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Sample records for surface ab initio

  1. Ab initio adiabatic and quasidiabatic potential energy surfaces of H ...

    Indian Academy of Sciences (India)

    Ion-diatom collisions; Ab initio potential energy surface; quasidiabitaziation; Nonadiabatic coupling matrix elements. 1. Introduction. Proton collisions with diatomic target molecules ..... energies. Acknowledgements. B.A. thanks IIT Madras and University Grants Com- mission, New Delhi for providing a research fellowship.

  2. Ab initio Potential Energy Surface for H-H2

    Science.gov (United States)

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

    1993-01-01

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

  3. Ab initio transport across bismuth selenide surface barriers

    KAUST Repository

    Narayan, Awadhesh

    2014-11-24

    © 2014 American Physical Society. We investigate the effect of potential barriers in the form of step edges on the scattering properties of Bi2Se3(111) topological surface states by means of large-scale ab initio transport simulations. Our results demonstrate the suppression of perfect backscattering, while all other scattering processes, which do not entail a complete spin and momentum reversal, are allowed. Furthermore, we find that the spin of the surface state develops an out-of-plane component as it traverses the barrier. Our calculations reveal the existence of quasibound states in the vicinity of the surface barriers, which appear in the form of an enhanced density of states in the energy window corresponding to the topological state. For double barriers we demonstrate the formation of quantum well states. To complement our first-principles results we construct a two-dimensional low-energy effective model and illustrate its shortcomings. Our findings are discussed in the context of a number of recent experimental works.

  4. An Ab Initio Based Potential Energy Surface for Water

    Science.gov (United States)

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

    1996-01-01

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

  5. An ab initio study of plutonium oxides surfaces; Etude ab initio des surfaces d'oxydes de Pu

    Energy Technology Data Exchange (ETDEWEB)

    Jomard, G.; Bottin, F.; Amadon, B

    2007-07-01

    By means of first-principles calculations, we have studied the atomic structure as well as the thermodynamic stability of various plutonium dioxide surfaces in function of their environment (in terms of oxygen partial pressure and temperature). All these simulations have been performed with the ABINIT code. It is well known that DFT fails to describe correctly plutonium-based materials since 5f electrons in such systems are strongly correlated. In order to go beyond DFT, we have treated PuO{sub 2} and {beta}-Pu{sub 2}O{sub 3} in a DFT+U framework. We show that the couple of parameters (U,J) that works well for pure Pu is also well designed for describing ground state (GS) properties of these two oxides. The major improvement with respect with DFT is that we are able to predict an insulating GS in agreement with experiments. The presence of a gap in the DOS (Density of States) of plutonium oxides should play a significant role in the predicted surface reactivity. However, performing DFT+U calculations on surfaces of plutonium oxide from scratch was too ambitious. That is why we decided, as a first step, to study the stability of the (100), (110) and (111) surfaces of PuO{sub 2} in a DFT-GGA framework. For each of these orientations, we considered various terminations. These ab initio results have been introduced in a thermodynamic model which allows us to predict the relative stability of the different terminations as a function of temperature and oxygen partial pressure (p{sub O{sub 2}}). We conclude that at room temperature and for p{sub O{sub 2}}{approx}10 atm., the polar O{sub 2}-(100) termination is favoured. The stabilization of such a polar stoichiometric surface is surprising and should be confirmed by DFT+U calculations before any final conclusion. (authors)

  6. Ab initio and work function and surface energy anisotropy of LaB6

    NARCIS (Netherlands)

    Uijttewaal, M. A.; de Wijs, G. A.; de Groot, R. A.

    2006-01-01

    Lanthanum hexaboride is one of the cathode materials most used in high-power electronics technology, but the many experimental results do not provide a consistent picture of the surface properties. Therefore, we report the first ab initio calculations of the work functions and surface energies of

  7. Ab initio treatment of the chemical reaction precursor complex Br(2P)-HCN. 1. Adiabatic and diabatic potential surfaces

    NARCIS (Netherlands)

    Fishchuk, A.V.; Merritt, J.M.; Avoird, A. van der

    2007-01-01

    The three adiabatic potential surfaces of the Br(P-2)-HCN complex that correlate to the P-2 ground state of the Br atom were calculated ab initio. With the aid of a geometry-dependent diabatic mixing angle, also calculated ab initio, these adiabatic potential surfaces were transformed into a set of

  8. Ab initio ground state phenylacetylene-argon intermolecular potential energy surface and rovibrational spectrum

    DEFF Research Database (Denmark)

    Cybulski, Hubert; Fernandez, Berta; Henriksen, Christian

    2012-01-01

    We evaluate the phenylacetylene-argon intermolecular potential energy surface by fitting a representative number of ab initio interaction energies to an analytic function. These energies are calculated at a grid of intermolecular geometries, using the CCSD(T) method and the aug-cc-pVDZ basis set ...

  9. Study on the surface hydroxyl group on solid breeding materials by ab-initio calculations

    Energy Technology Data Exchange (ETDEWEB)

    Tanaka, Satoru; Taniguchi, Masaki [Tokyo Univ. (Japan). Faculty of Engineering

    1996-10-01

    The nature of -OH on the surface of Li{sub 2}O was analyzed with the ab-initio quantum chemical calculation technique. Calculation results showed that the stretching vibration of O-H is affected by the chemical species around the -OH. (author)

  10. Ab Initio Studies on Hematite Surface and the Adsorption of Phosphate

    OpenAIRE

    Swati Chaudhury; Chandrika Varadachari; Kunal Ghosh

    2014-01-01

    This investigation explores the ab initio DFT method for understanding surface structure of hematite and the nature and energetics of phosphate adsorption. Using the full potential linearized plane wave method (FP-LAPW), we derived the structure and energies of various magnetic forms of hematite. The antiferromagnetic (AFM) form was observed to be the most stable. Hematite surfaces with Fe-termination, O-termination, or OH-termination were studied. The OH-terminated surface was the most stabl...

  11. Ab-initio study of surface segregation in aluminum alloys

    Energy Technology Data Exchange (ETDEWEB)

    Qin, Yifa, E-mail: yfqin10s@imr.ac.cn; Wang, Shaoqing

    2017-03-31

    Highlights: • A thorough study of surface segregation energies of 41 elements in Al is performed. • Segregation energies vary periodically with the atomic numbers of impurities. • 41 elements are classified into 3 groups according to the signs of segregation energies. • The results are validated by the surface/total concentration ratio in Al alloys. - Abstract: We have calculated surface segregation energies of 41 impurities by means of density functional theory calculations. An interesting periodical variation tendency was found for surface segregation energies derived. For the majority of main group elements, segregation energies are negative which means solute elements enrichment at Al surface is energetically more favorable than uniformly dissolution. Half of transition elements possess positive segregation energies and the energies are sensitive to surface crystallographic orientations. A strong correlation is found between the segregation energies at the Al surface and the surface energ of solute elements.

  12. A highly accurate {\\it ab initio} potential energy surface for methane

    CERN Document Server

    Owens, Alec; Yachmenev, Andrey; Tennyson, Jonathan; Thiel, Walter

    2016-01-01

    A new nine-dimensional potential energy surface (PES) for methane has been generated using state-of-the-art \\textit{ab initio} theory. The PES is based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set limit and incorporates a range of higher-level additive energy corrections. These include: core-valence electron correlation, higher-order coupled cluster terms beyond perturbative triples, scalar relativistic effects and the diagonal Born-Oppenheimer correction. Sub-wavenumber accuracy is achieved for the majority of experimentally known vibrational energy levels with the four fundamentals of $^{12}$CH$_4$ reproduced with a root-mean-square error of $0.70{\\,}$cm$^{-1}$. The computed \\textit{ab initio} equilibrium C{--}H bond length is in excellent agreement with previous values despite pure rotational energies displaying minor systematic errors as $J$ (rotational excitation) increases. It is shown that these errors can be significantly reduced by adjusting the e...

  13. Surface Tension of Ab Initio Liquid Water at the Water-Air Interface

    CERN Document Server

    Nagata, Yuki; Bonn, Mischa; Kühne, Thomas D

    2016-01-01

    We report calculations of the surface tension of the water-air interface using ab initio molecular dynamics (AIMD) simulations. We investigate the simulation cell size dependence of the surface tension of water from force field molecular dynamics (MD) simulations, which show that the calculated surface tension increases with increasing simulation cell size, thereby illustrating that a correction for finite size effects is required for the small system used in the AIMD simulation. The AIMD simulations reveal that the double-{\\xi} basis set overestimates the experimentally measured surface tension due to the Pulay stress, while the triple and quadruple-{\\xi} basis sets give similar results. We further demonstrate that the van der Waals corrections critically affect the surface tension. AIMD simulations without the van der Waals correction substantially underestimate the surface tension, while van der Waals correction with the Grimme's D2 technique results in the value for the surface tension that is too high. T...

  14. Full Dimensional Vibrational Calculations for Methane Using AN Accurate New AB Initio Based Potential Energy Surface

    Science.gov (United States)

    Majumder, Moumita; Dawes, Richard; Wang, Xiao-Gang; Carrington, Tucker; Li, Jun; Guo, Hua; Manzhos, Sergei

    2014-06-01

    New potential energy surfaces for methane were constructed, represented as analytic fits to about 100,000 individual high-level ab initio data. Explicitly-correlated multireference data (MRCI-F12(AE)/CVQZ-F12) were computed using Molpro [1] and fit using multiple strategies. Fits with small to negligible errors were obtained using adaptations of the permutation-invariant-polynomials (PIP) approach [2,3] based on neural-networks (PIP-NN) [4,5] and the interpolative moving least squares (IMLS) fitting method [6] (PIP-IMLS). The PESs were used in full-dimensional vibrational calculations with an exact kinetic energy operator by representing the Hamiltonian in a basis of products of contracted bend and stretch functions and using a symmetry adapted Lanczos method to obtain eigenvalues and eigenvectors. Very close agreement with experiment was produced from the purely ab initio PESs. References 1- H.-J. Werner, P. J. Knowles, G. Knizia, 2012.1 ed. 2012, MOLPRO, a package of ab initio programs. see http://www.molpro.net. 2- Z. Xie and J. M. Bowman, J. Chem. Theory Comput 6, 26, 2010. 3- B. J. Braams and J. M. Bowman, Int. Rev. Phys. Chem. 28, 577, 2009. 4- J. Li, B. Jiang and Hua Guo, J. Chem. Phys. 139, 204103 (2013). 5- S Manzhos, X Wang, R Dawes and T Carrington, JPC A 110, 5295 (2006). 6- R. Dawes, X-G Wang, A.W. Jasper and T. Carrington Jr., J. Chem. Phys. 133, 134304 (2010).

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

    Science.gov (United States)

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

    1995-01-01

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

  16. EFFECT OF SCANDIUM ON HIDROGEN DISSOCIATION ENERGY AT MAGNESIUM SURFACE: AB INITIO DFT STUDY

    Directory of Open Access Journals (Sweden)

    I Wayan Sutapa

    2010-07-01

    Full Text Available The dissociative chemisorption of hydrogen on both pure and Sc-incorporated Mg(0001 surfaces have been studied by ab initio density functional theory (DFT calculation. The calculated dissociation energy of hydrogen molecule on a pure Mg(0001 surface (1.200 eV is in good agreement with comparable theoretical studies. For the Sc-incorporated Mg(0001 surface, the activated barrier decreases to 0.780 eV due to the strong interaction between the molecular orbital of hydrogen and the d metal state of Sc. This could explain the experimentally observed improvement in absorption kinetics of hydrogen when transition metals have been introduced into the magnesium materials.   Keywords: Dissociation, Adsorption, Chemisorptions, DFT, Magnesium

  17. Toward spectroscopically accurate global ab initio potential energy surface for the acetylene-vinylidene isomerization

    Science.gov (United States)

    Han, Huixian; Li, Anyang; Guo, Hua

    2014-12-01

    A new full-dimensional global potential energy surface (PES) for the acetylene-vinylidene isomerization on the ground (S0) electronic state has been constructed by fitting ˜37 000 high-level ab initio points using the permutation invariant polynomial-neural network method with a root mean square error of 9.54 cm-1. The geometries and harmonic vibrational frequencies of acetylene, vinylidene, and all other stationary points (two distinct transition states and one secondary minimum in between) have been determined on this PES. Furthermore, acetylene vibrational energy levels have been calculated using the Lanczos algorithm with an exact (J = 0) Hamiltonian. The vibrational energies up to 12 700 cm-1 above the zero-point energy are in excellent agreement with the experimentally derived effective Hamiltonians, suggesting that the PES is approaching spectroscopic accuracy. In addition, analyses of the wavefunctions confirm the experimentally observed emergence of the local bending and counter-rotational modes in the highly excited bending vibrational states. The reproduction of the experimentally derived effective Hamiltonians for highly excited bending states signals the coming of age for the ab initio based PES, which can now be trusted for studying the isomerization reaction.

  18. D2 dissociative adsorption on and associative desorption from Si(100): Dynamic consequences of an ab initio potential energy surface

    DEFF Research Database (Denmark)

    Luntz, A. C.; Kratzer, Peter

    1996-01-01

    Dynamical calculations are reported for D-2 dissociative chemisorption on and associative desorption from a Si(100) surface. These calculations use the dynamically relevant effective potential which is based on an ab initio potential energy surface for the ''pre-paired'' species. Three coordinates...

  19. Rotational Energy Transfer of N2 Determined Using a New Ab Initio Potential Energy Surface

    Science.gov (United States)

    Huo, Winifred M.; Stallcop, James R.; Partridge, Harry; Langhoff, Stephen R. (Technical Monitor)

    1997-01-01

    A new N2-N2 rigid-rotor surface has been determined using extensive Ab Initio quantum chemistry calculations together with recent experimental data for the second virial coefficient. Rotational energy transfer is studied using the new potential energy surface (PES) employing the close coupling method below 200 cm(exp -1) and coupled state approximation above that. Comparing with a previous calculation based on the PES of van der Avoird et al.,3 it is found that the new PES generally gives larger cross sections for large (delta)J transitions, but for small (delta)J transitions the cross sections are either comparable or smaller. Correlation between the differences in the cross sections and the two PES will be attempted. The computed cross sections will also be compared with available experimental data.

  20. Surface tension of ab initio liquid water at the water-air interface.

    Science.gov (United States)

    Nagata, Yuki; Ohto, Tatsuhiko; Bonn, Mischa; Kühne, Thomas D

    2016-05-28

    We report calculations on the surface tension of the water-air interface using ab initio molecular dynamics (AIMD) simulations. We investigate the influence of the cell size on surface tension of water from force field molecular dynamics simulations. We find that the calculated surface tension increases with increasing simulation cell size, thereby illustrating that a correction for finite size effects is essential for small systems that are customary in AIMD simulations. Moreover, AIMD simulations reveal that the use of a double-ζ basis set overestimates the experimentally measured surface tension due to the Pulay stress while more accurate triple and quadruple-ζ basis sets give converged results. We further demonstrate that van der Waals corrections critically affect the surface tension. AIMD simulations without the van der Waals correction substantially underestimate the surface tension while the van der Waals correction with the Grimme's D2 technique results in a value for the surface tension that is too high. The Grimme's D3 van der Waals correction provides a surface tension close to the experimental value. Whereas the specific choices for the van der Waals correction and basis sets critically affect the calculated surface tension, the surface tension is remarkably insensitive to the details of the exchange and correlation functionals, which highlights the impact of long-range interactions on the surface tension. Our simulated values provide important benchmarks, both for improving van der Waals corrections and AIMD simulations of aqueous interfaces.

  1. Graphite-diamond phase coexistence study employing a neural-network mapping of the ab initio potential energy surface

    Science.gov (United States)

    Khaliullin, Rustam Z.; Eshet, Hagai; Kühne, Thomas D.; Behler, Jörg; Parrinello, Michele

    2010-03-01

    An interatomic potential for the diamond and graphite phases of carbon has been created using a neural-network (NN) representation of the ab initio potential energy surface. The NN potential combines the accuracy of a first-principles description of both phases with the efficiency of empirical force fields and allows one to perform a molecular-dynamics study, of ab initio quality, of the thermodynamics of graphite-diamond coexistence. Good agreement between the experimental and calculated coexistence curves is achieved if nuclear quantum effects are included in the simulation.

  2. Ab initio intermolecular potential energy surface and thermophysical properties of nitrous oxide

    Energy Technology Data Exchange (ETDEWEB)

    Crusius, Johann-Philipp, E-mail: johann-philipp.crusius@uni-rostock.de; Hassel, Egon [Lehrstuhl für Technische Thermodynamik, Universität Rostock, 18059 Rostock (Germany); Hellmann, Robert, E-mail: robert.hellmann@uni-rostock.de; Bich, Eckard [Institut für Chemie, Universität Rostock, 18059 Rostock (Germany)

    2015-06-28

    We present an analytical intermolecular potential energy surface (PES) for two rigid nitrous oxide (N{sub 2}O) molecules derived from high-level quantum-chemical ab initio calculations. Interaction energies for 2018 N{sub 2}O–N{sub 2}O configurations were computed utilizing the counterpoise-corrected supermolecular approach at the CCSD(T) level of theory using basis sets up to aug-cc-pVQZ supplemented with bond functions. A site-site potential function with seven sites per N{sub 2}O molecule was fitted to the pair interaction energies. We validated our PES by computing the second virial coefficient as well as shear viscosity and thermal conductivity in the dilute-gas limit. The values of these properties are substantiated by the best experimental data.

  3. Ab initio potential energy surface and vibration-rotation energy levels of beryllium monohydroxide.

    Science.gov (United States)

    Koput, Jacek

    2017-01-05

    The accurate potential energy surface of beryllium monohydroxide, BeOH, in its ground electronic state X 2A' has been determined from ab initio calculations using the coupled-cluster approach in conjunction with the correlation-consistent core-valence basis sets up to septuple-zeta quality. The higher-order electron correlation, scalar relativistic, and adiabatic effects were taken into account. The BeOH molecule was confirmed to be bent at equilibrium, with the BeOH angle of 141.2° and the barrier to linearity of 129 cm-1 . The vibration-rotation energy levels of the BeOH and BeOD isotopologues were predicted using a variational approach and compared with recent experimental data. The results can be useful in a further analysis of high-resolution vibration-rotation spectra of these interesting species. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  4. Classical trajectory studies of gas phase reaction dynamics and kinetics using ab initio potential energy surfaces

    Science.gov (United States)

    Jaffe, Richard L.; Pattengill, Merle D.; Schwenke, David W.

    1989-01-01

    Strategies for constructing global potential energy surfaces from a limited number of accurate ab initio electronic energy calculations are discussed. Generally, these data are concentrated in small regions of configuration space (e.g., in the vicinity of saddle points and energy minima) and difficulties arise in generating a potential function that is globally well-behaved. Efficient computer codes for carrying out classical trajectory calculations on vector and parallel processors are also described. Illustrations are given from recent work on the following chemical systems: Ca + HF yields CaF + H, H + H + H2 yields H2 + H2, N + O2 yields NO + O and O + N2 yields NO + N. The dynamics and kinetics of metathesis, dissociation, recombination, energy transfer and complex formation processes will be discussed.

  5. Ab initio potential energy surface and vibration-rotation energy levels of sulfur dioxide.

    Science.gov (United States)

    Koput, Jacek

    2017-05-05

    An accurate potential energy surface of sulfur dioxide, SO2 , in its ground electronic state X∼ 1A1 has been determined from ab initio calculations using the coupled-cluster approach in conjunction with the correlation-consistent basis sets up to septuple-zeta quality. The results obtained with the conventional and explicitly correlated coupled-cluster methods are compared. The role of the core-electron correlation, higher-order valence-electron correlation, scalar relativistic, and adiabatic effects in determining the structure and dynamics of the SO2 molecule is discussed. The vibration-rotation energy levels of the 32 SO2 and 34 SO2 isotopologues were predicted using a variational approach. It was shown that the inclusion of the aforementioned effects was mandatory to attain the "spectroscopic" accuracy. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  6. Ab initio STM and STS simulations on magnetic and nonmagnetic metallic surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Dick, Alexey

    2008-04-14

    The aim of this work was to provide an in-depth understanding of a new generation of scan- ning tunneling microscopy experiments, performed employing different regimes of the STM: the spectroscopy-mode (the so-called Fourier Transformed STM, FT-STM), and the spin-sensitive mode (the so-called spin-polarized STM, SP-STM). In the present thesis ab initio tools are proposed that are based on DFT calculations to theoretically predict and analyze such types of the STM. The first part of this thesis focusses on the simulation of FT-STM, the mode that allows to probe local dispersion properties of the electrons at the surface. In order to provide the theoretical counterpart of the experimental FT-STM spectra we have introduced a new implicit approach that is derived from Tersoff-Hamann theory of the STM. The importance of an accurate description of surface wavefunctions at 5-15 A above the surface as well as the spurious quantum- size effects have been discussed in detail together with approaches to obtain converged FT-STM images. We applied our method to FT-STM experiments performed on Ag(110) surfaces. In the second part of the thesis we discuss the modeling of the spin-resolved STM, the mode that allows to characterize the magnetic structure of a surface. As a case system we studied here the magnetically-ordered transition-metal nitride surface Mn{sub 3}N{sub 2}(010). Because SP-STM experiments did not allow a conclusive understanding of the surface structure, we have first employed ab initio thermodynamics to figure out the most stable magnetic and atomic configuration of the surface that are consistent with experiments. To simulate SP-STM images on the most stable Mn{sub 3}N{sub 2}(010) surface we have employed the spin-generalized transfer-Hamiltonian formalism, assuming that the tip wavefunctions have dominant radial symmetry (s-like tip). (orig.)

  7. Electronic Structure of Hydrogenated and Surface-Modified GaAs Nanocrystals: Ab Initio Calculations

    Directory of Open Access Journals (Sweden)

    Hamsa Naji Nasir

    2012-01-01

    Full Text Available Two methods are used to simulate electronic structure of gallium arsenide nanocrystals. The cluster full geometrical optimization procedure which is suitable for small nanocrystals and large unit cell that simulates specific parts of larger nanocrystals preferably core part as in the present work. Because of symmetry consideration, large unit cells can reach sizes that are beyond the capabilities of first method. The two methods use ab initio Hartree-Fock and density functional theory, respectively. The results show that both energy gap and lattice constant decrease in their value as the nanocrystals grow in size. The inclusion of surface part in the first method makes valence band width wider than in large unit cell method that simulates the core part only. This is attributed to the broken symmetry and surface passivating atoms that split surface degenerate states and adds new levels inside and around the valence band. Bond length and tetrahedral angle result from full geometrical optimization indicate good convergence to the ideal zincblende structure at the centre of hydrogenated nanocrystal. This convergence supports large unit cell methodology. Existence of oxygen atoms at nanocrystal surface melts down density of states and reduces energy gap.

  8. Ab initio-based approach to structural change of compound semiconductor surfaces during MBE growth

    Science.gov (United States)

    Ito, Tomonori; Akiyama, Toru; Nakamura, Kohji

    2009-01-01

    Phase diagrams of GaAs and GaN surfaces are systematically investigated by using our ab initio-based approach in conjunction with molecular beam epitaxy (MBE). The phase diagrams are obtained as a function of growth parameters such as temperature and beam equivalent pressure (BEP). The versatility of our approach is exemplified by the phase diagram calculations for GaAs(0 0 1) surfaces, where the stable phases and those phase boundaries are successfully determined as functions of temperature and As 2 and As 4 BEPs. The initial growth processes are clarified by the phase diagram calculations for GaAs(1 1 1)B-(2×2). The calculated results demonstrate that the As-trimer desorption on the GaAs(1 1 1)B-(2×2) with Ga adatoms occurs beyond 500-700 K while the desorption without Ga adatoms does beyond 800-1000 K. This self-surfactant effect induced by Ga adsorption crucially affects the initial growth of GaAs on the GaAs(1 1 1)B-(2×2). Furthermore, the phase diagram calculations for GaN(0 0 0 1) suggests that Ga adsorption or desorption during GaN MBE growth can easily change the pseudo-(1×1) to the (2×2)-Ga via newly found (1×1) and vice versa. On the basis of this finding, the possibility of ghost island formation during MBE growth is discussed.

  9. Ab Initio-Based Predictions of Hydrocarbon Combustion Chemistry

    Science.gov (United States)

    2015-07-15

    There are two prime objectives of the research. One is to develop and apply efficient methods for using ab initio potential energy surfaces (PESs...31-Mar-2015 Approved for Public Release; Distribution Unlimited Final Report: Ab Initio-Based Predictions of Hydrocarbon Combustion Chemistry The...Office P.O. Box 12211 Research Triangle Park, NC 27709-2211 hydrocarbon combustion, ab initio quantum chemistry, potential energy surfaces, chemical

  10. Ab initio calculations of biomolecules

    Science.gov (United States)

    Leś, Andrzej; Adamowicz, Ludwik

    1995-08-01

    Ab initio quantum mechanical calculations are valuable tools for interpretation and elucidation of elemental processes in biochemical systems. With the ab initio approach one can calculate data that sometimes are difficult to obtain by experimental techniques. The most popular computational theoretical methods include the Hartree-Fock method as well as some lower-level variational and perturbational post-Hartree Fock approaches which allow to predict molecular structures and to calculate spectral properties. We have been involved in a number of joined theoretical and experimental studies in the past and some examples of these studies are given in this presentation. The systems chosen cover a wide variety of simple biomolecules, such as precursors of nucleic acids, double-proton transferring molecules, and simple systems involved in processes related to first stages of substrate-enzyme interactions. In particular, examples of some ab initio calculations used in the assignment of IR spectra of matrix isolated pyrimidine nucleic bases are shown. Some radiation-induced transformations in model chromophores are also presented. Lastly, we demonstrate how the ab-initio approach can be used to determine the initial several steps of the molecular mechanism of thymidylate synthase inhibition by dUMP analogues.

  11. Ab initio potential for solids

    DEFF Research Database (Denmark)

    Chetty, N.; Stokbro, Kurt; Jacobsen, Karsten Wedel

    1992-01-01

    . At the most approximate level, the theory is equivalent to the usual effective-medium theory. At all levels of approximation, every term in the total-energy expression is calculated ab initio, that is, without any fitting to experiment or to other calculations. Every step in the approximation procedure can...

  12. Quantal Study of the Exchange Reaction for N + N2 using an ab initio Potential Energy Surface

    Science.gov (United States)

    Wang, Dunyou; Stallcop, James R.; Huo, Winifred M.; Dateo, Christopher E.; Schwenke, David W.; Partridge, Harry; Kwak, Dochan (Technical Monitor)

    2002-01-01

    The N + N2 exchange rate is calculated using a time-dependent quantum dynamics method on a newly determined ab initio potential energy surface (PES) for the ground A" state. This ab initio PES shows a double barrier feature in the interaction region with the barrier height at 47.2 kcal/mol, and a shallow well between these two barriers, with the minimum at 43.7 kcal/mol. A quantum dynamics wave packet calculation has been carried out using the fitted PES to compute the cumulative reaction probability for the exchange reaction of N + N2(J=O). The J - K shift method is then employed to obtain the rate constant for this reaction. The calculated rate constant is compared with experimental data and a recent quasi-classical calculation using a LEPS PES. Significant differences are found between the present and quasiclassical results. The present rate calculation is the first accurate 3D quantal dynamics study for N + N2 reaction system and the ab initio PES reported here is the first such surface for N3.

  13. A computational ab initio study of surface diffusion of sulfur on the CdTe (111 surface

    Directory of Open Access Journals (Sweden)

    Ebadollah Naderi

    2016-08-01

    Full Text Available In order to discern the formation of epitaxial growth of CdS shell over CdTe nanocrystals, kinetics related to the initial stages of the growth of CdS on CdTe is investigated using ab-initio methods. We report diffusion of sulfur adatom on the CdTe (111 A-type (Cd-terminated and B-type (Te-terminated surfaces within the density functional theory (DFT. The barriers are computed by applying the climbing Nudge Elastic Band (c-NEB method. From the results surface hopping emerges as the major mode of diffusion. In addition, there is a distinct contribution from kick-out type diffusion in which a CdTe surface atom is kicked out from its position and is replaced by the diffusing sulfur atom. Also, surface vacancy substitution contributes to the concomitant dynamics. There are sites on the B- type surface that are competitively close in terms of the binding energy to the lowest energy site of epitaxy on the surface. The kick-out process is more likely for B-type surface where a Te atom of the surface is displaced by a sulfur adatom. Further, on the B-type surface, subsurface migration of sulfur is indicated. Furthermore, the binding energies of S on CdTe reveal that on the A-type surface, epitaxial sites provide relatively higher binding energies and barriers than on B-type.

  14. A computational ab initio study of surface diffusion of sulfur on the CdTe (111) surface

    Energy Technology Data Exchange (ETDEWEB)

    Naderi, Ebadollah, E-mail: enaderi42@gmail.com [Department of Physics, Savitribai Phule Pune University (SPPU), Pune-411007 (India); Ghaisas, S. V. [Department of Electronic Science, Savitribai Phule Pune University (SPPU), Pune-411007 (India)

    2016-08-15

    In order to discern the formation of epitaxial growth of CdS shell over CdTe nanocrystals, kinetics related to the initial stages of the growth of CdS on CdTe is investigated using ab-initio methods. We report diffusion of sulfur adatom on the CdTe (111) A-type (Cd-terminated) and B-type (Te-terminated) surfaces within the density functional theory (DFT). The barriers are computed by applying the climbing Nudge Elastic Band (c-NEB) method. From the results surface hopping emerges as the major mode of diffusion. In addition, there is a distinct contribution from kick-out type diffusion in which a CdTe surface atom is kicked out from its position and is replaced by the diffusing sulfur atom. Also, surface vacancy substitution contributes to the concomitant dynamics. There are sites on the B- type surface that are competitively close in terms of the binding energy to the lowest energy site of epitaxy on the surface. The kick-out process is more likely for B-type surface where a Te atom of the surface is displaced by a sulfur adatom. Further, on the B-type surface, subsurface migration of sulfur is indicated. Furthermore, the binding energies of S on CdTe reveal that on the A-type surface, epitaxial sites provide relatively higher binding energies and barriers than on B-type.

  15. Collisional Dissociation of CO: ab initio Potential Energy Surfaces and Quasiclassical Trajectory Rate Coefficients

    Science.gov (United States)

    Schwenke, David W.; Jaffe, Richard L.; Chaban, Galina M.

    2016-01-01

    We have generated accurate global potential energy surfaces for CO+Ar and CO+O that correlate with atom-diatom pairs in their ground electronic states based on extensive ab initio electronic structure calculations and used these potentials in quasi-classical trajectory nuclear dynamics calculations to predict the thermal dissociation rate coefficients over 5000- 35000 K. Our results are not compatible with the 20-45 year old experimental results. For CO + Ar we obtain fairly good agreement with the experimental rate coefficients of Appleton et al. (1970) and Mick and Roth (1993), but our computed rate coefficients exhibit a stronger temperature dependence. For CO + O our dissociation rate coefficient is in close agreement with the value from the Park model, which is an empirical adjustment of older experimental results. However, we find the rate coefficient for CO + O is only 1.5 to 3.3 times larger than CO + Ar over the temperature range of the shock tube experiments (8000-15,000 K). The previously accepted value for this rate coefficient ratio is 15, independent of temperature. We also computed the rate coefficient for the CO + O ex- change reaction which forms C + O2. We find this reaction is much faster than previously believed and is the dominant process in the removal of CO at temperatures up to 16,000 K. As a result, the dissociation of CO is accomplished in two steps (react to form C+O2 and then O2 dissociates) that are endothermic by 6.1 and 5.1 eV, instead of one step that requires 11.2 eV to break the CO bond.

  16. Accurate high level ab initio-based global potential energy surface and dynamics calculations for ground state of CH2(+).

    Science.gov (United States)

    Li, Y Q; Zhang, P Y; Han, K L

    2015-03-28

    A global many-body expansion potential energy surface is reported for the electronic ground state of CH2 (+) by fitting high level ab initio energies calculated at the multireference configuration interaction level with the aug-cc-pV6Z basis set. The topographical features of the new global potential energy surface are examined in detail and found to be in good agreement with those calculated directly from the raw ab initio energies, as well as previous calculations available in the literature. In turn, in order to validate the potential energy surface, a test theoretical study of the reaction CH(+)(X(1)Σ(+))+H((2)S)→C(+)((2)P)+H2(X(1)Σg (+)) has been carried out with the method of time dependent wavepacket on the title potential energy surface. The total integral cross sections and the rate coefficients have been calculated; the results determined that the new potential energy surface can both be recommended for dynamics studies of any type and as building blocks for constructing the potential energy surfaces of larger C(+)/H containing systems.

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

    Science.gov (United States)

    Senese, Fredrick; Ake, Robert

    1992-01-01

    Ab initio quantum mechanical calculations on small hydration complexes involving the nitrate anion are reported. The self-consistent field method with accurate basis sets has been applied to compute completely optimized equilibrium geometries, vibrational frequencies, thermochemical parameters, and stable site labilities of complexes involving 1, 2, and 3 waters. The most stable geometries in the first hydration shell involve in-plane waters bridging pairs of nitrate oxygens with two equal and bent hydrogen bonds. A second extremely labile local minimum involves out-of-plane waters with a single hydrogen bond and lies about 2 kcal/mol higher. The potential in the region of the second minimum is extremely flat and qualitatively sensitive to changes in the basis set; it does not correspond to a true equilibrium structure.

  18. Ab initio surface core-level shifts and surface segregation energies

    DEFF Research Database (Denmark)

    Aldén, Magnus; Skriver, Hans Lomholt; Johansson, Börje

    1993-01-01

    We have calculated the surface core-level energy shifts of the 4d and 5d transition metals by means of local-density theory and a Green’s-function technique based on the linear muffin-tin orbitals method. Final-state effects are included by treating the core-ionized atom as an impurity located in...

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

    Science.gov (United States)

    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.

  20. Cooperative effects at water-crystalline silica interfaces strengthen surface silanol hydrogen bonding. An ab initio molecular dynamics study.

    Science.gov (United States)

    Musso, Federico; Mignon, Pierre; Ugliengo, Piero; Sodupe, Mariona

    2012-08-14

    Silica and silica based materials are widely used in chemistry and materials science due to their importance in many technological fields. The properties of these materials, which are crucial for their applications, are mainly determined by the presence of hydrogen bonding between surface silanols. Here, we present ab initio molecular dynamics simulations (AIMD) on different surfaces derived from the crystallographic α-quartz (100) and the α-cristobalite (001) and (101) faces, both free and at the interface with liquid water. The focus was on studying whether water adsorption can disrupt the H-bond pattern at the pristine free silica surface and how deep the perturbation due to the contact with the surface affects the structure of the water multilayer. Results highlight that the water phase is over structured at the interface with silica, as compared to water bulk. Furthermore, an apparent counterintuitive behavior has been observed for quartz (100) and cristobalite (001) surfaces: the interaction with water does not cleave the pre-existent H-bonds between the surface silanol groups. On the contrary, in several cases, it is observed that SiOH···OHSi H-bonds are even strengthened, as the result of a mutual cooperative H-donor/H-acceptor enhancement between silanols and water molecules, which may alter the adsorption capability of these silica surfaces.

  1. Near-infrared spectra and rovibrational dynamics on a four-dimensional ab initio potential energy surface of (HBr)2.

    Science.gov (United States)

    Castillo-Chará, J; McIntosh, A L; Wang, Z; Lucchese, R R; Bevan, J W

    2004-06-08

    Supersonic jet investigations of the (HBr)(2) dimer have been carried out using a tunable diode laser spectrometer to provide accurate data for comparison with results from a four-dimensional (4-D) ab initio potential energy surface (PES). The near-infrared nu(1) (+/-), nu(2) (+/-), and (nu(1)+nu(4))(-) bands of (H (79)Br)(2), (H (79)Br-H (81)Br), and (H (81)Br)(2) isotopomers have been recorded in the range 2500-2600 cm(-1) using a CW slit jet expansion with an upgraded near-infrared diode laser spectrometer. The 4-D PES has been calculated for (HBr)(2) using second-order Møller-Plesset perturbation theory with an augmented and polarized 6-311G basis set. The potential is characterized by a global minimum occurring at the H bond structure with the distance between the center of masses (CM) of the monomer being R(CM)=4.10 A with angles theta(A)=10 degrees, theta(B)=100 degrees and a well depth of 692.2 cm(-1), theta(A) is the angle the HBr bond of monomer A makes with the vector from the CM of A to the CM of B, and theta(B) is the corresponding angle monomer B makes with the same CM-CM vector. The barrier for the H interchange occurs at the closed C(2h) structure for which R(CM)=4.07 A, theta(A)=45 degrees, theta(B)=135 degrees, and the barrier height is 73.9 cm(-1). The PES was fitted using a linear-least squares method and the rovibrational energy levels of the complex were calculated by a split pseudospectral method. The spectroscopic data provide accurate molecular parameters for the dimer that are then compared with the results predicted on the basis of the 4-D ab initio PES. (c) 2004 American Institute of Physics.

  2. Diffusion and reaction pathways of water near fully hydrated TiO2 surfaces from ab initio molecular dynamics

    Science.gov (United States)

    Agosta, Lorenzo; Brandt, Erik G.; Lyubartsev, Alexander P.

    2017-07-01

    Ab initio molecular dynamics simulations are reported for water-embedded TiO2 surfaces to determine the diffusive and reactive behavior at full hydration. A three-domain model is developed for six surfaces [rutile (110), (100), and (001), and anatase (101), (100), and (001)] which describes waters as "hard" (irreversibly bound to the surface), "soft" (with reduced mobility but orientation freedom near the surface), or "bulk." The model explains previous experimental data and provides a detailed picture of water diffusion near TiO2 surfaces. Water reactivity is analyzed with a graph-theoretic approach that reveals a number of reaction pathways on TiO2 which occur at full hydration, in addition to direct water splitting. Hydronium (H3O+) is identified to be a key intermediate state, which facilitates water dissociation by proton hopping between intact and dissociated waters near the surfaces. These discoveries significantly improve the understanding of nanoscale water dynamics and reactivity at TiO2 interfaces under ambient conditions.

  3. MoS{sub 2} on an amorphous HfO{sub 2} surface: An ab initio investigation

    Energy Technology Data Exchange (ETDEWEB)

    Scopel, W. L., E-mail: wlscopel@if.uff.br [Departamento de Física, Universidade Federal do Espírito Santo, Vitória, Brazil and Departamento de Ciências Exatas, Universidade Federal Fluminense, Volta Redonda, Rio de Janerio (Brazil); Miwa, R. H., E-mail: hiroki@infis.ufu.br; Schmidt, T. M., E-mail: tome@infis.ufu.br [Instituto de Física, Universidade Federal de Uberlândia, Uberlândia, Minas Gerais (Brazil); Venezuela, P., E-mail: vene@if.uff.br [Instituto de Física, Universidade Federal Fluminense, Niterói, Rio de Janerio (Brazil)

    2015-05-21

    The energetic stability, electronic and structural properties of MoS{sub 2} adsorbed on an amorphous a-HfO{sub 2} surface (MoS{sub 2}/HfO{sub 2}) are examined through ab initio theoretical investigations. Our total energy results indicate that the formation of MoS{sub 2}/HfO{sub 2} is an exothermic process with an adsorption energy of 34 meV/Å{sup 2}, which means that it is more stable than similar systems like graphene/HfO{sub 2} and MoS{sub 2}/SiO{sub 2}. There are no chemical bonds at the MoS{sub 2}-HfO{sub 2} interface. Upon formation of MoS{sub 2}/HfO{sub 2}, the electronic charge distribution is mostly localized at the interface region with no net charge transfer between the adsorbed MoS{sub 2} sheet and –HfO{sub 2} surface. However, the MoS{sub 2} sheet becomes n-type doped when there are oxygen vacancies in the HfO{sub 2} surface. Further investigation of the electronic distribution reveals that there are no electron- and hole-rich regions (electron-hole puddles) on the MoS{sub 2} sheet, which makes this system promising for use in high-speed nanoelectronic devices.

  4. Accurate ab initio dipole moment surfaces of ozone: First principle intensity predictions for rotationally resolved spectra in a large range of overtone and combination bands

    Science.gov (United States)

    Tyuterev, Vladimir G.; Kochanov, Roman V.; Tashkun, Sergey A.

    2017-02-01

    Ab initio dipole moment surfaces (DMSs) of the ozone molecule are computed using the MRCI-SD method with AVQZ, AV5Z, and VQZ-F12 basis sets on a dense grid of about 1950 geometrical configurations. The analytical DMS representation used for the fit of ab initio points provides better behavior for large nuclear displacements than that of previous studies. Various DMS models were derived and tested. Vibration-rotation line intensities of 16O3 were calculated from these ab initio surfaces by the variational method using two different potential functions determined in our previous works. For the first time, a very good agreement of first principle calculations with the experiment was obtained for the line-by-line intensities in rotationally resolved ozone spectra in a large far- and mid-infrared range. This includes high overtone and combination bands up to Δ V = 6. A particular challenge was a correct description of the B-type bands (even Δ V3 values) that represented major difficulties for the previous ab initio investigations and for the empirical spectroscopic models. The major patterns of various B-type bands were correctly described without empirically adjusted dipole moment parameters. For the 10 μ m range, which is of key importance for the atmospheric ozone retrievals, our ab initio intensity results are within the experimental error margins. The theoretical values for the strongest lines of the ν3 band lie in general between two successive versions of HITRAN (HIgh-resolution molecular TRANsmission) empirical database that corresponded to most extended available sets of observations. The overall qualitative agreement in a large wavenumber range for rotationally resolved cold and hot ozone bands up to about 6000 cm-1 is achieved here for the first time. These calculations reveal that several weak bands are yet missing from available spectroscopic databases.

  5. Ab initio Potential-Energy Surfaces and Electron-Spin-Exchange Cross Sections for H-O2 Interactions

    Science.gov (United States)

    Stallcop, James R.; Partridge, Harry; Levin, Eugene

    1996-01-01

    Accurate quartet- and doublet-state potential-energy surfaces for the interaction of a hydrogen atom and an oxygen molecule in their ground states have been determined from an ab initio calculation using large-basis sets and the internally contracted multireference configuration interaction method. These potential surfaces have been used to calculate the H-O2 electron-spin-exchange cross section; the square root of the cross section (in a(sub 0)), not taking into account inelastic effects, can be obtained approximately from the expressions 2.390E(sup -1/6) and 5.266-0.708 log10(E) at low and high collision energies E (in E(sub h)), respectively. These functional forms, as well as the oscillatory structure of the cross section found at high energies, are expected from the nature of the interaction energy. The mean cross section (the cross section averaged over a Maxwellian velocity distribution) agrees reasonably well with the results of measurements.

  6. Ab initio thermodynamics for the growth of ultra-thin Cu film on a perfect Mg O(001) surface

    Energy Technology Data Exchange (ETDEWEB)

    Zhukovskii, Yuri F. [Institute for Solid State Physics, University of Latvia, Kengaraga str. 8, Riga LV-1063 (Latvia)]. E-mail: quantzh@latnet.lv; Fuks, David [Materials Engineering Department, Ben-Gurion University of the Negev, POB 653, Beer-Sheva IL-84105 (Israel); Kotomin, Eugene A. [Institute for Solid State Physics, University of Latvia, Kengaraga str. 8, Riga LV-1063 (Latvia); Dorfman, Simon [Department of Physics, Israel Institute of Technology-Technion, Haifa IL-32000 (Israel)

    2005-12-15

    Controlled growth of thin metallic films on oxide substrates is important for numerous micro-and nano electronic applications. Our ab initio study is devoted to the periodic slab simulations for a series of ordered 2a Cu superlattices on the regular Mg O(001) substrate. Submonolayer and monolayer substrate Cu coverages were calculated using the Daft-Gaga method, as implemented into the Crystal-98 code. The results of ab initio calculations have been combined with thermodynamic theory which allows US to predict the growth mode of ultra-thin metal films (spinodal decomposition vs. nucleation-and-growth regime) as a function of the metal coverage and the temperature, and to estimate the metal density in clusters. We show that 3a cluster formation becomes predominant already at low Cu coverages, in agreement with the experiment.

  7. Ab initio potential energy surface and vibration-rotation energy levels of silicon dicarbide, SiC2.

    Science.gov (United States)

    Koput, Jacek

    2016-10-05

    The accurate ground-state potential energy surface of silicon dicarbide, SiC2 , has been determined from ab initio calculations using the coupled-cluster approach. Results obtained with the conventional and explicitly correlated coupled-cluster methods were compared. The core-electron correlation, higher-order valence-electron correlation, and scalar relativistic effects were taken into account. The potential energy barrier to the linear SiCC configuration was predicted to be 1782 cm(-1) . The vibration-rotation energy levels of the SiC2 , (29) SiC2 , (30) SiC2 , and SiC(13) C isotopologues were calculated using a variational method. The experimental vibration-rotation energy levels of the main isotopologue were reproduced to high accuracy. In particular, the experimental energy levels of the highly anharmonic vibrational ν3 mode of SiC2 were reproduced to within 6.7 cm(-1) , up to as high as the v3  = 16 state. © 2016 Wiley Periodicals, Inc.

  8. An ab initio study of hydroxylated graphane

    Science.gov (United States)

    Buonocore, Francesco; Capasso, Andrea; Lisi, Nicola

    2017-09-01

    Graphene-based derivatives with covalent functionalization and well-defined stoichiometry are highly desirable in view of their application as functional surfaces. Here, we have evaluated by ab initio calculations the energy of formation and the phase diagram of hydroxylated graphane structures, i.e., fully functionalized graphene derivatives coordinated with -H and -OH groups. We compared these structures to different hydrogenated and non-hydrogenated graphene oxide derivatives, with high level of epoxide and hydroxyl groups functionalization. Based on our calculations, stable phases of hydroxylated graphane with low and high contents of hydrogen are demonstrated for high oxygen and hydrogen partial pressure, respectively. Stable phases of graphene oxide with a mixed carbon hybridization are also found. Notably, the synthesis of hydroxylated graphane has been recently reported in the literature.

  9. Ab initio valence calculations in chemistry

    CERN Document Server

    Cook, D B

    1974-01-01

    Ab Initio Valence Calculations in Chemistry describes the theory and practice of ab initio valence calculations in chemistry and applies the ideas to a specific example, linear BeH2. Topics covered include the Schrödinger equation and the orbital approximation to atomic orbitals; molecular orbital and valence bond methods; practical molecular wave functions; and molecular integrals. Open shell systems, molecular symmetry, and localized descriptions of electronic structure are also discussed. This book is comprised of 13 chapters and begins by introducing the reader to the use of the Schrödinge

  10. Orbital-free ab initio molecular dynamics study of the static structure and dynamic properties of the free liquid surface of Sn

    Directory of Open Access Journals (Sweden)

    del Rio B. G.

    2017-01-01

    Full Text Available We report results of an orbital-free ab initio molecular dynamics (OF-AIMD study of the free liquid surface (FLS of Sn at 1000 K and 600 K. A key ingredient in the OF-AIMD method is the local pseudopotential describing the ions-valence electrons interaction. We have used a force-matching method to derive a local pseudopotential suitable to account for the variation of the forces from the bulk to the FLS. We obtain very good results for structural properties, such as the reflectivity, including the characteristic shoulder it presents in x-ray experiments. Moreover we have been able to study ab initio for the first time the evolution in some dynamical properties as we move from the central region, where the system behaves like the bulk liquid, to the FLS.

  11. Effects of surface vibrations on interlayer mass transport: Ab initio molecular dynamics investigation of Ti adatom descent pathways and rates from TiN/TiN(001) islands

    Science.gov (United States)

    Sangiovanni, D. G.; Mei, A. B.; Edström, D.; Hultman, L.; Chirita, V.; Petrov, I.; Greene, J. E.

    2018-01-01

    We carried out density-functional ab initio molecular dynamics (AIMD) simulations of Ti adatom (T iad ) migration on, and descent from, square TiN 〈100 〉 epitaxial islands on TiN(001) at temperatures (T ) ranging from 1200 to 2400 K. Adatom-descent energy barriers determined via ab initio nudged-elastic-band calculations at 0 Kelvin suggest that Ti interlayer transport on TiN(001) occurs essentially exclusively via direct hopping onto a lower layer. However, AIMD simulations reveal comparable rates for T iad descent via direct hopping vs push-out/exchange with a Ti island-edge atom for T ≥1500 K . We demonstrate that this effect is due to surface vibrations, which yield considerably lower activation energies at finite temperatures by significantly modifying the adatom push-out/exchange reaction pathway.

  12. Ab-initio density functional study of O on the Ag(001) surface

    OpenAIRE

    Gajdos, M.; A. Eichler; Hafner, J.

    2003-01-01

    The adsorption of oxygen on the Ag(001) is investigated by means of density functional techniques. Starting from a characterization of the clean silver surfaces oxygen adsorption in several modifications (molecularly, on-surface, sub-surface, Ag$_2$O) for varying coverage was studied. Besides structural parameters and adsorption energies also work-function changes, vibrational frequencies and core level energies were calculated for a better characterization of the adsorption structures and an...

  13. Enhanced atomic oxygen adsorption on defective nickel surfaces: An ab initio study

    Science.gov (United States)

    Cherbal, N.; Megchiche, E. H.; Zenia, H.; Lounis, K.; Amarouche, M.

    2017-09-01

    In this work we have examined the influence of the presence of a monovacancy on the atomic oxygen adsorption process at nickel surfaces of orientation (111), (100), and (110). The presence of such a defect was neglected in earlier studies. And for the first time, we have studied oxygen segregation on a defective (111) surface. The results reveal a varying sensitivity of the oxygen adsorption energy to the state of the surfaces. When compared to the perfect surface, we have registered an energy gain of 0.22 eV in the process of oxygen adsorption on the (111) surface when a vacancy is present on it. However, the energetic gains for the other two surfaces, (100) and (110), are much less than that of the (111) surface: they are of the order of 0.1 eV. Comparing to the perfect surfaces, we have found that charge reconstruction in the neighborhood of the vacancy plays a major role in giving rise to the aforementioned energetic gains. Indeed, we find an increase in the charge density on the nickel atoms surrounding the vacancy, which leads to strengthening of the ionic Ni-O bond if the oxygen is adsorbed in its vicinity. As a means of studying the effect of the presence of the vacancy on the first stages of the growth of an oxide layer, we have looked at the segregation process of oxygen atoms at the three surfaces. Our results show that up to four oxygen atoms can aggregate favorably at the adsorption sites inside and in the vicinity of the monovacancy at the (111) surface. This number is reduced to two oxygen atoms at the (110) surface, and to only one oxygen atom at the (100) surface.

  14. Ab initio molecular dynamics calculations on reactions of molecules with metal surfaces

    NARCIS (Netherlands)

    Nattino, Francesco

    2015-01-01

    Reactions on metal surfaces are of scientific interest due to the tremendous relevance of heterogeneous catalysis. Single crystal surfaces under controlled physical conditions are generally employed as a model for the real catalysts, with the aim of improving the fundamental understanding of the

  15. Ab initio potential energy and dipole moment surfaces for CS2: determination of molecular vibrational energies.

    Science.gov (United States)

    Pradhan, Ekadashi; Carreón-Macedo, José-Luis; Cuervo, Javier E; Schröder, Markus; Brown, Alex

    2013-08-15

    The ground state potential energy and dipole moment surfaces for CS2 have been determined at the CASPT2/C:cc-pVTZ,S:aug-cc-pV(T+d)Z level of theory. The potential energy surface has been fit to a sum-of-products form using the neural network method with exponential neurons. A generic interface between neural network potential energy surface fitting and the Heidelberg MCTDH software package is demonstrated. The potential energy surface has also been fit using the potfit procedure in MCTDH. For fits to the low-energy regions of the potential, the neural network method requires fewer parameters than potfit to achieve high accuracy; global fits are comparable between the two methods. Using these potential energy surfaces, the vibrational energies have been computed for the four most abundant CS2 isotopomers. These results are compared to experimental and previous theoretical data. The current potential energy surfaces are shown to accurately reproduce the low-lying vibrational energies within a few wavenumbers. Hence, the potential energy and dipole moments surfaces will be useful for future study on the control of quantum dynamics in CS2.

  16. On the construction of diabatic and adiabatic potential energy surfaces based on ab initio valence bond theory.

    Science.gov (United States)

    Song, Lingchun; Gao, Jiali

    2008-12-18

    A theoretical model is presented for deriving effective diabatic states based on ab initio valence bond self-consistent field (VBSCF) theory by reducing the multiconfigurational VB Hamiltonian into an effective two-state model. We describe two computational approaches for the optimization of the effective diabatic configurations, resulting in two ways of interpreting such effective diabatic states. In the variational diabatic configuration (VDC) method, the energies of the diabatic states are variationally minimized. In the consistent diabatic configuration (CDC) method, both the configuration coefficients and orbital coefficients are simultaneously optimized to minimize the adiabatic ground-state energy in VBSCF calculations. In addition, we describe a mixed molecular orbital and valence bond (MOVB) approach to construct the CDC diabatic and adiabatic states for a chemical reaction. Note that the VDC-MOVB method has been described previously. Employing the symmetric S(N)2 reaction between NH(3) and CH(3)NH(3)(+) as a test system, we found that the results from ab initio VBSCF and from ab initio MOVB calculations using the same basis set are in good agreement, suggesting that the computationally efficient MOVB method is a reasonable model for VB simulations of condensed phase reactions. The results indicate that CDC and VDC diabatic states converge, respectively, to covalent and ionic states as the molecular geometries are distorted from the minimum of the respective diabatic state along the reaction coordinate. Furthermore, the resonance energy that stabilizes the energy of crossing between the two diabatic states, resulting in the transition state of the adiabatic ground-state reaction, has a strong dependence on the overlap integral between the two diabatic states and is a function of both the exchange integral and the total diabatic ground-state energy.

  17. Manipulating magnetism and conductance of an adatom-molecule junction on a metal surface: An ab initio study

    DEFF Research Database (Denmark)

    Tao, Kun; Stepanyuk, V.S.; Bruno, P.

    2008-01-01

    The state of the art ab initio calculations reveal the effect of a scanning tunneling microscopy tip on magnetic properties and conductance of a benzene-adatom sandwich on Cu(001). We concentrate on a benzene-Co system interacting with a Cr tip. Our studies give a clear evidence that magnetism...... and conductance in molecule-adatom junctions can be tailored by the STM tip. Varying the tip-substrate distance the magnetic moment of the Co adatom can be switched on/off. The interplay between spin-polarized electron transport through the junction and its magnetic properties is demonstrated. A spin...

  18. Accurate ab initio potential energy surface, dynamics, and thermochemistry of the F+CH4-->HF+CH3 reaction.

    Science.gov (United States)

    Czakó, Gábor; Shepler, Benjamin C; Braams, Bastiaan J; Bowman, Joel M

    2009-02-28

    An accurate full-dimensional global potential energy surface (PES) for the F+CH(4)-->HF+CH(3) reaction has been developed based on 19 384 UCCSD(T)/aug-cc-pVTZ quality ab initio energy points obtained by an efficient composite method employing explicit UCCSD(T)/aug-cc-pVDZ and UMP2/aug-cc-pVXZ [X=D,T] computations. The PES contains a first-order saddle point, (CH(4)- -F)(SP), separating reactants from products, and also minima describing the van der Waals complexes, (CH(4)- - -F)(vdW) and (CH(3)- - -HF)(vdW), in the entrance and exit channels, respectively. The structures of these stationary points, as well as those of the reactants and products have been computed and the corresponding energies have been determined using basis set extrapolation techniques considering (a) electron correlation beyond the CCSD(T) level, (b) effects of the scalar relativity and the spin-orbit couplings, (c) diagonal Born-Oppenheimer corrections (DBOC), and (d) zero-point vibrational energies and thermal correction to the enthalpy at 298 K. The resulting saddle point barrier and ground state vibrationally adiabatic barrier heights (V(SP) and V(VAGS)), dissociation energy of (CH(3)- - -HF)(vdW) (D(e) and D(0)), and the reaction enthalpy (DeltaH(e) ( degrees ), DeltaH(0) ( degrees ), and DeltaH(298) ( degrees )) are (240+/-40 and 245+/-200 cm(-1)), (1070+/-10 and 460+/-50 cm(-1)), and (-10000+/-50, -11200+/-80, and -11000+/-80 cm(-1)), respectively. Variational vibrational calculations have been carried out for (CH(3)- - -HF)(vdW) in full (12) dimensions. Quasiclassical trajectory calculations of the reaction using the new PES are reported. The computed HF vibrational and rotational distributions are in excellent agreement with experiment.

  19. Rotational Energy Transfer of N2 Gas Determined Using a New Ab Initio Potential Energy Surface

    Science.gov (United States)

    Huo, Winifred M.; Stallcop, James R.; Partridge, Harry; Langhoff, Stephen R. (Technical Monitor)

    1997-01-01

    Rotational energy transfer between two N2 molecules is a fundamental process of some importance. Exchange is expected to play a role, but its importance is somewhat uncertain. Rotational energy transfer cross sections of N2 also have applications in many other fields including modeling of aerodynamic flows, laser operations, and linewidth analysis in nonintrusive laser diagnostics. A number of N2-N2 rigid rotor potential energy surface (PES) has been reported in the literature.

  20. {ital Ab} {ital initio} calculations of biomolecules

    Energy Technology Data Exchange (ETDEWEB)

    Les, A. [Department of Chemistry, University of Warsaw, 02-093 Warsaw (Poland)]|[Department of Chemistry, University of Arizona, Tucson, Arizona 85721 (United States); Adamowicz, L. [Department of Theoretical Chemistry, University of Lund, Lund, S-22100 (Sweden)]|[Department of Chemistry, University of Arizona, Tucson, Arizona 85721 (United States)

    1995-08-01

    {ital Ab} {ital initio} quantum mechanical calculations are valuable tools for interpretation and elucidation of elemental processes in biochemical systems. With the {ital ab} {ital initio} approach one can calculate data that sometimes are difficult to obtain by experimental techniques. The most popular computational theoretical methods include the Hartree-Fock method as well as some lower-level variational and perturbational post-Hartree Fock approaches which allow to predict molecular structures and to calculate spectral properties. We have been involved in a number of joined theoretical and experimental studies in the past and some examples of these studies are given in this presentation. The systems chosen cover a wide variety of simple biomolecules, such as precursors of nucleic acids, double-proton transferring molecules, and simple systems involved in processes related to first stages of substrate-enzyme interactions. In particular, examples of some {ital ab} {ital initio} calculations used in the assignment of IR spectra of matrix isolated pyrimidine nucleic bases are shown. Some radiation-induced transformations in model chromophores are also presented. Lastly, we demonstrate how the {ital ab}-{ital initio} approach can be used to determine the initial several steps of the molecular mechanism of thymidylate synthase inhibition by dUMP analogues.

  1. AB INITIO STUDY, INVESTIGATION OF NMR SHIELDING ...

    African Journals Online (AJOL)

    Preferred Customer

    Ab initio study, investigation of NMR shielding tensors, NBO and vibrational frequency. Bull. Chem. Soc. Ethiop. 2010, 24(2). 231. Gas phase results. In order to study mechanism of the reactions, structure corresponding to reactants, transition states and products were optimized in level of theory. Figure 1 shows the ...

  2. Synthesis, characterization, ab initio calculations, thermal behaviour ...

    Indian Academy of Sciences (India)

    Administrator

    through titration of the ligands with the metal ions at constant ionic strength (0⋅1 M NaClO4) and at 25°C. According to the thermodynamic studies, as the steric character of the ligand increases, the complexation tendency to VO(IV) center decreases. Also, the ab initio calculations were carried out to determine the structural ...

  3. Ab Initio molecular dynamics with excited electrons

    NARCIS (Netherlands)

    Alavi, A.; Kohanoff, J.; Parrinello, M.; Frenkel, D.

    1994-01-01

    A method to do ab initio molecular dynamics suitable for metallic and electronically hot systems is described. It is based on a density functional which is costationary with the finite-temperature functional of Mermin, with state being included with possibly fractional occupation numbers.

  4. Ab initio study of the adsorption of antimony and arsenic on the Si(110) surface

    Energy Technology Data Exchange (ETDEWEB)

    Huitzil-Tepanecatl, Arely [Postgrado en Fisica Aplicada, Facultad de Ciencias Fisico-Matematicas, BUAP, Apartado Postal 52, Puebla 72000 (Mexico); Cocoletzi, Gregorio H., E-mail: cocoletz@sirio.ifuap.buap.m [Centro de Investigacion Cientifica y de Educacion Superior de Ensenada, Km. 107 Carretera Tijuana-Ensenada, Codigo Postal 22860, Apartado Postal 2732 Ensenada, Baja California (Mexico); Centro de Nanociencia y Nanotecnologia, Universidad Nacional Autonoma de Mexico, Apartado Postal 2681, Ensenada, Baja California, 22800 (Mexico); Instituto de Fisica, Universidad Autonoma de Puebla, Apartado Postal J-48, Puebla 72570 (Mexico); Takeuchi, Noboru [Centro de Nanociencia y Nanotecnologia, Universidad Nacional Autonoma de Mexico, Apartado Postal 2681, Ensenada, Baja California, 22800 (Mexico)

    2010-10-29

    We have performed first principles total energy calculations to investigate the adsorption of Sb and As adatoms on the Si(110) surface using a (2 x 3) supercell. The energetics and atomic structures have been investigated in four atomic configurations. One structure is obtained by placing 1/3 of a monolayer (ML) of Sb (As) atoms on the Si(110) surface. The other three geometries are obtained by depositing 1 ML of Sb (As) atoms on the surface. In the first case the structure is formed by four trimers, in the second case the geometry is formed by zigzag atomic chains and in the third case the structure contains 'microfacets'. The energetics results of the Sb adsorption show that for low coverage the tetrahedrons formed by the adsorption of 1/3 ML is the most stable configuration, while in the monolayer region the zigzag atomic chain is the most stable structure. However, the total energies of the trimer and microfacet structures are slightly higher, indicating that under some conditions, they may be formed. In an experimental report it has been suggested that the adsorption of 1/3 and 1 ML of Sb corresponds to the low and high coverage in the experiments of Zotov et al. [A. V. Zotov, V. G. Lifshifts, and A. N. Demidchik, Surf. Sci. 274, L583 (1992)]. On the other hand, our results of the As adsorption show that for low coverage, the tetrahedrons in the adsorption of 1/3 ML also give the most stable configuration. However, at the 1 ML coverage, a structure formed by microfacets is the most stable structure, in agreement with previous results.

  5. Interaction of C2H with molecular hydrogen: Ab initio potential energy surface and scattering calculations.

    Science.gov (United States)

    Dagdigian, Paul J

    2018-01-14

    The potential energy surface (PES) describing the interaction of the ethynyl (C2H) radical in its ground X̃2Σ+ electronic state with molecular hydrogen has been computed through restricted coupled cluster calculations including single, double, and (perturbative) triple excitations [RCCSD(T)], with the assumption of fixed molecular geometries. The computed points were fit to an analytical form suitable for time-independent quantum scattering calculations of rotationally inelastic cross sections and rate constants. A representative set of energy dependent state-to-state cross sections is presented and discussed. The PES and cross sections for collisions of H2(j = 0) are compared with a previous study [F. Najar et al., Chem. Phys. Lett. 614, 251 (2014)] of collisions of C2H with H2 treated as a spherical collision partner. Good agreement is found between the two sets of calculations when the H2 molecule in the present calculation is spherically averaged.

  6. Ti, Al and N adatom adsorption and diffusion on rocksalt cubic AlN (001) and (011) surfaces: Ab initio calculations

    Science.gov (United States)

    Mastail, C.; David, M.; Nita, F.; Michel, A.; Abadias, G.

    2017-11-01

    We use ab initio calculations to determine the preferred nucleation sites and migration pathways of Ti, Al and N adatoms on cubic NaCl-structure (B1) AlN surfaces, primary inputs towards a further thin film growth modelling of the TiAlN alloy system. The potential energy landscape is mapped out for both metallic species and nitrogen adatoms for two different AlN surface orientations, (001) and (110), using density functional theory. For all species, the adsorption energies on AlN(011) surface are larger than on AlN(001) surface. Ti and Al adatom adsorption energy landscapes determined at 0 K by ab initio show similar features, with stable binding sites being located in, or near, epitaxial surface positions, with Ti showing a stronger binding compared to Al. In direct contrast, N adatoms (Nad) adsorb preferentially close to N surface atoms (Nsurf), thus forming strong N2-molecule-like bonds on both AlN(001) and (011). Similar to N2 desorption mechanisms reported for other cubic transition metal nitride surfaces, in the present work we investigate Nad/Nsurf desorption on AlN(011) using a drag calculation method. We show that this process leaves a Nsurf vacancy accompanied with a spontaneous surface reconstruction, highlighting faceting formation during growth.

  7. Thermal Rate Coefficients and Kinetic Isotope Effects for the Reaction OH + CH4→ H2O + CH3on an Ab Initio Based Potential Energy Surface.

    Science.gov (United States)

    Li, Jun; Guo, Hua

    2018-02-26

    Thermal rate coefficients for the title reaction and its various isotopologues are computed using a tunneling-corrected transition-state theory on a global potential energy surface recently developed by fitting a large number of high-level ab initio points. The calculated rate coefficients are found to agree well with the measured ones in a wide temperature range, validating the accuracy of the potential energy surface. Strong non-Arrhenius effects are found at low temperatures. In addition, the calculations reproduced the primary and secondary kinetic isotope effects. These results confirm the strong influence of tunneling to this heavy-light-heavy hydrogen abstraction reaction.

  8. Ab initio study of magnetocrystalline anisotropy, magnetostriction, and Fermi surface of L10 FeNi (tetrataenite)

    Science.gov (United States)

    Werwiński, Mirosław; Marciniak, Wojciech

    2017-12-01

    We present results of ab initio calculations of several L10 FeNi characteristics, such as the summary of the magnetocrystalline anisotropy energies (MAEs), the full potential calculations of the anisotropy constant K 3, and the combined analysis of the Fermi surface and 3D {k} -resolved MAE. Other calculated parameters are the spin and orbital magnetic moments, the magnetostrictive coefficient λ0 0 1 , the bulk modulus B 0, and the lattice parameters. The MAEs summary shows rather big discrepancies among the experimental MAEs from the literature and also among the calculated MAE’s. The MAEs calculated in this work with the full potential and generalized gradient approximation (GGA) are equal to 0.47 MJ m-3 from WIEN2k, 0.34 MJ m-3 from FPLO, and 0.23 MJ m-3 from FP-SPR-KKR code. These results suggest that the MAE in GGA is below 0.5 MJ m-3 . It is expected that due to the limitations of the GGA, this value is underestimated. The L10 FeNi has further potential to improve its MAE by modifications, like e.g. tetragonal strain or alloying. The presented 3D {k} -resolved map of the MAE combined with the Fermi surface gives a complete picture of the MAE contributions in the Brillouin zone. The obtained, from the full potential FP-SPR-KKR method, magnetocrystalline anisotropy constants K 2 and K 3 are several orders of magnitude smaller than the MAE/K 1 and equal to -2.0 kJ m-3 and 110 J m-3 , respectively. The calculated spin and orbital magnetic moments of the L10 FeNi are equal to 2.72 and 0.054 μB for Fe and 0.53 and 0.039 μB for Ni atoms, respectively. The calculations of geometry optimization lead to a c/a ratio equal to 1.0036, B 0 equal to 194 GPa, and λ0 0 1 equal to 9.4  ×  10‑6.

  9. Phonocatalysis. An ab initio simulation experiment

    Directory of Open Access Journals (Sweden)

    Kwangnam Kim

    2016-06-01

    Full Text Available 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.

  10. Energy loss and surface temperature effects in ab initio molecular dynamics simulations: N adsorption on Ag(111) as a case study

    Science.gov (United States)

    Novko, Dino; Lončarić, Ivor; Blanco-Rey, María; Juaristi, J. Iñaki; Alducin, Maite

    2017-08-01

    We study surface temperature effects on the adsorption and relaxation of N atoms on Ag(111). To this aim, we perform ab initio molecular dynamics simulations with electronic friction, in which the surface is coupled to a thermostat that fixes the desired surface temperature. Simulations performed at 80 and 700 K show that the surface temperature has minor effects on magnitudes such as the initial adsorption probability, the relaxation rate of the adsorbing N, and the energy lost in electronic excitations. Slight differences are identified in the adsorption paths with the appearance of subsurface absorption events at 700 K that are not observed at 80 K. Furthermore, we perform additional simulations without a thermostat in order to examine the validity of commonly used ab initio molecular dynamics simulations in which no heat dissipation from the simulation cell is allowed. Our results show that such a methodology may not suffice to simulate the low-temperature regime since the surface becomes unphysically heated within a few picoseconds upon adsorption of the N atom. However, neither in this unfavorable case are the magnitudes defining the dynamics of the adsorbates at the same time scale significantly modified from those obtained at constant surface temperature.

  11. Ab initio electronic structure calculations for Mn linear chains deposited on CuN/Cu(001) surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Barral, Maria Andrea [Departamento de Fisica ' Juan Jose Giambiagi' , Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, 1428 Buenos Aires (Argentina)]. E-mail: barral@df.uba.ar; Weht, Ruben [Departamento de Fisica, Comision Nacional de Energia Atomica, Avenida del Libertador 8250, 1429 Buenos Aires (Argentina); Lozano, Gustavo [Departamento de Fisica ' Juan Jose Giambiagi' , Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, 1428 Buenos Aires (Argentina); Maria Llois, Ana [Departamento de Fisica ' Juan Jose Giambiagi' , Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, 1428 Buenos Aires (Argentina); Departamento de Fisica, Comision Nacional de Energia Atomica, Avenida del Libertador 8250, 1429 Buenos Aires (Argentina)

    2007-09-01

    In a recent experiment, scanning tunneling microscopy has been used to obtain a direct probe of the magnetic interaction in linear manganese chains arranged by atomic manipulation on thin insulating copper nitride islands grown on Cu(001). The local spin excitation spectra of these chains have been measured with inelastic electron tunneling spectroscopy. Analyzing the spectroscopic results with a Heisenberg Hamiltonian the interatomic coupling strength within the chains has been obtained. It has been found that the coupling strength depends on the deposition sites of the Mn atoms on the islands. In this contribution, we perform ab initio calculations for different arrangements of infinite Mn chains on CuN in order to understand the influence of the environment on the value of the magnetic interactions.

  12. MULTIMODE quantum calculations of intramolecular vibrational energies of the water dimer and trimer using ab initio-based potential energy surfaces

    Science.gov (United States)

    Wang, Yimin; Carter, Stuart; Braams, Bastiaan J.; Bowman, Joel M.

    2008-02-01

    We report vibrational configuration interaction calculations of the monomer fundamentals of (H2O)2, (D2O)2, (H2O)3, and (D2O)3 using the code MULTIMODE and full dimensional ab initio-based global potential energies surfaces (PESs). For the dimer the HBB PES [Huang et al., J. Chem. Phys 128, 034312 (2008)] is used and for the trimer a new PES, reported here, is used. The salient properties of the new trimer PES are presented and compared to previous single-point calculations and the vibrational energies are compared with experiments.

  13. Highly scalable Ab initio genomic motif identification

    KAUST Repository

    Marchand, Benoit

    2011-01-01

    We present results of scaling an ab initio motif family identification system, Dragon Motif Finder (DMF), to 65,536 processor cores of IBM Blue Gene/P. DMF seeks groups of mutually similar polynucleotide patterns within a set of genomic sequences and builds various motif families from them. Such information is of relevance to many problems in life sciences. Prior attempts to scale such ab initio motif-finding algorithms achieved limited success. We solve the scalability issues using a combination of mixed-mode MPI-OpenMP parallel programming, master-slave work assignment, multi-level workload distribution, multi-level MPI collectives, and serial optimizations. While the scalability of our algorithm was excellent (94% parallel efficiency on 65,536 cores relative to 256 cores on a modest-size problem), the final speedup with respect to the original serial code exceeded 250,000 when serial optimizations are included. This enabled us to carry out many large-scale ab initio motiffinding simulations in a few hours while the original serial code would have needed decades of execution time. Copyright 2011 ACM.

  14. Surface Adsorption Energetics Studied with "Gold Standard" Wavefunction Based Ab Initio Methods: Small Molecule Binding to TiO2(110).

    Science.gov (United States)

    Kubas, Adam M; Berger, Daniel; Oberhofer, Harald; Maganas, Dimitrios; Reuter, Karsten; Neese, Frank

    2016-10-03

    Coupled cluster theory with single, double and perturbative triple excitations (CCSD(T)) is widely considered to be the 'gold standard' of ab initio quantum chemistry. Using the domain-based pair natural orbital local correlation concept (DLPNO-CCSD(T)), these calculations can be performed on systems with hundreds of atoms at an accuracy of about 99.9% of the canonical CCSD(T) method. This allows for ab initio calculations providing reference adsorption energetics at solid surfaces with an accuracy approaching 1 kcal/mol. This is an invaluable asset, not least for the assessment of density-functional theory (DFT) as the prevalent approach for large-scale production calculations in energy or catalysis applications. Here we use DLPNO-CCSD(T) with embedded cluster models to compute entire adsorbate potential energy surfaces for the binding of a set of prototypical closed-shell molecules (H2O, NH3, CH4, CH3OH, CO2) to the rutile TiO2(110) surface. The DLPNO-CCSD(T) calculations show excellent agreement with available experimental data, even for the 'infamous' challenge of correctly predicting the CO2 adsorption geometry. The numerical efficiency of the approach is within one order of magnitude of hybrid-level DFT calculations, hence blurring the borders between reference and production technique.

  15. Character of intermolecular interaction in pyridine-argon complex: Ab initio potential energy surface, internal dynamics, and interrelations between SAPT energy components.

    Science.gov (United States)

    Makarewicz, Jan; Shirkov, Leonid

    2016-05-28

    The pyridine-Ar (PAr) van der Waals (vdW) complex is studied using a high level ab initio method. Its structure, binding energy, and intermolecular vibrational states are determined from the analytical potential energy surface constructed from interaction energy (IE) values computed at the coupled cluster level of theory with single, double, and perturbatively included triple excitations with the augmented correlation consistent polarized valence double-ζ (aug-cc-pVDZ) basis set complemented by midbond functions. The structure of the complex at its global minimum with Ar at a distance of 3.509 Å from the pyridine plane and shifted by 0.218 Å from the center of mass towards nitrogen agrees well with the corresponding equilibrium structure derived previously from the rotational spectrum of PAr. The PAr binding energy De of 392 cm(-1) is close to that of 387 cm(-1) calculated earlier at the same ab initio level for the prototypical benzene-Ar (BAr) complex. However, under an extension of the basis set, De for PAr becomes slightly lower than De for BAr. The ab initio vdW vibrational energy levels allow us to estimate the reliability of the methods for the determination of the vdW fundamentals from the rotational spectra. To disclose the character of the intermolecular interaction in PAr, the symmetry-adapted perturbation theory (SAPT) is employed for the analysis of different physical contributions to IE. It is found that SAPT components of IE can be approximately expressed in the binding region by only two of them: the exchange repulsion and dispersion energy. The total induction effect is negligible. The interrelations between various SAPT components found for PAr are fulfilled for a few other complexes involving aromatic molecules and Ar or Ne, which indicates that they are valid for all rare gas (Rg) atoms and aromatics.

  16. Prebiotic Atmospheric Chemistry on Titan: Formation Kinetics via Ab Initio Calculations for Potential Energy Surface (PES) Mapping

    Science.gov (United States)

    Gonzalez, Dayana; Mebel, Alexander

    2016-03-01

    It has been recently shown that Titan provides a unique perspective in our solar system: its atmosphere is comparable to a model of prebiotic Earth's. Provided the organic cationic and anionic molecular species identified by the Cassini spacecraft, this research characterizes reaction pathways for the reactions of methyl derivatives of the cyclopropenyl cation, the methyl cation with methyl- and dimethyl-acetylene, and reactions of resonance structures of protonated acrylonitrile with CH2NH. Isomerization and dissociation reactions involving methyl-cyclopropenyl cations, the perinaphthenyl cation and anion, and cations of pyrimidine and purine precursors of nucleobases will be examined to locate reaction pathways, intermediates, transition states, and products of the reactions. Gaussian '09 software is used for ab initio calculations to map out the PES. Geometry optimizations and vibrational frequency computations are preformed via the double-hybrid density functional B2PLYP-D3. Single-point energies are refined by use of the explicitly-correlated coupled-cluster CCSD(T)-F12 method. Rate constants are calculated using microcanonical RRKM theory, and pressure effects evaluated used the Master Equation approach; these allow for prediction of absolute rate constants and product branching ratios at different pressures and temperatures.

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

    Science.gov (United States)

    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.

  18. New analytical model for the ozone electronic ground state potential surface and accurate ab initio vibrational predictions at high energy range.

    Science.gov (United States)

    Tyuterev, Vladimir G; Kochanov, Roman V; Tashkun, Sergey A; Holka, Filip; Szalay, Péter G

    2013-10-07

    An accurate description of the complicated shape of the potential energy surface (PES) and that of the highly excited vibration states is of crucial importance for various unsolved issues in the spectroscopy and dynamics of ozone and remains a challenge for the theory. In this work a new analytical representation is proposed for the PES of the ground electronic state of the ozone molecule in the range covering the main potential well and the transition state towards the dissociation. This model accounts for particular features specific to the ozone PES for large variations of nuclear displacements along the minimum energy path. The impact of the shape of the PES near the transition state (existence of the "reef structure") on vibration energy levels was studied for the first time. The major purpose of this work was to provide accurate theoretical predictions for ozone vibrational band centres at the energy range near the dissociation threshold, which would be helpful for understanding the very complicated high-resolution spectra and its analyses currently in progress. Extended ab initio electronic structure calculations were carried out enabling the determination of the parameters of a minimum energy path PES model resulting in a new set of theoretical vibrational levels of ozone. A comparison with recent high-resolution spectroscopic data on the vibrational levels gives the root-mean-square deviations below 1 cm(-1) for ozone band centres up to 90% of the dissociation energy. New ab initio vibrational predictions represent a significant improvement with respect to all previously available calculations.

  19. GAUSSIAN 76: an ab initio molecular orbital program

    Energy Technology Data Exchange (ETDEWEB)

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

    1978-06-01

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

  20. GAUSSIAN 76: An ab initio Molecular Orbital Program

    Science.gov (United States)

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

    1978-01-01

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

  1. A potential energy surface for the process H2 + H2O yielding H + H + H2O - Ab initio calculations and analytical representation

    Science.gov (United States)

    Schwenke, David W.; Walch, Stephen P.; Taylor, Peter R.

    1991-01-01

    Extensive ab initio calculations on the ground state potential energy surface of H2 + H2O were performed using a large contracted Gaussian basis set and a high level of correlation treatment. An analytical representation of the potential energy surface was then obtained which reproduces the calculated energies with an overall root-mean-square error of only 0.64 mEh. The analytic representation explicitly includes all nine internal degrees of freedom and is also well behaved as the H2 dissociates; it thus can be used to study collision-induced dissociation or recombination of H2. The strategy used to minimize the number of energy calculations is discussed, as well as other advantages of the present method for determining the analytical representation.

  2. Ab initio quality neural-network potential for sodium

    Science.gov (United States)

    Eshet, Hagai; Khaliullin, Rustam Z.; Kühne, Thomas D.; Behler, Jörg; Parrinello, Michele

    2010-05-01

    An interatomic potential for high-pressure high-temperature (HPHT) crystalline and liquid phases of sodium is created using a neural-network (NN) representation of the ab initio potential-energy surface. It is demonstrated that the NN potential provides an ab initio quality description of multiple properties of liquid sodium and bcc, fcc, and cI16 crystal phases in the P-T region up to 120 GPa and 1200 K. The unique combination of computational efficiency of the NN potential and its ability to reproduce quantitatively experimental properties of sodium in the wide P-T range enables molecular-dynamics simulations of physicochemical processes in HPHT sodium of unprecedented quality.

  3. On the incorporation of the geometric phase in general single potential energy surface dynamics: A removable approximation to ab initio data.

    Science.gov (United States)

    Malbon, Christopher L; Zhu, Xiaolei; Guo, Hua; Yarkony, David R

    2016-12-21

    For two electronic states coupled by conical intersections, the line integral of the derivative coupling can be used to construct a complex-valued multiplicative phase factor that makes the real-valued adiabatic electronic wave function single-valued, provided that the curl of the derivative coupling is zero. Unfortunately for ab initio determined wave functions, the curl is never rigorously zero. However, when the wave functions are determined from a coupled two diabatic state Hamiltonian H(d) (fit to ab initio data), the resulting derivative couplings are by construction curl free, except at points of conical intersection. In this work we focus on a recently introduced diabatization scheme that produces the H(d) by fitting ab initio determined energies, energy gradients, and derivative couplings to the corresponding H(d) determined quantities in a least squares sense, producing a removable approximation to the ab initio determined derivative coupling. This approach and related numerical issues associated with the nonremovable ab initio derivative couplings are illustrated using a full 33-dimensional representation of phenol photodissociation. The use of this approach to provide a general framework for treating the molecular Aharonov Bohm effect is demonstrated.

  4. Discovering chemistry with an ab initio nanoreactor

    Science.gov (United States)

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

    2014-12-01

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

  5. Ab Initio Modeling of Molecular Radiation

    Science.gov (United States)

    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.

  6. Giant magnetoresistance An ab-initio description

    CERN Document Server

    Binder, J

    2000-01-01

    A new theoretical concept to study the microscopic origin of Giant Magnetoresistance (GMR) from first principles is presented. The method is based on ab-initio electronic structure calculations within the spin density functional theory using a Screened KORRINGA-KOHNROSTOKER method. Scattering at impurity atoms in the multilayers is described by means of a GREEN's-function method. The scattering potentials are calculated self-consistently. The transport properties are treated quasi-classically solving the BOLTZMANN equation including the electronic structure of the layered system and the anisotropic scattering. The solution of the BOLTZMANN equation is performed iteratively taking into account both scattering out and scattering in terms (vertex corrections). The method is applied to Co/Cu and Fe/Cr multilayers. Trends of scattering cross sections, residual resistivities and GMR ratios are discussed for various transition metal impurities at different positions in the Co/Cu or Fe/Cr multilayers. Furthermore the...

  7. Ab initio alpha-alpha scattering

    Science.gov (United States)

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

    2015-12-01

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

  8. Ab initio alpha-alpha scattering.

    Science.gov (United States)

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

    2015-12-03

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

  9. Graphitic nanofilms of zinc-blende materials: ab initio calculations

    Science.gov (United States)

    Hu, San-Lue; Zhao, Li; Li, Yan-Li

    2017-12-01

    Ab initio calculations on ultra-thin nanofilms of 25 kinds of zinc-blende semiconductors demonstrate their stable geometry structures growth along (1 1 1) surface. Our results show that the (1 1 1) surfaces of 9 kinds of zinc-blende semiconductors can transform into a stable graphitelike structure within a certain thickness. The tensile strain effect on the thickness of graphitic films is not obvious. The band gaps of stable graphitic films can be tuned over a wide range by epitaxial tensile strain, which is important for applications in microelectronic devices, solar cells and light-emitting diodes.

  10. Ab initio thermodynamics examination of sulfur species present on Rh, Ni, and binary Rh-Ni surfaces under steam reforming reaction conditions.

    Science.gov (United States)

    Lee, Kyungtae; Song, Chunshan; Janik, Michael J

    2012-04-03

    The stable form of adsorbed sulfur species and their coverage were investigated on Rh, Ni, and Rh-Ni binary metal surfaces using density functional theory calculations and the ab initio thermodynamics framework. S adsorption, SO(x) (x = 1-4) adsorption, and metal sulfide formation were examined on Rh(111) and Ni(111) pure metals. Both Rh and Ni metals showed a preference for S surface adsorption rather than SO(x) adsorption under steam reforming conditions. The transition temperature from a clean surface (reforming conditions of 4-100 ppm S and 800 °C, Rh(1)Ni(2) is covered with (1)/(9) ML of sulfur at the lower end of this range (4-33 ppm S). The possibility of sulfate formation on Rh catalysts was examined by considering higher oxygen pressures, a Rh(221) stepped surface, and the interface between a Rh(4) cluster and CeO(2)(111) surface. SO(x) surface species are stable only at high oxygen pressure or low temperatures outside those relevant to the steam reforming of hydrocarbons.

  11. The Role of Artificial Polarization in Optical Properties of FA2:Sr2+ Center and no Interactions at RbCl (001) Surface:. AN AB Initio Study

    Science.gov (United States)

    Assem, Mervat M.

    The role of artificial polarization in two different applications of the title color center, namely optical properties of FA2:Sr2+ center and adsorbate-substrate interactions, is investigated by using quantum mechanical CI-singles and DFT ab initio methods. Clusters of variable sizes were embedded in the simulated Coulomb field that closely approximate the Madelung field of the host surface, and ions that were the nearest neighbors to the defect site were allowed to relax to equilibrium. The sensitivity of the calculated transition energies (Stokes shifts) of FA2:Sr2+ center as well as related optical properties, such as optical-optical conversion efficiency, relaxed excited states of the defect-containing surface, orientational destruction of the point defect, recording sensitivity, the Glasner-Tompkins empirical rule, and the artificial polarization were examined. The dependence of NO and ON adsorption energies at RbCl (001) surface on artificial polarization were also examined, and the results were explained in terms of electrostatic potential curves. The coadsorption of NO molecules, and the charge transfer reactions between the NO molecules and the paramagnetic chlorine vacancy on RbCl surface were considered.

  12. Hydrogen-induced nanotunnel structure on the C-terminated β-SiC(0 0 1)-c(2 × 2) surface investigated by ab-initio calculations

    Energy Technology Data Exchange (ETDEWEB)

    Rosso, E.F. [Departamento de Química, Universidade Federal de Santa Maria, 97105-900, Santa Maria, RS (Brazil); Baierle, R.J., E-mail: rbaierle@smail.ufsm.br [Departamento de Física, Universidade Federal de Santa Maria, 97105-900, Santa Maria, RS (Brazil); Orellana, W. [Departamento de Ciencias Físicas, Universidad Andres Bello, República 220, 837-0134 Santiago (Chile); Miwa, R.H. [Instituto de Física, Universidade Federal de Uberlândia, 38408-100, Uberlândia, MG (Brazil)

    2015-12-01

    Graphical abstract: - Highlights: • β-SiC(0 0 1) surface. • Hydrogenation. • DFT calculations – PBE and HSE06 functional for the exchange correlation term. • Nanotunnel formation. • Electronic confinement. - Abstract: The structural and electronic properties of pristine and H-passivated C-terminated β-SiC(0 0 1)-c(2 × 2) surface are addressed by ab initio calculations. Here, we verify the formation of C chains composed by double-bonded dimers rows (C=C), separated by triple-bonded bridged dimers (C≡C). The surface states near the bandgap are confined along the C=C dimer rows, with no electronic contribution from the C≡C bridged dimers. After hydrogenation, the C-chains are strongly modified, forming subsurface voids or nanotunnel (NT) structures. By considering a plausible set of energy release steps for increasing hydrogenation, we obtain a C-rich NT ruled by the C=C dimer rows. Somewhat similar to that recently reported on the Si-rich termination, but 0.8 eV lower in energy. The electronic band structures of both Si-rich and C-rich NTs have been examined within the hybrid HSE06 functional, which are compared with those previously reported using a semilocal functional.

  13. Ab initio calculation of the Structural, Mechanical and ...

    African Journals Online (AJOL)

    ADOWIE PERE

    Corresponding Author: B. E. Iyorzor, Email: beniyorzor@uniben.edu. ABSTRACT: An ab initio ... by employing the first principles tight binding linear muffin-tin orbital method within the local density approximation (LDA) Kalpana et al (1998). Also the.

  14. Adsorption of ammonia at GaN(0001 surface in the mixed ammonia/hydrogen ambient - a summary of ab initio data

    Directory of Open Access Journals (Sweden)

    Paweł Kempisty

    2014-11-01

    Full Text Available Adsorption of ammonia at NH3/NH2/H-covered GaN(0001 surface was analyzed using results of ab initio calculations. The whole configuration space of partially NH3/NH2/H-covered GaN(0001 surface was divided into zones of differently pinned Fermi level: at the Ga broken bond state for dominantly bare surface (region I, at the valence band maximum (VBM for NH2 and H-covered surface (region II, and at the conduction band minimum (CBM for NH3-covered surface (region III. The electron counting rule (ECR extension was formulated for the case of adsorbed molecules. The extensive ab intio calculations show the validity of the ECR in case of all mixed H-NH2-NH3 coverages for the determination of the borders between the three regions. The adsorption was analyzed using the recently identified dependence of the adsorption energy on the charge transfer at the surface. For region I ammonia adsorbs dissociatively, disintegrating into a H adatom and a HN2 radical for a large fraction of vacant sites, while for region II adsorption of ammonia is molecular. The dissociative adsorption energy strongly depends on the Fermi level at the surface (pinned and in the bulk (unpinned while the molecular adsorption energy is determined by bonding to surface only, in accordance to the recently published theory. Adsorption of Ammonia in region III (Fermi level pinned at CBM leads to an unstable configuration both molecular and dissociative, which is explained by the fact that broken Ga-bonds are doubly occupied by electrons. The adsorbing ammonia brings 8 electrons to the surface, necessitating the transfer of these two electrons from the Ga broken bond state to the Fermi level. This is an energetically costly process. Adsorption of ammonia at H-covered site leads to the creation of a NH2 radical at the surface and escape of H2 molecule. The process energy is close to 0.12 eV, thus not large, but the direct inverse process is not possible due to the escape of the hydrogen

  15. Ab initio phonon scattering by dislocations

    Science.gov (United States)

    Wang, Tao; Carrete, Jesús; van Roekeghem, Ambroise; Mingo, Natalio; Madsen, Georg K. H.

    2017-06-01

    Heat management in thermoelectric and power devices as well as in random access memories poses a grand challenge and can make the difference between a working and an abandoned device design. Despite the prevalence of dislocations in all these technologies, the modeling of their thermal resistance is based on 50-year-old analytical approximations, whose simplicity was driven by practical limitations rather than physical insight. We introduce an efficient ab initio approach based on Green's functions computed by two-dimensional reciprocal space integration. By combining elasticity theory and density functional theory, we calculate the scattering strength of a 90∘ misfit edge dislocation in Si. Because of the breakdown of the Born approximation, earlier literature models fail, even qualitatively. We find that a dislocation density larger than 109cm-2 is necessary to substantially influence thermal conductivity at room temperature and above. We quantify how much of the reduction of thermal conductivity measured in nanograined samples can be explained by realistic dislocation concentrations.

  16. A new ab initio potential energy surface for the collisional excitation of HCN by para- and ortho-H{sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Denis-Alpizar, Otoniel, E-mail: otonieldenisalpizar@gmail.com [Université de Bordeaux, ISM, CNRS UMR 5255, 33405 Talence Cedex (France); Departamento de Física, Universidad de Matanzas, Matanzas 40100 (Cuba); Kalugina, Yulia [LOMC - UMR 6294, CNRS-Université du Havre, 25 rue Philippe Lebon, BP 540, 76058, Le Havre (France); Department of Optics and Spectroscopy, Tomsk State University, 36 Lenin av., Tomsk 634050 (Russian Federation); Stoecklin, Thierry [Université de Bordeaux, ISM, CNRS UMR 5255, 33405 Talence Cedex (France); Vera, Mario Hernández [LOMC - UMR 6294, CNRS-Université du Havre, 25 rue Philippe Lebon, BP 540, 76058, Le Havre (France); Instituto Superior de Tecnologías y Ciencias Aplicadas, Quinta de Los Molinos, Plaza, La Habana 10600 (Cuba); Lique, François, E-mail: francois.lique@univ-lehavre.fr [Departamento de Física, Universidad de Matanzas, Matanzas 40100 (Cuba)

    2013-12-14

    We present a new four-dimensional potential energy surface for the collisional excitation of HCN by H{sub 2}. Ab initio calculations of the HCN–H{sub 2} van der Waals complex, considering both molecules as rigid rotors, were carried out at the explicitly correlated coupled cluster with single, double, and perturbative triple excitations [CCSD(T)-F12a] level of theory using an augmented correlation-consistent triple zeta (aVTZ) basis set. The equilibrium structure is linear HCN–H{sub 2} with the nitrogen pointing towards H{sub 2} at an intermolecular separation of 7.20 a{sub 0}. The corresponding well depth is −195.20 cm{sup −1}. A secondary minimum of −183.59 cm{sup −1} was found for a T-shape configuration with the H of HCN pointing to the center of mass of H{sub 2}. We also determine the rovibrational energy levels of the HCN–para-H{sub 2} and HCN–ortho-H{sub 2} complexes. The calculated dissociation energies for the para and ortho complexes are 37.79 cm{sup −1} and 60.26 cm{sup −1}, respectively. The calculated ro-vibrational transitions in the HCN–H{sub 2} complex are found to agree by more than 0.5% with the available experimental data, confirming the accuracy of the potential energy surface.

  17. Accurate ab initio potential energy surface, thermochemistry, and dynamics of the Br(2P, 2P(3∕2)) + CH4 → HBr + CH3 reaction.

    Science.gov (United States)

    Czakó, Gábor

    2013-04-07

    Chemically accurate full-dimensional non-spin-orbit and spin-orbit (SO) ground-state potential energy surfaces (PESs) are obtained for the Br + CH4 → HBr + CH3 reaction by fitting 21 574 composite ab initio energy points. The composite method considers electron correlation methods up to CCSD(T), basis sets up to aug-cc-pwCVTZ-PP, correlation of the core electrons, scalar relativistic effects via an effective core potential (ECP), and SO corrections, thereby achieving an accuracy better than 0.5 kcal∕mol. Benchmark structures and relative energies are computed for the stationary points using the ab initio focal-point analysis (FPA) scheme based on both ECP and Douglas-Kroll approaches providing all-electron relativistic CCSDT(Q)∕complete-basis-set quality energies. The PESs accurately describe the saddle point of the abstraction reaction and the van der Waals complexes in the entrance and product channels. The SO-corrected PES provides a classical barrier height of 7285(7232 ± 50) cm(-1), De values of 867(799 ± 10) and 399(344 ± 10) cm(-1) for the complexes CH3-HBr and CH3-BrH, respectively, and reaction endothermicity of 7867(7857 ± 50) cm(-1), in excellent agreement with the new, FPA-based benchmark data shown in parentheses. The difference between the Br + CH4 asymptotes of the non-SO and SO PESs is 1240 cm(-1), in good agreement with the experiment (1228 cm(-1)). Quasiclassical trajectory calculations based on more than 13 million trajectories for the late-barrier Br + CH4(vk = 0, 1) [k = 1, 2, 3, 4] reactions show that the vibrational energy, especially the excitation of the stretching modes, activates the reaction much more efficiently than translational energy, in agreement with the extended Polanyi rules. Angular distributions show dominant backward scattering for the ground-state reaction and forward scattering for the stretching-excited reactions. The reactivity on the non-SO PES is about 3-5 times larger than that on the SO PES in a wide

  18. Iron -chromium alloys and free surfaces: from ab initio calculations to thermodynamic modeling; Demixtion et segregation superficielle dans les alliages fer-chrome: de la structure electronique aux modeles thermodynamiques

    Energy Technology Data Exchange (ETDEWEB)

    Levesque, M.

    2010-11-15

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

  19. Accurate ab initio potential energy surfaces for the 3A'' and 3A' electronic states of the O(3P)+HBr system.

    Science.gov (United States)

    de Oliveira-Filho, Antonio G S; Ornellas, Fernando R; Peterson, Kirk A

    2012-05-07

    In this work, we report the construction of potential energy surfaces for the (3)A('') and (3)A(') states of the system O((3)P) + HBr. These surfaces are based on extensive ab initio calculations employing the MRCI+Q/CBS+SO level of theory. The complete basis set energies were estimated from extrapolation of MRCI+Q/aug-cc-VnZ(-PP) (n = Q, 5) results and corrections due to spin-orbit effects obtained at the CASSCF/aug-cc-pVTZ(-PP) level of theory. These energies, calculated over a region of the configuration space relevant to the study of the reaction O((3)P) + HBr → OH + Br, were used to generate functions based on the many-body expansion. The three-body potentials were interpolated using the reproducing kernel Hilbert space method. The resulting surface for the (3)A('') electronic state contains van der Waals minima on the entrance and exit channels and a transition state 6.55 kcal/mol higher than the reactants. This barrier height was then scaled to reproduce the value of 5.01 kcal/mol, which was estimated from coupled cluster benchmark calculations performed to include high-order and core-valence correlation, as well as scalar relativistic effects. The (3)A(') surface was also scaled, based on the fact that in the collinear saddle point geometry these two electronic states are degenerate. The vibrationally adiabatic barrier heights are 3.44 kcal/mol for the (3)A('') and 4.16 kcal/mol for the (3)A(') state.

  20. Ab initio Studies of O2 Adsorption on (110 Nickel-Rich Pentlandite (Fe4Ni5S8 Mineral Surface

    Directory of Open Access Journals (Sweden)

    Peace P. Mkhonto

    2015-10-01

    Full Text Available Ab initio density functional theory was used to investigate the adsorption of oxygen molecule on the nickel-rich pentlandite (110 surface, which is important for mineral extraction. The three most reactive adsorption sites: Fe-top, Ni-top, and fcc-hollow have been considered. Firstly, the non-adsorbed pentlandite surface reflects the Ni atoms relaxing inwards. Consequently, their electronic structure showed high Fe 3d-orbital contribution than the Ni 3d-orbitals at the EF (indicating that the Fe atoms are more reactive than Ni. Secondly, the O2-adsorbed surface predicted lowest adsorption energy for Fe-top (-1.902 eV, as a more spontaneous reaction is likely to occur than on fcc-hollow (-1.891 eV and Ni-top (-0.040 eV sites, suggesting Fe preferential oxidation. The density of states indicates that the O2 show prevalence of electrons in the πp* antibonding orbitals, and are reduced to zero states at the valence band on metal-bonded oxygen (O1. The πp* orbital is observed to reside just above the EF for Fe-top and fcc-hollow site, while on Ni-top is half-occupied for both metal-bonded oxygen (O1 and terminal oxygen (O2. Finally, the isosurface charge density difference showed electron (charge depletion on Ni/Fe metals and accumulation on the O2 molecule. Bader analysis indicated that the oxidized Fe and Ni atoms adopt more positive charge, while O2 on Fe-top atoms possesses more negative charge than on Ni-top, resulting with O1 possessing a smaller charge than O2 atom.

  1. Ab initio nonadiabatic molecular dynamics of the ultrafast electron injection from a PbSe quantum dot into the TiO2 surface.

    Science.gov (United States)

    Long, Run; Prezhdo, Oleg V

    2011-11-30

    Following recent experiments [Science 2010, 328, 1543; PNAS 2011, 108, 965], we report an ab initio nonadiabatic molecular dynamics (NAMD) simulation of the ultrafast photoinduced electron transfer (ET) from a PbSe quantum dot (QD) into the rutile TiO(2) (110) surface. The system forms the basis for QD-sensitized semiconductor solar cells and demonstrates that ultrafast interfacial ET is instrumental for achieving high efficiencies in solar-to-electrical energy conversion. The simulation supports the observation that the ET successfully competes with energy losses due to electron-phonon relaxation. The ET proceeds by the adiabatic mechanism because of strong donor-acceptor coupling. High frequency polar vibrations of both QD and TiO(2) promote the ET, since these modes can rapidly influence the donor-acceptor state energies and coupling. Low frequency vibrations generate a distribution of initial conditions for ET, which shows a broad variety of scenarios at the single-molecule level. Compared to the molecule-TiO(2) interfaces, the QD-TiO(2) system exhibits pronounced differences that arise due to the larger size and higher rigidity of QDs relative to molecules. Both donor and acceptor states are more delocalized in the QD system, and the ET is promoted by optical phonons, which have relatively low frequencies in the QD materials composed of heavy elements. In contrast, in molecular systems, optical phonons are not thermally accessible under ambient conditions. Meanwhile, TiO(2) acceptor states resemble surface impurities due to the local influence of molecular chromophores. At the same time, the photoinduced ET at both QD-TiO(2) and molecule-TiO(2) interfaces is ultrafast and occurs by the adiabatic mechanism, as a result of strong donor-acceptor coupling. The reported state-of-the-art simulation generates a detailed time-domain atomistic description of the interfacial ET process that is fundamental to a wide variety of applications.

  2. Ab Initio Studies of Stratospheric Ozone Depletion Chemistry

    Science.gov (United States)

    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.

  3. Ab initio investigation of the surface properties of austenitic Fe-Ni-Cr alloys in aqueous environments

    Energy Technology Data Exchange (ETDEWEB)

    Rák, Zs., E-mail: zrak@ncsu.edu; Brenner, D.W.

    2017-04-30

    Highlights: • The trend in the surface energies of austenitic stainless steels is: (111) < (100) < (110). • On the (111) orientation Ni segregates to the surface and Cr segregates into the bulk. • The surface stability of the alloys in contact with water decrease with temperature and pH. - Abstract: The surface energetics of two austenitic stainless steel alloys (Type 304 and 316) and three Ni-based alloys (Alloy 600, 690, and 800) are investigated using theoretical methods within the density functional theory. The relative stability of the low index surfaces display the same trend for all alloys; the most closely packed orientation and the most stable is the (111), followed by the (100) and the (110) surfaces. Calculations on the (111) surfaces using various surface chemical and magnetic configurations reveal that Ni has the tendency to segregate toward the surface and Cr has the tendency to segregate toward the bulk. The magnetic frustration present on the (111) surfaces plays an important role in the observed segregation tendencies of Ni and Cr. The stability of the (111) surfaces in contact with aqueous solution are evaluated as a function of temperature, pH, and concentration of aqueous species. The results indicate that the surface stability of the alloys decrease with temperature and pH, and increase slightly with concentration. Under conditions characteristic to an operating pressurized water reactor, the Ni-based alloy series appears to be of better quality than the stainless steel series with respect to corrosion resistance and release of aqueous species when in contact with aqueous solutions.

  4. Insights on finite size effects in ab initio study of CO adsorption and dissociation on Fe 110 surface

    Energy Technology Data Exchange (ETDEWEB)

    Chakrabarty, Aurab, E-mail: aurab.chakrabarty@qatar.tamu.edu; Bouhali, Othmane [Texas A& M University at Qatar, P.O. Box 23874, Doha (Qatar); Mousseau, Normand [Département de Physique and RQMP, Université de Montréal, Case Postale 6128, Succursale Centre-ville, Montréal, Québec H3C 3J7 (Canada); Becquart, Charlotte S. [UMET, UMR CNRS 8207, ENSCL, Université Lille I, 59655 Villeneuve d' Ascq Cédex (France); El-Mellouhi, Fedwa [Qatar Environment and Energy Research Institute, Hamad Bin Khalifa University, P.O. Box 5825, Doha (Qatar)

    2016-08-07

    Adsorption and dissociation of hydrocarbons on metallic surfaces represent crucial steps on the path to carburization, eventually leading to dusting corrosion. While adsorption of CO molecules on Fe surface is a barrier-less exothermic process, this is not the case for the dissociation of CO into C and O adatoms and the diffusion of C beneath the surface that are found to be associated with large energy barriers. In practice, these barriers can be affected by numerous factors that combine to favour the CO-Fe reaction such as the abundance of CO and other hydrocarbons as well as the presence of structural defects. From a numerical point of view, studying these factors is challenging and a step-by-step approach is necessary to assess, in particular, the influence of the finite box size on the reaction parameters for adsorption and dissociation of CO on metal surfaces. Here, we use density functional theory (DFT) total energy calculations with the climbing-image nudged elastic band method to estimate the adsorption energies and dissociation barriers for different CO coverages with surface supercells of different sizes. We further compute the effect of periodic boundary condition for DFT calculations and find that the contribution from van der Waals interaction in the computation of adsorption parameters is important as they contribute to correcting the finite-size error in small systems. The dissociation process involves carbon insertion into the Fe surface causing a lattice deformation that requires a larger surface system for unrestricted relaxation. We show that, in the larger surface systems associated with dilute CO-coverages, C-insertion is energetically more favourable, leading to a significant decrease in the dissociation barrier. This observation suggests that a large surface system with dilute coverage is necessary for all similar metal-hydrocarbon reactions in order to study their fundamental electronic mechanisms, as an isolated phenomenon, free from

  5. Ab Initio Density Functional Calculations and Infra-Red Study of CO Interaction with Pd Atoms on θ-Al2O3(010) Surface.

    Science.gov (United States)

    Narula, Chaitanya K; Allard, Lawrence F; Wu, Zili

    2017-07-24

    The ab initio density functional theoretical studies show that energetics favor CO oxidation on single Pd atoms supported on θ-alumina. The diffuse reflectance infra-red spectroscopy (DRIFTS) results show that carbonates are formed as intermediates when single supported Pd atoms are exposed to a gaseous mixture of CO + O 2 . The rapid agglomeration of Pd atoms under CO oxidation conditions even at 6 °C leads to the presence of Pd particles along with single atoms during CO oxidation experiments. Thus, the observed CO oxidation has contributions from both single Pd atoms and Pd particles.

  6. Ab-initio investigation of structural, electronic and optical properties BSb compound in bulk and surface (110 states

    Directory of Open Access Journals (Sweden)

    H A Badehian

    2015-07-01

    Full Text Available In recent work the structural, electronic and optical properties of BSb compound in bulk and surface (110 states have been studied. Calculations have been performed using Full-Potential Augmented Plane Wave (FP-LAPW method by WIEN2k code in Density Functional Theory (DFT framework. The structural properties of the bulk such as lattice constant, bulk module and elastic constants have been investigated using four different approximations. The band gap energy of the bulk and the (110 surface of BSb were obtained about 1.082 and 0.38 eV respectively. Moreover the surface energy, the work function, the surface relaxation, surface state and the band structure of BSb (110 were investigated using symmetric and stoichiometric 15 layers slabs with the vacuum of 20 Bohr. In addition, the real and imaginary parts of the dielectric function of the bulk and the BSb (110 slab were calculated and compared to each other. Our obtained results have a good agreement with the available results.

  7. Ab initio molecular dynamics with enhanced sampling for surface reaction kinetics at finite temperatures: CH2⇌ CH + H on Ni(111) as a case study.

    Science.gov (United States)

    Sun, Geng; Jiang, Hong

    2015-12-21

    A comprehensive understanding of surface thermodynamics and kinetics based on first-principles approaches is crucial for rational design of novel heterogeneous catalysts, and requires combining accurate electronic structure theory and statistical mechanics modeling. In this work, ab initio molecular dynamics (AIMD) combined with the integrated tempering sampling (ITS) method has been explored to study thermodynamic and kinetic properties of elementary processes on surfaces, using a simple reaction CH2⇌CH+H on the Ni(111) surface as an example. By a careful comparison between the results from ITS-AIMD simulation and those evaluated in terms of the harmonic oscillator (HO) approximation, it is found that the reaction free energy and entropy from the HO approximation are qualitatively consistent with the results from ITS-AIMD simulation, but there are also quantitatively significant discrepancies. In particular, the HO model misses the entropy effects related to the existence of multiple adsorption configurations arising from the frustrated translation and rotation motion of adsorbed species, which are different in the reactant and product states. The rate constants are evaluated from two ITS-enhanced approaches, one using the transition state theory (TST) formulated in terms of the potential of mean force (PMF) and the other one combining ITS with the transition path sampling (TPS) technique, and are further compared to those based on harmonic TST. It is found that the rate constants from the PMF-based TST are significantly smaller than those from the harmonic TST, and that the results from PMF-TST and ITS-TPS are in a surprisingly good agreement. These findings indicate that the basic assumptions of transition state theory are valid in such elementary surface reactions, but the consideration of statistical averaging of all important adsorption configurations and reaction pathways, which are missing in the harmonic TST, are critical for accurate description of

  8. Ab initio molecular dynamics with enhanced sampling for surface reaction kinetics at finite temperatures: CH2 ⇌ CH + H on Ni(111) as a case study

    Science.gov (United States)

    Sun, Geng; Jiang, Hong

    2015-12-01

    A comprehensive understanding of surface thermodynamics and kinetics based on first-principles approaches is crucial for rational design of novel heterogeneous catalysts, and requires combining accurate electronic structure theory and statistical mechanics modeling. In this work, ab initio molecular dynamics (AIMD) combined with the integrated tempering sampling (ITS) method has been explored to study thermodynamic and kinetic properties of elementary processes on surfaces, using a simple reaction CH 2 ⇌ CH + H on the Ni(111) surface as an example. By a careful comparison between the results from ITS-AIMD simulation and those evaluated in terms of the harmonic oscillator (HO) approximation, it is found that the reaction free energy and entropy from the HO approximation are qualitatively consistent with the results from ITS-AIMD simulation, but there are also quantitatively significant discrepancies. In particular, the HO model misses the entropy effects related to the existence of multiple adsorption configurations arising from the frustrated translation and rotation motion of adsorbed species, which are different in the reactant and product states. The rate constants are evaluated from two ITS-enhanced approaches, one using the transition state theory (TST) formulated in terms of the potential of mean force (PMF) and the other one combining ITS with the transition path sampling (TPS) technique, and are further compared to those based on harmonic TST. It is found that the rate constants from the PMF-based TST are significantly smaller than those from the harmonic TST, and that the results from PMF-TST and ITS-TPS are in a surprisingly good agreement. These findings indicate that the basic assumptions of transition state theory are valid in such elementary surface reactions, but the consideration of statistical averaging of all important adsorption configurations and reaction pathways, which are missing in the harmonic TST, are critical for accurate description of

  9. Ab-initio modeling of oxygen on the surface passivation of 3C-SiC nanostructures

    Energy Technology Data Exchange (ETDEWEB)

    Cuevas, J.L.; Trejo, A.; Calvino, M.; Carvajal, E. [Instituto Politecnico Nacional, ESIME-Culhuacan, Av. Santa Ana 1000, 04430, D.F. (Mexico); Cruz-Irisson, M., E-mail: irisson@ipn.mx [Instituto Politecnico Nacional, ESIME-Culhuacan, Av. Santa Ana 1000, 04430, D.F. (Mexico)

    2012-08-15

    In this work the effect of OH on the electronic states of H-passivated 3C-SiC nanostructures, was studied by means of Density Functional Theory. We compare the electronic band structure for a [1 1 1]-oriented nanowire with total H, OH passivation and a combination of both. Also the electronic states of a porous silicon carbide case (PSiC) a C-rich pore surface in which the dangling bonds on the surface are saturated with H and OH was studied. The calculations show that the surface replacement of H with OH radicals is always energetically favorable and more stable. In all cases the OH passivation produced a similar effect than the H passivation, with electronic band gap of lower energy value than the H-terminated phase. When the OH groups are attached to C atoms, the band gap feature is changed from direct to indirect. The results indicate the possibility of band gap engineering on SiC nanostructures through the surface passivation species.

  10. Ab initio study of magnetism and interaction of graphene with the polar MnO(111) surface

    Science.gov (United States)

    Ilyasov, Victor V.; Popova, Inna G.; Ershov, Igor V.

    2017-10-01

    Simulation of graphene adsorption onto the oxygen-terminated polar manganese monoxide surface (111) was performed as a function of the hydrogen coverage based on the density functional theory. Local atomic reconstructions of the SLG/H:MnO(111) interface, and their thermodynamic, electronic and magnetic properties were methodically analyzed for different adsorption models. The bond lengths and the adsorption energy values were found for different reconstructions of the surface atomic structure in the SLG/H:MnO(111) systems, and the effects of graphene adsorption on the electronic spectrum of the SLG/H:MnO(111) interface were studied for its different reconstructions. The effective charges and the local magnetic moments on the carbon atoms and on the nearest-neighbor atoms were determined for the considered adsorption models. Charge transfer from the carbon atom to the nearest-neighbor atoms was found due to reconstruction of the local atomic and electronic structures, correlating with the interface hydrogenation rate. Hydrogenation of the interface surface provides for the p-n junction, turning graphene into an n-type semiconductor. The latter opens the way for creation of n-type graphene field-effect transistors. This paper predicts magnetism for zero-defect graphene adsorbed on the hydrogenated surface of MnO(111) magnetic insulator, and discusses the nature of such magnetism.

  11. ForceFit: a code to fit classical force fields to ab-initio potential energy surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Henson, Neil Jon [Los Alamos National Laboratory; Waldher, Benjamin [WSU; Kuta, Jadwiga [WSU; Clark, Aurora [WSU; Clark, Aurora E [NON LANL

    2009-01-01

    The ForceFit program package has been developed for fitting classical force field parameters based upon a force matching algorithm to quantum mechanical gradients of configurations that span the potential energy surface of the system. The program, which runs under Unix and is written in C++, is an easy to use, nonproprietary platform that enables gradient fitting of a wide variety of functional force field forms to quantum mechanical information obtained from an array of common electronic structure codes. All aspects of the fitting process are run from a graphical user interface, from the parsing of quantum mechanical data, assembling of a potential energy surface database, setting the force field and variables to be optimized, choosing a molecular mechanics code for comparison to the reference data, and finally, the initiation of a least squares minimization algorithm. Furthermore, the code is based on a modular templated code design that enables the facile addition of new functionality to the program.

  12. Adsorption of acetyl halide molecules on the surface of pristine and Al-doped graphene: Ab initio study

    Science.gov (United States)

    Rad, Ali Shokuhi; Kashani, Omid Razaghi

    2015-11-01

    We have scrutinized the adsorption energy, electronic structure, natural bond analysis (NBO), density of state (DOS) and global indices for adsorption of acetyl chloride (AC) and acetyl fluoride (AF) on the surface of pristine graphene as well as Al-doped graphene. The adsorption energies have been calculated for the most stable configurations of the molecules on the surface of pristine and Al-doped graphene. According to the calculated parameters, there is very weak physical adsorption of AC and AF on pristine graphene while strong adsorption takes place in the case of Al-doped graphene. The charge transfer from adsorbed molecules to Al-doped graphene surface was confirmed by the natural bond orbital as well as the Mulliken population analysis while there is no charge transfer with pristine graphene. Additionally, the density of states results reveal that orbital hybridization takes place between above-mentioned molecules and Al-doped graphene sheet, whereas there is no hybridization between the molecules and the pristine graphene. Our calculated adsorption energies for the most stable position configurations of AC and AF on Al-doped graphene were -68.8 kJ mol-1 (-52.6 kJ mol-1 BSSE corrected energy) and -78.4 kJ mol-1 (-64.3 kJ mol-1 BSSE corrected energy) which are correspond to chemisorptions process respectively. These results point to the appropriateness of Al-doped graphene as a powerful adsorbent for practical applications.

  13. Use of ab initio quantum chemical methods in battery technology

    Energy Technology Data Exchange (ETDEWEB)

    Deiss, E. [Paul Scherrer Inst. (PSI), Villigen (Switzerland)

    1997-06-01

    Ab initio quantum chemistry can nowadays predict physical and chemical properties of molecules and solids. An attempt should be made to use this tool more widely for predicting technologically favourable materials. To demonstrate the use of ab initio quantum chemistry in battery technology, the theoretical energy density (energy per volume of active electrode material) and specific energy (energy per mass of active electrode material) of a rechargeable lithium-ion battery consisting of a graphite electrode and a nickel oxide electrode has been calculated with this method. (author) 1 fig., 1 tab., 7 refs.

  14. Adsorption of acetyl halide molecules on the surface of pristine and Al-doped graphene: Ab initio study

    Energy Technology Data Exchange (ETDEWEB)

    Rad, Ali Shokuhi, E-mail: a.shokuhi@gmail.com [Department of Chemical Engineering, Qaemshahr Branch, Islamic Azad University, Qaemshahr (Iran, Islamic Republic of); Kashani, Omid Razaghi [Department of Polymer Engineering, Qaemshahr Branch, Islamic Azad University, Qaemshahr (Iran, Islamic Republic of)

    2015-11-15

    Graphical abstract: - Highlights: • The adsorption of acetyl chloride and acetyl fluoride on Al-doped graphene were investigated. • The doped Al induces some changes in the electronic structure of graphene. • Notable orbital hybridizations are achieved upon adsorption. • Al-doped graphene can be used as a superior sensor for Acetyl halides. - Abstract: We have scrutinized the adsorption energy, electronic structure, natural bond analysis (NBO), density of state (DOS) and global indices for adsorption of acetyl chloride (AC) and acetyl fluoride (AF) on the surface of pristine graphene as well as Al-doped graphene. The adsorption energies have been calculated for the most stable configurations of the molecules on the surface of pristine and Al-doped graphene. According to the calculated parameters, there is very weak physical adsorption of AC and AF on pristine graphene while strong adsorption takes place in the case of Al-doped graphene. The charge transfer from adsorbed molecules to Al-doped graphene surface was confirmed by the natural bond orbital as well as the Mulliken population analysis while there is no charge transfer with pristine graphene. Additionally, the density of states results reveal that orbital hybridization takes place between above-mentioned molecules and Al-doped graphene sheet, whereas there is no hybridization between the molecules and the pristine graphene. Our calculated adsorption energies for the most stable position configurations of AC and AF on Al-doped graphene were −68.8 kJ mol{sup −1} (−52.6 kJ mol{sup −1} BSSE corrected energy) and −78.4 kJ mol{sup −1} (−64.3 kJ mol{sup −1} BSSE corrected energy) which are correspond to chemisorptions process respectively. These results point to the appropriateness of Al-doped graphene as a powerful adsorbent for practical applications.

  15. The effect of protonation on the photodissociation processes in formamide - An ab initio surface hopping dynamics study

    Energy Technology Data Exchange (ETDEWEB)

    Antol, Ivana; Vazdar, Mario [Rudjer Boskovic Institute, Division of Organic Chemistry and Biochemistry, P.O.B. 180, HR-10002 Zagreb (Croatia); Barbatti, Mario [Institute for Theoretical Chemistry, University of Vienna, Waehringerstrasse 17, A-1090 Vienna (Austria); Eckert-Maksic, Mirjana [Rudjer Boskovic Institute, Division of Organic Chemistry and Biochemistry, P.O.B. 180, HR-10002 Zagreb (Croatia)], E-mail: mmaksic@emma.irb.hr

    2008-06-16

    Photodeactivation processes of protonated formamide were investigated using the multireference configuration interaction calculations with singles and doubles (MR-CISD) method while dynamics were simulated by employing the mixed quantum-classical direct trajectory method with surface hopping based on multi-configurational self-consistent wave functions. The dynamics calculations from the first excited singlet state in O-protonated formamide resembled those found for the second valence excited state of the parent molecule. Two deactivation processes were found: the C-N (major) and C-O (minor) dissociations with very short lifetimes (33 fs). Similarly, the major process for photodecomposition in the first excited state of N-protonated formamide resembles that for the parent formamide, and involves C-N dissociation with a lifetime around 390 fs. However, 55% of trajectories remained undissociated and undeactivated until 1000 fs, indicating the existence of other deactivation processes on a longer time scale.

  16. Ab initio reaction pathways for photodissociation and isomerization of nitromethane on four singlet potential energy surfaces with three roaming paths

    Energy Technology Data Exchange (ETDEWEB)

    Isegawa, Miho; Liu, Fengyi; Morokuma, Keiji [Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103 (Japan); Maeda, Satoshi [Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810 (Japan)

    2014-06-28

    Photodissociation pathways of nitromethane following π → π{sup *} electronic excitation are reported. The potential energy surfaces for four lowest singlet states are explored, and structures of many intermediates, dissociation limits, transition states, and minimum energy conical intersections were determined using the automated searching algorism called the global reaction route mapping strategy. Geometries are finally optimized at CASSCF(14e,11o) level and energies are computed at CAS(14o,11e)PT2 level. The calculated preferable pathways and important products qualitatively explain experimental observations. The major photodissociation product CH{sub 3} and NO{sub 2} ({sup 2}B{sub 2}) is formed by direct dissociation from the S{sub 1} state. Important pathways involving S{sub 1} and S{sub 0} states for production of various dissociation products CH{sub 3}NO + O ({sup 1}D), CH{sub 3}O(X{sup 2}E) + NO (X{sup 2}Π), CH{sub 2}NO + OH, and CH{sub 2}O + HNO, as well as various isomerization pathways have been identified. Three roaming processes also have been identified: the O atom roaming in O dissociation from CH{sub 3}NO{sub 2}, the OH radical roaming in OH dissociation from CH{sub 2}N(O)(OH), and the NO roaming in NO dissociation from CH{sub 3}ONO.

  17. An ab initio molecular orbital study of the potential energy surface of the HO2 + NO reaction

    Science.gov (United States)

    Sumathi, R.; Peyerimhoff, S. D.

    1997-08-01

    The potential energy surface of the HO2+NO reaction has been investigated at second order Moller-Plesset perturbation (MP2) and density functional (DFT) methods with the 6-311++G** basis set and at complete active space [CAS(8,8)] self-consistent field level using the 6-31G** basis set. The reaction is shown to give three different groups of products, viz., HO-NO2, NO2+OH, and HNO+O2. The thermodynamically stable HO-NO2 can be formed from the energized ONOOH adduct by the 1,2 migration of the OH group via a loose transition state (referred to as TS2) with a relatively higher barrier height compared to O-O bond fission. The other exothermic product, NO2+OH, arises from a direct O-O dissociation of ONOOH and is expected to be the most favorable process on account of its low barrier height. HNO+O2 can be formed by two different channels: (i) the direct hydrogen abstraction and/or (ii) the barrierless association of the reactants to form the peroxynitrous acid, ONOOH, which then undergoes 1,3 hydrogen migration, giving rise to the HN(O)OO biradical followed by N-O dissociation. Of the two channels, channel (i) has been found to be dominant. Owing to their higher barrier heights, HNO formation is expected only at high temperatures. NOH+O2 and HONO+O are not expected to compete in the kinetics of the HO2+NO system. The energetic of the key reactions, namely HO2+NO→HO-NO2 and HO2+NO→NO2+OH, has also been obtained at the QCISD/6-311++G(2df,2pd)//MP2/6-311++G** level.

  18. Experimental testing of ab initio potential energy surfaces: Stereodynamics of NO(A2Σ+) + Ne inelastic scattering at multiple collision energies.

    Science.gov (United States)

    Luxford, Thomas F M; Sharples, Thomas R; McKendrick, Kenneth G; Costen, Matthew L

    2016-11-07

    We present a crossed molecular beam velocity-map ion imaging study of state-to-state rotational energy transfer of NO(A2Σ+, v = 0, N = 0, j = 0.5) in collisions with Ne atoms. From these measurements, we report differential cross sections and angle-resolved rotational angular momentum alignment moments for product states N' = 3 and 5-10 for collisions at an average energy of 523 cm-1, and N' = 3 and 5-14 for collisions at an average energy of 1309 cm-1, respectively. The experimental results are compared to the results of close-coupled quantum scattering calculations on two literature ab initio potential energy surfaces (PESs) [Pajón-Suárez et al., Chem. Phys. Lett. 429, 389 (2006) and Cybulski and Fernández, J. Phys. Chem. A 116, 7319 (2012)]. The differential cross sections from both experiment and theory show clear rotational rainbow structures at both collision energies, and comparison of the angles observed for the rainbow peaks leads to the conclusion that Cybulski and Fernández PES better represents the NO(A2Σ+)-Ne interaction at the collision energies used here. Sharp, forward scattered (collision energies, which are not reproduced by theory on either PES. We identify these as L-type rainbows, characteristic of attractive interactions, and consistent with a shallow well in the collinear Ne-N-O geometry, similar to that calculated for the NO(A2Σ+)-Ar surface [Kłos et al., J. Chem. Phys. 129, 244303 (2008)], but absent from both of the NO(A2Σ+)-Ne surfaces tested here. The angle-resolved alignment moments calculated by quantum scattering theory are generally in good agreement with the experimental results, but both experiment and quantum scattering theories are dramatically different to the predictions of a classical rigid-shell, kinematic-apse conservation model. Strong oscillations are resolved in the experimental alignment moments as a function of scattering angle, confirming and extending the preliminary report of this behavior [Steill et al., J

  19. Projector augmented wave method: ab initio molecular dynamics ...

    Indian Academy of Sciences (India)

    http://www.ias.ac.in/article/fulltext/boms/026/01/0033-0041 ... A brief introduction to the projector augmented wave method is given and recent developments are reviewed. The projector augmented wave method is an all-electron method for efficient ab initio molecular dynamics simulations with full wave functions. It extends ...

  20. Hydrogen Bond Dynamics in Aqueous Solutions: Ab initio Molecular ...

    Indian Academy of Sciences (India)

    Rate equation for the decay of CHB(t) · Definition of Hydrogen Bonds · Results of Molecular Dynamics · Dynamics of anion-water and water-water hydrogen bonds · Structural relaxation of anion-water & water-water H-bonds · Ab initio Molecular Dynamics : · Slide 14 · Dynamics of hydrogen bonds : CPMD results · Slide 16.

  1. Projector augmented wave method: ab initio molecular dynamics ...

    Indian Academy of Sciences (India)

    Unknown

    Abstract. A brief introduction to the projector augmented wave method is given and recent developments are reviewed. The projector augmented wave method is an all-electron method for efficient ab initio molecular dynamics simulations with full wave functions. It extends and combines the traditions of existing augmented.

  2. Ab initio structure determination via powder X-ray diffraction

    Indian Academy of Sciences (India)

    Although the method of structure completion when once the starting model is provided is facile through the Rietveld refinement technique, the structure solution ab initio os still not push-button technology. In this article a survey of the recent development in this area is provided with an illustration of the structure determination ...

  3. Ab initio study of Pt induced nanowires on Ge(001)

    NARCIS (Netherlands)

    Vanpoucke, D.E.P.

    2009-01-01

    The aim of this thesis: “Ab Initio Study of Pt Induced Nanowires on Ge(001)”, is to model the experimentally observed ‘Pt nanowires’ on Ge(001). These one-atom-thick wires can be hundreds of nanometers long while remaining defect and kink free, providing the ultimate wire any chip designer dreams

  4. THEORETICAL STUDY (AB INITIO AND DFT METHODS) ON ...

    African Journals Online (AJOL)

    Theoretical study on acidic dissociation constant of xylenol orange in aqueous solution. Bull. Chem. Soc. Ethiop. 2017, 31(1). 129 modeled. Hartree-Fock ab initio and density functional geometry optimizations were performed with the Gaussian 09 program. The optimizations were done using HF/6-31+G(d) method. The.

  5. Analysis of some conventional ab initio gene finders using human ...

    African Journals Online (AJOL)

    Yomi

    2012-01-24

    Jan 24, 2012 ... parts of a given protein coding sequence so that the users be able to choose the best program(s) in accordance with their research goals. MATERIALS AND METHODS. Sequence data set. In assessing five ab initio gene prediction programs, a data set consisting of 110 known orthologous genes of human ...

  6. Ab initio computations on small copper compounds-CuO

    NARCIS (Netherlands)

    Boer, D.H.W. den; Kaleveld, E.W.

    1980-01-01

    Ab initio computations on CuO were performed with the Hartree-Fock method and a proper dissociation MC SCF procedure. In particular the influence of the GTO basis set for Cu in molecular computations has been studied. A potential energy curve and a Mulliken population analysis are presented. The

  7. Ab initio calculation of the Structural, Mechanical and ...

    African Journals Online (AJOL)

    ADOWIE PERE

    ABSTRACT: An ab initio plane-wave Pseudopotential calculations using the density functional theory (DFT) .... wave Pseudopotential PWPP method with the ..... Γ the longitudinal optical LO branch shows a sharp increasing amount of upward dispersion while the TO , a flat/horizontal dispersion it was also observed that the ...

  8. Realization of prediction of materials properties by ab initio ...

    Indian Academy of Sciences (India)

    Ab initio treatment is becoming realistic to predict physical, chemical, and even mechanical properties of academically and industrially interesting materials. There is, however, some limitation in size and time of the system up to the order of several hundred atoms and ∼ 1 pico second, even if we use the fastest ...

  9. The Properties of Some Simple Covalent Hydrides: An Ab Initio ...

    African Journals Online (AJOL)

    Some properties of the monomeric binary hydrides of the elements of the first two rows of the periodic table have been determined using ab initio molecular orbital theory. The properties in question are the energetic, structural, electronic, topological and vibrational characteristics. In general, a gradual convergence towards ...

  10. Resonance and Aromaticity : An Ab Initio Valence Bond Approach

    NARCIS (Netherlands)

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

    2012-01-01

    Resonance energy is one of the criteria to measure aromaticity. The effect of the use of different orbital models is investigated in the calculated resonance energies of cyclic conjugated hydrocarbons within the framework of the ab initio Valence Bond Self-Consistent Field (VBSCF) method. The VB

  11. Ab initio study of alanine polypeptide chain twisting

    DEFF Research Database (Denmark)

    Solov'yov, Ilia; Yakubovich, Alexander V.; Solov'yov, Andrey V.

    2006-01-01

    chains. These particular degrees of freedom are essential for the characterization of the proteins folding process. Calculations have been carried out within the ab initio theoretical framework based on the density functional theory and accounting for all the electrons in the system. We have determined...

  12. Cyanogen Azide. Ionization Potentials and Ab Initio SCF MO Calculation

    DEFF Research Database (Denmark)

    Bak, Börge; Jansen, Peter; Stafast, Herbert

    1975-01-01

    The Ne(I) and He(I) photoelectron(PE) spectra of cyanogen azide, NCN3, have been recorded at high resolution. Their interpretation is achieved by comparison with the PE spectrum of HN3 and an ab initio LCGO SCF MO calculation. Deviations from Koopmans' theorem of quite different magnitudes...

  13. Ab initio quantum dynamical study of the multi-state nonadiabatic photodissociation of pyrrole

    NARCIS (Netherlands)

    Faraji, S.; Vazdar, M.; Reddy, V. Sivaranjana; Eckert-Maksic, M.; Lischka, H.; Koeppel, H.

    2011-01-01

    There has been a substantial amount of theoretical investigations on the photodynamics of pyrrole, often relying on surface hopping techniques or, if fully quantal, confining the study to the lowest two or three singlet states. In this study we extend ab initio based quantum dynamical investigations

  14. Ab initio simulation of dislocation cores in metals; Simulation ab initio des coeurs de dislocation dans les metaux

    Energy Technology Data Exchange (ETDEWEB)

    Ventelon, L. [CEA Saclay, Dept. des Materiaux pour le Nucleaire (DEN/DANS/DMN/SRMP), 91 - Gif-sur-Yvette (France)

    2008-07-01

    In the framework of the multi scale simulation of metals and alloys plasticity, the aim of this study is to develop a methodology of ab initio dislocations study and to apply it to the [111] screw dislocation in the bc iron. (A.L.B.)

  15. Ab initio molecular dynamics study of the Eley-Rideal reaction of H + Cl-Au(111) → HCl + Au(111): Impact of energy dissipation to surface phonons and electron-hole pairs.

    Science.gov (United States)

    Zhou, Linsen; Zhou, Xueyao; Alducin, Maite; Zhang, Liang; Jiang, Bin; Guo, Hua

    2018-01-07

    The reaction between an impinging H atom and a Cl atom adsorbed on Au(111), which is a prototype for the Eley-Rideal mechanism, is investigated using ab initio molecular dynamics at different incidence angles. The reaction yielding gaseous HCl with large internal excitation proceeds via both direct and hot-atom mechanisms. Significant energy exchange with both surface phonons and electron-hole pairs has been observed. However, their impact on the reactivity and final state distributions was found to be limited, thanks to the large exothermicity and small barrier of the reaction.

  16. Modelling of nuclear glasses by classical and ab initio molecular dynamics; Modelisation de verres intervenant dans le conditionnement des dechets radioactifs par dynamiques moleculaires classique et ab initio

    Energy Technology Data Exchange (ETDEWEB)

    Ganster, P

    2004-10-15

    A calcium aluminosilicate glass of molar composition 67 % SiO{sub 2} - 12 % Al{sub 2}O{sub 3} - 21 % CaO was modelled by classical and ab initio molecular dynamics. The size effect study in classical MD shows that the systems of 100 atoms are more ordered than the larger ones. These effects are mainly due to the 3-body terms in the empirical potentials. Nevertheless, these effects are small and the structures generated are in agreement with experimental data. In such kind of glass, we denote an aluminium avoidance and an excess of non bridging oxygens which can be compensated by tri coordinated oxygens. When the dynamics of systems of 100 and 200 atoms is followed by ab initio MD, some local arrangements occurs (bond length, angular distributions). Thus, more realistic vibrational properties are obtained in ab initio MD. The modelling of thin films shows that aluminium atoms extend to the most external part of the surface and they are all tri-coordinated. Calcium atoms are set in the sub layer part of the surface and they produce a depolymerization of the network. In classical MD, tri-coordinated aluminium atoms produce an important electric field above the surface. With non bridging oxygens, they constitute attractive sites for single water molecules. (author)

  17. The Hydration Structure of Carbon Monoxide by Ab Initio Methods

    CERN Document Server

    Awoonor-Williams, Ernest

    2016-01-01

    The solvation of carbon monoxide (CO) in liquid water is important for understanding its toxicological effects and biochemical roles. In this paper, we use ab initio molecular dynamics (AIMD) and CCSD(T)-F12 calculations to assess the accuracy of the Straub and Karplus molecular mechanical (MM) model for CO(aq). The CCSD(T)-F12 CO--H2O potential energy surfaces show that the most stable structure corresponds to water donating a hydrogen bond to the C center. The MM-calculated surface it incorrectly predicts that the O atom is a stronger hydrogen bond acceptor than the C atom. The AIMD simulations indicate that CO is solvated like a hydrophobic solute, with very limited hydrogen bonding with water. The MM model tends to overestimate the degree of hydrogen bonding and overestimates the atomic radius of the C atom. The calculated Gibbs energy of hydration is in good agreement with experiment (9.3 kJ/mol calc. vs 10.7 kJ/mol exptl.). The calculated diffusivity of CO(aq) in TIP3P-model water was 5.19 x 10-5 cm2/s ...

  18. Quantum-mechanical study of the collision dynamics of O2(3Sigma(g)-) + O2(3Sigma(g)-) on a new ab initio potential energy surface.

    Science.gov (United States)

    Pérez-Ríos, Jesús; Bartolomei, Massimiliano; Campos-Martínez, José; Hernández, Marta I; Hernández-Lamoneda, Ramón

    2009-12-31

    The quantum mechanical theory for the scattering of two identical rigid rotors is reviewed and applied to the collision of O2(3Sigma(g)-) molecules using a new accurate ab initio potential energy surface (PES) for the quintet state of the composite system. The PES is based on calculations using restricted coupled-cluster theory with singles, doubles, and perturbative triple excitations [RCCSD(T)] [Bartolomei; et al. J. Chem. Phys. 2008, 128, 214304.]. This PES is extended here for large intermolecular distances using the ab initio long-range coefficients of Hettema et al. [J. Chem. Phys. 1994, 100, 1297.]. Elastic and rotationally inelastic integral cross sections have been obtained by means of close coupling calculations in the subthermal energy range (center-of-mass velocities below 500 m/s). Results are compared with those obtained using a PES derived from molecular beam experiments [Aquilanti; et al. J. Am. Chem. Soc. 1999, 121, 10794.]. General agreement is found between both PESs, although the experimentally derived PES appears as somewhat more anisotropic at least for the studied energy range. There is, however, a significant difference in the absolute value of the elastic cross sections that is due to differences in the long-range dispersion interaction. The performance of the ab initio PES for higher velocities (relevant to experiments) is also explored by retaining just the isotropic component of the interaction. A satisfactory agreement is found for the shape of the glory pattern but shifted toward lower absolute values of the cross sections.

  19. Lithium Insertion In Silicon Nanowires: An ab Initio Study

    KAUST Repository

    Zhang, Qianfan

    2010-09-08

    The ultrahigh specific lithium ion storage capacity of Si nanowires (SiNWs) has been demonstrated recently and has opened up exciting opportunities for energy storage. However, a systematic theoretical study on lithium insertion in SiNWs remains a challenge, and as a result, understanding of the fundamental interaction and microscopic dynamics during lithium insertion is still lacking. This paper focuses on the study of single Li atom insertion into SiNWs with different sizes and axis orientations by using full ab initio calculations. We show that the binding energy of interstitial Li increases as the SiNW diameter grows. The binding energies at different insertion sites, which can be classified as surface, intermediate, and core sites, are quite different. We find that surface sites are energetically the most favorable insertion positions and that intermediate sites are the most unfavorable insertion positions. Compared with the other growth directions, the [110] SiNWs with different diameters always present the highest binding energies on various insertion locations, which indicates that [110] SiNWs are more favorable by Li doping. Furthermore, we study Li diffusion inside SiNWs. The results show that the Li surface diffusion has a much higher chance to occur than the surface to core diffusion, which is consistent with the experimental observation that the Li insertion in SiNWs is layer by layer from surface to inner region. After overcoming a large barrier crossing surface-to-intermediate region, the diffusion toward center has a higher possibility to occur than the inverse process. © 2010 American Chemical Society.

  20. Computational methods for ab initio detection of microRNAs

    Directory of Open Access Journals (Sweden)

    Malik eYousef

    2012-10-01

    Full Text Available MicroRNAs are small RNA sequences of 18-24 nucleotides in length, which serve as templates to drive post transcriptional gene silencing. The canonical microRNA pathway starts with transcription from DNA and is followed by processing via the Microprocessor complex, yielding a hairpin structure. Which is then exported into the cytosol where it is processed by Dicer and then incorporated into the RNA induced silencing complex. All of these biogenesis steps add to the overall specificity of miRNA production and effect. Unfortunately, their modes of action are just beginning to be elucidated and therefore computational prediction algorithms cannot model the process but are usually forced to employ machine learning approaches. This work focuses on ab initio prediction methods throughout; and therefore homology-based miRNA detection methods are not discussed. Current ab initio prediction algorithms, their ties to data mining, and their prediction accuracy are detailed.

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

    Energy Technology Data Exchange (ETDEWEB)

    Srinivas, S.

    1999-06-16

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

  2. Local Structure Analysis in $Ab$ $Initio$ Liquid Water

    OpenAIRE

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

    2015-01-01

    Within the framework of density functional theory, the inclusion of exact exchange and non-local van der Waals/dispersion (vdW) 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 wi...

  3. Polariton Bose condensate in an open system: Ab initio approach

    Science.gov (United States)

    Elistratov, A. A.; Lozovik, Yu. E.

    2018-01-01

    In the framework of path-integral formalism and Keldysh technique for a nonequilibrium system we explore the kinetics of the polariton condensate in a quantum well embedded in an optical microcavity. We take into account pumping and leakage of excitons and photons. We make an ab initio derivation of the equations governing the dynamics of the condensates and reservoirs and show that the real open polariton system has a non-Markovian character at times comparable to the Rabi oscillation period.

  4. Ab initio study of phase equilibria in TiCx

    DEFF Research Database (Denmark)

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

    2002-01-01

    The phase diagram for the vacancy-ordered structures in the substoichiometric TiCx (x = 0.5-1.0) has been established from Monte Carlo simulations with the long-range pair and multisite effective interactions obtained from ab initio calculations. Three ordered superstructures of vacancies (Ti2C, ......3C2, and Ti6C5) are found to be ground state configurations. Their stability has been verified by full-potential total energy calculations of the fully relaxed structures....

  5. Kinetics of Electrocatalytic Reactions from First-Principles: A Critical Comparison with the Ab Initio Thermodynamics Approach.

    Science.gov (United States)

    Exner, Kai S; Over, Herbert

    2017-05-16

    Multielectron processes in electrochemistry require the stabilization of reaction intermediates (RI) at the electrode surface after every elementary reaction step. Accordingly, the bond strengths of these intermediates are important for assessing the catalytic performance of an electrode material. Current understanding of microscopic processes in modern electrocatalysis research is largely driven by theory, mostly based on ab initio thermodynamics considerations, where stable reaction intermediates at the electrode surface are identified, while the actual free energy barriers (or activation barriers) are ignored. This simple approach is popular in electrochemistry in that the researcher has a simple tool at hand in successfully searching for promising electrode materials. The ab initio TD approach allows for a rough but fast screening of the parameter space with low computational cost. However, ab initio thermodynamics is also frequently employed (often, even based on a single binding energy only) to comprehend on the activity and on the mechanism of an electrochemical reaction. The basic idea is that the activation barrier of an endergonic reaction step consists of a thermodynamic part and an additional kinetically determined barrier. Assuming that the activation barrier scales with thermodynamics (so-called Brønsted-Polanyi-Evans (BEP) relation) and the kinetic part of the barrier is small, ab initio thermodynamics may provide molecular insights into the electrochemical reaction kinetics. However, for many electrocatalytic reactions, these tacit assumptions are violated so that ab initio thermodynamics will lead to contradictions with both experimental data and ab initio kinetics. In this Account, we will discuss several electrochemical key reactions, including chlorine evolution (CER), oxygen evolution reaction (OER), and oxygen reduction (ORR), where ab initio kinetics data are available in order to critically compare the results with those derived from a

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

    Energy Technology Data Exchange (ETDEWEB)

    Draayer, Jerry P. [Louisiana State Univ., Baton Rouge, LA (United States)

    2014-09-28

    We have developed a novel ab initio symmetry-adapted no-core shell model (SA-NCSM), which has opened the intermediate-mass region for ab initio investigations, thereby providing an opportunity for first-principle symmetry-guided applications to nuclear structure and reactions for nuclear isotopes from the lightest p-shell systems to intermediate-mass nuclei. This includes short-lived proton-rich nuclei on the path of X-ray burst nucleosynthesis and rare neutron-rich isotopes to be produced by the Facility for Rare Isotope Beams (FRIB). We have provided ab initio descriptions of high accuracy for low-lying (including collectivity-driven) states of isotopes of Li, He, Be, C, O, Ne, Mg, Al, and Si, and studied related strong- and weak-interaction driven reactions that are important, in astrophysics, for further understanding stellar evolution, X-ray bursts and triggering of s, p, and rp processes, and in applied physics, for electron and neutrino-nucleus scattering experiments as well as for fusion ignition at the National Ignition Facility (NIF).

  7. Accurate ab initio vibrational energies of methyl chloride

    Energy Technology Data Exchange (ETDEWEB)

    Owens, Alec, E-mail: owens@mpi-muelheim.mpg.de [Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr (Germany); Department of Physics and Astronomy, University College London, Gower Street, WC1E 6BT London (United Kingdom); Yurchenko, Sergei N.; Yachmenev, Andrey; Tennyson, Jonathan [Department of Physics and Astronomy, University College London, Gower Street, WC1E 6BT London (United Kingdom); Thiel, Walter [Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr (Germany)

    2015-06-28

    Two new nine-dimensional potential energy surfaces (PESs) have been generated using high-level ab initio theory for the two main isotopologues of methyl chloride, CH{sub 3}{sup 35}Cl and CH{sub 3}{sup 37}Cl. The respective PESs, CBS-35{sup  HL}, and CBS-37{sup  HL}, are based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set (CBS) limit, and incorporate a range of higher-level (HL) additive energy corrections to account for core-valence electron correlation, higher-order coupled cluster terms, scalar relativistic effects, and diagonal Born-Oppenheimer corrections. Variational calculations of the vibrational energy levels were performed using the computer program TROVE, whose functionality has been extended to handle molecules of the form XY {sub 3}Z. Fully converged energies were obtained by means of a complete vibrational basis set extrapolation. The CBS-35{sup  HL} and CBS-37{sup  HL} PESs reproduce the fundamental term values with root-mean-square errors of 0.75 and 1.00 cm{sup −1}, respectively. An analysis of the combined effect of the HL corrections and CBS extrapolation on the vibrational wavenumbers indicates that both are needed to compute accurate theoretical results for methyl chloride. We believe that it would be extremely challenging to go beyond the accuracy currently achieved for CH{sub 3}Cl without empirical refinement of the respective PESs.

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

    Energy Technology Data Exchange (ETDEWEB)

    Bernard, St

    1998-12-31

    The quest for metallic hydrogen is a major goal for both theoretical and experimental condensed matter physics. Hydrogen and deuterium have been compressed up to 200 GPa in diamond anvil cells, without any clear evidence for a metallic behaviour. Loubeyere has recently suggested that hydrogen could metallize, at pressures within experimental range, in a new Van der Waals compound: Ar(H{sub 2}){sub 2} which is characterized at ambient pressure by an open and anisotropic sublattice of hydrogen molecules, stabilized by an argon skeleton. This thesis deals with a detailed ab initio investigation, by Car-Parrinello molecular dynamics methods, of the evolution under pressure of this compound. In a last chapter, we go to much higher pressures and temperatures, in order to compare orbital and orbital free ab initio methods for the dense hydrogen plasma. (author) 109 refs.

  9. Estudo da adsorção de hidrogênio e sulfeto na superfície de paládio: aspectos experimentais (eletroquímica e teóricos (ab initio e Teoria do Funcional da Densidade Experimental (electrochemistry and theoretical (ab initio and Density Functional Theory studies of hydrogen and sulfide adsorption on palladium (100 surface

    Directory of Open Access Journals (Sweden)

    Antônio Carlos D. Ângelo

    2001-08-01

    Full Text Available The adsorption of H and S2- species on Pd (100 has been studied with ab initio, density-functional calculations and electrochemical methods. A cluster of five Pd atoms with a frozen geometry described the surface. The computational calculations were performed through the GAUSSIAN94 program, and the basis functions adapted to a pseudo-potential obtained by using the Generator Coordinate Method adapted to the this program. Using the cyclic voltammetry technique through a Model 283 Potentiostat/Galvanostat E.G.&G-PAR obtained the electrochemical results. The calculated chemisorption geometry has a Pd-H distance of 1.55Å, and the potential energy surface was calculated using the Becke3P86//(GCM/DFT/SBK methodology. The adsorption of S2- ions on Pd surface obtained both through comparison between the experimental and theoretical results, at MP2 level, suggest a S2- absorption into the metallic cluster. The produced Pd-(S2- system was show to be very stable under the employed experimental conditions. The paper has shows the powerful aid of computational methods to interpret adsorption experimental data.

  10. A new ab initio potential energy surface of LiClH (1A') system and quantum dynamics calculation for Li + HCl (v = 0, j = 0-2) → LiCl + H reaction.

    Science.gov (United States)

    Tan, Rui Shan; Zhai, Huan Chen; Yan, Wei; Gao, Feng; Lin, Shi Ying

    2017-04-28

    A new ab initio potential energy surface (PES) for the ground state of Li + HCl reactive system has been constructed by three-dimensional cubic spline interpolation of 36 654 ab initio points computed at the MRCI+Q/aug-cc-pV5Z level of theory. The title reaction is found to be exothermic by 5.63 kcal/mol (9 kcal/mol with zero point energy corrections), which is very close to the experimental data. The barrier height, which is 2.99 kcal/mol (0.93 kcal/mol for the vibrationally adiabatic barrier height), and the depth of van der Waals minimum located near the entrance channel are also in excellent agreement with the experimental findings. This study also identified two more van der Waals minima. The integral cross sections, rate constants, and their dependence on initial rotational states are calculated using an exact quantum wave packet method on the new PES. They are also in excellent agreement with the experimental measurements.

  11. A new ab initio potential energy surface of LiClH (1A') system and quantum dynamics calculation for Li + HCl (v = 0, j = 0-2) → LiCl + H reaction

    Science.gov (United States)

    Tan, Rui Shan; Zhai, Huan Chen; Yan, Wei; Gao, Feng; Lin, Shi Ying

    2017-04-01

    A new ab initio potential energy surface (PES) for the ground state of Li + HCl reactive system has been constructed by three-dimensional cubic spline interpolation of 36 654 ab initio points computed at the MRCI+Q/aug-cc-pV5Z level of theory. The title reaction is found to be exothermic by 5.63 kcal/mol (9 kcal/mol with zero point energy corrections), which is very close to the experimental data. The barrier height, which is 2.99 kcal/mol (0.93 kcal/mol for the vibrationally adiabatic barrier height), and the depth of van der Waals minimum located near the entrance channel are also in excellent agreement with the experimental findings. This study also identified two more van der Waals minima. The integral cross sections, rate constants, and their dependence on initial rotational states are calculated using an exact quantum wave packet method on the new PES. They are also in excellent agreement with the experimental measurements.

  12. Ab initio work function of elemental metals

    DEFF Research Database (Denmark)

    Skriver, Hans Lomholt; Rosengaard, N. M.

    1992-01-01

    We have used a recently developed self-consistent Green’s-function technique based on tight-binding linear-muffin-tin-orbital theory to calculate the work function for the close-packed surfaces of 37 elemental metals. The results agree with the limited experimental data obtained from single...

  13. Ab Initio Studies of Metal Hexaboride Materials

    Science.gov (United States)

    Schmidt, Kevin M.

    Metal hexaborides are refractory ceramics with several qualities relevant to materials design, such as low work functions, high hardness, low thermal expansion coefficients, and high melting points, among many other properties of interest for industrial applications. Thermal and mechanical stability is a common feature provided by the covalently-bonded network boron atoms, and electronic properties can vary significantly with the resident metal. While these materials are currently employed as electron emitters and abrasives, promising uses of these materials also include catalytic applications for chemical dissociation reactions of various molecules such as hydrogen, water and carbon monoxide, for example. However, these extensions require a thorough understanding of particular mechanical and electronic properties. This dissertation is a collection of studies focused on understanding the behavior of metal hexaboride materials using computational modeling methods to investigate materials properties of these from both classical and quantum mechanical points of view. Classical modeling is performed using molecular dynamics methods with interatomic potentials obtained from density functional theory (DFT) calculations. Atomic mean-square displacements from the quasi-harmonic approximation and lattice energetic data are produced with DFT for developing the potentials. A generalized method was also developed for the inversion of cohesive energy curves of crystalline materials; pairwise interatomic potentials are extracted using detailed geometrical descriptions of the atomic interactions and a list of atomic displacements and degeneracies. The surface structure of metal hexaborides is studied with DFT using several model geometries to describe the terminal cation layouts, and these provide a basis for further studies on metal hexaboride interactions with hydrogen. The surface electronic structure calculations show that segregated regions of metal and boron

  14. Ab-Initio Physics of Electrochemistry

    Science.gov (United States)

    Letchworth Weaver, Kendra; Arias, Tomás

    2010-03-01

    We present a Joint Density Functional Theory (JDFT)footnotetextS. A. Petrosyan, A. A. Rigos, and T. A. Arias, J. Phys. Chem. B, 109, 15436-15444 (2005).^,footnotetextJ. Lischner and T. A. Arias, Phys. Rev. Lett. 101, 216401 (2008). capturing the key electrostatic interactions between electronic systems and a fluid environment. This novel theory is relevant to the study of electrochemical systems and includes the dielectric properties of the fluid and charge screening due to the presence of ions in solution. We also demonstrate how DFT calculations can address the fundamental physical issues underlying electrochemistry, including the definition of a consistent reference potential, the treatment of charged surfaces under periodic boundary conditions, and the study of the solid-electrolyte interface as a function of the applied potential. Results for interfacial capacitances and potentials of zero charge calculated using these techniques will be compared to experimental values. Our theory allows simulation of a variety of materials, such as intermetallics and complex oxides, in contact with an ionic liquid environment. This method has a wide range of potential applications including catalysis in fuel cells, batteries, and photoelectrochemical cells.

  15. Mechanisms for catalytic carbon nanofiber growth studied by ab initio density functional theory calculations

    DEFF Research Database (Denmark)

    Abild-Pedersen, Frank; Nørskov, Jens Kehlet; Rostrup-Nielsen, Jens

    2006-01-01

    Mechanisms and energetics of graphene growth catalyzed by nickel nanoclusters were studied using ab initio density functional theory calculations. It is demonstrated that nickel step-edge sites act as the preferential growth centers for graphene layers on the nickel surface. Carbon is transported......, and it is argued how these processes may lead to different nanofiber structures. The proposed growth model is found to be in good agreement with previous findings....

  16. Ab initio studies of the oxidation of methane with oxo-metal cations

    Science.gov (United States)

    Nachtigallová, Dana; Roeselová, Martina; Zahradník, Rudolf

    1997-05-01

    Ab initio calculations have been performed to study the oxidation of methane to methanol with oxo-metal cations of MO + type. Other possible reaction channels resulting from the reaction of CH 4 are investigated in the case of LiO +. It has been found that a high level of correlation energy needs to be included in order to obtain reaction energies in reasonable agreement with experiment. The calculated complexes found on the potential energy surface are of ionic character.

  17. Ab initio design on new push pull sila- and germastilbene

    Science.gov (United States)

    Amatatsu, Yoshiaki; Ohara, Yuhki

    2003-05-01

    Ab initio complete active space self-consistent field and second order Möller-Plesset perturbation calculations have been performed to examine the capabilities of the second order non-linear optics (NLO) of 4-dimethylamino,4 '-cyano,i-sila(or germa)stilbenes (i-DCSS, or i-DCSG) where the carbon at the position i of the parent 4-dimethylamino,4 '-cyanostilbene (DCS) is replaced by more electro-positive silicon or germanium atom. 1-DCSS and 1-DCSG, which have not been synthesized yet, were found to have better NLO properties than DCS.

  18. Tailoring magnetoresistance at the atomic level: An ab initio study

    KAUST Repository

    Tao, Kun

    2012-01-05

    The possibility of manipulating the tunneling magnetoresistance (TMR) of antiferromagnetic nanostructures is predicted in the framework of ab initio calculations. By the example of a junction composed of an antiferromagnetic dimer and a spin-polarized scanning tunneling microscopy tip we show that the TMR can be tuned and even reversed in sign by lateral and vertical movements of the tip. Moreover, our finite-bias calculations demonstrate that the magnitude and the sign of the TMR can also be tuned by an external voltage. © 2012 American Physical Society.

  19. Entropy of liquid water from ab initio molecular dynamics.

    Science.gov (United States)

    Zhang, Cui; Spanu, Leonardo; Galli, Giulia

    2011-12-08

    We have computed the entropy of liquid water using a two-phase thermodynamic model and trajectories generated by ab initio molecular dynamics simulations. We present the results obtained with semilocal, hybrid, and van der Waals density functionals. 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. The underestimate is more severe for the PBE and PBE0 functionals than for several van der Waals functionals. © 2011 American Chemical Society

  20. Stretching siloxanes: An ab initio molecular dynamics study

    Science.gov (United States)

    Lupton, E. M.; Nonnenberg, C.; Frank, I.; Achenbach, F.; Weis, J.; Bräuchle, C.

    2005-10-01

    We present an ab initio molecular dynamics study of siloxane elastomers placed under tensile stress for comparison with single molecule AFM experiments. Of particular interest is stress-induced chemical bond breaking in the high force regime, where a description of the molecular electronic structure is essential to determine the rupture mechanism. We predict an ionic mechanism for the bond breaking process with a rupture force of 4.4 nN for an isolated siloxane decamer pulled at a rate of 27.3 m/s and indicate lower values at experimental polymer lengths and pulling rates.

  1. Parallelisation of algorithms for ab initio computation of material properties

    CERN Document Server

    Rignanese, G M; Michenaud, J P; Gonze, X

    1995-01-01

    Parallel algorithms for ab initio calculations of vibrations modes of solids are presented and implemented under PVM. Load balancing and communication problems are dealt with in order to increase parallelism efficiency. For accurate time measurements, synchronisation of processes must be achieved. The results obtained by working with 1,2,4 and 8 processors of a Convex MetaSeries computer are presented, showing a very good efficiency. Further parallelisation of the codes (involving a three-dimensional Fast Fourier Transform) with compiler directives on a Convex Exemplar, is discussed.

  2. Ab initio modeling of small proteins by iterative TASSER simulations

    Directory of Open Access Journals (Sweden)

    Zhang Yang

    2007-05-01

    Full Text Available Abstract Background Predicting 3-dimensional protein structures from amino-acid sequences is an important unsolved problem in computational structural biology. The problem becomes relatively easier if close homologous proteins have been solved, as high-resolution models can be built by aligning target sequences to the solved homologous structures. However, for sequences without similar folds in the Protein Data Bank (PDB library, the models have to be predicted from scratch. Progress in the ab initio structure modeling is slow. The aim of this study was to extend the TASSER (threading/assembly/refinement method for the ab initio modeling and examine systemically its ability to fold small single-domain proteins. Results We developed I-TASSER by iteratively implementing the TASSER method, which is used in the folding test of three benchmarks of small proteins. First, data on 16 small proteins (α-root mean square deviation (RMSD of 3.8Å, with 6 of them having a Cα-RMSD α-RMSD α-RMSD of the I-TASSER models was 3.9Å, whereas it was 5.9Å using TOUCHSTONE-II software. Finally, 20 non-homologous small proteins (α-RMSD of 3.9Å was obtained for the third benchmark, with seven cases having a Cα-RMSD Conclusion Our simulation results show that I-TASSER can consistently predict the correct folds and sometimes high-resolution models for small single-domain proteins. Compared with other ab initio modeling methods such as ROSETTA and TOUCHSTONE II, the average performance of I-TASSER is either much better or is similar within a lower computational time. These data, together with the significant performance of automated I-TASSER server (the Zhang-Server in the 'free modeling' section of the recent Critical Assessment of Structure Prediction (CASP7 experiment, demonstrate new progresses in automated ab initio model generation. The I-TASSER server is freely available for academic users http://zhang.bioinformatics.ku.edu/I-TASSER.

  3. Ab initio study of a grain boundary in gold

    Science.gov (United States)

    Needels, M.; Rappe, A. M.; Bristowe, P. D.; Joannopoulos, J. D.

    1992-10-01

    The total energy of a grain boundary in a transition metal is calculated in an ab initio manner. Such calculations are now feasible using a plane-wave basis set provided that an optimally convergent pseudopotential is used. The investigation focuses on resolving two competing atomic models for the Σ=5 [001] twist boundary in gold. It is found that the model of lower energy, which involves small atomic displacements, corresponds to a structure determined both experimentally, using quantitative x-ray-diffraction techniques, and theoretically, using the embedded-atom method.

  4. Ab initio study of a grain boundary in gold

    Energy Technology Data Exchange (ETDEWEB)

    Needels, M.; Rappe, A.M.; Bristowe, P.D.; Joannopoulos, J.D. (Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States))

    1992-10-15

    The total energy of a grain boundary in a transition metal is calculated in an {ital ab} {ital initio} manner. Such calculations are now feasible using a plane-wave basis set provided that an optimally convergent pseudopotential is used. The investigation focuses on resolving two competing atomic models for the {Sigma}=5 (001) twist boundary in gold. It is found that the model of lower energy, which involves small atomic displacements, corresponds to a structure determined both experimentally, using quantitative x-ray-diffraction techniques, and theoretically, using the embedded-atom method.

  5. Machine Learning Force Field Parameters from Ab Initio Data.

    Science.gov (United States)

    Li, Ying; Li, Hui; Pickard, Frank C; Narayanan, Badri; Sen, Fatih G; Chan, Maria K Y; Sankaranarayanan, Subramanian K R S; Brooks, Bernard R; Roux, Benoît

    2017-09-12

    Machine learning (ML) techniques with the genetic algorithm (GA) have been applied to determine a polarizable force field parameters using only ab initio data from quantum mechanics (QM) calculations of molecular clusters at the MP2/6-31G(d,p), DFMP2(fc)/jul-cc-pVDZ, and DFMP2(fc)/jul-cc-pVTZ levels to predict experimental condensed phase properties (i.e., density and heat of vaporization). The performance of this ML/GA approach is demonstrated on 4943 dimer electrostatic potentials and 1250 cluster interaction energies for methanol. Excellent agreement between the training data set from QM calculations and the optimized force field model was achieved. The results were further improved by introducing an offset factor during the machine learning process to compensate for the discrepancy between the QM calculated energy and the energy reproduced by optimized force field, while maintaining the local "shape" of the QM energy surface. Throughout the machine learning process, experimental observables were not involved in the objective function, but were only used for model validation. The best model, optimized from the QM data at the DFMP2(fc)/jul-cc-pVTZ level, appears to perform even better than the original AMOEBA force field (amoeba09.prm), which was optimized empirically to match liquid properties. The present effort shows the possibility of using machine learning techniques to develop descriptive polarizable force field using only QM data. The ML/GA strategy to optimize force fields parameters described here could easily be extended to other molecular systems.

  6. Optical properties of highly compressed polystyrene: An ab initio study

    Science.gov (United States)

    Hu, S. X.; Collins, L. A.; Colgan, J. P.; Goncharov, V. N.; Kilcrease, D. P.

    2017-10-01

    Using all-electron density functional theory, we have performed an ab initio study on x-ray absorption spectra of highly compressed polystyrene (CH). We found that the K -edge shifts in strongly coupled, degenerate polystyrene cannot be explained by existing continuum-lowering models adopted in traditional plasma physics. To gain insights into the K -edge shift in warm, dense CH, we have developed a model designated as "single mixture in a box" (SMIAB), which incorporates both the lowering of the continuum and the rising of the Fermi surface resulting from high compression. This simple SMIAB model correctly predicts the K -edge shift of carbon in highly compressed CH in good agreement with results from quantum molecular dynamics (QMD) calculations. Traditional opacity models failed to give the proper K -edge shifts as the CH density increased. Based on QMD calculations, we have established a first-principles opacity table (FPOT) for CH in a wide range of densities and temperatures [ρ =0.1 -100 g /c m3 and T =2000 -1 000 000 K ]. The FPOT gives much higher Rosseland mean opacity compared to the cold-opacity-patched astrophysics opacity table for warm, dense CH and favorably compares to the newly improved Los Alamos atomic model for moderately compressed CH (ρCH≤10 g /c m3 ), but remains a factor of 2 to 3 higher at extremely high densities (ρCH≥50 g /c m3 ). We anticipate the established FPOT of CH will find important applications to reliable designs of high-energy-density experiments. Moreover, the understanding of K -edge shifting revealed in this study could provide guides for improving the traditional opacity models to properly handle the strongly coupled and degenerate conditions.

  7. Machine Learning Force Field Parameters from Ab Initio Data

    Energy Technology Data Exchange (ETDEWEB)

    Li, Ying [Argonne; Li, Hui [Department; Pickard, Frank C. [Laboratory; Narayanan, Badri [Center; Sen, Fatih G. [Center; Chan, Maria K. Y. [Center; Computational; Sankaranarayanan, Subramanian K. R. S. [Center; Computational; Brooks, Bernard R. [Laboratory; Roux, Benoît [Department; Center; Computational

    2017-08-11

    Machine learning (ML) techniques with the genetic algorithm (GA) have been applied to determine a polarizable force field parameters using only ab initio data from quantum mechanics (QM) calculations of molecular clusters at the MP2/6-31G(d,p), DFMP2(fc)/jul-cc-pVDZ, and DFMP2(fc)/jul-cc-pVTZ levels to predict experimental condensed phase properties (i.e., density and heat of vaporization). The performance of this ML/GA approach is demonstrated on 4943 dimer electrostatic potentials and 1250 cluster interaction energies for methanol. Excellent agreement between the training data set from QM calculations and the optimized force field model was achieved. The results were further improved by introducing an offset factor during the machine learning process to compensate for the discrepancy between the QM calculated energy and the energy reproduced by optimized force field, while maintaining the local “shape” of the QM energy surface. Throughout the machine learning process, experimental observables were not involved in the objective function, but were only used for model validation. The best model, optimized from the QM data at the DFMP2(fc)/jul-cc-pVTZ level, appears to perform even better than the original AMOEBA force field (amoeba09.prm), which was optimized empirically to match liquid properties. The present effort shows the possibility of using machine learning techniques to develop descriptive polarizable force field using only QM data. The ML/GA strategy to optimize force fields parameters described here could easily be extended to other molecular systems.

  8. Quasiclassical Trajectory Calculations of the Rate Constant of the OH + HBr → Br + H2O Reaction Using a Full-Dimensional Ab Initio Potential Energy Surface Over the Temperature Range 5 to 500 K.

    Science.gov (United States)

    de Oliveira-Filho, Antonio G S; Ornellas, Fernando R; Bowman, Joel M

    2014-02-20

    We report a permutationally invariant, ab initio potential energy surface (PES) for the OH + HBr → Br + H2O reaction. The PES is a fit to roughly 26 000 spin-free UCCSD(T)/cc-pVDZ-F12a energies and has no classical barrier to reaction. It is used in quasiclassical trajectory calculations with a focus on the thermal rate constant, k(T), over the temperature range 5 to 500 K. Comparisons with available experimental data over the temperature range 23 to 416 K are made using three approaches to treat the OH rotational and associated electronic partition function. All display an inverse temperature dependence of k(T) below roughly 160 K and a nearly constant temperature dependence above 160 K, in agreement with experiment. The calculated rate constant with no treatment of spin-orbit coupling is overall in the best agreement with experiment, being (probably fortuitously) within 20% of it.

  9. Ab Initio Potential Energy Surfaces for Both the Ground (X̃1A′ and Excited (A∼1A′′ Electronic States of HSiBr and the Absorption and Emission Spectra of HSiBr/DSiBr

    Directory of Open Access Journals (Sweden)

    Anyang Li

    2012-01-01

    Full Text Available Ab initio potential energy surfaces for the ground (X̃1A′ and excited (A˜A′′1 electronic states of HSiBr were obtained by using the single and double excitation coupled-cluster theory with a noniterative perturbation treatment of triple excitations and the multireference configuration interaction with Davidson correction, respectively, employing an augmented correlation-consistent polarized valence quadruple zeta basis set. The calculated vibrational energy levels of HSiBr and DSiBr of the ground and excited electronic states are in excellent agreement with the available experimental band origins. In addition, the absorption and emission spectra of HSiBr and DSiBr were calculated using an efficient single Lanczos propagation method and are in good agreement with the available experimental observations.

  10. Ab initio simulations and neutron scattering studies of structure and dynamics in PdH

    CERN Document Server

    Totolici, I E

    2001-01-01

    The work presented in this PhD thesis is concerned with the interpretation of the neutron scattering measurements from the palladium hydrogen system by means of ab initio electronic structure calculations. The motivation of performing such calculations was due to recent neutron scattering studies on this system that showed a strong directional dependence to the dynamical structure factor together with a complex dependence on energy. Here we attempt to describe the origin of these features by ab initio simulations of the dynamical structure factor. The method assumes an adiabatic separation of the motion of the proton and palladium atoms. The proton wave functions are calculated by a direct solution of the associated single-particle Schroedinger equation using a plane wave basis set method and a mapping of the adiabatic surface. The Fourier components of the adiabatic potential are obtained from LDA pseudopotential calculations. Using Fermi's golden rule within the Born approximation we were then able to calcu...

  11. Ab Initio Calculations and Raman and SERS Spectral Analyses of Amphetamine Species

    DEFF Research Database (Denmark)

    Berg, Rolf W.; Nørbygaard, Thomas; White, Peter C.

    2011-01-01

    For the first time, the differences between the spectra of amphetamine and amphetamine-H+ and between different conformers are thoroughly studied by ab initio model calculations, and Raman and surface-enhanced Raman spectroscopy (SERS) spectra are measured for different species of amphetamine....... The spectra of amphetamine and amphetamine-H+ sampleswere obtained and assigned according to a comparison of the experimental spectra and the ab initio MO calculations, performed using the Gaussian 03W program (Gaussian, Inc., Pittsburgh, PA). The analyses were based on complete geometry minimization...... of the conformational energy of the S-plus-amphetamine molecule and the S-plus-amphetamine-H+ ion. The harmonic frequency calculations provide information about the characteristic features of the Raman spectra and the nature of the bonding in the molecule. It is concluded that vibrational bands from salt anions...

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

    Energy Technology Data Exchange (ETDEWEB)

    Zen, Andrea, E-mail: a.zen@ucl.ac.uk [Dipartimento di Fisica, “La Sapienza” - Università di Roma, piazzale Aldo Moro 5, 00185 Rome (Italy); London Centre for Nanotechnology, University College London, London WC1E 6BT (United Kingdom); Luo, Ye, E-mail: xw111luoye@gmail.com; Mazzola, Guglielmo, E-mail: gmazzola@phys.ethz.ch; Sorella, Sandro, E-mail: sorella@sissa.it [SISSA–International School for Advanced Studies, Via Bonomea 26, 34136 Trieste (Italy); Democritos Simulation Center CNR–IOM Istituto Officina dei Materiali, 34151 Trieste (Italy); Guidoni, Leonardo, E-mail: leonardo.guidoni@univaq.it [Dipartimento di Fisica, “La Sapienza” - Università di Roma, piazzale Aldo Moro 5, 00185 Rome (Italy); Dipartimento di Scienze Fisiche e Chimiche, Università degli Studi dell’ Aquila, via Vetoio, 67100 L’ Aquila (Italy)

    2015-04-14

    Although liquid water is ubiquitous in chemical reactions at roots of life and climate on the earth, the prediction of its properties by high-level ab initio molecular dynamics simulations still represents a formidable task for quantum chemistry. In this article, we present a room temperature simulation of liquid water based on the potential energy surface obtained by a many-body wave function through quantum Monte Carlo (QMC) methods. The simulated properties are in good agreement with recent neutron scattering and X-ray experiments, particularly concerning the position of the oxygen-oxygen peak in the radial distribution function, at variance of previous density functional theory attempts. Given the excellent performances of QMC on large scale supercomputers, this work opens new perspectives for predictive and reliable ab initio simulations of complex chemical systems.

  13. Computer modeling of adsorption and decomposition pathways of boundary-layer lubricants on clean aluminum(111) surface, and adhesive metal transfer at the aluminum/steel interface: The ab-initio study

    Science.gov (United States)

    Zhong, Jun

    Density functional theory (DFT) is employed to study lubricant adsorption and decomposition pathways, and adhesive metal transfer on clean aluminum surfaces. In this dissertation, density functional theory (DFT-GGA) is used to investigate the optimal adsorption geometries and binding energies of vinyl-phosphonic and ethanoic acids on an A1(111) surface. Tri-bridged, bi-bridged and uni-dentate coordinations for adsorbates are examined to determine the optimal binding sites on the surface. An analysis of the charge density of states (DOS) of oxygen involved in reacting with aluminum ions reveals changes in the atomic bonding configuration. For these acid molecules, the favorable decomposition pathways lead to fragments of vinyl- and alkylchains bonding to the Al(111) surface with phosphorous and carbon ions. Final optimal decomposition geometries and binding energies for various decomposition stages are also discussed. In addition, ab-initio molecular dynamics (AIMD) is carried out to explore collisions of aliphatic lubricants like butanol-alcohol and butanoic-acid with the Al(111) surface. Simulation results indicate that functional oxygen groups on these molecules could react with the "islands of nascent aluminum" and oxidize the surface. Favorable decomposition pieces on the surface, which were corroborated with experiment and DFT calculations, are found to contribute to the effectiveness of a particular molecule for boundary thinfilm lubrication to reduce the wear of aluminum. Finally, ab-initio molecular dynamics is also applied to investigations of the interaction between aluminum and hematite surfaces with and without a vinyl-phosphonic acid (VPA) lubricant. Without the lubricant, hematite is found to react with Al strongly (thermit reaction). This removes relatively large fragments from the surface of the aluminum substrate when this substrate is rubbed with a harder steel-roller under an external shock contact-load exceeding the ability of the substrate to

  14. Physisorption of an organometallic platinum complex on silica. An ab initio study

    OpenAIRE

    Shen, Juan; Muthukumar, Kaliappan; Jeschke, Harald O.; Valenti, Roser

    2012-01-01

    The interaction of trimethyl methylcyclopentadienyl platinum (MeCpPtMe3) with a fully hydroxylated SiO2 surface has been explored by means of ab initio calculations. A large slab model cut out from the hydroxylated beta-cristobalite SiO2 (111) surface was chosen to simulate a silica surface. Density functional theory calculations were performed to evaluate the energies of MeCpPtMe3 adsorption to the SiO2 surface. Our results show that the physisorption of the molecule is dependent on both (i)...

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

    Science.gov (United States)

    Chaka, Anne M; Felmy, Andrew R

    2014-09-04

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

  16. Ab initio calculations of reactions of light nuclei

    Science.gov (United States)

    Hupin, Guillaume; Quaglioni, Sofia; Navrátil, Petr

    2017-09-01

    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 as a support tool for accurate evaluations of crucial reaction data for nuclear astrophysics, fusion-energy research, and other applications. We present an efficient many-body approach to nuclear bound and scattering states alike, known as the ab initio no-core shell model with continuum. In this approach, 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. We show that predictive results for nucleon and deuterium scattering on 4He nuclei can be obtained from the direct solution of the Schröedinger equation with modern nuclear potentials.

  17. Ab initio dynamics of the cytochrome P450 hydroxylation reaction

    Energy Technology Data Exchange (ETDEWEB)

    Elenewski, Justin E.; Hackett, John C, E-mail: jchackett@vcu.edu [Department of Physiology and Biophysics and The Massey Cancer Center, School of Medicine, Virginia Commonwealth University, 401 College Street, Richmond, Virginia 23219-1540 (United States)

    2015-02-14

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

  18. Microhydration of protonated glycine: an ab initio family tree.

    Science.gov (United States)

    Michaux, Catherine; Wouters, Johan; Perpète, Eric A; Jacquemin, Denis

    2008-02-28

    The incremental hydration of the glycine cation is investigated using an ab initio approach fully correcting for basis set superposition errors and explicitly incorporating electron-correlation effects. Structures with zero to four surrounding water molecules have been determined. It is demonstrated that the successive aggregates follow a Darwinian family tree, the most stable complexes systematically belonging to the same branch of the tree. In strong contrast with neutral glycine, the direct hydrogen bonding to the glycine cation is favored over bridging water structures. The agreement between experimental and theoretical hydration enthalpies and Gibbs free energies is impressive, as ab initio estimates almost systematically fit the experimental error bars. For GlyH(+)-(H2O) and GlyH(+)-(H2O)3, we show that two structures are generated by the experimental setup. The present approach also resolves most of the previous theory/experiment discrepancies and provides patterns for the evolution of the vibrational spectra: a decrease of the hydrogen-bond stretching frequency indicating second-shell water molecules. Additionally, the impact of bulk solvent solvation is investigated, as four discrete water molecules still do not fully hydrate the protonated glycine.

  19. Quantum Fragment Based ab Initio Molecular Dynamics for Proteins.

    Science.gov (United States)

    Liu, Jinfeng; Zhu, Tong; Wang, Xianwei; He, Xiao; Zhang, John Z H

    2015-12-08

    Developing ab initio molecular dynamics (AIMD) methods for practical application in protein dynamics is of significant interest. Due to the large size of biomolecules, applying standard quantum chemical methods to compute energies for dynamic simulation is computationally prohibitive. In this work, a fragment based ab initio molecular dynamics approach is presented for practical application in protein dynamics study. In this approach, the energy and forces of the protein are calculated by a recently developed electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method. For simulation in explicit solvent, mechanical embedding is introduced to treat protein interaction with explicit water molecules. This AIMD approach has been applied to MD simulations of a small benchmark protein Trpcage (with 20 residues and 304 atoms) in both the gas phase and in solution. Comparison to the simulation result using the AMBER force field shows that the AIMD gives a more stable protein structure in the simulation, indicating that quantum chemical energy is more reliable. Importantly, the present fragment-based AIMD simulation captures quantum effects including electrostatic polarization and charge transfer that are missing in standard classical MD simulations. The current approach is linear-scaling, trivially parallel, and applicable to performing the AIMD simulation of proteins with a large size.

  20. Two-component, ab initio potential energy surface for CO2—H2O, extension to the hydrate clathrate, CO2@(H2O)20, and VSCF/VCI vibrational analyses of both

    Science.gov (United States)

    Wang, Qingfeng Kee; Bowman, Joel M.

    2017-10-01

    We report an ab initio, full-dimensional, potential energy surface (PES) for CO2—H2O, in which two-body interaction energies are fit using a basis of permutationally invariant polynomials and combined with accurate potentials for the non-interacting monomers. This approach which we have termed "plug and play" is extended here to improve the precision of the 2-body fit in the long range. This is done by combining two separate fits. One is a fit to 47 593 2-body energies in the region of strong interaction and approaching the long range, and the second one is a fit to 6244 2-body energies in the long range. The two fits have a region of overlap which permits a smooth switch from one to the other. All energies are obtained at the CCSD(T)-F12b/aug-cc-pVTZ level of theory. Properties of the full PES, i.e., stationary points, harmonic frequencies of the global minimum, etc., are shown to be in excellent agreement with direct CCSD(T)-F12b/aug-cc-pVTZ results. Diffusion Monte Carlo calculations of the dimer zero-point energy (ZPE) are performed, and a dissociation energy, D0, of 787 cm-1 is obtained using that ZPE, De, and the rigorous ZPEs of the monomers. Using a benchmark De, D0 is 758 cm-1. Vibrational self-consistent field (VSCF)/virtual state configuration interaction (VCI) MULTIMODE calculations of intramolecular fundamentals are reported and are in good agreement with available experimental results. Finally, the full dimer PES is combined with an existing ab initio water potential to develop a potential for the CO2 hydrate clathrate CO2(H2O)20(512 water cage). A full normal-mode analysis of this hydrate clathrate is reported as are local-monomer VSCF/VCI calculations of the fundamentals of CO2.

  1. Two-component, ab initio potential energy surface for CO2-H2O, extension to the hydrate clathrate, CO2@(H2O)20, and VSCF/VCI vibrational analyses of both.

    Science.gov (United States)

    Wang, Qingfeng Kee; Bowman, Joel M

    2017-10-28

    We report an ab initio, full-dimensional, potential energy surface (PES) for CO2-H2O, in which two-body interaction energies are fit using a basis of permutationally invariant polynomials and combined with accurate potentials for the non-interacting monomers. This approach which we have termed "plug and play" is extended here to improve the precision of the 2-body fit in the long range. This is done by combining two separate fits. One is a fit to 47 593 2-body energies in the region of strong interaction and approaching the long range, and the second one is a fit to 6244 2-body energies in the long range. The two fits have a region of overlap which permits a smooth switch from one to the other. All energies are obtained at the CCSD(T)-F12b/aug-cc-pVTZ level of theory. Properties of the full PES, i.e., stationary points, harmonic frequencies of the global minimum, etc., are shown to be in excellent agreement with direct CCSD(T)-F12b/aug-cc-pVTZ results. Diffusion Monte Carlo calculations of the dimer zero-point energy (ZPE) are performed, and a dissociation energy, D0, of 787 cm-1 is obtained using that ZPE, De, and the rigorous ZPEs of the monomers. Using a benchmark De, D0 is 758 cm-1. Vibrational self-consistent field (VSCF)/virtual state configuration interaction (VCI) MULTIMODE calculations of intramolecular fundamentals are reported and are in good agreement with available experimental results. Finally, the full dimer PES is combined with an existing ab initio water potential to develop a potential for the CO2 hydrate clathrate CO2(H2O)20(512 water cage). A full normal-mode analysis of this hydrate clathrate is reported as are local-monomer VSCF/VCI calculations of the fundamentals of CO2.

  2. Embedded atom approach for gold–silicon system from ab initio ...

    Indian Academy of Sciences (India)

    In the present paper, an empirical embedded atom method (EAM) potential for gold–silicon (Au–Si) is developed by fitting to ab initio force (the 'force matching' method) and experimental data. The force database is generated within ab initio molecular dynamics (AIMD). The database includes liquid phase at various ...

  3. Ab initio studies of equations of state and chemical reactions of reactive structural materials

    Science.gov (United States)

    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

  4. Thermal neutron scattering law calculations using ab initio molecular dynamics

    Science.gov (United States)

    Wormald, Jonathan; Hawari, Ayman I.

    2017-09-01

    In recent years, methods for the calculation of the thermal scattering law (i.e. S(α,β), where α and β are dimensionless momentum and energy transfer variables, respectively) were developed based on ab initio lattice dynamics (AILD) and/or classical molecular dynamics (CMD). While these methods are now mature and efficient, further advancement in the application of such atomistic techniques is possible using ab initio molecular dynamics (AIMD) methods. In this case, temperature effects are inherently included in the calculation, e.g. phonon density of states (DOS), while using ab initio force fields that eliminate the need for parameterized semi-empirical force fields. In this work, AIMD simulations were performed to predict the phonon spectra as a function of temperature for beryllium and graphite, which are representative nuclear reactor moderator and reflector materials. Subsequently, the calculated phonon spectra were utilized to predict S(α,β) using the LEAPR module of the NJOY code. The AIMD models of beryllium and graphite were 5 × 5 × 5 crystal unit cells (250 atoms and 500 atoms respectively). Electronic structure calculations for the prediction of Hellman-Feynman forces were performed using density functional theory with a GGA exchange correlation functional and corresponding core electron pseudopotentials. AIMD simulations of 1000-10,000 time-steps were performed with the canonical ensemble (NVT thermostat) for several temperatures between 300 K and 900 K. The phonon DOS were calculated as the power spectrum of the AIMD predicted velocity autocorrelation functions. The resulting AIMD phonon DOS and corresponding inelastic thermal neutron scattering cross sections at 300 K, where anharmonic effects are expected to be small, were found to be in reasonable agreement with the results generated using traditional AILD. This illustrated the validity of the AIMD approach. However, since the impact of the temperature on the phonon DOS (e.g. broadening of

  5. Symplectic ab initio no-core shell model

    Energy Technology Data Exchange (ETDEWEB)

    Draayer, J. P.; Dytrych, T.; Sviratcheva, K. D.; Bahri, C. [Department of Physics and Astronomy, Lousiana State University, Baton Rouge, 70803 Lousiana (United States); Vary, J. P. [Department of Physics and Astronomy, Iowa State University, Ames, 50011 Iowa (United States)

    2008-12-15

    The present study confirms the significance of the symplectic Sp(3,R) symmetry in nuclear dynamics as unveiled, for the first time, by examinations of realistic nucleon-nucleon interactions as well as of eigenstates calculated in the framework of the ab initio No-Core Shell Model (NCSM). The results reveal that the NCSM wave functions for light nuclei highly overlap (at the {approx} 90% level) with only a few of the most deformed Sp(3,R)-symmetric basis states. This points to the possibility of achieving convergence of higher-lying collective modes and reaching heavier nuclei by expanding the NCSM basis space beyond its current limits through Sp(3,R) basis states. Furthermore the symplectic symmetry is found to be favored by the JISP 16 and CD-Bonn realistic nucleon-nucleon interactions, which points to a more fundamental origin of the symplectic symmetry. (Author)

  6. Ab initio and kinetic modeling studies of formic acid oxidation

    DEFF Research Database (Denmark)

    Marshall, Paul; Glarborg, Peter

    2015-01-01

    A detailed chemical kinetic model for oxidation of formic acid (HOCHO) in flames has been developed, based on theoretical work and data from literature. Ab initio calculations were used to obtain rate coefficients for reactions of HOCHO with H, O, and HO2. Modeling predictions with the mechanism...... have been compared to the experimental results of de Wilde and van Tiggelen (1968) who measured the laminar burning velocities for HOCHO flames over a range of stoichiometries and dilution ratios. The modeling predictions are generally satisfactory. The governing reaction mechanisms are outlined based...... on calculations with the kinetic model. Formic acid is consumed mainly by reaction with OH, yielding OCHO, which dissociates rapidly to CO2 + H, and HOCO, which may dissociate to CO + OH or CO2 + H, or react with H, OH, or O2 to form more stable products. The branching fraction of the HOCHO + OH reaction, as well...

  7. Ab initio study of electron-phonon coupling in rubrene

    Science.gov (United States)

    Ordejón, P.; Boskovic, D.; Panhans, M.; Ortmann, F.

    2017-07-01

    The use of ab initio methods for accurate simulations of electronic, phononic, and electron-phonon properties of molecular materials such as organic crystals is a challenge that is often tackled stepwise based on molecular properties calculated in gas phase and perturbatively treated parameters relevant for solid phases. In contrast, in this work we report a full first-principles description of such properties for the prototypical rubrene crystals. More specifically, we determine a Holstein-Peierls-type Hamiltonian for rubrene, including local and nonlocal electron-phonon couplings. Thereby, a recipe for circumventing the issue of numerical inaccuracies with low-frequency phonons is presented. In addition, we study the phenyl group motion with a molecular dynamics approach.

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

    Directory of Open Access Journals (Sweden)

    Varas Alejandro

    2016-08-01

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

  9. Ab Initio Calculations of Co Shielding in Model Complexes

    Directory of Open Access Journals (Sweden)

    Elaine A. Moore

    2002-08-01

    Full Text Available Abstract: Recent ab initio calculations of cobalt NMR shielding show that DFT-GIAO calculations using hybrid functionals are found to reproduce experimental values well. This method is used to calculate the variation of the cobalt NMR shielding tensor of sqaure pyramidal nitrosyl complexes with respect to the CoNO geometry and to differing basal ligands. The isotropic shielding is shown to have a large negative derivative with respect to CoX distance where X is a ligating atom.; the derivative with respect to NO distance is smaller but still significant. The zz component where z is along the CoN(NO bond is more sensitive to the basal ligands but the other two principal components are sensitive to the CoNO geometry.

  10. Ab initio studies on complexes formed by melamine and cyclotrione

    Directory of Open Access Journals (Sweden)

    LIANGIANG ZHU

    2007-04-01

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

  11. Integral approximations in ab initio, electron propagator calculations.

    Science.gov (United States)

    Flores-Moreno, Roberto; Ortiz, J V

    2009-09-28

    Treatments of interelectronic repulsion that avoid four-center integrals have been incorporated in ab initio, electron-propagator calculations with diagonal self-energy matrices. Whereas the formal scaling of arithmetic operations in the propagator calculations is unaffected, the reduction of storage requirements is substantial. Moreover, the scaling of integral transformations to the molecular orbital base is lowered by one order. Four-index, electron-repulsion integrals are regenerated from three-index intermediates. Test calculations with widely applied self-energy approximations demonstrate the accuracy of this approach. Only small errors are introduced when this technique is used with quasiparticle virtual orbitals, provided that conventional techniques of integral evaluation are used in the construction of density-difference matrices.

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

    Science.gov (United States)

    Wu, Henry; Mayeshiba, Tam; Morgan, Dane

    2016-01-01

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

  13. Ab initio MCDHF calculations of electron-nucleus interactions

    Science.gov (United States)

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

    2015-05-01

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

  14. Dispersion and Solvation Effects on the Structure and Dynamics of N719 Adsorbed to Anatase Titania (101) Surfaces in Room-Temperature Ionic Liquids: An ab Initio Molecular Simulation Study

    KAUST Repository

    Byrne, Aaron

    2015-12-24

    Ab initio, density functional theory (DFT)-based molecular dynamics (MD) has been carried out to investigate the effect of explicit solvation on the dynamical and structural properties of a [bmim][NTf2] room-temperature ionic liquid (RTIL), solvating a N719 sensitizing dye adsorbed onto an anatase titania (101) surface. The effect of explicit dispersion on the properties of this dye-sensitized solar cell (DSC) interface has also been studied. Upon inclusion of dispersion interactions in simulations of the solvated system, the average separation between the cations and anions decreases by 0.6 Å; the mean distance between the cations and the surface decreases by about 0.5 Å; and the layering of the RTIL is significantly altered in the first layer surrounding the dye, with the cation being on average 1.5 Å further from the center of the dye. Inclusion of dispersion effects when a solvent is not explicitly included (to dampen longer-range interactions) can result in unphysical "kinking" of the adsorbed dye\\'s configuration. The inclusion of solvent shifts the HOMO and LUMO levels of the titania surface by +3 eV. At this interface, the interplay between the effects of dispersion and solvation combines in ways that are often subtle, such as enhancement or inhibition of specific vibrational modes. © 2015 American Chemical Society.

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

    Science.gov (United States)

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

    2017-03-01

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

  16. Accurate ab initio potential energy surface, thermochemistry, and dynamics of the Cl(2P, 2P(3/2) + CH4 → HCl + CH3 and H + CH3Cl reactions.

    Science.gov (United States)

    Czakó, Gábor; Bowman, Joel M

    2012-01-28

    We report a high-quality, ab initio, full-dimensional global potential energy surface (PES) for the Cl((2)P, (2)P(3/2)) + CH(4) reaction, which describes both the abstraction (HCl + CH(3)) and substitution (H + CH(3)Cl) channels. The analytical PES is a least-squares fit, using a basis of permutationally invariant polynomials, to roughly 16,000 ab initio energy points, obtained by an efficient composite method, including counterpoise and spin-orbit corrections for the entrance channel. This composite method is shown to provide accuracy almost equal to all-electron CCSD(T)/aug-cc-pCVQZ results, but at much lower computational cost. Details of the PES, as well as additional high-level benchmark characterization of structures and energetics are reported. The PES has classical barrier heights of 2650 and 15,060 cm(-1) (relative to Cl((2)P(3/2)) + CH(4)(eq)), respectively, for the abstraction and substitution reactions, in good agreement with the corresponding new computed benchmark values, 2670 and 14,720 cm(-1). The PES also accurately describes the potential wells in the entrance and exit channels for the abstraction reaction. Quasiclassical trajectory calculations using the PES show that (a) the inclusion of the spin-orbit corrections in the PES decreases the cross sections by a factor of 1.5-2.5 at low collision energies (E(coll)); (b) at E(coll) ≈ 13,000 cm(-1) the substitution channel opens and the H/HCl ratio increases rapidly with E(coll); (c) the maximum impact parameter (b(max)) for the abstraction reaction is ~6 bohr; whereas b(max) is only ~2 bohr for the substitution; (d) the HCl and CH(3) products are mainly in the vibrational ground state even at very high E(coll); and (e) the HCl rotational distributions are cold, in excellent agreement with experiment at E(coll) = 1280 cm(-1). © 2012 American Institute of Physics

  17. High Accuracy ab Initio Calculations of Rotational-Vibrational Levels of the HCN/HNC System.

    Science.gov (United States)

    Makhnev, Vladimir Yu; Kyuberis, Aleksandra A; Zobov, Nikolai F; Lodi, Lorenzo; Tennyson, Jonathan; Polyansky, Oleg L

    2018-02-08

    Highly accurate ab initio calculations of vibrational and rotational-vibrational energy levels of the HCN/HNC (hydrogen cyanide/hydrogen isocyanide) isomerising system are presented for several isotopologues. All-electron multireference configuration interaction (MRCI) electronic structure calculations were performed using basis sets up to aug-cc-pCV6Z on a grid of 1541 geometries. The ab initio energies were used to produce an analytical potential energy surface (PES) describing the two minima simultaneously. An adiabatic Born-Oppenheimer diagonal correction (BODC) correction surface as well as a relativistic correction surface were also calculated. These surfaces were used to compute vibrational and rotational-vibrational energy levels up to 25 000 cm -1 which reproduce the extensive set of experimentally known HCN/HNC levels with a root-mean-square deviation σ = 1.5 cm -1 . We studied the effect of nonadiabatic effects by introducing opportune radial and angular corrections to the nuclear kinetic energy operator. Empirical determination of two nonadiabatic parameters results in observed energies up to 7000 cm -1 for four HCN isotopologues (HCN, DCN, H 13 CN, and HC 15 N) being reproduced with σ = 0.37 cm -1 . The height of the isomerization barrier, the isomerization energy and the dissociation energy were computed using a number of models; our best results are 16 809.4, 5312.8, and 43 729 cm -1 , respectively.

  18. Mode specificity in the OH + CHD{sub 3} reaction: Reduced-dimensional quantum and quasi-classical studies on an ab initio based full-dimensional potential energy surface

    Energy Technology Data Exchange (ETDEWEB)

    Song, Hongwei, E-mail: hwsong@wipm.ac.cn; Yang, Minghui [Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071 (China); Lu, Yunpeng [Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371 (Singapore); Li, Jun [School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 400044 (China); Guo, Hua [Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131 (United States)

    2016-04-28

    An initial state selected time-dependent wave packet method is applied to study the dynamics of the OH + CHD{sub 3} reaction with a six-dimensional model on a newly developed full-dimensional ab initio potential energy surface (PES). This quantum dynamical (QD) study is complemented by full-dimensional quasi-classical trajectory (QCT) calculations on the same PES. The QD results indicate that both translational energy and the excitation of the CH stretching mode significantly promote the reaction while the excitation of the umbrella mode has a negligible effect on the reactivity. For this early barrier reaction, interestingly, the CH stretching mode is more effective than translational energy in promoting the reaction except at very low collision energies. These QD observations are supported by QCT results. The higher efficacy of the CH stretching model in promoting this early barrier reaction is inconsistent with the prediction of the naively extended Polanyi’s rules, but can be rationalized by the recently proposed sudden vector projection model.

  19. Atomic structure of the indium-induced Ge(001)(¤n¤x4) surface reconstruction determined by scanning tunneling microscopy and ¤ab initio¤ calculations

    DEFF Research Database (Denmark)

    Falkenberg, G.; Bunk, O.; Johnson, R.L.

    2002-01-01

    . Sci. 123/124, 104 (1998) for In on Si(001). For the (4x4) subunit, we propose a model that includes the main features of the (3x4) subunit together with additional mixed Ge-In dimers. The atomic positions were optimized using ab initio total-energy calculations. The calculated local densities......Using scanning-tunneling microscopy (STM) and first-principles total-energy calculations, we have determined the atomic geometry of the superstructures formed by the adsorption of up to 0.5 monolayer of indium on Ge(001) and annealing at temperatures above 200 degreesC. A strong interaction between...... indium adatoms and the germanium substrate atoms leads to the formation of two different In-Ge subunits on the Ge(001) surface. In the subsaturation regime separate (nx4) subunits are observed where n can be either 3 or 4 and the STM images resemble those of the Si(001)-(3x4)-In and -Al reconstructions...

  20. Ab initio Molecular Orbital Studies of the Vibrational Spectra of some ...

    African Journals Online (AJOL)

    Ab initio Molecular Orbital Studies of the Vibrational Spectra of some van der Waals Complexes. Part 4. Complexes of Sulphur Dioxide with Carbon Dioxide, Carbonyl Sulphide, Carbon Disulphide and Nitrous Oxide.

  1. Experimental and ab initio investigations on textured Li–Mn–O spinel thin film cathodes

    Energy Technology Data Exchange (ETDEWEB)

    Fischer, J., E-mail: Julian.Fischer@kit.edu [Karlsruhe Institute of Technology (KIT), Institute for Applied Materials (IAM), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen (Germany); Music, D. [RWTH Aachen University, Materials Chemistry, Kopernikusstrasse 10, 52074 Aachen (Germany); Bergfeldt, T.; Ziebert, C.; Ulrich, S.; Seifert, H.J. [Karlsruhe Institute of Technology (KIT), Institute for Applied Materials (IAM), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen (Germany)

    2014-12-01

    This paper describes the tailored preparation of nearly identical lithium–manganese–oxide thin film cathodes with different global grain orientations. The thin films were synthesized by rf magnetron sputtering from a LiMn{sub 2}O{sub 4}-target in a pure argon plasma. Under appropriate processing conditions, thin films with a cubic spinel structure and a nearly similar density and surface topography but different grain orientation, i.e. (111)- and (440)-textured films, were achieved. The chemical composition was determined by inductively coupled plasma optical emission spectroscopy and carrier gas hot extraction. The constitution- and microstructure were evaluated by X-ray diffraction and Raman spectroscopy. The surface morphology and roughness were investigated by scanning electron and atomic force microscopy. The differently textured films represent an ideal model system for studying potential effects of grain orientation on the lithium ion diffusion and electrochemical behavior in LiMn{sub 2}O{sub 4}-based thin films. They are nearly identical in their chemical composition, atomic bonding behavior, surface-roughness, morphology and thickness. Our initial ab initio molecular dynamics data indicate that Li ion transport is faster in (111)-textured structure than in (440)-textured one. - Highlights: • Thin film model system of differently textured cubic Li–Mn–O spinels. • Investigation of the Li–Mn–O thin film mass density by X-ray reflectivity. • Ab initio molecular dynamics simulation on Li ion diffusion in LiMn{sub 2}O{sub 4}.

  2. Defining Condensed Phase Reactive Force Fields from ab Initio Molecular Dynamics Simulations: The Case of the Hydrated Excess Proton.

    Science.gov (United States)

    Knight, Chris; Maupin, C Mark; Izvekov, Sergei; Voth, Gregory A

    2010-10-12

    In this report, a general methodology is presented for the parametrization of a reactive force field using data from a condensed phase ab initio molecular dynamics (AIMD) simulation. This algorithm allows for the creation of an empirical reactive force field that accurately reproduces the underlying ab initio reactive surface while providing the ability to achieve long-time statistical sampling for large systems not possible with AIMD alone. In this work, a model for the hydrated excess proton is constructed where the hydronium cation and proton hopping portions of the model are statistically force-matched to the results of Car-Parrinello Molecular Dynamics (CPMD) simulations. The flexible nature of the algorithm also allows for the use of the more accurate classical simple point-charge flexible water (SPC/Fw) model to describe the water-water interactions while utilizing the ab initio data to create an overall multistate molecular dynamics (MS-MD) reactive model of the hydrated excess proton in water. The resulting empirical model for the system qualitatively reproduces thermodynamic and dynamic properties calculated from the ab initio simulation while being in good agreement with experimental results and previously developed multistate empirical valence bond (MS-EVB) models. The present methodology, therefore, bridges the AIMD technique with the MS-MD modeling of reactive events, while incorporating key strengths of both.

  3. Time-resolved photoelectron spectroscopy and ab initio multiple spawning studies of hexamethylcyclopentadiene

    DEFF Research Database (Denmark)

    Wolf, T. J. A.; Kuhlman, Thomas Scheby; Schalk, O.

    2014-01-01

    Time-resolved photoelectron spectroscopy and ab initio multiple spawning were applied to the ultrafast non-adiabatic dynamics of hexamethylcyclopentadiene. The high level of agreement between experiment and theory associates wavepacket motion with a distinct degree of freedom.......Time-resolved photoelectron spectroscopy and ab initio multiple spawning were applied to the ultrafast non-adiabatic dynamics of hexamethylcyclopentadiene. The high level of agreement between experiment and theory associates wavepacket motion with a distinct degree of freedom....

  4. Ab initio thermodynamic results for warm dense matter

    Science.gov (United States)

    Bonitz, Michael

    2016-10-01

    Warm dense matter (WDM) - an exotic state where electrons are quantum degenerate and ions may be strongly correlated - is ubiquitous in dense astrophysical plasmas and highly compressed laboratory systems including inertial fusion. Accurate theoretical predictions require precision thermodynamic data for the electron gas at high density and finite temperature around the Fermi temperature. First such data have been obtained by restricted path integral Monte Carlo (restricted PIMC) simulations and transformed into analytical fits for the free energy. Such results are also key input for novel finite temperature density functional theory. However, the RPIMC data of Ref. 1 are limited to moderate densities, and even there turned out to be surprisingly inaccurate, which is a consequence of the fermion sign problem. These problems were recently overcome by the development of alternative QMC approaches in Kiel (configuration PIMC and permutation blocking PIMC) and Imperial College (Density matrix QMC). The three methods have their strengths and limitations in complementary parameter regions and provide highly accurate thermodynamic data for the electronic contributions in WDM. While the original results were obtained for small particle numbers, recently accurate finite size corrections were derived allowing to compute ab initio thermodynamic data with an unprecedented accuracy of better than 0.3 percent. This provides the final step for the use as benchmark data for experiments and models of Warm dense matter. Co-authors: T. Schoof, S. Groth, T. Dornheim, F. D. Malone, M. Foulkes, and T. Sjostroem, Funded by: DFG via SFB-TR24 and project BO1366-10.

  5. Ab initio modelling of methane hydrate thermophysical properties.

    Science.gov (United States)

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

    2016-04-21

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

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

    Science.gov (United States)

    Oszlányi, Gábor; Sütő, András

    2016-07-01

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

  7. Challenges for large scale ab initio Quantum Monte Carlo

    Science.gov (United States)

    Kent, Paul

    2015-03-01

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

  8. Moderate-Cost Ab Initio Thermochemistry with Chemical Accuracy.

    Science.gov (United States)

    Ganyecz, Ádám; Kállay, Mihály; Csontos, József

    2017-09-12

    A moderate-cost ab initio composite model chemistry including the explicitly correlated CCSD(T*)(F12) and conventional coupled-cluster methods up to perturbative quadruple excitations along with correlation consistent basis sets is developed. The model, named diet-HEAT-F12, is also augmented with diagonal Born-Oppenheimer and scalar relativistic corrections. The methods and basis sets used for the calculation of the individual components are selected to reproduce, as close as possible, without using any fitted parameters, the benchmark HEAT contributions. A well-defined recipe for calculating size-dependent 95% confidence intervals was also worked out for the model. The reliability of the protocol was checked using the W4-11 data set as well as a disjoint set of 23 accurate atomization energies collected from the literature and obtained by the procedure of Feller, Peterson, and Dixon. The best error statistics for the test set was yielded by the diet-HEAT-F12 protocol among the models W3X, W3X-L, and W3-F12 considered.

  9. Ab initio no-core solutions for 6Li

    Science.gov (United States)

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

    2017-07-01

    We solve for properties of 6Li in the ab initio no-core full configuration (NCFC) approach and we separately solve for its ground state and {J}π ={2}2+ resonance with the Gamow shell model (GSM) in the Berggren basis. We employ both the JISP16 and chiral {{NNLO}}{opt} realistic nucleon-nucleon interactions and investigate the ground state energy, excitation energies, point proton root mean square (rms) radius and a suite of electroweak observables. We also extend and test methods to extrapolate the ground state energy, point proton rms radius, and electric quadrupole moment. We attain improved estimates of these observables in the NCFC approach by using basis spaces up through {N}\\max =18 that enable more definitive comparisons with experiment. Using the density matrix renormalization group approach with the JISP16 interaction, we find that we can significantly improve the convergence of the GSM treatment of the 6Li ground state and {J}π ={2}2+ resonance by adopting a natural orbital single-particle basis.

  10. Double-walled silicon nanotubes: an ab initio investigation

    Science.gov (United States)

    Lima, Matheus P.

    2018-02-01

    The synthesis of silicon nanotubes realized in the last decade demonstrates multi-walled tubular structures consisting of Si atoms in {{sp}}2 and the {{sp}}3 hybridizations. However, most of the theoretical models were elaborated taking as the starting point {{sp}}2 structures analogous to carbon nanotubes. These structures are unfavorable due to the natural tendency of the Si atoms to undergo {{sp}}3. In this work, through ab initio simulations based on density functional theory, we investigated double-walled silicon nanotubes proposing layered tubes possessing most of the Si atoms in an {{sp}}3 hybridization, and with few {{sp}}2 atoms localized at the outer wall. The lowest-energy structures have metallic behavior. Furthermore, the possibility to tune the band structure with the application of a strain was demonstrated, inducing a metal-semiconductor transition. Thus, the behavior of silicon nanotubes differs significantly from carbon nanotubes, and the main source of the differences is the distortions in the lattice associated with the tendency of Si to make four chemical bonds.

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

    Science.gov (United States)

    Gulian, Mamikon; Melkonyan, Gurgen; Gulian, Armen

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

  12. Ab-initio calculations for dilute magnetic semiconductors

    Energy Technology Data Exchange (ETDEWEB)

    Belhadji, Brahim

    2008-03-03

    This thesis focusses on ab-initio calculations for the electronic structure and the magnetic properties of dilute magnetic semiconductors (DMS). In particular we aim at the understanding of the complex exchange interactions in these systems. Our calculations are based on density functional theory, being ideally suited for a description of the material specific properties of the considered DMS. Moreover we use the KKR Green function method in connection with the coherent potential approximation (CPA), which allows to include the random substitutional disorder in a mean field-like approximation for the electronic structure. Finally we calculate the exchange coupling constants J{sub ij} between two impurities in a CPA medium by using the Lichtenstein formula and from this calculate the Curie temperature by a numerically exact Monte Carlo method. Based on this analysis we found and investigated four different exchange mechanisms being of importance in DMS systems: Double exchange, p-d exchange, antiferromagnetic superexchanges, and ferromagnetic superexchange. A second topic we have investigated in this thesis is the pressure dependence of the exchange interactions and the Curie temperatures in (Ga,Mn)As and (In,Mn)As, using the LDA and the LDA+U approximations. Exact calculations of T{sub C} by Monte Carlo simulations show a somehow different behavior. (orig.)

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

    Science.gov (United States)

    Velaga, Srinath C; Anderson, Brian J

    2014-01-16

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

  14. Ab Initio Computation of Dynamical Properties: Pressure Broadening

    Science.gov (United States)

    Wiesenfeld, Laurent; Drouin, Brian

    2014-06-01

    Rotational spectroscopy of polar molecules is the main observational tool in many areas of astrophysics, for gases of low densities (n ˜ 102 - 108 cm-3). Spectral line shapes in astrophysical media are largely dominated by turbulence-induced Doppler effects and natural line broadening are negligible. However line broadening remains an important tool for denser gases, like planetary high atmospheres. Understanding the excitation schemes of polar molecules requires the knowledge of excitation transfer rate due to collisional excitation, between the polar molecule and the ambient gas, usually H2. Transport properties in ionized media also require a precise knowledge of momentum transfer rates by elastic collisions. In order to assess the theoretically computed cross section and energy/momentum transfer rates, direct absolute experiments are scarce. The best way is to measure not individual scattering events but rather the global effect of the buffer gas, thanks to the pressure broadening cross sections, whose magnitude can be measured without any scaling parameters. At low temperatures, both elastic and inelastic scattering amplitudes are tested. At higher temperature, depending on the interaction strength, only inelastic scattering cross section are shown to play a significant role 1 ,2. Thanks to the advances of computer capabilities, it has become practical to compute spectral line parameters fromab initio quantum chemistry. In particular, the theory of rotational line broadening is readily incorporated into scattering quantum dynamical theory, like close-coupling schemes. The only approximations used in the computation are the isolated collision/isolated line approximations. We compute the non-binding interaction potential with high precision quantum chemistry and fit the resulting ab initio points onto a suitable functional. We have recently computed several such systems, for molecules in H2 buffer gas: H2O,3 H2CO,4 HCO+ .5 Detailed computations taking into

  15. Cosmic-Ray Modulation: an Ab Initio Approach

    Science.gov (United States)

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

    2014-10-01

    A better understanding of cosmic-ray modulation in the heliosphere can only be gained through a proper understanding of the effects of turbulence on the diffusion and drift of cosmic rays. We present an ab initio model for cosmic-ray modulation, incorporating for the first time the results yielded by a two-component turbulence transport model. This model is solved for periods of minimum solar activity, utilizing boundary values chosen so that model results are in fair to good agreement with spacecraft observations of turbulence quantities, not only in the solar ecliptic plane but also along the out-of-ecliptic trajectory of the Ulysses spacecraft. These results are employed as inputs for modelled slab and 2D turbulence energy spectra. The latter spectrum is chosen based on physical considerations, with a drop-off at the very lowest wavenumbers commencing at the 2D outerscale. There currently exist no models or observations for this quantity, and it is the only free parameter in this study. The modelled turbulence spectra are used as inputs for parallel mean free path expressions based on those derived from quasi-linear theory and perpendicular mean free paths from extended nonlinear guiding center theory. Furthermore, the effects of turbulence on cosmic-ray drifts are modelled in a self-consistent way, employing a recently developed model for drift along the wavy current sheet. The resulting diffusion coefficients and drift expressions are applied to the study of galactic cosmic-ray protons and antiprotons using a three-dimensional, steady-state cosmic-ray modulation code, and sample solutions in fair agreement with multiple spacecraft observations are presented.

  16. Cosmic-ray modulation: an ab initio approach

    Energy Technology Data Exchange (ETDEWEB)

    Engelbrecht, N.E.; Burger, R.A., E-mail: 12580996@nwu.ac.za [Center for Space Research, North-West University, Potchefstroom (South Africa)

    2014-07-01

    A better understanding of cosmic-ray modulation in the heliosphere can only be gained through a proper understanding of the effects of turbulence on the diffusion and drift of cosmic rays. We present an ab initio model for cosmic-ray modulation, incorporating for the first time the results yielded by a two-component turbulence transport model. This model is solved for periods of minimum solar activity, utilizing boundary values chosen so that model results are in fair to good agreement with spacecraft observations of turbulence quantities, not only in the solar ecliptic plane but also along the out-of-ecliptic trajectory of the Ulysses spacecraft. These results are employed as inputs for modelled slab and 2D turbulence energy spectra. The latter spectrum is chosen based on physical considerations, with a drop-off at the very lowest wavenumbers commencing at the 2D outerscale. There currently exist no models or observations for this quantity, and it is the only free parameter in this study. The modelled turbulence spectra are used as inputs for parallel mean free path expressions based on those derived from quasi-linear theory and perpendicular mean free paths from extended nonlinear guiding center theory. Furthermore, the effects of turbulence on cosmic-ray drifts are modelled in a self-consistent way, employing a recently developed model for drift along the wavy current sheet. The resulting diffusion coefficients and drift expressions are applied to the study of galactic cosmic-ray protons and antiprotons using a three dimensional, steady-state cosmic-ray modulation code, and sample solutions in fair agreement with multiple spacecraft observations are presented. (author)

  17. AN AB INITIO MODEL FOR COSMIC-RAY MODULATION

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-07-20

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

  18. The properties of Irn (n = 2-10) clusters and their nucleation on γ-Al₂O₃ and MgO surfaces: from ab initio studies.

    Science.gov (United States)

    Chen, Yongchang; Huo, Miao; Chen, Tong; Li, Qiang; Sun, Zhaolin; Song, Lijuan

    2015-01-21

    The structural stability and magnetic properties of iridium clusters Irn (n = 2-10) and their interaction on γ-Al2O3(001) and MgO(100) surfaces have been investigated from first principles calculations. It is found that the adsorption energy of Irn (n = 2-10)/γ-Al2O3(001) is lower than that of Irn/MgO(100); meanwhile, the strongest adsorption energy cluster for γ-Al2O3(001) is the tetrahedral Ir4 cluster, while for MgO(100) is a cubic Ir8 cluster. On the other hand, the nucleation of Irn (n = 2-10) clusters on both surfaces is thermodynamically favorable and exothermic. Moreover, the nucleation energy of Irn (n = 2-10) clusters on the γ-Al2O3(001) surface is close to the corresponding energy on the MgO(100) surface, except for Ir3, Ir4 and Ir6 clusters. Interestingly, the nucleation of Ir3 and Ir6 clusters on the MgO(100) surface is more favorable than that on the γ-Al2O3(001) surface, while the nucleation of the Ir4 cluster is reverse and very close to the gas phase Ir4 cluster. More importantly, deformation energy and charge density analysis show that the adsorbed Ir4 cluster on the γ-Al2O3(001) surface has obviously charge transfer between Ir atoms and surface Al, O atoms with negligible deformation. However, for the MgO(100) surface, the Ir4 cluster connects directly to three surface O atoms with severe distortion, which inhibits the activity of the tetrahedral Ir4 cluster as a catalyst.

  19. An ab initio study of the adsorption of Eu3+, Pu3+, Am3+, and Cm3+ hydroxide complexes on hematite (001) surface: Role of magnetism on adsorption

    Science.gov (United States)

    Yuan, Ke; Taylor, Sandra D.; Powell, Brian A.; Becker, Udo

    2017-10-01

    Inner-sphere hydroxide complexes of Eu3+, Pu3+, Am3+, and Cm3+ adsorbed to antiferromagnetic and ferromagnetic hematite (001) surfaces were modeled by using DFT (GGA + U) calculations in order to compare the electronic properties, atomic structures, and adsorption energies between the trivalent actinide analog Eu3+ and the corresponding actinides An3+. Eu3+ forms a tridentate-binuclear surface complex on the hematite surface with an Eu-Fe distance of 3.4-3.8 Å. Eu3+ is partially reduced upon adsorption, as indicated by the increase of original Eu3+ spin value from 6 to ∼7. Eu3+ adsorption on the ferromagnetic surface is energetically more favorable than on the antiferromagnetic surface, while the opposite is the case for all actinides An3+. When retaining a similar adsorption configuration (e.g., coordination number = 6), An3+ cations are adsorbed ∼0.2 Å closer to the surface compared to Eu3+. Partial density of states analyses indicate ionic bonding between O ions on the hematite surface and the Eu3+/An3+ adsorbates. An increasing number of bands above the Fermi energy were found when Eu3+ and An3+ were adsorbed to the ferromagnetic surface but not on the antiferromagnetic surface, indicating the ferromagnetic substrate becomes more semiconducting upon cation adsorption. These results show that the spin configurations of the hematite (001) surface have a weak but distinct influence on the cation adsorption energy. Although the antiferromagnetic spin configuration of hematite is dominant in nature, metastable ferromagnetic domains on nanohematite grains may influence the energetics of certain cation adsorption reactions.

  20. Efficient multidimensional free energy calculations for ab initio molecular dynamics using classical bias potentials

    Science.gov (United States)

    VandeVondele, Joost; Rothlisberger, Ursula

    2000-09-01

    We present a method for calculating multidimensional free energy surfaces within the limited time scale of a first-principles molecular dynamics scheme. The sampling efficiency is enhanced using selected terms of a classical force field as a bias potential. This simple procedure yields a very substantial increase in sampling accuracy while retaining the high quality of the underlying ab initio potential surface and can thus be used for a parameter free calculation of free energy surfaces. The success of the method is demonstrated by the applications to two gas phase molecules, ethane and peroxynitrous acid, as test case systems. A statistical analysis of the results shows that the entire free energy landscape is well converged within a 40 ps simulation at 500 K, even for a system with barriers as high as 15 kcal/mol.

  1. Vibrational predissociation dynamics of the aniline-neon Van der Waals complex: an ab initio study

    Energy Technology Data Exchange (ETDEWEB)

    Lopez-Tocon, I.; Otero, J.C.; Soto, J.; Becucci, M.; Pietraperzia, G.; Castellucci, E

    2004-08-02

    The aniline-neon van der Waals complex has been investigated from a theoretical point of view. The intermolecular distance, structure and rotational constants in the ground electronic state have been obtained by ab initio calculations using second-order Moeller-Plesset (MP2) theory. The potential energy surface has also been determined. It has been found that two conformers exist: the anti, where the neon atom and the NH bonds are located on opposite sides of the ring, is slightly more stable than the syn conformer. All the ab initio results agree with those obtained by the analysis of the rotational and laser induced fluorescence spectra of this complex. We have also modeled the interaction of the van der Waals bending mode with others internal motions of the aniline molecule such as the inversion mode of the amino group and the breathing mode of the ring. The theoretical results predict that there is a significant coupling between the van der Waals bending and the inversion mode in agreement with the experimental behavior found in both the ground and the first excited electronic states of this complex.

  2. Phenolic Polymer Solvation in Water and Ethylene Glycol, II: Ab Initio Computations.

    Science.gov (United States)

    Bauschlicher, Charles W; Bucholz, Eric W; Haskins, Justin B; Monk, Joshua D; Lawson, John W

    2017-04-06

    Ab initio techniques are used to study the interaction of ethylene glycol and water with a phenolic polymer. The water bonds more strongly with the phenolic OH than with the ring. The phenolic OH groups can form hydrogen bonds between themselves. For more than one water molecule, there is a competition between water-water and water-phenolic interactions. Ethylene glycol shows the same effects as those of water, but the potential energy surface is further complicated by CH2-phenolic interactions, different conformers of ethylene glycol, and two OH groups on each molecule. Thus, the ethylene glycol-phenolic potential is more complicated than the water-phenolic potential. The results of the ab initio calculations are compared to those obtained using a force field. These calibration studies show that the water system is easier to describe than the ethylene glycol system. The calibration studies confirm the reliability of force fields used in our companion molecular dynamics study of a phenolic polymer in water and ethylene solutions.

  3. Understanding the stability of Fe incorporation within Mn{sub 3}N{sub 2}(0 0 1) surfaces: An ab-initio study

    Energy Technology Data Exchange (ETDEWEB)

    Guerrero-Sánchez, J., E-mail: guerrero@ifuap.buap.mx [Department of Physics and Astronomy, Nanoscale and Quantum Phenomena Institute, Ohio University, Athens, OH 45701 (United States); Benemérita Universidad Autónoma de Puebla, Instituto de Física “Ing Luis Rivera Terrazas”, Apartado Postal J-48, Puebla 72570, México (Mexico); Centro de Nanociencias y Nanotecnologia, Universidad Nacional Autónoma de México, Apartado Postal 14, Ensenada, Baja California Codigo Postal 22800, México (Mexico); Mandru, Andrada-Oana [Department of Physics and Astronomy, Nanoscale and Quantum Phenomena Institute, Ohio University, Athens, OH 45701 (United States); Takeuchi, Noboru [Department of Physics and Astronomy, Nanoscale and Quantum Phenomena Institute, Ohio University, Athens, OH 45701 (United States); Centro de Nanociencias y Nanotecnologia, Universidad Nacional Autónoma de México, Apartado Postal 14, Ensenada, Baja California Codigo Postal 22800, México (Mexico); Cocoletzi, Gregorio H. [Benemérita Universidad Autónoma de Puebla, Instituto de Física “Ing Luis Rivera Terrazas”, Apartado Postal J-48, Puebla 72570, México (Mexico); Smith, Arthur R. [Department of Physics and Astronomy, Nanoscale and Quantum Phenomena Institute, Ohio University, Athens, OH 45701 (United States)

    2016-02-15

    Graphical abstract: - Highlights: • The Fe incorporation into inner layers of the Mn{sub 3}N{sub 2} surfaces is stable in all range of chemical potential. • Displaced Mn atoms forming cluster-like structures induce the stability of incorporated Fe atoms. • Antiferromagnetic alignment in the [0 0 1] direction and in-plane Ferromagnetic Fe–Fe and Fe–Mn alignments are the same as in Mn{sub 3}N{sub 2} bulk structure. • Incorporated Fe layers contribute to the metallic character of these surfaces. - Abstract: We present first principles spin-polarized calculations of the adsorption and incorporation of iron in the Mn{sub 3}N{sub 2}(0 0 1) surfaces. By means of a surface formation energy criterion, it is demonstrated that Fe incorporation is energetically stable for all studied surfaces. An Fe bilayer formation is achieved after Fe atoms displace Mn atoms in the sub-surface N-vacancy layers. An analysis of the magnetic coupling shows an antiferromagnetic alignment along the [0 0 1] direction as in the clean, ideal surfaces. Also, the in-plane magnetic coupling between Fe–Fe and Fe–Mn shows a ferromagnetic tendency, similar to the clean, ideally terminated surfaces. These results clearly indicate that Fe behaves like Mn when adsorbed into the Mn{sub 3}N{sub 2} surface. Density of states calculations of the stable structures show a slight deviation from the antiferromagnetic-like behavior, with the most important contribution around the Fermi level coming from the Fe-d and Mn-d orbitals.

  4. Refined ab initio intermolecular ground-state potential energy surface for the He-C2H2 van der Waals complex

    DEFF Research Database (Denmark)

    Fernández, Berta; Henriksen, Christian; Farrelly, David

    2013-01-01

    A refined CCSD(T) intermolecular potential energy surface is developed for the He-C2H2 van der Waals complex. For this, 206 points on the intermolecular potential energy surface, evaluated using the CCSD(T) method and the aug-cc-pVQZ basis set extended with a set of 3s3p2d1f1g midbond functions...

  5. Ab initio analysis of a vacancy and a self-interstitial near single crystal silicon surfaces: Implications for intrinsic point defect incorporation during crystal growth from a melt

    Energy Technology Data Exchange (ETDEWEB)

    Kamiyama, Eiji; Sueoka, Koji [Department of Communication Engineering, Okayama Prefectural University, 111 Kuboki, Soja, Okayama 719-1197 (Japan); Vanhellemont, Jan [Department of Solid State Sciences, Ghent University, Krijgslaan 281-S1, Gent 9000 (Belgium)

    2012-10-15

    The microscopic model of the Si (001) crystal surface was investigated by first principles calculations to clarify the behavior of intrinsic point defects near crystal surfaces. A c(4 x 2) structure model was used to describe the crystal surface in contact with vacuum. The calculations show lower formation energy near the surface and the existence of formation energy differences between the surface and the bulk for both types of intrinsic point defects. The tetrahedral (T)-site and the dumbbell (DB)-site, in which a Si atom is captured from the surface and forms a self-interstitial, are found as stable sites near the third atomic layer. The T-site has a barrier of 0.48 eV, whereas the DB-site has no barrier for the interstitial to penetrate into the crystal from the vacuum. Si atoms in a melt can migrate and reach at the third layer during crystal growth when bulk diffusion coefficient is used. Therefore, the melt/solid interface is always a source of intrinsic point defects. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  6. Beyond Born-Oppenheimer theory for ab initio constructed diabatic potential energy surfaces of singlet H3+ to study reaction dynamics using coupled 3D time-dependent wave-packet approach.

    Science.gov (United States)

    Ghosh, Sandip; Mukherjee, Saikat; Mukherjee, Bijit; Mandal, Souvik; Sharma, Rahul; Chaudhury, Pinaki; Adhikari, Satrajit

    2017-08-21

    The workability of beyond Born-Oppenheimer theory to construct diabatic potential energy surfaces (PESs) of a charge transfer atom-diatom collision process has been explored by performing scattering calculations to extract accurate integral cross sections (ICSs) and rate constants for comparison with most recent experimental quantities. We calculate non-adiabatic coupling terms among the lowest three singlet states of H3+ system (11A', 21A', and 31A') using MRCI level of calculation and solve the adiabatic-diabatic transformation equation to formulate the diabatic Hamiltonian matrix of the same process [S. Mukherjee et al., J. Chem. Phys. 141, 204306 (2014)] for the entire region of nuclear configuration space. The nonadiabatic effects in the D+ + H2 reaction has been studied by implementing the coupled 3D time-dependent wave packet formalism in hyperspherical coordinates [S. Adhikari and A. J. C. Varandas, Comput. Phys. Commun. 184, 270 (2013)] with zero and non-zero total angular momentum (J) on such newly constructed accurate (ab initio) diabatic PESs of H3+. We have depicted the convergence profiles of reaction probabilities for the reactive non-charge transfer, non-reactive charge transfer, and reactive charge transfer processes for different collisional energies with respect to the helicity (K) and total angular momentum (J) quantum numbers. Finally, total and state-to-state ICSs are calculated as a function of collision energy for the initial rovibrational state (v = 0, j = 0) of the H2 molecule, and consequently, those quantities are compared with previous theoretical and experimental results.

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

    Energy Technology Data Exchange (ETDEWEB)

    Han, Chang W. [Purdue Univ., West Lafayette, IN (United States); Iddir, Hakim [Argonne National Lab. (ANL), Argonne, IL (United States); Uzun, Alper [Koc Univ., Instanbul (Turkey); Curtiss, Larry A. [Argonne National Lab. (ANL), Argonne, IL (United States); Browning, Nigel D. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Gates, Bruce C. [Univ. of California, Davis, CA (United States); Ortalan, Volkan [Purdue Univ., West Lafayette, IN (United States)

    2015-11-06

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

  8. Ab-initio studies of the Sc adsorption and the ScN thin film formation on the GaN(000-1)-(2 × 2) surface

    Energy Technology Data Exchange (ETDEWEB)

    Guerrero-Sánchez, J., E-mail: guerrero@ifuap.buap.mx [Benemérita Universidad Autónoma de Puebla, Instituto de Física “Ing Luis Rivera Terrazas”, Apartado Postal J-48, Puebla 72570 (Mexico); Sánchez-Ochoa, F.; Cocoletzi, Gregorio H.; Rivas-Silva, J.F. [Benemérita Universidad Autónoma de Puebla, Instituto de Física “Ing Luis Rivera Terrazas”, Apartado Postal J-48, Puebla 72570 (Mexico); Takeuchi, Noboru [Universidad Nacional Autónoma de México, Centro de Nanociencia y Nanotecnología, Apartado Postal 2681, Ensenada, Baja California 22800 (Mexico)

    2013-12-02

    First principles total energy calculations have been performed to investigate the initial stages of the Sc adsorption and ScN thin film formation on the GaN(000-1)-(2 × 2) surface. Studies are done within the periodic density functional theory as implemented in the PWscf code of the Quantum ESPRESSO package. The Sc adsorption at high symmetry sites results in the bridge site as the most stable structure. When a Sc monolayer is deposited above the surface the T4 site results as the most stable geometry. The Sc migration into the first Ga monolayer induces the Ga displaced ad-atom to be adsorbed at the T4-2 site. A ScN bilayer may be obtained under the Ga monolayer. Finally a ScN bilayer may be formed in the wurtzite phase above the surface. The formation energy plots show that in the moderate Ga-rich conditions we obtain the formation of a ScN bilayer under the gallium monolayer. However at N-rich conditions the formation of ScN bilayer above the surface is the most favorable structure. We report the density of states to explain the electronic structure of the most favorable geometries. - Highlights: • Studies of the initial stages in the formation of Sc and ScN structures on GaN • In the adsorption of Sc on the GaN the Br site is the most favorable geometry. • When a Sc replaces a Ga of the first monolayer the displaced Ga occupies a T4-2 site. • For Ga-rich conditions there is formation of ScN under the Ga monolayer. • In N-rich conditions there is formation of ScN in the wurtzite phase.

  9. Ab initio R1 mechanism of photostimulated oxygen isotope exchange reaction on a defect TiO{sub 2} surface: The case of terminal oxygen atom exchange

    Energy Technology Data Exchange (ETDEWEB)

    Kevorkyants, Ruslan, E-mail: ruslan.kevorkyants@gmail.com; Sboev, Mikhail N.; Chizhov, Yuri V.

    2017-05-01

    Highlights: • DFT R1 mechanism of photostimulated oxygen isotope exchange between {sup 16}O{sup 18}O and terminal oxygen atom of a defect surface of nanocrystalline TiO{sub 2} is proposed. • The mechanism involves four adsorption intermediates and five transition states. • Activation energy of the reaction is 0.24 eV. • G-tensors of O{sub 3}{sup −} intermediates match EPR data on O{sub 2} adsorbed on UV-irradiated TiO{sub 2} surface. - Abstract: Based on density functional theory we propose R1 mechanism of photostimulated oxygen isotope exchange (POIEx) reaction between {sup 16}O{sup 18}O and terminal oxygen atom of a defect TiO{sub 2} surface, which is modeled by amorphous Ti{sub 8}O{sub 16} nanocluster in excited S{sup 1} electronic state. The proposed mechanism involves four adsorption intermediates and five transition states. The computed activation energy of the POIEx equals 0.24 eV. The computed g-tensors of the predicted ozonide O{sub 3}{sup −} chemisorption species match well EPR data on O{sub 2} adsorption on UV-irradiated nanocrystalline TiO{sub 2}. This match serves a mean of justification of the proposed R1 mechanism of the POIEx reaction. In addition, it is found that the proposed R1 POIEx reaction’s mechanism differs from R1 mechanism of thermo-assisted OIEx reaction on a surface of supported vanadium oxide catalyst VO{sub x}/TiO{sub 2} reported earlier.

  10. A room temperature CO$_2$ line list with ab initio computed intensities

    CERN Document Server

    Zak, Emil; Polyansky, Oleg L; Lodi, Lorenzo; Zobov, Nikolay F; Tashkun, Sergey A; Perevalov, Valery I

    2016-01-01

    Atmospheric carbon dioxide concentrations are being closely monitored by remote sensing experiments which rely on knowing line intensities with an uncertainty of 0.5% or better. We report a theoretical study providing rotation-vibration line intensities substantially within the required accuracy based on the use of a highly accurate {\\it ab initio} dipole moment surface (DMS). The theoretical model developed is used to compute CO$_2$ intensities with uncertainty estimates informed by cross comparing line lists calculated using pairs of potential energy surfaces (PES) and DMS's of similar high quality. This yields lines sensitivities which are utilized in reliability analysis of our results. The final outcome is compared to recent accurate measurements as well as the HITRAN2012 database. Transition frequencies are obtained from effective Hamiltonian calculations to produce a comprehensive line list covering all $^{12}$C$^{16}$O$_2$ transitions below 8000 cm$^{-1}$ and stronger than 10$^{-30}$ cm / molecule at ...

  11. Ab-initio Hartree-Fock study of tritium desorption from Li{sub 2}O

    Energy Technology Data Exchange (ETDEWEB)

    Taniguchi, Masaki; Tanaka, Satoru [Tokyo Univ. (Japan). Faculty of Engineering

    1998-03-01

    Dissociative adsorption of hydrogen on Li{sub 2}O (110) surface has been investigated with ab-initio Hartree-Fock quantum chemical calculation technique. Heat of adsorption and potential energy surface for H{sub 2} dissociative adsorption was evaluated by calculating the total energy of the system. Calculation results on adsorption heat indicated that H{sub 2} adsorption is endothermic. However, when oxygen vacancy exists adjacent to the adsorption sites, heat of adsorption energy became less endothermic and the activation energy required to dissociate the H-H bonding was smaller than that for the terrace site. This is considered to be caused by the excess charge localized near the defect. (author)

  12. Ab initio molecular dynamics study of ethylene adsorption onto Si(001) surface: short-time Fourier transform analysis of structural coordinate autocorrelation function.

    Science.gov (United States)

    Lee, Yung Ting; Lin, Jyh Shing

    2013-12-05

    The reaction dynamics of ethylene adsorption onto the Si(001) surface have been studied by combining density functional theory-based molecular dynamics simulations with molecular adsorption sampling scheme for investigating all kinds of reaction pathways and corresponding populations. Based on the calculated results, three possible reaction pathways--the indirect adsorption, the direct adsorption, and the repelling reaction--have been found. First, the indirect adsorption, in which the ethylene (C2H(4(ads))) forms the π-bonded C2H(4(ads)) with the buckled-down Si atom to adsorb on the Si(001) surface and then turns into the di-σ-bonded C2H(4(ads)), is the major reaction pathway. The short-time Fourier transform analysis of structural coordinate autocorrelation function is performed to further investigate the evolution of different vibrational modes along this indirect reaction pathway. This analysis illustrates that the Infrared (IR) inactive peak of the C=C stretching mode of the π-bonded C2 H4(ads) shifts to the IR inactive peak of the C-C stretching mode of di-σ-bonded C2H(4(ads)), which is in a good agreement with the IR inactive peak of the C=C stretching mode vanished in the vibrational spectrum at 150 K (Nagao et al., J. Am. Chem. Soc. 2004, 126, 9922). Second, the direct adsorption, in which the di-σ-bonded C2H(4(ads)) is formed directly with the Si intradimer or the Si interdimer on the Si(001) surface, is the less significant reaction pathway. This reaction pathway leads to the C-C stretching mode and the C-H stretching mode of the di-σ-bonded C2H(4(ads)) appeared in the vibrational spectra at 48 and 150 K, respectively (Nagao et al., J. Am. Chem. Soc. 2004, 126, 9922). Finally, the repelling reaction, in which the C2H(4(g)) first interacts with the Si dimer and then is repelled by Si atoms, is the least important reaction pathway. Consequently, neither the π-bonded C2H(4(ads)) nor the di-σ-bonded C2H(4(ads)) is formed on the Si(001) surface

  13. Ab Initio Calculations of the Electronic Properties of Polypyridine Transition Metal Complexes and Their Adsorption on Metal Surfaces in the Presence of Solvent and Counterions

    DEFF Research Database (Denmark)

    Jónsson, E. Ö.; Thygesen, Kristian Sommer; Ulstrup, Jens

    2011-01-01

    Os(II)/(III) and Co(II)/(III) polypyridine complexes in aqueous solution are robust molecular entities both in freely solute state and adsorbed on Au(111)- and Pt(111)-electrode surfaces. This class of robust coordination chemical compounds have recently been characterized by electrochemical...... of the complexes in the presence of the solvent, are conserved upon adsorption, whereas the structural features of the different oxidation states are completely lost upon adsorption under vacuum conditions. Detailed microscopic insight such as offered by the present study will be important in molecular...

  14. Correlated ab initio investigations on the intermolecular and intramolecular potential energy surfaces in the ground electronic state of the O2-(X2Πg)-HF(X1Σ+) complex

    Science.gov (United States)

    Fawzy, Wafaa M.; Elsayed, Mahmoud; Zhang, Yuchen

    2013-01-01

    This work reports the first highly correlated ab initio study of the intermolecular and intramolecular potential energy surfaces in the ground electronic state of the O_2^ - (X{}^2Π _g) - HF(X{}^1Σ^+) complex. Accurate electronic structure calculations were performed using the coupled cluster method including single and double excitations with addition of the perturbative triples correction [CCSD(T)] with the Dunning's correlation consistent basis sets aug-cc-pVnZ, n = 2-5. Also, the explicitly correlated CCSD(T)-F12a level of theory was employed with the AVnZ basis as well as the Peterson and co-workers VnZ-F12 basis sets with n = 2 and 3. Results of all levels of calculations predicted two equivalent minimum energy structures of planar geometry and Cs symmetry along the A″ surface of the complex, whereas the A' surface is repulsive. Values of the geometrical parameters and the counterpoise corrected dissociation energies (Cp-De) that were calculated using the CCSD(T)-F12a/VnZ-F12 level of theory are in excellent agreement with those obtained from the CCSD(T)/aug-cc-pV5Z calculations. The minimum energy structure is characterized by a very short hydrogen bond of length of 1.328 Å, with elongation of the HF bond distance in the complex by 0.133 Å, and De value of 32.313 Kcal/mol. Mulliken atomic charges showed that 65% of the negative charge is localized on the hydrogen bonded end of the superoxide radical and the HF unit becomes considerably polarized in the complex. These results suggest that the hydrogen bond is an incipient ionic bond. Exploration of the potential energy surface confirmed the identified minimum and provided support for vibrationally induced intramolecular proton transfer within the complex. The T-shaped geometry that possesses C2v symmetry presents a saddle point on the top of the barrier to the in-plane bending of the hydrogen above and below the axis that connects centers of masses of the monomers. The height of this barrier is 7

  15. New ab initio potential energy surface for BrH2 and rate constants for the H + HBr → H2 + Br abstraction reaction.

    Science.gov (United States)

    Jiang, Bin; Xie, Changjian; Xie, Daiqian

    2011-03-21

    A global potential energy surface (PES) for the electronic ground state of the BrH(2) system was constructed based on the multireference configuration interaction (MRCI) method including the Davidson's correction using a large basis set. In addition, the spin-orbit correction were computed using the Breit-Pauli Hamiltonian and the unperturbed MRCI wavefunctions in the Br + H(2) channel and the transition state region. Adding the correction to the ground state potential, the lowest spin-orbit correlated adiabatic potential was obtained. The characters of the new potential are discussed. Accurate initial state specified rate constants for the H + HBr → H(2) + Br abstraction reaction were calculated using a time-dependent wave packet method. The predicted rate constants were found to be in excellent agreement with the available experimental values and much better than those obtained from a previous PES.

  16. Boric acid adsorption on humic acids: Ab initio calculation of structures, stabilities, 11B NMR and 11B, 10B isotopic fractionations of surface complexes

    Science.gov (United States)

    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 Byrne, R.H., Yao, W

  17. Accurate quantum mechanical calculations of differential and integral cross sections and rate constant for the O+OH reaction using an ab initio potential energy surface.

    Science.gov (United States)

    Lin, Shi Ying; Guo, Hua; Honvault, Pascal; Xu, Chuanxiu; Xie, Daiqian

    2008-01-07

    The authors report accurate quantum mechanical studies of the O+OH reaction on the improved Xu-Xie-Zhang-Lin-Guo potential energy surface. The differential cross section was obtained at several energies near the reaction threshold using a time-independent method. The dominant forward and backward peaks in the angular distribution are consistent with a complex-forming mechanism, which is also confirmed by the extensive rotational excitation in the O2 product. However, the asymmetry of these peaks suggests a significant nonstatistical component. The initial state (upsilon i=0, j i=0) specified integral cross section, which was calculated up to 1.15 eV of collision energy using the Chebyshev wave packet method, shows no energy threshold and decreases with the increasing collision energy, consistent with the barrierless nature of the reaction. The resulting rate constant exhibits a negative temperature dependence for T>100 K and decays as the temperature is lowered, in qualitative agreement with available experimental data.

  18. Ab Initio Computational Study of Chromate Molecular Anion Adsorption on the Surfaces of Pristine and B- or N-Doped Carbon Nanotubes and Graphene.

    Science.gov (United States)

    Hizhnyi, Yuriy; Nedilko, Sergii; Borysiuk, Viktor; Shyichuk, Andrii

    2017-12-01

    Density functional theory (DFT) computations of the electronic structures of undoped, B- and N-doped CNT(3,3), CNT(5,5) carbon nanotubes, and graphene with adsorbed chromate anions CrO42- were performed within molecular cluster approach. Relaxed geometries, binding energies, charge differences of the adsorbed CrO42- anions, and electronic wave function contour plots were calculated using B3LYP hybrid exchange-correlation functional. Oscillator strengths of electronic transitions of CrO42- anions adsorbed on the surfaces of studied carbon nanostructures were calculated by the TD-DFT method. Calculations reveal covalent bonding between the anion and the adsorbents in all studied adsorption configurations. For all studied types of adsorbent structures, doping with N strengthens chemical bonding with CrO42- anions, providing a ~2-eV increase in binding energies comparatively to adsorption of the anion on undoped adsorbents. Additional electronic transitions of CrO42- anions appear in the orange-green spectral region when the anions are adsorbed on the N-doped low-diameter carbon nanotubes CNT(3,3) and CNT(5,5).

  19. Ab Initio Computational Study of Chromate Molecular Anion Adsorption on the Surfaces of Pristine and B- or N-Doped Carbon Nanotubes and Graphene

    Science.gov (United States)

    Hizhnyi, Yuriy; Nedilko, Sergii; Borysiuk, Viktor; Shyichuk, Andrii

    2017-01-01

    Density functional theory (DFT) computations of the electronic structures of undoped, B- and N-doped CNT(3,3), CNT(5,5) carbon nanotubes, and graphene with adsorbed chromate anions CrO4 2- were performed within molecular cluster approach. Relaxed geometries, binding energies, charge differences of the adsorbed CrO4 2- anions, and electronic wave function contour plots were calculated using B3LYP hybrid exchange-correlation functional. Oscillator strengths of electronic transitions of CrO4 2- anions adsorbed on the surfaces of studied carbon nanostructures were calculated by the TD-DFT method. Calculations reveal covalent bonding between the anion and the adsorbents in all studied adsorption configurations. For all studied types of adsorbent structures, doping with N strengthens chemical bonding with CrO4 2- anions, providing a 2-eV increase in binding energies comparatively to adsorption of the anion on undoped adsorbents. Additional electronic transitions of CrO4 2- anions appear in the orange-green spectral region when the anions are adsorbed on the N-doped low-diameter carbon nanotubes CNT(3,3) and CNT(5,5).

  20. Accurate ab initio potential energy surface, thermochemistry, and dynamics of the F(-) + CH3F SN2 and proton-abstraction reactions.

    Science.gov (United States)

    Szabó, István; Telekes, Hajnalka; Czakó, Gábor

    2015-06-28

    We develop a full-dimensional global analytical potential energy surface (PES) for the F(-) + CH3F reaction by fitting about 50 000 energy points obtained by an explicitly correlated composite method based on the second-order Møller-Plesset perturbation-F12 and coupled-cluster singles, doubles, and perturbative triples-F12a methods and the cc-pVnZ-F12 [n = D, T] basis sets. The PES accurately describes the (a) back-side attack Walden inversion mechanism involving the pre- and post-reaction (b) ion-dipole and (c) hydrogen-bonded complexes, the configuration-retaining (d) front-side attack and (e) double-inversion substitution pathways, as well as (f) the proton-abstraction channel. The benchmark quality relative energies of all the important stationary points are computed using the focal-point analysis (FPA) approach considering electron correlation up to coupled-cluster singles, doubles, triples, and perturbative quadruples method, extrapolation to the complete basis set limit, core-valence correlation, and scalar relativistic effects. The FPA classical(adiabatic) barrier heights of (a), (d), and (e) are -0.45(-0.61), 46.07(45.16), and 29.18(26.07) kcal mol(-1), respectively, the dissociation energies of (b) and (c) are 13.81(13.56) and 13.73(13.52) kcal mol(-1), respectively, and the endothermicity of (f) is 42.54(38.11) kcal mol(-1). Quasiclassical trajectory computations of cross sections, scattering (θ) and initial attack (α) angle distributions, as well as translational and internal energy distributions are performed for the F(-) + CH3F(v = 0) reaction using the new PES. Apart from low collision energies (Ecoll), the SN2 excitation function is nearly constant, the abstraction cross sections rapidly increase with Ecoll from a threshold of ∼40 kcal mol(-1), and retention trajectories via double inversion are found above Ecoll = ∼ 30 kcal mol(-1), and at Ecoll = ∼ 50 kcal mol(-1), the front-side attack cross sections start to increase very rapidly. At

  1. Structural properties of iron nitride on Cu(100): An ab-initio molecular dynamics study

    KAUST Repository

    Heryadi, Dodi

    2011-01-01

    Due to their potential applications in magnetic storage devices, iron nitrides have been a subject of numerous experimental and theoretical investigations. Thin films of iron nitride have been successfully grown on different substrates. To study the structural properties of a single monolayer film of FeN we have performed an ab-initio molecular dynamics simulation of its formation on a Cu(100) substrate. The iron nitride layer formed in our simulation shows a p4gm(2x2) reconstructed surface, in agreement with experimental results. In addition to its structural properties, we are also able to determine the magnetization of this thin film. Our results show that one monolayer of iron nitride on Cu(100) is ferromagnetic with a magnetic moment of 1.67 μ B. © 2011 Materials Research Society.

  2. Binding of TNT to amplifying fluorescent polymers: an ab initio and molecular dynamics study.

    Science.gov (United States)

    Enlow, Mark A

    2012-03-01

    Molecular modeling techniques were employed to study the interaction of trinitrotoluene with an amplifying fluorescent polymer used in explosive sensor devices. The pentiptycene moiety present in these polymers appears to be the most energetically favorable binding site for trinitrotoluene. Surface features of the polymer suggest that the small cavity feature of the pentiptycene moiety may be more available for binding to analyte compounds due to steric crowding about the large cavity. Binding energies between model binding sites of the polymer and various analyte compounds were more rigorously estimated by semiempirical and ab initio techniques. Binding energies were found to be largest with trinitrotoluene and other nitroaromatic compounds. Electrostatic and π-stacking interactions between trinitrotoluene and the model host were investigated by studying a series of modified host compounds. Copyright © 2011 Elsevier Inc. All rights reserved.

  3. On the role of hydrogen filled vacancies on the embrittlement of zirconium: An ab initio investigation

    Energy Technology Data Exchange (ETDEWEB)

    Olsson, Pär A.T., E-mail: Par.Olsson@mah.se [Materials Science and Applied Mathematics, Malmö University, SE-205 06 Malmö (Sweden); Kese, Kwadwo; Alvarez Holston, Anna-Maria [Studsvik Nuclear Corporation, Box 556, SE-611 10 Nyköping (Sweden)

    2015-12-15

    In this work we report the results of an ab initio study of the influence of hydrogen filled vacancies on the mechanical properties of zirconium. The modelling shows that hydrogen filled vacancies contribute to a lowering of the surface energy and an increase in the unstable stacking fault energy, which implies a reduction in ductility. The increase in unstable stacking fault energy suggests that the defects promote a change in the dislocation glide mechanism from prismatic to basal slip. To investigate the cleavage energetics, we model the decohesion process. For describing the interplanar interaction we adopt an extended version of Rose's universal binding energy relation, which is found to reproduce the behaviour accurately. The results of the modelling imply that the work of fracture and peak stress decrease as a result of the presence of hydrogen filled vacancies.

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

    Science.gov (United States)

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

    2016-04-01

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

  5. Ab initio study of long-period superstructures in close-packed A3B compounds

    DEFF Research Database (Denmark)

    Rosengaard, N. M.; Skriver, Hans Lomholt

    1994-01-01

    We have performed ab initio calculations of the stability of one-dimensional long-period superstructures in Cu3Pd, Cu3Al, and Ag3Mg by means of an interface Green's function technique based on the linear-muffin-tin-orbitals method within the tight-binding and atomic-sphere approximations. The ene......We have performed ab initio calculations of the stability of one-dimensional long-period superstructures in Cu3Pd, Cu3Al, and Ag3Mg by means of an interface Green's function technique based on the linear-muffin-tin-orbitals method within the tight-binding and atomic-sphere approximations...

  6. Physical origin of satellites in photoemission of doped graphene: an ab initio GW plus cumulant study.

    Science.gov (United States)

    Lischner, Johannes; Vigil-Fowler, Derek; Louie, Steven G

    2013-04-05

    We calculate the photoemission spectra of suspended and epitaxial doped graphene using an ab initio cumulant expansion of the Green's function based on the GW self-energy. Our results are compared to experiment and to standard GW calculations. For doped graphene on a silicon carbide substrate, we find, in contrast to earlier calculations, that the spectral function from GW only does not reproduce experimental satellite properties. However, ab initio GW plus cumulant theory combined with an accurate description of the substrate screening results in good agreement with experiment, but gives no plasmaron (i.e., no extra well-defined excitation satisfying Dyson's equation).

  7. Accurate evaluation of magnetic coupling between atoms with numerous open shells: An ab initio method

    Science.gov (United States)

    Gellé, A.; Varignon, J.; Lepetit, M.-B.

    2009-11-01

    We propose a new ab initio method designed for the accurate calculation of effective exchange integrals between atoms with numerous open shells. This method applies to ferromagnetic as well as antiferromagnetic exchange, direct or ligand-mediated exchange. Test calculations on high spin transition metal oxides such as KNiF3, Ba2CoS3 or YMnO3 exhibit a very good accuracy compared either to the best ab initio calculations —when those are feasible— and with experimental evaluations.

  8. Ab initio I-V characteristics of short C-20 chains

    DEFF Research Database (Denmark)

    Roland, C.; Larade, B.; Taylor, Jeremy Philip

    2002-01-01

    We have calculated the I-V characteristics of short chains of C-20 molecular cages between Al and Au leads with an ab initio formalism. The results indicate that a linear chain of such molecules acts primarily as metallic nanowires. The transmission, however, depends sensitively both on the orien......We have calculated the I-V characteristics of short chains of C-20 molecular cages between Al and Au leads with an ab initio formalism. The results indicate that a linear chain of such molecules acts primarily as metallic nanowires. The transmission, however, depends sensitively both...

  9. An ab initio investigation of a grain boundary in a transition metal oxide

    Energy Technology Data Exchange (ETDEWEB)

    Dawson, I.; Bristowe, P.D. [Univ. of Cambridge (United Kingdom). Dept. of Materials Science and Metallurgy; Payne, M.C.; Lee, M.H. [Univ. of Cambridge (United Kingdom). Cavendish Lab.

    1996-12-31

    The authors have used ab initio total energy plane wave pseudopotential methods to perform the first completely ab initio investigation of the atomic and electronic structure of a grain boundary in a transition metal oxide. The {Sigma} = 15 (210)[001] tilt boundary in rutile TiO{sub 2} is studied using the conjugate gradients iterative minimization technique for performing total energy calculations within the LDA and pseudopotential approximations. The stability of the experimentally observed translation state of the boundary is confirmed, and some insight is gained into its electronic structure.

  10. GAS PHASE ION CHEMISTRY OF COUMARINS: AB INITIO ...

    African Journals Online (AJOL)

    B. S. Chandravanshi

    Initio calculations favoured ionization by resonance electron capture for acetyl coumarin derivatives and dissociative electron capture by methyl substituted coumarins. Those coumarins that underwent resonance electron capture showed much higher intensities of M˙¯ than [M– H]¯ ions. These observations will be useful in ...

  11. Cryospectroscopic and ab initio anharmonic studies of acetylene-trimethylamine H-bonded complex

    Energy Technology Data Exchange (ETDEWEB)

    Rutkowski, K.S., E-mail: rutkowsk@molsp.phys.spbu.ru [Department of Physics, St. Petersburg University, Uljanovskaja 1, 198504 St. Petersburg (Russian Federation); Melikova, S.M. [Department of Physics, St. Petersburg University, Uljanovskaja 1, 198504 St. Petersburg (Russian Federation); Janski, J.; Koll, A. [Faculty of Chemistry, University of Wroclaw, 14 F. Joliot-Curie, 50-383 Wroclaw (Poland)

    2010-09-14

    Graphical abstract: FTIR spectroscopy in the range of fundamental and overtone bands and ab initio calculations show weak complex formation between acetylene and trimethylamine stabilized by a conventional H-bond predominantly. - Abstract: The FTIR spectra of C{sub 2}H{sub 2} in mixtures with trimethylamine (TMA) have been studied in liquefied Kr in the frequency range of {approx}800-7000 cm{sup -1}. The data obtained for C{sub 2}H{sub 2} subunit suggest the formation of 1:1 complexes stabilized by a moderate strength conventional H-bond. CH and CN stretching vibrations, related to the vicinal bonds of proton acceptor, were found to shift in opposite directions - blue in the former and red in the latter case. New weak bands, revealed in the range of {approx}6000-7000 cm{sup -1}, were ascribed to the overtone and combination bands of C-H stretching vibrations of acetylene which participates in the H-bond formation. The relative stability of the complex has been determined in a series of temperature (T = 118-157 K) measurements of integrated intensities of vibrational bands ascribed to monomer and complex species. Ab initio MP2/6-311++G(2d,2p) a priory counterpoise corrected calculations, made for acetylene, TMA, and the complex reproduce the main spectroscopic observations. They suggest that the most stable non-linear structure of the complex is very floppy. Evaluations of anharmonic effects on position and integrated intensity of selected bands of C-H stretching modes of C{sub 2}H{sub 2} subunit have been made within perturbation theory on the basis of single point potential energy surface (PES) and dipole moment function calculations.

  12. H/sub 3/ /sup +/: Ab initio calculation of the vibration spectrum

    Energy Technology Data Exchange (ETDEWEB)

    Carney, G.D.; Porter, R.N.

    1976-11-01

    The vibration spectrum of H/sub 3/ /sup +/ is calculated from the representation of a previously reported (J. Chem Phys. 60, 4251 (1974)) ab initio potential-energy surface in a fifth degree Simons--Parr--Finlan (SPF) expansion. Morse- and harmonic-oscillator basis functions are used to describe the motions of the three oscillators and the Harris--Engerholm--Gwinn quadrature technique is used to obtain matrix elements of the Hamiltonian in the basis of vibrational configurations. Our variational method is thus analogous to configuration--interaction calculations for electronic states. The ground state is found to have a zero-point energy of 4345 cm/sup -1/ and a vibrationally averaged geometry of R/sub 1/=R/sub 2/=0.91396 A, theta=60.0012degree, where theta is the angle between the two equivalent bonds. The transition frequencies for the E and A/sub 1/ fundamentals are nu-bar/sub E/=2516 cm/sup -1/ and nu-bar/sub A/=3185 cm/sup -1/ and those for the corresponding first overtones of the bending mode are 2nu-bar/sub E/=5004 +- 4 cm/sup -1/ and 2nu-bar/sub A/=4799 cm/sup -1/. The first overtone of the breathing mode is 6264 cm/sup -1/. The first-excited A/sub 1/ vibration state is metastable with a dipole--radiation lifetime of 3 sec. Transition frequencies, Einstein coefficients, and lifetimes are reported for a total of 21 transitions. Analysis of results for Dunham number and normal-coordinate expansions in comparison with those for SPF expansion show the latter to be superior for ab initio vibrational calculations. A scheme for possible direct measurement of the fundamental A/sub 1/ and E vibrational bands is suggested. (AIP)

  13. 14N NQR lineshape in nanocrystals: An ab initio investigation of urea

    Science.gov (United States)

    Gregorovič, Alan

    2017-05-01

    14N nuclear quadrupole resonance (NQR) lineshapes mostly contain information of low interest, although in nanocrystals they may display some unexpected behaviour. In this work, we present an ab initio computational study of the 14N NQR lineshapes in urea nanocrystals as a function of the nanocrystal size and geometry, focusing on the surface induced broadening of the lineshapes. The lineshapes were obtained through a calculation of the electric field gradient for each nitrogen site in the nanocrystal separately, taking into account the individual crystal field by embedding the molecule of interest in a suitable lattice of point multipoles representing other urea molecules in the nanocrystal. The small influence of distant molecules is found with a series expansion, using the in-crystal Sternheimer shieldings which we also calculated ab initio. We have considered nanocrystals with two geometries: a sphere and a cube, with characteristic sizes between 5 and 100 nm. Our calculations suggest that there is a dramatic difference between the linewidths for the two geometries. For spheres, we find a steep drop in linewidths at ˜10 nm; at 5 nm the linewidth is ˜11 kHz, whereas for sizes above 20 nm the linewidth is practically negligible (<100 Hz). For cubes, on the other hand, we find a steady 1/size decrease, from 12 kHz at 10 nm to 1.2 kHz at 100 nm. This analysis is important for 14N NQR spectroscopy of crystalline pharmaceuticals, where nanoparticles are increasingly more often embedded in some sort of matrix. Although this is only a theoretical analysis, we believe that this work can serve as a guidance for the forthcoming experimental analysis.

  14. Ab initio and DFT study of Octanitrocubane. | Ejuh | Journal of the ...

    African Journals Online (AJOL)

    The molecular stability, structure, dipole moment, charge transfer, polarizability and energy of Octonitrocubane have been studied by using ab- initio Quantum Mechanical calculations. We have used the Restricted Hartree-Fock (RHF) and density functional Becke3LYP (B3LYP) theories by employing 6-31G, 6- 31++G** and ...

  15. Raman and ab initio studies of simple and binary 1-alkyl-3-methylimidazolium ionic liquids

    DEFF Research Database (Denmark)

    Berg, R.W.; Deetlefs, M.; Seddon, K.R.

    2005-01-01

    Raman spectra of the ionic liquids, 1-butyl-3-methylimidazolium hexafluorophosphate ([C(4)mim][PF6]), 1-hexyl-3-methylimidazolium chloride ([C(6)mim]Cl), and 1-hexyl-3-methylimidazolium hexafluorophosphate ([C(6)mim][PF6]), and binary mixtures thereof, have been assigned using ab initio MP2...

  16. A fragment-based approach towards ab-initio treatment of polymeric ...

    Indian Academy of Sciences (India)

    Reshma S Pingale

    2017-06-20

    Jun 20, 2017 ... textiles, packaging, medical etc. have led to their extensive studies in both academic and industrial fields. Predicting the structure of these polymers is important for the study of their properties. The present work uses a 'divide and conquer'-type approach for the ab-initio studies of these polymeric systems.

  17. NMR chemical shift data and ab initio shielding calculations : emerging tools for protein structure determination

    NARCIS (Netherlands)

    Mulder, Frans A. A.; Filatov, Michael

    2010-01-01

    In this tutorial review, we discuss the utilization of chemical shift information as well as ab initio calculations of nuclear shieldings for protein structure determination. Both the empirical and computational aspects of the chemical shift are reviewed and the role of molecular dynamics and the

  18. Ab initio Molecular Orbital Studies of the Vibrational Spectra of some ...

    African Journals Online (AJOL)

    NJD

    2004-06-15

    Jun 15, 2004 ... The binary complexes formed between sulphur dioxide, as electron donor, and the series carbon dioxide, carbonyl sulphide and carbon disulphide, as electron acceptors, have been studied by means of ab initio molecular orbital theory. The optimized structures, the interaction energies and the vibrational ...

  19. Ab initio molecular dynamics study of the reaction of water with formaldehyde in sulfuric acid solution.

    NARCIS (Netherlands)

    Sprik, M.; Meijer, E.M.

    1998-01-01

    Ab initio molecular dynamics methods have been used to study the reaction mechanism of acidcatalyzed addition of water to formaldehyde in a model system of an aqueous solution of sulfuric acid. Using the method of constraints we find that an H

  20. Ab initio study of energy-level alignments in polymer-dye blends

    NARCIS (Netherlands)

    Pasveer, W.F.; Bobbert, P.A.; Michels, M.A.J.; Langeveld-Voss, B.M.W.; Schoo, H.F.M.; Bastiaansen, J.J.A.M.

    2003-01-01

    Polymers with a small amount of dye blended in offer an attractive possibility to change the color of the emitted light by changing the dye. We present ab initio calculations within density-functional theory of the HOMO/ LUMO energies for dipyrrolomethane dyes, polyphenylenevinylene and

  1. Gas phase ion chemistry of coumarins: ab initio calculations used to ...

    African Journals Online (AJOL)

    The gas phase ion chemistry of coumarins using electron ionization (EI), positive chemical ionization (PCI) and negative chemical ionization (NCI) in a time of flight and quadrupole mass spectrometer (qMS) coupled to a gas chromatograph is outlined. The observations in NCI mode were complimented with Ab initio ...

  2. Ab initio study on the paths of oxygen abstraction of hydrogen trioxide

    Indian Academy of Sciences (India)

    This means that the importance of SO2 + HO3 → SO3 (D3h) + HOO• reaction increases with increasing temperature and, this reaction plays an important role in the SO3(D3h) production as the main molecule of the formation of acid rain at high temperatures. Keywords. Ab initio calculations; atmospheric chemistry; hydrogen ...

  3. All electron ab initio investigations of the electronic states of the FeC molecule

    DEFF Research Database (Denmark)

    Shim, Irene; Gingerich, Karl A.

    1999-01-01

    The low lying electronic states of the molecule FeC have been investigated by performing all electron ab initio multi-configuration self-consistent-field (CASSCF) and multi reference configuration interaction (MRCI) calculations. The relativistic corrections for the one electron Darwin contact te...

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

    NARCIS (Netherlands)

    Zhang, X.; Sluiter, M.H.F.

    2015-01-01

    Vacancy properties in concentrated alloys continue to be of great interest because nowadays ab initio supercell simulations reach a scale where even defect properties in disordered alloys appear to be within reach. We show that vacancy properties cannot generally be extracted from supercell total

  5. Pressure induced structural phase transition in SnS—An ab initio study

    Indian Academy of Sciences (India)

    Unknown

    25. Pressure induced structural phase transition in SnS—An ab initio study. M RAJAGOPALAN*, G KALPANA and V PRIYAMVADHA. Department of Physics, Anna University, Chennai 600 025, India. MS received 21 June 2005; revised 16 November 2005. Abstract. The structural behaviour of SnS under pressure has been ...

  6. Advances in the ab initio description of nuclear three-cluster systems

    Directory of Open Access Journals (Sweden)

    Romero-Redondo Carolina

    2016-01-01

    Full Text Available We introduce the extension of the ab initio no-core shell model with continuum to describe three-body cluster systems. We present results for the ground state of 6He and show improvements with respect to the description obtained within the no-core shell model and the no-core shell model/resonating group methods.

  7. Sphinx: merging knowledge-based and ab initio approaches to improve protein loop prediction.

    Science.gov (United States)

    Marks, Claire; Nowak, Jaroslaw; Klostermann, Stefan; Georges, Guy; Dunbar, James; Shi, Jiye; Kelm, Sebastian; Deane, Charlotte M

    2017-05-01

    Loops are often vital for protein function, however, their irregular structures make them difficult to model accurately. Current loop modelling algorithms can mostly be divided into two categories: knowledge-based, where databases of fragments are searched to find suitable conformations and ab initio, where conformations are generated computationally. Existing knowledge-based methods only use fragments that are the same length as the target, even though loops of slightly different lengths may adopt similar conformations. Here, we present a novel method, Sphinx, which combines ab initio techniques with the potential extra structural information contained within loops of a different length to improve structure prediction. We show that Sphinx is able to generate high-accuracy predictions and decoy sets enriched with near-native loop conformations, performing better than the ab initio algorithm on which it is based. In addition, it is able to provide predictions for every target, unlike some knowledge-based methods. Sphinx can be used successfully for the difficult problem of antibody H3 prediction, outperforming RosettaAntibody, one of the leading H3-specific ab initio methods, both in accuracy and speed. Sphinx is available at http://opig.stats.ox.ac.uk/webapps/sphinx. deane@stats.ox.ac.uk. Supplementary data are available at Bioinformatics online.

  8. Ab Initio Molecular Orbital Studies on the Active Site of Papain

    NARCIS (Netherlands)

    Broer, Ria; Duijnen, P.Th. van; Nieuwpoort, W.C.

    1976-01-01

    Ab initio molecular orbital calcuiations using a contracted basis of gaussian orbitals on the system methanethiol/imidazole are reported. For the hydrogen bond S---H---N in this system, which was chosen as a model for the active site of papain, a double-well potential was found at a S-N separation

  9. Steel — ab Initio: Quantum Mechanics Guided Design of New Fe-Based Materials

    Science.gov (United States)

    Prahl, Ulrich; Bleck, Wolfgang; Saeed-Akbari, Alireza

    This contribution reports the results of the collaborative research unit SFB 761 "Steel — ab initio", a cooperative project between RWTH Aachen University and the Max-Planck-Institute for Iron Research in Düsseldorf (MPIE) financed by the German Research Foundation (DFG). For the first time, it is exploited how ab initio approaches may lead to a detailed understanding and thus to a specific improvement of material development. The challenge lies in the combination of abstract natural science theories with rather engineering-like established concepts. Aiming at the technological target of the development of a new type of structural materials based on Fe-Mn-C alloys, the combination of ab initio and engineering methods is new, but could be followed quite successfully. Three major topics are treated in this research unit: a) development of a new method for material- and process-development based on ab initio calculations; b) design of a new class of structural materials with extraordinary property combinations; c) acceleration of development time and reduction of experimental efforts and complexity for material- and process-development. In the present work, an overview of the results of the first five years as well as an outlook for the upcoming three-year period is given.

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

    DEFF Research Database (Denmark)

    Castelli, Ivano E.; Salvestrini, Paolo; Manini, Nicola

    2012-01-01

    As sp carbon chains (carbynes) are relatively rigid molecular objects, can we exploit them as construction elements in nanomechanics? To answer this question, we investigate their remarkable mechanical properties by ab initio total-energy simulations. In particular, we evaluate their linear...

  11. Ab initio study of spin-dependent transport in carbon nanotubes with iron and vanadium adatoms

    DEFF Research Database (Denmark)

    Fürst, Joachim Alexander; Brandbyge, Mads; Jauho, Antti-Pekka

    2008-01-01

    We present an ab initio study of spin-dependent transport in armchair carbon nanotubes with transition metal adsorbates: iron or vanadium. The method based on density functional theory and nonequilibrium Green's functions is used to compute the electronic structure and zero-bias conductance. The ...

  12. All-electron ab initio investigations of the electronic states of the NiC molecule

    DEFF Research Database (Denmark)

    Shim, Irene; Gingerich, Karl. A.

    1999-01-01

    The low-lying electronic states of NiC are investigated by all-electron ab initio multi-configuration self-consistent-field (CASSCF) calculations including relativistic corrections. The electronic structure of NiC is interpreted as perturbed antiferromagnetic couplings of the localized angular...

  13. One Size Fits All? Learning Conditions and Working Memory Capacity in "Ab Initio" Language Development

    Science.gov (United States)

    Sanz, Cristina; Lin, Hui-Ju; Lado, Beatriz; Stafford, Catherine A.; Bowden, Harriet W.

    2016-01-01

    The article summarizes results from two experimental studies (N = 23, N = 21) investigating the extent to which working memory capacity (WMC) intervenes in "ab initio" language development under two pedagogical conditions [± grammar lesson + input-based practice + explicit feedback]. The linguistic target is the use of morphosyntax to…

  14. Precise Ab-initio prediction of terahertz vibrational modes in crystalline systems

    DEFF Research Database (Denmark)

    Jepsen, Peter Uhd; Clark, Stewart J.

    2007-01-01

    We use a combination of experimental THz time-domain spectroscopy and ab-initio density functional perturbative theory to accurately predict the terahertz vibrational spectrum of molecules in the crystalline phase. Our calculations show that distinct vibrational modes found in solid-state materials...

  15. Ab initio Defect Energetics in LaBO3 Perovskite Solid Oxide Fuel Cell Materials

    DEFF Research Database (Denmark)

    Lee, Yueh-Lin; Morgan, Dane; Kleis, Jesper

    2009-01-01

    Perovskite materials of the form ABO3 are a promising family of compounds for use in solid oxide fuel cell (SOFC) cathodes. Study of the physics of these compounds under SOFC conditions with ab initio methods is particularly challenging due to high temperatures, exchange of oxygen with O2 gas...

  16. Ab initio study of solute transition-metal interactions with point defects in bcc Fe

    NARCIS (Netherlands)

    Olsson, P.; Klaver, T.P.C.; Domain, C.

    2010-01-01

    The properties of 3d, 4d, and 5d transition-metal elements in ?-Fe have been studied using ab initio density-functional theory. The intrinsic properties of the solutes have been characterized as well as their interaction with point defects. Vacancies and interstitials of (110) and (111) orientations

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

    DEFF Research Database (Denmark)

    Kreitmeir, M.; Bertagnolli, H.; Mortensen, Jens Jørgen

    2003-01-01

    Liquid hydrogen fluoride is a simple but interesting system for studies of the influence of hydrogen bonds on physical properties. We have performed ab initio molecular dynamics simulations of HF at several thermodynamic states, where we examine the microscopic structure of the liquid as well...

  18. Ab initio treatment of ion-water molecule collisions with a three-center pseudo potential

    OpenAIRE

    Martínez, Pablo A.; Errea, L. F.; Méndez, Laura González; Rabadán, Ismanuel

    2012-01-01

    We calculate electron capture cross sections in collisions of protons with water molecules, using two simple ab initio approaches. The formalism involves the calculation of one-electron scattering wave functions and the use of three-center pseudo potential to represent the electron H2O+ interaction. Several methods to obtain many-electron cross sections are considered

  19. An ab initio SCF calculation of the polarizability tensor of sulphur dioxide

    Science.gov (United States)

    Bacskay, George G.

    1983-08-01

    The principal components of the static electric dipole polarizability have been calculated by an ab initio coupled perturbed Hartree-Fock (CPHF) method. The calculated components are sufficiently accurate so that a choice can be made between the two different sets of experimentally consistent values in favor of the negative anisotropy parameter αxx-ᾱ.

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

    Science.gov (United States)

    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.

  1. Limitations of Ab Initio Predictions of Peptide Binding to MHC Class II Molecules

    DEFF Research Database (Denmark)

    Zhang, Hao; Lund, Ole; Nielsen, Morten

    2010-01-01

    potentials derived from the analysis of known protein structures; energetic evaluation of different peptide snapshots in a molecular dynamics simulation; and direct analysis of contacts made in known 3D structures of peptide:MHC complexes. These methods are ab initio in that they require structural data...

  2. Hexamethylcyclopentadiene: time-resolved photoelectron spectroscopy and ab initio multiple spawning simulations

    DEFF Research Database (Denmark)

    Wolf, T. J. A.; Kuhlman, Thomas Scheby; Schalk, O.

    2014-01-01

    comparing time-resolved photoelectron spectroscopy (TRPES) with ab initio multiple spawning (AIMS) simulations on the MS-MR-CASPT2 level of theory. We disentangle the relationship between two phenomena that dominate the immediate molecular response upon light absorption: a spectrally dependent delay...

  3. Ab initio energetics of LaBO3(001) (B=Mn, Fe, Co, and Ni) for solid oxide fuel cell cathodes

    DEFF Research Database (Denmark)

    Lee, Yueh-Lin; Kleis, Jesper; Rossmeisl, Jan

    2009-01-01

    LaBO3 (B=Mn, Fe, Co, and Ni) perovskites form a family of materials of significant interest for cathodes of solid oxide fuel cells (SOFCs). In this paper ab initio methods are used to study both bulk and surface properties of relevance for SOFCs, including vacancy formation and oxygen binding ene...

  4. Analysis of some conventional ab initio gene finders using human ...

    African Journals Online (AJOL)

    Yomi

    2012-01-24

    Jan 24, 2012 ... using human and mouse DNA sequences .... two different levels: coding nucleotide sequence and exonic .... Table 3. Predicted number of exons in each class on multi-exon genes in three .... measures, hexamer frequency, usually in the form of ..... combination of gene prediction results from multiple ab.

  5. GAS PHASE ION CHEMISTRY OF COUMARINS: AB INITIO ...

    African Journals Online (AJOL)

    B. S. Chandravanshi

    ABSTRACT. The gas phase ion chemistry of coumarins using electron ionization (EI), positive chemical ionization (PCI) and negative chemical ionization (NCI) in a time of flight and quadrupole mass spectrometer. (qMS) coupled to a gas chromatograph is outlined. The observations in NCI mode were complimented with Ab.

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

    Science.gov (United States)

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

    2009-05-14

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

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

    Science.gov (United States)

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

    2015-05-01

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

  8. A Review of Solid-Solution Models of High-Entropy Alloys Based on Ab Initio Calculations

    Directory of Open Access Journals (Sweden)

    Fuyang Tian

    2017-11-01

    Full Text Available Similar to the importance of XRD in experiments, ab initio calculations, as a powerful tool, have been applied to predict the new potential materials and investigate the intrinsic properties of materials in theory. As a typical solid-solution material, the large degree of uncertainty of high-entropy alloys (HEAs results in the difficulty of ab initio calculations application to HEAs. The present review focuses on the available ab initio based solid-solution models (virtual lattice approximation, coherent potential approximation, special quasirandom structure, similar local atomic environment, maximum-entropy method, and hybrid Monte Carlo/molecular dynamics and their applications and limits in single phase HEAs.

  9. Serious Gaming for Test & Evaluation of Clean-Slate (Ab Initio) National Airspace System (NAS) Designs

    Science.gov (United States)

    Allen, B. Danette; Alexandrov, Natalia

    2016-01-01

    Incremental approaches to air transportation system development inherit current architectural constraints, which, in turn, place hard bounds on system capacity, efficiency of performance, and complexity. To enable airspace operations of the future, a clean-slate (ab initio) airspace design(s) must be considered. This ab initio National Airspace System (NAS) must be capable of accommodating increased traffic density, a broader diversity of aircraft, and on-demand mobility. System and subsystem designs should scale to accommodate the inevitable demand for airspace services that include large numbers of autonomous Unmanned Aerial Vehicles and a paradigm shift in general aviation (e.g., personal air vehicles) in addition to more traditional aerial vehicles such as commercial jetliners and weather balloons. The complex and adaptive nature of ab initio designs for the future NAS requires new approaches to validation, adding a significant physical experimentation component to analytical and simulation tools. In addition to software modeling and simulation, the ability to exercise system solutions in a flight environment will be an essential aspect of validation. The NASA Langley Research Center (LaRC) Autonomy Incubator seeks to develop a flight simulation infrastructure for ab initio modeling and simulation that assumes no specific NAS architecture and models vehicle-to-vehicle behavior to examine interactions and emergent behaviors among hundreds of intelligent aerial agents exhibiting collaborative, cooperative, coordinative, selfish, and malicious behaviors. The air transportation system of the future will be a complex adaptive system (CAS) characterized by complex and sometimes unpredictable (or unpredicted) behaviors that result from temporal and spatial interactions among large numbers of participants. A CAS not only evolves with a changing environment and adapts to it, it is closely coupled to all systems that constitute the environment. Thus, the ecosystem that

  10. Scattering study of the Ne + NeH{sup +}(v{sub 0} = 0, j{sub 0} = 0) → NeH{sup +} + Ne reaction on an ab initio based analytical potential energy surface

    Energy Technology Data Exchange (ETDEWEB)

    Koner, Debasish; Panda, Aditya N., E-mail: adi07@iitg.ernet.in [Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781039 (India); Barrios, Lizandra; González-Lezana, Tomás, E-mail: t.gonzalez.lezana@csic.es [IFF-CSIC, Instituto de Física Fundamental, CSIC, Serrano 123, Madrid 28006 (Spain)

    2016-01-21

    Initial state selected dynamics of the Ne + NeH{sup +}(v{sub 0} = 0, j{sub 0} = 0) → NeH{sup +} + Ne reaction is investigated by quantum and statistical quantum mechanical (SQM) methods on the ground electronic state. The three-body ab initio energies on a set of suitably chosen grid points have been computed at CCSD(T)/aug-cc-PVQZ level and analytically fitted. The fitting of the diatomic potentials, computed at the same level of theory, is performed by spline interpolation. A collinear [NeHNe]{sup +} structure lying 0.72 eV below the Ne + NeH{sup +} asymptote is found to be the most stable geometry for this system. Energies of low lying vibrational states have been computed for this stable complex. Reaction probabilities obtained from quantum calculations exhibit dense oscillatory structures, particularly in the low energy region and these get partially washed out in the integral cross section results. SQM predictions are devoid of oscillatory structures and remain close to 0.5 after the rise at the threshold thus giving a crude average description of the quantum probabilities. Statistical cross sections and rate constants are nevertheless in sufficiently good agreement with the quantum results to suggest an important role of a complex-forming dynamics for the title reaction.

  11. Oxygen adsorption on beta-cristobalite polymorph: ab initio modeling and semiclassical time-dependent dynamics.

    Science.gov (United States)

    Rutigliano, M; Zazza, C; Sanna, N; Pieretti, A; Mancini, G; Barone, V; Cacciatore, M

    2009-12-31

    The adsorption dynamics of atomic oxygen on a model beta-cristobalite silica surface has been studied by combining ab initio electronic structure calculations with a molecular dynamics semiclassical approach. We have evaluated the interaction potential of atomic and molecular oxygen interacting with an active Si site of a model beta-cristobalite surface by performing DFT electronic structure calculations. As expected, O is strongly chemisorbed, E(b) = 5.57 eV, whereas molecular oxygen can be weakly adsorbed with a high-energy barrier to the adsorption state of approximately 2 eV. The binding energies calculated for silica clusters of different sizes have revealed the local nature of the O,O(2)-silica interaction. Semiclassical collision dynamic calculations show that O is mainly adsorbed in single-bounce collisions, with a smaller probability for adsorption via a multicollision mechanism. The probability for adsorption/desorption (reflected) collisions at the three impact energies is small but not negligible at the higher energy considered in the trajectory calculations, about P(r) = 0.2 at E(kin) = 0.8 eV. The calculations give evidence of a complex multiphonon excitation-deexcitation mechanism underlying the dynamics of stable adsorption and inelastic reflection collisions.

  12. Dissolution of NaCl nanocrystals: an ab initio molecular dynamics study.

    Science.gov (United States)

    Holmberg, Nico; Chen, Jian-Cheng; Foster, Adam S; Laasonen, Kari

    2014-09-07

    The dissolution of NaCl has been systematically investigated by employing ab initio molecular dynamics (AIMD) on different NaCl nanocrystals as well as on a surface system immersed in water. We discovered a complex dissolution process simultaneously involving multiple ions initiated at the corner sites of the crystal. Our simulations indicated a difference in the dissolution rates of sodium and chlorine. While sodiums readily became partially solvated, chlorines more frequently transitioned into the fully solvated state leading to an overall greater dissolution rate for Cl. We determined that this difference arises due to faster water mediated elongations of individual ionic bonds to Na, but a significantly slower process for the last bond in comparison to Cl. In an attempt to investigate this phenomenon further, we performed metadynamics based free energy simulations on a surface slab presenting corner sites similar to those in cubic crystals, aiming to extract the dissolution free energy profile of corner ions. In qualitative agreement with the nanocrystal simulations, this revealed a shallower first free energy minimum for Na, but no statistically significant difference in the corresponding barriers and inconclusive results for the latter stage. Finally, simulations of smaller NaCl crystals illustrated how dissolution proceeds beyond the point of crystal lattice collapse, highlighting the strength of solvated ion interactions.

  13. Ab initio ro-vibronic spectroscopy of SiCCl (X{sup ~2}Π)

    Energy Technology Data Exchange (ETDEWEB)

    Brites, Vincent [Université d’Evry Val d’Essonne, Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, LAMBE CNRS UMR 8587, Boulevard F. Mitterrand, 91025 Evry Cedex (France); Mitrushchenkov, Alexander O.; Léonard, Céline, E-mail: celine.leonard@u-pem.fr [Université Paris-Est, Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, 5 bd Descartes, 77454 Marne-la-Vallée (France); Peterson, Kirk A. [Department of Chemistry, Washington State University, Pullman, Washington 99164 (United States)

    2014-07-21

    The full dimensional potential energy surfaces of the {sup 2}A{sup ′} and {sup 2}A{sup ′′} electronic components of X{sup ~2}Π SiCCl have been computed using the explicitly correlated coupled cluster method, UCCSD(T)-F12b, combined with a composite approach taking into account basis set incompleteness, core-valence correlation, scalar relativity, and higher order excitations. The spin-orbit and dipole moment surfaces have also been computed ab initio. The ro-vibronic energy levels and absorption spectrum at 5 K have been determined from variational calculations. The influence of each correction on the fundamental frequencies is discussed. An assignment is proposed for bands observed in the LIF experiment of Smith et al. [J. Chem. Phys. 117, 6446 (2002)]. The overall agreement between the experimental and calculated ro-vibronic levels is better than 7 cm{sup −1} which is comparable with the 10–20 cm{sup −1} resolution of the emission spectrum.

  14. Ab initio atomic thermodynamics investigation on oxygen defects in the anatase TiO{sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Cheng, Zhijun [College of Science, University of Shanghai for Science and Technology, Shanghai 200093 (China); Liu, Tingyu, E-mail: liutyyxj@163.com [College of Science, University of Shanghai for Science and Technology, Shanghai 200093 (China); Yang, Chenxing; Gan, Haixiu [College of Science, University of Shanghai for Science and Technology, Shanghai 200093 (China); Chen, Jianyu [Key Laboratory of Materials for High Power Laser, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai 201800 (China); Zhang, Feiwu [Nanochemistry Research Institute, Curtin University, GPO Box U1987, Perth, WA 6845 (Australia)

    2013-01-05

    Highlights: Black-Right-Pointing-Pointer Three typical oxygen defects under the different annealing conditions have been studied. Black-Right-Pointing-Pointer The oxygen vacancy is easier to form at the surface than in the bulk. Black-Right-Pointing-Pointer The adsorption of O{sub 2} whose orientation is parallel to the surface should be more favorable. Black-Right-Pointing-Pointer The reduction reaction may firstly undertake at the surface during the annealing treatment. Black-Right-Pointing-Pointer The interstitial oxygen has important contribution to lead to the reduction of the band gap. - Abstract: In the framework of the ab initio atomic thermodynamics, the preliminary analysis of the oxygen defects in anatase TiO{sub 2} has been done by investigating the influence of the annealing treatment under representative conditions on three typical oxygen defects, that is, oxygen vacancy, oxygen adsorption and oxygen interstitial. Our results in this study agree well with the related experimental results. The molecular species of the adsorbed O{sub 2} is subject to the ratio of the number of the O{sub 2} to that of the vacancy, as well as to the initial orientation of O{sub 2} relative to the surface (101). Whatever the annealing condition is, the oxygen vacancy is easier to form at the surface than in the bulk indicating that the reduction reaction may firstly undertake at the surface during the annealing treatment, which is consistent with the phase transformation experiments. The molecular ion, peroxide species, caused by the interstitial oxygen has important contribution to the top of the valence band and lead to the reduction of the band gap.

  15. Ab initio quantum-enhanced optical phase estimation using real-time feedback control

    DEFF Research Database (Denmark)

    Berni, Adriano; Gehring, Tobias; Nielsen, Bo Melholt

    2015-01-01

    as demonstrated in a variety of different optical systems(3-8). Most of these accounts, however, deal with the measurement of a very small shift of an already known phase, which is in stark contrast to ab initio phase estimation where the initial phase is unknown(9-12). Here, we report on the realization...... of a quantum-enhanced and fully deterministic ab initio phase estimation protocol based on real-time feedback control. Using robust squeezed states of light combined with a real-time Bayesian adaptive estimation algorithm, we demonstrate deterministic phase estimation with a precision beyond the quantum shot...... noise limit. The demonstrated protocol opens up new opportunities for quantum microscopy, quantum metrology and quantum information processing....

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

    DEFF Research Database (Denmark)

    Fürst, Joachim Alexander; Brandbyge, Mads; Jauho, Antti-Pekka

    2010-01-01

    An atomic carbon chain joining two graphene flakes was recently realized in a ground-breaking experiment by Jin et al. (Phys. Rev. Lett., 102 (2009) 205501). We present ab initio results for the electron transport properties of such chains and demonstrate complete spin-polarization of the transmi......An atomic carbon chain joining two graphene flakes was recently realized in a ground-breaking experiment by Jin et al. (Phys. Rev. Lett., 102 (2009) 205501). We present ab initio results for the electron transport properties of such chains and demonstrate complete spin......-polarization of the transmission in large energy ranges. The effect is due to the spin-polarized zig-zag edge terminating each graphene flake causing a spin-splitting of the graphene pi(z) bands, and the chain states. Transmission occurs when the graphene p-states resonate with similar states in the strongly hybridized edges...

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

    Energy Technology Data Exchange (ETDEWEB)

    Rio, B. G. del; González, L. E. [Departamento de Física Teórica, Atómica y Óptica, Universidad de Valladolid, 47011 Valladolid (Spain)

    2015-08-17

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

  18. Electronic structure of the Ca3Co4O9 compound from ab initio local interactions

    Science.gov (United States)

    Soret, Julien; Lepetit, Marie-Bernadette

    2012-04-01

    We used fully correlated ab initio calculations to determine the effective parameters of Hubbard and t-J models for the thermoelectric misfit compound Ca3Co4O9. As for the NaxCoO2 family, the Fermi level orbitals are the a1g orbitals of the cobalt atoms; the eg' being always lower in energy by more than 240 meV. The electron correlation is found very large U/t˜26 as well as the parameters fluctuations as a function of the structural modulation. The main consequences are a partial a1g electrons localization and a fluctuation of the in-plane magnetic exchange from antiferromagnetic to ferromagnetic. The behavior of the Seebeck coefficient and the figure of merit are discussed in view of the ab initio results, as well as the 496 K phase transition.

  19. Constrained dynamics and extraction of normal modes from ab initio molecular dynamics: application to ammonia.

    Science.gov (United States)

    Siddick, M M; Ackland, G J; Morrison, C A

    2006-08-14

    We present a methodology for extracting phonon data from ab initio Born-Oppenheimer molecular dynamics calculations of molecular crystals. Conventional ab initio phonon methods based on perturbations are difficult to apply to lattice modes because the perturbation energy is dominated by intramolecular modes. We use constrained molecular dynamics to eliminate the effect of bond bends and stretches and then show how trajectories can be used to isolate and define in particular, the eigenvalues and eigenvectors of modes irrespective of their symmetry or wave vector. This is done by k-point and frequency filtering and projection onto plane wave states. The method is applied to crystalline ammonia: the constrained molecular dynamics allows a significant speed-up without affecting structural or vibrational modes. All Gamma point lattice modes are isolated: the frequencies are in agreement with previous studies; however, the mode assignments are different.

  20. CONFORMATIONAL EQUILIBRIUM AND SPECTROSCOPIC PROPERTIES OF CALIX[4]ARENE: THEORETICAL STUDY USING AB INITIO METHOD

    Directory of Open Access Journals (Sweden)

    Hanggara Sudrajat

    2010-06-01

    Full Text Available Molecular structures were optimized for the calix[4]arene by ab initio method at the Hartree-Fock level of theory using LANL2DZ and 6-311G basis sets. Conformational equilibrium of four calix[4]arene conformers are reported. The results are compared with experiment, force field, and semiempirical molecular orbital calculations. General trends in relative stabilities of calix[4]arene decrease in following order: cone > partial-cone > 1,2-alternate > 1,3-alternate. The most stable conformer is the cone conformer that is stabilized by an array of four hydrogen bonds and these results agree with the reported experimental observations. All structures were analyzed using theoretical IR, UV-Vis, and 1H NMR spectra attributed to the conformational equilibrium at the Hartree-Fock level of theory using LANL2DZ basis set.     Keywords: ab initio calculation, calix[4]arene, conformations, cone

  1. Ab initio calculations on the magnetic properties of transition metal complexes

    Energy Technology Data Exchange (ETDEWEB)

    Bodenstein, Tilmann; Fink, Karin [Karlsruhe Institute of Technology, Institute of Nanotechnology, POB 3640, 76021 Karlsruhe (Germany)

    2015-12-31

    We present a protocol for the ab initio determination of the magnetic properties of mono- and polynuclear transition metal compounds. First, we obtain the low lying electronic states by multireference methods. Then, we include spin-orbit coupling and an external magnetic field for the determination of zero-field splitting and g-tensors. For the polynuclear complexes the magnetic exchange coupling constants are determined by a modified complete active space self consistent field method. Based on the results of the ab initio calculations, magnetic data such as magnetic susceptibility or magnetization are simulated and compared to experimental data. The results obtained for the polynuclear complexes are further analysed by calculations on model complexes where part of the magnetic centers are substituted by diamagnetic ions. The methods are applied to different Co and Ni containing transition metal complexes.

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

    Energy Technology Data Exchange (ETDEWEB)

    Halasyamani, Shiv [Univ. of Houston, TX (United States); Fennie, Craig [Cornell Univ., Ithaca, NY (United States)

    2016-11-03

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

  3. Ab initio molecular dynamics with nuclear quantum effects at classical cost: ring polymer contraction for density functional theory

    CERN Document Server

    Marsalek, Ondrej

    2015-01-01

    Path integral molecular dynamics simulations, combined with an ab initio evaluation of interactions using electronic structure theory, incorporate the quantum mechanical nature of both the electrons and nuclei, which are essential to accurately describe systems containing light nuclei. However, path integral simulations have traditionally required a computational cost around two orders of magnitude greater than treating the nuclei classically, making them prohibitively costly for most applications. Here we show that the cost of path integral simulations can be dramatically reduced by extending our ring polymer contraction approach to ab initio molecular dynamics simulations. By using density functional tight binding as a reference system, we show that our ab initio ring polymer contraction (AI-RPC) scheme gives rapid and systematic convergence to the full path integral density functional theory result. We demonstrate the efficiency of this approach in ab initio simulations of liquid water and the reactive pro...

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

    Science.gov (United States)

    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

  5. Speciation of magnesium in monohydrocalcite: XANES, ab initio and geochemical modeling

    Science.gov (United States)

    Fukushi, Keisuke; Suzuki, Yuma; Kawano, Jun; Ohno, Takeshi; Ogawa, Masahiro; Yaji, Toyonari; Takahashi, Yoshio

    2017-09-01

    Monohydrocalcite (MHC: CaCO3·H2O), a rare carbonate mineral formed under surface conditions, is usually observed in nature as containing a variable amount of Mg, with a 0.007-0.45 Mg/Ca mole ratio. The variable Mg composition in MHC is anticipated as a promising proxy to assess paleo-hydrochemistry especially in saline lakes. Although the roles of Mg on the formation and stability of MHC have been studied intensively, the Mg speciation in MHC has remained unclear and controversial. This study examined Mg speciation in MHC using X-ray absorption near edge structure (XANES), ab initio molecular simulation, and geochemical modeling. Mg-XANES spectra of MHC with different Mg/Ca ratios prepared from mixing solutions of Na2CO3, CaCl2 and MgCl2 revealed that the Mg in MHC is a mixture of amorphous Mg carbonate (AMC) and other Mg containing phase. The contribution of AMC to total Mg is negatively correlated to the crystallinity of MHC. Results show that AMC might play a protective role in the crystallization and the transformation to stable calcium carbonates. Ab initio calculation of Mg2+ substitution into MHC showed that a limited amount of Mg2+ can be incorporated into the MHC structure. Six-fold coordination of Mg2+ is substituted for eight-fold coordination of Ca2+ in the MHC structure. The other type of Mg in MHC revealed from the XANES analyses most likely corresponds to the structural Mg in MHC. The contribution of the structural Mg is almost constant at 0.06 in Mg/Ca, representing the limit of solid solubility of Mg in MHC. The solubility products of the MHC with the limit of solid solubility of Mg and the AMC associated with MHC were estimated from the reacted solution compositions. Prediction of the Mg/Ca ratio as a function of the initial solution conditions using solubility reasonably reproduces the observed apparent Mg/Ca ratios in MHC from the present study and earlier studies. The apparent Mg/Ca ratio of MHC is useful to elucidate water chemistry

  6. The electronic structure of LaO: Ligand field versus ab initio calculations

    Science.gov (United States)

    Schamps, Joël; Bencheikh, Mohammed; Barthelat, Jean-Claude; Field, Robert W.

    1995-11-01

    The potentially pathological example of LaO has been chosen to test the application of ligand field theory (LFT) to metal monoxides. The test consists of a comparison of closed-shell ligand LFT (CSLLFT) results (in which a 2+/2- ionic M2+O2- model is a priori postulated with a point-charge ligand) against ab initio multiconfiguration self-consistent-field-multireference configuration interaction (MCSCF-MRCI) results (in which no ionicity is assumed a priori and an internal structure is allowed for the ligand). Special care has been devoted to the determination of a La3+ pseudopotential and its associated atomic basis set in order to keep the ab initio model close to the LFT one, yet at the same time capable of clearly exhibiting the consequences and the importance of the restrictions imposed in the CSLLFT model. The ab initio calculations reveal that the effective (Mulliken) ionicity in LaO is not La2+O2- but quite close to La+O-. Despite this, the (2+/2-) ionic CSLLFT model leads to the correct orbital occupations in the ground state but this model cannot account for the significant covalency contribution via the nominal 2pσ and 2pπ oxygen orbitals. The CSLLFT calculations correctly reproduce the excitation energies of the four lowest-lying observed states of LaO: these states are calculated to within 2000 cm-1 and globally better than via ab initio calculations. However, the (2+/2-) ionic CSLLFT model is shown to ignore the existence of a manifold of low-lying quartet (and doublet) states of (1+/1-) ionicity that might be relevant for interpreting features of the spectrum. This result exemplifies the need for developing, beyond the first attempts made in this direction, a computationally manageable open-shell ligand theory for the frequently encountered case of predominantly ionic structures with an open-shell ligand.

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

    DEFF Research Database (Denmark)

    Rosengaard, N. M.; Skriver, Hans Lomholt

    1994-01-01

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

  8. Ab initio study of the electronic spectrum of BeO

    Directory of Open Access Journals (Sweden)

    MILJENKO PERIC

    1999-12-01

    Full Text Available Low-lying singlet and triplet electronic states of the BeO molecule are calculated by means of the quantum chemical ab initio method. It was found that all states in the energy range from 0 to 50000 cm-1 are of valence character. Particular attention was paid to the investigation of the dissociative behavior of the states considered. The vibrational structure of the AIP<-XIS and BIS+<-XIS+ spectral systems was calculated.

  9. Initial Chemical Events in CL-20 Under Extreme Conditions: An Ab Initio Molecular Dynamics Study

    Science.gov (United States)

    2006-11-01

    established the existence of four CL-20 polymorphs and they have been studied (Foltz et al., 1994; Politzer 1991). Fourier Transform Raman Spectroscopy...1,3,5,7- tetrazocine ( HMX ) (Chakraborty et al., 2001; Zhang, 2003; Lewis et al., 2000; Manaa, 2002) have been also predicted using ab initio levels...cage, the differences in crystal lattice packing, and the number of molecules per unit cell define four possible polymorphs [16-18,23]. Among them

  10. Electric-field control of magnetism in graphene quantum dots: Ab initio calculations

    OpenAIRE

    Agapito, Luis A.; Kioussis, Nicholas; Kaxiras, Efthimios

    2010-01-01

    Employing ab initio calculations we predict that the magnetic states of hydrogenated diamond-shaped zigzag graphene quantum dots (GQDs), each exhibiting unique electronic structure, can be selectively tuned with gate voltage, through Stark or hybridization electric-field modulation of the spatial distribution and energy of the spin-polarized molecular orbitals, leading to transitions between these states. Electrical read-out of the GQD magnetic state can be accomplished by exploiting the dist...

  11. Electric-field control of magnetism in graphene quantum dots: Ab initio calculations.

    Science.gov (United States)

    Agapito, Luis A; Kioussis, Nicholas; Kaxiras, Efthimios

    2010-11-23

    Employing ab initio calculations we predict that the magnetic states of hydrogenated diamond-shaped zigzag graphene quantum dots (GQDs), each exhibiting unique electronic structure, can be selectively tuned with gate voltage, through Stark or hybridization electric-field modulation of the spatial distribution and energy of the spin-polarized molecular orbitals, leading to transitions between these states. Electrical read-out of the GQD magnetic state can be accomplished by exploiting the distinctive electrical properties of the various magnetic configurations.

  12. Ab Initio Study of Atropisomers of Derivatives of N-Benzyl-2-phenylpyridinium Ions

    Directory of Open Access Journals (Sweden)

    Firouzeh Nemati

    2012-01-01

    Full Text Available Ab initio calculation at RHF/6-31G* level of theory for geometry optimization of conformers of N-benzyl-2-phenylpyridinium ions are reported. The series of electron-withdrawing and electron-donating groups have been replaced by 3-H phenyl and benzyl of N-benzyl-2-phenylpyridinium ions and the energy difference between the syn- and anti- forms discussed in terms of π-π stacking.

  13. Transformation of ab initio force fields in calculations of molecular vibrations using regundand vibrational coordinates

    Science.gov (United States)

    Pitsevich, G. A.; Kostopravova, A. V.; Umreiko, D. S.; Ksenofontov, M. A.

    2011-11-01

    A technique was suggested to transform ab initio molecular force fields calculated using a set of independent vibrational coordinates into a form corresponding to a complete set of regundand coordinates and reflecting the molecular symmetry. Conditions necessary for the appropriate transformations to be possible are formulated. The possibility of transforming the force field for the simplest fragment containing regundand coordinates was demonstrated using ethylene as an example.

  14. Mechanics properties of Mono-layer Hexagonal Boron Nitride: Ab initio study

    OpenAIRE

    Peng, Qing; Zamiri, Amir R.; De, Suvranu

    2011-01-01

    We introduced a method to obtain the continuum description of the elastic properties of mono- layer h-BN through ab initio density functional theory. This thermodynamically rigorous contin- uum description of the elastic response is formulated by expanding the elastic strain energy density in a Taylor series in strain truncated after the fifth-order term. we obtained a total of fourteen nonzero independent elastic constants for the up to tenth-order tensor. We predicted the pressure dependent...

  15. Development of Ab-initio Multibody Energy Expansions for the Design of Metallic Materials with Extremal Properties

    Science.gov (United States)

    2010-10-31

    multiscale deformation processes", Computational Materias Science, Vol. 48, Issue 2, pp. 213--227, 2010 Zheng Li, Bin Wen and N. Zabaras, "Computing...expansions: An ab initio based transferable potential for computational thermodynamics", presented at the `Computational thermodynamics and kinetics...DD882) Inventions (DD882) Scientific Progress Technology Transfer 1 Development of ab-initio multibody energy expansions for the design of

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

    Directory of Open Access Journals (Sweden)

    Anne T. Tuukkanen

    2016-11-01

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

  17. Trapping of hydrogen and helium at dislocations in tungsten: an ab initio study

    Science.gov (United States)

    Bakaev, A.; Grigorev, P.; Terentyev, D.; Bakaeva, A.; Zhurkin, E. E.; Mastrikov, Yu. A.

    2017-12-01

    The interaction of H or He atoms with a core of edge and screw dislocations (SDs), with Burgers vector a 0/2≤ft , is studied by means of ab initio calculations. The results show that the edge dislocations are stronger traps for H and He compared to the SDs, while the H/He affinity to both types of dislocation is significantly weaker than to a single vacancy. The lowest energy atomic configurations are rationalized on the basis of the charge density distribution and elasticity theory considerations. The results obtained contribute to the rationalization of the thermal desorption spectroscopy analysis by attributing certain peaks of the release of plasma components to the detrapping from dislocations. Complementary molecular statics (MS) calculations are performed to validate the accuracy of the recently developed W-H-He embedded atom method (EAM) and bond-order potentials. It is revealed that the EAM potential can reproduce correctly the magnitude of the interaction of H with both dislocations as compared to the ab initio results. All the potentials underestimate significantly the He-dislocation interaction and cannot describe correctly the lowest energy positions for H and He around the dislocation core. The reason for the discrepancy between ab initio and the MS results is rationalized by the analysis of the fully relaxed atomic configurations.

  18. Cryospectroscopic and ab initio anharmonic studies of acetylene-trimethylamine H-bonded complex

    Science.gov (United States)

    Rutkowski, K. S.; Melikova, S. M.; Janski, J.; Koll, A.

    2010-09-01

    The FTIR spectra of C 2H 2 in mixtures with trimethylamine (TMA) have been studied in liquefied Kr in the frequency range of ˜800-7000 cm -1. The data obtained for C 2H 2 subunit suggest the formation of 1:1 complexes stabilized by a moderate strength conventional H-bond. CH and CN stretching vibrations, related to the vicinal bonds of proton acceptor, were found to shift in opposite directions - blue in the former and red in the latter case. New weak bands, revealed in the range of ˜6000-7000 cm -1, were ascribed to the overtone and combination bands of C sbnd H stretching vibrations of acetylene which participates in the H-bond formation. The relative stability of the complex has been determined in a series of temperature ( T = 118-157 K) measurements of integrated intensities of vibrational bands ascribed to monomer and complex species. Ab initio MP2/6-311++G(2d,2p) a priory counterpoise corrected calculations, made for acetylene, TMA, and the complex reproduce the main spectroscopic observations. They suggest that the most stable non-linear structure of the complex is very floppy. Evaluations of anharmonic effects on position and integrated intensity of selected bands of C sbnd H stretching modes of C 2H 2 subunit have been made within perturbation theory on the basis of single point potential energy surface (PES) and dipole moment function calculations.

  19. Nonequilibrium Chemical Effects in Single-Molecule SERS Revealed by Ab Initio Molecular Dynamics Simulations

    Energy Technology Data Exchange (ETDEWEB)

    Fischer, Sean A.; Apra, Edoardo; Govind, Niranjan; Hess, Wayne P.; El-Khoury, Patrick Z.

    2017-02-03

    Recent developments in nanophotonics have paved the way for achieving significant advances in the realm of single molecule chemical detection, imaging, and dynamics. In particular, surface-enhanced Raman scattering (SERS) is a powerful analytical technique that is now routinely used to identify the chemical identity of single molecules. Understanding how nanoscale physical and chemical processes affect single molecule SERS spectra and selection rules is a challenging task, and is still actively debated. Herein, we explore underappreciated chemical phenomena in ultrasensitive SERS. We observe a fluctuating excited electronic state manifold, governed by the conformational dynamics of a molecule (4,4’-dimercaptostilbene, DMS) interacting with a metallic cluster (Ag20). This affects our simulated single molecule SERS spectra; the time trajectories of a molecule interacting with its unique local environment dictates the relative intensities of the observable Raman-active vibrational states. Ab initio molecular dynamics of a model Ag20-DMS system are used to illustrate both concepts in light of recent experimental results.

  20. Ab initio quantum mechanical/molecular mechanical simulation of electron transfer process: fractional electron approach.

    Science.gov (United States)

    Zeng, Xiancheng; Hu, Hao; Hu, Xiangqian; Cohen, Aron J; Yang, Weitao

    2008-03-28

    Electron transfer (ET) reactions are one of the most important processes in chemistry and biology. Because of the quantum nature of the processes and the complicated roles of the solvent, theoretical study of ET processes is challenging. To simulate ET processes at the electronic level, we have developed an efficient density functional theory (DFT) quantum mechanical (QM)/molecular mechanical (MM) approach that uses the fractional number of electrons as the order parameter to calculate the redox free energy of ET reactions in solution. We applied this method to study the ET reactions of the aqueous metal complexes Fe(H(2)O)(6)(2+/3+) and Ru(H(2)O)(6)(2+/3+). The calculated oxidation potentials, 5.82 eV for Fe(II/III) and 5.14 eV for Ru(II/III), agree well with the experimental data, 5.50 and 4.96 eV, for iron and ruthenium, respectively. Furthermore, we have constructed the diabatic free energy surfaces from histogram analysis based on the molecular dynamics trajectories. The resulting reorganization energy and the diabatic activation energy also show good agreement with experimental data. Our calculations show that using the fractional number of electrons (FNE) as the order parameter in the thermodynamic integration process leads to efficient sampling and validate the ab initio QM/MM approach in the calculation of redox free energies.

  1. Formation of star nanowires of sulfur-doped zinc oxide: Ab initio calculations

    Directory of Open Access Journals (Sweden)

    Qiu-Bao Lin

    2016-09-01

    Full Text Available ZnO nanowires are hexagonally shaped under normal growth conditions, but are transformed from a hexagon to hexagram ones when sulfur dopants are added into the growth solution. The formation mechanism of the hexagram-shaped ZnO nanowires is further studied by the ab initio calculations in this paper. The present calculations support the fact that the hexagonally shaped ZnO nanowires are transformed to hexagram shaped ones when the O atoms on the side surfaces of the nanowires are replaced by S atoms in certain quantities. It indicates that the ratio of sulfur content plays an important role in the hexagram formation. The results of the electronic charge densities indicate that the charge transfer makes the S-Zn bond longer than that of O-Zn. The new charge distribution on the side planes due to the S atoms replacement leads to the formation of the hexagram-shaped nanowires. The calculation on the electronic properties shows that a sulfur-doped hexagram ZnO nanowire is an indirect band gap semiconductor with a narrow gap. When dopant is increased, the gap will decrease.

  2. Nucleation of aluminum nanoclusters on graphene: an ab-initio molecular dynamics study

    Science.gov (United States)

    Alnemrat, Sufian; Mayo, Dennis; de Carlo, Samantha; Eichhorn, Bryan; Hooper, Joseph

    2015-06-01

    Recent experimental results have shown that liquid AlCl and AlBr can, in the presence of a reducing agent, nucleate and grow 10-20 nm aluminum nanoparticles on functionalized graphene sheets. This may offer a route to patterned 2D structures of Al nanoparticles and clusters. Here we present DFT and ab initio molecular dynamics simulations of possible nucleation processes on defect-laden graphene beginning with the AlCl precursor. Static calculations show that AlCl weakly physisorbs on perfect graphene, with binding energies less than 0.5 eV and very small barriers for diffusion along the surface. Covalent bonding is seen on graphene only at vacancy sites. Car-Parrinello molecular dynamics is used to study possible cluster nucleation mechanisms near characteristic vacancies. Simulations at 500 and 1000 K show that the AlCl is very reactive in the presence of the defect, quickly agglomerating and forming long AlCl chains with strong Al-Al bonds.

  3. Amino acid alanine reactivity with the fingerprint reagent ninhydrin. A detailed ab initio computational study.

    Science.gov (United States)

    Petraco, Nicholas D K; Proni, Gloria; Jackiw, Jennifer J; Sapse, Anne-Marie

    2006-11-01

    Ninhydrin is one of the most widely used reagents for chemical development of fingerprints on porous surfaces. The detection is based on the reaction of ninhydrin with a monoacidic component of the fingerprint to form an intensively colored compound named Ruhemann's Purple. A computational study of the mechanisms and reaction energetics of the formation of Ruhemann's Purple from ninhydrin and alanine is presented. Such a study is significant from a forensic science point of view because of the strong interest in the forensic chemistry and law enforcement communities in developing alternatives to the current generation of ninhydrin like chemicals for the detection and development of latent fingerprints. Information about the mechanism of reaction between ninhydrin and amino acids can ultimately help to design compounds with stronger chromo-fluorogenic properties in aid of detecting fingerprints at crime scenes. The three most accepted mechanisms of formation have been considered using ab initio quantum mechanical calculations. At relatively high temperature ( approximately 100 degrees C) all three mechanisms are energetically feasible. However since it is recommended that forensic analyses be performed at room temperature, a revised mechanism is proposed for the formation of Ruhemann's Purple under this condition.

  4. Ab Initio Confirmation of a Harpoon-Type Electron Transfer in a Helium Droplet.

    Science.gov (United States)

    de Lara-Castells, María Pilar; Hauser, Andreas W; Mitrushchenkov, Alexander O

    2017-09-07

    An ab initio study of a long-range electron transfer or "harpoon"-type process from Cs and Cs2 to C60 in a superfluid helium droplet is presented. The heliophobic Cs or Cs2 species are initially located at the droplet surface, while the heliophilic C60 molecule is fully immersed in the droplet. First, probabilities for the electron transfer in the gas phase are calculated for reactants with velocities below the critical Landau velocity of 57 m/s to account for the superfluid helium environment. Next, reaction pathways are derived that also include the repulsive contribution from the extrusion of helium upon the approach of the two reactants. Our results are in perfect agreement with recent experimental measurements of electron ionization mass spectroscopy [ Renzler , M. ; et al., J. Chem. Phys. 2016 , 145 , 181101 ], showing a high possibility for the formation of a Cs2-C60 complex inside of the droplet through a direct harpoon-type electron transfer involving the rotation of the molecule but a negligibly low reactivity for atomic Cs.

  5. Highly correlated ab initio study of the far infrared spectra of methyl acetate.

    Science.gov (United States)

    Senent, M L; Domínguez-Gómez, R; Carvajal, M; Kleiner, I

    2013-01-28

    Highly correlated ab initio calculations (CCSD(T)) are used to compute gas phase spectroscopic parameters of three isotopologues of the methyl acetate (CH(3)COOCH(3), CD(3)COOCH(3), and CH(3)COOCD(3)), searching to help experimental assignments and astrophysical detections. The molecule shows two conformers cis and trans separated by a barrier of 4457 cm(-1). The potential energy surface presents 18 minima that intertransform through three internal rotation motions. To analyze the far infrared spectrum at low temperatures, a three-dimensional Hamiltonian is solved variationally. The two methyl torsion barriers are calculated to be 99.2 cm(-1) (C-CH(3)) and 413.1 cm(-1) (O-CH(3)), for the cis-conformer. The three fundamental torsional band centers of CH(3)COOCH(3) are predicted to lie at 63.7 cm(-1) (C-CH(3)), 136.1 cm(-1) (O-CH(3)), and 175.8 cm(-1) (C-O torsion) providing torsional state separations. For the 27 vibrational modes, anharmonic fundamentals and rovibrational parameters are provided. Computed parameters are compared with those fitted using experimental data.

  6. Ab Initio Nonadiabatic Dynamics with Coupled Trajectories: A Rigorous Approach to Quantum (De)Coherence.

    Science.gov (United States)

    Min, Seung Kyu; Agostini, Federica; Tavernelli, Ivano; Gross, E K U

    2017-07-06

    We report the first nonadiabatic molecular dynamics study based on the exact factorization of the electron-nuclear wave function. Our approach (a coupled-trajectory mixed quantum-classical, CT-MQC, scheme) is based on the quantum-classical limit derived from systematic and controlled approximations to the full quantum-mechanical problem formulated in the exact-factorization framework. Its strength is the ability to correctly capture quantum (de)coherence effects in a trajectory-based approach to excited-state dynamics. We show this by benchmarking CT-MQC dynamics against a revised version of the popular fewest-switches surface-hopping scheme that is able to fix its well-documented overcoherence issue. The CT-MQC approach is successfully applied to investigation of the photochemistry (ring-opening) of oxirane in the gas phase, analyzing in detail the role of decoherence. This work represents a significant step forward in the establishment of the exact factorization as a powerful tool to study excited-state dynamics, not only for interpretation purposes but mainly for nonadiabatic ab initio molecular dynamics simulations.

  7. New Approach for Investigating Reaction Dynamics and Rates with Ab Initio Calculations.

    Science.gov (United States)

    Fleming, Kelly L; Tiwary, Pratyush; Pfaendtner, Jim

    2016-01-21

    Herein, we demonstrate a convenient approach to systematically investigate chemical reaction dynamics using the metadynamics (MetaD) family of enhanced sampling methods. Using a symmetric SN2 reaction as a model system, we applied infrequent metadynamics, a theoretical framework based on acceleration factors, to quantitatively estimate the rate of reaction from biased and unbiased simulations. A systematic study of the algorithm and its application to chemical reactions was performed by sampling over 5000 independent reaction events. Additionally, we quantitatively reweighed exhaustive free-energy calculations to obtain the reaction potential-energy surface and showed that infrequent metadynamics works to effectively determine Arrhenius-like activation energies. Exact agreement with unbiased high-temperature kinetics is also shown. The feasibility of using the approach on actual ab initio molecular dynamics calculations is then presented by using Car-Parrinello MD+MetaD to sample the same reaction using only 10-20 calculations of the rare event. Owing to the ease of use and comparatively low-cost of computation, the approach has extensive potential applications for catalysis, combustion, pyrolysis, and enzymology.

  8. Nonequilibrium Chemical Effects in Single-Molecule SERS Revealed by Ab Initio Molecular Dynamics Simulations.

    Science.gov (United States)

    Fischer, Sean A; Aprà, Edoardo; Govind, Niranjan; Hess, Wayne P; El-Khoury, Patrick Z

    2017-02-16

    Recent developments in nanophotonics have paved the way for achieving significant advances in the realm of single-molecule chemical detection, imaging, and dynamics. In particular, surface-enhanced Raman scattering (SERS) is a powerful analytical technique that is now routinely used to identify the chemical identity of single molecules. Understanding how nanoscale physical and chemical processes affect single-molecule SERS spectra and selection rules is a challenging task and is still actively debated. Herein, we explore underappreciated chemical phenomena in ultrasensitive SERS. We observe a fluctuating excited electronic state manifold, governed by the conformational dynamics of a molecule (4,4'-dimercaptostilbene, DMS) interacting with a metallic cluster (Ag20). This affects our simulated single-molecule SERS spectra; the time trajectories of a molecule interacting with its unique local environment dictates the relative intensities of the observable Raman-active vibrational states. Ab initio molecular dynamics of a model Ag20-DMS system are used to illustrate both concepts in light of recent experimental results.

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

    Science.gov (United States)

    Luo, Han

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

  10. An ab-initio coupled mode theory for near field radiative thermal transfer.

    Science.gov (United States)

    Chalabi, Hamidreza; Hasman, Erez; Brongersma, Mark L

    2014-12-01

    We investigate the thermal transfer between finite-thickness planar slabs which support surface phonon polariton modes (SPhPs). The thickness-dependent dispersion of SPhPs in such layered materials provides a unique opportunity to manipulate and enhance the near field thermal transfer. The key accomplishment of this paper is the development of an ab-initio coupled mode theory that accurately describes all of its thermal transfer properties. We illustrate how the coupled mode parameters can be obtained in a direct fashion from the dispersion relation of the relevant modes of the system. This is illustrated for the specific case of a semi-infinite SiC substrate placed in close proximity to a thin slab of SiC. This is a system that exhibits rich physics in terms of its thermal transfer properties, despite the seemingly simple geometry. This includes a universal scaling behavior of the thermal conductance with the slab thickness and spacing. The work highlights and further increases the value of coupled mode theories in rapidly calculating and intuitively understanding near-field transfer.

  11. Peroxynitrous Acid Dimer: Ab Initio Density Functional Study

    Science.gov (United States)

    Pathak, Rajeev

    2012-02-01

    Peroxynitrous acid (PNA) HOONO, isomeric to nitric acid, is a very strong oxidant. A novel dimeric hydrogen-bonded cluster of peroxynitrous acid (PNA-D) is proposed herein; ab inito quantum chemical investigations performed whereupon lead to several stable structures that have a direct bearing on the reactivity of the participating monomers, quantified in terms of the molecular electrostatic potential. The electron-correlation lending stability to PNA and its dimers is gauged through several density functionals namely B3LYP, B3PW91, M06-2X, M06-L, and φ-B97X, etc.; as well as from popular wave-function based second order Møller-Plesset (MP2) perturbation theory, using the basis sets 6-311++G(d,p) and 6-311++G(2d,2p). The infra-red vibrational spectra reveal spectral shifts and intensity redistribution after dimerization. While the lowest energy PNA-D has a perfect inversion symmetry; the other stable dimers emerge as combinations of monomers in different orientation.

  12. Hydrogen Bonds and the Vibrational Modes of Water at Interfaces: ab-initio Molecular Dynamics meets Neutron Scattering

    Science.gov (United States)

    Kumar, Nitin; Neogi, Sanghamitra; Kent, Paul; Bandura, Andrei; Kubicki, James; Wesolowski, David; Sofo, Jorge

    2008-03-01

    We study the vibrational density of states (VDOS) of a thin water layer on the rutile (110) surface. The VDOS is obtained from the velocity-velocity autocorrelation function calculated from trajectories of large scale ab-initio molecular dynamics simulations. The rutile surface induces a shift to lower frequencies of the stretching modes with respect to pure water. The water vapor surface shows a peak at the vibrational frequency of free hydroxyls. Overall, the average stretching mode vibrational frequency increases with decreasing hydrogen bonding density. This density depends strongly on temperature. The water dissociation percentage at the surface can be correlated with the ratio between the weights of the stretching and the bending modes. Our results are in good agreement with inelastic neutron scattering measurements done on wet titania nanoparticles.

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

    Science.gov (United States)

    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.

  14. Ab initio simulations of water splitting on hematite

    Science.gov (United States)

    Seriani, Nicola

    2017-11-01

    In recent years, hematite has attracted great interest as a photocatalyst for water splitting, but many questions remain unanswered about the mechanisms and the main limiting factors. For this reason, density functional theory has been used to understand the optical, electronic and chemical properties of this material at an atomistic level. Bulk doping can be used to reduce the band gap, and to increase photoabsorption and charge mobility. Charge transport takes place through adiabatic polaron hopping. The stable (0 0 0 1) surface has a stoichiometric termination when exposed to oxygen, it becomes hydroxylated in water, and it has an oxygen-rich termination under illumination in a photoelectrochemical setup. On the oxygen-rich termination, surface states are present that might act as recombination centres for electrons and holes. On the contrary, on the hydroxylated termination surface states appear only on reaction intermediates. The intrinsic surface states disappear in the presence of an overlayer of gallium oxide. The reaction of water oxidation is assumed to proceed by four proton-coupled electron transfers and it is shown to involve a nucleophilic attack with the formation of an OOH group. Calculated overpotentials are in the range of 0.5–0.6 V. Open questions and future research directions are briefly discussed.

  15. Amino acids interacting with defected carbon nanotubes: ab initio calculations

    Directory of Open Access Journals (Sweden)

    M. Darvish Ganji

    2016-09-01

    Full Text Available The adsorption of a number of amino acids on a defected single-walled carbon nanotube (SWCNT is investigated by using the density-functional theory (DFT calculations. The adsorption energies and equilibrium distances are calculated for various configurations such as amino acid attaching to defect sites heptagon, pentagon and hexagon in defective tube and also for several molecular orientations with respect to the nanotube surface. The results showed that amino acids prefer to be physisorbed on the outer surface of the defected nanotube with different interaction strength following the hierarchy histidine > glycine > phenylalanine > cysteine. Comparing these findings with those obtained for perfect SWCNTs reveals that the adsorption energy of the amino acids increase for adsorption onto defected CNTs. The adsorption nature has also been evaluated by means of electronics structures analysis within the Mulliken population and DOS spectra for the interacting entities.

  16. Non-adiabatic ab initio molecular dynamics of supersonic beam epitaxy of silicon carbide at room temperature

    Energy Technology Data Exchange (ETDEWEB)

    Taioli, Simone [Interdisciplinary Laboratory for Computational Science, FBK-Center for Materials and Microsystems and University of Trento, Trento (Italy); Department of Physics, University of Trento, Trento (Italy); Istituto Nazionale di Fisica Nucleare, Sezione di Perugia (Italy); Department of Chemistry, University of Bologna, Bologna (Italy); Garberoglio, Giovanni [Interdisciplinary Laboratory for Computational Science, FBK-Center for Materials and Microsystems and University of Trento, Trento (Italy); Simonucci, Stefano [Interdisciplinary Laboratory for Computational Science, FBK-Center for Materials and Microsystems and University of Trento, Trento (Italy); Istituto Nazionale di Fisica Nucleare, Sezione di Perugia (Italy); Department of Physics, University of Camerino, Camerino (Italy); Beccara, Silvio a [Interdisciplinary Laboratory for Computational Science, FBK-Center for Materials and Microsystems and University of Trento, Trento (Italy); Department of Physics, University of Trento, Trento (Italy); Aversa, Lucrezia [Institute of Materials for Electronics and Magnetism, IMEM-CNR, Trento (Italy); Nardi, Marco [Institute of Materials for Electronics and Magnetism, IMEM-CNR, Trento (Italy); Institut fuer Physik, Humboldt-Universitaet zu Berlin, Berlin (Germany); Verucchi, Roberto [Institute of Materials for Electronics and Magnetism, FBK-CNR, Trento (Italy); Iannotta, Salvatore [Institute of Materials for Electronics and Magnetism, IMEM-CNR, Parma (Italy); Dapor, Maurizio [Interdisciplinary Laboratory for Computational Science, FBK-Center for Materials and Microsystems and University of Trento, Trento (Italy); Department of Materials Engineering and Industrial Technologies, University of Trento, Trento (Italy); Istituto Nazionale di Fisica Nucleare, Sezione di Padova (Italy); and others

    2013-01-28

    In this work, we investigate the processes leading to the room-temperature growth of silicon carbide thin films by supersonic molecular beam epitaxy technique. We present experimental data showing that the collision of fullerene on a silicon surface induces strong chemical-physical perturbations and, for sufficient velocity, disruption of molecular bonds, and cage breaking with formation of nanostructures with different stoichiometric character. We show that in these out-of-equilibrium conditions, it is necessary to go beyond the standard implementations of density functional theory, as ab initio methods based on the Born-Oppenheimer approximation fail to capture the excited-state dynamics. In particular, we analyse the Si-C{sub 60} collision within the non-adiabatic nuclear dynamics framework, where stochastic hops occur between adiabatic surfaces calculated with time-dependent density functional theory. This theoretical description of the C{sub 60} impact on the Si surface is in good agreement with our experimental findings.

  17. The Effectiveness of Newton's Method for Improving Ab Initio Force Fields with Applications to CO2 and H2CO

    Science.gov (United States)

    Mardis; Sibert

    1998-02-01

    Ab initio force field parameters are refined using modifications to Newton's method in which a figure of merit function is approximated as a Taylor Series truncated at second order. We investigate two versions of Newton's method: the Discrete Newton method where the Hessian is approximated by finite differences and the Gauss-Newton method where the Hessian is approximated as the product of first derivatives. The applicability of both rests on the capability of current ab initio methods to calculate quartic force fields that accurately reproduce experimental observables such as band centers and inertial constants. As examples, we calculate refined potential energy surfaces for CO2 and H2CO. We show that an algorithm depending solely on Newton's methods requires only a small number of iterations. Additionally, Newton-based methods provide a great deal of information about the sensitivity of the force field parameters to the observables being fit. We also demonstrate that the less computationally demanding Gauss-Newton method gives results similar to the less approximate Discrete Newton method. Copyright 1998 Academic Press. Copyright 1998Academic Press

  18. Rotational study of the NH3-CO complex: millimeter-wave measurements and ab initio calculations.

    Science.gov (United States)

    Surin, L A; Potapov, A; Dolgov, A A; Tarabukin, I V; Panfilov, V A; Schlemmer, S; Kalugina, Y N; Faure, A; van der Avoird, A

    2015-03-21

    The rotational spectrum of the van der Waals complex NH3-CO has been measured with the intracavity OROTRON jet spectrometer in the frequency range of 112-139 GHz. Newly observed and assigned transitions belong to the K = 0-0, K = 1-1, K = 1-0, and K = 2-1 subbands correlating with the rotationless (jk)NH3 = 00 ground state of free ortho-NH3 and the K = 0-1 and K = 2-1 subbands correlating with the (jk)NH3 = 11 ground state of free para-NH3. The (approximate) quantum number K is the projection of the total angular momentum J on the intermolecular axis. Some of these transitions are continuations to higher J values of transition series observed previously [C. Xia et al., Mol. Phys. 99, 643 (2001)], the other transitions constitute newly detected subbands. The new data were analyzed together with the known millimeter-wave and microwave transitions in order to determine the molecular parameters of the ortho-NH3-CO and para-NH3-CO complexes. Accompanying ab initio calculations of the intermolecular potential energy surface (PES) of NH3-CO has been carried out at the explicitly correlated coupled cluster level of theory with single, double, and perturbative triple excitations and an augmented correlation-consistent triple zeta basis set. The global minimum of the five-dimensional PES corresponds to an approximately T-shaped structure with the N atom closest to the CO subunit and binding energy De = 359.21 cm(-1). The bound rovibrational levels of the NH3-CO complex were calculated for total angular momentum J = 0-6 on this intermolecular potential surface and compared with the experimental results. The calculated dissociation energies D0 are 210.43 and 218.66 cm(-1) for ortho-NH3-CO and para-NH3-CO, respectively.

  19. Sampling the potential energy surface of a DNA duplex damaged by a food carcinogen: Force field parameterization by ab initio quantum calculations and conformational searching using molecular mechanics computations

    Science.gov (United States)

    Wu, Xiangyang

    1999-07-01

    The heterocyclic amine 2-amino-3-methylimidazo (4, 5-f) quinoline (IQ) is one of a number of carcinogens found in barbecued meat and fish. It induces tumors in mammals and is probably involved in human carcinogenesis, because of great exposure to such food carcinogens. IQ is biochemically activated to a derivative which reacts with DNA to form a covalent adduct. This adduct may deform the DNA and consequently cause a mutation. which may initiate carcinogenesis. To understand this cancer initiating event, it is necessary to obtain atomic resolution structures of the damaged DNA. No such structures are available experimentally due to synthesis difficulties. Therefore, we employ extensive molecular mechanics and dynamics calculations for this purpose. The major IQ-DNA adduct in the specific DNA sequence d(5'G1G2C G3CCA3') - d(5'TGGCGCC3') with IQ modified at G3 is studied. The d(5'G1G2C G3CC3') sequence has recently been shown to be a hot-spot for mutations when IQ modification is at G3. Although this sequence is prone to -2 deletions via a ``slippage mechanism'' even when unmodified, a key question is why IQ increases the mutation frequency of the unmodified DNA by about 104 fold. Is there a structural feature imposed by IQ that is responsible? The molecular mechanics and dynamics program AMBER for nucleic acids with the latest force field was chosen for this work. This force field has been demonstrated to reproduce well the B-DNA structure. However, some parameters, the partial charges, bond lengths and angles, dihedral parameters of the modified residue, are not available in the AMBER database. We parameterized the force field using high level ab initio quantum calculations. We created 800 starting conformations which uniformly sampled in combination at 18° intervals three torsion angles that govern the IQ-DNA orientations, and energy minimized them. The most important structures are abnormal; the IQ damaged guanine is rotated out of its standard B

  20. AsH3 ultraviolet photochemistry: an ab initio view.

    Science.gov (United States)

    Alekseyev, Aleksey B; Buenker, Robert J; Liebermann, Heinz-Peter

    2012-06-14

    Multireference configuration interaction calculations have been carried out for low-lying electronic states of AsH(3). Bending potentials for the nine lowest states of AsH(3) are obtained in C(3v) symmetry for As-H distances fixed at the ground state equilibrium value of 2.850 a(0), as well as for the minimum energy path constrained to R(1) = R(2) = R(3). The calculated equilibrium geometry and bond energy for the X (1)A(1) ground state agree very well with the previous experimental and theoretical data. It is shown that the lowest excited singlet state belongs to the (1)A(1) symmetry (in C(3v)), in contradiction to the previous calculations. This state is characterized by a planar equilibrium geometry. Asymmetric stretch potential energy surface (PES) cuts along the H(2)As-H recoil coordinate (at R(1) = R(2) = 2.850 a(0), θ = 123.9° and 90°) for numerous excited states and two-dimensional PESs for the X and à states up to the dissociation limits are obtained for the first time. The à (1)A(1), B(1)E-X (1)A(1) transition moments are calculated as well and used together with the PES data for the analysis of possible photodecay channels of arsine in its first absorption band.

  1. Ab initio theory of helix <-> coil phase transition

    DEFF Research Database (Denmark)

    Yakubovich, Alexander V.; Solov'yov, Ilia; Solov'yov, Andrey V.

    2008-01-01

    In this paper, we suggest a theoretical method based on the statistical mechanics for treating the alpha-helix <-> random coil transition in alanine polypeptides. We consider this process as a first-order phase transition and develop a theory which is free of model parameters and is based solely ...... twisting. The suggested theory is general and with some modification can be applied for the description of phase transitions in other complex molecular systems (e.g. proteins, DNA, nanotubes, atomic clusters, fullerenes).......In this paper, we suggest a theoretical method based on the statistical mechanics for treating the alpha-helix random coil transition in alanine polypeptides. We consider this process as a first-order phase transition and develop a theory which is free of model parameters and is based solely...... on fundamental physical principles. It describes essential thermodynamical properties of the system such as heat capacity, the phase transition temperature and others from the analysis of the polypeptide potential energy surface calculated as a function of two dihedral angles, responsible for the polypeptide...

  2. An ab Initio Exploration of the Bergman Cyclization.

    Science.gov (United States)

    Luxon, Adam R; Orms, Natalie; Kanters, René; Krylov, Anna I; Parish, Carol A

    2018-01-11

    The Bergman cyclization is an important reaction in which an enediyne cyclizes to produce a highly reactive diradical species, p-benzyne. Enediyne motifs are found in natural antitumor antibiotic compounds, such as calicheammicin and dynemicin. Understanding the energetics of cyclization is required to better control the initiation of the cyclization, which induces cell death. We computed the singlet and triplet potential energy surfaces for the Bergman cyclization of (Z)-hex-3-ene-1,5-diyne using the CCSD and EOM-SF-CCSD methods. The triplet enediyne and transition state were found to have C2 symmetry, which contrasts with the singlet reactant and transition state that possess C2v symmetry. We analyzed the frontier orbitals of both cyclization pathways to explain the large energetic barrier of the triplet cyclization. Reaction energies were calculated using CCSD(T)/cc-pVTZ single-point calculations on structures optimized with CCSD/cc-pVDZ. The singlet reaction was found to be slightly endothermic (ΔHrxn = 13.76 kcal/mol) and the triplet reaction was found to be highly exothermic (ΔHrxn = -33.29 kcal/mol). The adiabatic singlet-triplet gap of p-benzyne, computed with EOM-SF-CCSD/cc-pVTZ, was found to be 3.56 kcal/mol, indicating a singlet ground state.

  3. MONTE CARLO SIMULATION OF I-, Br-, AND Cl- IN WATER USING AB INITIO PAIR POTENSIAL FUNCTIONS

    Directory of Open Access Journals (Sweden)

    Harno Dwi Pranowo

    2010-06-01

    Full Text Available Monte Carlo simulations were performed for I-, Br- and Cl-, in water using ab initio pair potential. The systems consisting of one anion in 215 solvent molecules have been simulated at 298 K. Anion-water pair potentials have been newly developed based on ab initio calculations of split valence basis set plus polarization quality. The structure of the solvated ion is discussed in terms of radial distribution functions, coordination number and pair potential distribution. Structural properties were investigated by means of radial distribution functions and their running integration numbers, leading for the first solvation shell to an average 12.60 H2O around I- with I--O distance of 3.74 Å and I--H distance of 2.86 Å, 11.84 H2O around Br- with Br--O distance of 3.40 Å and Br--H distance of 2.42 Å, and 10.68 H2O around Cl- with Cl--O distance of 3.20 Å and Cl--H distance of 2.24 Å, respectively. The structure of the water-anion complexes are agreed with dipole orientation. Pair energy distribution of hydrated anions showed that the pair interaction energy are increase from I-, Cl-, to Br-, namely, -6.28, -9.98 and -13.67 kcal/mol, respectively. The coordination number distribution analysis for the first solvation shell of the all hydrated anions indicated a high exchange rate for the first solvation shell ligands.   Keywords: Monte Carlo simulation, halogen anion, ab initio

  4. Efficient approach to compute melting properties fully from ab initio with application to Cu

    Science.gov (United States)

    Zhu, Li-Fang; Grabowski, Blazej; Neugebauer, Jörg

    2017-12-01

    Applying thermodynamic integration within an ab initio-based free-energy approach is a state-of-the-art method to calculate melting points of materials. However, the high computational cost and the reliance on a good reference system for calculating the liquid free energy have so far hindered a general application. To overcome these challenges, we propose the two-optimized references thermodynamic integration using Langevin dynamics (TOR-TILD) method in this work by extending the two-stage upsampled thermodynamic integration using Langevin dynamics (TU-TILD) method, which has been originally developed to obtain anharmonic free energies of solids, to the calculation of liquid free energies. The core idea of TOR-TILD is to fit two empirical potentials to the energies from density functional theory based molecular dynamics runs for the solid and the liquid phase and to use these potentials as reference systems for thermodynamic integration. Because the empirical potentials closely reproduce the ab initio system in the relevant part of the phase space the convergence of the thermodynamic integration is very rapid. Therefore, the proposed approach improves significantly the computational efficiency while preserving the required accuracy. As a test case, we apply TOR-TILD to fcc Cu computing not only the melting point but various other melting properties, such as the entropy and enthalpy of fusion and the volume change upon melting. The generalized gradient approximation (GGA) with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional and the local-density approximation (LDA) are used. Using both functionals gives a reliable ab initio confidence interval for the melting point, the enthalpy of fusion, and entropy of fusion.

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

    Science.gov (United States)

    St. John, Alexander; Wexler, Carlos

    2015-03-01

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

  6. Ramsdellite-structured LiTiO 2: A new phase predicted from ab initio calculations

    Science.gov (United States)

    Koudriachova, M. V.

    2008-06-01

    A new phase of highly lithiated titania with potential application as an anode in Li-rechargeable batteries is predicted on the basis of ab initio calculations. This phase has a composition LiTiO2 and may be accessed through electrochemical lithiation of ramsdellite-structured TiO2 at the lowest potential reported for titanium dioxide based materials. The potential remains constant over a wide range of Li-concentrations. The new phase is metastable with respect to a tetragonally distorted rock salt structure, which hitherto has been the only known polymorph of LiTiO2.

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

    Science.gov (United States)

    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.

  8. Ab Initio Calculations of Deuterium Isotope Effects on Chemical Shifts of Salt-Bridged Lysines

    DEFF Research Database (Denmark)

    Ullah, Saif; Ishimoto, Takayoshi; Williamson, Mike P.

    2011-01-01

    . This method enables the determination of both the electronic and the protonic (deuteronic) wave functions simultaneously and can directly calculate the geometrical difference induced by H/D isotope effects. The calculations show that the one-bond deuterium isotope effects on 15N nuclear shielding, 1Δ15N......Deuterium isotope effects measure the change in chemical shift on substitution of a proton by deuterium. They have been calculated by direct treatment of the H/D nuclear quantum effect using a multicomponent ab initio molecular orbital method based on a non-Born−Oppenheimer approximation...

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

    Science.gov (United States)

    Pietrucci, Fabio; Andreoni, Wanda

    2011-08-01

    Social permutation invariant coordinates are introduced describing the bond network around a given atom. They originate from the largest eigenvalue and the corresponding eigenvector of the contact matrix, are invariant under permutation of identical atoms, and bear a clear signature of an order-disorder transition. Once combined with ab initio metadynamics, these coordinates are shown to be a powerful tool for the discovery of low-energy isomers of molecules and nanoclusters as well as for a blind exploration of isomerization, association, and dissociation reactions.

  10. Experimental and ab initio DFT calculated Raman Spectrum of Sudan I, a Red Dye

    DEFF Research Database (Denmark)

    Kunov-Kruse, Andreas Jonas; Kristensen, Steffen Buus; Liu, Chuan

    2011-01-01

    . Comparison was made with other azo dyes in the literature on natural, abundant plant pigments. The results show that there is a possibility in foodstuff analysis to distinguish Sudan I from other dyes by using Raman spectroscopy with more than one laser wavelength for resonance enhancement of the different......The red dye Sudan I was investigated by Raman spectroscopy using different excitation wavelengths (1064, 532 and 244 nm). A calculation of the Raman spectrum based on quantum mechanical ab initio density functional theory (DFT) was made using the RB3LYP method with the 3-21G and 6-311+G(d,p) basis...

  11. Temperature-Dependent Diffusion Coefficients from ab initio Computations: Hydrogen in Nickel

    Energy Technology Data Exchange (ETDEWEB)

    E Wimmer; W Wolf; J Sticht; P Saxe; C Geller; R Najafabadi; G Young

    2006-03-16

    The temperature-dependent mass diffusion coefficient is computed using transition state theory. Ab initio supercell phonon calculations of the entire system provide the attempt frequency, the activation enthalpy, and the activation entropy as a function of temperature. Effects due to thermal lattice expansion are included and found to be significant. Numerical results for the case of hydrogen in nickel demonstrate a strong temperature dependence of the migration enthalpy and entropy. Trapping in local minima along the diffusion path has a pronounced effect especially at low temperatures. The computed diffusion coefficients with and without trapping bracket the available experimental values over the entire temperature range between 0 and 1400 K.

  12. Heat capacities of xenotime-type ceramics: An accurate ab initio prediction

    Science.gov (United States)

    Ji, Yaqi; Beridze, George; Bosbach, Dirk; Kowalski, Piotr M.

    2017-10-01

    Because of ability to incorporate actinides into their structure, the lanthanide phosphate ceramics (LnPO4) are considered as potential matrices for the disposal of nuclear waste. Here we present highly reliable ab initio prediction of the variation of heat capacities and the standard entropies of these compounds in zircon structure along lanthanide series (Ln = Dy, …,Lu) and validate them against the existing experimental data. These data are helpful for assessment of thermodynamic parameters of these materials in the context of using them as matrices for immobilization of radionuclides for the purpose of nuclear waste management.

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

    Science.gov (United States)

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

    2014-02-05

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

  14. Monte Carlo methods in AB initio quantum chemistry quantum Monte Carlo for molecules

    CERN Document Server

    Lester, William A; Reynolds, PJ

    1994-01-01

    This book presents the basic theory and application of the Monte Carlo method to the electronic structure of atoms and molecules. It assumes no previous knowledge of the subject, only a knowledge of molecular quantum mechanics at the first-year graduate level. A working knowledge of traditional ab initio quantum chemistry is helpful, but not essential.Some distinguishing features of this book are: Clear exposition of the basic theory at a level to facilitate independent study. Discussion of the various versions of the theory: diffusion Monte Carlo, Green's function Monte Carlo, and release n

  15. Ionization energies of aqueous nucleic acids: Photoelectron spectroscopy of pyridine nucleosides and ab initio calculations

    Czech Academy of Sciences Publication Activity Database

    Slavíček, Petr; Winter, B.; Faubel, M.; Bradforth, S. E.; Jungwirth, Pavel

    2009-01-01

    Roč. 131, č. 18 (2009), s. 6460-6467 ISSN 0002-7863 R&D Projects: GA MŠk LC512; GA ČR GA203/08/0114 Grant - others:GA ČR(CZ) GP203/07/P449 Institutional research plan: CEZ:AV0Z40550506; CEZ:AV0Z40400503 Keywords : DNA bases * photoelectron spectroscopy * ab initio calculations Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 8.580, year: 2009

  16. Orbital free ab initio study of static and dynamic properties of some liquid transition metals

    Directory of Open Access Journals (Sweden)

    Bhuiyan G. M.

    2017-01-01

    Full Text Available Several static and dynamic properties of liquid transition metals Cr, Mn and Co are studied for the first time using the orbital free ab-initio molecular dynamics simulation (OF-AIMD. This method is based on the density functional theory (DFT which accounts for the electronic energy of the system whereas the interionic forces are derived from the electronic energy via the Hellman-Feynman theorem. The external energy functional is treated with a local pseudopotential. Results are reported for static structure factors, isothermal compressibility, diffusion coeffcients, sound velocity and viscosity and comparison is performed with the available experimental data and other theoretical calculations.

  17. Quantum chemistry the development of ab initio methods in molecular electronic structure theory

    CERN Document Server

    Schaefer III, Henry F

    2004-01-01

    This guide is guaranteed to prove of keen interest to the broad spectrum of experimental chemists who use electronic structure theory to assist in the interpretation of their laboratory findings. A list of 150 landmark papers in ab initio molecular electronic structure methods, it features the first page of each paper (which usually encompasses the abstract and introduction). Its primary focus is methodology, rather than the examination of particular chemical problems, and the selected papers either present new and important methods or illustrate the effectiveness of existing methods in predi

  18. Scalable numerical approach for the steady-state ab initio laser theory

    Science.gov (United States)

    Esterhazy, S.; Liu, D.; Liertzer, M.; Cerjan, A.; Ge, L.; Makris, K. G.; Stone, A. D.; Melenk, J. M.; Johnson, S. G.; Rotter, S.

    2014-08-01

    We present an efficient and flexible method for solving the non-linear lasing equations of the steady-state ab initio laser theory. Our strategy is to solve the underlying system of partial differential equations directly, without the need of setting up a parametrized basis of constant flux states. We validate this approach in one-dimensional as well as in cylindrical systems, and demonstrate its scalability to full-vector three-dimensional calculations in photonic-crystal slabs. Our method paves the way for efficient and accurate simulations of microlasers which were previously inaccessible.

  19. FTIR cryospectroscopic and ab initio studies of desflurane-dimethyl ether H-bonded complexes

    Science.gov (United States)

    Melikova, S. M.; Rutkowski, K. S.; Rospenk, M.

    2017-09-01

    The IR spectra of mixtures of desflurane and dimethyl ether are studied with the help of FTIR cryospectroscopy in liquefied Kr at T 118-158 K. Comparative analysis of the experimental data and results of ab initio calculations show that either of the two C-H groups of desflurane is involved in heterodimer formation of comparable strengths. The blue frequency shift is found for stretching vibrations of those C-H donors which directly participate in H-bond formation. Additionally the complexes are stabilized by weaker contacts between hydrogen atoms of dimethyl ether and fluorine atoms of desflurane.

  20. Orbital free ab initio study of static and dynamic properties of some liquid transition metals

    Science.gov (United States)

    Bhuiyan, G. M.; Molla, Mohammad Riazuddin; Ziauddin Ahmed, A. Z.; Gonzalez, L. E.; Gonzalez, D. J.

    2017-08-01

    Several static and dynamic properties of liquid transition metals Cr, Mn and Co are studied for the first time using the orbital free ab-initio molecular dynamics simulation (OF-AIMD). This method is based on the density functional theory (DFT) which accounts for the electronic energy of the system whereas the interionic forces are derived from the electronic energy via the Hellman-Feynman theorem. The external energy functional is treated with a local pseudopotential. Results are reported for static structure factors, isothermal compressibility, diffusion coeffcients, sound velocity and viscosity and comparison is performed with the available experimental data and other theoretical calculations.

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

    Science.gov (United States)

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

    2014-03-14

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

  2. Curved-line search algorithm for ab initio atomic structure relaxation

    Science.gov (United States)

    Chen, Zhanghui; Li, Jingbo; Li, Shushen; Wang, Lin-Wang

    2017-09-01

    Ab initio atomic relaxations often take large numbers of steps and long times to converge, especially when the initial atomic configurations are far from the local minimum or there are curved and narrow valleys in the multidimensional potentials. An atomic relaxation method based on on-the-flight force learning and a corresponding curved-line search algorithm is presented to accelerate this process. Results demonstrate the superior performance of this method for metal and magnetic clusters when compared with the conventional conjugate-gradient method.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-03-01

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

  4. Polarization and charge-transfer effects in aqueous solution via ab initio QM/MM simulations.

    Science.gov (United States)

    Mo, Yirong; Gao, Jiali

    2006-02-23

    Combined ab initio quantum mechanical and molecular mechanical (QM/MM) simulations coupled with the block-localized wave function energy decomposition (BLW-ED) method have been conducted to study the solvation of two prototypical ionic systems, acetate and methylammonium ions in aqueous solution. Calculations reveal that the electronic polarization between the targeted solutes and water is the primary many-body effect, whereas the charge-transfer term only makes a small fraction of the total solute-solvent interaction energy. In particular, the polarization effect is dominated by the solvent (water) polarization.

  5. Ab initio studies of complexes of ozone with some positive ions

    Science.gov (United States)

    Snyder, G.; Sapse, D.

    1994-02-01

    Ab initio calculations using the 6-31G * and the 6-311G * basis sets are performed on HeO +3, LiO +3 and N 2O +3 comp the HeO +3 and N 2O +3 complexes the positive charge is on the oxygen and the complexes are not bound with respect to dissociation into He or N 2 and O +3. In the LiO +3 complex the positive charge is on lithium and the complex is strongly bound with respect to the Li + and O 3.

  6. First Benchmark of Relativistic Photoionization Theories against 3D ab initio Simulation.

    Science.gov (United States)

    Hafizi, B; Gordon, D F; Palastro, J P

    2017-03-31

    Photoelectron spectra and ionization rates encompassing relativistic intensities and hydrogenlike ions with relativistic binding energies are obtained using a quasiclassical S-matrix approach. These results, along with those based on the imaginary time method, are compared with three-dimensional, ½-period ab initio simulations for a wide range of ionization potentials and electric field amplitudes. Significant differences between the three results are demonstrated. Time-dependent simulations indicate that the peak ionization current can occur before the peak of the electric field.

  7. Ab initio study of new sp3 silicon and germanium allotropes predicted from the zeolite topologies

    Science.gov (United States)

    Saleev, Vladimir A.; Shipilova, Alexandra V.; Proserpio, Davide M.; Fadda, Giuseppe

    2017-08-01

    We study the structural, elastic, vibrational, electronic, and optical properties of six new silicon and germanium allotropes using ab initio quantum mechanical methods. These allotropes have been found first for carbon by using topological methods on a large sample of zeolites; this is extended here to Si and Ge, given their chemical similarity with C and their importance for the semiconductor industry and for photovoltaics. Some Si allotropes show excellent absorbance of solar light, making them an interesting alternatives to amorphous Si, whereas an allotrope of Ge has a very small band gap, in agreement with the metallic nature of amorphous Ge.

  8. Ab initio determination of the structure of a grain boundary by simulated quenching

    Energy Technology Data Exchange (ETDEWEB)

    Payne, M.C.; Bristowe, P.D.; Joannopoulos, J.D.

    1987-03-30

    Results of the first completely ab initio investigation of the microscopic structure of a grain boundary in a semiconductor are presented. By use of the molecular-dynamics--simulated annealing method for performing total-energy calculations within the local-density--functional and pseudopotential approximation, the ..sigma.. = 5 (001) twist boundary in germanium is studied. A number of rotation-and-translation states are investigated leading to a prediction for the structure of this geometry. Evidence for the possible presence of novel defects and glasslike tunneling mode states at grain boundaries is presented.

  9. Ab-initio determination of the structure of a grain boundary by simulated quenching

    Energy Technology Data Exchange (ETDEWEB)

    Payne, M.C.; Bristowe, P.D.; Joannopoulos, J.D.

    1987-02-01

    Results of the first completely ab-initio investigation of the microscopic structure of a grain boundary in a semiconductor are presented. Using the molecular dynamics simulated annealing method for performing total energy calculations within the local density functional and pseudopotential approximations, the ..sigma.. = 5(001) twist boundary in germanium is studied. A number of rotation-and-translation states are investigated leading to a prediction for the structure of this geometry. Evidence for the possible presence of novel defects and glass-like tunneling mode states at grain boundaries is presented.

  10. Ab initio determination of the structure of a grain boundary by simulated quenching

    Science.gov (United States)

    Payne, M. C.; Bristowe, P. D.; Joannopoulos, J. D.

    1987-03-01

    Results of the first completely ab initio investigation of the microscopic structure of a grain boundary in a semiconductor are presented. By use of the molecular-dynamics-simulated annealing method for performing total-energy calculations within the local-density-functional and pseudopotential approximations, the Sigma = 5 (001) twist boundary is germanium is studied. A number of rotation-and-translation states are investigated leading to a prediction for the structure of this geometry. Evidence for the possible presence of novel defects and glasslike tunneling-mode states at grain boundaries is presented.

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

    Energy Technology Data Exchange (ETDEWEB)

    Kurova, N. V., E-mail: kurova_natasha@mail.ru; Burdov, V. A. [Lobachevskii Nizhni Novgorod State University (Russian Federation)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  13. SPASER as a complex system: femtosecond dynamics traced by ab-initio simulations

    KAUST Repository

    Gongora, J. S. Totero

    2016-03-14

    Integrating coherent light sources at the nanoscale with spasers is one of the most promising applications of plasmonics. A spaser is a nano-plasmonic counterpart of a laser, with photons replaced by surface plasmon polaritons and the resonant cavity replaced by a nanoparticle supporting localized plasmonic modes. Despite the large body of experimental and theoretical studies, the understanding of the fundamental properties of the spaser emission is still challenging. In this work, we investigated the ultrafast dynamics of the emission from a core-shell spaser by developing a rigorous first-principle numerical model. Our results show that the spaser is a highly nonlinear system with many interacting degrees of freedom, whose emission sustain a rich manifold of different spatial phases. In the regime of strong interaction we observed that the spaser emission manifests an irreversible ergodic evolution, where energy is equally shared among all the available degrees of freedom. Under this condition, the spaser generates ultrafast vortex lasing modes that are spinning on the femtosecond scale, acquiring the character of a nanoparticle with an effective spin. Interestingly, the spin orientation is defined by spontaneous symmetry breaking induced by quantum noise, which is a fundamental component of our ab-initio model. This opens up interesting possibilities of achieving unidirectional emission from a perfectly spherical nanoparticle, stimulating a broad range of applications for nano-plasmonic lasers as unidirectional couplers, random information sources and novel form of photonics neural-networks. © (2016) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.

  14. The Conformational Landscape of L-Threonine Matrix Isolation Infrared and {AB-INITIO Studies

    Science.gov (United States)

    Dubey, Pankaj; Mukhopadhyay, Anamika; Viswanathan, K. S.

    2017-06-01

    Amino acids, containing hydroxy side chains such as L-threonine and tyrosine play an important role in molecular recognition, such as in the docking of propofol, which is a commonly used anaesthetic. A rich conformational landscape of these amino acids makes them interesting candidates in the study of intra and intermolecular interactions. In this work, the conformational landscape of L-threonine was studied, as it can be expected to serve as a basis for understanding structure and functions of polypeptides and other biomolecules. The matrix isolation technique (MI) coupled with a high temperature effusive molecular beam (EMB) nozzle was used to trap conformers of amino acid, which were then characterized using FTIR spectroscopy. The usefulness of MI-EMB-FTIR spectroscopy is that it can trap structures corresponding to the local minima along with the global minimum and hence allows for a better exploration of the potential energy surface. A major challenge in conformational analysis of amino acids using matrix isolation FTIR arises from its non-volatile nature. A home built heating system which was mounted close to the cryotip, was used to evaporate the non-volatile amino acids. Our infrared spectra show that three conformations were trapped in the matrix. Experimental results were supported by {ab-initio calculations performed using the CCSD(T), MP2 and M06-2X methods together with 6-311++G(d,p) and aug/cc-pVDZ basis sets. The side chains of the amino acids appeared to have an influence on the preferential stabilisation of a particular backbone structure of amino acids. Factors such as entropy, anomeric effect and intramolecular H-bonding were also found to play an important role in determining conformal preferences, which will be discussed.

  15. Guiding exploration in conformational feature space with Lipschitz underestimation for ab-initio protein structure prediction.

    Science.gov (United States)

    Hao, Xiaohu; Zhang, Guijun; Zhou, Xiaogen

    2018-02-06

    Computing conformations which are essential to associate structural and functional information with gene sequences, is challenging due to the high dimensionality and rugged energy surface of the protein conformational space. Consequently, the dimension of the protein conformational space should be reduced to a proper level, and an effective exploring algorithm should be proposed. In this paper, a plug-in method for guiding exploration in conformational feature space with Lipschitz underestimation (LUE) for ab-initio protein structure prediction is proposed. The conformational space is converted into ultrafast shape recognition (USR) feature space firstly. Based on the USR feature space, the conformational space can be further converted into Underestimation space according to Lipschitz estimation theory for guiding exploration. As a consequence of the use of underestimation model, the tight lower bound estimate information can be used for exploration guidance, the invalid sampling areas can be eliminated in advance, and the number of energy function evaluations can be reduced. The proposed method provides a novel technique to solve the exploring problem of protein conformational space. LUE is applied to differential evolution (DE) algorithm, and metropolis Monte Carlo(MMC) algorithm which is available in the Rosetta; When LUE is applied to DE and MMC, it will be screened by the underestimation method prior to energy calculation and selection. Further, LUE is compared with DE and MMC by testing on 15 small-to-medium structurally diverse proteins. Test results show that near-native protein structures with higher accuracy can be obtained more rapidly and efficiently with the use of LUE. Copyright © 2018 Elsevier Ltd. All rights reserved.

  16. Collisions induced dissociation and Ab initio study of azobenzene derivatives bond structure and electronic configuration

    Science.gov (United States)

    Rezaee, Mohammadreza; Compton, Robert

    2015-05-01

    Collision induced dissociation (CID) and ab initio calculations were utilized to study a few derivatives of azobenzene molecule and their product ions. High level computational methods along with large basis set size yield values in close agreement with the experimental results. Möller-Plesset and coupled-cluster theory including perturbative triple excitations, CCSD(T), method were performed to obtain a high accuracy estimation of the bond dissociation energy value. The electron affinities have been studied experimentally using the photoelectron spectroscopy method as well as theoretically using ab inito calculations. For the trans-2,2',6,6' tetra-fluoro azobenzene the bond dissociation has been experimentally determined to be 1.88 eV and the vertical detachment energy is 1.78 eV.

  17. GW-based ab initio downfolding aiming at strongly correlated electron system

    Science.gov (United States)

    Nakamura, Kazuma; Kosugi, Taichi; Yoshimoto, Yoshihide; Arita, Ryotaro; Imada, Masatoshi

    2008-03-01

    Aiming at ab initio description of real complex systems under effects of strong electron correlations, we develop a GW-based downfolding scheme formulated in the plane-wave basis set. Our method is successfully applied to organic conductors, the family of (BEDT-TTF)2X. At the heart of our downfolding scheme lies utilizing the energy hierarchy of the system [1]: The low-energy hierarchy near the Fermi level (ɛ f±2˜3 eV) determines physics while is affected by the remaining high-energy part of hierarchy. We renormalize the high-energy part into low energy, based on the GW scheme. The renormalization generates a low-energy model characterized by renormalized transfers and effective screened Coulomb/exchange interactions, having frequency dependence arising from retarded screening by eliminated high-energy electrons. Thus, the low-energy frequency-dependent effective model is mapped out from the whole high- plus low-energy system in an ab initio procedure. [1] F. Aryasetiawan et al., Phys. Rev. B 70, 19514 (2004); I. V. Solovyev and M. Imada, ibid. 71, 045103 (2005).

  18. Ab initio molecular dynamics of the reaction of quercetin with superoxide radical

    Energy Technology Data Exchange (ETDEWEB)

    Lespade, Laure, E-mail: l.lespade@ism.u-bordeaux1.fr

    2016-08-22

    Highlights: • Ab initio molecular dynamics is performed to describe the reaction of quercetin and superoxide. • The reaction occurs near the sites 4′ and 7 when the system contains sufficiently water molecules. • The difference of reactivity of superoxide compared to commonly used radicals as DPPH{sup ·} or ABTS{sup ·+} is explained. - Abstract: Superoxide plays an important role in biology but in unregulated concentrations it is implicated in a lot of diseases such as cancer or atherosclerosis. Antioxidants like flavonoids are abundant in plant and are good scavengers of superoxide radical. The modeling of superoxide scavenging by flavonoids from the diet still remains a challenge. In this study, ab initio molecular dynamics of the reaction of the flavonoid quercetin toward superoxide radical has been carried out using Car–Parrinello density functional theory. The study has proven different reactant solvation by modifying the number of water molecules surrounding superoxide. The reaction consists in the gift of a hydrogen atom of one of the hydroxyl groups of quercetin to the radical. When it occurs, it is relatively fast, lower than 100 fs. Calculations show that it depends largely on the environment of the hydroxyl group giving its hydrogen atom, the geometry of the first water layer and the presence of a certain number of water molecules in the second layer, indicating a great influence of the solvent on the reactivity.

  19. Time-Domain Ab Initio Modeling of Photoinduced Dynamics at Nanoscale Interfaces

    Science.gov (United States)

    Wang, Linjun; Long, Run; Prezhdo, Oleg V.

    2015-04-01

    Nonequilibrium processes involving electronic and vibrational degrees of freedom in nanoscale materials are under active experimental investigation. Corresponding theoretical studies are much scarcer. The review starts with the basics of time-dependent density functional theory, recent developments in nonadiabatic molecular dynamics, and the fusion of the two techniques. Ab initio simulations of this kind allow us to directly mimic a great variety of time-resolved experiments performed with pump-probe laser spectroscopies. The focus is on the ultrafast photoinduced charge and exciton dynamics at interfaces formed by two complementary materials. We consider purely inorganic materials, inorganic-organic hybrids, and all organic interfaces, involving bulk semiconductors, metallic and semiconducting nanoclusters, graphene, carbon nanotubes, fullerenes, polymers, molecular crystals, molecules, and solvent. The detailed atomistic insights available from time-domain ab initio studies provide a unique description and a comprehensive understanding of the competition between electron transfer, thermal relaxation, energy transfer, and charge recombination processes. These advances now make it possible to directly guide the development of organic and hybrid solar cells, as well as photocatalytic, electronic, spintronic, and other devices relying on complex interfacial dynamics.

  20. Estudio ab initio del mecanismo de la reacción HSO + O3

    Science.gov (United States)

    Nebot Gil, I.

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

  1. Accurate disulfide-bonding network predictions improve ab initio structure prediction of cysteine-rich proteins.

    Science.gov (United States)

    Yang, Jing; He, Bao-Ji; Jang, Richard; Zhang, Yang; Shen, Hong-Bin

    2015-12-01

    Cysteine-rich proteins cover many important families in nature but there are currently no methods specifically designed for modeling the structure of these proteins. The accuracy of disulfide connectivity pattern prediction, particularly for the proteins of higher-order connections, e.g., >3 bonds, is too low to effectively assist structure assembly simulations. We propose a new hierarchical order reduction protocol called Cyscon for disulfide-bonding prediction. The most confident disulfide bonds are first identified and bonding prediction is then focused on the remaining cysteine residues based on SVR training. Compared with purely machine learning-based approaches, Cyscon improved the average accuracy of connectivity pattern prediction by 21.9%. For proteins with more than 5 disulfide bonds, Cyscon improved the accuracy by 585% on the benchmark set of PDBCYS. When applied to 158 non-redundant cysteine-rich proteins, Cyscon predictions helped increase (or decrease) the TM-score (or RMSD) of the ab initio QUARK modeling by 12.1% (or 14.4%). This result demonstrates a new avenue to improve the ab initio structure modeling for cysteine-rich proteins. http://www.csbio.sjtu.edu.cn/bioinf/Cyscon/ zhng@umich.edu or hbshen@sjtu.edu.cn. Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  2. Acetalization of 2-Hydroxybenzaldehyde mechanism using halogen acid catalysts based on ab initio methods

    Science.gov (United States)

    Yusuf, Muhammad; Roza, Destria; Nasution, Ahmad Kamil

    2017-11-01

    The computational calculation was performed on the acetalization of 2-hydroxybenzaldehyde by using ab initio method. Ab initio method is derived directly from theoretical principles with no inclusion of experimental data and this is an approximate quantum mechanical calculation. The aim of this research was to studies the acetalization of 2-hydroxybenzaldehyde mechanism using halogen acid catalysts. Computational calculation which was applied on the acetalization of 2-hydroxybenzaldehyde using halogen acid catalysts provided possible reaction steps. The first step was formation of a labile hemiacetal because it is essentially tetrahedral intermediates containing a leaving group. The second step was formation of a stable acetal. The results of computational calculation of acetalization of 2-hydroxybenzaldehyde provided possible energy change in the each step of the reaction process. A labile hemiacetal showed higher energy (481.04 kJ/mol) than 2-hydroxybenzaldehyde dimethyl acetal (65.32 kJ/mol) and 2-hydroxybenzaldehyde (0 kJ/mol) due to its instability. In general, acetalization of 2-hydroxybenzaldehyde reaction is a reversible reaction. The effect of Lewis acidity on halogen acid catalysts was also studied in this research. Based on the Mulliken charge on the H atom, it is found that HF has the highest Lewis acidity compared to other halogen acids with order HF> HCl> HBr> HI. As a result, HF was the efficient catalysts for acetalization of 2-Hydroxybenzaldehyde.

  3. Ab initio study of structural, electronic, and thermal properties of Ir1-xRhx alloys

    Directory of Open Access Journals (Sweden)

    Sh. Ahmed

    2015-06-01

    Full Text Available The structural, electronic, mechanical and thermal properties of Ir1-xRhx alloys was studied systematically using ab initio density functional theory at different concentration (x = 0.00, 0.25, 0.50, 0.75, 1.00. The Special Quasirandom Structure method was used to make the alloys with FCC structure with four atoms per unit cell. The ground state properties such as lattice constant and bulk modulus were calculated to find the equilibrium atomic position for stable alloys. The calculated ground state properties are in good agreement with the experimental and previously presented other theoretical data. The electronic band structure and density of states were calculated to study the electronic properties for these alloys at different concentration. The electronic properties substantiate metallic behavior of alloys. The first principle density functional perturbation theory as implemented in quasiharmonic approximation was used for the calculation of thermal properties. We have calculated the thermal properties such the Debye temperatures, vibration energy, entropy, constant-volume specific heat and internal energy. The ab initio linear-response method was used for phonon densities of states calculations.

  4. Transition strengths in 21 , 22 , 23Mg as tests of ab initio theory

    Science.gov (United States)

    Henderson, Jack; Ruotsalainen, Panu; Hackman, Greg; Experiment S1480 Team; Experiment S1624 Team; Experiment S1646 Team

    2017-09-01

    Effective charges compensate for insufficiencies arising from truncations of the nuclear model-space by performing a crude inflation of nucleon charges to account for missing electric-quadrupole (E 2) transition strength. Recent theoretical developments in ab initio nuclear theory might allow for the calculation of this strength using evolved effective-operators arising from first-principles, removing the need for effective charges and enhancing predictive power. To that end, Coulomb excitation measurements were performed of neutron-deficient 21 , 22 , 23Mg at TRIUMF-ISAC, with the goal of extracting precision E 2 strengths for comparison with state-of-the-art models. Results will be presented and compared with ab initio in-medium similarity renormalization group (IM-SRG) and symplectic no-core shell-model calculations, as well as phenomenological shell-model results. Results will also be presented in the context of mirror-pairs in the sd -shell, providing a systematic evaluation of the reproduction of E 2 strength with respect to isospin.

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

    Energy Technology Data Exchange (ETDEWEB)

    Mueller, B.Y.; Haag, M.; Fähnle, M., E-mail: faehnle@is.mpg.de

    2016-09-15

    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. - Highlights: • The contribution of electron–electron spin-flip scattering to the ultrafast demagnetization of ferromagnets after laser excitation is investigated. • Dynamical change of the band structure is taken into account on an ab initio level. • Large influence of the dynamical band structure on the magnetization dynamics is observed. • We trace electron dynamics and explain the thermalization and relaxation process after laser irradiation. • Treating the dynamical band structure yields a demagnetization comparable to the experimental one.

  6. Ab initio quantum chemistry in parallel-portable tools and applications

    Energy Technology Data Exchange (ETDEWEB)

    Harrison, R.J.; Shepard, R. (Argonne National Lab., IL (United States)); Kendall, R.A. (Battelle Pacific Northwest Lab., Richland, WA (United States))

    1991-01-01

    In common with many of the computational sciences, ab initio chemistry faces computational constraints to which a partial solution is offered by the prospect of highly parallel computers. Ab initio codes are large and complex (O(10{sup 5}) lines of FORTRAN), representing a significant investment of communal effort. The often conflicting requirements of portability and efficiency have been successfully resolved on vector computers by reliance on matrix oriented kernels. This proves inadequate even upon closely-coupled shared-memory parallel machines. We examine the algorithms employed during a typical sequence of calculations. Then we investigate how efficient portable parallel implementations may be derived, including the complex multi-reference singles and doubles configuration interaction algorithm. A portable toolkit, modeled after the Intel iPSC and the ANL-ACRF PARMACS, is developed, using shared memory and TCP/IP sockets. The toolkit is used as an initial platform for programs portable between LANS, Crays and true distributed-memory MIMD machines. Timings are presented. 53 refs., 4 tabs.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-03-05

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

  8. Ab initio molecular dynamics of solvation effects on reactivity at electrified interfaces

    Science.gov (United States)

    Herron, Jeffrey A.; Morikawa, Yoshitada; Mavrikakis, Manos

    2016-08-01

    Using ab initio molecular dynamics as implemented in periodic, self-consistent (generalized gradient approximation Perdew-Burke-Ernzerhof) density functional theory, we investigated the mechanism of methanol electrooxidation on Pt(111). We investigated the role of water solvation and electrode potential on the energetics of the first proton transfer step, methanol electrooxidation to methoxy (CH3O) or hydroxymethyl (CH2OH). The results show that solvation weakens the adsorption of methoxy to uncharged Pt(111), whereas the binding energies of methanol and hydroxymethyl are not significantly affected. The free energies of activation for breaking the C-H and O-H bonds in methanol were calculated through a Blue Moon Ensemble using constrained ab initio molecular dynamics. Calculated barriers for these elementary steps on unsolvated, uncharged Pt(111) are similar to results for climbing-image nudged elastic band calculations from the literature. Water solvation reduces the barriers for both C-H and O-H bond activation steps with respect to their vapor-phase values, although the effect is more pronounced for C-H bond activation, due to less disruption of the hydrogen bond network. The calculated activation energy barriers show that breaking the C-H bond of methanol is more facile than the O-H bond on solvated negatively biased or uncharged Pt(111). However, with positive bias, O-H bond activation is enhanced, becoming slightly more facile than C-H bond activation.

  9. Comparison between s - and d -electron mediated transport in a photoswitching dithienylethene molecule using ab initio transport methods

    KAUST Repository

    Odell, Anders

    2011-10-03

    The influence of the electrode\\'s Fermi surface on the transport properties of a photoswitching molecule is investigated with state-of-the-art ab initio transport methods. We report results for the conducting properties of the two forms of dithienylethene attached either to Ag or to nonmagnetic Ni leads. The I-V curves of the Ag/dithienylethene/Ag device are found to be very similar to those reported previously for Au. In contrast, when Ni is used as the electrode material the zero-bias transmission coefficient is profoundly different as a result of the role played by the Ni d bands in the bonding between the molecule and the electrodes. Intriguingly, despite these differences the overall conducting properties depend little on the electrode material. We thus conclude that electron transport in dithienylethene is, for the cases studied, mainly governed by the intrinsic electronic structure of the molecule. © 2011 American Physical Society.

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

    Energy Technology Data Exchange (ETDEWEB)

    Riedl, H., E-mail: helmut.riedl@tuwien.ac.at [Christian Doppler Laboratory for Application Oriented Coating Development at the Institute of Materials Science and Technology, TU Wien, A-1040 Wien (Austria); Zálešák, J. [Erich Schmid Institute for Materials Science, Austria Academy of Science, A-8700 Leoben (Austria); Department of Physical Metallurgy and Materials Testing, Montanuniversität Leoben, A-8700 Leoben (Austria); Arndt, M. [Oerlikon Balzers, Oerlikon Surface Solutions AG, LI-9496 Balzers (Liechtenstein); Polcik, P. [Plansee Composite Materials GmbH, D-86983 Lechbruck am See (Germany); Holec, D. [Christian Doppler Laboratory for Application Oriented Coating Development at the Institute of Materials Science and Technology, TU Wien, A-1040 Wien (Austria); Department of Physical Metallurgy and Materials Testing, Montanuniversität Leoben, A-8700 Leoben (Austria); Mayrhofer, P. H. [Christian Doppler Laboratory for Application Oriented Coating Development at the Institute of Materials Science and Technology, TU Wien, A-1040 Wien (Austria); Institute of Materials Science and Technology, TU Wien, A-1040 Vienna (Austria)

    2015-09-28

    The formation of transfer material products on coated cutting and forming tools is a major failure mechanism leading to various sorts of wear. To describe the atomistic processes behind the formation of transfer materials, we use ab initio to study the adsorption energy as well as the implantation barrier of Al and Fe atoms for (001)-oriented surfaces of TiN, Ti{sub 0.50}Al{sub 0.50}N, Ti{sub 0.90}Si{sub 0.10}N, CrN, and Cr{sub 0.90}Si{sub 0.10}N. The interactions between additional atoms and nitride-surfaces are described for pure adhesion, considering no additional stresses, and for the implantation barrier. The latter, we simplified to the stress required to implant Al and Fe into sub-surface regions of the nitride material. The adsorption energies exhibit pronounced extrema at high-symmetry positions and are generally highest at nitrogen sites. Here, the binary nitrides are comparable to their ternary counterparts and the average adhesive energy is higher (more negative) on CrN than TiN based systems. Contrary, the implantation barrier for Al and Fe atoms is higher for the ternary systems Ti{sub 0.50}Al{sub 0.50}N, Ti{sub 0.90}Si{sub 0.10}N, and Cr{sub 0.90}Si{sub 0.10}N than for their binary counterparts TiN and CrN. Based on our results, we can conclude that TiN based systems outperform CrN based systems with respect to pure adhesion, while the Si-containing ternaries exhibit higher implantation barriers for Al and Fe atoms. The data obtained are important to understand the atomistic interaction of metal atoms with nitride-based materials, which is valid not just for machining operations but also for any combination such as interfaces between coatings and substrates or multilayer and phase arrangements themselves.

  11. Kinetic products in coordination networks: ab initio X-ray powder diffraction analysis.

    Science.gov (United States)

    Martí-Rujas, Javier; Kawano, Masaki

    2013-02-19

    Porous coordination networks are materials that maintain their crystal structure as molecular "guests" enter and exit their pores. They are of great research interest with applications in areas such as catalysis, gas adsorption, proton conductivity, and drug release. As with zeolite preparation, the kinetic states in coordination network preparation play a crucial role in determining the final products. Controlling the kinetic state during self-assembly of coordination networks is a fundamental aspect of developing further functionalization of this class of materials. However, unlike for zeolites, there are few structural studies reporting the kinetic products made during self-assembly of coordination networks. Synthetic routes that produce the necessary selectivity are complex. The structural knowledge obtained from X-ray crystallography has been crucial for developing rational strategies for design of organic-inorganic hybrid networks. However, despite the explosive progress in the solid-state study of coordination networks during the last 15 years, researchers still do not understand many chemical reaction processes because of the difficulties in growing single crystals suitable for X-ray diffraction: Fast precipitation can lead to kinetic (metastable) products, but in microcrystalline form, unsuitable for single crystal X-ray analysis. X-ray powder diffraction (XRPD) routinely is used to check phase purity, crystallinity, and to monitor the stability of frameworks upon guest removal/inclusion under various conditions, but rarely is used for structure elucidation. Recent advances in structure determination of microcrystalline solids from ab initio XRPD have allowed three-dimensional structure determination when single crystals are not available. Thus, ab initio XRPD structure determination is becoming a powerful method for structure determination of microcrystalline solids, including porous coordination networks. Because of the great interest across scientific

  12. Specific interactions between mycobacterial FtsZ protein and curcumin derivatives: Molecular docking and ab initio molecular simulations

    Science.gov (United States)

    Fujimori, Mitsuki; Sogawa, Haruki; Ota, Shintaro; Karpov, Pavel; Shulga, Sergey; Blume, Yaroslav; Kurita, Noriyuki

    2018-01-01

    Filamentous temperature-sensitive Z (FtsZ) protein plays essential role in bacteria cell division, and its inhibition prevents Mycobacteria reproduction. Here we adopted curcumin derivatives as candidates of novel inhibitors and investigated their specific interactions with FtsZ, using ab initio molecular simulations based on protein-ligand docking, classical molecular mechanics and ab initio fragment molecular orbital (FMO) calculations. Based on FMO calculations, we specified the most preferable site of curcumin binding to FtsZ and highlighted the key amino acid residues for curcumin binding at an electronic level. The result will be useful for proposing novel inhibitors against FtsZ based on curcumin derivatives.

  13. The role of Zn2+ dopants in the acid-basic catalysis on MgO(001) surface: Ab initio simulations of the dissociative chemisorption of R-O-R‧ and R-S-R‧ (R, R ‧ = H , CH3, C2H5)

    Science.gov (United States)

    Fonseca, Carla G.; Tavares, Sérgio R.; Soares, Carla V.; daFonseca, Bruno G.; Henrique, Fábio J. F. S.; Vaiss, Viviane S.; Souza, Wladmir F.; Chiaro, Sandra S. X.; Diniz, Renata; Leitão, Alexandre A.

    2017-07-01

    Ab initio calculations were performed to study the effect of the Zn2+ dopant on the reactivity and the catalytic activity of the MgO(001) surface toward molecular adsorption and dissociation reactions of the H2O, H2S, CH3CH2OH, CH3CH2SH and CH3SCH3 molecules. The electronic analysis showed that Zn2+ cation increased the reactivity of the surface locally. All molecules dissociate on both surfaces except for water and ethanol which only dissociate on the MgO:Zn(001) surface, confirming the increased reactivity in this surface. The ΔG ° for the dissociation reactions of the CH3CH2SH and CH3SCH3 molecules on pure MgO(001) surface is positive in the entire temperature range. On the other hand, the ΔG ° for H2S molecule is negative until 148.7 °C. In the case of the MgO:Zn(001) surface, the CH3CH2SH molecule dissociates in the entire temperature range and, for H2S molecule, the dissociation is spontaneous until 349.7 °C. The rate constants obtained for the dissociation reactions were very large because the reaction barriers are very low in both surfaces for all the studied molecules, except for CH3SCH3 molecule. The Zn-doped MgO(001) surface, besides being more reactive, presented a better catalytic activity than the MgO(001) surface for the dissociation of this molecule.

  14. Combining quantum wavepacket ab initio molecular dynamics with QM/MM and QM/QM techniques: Implementation blending ONIOM and empirical valence bond theory.

    Science.gov (United States)

    Sumner, Isaiah; Iyengar, Srinivasan S

    2008-08-07

    We discuss hybrid quantum-mechanics/molecular-mechanics (QM/MM) and quantum mechanics/quantum mechanics (QM/QM) generalizations to our recently developed quantum wavepacket ab initio molecular dynamics methodology for simultaneous dynamics of electrons and nuclei. The approach is a synergy between a quantum wavepacket dynamics, ab initio molecular dynamics, and the ONIOM scheme. We utilize this method to include nuclear quantum effects arising from a portion of the system along with a simultaneous description of the electronic structure. The generalizations provided here make the approach a potentially viable alternative for large systems. The quantum wavepacket dynamics is performed on a grid using a banded, sparse, and Toeplitz representation of the discrete free propagator, known as the "distributed approximating functional." Grid-based potential surfaces for wavepacket dynamics are constructed using an empirical valence bond generalization of ONIOM and further computational gains are achieved through the use of our recently introduced time-dependent deterministic sampling technique. The ab initio molecular dynamics is achieved using Born-Oppenheimer dynamics. All components of the methodology, namely, quantum dynamics and ONIOM molecular dynamics, are harnessed together using a time-dependent Hartree-like procedure. We benchmark the approach through the study of structural and vibrational properties of molecular, hydrogen bonded clusters inclusive of electronic, dynamical, temperature, and critical quantum nuclear effects. The vibrational properties are constructed through a velocity/flux correlation function formalism introduced by us in an earlier publication.

  15. Quantitative Comparison of a New Ab Initio Micrometeor Ablation Model with an Observationally Verifiable Standard Model

    Science.gov (United States)

    Meisel, David D.; Szasz, Csilla; Kero, Johan

    2008-06-01

    The Arecibo UHF radar is able to detect the head-echos of micron-sized meteoroids up to velocities of 75 km/s over a height range of 80 140 km. Because of their small size there are many uncertainties involved in calculating their above atmosphere properties as needed for orbit determination. An ab initio model of meteor ablation has been devised that should work over the mass range 10-16 kg to 10-7 kg, but the faint end of this range cannot be observed by any other method and so direct verification is not possible. On the other hand, the EISCAT UHF radar system detects micrometeors in the high mass part of this range and its observations can be fit to a “standard” ablation model and calibrated to optical observations (Szasz et al. 2007). In this paper, we present a preliminary comparison of the two models, one observationally confirmable. Among the features of the ab initio model that are different from the “standard” model are: (1) uses the experimentally based low pressure vaporization theory of O’Hanlon (A users’s guide to vacuum technology, 2003) for ablation, (2) uses velocity dependent functions fit from experimental data on heat transfer, luminosity and ionization efficiencies measured by Friichtenicht and Becker (NASA Special Publication 319: 53, 1973) for micron sized particles, (3) assumes a density and temperature dependence of the micrometeoroids and ablation product specific heats, (4) assumes a density and size dependent value for the thermal emissivity and (5) uses a unified synthesis of experimental data for the most important meteoroid elements and their oxides through least square fits (as functions of temperature, density, and/or melting point) of the tables of thermodynamic parameters given in Weast (CRC Handbook of Physics and Chemistry, 1984), Gray (American Institute of Physics Handbook, 1972), and Cox (Allen’s Astrophysical Quantities 2000). This utilization of mostly experimentally determined data is the main reason for

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

    Science.gov (United States)

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

    2014-03-01

    Recent developments in path integral methodology have significantly reduced the computational expense of including quantum mechanical effects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of these developments requires a considerable programming effort, which has hindered their adoption. Here we describe i-PI, an interface written in Python that has been designed to minimise the effort required to bring state-of-the-art path integral techniques to an electronic structure program. While it is best suited to first principles calculations and path integral molecular dynamics, i-PI can also be used to perform classical molecular dynamics simulations, and can just as easily be interfaced with an empirical forcefield code. To give just one example of the many potential applications of the interface, we use it in conjunction with the CP2K electronic structure package to showcase the importance of nuclear quantum effects in high-pressure water. Catalogue identifier: AERN_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AERN_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 138626 No. of bytes in distributed program, including test data, etc.: 3128618 Distribution format: tar.gz Programming language: Python. Computer: Multiple architectures. Operating system: Linux, Mac OSX, Windows. RAM: Less than 256 Mb Classification: 7.7. External routines: NumPy Nature of problem: Bringing the latest developments in the modelling of nuclear quantum effects with path integral molecular dynamics to ab initio electronic structure programs with minimal implementational effort. Solution method: State-of-the-art path integral molecular dynamics techniques are implemented in a Python interface. Any electronic structure code can be patched to receive the atomic

  17. Ab initio identification of human microRNAs based on structure motifs

    Directory of Open Access Journals (Sweden)

    Wiuf Carsten

    2007-12-01

    Full Text Available Abstract Background MicroRNAs (miRNAs are short, non-coding RNA molecules that are directly involved in post-transcriptional regulation of gene expression. The mature miRNA sequence binds to more or less specific target sites on the mRNA. Both their small size and sequence specificity make the detection of completely new miRNAs a challenging task. This cannot be based on sequence information alone, but requires structure information about the miRNA precursor. Unlike comparative genomics approaches, ab initio approaches are able to discover species-specific miRNAs without known sequence homology. Results MiRPred is a novel method for ab initio prediction of miRNAs by genome scanning that only relies on (predicted secondary structure to distinguish miRNA precursors from other similar-sized segments of the human genome. We apply a machine learning technique, called linear genetic programming, to develop special classifier programs which include multiple regular expressions (motifs matched against the secondary structure sequence. Special attention is paid to scanning issues. The classifiers are trained on fixed-length sequences as these occur when shifting a window in regular steps over a genome region. Various statistical and empirical evidence is collected to validate the correctness of and increase confidence in the predicted structures. Among other things, we propose a new criterion to select miRNA candidates with a higher stability of folding that is based on the number of matching windows around their genome location. An ensemble of 16 motif-based classifiers achieves 99.9 percent specificity with sensitivity remaining on an acceptable high level when requiring all classifiers to agree on a positive decision. A low false positive rate is considered more important than a low false negative rate, when searching larger genome regions for unknown miRNAs. 117 new miRNAs have been predicted close to known miRNAs on human chromosome 19. All

  18. Ab initio kinetics and thermal decomposition mechanism of mononitrobiuret and 1,5-dinitrobiuret

    Science.gov (United States)

    Sun, Hongyan; Vaghjiani, Ghanshyam L.

    2015-05-01

    Mononitrobiuret (MNB) and 1,5-dinitrobiuret (DNB) are tetrazole-free, nitrogen-rich, energetic compounds. For the first time, a comprehensive ab initio kinetics study on the thermal decomposition mechanisms of MNB and DNB is reported here. In particular, the intramolecular interactions of amine H-atom with electronegative nitro O-atom and carbonyl O-atom have been analyzed for biuret, MNB, and DNB at the M06-2X/aug-cc-pVTZ level of theory. The results show that the MNB and DNB molecules are stabilized through six-member-ring moieties via intramolecular H-bonding with interatomic distances between 1.8 and 2.0 Å, due to electrostatic as well as polarization and dispersion interactions. Furthermore, it was found that the stable molecules in the solid state have the smallest dipole moment amongst all the conformers in the nitrobiuret series of compounds, thus revealing a simple way for evaluating reactivity of fuel conformers. The potential energy surface for thermal decomposition of MNB was characterized by spin restricted coupled cluster theory at the RCCSD(T)/cc-pV∞ Z//M06-2X/aug-cc-pVTZ level. It was found that the thermal decomposition of MNB is initiated by the elimination of HNCO and HNN(O)OH intermediates. Intramolecular transfer of a H-atom, respectively, from the terminal NH2 group to the adjacent carbonyl O-atom via a six-member-ring transition state eliminates HNCO with an energy barrier of 35 kcal/mol and from the central NH group to the adjacent nitro O-atom eliminates HNN(O)OH with an energy barrier of 34 kcal/mol. Elimination of HNN(O)OH is also the primary process involved in the thermal decomposition of DNB, which processes C2v symmetry. The rate coefficients for the primary decomposition channels for MNB and DNB were quantified as functions of temperature and pressure. In addition, the thermal decomposition of HNN(O)OH was analyzed via Rice-Ramsperger-Kassel-Marcus/multi-well master equation simulations, the results of which reveal the formation

  19. Ab Initio Kinetics and Thermal Decomposition Mechanism of Mononitrobiuret and 1,5- Dinitrobiuret

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Hongyan; Vaghjiani, Ghanshyam G.

    2015-05-26

    Mononitrobiuret (MNB) and 1,5-dinitrobiuret (DNB) are tetrazole-free, nitrogen-rich, energetic compounds. For the first time, a comprehensive ab initio kinetics study on the thermal decomposition mechanisms of MNB and DNB is reported here. In particular, the intramolecular interactions of amine H-atom with electronegative nitro O-atom and carbonyl O-atom have been analyzed for biuret, MNB, and DNB at the M06-2X/aug-cc-pVTZ level of theory. The results show that the MNB and DNB molecules are stabilized through six-member-ring moieties via intramolecular H-bonding with interatomic distances between 1.8 and 2.0 Å, due to electrostatic as well as polarization and dispersion interactions. Furthermore, it was found that the stable molecules in the solid state have the smallest dipole moment amongst all the conformers in the nitrobiuret series of compounds, thus revealing a simple way for evaluating reactivity of fuel conformers. The potential energy surface for thermal decomposition of MNB was characterized by spin restricted coupled cluster theory at the RCCSD(T)/cc-pV∞ Z//M06-2X/aug-cc-pVTZ level. It was found that the thermal decomposition of MNB is initiated by the elimination of HNCO and HNN(O)OH intermediates. Intramolecular transfer of a H-atom, respectively, from the terminal NH2 group to the adjacent carbonyl O-atom via a six-member-ring transition state eliminates HNCO with an energy barrier of 35 kcal/mol and from the central NH group to the adjacent nitro O-atom eliminates HNN(O)OH with an energy barrier of 34 kcal/mol. Elimination of HNN(O)OH is also the primary process involved in the thermal decomposition of DNB, which processes C2v symmetry. The rate coefficients for the primary decomposition channels for MNB and DNB were quantified as functions of temperature and pressure. In addition, the thermal decomposition of HNN(O)OH was analyzed via Rice–Ramsperger–Kassel–Marcus/multi-well master equation simulations, the results of which reveal the

  20. Ab initio molecular geometry and anharmonic vibrational spectra of thiourea and thiourea-d4.

    Science.gov (United States)

    Kowal, Andrzej T

    2011-03-01

    Potential energy surface (PES) of thiourea, SC(NH(2))(2), has been searched for stable conformers under C(1), C(s), C(2), and C(2v) symmetry constraints by post-Hartree-Fock ab initio methods with electron correlation level varying from second-order Moeller-Plesset perturbation theory (MP2) to quadratic configuration interaction with single and double excitations (QCISD) and basis sets of double- and triple-zeta quality within 6-31+G(d,p) to aug-cc-pVTZ range. Thiourea conformers of C(2) and C(s) symmetry have been found as stationary points on the PES with no imaginary frequencies at MP2/6-31+G(d,p) level, whereas only the C(2) conformer seems as true minimum when basis sets containing more polarization and/or diffuse functions were used. At QCISD/cc-pVTZ level, only the C(2) thiourea conformer has been found as true minimum on the PES. Anharmonic vibrational spectra of C(2) conformers of thiourea and thiourea-d(4) have been computed by vibrational self-consistent field (VSCF) and correlation-corrected VSCF methods using quartic force field approximation at MP2/TZV+(2d,2p), and MP2/6-311+G(3df,2p) level and direct approach at MP2/6-31+G(2d,p) level. Both quartic force field and direct VSCF methods used PES expansion in curvilinear (internal) coordinates. Wavenumbers of fundamental, first overtone, and combination transitions of C(2) symmetry conformer have been calculated for natural abundance thiourea and thiourea-d(4) isotopomer. Anharmonic corrections originating from mean field and mode coupling effects vary from 5 to 60 cm(-1), whereas mode-mode correlation contribution seems significant in the case of ν(N-H) stretching and δ(NH(2)) deformation modes (15-5 cm(-1)). Application of internal coordinates in the VSCF calculation results in slight underestimation of δ(NH(2)) deformation mode fundamentals and correct description of out-of-plane large-amplitude τ(SCNH) modes. Copyright © 2010 Wiley Periodicals, Inc.

  1. Ab Initio SCF MO Calculation of Ionisation Energies and Charge Distributions of TCNQ and Its Mono- and Divalent Anions

    NARCIS (Netherlands)

    Jonkman, H.T.; Velde, G.A. van der; Nieuwpoort, W.C.

    1974-01-01

    Ab initio SCF MO calculations using a contracted double zeta basis set of 168 gaussian type functions were performed on TCNQ+, TCNQ, TCNQ- and TCNQ2-. The ionisation potentials obtained from total energy differences are generally 0.25-0.50 eV higher than the corresponding negative orbital energies

  2. Quantum wavepacket ab initio molecular dynamics: an approach for computing dynamically averaged vibrational spectra including critical nuclear quantum effects.

    Science.gov (United States)

    Sumner, Isaiah; Iyengar, Srinivasan S

    2007-10-18

    We have introduced a computational methodology to study vibrational spectroscopy in clusters inclusive of critical nuclear quantum effects. This approach is based on the recently developed quantum wavepacket ab initio molecular dynamics method that combines quantum wavepacket dynamics with ab initio molecular dynamics. The computational efficiency of the dynamical procedure is drastically improved (by several orders of magnitude) through the utilization of wavelet-based techniques combined with the previously introduced time-dependent deterministic sampling procedure measure to achieve stable, picosecond length, quantum-classical dynamics of electrons and nuclei in clusters. The dynamical information is employed to construct a novel cumulative flux/velocity correlation function, where the wavepacket flux from the quantized particle is combined with classical nuclear velocities to obtain the vibrational density of states. The approach is demonstrated by computing the vibrational density of states of [Cl-H-Cl]-, inclusive of critical quantum nuclear effects, and our results are in good agreement with experiment. A general hierarchical procedure is also provided, based on electronic structure harmonic frequencies, classical ab initio molecular dynamics, computation of nuclear quantum-mechanical eigenstates, and employing quantum wavepacket ab initio dynamics to understand vibrational spectroscopy in hydrogen-bonded clusters that display large degrees of anharmonicities.

  3. Ab initio study of ferromagnetic La 0.5 Ba 0.5 CoO 3

    Indian Academy of Sciences (India)

    /fulltext/jcsc/115/05-06/0439-0446. Keywords. Ferromagnet; lanthanum barium cobalt oxide; phase transition; phonons. Abstract. We study structure and magnetic properties of La0.5Ba0.5CoO3 (LBCO) using ab initio density functional theory ...

  4. Collective solvent coordinates for the infrared spectrum of HOD in D2O based on an ab initio electrostatic map

    NARCIS (Netherlands)

    Hayashi, T; Jansen, TL; Zhuang, W; Mukamel, S

    2005-01-01

    An ab initio MP2 vibrational Hamiltonian of HOD in an external electrostatic potential parametrized by the electric field and its gradient-tensor is constructed. By combining it with the fluctuating electric field induced by the D2O solvent obtained from molecular dynamics simulations, we calculate

  5. Ab initio description of nonlinear dynamics of coupled microdisk resonators with application to self-trapping dynamics

    OpenAIRE

    Ramezani, Hamidreza; Kottos, Tsampikos; Shuvayev, Vladimir; Deych, Lev

    2011-01-01

    Ab initio approach is used to describe the time evolution of the amplitudes of whispering gallery modes in a system of coupled microdisk resonators with Kerr nonlinearity. It is shown that this system demonstrates a transition between Josephson-like nonlinear oscillations and self-trapping behavior. Manifestation of this transition in the dynamics of radiative losses is studied.

  6. Ab initio studies on [bmim][PF6]–CO2 mixture and CO2 clusters

    Indian Academy of Sciences (India)

    Wintec

    on CO2 clusters reveals the greater tendency of the clusters with more CO2 units, to deviate from the linear geometry. Keywords. Ionic liquids; supercritical carbon dioxide; ab initio; molecular dynamics. 1. Introduction. The increase in the pollution level due to the solvents used currently in industries demands alternative ...

  7. Ab initio calculations on 2-imidazolyl-2-thiazolyl azo compounds - an investigation of potential near-infrared absorbing structures

    DEFF Research Database (Denmark)

    Åstrand, P.-O.; Bak, K.L.; Sauer, S.P.A.

    2001-01-01

    The two lowest singlet excitation energies of 26 2-imidazolyl-2-thiazolylazo compounds have been investigated by ab initio methods within the second-order polarization propagator approximation (SOPPA). Various combinations of 4- and 5-substituents at both the imidazole and thiazole units have bee...

  8. Ab initio van der waals interactions in simulations of water alter structure from mainly tetrahedral to high-density-like

    DEFF Research Database (Denmark)

    Møgelhøj, Andreas; Kelkkanen, Kari André; Wikfeldt, K Thor

    2011-01-01

    The structure of liquid water at ambient conditions is studied in ab initio molecular dynamics simulations in the NVE ensemble using van der Waals (vdW) density-functional theory, i.e., using the new exchange-correlation functionals optPBE-vdW and vdW-DF2, where the latter has softer nonlocal...

  9. Brønsted acidity of protic ionic liquids: a modern ab initio valence bond theory perspective.

    Science.gov (United States)

    Patil, Amol Baliram; Mahadeo Bhanage, Bhalchandra

    2016-09-21

    Room temperature ionic liquids (ILs), especially protic ionic liquids (PILs), are used in many areas of the chemical sciences. Ionicity, the extent of proton transfer, is a key parameter which determines many physicochemical properties and in turn the suitability of PILs for various applications. The spectrum of computational chemistry techniques applied to investigate ionic liquids includes classical molecular dynamics, Monte Carlo simulations, ab initio molecular dynamics, Density Functional Theory (DFT), CCSD(t) etc. At the other end of the spectrum is another computational approach: modern ab initio Valence Bond Theory (VBT). VBT differs from molecular orbital theory based methods in the expression of the molecular wave function. The molecular wave function in the valence bond ansatz is expressed as a linear combination of valence bond structures. These structures include covalent and ionic structures explicitly. Modern ab initio valence bond theory calculations of representative primary and tertiary ammonium protic ionic liquids indicate that modern ab initio valence bond theory can be employed to assess the acidity and ionicity of protic ionic liquids a priori.

  10. Ab initio electronic structure and correlations in pristine and potassium-doped molecular crystals of copper phthalocyanine

    NARCIS (Netherlands)

    Giovannetti, G.; Brocks, G.; van den Brink, J.

    2008-01-01

    We investigate the effect that potassium intercalation has on the electronic structure of copper phthalocyanine (CuPc) molecular crystals by means of ab initio density functional calculations. Pristine CuPc (in its alpha and beta structures) is found to be an insulator containing local magnetic

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

    Science.gov (United States)

    Zhang, Yang

    2014-02-01

    We develop and test a new pipeline in CASP10 to predict protein structures based on an interplay of I-TASSER and QUARK for both free-modeling (FM) and template-based modeling (TBM) targets. The most noteworthy observation is that sorting through the threading template pool using the QUARK-based ab initio models as probes allows the detection of distant-homology templates which might be ignored by the traditional sequence profile-based threading alignment algorithms. Further template assembly refinement by I-TASSER resulted in successful folding of two medium-sized FM targets with >150 residues. For TBM, the multiple threading alignments from LOMETS are, for the first time, incorporated into the ab initio QUARK simulations, which were further refined by I-TASSER assembly refinement. Compared with the traditional threading assembly refinement procedures, the inclusion of the threading-constrained ab initio folding models can consistently improve the quality of the full-length models as assessed by the GDT-HA and hydrogen-bonding scores. Despite the success, significant challenges still exist in domain boundary prediction and consistent folding of medium-size proteins (especially beta-proteins) for nonhomologous targets. Further developments of sensitive fold-recognition and ab initio folding methods are critical for solving these problems. Copyright © 2013 Wiley Periodicals, Inc.

  12. Ab Initio Calculated and Experimentally Measured Raman Spectra of Spodumene (LiAlSi2O6)

    Science.gov (United States)

    Stangarone, C.; Prencipe, M.; Mantovani, L.; Bersani, D.; Tribaudino, M.; Lottici, P. P.

    2014-06-01

    Polarization Raman measurements on spodumene enabled the identification of all 30 active modes (14 Ag and 16 Bg). Ab initio CRYSTAL14 calculations (WC1LYP hamiltonian) give very good agreement for frequencies (ǀΔǀ< 4.8 cm^-1) and intensities.

  13. Structural and magnetic correlations in liquid oxygen an ab initio molecular dynamics study

    CERN Document Server

    Oda, T

    2003-01-01

    We have carried out an ab initio molecular dynamics simulation of liquid oxygen, a molecular fluid in which the individual O sub 2 units carry a molecular magnetic moment. In addition to the atomic and electronic structures, our simulation describes the evolution of the noncollinear magnetic structure. The atomic structure shows a strong preference for parallel alignment of first-neighbour molecules. The magnetic structure shows strong short-range antiferromagnetic correlations, in agreement with spin-polarized neutron diffraction data. The short-range correlations, observed in both the structural and magnetic properties, primarily result from appropriate trajectories of colliding O sub 2 molecules. Our simulation also reveals the occurrence of several long-living O sub 4 units which survive for time periods longer than four times the average residence time observed during collisions.

  14. Magnetic properties of vanadium doped CdTe: Ab initio calculations

    Energy Technology Data Exchange (ETDEWEB)

    Goumrhar, F. [Laboratory of Physics of High Energy, Modeling & Simulations (LPHE-MS), Faculty of Sciences, Mohammed V University of Rabat, Av. Ibn Batouta, B.P. 1014 Rabat (Morocco); Bahmad, L., E-mail: bahmad@fsr.ac.ma [Laboratory of Magnetism and High Energy Physics (LMPHE-URAC12), Faculty of Sciences, Mohammed V University of Rabat, Av. Ibn Batouta, B.P. 1014 Rabat (Morocco); Mounkachi, O. [Material and Nanomaterial Center, MAScIR Fondation, Rabat (Morocco); Benyoussef, A. [Laboratory of Magnetism and High Energy Physics (LMPHE-URAC12), Faculty of Sciences, Mohammed V University of Rabat, Av. Ibn Batouta, B.P. 1014 Rabat (Morocco); Material and Nanomaterial Center, MAScIR Fondation, Rabat (Morocco); Hassan II Academy of Sciences and Technology, Rabat (Morocco)

    2017-04-15

    In this paper, we are applying the ab initio calculations to study the magnetic properties of vanadium doped CdTe. This study is based on the Korringa–Kohn–Rostoker method (KKR) combined with the coherent potential approximation (CPA), within the local density approximation (LDA). This method is called KKR-CPA-LDA. We have calculated and plotted the density of states (DOS) in the energy diagram for different concentrations of dopants. We have also investigated the magnetic and half-metallic properties of this compound and shown the mechanism of exchange interaction. Moreover, we have estimated the Curie temperature T{sub c} for different concentrations. Finally, we have shown how the crystal field and the exchange splittings vary as a function of the concentrations.

  15. Progress towards an ab initio real-time treatment of warm dense matter

    Science.gov (United States)

    Baczewski, Andrew; Cangi, Attila; Hansen, Stephanie; Jensen, Daniel

    2017-10-01

    Time-dependent density functional theory (TDDFT) provides an accurate description of equilibrium properties of warm dense matter, such as the dynamic structure factor (Baczewski et al., Phys. Rev. Lett., 116(11), 2016). While non-equilibrium properties, such as stopping power, have also been demonstrated to be within the grasp of TDDFT, the ultrafast isochoric heating of condensed matter into the warm dense state, enabled by recent advances in XFELs, remains beyond its capabilities. In this talk, we will describe the successes of and continuing challenges for TDDFT for warm dense matter, and present progress towards a more complete ab initio treatment of isochoric x-ray heating. Sandia National Laboratories is a multi-mission laboratory managed and operated by National Technology and Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International, Inc., for the DOE's National Nuclear Security Administration under contract DE-NA0003525.

  16. Raman Spectroscopy and Ab-Initio Model Calculations on Ionic Liquids

    DEFF Research Database (Denmark)

    Berg, Rolf W.

    2007-01-01

    A review of the recent developments in the study and understanding of room temperature ionic liquids are given. An intimate picture of how and why these liquids are not crystals at ambient conditions is attempted, based on evidence from crystallographical results combined with vibrational...... spectroscopy and ab-initio molecular orbital calculations. A discussion is given, based mainly on some recent FT-Raman spectroscopic results on the model ionic liquid system of 1-butyl-3-methylimidazolium ([C4mim][X]) salts. The rotational isomerism of the [C4mim]þ cation is described: the presence of anti...... and gauche conformers that has been elucidated in remarkable papers by Hamaguchi et al. Such presence of a conformational equilibrium seems to be a general feature of the room temperature liquids. Then the ‘‘localized structure features’’ that apparently exist in ionic liquids are described. It is hoped...

  17. Ab-initio molecular dynamics study of lanthanides in liquid sodium

    Science.gov (United States)

    Li, Xiang; Samin, Adib; Zhang, Jinsuo; Unal, C.; Mariani, R. D.

    2017-02-01

    To mitigate the fuel cladding chemical interaction (FCCI) phenomena in liquid sodium cooled fast reactors, a fundamental understanding of the lanthanide (Ln) transport through liquid Nasbnd Cs filled pores in Usbnd Zr fuel is necessary. In this study, we investigate three abundant Ln fission products diffusion coefficients in liquid Na at multiple temperatures. By utilization of Ab-initio Molecular Dynamics, the Ln diffusivities are found to be in the magnitude order of liquid diffusion (10-5cm2 /s) and the temperature dependence of the diffusivity for different lanthanides in liquid sodium was explored. It is also observed that dilute concentration of Pr and Nd led to a significant change in Na diffusivity. The structural and electronic properties of Nasbnd Ln metallic systems have been investigated. The total coordination number shows dependence on both the temperature and the composition.

  18. Fast and reliable ab initio calculation of crystal field splittings in lanthanide complexes

    Science.gov (United States)

    Hallmen, P. P.; Köppl, C.; Rauhut, G.; Stoll, H.; van Slageren, J.

    2017-10-01

    Ab initio calculations of crystal field splittings and magnetic properties of lanthanide complexes are usually performed using state-averaged complete active space self-consistent field (CASSCF) calculations and a subsequent spin-orbit calculation mixing the CASSCF wave functions (CASSCF/state interaction with spin-orbit coupling). Because this approach becomes very time-consuming for large molecules, simplifications have been proposed in the literature to determine the state-averaged orbitals by configuration-averaged Hartree-Fock (CAHF) instead of CASSCF. We present an approach which is an extension of the CAHF method. We combine the techniques of local density fitting with CAHF and achieve a significant speedup compared to CASSCF without loss in accuracy. To assess the performance of our method, we apply it to three well-known molecules, namely, Er[N(SiMe3)2]3, Er(trensal), and the double-decker (NBu4)+ [Er(Pc)2]-.

  19. Ab Initio Quantum Monte Carlo Simulation of the Warm Dense Electron Gas in the Thermodynamic Limit

    Science.gov (United States)

    Dornheim, Tobias; Groth, Simon; Sjostrom, Travis; Malone, Fionn D.; Foulkes, W. M. C.; Bonitz, Michael

    2016-10-01

    We perform ab initio quantum Monte Carlo (QMC) simulations of the warm dense uniform electron gas in the thermodynamic limit. By combining QMC data with the linear response theory, we are able to remove finite-size errors from the potential energy over the substantial parts of the warm dense regime, overcoming the deficiencies of the existing finite-size corrections by Brown et al. [Phys. Rev. Lett. 110, 146405 (2013)]. Extensive new QMC results for up to N =1000 electrons enable us to compute the potential energy V and the exchange-correlation free energy Fxc of the macroscopic electron gas with an unprecedented accuracy of |Δ V |/|V |,|Δ Fxc|/|F |xc˜10-3 . A comparison of our new data to the recent parametrization of Fxc by Karasiev et al. [Phys. Rev. Lett. 112, 076403 (2014)] reveals significant deviations to the latter.

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

    CERN Document Server

    Coeck, S; Herbane, M; Kozlov, V Yu; Kraev, I S; Tandecki, M; Wauters, F; Beck, M; Delahaye, P; Herlert, A; Sturm, S; Severijns, N

    2007-01-01

    Various ab initio simulations on the behavior of ion clouds consisting of a small number of positively charged ions stored in the WITCH double Penning trap system are described. A general description of the simulation code used is presented and the expected behavior of the particles in the first of the two Penning traps is discussed. Special attention is paid to the influence of this behavior on the operation of the experimental setup. The effect of electric excitations on the ion motions is described in detail. Also the transfer of the ions between the two traps and consequences for their motion in the second Penning trap are addressed. Scaled Coulomb force simulations are used to estimate the size of the ion cloud inside the Penning traps for larger numbers of particles.

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

    KAUST Repository

    Ohto, Tatsuhiko

    2013-05-28

    Melamine on Cu(001) is mechanically unstable under the current of a scanning tunneling microscope tip and can switch among configurations. However, these are not equally accessible, and the switching critical current depends on the bias polarity. In order to explain such rich phenomenology, we have developed a scheme to evaluate the evolution of the reaction paths and activation barriers as a function of bias, which is rooted in the nonequilibrium Green\\'s function method implemented within density functional theory. This, combined with the calculation of the inelastic electron tunneling spectroscopy signal, allows us to identify the vibrational modes promoting the observed molecular conformational changes. Finally, once our ab initio results are used within a resonance model, we are able to explain the details of the switching behavior, such as its dependence on the bias polarity, and the noninteger power relation between the reaction rate constants and both the bias voltage and the electric current. © 2013 American Physical Society.

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

    DEFF Research Database (Denmark)

    Berg, Rolf W.

    2009-01-01

    that the structural resolving power of Raman spectroscopy will be appreciated by the reader, when used on crystals of known conformation and on the corresponding liquids, especially in combination with modern quantum mechanics calculations. It is hoped that these inetrdisciplinary methods will be applied to many more......A review of the recent developments in the study and understanding of room temperature ionic liquids are given. An intimate picture of how and why these liquids are not crystals at ambient conditions is attempted, based on evidence from crystallographical results combined with vibrational...... spectroscopy and ab-initio molecular orbital calculations. A discussion is given, based mainly on some recent FT- Raman spectroscopic results on the model ionic liquid system of 1-butyl-3-methyl-imidazolium ([C4C1Im]+X-) salts. The rotational isomerism of the [C4C1Im]+ cation is described: the presence of anti...

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

    Directory of Open Access Journals (Sweden)

    Xiaowei Li

    2015-01-01

    Full Text Available Structure and properties of Cu-doped diamond-like carbon films (DLC were investigated using ab initio calculations. The effect of Cu concentrations (1.56∼7.81 at.% on atomic bond structure was mainly analyzed to clarify the residual stress reduction mechanism. Results showed that with introducing Cu into DLC films, the residual compressive stress decreased firstly and then increased for each case with the obvious deterioration of mechanical properties, which was in agreement with the experimental results. Structural analysis revealed that the weak Cu-C bond and the relaxation of both the distorted bond angles and bond lengths accounted for the significant reduction of residual compressive stress, while at the higher Cu concentration the increase of residual stress attributed to the existence of distorted Cu-C structures and the increased fraction of distorted C-C bond lengths.

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

    Energy Technology Data Exchange (ETDEWEB)

    Li, Xiaowei; Ke, Peiling; Wang, Aiying, E-mail: aywang@nimte.ac.cn [Key Laboratory of Marine Materials and Related Technologies, Zhejiang Key Laboratory of Marine Materials and Protective Technologies, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo 315201 (China)

    2015-01-15

    Structure and properties of Cu-doped diamond-like carbon films (DLC) were investigated using ab initio calculations. The effect of Cu concentrations (1.56∼7.81 at.%) on atomic bond structure was mainly analyzed to clarify the residual stress reduction mechanism. Results showed that with introducing Cu into DLC films, the residual compressive stress decreased firstly and then increased for each case with the obvious deterioration of mechanical properties, which was in agreement with the experimental results. Structural analysis revealed that the weak Cu-C bond and the relaxation of both the distorted bond angles and bond lengths accounted for the significant reduction of residual compressive stress, while at the higher Cu concentration the increase of residual stress attributed to the existence of distorted Cu-C structures and the increased fraction of distorted C-C bond lengths.

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

    Science.gov (United States)

    Li, Xiaowei; Ke, Peiling; Wang, Aiying

    2015-01-01

    Structure and properties of Cu-doped diamond-like carbon films (DLC) were investigated using ab initio calculations. The effect of Cu concentrations (1.56˜7.81 at.%) on atomic bond structure was mainly analyzed to clarify the residual stress reduction mechanism. Results showed that with introducing Cu into DLC films, the residual compressive stress decreased firstly and then increased for each case with the obvious deterioration of mechanical properties, which was in agreement with the experimental results. Structural analysis revealed that the weak Cu-C bond and the relaxation of both the distorted bond angles and bond lengths accounted for the significant reduction of residual compressive stress, while at the higher Cu concentration the increase of residual stress attributed to the existence of distorted Cu-C structures and the increased fraction of distorted C-C bond lengths.

  6. Implementation of $ab$ $initio$ perturbed angular correlation observables for analysis of fluctuating quadrupole interactions

    CERN Document Server

    Barbosa, Marcelo

    A review about the nuclear properties, namely the nuclear moments (magnetic dipole moment and electric quadrupole moment) and their interaction with electromagnetic fields external to the nucleus (hyperfine interactions), as well as the angular distribution of radiation produced by $\\gamma$-decay, is presented. A detailed description about the theory of Perturbed Angular Correlations was done, including the comparison between $\\gamma-\\gamma$- correlations and $e^{-}- \\gamma$ correlations. For dynamic nuclear interactions, an introduction to the theory of stochastic states in PAC was performed. We focused on ab-initio implementation of observables for analyzing fluctuating quadrupole hyperfine interactions on time dependent perturbed angular correlations experiments. The development of computacional codes solving the full problem, adapted to fit data obtained on single crystals or polycrystals for two-state transient fields with any axial symmetry and orientation was the main purpose of this work. The final pa...

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

    Science.gov (United States)

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

    2011-09-09

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

  8. Ab Initio Assessment of the Bonding in Disulfonates Containing Divalent Nitrogen and Phosphorus Atoms

    DEFF Research Database (Denmark)

    Andersen, Vinca Bonde; Berg, Rolf W.; Shim, Irene

    2017-01-01

    The iminodisulfonate, [N(SO3)2]3–, and phosphinodisulfonate, [P(SO3)2]3–, ions have been investigated by performing ab initio MP2/6-311+G**calculations. The nitrogen and phosphorus atoms as part of the ions are shown to be divalent with a negative charge and two lone pairs on the nitrogen...... and phosphorus atoms. The experimentally known calcium sodium iminodisulfonate trihydrate and the analogous unknown compound calcium sodium phosphinodisulfonate trihydrate have also been investigated using the MP2/6-311+G** calculations. For the nitrogen compound, only minor changes occur in the iminodisulfonate...... ion when it becomes part of the calcium sodium iminodisulfonate trihydrate. For the phosphorus compound, the geometry of the phosphinodisulfonate ion changes significantly as part of calcium sodium phosphinodisulfonate trihydrate. Furthermore, the charges associated with the atoms in calcium sodium...

  9. Ab initio molecular dynamics simulation of pressure-induced phase transition in MgS

    Science.gov (United States)

    Begeç, Ebru; Eker, Sıtkı; Bozdemir, Süleyman

    2017-08-01

    Pressure-induced phase transition in MgS is studied using a constant pressure ab initio molecular dynamics method, and a solid evidence of existence of its high-pressure phase is provided. As predicted by total energy calculations, MgS undergoes a structural phase transformation from the rocksalt structure to a CsCl-type structure under hydrostatic pressure. The transformation mechanism is characterized, and two intermediate phases having P4/ nmm and P21/ m symmetries for the rocksalt-to-CsCl-type phase transformation of MgS are proposed, which is different from the previously proposed mechanisms. We also study this phase transition using the total energy calculations. Our predicted transition parameters and bulk properties are in good agreement with the earlier first principle simulations.

  10. Estudo ab-initio da a-alanina em meio aquoso

    Directory of Open Access Journals (Sweden)

    Sambrano Júlio Ricardo

    1999-01-01

    Full Text Available Ab initio Hartree-Fock (HF, Density Functional (B3LYP and electron correlation (MP2 methods have been used to caracterize the aqueous medium intramolecular hydrogen bond in a-alanine. The 6-31G* and 6-31++G** were taken from Gaussian94 library. We were concerned on the structure of three conformers of a-alanine, in their neutral form plus on the structure of the zwitterionic form (Z. The Z structure is a stationary point at the HF/6-31G* level but it is not when diffuse functions and electron correlation are included. This results shows that the Z form does not exist in the gas phase. The inclusion of solvent effects changed significantly the results obtained in gas phase, therefore this inclusion make the Z form a stationary point within all level of theory, and the relative energy depends dramatically on the level of calculation.

  11. AB INITIO STUDY OF AMMONIA CLUSTERS: (NH3n (n = 2-6

    Directory of Open Access Journals (Sweden)

    Herudi Kandau

    2010-06-01

    Full Text Available Hydrogen bonded neutral clusters of ammonia, (NH3n (n = 2-6, have been theoretically investigated employing the D95++(d,p (and wherever necessary, higher basis sets at the Hartree-Fock (HF level as well as with second-order Møller-Plesset (MP2 perturbation theory. While the ammonia trimer and tetramer exhibit perfect molecular symmetries and are nonpolar, the pentamer and hexamer both optimize with slight deviations from perfect symmetries and are seen to posses marginal, but nonzero dipole moments. The (NH3n linear clusters are seen to be chemically softer than the corresponding cyclic ones.   Keywords: ab initio calculation, ammonia clusters, Hartree-Fock, Møller-Plesset

  12. Spectroscopy of 50Sc and ab initio calculations of B (M 3 ) strengths

    Science.gov (United States)

    Garnsworthy, A. B.; Bowry, M.; Olaizola, B.; Holt, J. D.; Stroberg, S. R.; Cruz, S.; Georges, S.; Hackman, G.; MacLean, A. D.; Measures, J.; Patel, H. P.; Pearson, C. J.; Svensson, C. E.

    2017-10-01

    The GRIFFIN spectrometer at TRIUMF-ISAC has been used to study excited states and transitions in 50Sc following the β decay of 50Ca. Branching ratios were determined from the measured γ -ray intensities, and angular correlations of γ rays have been used to firmly assign the spins of excited states. The presence of an isomeric state that decays by an M 3 transition with a B (M 3 ) strength of 13.6(7) W.u. has been confirmed. We compare the first ab initio calculations of B (M 3 ) strengths in light- and medium-mass nuclei from the valence-space in-medium similarity renormalization group approach, using consistently derived effective Hamiltonians and effective M 3 operator. The experimental data are well reproduced for isoscalar M 3 transitions when using bare g factors, but the strength of isovector M 3 transitions are found to be underestimated by an order of magnitude.

  13. Quantifying Ab Initio Equation of State Errors for Hydrogen-Helium Mixtures

    Science.gov (United States)

    Clay, Raymond; Morales, Miguel

    2017-06-01

    In order to produce predictive models of Jovian planets, an accurate equation of state for hydrogen-helium mixtures is needed over pressure and temperature ranges spanning multiple orders of magnitude. While extensive theoretical work has been done in this area, previous controversies regarding the equation of state of pure hydrogen have demonstrated exceptional sensitivity to approximations commonly employed in ab initio calculations. To this end, we present the results of our quantum Monte Carlo based benchmarking studies for several major classes of density functionals. Additionally, we expand upon our published results by considering the impact that ionic finite size effects and density functional errors translate to errors in the equation of state. Sandia National Laboratories is a multi-mission laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

  14. Haber Process Made Efficient by Hydroxylated Graphene: Ab Initio Thermochemistry and Reactive Molecular Dynamics.

    Science.gov (United States)

    Chaban, Vitaly V; Prezhdo, Oleg V

    2016-07-07

    The Haber-Bosch process is the main industrial method for producing ammonia from diatomic nitrogen and hydrogen. We use a combination of ab initio thermochemical analysis and reactive molecular dynamics to demonstrate that a significant increase in the ammonia production yield can be achieved using hydroxylated graphene and related species. Exploiting the polarity difference between N2/H2 and NH3, as well as the universal proton acceptor behavior of NH3, we demonstrate a strong shift of the equilibrium of the Haber-Bosch process toward ammonia (ca. 50 kJ mol(-1) enthalpy gain and ca. 60-70 kJ mol(-1) free energy gain). The modified process is of significant importance to the chemical industry.

  15. High-accuracy extrapolated ab initio thermochemistry of the vinyl, allyl, and vinoxy radicals.

    Science.gov (United States)

    Tabor, Daniel P; Harding, Michael E; Ichino, Takatoshi; Stanton, John F

    2012-07-26

    Enthalpies of formation at both 0 and 298 K were calculated according to the HEAT (High-accuracy Extrapolated Ab initio Thermochemistry) protocol for the title molecules, all of which play important roles in combustion chemistry. At the HEAT345-(Q) level of theory, recommended enthalpies of formation at 0 K are 301.5 ± 1.3, 180.3 ± 1.8, and 23.4 ± 1.5 kJ mol(-1) for vinyl, allyl, and vinoxy, respectively. At 298 K, the corresponding values are 297.3, 168.6, and 16.1 kJ mol(-1), with the same uncertainties. The calculated values for the three radicals are in excellent agreement with the corresponding experimental values, but the uncertainties associated with the HEAT values for vinoxy are considerably smaller than those based on experimental studies.

  16. Selective sensing of ethylene and glucose using carbon-nanotube-based sensors: An ab initio investigation

    Science.gov (United States)

    Li, Yan; Hodak, Miroslav; Lu, Wenchang; Bernholc, Jerry

    Functionalized carbon nanotubes have great potential for nanoscale sensing applications, yet many aspects of their sensing mechanisms are not understood. We investigate two paradigmatic sensor configurations for detection of biologically important molecules through ab initio calculations: a non-covalently functionalized nanotube for glucose detection and a covalently functionalized nanotube for ethylene detection. Despite of their structural and chemical simplicities, glucose and ethylene control key life processes of humans and plants, respectively. We evaluate the sensors' electrical conductance and transmission coefficients at the full density-functional theory level via the non-equilibrium Green's function method. A clear atomistic picture emerges about the mechanisms involved in glucose and ethylene sensing. While functionalized semiconducting nanotubes exhibit good sensitivities in both cases, the current through metallic nanotubes is only weakly affected by analyte attachment. We also investigate the effects of band gaps of the nanotubes and changes to the receptors on the detection sensitivities. These quantitative results can guide the design of improved sensors.

  17. AB INITIO Modeling of Thermomechanical Properties of Mo-Based Alloys for Fossil Energy Conversion

    Energy Technology Data Exchange (ETDEWEB)

    Ching, Wai-Yim

    2013-12-31

    In this final scientific/technical report covering the period of 3.5 years started on July 1, 2011, we report the accomplishments on the study of thermo-mechanical properties of Mo-based intermetallic compounds under NETL support. These include computational method development, physical properties investigation of Mo-based compounds and alloys. The main focus is on the mechanical and thermo mechanical properties at high temperature since these are the most crucial properties for their potential applications. In particular, recent development of applying ab initio molecular dynamic (AIMD) simulations to the T1 (Mo{sub 5}Si{sub 3}) and T2 (Mo{sub 5}SiB{sub 2}) phases are highlighted for alloy design in further improving their properties.

  18. All Electron ab initio Investigations of the Electronic States of the MoN Molecule

    DEFF Research Database (Denmark)

    Shim, Irene; Gingerich, Karl A.

    1999-01-01

    The low lying electronic states of the molecule MoN have been investigated by performing all electron ab initio multi-configuration self-consistent-field (CASSCF) calculations. The relativistic corrections for the one electron Darwin contact term and the relativistic mass-velocity correction have...... been determined in perturbation calculations. The electronic ground state is confirmed as being 4 . The chemical bond of MoN has triple bond character due to the approximately fully occupied delocalized bonding and orbitals. The spectroscopic constants for the ground state and ten excited states have...... been derived. The excited doublet states, 2 , 2 , 2 , and 2 + are found to be lower lying than the 4 state that has been investigated experimentally. Elaborate multi configuration configuration interaction (MRCI) calculations have been carried out for the states 4 and 4 using various basis sets...

  19. A simplified ab initio cosmic-ray modulation model: construction and predictive capabilities

    Science.gov (United States)

    Moloto, Katlego; Burger, Renier; Engelbrecht, Nicholas

    2016-07-01

    A simplified ab initio approach is followed to model cosmic-ray modulation using a steady-state three-dimensional stochastic solver of the Parker transport equation. Standard diffusion coefficients based on Quasilinear Theory (QLT) and Nonlinear Guiding Center Theory (NLGC) are used. The spatial dependence of turbulence quantities required as input for the drift- and diffusion coefficients, follow from parametric fits to results from a turbulence transport model. Effective values are used for the solar wind speed, magnetic field magnitude and tilt angle in the modulation model. The unusually high cosmic-ray intensities observed during the 2009 solar minimum follow naturally from the current model for most of the energies considered. This demonstrates that changes in turbulence contribute significantly to than usual cosmic-ray intensities during the 2009 solar minimum. We also discuss and illustrate how this model can be used to predict future cosmic-ray intensities, and comment on the reliability of such predictions.

  20. An ab initio model for the modulation of galactic cosmic-ray electrons

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-12-20

    The modulation of galactic cosmic-ray electrons is studied using an ab initio three-dimensional steady state cosmic-ray modulation code in which the effects of turbulence on both the diffusion and drift of these cosmic-rays are treated as self-consistently as possible. A significant refinement is that a recent two-component turbulence transport model is used. This model yields results in reasonable agreement with observations of turbulence quantities throughout the heliosphere. The sensitivity of computed galactic electron intensities to choices of various turbulence parameters pertaining to the dissipation range of the slab turbulence spectrum, and to the choice of model of dynamical turbulence, is demonstrated using diffusion coefficients derived from the quasi-linear and extended nonlinear guiding center theories. Computed electron intensities and latitude gradients are also compared with spacecraft observations.

  1. An ab initio approach to the anisotropic perpendicular diffusion of galactic cosmic rays

    Science.gov (United States)

    Engelbrecht, Nicholas; Richardson, John; Burger, Renier

    2016-07-01

    The assumption that cosmic-ray diffusion perpendicular to the background magnetic field is anisotropic has been made in many numerical modulation studies. This was done in order to reproduce spacecraft observations of, for example, lower than expected latitude gradients of galactic protons. This assumption is usually justified in terms of observations of non-axisymmetric turbulent magnetic fluctuations, but is often implemented in a completely ad hoc manner. This study implements anisotropic perpendicular diffusion coefficients in an ab initio cosmic ray modulation model in a self-consistent manner, employing perpendicular mean free path expressions derived for the case where transverse magnetic fluctuations are non-axisymmetric. Voyager magnetic field observations are analysed to ascertain the nature of this non-axisymmetry, and modulation model solutions for various assumptions as to the spatial dependence of this non-axisymmetry, also taking into account the Voyager observations, are presented.

  2. AB-INITIO SIMULATION OF ELECTRONIC FEATURES OF HYPERFINE RARE EARTH OXIDE FILMS FOR SENSORY NANOSYSTEMS

    Directory of Open Access Journals (Sweden)

    A. V. Gulay

    2014-01-01

    Full Text Available Ab-Initio simulation of electronic features of sensoring nanomaterials based on rare earth oxides has been made by the example of yttrium oxide. The simulation method for thin films of nanometer scale consisted in the simulation of the material layer of the thickness equal to unit crystal cell size has been proposed within the VASP simulation package. The atomic bond breakdown in the crystal along one of the coordinate axes is simulated by the increase of a distance between the atomic layers along this axis up to values at which the value of free energy is stabilized. It has been found that the valence and conductivity bands are not revealed explicitly and the band gap is not formed in the hyperfine rare earth oxide film (at the film thickness close to 1 nm. In fact the hyperfine rare earth oxide film loses dielectric properties which were exhibited clear enough in continuum.

  3. An ab initio approach to free-energy reconstruction using logarithmic mean force dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Nakamura, Makoto, E-mail: nakamura@cphys.s.kanazawa-u.ac.jp; Obata, Masao [Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa 920-1192 (Japan); Morishita, Tetsuya [Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8568 (Japan); Oda, Tatsuki, E-mail: oda@cphys.s.kanazawa-u.ac.jp [Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa 920-1192 (Japan); Institute of Science and Engineering, Kanazawa University, Kanazawa 920-1192 (Japan)

    2014-05-14

    We present an ab initio approach for evaluating a free energy profile along a reaction coordinate by combining logarithmic mean force dynamics (LogMFD) and first-principles molecular dynamics. The mean force, which is the derivative of the free energy with respect to the reaction coordinate, is estimated using density functional theory (DFT) in the present approach, which is expected to provide an accurate free energy profile along the reaction coordinate. We apply this new method, first-principles LogMFD (FP-LogMFD), to a glycine dipeptide molecule and reconstruct one- and two-dimensional free energy profiles in the framework of DFT. The resultant free energy profile is compared with that obtained by the thermodynamic integration method and by the previous LogMFD calculation using an empirical force-field, showing that FP-LogMFD is a promising method to calculate free energy without empirical force-fields.

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

    Directory of Open Access Journals (Sweden)

    Casper Steinmann

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

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

    Science.gov (United States)

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

    2013-01-01

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

  6. X-ray absorption of liquid water by advanced ab initio methods

    Science.gov (United States)

    Sun, Zhaoru; Chen, Mohan; Zheng, Lixin; Wang, Jianping; Santra, Biswajit; Shen, Huaze; Xu, Limei; Kang, Wei; Klein, Michael L.; Wu, Xifan

    2017-09-01

    Oxygen K -edge x-ray absorption spectra of liquid water are computed based on configurations from advanced ab initio molecular dynamics simulations, as well as an electron excitation theory from the GW method. One the one hand, the molecular structures of liquid water are accurately predicted by including both van der Waals interactions and a hybrid functional (PBE0). On the other hand, the dynamic screening effects on electron excitation are approximately described by the recently developed enhanced static Coulomb-hole and screened-exchange approximation of W. Kang and M. S. Hybertsen [Phys. Rev. B 82, 195108 (2010), 10.1103/PhysRevB.82.195108]. The resulting spectra of liquid water are in better quantitative agreement with the experimental spectra due to the softened hydrogen bonds and the slightly broadened spectra originating from the better screening model.

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

    Energy Technology Data Exchange (ETDEWEB)

    Xiong, L H; Lou, H B; Wang, X D; Debela, T T; Cao, Q P; Zhang, D X; Wang, S Y; Wang, C Z; Jiang, J Z

    2014-04-01

    The local atomic structure evolution in Al2Au alloy during solidification from 2000 K to 400 K was studied by ab initio molecular dynamics simulations and analyzed using the structure factor, pair correlation functions, bond angle distributions, the Honeycutt-Anderson (HA) index and Voronoi tessellation methods. It was found that the icosahedral-like clusters are negligible in the Al2Au stable liquid and supercooled liquid states, and the most abundant clusters are those having HA indices of 131 and 120 or Voronoi indices of < 0,4,4,0 >, < 0,3, 6,0 > and < 0,4,4,2 > with coordination numbers of 8, 9 and 10, respectively. These clusters are similar to the local atomic structures in the CaF2-type Al2Au crystal, revealing the existence of structure heredity between liquid and crystalline phase in Al2Au alloy. (C) 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

  8. Structure and dynamics of liquid Zn: an analysis of ab-initio simulations

    Directory of Open Access Journals (Sweden)

    del Rio B. G.

    2017-01-01

    Full Text Available The static and dynamic properties of liquid Zn have been studied using an ab initio molecular dynamics method. Results are reported for the thermodynamic states at 723K near which inelastic neutron and x-ray scattering data are available. The calculated static structure shows very good agreement with experimental measurements, including an asymmetric main peak. The dynamic structure reveals the existence of propagating density fluctuations, and the associated dispersion relation has also been calculated. 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 several liquid metals under high pressures; the second region is around qp/2, as suggested by inelastic scattering experiments for liquid Zn and other metals.

  9. Ab initio multiscale simulation of high-order harmonic generation in solids

    Science.gov (United States)

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

    2018-01-01

    High-order-harmonic generation by a highly nonlinear interaction of infrared laser fields with matter allows for the generation of attosecond pulses in the XUV spectral regime. This process, well established for atoms, has been recently extended to the condensed phase. Remarkably well-pronounced harmonics up to order ˜30 have been observed for dielectrics. We establish a route toward an ab initio multiscale simulation of solid-state high-order-harmonic generation. We find that mesoscopic effects of the extended system, in particular the realistic sampling of the entire Brillouin zone, the pulse propagation in the dense medium, and the inhomogeneous illumination of the crystal, have a strong effect on the harmonic spectra. Our results provide an explanation for the formation of clean harmonics and have implications for a wide range of nonlinear optical processes in dense media.

  10. Sensitivity of core-level spectroscopy to electrostatic environments of nitrile groups: An ab initio study

    Directory of Open Access Journals (Sweden)

    Abid Hussain

    2017-09-01

    Full Text Available Ab initio quantum chemistry calculations have been performed to probe the influence of hydrogen bonding on the electronic structure of hydrogen cyanide (HCN. Our calculations determine the origin of nitrogen-specific Raman spectral features from resonant inelastic X-ray scattering occurring in the presence of a water molecule and an electric dipole field. The similarity of the two interactions in altering the electronic structure of the nitrogen atom differs only in the covalent contributions from the water molecule. The CN stretching mode as a structural probe was also investigated to study the electronic origin of the anomalous frequency shift of the nitrile group when subjected to hydrogen bonding and an electrostatic dipole field. The major changes in the electronic structure of HCN are electrostatic in nature and originate from dipole-dipole interactions. The relative shifts of the CN stretching frequency are in good agreement with those experimentally observed.

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

    Science.gov (United States)

    Šipr, O; Ebert, H; Minár, J

    2015-02-11

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

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

    Directory of Open Access Journals (Sweden)

    Karl-Heinz Böhm

    2014-04-01

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

  13. Ab initio contribution to the study of complexes formed during dilute FeCu alloys radiation

    CERN Document Server

    Becquart, C S

    2003-01-01

    Cu plays an important role in the embrittlement of pressure vessel steels under radiation and entities containing both Cu atoms and vacancies seem to appear as a consequence of displacement cascades. The characterisation of the stability as well as the migration of small Cu-vacancy complexes is thus necessary to understand and simulate the formation of these entities. For instance, cascade ageing studied by kinetic Monte Carlo or by rate theory models requires a good characterisation of such complexes which are parameters for these methods. We have investigated, by ab initio calculations based on the density functional theory, point defects and small defects in dilute FeCu alloys. The structure of small Cu clusters and Cu-vacancy complexes has been determined, as well as their formation and binding energies. Their relative stability is discussed. Vacancy migration energies in the presence of Cu atoms have been calculated and analysed. All the results are compared to the figures obtained with empirical interat...

  14. Ab initio calculation of ICD widths in photoexcited HeNe

    Energy Technology Data Exchange (ETDEWEB)

    Jabbari, G.; Klaiman, S.; Chiang, Y.-C.; Gokhberg, K., E-mail: kirill@pci.uni-heidelberg.de [Theoretische Chemie, Physikalisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 229, D-69120 Heidelberg (Germany); Trinter, F.; Jahnke, T. [Institut für Kernphysik, Goethe-Universität Frankfurt, Max-von-Laue-Str. 1, D-60438 Frankfurt (Germany)

    2014-06-14

    Excitation of HeNe by synchrotron light just below the frequency of the 1s → 3p transition of isolated He has been recently shown to be followed by resonant interatomic Coulombic decay (ICD). The vibrationally resolved widths of the ICD states were extracted with high precision from the photoion spectra. In this paper, we report the results of ab initio calculations of these widths. We show that interaction between electronic states at about the equilibrium distance of HeNe makes dark states of He accessible for the photoexcitation and subsequent electronic decay. Moreover, the values of the calculated widths are shown to be strongly sensitive to the presence of the non-adiabatic coupling between the electronic states participating in the decay. Therefore, only by considering the complete manifold of interacting decaying electronic states a good agreement between the measured and computed ICD widths can be achieved.

  15. Electron-phonon scattering rates in complex polar crystals from ab initio calculations

    Energy Technology Data Exchange (ETDEWEB)

    Prange, Micah P.; Campbell, Luke W.; Kerisit, Sebastien N.

    2017-09-17

    The thermalization of fast electrons by phonons is studied in CsI, NaI, SrI2, and YAP. This numerical study uses an improvement to a recently developed ab initio method based on a density functional perturbation theoretical description of the phonon modes that provides a way to go beyond widely used phonon models based on binary crystals. Improvements to this method are described, and scattering rates are presented and discussed. The results here treat polar and nonpolar scattering on equal footing and allow an assessment of the relative importance of the two types of scattering. The relative activity of the numerous phonon modes in materials with complicated structures is discussed, and a simple criterion for finding the modes that scatter strongly is presented.

  16. Ab initio molecular orbital calculations of the static polarizabilities of xanthone analogues

    Science.gov (United States)

    Sugino, Takushi; Kambe, Nobuaki; Sonoda, Noboru; Sakaguchi, Toru; Ohta, Koji

    1996-03-01

    The static polarizabilities, α, of various xanthone analogues ( 1-19) were estimated by ab initio molecular orbital calculations using the coupled perturbed Hartree-Fock (CPHF) method. The influence of basis sets on the calculated values was examined in detail and the reliability of the ECP approach was confirmed. A good linear relationship was found between the Δα values calculated using the 3-21G basis set and those using larger basis sets. The introduction of substituents generally increases , whereas Δα is strongly affected by the nature of the substituents and by the molecular geometries. According to Prasad's equation, γ orient was calculated from Δα and compared with experimental values.

  17. A direct ab initio molecular dynamics (MD) study on the repair reactions of stacked thymine dimer

    Science.gov (United States)

    Tachikawa, Hiroto; Kawabata, Hiroshi

    2008-09-01

    DNA repair reactions of the thymine dimer (T) 2 following the hole capture have been investigated by means of direct ab initio molecular dynamics (MD) method in order to elucidate the mechanism of repair processes of thymine dimer interacting with a photo-enzyme. The thymine dimer has two C-C single bonds between thymine rings at neutral state expressed by (T dbnd T). After the hole capture of (T dbnd T), one of the C-C bonds was preferentially broken, while the structure of (T dbnd T) + was spontaneously changed to an intermediate having a C-C single bond expressed by (T-T) +. Time scale of the C-C bond breaking and formation of the intermediate was estimated to be 60-180 fs. The mechanism of repair reactions of the thymine dimer was discussed on the basis of theoretical results.

  18. NestedMICA as an ab initio protein motif discovery tool

    Directory of Open Access Journals (Sweden)

    Down Thomas A

    2008-01-01

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

  19. Ab initio modeling of the herpesvirus VP26 core domain assessed by CryoEM density.

    Directory of Open Access Journals (Sweden)

    Matthew L Baker

    2006-10-01

    Full Text Available Efforts in structural biology have targeted the systematic determination of all protein structures through experimental determination or modeling. In recent years, 3-D electron cryomicroscopy (cryoEM has assumed an increasingly important role in determining the structures of these large macromolecular assemblies to intermediate resolutions (6-10 A. While these structures provide a snapshot of the assembly and its components in well-defined functional states, the resolution limits the ability to build accurate structural models. In contrast, sequence-based modeling techniques are capable of producing relatively robust structural models for isolated proteins or domains. In this work, we developed and applied a hybrid modeling approach, utilizing cryoEM density and ab initio modeling to produce a structural model for the core domain of a herpesvirus structural protein, VP26. Specifically, this method, first tested on simulated data, utilizes the cryoEM density map as a geometrical constraint in identifying the most native-like models from a gallery of models generated by ab initio modeling. The resulting model for the core domain of VP26, based on the 8.5-A resolution herpes simplex virus type 1 (HSV-1 capsid cryoEM structure and mutational data, exhibited a novel fold. Additionally, the core domain of VP26 appeared to have a complementary interface to the known upper-domain structure of VP5, its cognate binding partner. While this new model provides for a better understanding of the assembly and interactions of VP26 in HSV-1, the approach itself may have broader applications in modeling the components of large macromolecular assemblies.

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

    Science.gov (United States)

    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

  1. Ab-initio electronic and magnetic properties of Fe-Al alloys

    Directory of Open Access Journals (Sweden)

    Apiñaniz, E.

    2000-06-01

    Full Text Available This work presents ab-initio self-consistent calculations performed with the TB-LMTO code to study the different phases of the Fe-Al phase diagram, corresponding to the ordered structures B2, DO3 and B32 and for Fe50Al50 and Fe3Al compositions. Both, unpolarized and spin-polarized calculations have been performed to deduce the energetic difference between the paramagnetic and ferromagnetic state of the corresponding structure. Calculations for the disordered structures have also been performed for the previously mentioned compositions. These results show that by disordering the alloy magnetism is enhanced and that the equilibrium lattice parameter increases.

    En este trabajo se presentan cálculos autoconsistentes ab-initio realizados con el método TB-LMTO (Tight Binding Linear Muffin Tin Orbital con el fin de estudiar las diferentes estructuras que se presentan en el diagrama de fases de las aleaciones Fe-Al. Se han estudiado las estructuras ordenadas B2, DO3 y B32 para las siguientes concentraciones: Fe50Al50 y Fe3Al. Asimismo, se han realizado cálculos teniendo y sin tener en cuenta la polarización de spin con el fin de poder deducir la diferencia energética entre los estados ferromágneticos y paramágneticos de la misma estructura. Por otra parte se han realizado estos mismos cálculos para estructuras desordenadas y las mismas concentraciones. Los resultados muestran que mediante el desorden aumenta el magnetismo de estas aleaciones y crece el parámetro de red.

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

    Science.gov (United States)

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

    2016-09-01

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

  3. Ab initio molecular dynamics with nuclear quantum effects at classical cost: Ring polymer contraction for density functional theory.

    Science.gov (United States)

    Marsalek, Ondrej; Markland, Thomas E

    2016-02-07

    Path integral molecular dynamics simulations, combined with an ab initio evaluation of interactions using electronic structure theory, incorporate the quantum mechanical nature of both the electrons and nuclei, which are essential to accurately describe systems containing light nuclei. However, path integral simulations have traditionally required a computational cost around two orders of magnitude greater than treating the nuclei classically, making them prohibitively costly for most applications. Here we show that the cost of path integral simulations can be dramatically reduced by extending our ring polymer contraction approach to ab initio molecular dynamics simulations. By using density functional tight binding as a reference system, we show that our ring polymer contraction scheme gives rapid and systematic convergence to the full path integral density functional theory result. We demonstrate the efficiency of this approach in ab initio simulations of liquid water and the reactive protonated and deprotonated water dimer systems. We find that the vast majority of the nuclear quantum effects are accurately captured using contraction to just the ring polymer centroid, which requires the same number of density functional theory calculations as a classical simulation. Combined with a multiple time step scheme using the same reference system, which allows the time step to be increased, this approach is as fast as a typical classical ab initio molecular dynamics simulation and 35× faster than a full path integral calculation, while still exactly including the quantum sampling of nuclei. This development thus offers a route to routinely include nuclear quantum effects in ab initio molecular dynamics simulations at negligible computational cost.

  4. Strong electric fields at a prototypical oxide/water interface probed by ab initio molecular dynamics: MgO(001).

    Science.gov (United States)

    Laporte, Sara; Finocchi, Fabio; Paulatto, Lorenzo; Blanchard, Marc; Balan, Etienne; Guyot, François; Saitta, Antonino Marco

    2015-08-21

    We report a density-functional theory (DFT)-based study of the interface of bulk water with a prototypical oxide surface, MgO(001), and focus our study on the often-overlooked surface electric field. In particular, we observe that the bare MgO(001) surface, although charge-neutral and defectless, has an intense electric field on the Å scale. The MgO(001) surface covered with 1 water monolayer (1 ML) is investigated via a supercell accounting for the experimentally-observed (2 × 3) reconstruction, stable at ambient temperature, and in which two out of six water molecules are dissociated. This 1 ML-hydrated surface is also found to have a high, albeit short-ranged, normal component of the field. Finally, the oxide/water interface is studied via room-temperature ab initio molecular dynamics (AIMD) using 34 H2O molecules between two MgO(001) surfaces. To our best knowledge this is the first AIMD study of the MgO(001)/liquid water interface in which all atoms are treated using DFT and including several layers above the first adsorbed layer. We observe that the surface electric field, averaged over the AIMD trajectories, is still very strong on the fully-wet surface, peaking at about 3 V Å(-1). Even in the presence of bulk-like water, the structure of the first layer in contact with the surface remains similar to the (2 × 3)-reconstructed ice ad-layer on MgO(001). Moreover, we observe proton exchange within the first layer, and between the first and second layers - indeed, the O-O distances close to the surface are found to be distributed towards shorter distances, a property which has been shown to directly promote proton transfer.

  5. Molecular tailoring approach: a route for ab initio treatment of large clusters.

    Science.gov (United States)

    Sahu, Nityananda; Gadre, Shridhar R

    2014-09-16

    Conspectus Chemistry on the scale of molecular clusters may be dramatically different from that in the macroscopic bulk. Greater understanding of chemistry in this size regime could greatly influence fields such as materials science and atmospheric and environmental chemistry. Recent advances in experimental techniques and computational resources have led to accurate investigations of the energies and spectral properties of weakly bonded molecular clusters. These have enabled researchers to learn how the physicochemical properties evolve from individual molecules to bulk materials and to understand the growth patterns of clusters. Experimental techniques such as infrared, microwave, and photoelectron spectroscopy are the most popular and powerful tools for probing molecular clusters. In general, these experimental techniques do not directly reveal the atomistic details of the clusters but provide data from which the structural details need to be unearthed. Furthermore, the resolution of the spectral properties of energetically close cluster conformers can be prohibitively difficult. Thus, these investigations of molecular aggregates require a combination of experiments and theory. On the theoretical front, researchers have been actively engaged in quantum chemical ab initio calculations as well as simulation-based studies for the last few decades. To obtain reliable results, there is a need to use correlated methods such as Møller-Plesset second order method, coupled cluster theory, or dispersion corrected density functional theory. However, due to nonlinear scaling of these methods, optimizing the geometry of large clusters still remains a formidable quantum chemistry challenge. Fragment-based methods, such as divide-and-conquer, molecular tailoring approach (MTA), fragment molecular orbitals, and generalized energy-based fragmentation approach, provide alternatives for overcoming the scaling problem for spatially extended molecular systems. Within MTA, a large

  6. Ab initio kinetics and thermal decomposition mechanism of mononitrobiuret and 1,5-dinitrobiuret

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Hongyan, E-mail: hongyan.sun1@gmail.com, E-mail: ghanshyam.vaghjiani@us.af.mil; Vaghjiani, Ghanshyam L., E-mail: hongyan.sun1@gmail.com, E-mail: ghanshyam.vaghjiani@us.af.mil [Propellants Branch, Rocket Propulsion Division, Aerospace Systems Directorate, Air Force Research Laboratory, AFRL/RQRP, 10 E. Saturn Blvd., Edwards AFB, California 93524 (United States)

    2015-05-28

    Mononitrobiuret (MNB) and 1,5-dinitrobiuret (DNB) are tetrazole-free, nitrogen-rich, energetic compounds. For the first time, a comprehensive ab initio kinetics study on the thermal decomposition mechanisms of MNB and DNB is reported here. In particular, the intramolecular interactions of amine H-atom with electronegative nitro O-atom and carbonyl O-atom have been analyzed for biuret, MNB, and DNB at the M06-2X/aug-cc-pVTZ level of theory. The results show that the MNB and DNB molecules are stabilized through six-member-ring moieties via intramolecular H-bonding with interatomic distances between 1.8 and 2.0 Å, due to electrostatic as well as polarization and dispersion interactions. Furthermore, it was found that the stable molecules in the solid state have the smallest dipole moment amongst all the conformers in the nitrobiuret series of compounds, thus revealing a simple way for evaluating reactivity of fuel conformers. The potential energy surface for thermal decomposition of MNB was characterized by spin restricted coupled cluster theory at the RCCSD(T)/cc-pV∞ Z//M06-2X/aug-cc-pVTZ level. It was found that the thermal decomposition of MNB is initiated by the elimination of HNCO and HNN(O)OH intermediates. Intramolecular transfer of a H-atom, respectively, from the terminal NH{sub 2} group to the adjacent carbonyl O-atom via a six-member-ring transition state eliminates HNCO with an energy barrier of 35 kcal/mol and from the central NH group to the adjacent nitro O-atom eliminates HNN(O)OH with an energy barrier of 34 kcal/mol. Elimination of HNN(O)OH is also the primary process involved in the thermal decomposition of DNB, which processes C{sub 2v} symmetry. The rate coefficients for the primary decomposition channels for MNB and DNB were quantified as functions of temperature and pressure. In addition, the thermal decomposition of HNN(O)OH was analyzed via Rice–Ramsperger–Kassel–Marcus/multi-well master equation simulations, the results of which

  7. Ab-initio study of B2-type technetium AB (A=Tc, B=Nb and Ta) intermetallic compounds

    Science.gov (United States)

    Acharya, Nikita; Fatima, Bushra; Sanyal, Sankar P.

    2016-05-01

    The structural, electronic and elastic properties of AB type (A = Tc, B = Nb and Ta) technetium intermetallic compounds are studied using full potential linearized plane wave (FP-LAPW) method within generalized gradient approximation (GGA). The calculated lattice parameters agree well with the experimental results. The elastic constants obey the stability criteria for cubic system. Ductility for these compounds has been analyzed using the Pugh's rule and Cauchy's pressure and found that all the compounds are ductile in nature. Bonding nature is discussed in terms of Fermi surface and band structures.

  8. Adsorption effect on the formation of conductive path in defective TiO2: ab initio calculations

    Science.gov (United States)

    Li, Lei; Li, Wenshi; Qin, Han; Yang, Jianfeng; Mao, Ling-Feng

    2017-10-01

    Although the metal/TiO2/metal junctions providing resistive switching properties have attracted lots of attention in recent decades, revealing the atomic-nature of conductive path in TiO2 active layer remains a critical challenge. Here the effects of metal adsorption on defective TiO2(1 1 0) surface are theoretically investigated via ab initio calculations. The dependence of the conductive path on the adsorption of Ti/Zr/Cu/Pt/O atoms above a lattice Ti-ion in (1 1 0) plane and at 〈1 1 0〉 direction of the defective TiO2(0 0 1) surface are compared. It is found that Ti adsorptions in both sites give larger contributions to the presence of conductive path with more stability and larger transport coefficients at Fermi level, whereas the O adsorptions at both sites fail to produce conductive path. Moreover, the adsorptions of Zr/Cu/Pt atoms reduce the existence possibility of conductive path, especially absorbed above the lattice Ti-ion at 〈1 1 0〉 direction. Thus, it is helpful to clarify the interaction of the metal electrode and oxide layer in resistive random access memory.

  9. Ab initio density functional theory study on the atomic and electronic structure of GaP/Si(001) heterointerfaces

    Science.gov (United States)

    Romanyuk, O.; Supplie, O.; Susi, T.; May, M. M.; Hannappel, T.

    2016-10-01

    The atomic and electronic band structures of GaP/Si(001) heterointerfaces were investigated by ab initio density functional theory calculations. Relative total energies of abrupt interfaces and mixed interfaces with Si substitutional sites within a few GaP layers were derived. It was found that Si diffusion into GaP layers above the first interface layer is energetically unfavorable. An interface with Si/Ga substitution sites in the first layer above the Si substrate is energetically the most stable one in thermodynamic equilibrium. The electronic band structure of the epitaxial GaP/Si(001) heterostructure terminated by the (2 ×2 ) surface reconstruction consists of surface and interface electronic states in the common band gap of two semiconductors. The dispersion of the states is anisotropic and differs for the abrupt Si-Ga, Si-P, and mixed interfaces. Ga 2 p , P 2 p , and Si 2 p core-level binding-energy shifts were computed for the abrupt and the lowest-energy heterointerface structures. Negative and positive core-level shifts due to heterovalent bonds at the interface are predicted for the abrupt Si-Ga and Si-P interfaces, respectively. The distinct features in the heterointerface electronic structure and in the core-level shifts open new perspectives in the experimental characterization of buried polar-on-nonpolar semiconductor heterointerfaces.

  10. High pressure behaviour of uranium dicarbide (UC{sub 2}): Ab-initio study

    Energy Technology Data Exchange (ETDEWEB)

    Sahoo, B. D., E-mail: bdsahoo@barc.gov.in; Mukherjee, D.; Joshi, K. D.; Kaushik, T. C. [Applied Physics Division, Bhabha Atomic Research Centre, Mumbai 400085 (India)

    2016-08-28

    The structural stability of uranium dicarbide has been examined under hydrostatic compression employing evolutionary structure search algorithm implemented in the universal structure predictor: evolutionary Xtallography (USPEX) code in conjunction with ab-initio electronic band structure calculation method. The ab-initio total energy calculations involved for this purpose have been carried out within both generalized gradient approximations (GGA) and GGA + U approximations. Our calculations under GGA approximation predict the high pressure structural sequence of tetragonal → monoclinic → orthorhombic for this material with transition pressures of ∼8 GPa and 42 GPa, respectively. The same transition sequence is predicted by calculations within GGA + U also with transition pressures placed at ∼24 GPa and ∼50 GPa, respectively. Further, on the basis of comparison of zero pressure equilibrium volume and equation of state with available experimental data, we find that GGA + U approximation with U = 2.5 eV describes this material better than the simple GGA approximation. The theoretically predicted high pressure structural phase transitions are in disagreement with the only high experimental study by Dancausse et al. [J. Alloys. Compd. 191, 309 (1993)] on this compound which reports a tetragonal to hexagonal phase transition at a pressure of ∼17.6 GPa. Interestingly, during lowest enthalpy structure search using USPEX, we do not see any hexagonal phase to be closer to the predicted monoclinic phase even within 0.2 eV/f. unit. More experiments with varying carbon contents in UC{sub 2} sample are required to resolve this discrepancy. The existence of these high pressure phases predicted by static lattice calculations has been further substantiated by analyzing the elastic and lattice dynamic stability of these structures in the pressure regimes of their structural stability. Additionally, various thermo-physical quantities such as

  11. Mechanical properties of Fe rich Fe–Si alloys: ab initio local bulk-modulus viewpoint

    Science.gov (United States)

    Bhattacharya, Somesh Kr; Kohyama, Masanori; Tanaka, Shingo; Shiihara, Yoshinori; Saengdeejing, Arkapol; Chen, Ying; Mohri, Tetsuo

    2017-11-01

    Fe-rich Fe–Si alloys show peculiar bulk-modulus changes depending on the Si concentration in the range of 0–15 at.%Si. In order to clarify the origin of this phenomenon, we have performed density-functional theory calculations of supercells of Fe–Si alloy models with various Si concentrations. We have applied our recent techniques of ab initio local energy and local stress, by which we can obtain a local bulk modulus of each atom or atomic group as a local constituent of the cell-averaged bulk modulus. A2-phase alloy models are constructed by introducing Si substitution into bcc Fe as uniformly as possible so as to prevent mutual neighboring, while higher Si concentrations over 6.25 at.%Si lead to contacts between SiFe8 cubic clusters via sharing corner Fe atoms. For 12.5 at.%Si, in addition to an A2 model, we deal with partial D03 models containing local D03-like layers consisting of edge-shared SiFe8 cubic clusters. For the cell-averaged bulk modulus, we have successfully reproduced the Si-concentration dependence as a monotonic decrease until 11.11 at.%Si and a recovery at 12.5 at.%Si. The analysis of local bulk moduli of SiFe8 cubic clusters and Fe regions is effective to understand the variations of the cell-averaged bulk modulus. The local bulk moduli of Fe regions become lower for increasing Si concentration, due to the suppression of bulk-like d–d bonding states in narrow Fe regions. For higher Si concentrations till 11.11 at.%Si, corner-shared contacts or 1D chains of SiFe8 clusters lead to remarkable reduction of local bulk moduli of the clusters. At 12 at.%Si, on the other hand, two- or three-dimensional arrangements of corner- or edge-shared SiFe8 cubic clusters show greatly enhanced local bulk moduli, due to quite different bonding nature with much stronger p-d hybridization. The relation among the local bulk moduli, local electronic and magnetic structures, and local configurations such as connectivity of SiFe8 clusters and Fe-region sizes has

  12. Theoretical study of silicon carbide under irradiation at the nano scale: classical and ab initio modelling; Etude theorique a l'echelle nanometrique du carbure de silicium sous irradiation: modelisation classique et ab initio

    Energy Technology Data Exchange (ETDEWEB)

    Lucas, G

    2006-10-15

    The behaviour of silicon carbide under irradiation has been studied using classical and ab initio simulations, focusing on the nano scale elementary processes. First, we have been interested in the calculation of threshold displacement energies, which are difficult to determine both experimentally and theoretically, and also the associated Frenkel pairs. In the framework of this thesis, we have carried out simulations in classical and ab initio molecular dynamics. For the classical approach, two types of potentials have been used: the Tersoff potential, which led to non satisfactory results, and a new one which has been developed during this thesis. This potential allows a better modelling of SiC under irradiation than most of the empirical potentials available for SiC. It is based on the EDIP potential, initially developed to describe defects in silicon, that we have generalized to SiC. For the ab initio approach, the feasibility of the calculations has been validated and average energies of 19 eV for the C and 38 eV for the Si sublattices have been determined, close to the values empirically used in the fusion community. The results obtained with the new potential EDIP are globally in agreement with those values. Finally, the elementary processes involved in the crystal recovery have been studied by calculating the stability of the created Frenkel pairs and determining possible recombination mechanisms with the nudged elastic band method. (author)

  13. Efficient Ab-Initio Electron Transport Calculations for Heterostructures by the Nonequilibrium Green’s Function Method

    Directory of Open Access Journals (Sweden)

    Hirokazu Takaki

    2014-01-01

    Full Text Available We present an efficient computation technique for ab-initio electron transport calculations based on density functional theory and the nonequilibrium Green’s function formalism for application to heterostructures with two-dimensional (2D interfaces. The computational load for constructing the Green’s functions, which depends not only on the energy but also on the 2D Bloch wave vector along the interfaces and is thus catastrophically heavy, is circumvented by parallel computational techniques with the message passing interface, which divides the calculations of the Green’s functions with respect to energy and wave vectors. To demonstrate the computational efficiency of the present code, we perform ab-initio electron transport calculations of Al(100-Si(100-Al(100 heterostructures, one of the most typical metal-semiconductor-metal systems, and show their transmission spectra, density of states (DOSs, and dependence on the thickness of the Si layers.

  14. Ab initio and template-based prediction of multi-class distance maps by two-dimensional recursive neural networks

    Directory of Open Access Journals (Sweden)

    Martin Alberto JM

    2009-01-01

    Full Text Available Abstract Background Prediction of protein structures from their sequences is still one of the open grand challenges of computational biology. Some approaches to protein structure prediction, especially ab initio ones, rely to some extent on the prediction of residue contact maps. Residue contact map predictions have been assessed at the CASP competition for several years now. Although it has been shown that exact contact maps generally yield correct three-dimensional structures, this is true only at a relatively low resolution (3–4 Å from the native structure. Another known weakness of contact maps is that they are generally predicted ab initio, that is not exploiting information about potential homologues of known structure. Results We introduce a new class of distance restraints for protein structures: multi-class distance maps. We show that Cα trace reconstructions based on 4-class native maps are significantly better than those from residue contact maps. We then build two predictors of 4-class maps based on recursive neural networks: one ab initio, or relying on the sequence and on evolutionary information; one template-based, or in which homology information to known structures is provided as a further input. We show that virtually any level of sequence similarity to structural templates (down to less than 10% yields more accurate 4-class maps than the ab initio predictor. We show that template-based predictions by recursive neural networks are consistently better than the best template and than a number of combinations of the best available templates. We also extract binary residue contact maps at an 8 Å threshold (as per CASP assessment from the 4-class predictors and show that the template-based version is also more accurate than the best template and consistently better than the ab initio one, down to very low levels of sequence identity to structural templates. Furthermore, we test both ab-initio and template-based 8

  15. Efficacy of the SU(3) scheme for ab initio large-scale calculations beyond the lightest nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Dytrych, T. [Academy of Sciences of the Czech Republic (ASCR), Prague (Czech Republic); Louisiana State Univ., Baton Rouge, LA (United States); Maris, Pieter [Iowa State Univ., Ames, IA (United States); Launey, K. D. [Louisiana State Univ., Baton Rouge, LA (United States); Draayer, J. P. [Louisiana State Univ., Baton Rouge, LA (United States); Vary, James [Iowa State Univ., Ames, IA (United States); Langr, D. [Czech Technical Univ., Prague (Czech Republic); Aerospace Research and Test Establishment, Prague (Czech Republic); Saule, E. [Univ. of North Carolina, Charlotte, NC (United States); Caprio, M. A. [Univ. of Notre Dame, IN (United States); Catalyurek, U. [The Ohio State Univ., Columbus, OH (United States). Dept. of Electrical and Computer Engineering; Sosonkina, M. [Old Dominion Univ., Norfolk, VA (United States)

    2016-06-09

    We report on the computational characteristics of ab initio nuclear structure calculations in a symmetry-adapted no-core shell model (SA-NCSM) framework. We examine the computational complexity of the current implementation of the SA-NCSM approach, dubbed LSU3shell, by analyzing ab initio results for 6Li and 12C in large harmonic oscillator model spaces and SU(3)-selected subspaces. We demonstrate LSU3shell's strong-scaling properties achieved with highly-parallel methods for computing the many-body matrix elements. Results compare favorably with complete model space calculations and signi cant memory savings are achieved in physically important applications. In particular, a well-chosen symmetry-adapted basis a ords memory savings in calculations of states with a fixed total angular momentum in large model spaces while exactly preserving translational invariance.

  16. Ab initio Investigations of the Equilibria between Trichlorothioacetyl Chloride, Tetrachlorothiirane, and Trichloroethenesulfenyl Chloride, their Reactants and Decomposition Products

    DEFF Research Database (Denmark)

    Pedersen, Kim Vestergaard; Christensen, Henrik; Shim, Irene

    2004-01-01

    Trichlorothioacetyl chloride 1, tetrachlorothiirane 2, and trichloroethenesulfenyl chloride 3 and the equilibria between them have been investigated by ab initio Hartree-Fock (HF), Møller-Plesset second order perturbation (MP2) calculations, and by Gaussian-3 theory, G3(MP2). The transition states...... of the isomerization reactions have been identified. Also investigated were possible reactions leading to the isomers and their possible decomposition products. The results show that the unobserved isomerization reactions are feasible....

  17. Deuteron-induced nucleon transfer reactions within an ab initio framework: First application to p -shell nuclei

    Science.gov (United States)

    Raimondi, Francesco; Hupin, Guillaume; Navrátil, Petr; Quaglioni, Sofia

    2016-05-01

    Background: Low-energy transfer reactions in which a proton is stripped from a deuteron projectile and dropped into a target play a crucial role in the formation of nuclei in both primordial and stellar nucleosynthesis, as well as in the study of exotic nuclei using radioactive beam facilities and inverse kinematics. Ab initio approaches have been successfully applied to describe the 3H (d ,n )4He and 3He(d ,p )4He fusion processes. Purpose: An ab initio treatment of transfer reactions would also be desirable for heavier targets. In this work, we extend the ab initio description of (d ,p ) reactions to processes with light p -shell nuclei. As a first application, we study the elastic scattering of deuterium on 7Li and the 7Li(d ,p )8Li transfer reaction based on a two-body Hamiltonian. Methods: We use the no-core shell model to compute the wave functions of the nuclei involved in the reaction, and describe the dynamics between targets and projectiles with the help of microscopic-cluster states in the spirit of the resonating group method. Results: The shapes of the excitation functions for deuterons impinging on 7Li are qualitatively reproduced up to the deuteron breakup energy. The interplay between d -7Li and p -8Li particle-decay channels determines some features of the 9Be spectrum above the d +7Li threshold. Our prediction for the parity of the 17.298 MeV resonance is at odds with the experimental assignment. Conclusions: Deuteron stripping reactions with p -shell targets can now be computed ab initio, but calculations are very demanding. A quantitative description of the 7Li(d ,p )8Li reaction will require further work to include the effect of three-nucleon forces and additional decay channels and to improve the convergence rate of our calculations.

  18. Weak interactions in Graphane/BN systems under static electric fields—A periodic ab-initio study

    Energy Technology Data Exchange (ETDEWEB)

    Steinkasserer, Lukas Eugen Marsoner, E-mail: marsoner@zedat.fu-berlin.de [Institut für Chemie und Biochemie, Freie Universität Berlin, Takustraße 3, 14195 Berlin (Germany); MacDiarmid Institute for Advanced Materials and Nanotechnology, School of Chemical and Physical Sciences, Victoria University of Wellington, P.O. Box 600, 6140 Wellington (New Zealand); Gaston, Nicola [MacDiarmid Institute for Advanced Materials and Nanotechnology, School of Chemical and Physical Sciences, Victoria University of Wellington, P.O. Box 600, 6140 Wellington (New Zealand); Paulus, Beate [Institut für Chemie und Biochemie, Freie Universität Berlin, Takustraße 3, 14195 Berlin (Germany)

    2015-04-21

    Ab-initio calculations via periodic Hartree-Fock (HF) and local second-order Møller-Plesset perturbation theory (LMP2) are used to investigate the adsorption properties of combined Graphane/boron nitride systems and their response to static electric fields. It is shown how the latter can be used to alter both structural as well as electronic properties of these systems.

  19. Ab initio CPHF calculations of first hyperpolarizabilities of nitrogen-containing polyenes with donor—acceptor substituents

    Science.gov (United States)

    Tsunekawa, Tetsuya; Yamaguchi, Kizashi

    1992-03-01

    Ab initio CPHF calculations of static hyperpolarizabilities (β) were carried out in order to clarify the effects of nitrogen-atom substitution in π-conjugated chains with donor—acceptor substituents. The β values decrease gradually with the number of nitrogen atoms, and change drastically with the position of nitrogen-atom substitution in the polyenes. The effects of nitrogen-atom substitution are explained by the energy levels and the shapes of the frontier orbitals.

  20. Ab initio study of energetics and magnetism of sigma phase in Co–Mo and Fe–Mo systems

    Czech Academy of Sciences Publication Activity Database

    Pavlů, Jana; Vřešťál, Jan; Šob, Mojmír

    2016-01-01

    Roč. 24, č. 2 (2016), č. článku Art. Number 025009. ISSN 0965-0393 R&D Projects: GA ČR GA14-15576S Institutional support: RVO:68081723 Keywords : intermetallics * magnetic properties * phase stability * thermodynamic properties * site occupancy * ab-initio calculations Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.891, year: 2016

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

    Science.gov (United States)

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

    2012-04-01

    A simple (5 + 6 + 7)-sp3 carbon (denoted as F-carbon) with eight atoms per unit cell predicted by a newly developed ab initio particle-swarm optimization methodology on crystal structure prediction is proposed. F-carbon can be seen as the reconstruction of AA-stacked or 3R-graphite, and is energetically more stable than 2H-graphite beyond 13.9 GPa. Band structure and hardness calculations indicate that F-carbon is a transparent superhard carbon with a gap of 4.55 eV at 15 GPa and a hardness of 93.9 GPa at zero pressure. Compared with the previously proposed Bct-, M- and W-carbons, the simulative x-ray diffraction pattern of F-carbon also well matches the superhard intermediate phase of the experimentally cold-compressed graphite. The possible transition route and energy barrier were observed using the variable cell nudged elastic band method. Our simulations show that the cold compression of graphite can produce some reversible metastable carbons (e.g. M- and F-carbons) with energy barriers close to diamond or lonsdaleite.

  2. Matrix Isolation and ab initio study of the noncovalent complexes between formamide and acetylene.

    Science.gov (United States)

    Mardyukov, Artur; Sánchez-García, Elsa; Sander, Wolfram

    2009-02-12

    Matrix isolation spectroscopy in combination with ab initio calculations is a powerful technique for the identification of weakly bound intermolecular complexes. Here, weak complexes between formamide and acetylene are studied, and three 1:1 complexes with binding energies of -2.96, -2.46, and -1.79 kcal/mol have been found at the MP2 level of theory (MP2/cc-pVTZ + ZPE + BSSE). The two most stable dimers A and B are identified in argon and nitrogen matrices by comparison between the experimental and calculated infrared frequencies. Both complexes are stabilized by the formamide C=O...HC acetylene and H...pi interactions. Large shifts have been observed experimentally for the C-H stretching vibrations of the acetylene molecule, in very good agreement with the calculated values. Eight 1:2 FMA-acetylene trimers (T-A to T-H) with binding energies between -5.44 and -2.62 kcal/mol (MP2/aug-cc-pVDZ + ZPE + BSSE) were calculated. The two most stable trimers T-A and T-B are very close in energy and have similar infrared spectra. Several weak bands that are in agreement with the calculated frequencies of the trimers T-A and T-B are observed under matrix isolation conditions. However, the differences are too small for a definitive assignment.

  3. Ab Initio Enhanced calphad Modeling of Actinide-Rich Nuclear Fuels

    Energy Technology Data Exchange (ETDEWEB)

    Morgan, Dane [Univ. of Wisconsin, Madison, WI (United States); Yang, Yong Austin [Univ. of Wisconsin, Madison, WI (United States)

    2013-10-28

    The process of fuel recycling is central to the Advanced Fuel Cycle Initiative (AFCI), where plutonium and the minor actinides (MA) Am, Np, and Cm are extracted from spent fuel and fabricated into new fuel for a fast reactor. Metallic alloys of U-Pu-Zr-MA are leading candidates for fast reactor fuels and are the current basis for fast spectrum metal fuels in a fully recycled closed fuel cycle. Safe and optimal use of these fuels will require knowledge of their multicomponent phase stability and thermodynamics (Gibbs free energies). In additional to their use as nuclear fuels, U-Pu-Zr-MA contain elements and alloy phases that pose fundamental questions about electronic structure and energetics at the forefront of modern many-body electron theory. This project will validate state-of-the-art electronic structure approaches for these alloys and use the resulting energetics to model U-Pu-Zr-MA phase stability. In order to keep the work scope practical, researchers will focus on only U-Pu-Zr-{Np,Am}, leaving Cm for later study. The overall objectives of this project are to: Provide a thermodynamic model for U-Pu-Zr-MA for improving and controlling reactor fuels; and, Develop and validate an ab initio approach for predicting actinide alloy energetics for thermodynamic modeling.

  4. Ab initio calculations of structural and magnetic properties of Ni-Co-Mn-Cr-Sn alloys

    Directory of Open Access Journals (Sweden)

    Zagrebin Mikhail

    2015-01-01

    Full Text Available The composition dependences of crystal lattice parameters, bulk modulus, magnetic moments, magnetic exchange parameters in Ni2-yCoyMn1.5-xCrxSn0.5 (y = 0.2, 0.4; 0.0 ≤ x ≤ 0.4 Heusler alloys are investigated with the help of ab initio calculations. Our simulations have shown that crystal lattice parameter firstly increased and then decreased with Cr content (x increasing. The strongest ferromagnetic interaction for Ni1.6Co0.4Mn1.4Cr0.1Sn0.5 is nearest-neighbor interaction between Co and Mn1 (on own sites. The strongest antiferromagnetic interaction is observed between nearest-neighbor Mn1-Cr atoms in the first coordination sphere and it is equal to -15meV. Total magnetic moment of Ni2-yCoyMn1.5-xCrxSn0.5 (y =0.2, 0.4; 0.0 ≤ x ≤ 0.4 takes value in region from 6.1 μB to 6.6 μB.

  5. Ab initio study on the structural and electronic properties of water surrounding a multifunctional nanoprobe

    Science.gov (United States)

    Xia, Xiuli; Shao, Yuanzhi

    2018-02-01

    We report the magneto-electric behavior of a dual-modality biomedical nanoprobe, a ternary nanosystem consisting of gold and gadolinia clusters and water molecules, with the effect of both nanoclusters on the structural and electronic properties of water. The hydrogen-oxygen bond lengths and angles as well as electronic charges of water molecules surrounding both nanoclusters were calculated using Hubbard U corrected density functional theory aided by molecular dynamics approach. The calculations reveal existence of a magneto-electric interaction between gold and gadolinium oxide nanoclusters, which influences the physical properties of surrounding water remarkably. A broader (narrower) distribution of Hsbnd O bond lengths (Hsbnd Osbnd H bond angles) was observed at the presence of either gold or gadolinia nanoclusters. The presence of Gd6O9 cluster leads to the larger charges of neighbour oxygen atoms. The distribution of oxygen atom charges becomes border when both Gd6O9 and Au13 clusters coexist. Ab initio calculation provides a feasible approach to explore the most essential interactions among functional components of a multimodal nanoprobe applied in aqueous environment.

  6. Light focusing through a multiple scattering medium: ab initio computer simulation

    Science.gov (United States)

    Danko, Oleksandr; Danko, Volodymyr; Kovalenko, Andrey

    2018-01-01

    The present study considers ab initio computer simulation of the light focusing through a complex scattering medium. The focusing is performed by shaping the incident light beam in order to obtain a small focused spot on the opposite side of the scattering layer. MSTM software (Auburn University) is used to simulate the propagation of an arbitrary monochromatic Gaussian beam and obtain 2D distribution of the optical field in the selected plane of the investigated volume. Based on the set of incident and scattered fields, the pair of right and left eigen bases and corresponding singular values were calculated. The pair of right and left eigen modes together with the corresponding singular value constitute the transmittance eigen channel of the disordered media. Thus, the scattering process is described in three steps: 1) initial field decomposition in the right eigen basis; 2) scaling of decomposition coefficients for the corresponding singular values; 3) assembling of the scattered field as the composition of the weighted left eigen modes. Basis fields are represented as a linear combination of the original Gaussian beams and scattered fields. It was demonstrated that 60 independent control channels provide focusing the light into a spot with the minimal radius of approximately 0.4 μm at half maximum. The intensity enhancement in the focal plane was equal to 68 that coincided with theoretical prediction.

  7. Transport coefficients of helium-neon mixtures at low density computed from ab initio potentials.

    Science.gov (United States)

    Sharipov, Felix; Benites, Victor J

    2017-12-14

    The viscosity, thermal conductivity, diffusion coefficient, and thermal diffusion factor of helium-neon mixtures at low density are calculated for a wide range of temperature and for various molar fractions. The Chapman-Enskog method is employed considering the 10th order of the Sonine polynomial expansion. Ab initio potentials for intermolecular interactions are used to calculate the omega-integrals. The relative numerical error of the present results obtained for the potentials used here is less than 7 × 10-5 for the thermal diffusion factor and 2 × 10-5 for all the other coefficients. Since each employed potential has a different accuracy, the uncertainty related to such accuracies was analyzed, considering the contribution of each potential uncertainty. It was found that the total uncertainty due to the potentials is larger than the numerical error and it varies depending on the temperature and molar fraction. A comparison of the calculated transport coefficients with those available in the open literature shows that the present calculations provide the most accurate values currently available for the transport coefficients of helium-neon binary mixtures at low density.

  8. A fragment-based approach towards ab-initio treatment of polymeric materials

    Science.gov (United States)

    Pingale, Reshma S.; Pingale, Subhash S.; Kshirsagar, Anjali

    2017-07-01

    The broad range of applications of π -conjugated polymeric materials in industries such as automobiles, textiles, packaging, medical etc. have led to their extensive studies in both academic and industrial fields. Predicting the structure of these polymers is important for the study of their properties. The present work uses a `divide and conquer'-type approach for the ab-initio studies of these polymeric systems. The method employs a fragmentation technique with independent fragment optimization for obtaining optimized geometries of the oligomers of various polymeric materials such as polyfuran, polypyrrole, polythiophene and other such π -conjugated polymers. A few test calculations performed in the study provide fair concurrence between the energies and the HOMO-LUMO energy gaps obtained using the fragmentation-based approach with those obtained using the full optimization of the whole oligomer. Also, a significant reduction in time complexity occurs for the present fragment-based approach compared to the parent system optimization. The results are encouraging and prompt for studies of large polymeric materials.

  9. Ab initio guided design of structural materials with superior mechanical properties

    Science.gov (United States)

    Neugebauer, Jorg

    Modern engineering materials have evolved from simple single phase materials to nano-composites that employ dynamic mechanisms down to the atomistic scale. The structural and thermodynamic complexity of this new generation of structural materials presents a challenge to their design since experimental trial-and-error approaches as successfully used in the past are often no longer feasible. Ab initio approaches provide perfect tools to new design routes but face serious challenges: Finite temperature free energies of the various phases are almost degenerate, requiring advanced theoretical formalisms that accurately capture all relevant entropic contributions. In addition, their hierarchical nature with respect to length and time makes them challenging for any atomistic approach. Combining accurate first principles calculations with mesoscopic/macroscopic thermodynamic and/or kinetic concepts allows us now to address these issues and to determine free energies and derived thermodynamic quantities with a hitherto unprecedented accuracy. The flexibility and the predictive power of these approaches but also their present limitations will be discussed for examples ranging from modern ultra-high strength steels to light weight metallic alloys.

  10. Yttrium aluminium garnet under pressure: Structural, elastic, and vibrational properties from ab initio studies

    Energy Technology Data Exchange (ETDEWEB)

    Monteseguro, V. [Departamento de Física and MALTA Consolider Team, Universidad de La Laguna, 38200 San Cristóbal de La Laguna, Santa Cruz de Tenerife (Spain); Rodríguez-Hernández, P.; Muñoz, A., E-mail: amunoz@ull.es [Departamento de Física and MALTA Consolider Team, Universidad de La Laguna, 38200 San Cristóbal de La Laguna, Santa Cruz de Tenerife (Spain); Instituto de Materiales y Nanotecnología. Universidad de La Laguna, 38200 San Cristóbal de La Laguna, Santa Cruz de Tenerife (Spain)

    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.

  11. Ab initio computational study of vincristine as a biological active compound: NMR and NBO analyses

    Directory of Open Access Journals (Sweden)

    Shiva Joohari

    2015-06-01

    Full Text Available Vincristine is a biological active alkaloid that has been used clinically against a variety of neoplasms. In the current study we have theoretically investigated the magnetic properties of titled compound to predict physical and chemical properties of vincristine as a biological inhibitor. Ab initio computation using HF and B3LYP with 3-21G(d and 6-31G(d level of theory have been performed and then magnetic shielding tensor (, ppm, shielding asymmetry (, magnetic shielding anisotropy (aniso, ppm, the skew of a tensor (K, chemical shift anisotropy ( and chemical shift ( were calculated to indicate the details of the interaction mechanism between microtubules and vincristine. Moreover, EHOMO, ELUMO and Ebg were evaluated. The maximum and minimum values of Ebg were found in HF/3-21g and B3LYP/3-21g respectively. It was also uggested that O24, O37, O49 and O55 with minimum values of iso, are active sites of titled compound. Furthermore the calculated chemical shifts were compared with experimental data in DMSO and CDCl3 solvents.

  12. Nanolines of transition metals ruled by grain boundaries in graphene: An ab initio study

    Energy Technology Data Exchange (ETDEWEB)

    Lima, F.D.C. de, E-mail: felipe.lima@ufu.br; Miwa, R.H., E-mail: hiroki@infis.ufu.br

    2017-06-15

    We have performed an ab initio investigation of the energetic stability, and the electronic properties of transition metals (TMs = Mn, Fe, Co, and Ru) adsorbed on graphene, upon the presence of grain boundaries (GBs); where we found an energetic preference for the TMs lying on the GB sites (TM/GB). Further energy barrier calculations, of the transition metals in TM/GB, reveal that the GBs promote the formation of energetically favorable diffusion channels on graphene. By increasing the concentration of the TM adatoms, the energetic stability of the TM/GB systems has been strengthened; giving rise to TM nanolines (TM-NLs). The electronic properties of those TM-NLs were characterized through extensive electronic band structure calculations, where the energy bands of the TM/GB systems indicate the appearance of an anisotropic spin-polarized electronic current along the TM-NLs on graphene. - Highlights: • Formation of transition metal (TM) nanolines on graphene ruled by extended defects. • Those extended defects give rise to diffusion pipes of TMs on graphene. • The electronic band structure calculations indicate the formation of spin-polarized current upon the presence of TM nanolines. • The formation of those TM nanolines support the recent experimental findings.

  13. Towards the ab initio based theory of phase transformations in iron and steel

    Science.gov (United States)

    Razumov, I. K.; Gornostyrev, Yu. N.; Katsnelson, M. I.

    2017-04-01

    Despite of the appearance of numerous new materials, the iron based alloys and steels continue to play an essential role in modern technology. The properties of a steel are determined by its structural state (ferrite, cementite, pearlite, bainite, martensite, and their combination) that is formed under thermal treatment as a result of the shear lattice reconstruction γ (fcc) → α (bcc) and carbon diffusion redistribution. We present a review on a recent progress in the development of a quantitative theory of the phase transformations and microstructure formation in steel that is based on an ab initio parameterization of the Ginzburg-Landau free energy functional. The results of computer modeling describe the regular change of transformation scenario under cooling from ferritic (nucleation and diffusion-controlled growth of the α phase) to martensitic (the shear lattice instability γ → α). It has been shown that the increase in short-range magnetic order with decreasing the temperature plays a key role in the change of transformation scenarios. Phase-field modeling in the framework of a discussed approach demonstrates the typical transformation patterns.

  14. Towards Highly Scalable Ab Initio Molecular Dynamics (AIMD) Simulations on the Intel Knights Landing Manycore Processor

    Energy Technology Data Exchange (ETDEWEB)

    Jacquelin, Mathias; De Jong, Wibe A.; Bylaska, Eric J.

    2017-07-03

    The Ab Initio Molecular Dynamics (AIMD) method allows scientists to treat the dynamics of molecular and condensed phase systems while retaining a first-principles-based description of their interactions. This extremely important method has tremendous computational requirements, because the electronic Schr¨odinger equation, approximated using Kohn-Sham Density Functional Theory (DFT), is solved at every time step. With the advent of manycore architectures, application developers have a significant amount of processing power within each compute node that can only be exploited through massive parallelism. A compute intensive application such as AIMD forms a good candidate to leverage this processing power. In this paper, we focus on adding thread level parallelism to the plane wave DFT methodology implemented in NWChem. Through a careful optimization of tall-skinny matrix products, which are at the heart of the Lagrange multiplier and nonlocal pseudopotential kernels, as well as 3D FFTs, our OpenMP implementation delivers excellent strong scaling on the latest Intel Knights Landing (KNL) processor. We assess the efficiency of our Lagrange multiplier kernels by building a Roofline model of the platform, and verify that our implementation is close to the roofline for various problem sizes. Finally, we present strong scaling results on the complete AIMD simulation for a 64 water molecules test case, that scales up to all 68 cores of the Knights Landing processor.

  15. Ab Initio Dynamical Correlations from Auxiliary-field quantum Monte Carlo: applications in the Hubbard model

    Science.gov (United States)

    Vitali, Ettore; Shi, Hao; Qin, Mingpu; Zhang, Shiwei

    The possibility of calculating dynamical correlation functions from first principles provides a unique opportunity to explore the manifold of the excited states of a quantum many-body system. Such calculations allow us to predict interesting physical properties like spectral functions, excitation spectra and charge and spin gaps, which are more difficult to access from usual equilibrium calculations. We address the ab-initio calculation of dynamical Green functions and two-body correlation functions in the Auxiliary-field Quantum Monte Carlo method, using the two-dimensional Hubbard model as an example. When the sign problem is not present, an unbiased estimation of imaginary time correlation functions is obtained. We discuss in detail the complexity and the stability of the calculations. Moreover, we propose a new approach which is expected to be very useful when dealing with dilute systems, e.g. for cold gases, allowing calculations with a very favorable complexity in the system size. Supported by NSF, DOE SciDAC, and Simons Foundation.

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

    Science.gov (United States)

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

    2017-05-01

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

  17. Ab initio molecular dynamics of the reaction of quercetin with superoxide radical

    Science.gov (United States)

    Lespade, Laure

    2016-08-01

    Superoxide plays an important role in biology but in unregulated concentrations it is implicated in a lot of diseases such as cancer or atherosclerosis. Antioxidants like flavonoids are abundant in plant and are good scavengers of superoxide radical. The modeling of superoxide scavenging by flavonoids from the diet still remains a challenge. In this study, ab initio molecular dynamics of the reaction of the flavonoid quercetin toward superoxide radical has been carried out using Car-Parrinello density functional theory. The study has proven different reactant solvation by modifying the number of water molecules surrounding superoxide. The reaction consists in the gift of a hydrogen atom of one of the hydroxyl groups of quercetin to the radical. When it occurs, it is relatively fast, lower than 100 fs. Calculations show that it depends largely on the environment of the hydroxyl group giving its hydrogen atom, the geometry of the first water layer and the presence of a certain number of water molecules in the second layer, indicating a great influence of the solvent on the reactivity.

  18. Large scale ab initio molecular dynamics using the OpenAtom software

    Science.gov (United States)

    Ismail-Beigi, Sohrab; Mandal, Subhasish; Kim, Minjung; Mikida, Eric; Bohm, Eric; Jindal, Prateek; Jain, Nikhil; Kale, Laxmikant; Martyna, Glenn

    First principles molecular dynamics approaches permit one to simulate dynamic and time-dependent phenomena in physics, chemistry, and materials science without the use of empirical potentials or ad hoc assumptions about the interatomic interactions since they describe electrons, nuclei and their interactions explicitly. We describe our collaborative efforts in developing and enhancing the OpenAtom open source ab initio density functional software package based on plane waves and pseudopotentials (http://charm.cs.uiuc.edu/OpenAtom/). OpenAtom takes advantage of the Charm++ parallel framework. We present parallel scaling results on a large metal organic framework (MOF) material of scientific and potential technological interest for hydrogen storage. In the process, we highlight the capabilities of the software which include molecular dynamics (Car-Parrinello or Born-Oppenheimer), k-points, spin, path integral beads for quantum nuclear effects, and parallel tempering for exploration of complex phase spaces. Particular efforts have been made to ensure that the different capabilities interoperate in various combinations with high performance and scaling. Comparison to other available open source software will also be assessed. This collaboration is supported NSF SI2-SSI Grant ACI-1339804.

  19. ESTUDIO TEÓRICO DE LA MOLÉCULA DE HIDROGENO CALCULO AB-INITIO

    Directory of Open Access Journals (Sweden)

    N. Quitián

    2010-09-01

    Full Text Available Utilizando la técnica LCGO-SCF-MO (Combinación Lineal de los Orbitales Moleculares en Orbitales Gausianos, en el método del Campo Auto-Coherente, se determinaron las energías de orbital, la energía electrónica total, la energía de repulsión nuclear y la energía de Hartree-Fock de la molécula de hidrógeno en su estado fundamental, mediante un cálculo ab initio y utilizando una base de funciones gausianas. Los orbitales moleculares fueron desarrollados en términos de una función Is contraída por átomo de hidrógeno, obtenida por la minimización de los coeficientes y de los exponentes de los orbitales gausianos para el átomo aislado. Los resultados obtenidos nos permiten afirmar que la base molecular mejora sensiblemente los resultados, acercándose más al límite de Hartree-Fock.

  20. Ab initio theory of exchange interactions and the Curie temperature of bulk Gd

    CERN Document Server

    Turek, I; Bihlmayer, G; Bluegel, S

    2003-01-01

    An ab initio approach to the magnetic properties of bulk hexagonal Gd is developed that is based on the local spin-density approximation with the 4f electrons treated as localized core electrons. The effective one-electron problem is solved using the tight-binding linear muffin-tin orbital method in the atomic-sphere approximation with the valence basis consisting of s-, p-and d-type orbitals. The approach leads to a correct description of the ground-state properties like the stability of the ferromagnetic structure, the magnetic moment and the equilibrium lattice constant. Application of a real-space Green-function formalism yields the exchange pair interactions between distant neighbours that are inevitable for quantitative studies of magnetic excitations. The distance dependence and anisotropy of the exchange pair interactions are presented and the Curie temperature in the mean-field approximation is evaluated. The obtained value of 334 K is in much better agreement with the experimental value of 293 K tha...