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Sample records for ab-initio band structure

  1. Ab initio theory for ultrafast magnetization dynamics with a dynamic band structure

    NASA Astrophysics Data System (ADS)

    Mueller, B. Y.; Haag, M.; Fähnle, M.

    2016-09-01

    Laser-induced modifications of magnetic materials on very small spatial dimensions and ultrashort timescales are a promising field for novel storage and spintronic devices. Therefore, the contribution of electron-electron spin-flip scattering to the ultrafast demagnetization of ferromagnets after an ultrashort laser excitation is investigated. In this work, the dynamical change of the band structure resulting from the change of the magnetization in time is taken into account on an ab initio level. We find a large influence of the dynamical band structure on the magnetization dynamics and we illustrate the thermalization and relaxation process after laser irradiation. Treating the dynamical band structure yields a demagnetization comparable to the experimental one.

  2. Ab initio quasiparticle band structure of ABA and ABC-stacked graphene trilayers

    NASA Astrophysics Data System (ADS)

    Menezes, Marcos G.; Capaz, Rodrigo B.; Louie, Steven G.

    2014-01-01

    We obtain the quasiparticle band structure of ABA and ABC-stacked graphene trilayers through ab initio density-functional theory (DFT) and many-body quasiparticle calculations within the GW approximation. To interpret our results, we fit the DFT and GW π bands to a low-energy tight-binding model, which is found to reproduce very well the observed features near the K point. The values of the extracted hopping parameters are reported and compared with available theoretical and experimental data. For both stackings, the self-energy corrections lead to a renormalization of the Fermi velocity, an effect also observed in previous calculations on monolayer graphene. They also increase the separation between the higher-energy bands, which is proportional to the nearest-neighbor interlayer hopping parameter γ1. Both features are brought to closer agreement with experiment through the self-energy corrections. Finally, other effects, such as trigonal warping, electron-hole asymmetry, and energy gaps, are discussed in terms of the associated parameters.

  3. Ab initio calculations of quasiparticle band structure in correlated systems: LDA++ approach

    NASA Astrophysics Data System (ADS)

    Lichtenstein, A. I.; Katsnelson, M. I.

    1998-03-01

    We discuss a general approach to a realistic theory of the electronic structure in materials containing correlated d or f electrons. The main feature of this approach is the taking into account of the energy dependence of the electron self-energy with the momentum dependence being neglected (local approximation). It allows us to consider such correlation effects as the non-Fermi-step form of the distribution function, the enhancement of the effective mass including Kondo resonances,'' the appearance of the satellites in the electron spectra, etc. To specify the form of the self-energy, it is useful to distinguish (according to the ratio of the on-site Coulomb energy U to the bandwidth W) three regimes-strong, moderate, and weak correlations. In the case of strong interactions (U/W>1-rare-earth system) the Hubbard-I approach is the most suitable. Starting from an exact atomic Green function with the constrained density matrix nmm' the band-structure problem is formulated as the functional problem on nmm' for f electrons and the standard local-denisty-approximation functional for delocalized electrons. In the case of moderate correlations (U/W~1-metal-insulator regime, Kondo systems) we start from the d=∞ dynamical mean-field iterative perturbation scheme of Kotliar and co-workers and also make use of our multiband atomic Green function for constrained nmm'. Finally for the weak interactions (U/W<1-transition metals) the self-consistent diagrammatic fluctuation-exchange approach of Bickers and Scalapino is generalized to the realistic multiband case. We present two-band, two-dimensional model calculations for all three regimes. A realistic calculation in the Hubbard-I scheme with the exact solution of the on-site multielectron problem for f(d) shells was performed for mixed-valence 4f compound TmSe, and for the classical Mott insulator NiO.

  4. Structural, vibrational, and quasiparticle band structure of 1,1-diamino-2,2-dinitroethelene from ab initio calculations

    SciTech Connect

    Appalakondaiah, S.; Vaitheeswaran, G.; Lebègue, S.

    2014-01-07

    The effects of pressure on the structural and vibrational properties of the layered molecular crystal 1,1-diamino-2,2-dinitroethelene (FOX-7) are explored by first principles calculations. We observe significant changes in the calculated structural properties with different corrections for treating van der Waals interactions to Density Functional Theory (DFT), as compared with standard DFT functionals. In particular, the calculated ground state lattice parameters, volume and bulk modulus obtained with Grimme's scheme, are found to agree well with experiments. The calculated vibrational frequencies demonstrate the dependence of the intra and inter-molecular interactions on FOX-7 under pressure. In addition, we also found a significant increment in the N–H...O hydrogen bond strength under compression. This is explained by the change in bond lengths between nitrogen, hydrogen, and oxygen atoms, as well as calculated IR spectra under pressure. Finally, the computed band gap is about 2.3 eV with generalized gradient approximation, and is enhanced to 5.1 eV with the GW approximation, which reveals the importance of performing quasiparticle calculations in high energy density materials.

  5. Influence of the sequence on the ab initio band structures of single and double stranded DNA models

    NASA Astrophysics Data System (ADS)

    Bogár, Ferenc; Bende, Attila; Ladik, János

    2014-06-01

    The solid state physical approach is widely used for the characterization of electronic properties of DNA. In the simplest case the helical symmetry is explicitly utilized with a repeat unit containing only a single nucleotide or nucleotide pair. This model provides a band structure that is easily interpretable and reflects the main characteristic features of the single nucleotide or a nucleotide pair chain, respectively. The chemical variability of the different DNA chains is, however, almost completely neglected in this way. In the present work we have investigated the effect of the different sequences on the band structure of periodic DNA models. For this purpose we have applied the Hartree-Fock crystal orbital method for single and double stranded DNA chains with two different subsequent nucleotides in the repeat unit of former and two different nucleotide pairs in the latter case, respectively. These results are compared to simple helical models with uniform sequences. The valence and conduction bands related to the stacked nucleotide bases of single stranded DNA built up only from guanidine as well as of double stranded DNA built up only from guanidine-cytidine pairs showed special properties different from the other cases. Namely, they had higher conduction and lower valence band positions and this way larger band gaps and smaller widths of these bands. With the introduction of non-uniform guanidine containing sequences band structures became more similar to each other and to the band structures of other sequences without guanidine. The maximal bandwidths of the non-uniform sequences are considerably smaller than in the case of uniform sequences implying smaller charge carrier mobilities both in the conduction and valence bands.

  6. 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).

  7. Macromolecular ab initio phasing enforcing secondary and tertiary structure

    PubMed Central

    Millán, Claudia; Sammito, Massimo; Usón, Isabel

    2015-01-01

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

  8. Macromolecular ab initio phasing enforcing secondary and tertiary structure.

    PubMed

    Millán, Claudia; Sammito, Massimo; Usón, Isabel

    2015-01-01

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

  9. Macromolecular ab initio phasing enforcing secondary and tertiary structure.

    PubMed

    Millán, Claudia; Sammito, Massimo; Usón, Isabel

    2015-01-01

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

  10. Unified ab initio approaches to nuclear structure and reactions

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  11. Finite Elements in Ab Initio Electronic-Structure Calulations

    NASA Astrophysics Data System (ADS)

    Pask, J. E.; Sterne, P. A.

    Over the course of the past two decades, the density functional theory (DFT) (see e.g., [1]) of Hohenberg, Kohn, and Sham has proven to be an accurate and reliable basis for the understanding and prediction of a wide range of materials properties from first principles (ab initio), with no experimental input or empirical parameters. However, the solution of the Kohn-Sham equations of DFT is a formidable task and this has limited the range of physical systems which can be investigated by such rigorous, quantum mechanical means. In order to extend the interpretive and predictive power of such quantum mechanical theories further into the domain of "real materials", involving nonstoichiometric deviations, defects, grain boundaries, surfaces, interfaces, and the like; robust and efficient methods for the solution of the associated quantum mechanical equations are critical. The finite-element (FE) method (see e.g., [2]) is a general method for the solution of partial differential and integral equations which has found wide application in diverse fields ranging from particle physics to civil engineering. Here, we discuss its application to large-scale ab initio electronic-structure calculations.

  12. Ab initio X-Ray Absorption Fine Structure Cumulants

    NASA Astrophysics Data System (ADS)

    Vila, F.; Rehr, J. J.; Rossner, H. H.; Krappe, H. J.

    2006-03-01

    Theoretical calculations of vibrational effects in x-ray absorption spectra typically employ semi-phenomenological models, e.g. empirical force constants or correlated Debye or Einstein models. Instead we introduce an efficient and generally applicable ab initio approach based on electronic structure calculations of the dynamical matrix together with the Lanczos recursion algorithm [1] and relations between the cumulants. The approach yields 1) the thermal expansion coefficients (first cumulant of the vibrational distribution function); 2) correlated Debye-Waller factors (second cumulants) and 3) anharmonic contributions (third cumulants). Results are presented for crystalline (Cu, Au, Ge, GaAs) and molecular (GeCl4, C6H6) systems. Our results for the Debye-Waller factors agree well with experiment. [1]H.J. Krappe and H.H. Rossner, Phys. Rev. B70, 104102 (2004).

  13. The Crystal Structure of Impurity Centers Tm^{2+} and Eu^{2+} in SrCl2 : Ab Initio Calculations

    NASA Astrophysics Data System (ADS)

    Chernyshev, V. A.; Serdcev, A. V.; Petrov, V. P.; Nikiforov, A. E.

    2016-01-01

    Ab initio calculations of the impurity centers Tm^{2+} thulium and europium Eu^{2+} in SrCl2 and MeF2 (Me = Ca, Sr, Ba) were carried out at low (zero) temperature. The crystal structure of impurity centers was investigated. Charge density maps show that the bonds formed by the rare-earth ions have an ionic character. The crystal structures, lattice dynamics, and band structures of MeF2 and SrCl2 were calculated at low temperature. Ab initio calculations were performed in periodic CRYSTAL code within the framework of the MO LCAO approach by using hybrid DFT functionals.

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

    SciTech Connect

    Bergli, Elise; Hjorth-Jensen, Morten

    2011-05-15

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

  15. Metal-to-Insulator Transition in Au Chains on Si(111)-5×2-Au by Band Filling: Infrared Plasmonic Signal and Ab Initio Band Structure Calculation.

    PubMed

    Hötzel, Fabian; Seino, Kaori; Chandola, Sandhya; Speiser, Eugen; Esser, Norbert; Bechstedt, Friedhelm; Pucci, Annemarie

    2015-09-17

    The Si(111)-5×2-Au surface is increasingly of interest because it is one of the rare atomic chain systems with quasi-one-dimensional properties. For the deposition of 0.7 monolayers of Au, these chains are metallic. Upon the evaporation of an additional submonolayer amount of gold, the surface becomes insulating but keeps the 5×2 symmetry. This metal-to-insulator transition was in situ monitored based on the infrared plasmonic signal change with coverage. The phase transition is theoretically explained by total-energy and band-structure calculations. Accordingly, it can be understood in terms of the occupation of the originally half-filled one-dimensional band at the Fermi level. By annealing the system, the additional gold is removed from the surface and the plasmonic signal is recovered, which underlines the stability of the metallic structure. So, recent results on the infrared plasmonic signals of the Si(111)-5 × 2-Au surface are supported. The understanding of potential one-dimensional electrical interconnects is improved.

  16. Ab initio calculations of the electronic structure of silicon nanocrystals doped with shallow donors (Li, P)

    SciTech Connect

    Kurova, N. V. Burdov, V. A.

    2013-12-15

    The results of ab initio calculations of the electronic structure of Si nanocrystals doped with shallow donors (Li, P) are reported. It is shown that phosphorus introduces much more significant distortions into the electronic structure of the nanocrystal than lithium, which is due to the stronger central cell potential of the phosphorus ion. It is found that the Li-induced splitting of the ground state in the conduction band of the nanocrystal into the singlet, doublet, and triplet retains its inverse structure typical for bulk silicon.

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

    PubMed

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

    2015-08-01

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

  18. Band offset of the ZnO/Cu2O heterojunction from ab initio calculations

    NASA Astrophysics Data System (ADS)

    Zemzemi, M.; Alaya, S.

    2013-12-01

    The ZnO/Cu2O system has known a recent revival of interest in solar cells for its potential use as a heterojunction able to highly perform under visible light. In this work, we are interested on the characterization of the interface through nanoscale modelization based on ab initio (Density Functional Theory (DFT), Local Density Approximation (LDA), Generalized Gradient Approximation (GGA-PBE), and Pseudopotential (PP)). This work aims to build a supercell containing a heterojunction ZnO/Cu2O and study the structural properties and the discontinuity of the valence band (band offset) from a semiconductor to another. We built a zinc oxide in the wurtzite structure along the [0 0 0 1] on which we placed the copper oxide in the hexagonal structure (CdI2-type). We choose the method of Van de Walle and Martin to calculate the energy offset. This approach fits well with the DFT. Our calculations of the band offset gave us a value that corresponds to other experimental and theoretical values.

  19. Comparison of the electronic band structures of LiCaAlF6 and LiSrAlF6 ultraviolet laser host media from ab initio calculations

    NASA Astrophysics Data System (ADS)

    Viet Luong, Mui; Cadatal-Raduban, Marilou; Empizo, Melvin John F.; Arita, Ren; Minami, Yuki; Shimizu, Toshihiko; Sarukura, Nobuhiko; Azechi, Hiroshi; Pham, Minh Hong; Nguyen, Hung Dai; Kawazoe, Yoshiyuki

    2015-12-01

    We report the electronic structures and density of states (DOS) of perfect LiCAF and LiSAF crystals calculated from density functional theory (DFT) with local density approximation (LDA) using optimized lattice constants. DOS calculations reveal that the valence band is mainly derived from F 2p, thereby resulting to a very narrow valence band manifold. Meanwhile, the conduction band is mainly derived from Ca 4s or Sr 5s resulting to Sr having a broader band dispersion compared to Ca. Both fluoride compounds have indirect band gaps with LiCAF having a band gap of 8.02 eV and LiSAF a band gap of 7.92 eV. This is, to the best of our knowledge, the first report on the electronic structure of LiSAF calculated using DFT with LDA. Our results suggest that when doped with Ce3+, the shorter 5d-conduction band distance in Ce:LiSAF combined with the difficulty of growing high-purity crystals lead to the more pronounced excited state absorption (ESA) and solarization effect experimentally observed in Ce:LiSAF, limiting its potential as a laser material compared with Ce:LiCAF.

  20. Ab initio study of pressure induced structural and electronic properties in TmPo

    SciTech Connect

    Makode, Chandrabhan Pataiya, Jagdish; Sanyal, Sankar P.; Panwar, Y. S.; Aynyas, Mahendra

    2015-06-24

    We report an ab initio calculation of pressure induced structural phase transition and electronic properties of Thulium Polonide (TmPo).The total energy as a function of volume is obtained by means of self-consistent tight binding linear muffin-tin-orbital (TB-LMTO) method within the local density approximation (LDA). It is found that TmPo is stable in NaCl-type (B{sub 1}-phase) structure to CsCl-type (B{sub 2}-phase) structure of this compound in the pressure range of 7.0 GPa. We also calculate the lattice parameter (a{sub 0}), bulk modulus (B{sub 0}), band structure and density of states. From energy diagram it is observed that TmPo exhibit metallic behavior. The calculated values of equilibrium lattice parameter and bulk modulus are in general good agreement.

  1. DFT-based ab initio study of structural and electronic properties of lithium fluorooxoborate LiB6O9F and experimentally observed second harmonic generation

    NASA Astrophysics Data System (ADS)

    Andriyevsky, B.; Doll, K.; Cakmak, G.; Jansen, M.; Niemer, A.; Betzler, K.

    2011-09-01

    An ab initio density functional theory-based study of the electronic band structure, the elastic, electric, elastoelectric, and linear and nonlinear optical properties of the new ion conductor LiB6O9F, has been performed. The computed band structure reveals a wide direct band gap. The coefficients of the second order nonlinear susceptibility χ(2) were found to be comparable to those of KH2PO4. Corresponding experimental investigations of second harmonic generation comply with the respective ab initio calculations.

  2. 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.

  3. Ab Initio Classical Dynamics Simulations of CO_2 Line-Mixing Effects in Infrared Bands

    NASA Astrophysics Data System (ADS)

    Lamouroux, Julien; Hartmann, Jean-Michel; Tran, Ha; Snels, Marcel; Stefani, Stefania; Piccioni, Giuseppe

    2013-06-01

    Ab initio calculations of line-mixing effects in CO_2 infrared bands are presented and compared with experiments. The predictions were carried using requantized Classical Dynamics Molecular Simulations (rCDMS) based on an approach previously developed and successfully tested for CO_2 isolated line shapes. Using classical dynamics equations, the force and torque applied to each molecule by the surrounding molecules (described by an ab initio intermolecular potential) are computed at each time step. This enables, using a requantization procedure, to predict dipole and isotropic polarizability auto-correlation functions whose Fourier-Laplace transforms yield the spectra. The quality of the rCDMS calculations is demonstrated by comparisons with measured spectra in the spectral regions of the 3ν_3 and 2ν_1+2ν_2+ν_3 Infrared bands. J.-M. Hartmann, H. Tran, N. H. Ngo, et al., Phys. Rev. Lett. A {87} (2013), 013403. H. Tran, C. Boulet, M. Snels, S. Stefani, J. Quant. Spectrosc. Radiat. Transfer {112} (2011), 925-936.

  4. Ab initio theory of magnetic-field-induced odd-frequency two-band superconductivity in MgB2

    NASA Astrophysics Data System (ADS)

    Aperis, Alex; Maldonado, Pablo; Oppeneer, Peter M.

    2015-08-01

    We develop the anisotropic Eliashberg framework for superconductivity in the presence of an applied magnetic field. Using as input the ab initio calculated electron and phonon band structures and electron-phonon coupling, we solve self-consistently the anisotropic Eliashberg equations for the archetypal superconductor MgB2. We find two self-consistent solutions, time-even two-band superconductivity, as well as unconventional time-odd s -wave spin triplet two-band superconductivity emerging with applied field. We provide the full momentum, frequency, and spin-resolved dependence and magnetic field-temperature phase diagrams of the time-even and time-odd superconducting pair amplitudes and predict fingerprints of this novel odd-frequency state in tunneling experiments.

  5. Electronic structure of ScN determined using optical spectroscopy, photoemission, and ab initio calculations

    SciTech Connect

    Gall, D.; Sta''dele, M.; Ja''rrendahl, K.; Petrov, I.; Desjardins, P.; Haasch, R. T.; Lee, T.-Y.; Greene, J. E.

    2001-03-15

    Experimental and ab initio computational methods are employed to conclusively show that ScN is a semiconductor rather than a semimetal; i.e., there is a gap between the N 2p and the Sc 3d bands. Previous experimental investigators reported, in agreement with band structure calculations showing a band overlap of 0.2 eV, that ScN is a semimetal while others concluded that it is a semiconductor with a band gap larger than 2 eV. We have grown high quality, single crystalline ScN layers on MgO(001) and on TiN(001) buffer layers on MgO(001) by ultrahigh vacuum reactive magnetron sputter deposition. ScN optical properties were determined by transmission, reflection, and spectroscopic ellipsometry while in-situ x-ray and ultraviolet valence band photoelectron spectroscopy were used to determine the density of states (DOS) below the Fermi level. The measured DOS exhibits peaks at 3.8 and 5.2 eV stemming from the N 2p bands and at 15.3 eV due to the N 2s bands. The imaginary part of the measured dielectric function {epsilon}{sub 2} consists of two primary features due to direct X- and {Gamma}-point transitions at photon energies of 2.7 and 3.8 eV, respectively. For comparison, the ScN band structure was calculated using an ab initio Kohn--Sham approach which treats the exchange interactions exactly within density-functional theory. Calculated DOS and the complex dielectric function are in good agreement with our ScN valence-band photoelectron spectra and measured optical properties, respectively. We conclude, combining experimental and computational results, that ScN is a semiconductor with an indirect {Gamma}--X bandgap of 1.3{+-}0.3eV and a direct X-point gap of 2.4{+-}0.3eV.

  6. The C4H radical and the diffuse interstellar bands. An ab initio study

    NASA Technical Reports Server (NTRS)

    Kolbuszewski, Marcin

    1994-01-01

    An ab initio study of the low-lying electronic states of C4H has been presented where the species studied has a chi(2)sigma(+) ground state and two low lying pi states. Based on the vertical and adiabatic excitation energies between those states it is suggested that the 4428 A diffuse interstellar band is not carried by C4H. The application of the particle in a box model shows strong coincidences between the strong DIB's and predicted wavelengths of pi-pi transitions in C(2n)H series. Based on those coincidences, it is suggested the C(2n)H species as good candidates for carriers of diffuse interstellar bands.

  7. 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.

  8. Structural properties of rutherfordium: An ab-initio study

    NASA Astrophysics Data System (ADS)

    Gyanchandani, Jyoti; Sikka, S. K.

    2012-01-01

    The structural and electronic properties of rutherfordium, the latest group IV B element, have been evaluated by first principles density functional theory in scalar relativistic formalism with and without spin-orbit coupling and compared with its 5d homologue Hf. It is found that Rf will crystallize in the hexagonal close packed structure as in Hf. However, under pressure, it will have different sequence of phase transitions than Hf: hcp→bcc instead of hcp→ω→bcc. An explanation is offered for this difference in terms of the competition between the band structure and the Ewald energy contributions.

  9. 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.

  10. The infrared band intensities and other properties of the homodimers of the methyl and silyl halides: An ab initio study

    NASA Astrophysics Data System (ADS)

    Ford, Thomas A.

    2012-02-01

    The properties of the homodimers of methyl and silyl fluoride, chloride and bromide have been determined by means of ab initio molecular orbital calculations. The interaction energies, molecular structures, vibrational spectra and molecular orbital properties have been investigated, and some common features within each family have been observed. A number of systematic differences in the properties of the dimers have also been noted and rationalized. Typically, discussion of the results of such calculations has focused on the vibrational wavenumber shifts occurring on complexation, and the accompanying changes in the infrared band intensities have received relatively little attention. This paper aims to reposition infrared intensities as valid and useful parameters with which to interpret the formation of the homodimers of polar molecules.

  11. Ab initio calculations of the electronic structure and bonding characteristics of LaB6

    NASA Astrophysics Data System (ADS)

    Hossain, Faruque M.; Riley, Daniel P.; Murch, Graeme E.

    2005-12-01

    Lanthanum hexaboride ( LaB6 , NIST SRM-660a) is widely used as a standard reference material for calibrating the line position and line shape parameters of powder diffraction instruments. The accuracy of this calibration technique is highly dependent on how completely the reference material is characterized. Critical to x-ray diffraction, this understanding must include the valence of the La atomic position, which in turn will influence the x-ray form factor (f) and hence the diffracted intensities. The electronic structure and bonding properties of LaB6 have been investigated using ab initio plane-wave pseudopotential total energy calculations. The electronic properties and atomic bonding characteristics were analyzed by estimating the energy band structure and the density of states around the Fermi energy level. The calculated energy band structure is consistent with previously reported experimental findings; de Haas-van Alphen and two-dimensional angular correlation of electron-positron annihilation radiation. In addition, the bond strengths and types of atomic bonds in the LaB6 compound were estimated by analyzing the Mulliken charge density population. The calculated result revealed the coexistence of covalent, ionic, and metallic bonding in the LaB6 system and partially explains its high efficiency as a thermionic emitter.

  12. Ab initio NMR Confirmed Evolutionary Structure Prediction for Organic Molecular Crystals

    NASA Astrophysics Data System (ADS)

    Pham, Cong-Huy; Kucukbenli, Emine; de Gironcoli, Stefano

    2015-03-01

    Ab initio crystal structure prediction of even small organic compounds is extremely challenging due to polymorphism, molecular flexibility and difficulties in addressing the dispersion interaction from first principles. We recently implemented vdW-aware density functionals and demonstrated their success in energy ordering of aminoacid crystals. In this work we combine this development with the evolutionary structure prediction method to study cholesterol polymorphs. Cholesterol crystals have paramount importance in various diseases, from cancer to atherosclerosis. The structure of some polymorphs (e.g. ChM, ChAl, ChAh) have already been resolved while some others, which display distinct NMR spectra and are involved in disease formation, are yet to be determined. Here we thoroughly assess the applicability of evolutionary structure prediction to address such real world problems. We validate the newly predicted structures with ab initio NMR chemical shift data using secondary referencing for an improved comparison with experiments.

  13. 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

  14. 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.

  15. Structures of 13-atom clusters of fcc transition metals by ab initio and semiempirical calculations

    NASA Astrophysics Data System (ADS)

    Longo, R. C.; Gallego, L. J.

    2006-11-01

    We report the results of ab initio calculations of the structures and magnetic moments of Ni13 , Pd13 , Pt13 , Cu13 , Ag13 , and Au13 that were performed using a density-functional method that employs linear combinations of pseudoatomic orbitals as basis sets (SIESTA). Our structural results for Pt13 , Cu13 , Ag13 , and Au13 show that a buckled biplanar structure (BBP) is more stable than the icosahedral configuration, in keeping with results obtained recently by Chang and Chou [Phys. Rev. Lett. 93, 133401 (2004)] using the Vienna ab initio simulation package with a plane-wave basis. However, for Ni13 and Pd13 we found that the icosahedral structure is more stable than BBP. For all these clusters, two semiempirical methods based on spherically symmetric potentials both found the icosahedral structure to be the more stable, while the modified embedded atom model method, which uses a direction-dependent potential, found BBP to be the more stable structure. When low-energy structures found in recent ab initio studies of Pt13 , Cu13 , and Au13 other than Chang and Chou were optimized with SIESTA, those reported for Pt13 and Cu13 were found to be less stable than BBP, but the two-dimensional planar configuration reported for Au13 proved to be more stable than BBP.

  16. Electronic and structural properties of nitrogen adsorbed Nb(100) surfaces: An ab initio study

    NASA Astrophysics Data System (ADS)

    Carvalho, P. A. S.; Miwa, R. H.

    2013-08-01

    We have performed an ab initio total energy investigation of the electronic and structural properties of nitrogen adsorbed Nb(100) surface, N/Nb(100). We find an energetic preference for the nitrogen adsorption on the hollow sites of the Nb(100) surface. Upon the presence of N adatoms, there is a reduction of the electronic density of states near the Fermi level. However, the metallic character of the Nb(100) surface has been maintained. The (occupied) electronic states of N adatoms are resonant within the valence band of Nb(100), mostly lying at 4 eV below the Fermi level. Further investigations reveal the formation of energetically stable N/Nb(100)-(n × 1) phase, being the (2 × 1), (5 × 1), and (10 × 1) the most likely ones. Those (n × 1) structures are composed by NbN stripes separated by N vacancy lines. Our scanning tunneling microscopy simulations indicate the formation of bright lines lying on the Nb atoms neighboring the (dark) N vacancy lines, giving rise to an anisotropic electronic structure on the N/Nb(100)-(n × 1) surface. That is, the metallic character of the surface has been strengthened along the vacancy-lines.

  17. Ab initio calculation of structural stability, electronic and optical properties of Ag{sub 2}Se

    SciTech Connect

    Rameshkumar, S.; Jayalakshmi, V.; Jaiganesh, G.; Palanivel, B.

    2015-06-24

    The structural stability, electronic and optical properties of Ag{sub 2}Se compound is studied using ab initio packages. Ag{sub 2}Se is found to crystallize in orthorhombic structure with two different space groups i.e. P2{sub 1}2{sub 1}2{sub 1} (No. 19) and P222{sub 1} (No. 17). For this compound in these two space groups, the total energy has been computed as a function of volume. Our calculated results suggest that the P2{sub 1}2{sub 1}2{sub 1}–phase is more stable than that of the P222{sub 1}–phase. The band structure calculation show that Ag{sub 2}Se is semimetallic with an overlap of about 0.014 eV in P2{sub 1}2{sub 1}2{sub 1}–phase whereas is metallic in nature in P222{sub 1}–phase. Moreover, the optical properties including the dielectric function, energy loss spectrum are obtained and analysed.

  18. Incorporating Ab Initio energy into threading approaches for protein structure prediction

    PubMed Central

    2011-01-01

    Background Native structures of proteins are formed essentially due to the combining effects of local and distant (in the sense of sequence) interactions among residues. These interaction information are, explicitly or implicitly, encoded into the scoring function in protein structure prediction approaches—threading approaches usually measure an alignment in the sense that how well a sequence adopts an existing structure; while the energy functions in Ab Initio methods are designed to measure how likely a conformation is near-native. Encouraging progress has been observed in structure refinement where knowledge-based or physics-based potentials are designed to capture distant interactions. Thus, it is interesting to investigate whether distant interaction information captured by the Ab Initio energy function can be used to improve threading, especially for the weakly/distant homologous templates. Results In this paper, we investigate the possibility to improve alignment-generating through incorporating distant interaction information into the alignment scoring function in a nontrivial approach. Specifically, the distant interaction information is introduced through employing an Ab Initio energy function to evaluate the “partial” decoy built from an alignment. Subsequently, a local search algorithm is utilized to optimize the scoring function. Experimental results demonstrate that with distant interaction items, the quality of generated alignments are improved on 68 out of 127 query-template pairs in Prosup benchmark. In addition, compared with state-to-art threading methods, our method performs better on alignment accuracy comparison. Conclusions Incorporating Ab Initio energy functions into threading can greatly improve alignment accuracy. PMID:21342587

  19. 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.

  20. Ab initio nuclear structure from lattice effective field theory

    SciTech Connect

    Lee, Dean

    2014-11-11

    This proceedings article reviews recent results by the Nuclear Lattice EFT Collaboration on an excited state of the {sup 12}C nucleus known as the Hoyle state. The Hoyle state plays a key role in the production of carbon via the triple-alpha reaction in red giant stars. We discuss the structure of low-lying states of {sup 12}C as well as the dependence of the triple-alpha reaction on the masses of the light quarks.

  1. Hydration structure of salt solutions from ab initio molecular dynamics

    SciTech Connect

    Bankura, Arindam; Carnevale, Vincenzo; Klein, Michael L.

    2013-01-07

    The solvation structures of Na{sup +}, K{sup +}, and Cl{sup -} ions in aqueous solution have been investigated using density functional theory (DFT) based Car-Parrinello (CP) molecular dynamics (MD) simulations. CPMD trajectories were collected for systems containing three NaCl or KCl ion pairs solvated by 122 water molecules using three different but commonly employed density functionals (BLYP, HCTH, and PBE) with electron correlation treated at the level of the generalized gradient approximation (GGA). The effect of including dispersion forces was analyzed through the use of an empirical correction to the DFT-GGA scheme. Special attention was paid to the hydration characteristics, especially the structural properties of the first solvation shell of the ions, which was investigated through ion-water radial distribution functions, coordination numbers, and angular distribution functions. There are significant differences between the present results obtained from CPMD simulations and those provided by classical MD based on either the CHARMM force field or a polarizable model. Overall, the computed structural properties are in fair agreement with the available experimental results. In particular, the observed coordination numbers 5.0-5.5, 6.0-6.4, and 6.0-6.5 for Na{sup +}, K{sup +}, and Cl{sup -}, respectively, are consistent with X-ray and neutron scattering studies but differ somewhat from some of the many other recent computational studies of these important systems. Possible reasons for the differences are discussed.

  2. Hydration structure of salt solutions from ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Bankura, Arindam; Carnevale, Vincenzo; Klein, Michael L.

    2013-01-01

    The solvation structures of Na^+, K^+, and Cl^- ions in aqueous solution have been investigated using density functional theory (DFT) based Car-Parrinello (CP) molecular dynamics (MD) simulations. CPMD trajectories were collected for systems containing three NaCl or KCl ion pairs solvated by 122 water molecules using three different but commonly employed density functionals (BLYP, HCTH, and PBE) with electron correlation treated at the level of the generalized gradient approximation (GGA). The effect of including dispersion forces was analyzed through the use of an empirical correction to the DFT-GGA scheme. Special attention was paid to the hydration characteristics, especially the structural properties of the first solvation shell of the ions, which was investigated through ion-water radial distribution functions, coordination numbers, and angular distribution functions. There are significant differences between the present results obtained from CPMD simulations and those provided by classical MD based on either the CHARMM force field or a polarizable model. Overall, the computed structural properties are in fair agreement with the available experimental results. In particular, the observed coordination numbers 5.0-5.5, 6.0-6.4, and 6.0-6.5 for Na^+, K^+, and Cl^-, respectively, are consistent with X-ray and neutron scattering studies but differ somewhat from some of the many other recent computational studies of these important systems. Possible reasons for the differences are discussed.

  3. Ab initio structure determination of n-diamond.

    PubMed

    Li, Da; Tian, Fubo; Chu, Binhua; Duan, Defang; Sha, Xiaojing; Lv, Yunzhou; Zhang, Huadi; Lu, Nan; Liu, Bingbing; Cui, Tian

    2015-08-24

    A systematic computational study on the crystal structure of n-diamond has been performed using first-principle methods. A novel carbon allotrope with hexagonal symmetry R32 space group has been predicted. We name it as HR-carbon. HR-carbon composed of lonsdaleite layers and unique C3 isosceles triangle rings, is stable over graphite phase above 14.2 GPa. The simulated x-ray diffraction pattern, Raman, and energy-loss near-edge spectrum can match the experimental results very well, indicating that HR-carbon is a likely candidate structure for n-diamond. HR-carbon has an incompressible atomic arrangement because of unique C3 isosceles triangle rings. The hardness and bulk modulus of HR-carbon are calculated to be 80 GPa and 427 GPa, respectively, which are comparable to those of diamond. C3 isosceles triangle rings are very important for the stability and hardness of HR-carbon.

  4. Structural and magnetic properties of Tcn@C60 endohedral metallofullerenes: An ab initio study

    NASA Astrophysics Data System (ADS)

    Kim, Eunja; Weck, Philippe F.; Czerwinski, Kenneth R.; Tománek, David

    2010-03-01

    We use ab initio spin density functional calculations to study the equilibrium structure and magnetic properties of Tcn@C60 endohedral metallofullerenes. The radionuclide ^99mTc is well established in biomedicine as a potent in vivo diagnostic radiopharmaceutical; its encapsulation in the inert C60 shell is expected to limit possible cytotoxicity of radiometal nanoparticles catabolized by the biological host. We find that C60 can endohedrally accommodate Tcn clusters with up to n=7. The encapsulation does not change significantly the structure of the enclosed clusters, but reduces the magnetic moment due to a stronger Tc--C hybridization for the larger clusters.

  5. Electronic Structures of Anti-Ferromagnetic Tetraradicals: Ab Initio and Semi-Empirical Studies.

    PubMed

    Zhang, Dawei; Liu, Chungen

    2016-04-12

    The energy relationships and electronic structures of the lowest-lying spin states in several anti-ferromagnetic tetraradical model systems are studied with high-level ab initio and semi-empirical methods. The Full-CI method (FCI), the complete active space second-order perturbation theory (CASPT2), and the n-electron valence state perturbation theory (NEVPT2) are employed to obtain reference results. By comparing the energy relationships predicted from the Heisenberg and Hubbard models with ab initio benchmarks, the accuracy of the widely used Heisenberg model for anti-ferromagnetic spin-coupling in low-spin polyradicals is cautiously tested in this work. It is found that the strength of electron correlation (|U/t|) concerning anti-ferromagnetically coupled radical centers could range widely from strong to moderate correlation regimes and could become another degree of freedom besides the spin multiplicity. Accordingly, the Heisenberg-type model works well in the regime of strong correlation, which reproduces well the energy relationships along with the wave functions of all the spin states. In moderately spin-correlated tetraradicals, the results of the prototype Heisenberg model deviate severely from those of multi-reference electron correlation ab initio methods, while the extended Heisenberg model, containing four-body terms, can introduce reasonable corrections and maintains its accuracy in this condition. In the weak correlation regime, both the prototype Heisenberg model and its extended forms containing higher-order correction terms will encounter difficulties. Meanwhile, the Hubbard model shows balanced accuracy from strong to weak correlation cases and can reproduce qualitatively correct electronic structures, which makes it more suitable for the study of anti-ferromagnetic coupling in polyradical systems. PMID:26963572

  6. Structure and lattice dynamics of PrFe3(BO3)4: Ab initio calculation

    NASA Astrophysics Data System (ADS)

    Chernyshev, V. A.; Nikiforov, A. E.; Petrov, V. P.

    2016-06-01

    The crystal structure and phonon spectrum of PrFe3(BO3)4 are ab initio calculated in the context of the density functional theory. The ion coordinates in the unit cell of a crystal and the lattice parameters are evaluated from the calculations. The types and frequencies of the fundamental vibrations, as well as the line intensities of the IR spectrum, are determined. The elastic constants of the crystal are calculated. A "seed" frequency of the vibration strongly interacting with the electron excitation on the praseodymium ion is obtained for low-frequency A 2 mode. The calculated results are in agreement with the known experimental data.

  7. 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.

  8. Simple synthesis, structure and ab initio study of 1,4-benzodiazepine-2,5-diones

    NASA Astrophysics Data System (ADS)

    Jadidi, Khosrow; Aryan, Reza; Mehrdad, Morteza; Lügger, Thomas; Ekkehardt Hahn, F.; Ng, Seik Weng

    2004-04-01

    A simple procedure for the synthesis of pyrido[2,1-c][1,4] benzodiazepine-6,12-dione ( 1) and 1,4-benzodiazepine-2,5-diones ( 2a- 2d), using microwave irradiation and/or conventional heating is reported. The configuration of 1 was determined by single-crystal X-ray diffraction. A detailed ab initio B3LYP/6-31G* calculation of structural parameters and substituent effects on ring inversion barriers (Δ G#) and also free energy differences (Δ G0) for benzodiazepines are reported.

  9. Ab Initio Protein Structure Assembly Using Continuous Structure Fragments and Optimized Knowledge-based Force Field

    PubMed Central

    Xu, Dong; Zhang, Yang

    2012-01-01

    Ab initio protein folding is one of the major unsolved problems in computational biology due to the difficulties in force field design and conformational search. We developed a novel program, QUARK, for template-free protein structure prediction. Query sequences are first broken into fragments of 1–20 residues where multiple fragment structures are retrieved at each position from unrelated experimental structures. Full-length structure models are then assembled from fragments using replica-exchange Monte Carlo simulations, which are guided by a composite knowledge-based force field. A number of novel energy terms and Monte Carlo movements are introduced and the particular contributions to enhancing the efficiency of both force field and search engine are analyzed in detail. QUARK prediction procedure is depicted and tested on the structure modeling of 145 non-homologous proteins. Although no global templates are used and all fragments from experimental structures with template modeling score (TM-score) >0.5 are excluded, QUARK can successfully construct 3D models of correct folds in 1/3 cases of short proteins up to 100 residues. In the ninth community-wide Critical Assessment of protein Structure Prediction (CASP9) experiment, QUARK server outperformed the second and third best servers by 18% and 47% based on the cumulative Z-score of global distance test-total (GDT-TS) scores in the free modeling (FM) category. Although ab initio protein folding remains a significant challenge, these data demonstrate new progress towards the solution of the most important problem in the field. PMID:22411565

  10. 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.

  11. Ab initio investigations of the electronic structure and chemical bonding of Li2ZrN2

    NASA Astrophysics Data System (ADS)

    Matar, S. F.; Pöttgen, R.; Al Alam, A. F.; Ouaini, N.

    2012-06-01

    The electronic structure of the ternary nitride Li2ZrN2 is examined from ab initio with DFT computations for an assessment of the properties of chemical bonding. The compound is found insulating with 1.8 eV band gap; it becomes metallic and less ionic upon removal of one equivalent of Li. The chemical interaction is found mainly between Zr and N on one hand and Li and N on the other hand. While all pair interactions are bonding, antibonding N-N interactions are found dominant at the top of the valence band of Li2ZrN2 and they become less intense upon removal of Li. From energy differences the partial delithiation leading to Li2-xZrN2 (x=∼1) is favored.

  12. Symmetry-Adapted Ab Initio Shell Model for Nuclear Structure Calculations

    NASA Astrophysics Data System (ADS)

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

    2012-05-01

    An innovative concept, the symmetry-adapted ab initio shell model, that capitalizes on partial as well as exact symmetries that underpin the structure of nuclei, is discussed. This framework is expected to inform the leading features of nuclear structure and reaction data for light and medium mass nuclei, which are currently inaccessible by theory and experiment and for which predictions of modern phenomenological models often diverge. We use powerful computational and group-theoretical algorithms to perform ab initio CI (configuration-interaction) calculations in a model space spanned by SU(3) symmetry-adapted many-body configurations with the JISP16 nucleon-nucleon interaction. We demonstrate that the results for the ground states of light nuclei up through A = 16 exhibit a strong dominance of low-spin and high-deformation configurations together with an evident symplectic structure. This, in turn, points to the importance of using a symmetry-adapted framework, one based on an LS coupling scheme with the associated spatial configurations organized according to deformation.

  13. Structure and dynamics of bioactive phosphosilicate glasses and melts from ab initio molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Tilocca, Antonio

    2007-12-01

    Ab initio (Car-Parrinello) molecular dynamics simulations were carried out to investigate the melt precursor of a modified phosphosilicate glass with bioactive properties, and to quench the melt to the vitreous state. The properties of the 3000K liquid were extensively compared with those of the final glass structure. The melt is characterized by a significant fraction of structural defects (small rings, undercoordinated and overcoordinated ions), often combined together. The creation or removal of these coordinative defects in the liquid (through Si-O bond formation or dissociation) reflects frequent exchanges within the silicate first coordination shell, which in turn dynamically modify the intertetrahedral connectivity of silicate groups. The observed dynamical variation in both the identity and the number of silicate groups linked to a tagged Si ( Qn speciation) are considered key processes in the viscous flow of silicate melts [I. Farnan and J. F. Stebbins, Science 265, 1206 (1994)]. On the other hand, phosphate groups do not show an equally marked exchange activity in the coordination shell, but can still form links with Si. Once formed, these Si-O-P bridges are rather stable, and in fact they are retained in the glass phase obtained after cooling; their formation within the present full ab initio melt-and-quench approach strongly supports their presence in melt-derived phosphosilicate glasses with bioactive applications. On the other hand, the simulations show that the fraction of structural defects rapidly decreases during the cooling, and the glass is essentially free of miscoordinated ions and small rings.

  14. Ab initio study of structural and electronic properties of Cun@C60

    NASA Astrophysics Data System (ADS)

    Dhiman, Shobhna; Kumar, Ranjan; Dharamvir, Keya

    2013-06-01

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

  15. Structural and electronic properties of aqueous NaCl solutions from ab initio molecular dynamics simulations with hybrid density functionals

    NASA Astrophysics Data System (ADS)

    Gaiduk, Alex P.; Zhang, Cui; Gygi, François; Galli, Giulia

    2014-06-01

    We present a study of a dilute solution (1 M) of NaCl in water, carried out using ab initio molecular dynamics with semilocal and hybrid functionals. We showed that the structural and electronic properties of the solute and the solvent are the same as those obtained in the infinite dilution limit, i.e. for aqueous ions in the presence of a uniform compensating background. Compared to semilocal functionals, simulations with hybrid functionals yield a less structured solution with a smaller number of hydrogen bonds and a larger coordination number for the Cl- anion. In addition, hybrid functionals predict qualitatively correct positions of the energy levels of the ions with respect to the valence band of water.

  16. Evolved chiral NN +3N Hamiltonians for ab initio nuclear structure calculations

    NASA Astrophysics Data System (ADS)

    Roth, Robert; Calci, Angelo; Langhammer, Joachim; Binder, Sven

    2014-08-01

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

  17. Microwave spectrum, r(0) structure, dipole moment, barrier to internal rotation, and Ab initio calculations for fluoromethylsilane.

    PubMed

    Durig, James R; Panikar, Savitha S; Groner, Peter; Nanaie, Hossein; Bürger, Hans; Moritz, Peter

    2010-04-01

    The microwave spectra of seven isotopomers of fluoromethylsilane, CH(2)FSiH(3), in the ground vibrational state were measured and analyzed in the frequency range 18-40 GHz. The rotational and centrifugal distortion constants were evaluated by the least-squares treatment of the observed frequencies of a- and b-type R- and b-type Q-transitions. The values for the components of the dipole moment were obtained from the measurements of Stark effects from both a- and b-type transitions and the determined values are: |mu(a)| = 1.041(5), |mu(b)| = 1.311(6), and |mu(t)| = 1.674(4) D. Structural parameters have been determined and the heavy atom distances (r(0)) in Angstroms are: Si-C = 1.8942(57) and C-F = 1.4035(55) and the angle in degree, angleSiCF = 109.58(14). A semi-experimental r(e) structure was also determined from experimental ground state rotational constants and vibration-rotation constants derived from ab initio force fields. The internal torsional fundamental, SiH(3), was observed at 149.2 cm(-1) with two accompanying hot bands at 138.8 and 127.5 cm(-1). The barrier to internal rotation was obtained as 717.3(16) cm(-1) (2.051(46) kcal mol(-1)) by combining the analysis of the microwave A and E splittings and the torsional fundamental and hot band frequencies. Ab initio calculations have been carried out with full electron correlation by the second-order perturbation method with several different basis sets up to MP2/6-311+G(d,p) to obtain geometrical parameters, barriers to internal rotation, and centrifugal distortion constants. Adjusted r(0) structural parameters have been obtained by combining the ab initio MP2/6-311+G(d,p) predicted values with the determined rotational constants for the fluoride as well as with the previously reported microwave data for the chloro- and bromo- compounds. These experimental results are compared to the corresponding parameters for the carbon analogues.

  18. Ab initio study of electron-ion structure factors in binary liquids with different types of chemical bonding

    SciTech Connect

    Klevets, Ivan; Bryk, Taras

    2014-12-07

    Electron-ion structure factors, calculated in ab initio molecular dynamics simulations, are reported for several binary liquids with different kinds of chemical bonding: metallic liquid alloy Bi–Pb, molten salt RbF, and liquid water. We derive analytical expressions for the long-wavelength asymptotes of the partial electron-ion structure factors of binary systems and show that the analytical results are in good agreement with the ab initio simulation data. The long-wavelength behaviour of the total charge structure factors for the three binary liquids is discussed.

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

    PubMed

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

    2015-01-28

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

  20. 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.

  1. Integration of QUARK and I-TASSER for Ab Initio Protein Structure Prediction in CASP11.

    PubMed

    Zhang, Wenxuan; Yang, Jianyi; He, Baoji; Walker, Sara Elizabeth; Zhang, Hongjiu; Govindarajoo, Brandon; Virtanen, Jouko; Xue, Zhidong; Shen, Hong-Bin; Zhang, Yang

    2016-09-01

    We tested two pipelines developed for template-free protein structure prediction in the CASP11 experiment. First, the QUARK pipeline constructs structure models by reassembling fragments of continuously distributed lengths excised from unrelated proteins. Five free-modeling (FM) targets have the model successfully constructed by QUARK with a TM-score above 0.4, including the first model of T0837-D1, which has a TM-score = 0.736 and RMSD = 2.9 Å to the native. Detailed analysis showed that the success is partly attributed to the high-resolution contact map prediction derived from fragment-based distance-profiles, which are mainly located between regular secondary structure elements and loops/turns and help guide the orientation of secondary structure assembly. In the Zhang-Server pipeline, weakly scoring threading templates are re-ordered by the structural similarity to the ab initio folding models, which are then reassembled by I-TASSER based structure assembly simulations; 60% more domains with length up to 204 residues, compared to the QUARK pipeline, were successfully modeled by the I-TASSER pipeline with a TM-score above 0.4. The robustness of the I-TASSER pipeline can stem from the composite fragment-assembly simulations that combine structures from both ab initio folding and threading template refinements. Despite the promising cases, challenges still exist in long-range beta-strand folding, domain parsing, and the uncertainty of secondary structure prediction; the latter of which was found to affect nearly all aspects of FM structure predictions, from fragment identification, target classification, structure assembly, to final model selection. Significant efforts are needed to solve these problems before real progress on FM could be made. Proteins 2016; 84(Suppl 1):76-86. © 2015 Wiley Periodicals, Inc.

  2. Ab Initio Calculation of Structure and Thermodynamic Properties of Zintl Aluminide SrAl2

    NASA Astrophysics Data System (ADS)

    Fu, Zhi-Jian; Jia, Li-Jun; Xia, Ji-Hong; Tang, Ke; Li, Zhao-Hong; Sun, Xiao-Wei; Chen, Qi-Feng

    2015-12-01

    The structural and thermodynamic properties of the orthorhombic and cubic structure SrAl2 at pressure and temperature are investigated by using the ab initio plane-wave pseudopotential density functional theory methodwithin the generalised gradient approximation (GGA). The calculated lattice parameters are in agreement with the available experimental data and other theoretical results. The phase transition predicted takes place at 0.5 GPa from the orthorhombic to the cubic structure at zero temperature. The thermodynamic properties of the zinc-blende structure SrAl2 are calculated by the quasi-harmonic Debye model. The pressure-volume relationship and the variations inthe thermal expansion α are obtained systematically in the pressure and temperature ranges of 0-5 GPa and 0-500 K, respectively.

  3. Structural phase transition of CdTe: an ab initio study.

    PubMed

    Alptekin, Sebahaddin

    2013-01-01

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

  4. 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.

  5. 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.

  6. 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.

  7. Ab initio structure determination of new compound Ba 3(BO 3)(PO 4)

    NASA Astrophysics Data System (ADS)

    Ma, H. W.; Liang, J. K.; Wu, L.; Liu, G. Y.; Rao, G. H.; Chen, X. L.

    2004-10-01

    The crystal structure of new compound Ba3BPO7 was determined by ab initio method from high-resolution conventional X-ray powder diffraction data. The Rietveld refinement converged to Rp=5.92%, Rwp=8.87%, Rexp=5.00% with the following details: Hexagonal, space group P63mc, a=5.4898 (1) Å, c=14.7551(1) Å, Z=2. The basic unit of the structure is the [BaO10]-[BO3]-[PO4] polar polyhedra-chain composed of Ba1-B-P-O cluster. These chains, running along c-axis, stack in a HCP mode to build the whole structure with triangular prism channels. The channels are parallel to c-axis too, in which Ba2 and Ba3 are located.

  8. Structure, dynamics, and electronic structure of liquid Ag-Se alloys investigated by ab initio simulation

    NASA Astrophysics Data System (ADS)

    Kirchhoff, F.; Holender, J. M.; Gillan, M. J.

    1996-07-01

    Ab initio molecular-dynamics simulations have been used to investigate the structure, dynamics, and electronic properties of the liquid alloy Ag1-xSex at 1350 K and at the three compositions x=0.33, 0.42, and 0.65. To provide a point of reference, calculations are also presented for the equilibrium structure and the electronic structure of the α-Ag2Se crystal. The calculations are based on density-functional theory in the local-density approximation and on the pseudopotential plane-wave method. For the solid, we find excellent agreement with experiment for the equilibrium lattice parameters and the atomic coordinates of the 12-atom orthorhombic unit cell, and we present an analysis of the electronic density of states and density distribution. The reliability of the liquid simulations is confirmed by detailed comparisons with very recent neutron-diffraction results for the partial structure factors and radial distribution functions (RDF) of the stoichiometric liquid Ag2Se. Comparison with the predictions of an empirical interaction model due to Rino et al. is also given for l-Ag2Se. The ab initio simulations show a dramatic change of the Se-Se RDF with increasing Se content. This change is due to the formation of Se clusters bound by covalent bonds, the Se-Se bond length being almost the same as in pure c-Se and l-Se. The clusters are predominantly chainlike, but for higher x there is a significant fraction of threefold coordinated Se atoms. It is shown that the equilibrium fractions of Se present as isolated atoms and in clusters can be understood on a simple charge-balance model based on an ionic interpretation. The Ag diffusion coefficient in the simulated stoichiometric liquid is consistent with experimental values measured in the high-temperature superionic solid. The Ag and Se diffusion coefficients both increase with Se content, in spite of the Se clustering. An analysis of the Se-Se bond dynamics reveals surprisingly short bond lifetimes of less than 1 ps

  9. Ab initio molecular dynamics: Relationship between structural phases and the sound velocity in dense hydrogen

    NASA Astrophysics Data System (ADS)

    Guerrero, Carlo L.; Cuesta-Lopez, Santiago; Perlado, Jose M.

    2014-10-01

    The phase diagram and the possible stable structures of molecular solid hydrogen are intriguing physical phenomena that still remain to be fully unveiled. Particularly, its transition to metallic hydrogen at high pressures is currently a hot topic of discussion. This letter reports a simulation method that links the ab initio, quantum molecular dynamic and mechanical properties calculations to study the relation between the structural phase transitions and sound velocity in solid molecular hydrogen. The pressure range studied is from 0.1 GPa to 180 GPa, at 15 K temperature, thereby our aim is to simulate the conditions of manufacture, handling and early stages of compression of the target fuel used in confinement inertial fusion. Phase I degeneration below 1 GPa is discussed.

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

    NASA Astrophysics Data System (ADS)

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

    2014-07-01

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

  11. Ab Initio Investigation of the Structures of Fe-Doped Carbon Clusters

    NASA Astrophysics Data System (ADS)

    Lovato, Christella; Brownrigg, Clifton; Hira, Ajit

    2012-02-01

    We continue our interest in the theoretical study of carbon clusters to examine the effects of the doping of small carbon clusters (Cn, n = 2 - 15) with iron atoms. This work applies the hybrid ab initio methods of quantum chemistry to derive the different FemCn (m = 1-3) geometries. Of particular interest are linear, fan, and cyclic geometries. Electronic energies, rotational constants, dipole moments, and vibrational frequencies for these geometries are calculated. Exploration of the singlet, triplet, quintet, and septet potential energy surfaces is performed. The type of bonding in terms of competition between sp^2 and sp^3 hybridization is examined, with a view to addressing the possibility of the stabilization of the doped carbon nano-particles in a diamond type structure. The potential for the existence of new pathways to the fabrication of nanotubes is explored.

  12. One-Electron Reduction of Substituted Chlorinated Methanes as Determined from Ab Initio Electronic Structure Theory

    SciTech Connect

    Bylaska, Eric J.; Dixon, David A.; Felmy, Andrew R.; Tratnyek, Paul G.

    2002-12-17

    Substituted chloromethyl radicals and anions are potential intermediates in the reduction of substituted chlorinated methanes (CHxCl3-xL, with L- ) F-, OH-, SH-, NO3 -, HCO3 - and (x 0-3). Thermochemical properties, Hf (298.15 K), S(298.15 K,1 bar), and GS(298.15 K, 1 bar), were calculated by using ab initio electronic structure methods for the substituted chloromethyl radicals and anions: CHyCl2-yL and CHyCl2-yL-, for y 0-2. In addition, thermochemical properties were calculated for the aldehyde, ClHCO, and the gemchlorohydrin anions, CCl3O-, CHCl2O-, and CH2ClO-. The thermochemical properties of these additional compounds were calculated because the nitrate-substituted compounds, CHyCl2-y(NO3) and CHyCl2-y(NO3)-,

  13. Structure and lattice dynamics of rare-earth ferroborate crystals: Ab initio calculation

    NASA Astrophysics Data System (ADS)

    Chernyshev, V. A.; Nikiforov, A. E.; Petrov, V. P.; Serdtsev, A. V.; Kashchenko, M. A.; Klimin, S. A.

    2016-08-01

    The ab initio calculation of the crystal structure and the phonon spectrum of crystals RFe3(BO3)4 ( R = Pr, Nd, Sm) has been performed in the framework of the density functional theory. The ion coordinates in the unit cell, the lattice parameters, the frequencies and the types of fundamental vibrations, and also the intensities of lines in the Raman spectrum and infrared reflection spectra have been found. The elastic constants of the crystals have been calculated. For low-frequency A 2 mode in PrFe3(BO3)4, a "seed" vibration frequency that strongly interacts with the electronic excitation on a praseodymium ion was found. The calculation results satisfactory agree with the experimental data.

  14. Rotational spectra, conformational structures, and dipole moments of thiodiglycol by jet-cooled FTMW and ab initio calculations

    NASA Astrophysics Data System (ADS)

    Xu, Li-Hong; Liu, Qiang; Suenram, R. D.; Lovas, F. J.; Hight Walker, A. R.; Jensen, J. O.; Samuels, A. C.

    2004-12-01

    The rotational spectra of three low-energy conformers of thiodiglycol (TDG) (HOCH 2CH 2SCH 2CH 2OH) have been measured in a molecular beam using a pulsed-nozzle Fourier-transform microwave spectrometer. To determine the likely conformational structures with ab initio approach, conformational structures of 2-(ethylthio)ethanol (HOEES) (CH 3CH 2SCH 2CH 2OH) were used as starting points together with the consideration of possible intramolecular hydrogen bonding in TDG. Three lower-energy conformers have been found for TDG at the MP2=Full/6311G** level and ab initio results agree nicely with experimentally determined rotational constants. In addition, Stark measurements were performed for two of the three conformers for dipole moment determinations, adding to our confidence of the conformational structure matches between experimental observations and ab initio calculations. Of the three lower-energy conformers, one displays a compact folded-like structure with strong hydrogen bonding between the two hydroxyl groups and the central sulfide atom. Two other conformers have relatively open chain-like structures with hydrogen bonding between each of the hydroxyl groups to the central sulfur atom, of which one has pure b-type dipole moment according to the ab initio results.

  15. Structure and conformation studies from temperature dependent infrared spectra of xenon solutions and ab initio calculations of cyclobutylgermane.

    PubMed

    Guirgis, Gamil A; Klaassen, Joshua J; Deodhar, Bhushan S; Sawant, Dattatray K; Panikar, Savitha S; Dukes, Horace W; Wyatt, Justin K; Durig, James R

    2012-12-01

    The infrared spectra (3500-220 cm(-1)) of cyclobutylgermane, c-C(4)H(7)GeH(3) have been recorded of the gas. Also variable temperature (-65 to -100 °C) studies of the infrared spectra (3500-400 cm(-1)) of the sample dissolved in liquid xenon were recorded and both the equatorial and axial conformers were identified. The enthalpy difference has been determined from 10 band pairs 8 temperatures to give 112 ± 11 cm(-1) (1.34 ± 0.13 kJ mol(-1)) with the equatorial conformer the more stable form. The percentage of the axial conformer present at ambient temperature is estimated to be 37 ± 1%. From ab initio calculations conformational stabilities have been predicted from both MP2(full) and density functional theory calculations from a variety of basic sets. The r(0) structure parameters have been obtained for both conformers from the previously reported rotational constants from the three isotopologues. The determined heavy atom distances for the equatorial [axial] form are (Å) Ge-C(α)=1.952(3) [1.950(3)], [Formula: see text] , [Formula: see text] [1.551(3)] and angles in degrees (°) ∠GeC(α)C(β)=118.6(5) [113.4(5)], [Formula: see text] , ∠C(α)C(β)C(γ)=87.8(5) [88.8(5)], [Formula: see text] and a puckering angle of 29.1(5) [25.1(5)]. Data from ab initio calculations were used to predict vibrational harmonic force constants, fundamental wavenumbers, infrared intensities, Raman activities and depolarization ratios for both conformers. The results are compared to the corresponding properties of some related molecules.

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

    PubMed

    Zhang, Yang

    2014-02-01

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

  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 crystal structure prediction. A case study: NaBH{sub 4}

    SciTech Connect

    Caputo, Riccarda; Tekin, Adem

    2011-07-15

    Crystal structure prediction from first principles is still one of the most challenging and interesting issue in condensed matter science. we explored the potential energy surface of NaBH{sub 4} by a combined ab-initio approach, based on global structure optimizations and quantum chemistry. In particular, we used simulated annealing (SA) and density functional theory (DFT) calculations. The methodology enabled the identification of several local minima, of which the global minimum corresponded to the tetragonal ground-state structure (P4{sub 2}/nmc), and the prediction of higher energy stable structures, among them a monoclinic (Pm) one was identified to be 22.75 kJ/mol above the ground-state at T=298 K. In between, orthorhombic and cubic structures were recovered, in particular those with Pnma and F4-bar 3m symmetries. - Graphical abstract: The total electron energy difference of the calculated stable structures. Here, the tetragonal (IT 137) and the monoclinic (IT 6) symmetry groups corresponded to the lowest and the highest energy structures, respectively. Highlights: > Potential energy surface of NaBH{sub 4} is investigated. > This is done a combination of global structure optimizations based on simulated annealing and density functional calculations. > We successfully reproduced experimentally found tetragonal and orthorhombic structures of NaBH{sub 4}. > Furthermore, we found a new stable high energy structure.

  19. Structure, dynamics, and reactivity of hydrated electrons by ab initio molecular dynamics.

    PubMed

    Marsalek, Ondrej; Uhlig, Frank; VandeVondele, Joost; Jungwirth, Pavel

    2012-01-17

    Understanding the properties of hydrated electrons, which were first observed using pulse radiolysis of water in 1962, is crucial because they are key species in many radiation chemistry processes. Although time-resolved spectroscopic studies and molecular simulations have shown that an electron in water (prepared, for example, by water photoionization) relaxes quickly to a localized, cavity-like structure ∼2.5 Å in radius, this picture has recently been questioned. In another experimental approach, negatively charged water clusters of increasing size were studied with photoelectron and IR spectroscopies. Although small water clusters can bind an excess electron, their character is very different from bulk hydrated species. As data on electron binding in liquid water have become directly accessible experimentally, the cluster-to-bulk extrapolations have become a topic of lively debate. Quantum electronic structure calculations addressing experimental measurables have, until recently, been largely limited to small clusters; extended systems were approached mainly with pseudopotential calculations combining a classical description of water with a quantum mechanical treatment of the excess electron. In this Account, we discuss our investigations of electrons solvated in water by means of ab initio molecular dynamics simulations. This approach, applied to a model system of a negatively charged cluster of 32 water molecules, allows us to characterize structural, dynamical, and reactive aspects of the hydrated electron using all of the system's valence electrons. We show that under ambient conditions, the electron localizes into a cavity close to the surface of the liquid cluster. This cavity is, however, more flexible and accessible to water molecules than an analogous area around negatively charged ions. The dynamical process of electron attachment to a neutral water cluster is strongly temperature dependent. Under ambient conditions, the electron relaxes in the

  20. 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.

  1. 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).

  2. AB Initio Study of the Structure and Spectroscopic Properties of Halogenated Thioperoxy Radicals

    NASA Technical Reports Server (NTRS)

    Munoz, Luis A.; Binning, R. C., Jr.; Weiner, Brad R.; Ishikawa, Yasuyuki

    1997-01-01

    Thioperoxy (XSO or XOS) radicals exist in a variety of chemical environments, and they have as a consequence drawn some interest. HSO, an important species in the chemistry of the troposphere, has been examined both experimentally. The halogenated (X = F, Cl or Br) peroxy species and isovalent thioperoxy species have been studied less, but they too are potentially interesting because oxidized sulfur species and halogen sources are present in the atmosphere. Learning the fate of XSO and XOS radicals is important to understanding the atmospheric oxidation chemistry of sulfur compounds. Of these, FSO and ClSO are particularly interesting because they have been directly detected spectroscopically. Recent studies in our laboratory on the photochemistry of thionyl halides (X2SO; where X = F or Cl) have suggested new ways to generate XSO species. The laser-induced photodissociation of thionyl fluoride, F2SO, at 193 nm and thionyl chloride, ClSO, at 248 nm is characterized by a radical mechanism, X2SO -> XSO + X. The structure of FSO has been characterized experimentally by Endo et cd. employing microwave spectroscopy. Using the unrestricted Hartree-Fock (UHF) self-consistent field (SCF) method, Sakai and Morokuma computed the electronic structure of the ground (sup 2)A" and the first excited (sup 2)A' states of FSO. Electron correlation was not taken into account in their study. In a laser photodissociation experiment, Huber et al. identified ClSO mass spectromctrically. ClSO has also been detected in low temperature matrices by EPR and in the gas phase by far IR laser magnetic resonance. Although the structure of FSO is known in detail, the only study, experimental or theoretical, of CISO has been an ab initio HFSCF study by Hinchliffe. Electron correlation corrections were also excluded from this study. In order to better understand the isomerization and dissociation dynamics of the radical species, we have performed ab initio correlated studies of the potential energy

  3. 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.

  4. 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.

  5. A Parallel Framework for Multipoint Spiral Search in ab Initio Protein Structure Prediction

    PubMed Central

    Rashid, Mahmood A.; Newton, M. A. Hakim; Hoque, Md Tamjidul; Sattar, Abdul

    2014-01-01

    Protein structure prediction is computationally a very challenging problem. A large number of existing search algorithms attempt to solve the problem by exploring possible structures and finding the one with the minimum free energy. However, these algorithms perform poorly on large sized proteins due to an astronomically wide search space. In this paper, we present a multipoint spiral search framework that uses parallel processing techniques to expedite exploration by starting from different points. In our approach, a set of random initial solutions are generated and distributed to different threads. We allow each thread to run for a predefined period of time. The improved solutions are stored threadwise. When the threads finish, the solutions are merged together and the duplicates are removed. A selected distinct set of solutions are then split to different threads again. In our ab initio protein structure prediction method, we use the three-dimensional face-centred-cubic lattice for structure-backbone mapping. We use both the low resolution hydrophobic-polar energy model and the high-resolution 20 × 20 energy model for search guiding. The experimental results show that our new parallel framework significantly improves the results obtained by the state-of-the-art single-point search approaches for both energy models on three-dimensional face-centred-cubic lattice. We also experimentally show the effectiveness of mixing energy models within parallel threads. PMID:24744779

  6. A combined photoelectron spectroscopy and relativistic ab initio studies of the electronic structures of UFO and UFO-

    NASA Astrophysics Data System (ADS)

    Roy, Soumendra K.; Jian, Tian; Lopez, Gary V.; Li, Wei-Li; Su, Jing; Bross, David H.; Peterson, Kirk A.; Wang, Lai-Sheng; Li, Jun

    2016-02-01

    The observation of the gaseous UFO- anion is reported, which is investigated using photoelectron spectroscopy and relativisitic ab initio calculations. Two strong photoelectron bands are observed at low binding energies due to electron detachment from the U-7sσ orbital. Numerous weak detachment bands are also observed due to the strongly correlated U-5f electrons. The electron affinity of UFO is measured to be 1.27(3) eV. High-level relativistic quantum chemical calculations have been carried out on the ground state and many low-lying excited states of UFO to help interpret the photoelectron spectra and understand the electronic structure of UFO. The ground state of UFO- is linear with an O-U-F structure and a 3H4 spectral term derived from a U 7sσ25fφ15fδ1 electron configuration, whereas the ground state of neutral UFO has a 4H7/2 spectral term with a U 7sσ15fφ15fδ1 electron configuration. Strong electron correlation effects are found in both the anionic and neutral electronic configurations. In the UFO neutral, a high density of electronic states with strong configuration mixing is observed in most of the scalar relativistic and spin-orbit coupled states. The strong electron correlation, state mixing, and spin-orbit coupling of the electronic states make the excited states of UFO very challenging for accurate quantum chemical calculations.

  7. Structure and vibrational modes of AgI-doped AsSe glasses: Raman scattering and ab initio calculations

    SciTech Connect

    Kostadinova, O.; Chrissanthopoulos, A.; Petkova, T.; Petkov, P.; Yannopoulos, S.N.

    2011-02-15

    We report an investigation of the structure and vibrational modes of (AgI){sub x} (AsSe){sub 100-x}, bulk glasses using Raman spectroscopy and first principles calculations. The short- and medium-range structural order of the glasses was elucidated by analyzing the reduced Raman spectra, recorded at off-resonance conditions. Three distinct local environments were revealed for the AsSe glass including stoichiometric-like and As-rich network sub-structures, and cage-like molecules (As{sub 4}Se{sub n}, n=3, 4) decoupled from the network. To facilitate the interpretation of the Raman spectra ab initio calculations are employed to study the geometric and vibrational properties of As{sub 4}Se{sub n} molecular units that are parts of the glass structure. The incorporation of AgI causes appreciable structural changes into the glass structure. AgI is responsible for the population reduction of molecular units and for the degradation of the As-rich network-like sub-structure via the introduction of As-I terminal bonds. Ab initio calculations of mixed chalcohalide pyramids AsSe{sub m}I{sub 3-m} provided useful information augmenting the interpretation of the Raman spectra. -- Graphical abstract: Raman scattering and ab initio calculations are employed to study the structure of AgI-AsSe superionic glasses. The role of mixed chalcohalide pyramidal units as illustrated in the figure is elucidated. Display Omitted Research highlights: {yields} Doping binary As-Se glasses with AgI cause dramatic changes in glass structure. {yields} Raman scattering and ab initio calculations determine changes in short- and medium-range order. {yields} Three local environments exist in AsSe glass including a network sub-structure and cage-like molecules. {yields} Mixed chalcohalide pyramids AsSe{sub m}I{sub 3-m} dominate the AgI-doped glass structure.

  8. Ab initio structure determination from prion nanocrystals at atomic resolution by MicroED

    PubMed Central

    Sawaya, Michael R.; Rodriguez, Jose; Cascio, Duilio; Collazo, Michael J.; Shi, Dan; Reyes, Francis E.; Gonen, Tamir; Eisenberg, David S.

    2016-01-01

    Electrons, because of their strong interaction with matter, produce high-resolution diffraction patterns from tiny 3D crystals only a few hundred nanometers thick in a frozen-hydrated state. This discovery offers the prospect of facile structure determination of complex biological macromolecules, which cannot be coaxed to form crystals large enough for conventional crystallography or cannot easily be produced in sufficient quantities. Two potential obstacles stand in the way. The first is a phenomenon known as dynamical scattering, in which multiple scattering events scramble the recorded electron diffraction intensities so that they are no longer informative of the crystallized molecule. The second obstacle is the lack of a proven means of de novo phase determination, as is required if the molecule crystallized is insufficiently similar to one that has been previously determined. We show with four structures of the amyloid core of the Sup35 prion protein that, if the diffraction resolution is high enough, sufficiently accurate phases can be obtained by direct methods with the cryo-EM method microelectron diffraction (MicroED), just as in X-ray diffraction. The success of these four experiments dispels the concern that dynamical scattering is an obstacle to ab initio phasing by MicroED and suggests that structures of novel macromolecules can also be determined by direct methods. PMID:27647903

  9. 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.

  10. Local Structure in Ab Initio Liquid Water: Signatures of Amorphous Phases

    NASA Astrophysics Data System (ADS)

    Santra, Biswajit; Distasio, Robert A., Jr.; Martelli, Fausto; Car, Roberto

    Within the framework of density functional theory, the inclusion of exact exchange and non-local van der Waals/dispersion interactions is crucial for predicting a microscopic structure of ambient liquid water that quantitatively agrees with experiment. In this work, we have used the local structure index (LSI) order parameter to analyze the local structure in such highly accurate ab initio liquid water. At ambient conditions, the LSI probability distribution, P(I), was unimodal with most water molecules characterized by more disordered high-density-like local environments. With thermal excitations removed, the resultant bimodal P(I) in the inherent potential energy surface (IPES) exhibited a 3:1 ratio between high- and low-density-like molecules, with the latter forming small connected clusters amid the predominant population. By considering the spatial correlations and hydrogen bond network topologies among water molecules with the same LSI identities, we demonstrate that the signatures of the experimentally observed low- and high-density amorphous phases of ice are present in the IPES of ambient liquid water This work was supported by the DOE: DE-SC0008626, DE-SC0005180.

  11. A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction

    PubMed Central

    Spencer, Matt; Eickholt, Jesse; Cheng, Jianlin

    2014-01-01

    Ab initio protein secondary structure (SS) predictions are utilized to generate tertiary structure predictions, which are increasingly demanded due to the rapid discovery of proteins. Although recent developments have slightly exceeded previous methods of SS prediction, accuracy has stagnated around 80% and many wonder if prediction cannot be advanced beyond this ceiling. Disciplines that have traditionally employed neural networks are experimenting with novel deep learning techniques in attempts to stimulate progress. Since neural networks have historically played an important role in SS prediction, we wanted to determine whether deep learning could contribute to the advancement of this field as well. We developed an SS predictor that makes use of the position-specific scoring matrix generated by PSI-BLAST and deep learning network architectures, which we call DNSS. Graphical processing units and CUDA software optimize the deep network architecture and efficiently train the deep networks. Optimal parameters for the training process were determined, and a workflow comprising three separately trained deep networks was constructed in order to make refined predictions. This deep learning network approach was used to predict SS for a fully independent test data set of 198 proteins, achieving a Q3 accuracy of 80.7% and a Sov accuracy of 74.2%. PMID:25750595

  12. Vibrational modes of methane in the structure H clathrate hydrate from ab initio molecular dynamics simulation.

    PubMed

    Hiratsuka, Masaki; Ohmura, Ryo; Sum, Amadeu K; Yasuoka, Kenji

    2012-10-14

    Vibrational spectra of guest molecules in clathrate hydrates are frequently measured to determine the characteristic signatures of the molecular environment and dynamical properties of guest-host interactions. Here, we present results of our study on the vibrational frequencies of methane molecules in structure H clathrate hydrates, namely, in the 5(12) and 4(3)5(6)6(3) cages, as the frequencies of stretching vibrational modes in these environments are still unclear. The vibrational spectra of methane molecules in structure H clathrate hydrate were obtained from ab initio molecular dynamics simulation and computed from Fourier transform of autocorrelation functions for each distinct vibrational mode. The calculated symmetric and asymmetric stretching vibrational frequencies of methane molecules were found to be lower in the 4(3)5(6)6(3) cages than in the 5(12) cages (3.8 cm(-1) for symmetric stretching and 6.0 cm(-1) for asymmetric stretching). The C-H bond length and average distance between methane molecules and host-water molecules in 4(3)5(6)6(3) cages were slightly longer than those in the 5(12) cages.

  13. Structure-property relationship in py-hexahydrocinchonidine diastereomers: ab initio and NMR study.

    PubMed

    Szöllösi, György; Chatterjee, Abhijit; Forgó, Péter; Bartók, Mihály; Mizukami, Fujio

    2005-02-10

    Two py-hexahydrocinchonidine diastereomers were selectively obtained in the heterogeneous catalytic hydrogenation of cinchonidine over supported Pt catalyst. The two isolated compounds when used as chiral base catalysts in the Michael addition of a beta-keto ester to methyl vinyl ketone gave products of opposite configuration in excess. To trace the reason of this behavior, in the present study, the structures of the two diastereomers were fully optimized by ab initio quantum chemical calculation. These results were then compared with several nuclear Overhauser enhancement spectroscopy (NOESY) signal intensities from the spectra of the two compounds. Further we performed a conformational search on all the optimized geometries independently for the two flexible torsional angles, which are linking the quinuclidine and tetrahydroquinoline moieties present in these molecules. This study allowed us to propose the configuration of the C(4)(') chiral center. Thus, the product mixture resulted in the hydrogenation of cinchonidine containing the 4'-(S)-diastereomer in excess (de = 20%). According to the computation results the 4'-(S)-diastereomer is more stable than the 4'-(R)-diastereomer. The 4'-(S)-conformer obtained by computation has lower electronic energy than the structures obtained for the 4'-(R)-diastereomer, which may explain the excess formation of the first one. The results of the Michael addition catalyzed by these diastereomers were interpreted on the basis of these conclusions.

  14. A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction.

    PubMed

    Spencer, Matt; Eickholt, Jesse; Jianlin Cheng

    2015-01-01

    Ab initio protein secondary structure (SS) predictions are utilized to generate tertiary structure predictions, which are increasingly demanded due to the rapid discovery of proteins. Although recent developments have slightly exceeded previous methods of SS prediction, accuracy has stagnated around 80 percent and many wonder if prediction cannot be advanced beyond this ceiling. Disciplines that have traditionally employed neural networks are experimenting with novel deep learning techniques in attempts to stimulate progress. Since neural networks have historically played an important role in SS prediction, we wanted to determine whether deep learning could contribute to the advancement of this field as well. We developed an SS predictor that makes use of the position-specific scoring matrix generated by PSI-BLAST and deep learning network architectures, which we call DNSS. Graphical processing units and CUDA software optimize the deep network architecture and efficiently train the deep networks. Optimal parameters for the training process were determined, and a workflow comprising three separately trained deep networks was constructed in order to make refined predictions. This deep learning network approach was used to predict SS for a fully independent test dataset of 198 proteins, achieving a Q3 accuracy of 80.7 percent and a Sov accuracy of 74.2 percent.

  15. 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.

  16. Ab initio molecular orbital study of the structures of purine hydrates

    SciTech Connect

    Colson, A.O.; Sevilla, M.D.

    1996-03-14

    The structures of the isomers of purine hydrates [4(5)-hydroxy-5(4)-hydropurines] have been geometry optimized with ab initio quantum chemical methods at the 6-31G{sup *} basis set and with the semiempirical method PM3. These hydrates which can result from reduction of radical species formed by attack of hydroxyl radical at the 4,5 double bond in the purines, show significant geometrical distortion when compared to the natural bases. More specifically, the cis isomers adopt a `butterfly` conformation, while in the trans isomers, the pyrimidine and imidazole rings tilt opposite to each other. Our results predict the cis purine hydrate isomers are far more stable than the trans isomers by 10-18 kcal/mol at the 6-31G{sup *} level, whereas the 4-hydroxy-5-hydropurines are found to be slightly more energetically stable than the 5-hydroxy-4-hydropurines. The `butterfly` conformation of the cis isomers constitutes a bulky lesion which will result in a significant distortion of the DNA helix. 33 refs., 2 figs., 3 tabs.

  17. 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.; Lu, D.; Frenkel, A. I.

    2016-06-30

    We adopted ab-initio X-ray Absorption Near Edge Structure (XANES) modelling for structural refinement of local environments around metal impurities in a large variety of materials. Our method enables both direct modelling, where the candidate structures are known, and the inverse modelling, where the unknown structural motifs are deciphered from the experimental spectra. We present also estimates of systematic errors, and their influence on the stability and accuracy of the obtained results. We illustrate our approach by following the evolution of local environment of palladium atoms in palladium-doped gold thiolate clusters upon chemical and thermal treatments.

  18. Structure models: From shell model to ab initio methods. A brief introduction to microscopic theories for exotic nuclei

    NASA Astrophysics Data System (ADS)

    Bacca, Sonia

    2016-04-01

    A brief review of models to describe nuclear structure and reactions properties is presented, starting from the historical shell model picture and encompassing modern ab initio approaches. A selection of recent theoretical results on observables for exotic light and medium-mass nuclei is shown. Emphasis is given to the comparison with experiment and to what can be learned about three-body forces and continuum properties.

  19. Structure and dynamics of La(III) in aqueous solution An ab initio QM/MM MD approach

    NASA Astrophysics Data System (ADS)

    Hofer, Thomas S.; Scharnagl, Harald; Randolf, Bernhard R.; Rode, Bernd M.

    2006-08-01

    Ab initio QM/MM MD simulations have allowed to clarify some of the ambiguities arising from various studies on the hydrated La(III) ion. Both nine- and ten-coordinated hydrates co-exist and interchange in a dissociative process on the nano- or even subnanosecond scale, and thus much faster than any other trivalent main group or transition metal ions. The weak ion-ligand bond (53 N/m) supplies a reasonable explanation for it. The simulation results for La(III) are also compared to those for the isoelectronic ions Cs(I) and Ba(II) obtained by the same ab initio MD procedure, leading to conclusions on the influence of central ion charge on structural and dynamic properties of hydrate complexes.

  20. Real-structure effects: Band gaps of Mg_xZn_{1-x}O, Cd_xZn_{1-x}O, and n-type ZnO from ab-initio calculations

    SciTech Connect

    Schleife, A; Bechstedt, F

    2012-02-15

    Many-body perturbation theory is applied to compute the quasiparticle electronic structures and the optical-absorption spectra (including excitonic effects) for several transparent conducting oxides. We discuss HSE+G{sub 0}W{sub 0} results for band structures, fundamental band gaps, and effective electron masses of MgO, ZnO, CdO, SnO{sub 2}, SnO, In{sub 2}O{sub 3}, and SiO{sub 2}. The Bethe-Salpeter equation is solved to account for excitonic effects in the calculation of the frequency-dependent absorption coefficients. We show that the HSE+G{sub 0}W{sub 0} approach and the solution of the Bethe-Salpeter equation are very well-suited to describe the electronic structure and the optical properties of various transparent conducting oxides in good agreement with experiment.

  1. Crystal structure and magnetism in α -RuCl3 : An ab initio study

    NASA Astrophysics Data System (ADS)

    Kim, Heung-Sik; Kee, Hae-Young

    2016-04-01

    α -RuCl3 has been proposed recently as an excellent playground for exploring Kitaev physics on a two-dimensional (2D) honeycomb lattice. However, structural clarification of the compound has not been completed, which is crucial in understanding the physics of this system. Here, using ab initio electronic structure calculations, we study a full three-dimensional (3D) structure of α -RuCl3 , including the effects of spin-orbit coupling (SOC) and electronic correlations. The three major results are as follows: (i) SOC suppresses dimerization of Ru atoms, which exists in other Ru compounds such as isostructural Li2RuO3 , and makes the honeycomb closer to an ideal one. (ii) The nearest-neighbor Kitaev exchange interaction between the jeff=1 /2 pseudospin strongly depends on the Ru-Ru distance and the Cl position, originating from the nature of the edge-sharing geometry. (iii) The optimized 3D structure without electronic correlations has P 3 ¯1 m space-group symmetry independent of SOC, but including electronic correlation changes the optimized 3D structure to either C 2 /m or C m c 21 within 0.1 meV per formula unit (f.u.) energy difference. The reported P 3112 structure is also close in energy. The interlayer spin-exchange coupling is a few percent of the in-plane spin-exchange terms, confirming that α -RuCl3 is close to a 2D system. We further suggest how to increase the Kitaev term via tensile strain, which sheds light in realizing the Kitaev spin-liquid phase in this system.

  2. AB Initio Protein Tertiary Structure Prediction: Comparative-Genetic Algorithm with Graph Theoretical Methods

    SciTech Connect

    Gregurick, S. K.

    2001-04-20

    During the period from September 1, 1998 until September 1, 2000 I was awarded a Sloan/DOE postdoctoral fellowship to work in collaboration with Professor John Moult at the Center for Advanced Research in Biotechnology (CARB). Our research project, ''Ab Initio Protein Tertiary Structure Prediction and a Comparative Genetic algorithm'', yielded promising initial results. In short, the project is designed to predict the native fold, or native tertiary structure, of a given protein by inputting only the primary sequence of the protein (one or three letter code). The algorithm is based on a general learning, or evolutionary algorithm and is called Genetic Algorithm (GAS). In our particular application of GAS, we search for native folds, or lowest energy structures, using two different descriptions for the interactions of the atoms and residues in a given protein sequence. One potential energy function is based on a free energy description, while the other function is a threading potential derived by Moult and Samudrala. This modified genetic algorithm was loosely termed a Comparative Genetic Algorithm and was designed to search for native folded structures on both potential energy surfaces, simultaneously. We tested the algorithm on a series of peptides ranging from 11 to 15 residues in length, which are thought to be independent folding units and thereby will fold to native structures independent of the larger protein environment. Our initial results indicated a modest increase in accuracy, as compared to a standard Genetic Algorithm. We are now in the process of improving the algorithm to increase the sensitivity to other inputs, such as secondary structure requirements. The project did not involve additional students and as of yet, the work has not been published.

  3. Ab initio determination of dark structures in radiationless transitions for aromatic carbonyl compounds.

    PubMed

    Fang, Wei-Hai

    2008-03-01

    photoexcitation of aromatic carbonyl compounds. The importance of ab initio determination of transient structures in the photodissociation dynamics has been demonstrated for the case of the aromatic carbonyl compounds. In addition, the detailed knowledge of mechanistic photochemistry for aromatic carbonyl compounds forms the basis for further investigating photodissociation dynamics of a polyatomic molecule.

  4. Ab initio structure determination and refinement of a scorpion protein toxin.

    PubMed

    Smith, G D; Blessing, R H; Ealick, S E; Fontecilla-Camps, J C; Hauptman, H A; Housset, D; Langs, D A; Miller, R

    1997-09-01

    The structure of toxin II from the scorpion Androctonus australis Hector has been determined ab initio by direct methods using SnB at 0.96 A resolution. For the purpose of this structure redetermination, undertaken as a test of the minimal function and the SnB program, the identity and sequence of the protein was withheld from part of the research team. A single solution obtained from 1 619 random atom trials was clearly revealed by the bimodal distribution of the final value of the minimal function associated with each individual trial. Five peptide fragments were identified from a conservative analysis of the initial E-map, and following several refinement cycles with X-PLOR, a model was built of the complete structure. At the end of the X-PLOR refinement, the sequence was compared with the published sequence and 57 of the 64 residues had been correctly identified. Two errors in sequence resulted from side chains with similar size while the rest of the errors were a result of severe disorder or high thermal motion in the side chains. Given the amino-acid sequence, it is estimated that the initial E-map could have produced a model containing 99% of all main-chain and 81% of side-chain atoms. The structure refinement was completed with PROFFT, including the contributions of protein H atoms, and converged at a residual of 0.158 for 30 609 data with F >or= 2sigma(F) in the resolution range 8.0-0.964 A. The final model consisted of 518 non-H protein atoms (36 disordered), 407 H atoms, and 129 water molecules (43 with occupancies less than unity). This total of 647 non-H atoms represents the largest light-atom structure solved to date.

  5. Structural study of methyl isonicotinate by gas phase electron diffraction combined with ab initio calculations

    NASA Astrophysics Data System (ADS)

    Kiyono, Hajime; Kuze, Nobuhiko; Fujiwara, Hideo; Takeuchi, Hiroshi; Egawa, Toru; Konaka, Shigehiro

    1996-02-01

    The molecular structure of methyl isonicotinate was studied by gas phase electron diffraction combined with ab initio calculations. The molecular skeleton was assumed to be planar. The determined values of principal structure parameters ( rg and ∠ α) are as follows: r( NC) = 1.343(5) Å, r( C…C) ring = 1.401(3) Å, r( Cγ C) = 1.499(9) Å, r( C O) = 1.205(5) Å, r( C( O) O) = 1.331(8) Å, r( OC Me) = 1.430(8) Å, = 1.103(10) Å, ∠CNC = 117.6(9)°, ∠C βC γC β = 118.7(9)°, ∠C β,trans C γC(O) = 118.6(12), ∠C γCO = 121.4(12)°, ∠C γCO = 114.2(10)°, ∠COC = 115.4(15)°, where angled brackets denote average values and C γ,trans denotes the carbon atom which is trans to the carbonyl oxygen atom. Values in parentheses are the estimated limits of error (3σ) referring to the last significant digit. The structure of the ring in methyl isonicotinate agrees with that of pyridine within experimental error. In contrast, the structure parameters of the COOCH 3 group are significantly different from those of methyl acrylate and methyl acetate. These differences have been discussed in terms of hyperconjugation and steric effects.

  6. Input/Output of ab-initio nuclear structure calculations for improved performance and portability

    SciTech Connect

    Laghave, Nikhil

    2010-01-01

    Many modern scientific applications rely on highly computation intensive calculations. However, most applications do not concentrate as much on the role that input/output operations can play for improved performance and portability. Parallelizing input/output operations of large files can significantly improve the performance of parallel applications where sequential I/O is a bottleneck. A proper choice of I/O library also offers a scope for making input/output operations portable across different architectures. Thus, use of parallel I/O libraries for organizing I/O of large data files offers great scope in improving performance and portability of applications. In particular, sequential I/O has been identified as a bottleneck for the highly scalable MFDn (Many Fermion Dynamics for nuclear structure) code performing ab-initio nuclear structure calculations. We develop interfaces and parallel I/O procedures to use a well-known parallel I/O library in MFDn. As a result, we gain efficient I/O of large datasets along with their portability and ease of use in the down-stream processing. Even situations where the amount of data to be written is not huge, proper use of input/output operations can boost the performance of scientific applications. Application checkpointing offers enormous performance improvement and flexibility by doing a negligible amount of I/O to disk. Checkpointing saves and resumes application state in such a manner that in most cases the application is unaware that there has been an interruption to its execution. This helps in saving large amount of work that has been previously done and continue application execution. This small amount of I/O provides substantial time saving by offering restart/resume capability to applications. The need for checkpointing in optimization code NEWUOA has been identified and checkpoint/restart capability has been implemented in NEWUOA by using simple file I/O.

  7. Ab initio molecular dynamics study of the interlayer and micropore structure of aqueous montmorillonite clays

    NASA Astrophysics Data System (ADS)

    Suter, James L.; Kabalan, Lara; Khader, Mahmoud; Coveney, Peter V.

    2015-11-01

    Ab initio molecular dynamics simulations have been performed to gain an understanding of the interfacial microscopic structure and reactivity of fully hydrated clay edges. The models studied include both micropore and interlayer water. We identify acidic sites through dissociation mechanisms; the resulting ions can be stabilized by both micropore and interlayer water. We find clay edges possess a complex amphoteric behavior, which depends on the face under consideration and the location of isomorphic substitution. For the neutral (1 1 0) surface, we do not observe any dissociation on the timescale accessible. The edge terminating hydroxyl groups participate in a hydrogen bonded network of water molecules that spans the interlayer between periodic images of the clay framework. With isomorphic substitutions in the tetrahedral layer of the (1 1 0) clay edge, we find the adjacent exposed apical oxygen behaves as a Brönsted base and abstracts a proton from a nearby water molecule, which in turn removes a proton from an AlOH2 group. With isomorphic substitutions in the octahedral layer of the (1 1 0) clay edge the adjacent exposed apical oxygen atom does not abstract a proton from the water molecules, but increases the number of hydrogen bonded water molecules (from one to two). Acid treated clays are likely to have both sites protonated. The (0 1 0) surface does not have the same interfacial hydrogen bonding structure; it is much less stable and we observe dissociation of half the terminal SiOH groups (tbnd Sisbnd Osbnd H → tbnd Sisbnd O- + H+) in our models. The resulting anions are stabilized by solvation from both micropore and interlayer water molecules. This suggests that, when fully hydrated, the (0 1 0) surface can act as a Brönsted acid, even at neutral pH.

  8. Electronic band structure and optical properties of titanium oxyphosphates Li{sub 0.50}Co{sub 0.25}TiO(PO{sub 4}) single crystals: An ab-initio calculations

    SciTech Connect

    Reshak, Ali Hussain; Khenata, R.; Auluck, S.

    2011-08-15

    From the refined atomic positions obtained by Belmal et al. (2004) using X-ray diffraction for Li{sub 0.50}Co{sub 0.25}TiO(PO{sub 4}), we have performed a structural optimization by minimizing the forces acting on the atoms keeping the lattice parameters fixed at the experimental values. With this relaxed (optimized) geometry we have performed a comprehensive theoretical study of electronic properties and dispersion of the linear optical susceptibilities using the full potential linear augmented plane wave (FP-LAPW) method. The generalized gradient approximation (GGA) exchange-correlation potential was applied. In addition, the Engel-Vosko generalized gradient approximation (EVGGA) was used for comparison with GGA because it is known that EVGGA approach yields better band splitting compared to the GGA. We have calculated the band structure, and the total and partial densities of states. The electron charge densities and the bonding properties were analyzed and discussed. The complex dielectric optical susceptibilities were discussed in detail. - Graphical abstract: It is shown that P is tetrahedrally coordinated by four O ions. Highlights: > Comprehensive theoretical study of electronic and optical properties was performed. > Using X-ray diffraction data we have performed a structural optimization. > The electron charge densities and the bonding properties were analyzed and discussed. > Fermi surface was analyzed since it is useful for predicting thermal, magnetic, and optical properties. > The density of states at E{sub F} and the electronic specific heat coefficient were calculated.

  9. A combined photoelectron spectroscopy and relativistic ab initio studies of the electronic structures of UFO and UFO(-).

    PubMed

    Roy, Soumendra K; Jian, Tian; Lopez, Gary V; Li, Wei-Li; Su, Jing; Bross, David H; Peterson, Kirk A; Wang, Lai-Sheng; Li, Jun

    2016-02-28

    The observation of the gaseous UFO(-) anion is reported, which is investigated using photoelectron spectroscopy and relativisitic ab initio calculations. Two strong photoelectron bands are observed at low binding energies due to electron detachment from the U-7sσ orbital. Numerous weak detachment bands are also observed due to the strongly correlated U-5f electrons. The electron affinity of UFO is measured to be 1.27(3) eV. High-level relativistic quantum chemical calculations have been carried out on the ground state and many low-lying excited states of UFO to help interpret the photoelectron spectra and understand the electronic structure of UFO. The ground state of UFO(-) is linear with an O-U-F structure and a (3)H4 spectral term derived from a U 7sσ(2)5fφ(1)5fδ(1) electron configuration, whereas the ground state of neutral UFO has a (4)H(7/2) spectral term with a U 7sσ(1)5fφ(1)5fδ(1) electron configuration. Strong electron correlation effects are found in both the anionic and neutral electronic configurations. In the UFO neutral, a high density of electronic states with strong configuration mixing is observed in most of the scalar relativistic and spin-orbit coupled states. The strong electron correlation, state mixing, and spin-orbit coupling of the electronic states make the excited states of UFO very challenging for accurate quantum chemical calculations. PMID:26931704

  10. A combined photoelectron spectroscopy and relativistic ab initio studies of the electronic structures of UFO and UFO(-).

    PubMed

    Roy, Soumendra K; Jian, Tian; Lopez, Gary V; Li, Wei-Li; Su, Jing; Bross, David H; Peterson, Kirk A; Wang, Lai-Sheng; Li, Jun

    2016-02-28

    The observation of the gaseous UFO(-) anion is reported, which is investigated using photoelectron spectroscopy and relativisitic ab initio calculations. Two strong photoelectron bands are observed at low binding energies due to electron detachment from the U-7sσ orbital. Numerous weak detachment bands are also observed due to the strongly correlated U-5f electrons. The electron affinity of UFO is measured to be 1.27(3) eV. High-level relativistic quantum chemical calculations have been carried out on the ground state and many low-lying excited states of UFO to help interpret the photoelectron spectra and understand the electronic structure of UFO. The ground state of UFO(-) is linear with an O-U-F structure and a (3)H4 spectral term derived from a U 7sσ(2)5fφ(1)5fδ(1) electron configuration, whereas the ground state of neutral UFO has a (4)H(7/2) spectral term with a U 7sσ(1)5fφ(1)5fδ(1) electron configuration. Strong electron correlation effects are found in both the anionic and neutral electronic configurations. In the UFO neutral, a high density of electronic states with strong configuration mixing is observed in most of the scalar relativistic and spin-orbit coupled states. The strong electron correlation, state mixing, and spin-orbit coupling of the electronic states make the excited states of UFO very challenging for accurate quantum chemical calculations.

  11. Structures and relative stabilities of ammonia clusters at different temperatures: DFT vs. ab initio.

    PubMed

    Malloum, Alhadji; Fifen, Jean Jules; Dhaouadi, Zoubeida; Engo, Serge Guy Nana; Jaidane, Nejm-Eddine

    2015-11-21

    A hydrogen bond network in ammonia clusters plays a key role in understanding the properties of species embedded in ammonia. This network is dictated by the structures of neutral ammonia clusters. In this work, structures of neutral ammonia clusters (NH3)n(=2-10) have been studied at M06-2X/6-31++G(d,p) and MP2/6-31++g(d,p) levels of theory. The analysis of the relative stabilities of various hydrogen bond types has also been studied and vibrational spectroscopy of the ammonia pentamer and decamer is investigated. We noted that M06-2X provides lower electronic energies, greater binding energies and higher structural resolution than MP2. We also noted that at the M06-2X level of theory, the binding energy converges to the experimental vaporization enthalpy faster than that at the MP2 level of theory. As a result, it is found that the M06-2X functional could be more suitable than the MP2 ab initio method in the description of structures and energies of ammonia clusters. However, we found that the electronic energy differences obtained at both levels of computation follow a linear relation with n (number of ammonia molecules in a cluster). As far as the structures of ammonia clusters are concerned, we proposed new "significant" isomers that have not been reported previously. The most remarkable is the global minimum electronic energy structure of the ammonia hexamer, which has an inversion centre and confirms experimental observation. Moreover, we reported the relative stabilities of neutral ammonia clusters for temperatures ranging from 25 to 400 K. The stability of isomers changes with the increase of the temperature. As a result, the branched and less bonded isomers are the most favored at high temperatures and disfavored at low temperatures, while compact and symmetric isomers dominate the population of clusters at low temperatures. In fine, from this work, the global minimum energy structures of ammonia clusters are known for the first time at a given temperature

  12. An ab initio study of the fcc and hcp structures of helium

    NASA Astrophysics Data System (ADS)

    Røeggen, I.

    2006-05-01

    The hexagonal close packed (hcp) and face centered cubic (fcc) structures of helium are studied by using a new ab initio computational model for large complexes comprising small subsystems. The new model is formulated within the framework of the energy incremental scheme. In the calculation of intra- and intersystem energies, model systems are introduced. To each subsystem associated is a set of partner subsystems defined by a vicinity criterion. In the independent calculations of intra- and intersystem energies, the calculations are performed on model subsystems defined by the subsystems considered and their partner subsystems. A small and a large basis set are associated with each subsystem. For partner subsystems in a model system, the small basis set is adopted. By introducing a particular decomposition scheme, the intermolecular potential is written as a sum of effective one-body potentials. The binding energy per atom in an infinite crystal of atoms is the negative value of this one-body potential. The one- body potentials for hcp and fcc structures are calculated for the following nearest neighbor distances (d0): 4.6, 5.1, 5.4, 5.435, 5.5, 5.61, and 6.1a.u. The equilibrium distance is 5.44a.u. for both structures. The equilibrium dimer distance is 5.61a.u. For the larger distances, i.e., d0>5.4a.u., the difference of the effective one-body potentials for the two structures is less than 0.2μEh. However, the hcp structure has the lowest effective one-body potential for all the distances considered. For the smallest distance the difference in the effective one-body potential is 3.9μEh. Hence, for solid helium, i.e., helium under high pressure, the hcp structure is the preferred one. The error in the calculated effective one-body potential for the distance d0=5.61a.u. is of the order of 1μEh (≈0.5%).

  13. Structure and mechanical properties of cement and intermetallic compounds via ab-initio simulations

    NASA Astrophysics Data System (ADS)

    Dharmawardhana, Chamila Chathuranga

    Calcium silicate hydrates comprise a class of minerals formed synthetically during Portland cement hydration or naturally through various geological processes. The importance of these minerals is immense since they are the primary binding phases for Portland cement derived construction materials. Efforts spanning centuries have been devoted to understand the structural aspects of cohesion in these minerals. In recent years, the focus has progressively turned to atomic level comprehension. Structurally these minerals can range from crystalline to highly disordered amorphous phases. This thesis focuses upon unraveling the nature of chemical bonding in a large subset of calcium silicate hydrate (CSH) crystals. Thus their electronic structure was calculated and bonding mechanisms were investigated quantitatively. Results highlight a wide range of contributions from each type of bonding (Si-O, Ca-O, O-H and hydrogen bond) with respect to silicate polymerization, crystal symmetry, water and OH content. Consequently, total bond order density (TBOD) was designated as the overall single criterion for characterizing crystal cohesion. The TBOD categorization indicates that a rarely known orthorhombic phase Suolunite is closest to the ideal composition and structure of cement. Present work finds the relationship of partial bond order density (PBOD) of each bond species, especially HBs to the mechanical properties of CSH crystals. This can be used as a basis to validate existing C-S-H models and to build improved ones. This work goes further and validates the recently proposed models (2014) for C-S-H (I) phase on the same basis of proposed electronic structure parameters. Then the respective Calcium aluminosilicate hydrates C-A-S-H (I) phase models are proposed. Finally, these results lead to improved interpretations and construction of realistic atomistic models of cement hydrates. Ab initio molecular dynamics (AIMD) could be vital to solve critical problems in complex

  14. Excited state structure of 4-(dimethylamino)benzonitrile studied by femtosecond mid-infrared spectroscopy and ab initio calculations

    NASA Astrophysics Data System (ADS)

    Chudoba, C.; Kummrow, A.; Dreyer, J.; Stenger, J.; Nibbering, E. T. J.; Elsaesser, T.; Zachariasse, K. A.

    1999-08-01

    Combining femtosecond transient vibrational spectroscopy and high-level calculations is a powerful tool in the determination of excited-state structures. Striking differences in the experimental vibrational pattern of the locally excited states of 4-(dimethylamino)benzonitrile (DMABN) and 4-aminobenzonitrile (ABN) are explained on the basis of molecular structures obtained from ab initio complete-active-space self-consistent-field (CASSCF) calculations, giving evidence for a strong sensitivity of the molecular structure on modest changes in the substituents. The 4.0 ps charge-transfer time for DMABN in acetonitrile is resolved for the first time by tracking the downshifted CN stretching mode.

  15. Origin of the Hadži ABC structure: An ab initio study

    SciTech Connect

    Van Hoozen, Brian L.; Petersen, Poul B.

    2015-11-14

    Medium and strong hydrogen bonds are well known to give rise to broad features in the vibrational spectrum often spanning several hundred wavenumbers. In some cases, these features can span over 1000 cm{sup −1} and even contain multiple broad peaks. One class of strongly hydrogen-bonded dimers that includes many different phosphinic, phosphoric, sulfinic, and selenic acid homodimers exhibits a three-peaked structure over 1500 cm{sup −1} broad. This unusual feature is often referred to as the Hadži ABC structure. The origin of this feature has been debated since its discovery in the 1950s. Only a couple of theoretical studies have attempted to interpret the origin of this feature; however, no previous study has been able to reproduce this feature from first principles. Here, we present the first ab initio calculation of the Hadži ABC structure. Using a reduced dimensionality calculation that includes four vibrational modes, we are able to reproduce the three-peak structure and much of the broadness of the feature. Our results indicate that Fermi resonances of the in-plane bend, out-of-plane bend, and combination of these bends play significant roles in explaining this feature. Much of the broadness of the feature and the ability of the OH stretch mode to couple with many overtone bending modes are captured by including an adiabatically separated dimer stretch mode in the model. This mode modulates the distance between the monomer units and accordingly the strength of the hydrogen-bonds causing the OH stretch frequency to shift from 2000 to 3000 cm{sup −1}. Using this model, we were also able to reproduce the vibrational spectrum of the deuterated isotopologue which consists of a single 500 cm{sup −1} broad feature. Whereas previous empirical studies have asserted that Fermi resonances contribute very little to this feature, our study indicates that while not appearing as a separate peak, a Fermi resonance of the in-plane bend contributes substantially to

  16. From Geometry Optimization to Time Dependent Molecular Structure Modeling: Method Developments, ab initio Theories and Applications

    NASA Astrophysics Data System (ADS)

    Liang, Wenkel

    This dissertation consists of two general parts: (I) developments of optimization algorithms (both nuclear and electronic degrees of freedom) for time-independent molecules and (II) novel methods, first-principle theories and applications in time dependent molecular structure modeling. In the first part, we discuss in specific two new algorithms for static geometry optimization, the eigenspace update (ESU) method in nonredundant internal coordinate that exhibits an enhanced performace with up to a factor of 3 savings in computational cost for large-sized molecular systems; the Car-Parrinello density matrix search (CP-DMS) method that enables direct minimization of the SCF energy as an effective alternative to conventional diagonalization approach. For the second part, we consider the time dependence and first presents two nonadiabatic dynamic studies that model laser controlled molecular photo-dissociation for qualitative understandings of intense laser-molecule interaction, using ab initio direct Ehrenfest dynamics scheme implemented with real-time time-dependent density functional theory (RT-TDDFT) approach developed in our group. Furthermore, we place our special interest on the nonadiabatic electronic dynamics in the ultrafast time scale, and presents (1) a novel technique that can not only obtain energies but also the electron densities of doubly excited states within a single determinant framework, by combining methods of CP-DMS with RT-TDDFT; (2) a solvated first-principles electronic dynamics method by incorporating the polarizable continuum solvation model (PCM) to RT-TDDFT, which is found to be very effective in describing the dynamical solvation effect in the charge transfer process and yields a consistent absorption spectrum in comparison to the conventional linear response results in solution. (3) applications of the PCM-RT-TDDFT method to study the intramolecular charge-transfer (CT) dynamics in a C60 derivative. Such work provides insights into the

  17. Band-gap engineering in chemically conjugated bilayer graphene: Ab initio calculations

    NASA Astrophysics Data System (ADS)

    Duong, Dinh Loc; Lee, Seung Mi; Chae, Sang Hul; Ta, Quang Huy; Lee, Si Young; Han, Gang Hee; Bae, Jung Jun; Lee, Young Hee

    2012-05-01

    One-side chemical conjugation of bilayer graphene has limitations not only on opening a band gap of less than 0.2 eV due to a small electric field across bilayer graphene but also on generating highly degenerate semiconducting properties by shifting the Fermi level into either a valence band or a conduction band due to the requirement of heavy doping concentration. Here, we proposed a new strategy of band-gap engineering of bilayer graphene by chemically conjugating double sides of bilayer graphene, one side with an electron-donating group and another side with an electron-withdrawing group. The compensated charges not only created a large band gap of 0.3 eV by invoking an internally strong local dipole field in bilayer graphene but also removed degeneracy by shifting the Fermi level within the band gap. Our approach is easy and straightforward, environmentally stable, and scalable for integration, which is in good contrast with the previous reports of fabricating nanoribbons and high electric field operation.

  18. Structural stability and lattice defects in copper: Ab initio, tight-binding, and embedded-atom calculations

    SciTech Connect

    Mishin, Y.; Mehl, M. J.; Papaconstantopoulos, D. A.; Voter, A. F.; Kress, J. D.

    2001-06-01

    We evaluate the ability of the embedded-atom method (EAM) potentials and the tight-binding (TB) method to predict reliably energies and stability of nonequilibrium structures by taking Cu as a model material. Two EAM potentials are used here. One is constructed in this work by using more fitting parameters than usual and including ab initio energies in the fitting database. The other potential was constructed previously using a traditional scheme. Excellent agreement is observed between ab initio, TB, and EAM results for the energies and stability of several nonequilibrium structures of Cu, as well as for energies along deformation paths between different structures. We conclude that not only TB calculations but also EAM potentials can be suitable for simulations in which correct energies and stability of different atomic configurations are essential, at least for Cu. The bcc, simple cubic, and diamond structures of Cu were identified as elastically unstable, while some other structures (e.g., hcp and 9R) are metastable. As an application of this analysis, nonequilibrium structures of epitaxial Cu films on (001)-oriented fcc or bcc substrates are evaluated using a simple model and atomistic simulations with an EAM potential. In agreement with experimental data, the structure of the film can be either deformed fcc or deformed hcp. The bcc structure cannot be stabilized by epitaxial constraints.

  19. 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.

  20. Electronic structure and metallization of cubic GdH3 under pressure: Ab initio many-body GW calculations

    NASA Astrophysics Data System (ADS)

    Kong, Bo; Zhang, Yachao

    2016-07-01

    The electronic structures of the cubic GdH3 are extensively investigated using the ab initio many-body GW calculations treating the Gd 4f electrons either in the core (4f-core) or in the valence states (4f-val). Different degrees of quasiparticle (QP) self-consistent calculations with the different starting points are used to correct the failures of the GGA/GGA + U/HSE03 calculations. In the 4f-core case, GGA + G0W0 calculations give a fundamental band gap of 1.72 eV, while GGA+ GW0 or GGA + GW calculations present a larger band gap. In the 4f-val case, the nonlocal exchange-correlation (xc) functional HSE03 can account much better for the strong localization of the 4f states than the semilocal or Hubbard U corrected xc functional in the Kohn-Sham equation. We show that the fundamental gap of the antiferromagnetic (AFM) or ferromagnetic (FM) GdH3 can be opened up by solving the QP equation with improved starting point of eigenvalues and wave functions given by HSE03. The HSE03 + G0W0 calculations present a fundamental band gap of 2.73 eV in the AFM configuration, and the results of the corresponding GW0 and GW calculations are 2.89 and 3.03 eV, respectively. In general, for the cubic structure, the fundamental gap from G0W0 calculations in the 4f-core case is the closest to the real result. By G0W0 calculations in the 4f-core case, we find that H or Gd defects can strongly affect the band structure, especially the H defects. We explain the mechanism in terms of the possible electron correlation on the hydrogen site. Under compression, the insulator-to-metal transition in the cubic GdH3 occurs around 40 GPa, which might be a satisfied prediction.

  1. Orbital free ab initio simulations of liquid alkaline earth metals: from pseudopotential construction to structural and dynamic properties.

    PubMed

    Rio, Beatriz G del; González, Luis E

    2014-11-19

    We have performed a comprehensive study of the properties of liquid Be, Ca and Ba, through the use of orbital free ab initio simulations. To this end we have developed a force-matching method to construct the necessary local pseudopotentials from standard ab initio calculations. The structural magnitudes are analyzed, including the average and local structures and the dynamic properties are studied. We find several common features, like an asymmetric second peak in the structure factor, a large amount of local structures with five-fold symmetry, a quasi-universal behaviour of the single-particle dynamic properties and a large degree of positive dispersion in the propagation of collective density fluctuations, whose damping is dictated by slow thermal relaxations and fast viscoelastic ones. Some peculiarities in the dynamic properties are however observed, like a very high sound velocity and a large violation of the Stokes-Einstein relation for Be, or an extremely high positive dispersion and a large slope in the dispersion relation of shear waves at the onset of the wavevector region where they are supported for Ba. PMID:25347355

  2. Ab initio phasing by molecular averaging in real space with new criteria: application to structure determination of a betanodavirus.

    PubMed

    Yoshimura, Masato; Chen, Nai Chi; Guan, Hong Hsiang; Chuankhayan, Phimonphan; Lin, Chien Chih; Nakagawa, Atsushi; Chen, Chun Jung

    2016-07-01

    Molecular averaging, including noncrystallographic symmetry (NCS) averaging, is a powerful method for ab initio phase determination and phase improvement. Applications of the cross-crystal averaging (CCA) method have been shown to be effective for phase improvement after initial phasing by molecular replacement, isomorphous replacement, anomalous dispersion or combinations of these methods. Here, a two-step process for phase determination in the X-ray structural analysis of a new coat protein from a betanodavirus, Grouper nervous necrosis virus, is described in detail. The first step is ab initio structure determination of the T = 3 icosahedral virus-like particle using NCS averaging (NCSA). The second step involves structure determination of the protrusion domain of the viral molecule using cross-crystal averaging. In this method, molecular averaging and solvent flattening constrain the electron density in real space. To quantify these constraints, a new, simple and general indicator, free fraction (ff), is introduced, where ff is defined as the ratio of the volume of the electron density that is freely changed to the total volume of the crystal unit cell. This indicator is useful and effective to evaluate the strengths of both NCSA and CCA. Under the condition that a mask (envelope) covers the target molecule well, an ff value of less than 0.1, as a new rule of thumb, gives sufficient phasing power for the successful construction of new structures. PMID:27377380

  3. Ab initio phasing by molecular averaging in real space with new criteria: application to structure determination of a betanodavirus

    PubMed Central

    Yoshimura, Masato; Chen, Nai-Chi; Guan, Hong-Hsiang; Chuankhayan, Phimonphan; Lin, Chien-Chih; Nakagawa, Atsushi; Chen, Chun-Jung

    2016-01-01

    Molecular averaging, including noncrystallographic symmetry (NCS) averaging, is a powerful method for ab initio phase determination and phase improvement. Applications of the cross-crystal averaging (CCA) method have been shown to be effective for phase improvement after initial phasing by molecular replacement, isomorphous replacement, anomalous dispersion or combinations of these methods. Here, a two-step process for phase determination in the X-ray structural analysis of a new coat protein from a betanodavirus, Grouper nervous necrosis virus, is described in detail. The first step is ab initio structure determination of the T = 3 icosahedral virus-like particle using NCS averaging (NCSA). The second step involves structure determination of the protrusion domain of the viral molecule using cross-crystal averaging. In this method, molecular averaging and solvent flattening constrain the electron density in real space. To quantify these constraints, a new, simple and general indicator, free fraction (ff), is introduced, where ff is defined as the ratio of the volume of the electron density that is freely changed to the total volume of the crystal unit cell. This indicator is useful and effective to evaluate the strengths of both NCSA and CCA. Under the condition that a mask (envelope) covers the target molecule well, an ff value of less than 0.1, as a new rule of thumb, gives sufficient phasing power for the successful construction of new structures. PMID:27377380

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

    SciTech Connect

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

    2013-11-21

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

  5. Joint Density Functional Theory for the electrode/electrolyte interface: Benchmarking liquid structure with experiment and ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Letchworth-Weaver, Kendra; Umbright, Christine; Chan, Maria; Fenter, Paul; Arias, T. A.

    Understanding the physics of the interface between a charged electrode surface and a fluid electrolyte would inform design of electrochemical energy storage and conversion devices. However, such studies require a simultaneously accurate yet inherently multi-scale theory. Joint density-functional theory (JDFT) bridges the relevant length-scales by joining a fully ab initio description of the electrode with a low computational cost, yet atomically detailed classical DFT description of the liquid electrolyte structure. Leveraging JDFT within our framework to treat charged systems in periodic boundary conditions, we can predict the voltage-dependent structure and energetics of solvated ions at the interface between graphitic and single-crystalline metallic electrodes and technologically relevant liquid electrolytes. First, we elucidate the physical origin of the experimentally measured voltage-dependent differential capacitance of an Ag(111) electrode in aqueous NaF electrolyte, examining the crucial role of ion de-solvation and physisorption onto the electrode surface. We go on to compare the JDFT-predicted interfacial liquid structure next to a graphitic electrode with results obtained from X-ray reflectivity measurements and ab initio molecular dynamics simulations.

  6. Positive semidefinite tensor factorizations of the two-electron integral matrix for low-scaling ab initio electronic structure

    SciTech Connect

    Hoy, Erik P.; Mazziotti, David A.

    2015-08-14

    Tensor factorization of the 2-electron integral matrix is a well-known technique for reducing the computational scaling of ab initio electronic structure methods toward that of Hartree-Fock and density functional theories. The simplest factorization that maintains the positive semidefinite character of the 2-electron integral matrix is the Cholesky factorization. In this paper, we introduce a family of positive semidefinite factorizations that generalize the Cholesky factorization. Using an implementation of the factorization within the parametric 2-RDM method [D. A. Mazziotti, Phys. Rev. Lett. 101, 253002 (2008)], we study several inorganic molecules, alkane chains, and potential energy curves and find that this generalized factorization retains the accuracy and size extensivity of the Cholesky factorization, even in the presence of multi-reference correlation. The generalized family of positive semidefinite factorizations has potential applications to low-scaling ab initio electronic structure methods that treat electron correlation with a computational cost approaching that of the Hartree-Fock method or density functional theory.

  7. Positive semidefinite tensor factorizations of the two-electron integral matrix for low-scaling ab initio electronic structure.

    PubMed

    Hoy, Erik P; Mazziotti, David A

    2015-08-14

    Tensor factorization of the 2-electron integral matrix is a well-known technique for reducing the computational scaling of ab initio electronic structure methods toward that of Hartree-Fock and density functional theories. The simplest factorization that maintains the positive semidefinite character of the 2-electron integral matrix is the Cholesky factorization. In this paper, we introduce a family of positive semidefinite factorizations that generalize the Cholesky factorization. Using an implementation of the factorization within the parametric 2-RDM method [D. A. Mazziotti, Phys. Rev. Lett. 101, 253002 (2008)], we study several inorganic molecules, alkane chains, and potential energy curves and find that this generalized factorization retains the accuracy and size extensivity of the Cholesky factorization, even in the presence of multi-reference correlation. The generalized family of positive semidefinite factorizations has potential applications to low-scaling ab initio electronic structure methods that treat electron correlation with a computational cost approaching that of the Hartree-Fock method or density functional theory.

  8. Positive semidefinite tensor factorizations of the two-electron integral matrix for low-scaling ab initio electronic structure.

    PubMed

    Hoy, Erik P; Mazziotti, David A

    2015-08-14

    Tensor factorization of the 2-electron integral matrix is a well-known technique for reducing the computational scaling of ab initio electronic structure methods toward that of Hartree-Fock and density functional theories. The simplest factorization that maintains the positive semidefinite character of the 2-electron integral matrix is the Cholesky factorization. In this paper, we introduce a family of positive semidefinite factorizations that generalize the Cholesky factorization. Using an implementation of the factorization within the parametric 2-RDM method [D. A. Mazziotti, Phys. Rev. Lett. 101, 253002 (2008)], we study several inorganic molecules, alkane chains, and potential energy curves and find that this generalized factorization retains the accuracy and size extensivity of the Cholesky factorization, even in the presence of multi-reference correlation. The generalized family of positive semidefinite factorizations has potential applications to low-scaling ab initio electronic structure methods that treat electron correlation with a computational cost approaching that of the Hartree-Fock method or density functional theory. PMID:26277123

  9. Precise Lifetime Measurements in Light Nuclei for Benchmarking Modern Ab-initio Nuclear Structure Models

    SciTech Connect

    Lister, C.J.; McCutchan, E.A.

    2014-06-15

    A new generation of ab-initio calculations, based on realistic two- and three-body forces, is having a profound impact on our view of how nuclei work. To improve the numerical methods, and the parameterization of 3-body forces, new precise data are needed. Electromagnetic transitions are very sensitive to the dynamics which drive mixing between configurations. We have made a series of precise (< 3%) measurements of electromagnetic transitions in the A=10 nuclei {sup 10}C and {sup 10}Be by using the Doppler Shift Attenuation method carefully. Many interesting features can be reproduced including the strong α clustering. New measurements on {sup 8}Be and {sup 12}Be highlight the interplay between the alpha clusters and their valence neutrons.

  10. Optimized Structures and Proton Affinities of Fluorinated Dimethyl Ethers: An Ab Initio Study

    NASA Technical Reports Server (NTRS)

    Orgel, Victoria B.; Ball, David W.; Zehe, Michael J.

    1996-01-01

    Ab initio methods have been used to investigate the proton affinity and the geometry changes upon protonation for the molecules (CH3)2O, (CH2F)2O, (CHF2)2O, and (CF3)2O. Geometry optimizations were performed at the MP2/3-2 I G level, and the resulting geometries were used for single-point energy MP2/6-31G calculations. The proton affinity calculated for (CH3)2O was 7 Kjoule/mole from the experimental value, within the desired variance of +/- 8Kjoule/mole for G2 theory, suggesting that the methodology used in this study is adequate for energy difference considerations. For (CF3)20, the calculated proton affinity of 602 Kjoule/mole suggests that perfluorinated ether molecules do not act as Lewis bases under normal circumstances; e.g. degradation of commercial lubricants in tribological applications.

  11. Structure electronique de nanorubans de graphene avec des contacts metalliques: Une etude ab initio

    NASA Astrophysics Data System (ADS)

    Archambault, Chloe

    Graphene, a graphite monolayer presenting novel exciting properties, has attracted much attention recently in the scientific community as well as in the high-technology industry. In electronics, nanoribbons -- narrow strips of graphene which happen to be semiconducting-- could possibly allow further miniaturization of electronic devices such as transistors because of their atomic thickness. On the other hand, once making devices, the problem of metallic contacts, which can have critical impact at the nanoscopic scale, cannot be evaded. For example, metal induced gap states may short-circuit very short devices. With this in mind, the interaction of gold, palladium and titanium contacts with finite size graphene nanoribbons has been studied using ab initio density functional theory calculations. This theoretical approach made it possible to study separately and then conjugate four important aspects of the metal-ribbon interaction: bonding, charge transfer, electrostatics and metal induced gap states. Another goal of this project was to study size effects related to the ribbons' dimensions and to estimate the minimal channel length necessary for a device to operate as expected without the unwanted effect of induced gap states. Aside from the high precision achieved, these calculations stand out from earlier studies because they take into account finite size effects which often prevail in small ribbons. Using this model for the metal-nanoribbon junction, it was shown that, as for two-dimensional graphene, the bonding between a ribbon and a metal can be of two types depending on the electronic configuration of the metal. In the first case, physisorption, weak bonding resulting in a large separation distance between ribbon and electrode, is illustrated by the gold contact. On the other hand, titanium, because of its high density of states at the Fermi level, binds more strongly with graphene nanoribbons. This chemisorption is characterized by strong hybridization between

  12. An ab initio MO study of butalene

    NASA Astrophysics Data System (ADS)

    Ohta, Katsuhisa; Shima, Toru

    1994-01-01

    Butalene as a structural isomer of p-benzyne has been studied by using an ab initio GVB wavefunction. The geometry of butalene, which is shown to be almost rectangular, is first optimized as a local minimum on the energy surface at the ab initio level. However, the energy barrier of conversion to p-benzyne is as small as 1.6 kcal/mol, and experimental isolation of butalene is predicted to be difficult from a force-constant analysis.

  13. Interplay between the structure and dynamics in liquid and undercooled boron: An ab initio molecular dynamics simulation study

    SciTech Connect

    Jakse, N.; Pasturel, A.

    2014-12-21

    In the present work, the structural and dynamic properties of liquid and undercooled boron are investigated by means of ab initio molecular dynamics simulation. Our results show that both liquid and undercooled states present a well pronounced short-range order (SRO) mainly due to the formation of inverted umbrella structural units. Moreover, we observe the development of a medium-range order (MRO) in the undercooling regime related to the increase of inverted umbrella structural units and of their interconnection as the temperature decreases. We also evidence that this MRO leads to a partial crystallization in the β-rhombohedral crystal below T = 1900 K. Finally, we discuss the role played by the SRO and MRO in the nearly Arrhenius evolution of the diffusion and the non-Arrhenius temperature dependence of the shear viscosity, in agreement with the experiment.

  14. Microwave, infrared and Raman spectra, r0 structural parameters, ab initio calculations and vibrational assignment of 1-fluoro-1-silacyclopentane.

    PubMed

    Durig, James R; Panikar, Savitha S; Obenchain, Daniel A; Bills, Brandon J; Lohan, Patrick M; Peebles, Rebecca A; Peebles, Sean A; Groner, Peter; Guirgis, Gamil A; Johnston, Michael D

    2012-01-28

    The microwave spectrum (6500-18 ,500 MHz) of 1-fluoro-1-silacyclopentane, c-C(4)H(8)SiHF has been recorded and 87 transitions for the (28)Si, (29)Si, (30)Si, and (13)C isotopomers have been assigned for a single conformer. Infrared spectra (3050-350 cm(-1)) of the gas and solid and Raman spectrum (3100-40 cm(-1)) of the liquid have also been recorded. The vibrational data indicate the presence of a single conformer with no symmetry which is consistent with the twist form. Ab initio calculations with a variety of basis sets up to MP2(full)/aug-cc-pVTZ predict the envelope-axial and envelope-equatorial conformers to be saddle points with nearly the same energies but much lower energy than the planar conformer. By utilizing the microwave rotational constants for seven isotopomers ((28)Si, (29)Si, (30)Si, and four (13)C) combined with the structural parameters predicted from the MP2(full)/6-311+G(d,p) calculations, adjusted r(0) structural parameters have been obtained for the twist conformer. The heavy atom distances in Å are: r(0)(SiC(2)) = 1.875(3); r(0)(SiC(3)) = 1.872(3); r(0)(C(2)C(4)) = 1.549(3); r(0)(C(3)C(5)) = 1.547(3); r(0)(C(4)C(5)) = 1.542(3); r(0)(SiF) = 1.598(3) and the angles in degrees are: [angle]CSiC = 96.7(5); [angle]SiC(2)C(4) = 103.6(5); [angle]SiC(3)C(5) = 102.9(5); [angle]C(2)C(4)C(5) = 108.4(5); [angle]C(3)C(5)C(4) = 108.1(5); [angle]F(6)Si(1)C(2) = 110.7(5); [angle]F(6)Si(1)C(3) = 111.6(5). The heavy atom ring parameters are compared to the corresponding r(s) parameters. Normal coordinate calculations with scaled force constants from MP2(full)/6-31G(d) calculations were carried out to predict the fundamental vibrational frequencies, infrared intensities, Raman activities, depolarization values, and infrared band contours. These experimental and theoretical results are compared to the corresponding quantities of some other five-membered rings.

  15. Metallic VS2 Monolayer Polytypes as Potential Sodium-Ion Battery Anode via ab Initio Random Structure Searching.

    PubMed

    Putungan, Darwin Barayang; Lin, Shi-Hsin; Kuo, Jer-Lai

    2016-07-27

    We systematically investigated the potential of single-layer VS2 polytypes as Na-battery anode materials via density functional theory calculations. We found that sodiation tends to inhibit the 1H-to-1T structural phase transition, in contrast to lithiation-induced transition on monolayer MoS2. Thus, VS2 can have better structural stability in the cycles of charging and discharging. Diffussion of Na atom was found to be very fast on both polytypes, with very small diffusion barriers of 0.085 eV (1H) and 0.088 eV (1T). Ab initio random structure searching was performed in order to explore stable configurations of Na on VS2. Our search found that both the V top and the hexagonal center sites are preferred adsorption sites for Na, with the 1H phase showing a relatively stronger binding. Notably, our random structures search revealed that Na clusters can form as a stacked second layer at full Na concentration, which is not reported in earlier works wherein uniform, single-layer Na adsorption phases were assumed. With reasonably high specific energy capacity (232.91 and 116.45 mAh/g for 1H and 1T phases, respectively) and open-circuit voltage (1.30 and 1.42 V for 1H and 1T phases, respectively), VS2 is a promising alternative material for Na-ion battery anodes with great structural sturdiness. Finally, we have shown the capability of the ab initio random structure searching in the assessment of potential materials for energy storage applications. PMID:27373121

  16. Metallic VS2 Monolayer Polytypes as Potential Sodium-Ion Battery Anode via ab Initio Random Structure Searching.

    PubMed

    Putungan, Darwin Barayang; Lin, Shi-Hsin; Kuo, Jer-Lai

    2016-07-27

    We systematically investigated the potential of single-layer VS2 polytypes as Na-battery anode materials via density functional theory calculations. We found that sodiation tends to inhibit the 1H-to-1T structural phase transition, in contrast to lithiation-induced transition on monolayer MoS2. Thus, VS2 can have better structural stability in the cycles of charging and discharging. Diffussion of Na atom was found to be very fast on both polytypes, with very small diffusion barriers of 0.085 eV (1H) and 0.088 eV (1T). Ab initio random structure searching was performed in order to explore stable configurations of Na on VS2. Our search found that both the V top and the hexagonal center sites are preferred adsorption sites for Na, with the 1H phase showing a relatively stronger binding. Notably, our random structures search revealed that Na clusters can form as a stacked second layer at full Na concentration, which is not reported in earlier works wherein uniform, single-layer Na adsorption phases were assumed. With reasonably high specific energy capacity (232.91 and 116.45 mAh/g for 1H and 1T phases, respectively) and open-circuit voltage (1.30 and 1.42 V for 1H and 1T phases, respectively), VS2 is a promising alternative material for Na-ion battery anodes with great structural sturdiness. Finally, we have shown the capability of the ab initio random structure searching in the assessment of potential materials for energy storage applications.

  17. The infrared spectra and structure of o-sulfobenzimide (saccharin) and of its nitranion: An ab initio force field treatment

    NASA Astrophysics Data System (ADS)

    Binev, Ivan G.; Stamboliyska, Bistra A.; Velcheva, Evelina A.

    1996-08-01

    The structure of o-sulfobenzimide (saccharin) and of its nitranion has been studied on the basis of both infrared spectra and ab initio force field calculations. A good agreement has been found between the theoretical and experimental spectroscopic characteristics of the particles studied. The theoretical method used gives a good description of the strong spectral changes caused by the conversion of the saccharin molecule into the corresponding nitranion. The structural changes which accompany this conversion are essential and they spread over the whole sulfocarboximide group and the adjacent bonds. The nitranionic charge is delocalized over the phenylene group (0.29 e -), sulfonyl group (0.26 e -), nitranionic center (0.25 e -), and carbonyl group (0.20 e -).

  18. Molecular structure and conformational composition of 1,1-dichlorobutane: a gas-phase electron diffraction and ab initio investigation

    NASA Astrophysics Data System (ADS)

    Aarset, Kirsten; Hagen, Kolbjørn; Stølevik, Reidar

    1997-09-01

    Gas-phase electron diffraction data obtained at 23°C, together with results from ab initio molecular orbital calculations ( {HF}/{6-31 G(d)}). were used to determine the structure and conformational composition of 1,1-dichlorobutane. Of the five distinguishable conformers (AA, G + A, AG +, G + G + and G + G -), the G + A conformer was found to be the low-energy form, and the investigation also indicated that certain amounts of the AA and G + G - conformers might be present. The symbols describing the conformers refer to torsion about the C 1C 2 and C 2C 3 bonds, anti (A) with H 5C 1C 2C 3 and C 1C 2C 3C 4 torsion angles of 180° and gauche (G + or G -) with torsion angles of + 60° or 300° (-60°) respectively. The results for the principal distances ( rg) and angles (∠ α) from the combined electron diffraction/ab initio study for the G + A conformer, with estimated 2σ uncertainties, were as follows: r( C1 C2) = 1.521(4) Å, r( C2 C3) = 1.539(4) Å, r( C3 C4) = 1.546(4) Å, r( C Cl6) = 1.782(3) Å, r( CCl7) = 1.782(3) Å, = 1.106(6) Å, ∠C 1C 2C 3 = 114.4(13)°, ∠C 2C 3C 4 = 112.5(13)°, ∠CCCl 6 = 110.4(7)°, ∠CCCl 7 = 111.9(7)°, <∠CCH> = 108.9(47)°. Only average values for r(CC), r(CCl), r(CH), ∠CCC, ∠CCX and ∠CCH were determined in the least-square refinements; the differences between the values for these parameters in the same conformer and between the different conformers were kept constant at the values obtained from the ab initio molecular orbital calculations.

  19. Ab initio study of the molecular structure and vibrational spectrum of nitric acid and its protonated forms

    NASA Technical Reports Server (NTRS)

    Lee, Timothy J.; Rice, Julia E.

    1992-01-01

    The equilibrium structures, harmonic vibrational frequencies, IR intensities, and relative energetics of HNO3 and its protonated form H2NO3+ were investigated using double-zeta plus polarization and triple-zeta plus polarization basis sets in conjunction with high-level ab initio methods. The latter include second-order Moller-Plesset perturbation theory, the single and double excitation coupled cluster (CCSD) methods, a perturbational estimate of the effects of connected triple excitations (CCSD(T)), and the self-consistent field. To determine accurate energy differences CCSD(T) energies were computed using large atomic natural orbital basis sets. Four different isomers of H2NO3+ were considered. The lowest energy form of protonated nitric acid was found to correspond to a complex between H2O and NO2+, which is consistent with earlier theoretical and experimental studies.

  20. Ab initio investigation of the structure and nonlinear optical properties of five-membered heterocycles containing sulfur

    NASA Astrophysics Data System (ADS)

    Spassova, Milena; Enchev, Venelin

    2004-03-01

    An ab initio HF and MP2 study of the static (hyper)polarizabilities of 2,4-substituted imidazoles and thiazoles is presented. The comparison of the two types of five-membered heterocycles suggests, that the exocyclic heteroatoms have much more influence upon the calculated hyperpolarizabilities, than the ring heteroatoms. It has been found, that adding diffuse functions to the 6-31G** basis set and inclusion of the electron correlation result in drastic changes in the second hyperpolarizability. The changes are more pronounced for the structures with larger number of sulfur atoms. A HF/6-31G** investigation of a push-pull system, in which thiorhodanine has been chosen as acceptor fragment shows an enhancement of the molecular polarizabilities with respect to the corresponding typical donor-acceptor NH 2/NO 2 polyene.

  1. The Free Energies of Reactions of Chlorinated Methanes with Aqueous Monovalent Anions: Applications of ab initio Electronic Structure Theory

    SciTech Connect

    Bylaska, Eric J.; Dixon, David A.; Felmy, Andrew R.

    2000-01-01

    The presence of different anionic species in natural waters can significantly alter the degradation rates of chlorinated methanes and other organic compounds. Favorable reaction energetics is a necessary feature of these nucleophilic substitution reactions that can result in the degradation of the chlorinated methanes. In this study, ab initio electronic structure theory is used to evaluate the free energies of reaction of a series of monovalent anionic species (OH-, SH-, NO3 -, HCO3 -, HSO3 -, HSO4 -, H2PO4 -, and F-) that can occur in natural waters with the chlorinated methanes, CCl4, CCl3H, CCl2H2, and CClH3. The results of this investigation show that nucleophilic substitution reactions of OH-, SH-, HCO3 -, and F- are significantly exothermic for chlorine displacement, NO3 - reactions are slightly exothermic to thermoneutral, HSO3

  2. Phase constitution and interface structure of nano-sized Ag-Cu/AlN multilayers: Experiment and ab initio modeling

    SciTech Connect

    Pigozzi, Giancarlo; Janczak-Rusch, Jolanta; Passerone, Daniele; Antonio Pignedoli, Carlo; Patscheider, Joerg; Jeurgens, Lars P. H.; Antusek, Andrej; Parlinska-Wojtan, Magdalena; Bissig, Vinzenz

    2012-10-29

    Nano-sized Ag-Cu{sub 8nm}/AlN{sub 10nm} multilayers were deposited by reactive DC sputtering on {alpha}-Al{sub 2}O{sub 3}(0001) substrates. Investigation of the phase constitution and interface structure of the multilayers evidences a phase separation of the alloy sublayers into nanosized grains of Ag and Cu. The interfaces between the Ag grains and the quasi-single-crystalline AlN sublayers are semi-coherent, whereas the corresponding Cu/AlN interfaces are incoherent. The orientation relationship between Ag and AlN is constant throughout the entire multilayer stack. These observations are consistent with atomistic models of the interfaces as obtained by ab initio calculations.

  3. Recent advances in electronic structure theory and their influence on the accuracy of ab initio potential energy surfaces

    NASA Technical Reports Server (NTRS)

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

    1989-01-01

    Recent advances in electronic structure theory and the availability of high speed vector processors have substantially increased the accuracy of ab initio potential energy surfaces. The recently developed atomic natural orbital approach for basis set contraction has reduced both the basis set incompleteness and superposition errors in molecular calculations. Furthermore, full CI calculations can often be used to calibrate a CASSCF/MRCI approach that quantitatively accounts for the valence correlation energy. These computational advances also provide a vehicle for systematically improving the calculations and for estimating the residual error in the calculations. Calculations on selected diatomic and triatomic systems will be used to illustrate the accuracy that currently can be achieved for molecular systems. In particular, the F + H2 yields HF + H potential energy hypersurface is used to illustrate the impact of these computational advances on the calculation of potential energy surfaces.

  4. Recent advances in electronic structure theory and their influence on the accuracy of ab initio potential energy surfaces

    NASA Technical Reports Server (NTRS)

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

    1988-01-01

    Recent advances in electronic structure theory and the availability of high speed vector processors have substantially increased the accuracy of ab initio potential energy surfaces. The recently developed atomic natural orbital approach for basis set contraction has reduced both the basis set incompleteness and superposition errors in molecular calculations. Furthermore, full CI calculations can often be used to calibrate a CASSCF/MRCI approach that quantitatively accounts for the valence correlation energy. These computational advances also provide a vehicle for systematically improving the calculations and for estimating the residual error in the calculations. Calculations on selected diatomic and triatomic systems will be used to illustrate the accuracy that currently can be achieved for molecular systems. In particular, the F+H2 yields HF+H potential energy hypersurface is used to illustrate the impact of these computational advances on the calculation of potential energy surfaces.

  5. An ab initio study of the structural, elastic, electronic and optical properties of the newly synthesized nitridoaluminate LiCaAlN2

    NASA Astrophysics Data System (ADS)

    Haddadi, K.; Bouhemadou, A.; Bin-Omran, S.; Maabed, S.; Khenata, R.

    2015-01-01

    The structural parameters, elastic constants, electronic structure and optical properties of the recently reported monoclinic quaternary nitridoaluminate LiCaAlN2 are investigated in detail using the ab initio plane-wave pseudopotential method within the generalized gradient approximation. The calculated equilibrium structural parameters are in excellent agreement with the experimental data, which validate the reliability of the applied theoretical method. The chemical and structural stabilities of LiCaAlN2 are confirmed by calculating the cohesion energy and enthalpy of formation. Chemical band stiffness is calculated to explain the pressure dependence of the lattice parameters. Through the band structure calculation, LiCaAlN2 is predicted to be an indirect band gap of 2.725 eV. The charge-carrier effective masses are estimated from the band structure dispersions. The frequency-dependent dielectric function, absorption coefficient, refractive index, extinction coefficient, reflectivity coefficient and electron energy loss function spectra are calculated for polarized incident light in a wide energy range. Optical spectra exhibit a noticeable anisotropy. Single-crystal and polycrystalline elastic constants and related properties, including isotropic sound velocities and Debye temperatures, are numerically estimated. The calculated elastic constants and elastic compliances are used to analyse and visualize the elastic anisotropy of LiCaAlN2. The calculated elastic constants demonstrate the mechanical stability and brittle behaviour of the considered material.

  6. [Structural and Dipole Structure Peculiarities of Hoogsteen Base Pairs Formed in Complementary Nucleobases according to ab initio Quantum Mechanics Studies].

    PubMed

    Petrenko, Y M

    2015-01-01

    Ab initio quantum mechanics studies for the detection of structure and dipole structure peculiarities of Hoogsteen base pairs relative to Watson-Crick base pairs, were performed during our work. These base pairs are formed as a result of complementary interactions. It was revealed, that adenine-thymine Hoogsteen base pair and adenine-thymine Watson-Crick base pairs can be formed depending on initial configuration. Cytosine-guanine Hoogsteen pairs are formed only when cytosine was originally protonated. Both types of Hoogsteen pairs have noticeable difference in the bond distances and angles. These differences appeared in purine as well as in pyrimidine parts of the pairs. Hoogsteen pairs have mostly shorter hydrogen bond lengths and significantly larger angles of hydrogen bonds and larger angles between the hydrogen bonds than Watson-Crick base pairs. Notable differences are also observed with respect to charge distribution and dipole moment. Quantitative data on these differences are shown in our work. It is also reported that the values of local parameters (according to Cambridge classification of the parameters which determine DNA properties) in Hoogsteen base pairs, are greatly different from Watson-Crick ones.

  7. Surface structure of CdSe Nanorods revealed by combined X-rayabsorption fine structure measurements and ab-initio calculations

    SciTech Connect

    Aruguete, Deborah A.; Marcus, Matthew A.; Li, Liang-shi; Williamson, Andrew; Fakra, Sirine; Gygi, Francois; Galli, Giulia; Alivisatos, A. Paul

    2006-01-27

    We report orientation-specific, surface-sensitive structural characterization of colloidal CdSe nanorods with extended X-ray absorption fine structure spectroscopy and ab-initio density functional theory calculations. Our measurements of crystallographically-aligned CdSe nanorods show that they have reconstructed Cd-rich surfaces. They exhibit orientation-dependent changes in interatomic distances which are qualitatively reproduced by our calculations. These calculations reveal that the measured interatomic distance anisotropy originates from the nanorod surface.

  8. Structural and Thermal Properties of BaTe2O6: Combined Variable-Temperature Synchrotron X-ray Diffraction, Raman Spectroscopy, and ab Initio Calculations.

    PubMed

    Mishra, Karuna Kara; Achary, S Nagabhusan; Chandra, Sharat; Ravindran, T R; Sinha, Anil K; Singh, Manavendra N; Tyagi, Avesh K

    2016-09-01

    Variable-temperature Raman spectroscopic and synchrotron X-ray diffraction studies were performed on BaTe2O6 (orthorhombic, space group: Cmcm), a mixed-valence tellurium compound with a layered structure, to understand structural stability and anharmonicity of phonons. The structural and vibrational studies indicate no phase transition in it over a wider range of temperature (20 to 853 K). The structure shows anisotropic expansion with coefficients of thermal expansion in the order αb ≫ αa > αc, which was attributed to the anisotropy in bonding and structure of BaTe2O6. Temperature evolution of Raman modes of BaTe2O6 indicated a smooth decreasing trend in mode frequencies with increasing temperature, while the full width at half-maximum (fwhm) of all modes systematically increases due to a rise in phonon scattering processes. With the use of our earlier reported isothermal mode Grüneisen parameters, thermal properties such as thermal expansion coefficient and molar specific heat are calculated. The pure anharmonic (explicit) and quasiharmonic (implicit) contribution to the total anharmonicity is delineated and compared. The temperature dependence of phonon mode frequencies and their fwhm values are analyzed by anharmonicity models, and the dominating anharmonic phonon scattering mechanism is concluded in BaTe2O6. In addition to the lattice modes, several external modes of TeOn (n = 5, 6) are found to be strongly anharmonic. The ab initio electronic structure calculations indicated BaTe2O6 is a direct band gap semiconductor with gap energy of ∼2.1 eV. Oxygen orbitals, namely, O-2p states in the valence band maximum and the sp-hybridized states in the conduction band minimum, are mainly involved in the electronic transitions. In addition a number of electronic transitions are predicted by the electronic structure calculations. Experimental photoluminescence results are adequately explained by the ab initio calculations. Further details of the structural and

  9. 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.

  10. 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

    2007-07-01

    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).

  11. Ab initio molecular dynamics.

    PubMed

    Laasonen, Kari

    2013-01-01

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

  12. Ab Initio Assessment of the Structural and Optoelectronic Properties of Organic-ZnO Nanoclusters.

    PubMed

    Kumar, Pushpendra; Pal, Suman Kalyan

    2015-10-01

    Structural, electronic, and optical properties of a new coumarin dye, zinc oxide (ZnO) nanoclusters of varying sizes, and their complexes have been investigated using density functional theory (DFT). The band gap of oxide nanoclusters varies with size validating quantum confinement effect in small particles. Energy level diagrams of dye, ZnO nanoclusters, and redox electrolyte are in favor of efficient electron injection from dye to nanocluster and regeneration of the ionized dye. The adsorption of the organic dye to nanocluster is tested for anchoring through three different functional groups (cyano, carbonyl, and hydroxyl) of the dye. We have compared simulated absorption spectra of the dye, nanoclusters, and dye functionalized nanoclusters and discussed the matching with the solar irradiance spectrum. A strong new band appeared in the low energy side of the absorption spectra for dye adsorbed nanoclusters. Frontier molecular orbital calculations reveal that the first absorption band of dye-ZnO complexes is charge transfer (CT) in character. Excitation of this band leads to direct electron transfer to the conduction band (CB) of the nanocluster, making dye-ZnO complexes suitable for type II DSSCs as well. PMID:26348781

  13. Correction of erroneously packed protein's side chains in the NMR structure based on ab initio chemical shift calculations.

    PubMed

    Zhu, Tong; Zhang, John Z H; He, Xiao

    2014-09-14

    In this work, protein side chain (1)H chemical shifts are used as probes to detect and correct side-chain packing errors in protein's NMR structures through structural refinement. By applying the automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) method for ab initio calculation of chemical shifts, incorrect side chain packing was detected in the NMR structures of the Pin1 WW domain. The NMR structure is then refined by using molecular dynamics simulation and the polarized protein-specific charge (PPC) model. The computationally refined structure of the Pin1 WW domain is in excellent agreement with the corresponding X-ray structure. In particular, the use of the PPC model yields a more accurate structure than that using the standard (nonpolarizable) force field. For comparison, some of the widely used empirical models for chemical shift calculations are unable to correctly describe the relationship between the particular proton chemical shift and protein structures. The AF-QM/MM method can be used as a powerful tool for protein NMR structure validation and structural flaw detection.

  14. Ab-initio study of structural, mechanical and electronic properties of functionalized carbon nanotubes

    SciTech Connect

    Milowska, Karolina Z.; Birowska, Magdalena; Majewski, Jacek A.

    2013-12-04

    We present exemplary results of extensive studies of structural, mechanical and electronic properties of covalent functionalization of carbon nanotubes (CNTs). We report new results for metallic (9,0), and semiconducting (10,0) single-wall carbon nanotubes (CNT) functionalized with -COOH, -OH, and both groups with concentration up to 12.5%. Our studies are performed in the framework of the density functional theory (DFT). We discuss here the stability, local and global changes in structure, elastic moduli (Young's, Shear, and Bulk), electronic structure and resulting band gaps, as a function of the density of the adsorbed molecules.

  15. Pressure induced structural phase transition and electronic properties of actinide monophospides: Ab-initio calculations

    NASA Astrophysics Data System (ADS)

    Makode, Chandrabhan; Sanyal, Sankar P.

    2011-09-01

    We have investigated the structural and electronic properties of monophospides of thorium, uranium and neptunium. The total energy as a function of volume is obtained by means of the self-consistent tight binding linear muffin-tin-orbital (TB-LMTO) method within the local density approximation (LDA). From the present study with the help of total energy calculations it is found that ThP, UP and NpP are stable in NaCl-type structure at ambient pressure. The structural stability of ThP, UP and NpP changes under the application of pressure. We predict a structural phase transition from NaCl-type (B 1-phase) structure to CsCl-type (B 2-phase) structure for these phospides in the pressure range of 37.0-24.0 GPa (ThP-NpP). We also calculate lattice parameter ( a0), bulk modulus ( B0), band structure and density of states. From energy band diagram it is observed that ThP, UP and NpP exhibit metallic behavior. The calculated equilibrium lattice parameters and bulk modulus are in good agreement with experimental and theoretical work.

  16. Ab-initio study of electronic structure and elastic properties of ZrC

    NASA Astrophysics Data System (ADS)

    Mund, H. S.; Ahuja, B. L.

    2016-05-01

    The electronic and elastic properties of ZrC have been investigated using the linear combination of atomic orbitals method within the framework of density functional theory. Different exchange-correlation functionals are taken into account within generalized gradient approximation. We have computed energy bands, density of states, elastic constants, bulk modulus, shear modulus, Young's modulus, Poisson's ratio, lattice parameters and pressure derivative of the bulk modulus by calculating ground state energy of the rock salt structure type ZrC.

  17. Ab initio global optimization of the structures of Si{sub n}H, n=4-10, using parallel genetic algorithms

    SciTech Connect

    Ona, Ofelia; Facelli, Julio C.; Bazterra, Victor E.; Caputo, Maria C.; Ferraro, Marta B.

    2005-11-15

    The results of ab initio global optimizations of the structures of Si{sub n}H, n=4-10, atomic clusters using a parallel genetic algorithm are presented. Driving the global search with the parallel implementation of the genetic algorithm are presented and using the density functional theory as implemented in the Carr-Parinello molecular dynamics code to calculate atomic cluster energies and perform the local optimization of their structures, we have been able to demonstrate that it is possible to perform global optimizations of the structure of atomic clusters using ab initio methods. The results show that this approach is able to find many structures that were not previously reported in the literature. Moreover, in most cases the new structures have considerable lower energies than those previously known. The results clearly demonstrate that these calculations are now possible and in spite of their larger computational demands provide more reliable results.

  18. Isomers of small Pbn clusters (n=2-15) : Geometric and electronic structures based on ab initio molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Rajesh, C.; Majumder, C.; Rajan, M. G. R.; Kulshreshtha, S. K.

    2005-12-01

    The geometric and electronic structure of the Pbn clusters (n=2-15) has been calculated to elucidate its structural evolution and compared with other group-IV elemental clusters. The search for several low-lying isomers was carried out using the ab initio molecular dynamics simulations under the framework of the density functional theory formalism. The results suggest that unlike Si, Ge, and Sn clusters, which favor less compact prolate shape in the small size range, Pb clusters favor compact spherical structures consisting of fivefold or sixfold symmetries. The difference in the growth motif can be attributed to their bulk crystal structure, which is diamond-like for Si, Ge, and Sn but fcc for Pb. The relative stability of Pbn clusters is analyzed based on the calculated binding energies and second difference in energy. The results suggest that n=4 , 7, 10, and 13 clusters are more stable than their respective neighbors, reflecting good agreement with experimental observation. Based on the fragmentation pattern it is seen that small clusters up to n=12 favor monomer evaporation, larger ones fragment into two stable daughter products. The experimental observation of large abundance for n=7 and lowest abundance of n=14 have been demonstrated from their fragmentation pattern. Finally a good agreement of our theoretical results with that of the experimental findings reported earlier implies accurate predictions of the ground state geometries of these clusters.

  19. Vibrational spectroscopy and ab initio MO study of the molecular structure and vibrational spectra of α- and γ-pyrones

    NASA Astrophysics Data System (ADS)

    Fausto, Rui; Quinteiro, Graciete; Breda, Susana

    2001-12-01

    The molecular structures and vibrational spectra of the monomeric forms of α- and γ-pyrones were investigated by ab initio MO calculations, undertaken at the HF/6-31G ∗ level of theory, and vibrational spectroscopy, including matrix-isolation FTIR spectroscopy. A complete assignment of the vibrational spectra of the studied compounds isolated in an argon matrix, at 8 K, or in the condensed phases, at room temperature, is presented and the vibrational data correlated with some important structural parameters. It is shown that the intermolecular interactions in the room temperature condensed phases do not affect the structure and vibrational properties of the studied molecules strongly, though the vibrational results clearly reveal minor changes induced in the carbonyl groups that indirectly affect the electron distribution in the whole pyrone rings, leading to an increase in their π-electron delocalization. For the isolated monomers, both structural and vibrational results point to a relatively weak π-electron delocalization in both α- and γ-pyrone moieties.

  20. Ab initio study of the structural, electronic and optical properties of ZnTe compound

    SciTech Connect

    Bahloul, B.; Deghfel, B.; Amirouche, L.; Bounab, S.; Bentabet, A.; Bouhadda, Y.; Fenineche, N.

    2015-03-30

    Structural, electronic and optical properties of ZnTe compound were calculated using Density Functional Theory (DFT) based on the pseudopotentials and planewaves (PP-PW) method as implemented in the ABINIT computer code, where the exchange–correlation functional is approximated using the local density approximation (LDA) and the generalized gradient approximation (GGA). The obtained results from either LDA or GGa calculation for lattice parameter, energy band gap and optical parameters, such as the fundamental absorption edge, the peaks observed in the imaginary part of the dielectric function, the macroscopic dielectric constants and the optical dielectric constant, are compared with the available theoretical results and experimental data.

  1. Ab initio Study of the Structural, Tautomeric, Pairing and Electronic Properties of Seleno-Derivatives of Thymine

    SciTech Connect

    Vazquez-Mayagoitia, Alvaro; Fuentes-Cabrera, Miguel A; Sumpter, Bobby G; Luque, Javier; Huertas, Oscar; Orozco, Modesto; Felice, Rosa; Brancolini, Giorgia; Migliore, Agostino

    2009-01-01

    The structural, tautomeric, hydrogen-bonding, stacking and electronic properties of a seleno-derivative of thymine (T), denoted here as 4SeT and created by replacing O4 in T with Se, are investigated by means of ab initio computational techniques. The structural properties of T and 4SeT are very similar and the geometrical differences are mainly limited to the adjacent environment of the C-Se bond. The canonical keto form is the most stable tautomer, in gas phase and in aqueous solution, for both T and 4SeT. It is argued that the competition between two opposite trends, i.e. a decrease in the base-pairing ability and an increase of the stacking interaction upon incorporation of 4SeT into a duplex, likely explains the similar experimental melting points of a seleno-derivative duplex (Se-DNA) and its native counterpart. Interestingly, the underlying electronic structure shows that replacement of O4 with Se promotes a reduction in the HOMO-LUMO gap and an increase in inter-plane coupling, which suggests that Se-DNA could be potentially useful for nanodevice applications. This finding is further supported by the fact that transfer integrals between 4SeT---A stacked base pairs are larger than those determined for similarly stacked natural T---A pairs.

  2. The evolution of the structural, vibrational and electronic properties of the cyclic ethers - on ring size. An ab initio study

    NASA Astrophysics Data System (ADS)

    Ford, Thomas A.

    2014-09-01

    The molecular structures, vibrational spectra and atomic charges of the alicyclic ethers containing from two to five carbon atoms have been determined by means of ab initio calculations, at the level of second order Møller-Plesset perturbation theory and using Dunning's augmented correlation-consistent polarized valence triple-zeta basis set. Two isomers of the oxetane, tetrahydrofuran and tetrahydropyran molecules have been identified and their relative energies determined. Structural properties, such as the COC bond angles and the CH bond lengths, are found to increase steadily with increasing ring size and with decreasing ionization energy. The mean CH2 stretching and bending wavenumbers exhibit the reverse behaviour, while the mean wavenumbers of the CH2 wagging and twisting modes follow the same trend as the structural features. The ring mode wavenumbers vary in a less regular way. The charges of the oxygen, α-carbon and axial and equatorial α- and β-hydrogen atoms also do not show systematic dependences on ring size or ionization energy. The trends in the values of these properties have been rationalized.

  3. Hydration structures of U(III) and U(IV) ions from ab initio molecular dynamics simulations

    SciTech Connect

    Leung, Kevin; Nenoff, Tina M.

    2012-08-21

    We apply DFT+U-based ab initio molecular dynamics simulations to study the hydration structures of U(III) and U(IV) ions, pertinent to redox reactions associated with uranium salts in aqueous media. U(III) is predicted to be coordinated to 8 water molecules, while U(IV) has a hydration number between 7 and 8. At least one of the innershell water molecules of the hydrated U(IV) complex becomes spontaneously deprotonated. As a result, the U(IV)-O pair correlation function exhibits a satellite peak at 2.15 A associated with the shorter U(IV)-(OH{sup -}) bond. This feature is not accounted for in analysis of extended x-ray absorption fine structure and x-ray adsorption near edge structure measurements, which yield higher estimates of U(IV) hydration numbers. This suggests that it may be useful to include the effect of possible hydrolysis in future interpretation of experiments, especially when the experimental pH is close to the reported hydrolysis equilibrium constant value.

  4. Ab initio calculations of indium arsenide in the wurtzite phase: structural, electronic and optical properties

    NASA Astrophysics Data System (ADS)

    Dacal, Luis C. O.; Cantarero, A.

    2014-03-01

    Most III-V semiconductors, which acquire the zinc-blende phase as bulk materials, adopt the metastable wurtzite phase when grown in the form of nanowires. These are new semiconductors with new optical properties, in particular, a different electronic band gap when compared with that grown in the zinc-blende phase. The electronic gap of wurtzite InAs at the \\Gamma -point of the Brillouin zone ({{E}_{0}} gap) has been recently measured, {{E}_{0}}=0.46 eV at low temperature. The electronic gap at the A-point of the Brillouin zone (equivalent to the L-point in the zinc-blende structure, {{E}_{1}}) has also been obtained recently based on a resonant Raman scattering experiment. In this work, we calculate the band structure of InAs in the zinc-blende and wurtzite phases, using the full potential linearized augmented plane wave method, including spin-orbit interaction. The electronic band gap has been improved through the modified Becke-Johnson exchange-correlation potential. Both the {{E}_{0}} and {{E}_{1}} gaps agree very well with the experiment. From the calculations, a crystal field splitting of 0.122 eV and a spin-orbit splitting of 0.312 eV (the experimental value in zinc-blende InAs is 0.4 eV) has been obtained. Finally, we calculate the dielectric function of InAs in both the zinc-blende and wurtzite phases and a comparative discussion is given.

  5. Ab initio investigation of the structural and electronic properties of amorphous HgTe.

    PubMed

    Zhao, Huxian; Chen, Xiaoshuang; Lu, Jianping; Shu, Haibo; Lu, Wei

    2014-01-29

    We present the structure and electronic properties of amorphous mercury telluride obtained from first-principle calculations. The initial configuration of amorphous mercury telluride is created by computation alchemy. According to different exchange–correlation functions in our calculations, we establish two 256-atom models. The topology of both models is analyzed in terms of radial and bond angle distributions. It is found that both the Te and the Hg atoms tend to be fourfold, but with a wrong bond rate of about 10%. The fraction of threefold and fivefold atoms also shows that there are a significant number of dangling and floating bonds in our models. The electronic properties are also obtained. It is indicated that there is a bandgap in amorphous HgTe, in contrast to the zero bandgap for crystalline HgTe. The structures of the band tail and defect states are also discussed. PMID:24592480

  6. Structure, dynamics and stability of water/scCO2/mineral interfaces from ab initio molecular dynamics simulations

    PubMed Central

    Lee, Mal-Soon; Peter McGrail, B.; Rousseau, Roger; Glezakou, Vassiliki-Alexandra

    2015-01-01

    The boundary layer at solid-liquid interfaces is a unique reaction environment that poses significant scientific challenges to characterize and understand by experimentation alone. Using ab initio molecular dynamics (AIMD) methods, we report on the structure and dynamics of boundary layer formation, cation mobilization and carbonation under geologic carbon sequestration scenarios (T = 323 K and P = 90 bar) on a prototypical anorthite (001) surface. At low coverage, water film formation is enthalpically favored, but entropically hindered. Simulated adsorption isotherms show that a water monolayer will form even at the low water concentrations of water-saturated scCO2. Carbonation reactions readily occur at electron-rich terminal Oxygen sites adjacent to cation vacancies that readily form in the presence of a water monolayer. These results point to a carbonation mechanism that does not require prior carbonic acid formation in the bulk liquid. This work also highlights the modern capabilities of theoretical methods to address structure and reactivity at interfaces of high chemical complexity. PMID:26456362

  7. Structural transformation between long and short-chain form of liquid sulfur from ab initio molecular dynamics

    SciTech Connect

    Plašienka, Dušan Martoňák, Roman; Cifra, Peter

    2015-04-21

    We present results of ab initio molecular dynamics study of the structural transformation occurring in hot liquid sulfur under high pressure, which corresponds to the recently observed chain-breakage phenomenon and to the electronic transition reported earlier. The transformation is temperature-induced and separates two distinct polymeric forms of liquid sulfur: high-temperature form composed of short chain-like fragments with open endings and low-temperature form with very long chains. We offer a structural description of the two liquid forms in terms of chain lengths, cross-linking, and chain geometry and investigate several physical properties. We conclude that the transformation is accompanied by changes in energy (but not density) as well as in diffusion coefficient and electronic properties—semiconductor-metal transition. We also describe the analogy of the investigated process to similar phenomena that take place in two other chalcogens selenium and tellurium. Finally, we remark that the behavior of heated liquid sulfur at ambient pressure might indicate a possible existence of a critical point in the low-pressure region of sulfur phase diagram.

  8. Structure, dynamics and stability of water/scCO2/mineral interfaces from ab initio molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Lee, Mal-Soon; Peter McGrail, B.; Rousseau, Roger; Glezakou, Vassiliki-Alexandra

    2015-10-01

    The boundary layer at solid-liquid interfaces is a unique reaction environment that poses significant scientific challenges to characterize and understand by experimentation alone. Using ab initio molecular dynamics (AIMD) methods, we report on the structure and dynamics of boundary layer formation, cation mobilization and carbonation under geologic carbon sequestration scenarios (T = 323 K and P = 90 bar) on a prototypical anorthite (001) surface. At low coverage, water film formation is enthalpically favored, but entropically hindered. Simulated adsorption isotherms show that a water monolayer will form even at the low water concentrations of water-saturated scCO2. Carbonation reactions readily occur at electron-rich terminal Oxygen sites adjacent to cation vacancies that readily form in the presence of a water monolayer. These results point to a carbonation mechanism that does not require prior carbonic acid formation in the bulk liquid. This work also highlights the modern capabilities of theoretical methods to address structure and reactivity at interfaces of high chemical complexity.

  9. 42214 layered Fe-based superconductors: An ab initio study of their structural, magnetic, and electronic properties

    NASA Astrophysics Data System (ADS)

    Bucci, F.; Sanna, A.; Continenza, A.; Katrych, S.; Karpinski, J.; Gross, E. K. U.; Profeta, G.

    2016-01-01

    As a follow-up to the discovery of a new family of Fe-based superconductors, namely, the RE4Fe2As2Te1 -xO4 (42214) (RE = Pr, Sm, and Gd), we present a detailed ab initio study of these compounds highlighting the role of rare-earth (RE) atoms, external pressure, and Te content on their physical properties. Modifications of the structural, magnetic, and electronic properties of the pure (e.g., x =0.0 ) 42214 compounds and their possible correlations with the observed superconducting properties are calculated and discussed. The careful analysis of the results obtained shows that (i) changing the RE atoms allows one to tune the internal pressure acting on the As height with respect to the Fe planes; (ii) similarly to other Fe pnictides, the 42214 pure compounds show an antiferromagnetic-stripe magnetic ground state phase joined by an orthorhombic distortion (not experimentally found yet); (iii) smaller RE atoms increase the magnetic instability of the compounds possibly favoring the onset of the superconducting state; (iv) external pressure induces the vanishing of the magnetic order with a transition to the tetragonal phase and can be a possible experimental route towards higher superconducting critical temperature (Tc) ; and (v) Te vacancies act on the structural parameters, changing the As height and affecting the stability of the magnetic phase.

  10. Interfacing the Ab initio multiple spawning method with electronic structure methods in GAMESS: Photodecay of trans-Azomethane

    DOE PAGES

    Gaenko, Alexander; DeFusco, Albert; Varganov, Sergey A.; Martínez, Todd J.; Gordon, Mark S.

    2014-10-20

    This work presents a nonadiabatic molecular dynamics study of the nonradiative decay of photoexcited trans-azomethane, using the ab initio multiple spawning (AIMS) program that has been interfaced with the General Atomic and Molecular Electronic Structure System (GAMESS) quantum chemistry package for on-the-fly electronic structure evaluation. The interface strategy is discussed, and the capabilities of the combined programs are demonstrated with a nonadiabatic molecular dynamics study of the nonradiative decay of photoexcited trans-azomethane. Energies, gradients, and nonadiabatic coupling matrix elements were obtained with the state-averaged complete active space self-consistent field method, as implemented in GAMESS. The influence of initial vibrational excitationmore » on the outcome of the photoinduced isomerization is explored. Increased vibrational excitation in the CNNC torsional mode shortens the excited state lifetime. Depending on the degree of vibrational excitation, the excited state lifetime varies from ~60–200 fs. As a result, these short lifetimes are in agreement with time-resolved photoionization mass spectroscopy experiments.« less

  11. Structure of the glass-forming metallic liquids by ab-initio and classical molecular dynamics, a case study: Quenching the Cu60Ti20Zr20 alloy

    NASA Astrophysics Data System (ADS)

    Amokrane, S.; Ayadim, A.; Levrel, L.

    2015-11-01

    We consider the question of the amorphization of metallic alloys by melt quenching, as predicted by molecular dynamics simulations with semi-empirical potentials. The parametrization of the potentials is discussed on the example of the ternary Cu-Ti-Zr transition metals alloy, using the ab-initio simulation as a reference. The pair structure in the amorphous state is computed from a potential of the Stillinger-Weber form. The transferability of the parameters during the quench is investigated using two parametrizations: from solid state data, as usual and from a new parametrization on the liquid structure. When the adjustment is made on the pair structure of the liquid, a satisfactory transferability is found between the pure components and their alloys. The liquid structure predicted in this way agrees well with experiment, in contrast with the one obtained using the adjustment on the solid. The final structure, after quenches down to the amorphous state, determined with the new set of parameters is shown to be very close to the ab-initio one, the latter being in excellent agreement with recent X-rays diffraction experiments. The corresponding critical temperature of the glass transition is estimated from the behavior of the heat capacity. Discussion on the consistency between the structures predicted using semi-empirical potentials and ab-initio simulation, and comparison of different experimental data underlines the question of the dependence of the final structure on the thermodynamic path followed to reach the amorphous state.

  12. Electronic structure and anisotropic chemical bonding in TiNF from ab initio study

    SciTech Connect

    Matar, Samir F.

    2012-01-15

    Accounting for disorder in anatase titanium nitride fluoride TiNF is done through atoms re-distributions based on geometry optimizations using ultra soft pseudo potentials within density functional theory DFT. The fully geometry relaxed structures are found to keep the body centering of anatase (I4{sub 1}/amd No. 141). The new structural setups are identified with space groups I-4m2 No. 119 and Imm2 No. 44 which obey the 'group to subgroup' relationships with respect to anatase. In the ground state Imm2 structure identified from energy differences, TiNF is found semi-conducting with similar density of states features to anatase TiO{sub 2} and a chemical bonding differentiated between covalent like Ti-N versus ionic like Ti-F. Inter-anion N-F bonding is also identified. - Graphical Abstract: The geometry optimized ground state anatase derived TiNF structure with arrangement of open faceted TiN3F3 distorted octahedra. The insert shows the arrangement of octahedra in anatase TiO{sub 2}. Highlights: Black-Right-Pointing-Pointer Original approach of TiNF structure for addressing the electronic band structure. Black-Right-Pointing-Pointer Based on anatase, two different ordering scheme models with geometry optimization. Black-Right-Pointing-Pointer New structures obeying the group{yields}subgroup relationships with Imm2 ground state from energy. Black-Right-Pointing-Pointer In the ground state TiNF is found semi-conducting with similar density of states to anatase TiO{sub 2}. Black-Right-Pointing-Pointer Chemical bonding differentiated between covalent like Ti-N and ionic Ti-F.

  13. Ab initio calculations of the electronic structure of the low-lying states for the ultracold LiYb molecule

    NASA Astrophysics Data System (ADS)

    Tohme, Samir N.; Korek, Mahmoud; Awad, Ramadan

    2015-03-01

    Ab initio techniques have been applied to investigate the electronic structure of the LiYb molecule. The potential energy curves have been computed in the Born-Oppenheimer approximation for the ground and 29 low-lying doublet and quartet excited electronic states. Complete active space self-consistent field, multi-reference configuration interaction, and Rayleigh Schrödinger perturbation theory to second order calculations have been utilized to investigate these states. The spectroscopic constants, ωe, Re, Be, …, and the static dipole moment, μ, have been investigated by using the two different techniques of calculation with five different types of basis. The eigenvalues, Ev, the rotational constant, Bv, the centrifugal distortion constant, Dv, and the abscissas of the turning points, Rmin and Rmax, have been calculated by using the canonical functions approach. The comparison between the values of the present work, calculated by different techniques, and those available in the literature for several electronic states shows a very good agreement. Twenty-one new electronic states have been studied here for the first time.

  14. Ab initio calculations of the electronic structure of the low-lying states for the ultracold LiYb molecule

    SciTech Connect

    Tohme, Samir N.; Korek, Mahmoud E-mail: fkorek@yahoo.com; Awad, Ramadan

    2015-03-21

    Ab initio techniques have been applied to investigate the electronic structure of the LiYb molecule. The potential energy curves have been computed in the Born–Oppenheimer approximation for the ground and 29 low-lying doublet and quartet excited electronic states. Complete active space self-consistent field, multi-reference configuration interaction, and Rayleigh Schrödinger perturbation theory to second order calculations have been utilized to investigate these states. The spectroscopic constants, ω{sub e}, R{sub e}, B{sub e}, …, and the static dipole moment, μ, have been investigated by using the two different techniques of calculation with five different types of basis. The eigenvalues, E{sub v}, the rotational constant, B{sub v}, the centrifugal distortion constant, D{sub v}, and the abscissas of the turning points, R{sub min} and R{sub max}, have been calculated by using the canonical functions approach. The comparison between the values of the present work, calculated by different techniques, and those available in the literature for several electronic states shows a very good agreement. Twenty-one new electronic states have been studied here for the first time.

  15. Ab initio calculations of the electronic structure of the low-lying states for the ultracold LiYb molecule.

    PubMed

    Tohme, Samir N; Korek, Mahmoud; Awad, Ramadan

    2015-03-21

    Ab initio techniques have been applied to investigate the electronic structure of the LiYb molecule. The potential energy curves have been computed in the Born-Oppenheimer approximation for the ground and 29 low-lying doublet and quartet excited electronic states. Complete active space self-consistent field, multi-reference configuration interaction, and Rayleigh Schrödinger perturbation theory to second order calculations have been utilized to investigate these states. The spectroscopic constants, ωe, Re, Be, …, and the static dipole moment, μ, have been investigated by using the two different techniques of calculation with five different types of basis. The eigenvalues, Ev, the rotational constant, Bv, the centrifugal distortion constant, Dv, and the abscissas of the turning points, Rmin and Rmax, have been calculated by using the canonical functions approach. The comparison between the values of the present work, calculated by different techniques, and those available in the literature for several electronic states shows a very good agreement. Twenty-one new electronic states have been studied here for the first time. PMID:25796254

  16. Ab initio simulation of the electronic structure of Ta{sub 2}O{sub 5} crystal modifications

    SciTech Connect

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

    2013-06-15

    Ab initio simulation of the electronic structure crystalline {beta} and {delta} phases of tantalum(V) oxide (Ta{sub 2}O{sub 5}), representing a promising dielectric material for microelectronics, has been carried out. Both ideal crystals and those with neutral oxygen vacancies in various coordination positions have been studied. The simulation has been performed using the density functional theory with hybrid functionals involving the Hartree-Fock exchange energy. This approach gives a correct description of the bandgap width: 4.1 eV for {beta}-Ta{sub 2}O{sub 5} and 3.1 eV for {delta}-Ta{sub 2}O{sub 5}. The energy levels related to oxygen vacancies in various positions have been determined for the spectra of electron states in {beta}- and {delta}-Ta{sub 2}O{sub 5} polymorphs. It is established that the presence of oxygen vacancies in Ta{sub 2}O{sub 5} crystal modifications leads to the formation of characteristic absorption peaks in their electron energy loss spectra.

  17. Raman and infrared spectra, structure, vibrational assignment, normal coordinate analysis, and ab initio calculations of trifluoromethyl isocyanate

    NASA Astrophysics Data System (ADS)

    Durig, J. R.; Guirgis, G. A.; Eltayeb, S.

    1994-07-01

    The Raman (2500 to 30 cm -1) and infrared (2500 to 60 cm 1) spectra of gaseous and solid trifluoromethyl isocyanate, CF 3NCO, have been recorded. The Raman spectrum of the liquid has also been obtained and qualitative depolarization ratios have been measured. The CNC bend has been observed in the low-frequency Raman spectrum of the gas at 130 cm -1 as a relatively strong line which is split in the spectrum of the solid. However, the CF 3 torsional mode was not observed. The infrared spectrum of CF 3NCO dissolved in liquid xenon was also obtained and the observed spectrum indicates a very small barrier to internal rotation. With the exception of the torsion, a complete assignment of the vibrational fundamentals is proposed. The structural parameters, force constants, and vibrational frequencies have been determined from ab initio calculations utilizing a variety of basis sets and the theoretical results are compared to the experimental values when appropriate. These results have been compared with the corresponding quantities obtained for some similar molecules.

  18. Nonlocal Pseudopotentials and Long-Range Interactions in Ab Initio Finite-Element Electronic-Structure Calculations

    NASA Astrophysics Data System (ADS)

    Pask, J. E.; Sterne, P. A.

    2004-03-01

    The finite-element (FE) method is a general approach for the solution of partial differential equations. Like the planewave (PW) method, the FE method is a systematically improvable expansion approach. Unlike the PW method, however, its basis functions are strictly local in real space, which allows for variable resolution in real space and facilitates massively parallel implementation. We discuss the application of the FE method to ab initio electronic-structure calculations.(J.E. Pask, B.M. Klein, C.Y. Fong, and P.A. Sterne, Phys. Rev. B 59), 12352 (1999). In particular, we discuss the use of nonlocal pseudopotentials in bulk calculations, and the handling of long-range interactions in the construction of the Kohn-Sham effective potential and total energy. We show that the total energy converges variationally, and at the optimal theoretical rate consistent with the cubic completeness of the basis. This work was performed under the auspices of the U.S. Department of Energy by University of California, Lawrence Livermore National Laboratory under Contract W-7405-Eng-48.

  19. On the structure of crystalline and molten cryolite: Insights from the ab initio molecular dynamics in NpT ensemble

    NASA Astrophysics Data System (ADS)

    Bučko, Tomáš; Šimko, František

    2016-02-01

    Ab initio molecular dynamics simulations in isobaric-isothermal ensemble have been performed to study the low- and the high-temperature crystalline and liquid phases of cryolite. The temperature induced transitions from the low-temperature solid (α) to the high-temperature solid phase (β) and from the phase β to the liquid phase have been simulated using a series of MD runs performed at gradually increasing temperature. The structure of crystalline and liquid phases is analysed in detail and our computational approach is shown to reliably reproduce the available experimental data for a wide range of temperatures. Relatively frequent reorientations of the AlF6 octahedra observed in our simulation of the phase β explain the thermal disorder in positions of the F- ions observed in X-ray diffraction experiments. The isolated AlF63-, AlF52-, AlF4-, as well as the bridged Al 2 Fm 6 - m ionic entities have been identified as the main constituents of cryolite melt. In accord with the previous high-temperature NMR and Raman spectroscopic experiments, the compound AlF5 2 - has been shown to be the most abundant Al-containing species formed in the melt. The characteristic vibrational frequencies for the AlFn 3 - n species in realistic environment have been determined and the computed values have been found to be in a good agreement with experiment.

  20. On the structure of crystalline and molten cryolite: Insights from the ab initio molecular dynamics in NpT ensemble.

    PubMed

    Bučko, Tomáš; Šimko, František

    2016-02-14

    Ab initio molecular dynamics simulations in isobaric-isothermal ensemble have been performed to study the low- and the high-temperature crystalline and liquid phases of cryolite. The temperature induced transitions from the low-temperature solid (α) to the high-temperature solid phase (β) and from the phase β to the liquid phase have been simulated using a series of MD runs performed at gradually increasing temperature. The structure of crystalline and liquid phases is analysed in detail and our computational approach is shown to reliably reproduce the available experimental data for a wide range of temperatures. Relatively frequent reorientations of the AlF6 octahedra observed in our simulation of the phase β explain the thermal disorder in positions of the F(-) ions observed in X-ray diffraction experiments. The isolated AlF6(3-), AlF5(2-), AlF4(-), as well as the bridged Al2Fm(6-m) ionic entities have been identified as the main constituents of cryolite melt. In accord with the previous high-temperature NMR and Raman spectroscopic experiments, the compound AlF5(2-) has been shown to be the most abundant Al-containing species formed in the melt. The characteristic vibrational frequencies for the AlFn(3-n) species in realistic environment have been determined and the computed values have been found to be in a good agreement with experiment. PMID:26874492

  1. F K-edge X-ray absorption near-edge structure (XANES) of AlF3 polymorphs: combining ab initio calculations with Walsh correlation diagrams.

    PubMed

    Schroeder, Sven L M; Weiher, Norbert

    2006-04-21

    The X-ray absorption near-edge structures (XANES) at the F K-edge of alpha-AlF(3), beta-AlF(3) and a tetragonal AlF(3) phase are analysed by a combination of ab initio calculations with the FEFF8 code and a phenomenological discussion of local molecular orbital (MO) symmetries at the absorbing fluorine atoms. By means of a Walsh correlation diagram it is shown that the two intense absorption bands observed at the F K-edges of the AlF(3) polymorphs can be interpreted as transitions to anti-bonding MOs in [Al-F-Al]-units that have C(2v) and D(infinity h) point group symmetries. The energies of both anti-bonding orbitals are very insensitive to the angle between the Al-F bonds, which explains the close similarity of the XANES signatures from the three polymorphs. The FEFF8 analysis shows that the increased broadening of the XANES structure for beta-AlF(3) and the tetragonal AlF(3) phase is due to the superposition of the individual absorption spectra from the crystallographically distinct F species. The interpretation in terms of local MOs provides for the first time a "chemically intuitive" approach to investigations of solid fluorides by XANES spectroscopy and provides a simple conceptual framework for the discussion of the electronic structure in AlF(3) materials.

  2. Electronic structure, thermodynamic properties and hydrogenation of LaPtIn and CePtIn compounds by ab-initio methods

    NASA Astrophysics Data System (ADS)

    Jezierski, Andrzej; Szytuła, Andrzej

    2016-02-01

    The electronic structures and thermodynamic properties of LaPtIn and CePtIn are studied by means of ab-initio full-relativistic full-potential local orbital basis (FPLO) method within densities functional (DFT) methodologies. We have also examined the influence of hydrogen on the electronic structure and stability of CePtInH and LaPtInH systems. The positions of the hydrogen atoms have been found from the minimum of the total energy. Our calculations have shown that band structure and topology of the Fermi surfaces changed significantly during the hydrogenation. The thermodynamic properties (bulk modulus, Debye temperatures, constant pressure heat capacity) calculated in quasi-harmonic Debye-Grüneisen model are in a good agreement with the experimental data. We have applied different methods of the calculation of the equation of states (EOS) (Murnaghan, Birch-Murnaghan, Poirier-Tarantola, Vinet). The thermodynamic properties are presented for the pressure 0

  3. Structural, elastic, vibrational and electronic properties of amorphous Al2O3 from ab initio calculations.

    PubMed

    Davis, Sergio; Gutiérrez, Gonzalo

    2011-12-14

    First-principles molecular dynamics calculations of the structural, elastic, vibrational and electronic properties of amorphous Al(2)O(3), in a system consisting of a supercell of 80 atoms, are reported. A detailed analysis of the interatomic correlations allows us to conclude that the short-range order is mainly composed of AlO(4) tetrahedra, but, in contrast with previous results, also an important number of AlO(6) octahedra and AlO(5) units are present. The vibrational density of states presents two frequency bands, related to bond-bending and bond-stretching modes. It also shows other recognizable features present in similar amorphous oxides. We also present the calculation of elastic properties (bulk modulus and shear modulus). The calculated electronic structure of the material, including total and partial electronic density of states, charge distribution, electron localization function and the ionicity for each species, gives evidence of correlation between the ionicity and the coordination for each Al atom.

  4. Ab initio structural and vibrational properties of GaAs diamondoids and nanocrystals

    NASA Astrophysics Data System (ADS)

    Abdulsattar, Mudar Ahmed; Hussein, Mohammed T.; Hameed, Hadeel Ali

    2014-12-01

    Gallium arsenide diamondoids structural and vibrational properties are investigated using density functional theory at the PBE/6-31(d) level and basis including polarization functions. Variation of energy gap as these diamondoids increase in size is seen to follow confinement theory for diamondoids having nearly equiaxed dimensions. Density of energy states transforms from nearly single levels to band structure as we reach larger diamondoids. Bonds of surface hydrogen with As atoms are relatively localized and shorter than that bonded to Ga atoms. Ga-As bonds have a distribution range of values due to surface reconstruction and effect of bonding to hydrogen atoms. Experimental bulk Ga-As bond length (2.45 Å) is within this distribution range. Tetrahedral and dihedral angles approach values of bulk as we go to higher diamondoids. Optical-phonon energy of larger diamondoids stabilizes at 0.037 eV (297 cm-1) compared to experimental 0.035 eV (285.2 cm-1). Ga-As force constant reaches 1.7 mDyne/Å which is comparable to Ga-Ge force constant (1.74 mDyne/Å). Hydrogen related vibrations are nearly constant and serve as a fingerprint of GaAs diamondoids while Ga-As vibrations vary with size of diamondoids.

  5. Ab initio structural and vibrational properties of GaAs diamondoids and nanocrystals

    SciTech Connect

    Abdulsattar, Mudar Ahmed; Hussein, Mohammed T.; Hameed, Hadeel Ali

    2014-12-15

    Gallium arsenide diamondoids structural and vibrational properties are investigated using density functional theory at the PBE/6-31(d) level and basis including polarization functions. Variation of energy gap as these diamondoids increase in size is seen to follow confinement theory for diamondoids having nearly equiaxed dimensions. Density of energy states transforms from nearly single levels to band structure as we reach larger diamondoids. Bonds of surface hydrogen with As atoms are relatively localized and shorter than that bonded to Ga atoms. Ga-As bonds have a distribution range of values due to surface reconstruction and effect of bonding to hydrogen atoms. Experimental bulk Ga-As bond length (2.45 Å) is within this distribution range. Tetrahedral and dihedral angles approach values of bulk as we go to higher diamondoids. Optical-phonon energy of larger diamondoids stabilizes at 0.037 eV (297 cm{sup -1}) compared to experimental 0.035 eV (285.2 cm{sup -1}). Ga-As force constant reaches 1.7 mDyne/Å which is comparable to Ga-Ge force constant (1.74 mDyne/Å). Hydrogen related vibrations are nearly constant and serve as a fingerprint of GaAs diamondoids while Ga-As vibrations vary with size of diamondoids.

  6. Ab initio investigation of the structural, electronic, magnetic and optical properties of the perovskite TlMnX3 (X = F, Cl) compounds

    NASA Astrophysics Data System (ADS)

    Hamioud, Farida; Alghamdi, Ghadah S.; Al-Omari, Saleh; Mubarak, A. A.

    2016-03-01

    We have performed ab initio investigation of some physical properties of the perovskite TlMnX3 (X = F, Cl) compounds using the full-potential linearized augmented plane wave (FP-LAPW) method. The generalized gradient approximation (GGA) is employed as exchange-correlation potential. The calculated lattice constant and bulk modulus agree with previous studies. Both compounds are found to be elastically stable. TlMnF3 and TlMnCl3 are classified as anisotropic and ductile compounds. The calculations of the band structure of the studied compounds showed the semiconductor behavior with the indirect (M-X) energy gap. Both compounds are classified as a ferromagnetic due to the integer value of the total magnetic moment of the compounds. The different optical spectra are calculated from the real and the imaginary parts of the dielectric function and connected to the electronic structure of the compounds. The static refractive index n(0) is inversely proportional to the energy bandgap of the two compounds. Beneficial optics technology applications are predicted based on the optical spectra.

  7. An ab-initio study of adsorption of gaseous molecules on doped graphene structures

    NASA Astrophysics Data System (ADS)

    Balangi, H. R.; Shokri, A. A.

    2015-11-01

    In this work, electronic properties of bare and doped graphene layers in the presence of N, B and a type of defective impurities are investigated under adsorption of CO, NO, NH3 and NO2 molecules on it's external surface. We use a fully self-consistent density function theory (DFT) based calculations as implemented in SIESTA package. The local-density approximation (LDA) is considered for the exchange-correlation function. Total density of state (TDOS), partial density of state (PDOS) and charge density calculations are also considered to elucidate the difference in the CO, NO, NH3 and NO2 gases detection mechanism of pristine and doped graphene structures. With regard to that the charge transfer is occurring between the graphene sheet and gaseous molecules, the NO2 and NH3 molecules are considered as the recipient and donor of electrons, respectively. We show that the states contributed by the adsorbed CO and NO molecules are quite localized near the center of original band gap and they suggest that the charge transport in such systems cannot be enhanced considerably, while NO2 and NH3 molecules adsorption acts as the acceptor and donor, respectively. Our results can serve as a base for developments in designing nano-electronic devices.

  8. 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.

  9. Homologous series of layered structures in binary and ternary Bi-Sb-Te-Se systems: Ab initio study

    NASA Astrophysics Data System (ADS)

    Govaerts, K.; Sluiter, M. H. F.; Partoens, B.; Lamoen, D.

    2014-02-01

    In order to account explicitly for the existence of long-periodic layered structures and the strong structural relaxations in the most common binary and ternary alloys of the Bi-Sb-Te-Se system, we have developed a one-dimensional cluster expansion (CE) based on first-principles electronic structure calculations, which accounts for the Bi and Sb bilayer formation. Excellent interlayer distances are obtained with a van der Waals density functional. It is shown that a CE solely based on pair interactions is sufficient to provide an accurate description of the ground-state energies of Bi-Sb-Te-Se binary and ternary systems without making the data set of ab initio calculated structures unreasonably large. For the binary alloys A1-xQx (A =Sb, Bi; Q =Te, Se), a ternary CE yields an almost continuous series of (meta)stable structures consisting of consecutive A bilayers next to consecutive A2Q3 for 00.6, the binary alloy segregates into pure Q and A2Q3. The Bi-Sb system is described by a quaternary CE and is found to be an ideal solid solution stabilized by entropic effects at T ≠0 K but with an ordered structure of alternating Bi and Sb layers for x =0.5 at T =0 K. A quintuple CE is used for the ternary Bi-Sb-Te system, where stable ternary layered compounds with an arbitrary stacking of Sb2Te3,Bi2Te3, and Te-Bi-Te-Sb-Te quintuple units are found, optionally separated by mixed Bi/Sb bilayers. Electronic properties of the stable compounds were studied taking spin-orbit coupling into account.

  10. Molecular structural conformations and hydration of internally hydrogen-bonded salicylic acid: Ab initio and DFT studies

    NASA Astrophysics Data System (ADS)

    Anandan, K.; Kolandaivel, P.; Kumaresan, R.

    We studied molecular structural conformations and hydration of internally hydrogen-bonded salicylic acid using ab initio and density functional theory methods. Molecular geometries and energetical parameters were obtained in gaseous phase using MP2 and B3LYP levels of theory, implementing the 6-311G(2d,2p) atomic basis set. Chemical hardness and chemical potential were calculated at HF/6-311G(2d,2p) level of theory for all the optimized structures, and the principle of maximum hardness was tested. The condensed Fukui functions were calculated using the atomic charges obtained through a natural population analysis scheme for all optimized structures at B3LYP/6-311G(2d,2p) level of theory, and the most reactive sites of the molecules were identified. NMR studies were carried out for all the conformers in gaseous phase on the basis of Cheeseman et al.'s method at B3LYP/6-311G(2d,2p) level of theory; the calculated chemical shift values are discussed. The self-consistent reaction field theory (SCRF) was used to optimize all the conformers in aqueous phase (ɛ = 78.39) at B3LYP/6-311G(2d,2p) level of theory and the solvent effect was studied. The geometrical and energetical parameters of all the conformers are compared and analyzed. The dimeric structure of the most stable conformer in the gaseous phase was optimized at B3LYP/6-311G(2d,2p) level of theory and the interaction energy studied. Selected conformers were allowed to interact with water molecule; optimized parameters are discussed. Vibrational frequency analyses were performed at MP2/6-311G(2d,2p) level of theory and the stationary point corresponding to local minima without imaginary frequencies are obtained for all the optimized structures.

  11. Experimental and ab Initio Study of Catena(bis(μ2-iodo)-6-methylquinoline-copper(I)) under Pressure: Synthesis, Crystal Structure, Electronic, and Luminescence Properties.

    PubMed

    Aguirrechu-Comerón, Amagoia; Hernández-Molina, Rita; Rodríguez-Hernández, Plácida; Muñoz, Alfonso; Rodríguez-Mendoza, Ulises R; Lavín, Vı́ctor; Angel, Ross J; Gonzalez-Platas, Javier

    2016-08-01

    Copper(I) iodine compounds can exhibit interesting mechanochromic and thermochromic luminescent properties with important technological applications. We report the synthesis and structure determination by X-ray diffraction of a new polymeric staircase copper(I) iodine compound catena(bis(μ2-iodo)-6-methylquinoline-copper(I), [C10H9CuIN]. The structure is composed of isolated polymeric staircase chains of copper-iodine coordinated to organic ligands through Cu-N bonds. High pressure X-ray diffraction to 6.45 GPa shows that the material is soft, with a bulk modulus K0 = 10.2(2)GPa and a first derivative K'0 = 8.1(3), typical for organometallic compounds. The unit-cell compression is very anisotropic with the stiffest direction [302] arising from a combination of the stiff CuI ladders and the shear of the planar quinolone ligands over one another. Full structure refinements at elevated pressures show that pressures reduce the Cu···Cu distances in the compound. This effect is detected in luminescence spectra with the appearance of four sub-bands at 515, 600, 647, and 712 nm above 3.5 GPa. Red-shifts are observed, and they are tentatively associated with interactions between copper(I) ions due to the shortening of the Cu···Cu distances induced by pressure, below twice the van der Waals limit (2.8 Å). Additionally, ab initio simulations were performed, and they confirmed the structure and the results obtained experimentally for the equation of state. The simulation allowed the band structure and the electronic density of states of this copper(I) iodine complex to be determined. In particular, the band gap decreases slowly with pressure in a quadratic way with dEg/dP = -0.011 eV/GPa and d(2)Eg/dP(2) = 0.001 eV/GPa(2).

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

    NASA Astrophysics Data System (ADS)

    Aryal, Sita Ram

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

  13. The individual and collective effects of exact exchange and dispersion interactions on the ab initio structure of liquid water

    NASA Astrophysics Data System (ADS)

    DiStasio, Robert A.; Santra, Biswajit; Li, Zhaofeng; Wu, Xifan; Car, Roberto

    2014-08-01

    In this work, we report the results of a series of density functional theory (DFT) based ab initio molecular dynamics (AIMD) simulations of ambient liquid water using a hierarchy of exchange-correlation (XC) functionals to investigate the individual and collective effects of exact exchange (Exx), via the PBE0 hybrid functional, non-local van der Waals/dispersion (vdW) interactions, via a fully self-consistent density-dependent dispersion correction, and an approximate treatment of nuclear quantum effects, via a 30 K increase in the simulation temperature, on the microscopic structure of liquid water. Based on these AIMD simulations, we found that the collective inclusion of Exx and vdW as resulting from a large-scale AIMD simulation of (H2O)128 significantly softens the structure of ambient liquid water and yields an oxygen-oxygen structure factor, SOO(Q), and corresponding oxygen-oxygen radial distribution function, gOO(r), that are now in quantitative agreement with the best available experimental data. This level of agreement between simulation and experiment demonstrated herein originates from an increase in the relative population of water molecules in the interstitial region between the first and second coordination shells, a collective reorganization in the liquid phase which is facilitated by a weakening of the hydrogen bond strength by the use of a hybrid XC functional, coupled with a relative stabilization of the resultant disordered liquid water configurations by the inclusion of non-local vdW/dispersion interactions. This increasingly more accurate description of the underlying hydrogen bond network in liquid water also yields higher-order correlation functions, such as the oxygen-oxygen-oxygen triplet angular distribution, POOO(θ), and therefore the degree of local tetrahedrality, as well as electrostatic properties, such as the effective molecular dipole moment, that are in much better agreement with experiment.

  14. The individual and collective effects of exact exchange and dispersion interactions on the ab initio structure of liquid water

    SciTech Connect

    DiStasio, Robert A.; Santra, Biswajit; Li, Zhaofeng; Wu, Xifan; Car, Roberto

    2014-08-28

    In this work, we report the results of a series of density functional theory (DFT) based ab initio molecular dynamics (AIMD) simulations of ambient liquid water using a hierarchy of exchange-correlation (XC) functionals to investigate the individual and collective effects of exact exchange (Exx), via the PBE0 hybrid functional, non-local van der Waals/dispersion (vdW) interactions, via a fully self-consistent density-dependent dispersion correction, and an approximate treatment of nuclear quantum effects, via a 30 K increase in the simulation temperature, on the microscopic structure of liquid water. Based on these AIMD simulations, we found that the collective inclusion of Exx and vdW as resulting from a large-scale AIMD simulation of (H{sub 2}O){sub 128} significantly softens the structure of ambient liquid water and yields an oxygen-oxygen structure factor, S{sub OO}(Q), and corresponding oxygen-oxygen radial distribution function, g{sub OO}(r), that are now in quantitative agreement with the best available experimental data. This level of agreement between simulation and experiment demonstrated herein originates from an increase in the relative population of water molecules in the interstitial region between the first and second coordination shells, a collective reorganization in the liquid phase which is facilitated by a weakening of the hydrogen bond strength by the use of a hybrid XC functional, coupled with a relative stabilization of the resultant disordered liquid water configurations by the inclusion of non-local vdW/dispersion interactions. This increasingly more accurate description of the underlying hydrogen bond network in liquid water also yields higher-order correlation functions, such as the oxygen-oxygen-oxygen triplet angular distribution, P{sub OOO}(θ), and therefore the degree of local tetrahedrality, as well as electrostatic properties, such as the effective molecular dipole moment, that are in much better agreement with experiment.

  15. Vibrational Properties of Hydrogen-Bonded Systems Using the Multireference Generalization to the "On-the-Fly" Electronic Structure within Quantum Wavepacket ab Initio Molecular Dynamics (QWAIMD).

    PubMed

    Li, Junjie; Li, Xiaohu; Iyengar, Srinivasan S

    2014-06-10

    We discuss a multiconfigurational treatment of the "on-the-fly" electronic structure within the quantum wavepacket ab initio molecular dynamics (QWAIMD) method for coupled treatment of quantum nuclear effects with electronic structural effects. Here, multiple single-particle electronic density matrices are simultaneously propagated with a quantum nuclear wavepacket and other classical nuclear degrees of freedom. The multiple density matrices are coupled through a nonorthogonal configuration interaction (NOCI) procedure to construct the instantaneous potential surface. An adaptive-mesh-guided set of basis functions composed of Gaussian primitives are used to simplify the electronic structure calculations. Specifically, with the replacement of the atom-centered basis functions positioned on the centers of the quantum-mechanically treated nuclei by a mesh-guided band of basis functions, the two-electron integrals used to compute the electronic structure potential surface become independent of the quantum nuclear variable and hence reusable along the entire Cartesian grid representing the quantum nuclear coordinates. This reduces the computational complexity involved in obtaining a potential surface and facilitates the interpretation of the individual density matrices as representative diabatic states. The parametric nuclear position dependence of the diabatic states is evaluated at the initial time-step using a Shannon-entropy-based sampling function that depends on an approximation to the quantum nuclear wavepacket and the potential surface. This development is meant as a precursor to an on-the-fly fully multireference electronic structure procedure embedded, on-the-fly, within a quantum nuclear dynamics formalism. We benchmark the current development by computing structural, dynamic, and spectroscopic features for a series of bihalide hydrogen-bonded systems: FHF(-), ClHCl(-), BrHBr(-), and BrHCl(-). We find that the donor-acceptor structural features are in good

  16. Structure and dynamics of high-pressure Na close to the melting line: An ab initio molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Marqués, M.; González, D. J.; González, L. E.

    2016-07-01

    The melting curve of sodium for a pressure range up to 100 GPa has been evaluated by the orbital free ab initio molecular dynamics method. This method uses the electronic density as the basic variable combined with an approximate electronic kinetic energy functional and a local ionic pseudopotential and makes it possible to perform simulations with a large number of particles and for long simulation times. The calculated melting curve shows a maximum melting temperature at a pressure around 30 GPa followed by a steep decrease up to 100 GPa. For various pressures and temperatures we have evaluated several static properties, including average and local structure, electronic properties, like the electron localization function (ELF), and dynamic properties, both single-particle and collective ones, from which some transport coefficients are deduced. Despite the accurate reproduction of the available experimental data, we do not observe any indication of an early transition from a bcc-like to an fcc-like liquid, as suggested previously by other authors, but rather pressure-induced change in the variation of icosahedral-like order and bcc-like order, with no sign of fcc-like structures in the whole liquid range studied. We also consider the evolution of the ELF within this type of local arrangement upon pressurization. In the dynamic realm, we find an enlarged wave-vector region where atomic collisions play an important role in the dynamic properties of the system as pressure is increased and temperature decreased along the melting line, leading to a peculiar behavior of the dynamic properties.

  17. Ab-initio study of structural, electronic, and transport properties of zigzag GaP nanotubes.

    PubMed

    Srivastava, Anurag; Jain, Sumit Kumar; Khare, Purnima Swarup

    2014-03-01

    Stability and electronic properties of zigzag (3 ≤ n ≤ 16) gallium phosphide nanotubes (GaP NTs) have been analyzed by employing a systematic ab-intio approach based on density functional theory using generalized gradient approximation with revised Perdew Burke Ernzerhoff type parameterization. Diameter dependence of bond length, buckling, binding energy, and band gap has been investigated and the analysis shows that the bond length and buckling decreases with increasing diameter of the tube, highest binding energy of (16, 0) confirms this as the most stable amongst all the NTs taken into consideration. The present GaP NTs shows direct band gap and it increases with diameter of the tubes. Using a two probe model for (4, 0) NT the I-V relationship shows an exponential increase in current on applying bias voltage beyond 1.73 volt.

  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. Unravelling the impact of hydrocarbon structure on the fumarate addition mechanism--a gas-phase ab initio study.

    PubMed

    Bharadwaj, Vivek S; Vyas, Shubham; Villano, Stephanie M; Maupin, C Mark; Dean, Anthony M

    2015-02-14

    The fumarate addition reaction mechanism is central to the anaerobic biodegradation pathway of various hydrocarbons, both aromatic (e.g., toluene, ethyl benzene) and aliphatic (e.g., n-hexane, dodecane). Succinate synthase enzymes, which belong to the glycyl radical enzyme family, are the main facilitators of these biochemical reactions. The overall catalytic mechanism that converts hydrocarbons to a succinate molecule involves three steps: (1) initial H-abstraction from the hydrocarbon by the radical enzyme, (2) addition of the resulting hydrocarbon radical to fumarate, and (3) hydrogen abstraction by the addition product to regenerate the radical enzyme. Since the biodegradation of hydrocarbon fuels via the fumarate addition mechanism is linked to bio-corrosion, an improved understanding of this reaction is imperative to our efforts of predicting the susceptibility of proposed alternative fuels to biodegradation. An improved understanding of the fuel biodegradation process also has the potential to benefit bioremediation. In this study, we consider model aromatic (toluene) and aliphatic (butane) compounds to evaluate the impact of hydrocarbon structure on the energetics and kinetics of the fumarate addition mechanism by means of high level ab initio gas-phase calculations. We predict that the rate of toluene degradation is ∼100 times faster than butane at 298 K, and that the first abstraction step is kinetically significant for both hydrocarbons, which is consistent with deuterium isotope effect studies on toluene degradation. The detailed computations also show that the predicted stereo-chemical preference of the succinate products for both toluene and butane are due to the differences in the radical addition rate constants for the various isomers. The computational and kinetic modeling work presented here demonstrates the importance of considering pre-reaction and product complexes in order to accurately treat gas phase systems that involve intra and inter

  20. Pressure induced structural phase transition in actinide mono-bismuthides: Ab initio calculations

    NASA Astrophysics Data System (ADS)

    Pataiya, J.; Makode, C.; Aynyas, M.; Sanyal, Sankar P.

    2013-06-01

    The structural and electronic properties of mono-bismuthides of Plutonium and Americium have been investigated using tight binding linear muffin-tin-orbital (TB-LMTO) method within the local density approximation (LDA). From present study with the help of total energy calculations it is found that PuBi and AmBi are stable in NaCl - type structure under ambient pressure. The structure stability of PuBi and AmBi changes under the application of pressure. We predict a structural phase transition from NaCl-type (B1-phase) structure to CsCl-type (B2-phase) structure for these phospides in the pressure range of 45 - 4.5 GPa for PuBi and AmBi respectively. The calculated equilibrium lattice parameters and bulk modulus are in good agreement with experimental and theoretical work.

  1. Pressure Induced Structural Phase Transition in Actinide Monophospides: Ab Initio Calculations

    NASA Astrophysics Data System (ADS)

    Makode, Chandrabhan; Sanyal, Sankar P.

    2011-07-01

    The structural and electronic properties of monophospides of Thorium, Uranium and Neptunium have been investigated using tight binding linear muffin-in-orbital (TB-LMTO) method within the local density approximation (LDA). From present study with the help of total energy calculations it is found that ThP, UP and NpP are stable in NaCl- type structure under ambient pressure. The structure stability of ThP, UP and NpP changes under the application of pressure. We predict a structural phase transition from NaCl-type (B1-phase) structure to CsCl-type (B2-phase) structure for these phospides in the pressure range of 37.0-24.0 GPa (ThP to NpP). The calculated equilibrium lattice parameters and bulk modulus are in good agreement with experimental and theoretical work.

  2. Ab initio self-consistent x-ray absorption fine structure analysis for metalloproteins.

    PubMed

    Dimakis, Nicholas; Bunker, Grant

    2006-12-01

    X-ray absorption fine structure is a powerful tool for probing the structures of metals in proteins in both crystalline and noncrystalline environments. Until recently, a fundamental problem in biological XAFS has been that ad hoc assumptions must be made concerning the vibrational properties of the amino acid residues that are coordinated to the metal to fit the data. Here, an automatic procedure for accurate structural determination of active sites of metalloproteins is presented. It is based on direct multiple-scattering simulation of experimental X-ray absorption fine structure spectra combining electron multiple scattering calculations with density functional theory calculations of vibrational modes of amino acid residues and the genetic algorithm differential evolution to determine a global minimum in the space of fitting parameters. Structure determination of the metalloprotein active site is obtained through a self-consistent iterative procedure with only minimal initial information.

  3. Ab-Initio Determination of Novel Crystal Structures of the Thermoelectric Material MgAgSb

    SciTech Connect

    Kirkham, Melanie J; Moreira Dos Santos, Antonio F; Rawn, Claudia J; Lara-Curzio, Edgar; Sharp, Jeff W.; Thompson, Alan

    2012-01-01

    Materials with the half-Heusler structure possess interesting electrical and magnetic properties, including potential for thermoelectric applications. MgAgSb is compositionally and structurally related to many half-Heusler materials, but has not been extensively studied. This work presents the high-temperature X-ray diffraction analysis of MgAgSb between 27 and 420 C, complemented with thermoelectric property measurements. MgAgSb is found to exist in three different structures in this temperature region, taking the half-Heusler structure at high temperatures, a Cu2Sb-related structure at intermediate temperatures, and a previously unreported tetragonal structure at room temperature. All three structures are related by a distorted Mg-Sb rocksalt-type sublattice, differing primarily in the Ag location among the available tetrahedral sites. Transition temperatures between the three phases correlate well with discontinuities in the Seebeck coefficient and electrical conductivity; the best performance occurs with the novel room temperature phase. For application of MgAgSb as a thermoelectric material, it may be desirable to develop methods to stabilize the room temperature phase at higher temperatures.

  4. Ab-initio structure determination of {beta}-La{sub 2}WO{sub 6}

    SciTech Connect

    Chambrier, M-H.; Kodjikian, S.; Ibberson, R.M.; Goutenoire, F.

    2009-02-15

    The structure of the low-temperature form of {beta}-La{sub 2}WO{sub 6} has been determined from laboratory X-ray, neutron time-of-flight and electron diffraction data. This tungstate crystallizes in the non-centrosymmetric orthorhombic space group (no. 19) P2{sub 1}2{sub 1}2{sub 1}, with Z=8, a=7.5196(1) A, b=10.3476(1) A, c=12.7944(2) A, and a measured density 7.37(1) g cm{sup -3}. The structure consists of tungsten [WO{sub 6}] octahedra and tetrahedral [OLa{sub 4}]. Tungsten polyhedra are connected such that [W{sub 2}O{sub 11}]{sup 10-} units are formed. - Graphical abstract: Projection of La{sub 2}WO{sub 6} structure along [100]. The structure could be described by [W{sub 2}O{sub 11}]{sup -10} structural unit formed by two corner-sharing octahedra.

  5. Low-temperature structure of ξ'-Al-Pd-Mn optimized by ab initio methods

    NASA Astrophysics Data System (ADS)

    Frigan, Benjamin; Santana, Alejandro; Engel, Michael; Schopf, Daniel; Trebin, Hans-Rainer; Mihalkovič, Marek

    2011-11-01

    We have studied and resolved occupancy correlations in the existing average structure model of the complex metallic alloy ξ'-Al-Pd-Mn [Boudard , Philos. Mag. APMAADG0141-861010.1080/01418619608242169 74, 939 (1996)], which has approximately 320 atoms in the unit cell and many fractionally occupied sites. Model variants were constructed systematically in a tiling-decoration approach and subjected to simulated annealing by use of both density functional theory and molecular dynamics with empirical potentials. To obtain a measure for thermodynamic stability, we reproduce the Al-Pd-Mn phase diagram at T=0 K, and derive an enthalpy of formation for each structure. Our optimal structure resolves a cloud of fractionally occupied sites in pseudo-Mackay clusters. In particular, we demonstrate the presence of rotational degrees of freedom of an Al9 inner shell, which is caged within two icosahedrally symmetric outer shells Al30 and Pd12. Outside these clusters, the chemical ordering on a chain of three nearby sites surprisingly breaks the inversion symmetry of the surrounding structure, and couples to an Al/vacancy site nearby. Our refined tiling-decoration model applies to any structure within the ɛ-phases family, including the metastable decagonal quasicrystalline phase.

  6. Structural properties of iron-phosphate glasses: spectroscopic studies and ab initio simulations.

    PubMed

    Stoch, Pawel; Szczerba, Wojciech; Bodnar, Wiktor; Ciecinska, Malgorzata; Stoch, Agata; Burkel, Eberhard

    2014-10-01

    Vitrification is the most effective method for the immobilization of hazardous waste by incorporating toxic elements into a glass structure. Iron phosphate glasses are presently being considered as matrices for the storage of radioactive waste, even of those which cannot be vitrified using conventional borosilicate waste glass. In this study, a structural model of 60P2O5-40Fe2O3 glass is proposed. The model is based on the crystal structure of FePO4 which is composed of [FeO4][PO4] tetrahedral rings. The rings are optimized using the DFT method and the obtained theoretical FTIR and Raman spectra are being compared with their experimental counterparts. Moreover, the proposed model is in very good agreement with X-ray absorption fine structure spectroscopy (XANES/EXAFS) and Mössbauer spectroscopy measurements. According to the calculations the Fe(3+) is in tetrahedral and five-fold coordination. The maximal predicted load of waste constituents into the glass without rebuilding of the structure is 30 mol%. Below this content, waste constituents balance the charge of [FeO4](-) tetrahedra which leads to their strong bonding to the glass resulting in an increase of the chemical durability, transformation and melting temperatures and density. PMID:25115558

  7. Ab initio study of structural, electronic, magnetic alloys: XTiSb (X = Co, Ni and Fe)

    SciTech Connect

    Ibrir, M. Berri, S.; Lakel, S.; Alleg, S.; Bensalem, R.

    2015-03-30

    Structural, electronic and magnetic properties of three semi-Heusler compounds of CoTiSb, NiTiSb and FeTiSb were calculated by the method (FP-LAPW) which is based on the DFT code WIEN2k. We used the generalized gradient approximation (GGA (06)) for the term of the potential exchange and correlation (XC) to calculate structural properties, electronic properties and magnetic properties. Structural properties obtained as the lattice parameter are in good agreement with the experimental results available for the electronic and magnetic properties was that: CoTiSb is a semiconductor NiTiSb is a metal and FeTiSb is a half-metal ferromagnetic.

  8. Structural determination of the Bi(110) semimetal surface by LEED analysis and ab initio calculations

    SciTech Connect

    Sun, J.; Pohl, K.; Mikkelsen, A.; Fuglsang Jensen, M.; Hofmann, Ph.; Koroteev, Y. M.; Bihlmayer, G.; Chulkov, E. V.

    2006-12-15

    The surface structure of Bi(110) has been investigated by low-energy electron diffraction intensity analysis and by first-principles calculations. Diffraction patterns at a sample temperature of 110 K and normal incidence reveal a bulk truncated (1x1) surface without indication of any structural reconstruction despite the presence of dangling bonds on the surface layer. Good agreement is obtained between the calculated and measured diffraction intensities for this surface containing only one mirror-plane symmetry element and a buckled bilayer structure. No significant interlayer spacing relaxations are found. The Debye temperature for the surface layer is found to be lower than in the bulk, which is indicative of larger atomic vibrational amplitudes at the surface. Meanwhile, the second layer shows a Debye temperature close to the bulk value. The experimental results for the relaxations agree well with those of our first-principles calculation.

  9. Ab-initio structure determination of β-La 2WO 6

    NASA Astrophysics Data System (ADS)

    Chambrier, M.-H.; Kodjikian, S.; Ibberson, R. M.; Goutenoire, F.

    2009-02-01

    The structure of the low-temperature form of β-La 2WO 6 has been determined from laboratory X-ray, neutron time-of-flight and electron diffraction data. This tungstate crystallizes in the non-centrosymmetric orthorhombic space group (no. 19) P2 12 12 1, with Z=8, a=7.5196(1) Å, b=10.3476(1) Å, c=12.7944(2) Å, and a measured density 7.37(1) g cm -3. The structure consists of tungsten [WO 6] octahedra and tetrahedral [OLa 4]. Tungsten polyhedra are connected such that [W 2O 11] 10- units are formed.

  10. Structure and energetics of graphene oxide isomers: ab initio thermodynamic analysis.

    PubMed

    Chaban, Vitaly V; Prezhdo, Oleg V

    2015-10-28

    Graphene oxide (GO) holds significant promise for electronic devices and nanocomposite materials. A number of models were proposed for the GO structure, combining carboxyl, hydroxyl, carbonyl and epoxide groups at different locations. The complexity and variety of GO isomers, whose thermodynamic stability and formation kinetics depend on the applied conditions, make determination of the GO structure with atomistic precision challenging. We report high level theoretical investigation of multiple molecular configurations, which are anticipated in GO. We conclude that all oxygen containing groups at the GO surface are thermodynamically permitted, whereas the 'edge' positions are systematically more favorable than the 'center' and 'side' positions. We discuss a potentially novel type of chemical bond or bonding reinforcement in GO, which consists of a covalent bond and a strong electrostatic contribution from a polarized graphene plane. We observe and analyze significant modifications of the graphene geometry and electronic structure upon oxidation. The reported thermodynamic data guide experiments aimed at deciphering the GO chemical composition and structure, and form the basis for predicting GO properties required for nano-technological applications. PMID:26420562

  11. Structure and energetics of graphene oxide isomers: ab initio thermodynamic analysis

    NASA Astrophysics Data System (ADS)

    Chaban, Vitaly V.; Prezhdo, Oleg V.

    2015-10-01

    Graphene oxide (GO) holds significant promise for electronic devices and nanocomposite materials. A number of models were proposed for the GO structure, combining carboxyl, hydroxyl, carbonyl and epoxide groups at different locations. The complexity and variety of GO isomers, whose thermodynamic stability and formation kinetics depend on the applied conditions, make determination of the GO structure with atomistic precision challenging. We report high level theoretical investigation of multiple molecular configurations, which are anticipated in GO. We conclude that all oxygen containing groups at the GO surface are thermodynamically permitted, whereas the `edge' positions are systematically more favorable than the `center' and `side' positions. We discuss a potentially novel type of chemical bond or bonding reinforcement in GO, which consists of a covalent bond and a strong electrostatic contribution from a polarized graphene plane. We observe and analyze significant modifications of the graphene geometry and electronic structure upon oxidation. The reported thermodynamic data guide experiments aimed at deciphering the GO chemical composition and structure, and form the basis for predicting GO properties required for nano-technological applications.

  12. Ab Initio Approach for Prediction of Oxide Surface Structure, Stoichiometry, and Electrocatalytic Activity in Aqueous Solution.

    PubMed

    Rong, Xi; Kolpak, Alexie M

    2015-05-01

    The design of efficient, stable, and inexpensive catalysts for oxygen evolution and reduction is crucial for the development of electrochemical energy conversion devices such as fuel cells and metal-air batteries. Currently, such design is limited by challenges in atomic-scale experimental characterization and computational modeling of solid-liquid interfaces. Here, we begin to address these issues by developing a general-, first-principles-, and electrochemical-principles-based framework for prediction of catalyst surface structure, stoichiometry, and stability as a function of pH, electrode potential, and aqueous cation concentration. We demonstrate the approach by determining the surface phase diagram of LaMnO3, which has been studied for oxygen evolution and reduction and computing the reaction overpotentials on the relevant surface phases. Our results illustrate the critical role of solvated cation species in governing the catalyst surface structure and stoichiometry, and thereby catalytic activity, in aqueous solution.

  13. Ab initio simulations for the ion-ion structure factor of warm dense aluminum.

    PubMed

    Rüter, Hannes R; Redmer, Ronald

    2014-04-11

    We perform ab initio simulations based on finite-temperature density functional theory in order to determine the static and dynamic ion-ion structure factor in aluminum. We calculate the dynamic structure factor via the intermediate scattering function and extract the dispersion relation for the collective excitations. The results are compared with available experimental x-ray scattering data. Very good agreement is obtained for the liquid metal domain. In addition we perform simulations for warm dense aluminum in order to obtain the ion dynamics in this strongly correlated quantum regime. We determine the sound velocity for both liquid and warm dense aluminum which can be checked experimentally using narrow-bandwidth free electron laser radiation. PMID:24765982

  14. Ab initio studies of electronic and structural transitions in low-Z liquids under extreme conditions

    NASA Astrophysics Data System (ADS)

    Bonev, Stanimir

    2007-06-01

    The liquids of group I elements (H, Li, Na, and K) are studied using first principles theory. It will be shown that they undergo electronic and structural transitions analogous to that observed in their solids, but commencing at much lower pressure in the presence of disorder. These changes result in exotic melting behavior and in molten phases with unusual properties. The theoretical predictions will be compared with experimental data and ways for further experimental verification of the theoretical results will be suggested.

  15. Ab-initio structural search in solid oxygen at high pressure: from zero to finite temperature

    NASA Astrophysics Data System (ADS)

    Cogollo-Olivo, B. H.; Montoya, J. A.

    2016-08-01

    The crystal structure of solid oxygen in the terapascal (TPa) regime has been investigated with Density Functional Theory and the Random Search algorithm at zero temperature. We also considered the effect of the entropy at finite temperatures using the QuasiHarmonic Approximation, and we found that the regime of stability of solid oxygen differs strongly from the results predicted at zero temperature. Finally, we provide some insights of oxygen as a chalcogen element.

  16. A comparative study of the reported performance of ab initio protein structure prediction algorithms.

    PubMed

    Helles, Glennie

    2008-04-01

    Protein structure prediction is one of the major challenges in bioinformatics today. Throughout the past five decades, many different algorithmic approaches have been attempted, and although progress has been made the problem remains unsolvable even for many small proteins. While the general objective is to predict the three-dimensional structure from primary sequence, our current knowledge and computational power are simply insufficient to solve a problem of such high complexity. Some prediction algorithms do, however, appear to perform better than others, although it is not always obvious which ones they are and it is perhaps even less obvious why that is. In this review, the reported performance results from 18 different recently published prediction algorithms are compared. Furthermore, the general algorithmic settings most likely responsible for the difference in the reported performance are identified, and the specific settings of each of the 18 prediction algorithms are also compared. The average normalized r.m.s.d. scores reported range from 11.17 to 3.48. With a performance measure including both r.m.s.d. scores and CPU time, the currently best-performing prediction algorithm is identified to be the I-TASSER algorithm. Two of the algorithmic settings--protein representation and fragment assembly--were found to have definite positive influence on the running time and the predicted structures, respectively. There thus appears to be a clear benefit from incorporating this knowledge in the design of new prediction algorithms.

  17. Ground state structures of tantalum tetraboride and triboride: an ab initio study.

    PubMed

    Wei, Shuli; Li, Da; Lv, Yunzhou; Liu, Zhao; Xu, Chunhong; Tian, Fubo; Duan, Defang; Liu, Bingbing; Cui, Tian

    2016-07-21

    Tantalum-boron compounds, which are potential candidates for superhard multifunctional materials, may possess multiple stoichiometries and structures under pressure. Using first-principle methods, ground-state TaB3 with the monoclinic C2/m space group and high-pressure TaB4 with the orthorhombic Amm2 space group have been found. They are more stable than the previously proposed structures. High-pressure boron-rich Amm2-TaB4 can be quenched to ambient pressure. The ground-state C2/m-TaB3 and high-pressure Amm2-TaB4 are two potential ultra-incompressible and hard materials with a calculated hardness of 17.02 GPa and 30.02 GPa at ambient pressure, respectively. Detailed electronic structure and chemical bonding analysis proved that the high hardness value of Amm2-TaB4 mainly stems from the strong covalent boron-boron bonds in graphene-like B layers as well as B-B bonds between layers. PMID:27327210

  18. Structure and energy of point defects in TiC: An ab initio study

    NASA Astrophysics Data System (ADS)

    Sun, Weiwei; Ehteshami, Hossein; Korzhavyi, Pavel A.

    2015-04-01

    We employ first-principles calculations to study the atomic and electronic structure of various point defects such as vacancies, interstitials, and antisites in the stoichiometric as well as slightly off-stoichiometric Ti1 -cCc (including both C-poor and C-rich compositions, 0.49 ≤c ≤0.51 ). The atomic structure analysis has revealed that both interstitial and antisite defects can exist in split conformations involving dumbbells. To characterize the electronic structure changes caused by a defect, we introduce differential density of states (dDOS) defined as a local perturbation of the density of states (DOS) on the defect site and its surrounding relative to the perfect TiC. This definition allows us to identify the DOS peaks characteristic of the studied defects in several conformations. So far, characteristic defect states have been discussed only in connection with carbon vacancies. Here, in particular, we have identified dDOS peaks of carbon interstitials and dumbbells, which can be used for experimental detection of such defects in TiC. The formation energies of point defects in TiC are derived in the framework of a grand-canonical formalism. Among the considered defects, carbon vacancies and interstitials are shown to have, respectively, the lowest and the second-lowest formation energies. Their formation energetics are consistent with the thermodynamic data on the phase stability of nonstoichiometric TiC. A cluster type of point defect is found to be next in energy, a titanium [100] dumbbell terminated by two carbon vacancies.

  19. Ab initio powder structure analysis and theoretical study of two thiazole derivatives

    NASA Astrophysics Data System (ADS)

    Hazra, Dipak K.; Mukherjee, Monika; Mukherjee, Alok K.

    2013-05-01

    Crystal structures of 2-amino-5-methylthiazole (1) and 4-(6-methyl-2-benzothiazolyl) aniline (2) have been determined from laboratory X-ray powder diffraction data along with an analysis of the Hirshfeld surfaces and 2D-fingerprint plots, facilitating a comparison of intermolecular interactions. The DFT optimized molecular geometries in (1) and (2) agree closely with those obtained from the crystallographic studies. An interplay of Nsbnd H⋯N/S hydrogen bonds and C/Nsbnd H⋯π interactions connects the molecules of (1) and (2) into two-dimensional framework. Hirshfeld surface analysis of (1) indicates that the H⋯H and H⋯π contacts can account for 56.9% of the Hirshfeld surface area, whereas the corresponding fraction in (2) is 80.5%.

  20. Efficient preconditioning of the electronic structure problem in large scale ab initio molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Schiffmann, Florian; VandeVondele, Joost

    2015-06-01

    We present an improved preconditioning scheme for electronic structure calculations based on the orbital transformation method. First, a preconditioner is developed which includes information from the full Kohn-Sham matrix but avoids computationally demanding diagonalisation steps in its construction. This reduces the computational cost of its construction, eliminating a bottleneck in large scale simulations, while maintaining rapid convergence. In addition, a modified form of Hotelling's iterative inversion is introduced to replace the exact inversion of the preconditioner matrix. This method is highly effective during molecular dynamics (MD), as the solution obtained in earlier MD steps is a suitable initial guess. Filtering small elements during sparse matrix multiplication leads to linear scaling inversion, while retaining robustness, already for relatively small systems. For system sizes ranging from a few hundred to a few thousand atoms, which are typical for many practical applications, the improvements to the algorithm lead to a 2-5 fold speedup per MD step.

  1. Ab initio and DFT studies of the structure and vibrational spectra of anhydrous caffeine

    NASA Astrophysics Data System (ADS)

    Srivastava, Santosh K.; Singh, Vipin B.

    2013-11-01

    Vibrational spectra and molecular structure of anhydrous caffeine have been systematically investigated by second order Moller-Plesset (MP2) perturbation theory and density functional theory (DFT) calculations. Vibrational assignments have been made and many previous ambiguous assignments in IR and Raman spectra are amended. The calculated DFT frequencies and intensities at B3LYP/6-311++G(2d,2p) level, were found to be in better agreement with the experimental values. It was found that DFT with B3LYP functional predicts harmonic vibrational wave numbers more close to experimentally observed value when it was performed on MP2 optimized geometry rather than DFT geometry. The calculated TD-DFT vertical excitation electronic energies of the valence excited states of anhydrous caffeine are found to be in consonance to the experimental absorption peaks.

  2. Structure-function studies of DNA damage using AB INITIO quantum mechanics and molecular dynamics simulation

    SciTech Connect

    Miller, J.; Miaskiewicz, K.; Osman, R.

    1993-12-01

    Studies of ring-saturated pyrimidine base lesions are used to illustrate an integrated modeling approach that combines quantum-chemical calculations with molecular dynamics simulation. Electronic-structure calculations on the lesions in Isolation reveal strong conformational preferences due to interactions between equatorial substituents to the pyrimidine ring. Large distortions of DNA should result when these interactions force the methyl group of thymine to assume an axial orientation, as is the case for thymine glycol but not for dihydrothymine. Molecular dynamics simulations of the dodecamer d(CGCGAATTCGCG){sub 2} with and without a ring-saturated thymine lesion at position T7 support this conclusion. Implications of these studies for recognition of thymine lesions by endonuclease III are also discussed.

  3. Efficient preconditioning of the electronic structure problem in large scale ab initio molecular dynamics simulations

    SciTech Connect

    Schiffmann, Florian; VandeVondele, Joost

    2015-06-28

    We present an improved preconditioning scheme for electronic structure calculations based on the orbital transformation method. First, a preconditioner is developed which includes information from the full Kohn-Sham matrix but avoids computationally demanding diagonalisation steps in its construction. This reduces the computational cost of its construction, eliminating a bottleneck in large scale simulations, while maintaining rapid convergence. In addition, a modified form of Hotelling’s iterative inversion is introduced to replace the exact inversion of the preconditioner matrix. This method is highly effective during molecular dynamics (MD), as the solution obtained in earlier MD steps is a suitable initial guess. Filtering small elements during sparse matrix multiplication leads to linear scaling inversion, while retaining robustness, already for relatively small systems. For system sizes ranging from a few hundred to a few thousand atoms, which are typical for many practical applications, the improvements to the algorithm lead to a 2-5 fold speedup per MD step.

  4. Ab initio electronic structure study of a model water splitting dimer complex.

    PubMed

    Fernando, Amendra; Aikens, Christine M

    2015-12-28

    A model manganese dimer electrocatalyst bridged by μ-OH ligands is used to investigate changes in spin states that may occur during water oxidation. We have employed restricted open-shell Hartree-Fock (ROHF), second-order Møller-Plesset perturbation theory (MP2), complete active space self-consistent field (CASSCF), and multireference second-order Møller-Plesset perturbation theory (MRMP2) calculations to investigate this system. Multiconfigurational methods like CASSCF and MRMP2 are appropriate methods to study these systems with antiferromagnetically-coupled electrons. Orbital occupations and distributions have been closely analyzed to understand the electronic details and contributions to the water splitting from manganese and oxygen atoms. The presence of Mn(IV)O˙ radical moieties has been observed in this catalytic pathway. Multiple nearly degenerate excited states were found close to the ground state in all structures. This suggests competing potential energy landscapes near the ground state may influence the reactivity of manganese complexes such as the dimers studied in this work.

  5. Ab initio approach to structural, electronic, and ferroelectric properties of antimony sulphoiodide

    NASA Astrophysics Data System (ADS)

    Amoroso, Danila; Picozzi, Silvia

    2016-06-01

    By means of first-principles calculations for the SbSI semiconductor, we show that bare density functional theory fails to reproduce the experimentally observed ferroelectric phase, whereas a more advanced approach, based on hybrid functionals, correctly works. When comparing the paraelectric and ferroelectric phases, our results show polar displacements along the c direction of the Sb and S sublattices with respect to the iodine framework, leading to a predicted spontaneous polarization of P ≃20 μ C/cm2 , in good agreement with experiments. In the ferroelectric phase, the semiconducting behavior of SbSI is confirmed by relatively large values for the indirect and direct gaps (≃2.15 eV and 2.3 eV , respectively). An analysis of the electronic structure, in terms of density of states, charge density distribution, and anomalies in the Born effective charges, reveals (i) the clear presence of a Sb(III) lone pair and (ii) a large covalency in the SbSI bonding, based on the hybridization between Sb and S ions, in turn more ionically bonded to iodine anions. Finally, the interplay between ferroelectricity and spin-orbit coupling reveals a coexistence of Dresselhaus and Rashba relativistic effects and a spin texture that can be reversed by switching the polarization, of potential appeal in electrically controlled spintronics.

  6. Structural, electronic and magnetic properties of carbon doped boron nitride nanowire: Ab initio study

    NASA Astrophysics Data System (ADS)

    Jalilian, Jaafar; Kanjouri, Faramarz

    2016-11-01

    Using spin-polarized density functional theory calculations, we demonstrated that carbon doped boron nitride nanowire (C-doped BNNW) has diverse electronic and magnetic properties depending on position of carbon atoms and their percentages. Our results show that only when one carbon atom is situated on the edge of the nanowire, C-doped BNNW is transformed into half-metal. The calculated electronic structure of the C-doped BNNW suggests that doping carbon can induce localized edge states around the Fermi level, and the interaction among localized edge states leads to semiconductor to half-metal transition. Overall, the bond reconstruction causes of appearance of different electronic behavior such as semiconducting, half-metallicity, nonmagnetic metallic, and ferromagnetic metallic characters. The formation energy of the system shows that when a C atom is doped on surface boron site, system is more stable than the other positions of carbon impurity. Our calculations show that C-doped BNNW may offer unique opportunities for developing nanoscale spintronic materials.

  7. Electronic structure of Sc C[sub 60]. An ab initio theoretical study

    SciTech Connect

    Guo, T.; Odom, G.K.; Scuseria, G.E. )

    1994-08-11

    We have studied the electronic structure of Sc C[sub 60] at the self-consistent-field Hartree-Fock (SCF-HF) level of theory employing a double-zeta (DZ) basis set. Binding energies have also been calculated employing a hybrid of HF and density functional theory (herein denoted as HF-BLYP). Several electronic states in C[sub 50] and C[sub 30] symmetry were considered. A double-minimum configuration is found for the open-shell [sup 4]A[sub 2] electronic ground state in C[sub 50] symmetry. The lowest energy minimum has Sc located 1.175 [angstrom] away from the center of the cage, approaching a C[sub 60] pentagon along a C[sub 5] axis. Bonding between the Sc atom and the cage occurs by donation of the 4s electrons to the lowest unoccupied orbital of C[sub 60] and by 3d electron interaction with the antibonding orbital associated with the five double bonds radiating from the pentagon closest to Sc ([approximately] 2.5 [angstrom]). The other local minimum has Sc located at the center of the cage and is predicted to be 1.2 eV higher in energy at the highest level of theory employed in this work (DZ/HF-BLYP). The energy barrier for moving Sc from the center of the cage to the lowest energy position is predicted to be 0.1 eV at the same level of theory. 33 refs., 2 figs., 2 tabs.

  8. Solvation processes in steam: Ab initio calculations of ion solvent structures and clustering equilibria

    NASA Astrophysics Data System (ADS)

    Lemke, Kono H.; Seward, Terry M.

    2008-07-01

    Reports of the high ion content of steam and low-density supercritical fluids date back to the work of Carlon [Carlon H. R. (1980) Ion content of air humidified by boiling water. J. Appl.Phys.51, 171-173], who invoked ion and neutral-water clustering as mechanism to explain why ions partition into the low-density aqueous phase. Mass spectrometric, vibrational spectroscopic measurements and quantum chemical calculations have refined this concept by proposing strongly bound ion-solvent aggregates and water clusters such as Eigen- and Zundel-type proton clusters H 3O +·(H 2O) m and the more weakly bound water oligomers (H 2O) m. The extent to which these clusters affect fluid chemistry is determined by their abundance, however, little is known regarding the stability of such moieties in natural low-density high-temperature fluids. Here we report results from quantum chemical calculations using chemical-accuracy multi-level G3 (Curtiss-Pople) and CBS-Q theory (Peterson) to address this question. In particular, we have investigated the cluster structures and clustering equilibria for the ions HO·(HO)m(HS)n,NH4+·(HO)m(HS)n and H 3S +·(H 2O) m(H 2S) n, where m ⩽ 6 and n ⩽ 4, at 300-1000 K and 1 bar as well as under vapor-liquid equilibrium conditions between 300 and 646 K. We find that incremental hydration enthalpies and entropies derived from van't Hoff analyses for the attachment of H 2O and H 2S onto H 3O +, NH4+ and H 3S + are in excellent agreement with experimental values and that the addition of water to all three ions is energetically more favorable than solvation by H 2S. As clusters grow in size, the energetic trends of cluster hydration begin to reflect those for bulk H 2O liquids, i.e. calculated hydration enthalpies and entropies approach values characteristic of the condensation of bulk water (Δ Ho = -44.0 kJ mol -1, Δ So = -118.8 J K mol -1). Water and hydrogen sulfide cluster calculations at higher temperatures indicate that a significant

  9. Structures and stability of medium silicon clusters. II. Ab initio molecular orbital calculations of Si12-Si20

    NASA Astrophysics Data System (ADS)

    Zhu, X. L.; Zeng, X. C.; Lei, Y. A.; Pan, B.

    2004-05-01

    Ab initio all-electron molecular-orbital calculations are carried out to study the structures and relative stability of low-energy silicon clusters (Sin,n=12-20). Selected geometric isomers include those predicted by Ho et al. [Nature (London) 392, 582 (1998)] based on an unbiased search with tight-binding/genetic algorithm, as well as those found by Rata et al. [Phys. Rev. Lett. 85, 546 (2000)] based on density-functional tight-binding/single-parent evolution algorithm. These geometric isomers are optimized at the Møller-Plesset (MP2) MP2/6-31G(d) level. The single-point energy at the coupled-cluster single and double substitutions (including triple excitations) [CCSD(T)] CCSD(T)/6-31G(d) level for several low-lying isomers are further computed. Harmonic vibrational frequency analysis at the MP2/6-31G(d) level of theory is also undertaken to assure that the optimized geometries are stable. For Si12-Si17 and Si19 the isomer with the lowest-energy at the CCSD(T)/6-31G(d) level is the same as that predicted by Ho et al., whereas for Si18 and Si20, the same as predicted by Rata et al. However, for Si14 and Si15, the vibrational frequency analysis indicates that the isomer with the lowest CCSD(T)/6-31G(d) single-point energy gives rise to imaginary frequencies. Small structural perturbation onto the Si14 and Si15 isomers can remove the imaginary frequencies and results in new isomers with slightly lower MP2/6-31G(d) energy; however the new isomers have a higher single-point energy at the CCSD(T)/6-31G(d) level. For most Sin (n=12-18,20) the low-lying isomers are prolate in shape, whereas for Si19 a spherical-like isomer is slightly lower in energy at the CCSD(T)/6-31G(d) level than low-lying prolate isomers.

  10. Excitons and band edge alignment in CdSe/CdS core-shell nanocrystals: ab initio

    NASA Astrophysics Data System (ADS)

    Zherebetskyy, Danylo; Wang, Lin-Wang; Computational Materials Science; Nanoscience Team

    Quantum confinement is a foundational nanoscience concept that allows tuning electronic properties of quantum dots. Core-shell quantum dots are promising nanoparticles and found applications as light-emitting optoelectronic devices and biomarkers due to their robustness and tunability of both core and shell. The fluorescent quantum yield of these quantum dots can achieve 100% even at room temperature. However, to understand many phenomena of carrier dynamics, photoluminescence efficient and Auger effects, fine electronic structures of the exciton are needed. Here, using large scale electronic structure calculations based on charge patching method, we have investigated the exciton binding energy, band alignment between core and shell, charge separation between electron and hole. We will discuss how these can be tuned by changing the core/shell dimensions.

  11. Electronic structure and magnetic properties of doped Al1- x Ti x N ( x = 0.03, 0.25) compositions based on cubic aluminum nitride from ab initio simulation data

    NASA Astrophysics Data System (ADS)

    Bannikov, V. V.; Beketov, A. R.; Baranov, M. V.; Elagin, A. A.; Kudyakova, V. S.; Shishkin, R. A.

    2016-05-01

    The phase stability, electronic structure, and magnetic properties of Al1- x Ti x N compositions based on the metastable aluminum nitride modification with the rock-salt structure at low ( x = 0.03) and high ( x = 0.25) concentrations of titanium in the system have been investigated using the results of ab initio band calculations. It has been shown that, at low values of x, the partial substitution is characterized by a positive enthalpy, which, however, changes sign with an increase in the titanium concentration. According to the results of the band structure calculations, the doped compositions have electronic conductivity. For x = 0.03, titanium impurity atoms have local magnetic moments (˜0.6 μB), and the electronic spectrum is characterized by a 100% spin polarization of near-Fermi states. Some of the specific features of the chemical bonding in Al1- x Ti x N cubic phases have been considered.

  12. Structure and Dynamics of the Instantaneous Water/Vapor Interface Revisited by Path-Integral and Ab Initio Molecular Dynamics Simulations.

    PubMed

    Kessler, Jan; Elgabarty, Hossam; Spura, Thomas; Karhan, Kristof; Partovi-Azar, Pouya; Hassanali, Ali A; Kühne, Thomas D

    2015-08-01

    The structure and dynamics of the water/vapor interface is revisited by means of path-integral and second-generation Car-Parrinello ab initio molecular dynamics simulations in conjunction with an instantaneous surface definition [Willard, A. P.; Chandler, D. J. Phys. Chem. B 2010, 114, 1954]. In agreement with previous studies, we find that one of the OH bonds of the water molecules in the topmost layer is pointing out of the water into the vapor phase, while the orientation of the underlying layer is reversed. Therebetween, an additional water layer is detected, where the molecules are aligned parallel to the instantaneous water surface.

  13. Ab initio calculations of the 2p3/2-2p1/2 fine-structure splitting in boronlike ions

    NASA Astrophysics Data System (ADS)

    Artemyev, A. N.; Shabaev, V. M.; Tupitsyn, I. I.; Plunien, G.; Surzhykov, A.; Fritzsche, S.

    2013-09-01

    We have performed ab initio QED calculations of the (1s)2(2s)22p3/2-(1s)2(2s)22p1/2 fine-structure splitting along the boron isoelectronic sequence for all ions with 17≤Z≤100. This level splitting was evaluated within the extended Furry picture and by making use of four different screening potentials in order to estimate the effects of interelectronic correlations. The accuracy of the predicted transition energies has been improved significantly when compared with previous computations.

  14. Structures and vibrational spectra of pinacol.. 1. Infrared and matrix infrared spectra of monomeric pinacol. Ab initio calculations on conformers and vibrational frequencies

    NASA Astrophysics Data System (ADS)

    Dahlqvist, Martti; Hotokka, Matti; Räsänen, Markku

    1998-04-01

    The infrared spectra of monomeric pinacol molecules (2,3-dimethyl-2,3-butanediol; (CH 3) 2C(OH)C(OH)(CH 3) 2) have been recorded in the gas phase and dilute nonpolar solutions, and in an argon matrix. The vibrational data are consistent with the intramolecularly hydrogen-bonded G-type (gauche with respect to the central C-C bond) conformers and there is no evidence for the T-type (trans with respect to the central C-C bond) conformers, which have been observed in the condensed phases. This was confirmed by studying the infrared region 835-815 cm -1, which was found to be the most indicative to show spectral changes within the type of the conformers. In this region the band of the T-type conformers (assigned to the hybridized asymmetric vibration of the central CC and CO stretching modes) disappears when going from the condensed phases to phases, where pinacol molecules are monomeric. Ab initio HF/6-311G** (MP2/6-311G**) calculations support the experimental findings; the calculated relative energies for the tGg', gGg', g'Gg', tTt, and gTg' conformers are 0.0 (0.0), 3.4 (3.4), 5.1 (5.9), 7.9 (11.3), and 12.0 (14.0) kJ mol -1, respectively. Consequently, only the G-type conformers are sufficiently populated to give rise to observable spectral lines. Both experimental findings and theoretical calculations demonstrated that the bands in the argon matrix spectrum of pinacol are due to the most stable tGg' conformer. Although the ab initio calculations predict that also the gGg' and g'Gg' conformers are present in the gas phase and in dilute nonpolar solutions their existence could not be confirmed experimentally. Hence, we conclude that the conformation sensitive bands may coincide in the spectra. The HF/6-311G** ab initio calculations for vibrational frequencies of pinacol are consistent with this conclusion, suggesting only small differences between the wavenumbers of the G-type conformers. Pinacol does not show infrared-induced photorotamerization in the low

  15. Molecular structures and conformational compositions of 2-chlorobutane and 2-bromobutane; an investigation using gas-phase electron-diffraction data and ab initio molecular orbital calculations

    NASA Astrophysics Data System (ADS)

    Aarset, Kirsten; Hagen, Kolbjørn; Stølevik, Reidar

    2001-06-01

    The structure and conformational composition of 2-chlorobutane and 2-bromobutane have been studied by gas-phase electron diffraction (GED) at 25°C, together with ab initio molecular orbital calculations (HF/6-311+G(d,p)). These molecules may exist as three distinguishable conformers (G+, A, and G-). The symbols refer to anti (A) with a torsion angle Φ2(X 8-C 2-C 3-C 4) of about 180° and gauche (G+ and G-) with torsion angles Φ2(X 8-C 2-C 3-C 4) of about +60° and 300°(-60°), respectively. It was not possible; from our GED-data alone, to accurately determine the conformational composition because the distance distributions for two of the conformers (G+ and G-) are very similar. The conformational composition for 2-chlorobutane obtained from the ab initio calculations (G+ 62%, A 25% G- 13%) was found to fit the experimental data quite well. For 2-bromobutane the ab initio calculated conformational composition (G+ 58%, A 28% G- 14%) did not, however, fit the experimental data. Here a much better fit was obtained by using only 10% of the A conformer and using the relative energy for the two gauche conformers, as obtained in the ab initio molecular orbital calculations, to calculate the relative amounts of the two gauche forms (G+ 73%, A 10% G- 17%). The results for the principal distances ( rg) and angles ∠ α for the G+ conformer of 2-chlorobutane, with estimated 2 σ uncertainties, obtained from the combined GED/ab initio study are: r( C1- C2)=1.524(3) Å, r( C2- C3)=1.528(3) Å, r( C3- C4)=1.539(3) Å, r( C- Cl)=1.812(3) Å, r( C- H) ave=1.098(4) Å, ∠C 1C 2C 3=111.5(16)°, ∠C 2C 3C 4=113.3(5)°, ∠C 1C 2C1=110.4(9)°. The results for the G+ conformer of 2-bromobutane are: r( C1- C2)=1.526(4) Å, r( C2- C3)=1.530(4) Å, r( C3- C4)=1.540(4) Å, r( C- Br)=1.982(5) Å, r( C- H) ave=1.111(8) Å, ∠C 1C 2C 3=112.5(16)°, ∠C 2C 3C 4=114.6(15)°, ∠C 1C 2Br=110.1(16)°. Only average values for r(C-C), r(C-H), ∠CCC, and ∠CCH could be determined in the

  16. 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.

  17. The Most Stable Structures of Si Clusters Based on ab initio Calculation of TB-LMTO and Real-Space Green's Function Method

    NASA Astrophysics Data System (ADS)

    Xie, Z. L.; Dy, K. S.; Wu, S. Y.

    1996-03-01

    An efficient ab initio scheme has been developed by using TB LMTO method to calculate the electronic structure and the full electron density of atomic clusters. In this scheme, the real-space Green's function (RSG) is used to obtain the full electronic density which includes the correction for non-spherical effects. Meanwhile, the real space Green's function can facilitate the calculation of the electronic structure for large clusters with restricted computer memory and CPU resources by using matrix reversion method developed by Wu and his co-workers. With the full electron density of atomic clusters, the total energies of clusters can be calculated. We have applied this ab initio scheme to evaluate the structural properties for Si clusters of 11-14 atoms. Diffrent geometrical arrangements have been examined as posible candidates of the most stable structure for each size cluster, and by calculating their cohesive energies, the most stable structure can be determined for a given size cluster. Our calculations have given similar results of previous investigations using the tight-binding molecular dynamics method.

  18. Experimental and ab Initio Study of Catena(bis(μ2-iodo)-6-methylquinoline-copper(I)) under Pressure: Synthesis, Crystal Structure, Electronic, and Luminescence Properties.

    PubMed

    Aguirrechu-Comerón, Amagoia; Hernández-Molina, Rita; Rodríguez-Hernández, Plácida; Muñoz, Alfonso; Rodríguez-Mendoza, Ulises R; Lavín, Vı́ctor; Angel, Ross J; Gonzalez-Platas, Javier

    2016-08-01

    Copper(I) iodine compounds can exhibit interesting mechanochromic and thermochromic luminescent properties with important technological applications. We report the synthesis and structure determination by X-ray diffraction of a new polymeric staircase copper(I) iodine compound catena(bis(μ2-iodo)-6-methylquinoline-copper(I), [C10H9CuIN]. The structure is composed of isolated polymeric staircase chains of copper-iodine coordinated to organic ligands through Cu-N bonds. High pressure X-ray diffraction to 6.45 GPa shows that the material is soft, with a bulk modulus K0 = 10.2(2)GPa and a first derivative K'0 = 8.1(3), typical for organometallic compounds. The unit-cell compression is very anisotropic with the stiffest direction [302] arising from a combination of the stiff CuI ladders and the shear of the planar quinolone ligands over one another. Full structure refinements at elevated pressures show that pressures reduce the Cu···Cu distances in the compound. This effect is detected in luminescence spectra with the appearance of four sub-bands at 515, 600, 647, and 712 nm above 3.5 GPa. Red-shifts are observed, and they are tentatively associated with interactions between copper(I) ions due to the shortening of the Cu···Cu distances induced by pressure, below twice the van der Waals limit (2.8 Å). Additionally, ab initio simulations were performed, and they confirmed the structure and the results obtained experimentally for the equation of state. The simulation allowed the band structure and the electronic density of states of this copper(I) iodine complex to be determined. In particular, the band gap decreases slowly with pressure in a quadratic way with dEg/dP = -0.011 eV/GPa and d(2)Eg/dP(2) = 0.001 eV/GPa(2). PMID:27429246

  19. Conformational Characteristics of Poly(tetrafluoroethylene) (PTFE) Based Upon Ab Initio Electronic Structure Calculations on Model Molecules

    NASA Technical Reports Server (NTRS)

    Smith, Grant D.; Jaffe, R. L.; Yoon, D. Y.; Arnold, James O. (Technical Monitor)

    1994-01-01

    Conformational energy contours of perfluoroalkanes, determined from ab initio calculations, confirm the well-known spitting of trans states into two minima at plus or minus 17 degrees but also show that the gauche states split as well, with minima at plus or minus 124 degrees and plus or minus 84 in order to relieve steric crowding. The directions of such split distortions from the perfectly staggered states are strongly coupled for adjacent pairs of bonds in a manner identical to the intradyad pair for poly (isobutylene) chains. These conformational characteristics are fully represented by a six-state rotational isomeric state (RIS) model for PTFE comprised of t(+), t(-), g(sup +)+, g(sup +)-, g(sup -) + and g(sup -)-states, located at the split energy minima. The resultant 6 x 6 statistical weight matrix is described by first-order interaction parameters for the g+(+) (ca. 0.6 kcal/mol) and g+- (ca. 2.0 kcal/mol) states, and second order parameters for the g(sup +)+g(sup +)+ (ca 0.6 kcal/mol) and g(sup +)+g(sup -)+ (ca. 1.0 kcal/mol) states. This six-state RIS model, without adjustment of the geometric or energy parameters as determined from the ab initio calculations, predicts the unperturbed chain dimensions and the fraction of gauche bonds as a function of temperature for PTFE in good agreement with available experimental values.

  20. Structural, elastic and thermodynamic properties of tetragonal and orthorhombic polymorphs of Sr2GeN2: an ab initio investigation

    NASA Astrophysics Data System (ADS)

    Bedjaoui, A.; Bouhemadou, A.; Bin-Omran, S.

    2016-04-01

    The structural, elastic and thermodynamic properties of the α (tetragonal) and β (orthorhombic) polymorphs of the Sr2GeN2 compound have been examined in detail using ab initio density functional theory pseudopotential plane-wave calculations. Apart the structural properties at the ambient conditions, all present reported results are predicted for the first time. The calculated equilibrium lattice parameters and inter-atomic bond-lengths of the considered polymorphs are in good agreement with the available experimental data. It is found that α-Sr2GeN2 is energetically more stable than β-Sr2GeN2. The two examined polymorphs are very similar in their crystal structures and have almost identical local environments. The single-crystal and polycrystalline elastic parameters and related properties - including elastic constants, bulk, shear and Young's moduli, Poisson's ratio, anisotropy indexes, Pugh's criterion, elastic wave velocities and Debye temperature - have been predicted. Temperature and pressure dependence of some macroscopic properties - including the unit-cell volume, bulk modulus, volume thermal expansion coefficient, heat capacity and Debye temperature - have been evaluated using ab initio calculations combined with the quasi-harmonic Debye model.

  1. Bonding Structure of Phenylacetylene on Hydrogen-Terminated Si(111) and Si(100): Surface Photoelectron Spectroscopy Analysis and Ab Initio Calculations

    SciTech Connect

    M Kondo; T Mates; D Fischer; F Wudl; E Kramer

    2011-12-31

    Interfaces between phenylacetylene (PA) monolayers and two silicon surfaces, Si(111) and Si(100), are probed by X-ray photoelectron spectroscopy (XPS), ultraviolet photoelectron spectroscopy (UPS), and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy, and the results are analyzed using ab initio molecular orbital calculations. The monolayer systems are prepared via the surface hydrosilylation reaction between PA and hydrogen-terminated silicon surfaces. The following spectral features are obtained for both of the PA-Si(111) and PA-Si(100) systems: a broad {pi}-{pi}* shakeup peak at 292 eV (XPS), a broad first ionization peak at 3.8 eV (UPS), and a low-energy C 1s {yields} {pi}* resonance peak at 284.3 eV (NEXAFS). These findings are ascribed to a styrene-like {pi}-conjugated molecular structure at the PA-Si interface by comparing the experimental data with theoretical analysis results. A conclusion is drawn that the vinyl group can keep its {pi}-conjugation character on the hydrogen-terminated Si(100) [H:Si(100)] surface composed of the dihydride (SiH{sub 2}) groups as well as on hydrogen-terminated Si(111) having the monohydride (SiH) group. The formation mechanism of the PA-Si(100) interface is investigated within cluster ab initio calculations, and the possible structure of the H:Si(100) surface is discussed based on available data.

  2. Structural and vibrational study of 2-MethoxyEthylAmmonium Nitrate (2-OMeEAN): Interpretation of experimental results with ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Campetella, M.; Bovi, D.; Caminiti, R.; Guidoni, L.; Bencivenni, L.; Gontrani, L.

    2016-07-01

    In this work we report an analysis of the bulk phase of 2-methoxyethylammonium nitrate based on ab initio molecular dynamics. The structural and dynamical features of the ionic liquid have been characterized and the computational findings have been compared with the experimental X-ray diffraction patterns, with infrared spectroscopy data, and with the results obtained from molecular dynamics simulations. The experimental infrared spectrum was interpreted with the support of calculated vibrational density of states as well as harmonic frequency calculations of selected gas phase clusters. Particular attention was addressed to the high frequency region of the cation (ω > 2000 cm-1), where the vibrational motions involve the NH3+ group responsible for hydrogen bond formation, and to the frequency range 1200-1400 cm-1 where the antisymmetric stretching mode (ν3) of nitrate is found. Its multiple absorption lines in the liquid arise from the removal of the degeneracy present in the D3h symmetry of the isolated ion. Our ab initio molecular dynamics leads to a rationalization of the frequency shifts and splittings, which are inextricably related to the structural modifications induced by a hydrogen bonding environment. The DFT calculations lead to an inhomogeneous environment.

  3. Molecular structure of poly(methyl methacrylate) surface: Combination of interface-sensitive infrared-visible sum frequency generation, molecular dynamics simulations, and ab initio calculations

    NASA Astrophysics Data System (ADS)

    Zhu, He; Jha, Kshitij C.; Bhatta, Ram S.; Tsige, Mesfin; Dhinojwala, Ali

    2015-03-01

    The chemical composition and molecular structure of polymeric surfaces are important in understanding wetting, adhesion, and friction. Here, we combine interface-sensitive sum frequency generation spectroscopy (SFG), all-atom molecular dynamics (MD) simulations, and ab initio calculations to understand the composition and the orientation of chemical groups on poly(methyl methacrylate) (PMMA) surface as a function of tacticity and temperature. The SFG spectral features for isotactic and syndiotactic PMMA surfaces are similar and the dominant peak in the spectra corresponds to the ester-methyl groups. The SFG spectra for solid and melt states are very similar for both syndiotactic and isotactic PMMA. In comparison, the MD simulation results show that both the ester-methyl and the α-methyl groups of syndiotactic-PMMA are ordered and tilted towards the surface normal. For the isotactic-PMMA, the α-methyl groups are less ordered compared to their ester-methyl groups. The backbone methylene groups have a broad angular distribution and on average tilt along the surface plane, independent of tacticity and temperature. We have compared the SFG results with theoretical spectra calculated using MD simulations and ab initio calculations. National Science Foundation.

  4. Ab initio investigation of the structure, stability, and atmospheric distribution of molecular clusters containing H2O, CO2, and N2O

    NASA Astrophysics Data System (ADS)

    Lemke, Kono H.; Seward, Terry M.

    2008-10-01

    We present results from ab initio calculations for the structures and energetic properties of neutral clusters containing water, carbon dioxide, and nitrous oxide using the complete basis set CBS-Q multilevel procedure. Gas phase hydration energies ΔG0, enthalpies ΔH0, and entropies ΔS0 for the stepwise attachment of water onto clusters according to X·(H2O)n + H2O ↔ X·(H2O)n+1 (X = CO2, N2O, and H2O) are reported for n ≤ 4. In particular, our results demonstrate that values for the incremental hydration enthalpies and entropies of all three gases CO2, N2O, and H2O asymptotically approach values characteristic of bulk water (i.e., -44.0 kJ mol-1 for the enthalpy and -118.8 J K-1 mol-1 for the entropy of condensation) following attachment of around three to four water molecules. Our ab initio calculations indicate that water attachment onto CO2, N2O, and H2O is a thermodynamically favorable process, such that hydrated CO2·(H2O)n, N2O·(H2O)n, and H2O·(H2O)n clusters would form a significant atmospheric repository of these species.

  5. A search for manifestation of two types of collective excitations in dynamic structure of a liquid metal: Ab initio study of collective excitations in liquid Na.

    PubMed

    Bryk, Taras; Wax, J-F

    2016-05-21

    Using a combination of ab initio molecular dynamics and several fit models for dynamic structure of liquid metals, we explore an issue of possible manifestation of non-acoustic collective excitations in longitudinal dynamics having liquid Na as a case study. A model with two damped harmonic oscillators (DHOs) in time domain is used for analysis of the density-density time correlation functions. Another similar model with two propagating contributions and three lowest exact sum rules is considered, as well as an extended hydrodynamic model known as thermo-viscoelastic one which permits two types of propagating modes outside the hydrodynamic region to be used for comparison with ab initio obtained time correlation functions and calculations of dispersions of collective excitations. Our results do not support recent suggestions that, even in simple liquid metals, non-hydrodynamics transverse excitations contribute to the longitudinal collective dynamics and can be detected as a DHO-like spectral shape at their transverse frequency. We found that the thermo-viscoelastic dynamic model permits perfect description of the density-density and current-current time correlation functions of the liquid Na in a wide range of wave numbers, which implies that the origin of the non-hydrodynamic collective excitations contributing to longitudinal dynamics can be short-wavelength heat waves. PMID:27208952

  6. 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.

  7. Quasiparticle electronic structure and optical absorption of diamond nanoparticles from ab initio many-body perturbation theory

    SciTech Connect

    Yin, Huabing; Ma, Yuchen Mu, Jinglin; Liu, Chengbu; Hao, Xiaotao; Yi, Zhijun

    2014-06-07

    The excited states of small-diameter diamond nanoparticles in the gas phase are studied using the GW method and Bethe-Salpeter equation (BSE) within the ab initio many-body perturbation theory. The calculated ionization potentials and optical gaps are in agreement with experimental results, with the average error about 0.2 eV. The electron affinity is negative and the lowest unoccupied molecular orbital is rather delocalized. Precise determination of the electron affinity requires one to take the off-diagonal matrix elements of the self-energy operator into account in the GW calculation. BSE calculations predict a large exciton binding energy which is an order of magnitude larger than that in the bulk diamond.

  8. Ab initio calculation of structure and transport properties of He…X (X = Zn, Cd, Hg) van der Waals complexes.

    PubMed

    Sládek, Vladimír; Lukeš, Vladimír; Ilčin, Michal; Biskupič, Stanislav

    2012-03-15

    The ground state ab initio CCSD(T) potential curves using various basis sets (aug-cc-pVXZ-PP (X = D, T, Q, 5)) is obtained for the dimers of helium with IIb group metals. The effect of the position of the (mid) bond-functions on the interaction energy is discussed. A Symmetry Adapted Perturbation Theory decomposition of the interaction energy is provided and the trends in the dimer stabilizing and destabilizing contributions are depicted. The spline fitted potential curves are applied together with rigorous statistical formulae in order to obtain the transport coefficients (viscosity coefficients, diffusion coefficients) and the second virial coefficient both for pure constituents and mixtures. The obtained theoretical results are compared with available experimental data. Molecular dynamics is used to obtain reliable values of the diffusion coefficients for all the systems under study.

  9. A novel supramolecular compound of cadmium(II): Synthesis, characterization, crystal structure, ab initio HF, DFT calculations and solution study

    NASA Astrophysics Data System (ADS)

    Aghabozorg, Hossein; Manteghi, Faranak; Ghadermazi, Mohammad; Mirzaei, Masoud; Salimi, Ali R.; Shokrollahi, Ardeshir; Derki, Somayyeh; Eshtiagh-Hosseini, Hossein

    2009-02-01

    A novel compound with formula unit (pipzH 2)[Cd(pydc) 2]·6H 2O, was synthesized and characterized by IR, 1H NMR and 13C NMR spectroscopy, elemental analysis, single crystal X-ray diffractometry. Moreover, the solution behavior was studied, and ab initio HF, DFT calculations were carried out. The compound belongs to a great family of supramolecular metal complexes derived from a proton transfer ion pair i.e. (pipzH 2)(pydc), where pipz is piperazine and pydcH 2 is pyridine-2,6-dicarboxylic acid. The compound shows a distorted octahedral geometry around the six-coordinated Cd II atom. A variety of intermolecular O sbnd H···O, N sbnd H···O and C sbnd H···O hydrogen bonds are responsible to extend the supramolecular network of the compound. The geometry parameters of [Cd(pydc) 2] 2- complex and free (pydc) 2- ligand have been optimized with the B3LYP method of density functional theory (DFT) and ab initio Hartree-Fock (HF) methods for comparison. The effect of basis sets has been investigated using four combination basis sets. The electronic properties of the Cd II compound and free (pydc) 2- ligand have been investigated based on the natural bond orbital (NBO) analysis at the B3LYP/A level of theory which verifies that the synergistic effect have been occurred in the compound. In solution study, the protonation constants of pipz and pydc, the equilibrium constants for pydc/pipz proton transfer system and the stoichiometry and stability of the system with Cd 2+ ion in aqueous solution were investigated by potentiometric pH titrations. The stoichiometry of one of the most abundant complexed species in solution was found to be the same as that of the crystalline cadmium complex.

  10. 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)

  11. ASTRO-FOLD: A Combinatorial and Global Optimization Framework for Ab Initio Prediction of Three-Dimensional Structures of Proteins from the Amino Acid Sequence

    PubMed Central

    Klepeis, J. L.; Floudas, C. A.

    2003-01-01

    The field of computational biology has been revolutionized by recent advances in genomics. The completion of a number of genome projects, including that of the human genome, has paved the way toward a variety of challenges and opportunities in bioinformatics and biological systems engineering. One of the first challenges has been the determination of the structures of proteins encoded by the individual genes. This problem, which represents the progression from sequence to structure (genomics to structural genomics), has been widely known as the structure-prediction-in-protein-folding problem. We present the development and application of ASTRO-FOLD, a novel and complete approach for the ab initio prediction of protein structures given only the amino acid sequences of the proteins. The approach exhibits many novel components and the merits of its application are examined for a suite of protein systems, including a number of targets from several critical-assessment-of-structure-prediction experiments. PMID:14507680

  12. Ab-initio study of the magnetism, structure and spin dependent electronic states of Ti substituted MO (M = Mg, Ca, Sr)

    SciTech Connect

    Jaiganesh, G. Jaya, S. Mathi

    2015-06-24

    The magnetism, structure and spin polarized electronic structure of Ti substituted MO (M = Mg, Ca, Sr) are studied using the ab-initio techniques within the framework of the density functional theory. Appropriately constructed supercell along with the full structural optimization of these cells is used for studying the influence of Ti substitution on the magnetism and electronic structure of these compounds. We find from our calculations that the Ti substituted MO compounds energetically favor magnetically ordered state. The Ti concentration is found to be important in deciding the magnetic order and we have observed antiferromagnetic order for the Ti concentration of 0.25. The Ti substituted MO compounds are thus an interesting class of materials that deserve further studies.

  13. Magneto-Structural Correlations in a Series of Pseudotetrahedral [Co(II)(XR)4](2-) Single Molecule Magnets: An ab Initio Ligand Field Study.

    PubMed

    Suturina, Elizaveta A; Maganas, Dimitrios; Bill, Eckhard; Atanasov, Mihail; Neese, Frank

    2015-10-19

    Over the past several decades, tremendous efforts have been invested in finding molecules that display slow relaxation of magnetization and hence act as single-molecule magnets (SMMs). While initial research was strongly focused on polynuclear transition metal complexes, it has become increasingly evident that SMM behavior can also be displayed in relatively simple mononuclear transition metal complexes. One of the first examples of a mononuclear SMM that shows a slow relaxation of the magnetization in the absence of an external magnetic field is the cobalt(II) tetra-thiolate [Co(SPh)4](2-). Fascinatingly, substitution of the donor ligand atom by oxygen or selenium dramatically changes zero-field splitting (ZFS) and relaxation time. Clearly, these large variations call for an in-depth electronic structure investigation in order to develop a qualitative understanding of the observed phenomena. In this work, we present a systematic theoretical study of a whole series of complexes (PPh4)2[Co(XPh)4] (X = O, S, Se) using multireference ab initio methods. To this end, we employ the recently proposed ab initio ligand field theory, which allows us to translate the ab initio results into the framework of ligand field theory. Magneto-structural correlations are then developed that take into account the nature of metal-ligand covalent bonding, ligand spin-orbit coupling, and geometric distortions away from pure tetrahedral symmetry. The absolute value of zero-field splitting increases when the ligand field strength decreases across the series from O to Te. The zero-field splitting of the ground state of the hypothetical [Co(TePh)4](2-) complex is computed to be about twice as large as for the well-known (PPh4)2[Co(SPh)4] compound. It is shown that due to the π-anisotropy of the ligand donor atoms (S, Se) magneto-structural correlations in [Co(OPh)4](2-) complex differ from [Co(S/SePh)4](2-). In the case of almost isotropic OPh ligand, only variations in the first

  14. Conformational stability, structural parameters and vibrational assignment from variable temperature infrared spectra of krypton solutions and ab initio calculations of ethylisothiocyanate.

    PubMed

    Durig, James R; Zheng, Chao

    2007-11-01

    Variable temperature (-105 to -150 degrees C) studies of the infrared spectra (3500-400 cm(-1)) of ethylisothiocyanate, CH(3)CH(2)NCS, dissolved in liquid krypton have been recorded. Additionally the infrared spectra of the gas and solid have been re-investigated. These spectroscopic data indicate a single conformer in all physical states with a large number of molecules in the gas phase at ambient temperature in excited states of the CN torsional mode which has a very low barrier to conformational interchange. To aid in the analyses of the vibrational and rotational spectra, ab initio calculations have been carried out by the perturbation method to the second order (MP2) with valence and core electron correlation using a variety of basis sets up to 6-311+G(2df,2pd). With the smaller basis sets up to 6-311+G(d,p) and cc-PVDZ, the cis conformer is indicated as a transition state with all larger basis sets the cis conformer is the only stable form. The predicted energy difference from these calculations between the cis form and the higher energy trans conformer is about 125 cm(-1) which represents essentially the barrier to internal rotation of the NCS group (rotation around NC axis). Density functional theory calculation by the B3LYP method with the same basis sets predicts this barrier to be about 25 cm(-1). By utilizing the previously reported microwave rotational constants with the structural parameters predicted by the ab initio MP2(full)/6-311+G(d,p) calculations, adjusted r(0) structural parameters have been obtained for the cis form. The determined heavy atom parameters are: r(NC)=1.196(5), r(CS)=1.579(5), r(CN)=1.439(5), r(CC)=1.519(5)A for the distances and angles of angleCCN=112.1(5), angleCNC=146.2(5), angleNCS=174.0(5) degrees . The centrifugal distortion constants, dipole moments, conformational stability, vibrational frequencies, infrared intensities and Raman activities have been predicted from ab initio calculations and compared to experimental

  15. Ab initio structure determination of nanocrystals of organic pharmaceutical compounds by electron diffraction at room temperature using a Timepix quantum area direct electron detector

    PubMed Central

    van Genderen, E.; Clabbers, M. T. B.; Das, P. P.; Stewart, A.; Nederlof, I.; Barentsen, K. C.; Portillo, Q.; Pannu, N. S.; Nicolopoulos, S.; Gruene, T.; Abrahams, J. P.

    2016-01-01

    Until recently, structure determination by transmission electron microscopy of beam-sensitive three-dimensional nanocrystals required electron diffraction tomography data collection at liquid-nitrogen temperature, in order to reduce radiation damage. Here it is shown that the novel Timepix detector combines a high dynamic range with a very high signal-to-noise ratio and single-electron sensitivity, enabling ab initio phasing of beam-sensitive organic compounds. Low-dose electron diffraction data (∼0.013 e− Å−2 s−1) were collected at room temperature with the rotation method. It was ascertained that the data were of sufficient quality for structure solution using direct methods using software developed for X-ray crystallography (XDS, SHELX) and for electron crystallography (ADT3D/PETS, SIR2014). PMID:26919375

  16. Ab initio structure determination of nanocrystals of organic pharmaceutical compounds by electron diffraction at room temperature using a Timepix quantum area direct electron detector.

    PubMed

    van Genderen, E; Clabbers, M T B; Das, P P; Stewart, A; Nederlof, I; Barentsen, K C; Portillo, Q; Pannu, N S; Nicolopoulos, S; Gruene, T; Abrahams, J P

    2016-03-01

    Until recently, structure determination by transmission electron microscopy of beam-sensitive three-dimensional nanocrystals required electron diffraction tomography data collection at liquid-nitrogen temperature, in order to reduce radiation damage. Here it is shown that the novel Timepix detector combines a high dynamic range with a very high signal-to-noise ratio and single-electron sensitivity, enabling ab initio phasing of beam-sensitive organic compounds. Low-dose electron diffraction data (∼ 0.013 e(-) Å(-2) s(-1)) were collected at room temperature with the rotation method. It was ascertained that the data were of sufficient quality for structure solution using direct methods using software developed for X-ray crystallography (XDS, SHELX) and for electron crystallography (ADT3D/PETS, SIR2014). PMID:26919375

  17. Structural changes upon reduction of dipyrido[2,3-a:3',2'-c]phenazine probed by vibrational spectroscopy, ab initio calculations, and deuteration studies.

    PubMed

    Howell, Sarah L; Matthewson, Benjamin J; Polson, Matthew I J; Burrell, Anthony K; Gordon, Keith C

    2004-05-01

    A series of bridging ligands, dipyrido[2,3-a:3',2'-c]phenazine (ppb), dipyrido[2,3-a:3',2'-c]-6,7-dichlorophenazine (ppbCl2), and dipyrido[2,3-a:3',2'-c]-6,7-dimethylphenazine (ppbMe2), and their binuclear copper(I) complexes have been synthesized, and their spectral properties were measured. The single-crystal structure of the complex, [(PPh3)2Cu(mu-ppbCl2)Cu(PPh3)2](BF4)2 in the monoclinic space group P21/c, 18.2590(1), 21.1833(3), 23.2960(3) A with Z = 4 is reported. The copper(I) complexes are deeply colored through MLCT transitions in the visible region. The vibrational spectra of the ligands have been modeled using ab initio hybrid density functional theory (DFT) methods (B3LYP/6-31G(d)) and compared to experimental FT-Raman and IR data. The DFT calculations are used to interpret the resonance Raman spectra, and thus the electronic spectra, of the complexes. The preferential enhancement of modes associated with the phenanthroline section of the ligands with blue excitation (lambda(exc) = 457.9 nm) over phenazine-based modes with redder excitation (lambda(exc) = 514.5 and 632.8 nm) suggests the 2 MLCT transitions terminated on different unoccupied MOs are present under the visible absorption envelope. The radical anion species of the ligands are prepared by the electrochemical reduction of the binuclear copper(I) complexes; no evidence of dechelation prevalent in other copper(I) complexes is observed. The resonance Raman spectra of the reduced complexes are dramatically different from those of the parent species. Across the series common bands are observed at about 1590 and 1570 cm(-1) which do not shift with reduction but are altered in intensity. The normal-mode analysis of the radical anion species suggests that these normal modes primarily involve bond length distortions that are unaffected by reduction.

  18. The Energetics of the Hydrogenolysis, Dehydrohalogenation, and Hydrolysis of 4,4'-Dichloro-diphenyl-trichloroethane from Ab Initio Electronic Structure Theory

    SciTech Connect

    Bylaska, Eric J.; Dixon, David A.; Felmy, Andrew R.; Apra, Edoardo; Windus, Theresa L.; Zhan, Chang-Guo; Tratnyek, Paul G.

    2004-07-08

    Electronic structure methods were used to calculate the aqueous reaction energies for hydrogenolysis, dehydrochlorination, and nucleophilic substitution by OH- of 4,4¢-DDT. Thermochemical properties ¢Hf° (298.15 K), S° (298.15 K, 1 bar), ¢GS (298.15 K, 1 bar) were calculated by using ab initio electronic structure calculations, isodesmic reactions schemes, gas-phase entropy estimates, and continuum solvation models for a series of DDT type structures (p-C6H4Cl)2-CH-CCl3, (p-C6H4Cl)2-CH-CCl2¥, (p-C6H4Cl)2-CHCHCl2, (p-C6H4Cl)2-CdCCl2, (p-C6H4Cl)2-CH-CCl2OH, (p-C6H4Cl)2-CH-CCl(dO), and (p-C6H4-Cl)2-CH-COOH. On the basis of these thermochemical estimates, the overall aqueous reaction energetics of hydrogenolysis, dehydrochlorination, and hydrolysis of 4,4¢-DDT were estimated. The results of this investigation showed that the dehydrochlorination and hydrolysis reactions have strongly favorable thermodynamics in the standard state, as well as under a wide range of pH conditions. For hydrogenolysis with the reductant aqueous Fe(II), the thermodynamics are strongly dependent on pH, and the stability region of the (p-C6H4Cl)2-CH-CCl2¥(aq) species is a key to controlling the reactivity in hydrogenolysis. These results illustrate the use of ab initio electronic structure methods to identify the potentially important environmental degradation reactions by calculation of the reaction energetics of a potentially large number of organic compounds with aqueous species in natural waters.

  19. Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding

    PubMed Central

    Almond, David; Cardozo, Timothy

    2010-01-01

    The antigenic diversity of HIV-1 has long been an obstacle to vaccine design, and this variability is especially pronounced in the V3 loop of the virus' surface envelope glycoprotein. We previously proposed that the crown of the V3 loop, although dynamic and sequence variable, is constrained throughout the population of HIV-1 viruses to an immunologically relevant β-hairpin tertiary structure. Importantly, there are thousands of different V3 loop crown sequences in circulating HIV-1 viruses, making 3D structural characterization of trends across the diversity of viruses difficult or impossible by crystallography or NMR. Our previous successful studies with folding of the V3 crown1, 2 used the ab initio algorithm 3 accessible in the ICM-Pro molecular modeling software package (Molsoft LLC, La Jolla, CA) and suggested that the crown of the V3 loop, specifically from positions 10 to 22, benefits sufficiently from the flexibility and length of its flanking stems to behave to a large degree as if it were an unconstrained peptide freely folding in solution. As such, rapid ab initio folding of just this portion of the V3 loop of any individual strain of the 60,000+ circulating HIV-1 strains can be informative. Here, we folded the V3 loop of the R2 strain to gain insight into the structural basis of its unique properties. R2 bears a rare V3 loop sequence thought to be responsible for the exquisite sensitivity of this strain to neutralization by patient sera and monoclonal antibodies4, 5. The strain mediates CD4-independent infection and appears to elicit broadly neutralizing antibodies. We demonstrate how evaluation of the results of the folding can be informative for associating observed structures in the folding with the immunological activities observed for R2. PMID:20864931

  20. The Band Structure of Polymers: Its Calculation and Interpretation. Part 3. Interpretation.

    ERIC Educational Resources Information Center

    Duke, B. J.; O'Leary, Brian

    1988-01-01

    In this article, the third part of a series, the results of ab initio polymer calculations presented in part 2 are discussed. The electronic structure of polymers, symmetry properties of band structure, and generalizations are presented. (CW)

  1. Orbital-free ab initio molecular dynamics study of the free liquid surface of Sn. From pseudopotential generation to structural and dynamic properties

    NASA Astrophysics Data System (ADS)

    Gonzalez Del Rio, Beatriz; Gonzalez Tesedo, Luis Enrique

    We report results of an orbital-free ab initio molecular dynamics (OF-AIMD) study of the free liquid surface of Sn at 1000 K. A key ingredient in the OF-AIMD method is the local ionic pseudopotential describing the ions-valence electrons interaction. We have developed a force-matching method to derive a local ionic pseudopotential suitable to account for a rapidly varying density system, such as in a free liquid surface. We obtain very good results for several structural properties. We have also studied the evolution of some dynamical properties when going from the central region (where the system behaves like the bulk liquid) towards the free liquid surface. We aknowledge the spanish MSI (Project FIS2012-33126) and the University of Valladolid for the provision of a PhD grant.

  2. Optical properties of crystalline and amorphous silicon slabs with adsorbed metal clusters and with dopants: A combined ab-initio electronic structure and density matrix treatment

    NASA Astrophysics Data System (ADS)

    Kilin, Dimitri; Micha, David; Ramirez, Jessica

    2011-03-01

    The optical absorbance and surface photovoltage of slabs of Si with varying number of layers have been calculated starting from their atomic structure. Results have been obtained for nanostructured surfaces with adsorbed metal clusters and for group III and V dopants, from ab initio DFT with periodic boundary conditions for extended systems, and from time-dependent DFT for supercells. Density matrix equations of motion (EOM) have been parametrized in a basis set of Kohn-Sham orbitals, for both crystalline and amorphous Si slabs. Results for properties and from electronic charge distributions provide insight on slab confinement effects for electronically excited states and for particle-hole creation. In addition, the integrodifferential EOMs have been solved for an initial femtosecond pulse excitation to analyze the nature of electron transfer at the surfaces, relevant to photovoltaics. Work supported by the NSF and by the Dreyfus Foundation to DM.

  3. Molecular structure, vibrational spectra and HOMO, LUMO analysis of yohimbine hydrochloride by density functional theory and ab initio Hartree-Fock calculations

    NASA Astrophysics Data System (ADS)

    Joshi, Bhawani Datt; Srivastava, Anubha; Tandon, Poonam; Jain, Sudha

    2011-11-01

    Yohimbine hydrochloride (YHCl) is an aphrodisiac and promoted for erectile dysfunction, weight loss and depression. The optimized geometry, total energy, potential energy surface and vibrational wavenumbers of yohimbine hydrochloride have been determined using ab initio, Hartree-Fock (HF) and density functional theory (DFT/B3LYP) method with 6-311++G(d,p) basis set. A complete vibrational assignment is provided for the observed Raman and IR spectra of YHCl. The UV absorption spectrum was examined in ethanol solvent and compared with the calculated one in gas phase as well as in solvent environment (polarizable continuum model, PCM) using TD-DFT/6-31G basis set. These methods are proposed as a tool to be applied in the structural characterization of YHCl. The calculated highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) with frontier orbital gap are presented.

  4. Photoexcited Nuclear Dynamics with Ab Initio Electronic Structure Theory: Is TD-DFT Ready For the Challenge?

    NASA Astrophysics Data System (ADS)

    Subotnik, Joseph

    In this talk, I will give a broad overview of our work in nonadiabatic dynamics, i.e. the dynamics of strongly coupled nuclear-electronic motion whereby the relaxation of a photo-excited electron leads to the heating up of phonons. I will briefly discuss how to model such nuclear motion beyond mean field theory. Armed with the proper framework, I will then focus on how to calculate one flavor of electron-phonon couplings, known as derivative couplings in the chemical literature. Derivative couplings are the matrix elements that couple adiabatic electronic states within the Born-Oppenheimer treatment, and I will show that these matrix elements show spurious poles using formal (frequency-independent) time-dependent density functional theory. To correct this TD-DFT failure, a simple approximation will be proposed and evaluated. Finally, time permitting, I will show some ab initio calculations whereby one can use TD-DFT derivative couplings to study electronic relaxation through a conical intersection.

  5. What Are the Ground State Structures of C20 and C24? An Explicitly Correlated Ab Initio Approach.

    PubMed

    Manna, Debashree; Martin, Jan M L

    2016-01-14

    A new benchmark study has been performed for six isomers of C20 and four isomers of C24 using explicitly correlated methods, together with coupled cluster theory with large basis sets and DFT with advanced functionals. The relative energy trends obtained are extremely sensitive to the methods used. Combining our best CCSD(T)-MP2 difference with our best MP2 basis set limit, the dehydrocorannulene bowl is found to be the most stable for C20, followed by the cage at about 8 kcal/mol, and the ring at about 46 kcal/mol. For C24, the D3d cage is found to be the most stable isomer, followed at only a few kilocalories per mole by dehydrocoronene, and at larger separations by then octahedral cage and the ring, respectively. This makes C24 the smallest classical fullerene. The estimated residual basis set error of the estimated CCSD(T) basis set limit is conservatively expected to be ±1 kcal/mol. In general, DFT exhibits large errors for relative energies with RMSD values in the 8-34 kcal/mol range. However, among the DFT functionals, the DSD-PBEP86-D3BJ double hybrid comes close to our best ab initio results, while the ωB97X-V range-separated hybrid is in semiquantitative agreement. PMID:26654916

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

    PubMed

    Olsson, P; Vidal, J; Lincot, D

    2011-10-12

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

  7. Conformational analysis of an acyclic tetrapeptide: ab-initio structure determination from X-ray powder diffraction, Hirshfeld surface analysis and electronic structure.

    PubMed

    Das, Uday; Naskar, Jishu; Mukherjee, Alok Kumar

    2015-12-01

    A terminally protected acyclic tetrapeptide has been synthesized, and the crystal structure of its hydrated form, Boc-Tyr-Aib-Tyr-Ile-OMe·2H2O (1), has been determined directly from powder X-ray diffraction data. The backbone conformation of tetrapeptide (1) exhibiting two consecutive β-turns is stabilized by two 4 → 1 intramolecular N-H · · · O hydrogen bonds. In the crystalline state, the tetrapeptide molecules are assembled through water-mediated O-H · · · O hydrogen bonds to form two-dimensional molecular sheets, which are further linked by intermolecular C-H · · · O hydrogen bonds into a three-dimensional supramolecular framework. The molecular electrostatic potential (MEP) surface of (1) has been used to supplement the crystallographic observations. The nature of intermolecular interactions in (1) has been analyzed quantitatively through the Hirshfeld surface and two-dimensional fingerprint plot. The DFT optimized molecular geometry of (1) agrees closely with that obtained from the X-ray structure analysis. The present structure analysis of Boc-Tyr-Aib-Tyr-Ile-OMe·2H2 O (1) represents a case where ab-initio crystal structure of an acyclic tetrapeptide with considerable molecular flexibility has been accomplished from laboratory X-ray powder diffraction data.

  8. 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.

  9. Structural, elastic, electronic and optical properties of Cu3MTe4 (M = Nb, Ta) sulvanites — An ab initio study

    NASA Astrophysics Data System (ADS)

    Ali, M. A.; Roknuzzaman, M.; Nasir, M. T.; Islam, A. K. M. A.; Naqib, S. H.

    2016-04-01

    The elastic, electronic, and optical properties of Cu3MTe4 (M = Nb, Ta) are investigated for the first time using the density-functional formalism. The optimized crystal structure is obtained and the lattice parameters are compared with available experimental data. Different elastic moduli are calculated. The Born criteria for mechanical stability are found to be fulfilled from the estimated values of the elastic moduli, Cij. The band structure and the electronic energy density of states (EDOS) are also determined. The band structure calculations show semiconducting behavior for both the compounds. The theoretically calculated values of the band gaps are found to be strongly dependent on the nature of the functional representing the exchange correlations. Technologically significant optical parameters (e.g., dielectric function, refractive index, absorption coefficient, optical conductivity, reflectivity, and loss function) have been determined. Important conclusions are drawn based on the theoretical findings.

  10. Ab initio RNA folding

    NASA Astrophysics Data System (ADS)

    Cragnolini, Tristan; Derreumaux, Philippe; Pasquali, Samuela

    2015-06-01

    RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, the experimental determination of RNA structures through x-ray crystallography and NMR seems to have reached a plateau in the number of structures resolved each year, but as more and more RNA sequences are being discovered, the need for structure prediction tools to complement experimental data is strong. Theoretical approaches to RNA folding have been developed since the late nineties, when the first algorithms for secondary structure prediction appeared. Over the last 10 years a number of prediction methods for 3D structures have been developed, first based on bioinformatics and data-mining, and more recently based on a coarse-grained physical representation of the systems. In this review we are going to present the challenges of RNA structure prediction and the main ideas behind bioinformatic approaches and physics-based approaches. We will focus on the description of the more recent physics-based phenomenological models and on how they are built to include the specificity of the interactions of RNA bases, whose role is critical in folding. Through examples from different models, we will point out the strengths of physics-based approaches, which are able not only to predict equilibrium structures, but also to investigate dynamical and thermodynamical behavior, and the open challenges to include more key interactions ruling RNA folding.

  11. Ab initio study on the effect of structural relaxation on the electronic and optical properties of P-doped Si nanocrystals

    SciTech Connect

    Pi, Xiaodong; Ni, Zhenyi; Yang, Deren E-mail: christophe.delerue@isen.fr; Delerue, Christophe E-mail: christophe.delerue@isen.fr

    2014-11-21

    In contrast to the conventional doping of bulk silicon (Si), the doping of Si nanocrystals (NCs) that are often smaller than 5 nm in diameter may lead to serious structural changes. Since the electronic and optical properties of Si NCs are intimately associated with their structures, it is critical to understand how doping impacts the structures of Si NCs. By means of ab initio calculation we now compare 1.4 nm phosphorus (P)-doped Si NCs without structural relaxation and those with structural relaxation. Structural changes induced by structural relaxation are manifested by the stretching and compressing of bonds and apparent variations in bond angles. With the increase of the concentration of P structural changes induced by structural relaxation become more serious. It is found that structural relaxation makes differences in the energy-level schemes of P-doped Si NCs. Structural relaxation also causes the binding energy of an electron in a P-doped Si NC to more significantly increase as the concentration of P increases. With the increase of the concentration of P structural relaxation leads to more pronounced changes in the optical absorption of P-doped Si NCs.

  12. 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.

  13. 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.

  14. Ab initio structural modeling of and experimental validation for Chlamydia trachomatis protein CT296 reveal structural similarity to Fe(II) 2-oxoglutarate-dependent enzymes

    SciTech Connect

    Kemege, Kyle E.; Hickey, John M.; Lovell, Scott; Battaile, Kevin P.; Zhang, Yang; Hefty, P. Scott

    2012-02-13

    Chlamydia trachomatis is a medically important pathogen that encodes a relatively high percentage of proteins with unknown function. The three-dimensional structure of a protein can be very informative regarding the protein's functional characteristics; however, determining protein structures experimentally can be very challenging. Computational methods that model protein structures with sufficient accuracy to facilitate functional studies have had notable successes. To evaluate the accuracy and potential impact of computational protein structure modeling of hypothetical proteins encoded by Chlamydia, a successful computational method termed I-TASSER was utilized to model the three-dimensional structure of a hypothetical protein encoded by open reading frame (ORF) CT296. CT296 has been reported to exhibit functional properties of a divalent cation transcription repressor (DcrA), with similarity to the Escherichia coli iron-responsive transcriptional repressor, Fur. Unexpectedly, the I-TASSER model of CT296 exhibited no structural similarity to any DNA-interacting proteins or motifs. To validate the I-TASSER-generated model, the structure of CT296 was solved experimentally using X-ray crystallography. Impressively, the ab initio I-TASSER-generated model closely matched (2.72-{angstrom} C{alpha} root mean square deviation [RMSD]) the high-resolution (1.8-{angstrom}) crystal structure of CT296. Modeled and experimentally determined structures of CT296 share structural characteristics of non-heme Fe(II) 2-oxoglutarate-dependent enzymes, although key enzymatic residues are not conserved, suggesting a unique biochemical process is likely associated with CT296 function. Additionally, functional analyses did not support prior reports that CT296 has properties shared with divalent cation repressors such as Fur.

  15. Ab Initio Structural Modeling of and Experimental Validation for Chlamydia trachomatis Protein CT296 Reveal Structural Similarity to Fe(II) 2-Oxoglutarate-Dependent Enzymes▿

    PubMed Central

    Kemege, Kyle E.; Hickey, John M.; Lovell, Scott; Battaile, Kevin P.; Zhang, Yang; Hefty, P. Scott

    2011-01-01

    Chlamydia trachomatis is a medically important pathogen that encodes a relatively high percentage of proteins with unknown function. The three-dimensional structure of a protein can be very informative regarding the protein's functional characteristics; however, determining protein structures experimentally can be very challenging. Computational methods that model protein structures with sufficient accuracy to facilitate functional studies have had notable successes. To evaluate the accuracy and potential impact of computational protein structure modeling of hypothetical proteins encoded by Chlamydia, a successful computational method termed I-TASSER was utilized to model the three-dimensional structure of a hypothetical protein encoded by open reading frame (ORF) CT296. CT296 has been reported to exhibit functional properties of a divalent cation transcription repressor (DcrA), with similarity to the Escherichia coli iron-responsive transcriptional repressor, Fur. Unexpectedly, the I-TASSER model of CT296 exhibited no structural similarity to any DNA-interacting proteins or motifs. To validate the I-TASSER-generated model, the structure of CT296 was solved experimentally using X-ray crystallography. Impressively, the ab initio I-TASSER-generated model closely matched (2.72-Å Cα root mean square deviation [RMSD]) the high-resolution (1.8-Å) crystal structure of CT296. Modeled and experimentally determined structures of CT296 share structural characteristics of non-heme Fe(II) 2-oxoglutarate-dependent enzymes, although key enzymatic residues are not conserved, suggesting a unique biochemical process is likely associated with CT296 function. Additionally, functional analyses did not support prior reports that CT296 has properties shared with divalent cation repressors such as Fur. PMID:21965559

  16. An ab initio study of electronic structure and spectra of 8-bromoguanine: a comparative study with guanine.

    PubMed

    Mishra, S K; Mishra, P C

    2001-10-01

    Ground state geometries of the four tautomeric forms keto-N9H, keto-N7H, enol-N9H and enol-N7H of 8-bromoguanine (8BG) were optimized using the ab initio RHF procedure employing a mixed basis set consisting of the 6-311 + G* basis set for the nitrogen atom of the amino group and the bromine atom, and the 4-31G basis set for all other atoms. These calculations were followed by correlation correction of the total energy at the MP2 level using the same basis set. The different tautomeric forms of 8BG in the ground state were solvated using the isodensity surface polarized continuum model (IPCM) of the SCRF theory both at the RHF and MP2 levels. Excited states were generated employing configuration interaction among singly excited configurations (CIS) obtained using a limited window of filled and empty molecular orbitals. Formation of hydrogen-bonded complexes between 8BG and three water molecules in the ground and excited states was considered in order to account for solvent effects approximately. Excited state geometry was optimized in each case for the lowest singlet excited state which was found to be of pi-pi* type. Vibrational frequency analysis was performed in order to ensure that the stationary points located on the potential energy surfaces by geometry optimization were minima. It is found that 8BG would occur in the ground state dominantly in the keto-N7H form both at the aqueous solution-air interface and inside the bulk liquid. The observed absorption and fluorescence spectra of 8BG can be explained satisfactorily considering only the keto-N7H form of the molecule. The enol tautomers of 8BG do not appear to be important from the point of view of ground state properties or electronic spectra. The observed differences between the behaviors of guanine and 8BG can be easily explained on the basis of the results obtained.

  17. Ab-initio calculation of electronic structure and optical properties of AB-stacked bilayer α-graphyne

    NASA Astrophysics Data System (ADS)

    Behzad, Somayeh

    2016-09-01

    Monolayer α-graphyne is a new two-dimensional carbon allotrope with many special features. In this work the electronic properties of AA- and AB-stacked bilayers of this material and then the optical properties are studied, using first principle plane wave method. The electronic spectrum has two Dirac cones for AA stacked bilayer α-graphyne. For AB-stacked bilayer, the interlayer interaction changes the linear bands into parabolic bands. The optical spectra of the most stable AB-stacked bilayer closely resemble to that of the monolayer, except for small shifts of peak positions and increasing of their intensity. For AB-stacked bilayer, a pronounced peak has been found at low energies under the perpendicular polarization. This peak can be clearly ascribed to the transitions at the Dirac point as a result of the small degeneracy lift in the band structure.

  18. 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.

  19. The gas-phase molecular structure of 1,1-diethynylsilacyclobutane as determined by means of electron diffraction and ab initio calculations

    NASA Astrophysics Data System (ADS)

    Dakkouri, Marwan; Grosser, Martin

    2002-06-01

    As a continuation of our systematic investigation of the effect of substituents on the ring geometry and dynamics in silacyclobutanes and in order to explore the role of the silicon atom as a mediator for electronic interactions between the attached fragments, we studied the molecular structure of 1,1-diethynylsilacyclobutane (DESCB) by means of gas-phase electron diffraction and ab initio calculations. The structural refinement of the electron diffraction data yielded the following bond lengths ( ra) and bond angles (uncertainties are 3σ): r( Si- C)=1.874(2) Å, r( Si- C)=1.817(1) Å, r(- C C-)=1.209(1) Å, r( C- C)=1.563(2) Å, ∠(C-Si-C)=79.2(6)°, ∠(C-Si-C)=106.5(6)°. The geminal Si-CC moieties were found to be bent outwards by 3.1(15)° and the puckering angle was determined to be 30.0(15)°. The evidently short Si-C bond length, which was also reproduced by the ab initio calculations, could be rationalized as being the consequence of the electronic interaction between the outer π charges of the triple bond and the 3pπ orbitals at the silicon atom. It is also likely that the conjugation of the geminal ethynyl groups leads to an enhancement of this bond contraction. Electrostatic interactions and the subsequent reduction of the covalent radius of the silicon atom may also contribute to this bond shortening. It has been found that the endocyclic Si-C bond length fits nicely within a scheme describing a monotonous decrease of the Si-C bond length with the increase of the electronegativity of the substituent in various geminally substituted silacyclobutanes. A series of related silacyclobutanes and acyclic diethynylsilanes have been studied by applying various ab initio methods and their optimized structures were compared to the structure of DESCB. Among these compounds are 1,1-dicyanosilacyclobutane (DCYSCB), which is isoelectronic to DESCB, 1,1-diethynylcyclobutane (DECB) which is isovalent to DESCB, monoethynylsilacyclobutane (MESCB

  20. Structure of 1:1 complex of 1-naphthylmethyl ester of monensin A with sodium perchlorate studied by X-ray, FT-IR and ab initio methods

    NASA Astrophysics Data System (ADS)

    Huczyński, Adam; Janczak, Jan; Brzezinski, Bogumil

    2012-12-01

    A new crystalline complex formed between 1-naphthylmethyl ester of the naturally occurring antibiotic - monensin A (MON8) with sodium perchlorate has been obtained and studied using X-ray crystallography and FT-IR spectroscopy. The X-ray data of the complex show that MON8 forms a pseudo-cyclic structure stabilised by one weak intramolecular hydrogen bond and the sodium cation co-ordinated by two oxygen atoms of hydroxyl groups and four etheric oxygen atoms in the hydrophilic sphere. Within this structure the oxygen atoms of the ester groups are not involved in the coordination of sodium cation. In contrast to the solid state structure of the complex, in acetonitrile solution an equilibrium between two structures, in which the oxygen atom of the carbonyl ester group is either involved or not involved in the complexation of the sodium cation, is found. In acetonitrile this equilibrium is shifted towards the latter structure i.e. the structure existing in the solid state. The gas-phase structure of [MON8sbnd Na]+ cation as shown the ab initio MO calculations is comparable with the crystal one. Three-dimensional molecular electrostatic potential calculated for the neutral MON8 and [MON8sbnd Na]+ molecules is helpful for understanding the structural aspects of the sodium complex formation.

  1. An ab initio potential function for the ν13 vibrational mode of 1,3-butadiene

    NASA Astrophysics Data System (ADS)

    Senent, M. L.

    1995-06-01

    The restricted potential of the ν13 torsional mode of 1,3-butadiene has been determined from ab initio calculations. The relative energy and geometry of the second rotamer were calculated with the optimized couple cluster method with double substitutions. This ab initio level provides that the second stable structure attaches to a gauche form situated at 140.8°. The potential energy function was obtained by fitting to a symmetry-adapted Fourier series the total electronic energies of several selected conformations. These energies were calculated by the Möller-Plesset perturbation theory up to the second order (MP2) with full and partial optimization of the geometry. Torsional Raman band positions and fundamental frequencies were determined from the periodic potentials with a good agreement with experimental data. The convenience of performing fully optimized calculations to determine the restricted function is also refuted.

  2. Prediction of new stable structure, promising electronic and thermodynamic properties of MoS3: Ab initio calculations

    NASA Astrophysics Data System (ADS)

    Pan, Yong; Guan, Weiming

    2016-09-01

    MoS3 has attracted considerable attention as potential hydrogen storage material due to the interaction between the hydrogen and unsaturated sulfur atoms. However, its structure and physical properties are unknown. By means of first-principles approach and Inorganic crystal structure Database (ISCD), we systematically investigated the structure, relevant physical and thermodynamic properties of MoS3. Phonon dispersion, electronic structure, band structure and heat capacity are calculated in detail. We predicted the orthorhombic B2ab (SrS3-type) and tetragonal P-421m (BaS3-type) structures of MoS3, which prefers to form the SrS3-type (Space group: B2ab, No.41) structure at the ground state. High pressure results in structural transition from SrS3-type structure to BaS3-type structure. This sulfide exhibits a degree of metallic behavior. The calculated heat capacity of MoS3 with SrS3-type structure is about of 39 J/(mol·K).

  3. Synchrotron-based far-infrared spectroscopic investigation and ab initio calculations of 3-oxetanone: observation and analysis of the ν7 band and the Coriolis coupled ν16 and ν20 bands.

    PubMed

    Chen, Ziqiu; van Wijngaarden, Jennifer

    2012-09-27

    Rotationally resolved vibrational spectra of the four-membered heterocycle 3-oxetanone (c-C(3)H(4)O(2)) have been investigated in the 360-720 cm(-1) region with a resolution of 0.000 959 cm(-1) using synchrotron radiation from the Canadian Light Source. The observed bands correspond to motions best described as C═O deformation out-of-plane (ν(20)) at 399.6 cm(-1), C═O deformation in-plane (ν(16)) at 448.2 cm(-1), and the ring deformation (ν(7)) at 685.0 cm(-1). Infrared ground state combination differences along with previously reported pure rotational transitions were used to obtain the ground state spectroscopic parameters. Band centers, rotational and centrifugal distortion constants for the ν(7), ν(16), and ν(20) vibrational excited states were accurately determined by fitting a total of 10,319 assigned rovibrational transitions in a global analysis. The two adjacent carbonyl deformation bands, ν(16) and ν(20), were found to be mutually perturbed through a first-order a-type Coriolis interaction which was accounted for in the multiband analysis. The band centers agree within 3% of the ab initio estimates using DFT theory.

  4. Rotational spectra and structure of the Ar2-H2S complex: pulsed nozzle Fourier transform microwave spectroscopic and ab initio studies.

    PubMed

    Mandal, Pankaj K; Ramdass, Dharmender J; Arunan, E

    2005-07-21

    This paper reports the rotational spectrum and structure of the Ar2-H2S complex and its HDS and D2S isotopomers. The ground state structure has heavy-atom C2v symmetry with the two Ar atoms indistinguishable and H2S freely rotating as evinced by the fact that asymmetric top energy levels with Kp=odd levels are missing. The rotational constants for the parent isotopomer are: A=1733.115(1) MHz, B=1617.6160(5) MHz and C=830.2951(2) MHz. Unlike the Ar-H2S complex, the Ar2-H2S does not show an anomalous isotopic shift in rotational constants on deuterium substitution. However, the intermolecular potential is still quite floppy, leading to very different centrifugal distortion constants for the three isotopomers. The Ar-Ar and Ar-c.m.(H2S) distances are determined to be 3.820 A and 4.105 A, respectively. The A rotational constants for Ar2-H2S/HDS/D2S isotopomers are very close to each other and to the B constant of free Ar2, indicating that H2S does not contribute to the moment of inertia about the a-axis. Ab initio calculations at MP2 level with aug-cc-pVQZ basis set lead to an equilibrium C2v minimum structure with the Ar-Ar line perpendicular to the H-H line and the S away from Ar2. The centrifugal distortion constants, calculated using the ab initio force field, are in reasonable agreement with the experimental values. However, they do not show the variation observed for different isotopmers. The binding energy of Ar2-H2S has been determined to be 507 cm-1(6.0 kJ mol-1) by CBS extrapolation after correcting for basis set superposition error. Potential energy scans point out that the barrier for internal rotation of H2S about its b axis is only 10 cm-1 and it is below the zero point energy (13.5 cm-1) in this torsional degree of freedom. Internal rotation of H2S about its a- and c-axes also have small barriers of about 50 cm-1 only, suggesting that H2S is extremely floppy within the complex.

  5. Spectra-structure correlations in solid metal saccharinates. II. Ab initio molecular structures and vibrational spectra of N-substituted saccharins at the HF level

    NASA Astrophysics Data System (ADS)

    Naumov, Panče; Jovanovski, Gligor; Ohashi, Yuji

    2002-02-01

    Ground-state ab initio molecular geometries and vibrational spectra of 24 N-substituted isolated saccharins with small-size B, Br, C, Cl, F, N, O, P or S-groups and the parent molecule are predicted at RHF/6-31G level to examine the molecular structural changes stemming from N-substitution of saccharin (o-sulfobenzimide). Trends in the molecular geometrical parameters of the sulfimide ring and the carbonyl stretching frequency are discussed in relation to the electronic properties of the substituent and the solid state effects. The results are compared with the crystallographic data for N-substituted saccharins and metal saccharinato salts/complexes retrieved from the Cambridge Structural Database. The ability of several theoretical methods to describe the substitution/deprotonation of the conjugated CONHSO 2 structure is summarized. Electronic properties of the substituent affect significantly only the immediate CN and SN bonds by as much as ±0.014 Å, while other bonds are relatively less influenced (±0.004 Å). Combined with the effects of the crystal packing and thermal vibrations, they impose flexibility on the intramolecular lengths up to ±0.02 Å. High correlation ( R=0.966) between the theoretical ν(CO) frequencies and CO distances is predictable for both of these parameters, but is lowered notably in the crystal by both vibrational and solid-state circumstances. From the structural viewpoint, the N sac-X bonds (X = B, Br, C, Cl, F, N, O, P, S; sac denotes saccharin) behave similarly to the purely covalent N sac-metal bonds.

  6. Structure, energetics, and electronic properties of the surface of a promoted MoS{sub 2} catalyst: An ab initio local density functional study

    SciTech Connect

    Raybaud, P.; Hafner, J.; Kresse, G.; Kasztelan, S.; Toulhoat, H.

    2000-02-15

    The determination of the local structure of cobalt- or nickel-promoted MoS{sub 2}-based hydrodesulfurization catalysts is of interest for understanding the mechanism leading to an increased activity brought by cobalt or nickel, the so-called synergetic effect. For that reason, the authors carried out ab initio calculations using density functional theory under the generalized gradient approximation for periodic systems. The edge substitution model emerges as the most stable structure and provides an excellent agreement with local structures experimentally determined on real catalysts by in situ extended X-ray absorption fine structure. The authors studied the absorption of sulfur on the active edge surface of the promoted MoS{sub 2} catalyst and determined the equilibrium coverage under sulfiding conditions. It is demonstrated that the incorporation of promoter atoms has a strong influence on the sulfur-metal bond energy at the surface and in particular leads to a reduction of the equilibrium S coverage of the active metal sites. A comparative study on the effects of Co, Ni, and Cu atoms as promoters was performed. Detailed results on the surface electronic structure of promoted MoS{sub 2} are presented.

  7. 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.

  8. Ab initio non-relativistic spin dynamics

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

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

    PubMed

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

    2009-11-01

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

  10. Friction of water on graphene and hexagonal boron nitride from ab initio methods: very different slippage despite very similar interface structures.

    PubMed

    Tocci, Gabriele; Joly, Laurent; Michaelides, Angelos

    2014-12-10

    Friction is one of the main sources of dissipation at liquid water/solid interfaces. Despite recent progress, a detailed understanding of water/solid friction in connection with the structure and energetics of the solid surface is lacking. Here, we show for the first time that ab initio molecular dynamics can be used to unravel the connection between the structure of nanoscale water and friction for liquid water in contact with graphene and with hexagonal boron nitride. We find that although the interface presents a very similar structure between the two sheets, the friction coefficient on boron nitride is ≈ 3 times larger than that on graphene. This comes about because of the greater corrugation of the energy landscape on boron nitride arising from specific electronic structure effects. We discuss how a subtle dependence of the friction on the atomistic details of a surface, which is not related to its wetting properties, may have a significant impact on the transport of water at the nanoscale, with implications for the development of membranes for desalination and for osmotic power harvesting.

  11. An ab initio calculation of magnetic structure factors for Cs3CoCl5 including spin-orbit and finite magnetic field effects

    NASA Astrophysics Data System (ADS)

    Wolff, Stephen K.; Jayatilaka, Dylan; Chandler, Graham S.

    1995-09-01

    Spin-orbit interaction plays a significant role in determining the magnetic density in some transition metal complexes. We present a new ab initio technique, based on an extension of unrestricted Hartree-Fock theory, which includes nonperturbatively these spin-orbit effects, and simultaneously also the effects of a finite magnetic field. We also present a new and efficient method for calculating magnetic structure factors, based on the current density rather than magnetic dipole moment density, for a crystal composed of noninteracting molecular fragments. These structure factors are directly comparable to polarized neutron diffraction experiments. Results for the Cs3CoCl5 crystal are compared with experiment and previous studies. Without one-electron spin-orbit coupling terms, the magnitudes of the predicted structure factors are on average 10-15 % too low, whereas, with the spin-orbit terms, the magnitudes are 25-30% too high. Using an effective nuclear charge for Co in the spin-orbit term brings the results into much better agreement, and suggests that the two-electron spin-orbit shielding terms omitted in the present work are important. For over one quarter of the reflections studied, the magnetic contribution to the structure factors is more than 20% of the nuclear contribution.

  12. Pressure-induced changes in structural and dynamic properties of liquid Fe close to the melting line. An ab initio study.

    PubMed

    Marqués, Miriam; González, Luis E; González, David J

    2016-02-24

    The static and dynamic properties of liquid Fe at high pressure and temperature have been studied using an ab initio molecular dynamics method. We have focused on four thermodynamic states at pressures of 27, 42, 50 and 58 GPa for which x-ray scattering data are available. The calculated static structure shows very good agreement with the available experimental data, including an asymmetric second peak which becomes more marked with increasing pressure. The dynamical structure reveals the existence of propagating density fluctuations and the associated dispersion relation has also been determined. The relaxation mechanisms for the density fluctuations have been analyzed in terms of a model with two decay channels (fast and slow, respectively). We found that the thermal relaxation proceeds along the slow decaying channel whereas the fast one is that of the viscoelastic relaxation. The possible coupling between longitudinal and transverse excitation modes has been investigated by looking at specific signatures in two wavevector regions: the first one is located around the position of the main peak of the structure factor, qp, as suggested by the recently reported appearance of high frequency transverse waves in liquid Li under high pressures; the second region is around qp/2, as suggested by the recent finding of transverse acoustic modes in inelastic x-ray scattering intensities of liquid Fe at ambient pressure. Finally, results are also reported for several transport coefficients. PMID:26811899

  13. Ab initio investigations of A-site doping on the structure and electric polarization of HoMnO{sub 3}

    SciTech Connect

    S, Sathya Sheela; C, Kanagaraj; Natesan, Baskaran

    2015-06-24

    We have investigated the effect of A-site doping on the structure and electric polarization of orthorhombic HoMnO{sub 3} using ab initio density functional theory calculations. We find that the substitution of rare earth ions, such as Lu, Y and La in place of Ho in orthorhombic HoMnO{sub 3} modifies the local structure around Mn ions drastically, and leads to the formation of two distinct Mn sites Mn(0) and Mn(1). As a result, large variance between Mn(0)O{sub 6} and Mn(1)O{sub 6} octahedral distortions arises. This variance in the octahedral distortions drives the disparate hopping of electrons between the e{sub g} orbitals enhancing the electronic polarization with increasing rare earth ion radius. The largest polarization of 7 µC/cm{sup 2} is obtained for La doped HoMnO{sub 3}. This increase in polarization has been explained on the basis of radius mismatch induced local structural effects.

  14. Ab initio thermodynamic study of the structure and chemical bonding of a β-Ni1-xAlx/α-Al2O3 interface

    NASA Astrophysics Data System (ADS)

    Li, Hongtao; Feng, Jiwei; Zhang, Wenqing; Jiang, Wan; Gu, Hui; Smith, John R.

    2009-11-01

    The properties of an interface between a metallic alloy and an oxide are computed by combining ab initio quantum mechanics with thermodynamics. Results for the stability, structures, and chemical compositions of the β-Ni1-xAlx/α-Al2O3 interface are presented. We found that there are two types of stable structures for the interface. Type I is characterized by joining an Al-rich Ni-Al alloy with an Al-rich Al2O3 surface (terminated by two Al atomic layers). Type II is a junction of a Ni-rich Ni-Al alloy with an Al2O3 surface terminated by an oxygen atomic layer and with atomic migrations and interchanges within the interfacial region. Both types of interfaces exhibit Al accumulation on top of the oxide scale while an adjacent Ni-rich layer is found at the type-II interfaces. The atomic geometries, electronic structures, and chemical bonds of the two types of interfacial systems were analyzed. The calculated interfacial works of separation Wsep agree reasonably well with experimental data and earlier calculations.

  15. Pressure-induced changes in structural and dynamic properties of liquid Fe close to the melting line. An ab initio study.

    PubMed

    Marqués, Miriam; González, Luis E; González, David J

    2016-02-24

    The static and dynamic properties of liquid Fe at high pressure and temperature have been studied using an ab initio molecular dynamics method. We have focused on four thermodynamic states at pressures of 27, 42, 50 and 58 GPa for which x-ray scattering data are available. The calculated static structure shows very good agreement with the available experimental data, including an asymmetric second peak which becomes more marked with increasing pressure. The dynamical structure reveals the existence of propagating density fluctuations and the associated dispersion relation has also been determined. The relaxation mechanisms for the density fluctuations have been analyzed in terms of a model with two decay channels (fast and slow, respectively). We found that the thermal relaxation proceeds along the slow decaying channel whereas the fast one is that of the viscoelastic relaxation. The possible coupling between longitudinal and transverse excitation modes has been investigated by looking at specific signatures in two wavevector regions: the first one is located around the position of the main peak of the structure factor, qp, as suggested by the recently reported appearance of high frequency transverse waves in liquid Li under high pressures; the second region is around qp/2, as suggested by the recent finding of transverse acoustic modes in inelastic x-ray scattering intensities of liquid Fe at ambient pressure. Finally, results are also reported for several transport coefficients.

  16. Ab initio Study of HZnF

    NASA Astrophysics Data System (ADS)

    Hayashi, S.; Léonard, C.; Chambaud, G.

    2009-11-01

    On the basis of highly correlated ab initio calculations, an accurate determination of the electronic structure and of the rovibrational spectroscopy has been performed for the electronic ground state of the HZnF system. Using effective core pseudopotentials for the Zn and F atoms and associated aug-cc-pVQZ basis sets, we have calculated, at the multireference configuration interaction level including the Davidson correction, the three-dimensional potential energy surface of the X1Σ+ ground state. The rovibrational energy levels have been obtained variationally, and the results have been discussed and compared with existing experimental data on the ground state of the close system HZnCl, which exhibits a complicated vibration-rotation spectrum. Our analysis shows that the nature of the H-ZnF bond is quite similar to that of the H-ZnCl bond, according to their bond lengths, harmonic frequencies of the H-Zn stretching mode, and dissociation energies into H and ZnF/ZnCl. The ab initio study of the electronic ground and excited states of ZnH and ZnH+ are also presented using similar level of calculations. Characteristic constants are given for the first bounded electronic states correlating to the first two dissociation asymptotes of the neutral and ionic diatomics.

  17. Ab initio description of the diluted magnetic semiconductor Ga1-xMnxAs: Ferromagnetism, electronic structure, and optical response

    NASA Astrophysics Data System (ADS)

    Craco, L.; Laad, M. S.; Müller-Hartmann, E.

    2003-12-01

    Motivated by a study of various experiments describing the electronic and magnetic properties of the diluted magnetic semiconductor Ga1-xMnxAs, we investigate its physical response in detail using a combination of first-principles band structure with methods based on dynamical mean field theory to incorporate strong, dynamical correlations, and intrinsic as well as extrinsic disorder in one single theoretical picture. We show how ferromagnetism is driven by double exchange (DE), in agreement with very recent observations, along with a good quantitative description of the details of the electronic structure, as probed by scanning tunneling microscopy and optical conductivity. Our results show how ferromagnetism can be driven by DE even in diluted magnetic semiconductors with small carrier concentration.

  18. 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.

  19. Characterization of structure and dynamics of an aqueous scandium(III) ion by an extended ab initio QM/MM molecular dynamics simulation.

    PubMed

    Vchirawongkwin, Viwat; Kritayakornupong, Chinapong; Tongraar, Anan; Rode, Bernd M

    2012-10-14

    Hydration structure and dynamics of an aqueous Sc(III) solution were characterized by means of an extended ab initio quantum mechanical/molecular dynamical (QM/MM) molecular dynamics simulation at Hartree-Fock level. A monocapped trigonal prismatic structure composed of seven water molecules surrounding scandium(III) ion was proposed by the QM/MM simulation including the quantum mechanical effects for the first and second hydration shells. The mean Sc(III)-O bond length of 2.14 Å was identified for six prism water molecules with one capping water located at around 2.26 Å, reproducing well the X-ray diffraction data. The Sc(III)-O stretching frequency of 432 cm(-1) corresponding to a force constant of 130 N m(-1), evaluated from the enlarged QM/MM simulation, is in good agreement with the experimentally determined value of 430 cm(-1) (128 N m(-1)). Various water exchange processes in the second hydration shell of the hydrated Sc(III) ion predict a mean ligand residence time of 7.3 ps.

  20. Interfacing the Ab initio multiple spawning method with electronic structure methods in GAMESS: Photodecay of trans-Azomethane

    SciTech Connect

    Gaenko, Alexander; DeFusco, Albert; Varganov, Sergey A.; Martínez, Todd J.; Gordon, Mark S.

    2014-10-20

    This work presents a nonadiabatic molecular dynamics study of the nonradiative decay of photoexcited trans-azomethane, using the ab initio multiple spawning (AIMS) program that has been interfaced with the General Atomic and Molecular Electronic Structure System (GAMESS) quantum chemistry package for on-the-fly electronic structure evaluation. The interface strategy is discussed, and the capabilities of the combined programs are demonstrated with a nonadiabatic molecular dynamics study of the nonradiative decay of photoexcited trans-azomethane. Energies, gradients, and nonadiabatic coupling matrix elements were obtained with the state-averaged complete active space self-consistent field method, as implemented in GAMESS. The influence of initial vibrational excitation on the outcome of the photoinduced isomerization is explored. Increased vibrational excitation in the CNNC torsional mode shortens the excited state lifetime. Depending on the degree of vibrational excitation, the excited state lifetime varies from ~60–200 fs. As a result, these short lifetimes are in agreement with time-resolved photoionization mass spectroscopy experiments.

  1. Tunneling Splittings in Vibronic Structure of CH_3F^+ ( X^2E): Studied by High Resolution Photoelectron Spectra and AB Initio Theoretical Method

    NASA Astrophysics Data System (ADS)

    Mo, Yuxiang; Gao, Shuming; Dai, Zuyang; Li, Hua

    2013-06-01

    We report a combined experimental and theoretical study on the vibronic structure of CH_3F^+. The results show that the tunneling splittings of vibrational energy levels occur in CH_3F^+ due to the Jahn-Teller effect. Experimentally, we have measured a high resolution ZEKE spectrum of CH_3F up to 3500 cm^-^1 above the ground state. Theoretically, we performed an ab initio calculation based on the diabatic model. The adiabatic potential energy surfaces (APES) of CH_3F^+ have been calculated at the MRCI/CAS/avq(t)z level and expressed by Taylor expansions with normal coordinates as variables. The energy gradients for the lower and upper APES, the derivative couplings between them and also the energies of the APES have been used to determine the coefficients in the Taylor expansion. The spin-vibronic energy levels have been calculated by accounting all six vibrational modes and their couplings. The experimental ZEKE spectra were assigned based on the theoretical calculations. W. Domcke, D. R. Yarkony, and H. Köpple (Eds.), Conical Intersections: Eletronic Structure, Dynamics and Spectroscopy (World Scientific, Singapore, 2004). M. S. Schuurman, D. E. Weinberg, and D. R. Yarkony, J. Chem. Phys. 127, 104309 (2007).

  2. Nuclear Zero Point Effects as a Function of Density in Ice-like Structures and Liquid Water from vdW-DF Ab Initio Calculations

    NASA Astrophysics Data System (ADS)

    Pamuk, Betül; Allen, Philip B.; Soler, Jose M.; Fernández-Serra, Marivi

    2014-03-01

    The contributions of nuclear zero point vibrations to the structures of liquid water and ice are not negligible. Recently, we have explained the source of an anomalous isotope shift in hexagonal ice, representing itself as an increase in the lattice volume when H is replaced by D, by calculating free energy within the quasiharmonic approximation, with ab initio density functional theory. In this work, we extend our studies to analyze the zero point effect in other ice-like structures under different densities: clathrate hydrates, LDL and HDL-like amorphous ices with different densities, and a highly dense ice phase, ice VIII. We show that there is a transition from anomalous isotope effect to normal isotope effect as the density increases. We also analyze nuclear zero point effects in liquid water using different vdW-DFs and make connections to this anomalous-normal isotope effect transition in ice. This work is supported by DOE Early Career Award No. DE-SC0003871.

  3. Ab initio structural and spectroscopic study of HPS{sup x} and HSP{sup x} (x = 0,+1,−1) in the gas phase

    SciTech Connect

    Yaghlane, Saida Ben; Cotton, C. Eric; Francisco, Joseph S. E-mail: hochlaf@univ-mlv.fr; Linguerri, Roberto; Hochlaf, Majdi E-mail: hochlaf@univ-mlv.fr

    2013-11-07

    Accurate ab initio computations of structural and spectroscopic parameters for the HPS/HSP molecules and corresponding cations and anions have been performed. For the electronic structure computations, standard and explicitly correlated coupled cluster techniques in conjunction with large basis sets have been adopted. In particular, we present equilibrium geometries, rotational constants, harmonic vibrational frequencies, adiabatic ionization energies, electron affinities, and, for the neutral species, singlet-triplet relative energies. Besides, the full-dimensional potential energy surfaces (PESs) for HPS{sup x} and HSP{sup x} (x = −1,0,1) systems have been generated at the standard coupled cluster level with a basis set of augmented quintuple-zeta quality. By applying perturbation theory to the calculated PESs, an extended set of spectroscopic constants, including τ, first-order centrifugal distortion and anharmonic vibrational constants has been obtained. In addition, the potentials have been used in a variational approach to deduce the whole pattern of vibrational levels up to 4000 cm{sup −1} above the minima of the corresponding PESs.

  4. Structure of (SiO) sub 2 : A comparison between (AlF) sub 2 , (SiO) sub 2 , and (PN) sub 2. Matrix infrared investigation and ab initio calculation

    SciTech Connect

    Schnoeckel, H.; Mehner, T.; Plitt, H.S.; Schunck, S. )

    1989-06-21

    The structure of dimeric SiO is reexamined by a study of the IR spectra of the matrix-isolated species. Spectra of isotopomers from experiments with {sup 29}Si- and {sup 18}O-enriched samples are discussed with the help of normal-coordinate analysis. The results are in line with data of the geometrical and electronic structure obtained by ab initio SCF calculations. The dimerization energy calculated by quantum chemical methods agrees well with experimental data, which have been recalculated. With the help of additional ab initio calculations on the isoelectronic species PN and AlF, interesting correlations between their tendency toward dimerization can be obtained. Structural data of SiO are compared with the analogous ones of similar molecules (e.g., BF).

  5. Structure of the glass-forming metallic liquids by ab-initio and classical molecular dynamics, a case study: Quenching the Cu{sub 60}Ti{sub 20}Zr{sub 20} alloy

    SciTech Connect

    Amokrane, S.; Ayadim, A.; Levrel, L.

    2015-11-21

    We consider the question of the amorphization of metallic alloys by melt quenching, as predicted by molecular dynamics simulations with semi-empirical potentials. The parametrization of the potentials is discussed on the example of the ternary Cu-Ti-Zr transition metals alloy, using the ab-initio simulation as a reference. The pair structure in the amorphous state is computed from a potential of the Stillinger-Weber form. The transferability of the parameters during the quench is investigated using two parametrizations: from solid state data, as usual and from a new parametrization on the liquid structure. When the adjustment is made on the pair structure of the liquid, a satisfactory transferability is found between the pure components and their alloys. The liquid structure predicted in this way agrees well with experiment, in contrast with the one obtained using the adjustment on the solid. The final structure, after quenches down to the amorphous state, determined with the new set of parameters is shown to be very close to the ab-initio one, the latter being in excellent agreement with recent X-rays diffraction experiments. The corresponding critical temperature of the glass transition is estimated from the behavior of the heat capacity. Discussion on the consistency between the structures predicted using semi-empirical potentials and ab-initio simulation, and comparison of different experimental data underlines the question of the dependence of the final structure on the thermodynamic path followed to reach the amorphous state.

  6. Structural and magnetic properties of MnPd/Fe grown on MgO(100) substrate: Ab initio studies

    NASA Astrophysics Data System (ADS)

    Malonda-Boungou, B. R.; Magnoungou, J. H. J.; M'Passi-Mabiala, B.; Demangeat, C.

    2016-07-01

    Structural and magnetic properties of ultrathin films MnPd/Fe grown on MgO(001) are investigated using a self-consistent pseudopotential plane waves method based on density functional theory in the Perdew-Burke-Ernzerhof generalized gradient approximation. The results obtained reveal the presence of an antiferromagnetic coupling between successive Mn [100] rows, combined with a ripple where Mn outward atoms exhibit a positive magnetic moment, in the case of Mn overlayer on Fe/MgO(001). In the case of MnPd monolayer ordered alloy, the c(2 × 2) structure formation is more favorable than the p(1 × 2) one, exhibiting a ferromagnetic coupling between Mn neighbor atoms with a positive induced ferromagnetic moment on Pd atoms. Pd atoms are pushed outward. For 1-ML MnxPd1 - x on Fe/MgO, the Mn absolute mean magnetization per atom increases as x coverage increases, whereas the Pd mean induced magnetic moment decreases. For systems alternating Mn and Pd monolayers on Fe/MgO(001), a complex magnetic structure is shown on Mn monolayers: changing from Mn neighboring antiferromagnetic coupling to Mn [010] rows antiferromagnetic behavior. The correlation is made between the electronic structure and the magnetic properties, by comparing filled with partially filled components (Pd, Mn and Fe) d-bands. The magnetization easy-axis changes between the in-plane and the out-of-plane orientations from Fe/MgO to MnPd/Fe/MgO systems.

  7. Ab Initio Investigation of the Structure, Stability and Atmospheric Distribution of Molecular Clusters Containing H2O, CO2 and N2O.

    NASA Astrophysics Data System (ADS)

    Lemke, K. H.; Seward, T. M.

    2007-12-01

    We present results from ab initio calculations for the structures, energetics and atmospheric abundances of neutral clusters containing water, carbon dioxide and nitrous oxide up to 45km altitude using the complete basis set CBS-Q and G3 multi-level procedures. Gas phase hydration energies, enthalpies and entropies for the stepwise attachment of water onto clusters according to X(H2O)n + H2O = X(H2O)n+1 (where X = H2O, CO2 and N2O) are reported for up to n=5. In particular, our results demonstrate that values for the incremental hydration enthalpies and entropies of all three gases H2O, CO2 and N2O asymptotically approach values characteristic of bulk liquid water (i.e. -44.0 kJ/mol for the enthalpy and -118.8 J/Kmol for the entropy of condensation) following attachment of around 3-4 water molecules. Interestingly, our calculated number densities for the water dimer at 292Kelvin are in excellent agreement with recent values obtained from IR measurements of atmospheric media (Pfeilsticker et al., 2003, Science). Our quantum chemical calculations indicate that water attachment onto H2O, CO2 and N2O is a thermodynamically favorable process, such that hydrated clusters would form a significant atmospheric repository of these species.

  8. Molecular structure, vibrational spectra, NBO analysis and molecular packing prediction of 3-nitroacetanilide by ab initio HF and density functional theory.

    PubMed

    Li, Xiao-Hong; Li, Tong-Wei; Ju, Wei-Wei; Yong, Yong-Liang; Zhang, Xian-Zhou

    2014-01-24

    Quantum chemical calculations of geometries and vibrational wavenumbers of 3-nitroacetanilide (C8H8N2O3) in the ground state were carried out by using ab initio HF and density functional theory (DFT/B3LYP) methods with 6-31+G(*) basis set. The -311++G(**) basis set is also used for B3LYP level. The scaled harmonic vibrational frequencies have been compared with experimental FT-IR spectra. Theoretical vibrational spectra of the title compound were interpreted by means of potential energies distributions (PEDs) using MOLVIB program. The theoretical spectrograms for IR spectra of the title compound have been constructed. The shortening of C-H bond length and the elongation of N-H bond length suggest the existence of weak C-H⋯O and N-H⋯O hydrogen bonds, which is confirmed by the natural bond orbital analysis. In addition, the crystal structure obtained by molecular mechanics belongs to the P2(1) space group, with lattice parameters Z=4, a=14.9989 Å, b=4.0367 Å, c=12.9913 Å, ρ=0.998 g cm(-3).

  9. Structure, electronic density of states and electric field gradients of icosahedral AlCuFe: An ab initio study of the original and a modified Cockayne model

    NASA Astrophysics Data System (ADS)

    Zijlstra, E. S.; Kortus, J.; Krajčí, M.; Stadnik, Z. M.; Bose, S. K.

    2004-03-01

    We present a detailed analysis of electronic properties of the Cockayne model of icosahedral AlCuFe, both in its original form and after a structural relaxation using the ab initio density functional approach. The electronic density of states (DOS) and electric field gradients (EFG’s) of the Al and Fe atoms in the original and the relaxed Cockayne models were calculated and compared with available photoemission, Mössbauer, and nuclear quadrupole resonance spectroscopy data. The relaxed and the original models show significantly different electronic properties. Both models are deficient in describing the available experimental data. The DOS’s show two Fe-d peaks, where there is only one such peak in the photoemission spectroscopy data. These models also cannot account for the shape of the Mössbauer spectra. We show that the interchange between 12 Cu and 12 Fe atoms, each belonging to a single symmetry class, results in a smaller number of Cu-Fe nearest-neighbor pairs and a lowering of the total energy by an amount of ΔE˜50 meV/atom. This “modified” version of the Cockayne model was further relaxed for the final comparison between the calculation and experimental results. The modified model shows a considerable improvement: The DOS has only one Fe-d peak, in agreement with photoemission spectroscopy data, and the calculated EFG’s account very well for the experimental Mössbauer spectra.

  10. HfO_2and ZrO2 : Comparison of Structures and Thermodynamic and Electronic Properties Based on Ab Initio Calculations and Experiment

    NASA Astrophysics Data System (ADS)

    Demkov, Alexander A.; Navrotsky, Alexandra

    2001-03-01

    The International Technology Roadmap for Semiconductors (ITRS) predicts that the strategy of scaling complementary metal-oxide-semiconductor (CMOS) devices will come to an abrupt end around the year 2012. The main reason for this will be the unacceptably high leakage current through the silicon dioxide gate with a thickness below 20 ÅFinding a gate insulator alternative to SiO2 has proven to be far from trivial. Hafnium and zirconium dioxides and silicates have been recently considered as gate dielectrics with intermediate dielectric constants. Hafnia and ziconia are important ceramic materials as well, and their phase relations are rather well studied. There is also interest in hafnia as a constituent of ceramic waste forms for plutonium, based on its refractory nature and high neutron absorption cross section. We use a combination of the ab-initio calculations and calorimetry to investigate thermodynamic and electronic properties of hafnia and zirconia. We describe the cubic to tetragonal phase transition in the fluorite structure by computing the total energy surface for zone-edge distortions correct to fourth order in the soft-mode displacement with the strain coupling renormalization included. We compare the two materials using some simple chemical concepts.

  11. 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.

  12. Ab initio calculations of structural, electronic, optical and thermodynamic properties of alkaline earth tellurides BaxSr1-XTe

    NASA Astrophysics Data System (ADS)

    Bahloul, B.; Bentabet, A.; Amirouche, L.; Bouhadda, Y.; Bounab, S.; Deghfel, B.; Fenineche, N.

    2014-03-01

    Structural, electronic and thermodynamic properties of SrTe and BaTe compounds and their ternary mixed crystals BaxSr1-xTe in the rock-salt structure have been studied with density functional theory (DFT), whereas the optical properties have been obtained by using empirical methods such as the modified Moss relation. The exchange-correlation potential was calculated using the generalized gradient approximation (GGA) of Perdew-Burke-Ernzerhof (PBE) and the local density approximation (LDA) of Teter-Pade (TP). In the present work, we used the virtual-crystal approximation (VCA) to study the effect of composition (x). The calculated lattice parameters at equilibrium volume and the bulk modulus for x=0 and x=1 are in good agreement with the literature data. Furthermore, the BaxSr1-xTe alloys are found to be an indirect band gap semiconductor. In addition, we have also predicted the heat capacities (CV), the entropy(S), the internal energy (U) and the Helmholtz free energy (F) of the parent compounds SrTe and BaTe.

  13. Ab initio study of structural, mechanical, thermal and electronic properties of perovskites Sr(Li,Pd)H3

    NASA Astrophysics Data System (ADS)

    Benlamari, S.; Amara Korba, S.; Lakel, S.; Meradji, H.; Ghemid, S.; El Haj Hassan, F.

    2016-01-01

    The structural, elastic, thermal and electronic properties of perovskite hydrides SrLiH3 and SrPdH3 have been investigated using the all-electron full-potential linear augmented plane wave (FP-LAPW) method based on the density functional theory (DFT). For the exchange-correlation potential, local-density approximation (LDA) and generalized gradient approximation (GGA) have been used to calculate theoretical lattice parameters, bulk modulus, and its pressure derivative. The present results are in good agreement with available theoretical and experimental data. The three independent elastic constants (C11, C12 and C44) are also reported. From electronic band structure and density of states (DOSs), it is found that SrLiH3 is an insulator characterized by an indirect gap of 3.48 eV, while SrPdH3 is metallic with a calculated DOSs at Fermi energy of 0.745 states/eV-unit cell. Poisson’s ratio (σ), Young’s modulus (E), shear modulus (G), anisotropy factor (A), average sound velocities (vm) and density (ρ) of these compounds are also estimated for the first time. The Debye temperature is deduced from the average sound velocity. Variation of elastic constants and bulk modulus of these compounds as a function of pressure is also reported. Pressure and thermal effects on some macroscopic properties are predicted using the quasi-harmonic Debye model.

  14. Computation and interpretation of vibrational spectra on the structure of Losartan using ab initio and Density Functional methods.

    PubMed

    Latha, B; Gunasekaran, S; Srinivasan, S; Ramkumaar, G R

    2014-11-11

    The solid phase FTIR and FT-Raman spectra of Losartan have been recorded in the region 400-4000 cm(-1). The spectra were interpreted in terms of fundamental modes, combination and overtone bands. The structure of the molecule was optimized and the structural characteristics were determined by Quantum chemical methods. The vibrational frequencies yield good agreement between observed and calculated values. The infrared and Raman spectra were also predicted from the calculated intensities. 1H and 13C NMR spectra were recorded and resonance chemical shifts of the molecule were calculated. UV-Visible spectrum of the compound was recorded in the region 200-600 nm and the electronic properties HOMO and LUMO energies calculated by TD-HF approach. NBO atomic charges of the molecules and second order perturbation theory analysis of Fock matrix also calculated and interpreted. The geometrical parameters, energies, harmonic vibrational frequencies, IR intensities, Raman intensities, and absorption wavelengths were compared with experimental and theoretical data of the molecule.

  15. Computation and interpretation of vibrational spectra on the structure of Losartan using ab initio and Density Functional methods

    NASA Astrophysics Data System (ADS)

    Latha, B.; Gunasekaran, S.; Srinivasan, S.; Ramkumaar, G. R.

    2014-11-01

    The solid phase FTIR and FT-Raman spectra of Losartan have been recorded in the region 400-4000 cm-1. The spectra were interpreted in terms of fundamental modes, combination and overtone bands. The structure of the molecule was optimized and the structural characteristics were determined by Quantum chemical methods. The vibrational frequencies yield good agreement between observed and calculated values. The infrared and Raman spectra were also predicted from the calculated intensities. (1)H and (13)C NMR spectra were recorded and resonance chemical shifts of the molecule were calculated. UV-Visible spectrum of the compound was recorded in the region 200-600 nm and the electronic properties HOMO and LUMO energies calculated by TD-HF approach. NBO atomic charges of the molecules and second order perturbation theory analysis of Fock matrix also calculated and interpreted. The geometrical parameters, energies, harmonic vibrational frequencies, IR intensities, Raman intensities, and absorption wavelengths were compared with experimental and theoretical data of the molecule.

  16. The structure and binding energies of the van der Waals complexes of Ar and N2 with phenol and its cation, studied by high level ab initio and density functional theory calculations

    NASA Astrophysics Data System (ADS)

    Vincent, Mark A.; Hillier, Ian H.; Morgado, Claudio A.; Burton, Neil A.; Shan, Xiao

    2008-01-01

    We have investigated, using both ab initio and density functional theory methods, the minimum energy structures and corresponding binding energies of the van der Waals complexes between phenol and argon or the nitrogen molecule, and the corresponding complexes involving the phenol cation. Structures were obtained at the MP2 level using a large basis, and the corresponding energies were corrected for basis set superposition error (BSSE), higher order electron correlation effects, and for basis set size. The structures of the global minima were further refined for the effects of BSSE and the corresponding binding energies were evaluated. For each neutral species, we find only a single true minimum, π bonded for argon and OH bonded for nitrogen. For both cationic species, we find that the OH-bonded complex is preferred over other minima which we have identified as having Ar or N2 between exogeneous atoms. The ab initio calculations are generally in excellent agreement with experimental binding energies and rotational constants. We find that the B3LYP functional is particularly poor at describing these complexes, while a density functional theory (DFT) method with an empirical correction for dispersive interactions (DFT-D) is very successful, as are some of the new functionals proposed by Zhao and Truhlar [J. Phys. Chem. A 109, 5656 (2005); J. Chem. Theory Comput. 2, 1009 (2006); Phys. Chem. Chem. Phys. 7, 2701 (2005); J. Phys. Chem. A 108, 6908 (2004)]. Both the ab initio and DFT-D methods accurately predict the intermolecular vibrational modes.

  17. The structure and binding energies of the van der Waals complexes of Ar and N2 with phenol and its cation, studied by high level ab initio and density functional theory calculations.

    PubMed

    Vincent, Mark A; Hillier, Ian H; Morgado, Claudio A; Burton, Neil A; Shan, Xiao

    2008-01-28

    We have investigated, using both ab initio and density functional theory methods, the minimum energy structures and corresponding binding energies of the van der Waals complexes between phenol and argon or the nitrogen molecule, and the corresponding complexes involving the phenol cation. Structures were obtained at the MP2 level using a large basis, and the corresponding energies were corrected for basis set superposition error (BSSE), higher order electron correlation effects, and for basis set size. The structures of the global minima were further refined for the effects of BSSE and the corresponding binding energies were evaluated. For each neutral species, we find only a single true minimum, pi bonded for argon and OH bonded for nitrogen. For both cationic species, we find that the OH-bonded complex is preferred over other minima which we have identified as having Ar or N(2) between exogeneous atoms. The ab initio calculations are generally in excellent agreement with experimental binding energies and rotational constants. We find that the B3LYP functional is particularly poor at describing these complexes, while a density functional theory (DFT) method with an empirical correction for dispersive interactions (DFT-D) is very successful, as are some of the new functionals proposed by Zhao and Truhlar [J. Phys. Chem. A 109, 5656 (2005); J. Chem. Theory Comput. 2, 1009 (2006); Phys. Chem. Chem. Phys. 7, 2701 (2005); J. Phys. Chem. A 108, 6908 (2004)]. Both the ab initio and DFT-D methods accurately predict the intermolecular vibrational modes.

  18. Electronic structure and mechanical properties of ternary ZrTaN alloys studied by ab initio calculations and thin-film growth experiments

    NASA Astrophysics Data System (ADS)

    Abadias, G.; Kanoun, M. B.; Goumri-Said, S.; Koutsokeras, L.; Dub, S. N.; Djemia, Ph.

    2014-10-01

    The structure, phase stability, and mechanical properties of ternary alloys of the Zr-Ta-N system are investigated by combining thin-film growth and ab initio calculations. Zr1-xTaxN films with 0≤x≤1 were deposited by reactive magnetron cosputtering in Ar +N2 plasma discharge and their structural properties characterized by x-ray diffraction. We considered both ordered and disordered alloys, using supercells and special quasirandom structure approaches, to account for different possible metal atom distributions on the cation sublattice. Density functional theory within the generalized gradient approximation was employed to calculate the electronic structure as well as predict the evolution of the lattice parameter and key mechanical properties, including single-crystal elastic constants and polycrystalline elastic moduli, of ternary Zr1-xTaxN compounds with cubic rocksalt structure. These calculated values are compared with experimental data from thin-film measurements using Brillouin light scattering and nanoindentation tests. We also study the validity of Vegard's empirical rule and the effect of growth-dependent stresses on the lattice parameter. The thermal stability of these Zr1-xTaxN films is also studied, based on their structural and mechanical response upon vacuum annealing at 850 °C for 3 h. Our findings demonstrate that Zr1-xTaxN alloys with Ta fraction 0.51⩽x⩽0.78 exhibit enhanced toughness, while retaining high hardness ˜30 GPa, as a result of increased valence electron concentration and phase stability tuning. Calculations performed for disordered or ordered structures both lead to the same conclusion regarding the mechanical behavior of these nitride alloys, in agreement with recent literature findings [H. Kindlund, D. G. Sangiovanni, L. Martinez-de-Olcoz, J. Lu, J. Jensen, J. Birch, I. Petrov, J. E. Greene, V. Chirita, and L. Hultman, APL Materials 1, 042104 (2013), 10.1063/1.4822440].

  19. A photoelectron spectroscopy and ab initio study of the structures and chemical bonding of the B{sub 25}{sup −} cluster

    SciTech Connect

    Piazza, Zachary A.; Li, Wei-Li; Wang, Lai-Sheng E-mail: lai-sheng-wang@brown.edu; Popov, Ivan A.; Boldyrev, Alexander I. E-mail: lai-sheng-wang@brown.edu; Pal, Rhitankar; Cheng Zeng, Xiao

    2014-07-21

    Photoelectron spectroscopy and ab initio calculations are used to investigate the structures and chemical bonding of the B{sub 25}{sup −} cluster. Global minimum searches reveal a dense potential energy landscape with 13 quasi-planar structures within 10 kcal/mol at the CCSD(T)/6-311+G(d) level of theory. Three quasi-planar isomers (I, II, and III) are lowest in energy and nearly degenerate at the CCSD(T) level of theory, with II and III being 0.8 and 0.9 kcal/mol higher, respectively, whereas at two density functional levels of theory isomer III is the lowest in energy (8.4 kcal/mol more stable than I at PBE0/6-311+G(2df) level). Comparison with experimental photoelectron spectroscopic data shows isomer II to be the major contributor while isomers I and III cannot be ruled out as minor contributors to the observed spectrum. Theoretical analyses reveal similar chemical bonding in I and II, both involving peripheral 2c-2e B−B σ-bonding and delocalized interior σ- and π-bonding. Isomer III has an interesting elongated ribbon-like structure with a π-bonding pattern analogous to those of dibenzopentalene. The high density of low-lying isomers indicates the complexity of the medium-sized boron clusters; the method dependency of predicting relative energies of the low-lying structures for B{sub 25}{sup −} suggests the importance of comparison with experiment in determining the global minima of boron clusters at this size range. The appearance of many low-lying quasi-planar structures containing a hexagonal hole in B{sub 25}{sup −} suggests the importance of this structural feature in maintaining planarity of larger boron clusters.

  20. Structure determination of propanal by joint analysis of gas electron diffraction, microwave and infrared spectroscopy, including constraints and a valence force field from geometry relaxed ab-initio calculations

    NASA Astrophysics Data System (ADS)

    Van Nuffel, P.; Van Den Enden, L.; Van Alsenoy, C.; Geise, H. J.

    1984-04-01

    The structure and conformational equilibrium of CH 3-SYN and CH 3-SKEW conformers of propanal were studied by joint analysis of gas electron diffraction, microwave and infrared data, including constraints obtained after ab-initio relaxations (4-21G basis set) of the molecule. A valence force field was calculated for both conformers and scaled upon experimental IR frequencies; theoretical frequencies and band intensities are compared to experimental ones. Rotamer populations of CH 3-SYN and CH 3-SKEW were found to be 81 and 19%, respectively, at 300 K. The following best-fitting rg/ rα parameters were obtained as: r(OC) = 1.209(4) Å, r(C2C3) = 1.515(9) Å, r(C3C4) = 1.521(9) Å for CH 3-SYN and (with lower reliability) 1.569(45) Å for CH 3-SKEW, = 1.127(4) Å, ∠O=CC = 124.5(3)°(SYN) and 125.1(3)° (SKEW), ∠CCC = 113.8(4)° (SYN) and 110.2(4)° (SKEW), torsion angle around C2C3 = 123.7(2.6)° for CH 3-SKEW.

  1. Ab initio cluster calculations on the electronic structure of oxygen vacancies at the polar ZnO(0001) surface and on the adsorption of H2, CO, and CO2 at these sites.

    PubMed

    Fink, Karin

    2006-04-01

    Oxygen vacancies at the polar O terminated (0001) surface of ZnO are of particular interest, because they are discussed as active sites in the methanol synthesis. In general, the polar ZnO surfaces are stabilized by OH groups, therefore O vacancies can be generated by removing either O atoms or OH or H2O groups from the surface. These defects differ in the number of electrons in the vacancy and the number of OH groups in the neighborhood. In the present study, the electronic structure and the adsorption properties of four different types of oxygen vacancies have been investigated by means of embedded cluster calculations. We performed ab initio calculations on F+ like surface excitations for the different defect types and found that the transition energies are above the optical band-gap, while F+ centers in bulk ZnO show a characteristic optical excitation at 3.19 eV. Furthermore, we studied the adsorption of CO2 and CO at the different defect sites by DFT calculations. We found that CO2 dissociates at electron rich vacancies into CO and an O atom which remains in the vacancy. At the OH vacancy which contains an unpaired electron CO2 adsorbed in the form of CO2-, while it adsorbed as a linear neutral molecule at the H2O defect. CO adsorbed preferentially at the H2O defect and the OH defect, both with a binding energy of 0.3 eV. PMID:16633631

  2. Conformational stability from variable temperature infrared spectra of krypton solutions, ab initio calculations, vibrational assignment, and r0 structural parameters of 1,3-difluoropropane.

    PubMed

    Durig, James R; Zheng, Chao; Williams, Michael J; Stidham, Howard D; Guirgis, Gamil A

    2004-06-01

    well as for the Cs conformers than the MP2 values. A complete vibrational assignment is proposed for the C2 conformer and many of the fundamentals have been identified for the C1 form based on the force constants, relative intensities and rotational-vibrational band contours obtained from the predicted equilibrium geometry parameters. By combining previously reported rotational constants for the C2 and C1 conformers with ab initio MP2/6-311 + G(d, p) predicted parameters, adjusted r0 parameters have been obtained for both conformers. Comparisons are made with the parameters obtained for some other molecules containing the FCH2 group. The spectroscopic and theoretical results are compared to the corresponding properties for some similar molecules.

  3. Ab initio studies of structural, electronic, optical, elastic and thermal properties of silver gallium dichalcogenides (AgGaX{sub 2}: X = S, Se, Te)

    SciTech Connect

    Sharma, Sheetal; Verma, A.S.; Jindal, V.K.

    2014-05-01

    Graphical abstract: - Highlights: • FP-LAPW method has been used to compute the solid state properties of AgGaX{sub 2} (X = S, Se, Te). • Electronic and optical properties reported with recently developed mBJ potential. • Thermal expansion, heat capacity, Debye temperature, entropy and Grüneisen parameter were evaluated. • Hardness was calculated for the first time at different temperature and pressure. - Abstract: We have performed ab initio calculations for the structural, electronic, optical, elastic and thermal properties of the silver gallium dichalcogenides (AgGaX{sub 2}: X = S, Se, Te). In this study, we have used the accurate full potential linearized augmented plane wave (FP-LAPW) method to find the equilibrium structural parameters and to compute the six elastic constants (C{sub 11}, C{sub 12}, C{sub 13}, C{sub 33}, C{sub 44} and C{sub 66}). We have reported electronic and optical properties with the recently developed density functional theory of Tran and Blaha, and this theory is used along with the Wu-Cohen generalized gradient approximation (WC-GGA) for the exchange-correlation potential. Furthermore, optical features such as dielectric functions, refractive indices, extinction coefficient, optical reflectivity, absorption coefficients and optical conductivities were calculated for photon energies up to 40 eV. The thermodynamical properties such as thermal expansion, heat capacity, debye temperature, entropy, Grüneisen parameter and bulk modulus were calculated employing the quasi-harmonic Debye model at different temperatures (0–900 K) and pressures (0–8 GPa) and the silent results were interpreted. Hardness of the materials was calculated for the first time at different temperatures and pressures.

  4. Hydrogen bonded structure, polarity, molecular motion and frequency fluctuations at liquid-vapor interface of a water-methanol mixture: an ab initio molecular dynamics study.

    PubMed

    Choudhuri, Jyoti Roy; Chandra, Amalendu

    2014-10-01

    We have performed ab initio molecular dynamics simulations of a liquid-vapor interfacial system consisting of a mixture of water and methanol molecules. Detailed results are obtained for the structural and dynamical properties of the bulk and interfacial regions of the mixture. Among structural properties, we have looked at the inhomogeneous density profiles of water and methanol molecules, hydrogen bond distributions and also the orientational profiles of bulk and interfacial molecules. The methanol molecules are found to have a higher propensity to be at the interface than water molecules. It is found that the interfacial molecules show preference for specific orientations so as to form water-methanol hydrogen bonds at the interface with the hydrophobic methyl group pointing towards the vapor side. It is also found that for both types of molecules, the dipole moment decreases at the interface. It is also found that the local electric field of water influences the dipole moment of methanol molecules. Among the dynamical properties, we have calculated the diffusion, orientational relaxation, hydrogen bond dynamics, and vibrational frequency fluctuations in bulk and interfacial regions. It is found that the diffusion and orientation relaxation of the interfacial molecules are faster than those of the bulk. However, the hydrogen bond lifetimes are longer at the interface which can be correlated with the time scales found from the decay of frequency time correlations. The slower hydrogen bond dynamics for the interfacial molecules with respect to bulk can be attributed to diminished cooperative effects at the interface due to reduced density and number of hydrogen bonds.

  5. Structure and Hydrolysis of the U(IV), U(V), and U(VI) Aqua Ions from Ab Initio Molecular Simulations

    SciTech Connect

    Atta-Fynn, Raymond; Johnson, Donald F.; Bylaska, Eric J.; Ilton, Eugene S.; Schenter, Gregory K.; De Jong, Wibe A.

    2012-03-05

    Ab initio molecular dynamics simulations at 300 K based on density functional theory have been used to study the hydration shell geometries, solvent dipole, and first hydrolysis of the Uranium(IV) (U{sup 4+}) and Uranyl(V) (UO{sub 2}{sup +}) ions in aqueous solution. The solvent dipole and first of hydrolysis of aqueous Uranium(VI) (UO{sub 2}{sup 2+}) has also been probed. The first shell of U{sup 4+} is coordinated by 8-9 water ligands with an average U-O distance of 2.42 {angstrom}. The average first shell coordination number and distance are in agreement with experimental estimates of 8-11 and 2.40-2.44 {angstrom} respectively. The simulated EXAFS spectra of U{sup 4+} matched well with recent experimental data. The first shell of UO{sub 2}{sup +} is coordinated by 5 water ligands in the equatorial plane, with the average U=O{sub ax} and U-O distances being 1.85 {angstrom} and 2.54 {angstrom} respectively. Overall, the hydration shell structure of UO{sub 2}{sup +} matches closely with that of UO{sub 2}{sup 2+} except for small expansions in the average U=O{sub ax} and U-O distances. Each ion strongly polarizes their respective first shell water ligands. The computed acidity constant (pK{sub a}) of U{sup 4+} and UO{sub 2}{sup 2+} are 0.93 and 4.95, in good agreement with the experimental values of 0.54 and 5.24 respectively. The predicted pK{sub a} of UO{sub 2}{sup +} is 8.5.

  6. Electronic structure investigations of 4-aminophthal hydrazide by UV-visible, NMR spectral studies and HOMO-LUMO analysis by ab initio and DFT calculations.

    PubMed

    Sambathkumar, K; Jeyavijayan, S; Arivazhagan, M

    2015-08-01

    Combined experimental and theoretical studies were conducted on the molecular structure and vibrational spectra of 4-AminoPhthalhydrazide (APH). The FT-IR and FT-Raman spectra of APH were recorded in the solid phase. The molecular geometry and vibrational frequencies of APH in the ground state have been calculated by using the ab initio HF (Hartree-Fock) and density functional methods (B3LYP) invoking 6-311+G(d,p) basis set. The optimized geometric bond lengths and bond angles obtained by HF and B3LYP method show best agreement with the experimental values. Comparison of the observed fundamental vibrational frequencies of APH with calculated results by HF and density functional methods indicates that B3LYP is superior to the scaled Hartree-Fock approach for molecular vibrational problems. The difference between the observed and scaled wave number values of most of the fundamentals is very small. A detailed interpretation of the NMR spectra of APH was also reported. The theoretical spectrograms for infrared and Raman spectra of the title molecule have been constructed. UV-vis spectrum of the compound was recorded and the electronic properties, such as HOMO and LUMO energies, were performed by time dependent density functional theory (TD-DFT) approach. Finally the calculations results were applied to simulated infrared and Raman spectra of the title compound which show good agreement with observed spectra. And the temperature dependence of the thermodynamic properties of constant pressure (Cp), entropy (S) and enthalpy change (ΔH0→T) for APH were also determined. PMID:25829160

  7. Interactions of Metal Ions with Water: Ab Initio Molecular Orbital Studies of Structure, Bonding Enthalpies, Vibrational Frequencies and Charge Distributions. 1. Monohydrates.

    PubMed

    Trachtman, Mendel; Markham, George D.; Glusker, Jenny P.; George, Philip; Bock, Charles W.

    1998-08-24

    The formation and properties of a wide range of metal ion monohydrates, M(n)()(+)-OH(2), where n = 1 and 2, have been studied by ab initio molecular orbital calculations at the MP2(FULL)/6-311++G//MP2(FULL)/6-311++G and CCSD(T)(FULL)/6-311++G//MP2(FULL)/6-311++G computational levels. The ions M are from groups 1A, 2A, 3A, and 4A in the second, third, and fourth periods of the periodic table and the first transition series. Structural parameters, vibrational frequencies, bonding enthalpies, orbital occupancies and energies, and atomic charge distributions are reported. Trends in these properties are correlated with the progressive occupancy of the s, p, and d orbitals. Except for K(+)-OH(2) and Ca(2+)-OH(2), the O-H bond lengths and HOH angles are greater in the hydrates than in unbound water. The M-O bond lengths decrease proceeding from group 1A --> 4A but become larger in proceeding from the second --> fourth period. The bonding enthalpies, are found to be inversely linearly dependent on the M-O bond length M(n)()(+) according to equations of the form = A + B(1/M-O) for n = 1 and n = 2. Within each monohydrate the distribution of atomic charge reveals a small but definite transfer of charge from water to the metal ion. Compared to unbound water there is, in a metal-ion-bound water complex, an increase in the electronic (negative) charge on the oxygen atom, accompanied by a (significantly) larger decrease in the electronic charge on the hydrogen atoms. The bonding of the water molecule, although electrostatic in origin, is thus more complex than a simple interaction between a point charge on the metal ion, and the water dipole.

  8. Ab initio study of the influence of structural parameters on the potential energy surfaces of spin-crossover Fe(II) model compounds

    NASA Astrophysics Data System (ADS)

    Boilleau, Corentin; Suaud, Nicolas; Guihéry, Nathalie

    2012-12-01

    In spin-crossover (SCO) compounds exhibiting a light induced excited spin state trapping (LIESST) effect, the thermodynamic T1/2 and kinetic T(LIESST) temperature values depend on the features of the potential energy surfaces (PES) of the two lowest singlet and quintet states but also on vibrational contributions, collective effects, such as electrostatics, for instance, spin-orbit couplings to a lesser extent, etc. In this work, the question of the link between the shape of the PES of SCO compounds exhibiting a LIESST effect and their first coordination sphere structure is addressed from wave function theory based ab initio calculations. Fe(II) complexes based on model ligands suited to reproduce the main characteristics of the PES of such compounds are distorted to emphasize selectively the role played by the metal-ligand distances and the ligand-metal-ligand angles. The studied angular deformations are those usually observed in many Fe(L)2(NCS)2 complexes. It is shown that the larger the deformation between the low spin and high spin equilibrium geometries, the higher the energy barrier from the high spin state and the weaker the energy difference between the bottom of the wells. These results corroborate observations made by experimentalists on a large number of complexes. While the PES features only constitutes one of the contributions to these temperatures, it is worth noticing that, relating T1/2 to the energy difference between the bottoms of the singlet and quintet wells and the T(LIESST) to the energy barrier from the quintet bottom well, the same slope of the empirical law T(LIESST) = -0.3T1/2+T0 is observed.

  9. Structural evolution and electronic properties of medium-sized gallium clusters from ab initio genetic algorithm search.

    PubMed

    Sai, Linwei; Zhao, Jijun; Huang, Xiaoming; Wang, Jun

    2012-01-01

    Using genetic algorithm incorporated with density functional theory, we have explored the size evolution of structural and electronic properties of neutral gallium clusters of 20-40 atoms in terms of their ground state structures, binding energies, second differences of energy, HOMO-LUMO gaps, distributions of bond length and bond angle, and electron density of states. In the size range studied, the Ga(n) clusters exhibit several growth patterns, and the core-shell structures become dominant from Ga31. With high point group symmetries, Ga23 and Ga36 show particularly high stability and Ga36 owns a large HOMO-LUMO gap. The atomic structures and electronic states of Ga(n) clusters significantly differ from the a solid but resemble beta solid and liquid to certain extent.

  10. Ab initio investigation of competing antiferromagnetic structures in low Si-content FeMn(PSi) alloy.

    PubMed

    Li, Guijiang; Eriksson, Olle; Johansson, Börje; Vitos, Levente

    2016-06-01

    The antiferromagnetic structures of a low Si-content FeMn(PSi) alloy were investigated by first principles calculations. One possible antiferromagnetic structure in supercell along the c-axis was revealed in FeMnP0.75Si0.25 alloy. It was found that atomic disorder occupation between Fe atom on 3f and Mn atoms on 3g sites is responsible for the formation of antiferromagnetic structures. Furthermore the magnetic competition and the coupling between possible AFM supercells along the c and a-axis can promote a non-collinear antiferromagnetic structure. These theoretical investigations help to deeply understand the magnetic order in FeMn(PSi) alloys and benefit to explore the potential magnetocaloric materials in Fe2P-type alloys.

  11. Dimeric structure of the N-terminal domain of PriB protein from Thermoanaerobacter tengcongensis solved ab initio.

    PubMed

    Liebschner, Dorothee; Brzezinski, Krzysztof; Dauter, Miroslawa; Dauter, Zbigniew; Nowak, Marta; Kur, Józef; Olszewski, Marcin

    2012-12-01

    PriB is one of the components of the bacterial primosome, which catalyzes the reactivation of stalled replication forks at sites of DNA damage. The N-terminal domain of the PriB protein from the thermophilic bacterium Thermoanaerobacter tengcongensis (TtePriB) was expressed and its crystal structure was solved at the atomic resolution of 1.09 Å by direct methods. The protein chain, which encompasses the first 104 residues of the full 220-residue protein, adopts the characteristic oligonucleotide/oligosaccharide-binding (OB) structure consisting of a five-stranded β-barrel filled with hydrophobic residues and equipped with four loops extending from the barrel. In the crystal two protomers dimerize, forming a six-stranded antiparallel β-sheet. The structure of the N-terminal OB domain of T. tengcongensis shows significant differences compared with mesophile PriBs. While in all other known structures of PriB a dimer is formed by two identical OB domains in separate chains, TtePriB contains two consecutive OB domains in one chain. However, sequence comparison of both the N-terminal and the C-terminal domains of TtePriB suggests that they have analogous structures and that the natural protein possesses a structure similar to a dimer of two N-terminal domains.

  12. Dimeric structure of the N-terminal domain of PriB protein from Thermoanaerobacter tengcongensis solved ab initio

    PubMed Central

    Liebschner, Dorothee; Brzezinski, Krzysztof; Dauter, Miroslawa; Dauter, Zbigniew; Nowak, Marta; Kur, Józef; Olszewski, Marcin

    2012-01-01

    PriB is one of the components of the bacterial primosome, which catalyzes the reactivation of stalled replication forks at sites of DNA damage. The N-terminal domain of the PriB protein from the thermophilic bacterium Thermoanaerobacter tengcongensis (TtePriB) was expressed and its crystal structure was solved at the atomic resolution of 1.09 Å by direct methods. The protein chain, which encompasses the first 104 residues of the full 220-residue protein, adopts the characteristic oligonucleotide/oligosaccharide-binding (OB) structure consisting of a five-stranded β-barrel filled with hydrophobic residues and equipped with four loops extending from the barrel. In the crystal two protomers dimerize, forming a six-stranded antiparallel β-sheet. The structure of the N-terminal OB domain of T. tengcongensis shows significant differences compared with mesophile PriBs. While in all other known structures of PriB a dimer is formed by two identical OB domains in separate chains, TtePriB contains two consecutive OB domains in one chain. However, sequence comparison of both the N-terminal and the C-terminal domains of TtePriB suggests that they have analogous structures and that the natural protein possesses a structure similar to a dimer of two N-terminal domains. PMID:23151633

  13. Electronic and thermoelectric properties of InN studied using ab initio density functional theory and Boltzmann transport calculations

    NASA Astrophysics Data System (ADS)

    Borges, P. D.; Scolfaro, L.

    2014-12-01

    The thermoelectric properties of indium nitride in the most stable wurtzite phase (w-InN) as a function of electron and hole concentrations and temperature were studied by solving the semiclassical Boltzmann transport equations in conjunction with ab initio electronic structure calculations, within Density Functional Theory. Based on maximally localized Wannier function basis set and the ab initio band energies, results for the Seebeck coefficient are presented and compared with available experimental data for n-type as well as p-type systems. Also, theoretical results for electric conductivity and power factor are presented. Most cases showed good agreement between the calculated properties and experimental data for w-InN unintentionally and p-type doped with magnesium. Our predictions for temperature and concentration dependences of electrical conductivity and power factor revealed a promising use of InN for intermediate and high temperature thermoelectric applications. The rigid band approach and constant scattering time approximation were utilized in the calculations.

  14. Electronic and thermoelectric properties of InN studied using ab initio density functional theory and Boltzmann transport calculations

    SciTech Connect

    Borges, P. D. E-mail: lscolfaro@txstate.edu; Scolfaro, L. E-mail: lscolfaro@txstate.edu

    2014-12-14

    The thermoelectric properties of indium nitride in the most stable wurtzite phase (w-InN) as a function of electron and hole concentrations and temperature were studied by solving the semiclassical Boltzmann transport equations in conjunction with ab initio electronic structure calculations, within Density Functional Theory. Based on maximally localized Wannier function basis set and the ab initio band energies, results for the Seebeck coefficient are presented and compared with available experimental data for n-type as well as p-type systems. Also, theoretical results for electric conductivity and power factor are presented. Most cases showed good agreement between the calculated properties and experimental data for w-InN unintentionally and p-type doped with magnesium. Our predictions for temperature and concentration dependences of electrical conductivity and power factor revealed a promising use of InN for intermediate and high temperature thermoelectric applications. The rigid band approach and constant scattering time approximation were utilized in the calculations.

  15. Dimeric structure of the N-terminal domain of PriB protein from Thermoanaerobacter tengcongensis solved ab initio

    SciTech Connect

    Liebschner, Dorothee; Brzezinski, Krzysztof; Dauter, Miroslawa; Dauter, Zbigniew; Nowak, Marta; Kur, Józef; Olszewski, Marcin

    2012-12-01

    The N-terminal domain of the PriB protein from the thermophilic bacterium T. tengcongensis (TtePriB) was expressed and its crystal structure has been solved at the atomic resolution of 1.09 Å by direct methods. PriB is one of the components of the bacterial primosome, which catalyzes the reactivation of stalled replication forks at sites of DNA damage. The N-terminal domain of the PriB protein from the thermophilic bacterium Thermoanaerobacter tengcongensis (TtePriB) was expressed and its crystal structure was solved at the atomic resolution of 1.09 Å by direct methods. The protein chain, which encompasses the first 104 residues of the full 220-residue protein, adopts the characteristic oligonucleotide/oligosaccharide-binding (OB) structure consisting of a five-stranded β-barrel filled with hydrophobic residues and equipped with four loops extending from the barrel. In the crystal two protomers dimerize, forming a six-stranded antiparallel β-sheet. The structure of the N-terminal OB domain of T. tengcongensis shows significant differences compared with mesophile PriBs. While in all other known structures of PriB a dimer is formed by two identical OB domains in separate chains, TtePriB contains two consecutive OB domains in one chain. However, sequence comparison of both the N-terminal and the C-terminal domains of TtePriB suggests that they have analogous structures and that the natural protein possesses a structure similar to a dimer of two N-terminal domains.

  16. Structural and electronic properties of AlN(0001) surface under partial N coverage as determined by ab initio approach

    SciTech Connect

    Strak, Pawel; Sakowski, Konrad; Kempisty, Pawel

    2015-09-07

    Properties of bare and nitrogen-covered Al-terminated AlN(0001) surface were determined using density functional theory (DFT) calculations. At a low nitrogen coverage, the Fermi level is pinned by Al broken bond states located below conduction band minimum. Adsorption of nitrogen is dissociative with an energy gain of 6.05 eV/molecule at a H3 site creating an overlap with states of three neighboring Al surface atoms. During this adsorption, electrons are transferred from Al broken bond to topmost N adatom states. Accompanying charge transfer depends on the Fermi level. In accordance with electron counting rule (ECR), the DFT results confirm the Fermi level is not pinned at the critical value of nitrogen coverage θ{sub N}(1) = 1/4 monolayer (ML), but it is shifted from an Al-broken bond state to Np{sub z} state. The equilibrium thermodynamic potential of nitrogen in vapor depends drastically on the Fermi level pinning being shifted by about 4 eV for an ECR state at 1/4 ML coverage. For coverage above 1/4 ML, adsorption is molecular with an energy gain of 1.5 eV at a skewed on-top position above an Al surface atom. Electronic states of the admolecule are occupied as in the free molecule, no electron transfer occurs and adsorption of a N{sub 2} molecule does not depend on the Fermi level. The equilibrium pressure of molecular nitrogen above an AlN(0001) surface depends critically on the Fermi level position, being very low and very high for low and high coverage, respectively. From this fact, one can conclude that at typical growth conditions, the Fermi level is not pinned, and the adsorption and incorporation of impurities depend on the position of Fermi level in the bulk.

  17. Ab Initio Quantum Mechanical Study of the Structure and Stability of the Alkaline Earth Metal Oxides and Peroxides

    NASA Astrophysics Data System (ADS)

    Königstein, Markus; Catlow, C. Richard A.

    1998-10-01

    We report a detailed computationally study of the stability of the alkaline earth metal peroxidesMO2(M=Ba, Sr, Ca, Mg, Be) with respect to decomposition into the corresponding oxidesMOand molecular oxygen using Hartree-Fock and density functional theory (DFT) techniques. A comparison between calculated and experimental binding energies indicates that the DFT method is most suitable for a correct description of the peroxide bond. The DFT reaction energies for the peroxide decompositionMO2→MO+{1}/{2}O2show that only BaO2and SrO2are thermodynamically stable compounds, while CaO2(in the calcium carbide structure), MgO2, and BeO2(in the pyrite structure) are energetically unstable with reaction energies of -24.7, -26.8, and -128.7kJ/mol, respectively, and are therefore unlikely to exist as pure compounds. The published calcium carbide structure for CaO2is probably incorrect, at least for pure calcium peroxide, since apart from the thermodynamical instability the compound is more stable in the pyrite structure by 25.5 kJ/mol. Our analysis suggests that the water and/or hydrogen peroxide content of experimentally prepared MgO2samples is necessary for the stabilization of the structure, while BeO2is clearly unstable under ambient conditions. We studied also the effect of the zero point energies and the entropies on the decomposition free energies and, for this purpose, performed atomistic lattice simulations based on interatomic potentials, which we derived from ourab initiodata; the results indicate a negligible effect of the zero point energies, while the entropy terms favor the decomposition reaction by ca. 20 kJ/mol at 298.15 K.

  18. Revisiting structure and dynamics of Ag+ in 18.6% aqueous ammonia: An ab initio quantum mechanical charge field simulation

    NASA Astrophysics Data System (ADS)

    Prasetyo, Niko; Armunanto, Ria

    2016-05-01

    Structures and dynamics of Ag+ in 18.6% aqueous ammonia have been studied using Quantum Mechanical Charge Field Molecular Dynamics (QMCF-MD) simulation at the Hartree-Fock (HF) level theory employing LANL2DZ ECP basis set for Ag+ and Dunning DZP for solvent molecules. Structural properties are in excellent agreement with previous QM/MM and experiments studies. [Ag(NH3)2(H2O)3]+ was found as dominant species during simulation time. For 20 ps of simulation time, a labile first solvation shell was observed with both fast ammonia and water ligands exchanges. QMCF-MD framework describes first solvation shell more labile than conventional QM/MM MD simulation.

  19. Structure of the Al13Co4 (100) surface: Combination of surface x-ray diffraction and ab initio calculations

    NASA Astrophysics Data System (ADS)

    Gaudry, É.; Chatelier, C.; McGuirk, G. M.; Serkovic Loli, L. N.; de Weerd, M.-C.; Ledieu, J.; Fournée, V.; Felici, R.; Drnec, J.; Beutier, G.; de Boissieu, M.

    2016-10-01

    The structure of the quasicrystalline approximant Al13Co4 (100) has been determined by surface x-ray diffraction (SXRD) and complementary density-functional-theory (DFT) calculations. Thanks to the use of a two-dimensional pixel detector, which speeds up the data acquisition enormously, an exceptionally large set of experimental data, consisting of 124 crystal truncation rods, has been collected and used to refine this complex structure of large unit cell and low symmetry. Various models were considered for the SXRD analysis. The best fit is consistent with a surface termination at the puckered type of planes but with a depletion of the protruding Co atoms. The surface energy of the determined surface model was calculated using DFT, and it takes a rather low value of 1.09 J/m 2 . The results for the atomic relaxation of surface planes found by SXRD or DFT were in excellent agreement. This work opens up additional perspectives for the comprehension of related quasicrystalline surfaces.

  20. Ab initio molecular dynamics simulations of structural changes associated with the incorporation of fluorine in bioactive phosphate glasses.

    PubMed

    Christie, Jamieson K; Ainsworth, Richard I; de Leeuw, Nora H

    2014-08-01

    Phosphate-based bioactive glasses containing fluoride ions offer the potential of a biomaterial which combines the bioactive properties of the phosphate glass and the protection from dental caries by fluoride. We conduct accurate first-principles molecular dynamics simulations of two compositions of fluorinated phosphate-based glass to assess its suitability as a biomaterial. There is a substantial amount of F-P bonding and as a result the glass network will be structurally homogeneous on medium-range length scales, without the inhomogeneities which reduce the bioactivity of other fluorinated bioactive glasses. We observe a decrease in the network connectivity with increasing F content, caused by the replacement of bridging oxygen atoms by non-bridging fluorine atoms, but this decrease is small and can be opposed by an increase in the phosphate content. We conclude that the structural changes caused by the incorporation of fluoride into phosphate-based glasses will not adversely affect their bioactivity, suggesting that fluorinated phosphate glasses offer a superior alternative to their silicate-based counterparts.

  1. Structure, dynamics and stability of water/scCO2/mineral interfaces from ab initio molecular dynamics simulations

    DOE PAGES

    Lee, Mal -Soon; Peter McGrail, B.; Rousseau, Roger; Glezakou, Vassiliki -Alexandra

    2015-10-12

    Here, the interface between a solid and a complex multi-component liquid forms a unique reaction environment whose structure and composition can significantly deviate from either bulk or liquid phase and is poorly understood due the innate difficulty to obtain molecular level information. Feldspar minerals, as typified by the Ca-end member Anorthite, serve as prototypical model systems to assess the reactivity and ion mobility at solid/water-bearing supercritical fluid (WBSF) interfaces due to recent X-ray based measurements that provide information on water-film formation, and cation vacancies at these surfaces. Using density functional theory based molecular dynamics, which allows the evaluation of reactivitymore » and condensed phase dynamics on equal footing, we report on the structure and dynamics of water nucleation and surface aggregation, carbonation and Ca mobilization under geologic carbon sequestration scenarios (T = 323 K and P = 90 bar). We find that water has a strong enthalpic preference for aggregation on a Ca-rich, O-terminated anorthite (001) surface, but entropy strongly hinders the film formation at very low water concentrations. Carbonation reactions readily occur at electron-rich terminal Oxygen sites adjacent to cation vacancies, when in contact with supercritical CO2. Cation vacancies of this type can form readily in the presence of a water layer that allows for facile and enthalpicly favorable Ca2+ extraction and solvation. Apart from providing unprecedented molecular level detail of a complex three component (mineral, water and scCO2) system), this work highlights the ability of modern capabilities of AIMD methods to begin to qualitatively and quantitatively address structure and reactivity at solid-liquid interfaces of high chemical complexity. This work was supported by the US Department of Energy, Office of Fossil Energy (M.-S. L., B. P. M. and V.-A. G.) and the Office of Basic Energy Science, Division of Chemical Sciences

  2. Ab initio study on structural, electronic properties, and hardness of re-doped W2B5

    NASA Astrophysics Data System (ADS)

    Feng, ShiQuan; Li, XiaoDong; Su, Lei; Li, HaiNing; Yang, Hongyan; Cheng, Xinlu

    2016-11-01

    Using first principle calculations method, we calculated the structural stability, electronic properties and hardness for three Re-doped hexagonal W2B5 compounds. The electronic properties were carried out to discuss the effect of doped Re on the conductivity, chemical bonding components and orbital hybridization of W2B5. What is more, the hardness of these three doped crystals was calculated by a semiempirical method considering the role of metallic components. A Re-doped W2B5 compound with a greater hardness value than that of pure W2B5 was obtained. And the effect of doping on the hardness of hexagonal W2B5was discussed.

  3. DFT and ab initio study of structure of dyes derived from 2-hydroxy and 2,4-dihydroxy benzoic acids

    NASA Astrophysics Data System (ADS)

    Dabbagh, Hossein A.; Teimouri, Abbas; Najafi Chermahini, Alireza; Shahraki, Maryam

    2008-02-01

    We present a detailed analysis of the structural, infrared spectra and visible spectra of a series of azo dyes preparation of salicylic acid and 2,4-dihydroxy benzoic acid derivatives as the coupling component. The preparation of these azo dyes with salicylic acid and 2,4-dihydroxy benzoic acid derivatives (salicylic acid, methyl salicylate, ethyl salicylate, butyl salicylate, methyl 2,4-dihydroxy benzoate, ethyl 2,4-dihydroxy benzoate, salicylaldehyde, salicylamide, 2,4-dihydroxy benzamide, salicylaldoxime) have been investigated theoretically by performing HF and DFT levels of theory using the standard 6-31G* basis set. The optimized geometries and calculated vibrational frequencies are evaluated via comparison with experimental values. The vibrational spectral data obtained from solid phase FT-IR spectra are assigned modes based on the results of the theoretical calculations. The observed spectra are found to be in good agreement with the calculations.

  4. Environmental effects on the structure of metal ion-DOTA complexes: An ab initio study of radiopharmaceutical metals.

    SciTech Connect

    Lau, E Y; Lightstone, F C; Colvin, M E

    2006-02-10

    Quantum mechanical calculations were performed to study the differences between the important radiopharmaceutical metals yttrium (Y) and indium (In) bound by DOTA and modified DOTA molecules. Energies were calculated at the MP2/6-31+G(d)//HF/6-31G(d) levels, using effective core potentials on the Y and In ions. Although the minimum energy structures obtained are similar for both metal ion-DOTA complexes, changes in coordination and local environment significantly affect the geometries and energies of these complexes. Coordination by a single water molecule causes a change in the coordination number and a change in the position of the metal ion in In-DOTA; but, Y-DOTA is hardly affected by water coordination. When one of the DOTA carboxylates is replaced by an amide, the coordination energy for the amide arm shows a large variation between the Y and In ions. Optimizations including water and guandinium moieties to approximate the effects of antibody binding indicate a large energy cost for the DOTA-chelated In to adopt the ideal conformation for antibody binding.

  5. Comparison of ab initio and DFT electronic structure methods for peptides containing an aromatic ring: effect of dispersion and BSSE.

    PubMed

    Shields, Ashley E; van Mourik, Tanja

    2007-12-20

    We establish that routine B3LYP and MP2 methods give qualitatively wrong conformations for flexible organic systems containing pi systems and that recently developed methods can overcome the known inadequacies of these methods. This is illustrated for a molecule (a conformer of the Tyr-Gly dipeptide) for which B3LYP/6-31+G(d) and MP2/6-31+G(d) geometry optimizations yield strikingly different structures [Mol. Phys. 2006, 104, 559-570]: MP2 predicts a folded "closed-book" conformer with the glycine residue located above the tyrosine ring, whereas B3LYP predicts a more open conformation. By employing different levels of theory, including the local electron correlation methods LMP2 (local MP2) and LCCSD(T0) (local coupled cluster with single, double, and noniterative local triple excitations) and large basis sets (aug-cc-pVnZ, n=D, T, Q), it is shown that the folded MP2 minimum is an artifact caused by large intramolecular BSSE (basis set superposition error) effects in the MP2/6-31+G(d) calculations. The B3LYP functional gives the correct minimum, but the potential energy apparently rises too steeply when the glycine and tyrosine residues approach each other, presumably due to missing dispersion effects in the B3LYP calculations. The PWB6K and M05-2X functionals, designed to give good results for weak interactions, remedy this to some extent. The reduced BSSE in the LMP2 calculations leads to faster convergence with increasing basis set quality, and accurate results can be obtained with smaller basis sets as compared to canonical MP2. We propose LMP2 as a suitable method to study interactions with pi-electron clouds.

  6. First attempts at an elucidation of the interface structure resulting from the interaction between methacrylonitrile and a platinum anode: an experimental and theoretical (ab initio) study

    NASA Astrophysics Data System (ADS)

    Bureau, Christophe; Deniau, Guy; Valin, Françoise; Guittet, Marie-Joseph; Lécayon, Gérard; Delhalle, Joseph

    1996-06-01

    The aim of the present paper is to contribute to the elucidation of the molecular structures obtained on a platinum surface as this surface is submitted to an anodic potential (with respect to a silver reference electrode) when dipped into pure 2-methyl 2-propenenitrile (methacrylonitrile). Modified surfaces are examined using X- and UV-photoelectron spectroscopies (UPS and XPS). The results evidence the formation of an ultra-thin (20-40 Å) grafted oligomer film, which is not classical polymethacrylonitrile (PMAN), as obtained through a radical or anionic mechanism: spectral characteristics argue in the sense of a cationic polymerization of methacrylonitrile through its nitrile groups, as evidenced by a lowering of the gap as well as by the UPS and XPS (N 1s region) spectra. Molecular models of the reactants and reaction intermediates are proposed for the cationic polymerization of methacrylonitrile, and show that this polymerization is about as feasible as that of acetonitrile, at least on kinetic control grounds. Two different mechanisms are nonetheless possible, leading either to a quasi conjugated poly-imine type -(N  C) n-, or to a poly-cumulene type -(N  C  C) n- network. Theoretical consierations on reactants properties lead us to select the poly-imine way as the most plausible. Along with literature data concerning chemisorbed nitriles on platinum surfaces, a molecular model of the final state of the poly-imine reaction is then designed, comprising a three atom cluster to render the grafting site, and a dimer to render the grafted structure. A full geometry optimization is performed on the organic moiety at the Hartree-Fock (ab initio) level of theory, and a rough evaluation of the spectral footprint of the interface bond in the N 1s region is performed on the basis of Koopmans theorem with calibration on the bulk polymer peak. A preliminary 2.7 eV downward shift is predicted for N 1s interface nitrogens with respect to the polymer peak, which can

  7. 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.

  8. 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.

  9. Initial oxidation of TiAl: An ab-initio investigation

    SciTech Connect

    Bakulin, Alexander V. Kulkova, Svetlana E.; Hu, Qing-Miao; Yang, Rui

    2014-11-14

    We present ab-initio investigation of oxygen adsorption up to two monolayer coverage on the stoichiometric TiAl(100) surface to illustrate the initial oxidation stage. The formation of band gap near the Fermi level demonstrates the transformation from metal to oxide surface with increasing oxygen coverage. The oxidation of Ti rather than Al is observed from our electronic structure calculations. The energy barriers of oxygen diffusion between different sites on surface as well as in subsurface and bulk region are derived. It is shown that the diffusion of oxygen is much easier on the surface than that into the subsurface region.

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

    NASA Astrophysics Data System (ADS)

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

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

  11. 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.

  12. 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.

  13. Ab Initio Studies of Calcium Carbonate Hydration.

    PubMed

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

    2015-11-25

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

  14. 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

  15. Ab initio studies of anisotropic magnetism in uranium and cerium monopnictides and monochalcogenides

    NASA Astrophysics Data System (ADS)

    Collins, Eric Mason

    We have applied two ab initio based methods to investigate the origin in the electronic structure of the unusual magnetic behavior of the cerium and uranium monopnictides and monochalcogenides. First, we have carried out spin-polarized electronic structure calculations, based on the full potential linear muffin tin (FPLMTO) method, with spin polarization (orbital polarization only via spin-orbit coupling) and also with orbital polarization correction. Second, we have carried out ab initio based calculations synthesizing (1) a phenomenological theory of orbitally driven magnetism based on the Anderson and Kondo, lattice model which incorporates explicitly the hybridization induced and the Coulomb exchange interactions on an equal footing, and (2) FPLMTO electronic structure calculations allowing a first principles evaluation of all the parameters entering the model Hamiltonian. For the cerium compounds, we also include the crystal field interactions on an equal footing with the hybridization and Coulomb exchange interactions with a scaling determined by experiment. The results for the uranium compound calculations show that both methods are limited to the extremes to which they are best suited. The pure band structure calculations provide the best agreement for the lighter uranium compounds, while the model hamiltonian approach provides better agreement for the heavier uranium compounds. In the case of the cerium compounds, while the pure FPLMTO calculations yield values for the magnetic moment in agreement with experiment for the lighter cerium chalcogenides, they fail to give, even qualitatively, the magnetic properties for all other systems. On the other hand, the ab initio based model Hamiltonian calculations reveal for the first time the interplay of hybridization, Coulomb exchange, and crystal field interactions across the cerium series, and give results for the low-temperature moment and ordering temperature in excellent agreement with experiment, for the

  16. 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.

  17. Ab-initio calculations on melting of thorium

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

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

    PubMed Central

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

    2005-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-08-01

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

  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 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.

  2. 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.

  3. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-08-01

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

  5. 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.

  6. Ab initio calculations of reactions with light nuclei

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

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

    PubMed

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

    2014-08-01

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

  8. Ab-initio crystal structure of hydroxy adipate of nickel and hydroxy subarate of nickel and cobalt from synchrotron powder diffraction and magnetic properties

    SciTech Connect

    Mesbah, Adel; Carton, Anne; Aranda, Lionel; Mazet, Thomas; Porcher, Florence; Francois, Michel

    2008-12-15

    Organic-inorganic hybrid compounds Ni(II){sub 5}(OH){sub 6}(C{sub 6}H{sub 8}O{sub 4}){sub 2}(1), Ni(II){sub 5}(OH){sub 6}(C{sub 8}H{sub 12}O{sub 4}){sub 2}(2) and Co(II){sub 5}(OH){sub 6}(C{sub 8}H{sub 12}O{sub 4}){sub 2}(3) have a similar layered structure as determined ab initio from synchrotron powder diffraction analysis. The metal sites are octahedrally coordinated by O atoms. The slabs are built from edge-sharing octahedra in such a way that channels with an average size of 4 A are formed. Bis-bidentate and bridging dicarboxylate anions lead to a 3D framework. The compounds (1) and (2) order antiferromagnetically below T{sub N}=26.5 and 19.3 K, respectively, while (3) is ferrimagnetic with T{sub C}=16.2 K. Crystal data for compounds are as follows: (1)a=11.6504(1) A, b=6.8021(3) A, c=6.3603(1) A, {alpha}=73.52(1){sup o}, {beta}=99.69(1){sup o}, {gamma}=96.16(1){sup o}, R{sub B}=0.070, 668 reflections; (2)a=13.9325(1) A, b=6.7893(1) A, c=6.3534(4) A, {alpha}=73.63(1){sup o}, {beta}=95.14(1){sup o}, {gamma}=91.80(1){sup o}, R{sub B}=0.052, 804 reflections; (3)a=13.9806(1) A, b=6.9588(1) A, c=6.3967(1) A, {alpha}=73.05(1){sup o}, {beta}=94.51(1){sup o}, {gamma}=92.19(1){sup o}, R{sub B}=0.048, 410 reflections. The space group is P-1 for the three compounds. - Graphical abstract: The hybrid metal-organic compounds Ni(II){sub 5}(OH){sub 6}(C{sub 6}H{sub 8}O{sub 4}){sub 2}(1), Ni(II){sub 5}(OH){sub 6}(C{sub 8}H{sub 12}O{sub 4}){sub 2}(2) and Co(II){sub 5}(OH){sub 6}(C{sub 8}H{sub 12}O{sub 4}){sub 2}(3) have been synthesized by the hydrothermal route. The microporous metal hydroxide layers are bridged by dicarboxylates anions. (1) and (2) are antiferromagnetic with T{sub N}=26.5 and 19.3 K, respectively, while (3) is ferrimagnetic with T{sub C}=16.2 K.

  9. Ab initio study of heterojunction discontinuities in the ZnO/Cu2O system

    NASA Astrophysics Data System (ADS)

    Zemzemi, M.; Alaya, S.; Ben Ayadi, Z.

    2014-06-01

    Solar cells based on transparent conductive oxides such as ZnO/Cu2O constitute a very advanced way to build high-performance cells. In this work, we are interested in the characterization of the interface through nanoscale modeling based on ab initio approaches (density functional theory, local density approximation, and pseudopotential). This work aims to build a supercell containing a heterojunction ZnO/Cu2O and study the structural properties and the discontinuity of the valence band (band offset) from a semiconducting to another phase. We build a zinc oxide in the wurtzite structure along [0001] on which we place the copper oxide in the hexagonal (CdI2-type) structure. We choose the method of Van de Walle and Martin to calculate the energy offset. This approach fits well the density functional theory. Our calculation of the band offset gives a value that corresponds to other experimental and theoretical values.

  10. n-type conductivity in Si-doped amorphous AlN: an ab initio investigation

    NASA Astrophysics Data System (ADS)

    Durandurdu, Murat

    2016-04-01

    We report the electronic structure and topology of a heavily Si-doped amorphous aluminium nitride (Al37.5Si12.5N50) using ab initio simulations. The amorphous Al37.5Si12.5N50 system is found to be structurally similar to pure amorphous aluminium nitride. It has an average coordination number of about 3.9 and exhibits a small amount of Si-Si homopolar bonds. The formation of Si-Al bonds is not very favourable. Electronic structure calculations reveal that the Si doping has a negligible effect on the band gap width but causes delocalization of the valence band tail states and a shift of the Fermi level towards the conduction band. Thus, amorphous Al37.5Si12.5N50 alloys show n-type conductivity.

  11. An extensive ab initio study of the structures, vibrational spectra, quadratic force fields, and relative energetics of three isomers of Cl2O2

    NASA Technical Reports Server (NTRS)

    Lee, Timothy J.; Rohlfing, Celeste MCM.; Rice, Julia E.

    1992-01-01

    Quantum mechanical computational methods are employed for an ab initio investigation of: (1) the molecular properties of the lowest isomers of the ClO dimer; and (2) predicted molecular and thermochemical properties. Techniques employed include electron correlation and particularly singles and doubles coupled-cluster (CCSD) theory with or without perturbational estimates of the effects of connected triple excitations. The isomers ClOClO and ClClO2 are found to have higher energies than the ClOOCl isomer, and the theoretical vibrational frequencies of the isomers are well correlated with experimental data. Experimental values of the heat of formation for the isomers are also compared with calculations based on an isodesmic reaction with Cl2O, H2O, and HOOH.

  12. Spectra and structure of small ring compounds. LXVII vibrational spectra, variable temperature FT-IR spectra of krypton solutions, conformational stability and ab initio calculations of 1-bromosilacyclobutane.

    PubMed

    Gounev, T K; Guirgis, G A; Zhen, P; Durig, J R

    2000-11-15

    The infrared (3,200-30 cm(-1) spectra of gaseous and solid 1-bromosilacyclobutane, c-C3H6SiBrH, have been recorded. Additionally, the Raman spectra of the liquid (3,200- 30 cm(-1) with quantitative depolarization values and the solid have been recorded. Both the equatorial and the axial conformers have been identified in the fluid phases, Variable temperature ( - 105 to - 150 degrees C) studies of the infrared spectra of the sample dissolved in liquid krypton have been carried out. From these data the enthalpy difference has been determined to be 182 +/- 18 cm(-1) (2.18 +/- 0.22 kJ/mol) with the equatorial conformer the more stable rotamer and only conformer remaining in the annealing solid. At ambient temperature there is approximately 22% of the axial conformer present in the vapor phase. A complete vibrational assignment is proposed for both conformers based on infrared contours, relative intensities, depolarization values and group frequencies. The vibrational assignments are supported by normal coordinate calculations utilizing the force constants from ab initio MP2/6-31G(d) calculations. From the frequencies of the Si-H stretch, the Si-H bond distance of 1.483 A has been determined for both the equatorial and the axial conformers. Complete equilibrium geometries have been determined for both rotamers by ab initio calculations employing the 6-31G(d) and 6-311 +/- G(d,p) basis sets at levels of Hartree Fock (RHF) and/or Moller- Plesset with full electron correlation by the perturbation method to the second order (MP2). The results are discussed and compared to those obtained for some similar molecules.

  13. Band-gap Variation of "Semi-metallic" Zig-Zag Carbon Nanotubes under Uniaxial Strain: Accurate Ab-initio Studies

    NASA Astrophysics Data System (ADS)

    Guo, Guang-Yu; Chu, K. C.; Liu, Lei; Jayanthi, C. S.; Wu, Shi-Yu

    2003-03-01

    We have calculated the electronic properties of "semi-metallic" zigzag carbon nanotubes as a function of uniaxial strain using highly accurate all-electron projector augmented-wave (PAW) method. The calculated band gaps for unstrained nanotubes are in good agreement with available STM experimental results [1]. It is found that with increasing elongation, the band gap of all the "semi-metallic" nanotubes initially decreases linearly, then vanishes at a small strain, and then increases linearly for relatively small strains. The strain characterizing the semiconductor to metal transition is found to be inversely proportional to the square of the diameter of the nanotube. The calculated transition strain values are all within 1 thus easily verifiable experimentally. Analytic relations among band gaps, diameters, and strains of zig-zag nanotubes extracted from our accurate calculations will be reported. Acknowledgements: The work is supported by National Science Council of Taiwan (NSC 91-2112-M-002-054) as well as NSF (DMR-0112824) and DOE (DEFG02-00ER45832). [1] M. Ouyang, J.-L. Huang, C.L. Cheung, and C.M. Lieber, Science 292, 702 (2001).

  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. Ab Initio Study of Hot Carriers in the First Picosecond after Sunlight Absorption in Silicon

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

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

  16. Ab-initio study of napthelene based conducting polymer

    SciTech Connect

    Ruhela, Ankur; Kanchan, Reena; Srivastava, Anurag; Sinha, O. P.

    2014-04-24

    In this paper, we have identified structural and electronic properties of conducting polymers by using DFT based ATK-VNL ab-initio tool. Naphthalene derivative structures were stabilized by varying the bond length between two atoms of the molecule C-N and C-C. We have also studied the molecular energy spectrum of naphthalene derivatives and found the HOMOLUMO for the same. A comparison of structural and electronic properties of naphthalene derivatives by attaching the functional group of amine, have been performed and found that they show good semi conducting properties.

  17. Electronic states of lithium passivated germanium nanowires: An ab-initio study

    SciTech Connect

    Trejo, A.; Carvajal, E.; Vázquez-Medina, R.; Cruz-Irisson, M.

    2014-05-15

    A study of the electronic and structural properties of germanium nanowires (GeNWs) was performed using the ab-initio Density Functional Theory within the generalized gradient approximation where electron-ion interactions are described by ultrasoft pseudopotentials. To study the effects of the lithium in the surface of the GeNWs we compare the electronic band structures of Hydrogen passivated GeNWs with those of partial and totally Li passivated GeNWs. The nanowires were constructed in the [001], [111] and [110] directions, using the supercell model to create different wire diameters. The results show that in the case of partial Li passivation there are localized orbitals near the valence band maximum, which would create a p-doped-kind of state. The total Li passivation created metallic states for all the wires.

  18. Ab initio studies of structural features not easily amenable to experiment. 23. Molecular structures and conformational analysis of the dipeptide N-acetyl-N'-methyl glycyl amide and the significance of local geometries for peptide structures

    NASA Astrophysics Data System (ADS)

    Schäfer, Lothar; Van Alsenoy, C.; Scarsdale, J. N.

    1982-02-01

    The molecular structures of four conformations of N-acetyl-N'-methyl glycyl amide were refined by geometrically unconstrained ab initio gradient relaxation on the 4-21G level. The most stable form I contains a seven-membered ring closed by hydrogen bonding. A second local minimum II is less than 1 kcal/mol above I and represents the fully extended form with a five-membered hydrogen bonded ring. The two other minima refined, III and IV, are open forms which are 4-5 kcal/mol less stable than I. The refined geometries make it possible to estimate the significance of local geometries, in contrast to standard geometry, in the various conformations. It is found that bond distances in different conformations can vary by up to 0.02 Å, and important backbone bond angles can vary by up to 7°. Except for the symmetrical form II, small deviations from amide planarity (H-N-C = 0 angles of 3-10°) are the rule, even though the equilibrium structure of the unperturbed amide group in 4-21G space is planar. It can be concluded that local geometry relaxations at different points of the potential energy surface of a peptide system can amount to several Kcal/mol per residue and should be an important aspect of protein conformational analysis.

  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. Ab initio Computations of the Electronic, Mechanical, and Thermal Properties of Ultra High Temperature Ceramics (UHTC) ZrB2 and HfB2

    NASA Technical Reports Server (NTRS)

    Lawson, John W.; Bauschlicher, Charles W.; Daw, Murray

    2011-01-01

    Refractory materials such as metallic borides, often considered as ultra high temperature ceramics (UHTC), are characterized by high melting point, high hardness, and good chemical inertness. These materials have many applications which require high temperature materials that can operate with no or limited oxidation. Ab initio, first principles methods are the most accurate modeling approaches available and represent a parameter free description of the material based on the quantum mechanical equations. Using these methods, many of the intrinsic properties of these material can be obtained. We performed ab initio calculations based on density functional theory for the UHTC materials ZrB2 and HfB2. Computational results are presented for structural information (lattice constants, bond lengths, etc), electronic structure (bonding motifs, densities of states, band structure, etc), thermal quantities (phonon spectra, phonon densities of states, specific heat), as well as information about point defects such as vacancy and antisite formation energies.

  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. 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.

  3. Boric acid, “carbonic” acid, and N-containing oxyacids in aqueous solution: Ab initio studies of structure, pKa, NMR shifts, and isotopic fractionations

    NASA Astrophysics Data System (ADS)

    Tossell, J. A.

    2005-12-01

    B(OH) 3 and CO 2 are acidic species of considerable geochemical importance, yet the microscopic nature of the acid dissociation reactions for these B and C species is not well understood. Quantum mechanical methods have recently been applied to the direct ab initio calculation of p Ka values for many organic and inorganic weak acids, but the B and C acids have not yet been considered in detail. In the present study, p Ka values are calculated quantum mechanically for the oxyacids B(OH) 3, H 2CO 3 and HNO 3, which have experimental first p Ka values of 9.2, 6.4 and -1.3, respectively. We calculate the gas-phase reaction free energies at the highly accurate CBS-QB3 ab initio quantum mechanical level and reaction free energies of hydration using a polarizable continuum method. Using a thermodynamic cycle corresponding to the simple dissociation process HA A - + H +, in aqueous solution, we calculate p Ka values of 21.6, 3.8 to 2.2 and -0.8 for the three oxyacids mentioned above, closely matching experiment only for HNO 3. The discrepancies with experiment arise from the more complex nature of the acid dissociation process for B(OH) 3, which involves the addition of H 2O to B(OH) 3 and formation of the B(OH) 4- anion, and from the instability of hypothetical H 2CO 3 compared to the proper hydrated reactant complex CO 2. . . H 2O. When the proper microscopic description of the reactants and products is used the calculated p Ka values for the three acids become 11.1, 7.2 and -0.8, in considerably better agreement with experiment for B(OH) 3 and CO 2. . . H 2O. Thus p Ka calculations using this approach are accurate enough to give information on the actual acid species present in solution and the details of their acid dissociation processes at the microscopic level. 11B and 13C-NMR chemical shifts are also calculated for the various species and compared to experiment. By comparison of our calculations with experiment it is apparent that the 13C-NMR chemical shift has

  4. The MSRC ab initio methods benchmark suite: A measurement of hardware and software performance in the area of electronic structure methods

    NASA Astrophysics Data System (ADS)

    Feller, D. F.

    1993-07-01

    This collection of benchmark timings represents a snapshot of the hardware and software capabilities available for ab initio quantum chemical calculations at Pacific Northwest Laboratory's Molecular Science Research Center in late 1992 and early 1993. The 'snapshot' nature of these results should not be underestimated, because of the speed with which both hardware and software are changing. Even during the brief period of this study, we were presented with newer, faster versions of several of the codes. However, the deadline for completing this edition of the benchmarks precluded updating all the relevant entries in the tables. As will be discussed below, a similar situation occurred with the hardware. The timing data included in this report are subject to all the normal failures, omissions, and errors that accompany any human activity. In an attempt to mimic the manner in which calculations are typically performed, we have run the calculations with the maximum number of defaults provided by each program and a near minimum amount of memory. This approach may not produce the fastest performance that a particular code can deliver. It is not known to what extent improved timings could be obtained for each code by varying the run parameters. If sufficient interest exists, it might be possible to compile a second list of timing data corresponding to the fastest observed performance from each application, using an unrestricted set of input parameters. Improvements in I/O might have been possible by fine tuning the Unix kernel, but we resisted the temptation to make changes to the operating system. Due to the large number of possible variations in levels of operating system, compilers, speed of disks and memory, versions of applications, etc., readers of this report may not be able to exactly reproduce the times indicated. Copies of the output files from individual runs are available if questions arise about a particular set of timings.

  5. Ab initio quantum mechanical study of the structures and energies for the pseudorotation of 5{prime}-dehydroxy analogues of 2{prime}-deoxyribose and ribose sugars

    SciTech Connect

    Brameld, K.A.; Goddard, W.A. III

    1999-02-10

    The authors have used ab initio quantum mechanical (QM) methods to determine the potential energy of pseudorotation for 3,4-dihydroxy-5-methyl-2-(1-pyrollyl)tetrahydrofuran and 4-hydroxy-5-methyl-2-(1-pyrollyl)-tetrahydrofuran, close analogues of 2{prime}-deoxyribose and ribose sugars. The pyrrole is a substitute for the naturally occurring nucleic acid bases: adenine, thymine, guanine, cytosine, and uracil. At the highest calculation level (LMP2/cc-pVTZ(-f)//HF/6-31G**) for 2{prime}-deoxyribose, they find the C2{prime}-endo conformation is the global minimum. The C3{prime}-endo conformation is a local minimum 0.6 kcal/mol higher in energy, and an eastern barrier of 1.6 kcal/mol separates the two minima. Pseudorotation energies of ribose are quite complex and are strongly affected by local orientations of the 2{prime} and 3{prime} hydroxyl groups. When the hydroxyl groups are allowed to assume any conformation, the global minimum remains the C2{prime}-endo conformation. The eastern barrier increases slightly to 1.8 kcal/mol, and the C3{prime}-endo local minimum lies 0.6 kcal/mol above the global minimum. Constraining the torsion angle of the C3{prime} hydroxyl group to {minus}146{degree}, as is found in RNA polymers, results in the C3{prime}-endo conformation becoming the only energy minimum with a C2{prime}-endo conformation 1.9 kcal/mol higher in energy. Bond angles within the pentofuranose ring are correlated to the pseudorotational phase, as is observed by X-ray crystallography and is predicted by pseudorotation theory. Finally, a force field for use in molecular mechanics and dynamics simulations is presented which reproduces the QM potential energies for the 2{prime}-deoxyribose and ribose sugars.

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

    SciTech Connect

    Feller, D.F.

    1993-07-01

    This collection of benchmark timings represents a snapshot of the hardware and software capabilities available for ab initio quantum chemical calculations at Pacific Northwest Laboratory`s Molecular Science Research Center in late 1992 and early 1993. The ``snapshot`` nature of these results should not be underestimated, because of the speed with which both hardware and software are changing. Even during the brief period of this study, we were presented with newer, faster versions of several of the codes. However, the deadline for completing this edition of the benchmarks precluded updating all the relevant entries in the tables. As will be discussed below, a similar situation occurred with the hardware. The timing data included in this report are subject to all the normal failures, omissions, and errors that accompany any human activity. In an attempt to mimic the manner in which calculations are typically performed, we have run the calculations with the maximum number of defaults provided by each program and a near minimum amount of memory. This approach may not produce the fastest performance that a particular code can deliver. It is not known to what extent improved timings could be obtained for each code by varying the run parameters. If sufficient interest exists, it might be possible to compile a second list of timing data corresponding to the fastest observed performance from each application, using an unrestricted set of input parameters. Improvements in I/O might have been possible by fine tuning the Unix kernel, but we resisted the temptation to make changes to the operating system. Due to the large number of possible variations in levels of operating system, compilers, speed of disks and memory, versions of applications, etc., readers of this report may not be able to exactly reproduce the times indicated. Copies of the output files from individual runs are available if questions arise about a particular set of timings.

  7. A fragmentation and reassembly method for ab initio phasing.

    PubMed

    Shrestha, Rojan; Zhang, Kam Y J

    2015-02-01

    Ab initio phasing with de novo models has become a viable approach for structural solution from protein crystallographic diffraction data. This approach takes advantage of the known protein sequence information, predicts de novo models and uses them for structure determination by molecular replacement. However, even the current state-of-the-art de novo modelling method has a limit as to the accuracy of the model predicted, which is sometimes insufficient to be used as a template for successful molecular replacement. A fragment-assembly phasing method has been developed that starts from an ensemble of low-accuracy de novo models, disassembles them into fragments, places them independently in the crystallographic unit cell by molecular replacement and then reassembles them into a whole structure that can provide sufficient phase information to enable complete structure determination by automated model building. Tests on ten protein targets showed that the method could solve structures for eight of these targets, although the predicted de novo models cannot be used as templates for successful molecular replacement since the best model for each target is on average more than 4.0 Å away from the native structure. The method has extended the applicability of the ab initio phasing by de novo models approach. The method can be used to solve structures when the best de novo models are still of low accuracy. PMID:25664740

  8. Ab initio study of structural, electronic and optical properties of ternary CdO1-xSex alloys using special quasi-random structures

    NASA Astrophysics Data System (ADS)

    Muhammad, Rashid; Fayyaz, Hussain; Muhammad, Imran; A. Ahmad, S.; A. Noor, N.

    2014-01-01

    The structural, electronic, and optical properties of binary CdO, CdSe, and their ternary CdO1-xSex alloys (0 <= x <= 1) in the rock salt and zinc blend phases have been studied by the special quasi-random structure (SQS) method. All the calculations are performed using full-potential linearized augmented plane wave plus local orbital's (FP-LAPW+lo) method within the framework of density function theory (DFT). We use Wu—Cohen (WC) generalized gradient approximation (GGA) to calculate structural parameters, whereas both Wu—Cohen and Engel—Vosko (EV) GGA have been applied to calculate electronic structure of the materials. Our predicted results of lattice constant and bulk modulus show only a slight deviation from Vegard's law for the whole concentrations. The obtained band structure indicates that for the rock-salt phase, the ternary alloys present semi-metallic behavior, while for the zinc blend phase, semiconductor behavior with direct bandgap is observed with decreasing order of x except for CdSe. Finally, by incorporating the basic optical properties, we discuss the dielectric function, refractive index, optical reflectivity, the absorption coefficient, and optical conductivity in terms of incident photon energy up to 14 eV. The calculated results of both binaries are in agreement with existing experimental and theoretical values.

  9. Ab Initio No-Core Shell Model

    SciTech Connect

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

    2011-04-11

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

  10. Ab Initio Active Region Formation

    NASA Astrophysics Data System (ADS)

    Stein, Robert F.; Nordlund, A.

    2013-01-01

    The tachocline is not necessary to produce active regions with their global properties. Dynamo action within the convection zone can produce large scale reversing polarity magnetic fields as shown by ASH code and Charboneau et al simulations. Magneto-convection acting on this large scale field produces Omega-loops which emerge through the surface to produce active regions. The field first emerges as small bipoles with horizontal field over granules anchored in vertical fields in the intergranular lanes. The fields are quickly swept into the intergranular lanes and produce a mixed polarity "pepper and salt" pattern. The opposite polarities then migrate toward separate unipolar regions due to the underlying large scale loop structure. When sufficient flux concentrates, pores and sunspots form. We will show movies of magneto-convection simulations of the emerging flux, its migration, and concentration to form pores and spots, as well as the underlying magnetic field evolution. In addition, the same atmospheric data has been used as input to the LILIA Stokes Inversion code to calculate Stokes spectra for the Fe I 630 nm lines and then invert them to determine the magnetic field. Comparisons of the inverted field with the simulation field shows that small-scale, weak fields, less than 100 G, can not be accurately determined because of vertical gradients that are difficult to match in fitting the line profiles. Horizontal smoothing by telescope diffraction further degrades the inversion accuracy.

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

    SciTech Connect

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

    2015-02-01

    Two ab initio modelling programs solve complementary sets of targets, enhancing the success of AMPLE with small proteins. AMPLE clusters and truncates ab initio protein structure predictions, producing search models for molecular replacement. Here, an interesting degree of complementarity is shown between targets solved using the different ab initio modelling programs QUARK and ROSETTA. Search models derived from either program collectively solve almost all of the all-helical targets in the test set. Initial solutions produced by Phaser after only 5 min perform surprisingly well, improving the prospects for in situ structure solution by AMPLE during synchrotron visits. Taken together, the results show the potential for AMPLE to run more quickly and successfully solve more targets than previously suspected.

  12. High pressure behaviour of uranium dicarbide (UC2): Ab-initio study

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

    The structural stability of uranium dicarbide has been examined under hydrostatic compression employing evolutionary structure search algorithm implemented in the universal structure predictor: evolutionary Xtallography (USPEX) code in conjunction with ab-initio electronic band structure calculation method. The ab-initio total energy calculations involved for this purpose have been carried out within both generalized gradient approximations (GGA) and GGA + U approximations. Our calculations under GGA approximation predict the high pressure structural sequence of tetragonal → monoclinic → orthorhombic for this material with transition pressures of ˜8 GPa and 42 GPa, respectively. The same transition sequence is predicted by calculations within GGA + U also with transition pressures placed at ˜24 GPa and ˜50 GPa, respectively. Further, on the basis of comparison of zero pressure equilibrium volume and equation of state with available experimental data, we find that GGA + U approximation with U = 2.5 eV describes this material better than the simple GGA approximation. The theoretically predicted high pressure structural phase transitions are in disagreement with the only high experimental study by Dancausse et al. [J. Alloys. Compd. 191, 309 (1993)] on this compound which reports a tetragonal to hexagonal phase transition at a pressure of ˜17.6 GPa. Interestingly, during lowest enthalpy structure search using USPEX, we do not see any hexagonal phase to be closer to the predicted monoclinic phase even within 0.2 eV/f. unit. More experiments with varying carbon contents in UC2 sample are required to resolve this discrepancy. The existence of these high pressure phases predicted by static lattice calculations has been further substantiated by analyzing the elastic and lattice dynamic stability of these structures in the pressure regimes of their structural stability. Additionally, various thermo-physical quantities such as equilibrium volume, bulk modulus, Debye

  13. 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.

  14. Ab-initio study of the structural, linear and nonlinear optical properties of CdAl{sub 2}Se{sub 4} defect-chalcopyrite

    SciTech Connect

    Ouahrani, T.; Reshak, Ali H.; Khenata, R.; Amrani, B.; Mebrouki, M.; Otero-de-la-Roza, A.; Luana, V.

    2010-01-15

    The complex density functional theory (DFT) calculations of structural, electronic, linear and nonlinear optical properties for the defect chalcopyrite CdAl{sub 2}Se{sub 4} compound have been reported using the full potential linearized augmented plane wave (FP-LAPW) method as implemented in the WIEN2k code. We employed the Wu and Cohen generalized gradient approximation (GGA-WC), which is based on exchange-correlation energy optimization to calculate the total energy. Also we have used the Engel-Vosko GGA formalism, which optimizes the corresponding potential for band structure, density of states and the spectral features of the linear and nonlinear optical properties. This compound has a wide direct energy band gap of about 2.927 eV with both the valence band maximum and conduction band minimum located at the center of the Brillouin zone. The ground state quantities such as lattice parameters (a, c, x, y and z), bulk modulus B and its pressure derivative B' are evaluated. We have calculated the frequency-dependent complex epsilon(omega), its zero-frequency limit epsilon{sub 1}(0), refractive index n(omega), birefringence DELTAn(omega), the reflectivity R(omega) and electron energy loss function L(omega). Calculations are reported for the frequency-dependent complex second-order nonlinear optical susceptibilities. We find opposite signs of the contributions of the 2omega and 1omega inter/intra-band to the imaginary part for the dominant component through the wide optical frequency range. - Graphical abstract: Calculated band structure and total density of CdAl{sub 2}Se{sub 4}.

  15. Ab initio melting curve of osmium

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

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

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

    NASA Astrophysics Data System (ADS)

    Zhu, Xiaolei; Yarkony, David R.

    2016-01-01

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

  17. Magneto-structural correlations in a family of Fe(II)Re(IV)(CN)2 single-chain magnets: density functional theory and ab initio calculations.

    PubMed

    Zhang, Yi-Quan; Luo, Cheng-Lin; Wu, Xin-Bao; Wang, Bing-Wu; Gao, Song

    2014-04-01

    Until now, the expressions of the anisotropic energy barriers Δξ and ΔA, using the uniaxial magnetic anisotropy D, the intrachain coupling strength J, and the high-spin ground state S for single-chain magnets (SCMs) in the intermediate region between the Ising and the Heisenberg limits, were unknown. To explore this relationship, we used density functional theory and ab initio methods to obtain expressions of Δξ and ΔA in terms of D, J, and S of six R4Fe(II)-Re(IV)Cl4(CN)2 (R = diethylformamide (1), dibutylformamide (2), dimethylformamide (3), dimethylbutyramide (4), dimethylpropionamide (5), and diethylacetamide (6)) SCMs in the intermediate region. The ΔA value for compounds 1-3 was very similar to the magnetic anisotropic energy of a single Fe(II), while the value of Δξ was predicted using the exchange interaction of Fe(II) with the neighboring Re(IV), which could be expressed as 2JSReSFe. Similar to compounds 1-3, the anisotropy energy barrier ΔA of compounds 4 and 5 was also equal to (Di - Ei)SFe(2), but the correlation energy Δξ was closely equal to 2JSReSFe(cos 98.4 - cos 180) due to the reversal of the spins on the opposite Fe(II). For compound 6, one unit cell of Re(IV)Fe(II) was regarded as a domain wall since it had two different Re(IV)-Fe(II) couplings. Thus, the Δξ of compound 6 was expressed as 4J″SRe1Fe1SRe2Fe2, where J″ was the coupling constant of the neighboring unit cells of Re1Fe1 and Re2Fe2, and ΔA was equal to the anisotropic energy barrier of one domain wall given by DRe1Fe1(S(2)Re1Fe1 - 1/4). PMID:24673387

  18. Ab initio density functional theory investigation of the structural, electronic and optical properties of Ca3Sb2 in hexagonal and cubic phases

    NASA Astrophysics Data System (ADS)

    Arghavani Nia, Borhan; Sedighi, Matin; Shahrokhi, Masoud; Moradian, Rostam

    2013-11-01

    A density functional theory study of structural, electronical and optical properties of Ca3Sb2 compound in hexagonal and cubic phases is presented. In the exchange-correlation potential, generalized gradient approximation (PBE-GGA) has been used to calculate lattice parameters, bulk modulus, cohesive energy, dielectric function and energy loss spectra. The electronic band structure of this compound has been calculated using the above two approximations as well as another form of PBE-GGA, proposed by Engle and Vosko (EV-GGA). It is found that the hexagonal phase of Ca3Sb2 has an indirect gap in the Γ→N direction; while in the cubic phase there is a direct-gap at the Γ point in the PBE-GGA and EV-GGA. Effects of applying pressure on the band structure of the system studied and optical properties of these systems were calculated.

  19. Ab initio calculation and spectral properties of nano- and bulk materials

    SciTech Connect

    Kulagin, N. A.

    2013-01-15

    This paper presents the development of ab initio calculation of the electronic structure of either clusters, nano-crystals, doped and unperfected bulk crystals. In addition, analysis of selected experimental data for {gamma}- or plasma irradiated pure and doped wide-band gap oxides such as sapphire, {alpha}-Al{sub 2}O{sub 3}, garnet, Y{sub 3}Al{sub 5}O{sub 12}, Gd{sub 3}Sc{sub 2}Al{sub 3}O{sub 12} and perovskites YAlO{sub 3}, SrTiO{sub 3} is presented. Change in the crystals surface morphology and spectroscopic properties of sapphire, perovskites, garnets as well as ion oxidation state in pure and doped {gamma}- and plasma irradiated crystals are discussed in detail using the optical and X ray spectroscopy experimental results.

  20. Far-infrared spectrum and ab initio calculations for vinylene carbonate

    NASA Astrophysics Data System (ADS)

    Autrey, D.; del Rosario, A.; Laane, J.

    2000-09-01

    The far-infrared spectrum of vinylene carbonate shows five closely spaced bands near 233 cm -1, characteristic of a nearly harmonic ring-puckering potential energy function. Using a coordinate dependent kinetic energy expansion, the potential energy function was determined to be V ( cm-1)=1.652×10 5x 2-1.416×10 5x 4 where x is the puckering coordinate in Å. This shows the molecule to be much more rigid than the similar 3-cyclopenten-1-one due to π bonding interactions involving the oxygen atoms adjacent to the carbonyl group. Ab initio calculations with a B3LYP/6-311++G ∗∗ basis set yield structural data in good agreement with the previous microwave work and also predict vibrational frequencies that correspond closely to the experimental values.

  1. Infrared spectra, vibrational assignment, and ab initio calculations for N-bromo-hexafluoro-2-propanimine

    NASA Astrophysics Data System (ADS)

    Panikar, Savitha S.; Guirgis, Gamil A.; Sheehan, Tracie G.; Durig, Douglas T.; Durig, James R.

    2012-05-01

    The infrared spectra of gaseous and solid N-bromo-hexafluoro-2-propanimine, (CF3)2Cdbnd NBr, have been obtained from 2000 to 50 cm-1. The vibrational assignment for the normal modes is proposed based on infrared band contours, group frequencies and normal coordinate calculations utilizing Cs symmetry. The structural parameters have been obtained from ab initio MP2(full)/6-311 + G(d,p) calculations employing the Gaussian-03 program. Additionally, the frequencies and potential energy distributions for the normal modes have been calculated with the MP2(full)/6-31G(d). All of these results are compared to the corresponding data for some similar molecules.

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

    PubMed Central

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

    2015-01-01

    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. PMID:25664744

  3. 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.

  4. 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.

  5. An Efficient Time-Stepping Scheme for Ab Initio Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Tsuchida, Eiji

    2016-08-01

    In ab initio molecular dynamics simulations of real-world problems, the simple Verlet method is still widely used for integrating the equations of motion, while more efficient algorithms are routinely used in classical molecular dynamics. We show that if the Verlet method is used in conjunction with pre- and postprocessing, the accuracy of the time integration is significantly improved with only a small computational overhead. We also propose several extensions of the algorithm required for use in ab initio molecular dynamics. The validity of the processed Verlet method is demonstrated in several examples including ab initio molecular dynamics simulations of liquid water. The structural properties obtained from the processed Verlet method are found to be sufficiently accurate even for large time steps close to the stability limit. This approach results in a 2× performance gain over the standard Verlet method for a given accuracy. We also show how to generate a canonical ensemble within this approach.

  6. Charge transition levels of oxygen, lanthanum, and fluorine related defect structures in bulk hafnium dioxide (HfO2): An ab initio investigation

    NASA Astrophysics Data System (ADS)

    Leitsmann, Roman; Lazarevic, Florian; Nadimi, Ebrahim; Öttking, Rolf; Plänitz, Philipp; Erben, Elke

    2015-06-01

    Intrinsic defect structures and impurity atoms are one of the main sources of leakage current in metal-oxide-semiconductor devices. Using state of the art density functional theory, we have investigated oxygen, lanthanum, and fluorine related defect structures and possible combinations of them. In particular, we have calculated their charge transition levels in bulk m-HfO2. For this purpose, we have developed a new scaling scheme to account for the band gap underestimation within the density functional theory. The obtained results are able to explain the recent experimental observation of a reduction of the trap density near the silicon valence band edge after NF3 treatment and the associated reduction of the device degradation.

  7. Charge transition levels of oxygen, lanthanum, and fluorine related defect structures in bulk hafnium dioxide (HfO{sub 2}): An ab initio investigation

    SciTech Connect

    Leitsmann, Roman Lazarevic, Florian; Plänitz, Philipp; Nadimi, Ebrahim; Öttking, Rolf; Erben, Elke

    2015-06-28

    Intrinsic defect structures and impurity atoms are one of the main sources of leakage current in metal-oxide-semiconductor devices. Using state of the art density functional theory, we have investigated oxygen, lanthanum, and fluorine related defect structures and possible combinations of them. In particular, we have calculated their charge transition levels in bulk m-HfO{sub 2}. For this purpose, we have developed a new scaling scheme to account for the band gap underestimation within the density functional theory. The obtained results are able to explain the recent experimental observation of a reduction of the trap density near the silicon valence band edge after NF{sub 3} treatment and the associated reduction of the device degradation.

  8. 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.

  9. Entropy of Liquid Water from Ab Initio Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Spanu, Leonardo; Zhang, Cui; Galli, Giulia

    2012-02-01

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

  10. Ab initio centroid molecular dynamics: a fully quantum method for condensed-phase dynamics simulations

    NASA Astrophysics Data System (ADS)

    Pavese, Marc; Berard, Daniel R.; Voth, Gregory A.

    1999-01-01

    A fully quantum molecular dynamics method is presented which combines ab initio Car-Parrinello molecular dynamics with centroid molecular dynamics. The first technique allows the forces on the atoms to be obtained from ab initio electronic structure. The second technique, given the forces on the atoms, allows one to calculate an approximate quantum time evolution for the nuclei. The combination of the two, therefore, represents the first feasible approach to simulating the fully quantum dynamics of a many-body system. An application to excess proton translocation along a model water wire will be presented.

  11. Lattice dynamics of rare-earth titanates with the structure of pyrochlore R 2Ti2O7 ( R = Gd, Tb, Dy, Ho, Er, Tm, Yb, and Lu): Ab initio calculation

    NASA Astrophysics Data System (ADS)

    Chernyshev, V. A.; Petrov, V. P.; Nikiforov, A. E.

    2015-05-01

    The ab initio calculation has been performed for the crystal structure and the phonon spectrum of titanates with the structure of pyrochlore R 2Ti2O7 ( R = Gd-Lu). The frequencies and types of fundamental vibrations have been found. For R = Tb, Tm, and Yb, this calculation has been carried out for the first time; furthermore, there is no available information on experimental studies of the phonon spectrum for Tm and Yb. The influence of hydrostatic pressure to 35 GPa on the structure, dynamics, and elastic properties of the Gd2Ti2O7 lattice has been investigated. The dependence of the phonon frequencies on the pressure has been obtained. The calculations have predicted that the relative change in the pyrochlore structure volume during compression at pressures to 35 GPa is well described by the third-order Birch-Murnaghan equation of states. The results of the calculations agree with the available experimental data. It has been shown that the structural, dynamic, and elastic properties of the R 2Ti2O7 crystal lattice can be adequately described in the case where the inner shells of the RE ion up to 4 f are replaced by the pseudopotential.

  12. Structures and Electronic Properties of (KI)n(-/0) (n = 1-4) and K(KI)n(-/0) (n = 1-3) Clusters: Photoelectron Spectroscopy, Isomer-Depletion, and ab Initio Calculations.

    PubMed

    Hou, Gao-Lei; Feng, Gang; Zhao, Li-Juan; Xu, Hong-Guang; Zheng, Wei-Jun

    2015-11-12

    The (KI)n(-) (n = 1-4) and K(KI)n(-) (n = 1-3) clusters were studied by negative ion photoelectron spectroscopy and ab initio calculations. Comparison between the theoretical vertical detachment energies and the experimental values revealed that multiple isomers may coexist in the experiments. The existence of two isomers for K(KI)(-) and K(KI)2(-) were confirmed directly by isomer-depletion experiments, in which the low adiabatic detachment energy isomers were depleted by a 1064 nm laser beam before the anions were photodetached by a 532 nm laser beam. Our results show that the most stable structures of the K(KI)(-), (KI)2(-), and K(KI)2(-) anions are chain structures, while those of their neutral counterparts are planar. Three-dimensional structures start to appear at n = 3 for (KI)n(-/0) and K(KI)n(-/0). In the K(KI)n(-) cluster anions, the excess electron is localized on the extra K atom and forms an electron pair with the existing s electron of the K atom; the resulting negatively charged K prefers to interact with the other positively charged K atoms rather than with the I atoms. Both the anionic and neutral (KI)4 clusters have cuboid structures, which may be regarded as the smallest structural motif of KI crystal. PMID:26473992

  13. Ab initio density functional theory investigation of the structural, electronic and optical properties of Ca{sub 3}Sb{sub 2} in hexagonal and cubic phases

    SciTech Connect

    Arghavani Nia, Borhan; Sedighi, Matin; Shahrokhi, Masoud; Moradian, Rostam

    2013-11-15

    A density functional theory study of structural, electronical and optical properties of Ca{sub 3}Sb{sub 2} compound in hexagonal and cubic phases is presented. In the exchange–correlation potential, generalized gradient approximation (PBE-GGA) has been used to calculate lattice parameters, bulk modulus, cohesive energy, dielectric function and energy loss spectra. The electronic band structure of this compound has been calculated using the above two approximations as well as another form of PBE-GGA, proposed by Engle and Vosko (EV-GGA). It is found that the hexagonal phase of Ca{sub 3}Sb{sub 2} has an indirect gap in the Γ→N direction; while in the cubic phase there is a direct-gap at the Γ point in the PBE-GGA and EV-GGA. Effects of applying pressure on the band structure of the system studied and optical properties of these systems were calculated. - Graphical abstract: A density functional theory study of structural, electronic and optical properties of Ca{sub 3}Sb{sub 2} compound in hexagonal and cubic phases is presented. Display Omitted - Highlights: • Physical properties of Ca{sub 3}Sb{sub 2} in hexagonal and cubic phases are investigated. • It is found that the hexagonal phase is an indirect gap semiconductor. • Ca{sub 3}Sb{sub 2} is a direct-gap semiconductor at the Γ point in the cubic phase. • By increasing pressure the semiconducting band gap and anti-symmetry gap are decreased.

  14. Ab-initio study of structural and electronic properties of thin film and bulk forms of Bi2Q3 (Q = Se, Te) as topological insulators

    NASA Astrophysics Data System (ADS)

    Ranjbardizaj, Ahmad; Mizuseki, Hiroshi; Kawazoe, Yoshiyuki

    2013-03-01

    Bi2Q3 (Q =Se, Te) are the best-known bulk thermoelectric materials, which have been demonstrated to be topological insulators (TI). TI's are insulators with conductive surface states consisting of a single Dirac cones. These materials have layered structures consisting of stacked quintuple layers (QL), with relatively weak coupling between the QL's. Therefore, it might be easy to prepare the Bi2Q3 in the form of thin films with particular thicknesses using the available experimental techniques. In this study, the electronic and structural properties of bulk Bi2Se3 are investigated using density functional theory. Our results show that the Bi2Se3 is an indirect semiconductor with energy gap of ~ 0.27 eV. Additionally, the electronic structure dependence of Bi2Se3to the thicknesses of thin films (n-QL's with n =1,2...9) is considered. It is observed that the electronic structure of this kind of thin films depends on the number of QL's. For n-QL's with n larger than three, the thin film has a bulk band gap and has protected conducting states on its surface. Moreover, the effect of number of layers (n) on band-gap energy is studied. Similar calculations and discussions are carried out for Bi2Te3 and the results are compared to the Bi2Se3 case and also the available theoretical and experimental results.

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

    NASA Astrophysics Data System (ADS)

    Jhalani, Vatsal; Bernardi, Marco

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

  16. AB INITIO STUDY OF STRUCTURAL, ELECTRONIC AND OPTICAL PROPERTIES OF MgxCd1-xX (X = S, Se, Te) ALLOYS

    NASA Astrophysics Data System (ADS)

    Noor, N. A.; Shaukat, A.

    2012-12-01

    This study describes structural, electronic and optical properties of MgxCd1-xX (X = S, Se, Te) alloys in the complete range 0≤x ≤1 of composition x in the zinc-blende (ZB) phase with the help of full-potential linearized augmented plane wave plus local orbitals (FP-LAPW+lo) method within density functional theory (DFT). In order to calculate total energy, generalized gradient approximation (Wu-Cohen GGA) has been applied, which is based on optimization energy. For electronic structure calculations, the corresponding potential is being optimized by Engel-Vosko GGA formalism. Our calculations reveal the nonlinear variation of lattice constant and bulk modulus with different concentration for the end binary and their ternary alloys, which slightly deviates from Vegard's law. The calculated band structures show a direct band gap for all three alloys with increasing order in the complete range of the compositional parameter x. In addition, we have discussed the disorder parameter (gap bowing) and concluded that the total band gap bowing is substantially influenced by the chemical (electronegativity) contribution. The calculated density of states (DOS) of these alloys is discussed in terms of contribution from various s-, p- and d-states of the constituent atoms and charge density distributions plots are analyzed. Optical properties have been presented in the form of the complex dielectric function ɛ(ω), refractive index n(ω) and extinction coefficient k(ω) as function of the incident photon energy, and the results have been compared with existing experimental data and other theoretical calculations.

  17. Synthesis, spectroscopy, electrochemistry and thermogravimetry of copper(II) tridentate Schiff base complexes, theoretical study of the structures of compounds and kinetic study of the tautomerism reactions by ab initio calculations

    NASA Astrophysics Data System (ADS)

    Kianfar, Ali Hossein; Ramazani, Shapour; Fath, Roghaye Hashemi; Roushani, Mahmoud

    2013-03-01

    Attempts to spectroscopic and structural study of copper complexes, some Cu(II) Schiff base complexes were synthesized and characterized by means of electronic, IR, 1HNMR spectra and elemental analysis. The thermal analyses of the complexes were investigated and the first order kinetic parameters were derived for them. The cyclic voltammetric studies in acetonitrile were proposed a monomeric structure for complexes. The structures of compounds were determined by ab initio calculations. In the solid state, the ligands exist as keto-amine/enol-imine tautomeric forms with an intramolecular hydrogen bond (Nsbnd H⋯O) between amine and carbonyl group. The kinetic studies of the tautomerism and equilibrium constant of the reactions were calculated using transition state theory. The optimized molecular geometry and atomic charges were calculated using MP2 method with 6-31G(d) basis set for H, C, N and O atoms and LANL2DZ for the Cu atom. The results suggested that, in the complexes, Cu(II) ion is in pseudo square-planar NO3 coordination geometry. Also the bond lengths and angles were studied and compared.

  18. Determination of Structures and Energetics of Small- and Medium-Sized One-Carbon-Bridged Twisted Amides using ab Initio Molecular Orbital Methods: Implications for Amidic Resonance along the C-N Rotational Pathway.

    PubMed

    Szostak, Roman; Aubé, Jeffrey; Szostak, Michal

    2015-08-21

    Twisted amides containing nitrogen at the bridgehead position are attractive practical prototypes for the investigation of the electronic and structural properties of nonplanar amide linkages. Changes that occur during rotation around the N-C(O) axis in one-carbon-bridged twisted amides have been studied using ab initio molecular orbital methods. Calculations at the MP2/6-311++G(d,p) level performed on a set of one-carbon-bridged lactams, including 20 distinct scaffolds ranging from [2.2.1] to [6.3.1] ring systems, with the C═O bond on the shortest bridge indicate significant variations in structures, resonance energies, proton affinities, core ionization energies, frontier molecular orbitals, atomic charges, and infrared frequencies that reflect structural changes corresponding to the extent of resonance stabilization during rotation along the N-C(O) axis. The results are discussed in the context of resonance theory and activation of amides toward N-protonation (N-activation) by distortion. This study demonstrates that one-carbon-bridged lactams-a class of readily available, hydrolytically robust twisted amides-are ideally suited to span the whole spectrum of the amide bond distortion energy surface. Notably, this study provides a blueprint for the rational design and application of nonplanar amides in organic synthesis. The presented findings strongly support the classical amide bond resonance model in predicting the properties of nonplanar amides.

  19. An ab initio study of MgO epitaxial layers on a Co2MnSi (0 0 1) surface: influence of the interface structure on tunnelling conductance

    NASA Astrophysics Data System (ADS)

    Yu, H. L.; Jiang, X. F.; Zheng, Y.; Yang, G. W.

    2012-08-01

    The formation of MgO epitaxial layers on a Co2MnSi (0 0 1) surface was studied using the ab initio electronic structure calculations based on the density functional theory. The free energy calculations showed that the O-rich, O-top and Mg-rich configurations in the CoCo termination case, and the O-rich and O-top configurations in the MnSi termination case were thermodynamically stable. The magnetic and electronic properties of these stable configurations were investigated in detail, and the results indicated that only the Mg-rich configuration with CoCo termination exhibited near half-metallic properties at the interface. The influence of the interfacial structure on the tunnelling conductance of the Co2MnSi/MgO/Co2MnSi magnetic tunnel junctions (MTJs) was also discussed using the nonequilibrium Green's function method. The attained conductance showed that a large difference of up to 104 was observed in the magnitude of parallel conductance, which means that the interface structure plays a crucial role in the electronic transport of the MTJ. These findings are useful in designing MTJs with high performance.

  20. Structural, vibrational, electronic, NMR, NLO and reactivity analyses of (3Z)-3-(2-oxo-2-phenylethylidene)-1,3-dihydro-2H-indol-2-one (OPEDI) by ab initio HF and DFT calculations.

    PubMed

    Sridevi, C; Velraj, G

    2013-04-15

    This study represents the vibrational, electronic, NMR, NLO, reactivity and structural aspects of (3Z)-3-(2-oxo-2-phenylethylidene)-1,3-dihydro-2H-indol-2-one (OPEDI). A detailed interpretation of the FT-IR, FT-Raman, UV and NMR spectra were reported. Theoretical calculations were performed by ab initio HF and density functional theory (DFT)/B3LYP method using 6-311++G(d,p) basis sets. The most preferred Z isomer (cis-configuration) was confirmed through PES scan studies. The vibrational wavenumbers and potential energy distribution (PED) of various normal modes were calculated. The lower frontier orbital energy gap and high dipole moment of OPEDI illustrates the high reactivity. The stability and charge delocalization of the molecule was studied by natural bond orbital (NBO) analysis. OPEDI exhibited good nonlinear optical activity and was 13 times greater than that of urea. Molecular electrostatic potential (MEP) was carried out for predicting the reactive sites. The NMR results indicated that the observed chemical shifts depend not only on the structure of the molecule being studied, but also on the solvent used.

  1. 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

  2. Realistic multiband k .p approach from ab initio and spin-orbit coupling effects of InAs and InP in wurtzite phase

    NASA Astrophysics Data System (ADS)

    Faria Junior, Paulo E.; Campos, Tiago; Bastos, Carlos M. O.; Gmitra, Martin; Fabian, Jaroslav; Sipahi, Guilherme M.

    2016-06-01

    Semiconductor nanowires based on non-nitride III-V compounds can be synthesized under certain growth conditions to favor the appearance of the wurtzite crystal phase. Despite reports in the literature of ab initio band structures for these wurtzite compounds, we still lack effective multiband models and parameter sets that can be simply used to investigate physical properties of such systems, for instance, under quantum confinement effects. In order to address this deficiency, in this study we calculate the ab initio band structure of bulk InAs and InP in the wurtzite phase and develop an 8 ×8 k .p Hamiltonian to describe the energy bands around the Γ point. We show that our k .p model is robust and can be fitted to describe the important features of the ab initio band structure. The correct description of the spin-splitting effects that arise due to the lack of inversion symmetry in wurtzite crystals is obtained with the k -dependent spin-orbit term in the Hamiltonian, often neglected in the literature. All the energy bands display a Rashba-like spin texture for the in-plane spin expectation value. We also provide the density of states and the carrier density as functions of the Fermi energy. Alternatively, we show an analytical description of the conduction band, valid close to the Γ point. The same fitting procedure is applied to the 6 ×6 valence band Hamiltonian. However, we find that the most reliable approach is the 8 ×8 k .p Hamiltonian for both compounds. The k .p Hamiltonians and parameter sets that we develop in this paper provide a reliable theoretical framework that can be easily applied to investigate electronic, transport, optical, and spin properties of InAs- and InP-based nanostructures.

  3. 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

  4. 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.

  5. Discovering chemistry with an ab initio nanoreactor

    DOE PAGES

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

    2014-11-02

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

  6. 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.

  7. Study of B1 (NaCl-type) to B2 (CsCl-type) pressure-induced structural phase transition in BaS, BaSe and BaTe using ab initio computations

    NASA Astrophysics Data System (ADS)

    Zhou, X.; Roehl, J. L.; Lind, C.; Khare, S. V.

    2013-02-01

    We have studied the pressure-induced phase transitions from NaCl-type (B1) to CsCl-type (B2) structure in BaS, BaSe and BaTe by using ab initio density functional theory computations in the local density approximation. The Buerger and WTM mechanisms were explored by mapping the enthalpy contours in two- and four-dimensional configuration space for the two mechanisms, respectively. Transition pressures for BaS, BaSe and BaTe were determined to be 5.5 GPa, 4.9 GPa and 3.4 GPa, respectively. From these configuration space landscapes, a low enthalpy barrier path was constructed for the transitions to proceed at three different pressures. We obtained barriers of 0.18, 0.16 and 0.15 eV/pair (17.4, 15.4 and 14.5 kJ mol-1) for the Buerger mechanism and 0.13, 0.13 and 0.12 eV/pair (12.5, 12.5 and 11.6 kJ mol-1) for the WTM mechanism at the transition pressures for BaS, BaSe and BaTe, respectively, indicating that the WTM mechanism is slightly more favorable in these compounds. We describe the difference between the two mechanisms by differences in their symmetry and atomic coordination.

  8. Vibrational and ab initio molecular dynamics studies of bradykinin

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

  9. Ab initio alpha-alpha scattering.

    PubMed

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

    2015-12-01

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

  10. Ab initio alpha-alpha scattering.

    PubMed

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

    2015-12-01

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

  11. 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…

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

    NASA Astrophysics Data System (ADS)

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

    2011-05-01

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

  13. Ab initio and density functional theory calculations of molecular structure and vibrational spectra of 4-(2-Hydroxyethyl) piperazine-1-ethanesulfonic acid

    NASA Astrophysics Data System (ADS)

    Kumar, J. Sharmi; Devi, T. S. Renuga; Ramkumaar, G. R.; Bright, A.

    2016-01-01

    The FTIR and FT-Raman spectra of 4-(2-Hydroxyethyl) piperazine-1-ethanesulfonic acid were recorded and the structural and spectroscopic data of the molecule in the ground state were calculated using Hartree-Fock and Density Functional Method (B3LYP). The most stable conformer was optimized and the structural and vibrational parameters were determined. With the observed FTIR and FT-Raman data, a complete vibrational band assignment and analysis of the fundamental modes of the compound were carried out. Thermodynamic properties, Mulliken and natural atomic charge distribution were calculated using both Hartree-Fock and Density Functional Method and compared. UV-Visible and HOMO-LUMO analysis were carried out. 1H and 13C NMR chemical shifts of the molecule were calculated using gauge including atomic orbital method and were compared with experimental results. Stability of the molecule arising from hyperconjugative interactions and charge delocalization has been analyzed using natural bond orbital analysis. The first order hyperpolarizability (β) and molecular electrostatic potential of the molecule was computed using DFT calculations. The electron density based local reactivity descriptor such as Fukui functions were calculated to explain the chemically reactive site in the molecule.

  14. Ab initio and density functional theory calculations of molecular structure and vibrational spectra of 4-(2-Hydroxyethyl) piperazine-1-ethanesulfonic acid.

    PubMed

    Kumar, J Sharmi; Devi, T S Renuga; Ramkumaar, G R; Bright, A

    2016-01-01

    The FTIR and FT-Raman spectra of 4-(2-Hydroxyethyl) piperazine-1-ethanesulfonic acid were recorded and the structural and spectroscopic data of the molecule in the ground state were calculated using Hartree-Fock and Density Functional Method (B3LYP). The most stable conformer was optimized and the structural and vibrational parameters were determined. With the observed FTIR and FT-Raman data, a complete vibrational band assignment and analysis of the fundamental modes of the compound were carried out. Thermodynamic properties, Mulliken and natural atomic charge distribution were calculated using both Hartree-Fock and Density Functional Method and compared. UV-Visible and HOMO-LUMO analysis were carried out. (1)H and (13)C NMR chemical shifts of the molecule were calculated using gauge including atomic orbital method and were compared with experimental results. Stability of the molecule arising from hyperconjugative interactions and charge delocalization has been analyzed using natural bond orbital analysis. The first order hyperpolarizability (β) and molecular electrostatic potential of the molecule was computed using DFT calculations. The electron density based local reactivity descriptor such as Fukui functions were calculated to explain the chemically reactive site in the molecule.

  15. 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.

  16. Size effects on the structural, electronic, and optical properties of (5,0) finite-length carbon nanotube: An ab-initio electronic structure study

    NASA Astrophysics Data System (ADS)

    Tarighi Ahmadpour, Mahdi; Hashemifar, S. Javad; Rostamnejadi, Ali

    2016-07-01

    We use density functional computations to study the zero temperature structural, electronic, magnetic, and optical properties of (5,0) finite carbon nanotubes (FCNT), with length in the range of 4-44 Å. It is found that the structural and electronic properties of (5,0) FCNTs, in the ground state, converge at a length of about 30 Å, while the excited state properties exhibit long-range edge effects. We discuss that curvature effects enhance energy gap of FCNTs, in contrast to the known trend in the periodic limit. It is seen that compensation of curvature effects in two special small sizes may give rise to spontaneous magnetization. The obtained cohesive energies provide some insights into the effects of environment on the growth of FCNTs. The second-order difference of the total energies reveals an important magic size of about 15 Å. The optical and dynamical magnetic responses of the FCNTs to polarized electromagnetic pulses are studied by time dependent density functional theory. The results show that the static and dynamic magnetic properties mainly come from the edge carbon atoms. The optical absorption properties are described in terms of local field effects and characterized by Casida linear response method.

  17. Characterization and ab initio XRPD structure determination of a novel silicate with Vierer single chains: the crystal structure of NaYSi2O6.

    PubMed

    Többens, Daniel M; Kahlenberg, Volker; Kaindl, Reinhard

    2005-12-12

    The crystal structure of a sodium yttrium silicate with composition NaYSi2O6 has been determined from laboratory X-ray powder diffraction data by simulated annealing, and has been subsequently refined with the Rietveld technique. The compound is monoclinic with space group P2(1)/c and unit cell parameters of a=5.40787(2) A, b=13.69784(5) A, c=7.58431(3) A, and beta=109.9140(3) degrees at 23.5 degrees C (Z=4). The structure was found to be a single-chain silicate with a chain periodicity of four. The two symmetry dependent [Si4O12] chains in the unit cell are parallel to c. A prominent feature is the strong folding of the crankshaft-like chains within the b,c-plane resulting in intrachain Si-Si-Si angles close to 90 degrees. The coordination of the Y3+ ions by O2- is 7-fold in the form of slightly irregular pentagonal bipyramids, with oxygen atoms from four different chains contributing to the coordination polyhedron. Na+ ions are irregularly coordinated by 10 oxygens from two neighboring chains. No disorder of Na+ and Y3+ between the two nontetrahedral cation sites could be observed. Furthermore, micro-Raman spectra have been obtained from the polycrystalline material. PMID:16323944

  18. Differences in the surface electronic structure of Ge(001) and Si(001) from angle-resolved photoemission spectroscopy and ab-initio theory

    NASA Astrophysics Data System (ADS)

    Hatch, Richard C.; Seo, Hosung; Ponath, Patrick; Choi, Miri; Posadas, Agham B.; Demkov, Alexander A.

    2014-03-01

    Using high-resolution angle-resolved photoemission spectroscopy (ARPES) we compare the surface electronic structure of both Ge(001) and Si(001) surfaces. Unlike previous ARPES experiments, where the Ge(001) surfaces were prepared using cycles of ion sputtering and annealing, our Ge(001) surfaces were prepared using a combination of wet etching and oxygen plasma cleaning. This new technique has the advantage that it avoids the incomplete healing of surface roughening associated with sputtering and annealing cycles. The ARPES data show that the dimer-derived surface state that determines the charge neutrality level, and thus the Schottky barrier height in Si, is actually a surface resonance in Ge, and the highest occupied state is a bulk state. In order to avoid theory predicting an overlap of the valence and conduction bands, we employed first-principles, hybrid density functional theory (DFT). This theory effectively explains the presence of a number of photoemission features in both Si and Ge. We found it is necessary to incorporate spin-orbit interaction in the hybrid DFT calculations for Ge in order to model ARPES data, and we found a spin-orbit splitting of 0.28 eV both experimentally and theoretically.

  19. 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].

  20. 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.

  1. 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.

  2. Ab initio and RRKM calculations of o-benzyne pyrolysis

    NASA Astrophysics Data System (ADS)

    Deng, Wei-Qiao; Han, Ke-Li; Zhan, Ji-Ping; He, Guo-Zhong

    1998-05-01

    Recently, a new mechanism has been provided in the phenyl pyrolysis, that is, the phenyl dissociation favours the benzyne channel by losing an H atom [H. Wang, M. Frenklach, J. Phys. Chem., 98 (1994) 11465]. In this Letter, the dissociation of o-benzyne has been investigated by means of ab initio theory. The geometries and structures of o-benzyne with its pyrolysis products C 4H 2, C 2H 2 and also the transition state were optimized at the UHF/6-31G* level. The single point energies were refined by B3LYP/6-31G* calculations. The unimolecular rate constants for o-benzyne pyrolysis in different pressures were calculated by the Rice-Ramsperger-Kassel-Marcus (RRKM) method.

  3. Ab initio water pair potential with flexible monomers.

    PubMed

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

    2015-03-26

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

  4. Ab Initio Force Fields for Imidazolium-Based Ionic Liquids.

    PubMed

    McDaniel, Jesse G; Choi, Eunsong; Son, Chang Yun; Schmidt, J R; Yethiraj, Arun

    2016-07-21

    We develop ab initio force fields for alkylimidazolium-based ionic liquids (ILs) that predict the density, heats of vaporization, diffusion, and conductivity that are in semiquantitative agreement with experimental data. These predictions are useful in light of the scarcity of and sometimes inconsistency in experimental heats of vaporization and diffusion coefficients. We illuminate physical trends in the liquid cohesive energy with cation chain length and anion. These trends are different than those based on the experimental heats of vaporization. Molecular dynamics prediction of the room temperature dynamics of such ILs is more difficult than is generally realized in the literature due to large statistical uncertainties and sensitivity to subtle force field details. We believe that our developed force fields will be useful for correctly determining the physics responsible for the structure/property relationships in neat ILs.

  5. 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.

  6. 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

  7. Ab Initio Structure Determination of New Mixed Zirconium Hydroxide Nitrates Zr M(OH) 2(NO 3) 3 ( M=K, Rb) from X-Ray Powder Diffraction Data

    NASA Astrophysics Data System (ADS)

    Bénard-Rocherullé, P.; Louër, D.

    2000-01-01

    Two new mixed zirconium hydroxide nitrates ZrM(OH)2(NO3)3 (M=K, Rb) have been synthesized through a wet chemical process. The two crystal structures have been solved ab initio from powder diffraction data collected with conventional monochromatic X-rays. ZrK(OH)2(NO3)3 crystallizes with a monoclinic symmetry [a=16.569(3) Å, b=5.791(1) Å, c=9.813(2) Å, β=90.17(2)°, P21/n, Z=4) and ZrRb(OH)2(NO3)3 with an orthorhombic symmetry [a=10.126(3) Å, b=16.492(3) Å, c=5.855(2) Å, Pbcn, Z=4]. The heavy atoms have been located from an interpretation of Patterson functions. The coordinates of the remaining light atoms have been determined from successive three-dimensional Fourier maps. The final Rietveld refinement indicators were RF=0.042, Rp=0.077 (M=K) and RF=0.064, Rp=0.115 (M=Rb). Like the structures of α-Zr(OH)2(NO3)2·1.65H2O and β-Zr(OH)2(NO3)2·H2O, the structures of the mixed basic zirconium nitrates are built from edge-sharing ZrO8 polyhedra to form infinite neutral zigzag chains of chemical composition [Zr(OH)4/2(NO3)2]n. The main difference with respect to the hydrated phases is the nature of the cohesion in the structures based on ionic contacts involving intercalated K+ or Rb+ and NO-3 species in the mixed compounds and on a complex hydrogen-bonding network in the hydrated phases. The crystal chemistry of the zirconium hydroxide nitrates is discussed and three structure types are identified.

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

    The calculation and characterization of the IR spectrum of liquid water have remained a challenge for theory. In this paper, we address this challenge using a combination of ab initio approaches, namely, a quantum treatment of IR spectrum using the ab initio WHBB water potential energy surface and a refined ab initio dipole moment surface. The quantum treatment is based on the embedded local monomer method, in which the three intramolecular modes of each embedded H2O monomer are fully coupled and also coupled singly to each of six intermolecular modes. The new dipole moment surface consists of a previous spectroscopically accurate 1-body dipole moment surface and a newly fitted ab initio intrinsic 2-body dipole moment. A detailed analysis of the new dipole moment surface in terms of the coordinate dependence of the effective atomic charges is done along with tests of it for the water dimer and prism hexamer double-harmonic spectra against direct ab initio calculations. The liquid configurations are taken from previous molecular dynamics calculations of Skinner and co-workers, using the TIP4P plus E3B rigid monomer water potential. The IR spectrum of water at 300 K in the range of 0-4000 cm-1 is calculated and compared with experiment, using the ab initio WHBB potential and new ab initio dipole moment, the q-TIP4P/F potential, which has a fixed-charged description of the dipole moment, and the TTM3-F potential and dipole moment surfaces. The newly calculated ab initio spectrum is in very good agreement with experiment throughout the above spectral range, both in band positions and intensities. This contrasts to results with the other potentials and dipole moments, especially the fixed-charge q-TIP4P/F model, which gives unrealistic intensities. The calculated ab initio spectrum is analyzed by examining the contribution of various transitions to each band.

  9. 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.

  10. Ab initio derivation of model energy density functionals

    NASA Astrophysics Data System (ADS)

    Dobaczewski, Jacek

    2016-08-01

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

  11. On the hierarchical parallelization of ab initio simulations

    NASA Astrophysics Data System (ADS)

    Ruiz-Barragan, Sergi; Ishimura, Kazuya; Shiga, Motoyuki

    2016-02-01

    A hierarchical parallelization has been implemented in a new unified code PIMD-SMASH for ab initio simulation where the replicas and the Born-Oppenheimer forces are parallelized. It is demonstrated that ab initio path integral molecular dynamics simulations can be carried out very efficiently for systems up to a few tens of water molecules. The code was then used to study a Diels-Alder reaction of cyclopentadiene and butenone by ab initio string method. A reduction in the reaction energy barrier is found in the presence of hydrogen-bonded water, in accordance with experiment.

  12. Quantization and topological states in the spin Hall conductivity of low-dimensional systems: An ab initio study

    NASA Astrophysics Data System (ADS)

    Matthes, L.; Küfner, S.; Furthmüller, J.; Bechstedt, F.

    2016-03-01

    Ab initio relativistic band structure calculations are performed for the frequency-dependent spin Hall conductivity of two-dimensional atomically thin crystals and one-dimensional nanoribbons. We study the influence of topology, quantization, and topological edge states. As model systems fully halogenated germanene, GeI, and its zigzag nanoribbons are investigated. GeI represents a topological insulator (TI). For comparison, also the TI germanene and the trivial insulator hydrogenated germanene are studied. For the TIs we demonstrate the quantization of the static spin Hall conductivity. It is hardly influenced by temperature and Fermi level shift. Its frequency dependence is governed by the band-structure details. Topological edge states influence the conductivity mainly for vanishing frequencies.

  13. Microwave absorption enhancement, magnetic coupling and ab initio electronic structure of monodispersed (Mn1-xCox)3O4 nanoparticles

    NASA Astrophysics Data System (ADS)

    Zhao, Pengfei; Liang, Chongyun; Gong, Xiwen; Gao, Ran; Liu, Jiwei; Wang, Min; Che, Renchao

    2013-08-01

    Monodispersed manganese oxide (Mn1-xCox)3O4 (0 <= x <= 0.5) nanoparticles, less than 10 nm size, are respectively synthesized via a facile thermolysis method at a rather low temperature, ranging from 90 to 100 °C, without any inertia gas for protection. The influences of the Co dopant content on the critical reaction temperature required for the nanoparticle formation, electronic band structures, magnetic properties, and the microwave absorption capability of (Mn1-xCox)3O4 are comprehensively investigated by means of both experimental and theoretical approaches including powder X-ray diffraction (XRD), electron energy loss spectroscopy (EELS), super conductivity quantum interference device (SQUID) examination, and first-principle simulations. Co is successfully doped into the Mn atomic sites of the (Mn1-xCox)3O4 lattice, which is further confirmed by EELS data acquired from one individual nanoparticle. Therefore, continuous solid solutions of well-crystallized (Mn1-xCox)3O4 products are achieved without any impurity phase or phase separation. With increases in the Co dopant concentration x from 0 to 0.5, the lattice parameters change systemically, where the overall saturation magnetization at 30 K increases due to the more intense coupling of the 3d electrons between Mn and Co, as revealed by simulations. The microwave absorption properties of the (Mn1-xCox)3O4 nanoparticles are examined between 2 and 18 GHz. The maximum absorption peak -11.0 dB of the x = 0 sample is enhanced to -11.5 dB for x = 0.2, -12.7 dB for x = 0.25, -15.6 dB for x = 0.33, and -24.0 dB for x = 0.5 respectively, suggesting the Co doping effects. Our results might provide novel insights into the understanding of the influences of metallic ion doping on the electromagnetic properties of metallic oxide nanomaterials.Monodispersed manganese oxide (Mn1-xCox)3O4 (0 <= x <= 0.5) nanoparticles, less than 10 nm size, are respectively synthesized via a facile thermolysis method at a rather low

  14. Investigation of polarization effects in the gramicidin A channel from ab initio molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Timko, Jeff; Kuyucak, Serdar

    2012-11-01

    Polarization is an important component of molecular interactions and is expected to play a particularly significant role in inhomogeneous environments such as pores and interfaces. Here we investigate the effects of polarization in the gramicidin A ion channel by performing quantum mechanics/molecular mechanics molecular dynamics (MD) simulations and comparing the results with those obtained from classical MD simulations with non-polarizable force fields. We consider the dipole moments of backbone carbonyl groups and channel water molecules as well as a number of structural quantities of interest. The ab initio results show that the dipole moments of the carbonyl groups and water molecules are highly sensitive to the hydrogen bonds (H-bonds) they participate in. In the absence of a K+ ion, water molecules in the channel are quite mobile, making the H-bond network highly dynamic. A central K+ ion acts as an anchor for the channel waters, stabilizing the H-bond network and thereby increasing their average dipole moments. In contrast, the K+ ion has little effect on the dipole moments of the neighboring carbonyl groups. The weakness of the ion-peptide interactions helps to explain the near diffusion-rate conductance of K+ ions through the channel. We also address the sampling issue in relatively short ab initio MD simulations. Results obtained from a continuous 20 ps ab initio MD simulation are compared with those generated by sampling ten windows from a much longer classical MD simulation and running each window for 2 ps with ab initio MD. Both methods yield similar results for a number of quantities of interest, indicating that fluctuations are fast enough to justify the short ab initio MD simulations.

  15. Investigation of polarization effects in the gramicidin A channel from ab initio molecular dynamics simulations.

    PubMed

    Timko, Jeff; Kuyucak, Serdar

    2012-11-28

    Polarization is an important component of molecular interactions and is expected to play a particularly significant role in inhomogeneous environments such as pores and interfaces. Here we investigate the effects of polarization in the gramicidin A ion channel by performing quantum mechanics/molecular mechanics molecular dynamics (MD) simulations and comparing the results with those obtained from classical MD simulations with non-polarizable force fields. We consider the dipole moments of backbone carbonyl groups and channel water molecules as well as a number of structural quantities of interest. The ab initio results show that the dipole moments of the carbonyl groups and water molecules are highly sensitive to the hydrogen bonds (H-bonds) they participate in. In the absence of a K(+) ion, water molecules in the channel are quite mobile, making the H-bond network highly dynamic. A central K(+) ion acts as an anchor for the channel waters, stabilizing the H-bond network and thereby increasing their average dipole moments. In contrast, the K(+) ion has little effect on the dipole moments of the neighboring carbonyl groups. The weakness of the ion-peptide interactions helps to explain the near diffusion-rate conductance of K(+) ions through the channel. We also address the sampling issue in relatively short ab initio MD simulations. Results obtained from a continuous 20 ps ab initio MD simulation are compared with those generated by sampling ten windows from a much longer classical MD simulation and running each window for 2 ps with ab initio MD. Both methods yield similar results for a number of quantities of interest, indicating that fluctuations are fast enough to justify the short ab initio MD simulations.

  16. Silicene-derived phases on Ag(111) substrate versus coverage: Ab initio studies

    NASA Astrophysics Data System (ADS)

    Pflugradt, P.; Matthes, L.; Bechstedt, F.

    2014-01-01

    Silicene is systematically investigated as an epitaxial overlayer on an Ag(111) substrate based on the ab initio density functional theory. The geometry and stability of five silicene-silver adsorbate systems with four coincidence lattices, √7 ×√7 on √13 ×√13 , 3×3 on 4×4, 2×2 on √7 ×√7 , and √7 ×√7 on 2√3 ×2√3 , are related to the Si coverage, biaxial strain, and preparation conditions. Their phase diagram is calculated for varying chemical potential of the Si reservoir. The scanning tunneling microscopy images calculated for the optimized atomic geometries agree with those observed experimentally. The destruction of the original honeycomb symmetry and the strong adsorbate-substrate interaction significantly influence the electronic structure. Four peeled-off silicene sheets show conical linear bands, with small gaps. However, the band edges of the 3×3 on 4×4 geometry cannot be explained in terms of gap opening between Dirac cones for symmetry reasons. We confirm the conclusion that the linear bands observed by ARPES are due to folded Ag bands.

  17. 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)

  18. 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.

  19. Ab initio two-component Ehrenfest dynamics

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

  20. Phonocatalysis. An ab initio simulation experiment

    NASA Astrophysics Data System (ADS)

    Kim, Kwangnam; Kaviany, Massoud

    2016-06-01

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

  1. Molecular structure and vibrational assignment of melaminium phthalate by density functional theory (DFT) and ab initio Hartree-Fock (HF) calculations.

    PubMed

    Tarcan, Erdoğan; Altindağ, Ozgü; Avci, Davut; Atalay, Yusuf

    2008-11-01

    The molecular geometry, the normal mode frequencies and corresponding vibrational assignment of melaminium phthalate (C3H7N6+.C8H5O4(-)) in the ground state were performed by HF and B3LYP levels of theory using the 6-31G(d) basis set. The optimized bond length numbers with bond angles are in good agreement with the X-ray data. The vibrational spectra of melaminium phthalate which is calculated by HF and B3LYP methods, reproduces vibrational wave numbers with an accuracy which allows reliable vibrational assignments. The title compound has been studied in the 4000-100 cm(-1) region where the theoretical evaluation and assignment of all observed bands were made.

  2. Ab initio calculations on potential energy curves and radiative lifetimes for the band systems A(2)Π-X(2)Σ(+) of magnesium monohalides MgX (X=F, Cl, Br, I).

    PubMed

    Wu, Dong-lan; Tan, Bin; Qin, Jiu-ying; Wan, Hui-jun; Xie, An-dong; Yan, Bing; Ding, Da-jun

    2015-11-01

    Ab initio calculations on potential energy curves (PECs), spectroscopic constants, transition dipole moments, radiative transition probabilities and lifetimes for the ground state (X(2)Σ(+)) and the first excited state (A(2)Π) of MgX (X=F, Cl, Br, I) molecules are determined by high-level internally contracted multi-reference configuration interaction (ic-MRCI) method. In order to improve the calculation, the Davidson modification (+Q) and scalar relativistic correction are included. The present results show that most of spectroscopic constants are in accordance with the measurements, the equilibrium internuclear distance Re increases while the other spectroscopic constants reduce along with the increasing of the atomic number of the halogen from F to I. Diagonal vibrational transitions are found to be dominant for the A(2)Π→X(2)Σ(+) system of MgX molecules. The corresponding radiative lifetimes of ν'=0 are computed to be 7.24, 9.98, 18.94 and 22.72 ns for MgF, MgCl, MgBr, and MgI, respectively. The calculated result of MgF molecule is in good agreement with the recent theoretical result of 7.16 ns, with a small relative error percent of 1.11%.

  3. 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

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

    PubMed

    Drumm, Daniel W; Budi, Akin; Per, Manolo C; Russo, Salvy P; L Hollenberg, Lloyd C

    2013-02-27

    : 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%.

  5. Inductive and steric effects on the gas-phase structure of tert-butyl acetate. Electron diffraction and ab initio MO investigations

    SciTech Connect

    Takeuchi, Hiroshi; Enmi, Jun-ichiro; Onozaki, Manabu; Egawa, Toru; Konaka, Shigehiro

    1994-09-01

    Gas electron diffusion and HF/4-21 G calculations on geometric parameters and harmonic force constants are used to study the molecular structure of tert-butyl acetate. This determined that C{sub 1} = O{sub 2} is (cis) to O{sub 4}-C{sub 5} and the tert-butyl group is staggered to the C{sub 1}-O{sub 4} bond. The structural parameters are also determined. C{sub 1}-O{sub 4} bond length shortening is rationalized in terms of the resonance effect and the electron-releasing inductive effect of substituents. 29 refs., 4 figs., 4 tabs.

  6. Ab initio study of the structural phase transitions of the double perovskites Sr2MWO6 (M=Zn, Ca, Mg)

    NASA Astrophysics Data System (ADS)

    Petralanda, U.; Etxebarria, I.

    2014-02-01

    We study the interplay of structural distortions in double perovskites Sr2MWO6 (M = Zn, Ca, Mg) by means of first-principles calculations and group theoretical analysis. Structure relaxations of the cubic, tetragonal, and monoclinic phases show that the ground states of the three compounds are monoclinic, although the energy difference between the monoclinic and tetragonal structures is very small in the case of Sr2MgWO6. The symmetry analysis of the distortions involved in the experimental and calculated low-temperature structures shows that the amplitude of two primary distortions associated to rigid rotations of the MX6 and WO6 octahedra are dominant, although the amplitude of a third mode related to deformations of the MX6 groups can not be neglected. The energy maps of the space spanned by the three relevant modes are calculated, and the couplings among the modes are evaluated, showing that the role of a hard secondary mode (in the Landau sense) coupled trilinearly to the two primary instabilities is crucial to stabilize the monoclinic ground state. Results suggest that the key role of the trilinear coupling among three modes could be rather common. A phenomenological theory including the effects of the chemical pressure is also developed. We find that the evolution of the stiffness constants in terms of the atomic substitution follows an accurate linear dependence and that the influence of quantum saturation of the order parameters could stabilize the tetragonal phase of Sr2MgWO6.

  7. Epitaxial strain induced ferroelectricity in rocksalt binary compound: Hybrid functional Ab initio calculation and soft mode group theory analysis

    NASA Astrophysics Data System (ADS)

    Kim, Bog G.

    2011-05-01

    We have studied the detailed mechanism of epitaxial strain induced ferroelectricity in rocksalt binary compound by ab initio calculation and soft mode group theory analysis. By applying compressive strain, cubic binary rocksalt (F m3m) transforms into tetragonal (I 4/mmm) structure. With increasing compressive strain, tetragonal structure becomes unstable against spontaneous transformation to lower symmetry tetragonal structure (I 4/mm), evident both from ab initio calculation and from soft mode group theory analysis. For the tensile strain, phase transition sequence can be cubic binary rocksalt to tetragonal (I 4/mmm) and to orthorhombic structure (I m2m). From ab initio calculation and space group analysis, we propose that the epitaxial strain induced ferroelectricity of rocksalt binary compound is the generic property.

  8. Furanose ring conformation: the application of ab initio molecular orbital calculations to the structure and dynamics of erythrofuranose and threofuranose rings

    SciTech Connect

    Serianni, A.S.; Chipman, D.M.

    1987-09-02

    Ab initiao molecular orbital calculations have been conducted on four tetrofuranose anomers, ..cap alpha..- and ..beta..-D-erythrofuranose and ..cap alpha..- and ..beta..-D-threofuranose, to study the effect of ring conformation on molecular parameters (bond lengths, bond angles, bond torsions) and on total energies. Geometric optimizations of envelope and planar conformers were conducted using the STO-3G basis set; single-point calculations were also performed with the 3-21G basis set. Preferred solution conformations deduced from previous NMR studies are in good agreement with those predicted by calculation, indicating that the intrinsic structures of these furanoses dictate their preferred geometries, and that solvation by water (/sup 2/H/sub 2/O) does not appear to be a major conformational determinant. The ..beta..-D-erythro configuration, which is structurally related to the ..beta..-D-ribo configuration found in RNA, was found to have significantly different conformational behavior from the other three configurations.

  9. 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.

  10. 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

  11. Ab Initio Molecular Dynamics Simulations of an Excess Proton in a Triethylene Glycol-Water Solution: Solvation Structure, Mechanism, and Kinetics.

    PubMed

    McDonnell, Marshall T; Xu, Haixuan; Keffer, David J

    2016-06-16

    We investigate the solvation shell structures, the distribution of protonic defects, mechanistic details, kinetics, and dynamics of proton transfer for an excess proton in bulk water and for an excess proton in an aqueous solution of triethylene glycol (TEG) via Car-Parrinello molecular dynamics simulations. The PW91, PBE, and PBE with the Tkatchenko-Scheffler (TS) density-dependent dispersion functionals were used and compared for bulk water and the TEG-water mixtures. The excess proton is found to reside predominantly on water molecules but also resides on hydroxyl groups of TEG. The lifetimes associated with structural diffusion time scales of the protonated water were found to be on the order of ∼1 ps. All three functionals studied support the presolvation requirement for structural diffusion. The highest level of theory shows a reduction in the free energy barrier for water-water proton transfer in TEG-water mixtures compared to bulk water. The effect of TEG shows no strong change in the kinetics for TEG-water mixtures compared to bulk water for this same level of theory. The excess proton displays burst-rest behavior in the presence of TEG, similar to that found in bulk water. We find that the TEG chain disrupts the hydrogen-bond network, causing the solvation shell around water to be populated by TEG chain groups instead of other waters, reducing the rigidity of the hydrogen-bond network. Methylene is a dominant hydrogen bond donor for the protonated water in hydrogen-bond networks associated with proton transfer and structural diffusion. This is consistent with previous studies that have found the hydronium ion to be amphiphilic in nature and to have higher proton mobility at oil-water interfaces. PMID:27218455

  12. Theoretical prediction of the band offsets at the ZnO/anatase TiO2 and GaN/ZnO heterojunctions using the self-consistent ab initio DFT/GGA-1/2 method

    NASA Astrophysics Data System (ADS)

    Fang, D. Q.; Zhang, S. L.

    2016-01-01

    The band offsets of the ZnO/anatase TiO2 and GaN/ZnO heterojunctions are calculated using the density functional theory/generalized gradient approximation (DFT/GGA)-1/2 method, which takes into account the self-energy corrections and can give an approximate description to the quasiparticle characteristics of the electronic structure of semiconductors. We present the results of the ionization potential (IP)-based and interfacial offset-based band alignments. In the interfacial offset-based band alignment, to get the natural band offset, we use the surface calculations to estimate the change of reference level due to the interfacial strain. Based on the interface models and GGA-1/2 calculations, we find that the valence band maximum and conduction band minimum of ZnO, respectively, lie 0.64 eV and 0.57 eV above those of anatase TiO2, while lie 0.84 eV and 1.09 eV below those of GaN, which agree well with the experimental data. However, a large discrepancy exists between the IP-based band offset and the calculated natural band offset, the mechanism of which is discussed. Our results clarify band alignment of the ZnO/anatase TiO2 heterojunction and show good agreement with the GW calculations for the GaN/ZnO heterojunction.

  13. Theoretical prediction of the band offsets at the ZnO/anatase TiO2 and GaN/ZnO heterojunctions using the self-consistent ab initio DFT/GGA-1/2 method.

    PubMed

    Fang, D Q; Zhang, S L

    2016-01-01

    The band offsets of the ZnO/anatase TiO2 and GaN/ZnO heterojunctions are calculated using the density functional theory/generalized gradient approximation (DFT/GGA)-1/2 method, which takes into account the self-energy corrections and can give an approximate description to the quasiparticle characteristics of the electronic structure of semiconductors. We present the results of the ionization potential (IP)-based and interfacial offset-based band alignments. In the interfacial offset-based band alignment, to get the natural band offset, we use the surface calculations to estimate the change of reference level due to the interfacial strain. Based on the interface models and GGA-1/2 calculations, we find that the valence band maximum and conduction band minimum of ZnO, respectively, lie 0.64 eV and 0.57 eV above those of anatase TiO2, while lie 0.84 eV and 1.09 eV below those of GaN, which agree well with the experimental data. However, a large discrepancy exists between the IP-based band offset and the calculated natural band offset, the mechanism of which is discussed. Our results clarify band alignment of the ZnO/anatase TiO2 heterojunction and show good agreement with the GW calculations for the GaN/ZnO heterojunction. PMID:26747815

  14. Ab initio configuration interaction study of the structure and magnetic properties of radicals and radical ions derived from group 13 15 trihydrides

    NASA Astrophysics Data System (ADS)

    Carmichael, Ian

    1987-09-01

    The structures, characteristic vibrations and magnetic properties of two isoelectronic series of radicals and radical ions derived from group 13-15 trihydrides have been investigated by post-Hartree-Fock theoretical techniques. Møller-Plesset perturbation theory based on an unrestricted Hartree-Fock determinant has been employed to determine the structures and vibrational frequencies in the 9-electron series, BH -3, CH 3, and NH +3. These species are found to be planar. Spin density distributions and ionization energetics have been estimated using a variational configuration interaction procedure. A positive electron affinity for BH 3 has not been demonstrated. The effect of out-of-plane vibrations on the hyperfine coupling constants is determined at a similar level of theory. In the 17-electron series AlH -3, SiH 3, and PH +3, pyramidal structures are found by using and extended split-valence basis at the SCF level. The computed harmonic force field suggests that a tentative assignment of a matrix isolated infrared spectrum to SiH 3 is incorrect. This conclusion is reinforced by calculation of the vibrational intensity patterns. Hyperfine interaction tensors computed at the optimized geometries from the UHF wavefunction with a more complete polarized double-zeta basis set are in accord with experiment. Vibrational effects are estimated by averaging the UHF spin density over an energy surface determined by second-order perturbation theory. Corrections due to vibrations are smaller than in the carbon series and single-point configuration interaction calculations confirm the reliability of the UHF spin densities.

  15. Direct phase selection of initial phases from single-wavelength anomalous dispersion (SAD) for the improvement of electron density and ab initio structure determination

    SciTech Connect

    Chen, Chung-De; Huang, Yen-Chieh; Chiang, Hsin-Lin; Hsieh, Yin-Cheng; Guan, Hong-Hsiang; Chuankhayan, Phimonphan; Chen, Chun-Jung

    2014-09-01

    A novel direct phase-selection method to select optimized phases from the ambiguous phases of a subset of reflections to replace the corresponding initial SAD phases has been developed. With the improved phases, the completeness of built residues of protein molecules is enhanced for efficient structure determination. Optimization of the initial phasing has been a decisive factor in the success of the subsequent electron-density modification, model building and structure determination of biological macromolecules using the single-wavelength anomalous dispersion (SAD) method. Two possible phase solutions (ϕ{sub 1} and ϕ{sub 2}) generated from two symmetric phase triangles in the Harker construction for the SAD method cause the well known phase ambiguity. A novel direct phase-selection method utilizing the θ{sub DS} list as a criterion to select optimized phases ϕ{sub am} from ϕ{sub 1} or ϕ{sub 2} of a subset of reflections with a high percentage of correct phases to replace the corresponding initial SAD phases ϕ{sub SAD} has been developed. Based on this work, reflections with an angle θ{sub DS} in the range 35–145° are selected for an optimized improvement, where θ{sub DS} is the angle between the initial phase ϕ{sub SAD} and a preliminary density-modification (DM) phase ϕ{sub DM}{sup NHL}. The results show that utilizing the additional direct phase-selection step prior to simple solvent flattening without phase combination using existing DM programs, such as RESOLVE or DM from CCP4, significantly improves the final phases in terms of increased correlation coefficients of electron-density maps and diminished mean phase errors. With the improved phases and density maps from the direct phase-selection method, the completeness of residues of protein molecules built with main chains and side chains is enhanced for efficient structure determination.

  16. Ab initio investigations of the electronic structures and chemical bonding in LiCo6P4 and Li2Co12P7

    NASA Astrophysics Data System (ADS)

    Matar, Samir F.; Al-Alam, Adel; Ouaini, Naïm; Pöttgen, Rainer

    2013-06-01

    The electronic structures of the metal-rich phosphides LiCo6P4 and Li2Co12P7 were studied by DFT calculations. Both phosphides consist of three-dimensional [Co6P4] and [Co12P7] polyanionic networks which leave hexagonal channels for the lithium atoms. COOP data show strong Co-P and Co-Co bonding within the polyanions. The lithium atoms have trigonal prismatic phosphorus coordination. Total energy calculations indicate stability upon de-lithiation towards the Co6P4 and Co12P7 substructures

  17. Electric field gradients of CeMIn5 (M= Co, Rh, Ir) heavy-fermion systems studied by perturbed angular correlations and ab initio electronic structure calculations

    NASA Astrophysics Data System (ADS)

    Forker, M.; Silva, P. R. J.; Cavalcante, J. T. P. D.; Cavalcante, F. H. M.; Ramos, S. M.; Saitovitch, H.; Baggio-Saitovitch, E.; Alonso, R.; Taylor, M.; Errico, L. A.

    2013-04-01

    The electric field gradient (EFG) at the highly dilute nuclear probe 111Cd in the heavy fermion systems CeMIn5, M= Co, Rh, and Ir and YCoIn5 has been investigated by perturbed angular correlation (PAC) measurements of the nuclear electric quadrupole interaction (QI) of 111Cd on In sites. Pure and Sn-doped single crystals prepared by In-flux synthesis and polycrystalline samples prepared by arc melting have been studied. The samples were doped with the PAC probe 111Cd by diffusion of the mother isotope 111In. In all samples, several fractions of 111Cd probe nuclei subject to different QI's have been observed, among them a large fraction of 111Cd in unreacted In metal. Detailed calculations of the EFG at In nuclei and at Cd probes on In sites of pure and Sn-doped CeMIn5 were preformed, using the full-potential augmented plane wave+local orbital (APW+lo) formalism and taking into account different variables such as the electronic structure of the hyperfine probes, probe induced structural distortions, and impurity doping. The excellent agreement between the predicted EFG's and the experimental results allows us to assign two of the observed EFG components to the lattice sites 1c and 4i of the CeMIn5 compounds and to explain the pronounced difference of the EFG at In and Cd probes on the same lattice position. Structural distortions induced by the Cd probe and Sn-doping were found to have little effect on the EFG at the Cd probes. We also show that the local spin density approximation (LSDA) and LDA+U calculations predict very similar equilibrium structures and EFG's at the In/Cd sites. The extension of the experiments and the calculations from CeMIn5 to YCoIn5 and LaCoIn5 have established that the influence of the 4f electrons on the EFG's at impurity sites is negligibly small.

  18. Study of the structure, energetics, and vibrational properties of small ammonia clusters (NH3)n (n = 2-5) using correlated ab initio methods.

    PubMed

    Janeiro-Barral, Paula E; Mella, Massimo

    2006-10-01

    Equilibrium geometries, interaction energies, and harmonic frequencies of (NH3)n isomers (n = 2-5) have been computed using correlated calculations (MP2) in conjunction with Dunning's aug-cc-pVXZ (X = D, T, Q) basis sets and the Counterpoise procedure. Whenever available, literature values for the binding energy and geometry of dimers and trimers agree well with our data. Low lying isomers for (NH3)4 and (NH3)5 have been found to have similar binding energies (roughly 16 and 20 kcal/mol for the tetramer and pentamer, respectively), perhaps suggesting the presence of a very smooth energy landscape. Using BSSE corrected forces or freezing the monomer structure to its gas phase geometry have been found to have only a weak impact on the energetic and structural properties of the clusters. The effect of zero-point energy (ZPE) on the relative stability of the clusters has been estimated using harmonic frequencies. The latter also highlighted the presence of vibrational fingerprints for the presence of double acceptor ammonia molecules. Many-body effects for (NH3)n isomers (n = 2-4) have been investigated to explore the possibility of building a pairwise interaction model for ammonia. In the frame of the work presented, we have found the 3-body effect to account for 10-15% of the total interaction energy, whereas the 4-body effects may be neglected as first approximation.

  19. Self assembly of sandwich-layered 2D silver(I) coordination polymers stabilized by argentophilic interactions: Synthesis, crystal structures and ab initio intramolecular energetics

    NASA Astrophysics Data System (ADS)

    Zorlu, Yunus; Can, Hatice

    2014-11-01

    Two different two-dimensional silver(I) coordination polymers, namely {[Ag2(dcpa)}n (1) and {[Ag2(ma)]}n (2), where dcpa = 4,5-dichlorophthalate; ma = maleate, were synthesized and structurally analyzed by single crystal X-ray diffraction technique. Complexes 1 and 2 represent 2D coordination polymer with metal-organic sandwich type. Two independent Ag(I) ions in both complexes are linked to constructed 2D layer by μ8-η3:η2:η2:η1 (for complex 1) and μ8-η3:η3:η2:η2 (for complex 2) carboxylate bridging fashions. The 2D layers of 1 are further extended into a three-dimensional (3D) supramolecular network by weak Cl⋯Cl interactions while 2D layers of 2 are linked by weak CH⋯O interactions into a 3D supramolecular framework. These two complexes exhibit considerable short Ag-Ag argentophilic interactions. The long-range corrected density functional theory (DFT) method was used to investigate intramolecular energetics, which are responsible for these 2D structures. Natural bond orbital (NBO) analysis with long-range corrected DFT method assists to understand these intramolecular interactions.

  20. ``Phantom'' Modes in Ab Initio Tunneling Calculations: Implications for Theoretical Materials Optimization, Tunneling, and Transport

    NASA Astrophysics Data System (ADS)

    Barabash, Sergey V.; Pramanik, Dipankar

    2015-03-01

    Development of low-leakage dielectrics for semiconductor industry, together with many other areas of academic and industrial research, increasingly rely upon ab initio tunneling and transport calculations. Complex band structure (CBS) is a powerful formalism to establish the nature of tunneling modes, providing both a deeper understanding and a guided optimization of materials, with practical applications ranging from screening candidate dielectrics for lowest ``ultimate leakage'' to identifying charge-neutrality levels and Fermi level pinning. We demonstrate that CBS is prone to a particular type of spurious ``phantom'' solution, previously deemed true but irrelevant because of a very fast decay. We demonstrate that (i) in complex materials, phantom modes may exhibit very slow decay (appearing as leading tunneling terms implying qualitative and huge quantitative errors), (ii) the phantom modes are spurious, (iii) unlike the pseudopotential ``ghost'' states, phantoms are an apparently unavoidable artifact of large numerical basis sets, (iv) a presumed increase in computational accuracy increases the number of phantoms, effectively corrupting the CBS results despite the higher accuracy achieved in resolving the true CBS modes and the real band structure, and (v) the phantom modes cannot be easily separated from the true CBS modes. We discuss implications for direct transport calculations. The strategy for dealing with the phantom states is discussed in the context of optimizing high-quality high- κ dielectric materials for decreased tunneling leakage.

  1. Comparative ab initio study of half-Heusler compounds for optoelectronic applications

    NASA Astrophysics Data System (ADS)

    Gruhn, Thomas

    2010-09-01

    For the advancement of optoelectronic applications, such as thin-film solar cells or laser diodes, there is a strong demand for new semiconductor materials with tailored structural and electronic properties. The eight-electron half-Heusler compounds include many promising materials with a big variety of lattice constants and band gaps. So far only a small number of them have been investigated. With the help of ab initio calculations, we have studied all possible configurations of ternary 1:1:1 compounds in the half-Heusler structure. We have investigated 648 half-Heusler materials, including compounds of the types I-I-VI, I-II-V, I-III-IV, II-II-IV, and II-III-III. For all compounds, we have optimized the lattice constant and determined the most stable arrangement of elements on the half-Heusler lattice sites. Preferred configurations and semiconductivities are compared for the different half-Heusler types. A discussion of the lattice geometries provides a parameter-free function for estimating the lattice constants. The calculated band gaps and lattice constants are used to select potential substitute materials for CdS in the buffer layer of CuInSe2 and Cu(In,Ga)Se2 thin-film solar cells.

  2. Structure, dynamics and stability of water/scCO2/mineral interfaces from ab initio molecular dynamics simulations

    SciTech Connect

    Lee, Mal -Soon; Peter McGrail, B.; Rousseau, Roger; Glezakou, Vassiliki -Alexandra

    2015-10-12

    Here, the interface between a solid and a complex multi-component liquid forms a unique reaction environment whose structure and composition can significantly deviate from either bulk or liquid phase and is poorly understood due the innate difficulty to obtain molecular level information. Feldspar minerals, as typified by the Ca-end member Anorthite, serve as prototypical model systems to assess the reactivity and ion mobility at solid/water-bearing supercritical fluid (WBSF) interfaces due to recent X-ray based measurements that provide information on water-film formation, and cation vacancies at these surfaces. Using density functional theory based molecular dynamics, which allows the evaluation of reactivity and condensed phase dynamics on equal footing, we report on the structure and dynamics of water nucleation and surface aggregation, carbonation and Ca mobilization under geologic carbon sequestration scenarios (T = 323 K and P = 90 bar). We find that water has a strong enthalpic preference for aggregation on a Ca-rich, O-terminated anorthite (001) surface, but entropy strongly hinders the film formation at very low water concentrations. Carbonation reactions readily occur at electron-rich terminal Oxygen sites adjacent to cation vacancies, when in contact with supercritical CO2. Cation vacancies of this type can form readily in the presence of a water layer that allows for facile and enthalpicly favorable Ca2+ extraction and solvation. Apart from providing unprecedented molecular level detail of a complex three component (mineral, water and scCO2) system), this work highlights the ability of modern capabilities of AIMD methods to begin to qualitatively and quantitatively address structure and reactivity at solid-liquid interfaces of high chemical complexity. This work was supported by the US Department of Energy, Office of Fossil Energy (M.-S. L., B. P. M. and V.-A. G.) and the Office of Basic Energy Science, Division of

  3. Topologically close-packed phases in binary transition-metal compounds: matching high-throughput ab initio calculations to an empirical structure map

    NASA Astrophysics Data System (ADS)

    Hammerschmidt, T.; Bialon, A. F.; Pettifor, D. G.; Drautz, R.

    2013-11-01

    In steels and single-crystal superalloys the control of the formation of topologically close-packed (TCP) phases is critical for the performance of the material. The structural stability of TCP phases in multi-component transition-metal alloys may be rationalized in terms of the average valence-electron count \\bar {N} and the composition-dependent relative volume-difference \\overline {\\Delta V/V} . We elucidate the interplay of these factors by comparing density-functional theory calculations to an empirical structure map based on experimental data. In particular, we calculate the heat of formation for the TCP phases A15, C14, C15, C36, χ, μ and σ for all possible binary occupations of the Wyckoff positions. We discuss the isovalent systems V/Nb-Ta to highlight the role of atomic-size difference and observe the expected stabilization of C14/C15/C36/μ by \\overline {\\Delta V/V} at ΔN = 0 in V-Ta. In the systems V/Nb-Re, we focus on the well-known trend of A15 → σ → χ stability with increasing \\bar {N} and show that the influence of \\overline {\\Delta V/V} is too weak to stabilize C14/C15/C36/μ in Nb-Re. As an example for a significant influence of both \\bar {N} and \\overline {\\Delta V/V} , we also consider the systems Cr/Mo-Co. Here the sequence A15 → σ → χ is observed in both systems but in Mo-Co the large size-mismatch stabilizes C14/C15/C36/μ. We also include V/Nb-Co that cover the entire valence range of TCP stability and also show the stabilization of C14/C15/C36/μ. Moreover, the combination of a large volume-difference with a large mismatch in valence-electron count reduces the stability of the A15/σ/χ phases in Nb-Co as compared to V-Co. By comparison to non-magnetic calculations we also find that magnetism is of minor importance for the structural stability of TCP phases in Cr/Mo-Co and in V/Nb-Co.

  4. Ab initio study of 59Co NMR spectra in Co2FeAl1-xSix Heusler alloys

    NASA Astrophysics Data System (ADS)

    Nishihara, H.; Sato, K.; Akai, H.; Takiguchi, C.; Geshi, M.; Kanomata, T.; Sakon, T.; Wada, T.

    2015-05-01

    Ab initio electronic structure calculation of a series of Co2FeAl1-xSix Heusler alloys has been performed, using the Korringa-Kohn-Rostoker-coherent potential approximation method to explain experimental 59Co NMR spectra. Two prominent features are explained semi-quantitatively-a global shift of the 59Co resonance line due to alloying with Al and Si atoms in Co2FeAl1-xSix, and the effect of local disorder in creating distinct satellite lines of 59Co NMR in Co2FeAl. The importance is stressed of the positive contribution to the 59Co hyperfine field from valence electron polarization, which emerges from the half-metallic band structure inherent in Co-based Heusler alloys.

  5. Characterization of amorphous In{sub 2}O{sub 3}: An ab initio molecular dynamics study

    SciTech Connect

    Aliano, Antonio; Catellani, Alessandra; Cicero, Giancarlo

    2011-11-21

    In this work, we report on the structural and electronic properties of amorphous In{sub 2}O{sub 3} obtained with ab initio molecular dynamics. Our results show crystal-like short range InO{sub 6} polyhedra having average In-O distance consistent with x-ray spectroscopy data. Structural disorder yields band tailing and localized states, which are responsible of a strong reduction of the electronic gap. Most importantly, the appearance of a peculiar O-O bond imparts n-type character to the amorphous compound and provides contribution for interpreting spectroscopic measurements on indium based oxidized systems. Our findings portray characteristic features to attribute transparent semiconductive properties to amorphous In{sub 2}O{sub 3}.

  6. An ab initio study of the electronic structure and optical properties of CdS{sub 1-x}Te{sub x} alloys

    SciTech Connect

    Al-Douri, Y.; Ahmad, S.; Hashim, U.; Reshak, Ali Hussain; Baaziz, H.; Charifi, Z.; Khenata, R.

    2010-12-15

    The structural, electronic and optical properties of cubic CdS{sub 1-x}Te{sub x} alloys, with Te-concentrations varying from 0% up to 100% are investigated. The calculations are based on the total-energy calculations using the full potential-linearized augmented plane wave (FP-LAPW) method. The exchange and correlation potential is treated by the generalized-gradient approximation (GGA) for the total-energy calculations, while for electronic properties in addition to that the Engel-Vosko (EV-GGA) formalism was also applied. The ground state properties for all Te-concentrations are presented. The optical dielectric constant is also determined for both the binary and their related ternary alloys. (author)

  7. Structural and electronic properties of cyanide-coated fullerene C20@(CN)n(n=0-20): An ab initio approach

    NASA Astrophysics Data System (ADS)

    Demiray, Ferhat; Sıdır, İsa; Gülseven Sıdır, Yadigar

    2016-08-01

    Density functional theory calculations at the LDA level have been performed to investigate the geometrical structure, stabilities and electronic properties of cyanide-coated fullerene C20@(CN) n, with n=0-20 in the ground state. From the binding energy, dissociation energy and second-order energy, even-number-coated fullerenes are more stable than odd-number ones. C20 has been successfully coated with electron-withdrawing group CN, achieving fullerene electron acceptors which have low-LUMO levels. The lowest LUMO value obtained for C20@(CN)12 is -5.89 eV, which is comparable with or lower than that of C60 and C60@(CN)2 fullerenes. Each of the cyanide coatings makes the fullerenes more stable with a larger HOMO-LUMO gap. Designed cyanide-coated fullerene compounds are promising and progressive to achieve a wider range of donor materials and high efficiencies in organic photovoltaic devices.

  8. Molecular structure and vibrational spectra of three substituted 4-thioflavones by density functional theory and ab initio Hartree-Fock calculations

    NASA Astrophysics Data System (ADS)

    Li, Xiao-Hong; Liu, Xiang-Ru; Zhang, Xian-Zhou

    2011-01-01

    The vibrational frequencies of three substituted 4-thioflavones in the ground state have been calculated using the Hartree-Fock and density functional method (B3LYP) with 6-31G* and 6-31+G** basis sets. The structural analysis shows that there exists H-bonding in the selected compounds and the hydrogen bond lengths increase with the augment of the conjugate parameters of the substituent group on the benzene ring. A complete vibrational assignment aided by the theoretical harmonic wavenumber analysis was proposed. The theoretical spectrograms for FT-IR spectra of the title compounds have been constructed. In addition, it is noted that the selected compounds show significant activity against Shigella flexniri. Several electronic properties and thermodynamic parameters were also calculated.

  9. Direct phase selection of initial phases from single-wavelength anomalous dispersion (SAD) for the improvement of electron density and ab initio structure determination

    PubMed Central

    Chen, Chung-De; Huang, Yen-Chieh; Chiang, Hsin-Lin; Hsieh, Yin-Cheng; Guan, Hong-Hsiang; Chuankhayan, Phimonphan; Chen, Chun-Jung

    2014-01-01

    Optimization of the initial phasing has been a decisive factor in the success of the subsequent electron-density modification, model building and structure determination of biological macromolecules using the single-wavelength anomalous dispersion (SAD) method. Two possible phase solutions (ϕ1 and ϕ2) generated from two symmetric phase triangles in the Harker construction for the SAD method cause the well known phase ambiguity. A novel direct phase-selection method utilizing the θDS list as a criterion to select optimized phases ϕam from ϕ1 or ϕ2 of a subset of reflections with a high percentage of correct phases to replace the corresponding initial SAD phases ϕSAD has been developed. Based on this work, reflections with an angle θDS in the range 35–145° are selected for an optimized improvement, where θDS is the angle between the initial phase ϕSAD and a preliminary density-modification (DM) phase ϕDM NHL. The results show that utilizing the additional direct phase-selection step prior to simple solvent flattening without phase combination using existing DM programs, such as RESOLVE or DM from CCP4, significantly improves the final phases in terms of increased correlation coefficients of electron-density maps and diminished mean phase errors. With the improved phases and density maps from the direct phase-selection method, the completeness of residues of protein molecules built with main chains and side chains is enhanced for efficient structure determination. PMID:25195747

  10. Direct phase selection of initial phases from single-wavelength anomalous dispersion (SAD) for the improvement of electron density and ab initio structure determination.

    PubMed

    Chen, Chung-De; Huang, Yen-Chieh; Chiang, Hsin-Lin; Hsieh, Yin-Cheng; Guan, Hong-Hsiang; Chuankhayan, Phimonphan; Chen, Chun-Jung

    2014-09-01

    Optimization of the initial phasing has been a decisive factor in the success of the subsequent electron-density modification, model building and structure determination of biological macromolecules using the single-wavelength anomalous dispersion (SAD) method. Two possible phase solutions (φ1 and φ2) generated from two symmetric phase triangles in the Harker construction for the SAD method cause the well known phase ambiguity. A novel direct phase-selection method utilizing the θ(DS) list as a criterion to select optimized phases φ(am) from φ1 or φ2 of a subset of reflections with a high percentage of correct phases to replace the corresponding initial SAD phases φ(SAD) has been developed. Based on this work, reflections with an angle θ(DS) in the range 35-145° are selected for an optimized improvement, where θ(DS) is the angle between the initial phase φ(SAD) and a preliminary density-modification (DM) phase φ(DM)(NHL). The results show that utilizing the additional direct phase-selection step prior to simple solvent flattening without phase combination using existing DM programs, such as RESOLVE or DM from CCP4, significantly improves the final phases in terms of increased correlation coefficients of electron-density maps and diminished mean phase errors. With the improved phases and density maps from the direct phase-selection method, the completeness of residues of protein molecules built with main chains and side chains is enhanced for efficient structure determination.

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

    PubMed

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

    2004-08-20

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

  12. Ab-initio and DFT calculations on molecular structure, NBO, HOMO-LUMO study and a new vibrational analysis of 4-(Dimethylamino) Benzaldehyde.

    PubMed

    Rocha, Mariana; Di Santo, Alejandro; Arias, Juan Marcelo; Gil, Diego M; Ben Altabef, Aída

    2015-02-01

    The experimental and theoretical study on the molecular structure and a new vibrational analysis of 4-(Dimethylamino) Benzaldehyde (DMABA) is presented. The IR and Raman spectra were recorded in solid state. Optimized geometry, vibrational frequencies and various thermodynamic parameters of the title compound were calculated using DFT methods and are in agreement with the experimental values. A detailed interpretation of the IR and Raman spectra of the title compound were reported. The stability of the molecule arising from hyper-conjugative interactions and charge delocalization has been analyzed using NBO analysis and AIM approach. The HOMO and LUMO analysis were used to determine the charge transfer within the molecule and some molecular properties such as ionization potential, electron affinity, electronegativity, chemical potential, hardness, softness and global electrophilicity index. The TD-DFT approach was applied to assign the electronic transitions observed in the UV-visible spectrum measured experimentally. Molecular electrostatic potential map was performed by the DFT method. According to DSC measurements, the substance presents a melting point of 72.34°C and decomposes at temperatures higher than 193°C.

  13. Ab-initio and DFT calculations on molecular structure, NBO, HOMO-LUMO study and a new vibrational analysis of 4-(Dimethylamino) Benzaldehyde

    NASA Astrophysics Data System (ADS)

    Rocha, Mariana; Di Santo, Alejandro; Arias, Juan Marcelo; Gil, Diego M.; Altabef, Aída Ben

    2015-02-01

    The experimental and theoretical study on the molecular structure and a new vibrational analysis of 4-(Dimethylamino) Benzaldehyde (DMABA) is presented. The IR and Raman spectra were recorded in solid state. Optimized geometry, vibrational frequencies and various thermodynamic parameters of the title compound were calculated using DFT methods and are in agreement with the experimental values. A detailed interpretation of the IR and Raman spectra of the title compound were reported. The stability of the molecule arising from hyper-conjugative interactions and charge delocalization has been analyzed using NBO analysis and AIM approach. The HOMO and LUMO analysis were used to determine the charge transfer within the molecule and some molecular properties such as ionization potential, electron affinity, electronegativity, chemical potential, hardness, softness and global electrophilicity index. The TD-DFT approach was applied to assign the electronic transitions observed in the UV-visible spectrum measured experimentally. Molecular electrostatic potential map was performed by the DFT method. According to DSC measurements, the substance presents a melting point of 72.34 °C and decomposes at temperatures higher than 193 °C.

  14. Comment on: ``FTIR and FTRaman spectra, assignments, ab initio HF and DFT analysis of 4-nitrotoluene'' by S. Ramalingam et al., Spectrochemica Acta A 75 (2010) 1308-1314

    NASA Astrophysics Data System (ADS)

    Tomkinson, John

    2010-10-01

    The title paper reports the ab initio calculated structure and vibrational spectra of 4-nitrotoluene. The calculated structure is wrong and the assignments are inconsistent with earlier work. We have recalculated the ab initio structure and reassigned the spectra in agreement with the standard text.

  15. Comment on: "FTIR and FTRaman spectra, assignments, ab initio HF and DFT analysis of 4-nitrotoluene" by S. Ramalingam et al., Spectrochemica Acta A 75 (2010) 1308-1314.

    PubMed

    Tomkinson, John

    2010-10-01

    The title paper reports the ab initio calculated structure and vibrational spectra of 4-nitrotoluene. The calculated structure is wrong and the assignments are inconsistent with earlier work. We have recalculated the ab initio structure and reassigned the spectra in agreement with the standard text. PMID:20598628

  16. Boric acid adsorption on humic acids: Ab initio calculation of structures, stabilities, 11B NMR and 11B, 10B isotopic fractionations of surface complexes

    NASA Astrophysics Data System (ADS)

    Tossell, J. A.

    2006-10-01

    Boric acid, B(OH) 3, forms complexes in aqueous solution with a number of bidentate O-containing ligands, HL -, where H 2L is C 2O 4H 2 (oxalic acid), C 3O 4H 4 (malonic acid), C 2H 6O 2 (ethylene glycol), C 6H 6O 2 (catechol), C 10H 8O 2 (dioxynaphthalene) and C 2O 3H 4 (glycolic acid). McElligott and Byrne [McElligott, S., Byrne, R.H., 1998. Interaction of B(OH)30 and HCO3- in seawater: Formation of B(OH)CO3-. Aquat. Geochem.3, 345-356.] have also found B(OH) 3 to form an aqueous complex with HCO3-1. Recently Lemarchand et al. [Lemarchand, E., Schott, J., Gaillardeet, J., 2005. Boron isotopic fractionation related to boron sorption on humic acid and the structure of surface complexes formed. Geochim. Cosmochim. Acta69, 3519-3533] have studied the formation of surface complexes of B(OH) 3 on humic acid, determining 11B NMR shifts and fitted values of formation constants, and 11B, 10B isotope fractionations for a number of surface complexation models. Their work helps to clarify both the nature of the interaction of boric acid with the functional groups in humic acid and the nature of some of these coordinating sites on the humic acid. The determination of isotope fractionations may be seen as a form of vibrational spectroscopy, using the fractionating element as a local probe of the vibrational spectrum. We have calculated quantum mechanically the structures, stabilities, vibrational spectra, 11B NMR spectra and 11B, 10B isotope fractionations of a number of complexes B(OH) 2L - formed by reactions of the type: B(OH)3+HL-⇒B(OH)2L+HO using a 6-311G(d,p) basis set and the B3LYP method for determination of structures, vibrational frequencies and isotopic fractionations, the highly accurate Complete Basis Set-QB3 method for calculating the free energies and the GIAO HF method with a 6-311+G(2d,p) basis for the NMR shieldings. The calculations indicate that oxalic acid, malonic acid, catechol and glycolic acid all form stable complexes (Δ G < 0 for Reaction (1

  17. Acid-base interactions and secondary structures of poly-L-lysine probed by 15N and 13C solid state NMR and Ab initio model calculations.

    PubMed

    Dos, Alexandra; Schimming, Volkmar; Tosoni, Sergio; Limbach, Hans-Heinrich

    2008-12-11

    The interactions of the 15N-labeled amino groups of dry solid poly-L-lysine (PLL) with various halogen and oxygen acids HX and the relation to the secondary structure have been studied using solid-state 15N and 13C CPMAS NMR spectroscopy (CP = cross polarization and MAS = magic angle spinning). For comparison, 15N NMR spectra of an aqueous solution of PLL were measured as a function of pH. In order to understand the effects of protonation and hydration on the 15N chemical shifts of the amino groups, DFT and chemical shielding calculations were performed on isolated methylamine-acid complexes and on periodic halide clusters of the type (CH3NH3(+)X(-))n. The combined experimental and computational results reveal low-field shifts of the amino nitrogens upon interaction with the oxygen acids HX = HF, H2SO4, CH3COOH, (CH3)2POOH, H3PO4, HNO3, and internal carbamic acid formed by reaction of the amino groups with gaseous CO2. Evidence is obtained that only hydrogen-bonded species of the type (Lys-NH2***H-X)n are formed in the absence of water. 15N chemical shifts are maximum when H is located in the hydrogen bond center and then decrease again upon full protonation, as found for aqueous solution at low pH. By contrast, halogen acids interact in a different way. They form internal salts of the type (Lys-NH3(+)X(-))n via the interaction of many acid-base pairs. This salt formation is possible only in the beta-sheet conformation. By contrast, the formation of hydrogen-bonded complexes can occur both in beta-sheet domains as well as in alpha-helical domains. The 15N chemical shifts of the protonated ammonium groups increase when the size of the interacting halogen anions is increased from chloride to iodide and when the number of the interacting anions is increased. Thus, the observed high-field 15N shift of ammonium groups upon hydration is the consequence of replacing interacting halogen atoms by oxygen atoms.

  18. Geometries and electronic structures of the ground and low-lying excited states of FeCO: An ab initio study

    NASA Astrophysics Data System (ADS)

    Hirano, Tsuneo; Okuda, Rei; Nagashima, Umpei; Jensen, Per

    2012-12-01

    FeCO is a molecule of astrophysical interest. We report here theoretical calculations of its geometrical parameters, electronic structures, and molecular constants (such as dipole moment and spin-orbit coupling constant) in the electronic ground state tilde{X}3Σ - and the low-lying triplet and quintet excited states. The calculations were made at the MR-SDCI+Q_DK3/[5ZP ANO-RCC (Fe, C, O)] and MR-AQCC_DK3/[5ZP ANO-RCC (Fe, C, O)] levels of theory. A multi-reference calculation was required to describe correctly the wavefunctions of all states studied. For all triplet states, the σ-donation through the 10σ molecular orbital (MO) as well as the π-back-donation through the 4π MO are observed, and the dipole moment vector points from O toward Fe as expected. However, in the excited quintet states 5Π, 5Φ, and 5Δ, the almost negligible contribution of Fe 4s to the 10σ MO makes the dipole moment vector point from Fe toward O, i.e., in the same direction as in CO. In the tilde{X}3Σ - state, the electron provided by the σ-donation through the 10σ MO is shared between the Fe atom and the C end of the CO residue to form a coordinate-covalent Fe-C bond. In the tilde{a}5Σ - state (the high-spin counterpart of tilde{X}3Σ -), the σ-donation through the 10σ MO is not significant and so the Fe-C bond is rather ionic. The π-back-donation through the 4π MO is found to be of comparable importance in the two electronic states; it has a slightly larger magnitude in the tilde{X}3Σ - state. The difference in the molecular properties of the low-spin tilde{X}3Σ - and the high-spin tilde{a}5Σ - states can be understood in terms of the dynamical electron correlation effects.

  19. Methylchloride adsorbed on Si(0 0 1): an ab initio study

    NASA Astrophysics Data System (ADS)

    Preuss, M.; Schmidt, W. G.; Seino, K.; Bechstedt, F.

    2004-07-01

    We present ab initio calculations of the adsorption of methylchloride (CH 3Cl) on Si(0 0 1). Among multiple plausible adsorption geometries, we find five thermodynamically favorable configurations. These lead to strong geometrical changes in the Si surface structure as well as to significant charge transfer processes. The stability of the adsorption structures is discussed in terms of electrostatics. The results are compared to recent experimental and theoretical findings.

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

    PubMed

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

    2006-02-01

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