in tungsten is reported. These defects can be produced in the first wall of the future nuclear fusion reactors due to the high radiation fluxes present. The evolution of defects that appear in the bulk and end up reaching the surface has been followed. An energetic study has been combined with a detailed charge density analysis of the system by means of the SIESTA code. The resulting data have been validated by confronting them with those obtained with a more precise plane wave code, namely VASP. Meanwhile, the structural and the mechanical properties of the system have been positively compared with experimental measurements. Such comparisons have led us to present a new SIESTA basis for tungsten. This complete analysis establishes a nanoscopic view of the phenomena involving the presence of light atoms at native defects in tungsten, paying special attention to the vicinity of surfaces.

  10. Dissipative Particle Dynamics interaction parameters from ab initio calculations

    NASA Astrophysics Data System (ADS)

    Sepehr, Fatemeh; Paddison, Stephen J.

    2016-02-01

    Dissipative Particle Dynamics (DPD) is a commonly employed coarse-grained method to model complex systems. Presented here is a pragmatic approach to connect atomic-scale information to the meso-scale interactions defined between the DPD particles or beads. Specifically, electronic structure calculations were utilized for the calculation of the DPD pair-wise interaction parameters. An implicit treatment of the electrostatic interactions for charged beads is introduced. The method is successfully applied to derive the parameters for a hydrated perfluorosulfonic acid ionomer with absorbed vanadium cations.

  11. Ab initio calculation of the NMR shielding constants for histamine

    NASA Astrophysics Data System (ADS)

    Mazurek, A. P.; Dobrowolski, J. Cz.; Sadlej, J.

    1997-12-01

    The gage-independent atomic orbital (GIAO) approach is used within the coupled Hartree-Fock approximation to compute the 1H, 13C and 15N NMR shielding constants in two tautomeric forms of both the histamine molecule and its protonated form. An analysis of the results shows that the protonation on the end of the chain changes its nitrogen shielding constants of the pyridine and pyrrole type. These changes are much higher for the N(3)-H than for the N(1)-H tautomer.

  12. Chiral graphene nanoribbon inside a carbon nanotube: ab initio study.

    PubMed

    Lebedeva, Irina V; Popov, Andrey M; Knizhnik, Andrey A; Khlobystov, Andrei N; Potapkin, Boris V

    2012-08-07

    The dispersion-corrected density functional theory (DFT-D) is applied for investigation of structure and electronic properties of a sulfur-terminated graphene nanoribbon (S-GNR) encapsulated in a carbon nanotube. Two mechanisms of accommodation of the GNR in the carbon nanotube, distortion of the nanotube cross-section into an elliptic shape accompanied by bending of the GNR and transformation of the GNR to a helical conformation, are analyzed. Three types of elastic distortions of the nanotube and encapsulated GNR are revealed depending on the ratio of the diameter of the nanotube cavity to the GNR width. Helical states of the GNR are shown to be stabilized by the van der Waals attraction of sulfur atoms at neighbouring edges of adjacent turns of the GNR. The results of calculations are correlated with the experimental observations for the S-GNR synthesized recently inside the carbon nanotube. The hybrid DFT calculations of band structures of zigzag GNRs terminated with different atoms demonstrate that as opposed to O- and H-GNRs, the S-GNR is metallic even when deformed inside carbon nanotubes. Possible applications of GNRs encapsulated in carbon nanotubes are discussed.

  13. Structure enhancement methodology using theory and experiment: gas-phase molecular structures using a dynamic interaction between electron diffraction, molecular mechanics, and ab initio data.

    PubMed

    Kafka, Graeme R; Masters, Sarah L; Rankin, David W H

    2007-07-05

    A new method of incorporating ab initio theoretical data dynamically into the gas-phase electron diffraction (GED) refinement process has been developed to aid the structure determination of large, sterically crowded molecules. This process involves calculating a set of differences between parameters that define the positions of peripheral atoms (usually hydrogen), as determined using molecular mechanics (MM), and those which use ab initio methods. The peripheral-atom positions are then updated continually during the GED refinement process, using MM, and the returned positions are modified using this set of differences to account for the differences between ab initio and MM methods, before being scaled back to the average parameters used to define them, as refined from experimental data. This allows the molecule to adopt a completely asymmetric structure if required, without being constrained by the MM parametrization, whereas the calculations can be performed on a practical time scale. The molecular structures of tri-tert-butylphosphine oxide and tri-tert-butylphosphine imide have been re-examined using this new technique, which we call SEMTEX (Structure Enhancement Methodology using Theory and EXperiment).

  14. A crossed molecular beam and ab-initio investigation of the reaction of boron monoxide (BO; X2Σ+) with methylacetylene (CH3CCH; X1A1): competing atomic hydrogen and methyl loss pathways.

    PubMed

    Maity, Surajit; Parker, Dorian S N; Dangi, Beni B; Kaiser, Ralf I; Fau, Stefan; Perera, Ajith; Bartlett, Rodney J

    2013-11-21

    The gas-phase reaction of boron monoxide ((11)BO; X(2)Σ(+)) with methylacetylene (CH3CCH; X(1)A1) was investigated experimentally using crossed molecular beam technique at a collision energy of 22.7 kJ mol(-1) and theoretically using state of the art electronic structure calculation, for the first time. The scattering dynamics were found to be indirect (complex forming reaction) and the reaction proceeded through the barrier-less formation of a van-der-Waals complex ((11)BOC3H4) followed by isomerization via the addition of (11)BO(X(2)Σ(+)) to the C1 and/or C2 carbon atom of methylacetylene through submerged barriers. The resulting (11)BOC3H4 doublet radical intermediates underwent unimolecular decomposition involving three competing reaction mechanisms via two distinct atomic hydrogen losses and a methyl group elimination. Utilizing partially deuterated methylacetylene reactants (CD3CCH; CH3CCD), we revealed that the initial addition of (11)BO(X(2)Σ(+)) to the C1 carbon atom of methylacetylene was followed by hydrogen loss from the acetylenic carbon atom (C1) and from the methyl group (C3) leading to 1-propynyl boron monoxide (CH3CC(11)BO) and propadienyl boron monoxide (CH2CCH(11)BO), respectively. Addition of (11)BO(X(2)Σ(+)) to the C1 of methylacetylene followed by the migration of the boronyl group to the C2 carbon atom and/or an initial addition of (11)BO(X(2)Σ(+)) to the sterically less accessible C2 carbon atom of methylacetylene was followed by loss of a methyl group leading to the ethynyl boron monoxide product (HCC(11)BO) in an overall exoergic reaction (78 ± 23 kJ mol(-1)). The branching ratios of these channels forming CH2CCH(11)BO, CH3CC(11)BO, and HCC(11)BO were derived to be 4 ± 3%, 40 ± 5%, and 56 ± 15%, respectively; these data are in excellent agreement with the calculated branching ratios using statistical RRKM theory yielding 1%, 38%, and 61%, respectively.

  15. The hydriding resistance of plutonium oxides and mononitride: A view from ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Sun, Bo; Liu, Haifeng; Song, Haifeng

    2015-06-01

    Based on the non-local van der Waals density functional (vdW-DF)+ U scheme, we carry out the ab initio molecular dynamics study of the interaction dynamics for H2 molecules impingement against Pu-oxides and mononitride surfaces. We show that except for the weak physisorption, both PuO2 and PuN surfaces are so difficult of access that almost all of H2 molecules will bounce back to the vacuum when their initial kinetic energies are not sufficient. Although the dissociative adsorption of H2 on PuO2 surfaces is found to be exothermic, the collision-induced dissociation barriers of H2 are very high (up to 2.2 eV). However, PuO2 overlayer on Pu-metal can be reduced to α-Pu2O3 drived by oxygen-lean conditions, and H2 can penetrate and diffuse in α-Pu2O3 easily. As a result, α-Pu2O3 can promote the hydriding process of Pu. Unlike PuO2, PuN is found to be one kind of stable and uniform passivation layer against Pu-hydriding. Specifically, the incorporation of PuN and H-atom is proven to be thermodynamically unstable. Overall, our current study reveals the mechanical and chemical resistances of Pu-oxide and Pu-nitride to hydrogen corrosion, which have strong implications to the understanding of the surface corrosion and passivation of Pu metal. This work was supported by the FDST of CAEP under Grant No. 9090707.

  16. Diffusion within α-CuI studied using ab initio molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Mohn, Chris E.; Stølen, Svein; Hull, Stephen

    2009-08-01

    The structure and dynamics of superionic α-CuI are studied in detail by means of ab initio Born-Oppenheimer molecular dynamics simulations. The extreme cation disorder and a soft immobile face centred cubic sublattice are evident from the highly diffuse atomic density profiles. The Cu-Cu pair distribution function and distribution of Cu-I-Cu bond angles possess distinct peaks at 2.6 Å and 60° respectively, which are markedly lower than the values expected from the average cationic density, pointing to the presence of pronounced short-range copper-copper correlations. Comparison with lattice static calculations shows that these correlations and the marked shift in the cationic density profile in the lang111rang directions are associated with a locally distorted cation sublattice, and that the movements within the tetrahedral cavities involve rapid jumps into and out of shallow basins on the system potential energy surface. On average, the iodines are surrounded by three coppers within their first coordination shell, with the fourth copper being located in a transition zone between two neighbouring iodine cavities. However, time-resolved analysis reveals that the local structure actually involves a mixture of threefold-, fourfold- and fivefold-coordinated iodines. Examination of the ionic trajectories shows that the copper ions jump rapidly to nearest neighbouring tetrahedral cavities (aligned in the lang100rang directions) following a markedly curved trajectory and often involving short-lived (~1 ps) interstitial positions. The nature of the correlated diffusion underlying the unusually high fraction of coppers with short residence time can be attributed to the presence of a large number of 'unsuccessful' jumps and the likelihood of cooperative motion of pairs of coppers. The calculated diffusion coefficient at 750 K, DCu = 2.8 × 10-5 cm2 s-1, is in excellent agreement with that found experimentally.

  17. The ab initio calculation of spectra of open shell diatomic molecules

    NASA Astrophysics Data System (ADS)

    Tennyson, Jonathan; Lodi, Lorenzo; McKemmish, Laura K.; Yurchenko, Sergei N.

    2016-05-01

    The spectra (rotational, rotation-vibrational or electronic) of diatomic molecules due to transitions involving only closed-shell (1Σ ) electronic states follow very regular, simple patterns and their theoretical analysis is usually straightforward. On the other hand, open-shell electronic states lead to more complicated spectral patterns and, moreover, often appear as a manifold of closely lying electronic states, leading to perturbed spectra of even greater complexity. This is especially true when at least one of the atoms is a transition metal. Traditionally these complex cases have been analysed using approaches based on perturbation theory, with semi-empirical parameters determined by fitting to spectral data. Recently the needs of two rather diverse scientific areas have driven the demand for improved theoretical models of open-shell diatomic systems based on an ab initio approach; these areas are ultracold chemistry and the astrophysics of ‘cool’ stars, brown dwarfs and most recently extrasolar planets. However, the complex electronic structure of these molecules combined with the accuracy requirements of high-resolution spectroscopy render such an approach particularly challenging. This review describes recent progress in developing methods for directly solving the effective Schrödinger equation for open-shell diatomic molecules, with a focus on molecules containing a transtion metal. It considers four aspects of the problem: (i) the electronic structure problem; (ii) non-perturbative treatments of the curve couplings; (iii) the solution of the nuclear motion Schrödinger equation; (iv) the generation of accurate electric dipole transition intensities. Examples of applications are used to illustrate these issues.

  18. Ab initio calculation of Ti NMR shieldings for titanium oxides and halides

    NASA Astrophysics Data System (ADS)

    Tossell, J. A.

    Titanium NMR shielding constants have been calculated using ab initio coupled Hartree-Fock perturbation theory and polarized double-zeta basis sets for TiF 4, TiF 62-, TiCI 4, Ti(OH) 4, Ti(OH 2) 64+, Ti(OH) 4O, and Ti(OH) 3O -. In all cases the calculations were performed at Hartree-Fuck energy-optimized geometries. For Ti(OH) 4 a S4-symmetry geometry with nonlinear ∠ TiOH was employed. Relative shieldings are in reasonable agreement with experiment for TiF 62-, TiCI 4, and Ti(OR) 4, where R = H or alkyl. Ti(OH 2) 64+ is predicted to be more highly shielded than Ti(OH) 4 by about 340 ppm. The five-coordinate complex Ti(OH) 4O, whose calculated structure matches well that measured by extended X-ray absorption fine structure in K 2O · TiO 2 · SiO 2 glass, is actually deshielded compared to Ti(OH) 4 by about 40 ppm. X-ray absorption-near-edge spectral energies have also been calculated for TiF 4, TiCI 4, Ti(OH) 4, and Ti(OH) 4O using an equivalent ionic core virtual-orbital method and the observed reduction in term energy for the five-coordinate species compared to Ti(OH) 4 has been reproduced. Replacement of the H atoms in Ti(OH) 4 by point charges has only a slight effect upon σTi, suggesting a possible means of incorporating second-neighbor effects in NMR calculations for condensed phases.

  19. Complementary ab initio and X-ray nanodiffraction studies of Ta2O5

    PubMed Central

    Hollerweger, R.; Holec, D.; Paulitsch, J.; Bartosik, M.; Daniel, R.; Rachbauer, R.; Polcik, P.; Keckes, J.; Krywka, C.; Euchner, H.; Mayrhofer, P.H.

    2015-01-01

    The complex structure of Ta2O5 led to the development of various structural models. Among them, superstructures represent the most stable configurations. However, their formation requires kinetic activity and long-range ordering processes, which are hardly present during physical vapor deposition. Based on nano-beam X-ray diffraction and concomitant ab initio studies, a new metastable orthorhombic basic structure is introduced for Ta2O5 with lattice parameters a = 6.425 Å, b = 3.769 Å and c = 7.706 Å. The unit cell containing only 14 atoms, i.e. two formula unit blocks in the c direction, is characterized by periodically alternating the occupied oxygen site between two possible positions in succeeding 002-planes. This structure can be described by the space group 53 (Pncm) with four Wyckoff positions, and exhibits an energy of formation of −3.209 eV atom−1. Among all the reported basic structures, its energy of formation is closest to those of superstructures. Furthermore, this model exhibits a 2.5 eV band gap, which is closer to experimental data than the band gap of any other basic-structure model. The sputtered Ta2O5 films develop only a superstructure if annealed at temperatures >800 °C in air or vacuum. Based on these results and the conveniently small unit cell size, it is proposed that the basic-structure model described here is an ideal candidate for both structure and electronic state descriptions of orthorhombic Ta2O5 materials. PMID:25642136

  20. Thermodynamics and phonon dispersion of pyrope and grossular silicate garnets from ab initio simulations

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

    The phonon dispersion and thermodynamic properties of pyrope ({Mg}_3{Al}_2{Si}_3{O}_{12}) and grossular ({Ca}_3{Al}_2{Si}_3{O}_{12} ) have been computed by using an ab initio quantum mechanical approach, an all-electron variational Gaussian-type basis set and the B3LYP hybrid functional, as implemented in the Crystal program. Dispersion effects in the phonon bands have been simulated by using supercells of increasing size, containing 80, 160, 320, 640, 1280 and 2160 atoms, corresponding to 1, 2, 4, 8, 16 and 27 {k} points in the first Brillouin zone. Phonon band structures, density of states and corresponding inelastic neutron scattering spectra are reported. Full convergence of the various thermodynamic properties, in particular entropy ( S) and specific heat at constant volume (CV), with the number of {k} points is achieved with 27 {k} points. The very regular behavior of the S( T) and CV(T) curves as a function of the number of {k} points, determined by high numerical stability of the code, permits extrapolation to an infinite number of {k} points. The limiting value differs from the 27-{k} case by only 0.40 % at 100 K for S (the difference decreasing to 0.11 % at 1000 K) and by 0.29 % (0.05 % at 1000 K) for CV. The agreement with the experimental data is rather satisfactory. We also address the problem of the relative entropy of pyrope and grossular, a still debated question. Our lattice dynamical calculations correctly describe the larger entropy of pyrope than grossular by taking into account merely vibrational contributions and without invoking "static disorder" of the Mg ions in dodecahedral sites. However, as the computed entropy difference is found to be larger than the experimental one by a factor of 2-3, present calculations cannot exclude possible thermally induced structural changes, which could lead to further conformational contributions to the entropy.