Ab initio potential energy and dipole moment surfaces of the F(-)(H2O) complex.

PubMed

Kamarchik, Eugene; Toffoli, Daniele; Christiansen, Ove; Bowman, Joel M

2014-02-05

We present full-dimensional, ab initio potential energy and dipole moment surfaces for the F(-)(H2O) complex. The potential surface is a permutationally invariant fit to 16,114 coupled-cluster single double (triple)/aVTZ energies, while the dipole surface is a covariant fit to 11,395 CCSD(T)/aVTZ dipole moments. Vibrational self-consistent field/vibrational configuration interaction (VSCF/VCI) calculations of energies and the IR-spectrum are presented both for F(-)(H2O) and for the deuterated analog, F(-)(D2O). A one-dimensional calculation of the splitting of the ground state, due to equivalent double-well global minima, is also reported. Copyright © 2013 Elsevier B.V. All rights reserved.

Magnetic Excitations in Polyoxotungstate-Supported Lanthanoid Single-Molecule Magnets: An Inelastic Neutron Scattering and ab Initio Study.

PubMed

Vonci, Michele; Giansiracusa, Marcus J; Van den Heuvel, Willem; Gable, Robert W; Moubaraki, Boujemaa; Murray, Keith S; Yu, Dehong; Mole, Richard A; Soncini, Alessandro; Boskovic, Colette

2017-01-03

Inelastic neutron scattering (INS) has been used to investigate the crystal field (CF) magnetic excitations of the analogs of the most representative lanthanoid-polyoxometalate single-molecule magnet family: Na 9 [Ln(W 5 O 18 ) 2 ] (Ln = Nd, Tb, Ho, Er). Ab initio complete active space self-consistent field/restricted active space state interaction calculations, extended also to the Dy analog, show good agreement with the experimentally determined low-lying CF levels, with accuracy better in most cases than that reported for approaches based only on simultaneous fitting to CF models of magnetic or spectroscopic data for isostructural Ln families. In this work we demonstrate the power of a combined spectroscopic and computational approach. Inelastic neutron scattering has provided direct access to CF levels, which together with the magnetometry data, were employed to benchmark the ab initio results. The ab initio determined wave functions corresponding to the CF levels were in turn employed to assign the INS transitions allowed by selection rules and interpret the observed relative intensities of the INS peaks. Ultimately, we have been able to establish the relationship between the wave function composition of the CF split Ln III ground multiplets and the experimentally measured magnetic and spectroscopic properties for the various analogs of the Na 9 [Ln(W 5 O 18 ) 2 ] family.

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

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Rice, Julia E.

1992-01-01

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

Transitioning NWChem to the Next Generation of Manycore Machines

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bylaska, Eric J.; Apra, E; Kowalski, Karol

The NorthWest chemistry (NWChem) modeling software is a popular molecular chemistry simulation software that was designed from the start to work on massively parallel processing supercomputers [1-3]. It contains an umbrella of modules that today includes self-consistent eld (SCF), second order Møller-Plesset perturbation theory (MP2), coupled cluster (CC), multiconguration self-consistent eld (MCSCF), selected conguration interaction (CI), tensor contraction engine (TCE) many body methods, density functional theory (DFT), time-dependent density functional theory (TDDFT), real-time time-dependent density functional theory, pseudopotential plane-wave density functional theory (PSPW), band structure (BAND), ab initio molecular dynamics (AIMD), Car-Parrinello molecular dynamics (MD), classical MD, hybrid quantum mechanicsmore » molecular mechanics (QM/MM), hybrid ab initio molecular dynamics molecular mechanics (AIMD/MM), gauge independent atomic orbital nuclear magnetic resonance (GIAO NMR), conductor like screening solvation model (COSMO), conductor-like screening solvation model based on density (COSMO-SMD), and reference interaction site model (RISM) solvation models, free energy simulations, reaction path optimization, parallel in time, among other capabilities [4]. Moreover, new capabilities continue to be added with each new release.« less

Diffusion in liquid Germanium using ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

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

1996-03-01

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

Ab initio atomic recombination reaction energetics on model heat shield surfaces

NASA Technical Reports Server (NTRS)

Senese, Fredrick; Ake, Robert

1992-01-01

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

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

PubMed

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

2015-05-21

The calculation and characterization of the IR spectrum of liquid water have remained a challenge for theory. In this paper, we address this challenge using a combination of ab initio approaches, namely, a quantum treatment of IR spectrum using the ab initio WHBB water potential energy surface and a refined ab initio dipole moment surface. The quantum treatment is based on the embedded local monomer method, in which the three intramolecular modes of each embedded H2O monomer are fully coupled and also coupled singly to each of six intermolecular modes. The new dipole moment surface consists of a previous spectroscopically accurate 1-body dipole moment surface and a newly fitted ab initio intrinsic 2-body dipole moment. A detailed analysis of the new dipole moment surface in terms of the coordinate dependence of the effective atomic charges is done along with tests of it for the water dimer and prism hexamer double-harmonic spectra against direct ab initio calculations. The liquid configurations are taken from previous molecular dynamics calculations of Skinner and co-workers, using the TIP4P plus E3B rigid monomer water potential. The IR spectrum of water at 300 K in the range of 0-4000 cm(-1) is calculated and compared with experiment, using the ab initio WHBB potential and new ab initio dipole moment, the q-TIP4P/F potential, which has a fixed-charged description of the dipole moment, and the TTM3-F potential and dipole moment surfaces. The newly calculated ab initio spectrum is in very good agreement with experiment throughout the above spectral range, both in band positions and intensities. This contrasts to results with the other potentials and dipole moments, especially the fixed-charge q-TIP4P/F model, which gives unrealistic intensities. The calculated ab initio spectrum is analyzed by examining the contribution of various transitions to each band.

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

NASA Astrophysics Data System (ADS)

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

2015-05-01

The calculation and characterization of the IR spectrum of liquid water have remained a challenge for theory. In this paper, we address this challenge using a combination of ab initio approaches, namely, a quantum treatment of IR spectrum using the ab initio WHBB water potential energy surface and a refined ab initio dipole moment surface. The quantum treatment is based on the embedded local monomer method, in which the three intramolecular modes of each embedded H2O monomer are fully coupled and also coupled singly to each of six intermolecular modes. The new dipole moment surface consists of a previous spectroscopically accurate 1-body dipole moment surface and a newly fitted ab initio intrinsic 2-body dipole moment. A detailed analysis of the new dipole moment surface in terms of the coordinate dependence of the effective atomic charges is done along with tests of it for the water dimer and prism hexamer double-harmonic spectra against direct ab initio calculations. The liquid configurations are taken from previous molecular dynamics calculations of Skinner and co-workers, using the TIP4P plus E3B rigid monomer water potential. The IR spectrum of water at 300 K in the range of 0-4000 cm-1 is calculated and compared with experiment, using the ab initio WHBB potential and new ab initio dipole moment, the q-TIP4P/F potential, which has a fixed-charged description of the dipole moment, and the TTM3-F potential and dipole moment surfaces. The newly calculated ab initio spectrum is in very good agreement with experiment throughout the above spectral range, both in band positions and intensities. This contrasts to results with the other potentials and dipole moments, especially the fixed-charge q-TIP4P/F model, which gives unrealistic intensities. The calculated ab initio spectrum is analyzed by examining the contribution of various transitions to each band.

Ab Initio Calculations of Transport in Titanium and Aluminum Mixtures

NASA Astrophysics Data System (ADS)

Walker, Nicholas; Novak, Brian; Tam, Ka Ming; Moldovan, Dorel; Jarrell, Mark

In classical molecular dynamics simulations, the self-diffusion and shear viscosity of titanium about the melting point have fallen within the ranges provided by experimental data. However, the experimental data is difficult to collect and has been rather scattered, making it of limited value for the validation of these calculations. By using ab initio molecular dynamics simulations within the density functional theory framework, the classical molecular dynamics data can be validated. The dynamical data from the ab initio molecular dynamics can also be used to calculate new potentials for use in classical molecular dynamics, allowing for more accurate classical dynamics simulations for the liquid phase. For metallic materials such as titanium and aluminum alloys, these calculations are very valuable due to an increasing demand for the knowledge of their thermophysical properties that drive the development of new materials. For example, alongside knowledge of the surface tension, viscosity is an important input for modeling the additive manufacturing process at the continuum level. We are developing calculations of the viscosity along with the self-diffusion for aluminum, titanium, and titanium-aluminum alloys with ab initio molecular dynamics. Supported by the National Science Foundation through cooperative agreement OIA-1541079 and the Louisiana Board of Regents.

An ab initio CASSCF study of zero field splitting fluctuations in the octet ground state of aqueous [Gd(iii)(HPDO3A)(H2O)

NASA Astrophysics Data System (ADS)

Khan, Shehryar; Pollet, Rodolphe; Vuilleumier, Rodolphe; Kowalewski, Jozef; Odelius, Michael

2017-12-01

In this work, we present ab initio calculations of the zero-field splitting (ZFS) of a gadolinium complex [Gd(iii)(HPDO3A)(H2O)] sampled from an ab initio molecular dynamics (AIMD) simulation. We perform both post-Hartree-Fock (complete active space self-consistent field—CASSCF) and density functional theory (DFT) calculations of the ZFS and compare and contrast the methods with experimental data. Two different density functional approximations (TPSS and LC-BLYP) were investigated. The magnitude of the ZFS from the CASSCF calculations is in good agreement with experiment, whereas the DFT results in varying degrees overestimate the magnitude of the ZFS for both functionals and exhibit a strong functional dependence. It was found in the sampling over the AIMD trajectory that the fluctuations in the transient ZFS tensor derived from DFT are not correlated with those of CASSCF nor does the magnitude of the ZFS from CASSCF and DFT correlate. From the fluctuations in the ZFS tensor, we extract a correlation time of the transient ZFS which is on the sub-picosecond time scale, showing a faster decay than experimental estimates.

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

PubMed Central

Zhang, Yang

2014-01-01

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. PMID:23760925

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

PubMed

Zhang, Yang

2014-02-01

We develop and test a new pipeline in CASP10 to predict protein structures based on an interplay of I-TASSER and QUARK for both free-modeling (FM) and template-based modeling (TBM) targets. The most noteworthy observation is that sorting through the threading template pool using the QUARK-based ab initio models as probes allows the detection of distant-homology templates which might be ignored by the traditional sequence profile-based threading alignment algorithms. Further template assembly refinement by I-TASSER resulted in successful folding of two medium-sized FM targets with >150 residues. For TBM, the multiple threading alignments from LOMETS are, for the first time, incorporated into the ab initio QUARK simulations, which were further refined by I-TASSER assembly refinement. Compared with the traditional threading assembly refinement procedures, the inclusion of the threading-constrained ab initio folding models can consistently improve the quality of the full-length models as assessed by the GDT-HA and hydrogen-bonding scores. Despite the success, significant challenges still exist in domain boundary prediction and consistent folding of medium-size proteins (especially beta-proteins) for nonhomologous targets. Further developments of sensitive fold-recognition and ab initio folding methods are critical for solving these problems. Copyright © 2013 Wiley Periodicals, Inc.

Ab initio DNA synthesis by Bst polymerase in the presence of nicking endonucleases Nt.AlwI, Nb.BbvCI, and Nb.BsmI.

PubMed

Antipova, Valeriya N; Zheleznaya, Lyudmila A; Zyrina, Nadezhda V

2014-08-01

In the absence of added DNA, thermophilic DNA polymerases synthesize double-stranded DNA from free dNTPs, which consist of numerous repetitive units (ab initio DNA synthesis). The addition of thermophilic restriction endonuclease (REase), or nicking endonuclease (NEase), effectively stimulates ab initio DNA synthesis and determines the nucleotide sequence of reaction products. We have found that NEases Nt.AlwI, Nb.BbvCI, and Nb.BsmI with non-palindromic recognition sites stimulate the synthesis of sequences organized mainly as palindromes. Moreover, the nucleotide sequence of the palindromes appeared to be dependent on NEase recognition/cleavage modes. Thus, the heterodimeric Nb.BbvCI stimulated the synthesis of palindromes composed of two recognition sites of this NEase, which were separated by AT-reach sequences or (A)n (T)m spacers. Palindromic DNA sequences obtained in the ab initio DNA synthesis with the monomeric NEases Nb.BsmI and Nt.AlwI contained, along with the sites of these NEases, randomly synthesized sequences consisted of blocks of short repeats. These findings could help investigation of the potential abilities of highly productive ab initio DNA synthesis for the creation of DNA molecules with desirable sequence. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Electron transport in biomolecular gaseous and liquid systems: theory, experiment and self-consistent cross-sections

NASA Astrophysics Data System (ADS)

White, R. D.; Cocks, D.; Boyle, G.; Casey, M.; Garland, N.; Konovalov, D.; Philippa, B.; Stokes, P.; de Urquijo, J.; González-Magaña, O.; McEachran, R. P.; Buckman, S. J.; Brunger, M. J.; Garcia, G.; Dujko, S.; Petrovic, Z. Lj

2018-05-01

Accurate modelling of electron transport in plasmas, plasma-liquid and plasma-tissue interactions requires (i) the existence of accurate and complete sets of cross-sections, and (ii) an accurate treatment of electron transport in these gaseous and soft-condensed phases. In this study we present progress towards the provision of self-consistent electron-biomolecule cross-section sets representative of tissue, including water and THF, by comparison of calculated transport coefficients with those measured using a pulsed-Townsend swarm experiment. Water–argon mixtures are used to assess the self-consistency of the electron-water vapour cross-section set proposed in de Urquijo et al (2014 J. Chem. Phys. 141 014308). Modelling of electron transport in liquids and soft-condensed matter is considered through appropriate generalisations of Boltzmann’s equation to account for spatial-temporal correlations and screening of the electron potential. The ab initio formalism is applied to electron transport in atomic liquids and compared with available experimental swarm data for these noble liquids. Issues on the applicability of the ab initio formalism for krypton are discussed and addressed through consideration of the background energy of the electron in liquid krypton. The presence of self-trapping (into bubble/cluster states/solvation) in some liquids requires a reformulation of the governing Boltzmann equation to account for the combined localised–delocalised nature of the resulting electron transport. A generalised Boltzmann equation is presented which is highlighted to produce dispersive transport observed in some liquid systems.

Ab initio quantum chemical calculation of electron transfer matrix elements for large molecules

NASA Astrophysics Data System (ADS)

Zhang, Linda Yu; Friesner, Richard A.; Murphy, Robert B.

1997-07-01

Using a diabatic state formalism and pseudospectral numerical methods, we have developed an efficient ab initio quantum chemical approach to the calculation of electron transfer matrix elements for large molecules. The theory is developed at the Hartree-Fock level and validated by comparison with results in the literature for small systems. As an example of the power of the method, we calculate the electronic coupling between two bacteriochlorophyll molecules in various intermolecular geometries. Only a single self-consistent field (SCF) calculation on each of the monomers is needed to generate coupling matrix elements for all of the molecular pairs. The largest calculations performed, utilizing 1778 basis functions, required ˜14 h on an IBM 390 workstation. This is considerably less cpu time than would be necessitated with a supermolecule adiabatic state calculation and a conventional electronic structure code.

Molecular dynamics simulations of fluid methane properties using ab initio intermolecular interaction potentials.

PubMed

Chao, Shih-Wei; Li, Arvin Huang-Te; Chao, Sheng D

2009-09-01

Intermolecular interaction energy data for the methane dimer have been calculated at a spectroscopic accuracy and employed to construct an ab initio potential energy surface (PES) for molecular dynamics (MD) simulations of fluid methane properties. The full potential curves of the methane dimer at 12 symmetric conformations were calculated by the supermolecule counterpoise-corrected second-order Møller-Plesset (MP2) perturbation theory. Single-point coupled cluster with single and double and perturbative triple excitations [CCSD(T)] calculations were also carried out to calibrate the MP2 potentials. We employed Pople's medium size basis sets [up to 6-311++G(3df, 3pd)] and Dunning's correlation consistent basis sets (cc-pVXZ and aug-cc-pVXZ, X = D, T, Q). For each conformer, the intermolecular carbon-carbon separation was sampled in a step 0.1 A for a range of 3-9 A, resulting in a total of 732 configuration points calculated. The MP2 binding curves display significant anisotropy with respect to the relative orientations of the dimer. The potential curves at the complete basis set (CBS) limit were estimated using well-established analytical extrapolation schemes. A 4-site potential model with sites located at the hydrogen atoms was used to fit the ab initio potential data. This model stems from a hydrogen-hydrogen repulsion mechanism to explain the stability of the dimer structure. MD simulations using the ab initio PES show quantitative agreements on both the atom-wise radial distribution functions and the self-diffusion coefficients over a wide range of experimental conditions. Copyright 2008 Wiley Periodicals, Inc.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

2015-05-21

The calculation and characterization of the IR spectrum of liquid water have remained a challenge for theory. In this paper, we address this challenge using a combination of ab initio approaches, namely, a quantum treatment of IR spectrum using the ab initio WHBB water potential energy surface and a refined ab initio dipole moment surface. The quantum treatment is based on the embedded local monomer method, in which the three intramolecular modes of each embedded H{sub 2}O monomer are fully coupled and also coupled singly to each of six intermolecular modes. The new dipole moment surface consists of a previousmore » spectroscopically accurate 1-body dipole moment surface and a newly fitted ab initio intrinsic 2-body dipole moment. A detailed analysis of the new dipole moment surface in terms of the coordinate dependence of the effective atomic charges is done along with tests of it for the water dimer and prism hexamer double-harmonic spectra against direct ab initio calculations. The liquid configurations are taken from previous molecular dynamics calculations of Skinner and co-workers, using the TIP4P plus E3B rigid monomer water potential. The IR spectrum of water at 300 K in the range of 0–4000 cm{sup −1} is calculated and compared with experiment, using the ab initio WHBB potential and new ab initio dipole moment, the q-TIP4P/F potential, which has a fixed-charged description of the dipole moment, and the TTM3-F potential and dipole moment surfaces. The newly calculated ab initio spectrum is in very good agreement with experiment throughout the above spectral range, both in band positions and intensities. This contrasts to results with the other potentials and dipole moments, especially the fixed-charge q-TIP4P/F model, which gives unrealistic intensities. The calculated ab initio spectrum is analyzed by examining the contribution of various transitions to each band.« less

Self-consistent-field perturbation theory for the Schröautdinger equation

NASA Astrophysics Data System (ADS)

Goodson, David Z.

1997-06-01

A method is developed for using large-order perturbation theory to solve the systems of coupled differential equations that result from the variational solution of the Schröautdinger equation with wave functions of product form. This is a noniterative, computationally efficient way to solve self-consistent-field (SCF) equations. Possible applications include electronic structure calculations using products of functions of collective coordinates that include electron correlation, vibrational SCF calculations for coupled anharmonic oscillators with selective coupling of normal modes, and ab initio calculations of molecular vibration spectra without the Born-Oppenheimer approximation.

Ab initio study of Fe(+)-benzyne

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.

1993-01-01

The interaction of Fe(+) with benzyne is studied using the self-consistent-field (SCF), complete active space SCF, and modified-coupled-pair functional levels of theory. The most stable structure is planar, where the Fe(+) has inserted into the in-plane pi bond, although the C-C bond distance suggests that some in-plane pi bonding remains. This system is compared with Sc(+) bonding to benzyne and other ligands.

A high level Ab initio study of the anionic hydrogen-bonded complexes FH-CN-, FH-NC-, H2O-CN- and H2O-NC-

NASA Technical Reports Server (NTRS)

Lee, Timothy J.

1989-01-01

HF, H2O, CN- and their hydrogen-bonded complexes were studied using state-of-the-art ab initio quantum mechanical methods. A large Gaussian one particle basis set consisting of triple zeta plus double polarization plus diffuse s and p functions (TZ2P + diffuse) was used. The theoretical methods employed include self consistent field, second order Moller-Plesset perturbation theory, singles and doubles configuration interaction theory and the singles and doubles coupled cluster approach. The FH-CN- and FH-NC- and H2O-CN-, H2O-NC- pairs of complexes are found to be essentially isoenergetic. The first pair of complexes are predicted to be bound by approx. 24 kcal/mole and the latter pair bound by approximately 15 kcal/mole. The ab initio binding energies are in good agreement with the experimental values. The two being shorter than the analogous C-N hydrogen bond. The infrared (IR) spectra of the two pairs of complexes are also very similar, though a severe perturbation of the potential energy surface by proton exchange means that the accurate prediction of the band center of the most intense IR mode requires a high level of electronic structure theory as well as a complete treatment of anharmonic effects. The bonding of anionic hydrogen-bonded complexes is discussed and contrasted with that of neutral hydrogen-bonded complexes.

Dynamical correlation effects on photoisomerization: Ab initio multiple spawning dynamics with MS-CASPT2 for a model trans-protonated Schiff base

DOE PAGES

Liu, Lihong; Liu, Jian; Martinez, Todd J.

2015-12-17

Here, we investigate the photoisomerization of a model retinal protonated Schiff base (trans-PSB3) using ab initio multiple spawning (AIMS) based on multi-state second order perturbation theory (MSPT2). Discrepancies between the photodynamical mechanism computed with three-root state-averaged complete active space self-consistent field (SA-3-CASSCF, which does not include dynamic electron correlation effects) and MSPT2 show that dynamic correlation is critical in this photoisomerization reaction. Furthermore, we show that the photodynamics of trans-PSB3 is not well described by predictions based on minimum energy conical intersections (MECIs) or minimum energy conical intersection (CI) seam paths. Instead, most of the CIs involved in the photoisomerizationmore » are far from MECIs and minimum energy CI seam paths. Thus, both dynamical nuclear effects and dynamic electron correlation are critical to understanding the photochemical mechanism.« less

Correlation of electronic structure and magnetic moment in Ga1-xMnxN : First-principles, mean field and high temperature series expansions calculations

NASA Astrophysics Data System (ADS)

Masrour, R.; Hlil, E. K.

2016-08-01

Self-consistent ab initio calculations based on density-functional theory and using both full potential linearized augmented plane wave and Korring-Kohn-Rostoker-coherent potential approximation methods, are performed to investigate both electronic and magnetic properties of the Ga1-xMnxN system. Magnetic moments considered to lie along (001) axes are computed. Obtained data from ab initio calculations are used as input for the high temperature series expansions (HTSEs) calculations to compute other magnetic parameters such as the magnetic phase diagram and the critical exponent. The increasing of the dilution x in this system has allowed to verify a series of HTSEs predictions on the possibility of ferromagnetism in dilute magnetic insulators and to demonstrate that the interaction changes from antiferromagnetic to ferromagnetic passing through the spins glace phase.

An ab initio cluster study of the chemisorption of atomic cesium and hydrogen on reconstructed surfaces of gallium rich gallium arsenide

NASA Astrophysics Data System (ADS)

Schailey, Ronald

1999-11-01

Chemisorption properties of cesium and hydrogen atoms on the Ga-rich GaAs (100) (2 x 1), (2 x 2), and β(4 x 2) surfaces are investigated using ab initio self-consistent restricted open shell Hartree-Fock (ROHF) total energy calculations with Hay- Wadt effective core potentials. The effects of electron correlation have been included using many-body perturbation theory through second order, with the exception of β(4 x 2) symmetry due to computational limitations. The semiconductor surface is modeled by finite sized hydrogen saturated clusters. The effects of surface relaxation and reconstruction have been investigated in detail. Results are given for the energetics of chemisorption, charge population analysis, HOMO-LUMO gaps, and consequent possibilities of metallization for atomic cesium adsorption. For the chemisorption of atomic hydrogen, the experimentally verified mechanism of surface dimer bond breaking is investigated in detail.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ejembi, J. I.; Nwigboji, I. H.; Franklin, L.

2014-09-14

We present results from ab-initio, self-consistent density functional theory calculations of electronic and related properties of zinc blende boron phosphide (zb-BP). We employed a local density approximation potential and implemented the linear combination of atomic orbitals formalism. This technique follows the Bagayoko, Zhao, and Williams method, as enhanced by the work of Ekuma and Franklin. The results include electronic energy bands, densities of states, and effective masses. The calculated band gap of 2.02 eV, for the room temperature lattice constant of a=4.5383 Å, is in excellent agreement with the experimental value of 2.02±0.05 eV. Our result for the bulk modulus,more » 155.7 GPa, agrees with experiment (152–155 GPa). Our predictions for the equilibrium lattice constant and the corresponding band gap, for very low temperatures, are 4.5269 Å and 2.01 eV, respectively.« less

Kinetics study of the CN + CH4 hydrogen abstraction reaction based on a new ab initio analytical full-dimensional potential energy surface.

PubMed

Espinosa-Garcia, Joaquin; Rangel, Cipriano; Suleimanov, Yury V

2017-07-26

We have developed an analytical full-dimensional potential energy surface, named PES-2017, for the gas-phase hydrogen abstraction reaction between the cyano radical and methane. This surface is fitted using high-level ab initio information as input. Using the PES-2017 surface, a kinetics study was performed via two theoretical approaches: variational transition-state theory with multidimensional tunnelling (VTST-MT) and ring polymer molecular dynamics (RPMD). The results are compared with the experimental data. In the whole temperature range analysed, 300-1500 K, both theories agree within a factor of <2, reproducing the experimental behaviour taking into account the experimental uncertainties. At high temperatures, where the recrossing effects dominate and the RPMD theory is exact, both theories differ by a factor of about 20%; while at low temperatures this difference is larger, 45%. Note that in this temperature regime, the tunnelling effect is negligible. The CN + CH 4 /CD 4 kinetic isotope effects are important, reproducing the scarce experimental evidence. The good agreement with the ab initio information used in the fitting process (self-consistency test) and with the kinetic behaviour in a wide temperature range gives confidence and strength to the new surface.

An ab initio chemical reaction model for the direct simulation Monte Carlo study of non-equilibrium nitrogen flows.

PubMed

Mankodi, T K; Bhandarkar, U V; Puranik, B P

2017-08-28

A new ab initio based chemical model for a Direct Simulation Monte Carlo (DSMC) study suitable for simulating rarefied flows with a high degree of non-equilibrium is presented. To this end, Collision Induced Dissociation (CID) cross sections for N 2 +N 2 →N 2 +2N are calculated and published using a global complete active space self-consistent field-complete active space second order perturbation theory N 4 potential energy surface and quasi-classical trajectory algorithm for high energy collisions (up to 30 eV). CID cross sections are calculated for only a selected set of ro-vibrational combinations of the two nitrogen molecules, and a fitting scheme based on spectroscopic weights is presented to interpolate the CID cross section for all possible ro-vibrational combinations. The new chemical model is validated by calculating equilibrium reaction rate coefficients that can be compared well with existing shock tube and computational results. High-enthalpy hypersonic nitrogen flows around a cylinder in the transition flow regime are simulated using DSMC to compare the predictions of the current ab initio based chemical model with the prevailing phenomenological model (the total collision energy model). The differences in the predictions are discussed.

Maximally localized Wannier functions in LaMnO3 within PBE + U, hybrid functionals and partially self-consistent GW: an efficient route to construct ab initio tight-binding parameters for eg perovskites.

PubMed

Franchini, C; Kováčik, R; Marsman, M; Murthy, S Sathyanarayana; He, J; Ederer, C; Kresse, G

2012-06-13

Using the newly developed VASP2WANNIER90 interface we have constructed maximally localized Wannier functions (MLWFs) for the e(g) states of the prototypical Jahn-Teller magnetic perovskite LaMnO(3) at different levels of approximation for the exchange-correlation kernel. These include conventional density functional theory (DFT) with and without the additional on-site Hubbard U term, hybrid DFT and partially self-consistent GW. By suitably mapping the MLWFs onto an effective e(g) tight-binding (TB) Hamiltonian we have computed a complete set of TB parameters which should serve as guidance for more elaborate treatments of correlation effects in effective Hamiltonian-based approaches. The method-dependent changes of the calculated TB parameters and their interplay with the electron-electron (el-el) interaction term are discussed and interpreted. We discuss two alternative model parameterizations: one in which the effects of the el-el interaction are implicitly incorporated in the otherwise 'noninteracting' TB parameters and a second where we include an explicit mean-field el-el interaction term in the TB Hamiltonian. Both models yield a set of tabulated TB parameters which provide the band dispersion in excellent agreement with the underlying ab initio and MLWF bands.

Pseudo-conformer models for linear molecules: Joint treatment of spectroscopic, electron diffraction and ab initio data for the C3O2 molecule

NASA Astrophysics Data System (ADS)

Tarasov, Yury I.; Kochikov, Igor V.

2018-06-01

Dynamic analysis of the molecules with large-amplitude motions (LAM) based on the pseudo-conformer approach has been successfully applied to various molecules. Floppy linear molecules present a special class of molecular structures that possess a pair of conjugate LAM coordinates but allow one-dimensional treatment. In this paper, previously developed treatment for the semirigid molecules is applied to the carbon suboxide molecule. This molecule characterized by the extremely large CCC bending has been thoroughly investigated by spectroscopic and ab initio methods. However, the earlier electron diffraction investigations were performed within a static approach, obtaining thermally averaged parameters. In this paper we apply a procedure aimed at obtaining the short list of self-consistent reference geometry parameters of a molecule, while all thermally averaged parameters are calculated based on reference geometry, relaxation dependencies and quadratic and cubic force constants. We show that such a model satisfactorily describes available electron diffraction evidence with various QC bending potential energy functions when r.m.s. CCC angle is in the interval 151 ± 2°. This leads to a self-consistent molecular model satisfying spectroscopic and GED data. The parameters for linear reference geometry have been defined as re(CO) = 1.161(2) Å and re(CC) = 1.273(2) Å.

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

PubMed

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 simple ab initio thermodynamics treatment. We show that ab initio thermodynamics leads to erroneous conclusions about kinetic and mechanistic aspects for the CER over RuO 2 (110), while the kinetics of the OER over RuO 2 (110) and ORR over Pt(111) are reasonably well described. Microkinetics of an electrocatalyzed reaction is largely simplified by the quasi-equilibria of the RI preceding the rate-determining step (rds) with the reactants. Therefore, in ab initio kinetics the rate of an electrocatalyzed reaction is governed by the transition state (TS) with the highest free energy G rds # , defining also the rate-determining step (rds). Ab initio thermodynamics may be even more powerful, when using the highest free energy of an reaction intermediate G max (RI) rather than the highest free energy difference between consecutive reaction intermediates, ΔG loss , as a descriptor for the kinetics.

The Application of Some Hartree-Fock Model Calculation to the Analysis of Atomic and Free-Ion Optical Spectra

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hayhurst, Thomas Laine

1980-08-06

Techniques for applying ab-initio calculations to the is of atomic spectra are investigated, along with the relationship between the semi-empirical and ab-initio forms of Slater-Condon theory. Slater-Condon theory is reviewed with a focus on the essential features that lead to the effective Hamiltonians associated with the semi-empirical form of the theory. Ab-initio spectroscopic parameters are calculated from wavefunctions obtained via self-consistent field methods, while multi-configuration Hamiltonian matrices are constructed and diagonalized with computer codes written by Robert Cowan of Los Alamos Scientific Laboratory. Group theoretical analysis demonstrates that wavefunctions more general than Slater determinants (i.e. wavefunctions with radial correlations betweenmore » electrons) lead to essentially the same parameterization of effective Hamiltonians. In the spirit of this analysis, a strategy is developed for adjusting ab-initio values of the spectroscopic parameters, reproducing parameters obtained by fitting the corresponding effective Hamiltonian. Secondary parameters are used to "screen" the calculated (primary) spectroscopic parameters, their values determined by least squares. Extrapolations of the secondary parameters determined from analyzed spectra are attempted to correct calculations of atoms and ions without experimental levels. The adjustment strategy and extrapolations are tested on the K I sequence from K 0+ through Fe 7+, fitting to experimental levels for V 4+, and Cr 5+; unobserved levels and spectra are predicted for several members of the sequence. A related problem is also discussed: Energy levels of the Uranium hexahalide complexes, (UX 6) 2- for X= F, Cl, Br, and I, are fit to an effective Hamiltonian (the f 2 configuration in O h symmetry) with corrections proposed by Brian Judd.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Starrett, C. E.; Saumon, D.

Here, we present an approximation for calculating the equation of state (EOS) of warm and hot dense matter that is built on the previously published pseudoatom molecular dynamics (PAMD) model of dense plasmas [Starrett et al., Phys. Rev. E 91, 013104 (2015)]. And while the EOS calculation with PAMD was previously limited to orbital-free density functional theory (DFT), the new approximation presented here allows a Kohn-Sham DFT treatment of the electrons. The resulting EOS thus includes a quantum mechanical treatment of the electrons with a self-consistent model of the ionic structure, while remaining tractable at high temperatures. The method ismore » validated by comparisons with pressures from ab initio simulations of Be, Al, Si, and Fe. The EOS in the Thomas-Fermi approximation shows remarkable thermodynamic consistency over a wide range of temperatures for aluminum. We also calculate the principal Hugoniots of aluminum and silicon up to 500 eV. We find that the ionic structure of the plasma has a modest effect that peaks at temperatures of a few eV and that the features arising from the electronic structure agree well with ab initio simulations.« less

Materials Screening for the Discovery of New Half-Heuslers: Machine Learning versus ab Initio Methods.

PubMed

Legrain, Fleur; Carrete, Jesús; van Roekeghem, Ambroise; Madsen, Georg K H; Mingo, Natalio

2018-01-18

Machine learning (ML) is increasingly becoming a helpful tool in the search for novel functional compounds. Here we use classification via random forests to predict the stability of half-Heusler (HH) compounds, using only experimentally reported compounds as a training set. Cross-validation yields an excellent agreement between the fraction of compounds classified as stable and the actual fraction of truly stable compounds in the ICSD. The ML model is then employed to screen 71 178 different 1:1:1 compositions, yielding 481 likely stable candidates. The predicted stability of HH compounds from three previous high-throughput ab initio studies is critically analyzed from the perspective of the alternative ML approach. The incomplete consistency among the three separate ab initio studies and between them and the ML predictions suggests that additional factors beyond those considered by ab initio phase stability calculations might be determinant to the stability of the compounds. Such factors can include configurational entropies and quasiharmonic contributions.

Ab initio molecular dynamics of solvation effects on reactivity at electrified interfaces

DOE PAGES

Herron, Jeffrey A.; Morikawa, Yoshitada; Mavrikakis, Manos

2016-08-08

Using ab initio molecular dynamics (as implemented in periodic, self-consistent (GGA-PBE) density functional theory (DFT) we investigated the mechanism of methanol electro-oxidation on Pt(111). We investigated the role of solvation and electrode potential on the energetics of the first proton transfer step, methanol electro-oxidation to methoxy (CH 3O) or hydroxymethyl (CH 2OH). The results show that solvation weakens the adsorption of methoxy to uncharged Pt(111), while the binding energy 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 constrainedmore » 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. Solvation reduces the barrier for both C-H and O-H bond activation steps with respect to their vapor phase values, though 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). Furthermore, with positive bias, O-H bond activation is enhanced, becoming slightly more facile than C-H bond activation.« less

Ab initio molecular orbital studies of the positive muon and muonium in 4-arylmethyleneamino-TEMPO derivatives

NASA Astrophysics Data System (ADS)

Briere, T. M.; Jeong, J.; Das, T. P.; Ohira, S.; Nagamine, K.

2000-08-01

The muon and muonium bonding sites of the 4-arylmethyleneamino-2,2,6,6-tetramethylpiperidin-1-yloxyl radical crystals with aryl groups consisting of biphenyl and 4-pyridyl were studied via ab initio Hartree-Fock theory. The hyperfine fields, including both intramolecular and intermolecular interactions, were calculated at the sites of interest and compared to zero field μSR results.

Atomistic and Ab Initio Calculations or Ternary II-IV-V2 Semiconductors

DTIC Science & Technology

1999-12-07

consisting of two- and three-body terms is developed reproducing crystal lattice constants, elastic and dielectric constants very well. The calculated...the lattice . This difference may well be due to defect-induced lattice distortion which plays a key role in stabilizing the hole states in the... lattice . 15. SUBJECT TERMS Chalcopyrites, Defects, Atomistic and AB Initio Calculations 16. SECURITY CLASSIFICATION OF: a. REPORT u b. ABSTRACT U

Self-Instruction and Success: A Learner-Profile Study.

ERIC Educational Resources Information Center

Jones, Francis R.

1998-01-01

Interviews with adults experienced in foreign language self-instruction generated profiles of language experience at learner and self-instructed language-token levels. Results showed separations between languages with and without self-instruction. The most effective learning route was starting with classwork. Ab initio self-instruction produced…

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

DOE PAGES

Gaenko, Alexander; DeFusco, Albert; Varganov, Sergey A.; ...

2014-10-20

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

Ab-initio Calculation of the XANES of Lithium Phosphates and LiFePO4

NASA Astrophysics Data System (ADS)

Yiu, Y. M.; Yang, Songlan; Wang, Dongniu; Sun, Xueliang; Sham, T. K.

2013-04-01

Lithium iron phosphate has been regarded as a promising cathode material for the next generation lithium ion batteries due to its high specific capacity, superior thermal and cyclic stability [1]. In this study, the XANES (X-ray Absorption Near Edge Structure) spectra of lithium iron phosphate and lithium phosphates of various compositions at the Li K, P L3,2, Fe M3,2 and O K-edges have been simulated self-consistently using ab-initio calculations based on multiple scattering theory (the FEFF9 code) and DFT (Density Functional Theory, the Wien2k code). The lithium phosphates under investigation include LiFePO4, γ-Li3PO4, Li4P2O7 and LiPO3. The calculated spectra are compared to the experimental XANES recorded in total electron yield (TEY) and fluorescence yield (FLY). This work was carried out to assess the XANES of possible phases presented in LiFePO4 based Li ion battery applications [2].

On the bonding mechanism of CO to Pt(111) and its effect on the vibrational frequency of chemisorbed CO

NASA Astrophysics Data System (ADS)

Illas, F.; Zurita, S.; Márquez, A. M.; Rubio, J.

1997-04-01

The chemisorption of CO on the atop site of Pt(111) has been simulated by a Pt4 cluster model. Ab initio self consistent field (SCF) and complete active space self consistent field (CASSCF) cluster model wave functions have been obtained for the electronic ground state. Likewise, ab initio SCF wavefunctions have been obtained for two other electronic states. The optimum geometry and vibrational frequencies of chemisorbed CO are reported for the three states. The interaction energy and vibrational shift of chemisorbed CO, with respect to free gas phase CO, have been analyzed for the three electronic states. This analysis is carried out by means of the constrained space orbital variation (CSOV) method. In all cases the bond is found to be dominated by σ donation and π back-donation, known as Blyholder's mechanism. This mechanism is further supported by SCF calculations on a larger, Pt13, cluster model. For both clusters, the CSOV analysis of the vibrational frequency definitely shows that, contrary to previous recent studies, a major contribution to the experimentally observed vibrational shift comes from the π back-donation mechanism. However, we found that, contrary to common belief, σ donation also acts to lower the CO frequency and not to increase it. Physical reasons for such unexpected behaviour are given.

An ensemble approach to protein fold classification by integration of template-based assignment and support vector machine classifier.

PubMed

Xia, Jiaqi; Peng, Zhenling; Qi, Dawei; Mu, Hongbo; Yang, Jianyi

2017-03-15

Protein fold classification is a critical step in protein structure prediction. There are two possible ways to classify protein folds. One is through template-based fold assignment and the other is ab-initio prediction using machine learning algorithms. Combination of both solutions to improve the prediction accuracy was never explored before. We developed two algorithms, HH-fold and SVM-fold for protein fold classification. HH-fold is a template-based fold assignment algorithm using the HHsearch program. SVM-fold is a support vector machine-based ab-initio classification algorithm, in which a comprehensive set of features are extracted from three complementary sequence profiles. These two algorithms are then combined, resulting to the ensemble approach TA-fold. We performed a comprehensive assessment for the proposed methods by comparing with ab-initio methods and template-based threading methods on six benchmark datasets. An accuracy of 0.799 was achieved by TA-fold on the DD dataset that consists of proteins from 27 folds. This represents improvement of 5.4-11.7% over ab-initio methods. After updating this dataset to include more proteins in the same folds, the accuracy increased to 0.971. In addition, TA-fold achieved >0.9 accuracy on a large dataset consisting of 6451 proteins from 184 folds. Experiments on the LE dataset show that TA-fold consistently outperforms other threading methods at the family, superfamily and fold levels. The success of TA-fold is attributed to the combination of template-based fold assignment and ab-initio classification using features from complementary sequence profiles that contain rich evolution information. http://yanglab.nankai.edu.cn/TA-fold/. yangjy@nankai.edu.cn or mhb-506@163.com. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Equation of state of dense plasmas with pseudoatom molecular dynamics

DOE PAGES

Starrett, C. E.; Saumon, D.

2016-06-14

Here, we present an approximation for calculating the equation of state (EOS) of warm and hot dense matter that is built on the previously published pseudoatom molecular dynamics (PAMD) model of dense plasmas [Starrett et al., Phys. Rev. E 91, 013104 (2015)]. And while the EOS calculation with PAMD was previously limited to orbital-free density functional theory (DFT), the new approximation presented here allows a Kohn-Sham DFT treatment of the electrons. The resulting EOS thus includes a quantum mechanical treatment of the electrons with a self-consistent model of the ionic structure, while remaining tractable at high temperatures. The method ismore » validated by comparisons with pressures from ab initio simulations of Be, Al, Si, and Fe. The EOS in the Thomas-Fermi approximation shows remarkable thermodynamic consistency over a wide range of temperatures for aluminum. We also calculate the principal Hugoniots of aluminum and silicon up to 500 eV. We find that the ionic structure of the plasma has a modest effect that peaks at temperatures of a few eV and that the features arising from the electronic structure agree well with ab initio simulations.« less

Self-consistent ab initio Calculations for Photoionization and Electron-Ion Recombination Using the R-Matrix Method

NASA Astrophysics Data System (ADS)

Nahar, S. N.

2003-01-01

Most astrophysical plasmas entail a balance between ionization and recombination. We present new results from a unified method for self-consistent and ab initio calculations for the inverse processes of photoionization and (e + ion) recombination. The treatment for (e + ion) recombination subsumes the non-resonant radiative recombination and the resonant dielectronic recombination processes in a unified scheme (S.N. Nahar and A.K. Pradhan, Phys. Rev. A 49, 1816 (1994);H.L. Zhang, S.N. Nahar, and A.K. Pradhan, J.Phys.B, 32,1459 (1999)). Calculations are carried out using the R-matrix method in the close coupling approximation using an identical wavefunction expansion for both processes to ensure self-consistency. The results for photoionization and recombination cross sections may also be compared with state-of-the-art experiments on synchrotron radiation sources for photoionization, and on heavy ion storage rings for recombination. The new experiments display heretofore unprecedented detail in terms of resonances and background cross sections and thereby calibrate the theoretical data precisely. We find a level of agreement between theory and experiment at about 10% for not only the ground state but also the metastable states. The recent experiments therefore verify the estimated accuracy of the vast amount of photoionization data computed under the OP, IP and related works. features. Present work also reports photoionization cross sections including relativistic effects in the Breit-Pauli R-matrix (BPRM) approximation. Detailed features in the calculated cross sections exhibit the missing resonances due to fine structure. Self-consistent datasets for photoionization and recombination have so far been computed for approximately 45 atoms and ions. These are being reported in a continuing series of publications in Astrophysical J. Supplements (e.g. references below). These data will also be available from the electronic database TIPTOPBASE (http://heasarc.gsfc.nasa.gov)

Molecular dynamics simulations of fluid cyclopropane with MP2/CBS-fitted intermolecular interaction potentials

NASA Astrophysics Data System (ADS)

Ho, Yen-Ching; Wang, Yi-Siang; Chao, Sheng D.

2017-08-01

Modeling fluid cycloalkanes with molecular dynamics simulations has proven to be a very challenging task partly because of lacking a reliable force field based on quantum chemistry calculations. In this paper, we construct an ab initio force field for fluid cyclopropane using the second-order Møller-Plesset perturbation theory. We consider 15 conformers of the cyclopropane dimer for the orientation sampling. Single-point energies at important geometries are calibrated by the coupled cluster with single, double, and perturbative triple excitation method. Dunning's correlation consistent basis sets (up to aug-cc-pVTZ) are used in extrapolating the interaction energies at the complete basis set limit. The force field parameters in a 9-site Lennard-Jones model are regressed by the calculated interaction energies without using empirical data. With this ab initio force field, we perform molecular dynamics simulations of fluid cyclopropane and calculate both the structural and dynamical properties. We compare the simulation results with those using an empirical force field and obtain a quantitative agreement for the detailed atom-wise radial distribution functions. The experimentally observed gross radial distribution function (extracted from the neutron scattering measurements) is well reproduced in our simulation. Moreover, the calculated self-diffusion coefficients and shear viscosities are in good agreement with the experimental data over a wide range of thermodynamic conditions. To the best of our knowledge, this is the first ab initio force field which is capable of competing with empirical force fields for simulating fluid cyclopropane.

Ab initio and DFT study of hydrogen bond interactions between ascorbic acid and dimethylsulfoxide based on FT-IR and FT-Raman spectra

NASA Astrophysics Data System (ADS)

Niazazari, Naser; Zatikyan, Ashkhen L.; Markarian, Shiraz A.

2013-06-01

The hydrogen bonding of 1:1 complexes formed between L-ascorbic acid (LAA) and dimethylsulfoxide (DMSO) has been studied by means of ab initio and density functional theory (DFT) calculations. Solutions of L-ascorbic acid (AA) in dimethylsulfoxide (DMSO) have been studied by means of both FT-IR (4000-220 cm-1) and FT-Raman spectroscopy. Ab initio Hartree-Fock (HF) and DFT methods have been used to determine the structure and energies of stable conformers of various types of L-AA/DMSO complexes in gas phase and solution. The basis sets 6-31++G∗∗ and 6-311+G∗ were used to describe the structure, energy, charges and vibrational frequencies of interacting complexes in the gas phase. The optimized geometric parameters and interaction energies for various complexes at different theories have been estimated. Binding energies have been corrected for basis set superposition error (BSSE) and harmonic vibrational frequencies of the structures have been calculated to obtain the stable forms of the complexes. The self-consistent reaction field (SCRF) has been used to calculate the effect of DMSO as the solvent on the geometry, energy and charges of complexes. The solvent effect has been studied using the Onsager models. It is shown that the polarity of the solvent plays an important role on the structures and relative stabilities of different complexes. The results obtained show that there is a satisfactory correlation between experimental and theoretical predictions.

Optical absorption spectra and g factor of MgO: Mn2+explored by ab initio and semi empirical methods

NASA Astrophysics Data System (ADS)

Andreici Eftimie, E.-L.; Avram, C. N.; Brik, M. G.; Avram, N. M.

2018-02-01

In this paper we present a methodology for calculations of the optical absorption spectra, ligand field parameters and g factor for the Mn2+ (3d5) ions doped in MgO host crystal. The proposed technique combines two methods: the ab initio multireference (MR) and the semi empirical ligand field (LF) in the framework of the exchange charge model (ECM) respectively. Both methods of calculations are applied to the [MnO6]10-cluster embedded in an extended point charge field of host matrix ligands based on Gellé-Lepetit procedure. The first step of such investigations was the full optimization of the cubic structure of perfect MgO crystal, followed by the structural optimization of the doped of MgO:Mn2+ system, using periodic density functional theory (DFT). The ab initio MR wave functions approaches, such as complete active space self-consistent field (CASSCF), N-electron valence second order perturbation theory (NEVPT2) and spectroscopy oriented configuration interaction (SORCI), are used for the calculations. The scalar relativistic effects have also been taken into account through the second order Douglas-Kroll-Hess (DKH2) procedure. Ab initio ligand field theory (AILFT) allows to extract all LF parameters and spin-orbit coupling constant from such calculations. In addition, the ECM of ligand field theory (LFT) has been used for modelling theoptical absorption spectra. The perturbation theory (PT) was employed for the g factor calculation in the semi empirical LFT. The results of each of the aforementioned types of calculations are discussed and the comparisons between the results obtained and the experimental results show a reasonable agreement, which justifies this new methodology based on the simultaneous use of both methods. This study establishes fundamental principles for the further modelling of larger embedded cluster models of doped metal oxides.

Ab initio structures and polarizabilities of sodium clusters

NASA Astrophysics Data System (ADS)

Kronik, Leeor; Vasiliev, Igor; Jain, Manish; Chelikowsky, James R.

2001-09-01

We present quantitative ab initio calculations for Na cluster structures and polarizabilities, for all cluster sizes up to 20 atoms. Our calculations are performed by combining an ab initio core-corrected pseudopotential and a gradient-corrected density functional within a real space approach. We find the cluster bonding to be very floppy and catalog a host of low-energy quasi-degenerate isomers for all second-decade clusters. The existence of these isomers results in a band of polarizability values for each cluster size even at zero temperature. This eliminates any finer structure in the polarizability curve. We further show that the experimental polarizability values are consistently underestimated by calculations at zero temperature. By computing the effects of structure expansion and distortion due to a finite temperature we arrive at a quantitative agreement between theory and experiment.

The hydrogen diffusion in liquid aluminum alloys from ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

Jakse, N.; Pasturel, A.

2014-09-01

We study the hydrogen diffusion in liquid aluminum alloys through extensive ab initio molecular dynamics simulations. At the microscopic scale, we show that the hydrogen motion is characterized by a broad distribution of spatial jumps that does not correspond to a Brownian motion. To determine the self-diffusion coefficient of hydrogen in liquid aluminum alloys, we use a generalized continuous time random walk model recently developed to describe the hydrogen diffusion in pure aluminum. In particular, we show that the model successfully accounts the effects of alloying elements on the hydrogen diffusion in agreement with experimental features.

Ab initio implementation of quantum trajectory mean-field approach and dynamical simulation of the N{sub 2}CO photodissociation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xie, Binbin; Liu, Lihong; Cui, Ganglong

2015-11-21

In this work, the recently introduced quantum trajectory mean-field (QTMF) approach is implemented and employed to explore photodissociation dynamics of diazirinone (N{sub 2}CO), which are based on the high-level ab initio calculation. For comparison, the photodissociation process has been simulated as well with the fewest-switches surface hopping (FSSH) and the ab initio multiple spawning (AIMS) methods. Overall, the dynamical behavior predicted by the three methods is consistent. The N{sub 2}CO photodissociation at λ > 335 nm is an ultrafast process and the two C—N bonds are broken in a stepwise way, giving birth to CO and N{sub 2} as themore » final products in the ground state. Meanwhile, some noticeable differences were found in the QTMF, FSSH, and AIMS simulated time constants for fission of the C—N bonds, excited-state lifetime, and nonadiabatic transition ratios in different intersection regions. These have been discussed in detail. The present study provides a clear evidence that direct ab initio QTMF approach is one of the reliable tools for simulating nonadiabatic dynamics processes.« less

Common lines modeling for reference free Ab-initio reconstruction in cryo-EM.

PubMed

Greenberg, Ido; Shkolnisky, Yoel

2017-11-01

We consider the problem of estimating an unbiased and reference-free ab initio model for non-symmetric molecules from images generated by single-particle cryo-electron microscopy. The proposed algorithm finds the globally optimal assignment of orientations that simultaneously respects all common lines between all images. The contribution of each common line to the estimated orientations is weighted according to a statistical model for common lines' detection errors. The key property of the proposed algorithm is that it finds the global optimum for the orientations given the common lines. In particular, any local optima in the common lines energy landscape do not affect the proposed algorithm. As a result, it is applicable to thousands of images at once, very robust to noise, completely reference free, and not biased towards any initial model. A byproduct of the algorithm is a set of measures that allow to asses the reliability of the obtained ab initio model. We demonstrate the algorithm using class averages from two experimental data sets, resulting in ab initio models with resolutions of 20Å or better, even from class averages consisting of as few as three raw images per class. Copyright © 2017 Elsevier Inc. All rights reserved.

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

NASA Technical Reports Server (NTRS)

Good, Brian S.

2003-01-01

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

Convergence of quasiparticle self-consistent G W calculations of transition-metal monoxides

NASA Astrophysics Data System (ADS)

Das, Suvadip; Coulter, John E.; Manousakis, Efstratios

2015-03-01

Finding an accurate ab initio approach for calculating the electronic properties of transition-metal oxides has been a problem for several decades. In this paper, we investigate the electronic structure of the transition-metal monoxides MnO, CoO, and NiO in their undistorted rocksalt structure within a fully iterated quasiparticle self-consistent G W (QPsc G W ) scheme. We study the convergence of the QPsc G W method, i.e., how the quasiparticle energy eigenvalues and wave functions converge as a function of the QPsc G W iterations, and we compare the converged outputs obtained from different starting wave functions. We find that the convergence is slow and that a one-shot G0W0 calculation does not significantly improve the initial eigenvalues and states. It is important to notice that in some cases the "path" to convergence may go through energy band reordering which cannot be captured by the simple initial unperturbed Hamiltonian. When we reach a fully iterated solution, the converged density of states, band gaps, and magnetic moments of these oxides are found to be only weakly dependent on the choice of the starting wave functions and in reasonably good agreement with the experiment. Finally, this approach provides a clear picture of the interplay between the various orbitals near the Fermi level of these simple transition-metal monoxides. The results of these accurate ab initio calculations can provide input for models aiming at describing the low-energy physics in these materials.

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

NASA Astrophysics Data System (ADS)

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

2016-05-01

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

Ab Initio-Based Predictions of Hydrocarbon Combustion Chemistry

DTIC Science & Technology

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

Ab-initio Electronic, Transport and Related Properties of Zinc Blende Boron Arsenide (zb-BAs)

NASA Astrophysics Data System (ADS)

Nwigboji, Ifeanyi H.; Malozovsky, Yuriy; Bagayoko, Diola

We present results from ab-initio, self-consistent density functional theory (DFT) calculations of electronic, transport, and bulk properties of zinc blende boron arsenide (zb-BAs). We utilized a local density approximation (LDA) potential and the linear combination of atomic orbital (LCAO) formalism. Our computational technique follows the Bagayoko, Zhao, and Williams method, as enhanced by Ekuma and Franklin. Our results include electronic energy bands, densities of states, and effective masses. We explain the agreement between these findings, including the indirect band gap, and available, corresponding, experimental ones. This work confirms the capability of DFT to describe accurately properties of materials, provided the computations adhere to the conditions of validity of DFT [AIP Advances, 4, 127104 (2014)]. Acknowledgments: This work was funded in part by the National Science Foundation (NSF) and the Louisiana Board of Regents, through LASiGMA [Award Nos. EPS- 1003897, NSF (2010-15)-RII-SUBR] and NSF HRD-1002541, the US Department of Energy - National, Nuclear Security Administration (NNSA) (Award No. DE- NA0002630), LaSPACE, and LONI-SUBR.

Electronic, magnetic properties and phase diagrams of system with Fe4N compound: An ab initio calculations and Monte Carlo study

NASA Astrophysics Data System (ADS)

Masrour, R.; Jabar, A.; Hlil, E. K.

2018-05-01

Self-consistent ab initio calculations, based on Density Functional Theory (DFT) approach and using Full potential Linear Augmented Plane Wave (FLAPW) method, are performed to investigate the electronic and magnetic properties of the Fe4N compound. Polarized spin and spin-orbit coupling are included in calculations within the framework of the ferromagnetic state between Fe(I) and Fe(II) in Fe4N compound. We have used the obtained data from abinitio calculations as an input in Monte Carlo simulation to calculate the magnetic properties of this compounds such as the ground state phase diagrams, total and partial magnetization of Fe(I) and Fe(II) as well as the transition temperatures are computed. The variation of magnetization with the crystal field are also studied. The magnetic hysteresis cycle of the same Fe4N compound are determined for different values of temperatures and crystal field values. The two-step hysteresis loop are evidenced, which is typical for Fe4N structure. The ferromagnetic and superparamagnetic phase is observed as well.

Ab initio calculation of harmonic force fields and vibrational spectra for the arsine oxides and sulfides R sub 3 AsY (R = H, F; Y = O, S) and related compounds

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schneider, W.; Thiel, W.; Komornicki, A.

1990-04-05

Ab initio self-consistent-field calculations using effective core potentials and polarized double-zeta basis sets are reported for the arsenic compounds H{sub 3}As, H{sub 3}AsO, H{sub 3}AsS, F{sub 3}As, F{sub 3}AsO, F{sub 3}AsS, cis- and trans-H{sub 2}AsOH, and HAsO. The calculated geometries, rotational constants, vibrational frequencies, Coriolis coupling constants, centrifugal distortion constants, infrared band intensities, and force fields are compared with the available experimental data. Good agreement is found in the case of the known molecules, especially H{sub 3}As and F{sub 3}As, so that the predictions for the unknown molecules are expected to be realistic. The theoretical results confirm a recent spectroscopicmore » identification of H{sub 3}AsO, H{sub 2}AsOH, and HAsO and suggest reassignment of several observed frequencies.« less

The torsional energy profile of 1,2-diphenylethane: an ab initio study

NASA Astrophysics Data System (ADS)

Ivanov, Petko M.

1997-08-01

Ab initio molecular orbital calculations were carried out for the antiperiplanar (ap), the synclinal (sc), phenyl/phenyl eclipsed (syn barrier), and phenyl/H eclipsed (ap/sc barrier) conformations of 1,2-diphenylethane, and the energy ordering of conformations thus obtained was compared with the torsional energy profile estimated with the MM2 and MM3 molecular mechanics force fields. The basis set effect on the results was studied at the restricted Hartree-Fock (RHF) self-consistent field (SCF) level of theory, and the electron correlation energies were corrected by the second-order (MP2) Møller-Plesset perturbation treatment using the 6-31G * basis set. The performance of a DFT model (Becke-style three-parameter hybrid method using the correlation functional of Lee, Yang and Parr, B3LYP) was also tested to assess relative energies of the conformations using two basis sets, 6-31G * and 6-311G **. The RHF and B3LYP results are qualitatively the same, while the MP2 calculations produced significant differences in the geometries and reversed the order of preference for the antiperiplanar and the synclinal conformations.

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

NASA Technical Reports Server (NTRS)

Allen, B. Danette; Alexandrov, Natalia

2016-01-01

Incremental approaches to air transportation system development inherit current architectural constraints, which, in turn, place hard bounds on system capacity, efficiency of performance, and complexity. To enable airspace operations of the future, a clean-slate (ab initio) airspace design(s) must be considered. This ab initio National Airspace System (NAS) must be capable of accommodating increased traffic density, a broader diversity of aircraft, and on-demand mobility. System and subsystem designs should scale to accommodate the inevitable demand for airspace services that include large numbers of autonomous Unmanned Aerial Vehicles and a paradigm shift in general aviation (e.g., personal air vehicles) in addition to more traditional aerial vehicles such as commercial jetliners and weather balloons. The complex and adaptive nature of ab initio designs for the future NAS requires new approaches to validation, adding a significant physical experimentation component to analytical and simulation tools. In addition to software modeling and simulation, the ability to exercise system solutions in a flight environment will be an essential aspect of validation. The NASA Langley Research Center (LaRC) Autonomy Incubator seeks to develop a flight simulation infrastructure for ab initio modeling and simulation that assumes no specific NAS architecture and models vehicle-to-vehicle behavior to examine interactions and emergent behaviors among hundreds of intelligent aerial agents exhibiting collaborative, cooperative, coordinative, selfish, and malicious behaviors. The air transportation system of the future will be a complex adaptive system (CAS) characterized by complex and sometimes unpredictable (or unpredicted) behaviors that result from temporal and spatial interactions among large numbers of participants. A CAS not only evolves with a changing environment and adapts to it, it is closely coupled to all systems that constitute the environment. Thus, the ecosystem that contains the system and other systems evolves with the CAS as well. The effects of the emerging adaptation and co-evolution are difficult to capture with only combined mathematical and computational experimentation. Therefore, an ab initio flight simulation environment must accommodate individual vehicles, groups of self-organizing vehicles, and large-scale infrastructure behavior. Inspired by Massively Multiplayer Online Role Playing Games (MMORPG) and Serious Gaming, the proposed ab initio simulation environment is similar to online gaming environments in which player participants interact with each other, affect their environment, and expect the simulation to persist and change regardless of any individual player's active participation.

40 CFR 89.126 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2010 CFR

2010-07-01

... certificate void ab initio. (d) When the Administrator denies, suspends, revokes, or voids ab initio a... such fraud or other misconduct that makes the certification invalid ab initio. [59 FR 31335, June 17...

40 CFR 89.126 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2014 CFR

2014-07-01

... certificate void ab initio. (d) When the Administrator denies, suspends, revokes, or voids ab initio a... such fraud or other misconduct that makes the certification invalid ab initio. [59 FR 31335, June 17...

40 CFR 89.126 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2012 CFR

2012-07-01

... certificate void ab initio. (d) When the Administrator denies, suspends, revokes, or voids ab initio a... such fraud or other misconduct that makes the certification invalid ab initio. [59 FR 31335, June 17...

40 CFR 89.126 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2013 CFR

2013-07-01

... certificate void ab initio. (d) When the Administrator denies, suspends, revokes, or voids ab initio a... such fraud or other misconduct that makes the certification invalid ab initio. [59 FR 31335, June 17...

40 CFR 89.126 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2011 CFR

2011-07-01

... certificate void ab initio. (d) When the Administrator denies, suspends, revokes, or voids ab initio a... such fraud or other misconduct that makes the certification invalid ab initio. [59 FR 31335, June 17...

An ab initio potential energy surface for the formic acid dimer: zero-point energy, selected anharmonic fundamental energies, and ground-state tunneling splitting calculated in relaxed 1-4-mode subspaces.

PubMed

Qu, Chen; Bowman, Joel M

2016-09-14

We report a full-dimensional, permutationally invariant potential energy surface (PES) for the cyclic formic acid dimer. This PES is a least-squares fit to 13475 CCSD(T)-F12a/haTZ (VTZ for H and aVTZ for C and O) energies. The energy-weighted, root-mean-square fitting error is 11 cm -1 and the barrier for the double-proton transfer on the PES is 2848 cm -1 , in good agreement with the directly-calculated ab initio value of 2853 cm -1 . The zero-point vibrational energy of 15 337 ± 7 cm -1 is obtained from diffusion Monte Carlo calculations. Energies of fundamentals of fifteen modes are calculated using the vibrational self-consistent field and virtual-state configuration interaction method. The ground-state tunneling splitting is computed using a reduced-dimensional Hamiltonian with relaxed potentials. The highest-level, four-mode coupled calculation gives a tunneling splitting of 0.037 cm -1 , which is roughly twice the experimental value. The tunneling splittings of (DCOOH) 2 and (DCOOD) 2 from one to three mode calculations are, as expected, smaller than that for (HCOOH) 2 and consistent with experiment.

On the photoisomerization of 5-hydroxytropolone: An ab initio and nuclear wave function study

NASA Astrophysics Data System (ADS)

Paz, Juan J.; Moreno, Miquel; Lluch, José M.

1997-10-01

In this paper we perform ab initio calculations for the stable conformations and the transition states for the isomerization processes in 5-hydroxytropolone in both the ground (S0) and first excited (S1) singlet electronic states. The Hartree-Fock self-consistent field (SCF) level and a complete active space SCF (CASSCF) level for S0 are considered, whereas the configuration interaction all single excitation method (CIS) and the CASSCF levels are used to deal with the S1 state. Energies are reevaluated at all levels through perturbation theory up to second order: Møller-Plesset for the Hartree-Fock and CIS methods, and the CASPT2 method for CAS results. The ab initio results are then used to perform different monodimensional fits to the potential energy surfaces in order to analyze the wave functions for the nuclear motions in both electronic states. Our best results predict that for the S0 state two stable conformers, syn and anti, can exist in thermal equilibrium. In accordance with experimental expectations the syn isomer is the most stable. As for the S1 state, and again in accord with experimental spectroscopical data, the order of stability reverses, the anti being the most stable. A more interesting result is that analysis of the nuclear wave functions shows an important syn-anti mixing in the S1 state that does not appear in S0. This result explains the appearance of syn-anti and anti-syn crossover transitions observed in the electronic spectra of 5-hydroxytropolone so that syn-anti reaction may take place through photoisomerization.

Development and application of ab initio QM/MM methods for mechanistic simulation of reactions in solution and in enzymes

PubMed Central

Hu, Hao; Yang, Weitao

2013-01-01

Determining the free energies and mechanisms of chemical reactions in solution and enzymes is a major challenge. For such complex reaction processes, combined quantum mechanics/molecular mechanics (QM/MM) method is the most effective simulation method to provide an accurate and efficient theoretical description of the molecular system. The computational costs of ab initio QM methods, however, have limited the application of ab initio QM/MM methods. Recent advances in ab initio QM/MM methods allowed the accurate simulation of the free energies for reactions in solution and in enzymes and thus paved the way for broader application of the ab initio QM/MM methods. We review here the theoretical developments and applications of the ab initio QM/MM methods, focusing on the determination of reaction path and the free energies of the reaction processes in solution and enzymes. PMID:24146439

First-principles phase stability at high temperatures and pressure in Nb 90Zr 10 alloy

DOE PAGES

Landa, A.; Soderlind, P.

2016-08-18

The phase stability of Nb 90Zr 10 alloy at high temperatures and compression is explored by means of first-principles electronic-structure calculations. Utilizing the self-consistent ab initio lattice dynamics (SCAILD) approach in conjunction with density-functional theory, we show that pressure-induced mechanical instability of the body-centered cubic phase, which results in formation of a rhombohedral phase at around 50 GPa, will prevail significant heating. As a result, the body-centered cubic structure will recover before melting at ~1800 K.

Development of a Scaled Quantum Mechanical Force Field for Peptides in Aqueous Solution

DTIC Science & Technology

1996-03-01

differ. Raman and IR techniques are complimentary which helps in assignment of observed vibrational modes. As described in beginning organic ...1588 I NH, .i.sor(98) 2076 2100 24 CH3 55(95) 2125 2207 82 CH3 as’ (56), CH3 as’ (43) 2235 2253 18 CH3 as’(55), CH3 as’(41) 2888 COff .(100) 3155 NH...Application of self- consistent-field ab initio calculations to organic molecules I. Equilibrium struc- ture and force constants of hydrocarbons

Recent Theoretical Studies On Excitation and Recombination

NASA Technical Reports Server (NTRS)

Pradhan, Anil K.

2000-01-01

New advances in the theoretical treatment of atomic processes in plasmas are described. These enable not only an integrated, unified, and self-consistent treatment of important radiative and collisional processes, but also large-scale computation of atomic data with high accuracy. An extension of the R-matrix work, from excitation and photoionization to electron-ion recombination, includes a unified method that subsumes both the radiative and the di-electronic recombination processes in an ab initio manner. The extensive collisional calculations for iron and iron-peak elements under the Iron Project are also discussed.

Single-ion 4f element magnetism: an ab-initio look at Ln(COT)2(-).

PubMed

Gendron, Frédéric; Pritchard, Benjamin; Bolvin, Hélène; Autschbach, Jochen

2015-12-14

The electron densities associated with the Ln 4f shell, and spin and orbital magnetizations ('magnetic moment densities'), are investigated for the Ln(COT)2(-) series. The densities are obtained from ab-initio calculations including spin-orbit coupling. For Ln = Ce, Pr the magnetizations are also derived from crystal field models and shown to agree with the ab-initio results. Analysis of magnetizations from ab-initio calculations may be useful in assisting research on single molecule magnets.

4He+n+n continuum within an ab initio framework

DOE PAGES

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

2014-07-16

In this study, the low-lying continuum spectrum of the 6He nucleus is investigated for the first time within an ab initio framework that encompasses the 4He+n+n three-cluster dynamics characterizing its lowest decay channel. This is achieved through an extension of the no-core shell model combined with the resonating-group method, in which energy-independent nonlocal interactions among three nuclear fragments can be calculated microscopically, starting from realistic nucleon-nucleon interactions and consistent ab initio many-body wave functions of the clusters. The three-cluster Schrödinger equation is solved with three-body scattering boundary conditions by means of the hyperspherical-harmonics method on a Lagrange mesh. Using amore » soft similarity-renormalization-group evolved chiral nucleon-nucleon potential, we find the known J π = 2 + resonance as well as a result consistent with a new low-lying second 2 + resonance recently observed at GANIL at ~2.6 MeV above the He6 ground state. We also find resonances in the 2 –, 1 +, and 0 – channels, while no low-lying resonances are present in the 0 + and 1 – channels.« less

40 CFR 91.123 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2010 CFR

2010-07-01

....203(f), 91.206(d), 91.208(c) or 91.209(g), the Administrator may void such certificate ab initio. (d) When the Administrator denies, revokes, or voids ab initio a certificate of conformity, the engine... makes the certificate void ab initio. ...

40 CFR 86.1850-01 - Denial, suspension or revocation of certificate of conformity.

Code of Federal Regulations, 2010 CFR

2010-07-01

... conditions specified in § 86.1843-01, the Administrator may deem such certificate void ab initio. (e) When the Administrator denies, suspends, revokes, or voids ab initio a certificate, EPA will provide the... that makes the certification void ab initio. ...

40 CFR 86.1850-01 - Denial, suspension or revocation of certificate of conformity.

Code of Federal Regulations, 2014 CFR

2014-07-01

... conditions specified in § 86.1843-01, the Administrator may deem such certificate void ab initio. (e) When the Administrator denies, suspends, revokes, or voids ab initio a certificate, EPA will provide the... that makes the certification void ab initio. ...

40 CFR 91.123 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2013 CFR

2013-07-01

....203(f), 91.206(d), 91.208(c) or 91.209(g), the Administrator may void such certificate ab initio. (d) When the Administrator denies, revokes, or voids ab initio a certificate of conformity, the engine... makes the certificate void ab initio. ...

40 CFR 91.123 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2011 CFR

2011-07-01

....203(f), 91.206(d), 91.208(c) or 91.209(g), the Administrator may void such certificate ab initio. (d) When the Administrator denies, revokes, or voids ab initio a certificate of conformity, the engine... makes the certificate void ab initio. ...

40 CFR 91.123 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2012 CFR

2012-07-01

....203(f), 91.206(d), 91.208(c) or 91.209(g), the Administrator may void such certificate ab initio. (d) When the Administrator denies, revokes, or voids ab initio a certificate of conformity, the engine... makes the certificate void ab initio. ...

40 CFR 86.1850-01 - Denial, suspension or revocation of certificate of conformity.

Code of Federal Regulations, 2012 CFR

2012-07-01

... conditions specified in § 86.1843-01, the Administrator may deem such certificate void ab initio. (e) When the Administrator denies, suspends, revokes, or voids ab initio a certificate, EPA will provide the... that makes the certification void ab initio. ...

40 CFR 86.1850-01 - Denial, suspension or revocation of certificate of conformity.

Code of Federal Regulations, 2013 CFR

2013-07-01

... conditions specified in § 86.1843-01, the Administrator may deem such certificate void ab initio. (e) When the Administrator denies, suspends, revokes, or voids ab initio a certificate, EPA will provide the... that makes the certification void ab initio. ...

40 CFR 91.123 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2014 CFR

2014-07-01

....203(f), 91.206(d), 91.208(c) or 91.209(g), the Administrator may void such certificate ab initio. (d) When the Administrator denies, revokes, or voids ab initio a certificate of conformity, the engine... makes the certificate void ab initio. ...

40 CFR 86.1850-01 - Denial, suspension or revocation of certificate of conformity.

Code of Federal Regulations, 2011 CFR

2011-07-01

... conditions specified in § 86.1843-01, the Administrator may deem such certificate void ab initio. (e) When the Administrator denies, suspends, revokes, or voids ab initio a certificate, EPA will provide the... that makes the certification void ab initio. ...

Self-consistent mapping of the ab initio calculations to the multi-orbital p- d model: Magnetism in α-FeSi2 films as the effect of the local environment

NASA Astrophysics Data System (ADS)

Zhandun, V.; Zamkova, N.; Ovchinnikov, S.; Sandalov, I.

2017-11-01

To accurately translate the results obtained within density functional theory (DFT) to the language of many-body theory we suggest and test the following approach: the parameters of the formulated model are to be found from the requirement that the model self-consistent electron density and density of electron states are as close as possible to the ones found from the DFT-based calculations. The investigation of the phase diagram of the model allows us to find the critical regions in magnetic properties. Then the behavior of the real system in these regions is checked by the ab initio calculations. As an example, we studied the physics of magnetic moment (MM) formation due to substitutions of Si by Fe-atoms or vice versa in the otherwise non-magnetic alloy α-FeSi2. We find that the MM formation is essentially controlled by the interaction of Fe atoms with its next nearest atoms (NNN) and by their particular arrangement. The latter may result in different magnetic states at the same concentrations of constituents. Moreover, one of arrangements produces the counterintuitive result: a ferromagnetism arises due to an increase in Si concentration in Fe1-xSi2+ x ordered alloy. The existing phenomenological models associate the destruction of magnetic moment only with the number of Fe-Si nearest neighbors. The presented results show that the crucial role in MM formation is played by the particular local NNN environment of the metal atom in the transition metal-metalloid alloy.

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

PubMed

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

2016-05-13

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

Electron transport in extended carbon-nanotube/metal contacts: Ab initio based Green function method

NASA Astrophysics Data System (ADS)

Fediai, Artem; Ryndyk, Dmitry A.; Cuniberti, Gianaurelio

2015-04-01

We have developed a new method that is able to predict the electrical properties of the source and drain contacts in realistic carbon nanotube field effect transistors (CNTFETs). It is based on large-scale ab initio calculations combined with a Green function approach. For the first time, both internal and external parts of a realistic CNT-metal contact are taken into account at the ab initio level. We have developed the procedure allowing direct calculation of the self-energy for an extended contact. Within the method, it is possible to calculate the transmission coefficient through a contact of both finite and infinite length; the local density of states can be determined in both free and embedded CNT segments. We found perfect agreement with the experimental data for Pd and Al contacts. We have explained why CNTFETs with Pd electrodes are p -type FETs with ohmic contacts, which can carry current close to the ballistic limit (provided contact length is large enough), whereas in CNT-Al contacts transmission is suppressed to a significant extent, especially for holes.

Chiral self-recognition: direct spectroscopic detection of the homochiral and heterochiral dimers of propylene oxide in the gas phase.

PubMed

Su, Zheng; Borho, Nicole; Xu, Yunjie

2006-12-27

In this report, we describe rotational spectroscopic and high-level ab initio studies of the 1:1 chiral molecular adduct of propylene oxide dimer. The complexes are bound by weak secondary hydrogen bonds, that is, the O(epoxy)...H-C noncovalent interactions. Six homochiral and six heterochiral conformers were predicted to be the most stable configurations where each monomer acts as a proton acceptor and a donor simultaneously, forming two six- or five-membered intermolecular hydrogen-bonded rings. Rotational spectra of six, that is, three homochiral and heterochiral conformer pairs, out of the eight conformers that were predicted to have sufficiently large permanent electric dipole moments were measured and analyzed. The relative conformational stability order and the signs of the chiral recognition energies of the six conformers were determined experimentally and were compared to the ab initio computational results. The experimental observations and the ab initio calculations suggest that the concerted effort of these weak secondary hydrogen bonds can successfully lock the subunits in a particular orientation and that the overall binding strength is comparable to a classic hydrogen bond.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

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

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

DOE PAGES

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

2016-05-11

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

Ab initio study of the electron energy loss function in a graphene-sapphire-graphene composite system

NASA Astrophysics Data System (ADS)

Despoja, Vito; Djordjević, Tijana; Karbunar, Lazar; Radović, Ivan; Mišković, Zoran L.

2017-08-01

The propagator of a dynamically screened Coulomb interaction W in a sandwichlike structure consisting of two graphene layers separated by a slab of Al2O3 (or vacuum) is derived from single-layer graphene response functions and by using a local dielectric function for the bulk Al2O3 . The response function of graphene is obtained using two approaches within the random phase approximation (RPA): an ab initio method that includes all electronic bands in graphene and a computationally less demanding method based on the massless Dirac fermion (MDF) approximation for the low-energy excitations of electrons in the π bands. The propagator W is used to derive an expression for the effective dielectric function of our sandwich structure, which is relevant for the reflection electron energy loss spectroscopy of its surface. Focusing on the range of frequencies from THz to mid-infrared, special attention is paid to finding an accurate optical limit in the ab initio method, where the response function is expressed in terms of a frequency-dependent conductivity of graphene. It was shown that the optical limit suffices for describing hybridization between the Dirac plasmons in graphene layers and the Fuchs-Kliewer phonons in both surfaces of the Al2O3 slab, and that the spectra obtained from both the ab initio method and the MDF approximation in the optical limit agree perfectly well for wave numbers up to about 0.1 nm-1. Going beyond the optical limit, the agreement between the full ab initio method and the MDF approximation was found to extend to wave numbers up to about 0.3 nm-1 for doped graphene layers with the Fermi energy of 0.2 eV.

Operator evolution for ab initio electric dipole transitions of 4He

DOE PAGES

Schuster, Micah D.; Quaglioni, Sofia; Johnson, Calvin W.; ...

2015-07-24

A goal of nuclear theory is to make quantitative predictions of low-energy nuclear observables starting from accurate microscopic internucleon forces. A major element of such an effort is applying unitary transformations to soften the nuclear Hamiltonian and hence accelerate the convergence of ab initio calculations as a function of the model space size. The consistent simultaneous transformation of external operators, however, has been overlooked in applications of the theory, particularly for nonscalar transitions. We study the evolution of the electric dipole operator in the framework of the similarity renormalization group method and apply the renormalized matrix elements to the calculationmore » of the 4He total photoabsorption cross section and electric dipole polarizability. All observables are calculated within the ab initio no-core shell model. Furthermore, we find that, although seemingly small, the effects of evolved operators on the photoabsorption cross section are comparable in magnitude to the correction produced by including the chiral three-nucleon force and cannot be neglected.« less

Three-cluster dynamics within an ab initio framework

DOE PAGES

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

2013-09-26

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

Ab initio study of the structural properties of acetonitrile-water mixtures

NASA Astrophysics Data System (ADS)

Chen, Jinfan; Sit, Patrick H.-L.

2015-08-01

Structural properties of acetonitrile and acetonitrile-water mixtures are studied using Density Functional Theory (DFT) and ab initio molecular dynamics simulations. Stable molecular clusters consisted of several water and acetonitrile molecules are identified to provide microscopic understanding of the interaction among water and acetonitrile molecules. Ab initio molecular dynamics simulations are performed to study the liquid structure at the finite temperature. Three mixing compositions in which the mole fraction of acetonitrile equals 0.109, 0.5 and 0.891 are studied. These compositions correspond to three distinct structural regimes. At the 0.109 and 0.891 mole fraction of acetonitrile, the majority species are mostly connected among themselves and the minority species are either isolated or forming small clusters without disrupting the network of the majority species. At the 0.5 mole fraction of acetonitrile, large water and acetonitrile clusters persist throughout the simulation, exhibiting the microheterogeneous behavior in acetonitrile-water mixtures in the mid-range mixing ratio.

Using the Ab Initio Molecular Dynamics Method for Simulating the Peculiarities in the Temperature Dependence of Liquid Bismuth Properties

NASA Astrophysics Data System (ADS)

Yuryev, A. A.; Gelchinski, B. R.; Vatolin, N. A.

2018-03-01

The specific features pertinent to the temperature dependence of the electronic and atomic properties of liquid bismuth that have been observed in experiments are investigated according to the ab initio molecular dynamics method using the SIESTA open software package. The density of electronic states, the radial distribution function of atoms, and the self-diffusion coefficient are calculated for the temperature range from the melting point equal to 545 K to 1500 K. The calculated data are in good agreement with the experimental data. It is found that the position of the first peak in the radial distribution function of atoms and the self-diffusion coefficient are characterized by a nonmonotonic dependence under the conditions of superheating by approximately 150 K above the melting temperature. In the authors' opinion, this dependence feature is attributed to a change in the liquid short-range order structure.

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

NASA Astrophysics Data System (ADS)

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

2008-06-01

Reaching the native states of small proteins, a necessary step towards a comprehensive understanding of the folding mechanisms, has remained a tremendous challenge to ab initio protein folding simulations despite the extensive effort. In this work, the folding process of the B domain of protein A (BdpA) has been simulated by both conventional and replica exchange molecular dynamics using AMBER FF03 all-atom force field. Started from an extended chain, a total of 40 conventional (each to 1.0 μs) and two sets of replica exchange (each to 200.0 ns per replica) molecular dynamics simulations were performed with different generalized-Born solvation models and temperature control schemes. The improvements in both the force field and solvent model allowed successful simulations of the folding process to the native state as demonstrated by the 0.80 A˚ Cα root mean square deviation (RMSD) of the best folded structure. The most populated conformation was the native folded structure with a high population. This was a significant improvement over the 2.8 A˚ Cα RMSD of the best nativelike structures from previous ab initio folding studies on BdpA. To the best of our knowledge, our results demonstrate, for the first time, that ab initio simulations can reach the native state of BdpA. Consistent with experimental observations, including Φ-value analyses, formation of helix II/III hairpin was a crucial step that provides a template upon which helix I could form and the folding process could complete. Early formation of helix III was observed which is consistent with the experimental results of higher residual helical content of isolated helix III among the three helices. The calculated temperature-dependent profile and the melting temperature were in close agreement with the experimental results. The simulations further revealed that phenylalanine 31 may play critical to achieve the correct packing of the three helices which is consistent with the experimental observation. In addition to the mechanistic studies, an ab initio structure prediction was also conducted based on both the physical energy and a statistical potential. Based on the lowest physical energy, the predicted structure was 2.0 A˚ Cα RMSD away from the experimentally determined structure.

40 CFR 86.004-30 - Certification.

Code of Federal Regulations, 2010 CFR

2010-07-01

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40 CFR 86.004-30 - Certification.

Code of Federal Regulations, 2012 CFR

2012-07-01

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40 CFR 86.007-30 - Certification.

Code of Federal Regulations, 2014 CFR

2014-07-01

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40 CFR 86.004-30 - Certification.

Code of Federal Regulations, 2013 CFR

2013-07-01

... determined in accordance with this part. The certificate shall be void ab initio for those vehicles causing... the certificate was issued, and the certificate may be deemed void ab initio. (C) The manufacturer... determined in accordance with this part. The certificate shall be void ab initio for those vehicles causing...

Structural modeling of Ge6.25As32.5Se61.25 using a combination of reverse Monte Carlo and Ab initio molecular dynamics.

PubMed

Opletal, George; Drumm, Daniel W; Wang, Rong P; Russo, Salvy P

2014-07-03

Ternary glass structures are notoriously difficult to model accurately, and yet prevalent in several modern endeavors. Here, a novel combination of Reverse Monte Carlo (RMC) modeling and ab initio molecular dynamics (MD) is presented, rendering these complicated structures computationally tractable. A case study (Ge6.25As32.5Se61.25 glass) illustrates the effects of ab initio MD quench rates and equilibration temperatures, and the combined approach's efficacy over standard RMC or random insertion methods. Submelting point MD quenches achieve the most stable, realistic models, agreeing with both experimental and fully ab initio results. The simple approach of RMC followed by ab initio geometry optimization provides similar quality to the RMC-MD combination, for far fewer resources.

Inner Core Anisotropy: Can Seismic Observations be Reconciled with Ab Initio Calculations of Elasticity?

NASA Astrophysics Data System (ADS)

Song, X.; Jordan, T. H.

2016-12-01

Body-wave and normal-mode observations have revealed an inner-core structure that is radially layered, axially anisotropic, and hemispherically asymmetric. Previous theoretical studies have examined the consistency of these features with the elasticity of iron crystals thought to dominate inner-core composition, but a fully consistent model has been elusive. Here we compare the seismic observation with effective-medium models derived from ab initio calculations of the elasticity tensors for hcp-Fe and bcc-Fe. Our estimates are based on Jordan's (GJI, 2015) effective medium theory, which is derived from a self-consistent, second-order Born approximation. The theory provides closed-form expressions for the effective elastic parameters of 3D anisotropic, heterogeneous media in which the local anisotropy is a constant hexagonal stiffness tensor C stochastically oriented about a constant symmetry axis \\hat{s} and the statistics of the small-scale heterogeneities are transversely isotropic in the plane perpendicular to \\hat{s}. The stochastic model is then described by a dimensionless "aspect ratio of the heterogeneity", 0 ≤ η < ∞, and a dimensionless "orientation ratio of the anisotropy", 0 ≤ ξ < ∞. The latter determines the degree to which the axis of C is aligned with \\hat{s}. We compute the loci of models with \\hat{s} oriented along the Earth's rotational axis ( \\hat{s} = north) by varying ξ and η for various ab initio estimates of C. We show that a lot of widely used estimates of C are inconsistent with most published normal-mode models of inner-core anisotropy. In particular, if the P-wave fast axis aligns with the rotational axis, which is required to satisfy the body-wave observations, then these hcp-Fe models predict that the fast polarization of the S waves is in the plane perpendicular to \\hat{s}, which disagrees with most normal-mode models. We have attempted to resolve this discrepancy by examining alternative hcp-Fe models, including radially anisotropic distributions of stochastic anisotropy and heterogeneity (i.e., where \\hat{s} = \\hat{r}), as well as bcc-Fe models. Our calculations constrain the form of C needed to satisfy the seismological inferences.

Communication: Smoothing out excited-state dynamics: Analytical gradients for dynamically weighted complete active space self-consistent field

DOE Office of Scientific and Technical Information (OSTI.GOV)

Glover, W. J., E-mail: williamjglover@gmail.com

2014-11-07

State averaged complete active space self-consistent field (SA-CASSCF) is a workhorse for determining the excited-state electronic structure of molecules, particularly for states with multireference character; however, the method suffers from known issues that have prevented its wider adoption. One issue is the presence of discontinuities in potential energy surfaces when a state that is not included in the state averaging crosses with one that is. In this communication I introduce a new dynamical weight with spline (DWS) scheme that mimics SA-CASSCF while removing energy discontinuities due to unweighted state crossings. In addition, analytical gradients for DWS-CASSCF (and other dynamically weightedmore » schemes) are derived for the first time, enabling energy-conserving excited-state ab initio molecular dynamics in instances where SA-CASSCF fails.« less

First-principles studies of electronic, transport and bulk properties of pyrite FeS2

NASA Astrophysics Data System (ADS)

Banjara, Dipendra; Mbolle, Augustine; Malozovsky, Yuriy; Franklin, Lashounda; Bagayoko, Diola

We present results of ab-initio, self-consistent density functional theory (DFT) calculations of electronic, transport, and bulk properties of pyrite FeS2. We employed a local density approximation (LDA) potential and the linear combination of atomic orbitals (LCAO) formalism, following the Bagayoko, Zhao and Williams (BZW) method, as enhanced by Ekuma and Franklin (BZW-EF). The BZW-EF method requires successive, self consistent calculations with increasing basis sets to reach the ground state of the system under study. We report the band structure, the band gap, total and partial densities of states, effective masses, and the bulk modulus. Work funded in part by the US Department of Energy (DOE), National Nuclear Security Administration (NNSA) (Award No.DE-NA0002630), the National Science Foundation (NSF) (Award No, 1503226), LaSPACE, and LONI-SUBR.

Ab-initio Computation of the Electronic, transport, and Bulk Properties of Calcium Oxide.

NASA Astrophysics Data System (ADS)

Mbolle, Augustine; Banjara, Dipendra; Malozovsky, Yuriy; Franklin, Lashounda; Bagayoko, Diola

We report results from ab-initio, self-consistent, local Density approximation (LDA) calculations of electronic and related properties of calcium oxide (CaO) in the rock salt structure. We employed the Ceperley and Alder LDA potential and the linear combination of atomic orbitals (LCAO) formalism. Our calculations are non-relativistic. We implemented the LCAO formalism following the Bagayoko, Zhao, and Williams (BZW) method, as enhanced by Ekuma and Franklin (BZW-EF). The BZW-EF method involves a methodical search for the optimal basis set that yields the absolute minima of the occupied energies, as required by density functional theory (DFT). Our calculated, indirect band gap of 6.91eV, from towards the L point, is in excellent agreement with experimental value of 6.93-7.7eV, at room temperature (RT). We have also calculated the total (DOS) and partial (pDOS) densities of states as well as the bulk modulus. Our calculated bulk modulus is in excellent agreement with experiment. Work funded in part by the US Department of Energy (DOE), National Nuclear Security Administration (NNSA) (Award No.DE-NA0002630), the National Science Foundation (NSF) (Award No, 1503226), LaSPACE, and LONI-SUBR.

Ab initio study of single-crystalline and polycrystalline elastic properties of Mg-substituted calcite crystals.

PubMed

Zhu, L-F; Friák, M; Lymperakis, L; Titrian, H; Aydin, U; Janus, A M; Fabritius, H-O; Ziegler, A; Nikolov, S; Hemzalová, P; Raabe, D; Neugebauer, J

2013-04-01

We employ ab initio calculations and investigate the single-crystalline elastic properties of (Ca,Mg)CO3 crystals covering the whole range of concentrations from pure calcite CaCO3 to pure magnesite MgCO3. Studying different distributions of Ca and Mg atoms within 30-atom supercells, our theoretical results show that the energetically most favorable configurations are characterized by elastic constants that nearly monotonously increase with the Mg content. Based on the first principles-derived single-crystalline elastic anisotropy, the integral elastic response of (Ca,Mg)CO3 polycrystals is determined employing a mean-field self-consistent homogenization method. As in case of single-crystalline elastic properties, the computed polycrystalline elastic parameters sensitively depend on the chemical composition and show a significant stiffening impact of Mg atoms on calcite crystals in agreement with the experimental findings. Our analysis also shows that it is not advantageous to use a higher-scale two-phase mix of stoichiometric calcite and magnesite instead of substituting Ca atoms by Mg ones on the atomic scale. Such two-phase composites are not significantly thermodynamically favorable and do not provide any strong additional stiffening effect. Copyright © 2013 Elsevier Ltd. All rights reserved.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tohme, Samir N.; Korek, Mahmoud, E-mail: mahmoud.korek@bau.edu.lb, E-mail: fkorek@yahoo.com; Awad, Ramadan

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

Combined ab initio and density functional study on polaron to bipolaron transitions in oligophenyls and oligothiophenes

NASA Astrophysics Data System (ADS)

Irle, Stephan; Lischka, Hans

1997-08-01

Ab initio self-consistent-field (SCF), two-configuration SCF (TCSCF), and density functional theory (DFT) calculations on the charge-transfer complexes of doubly Li/Cl-doped oligothiophenes and oligo(p-phenyls) and on respective charged systems without counterions have been carried out in order to study polaron to bipolaron transitions. Oligomer chains up to octamers and the ring structures cyclo-dodecathiophene and cyclo-dodeca(p-phenyl) have been investigated. Special attention is paid to the open-shell biradical character of two isolated polaronic defects. It is found that the TCSCF and the spin-unrestricted DFT methods can be successfully applied. A bipolaron structure is obtained when the doping atoms are located on neighboring rings and when there is one undoped ring separating the two doped ones. If there are two or more undoped rings in between a two-polaron configuration (biradical) is found. The bipolaron system is calculated to be more stable than the two-polaron case when counterions are taken into account. The stabilities are reversed if the bare, doubly-charged systems are considered. A theoretical estimate for the barrier height of the polaron to bipolaron transition is given using model reaction coordinates.

A GENERALIZED TWO-COMPONENT MODEL OF SOLAR WIND TURBULENCE AND AB INITIO DIFFUSION MEAN-FREE PATHS AND DRIFT LENGTHSCALES OF COSMIC RAYS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wiengarten, T.; Fichtner, H.; Kleimann, J.

2016-12-10

We extend a two-component model for the evolution of fluctuations in the solar wind plasma so that it is fully three-dimensional (3D) and also coupled self-consistently to the large-scale magnetohydrodynamic equations describing the background solar wind. The two classes of fluctuations considered are a high-frequency parallel-propagating wave-like piece and a low-frequency quasi-two-dimensional component. For both components, the nonlinear dynamics is dominanted by quasi-perpendicular spectral cascades of energy. Driving of the fluctuations by, for example, velocity shear and pickup ions is included. Numerical solutions to the new model are obtained using the Cronos framework, and validated against previous simpler models. Comparing results frommore » the new model with spacecraft measurements, we find improved agreement relative to earlier models that employ prescribed background solar wind fields. Finally, the new results for the wave-like and quasi-two-dimensional fluctuations are used to calculate ab initio diffusion mean-free paths and drift lengthscales for the transport of cosmic rays in the turbulent solar wind.« less

Electronic and magnetic structures of Fe3O4 ferrimagnetic investigated by first principle, mean field and series expansions calculations

NASA Astrophysics Data System (ADS)

Masrour, R.; Hlil, E. K.; Hamedoun, M.; Benyoussef, A.; Mounkachi, O.; El Moussaoui, H.

2015-03-01

Self-consistent ab initio calculations, based on density functional theory (DFT) approach and using a full potential linear augmented plane wave (FLAPW) method, are performed to investigate both electronic and magnetic properties of the Fe3O4. Polarized spin and spin-orbit coupling are included in calculations within the framework of the antiferromagnetic state between two adjacent Fe plans. Magnetic moment considered to lie along (010) axes are computed. Obtained data from ab initio calculations are used as input for the high temperature series expansions (HTSEs) calculations to compute other magnetic parameters. The exchange interactions between the magnetic atoms Fe-Fe in Fe3O4 are given using the mean field theory. The high temperature series expansions (HTSEs) of the magnetic susceptibility of with the magnetic moments, mFe in Fe3O4 is given up to seventh order series in (1/kBT). The Néel temperature TN is obtained by HTSEs of the magnetic susceptibility series combined with the Padé approximant method. The critical exponent γ associated with the magnetic susceptibility is deduced as well.

Ab initio vel ex eventu

NASA Astrophysics Data System (ADS)

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

Der gegenwärtige Stand der physikalischen Erkenntnis, in Sonderheit die Atomistik und die Quantentheorie, ermöglicht (in wohldefinierten Energie-Bereichen) eine ab initio-Berechnung aller physikalischen und chemischen Prozesse und Strukturen. Die Schrödinger-Gleichung erlaubt zusammen mit den Prinzipien der Quantenstatistik (Pauli-Prinzip) aus dem Planckschen Wirkungsquantum h und den atomischen Konstanten die Berechnung aller Energieumsätze, Zeitabläufe etc., die insbesondere die chemische Physik bestimmen. Die Rechenresultate gelten auch quantitativ bis auf die unvermeidliche Stochastik.Die ab initio-Berechnungen korrespondieren einerseits und sind andererseits komplementär zu den auf den Methoden der theoretischen Chemie und der klassischen Thermodynamik beruhenden Ergebnissen ex eventu. Die theoretische Behandlung ab initio führt zu mathematischen Experimenten, die die Laboratoriums-Experimente ergänzen oder auch substituieren.Translated AbstractAb initio vel ex eventuThe present state of physical knowledge, in peculiar atomistic and quantum theory, makes an ab initio calculation of all physical and chemical processes and structures possible (in well defined reaches of energy). The Schrödinger equation together with the principles of quantum statistics (Pauli principle) permits from the Planck and atomistic constants to calculate all exchanges of energy, courses of time, etc. which govern chemical physics. The calculated results are valid even quantitatively apart from the unavoidable stochastics.These ab initio calculations on the one hand correspond and are on the other complimentary to results ex eventu based on the methods of theoretical chemistry and classical thermodynamics. Theoretical treatment ab initio leads to mathematical experiments which add to or even substitute experiments in the laboratory.

Towards Accurate Ab Initio Predictions of the Spectrum of Methane

NASA Technical Reports Server (NTRS)

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

2001-01-01

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

Ab Initio Studies of Stratospheric Ozone Depletion Chemistry

NASA Technical Reports Server (NTRS)

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

1995-01-01

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

A Force Balanced Fragmentation Method for ab Initio Molecular Dynamic Simulation of Protein.

PubMed

Xu, Mingyuan; Zhu, Tong; Zhang, John Z H

2018-01-01

A force balanced generalized molecular fractionation with conjugate caps (FB-GMFCC) method is proposed for ab initio molecular dynamic simulation of proteins. In this approach, the energy of the protein is computed by a linear combination of the QM energies of individual residues and molecular fragments that account for the two-body interaction of hydrogen bond between backbone peptides. The atomic forces on the caped H atoms were corrected to conserve the total force of the protein. Using this approach, ab initio molecular dynamic simulation of an Ace-(ALA) 9 -NME linear peptide showed the conservation of the total energy of the system throughout the simulation. Further a more robust 110 ps ab initio molecular dynamic simulation was performed for a protein with 56 residues and 862 atoms in explicit water. Compared with the classical force field, the ab initio molecular dynamic simulations gave better description of the geometry of peptide bonds. Although further development is still needed, the current approach is highly efficient, trivially parallel, and can be applied to ab initio molecular dynamic simulation study of large proteins.

Theoretical dissociation energies for the alkali and alkaline-earth monofluorides and monochlorides

NASA Technical Reports Server (NTRS)

Langhoff, S. R.; Bauschlicher, C. W., Jr.; Partridge, H.

1986-01-01

Spectroscopic parameters are accurately determined for the alkali and alkaline-earth monofluorides and monochlorides by means of ab initio self-consistent field and correlated wave function calculations. Numerical Hartree-Fock calculations are performed on selected systems to ensure that the extended Slater basis sets employed are near the Hartree-Fock limit. Since the bonding is predominantly electrostatic in origin, a strong correlation exists between the dissociation energy (to ions) and the spectroscopic parameter r(e). By dissociating to the ionic limits, most of the differential correlation effects can be embedded in the accurate experimental electron affinities and ionization potentials.

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

NASA Technical Reports Server (NTRS)

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

1995-01-01

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

Ab-initio study of liquid systems: Concentration dependence of electrical resistivity of binary liquid alloy Rb1-xCsx

NASA Astrophysics Data System (ADS)

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

2013-02-01

The electrical resistivity (ρL) of Rb1-XCsX binary alloys has been made calculated using Troullier Martins ab-initio pseudopotentials. The present results of the electrical resistivity (ρL) of Rb1-XCsX binary alloys have been found in good agreement with the experimental results. These results suggest that ab-initio approach for calculating electrical resistivity is quite successful in explaining the electronic transport properties of binary Liquid alloys. Hence ab-initio pseudopotentials can be used instead of model pseudopotentials having problem of transferability.

Topological Semimetals Studied by Ab Initio Calculations

NASA Astrophysics Data System (ADS)

Hirayama, Motoaki; Okugawa, Ryo; Murakami, Shuichi

2018-04-01

In topological semimetals such as Weyl, Dirac, and nodal-line semimetals, the band gap closes at points or along lines in k space which are not necessarily located at high-symmetry positions in the Brillouin zone. Therefore, it is not straightforward to find these topological semimetals by ab initio calculations because the band structure is usually calculated only along high-symmetry lines. In this paper, we review recent studies on topological semimetals by ab initio calculations. We explain theoretical frameworks which can be used for the search for topological semimetal materials, and some numerical methods used in the ab initio calculations.

Towards accurate ab initio predictions of the vibrational spectrum of methane

NASA Technical Reports Server (NTRS)

Schwenke, David W.

2002-01-01

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

AIDA: ab initio domain assembly for automated multi-domain protein structure prediction and domain–domain interaction prediction

PubMed Central

Xu, Dong; Jaroszewski, Lukasz; Li, Zhanwen; Godzik, Adam

2015-01-01

Motivation: Most proteins consist of multiple domains, independent structural and evolutionary units that are often reshuffled in genomic rearrangements to form new protein architectures. Template-based modeling methods can often detect homologous templates for individual domains, but templates that could be used to model the entire query protein are often not available. Results: We have developed a fast docking algorithm ab initio domain assembly (AIDA) for assembling multi-domain protein structures, guided by the ab initio folding potential. This approach can be extended to discontinuous domains (i.e. domains with ‘inserted’ domains). When tested on experimentally solved structures of multi-domain proteins, the relative domain positions were accurately found among top 5000 models in 86% of cases. AIDA server can use domain assignments provided by the user or predict them from the provided sequence. The latter approach is particularly useful for automated protein structure prediction servers. The blind test consisting of 95 CASP10 targets shows that domain boundaries could be successfully determined for 97% of targets. Availability and implementation: The AIDA package as well as the benchmark sets used here are available for download at http://ffas.burnham.org/AIDA/. Contact: adam@sanfordburnham.org Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25701568

Consistent integration of experimental and ab initio data into molecular and coarse-grained models

NASA Astrophysics Data System (ADS)

Vlcek, Lukas

As computer simulations are increasingly used to complement or replace experiments, highly accurate descriptions of physical systems at different time and length scales are required to achieve realistic predictions. The questions of how to objectively measure model quality in relation to reference experimental or ab initio data, and how to transition seamlessly between different levels of resolution are therefore of prime interest. To address these issues, we use the concept of statistical distance to define a measure of similarity between statistical mechanical systems, i.e., a model and its target, and show that its minimization leads to general convergence of the systems' measurable properties. Through systematic coarse-graining, we arrive at appropriate expressions for optimization loss functions consistently incorporating microscopic ab initio data as well as macroscopic experimental data. The design of coarse-grained and multiscale models is then based on factoring the model system partition function into terms describing the system at different resolution levels. The optimization algorithm takes advantage of thermodynamic perturbation expressions for fast exploration of the model parameter space, enabling us to scan millions of parameter combinations per hour on a single CPU. The robustness and generality of the new model optimization framework and its efficient implementation are illustrated on selected examples including aqueous solutions, magnetic systems, and metal alloys.

Ab initio quantum chemical study of electron transfer in carboranes

NASA Astrophysics Data System (ADS)

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

2005-05-01

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

Multiscale Quantum Mechanics/Molecular Mechanics Simulations with Neural Networks.

PubMed

Shen, Lin; Wu, Jingheng; Yang, Weitao

2016-10-11

Molecular dynamics simulation with multiscale quantum mechanics/molecular mechanics (QM/MM) methods is a very powerful tool for understanding the mechanism of chemical and biological processes in solution or enzymes. However, its computational cost can be too high for many biochemical systems because of the large number of ab initio QM calculations. Semiempirical QM/MM simulations have much higher efficiency. Its accuracy can be improved with a correction to reach the ab initio QM/MM level. The computational cost on the ab initio calculation for the correction determines the efficiency. In this paper we developed a neural network method for QM/MM calculation as an extension of the neural-network representation reported by Behler and Parrinello. With this approach, the potential energy of any configuration along the reaction path for a given QM/MM system can be predicted at the ab initio QM/MM level based on the semiempirical QM/MM simulations. We further applied this method to three reactions in water to calculate the free energy changes. The free-energy profile obtained from the semiempirical QM/MM simulation is corrected to the ab initio QM/MM level with the potential energies predicted with the constructed neural network. The results are in excellent accordance with the reference data that are obtained from the ab initio QM/MM molecular dynamics simulation or corrected with direct ab initio QM/MM potential energies. Compared with the correction using direct ab initio QM/MM potential energies, our method shows a speed-up of 1 or 2 orders of magnitude. It demonstrates that the neural network method combined with the semiempirical QM/MM calculation can be an efficient and reliable strategy for chemical reaction simulations.

Torsional anharmonicity in the conformational thermodynamics of flexible molecules

NASA Astrophysics Data System (ADS)

Miller, Thomas F., III; Clary, David C.

We present an algorithm for calculating the conformational thermodynamics of large, flexible molecules that combines ab initio electronic structure theory calculations with a torsional path integral Monte Carlo (TPIMC) simulation. The new algorithm overcomes the previous limitations of the TPIMC method by including the thermodynamic contributions of non-torsional vibrational modes and by affordably incorporating the ab initio calculation of conformer electronic energies, and it improves the conventional ab initio treatment of conformational thermodynamics by accounting for the anharmonicity of the torsional modes. Using previously published ab initio results and new TPIMC calculations, we apply the algorithm to the conformers of the adrenaline molecule.

HPAM: Hirshfeld Partitioned Atomic Multipoles

PubMed Central

Elking, Dennis M.; Perera, Lalith; Pedersen, Lee G.

2011-01-01

An implementation of the Hirshfeld (HD) and Hirshfeld-Iterated (HD-I) atomic charge density partitioning schemes is described. Atomic charges and atomic multipoles are calculated from the HD and HD-I atomic charge densities for arbitrary atomic multipole rank lmax on molecules of arbitrary shape and size. The HD and HD-I atomic charges/multipoles are tested by comparing molecular multipole moments and the electrostatic potential (ESP) surrounding a molecule with their reference ab initio values. In general, the HD-I atomic charges/multipoles are found to better reproduce ab initio electrostatic properties over HD atomic charges/multipoles. A systematic increase in precision for reproducing ab initio electrostatic properties is demonstrated by increasing the atomic multipole rank from lmax = 0 (atomic charges) to lmax = 4 (atomic hexadecapoles). Both HD and HD-I atomic multipoles up to rank lmax are shown to exactly reproduce ab initio molecular multipole moments of rank L for L ≤ lmax. In addition, molecular dipole moments calculated by HD, HD-I, and ChelpG atomic charges only (lmax = 0) are compared with reference ab initio values. Significant errors in reproducing ab initio molecular dipole moments are found if only HD or HD-I atomic charges used. PMID:22140274

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

PubMed

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.

Real-Space Multiple-Scattering Theory and Its Applications at Exascale

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eisenbach, Markus; Wang, Yang

In recent decades, the ab initio methods based on density functional theory (DFT) (Hohenberg and Kohn 1964, Kohn and Sham 1965) have become a widely used tool in computational materials science, which allows theoretical prediction of physical properties of materials from the first principles and theoretical interpretation of new physical phenomena found in experiments. In the framework of DFT, the original problem that requires solving a quantum mechanical equation for a many-electron system is reduced to a one-electron problem that involves an electron moving in an effective field, while the effective field potential is made up of an electrostatic potential,more » also known as Hartree potential, arising from the electronic and ion charge distribution in space and an exchange–correlation potential, which is a function of the electron density and encapsulates the exchange and correlation effects of the many-electron system. Even though the exact functional form of the exchange-correlation potential is formally unknown, a local density approximation (LDA) or a generalized gradient approximation (GGA) is usually applied so that the calculation of the exchange–correlation potential, as well as the exchange–correlation energy, becomes tractable while a required accuracy is retained. Based on DFT, ab initio electronic structure calculations for a material generally involve a self-consistent process that iterates between two computational tasks: (1) solving an one-electron Schrödinger equation, also known as Kohn–Sham equation, to obtain the electron density and, if needed, the magnetic moment density, and (2) solving the Poisson equation to obtain the electrostatic potential corresponding to the electron density and constructing the effective potential by adding the exchange–correlation potential to the electrostatic potential. This self-consistent process proceeds until a convergence criteria is reached.« less

Cyclic density functional theory: A route to the first principles simulation of bending in nanostructures

NASA Astrophysics Data System (ADS)

Banerjee, Amartya S.; Suryanarayana, Phanish

2016-11-01

We formulate and implement Cyclic Density Functional Theory (Cyclic DFT) - a self-consistent first principles simulation method for nanostructures with cyclic symmetries. Using arguments based on Group Representation Theory, we rigorously demonstrate that the Kohn-Sham eigenvalue problem for such systems can be reduced to a fundamental domain (or cyclic unit cell) augmented with cyclic-Bloch boundary conditions. Analogously, the equations of electrostatics appearing in Kohn-Sham theory can be reduced to the fundamental domain augmented with cyclic boundary conditions. By making use of this symmetry cell reduction, we show that the electronic ground-state energy and the Hellmann-Feynman forces on the atoms can be calculated using quantities defined over the fundamental domain. We develop a symmetry-adapted finite-difference discretization scheme to obtain a fully functional numerical realization of the proposed approach. We verify that our formulation and implementation of Cyclic DFT is both accurate and efficient through selected examples. The connection of cyclic symmetries with uniform bending deformations provides an elegant route to the ab-initio study of bending in nanostructures using Cyclic DFT. As a demonstration of this capability, we simulate the uniform bending of a silicene nanoribbon and obtain its energy-curvature relationship from first principles. A self-consistent ab-initio simulation of this nature is unprecedented and well outside the scope of any other systematic first principles method in existence. Our simulations reveal that the bending stiffness of the silicene nanoribbon is intermediate between that of graphene and molybdenum disulphide - a trend which can be ascribed to the variation in effective thickness of these materials. We describe several future avenues and applications of Cyclic DFT, including its extension to the study of non-uniform bending deformations and its possible use in the study of the nanoscale flexoelectric effect.

Ab initio molecular simulations with numeric atom-centered orbitals

NASA Astrophysics Data System (ADS)

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

2009-11-01

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

Unification of the phonon mode behavior in semiconductor alloys: Theory and ab initio calculations

NASA Astrophysics Data System (ADS)

Pagès, O.; Postnikov, A. V.; Kassem, M.; Chafi, A.; Nassour, A.; Doyen, S.

2008-03-01

We demonstrate how to overcome serious problems in understanding and classification of vibration spectra in semiconductor alloys, following from traditional use of the virtual crystal approximation (VCA). We show that such different systems as InGaAs (1- bond→1 -mode behavior), InGaP (modified 2-mode), and ZnTeSe (2- bond→1 -mode) obey, in fact, the same phonon mode behavior—hence probably a universal one—of a percolation type (1- bond→2 -mode). The change of paradigm from the “VCA insight” (an averaged microscopic one) to the “percolation insight” (a mesoscopic one) offers a promising link toward the understanding of alloy disorder. The discussion is supported by ab initio simulation of the phonon density of states at the zone center of representative supercells at intermediary composition (ZnTeSe) and at the impurity-dilute limits (all systems). In particular, we propose a simple ab initio “protocol” to estimate the basic input parameters of our semiempirical “percolation” model for the calculation of the 1- bond→2 -mode vibration spectra of zinc blende alloys. With this, the model turns self-sufficient.

Self-consistent electronic structure of disordered Fe/sub 0. 65/Ni/sub 0. 35/

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnson, D.D.; Pinski, F.J.; Stocks, G.M.

1985-04-15

We present the results of the first ab initio calculation of the electronic structure of the disordered alloy Fe/sub 0.65/Ni/sub 0.35/. The calculation is based on the multiple-scattering coherent-potential approach (KKR-CPA) and is fully self-consistent and spin polarized. Magnetic effects are included within local-spin-density functional theory using the exchange-correlation function of Vosko--Wilk--Nusair. The most striking feature of the calculation is that electrons of different spins experience different degrees of disorder. The minority spin electrons see a very large disorder, whereas the majority spin electrons see little disorder. Consequently, the minority spin density of states is smooth compared to the verymore » structured majority spin density of states. This difference is due to a subtle balance between exchange splitting and charge neutrality.« less

Self-consistent electronic structure of disordered Fe/sub 0/ /sub 65/Ni/sub 0/ /sub 35/

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnson, D.D.; Pinski, F.J.; Stocks, G.M.

1984-01-01

We present the results of the first ab-initio calculation of the electronic structure of a disordered Fe/sub 0/ /sub 65/Ni/sub 0/ /sub 35/ alloy. The calculation is based on the multiple-scattering coherent-potential approach (KKR-CPA) and is fully self-consistent and spin-polarized. Magnetic effects are included within local-spin-density functional theory using the exchange-correlation function of Vosko-Wilk-Nusair. The most striking feature of the calculation is that electrons of different spins experience different degrees of disorder. The minority spin electrons see a very large disorder; whereas, the majority spin electrons see little disorder. Consequently, the minority spin density of states is smooth compared tomore » the very structured majority spin density of states. This difference is due to a subtle balance between exchange-splitting and charge neutrality. 15 references, 2 figures.« less

A tungsten-rhenium interatomic potential for point defect studies

DOE PAGES

Setyawan, Wahyu; Gao, Ning; Kurtz, Richard J.

2018-05-28

A tungsten-rhenium (W-Re) classical interatomic potential is developed within the embedded atom method (EAM) interaction framework. A force-matching method is employed to fit the potential to ab initio forces, energies, and stresses. Simulated annealing is combined with the conjugate gradient technique to search for an optimum potential from over 1000 initial trial sets. The potential is designed for studying point defects in W-Re systems. It gives good predictions of the formation energies of Re defects in W and the binding energies of W self-interstitial clusters with Re. The potential is further evaluated for describing the formation energy of structures inmore » the σ and χ intermetallic phases. The predicted convex-hulls of formation energy are in excellent agreement with ab initio data. In pure Re, the potential can reproduce the formation energies of vacancy and self-interstitial defects sufficiently accurately, and gives the correct ground state self-interstitial configuration. Furthermore, by including liquid structures in the fit, the potential yields a Re melting temperature (3130 K) that is close to the experimental value (3459 K).« less

A tungsten-rhenium interatomic potential for point defect studies

NASA Astrophysics Data System (ADS)

Setyawan, Wahyu; Gao, Ning; Kurtz, Richard J.

2018-05-01

A tungsten-rhenium (W-Re) classical interatomic potential is developed within the embedded atom method interaction framework. A force-matching method is employed to fit the potential to ab initio forces, energies, and stresses. Simulated annealing is combined with the conjugate gradient technique to search for an optimum potential from over 1000 initial trial sets. The potential is designed for studying point defects in W-Re systems. It gives good predictions of the formation energies of Re defects in W and the binding energies of W self-interstitial clusters with Re. The potential is further evaluated for describing the formation energy of structures in the σ and χ intermetallic phases. The predicted convex-hulls of formation energy are in excellent agreement with ab initio data. In pure Re, the potential can reproduce the formation energies of vacancies and self-interstitial defects sufficiently accurately and gives the correct ground state self-interstitial configuration. Furthermore, by including liquid structures in the fit, the potential yields a Re melting temperature (3130 K) that is close to the experimental value (3459 K).

A tungsten-rhenium interatomic potential for point defect studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Setyawan, Wahyu; Gao, Ning; Kurtz, Richard J.

A tungsten-rhenium (W-Re) classical interatomic potential is developed within the embedded atom method (EAM) interaction framework. A force-matching method is employed to fit the potential to ab initio forces, energies, and stresses. Simulated annealing is combined with the conjugate gradient technique to search for an optimum potential from over 1000 initial trial sets. The potential is designed for studying point defects in W-Re systems. It gives good predictions of the formation energies of Re defects in W and the binding energies of W self-interstitial clusters with Re. The potential is further evaluated for describing the formation energy of structures inmore » the σ and χ intermetallic phases. The predicted convex-hulls of formation energy are in excellent agreement with ab initio data. In pure Re, the potential can reproduce the formation energies of vacancy and self-interstitial defects sufficiently accurately, and gives the correct ground state self-interstitial configuration. Furthermore, by including liquid structures in the fit, the potential yields a Re melting temperature (3130 K) that is close to the experimental value (3459 K).« less

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

NASA Astrophysics Data System (ADS)

Lique, François

2009-03-01

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

Dynamic Structure of a Molecular Liquid S0.5Cl0.5: Ab initio Molecular-Dynamics Simulations

NASA Astrophysics Data System (ADS)

Ohmura, Satoshi; Shimakura, Hironori; Kawakita, Yukinobu; Shimojo, Fuyuki; Yao, Makoto

2013-07-01

The static and dynamic structures of a molecular liquid S0.5Cl0.5 consisting of Cl--S--S--Cl (S2Cl2) type molecules are studied by means of ab initio molecular dynamics simulations. Both the calculated static and dynamic structure factors are in good agreement with experimental results. The dynamic structures are discussed based on van-Hove distinct correlation functions, molecular translational mean-square displacements (TMSD) and rotational mean-square displacements (RMSD). In the TMSD and RMSD, there are ballistic and diffusive regimes in the sub-picosecond and picosecond time regions, respectively. These time scales are consistent with the decay time observed experimentally. The interaction between molecules in the liquid is also discussed in comparison with that in another liquid chalcogen--halogen system Se0.5Cl0.5.

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

NASA Technical Reports Server (NTRS)

Good, Brian S.

2004-01-01

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

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

NASA Astrophysics Data System (ADS)

Dahlqvist, Martti; Hotokka, Matti; Räsänen, Markku

1998-04-01

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

Ab Initio Studies of Chlorine Oxide and Nitrogen Oxide Species of Interest in Stratospheric Chemistry

NASA Technical Reports Server (NTRS)

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

1995-01-01

The ability of modern state-of-the art ab initio quantum chemical techniques to characterize reliably the gas-phase molecular structure, vibrational spectrum, electronic spectrum, and thermal stability of chlorine oxide and nitrogen oxide species will be demonstrated by presentation of some example studies. In particular the geometrical structures, vibrational spectra, and heats of formation Of ClNO2, CisClONO, and trans-ClONO are shown to be in excellent agreement with the available experimental data, and where the experimental data are either not known or are inconclusive, the ab initio results are shown to fill in the gaps and to resolve the experimental controversy. In addition, ab initio studies in which the electronic spectra and the characterization of excited electronic states of ClONO2, HONO2, ClOOC17 ClOOH, and HOOH will also be presented. Again where available, the ab initio results are compared to experimental observations, and are used to aid in the interpretation of the experimental studies.

Computational Chemistry Comparison and Benchmark Database

National Institute of Standards and Technology Data Gateway

SRD 101 NIST Computational Chemistry Comparison and Benchmark Database (Web, free access)   The NIST Computational Chemistry Comparison and Benchmark Database is a collection of experimental and ab initio thermochemical properties for a selected set of molecules. The goals are to provide a benchmark set of molecules for the evaluation of ab initio computational methods and allow the comparison between different ab initio computational methods for the prediction of thermochemical properties.

Band gap depiction of quaternary FeMnTiAl alloy using Hubbard (U) potential

NASA Astrophysics Data System (ADS)

Bhat, Tahir Mohiuddin; Yousuf, Saleem; Khandy, Shakeel Ahmad; Gupta, Dinesh C.

2018-05-01

We have employed self-consistent ab-initio calculations to investigate new quaternary alloy FeMnTiAl by applying Hubbard potential (U). The alloy is found to be stable in ferromagnetic phase with cubic structure. The alloy shows half-metallic (HM) ferromagnet character. The values of minority band gap FeMnTiAl are found to be 0.33 eV respectively. Electronic charge density reveals that both types of bonds covalent as well as ionic are present in the alloy. Thus the new quaternary alloy can be proved as vital contender for spin valves and spin generator devices.

Multiobjective evolutionary algorithm with many tables for purely ab initio protein structure prediction.

PubMed

Brasil, Christiane Regina Soares; Delbem, Alexandre Claudio Botazzo; da Silva, Fernando Luís Barroso

2013-07-30

This article focuses on the development of an approach for ab initio protein structure prediction (PSP) without using any earlier knowledge from similar protein structures, as fragment-based statistics or inference of secondary structures. Such an approach is called purely ab initio prediction. The article shows that well-designed multiobjective evolutionary algorithms can predict relevant protein structures in a purely ab initio way. One challenge for purely ab initio PSP is the prediction of structures with β-sheets. To work with such proteins, this research has also developed procedures to efficiently estimate hydrogen bond and solvation contribution energies. Considering van der Waals, electrostatic, hydrogen bond, and solvation contribution energies, the PSP is a problem with four energetic terms to be minimized. Each interaction energy term can be considered an objective of an optimization method. Combinatorial problems with four objectives have been considered too complex for the available multiobjective optimization (MOO) methods. The proposed approach, called "Multiobjective evolutionary algorithms with many tables" (MEAMT), can efficiently deal with four objectives through the combination thereof, performing a more adequate sampling of the objective space. Therefore, this method can better map the promising regions in this space, predicting structures in a purely ab initio way. In other words, MEAMT is an efficient optimization method for MOO, which explores simultaneously the search space as well as the objective space. MEAMT can predict structures with one or two domains with RMSDs comparable to values obtained by recently developed ab initio methods (GAPFCG , I-PAES, and Quark) that use different levels of earlier knowledge. Copyright © 2013 Wiley Periodicals, Inc.

Ab initio calculation of proton-coupled electron transfer rates using the external-potential representation: A ubiquinol complex in solution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yamamoto, Takeshi; Kato, Shigeki

2007-06-14

In quantum-mechanical/molecular-mechanical (QM/MM) treatment of chemical reactions in condensed phases, one solves the electronic Schroedinger equation for the solute (or an active site) under the electrostatic field from the environment. This Schroedinger equation depends parametrically on the solute nuclear coordinates R and the external electrostatic potential V. This fact suggests that one may use R and V as natural collective coordinates for describing the entire system, where V plays the role of collective solvent variables. In this paper such an (R,V) representation of the QM/MM canonical ensemble is described, with particular focus on how to treat charge transfer processes inmore » this representation. As an example, the above method is applied to the proton-coupled electron transfer of a ubiquinol analog with phenoxyl radical in acetonitrile solvent. Ab initio free-energy surfaces are calculated as functions of R and V using the reference interaction site model self-consistent field method, the equilibrium points and the minimum free-energy crossing point are located in the (R,V) space, and then the kinetic isotope effects (KIEs) are evaluated approximately. The results suggest that a stiffer proton potential at the transition state may be responsible for unusual KIEs observed experimentally for related systems.« less

Ab initio electronic structure calculations for metallic intermediate band formation in photovoltaic materials

NASA Astrophysics Data System (ADS)

Wahnón, P.; Tablero, C.

2002-04-01

A metallic isolated band in the middle of the band gap of several III-V semiconductors has been predicted as photovoltaic materials with the possibility of providing substantially enhanced efficiencies. We have investigated the electronic band structures and lattice constants of GanAsmM and GanPmM with M=Sc, Ti, V, and Cr, to identify whether this isolated band is likely to exist by means of accurate calculations. For this task, we use the SIESTA program, an ab initio periodic density-functional method, fully self consistent in the local-density approximation. Norm-conserving, nonlocal pseudopotentials and confined linear combination of atomic orbitals have been used. We have carried out a case study of GanAsmTi and GanPmTi energy-band structure including analyses of the effect of the basis set, fine k-point mesh to ensure numerical convergence, structural parameters, and generalized gradient approximation for exchange and correlation corrections. We find the isolated intermediate band when one Ti atom replaces the position of one As (or P) atom in the crystal structure. For this kind of compound we show that the intermediate band relative position inside the band gap and width are sensitive to the dynamic relaxation of the crystal and the size of the basis set.

DFT and ab initio study of the unimolecular decomposition of the lowest singlet and triplet states of nitromethane

DOE Office of Scientific and Technical Information (OSTI.GOV)

Manaa, M.R.; Fried, L.E.

1998-11-26

The fully optimized potential energy curves for the unimolecular decomposition of the lowest singlet and triplet states of nitromethane through the C-NO{sub 2} bond dissociation pathway are calculated using various DFT and high-level ab initio electronic structure methods. The authors perform gradient corrected density functional theory (DFT) and multiconfiguration self-consistent field (MCSCF) to conclusively demonstrate that the triplet state of nitromethane is bound. The adiabatic curve of this state exhibits a 33 kcal/mol energy barrier as determined at the MCSCF level. DFT methods locate this barrier at a shorter C-N bond distance with 12--16 kcal/mol lower energy than does MCSCF.more » In addition to MCSCF and DFT, quadratic configuration interactions with single and double substitutions (QCISD) calculations are also performed for the singlet curve. The potential energy profiles of this state predicted by FT methods based on Becke`s 1988 exchange functional differ by as much as 17 kcal/mol from the predictions of MCSCF and QCISD in the vicinity of the equilibrium structure. The computational methods predict bond dissociation energies 5--9 kcal/mol lower than the experimental value. DFT techniques based on Becke`s 3-parameter exchange functional show the best overall agreement with the higher level methods.« less

Anharmonic force field and vibrational dynamics of CH2F2 up to 5000 cm(-1) studied by Fourier transform infrared spectroscopy and state-of-the-art ab initio calculations.

PubMed

Tasinato, Nicola; Regini, Giorgia; Stoppa, Paolo; Pietropolli Charmet, Andrea; Gambi, Alberto

2012-06-07

Difluoromethane (CH(2)F(2), HFC-32) is a molecule used in refrigerant mixtures as a replacement of the more environmentally hazardous, ozone depleting, chlorofluorocarbons. On the other hand, presenting strong vibration-rotation bands in the 9 μm atmospheric window, it is a greenhouse gas which contributes to global warming. In the present work, the vibrational and ro-vibrational properties of CH(2)F(2), providing basic data for its atmospheric modeling, are studied in detail by coupling medium resolution Fourier transform infrared spectroscopy to high-level electronic structure ab initio calculations. Experimentally a full quantum assignment and accurate integrated absorption cross sections are obtained up to 5000 cm(-1). Ab initio calculations are carried out by using CCSD(T) theory and large basis sets of either the correlation consistent or atomic natural orbital hierarchies. By using vibrational perturbation theory to second order a complete set of vibrational and ro-vibrational parameters is derived from the ab initio quartic anharmonic force fields, which well compares with the spectroscopic constants retrieved experimentally. An excellent agreement between theory and experiment is achieved for vibrational energy levels and integrated absorption cross sections: transition frequencies up to four quanta of vibrational excitation are reproduced with a root mean square deviation (RMSD) of 7 cm(-1) while intensities are predicted within few km mol(-1) from the experiment. Basis set performances and core correlation effects are discussed throughout the paper. Particular attention is focused in the understanding of the anharmonic couplings which rule the vibrational dynamics of the |ν(1)>, |2ν(8)>, |2ν(2)> three levels interacting system. The reliability of the potential energy and dipole moment surfaces in reproducing the vibrational eigenvalues and intensities as well as in modeling the vibrational and ro-vibrational mixings over the whole 400-5000 cm(-1) region is also demonstrated by spectacular spectral simulations carried out by using the ro-vibrational Hamiltonian constants, and the relevant coupling terms, obtained from the perturbation treatment of the ab initio anharmonic force field. The present results suggest CH(2)F(2) as a prototype molecule to test ab initio calculations and theoretical models.

Anharmonic force field and vibrational dynamics of CH2F2 up to 5000 cm-1 studied by Fourier transform infrared spectroscopy and state-of-the-art ab initio calculations

NASA Astrophysics Data System (ADS)

Tasinato, Nicola; Regini, Giorgia; Stoppa, Paolo; Charmet, Andrea Pietropolli; Gambi, Alberto

2012-06-01

Difluoromethane (CH2F2, HFC-32) is a molecule used in refrigerant mixtures as a replacement of the more environmentally hazardous, ozone depleting, chlorofluorocarbons. On the other hand, presenting strong vibration-rotation bands in the 9 μm atmospheric window, it is a greenhouse gas which contributes to global warming. In the present work, the vibrational and ro-vibrational properties of CH2F2, providing basic data for its atmospheric modeling, are studied in detail by coupling medium resolution Fourier transform infrared spectroscopy to high-level electronic structure ab initio calculations. Experimentally a full quantum assignment and accurate integrated absorption cross sections are obtained up to 5000 cm-1. Ab initio calculations are carried out by using CCSD(T) theory and large basis sets of either the correlation consistent or atomic natural orbital hierarchies. By using vibrational perturbation theory to second order a complete set of vibrational and ro-vibrational parameters is derived from the ab initio quartic anharmonic force fields, which well compares with the spectroscopic constants retrieved experimentally. An excellent agreement between theory and experiment is achieved for vibrational energy levels and integrated absorption cross sections: transition frequencies up to four quanta of vibrational excitation are reproduced with a root mean square deviation (RMSD) of 7 cm-1 while intensities are predicted within few km mol-1 from the experiment. Basis set performances and core correlation effects are discussed throughout the paper. Particular attention is focused in the understanding of the anharmonic couplings which rule the vibrational dynamics of the |ν1⟩, |2ν8⟩, |2ν2⟩ three levels interacting system. The reliability of the potential energy and dipole moment surfaces in reproducing the vibrational eigenvalues and intensities as well as in modeling the vibrational and ro-vibrational mixings over the whole 400-5000 cm-1 region is also demonstrated by spectacular spectral simulations carried out by using the ro-vibrational Hamiltonian constants, and the relevant coupling terms, obtained from the perturbation treatment of the ab initio anharmonic force field. The present results suggest CH2F2 as a prototype molecule to test ab initio calculations and theoretical models.

New DMFT capabilities in CASTEP

NASA Astrophysics Data System (ADS)

Plekhanov, Evgeny; Sacksteder, Vincent; Hasnip, Phil; Probert, Matt; Clark, Stewart; Weber, Cedric; Refson, Keith

We present the first implementation of Dynamical Mean-Field Theory in UK's major ab-initio code CASTEP. This implementation: i) is modular; ii) allows great flexibility in choosing local basis set for downfolding/upfolding of self-energy; iii) permits wide choice of impurity solvers (including external solver libraries); and iv) gives the user a possibility to use several self-consistency schemes and calculate total energy and forces. We explain in details the theoretical framework used. We benchmark our implementation on several strongly-correlated insulating systems with d- and f-shells: γ-Ce and Ce2O3 by using Hubbard I and CTHYB-QMC solvers. Our results appear to be in excellent agreement with the reference data published previously in the literature. EPSRC-funded project ''Strong Correlation meets Materials Modelling: DMFT and GW in CASTEP''.

Ab initio Quantum Chemical and Experimental Reaction Kinetics Studies in the Combustion of Bipropellants

DTIC Science & Technology

2017-03-24

NUMBER (Include area code) 24 March 2017 Briefing Charts 01 March 2017 - 31 March 2017 Ab initio Quantum Chemical and Experimental Reaction Kinetics...Laboratory AFRL/RQRS 1 Ara Road Edwards AFB, CA 93524 *Email: ghanshyam.vaghjiani@us.af.mil Ab initio Quantum Chemical and Experimental Reaction ...Clearance 17161 Zador et al., Prog. Energ. Combust. Sci., 37 371 (2011) Why Quantum Chemical Reaction Kinetics Studies? DISTRIBUTION A: Approved for

An ab initio study of the conformational energy map of acetylcholine

NASA Astrophysics Data System (ADS)

Segall, M. D.; Payne, M. C.; Boyes, R. N.

An ab initio density functional theory study is reported of the conformational energy map of acetylcholine, with respect to the two central dihedral angles of the molecule. The acetylcholine molecule pays a central role in neurotransmission and has been studied widely using semi-empirical computational modelling. The ab initio results are compared with a number of previous investigations and with experiment. The ab initio data indicate that the most stable conformation of acetylcholine is the trans , gauche arrangement of the central dihedral angles. Furthermore, Mulliken population analysis of the electronic structure of the molecule in this conformation indicates that the positive charge of the molecule is spread over the exterior of the cationic head of the molecule.

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

PubMed

Rana, Malay Kumar; Chandra, Amalendu

2013-05-28

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

Revisiting the Electronic Structure of FeS Monomers Using ab Initio Ligand Field Theory and the Angular Overlap Model.

PubMed

Chilkuri, Vijay Gopal; DeBeer, Serena; Neese, Frank

2017-09-05

Iron-sulfur (FeS) proteins are universally found in nature with actives sites ranging in complexity from simple monomers to multinuclear sites from two up to eight iron atoms. These sites include mononuclear (rubredoxins), dinuclear (ferredoxins and Rieske proteins), trinuclear (e.g., hydrogenases), and tetranuclear (various ferredoxins and high-potential iron-sulfur proteins). The electronic structure of the higher-nuclearity clusters is inherently extremely complex. Hence, it is reasonable to take a bottom-up approach in which clusters of increasing nuclearity are analyzed in terms of the properties of their lower nuclearity constituents. In the present study, the first step is taken by an in-depth analysis of mononuclear FeS systems. Two different FeS molecules with phenylthiolate and methylthiolate as ligands are studied in their oxidized and reduced forms using modern wave function-based ab initio methods. The ab initio electronic spectra and wave function are presented and analyzed in detail. The very intricate electronic structure-geometry relationship in these systems is analyzed using ab initio ligand field theory (AILFT) in conjunction with the angular overlap model (AOM) parametrization scheme. The simple AOM model is used to explain the effect of geometric variations on the electronic structure. Through a comparison of the ab initio computed UV-vis absorption spectra and the available experimental spectra, the low-energy part of the many-particle spectrum is carefully analyzed. We show ab initio calculated magnetic circular dichroism spectra and present a comparison with the experimental spectrum. Finally, AILFT parameters and the ab initio spectra are compared with those obtained experimentally to understand the effect of the increased covalency of the thiolate ligands on the electronic structure of FeS monomers.

Identification and Characterization of Molecular Bonding Structures by ab initio Quasi-Atomic Orbital Analyses.

PubMed

West, Aaron C; Duchimaza-Heredia, Juan J; Gordon, Mark S; Ruedenberg, Klaus

2017-11-22

The quasi-atomic analysis of ab initio electronic wave functions in full valence spaces, which was developed in preceding papers, yields oriented quasi-atomic orbitals in terms of which the ab initio molecular wave function and energy can be expressed. These oriented quasi-atomic orbitals are the rigorous ab initio counterparts to the conceptual bond forming atomic hybrid orbitals of qualitative chemical reasoning. In the present work, the quasi-atomic orbitals are identified as bonding orbitals, lone pair orbitals, radical orbitals, vacant orbitals and orbitals with intermediate character. A program determines the bonding characteristics of all quasi-atomic orbitals in a molecule on the basis of their occupations, bond orders, kinetic bond orders, hybridizations and local symmetries. These data are collected in a record and provide the information for a comprehensive understanding of the synergism that generates the bonding structure that holds the molecule together. Applications to a series of molecules exhibit the complete bonding structures that are embedded in their ab initio wave functions. For the strong bonds in a molecule, the quasi-atomic orbitals provide quantitative ab initio amplifications of the Lewis dot symbols. Beyond characterizing strong bonds, the quasi-atomic analysis also yields an understanding of the weak interactions, such as vicinal, hyperconjugative and radical stabilizations, which can make substantial contributions to the molecular bonding structure.

Ab initio interatomic potentials and the thermodynamic properties of fluids

NASA Astrophysics Data System (ADS)

Vlasiuk, Maryna; Sadus, Richard J.

2017-07-01

Monte Carlo simulations with accurate ab initio interatomic potentials are used to investigate the key thermodynamic properties of argon and krypton in both vapor and liquid phases. Data are reported for the isochoric and isobaric heat capacities, the Joule-Thomson coefficient, and the speed of sound calculated using various two-body interatomic potentials and different combinations of two-body plus three-body terms. The results are compared to either experimental or reference data at state points between the triple and critical points. Using accurate two-body ab initio potentials, combined with three-body interaction terms such as the Axilrod-Teller-Muto and Marcelli-Wang-Sadus potentials, yields systematic improvements to the accuracy of thermodynamic predictions. The effect of three-body interactions is to lower the isochoric and isobaric heat capacities and increase both the Joule-Thomson coefficient and speed of sound. The Marcelli-Wang-Sadus potential is a computationally inexpensive way to utilize accurate two-body ab initio potentials for the prediction of thermodynamic properties. In particular, it provides a very effective way of extending two-body ab initio potentials to liquid phase properties.

A walk through the approximations of ab initio multiple spawning

NASA Astrophysics Data System (ADS)

Mignolet, Benoit; Curchod, Basile F. E.

2018-04-01

Full multiple spawning offers an in principle exact framework for excited-state dynamics, where nuclear wavefunctions in different electronic states are represented by a set of coupled trajectory basis functions that follow classical trajectories. The couplings between trajectory basis functions can be approximated to treat molecular systems, leading to the ab initio multiple spawning method which has been successfully employed to study the photochemistry and photophysics of several molecules. However, a detailed investigation of its approximations and their consequences is currently missing in the literature. In this work, we simulate the explicit photoexcitation and subsequent excited-state dynamics of a simple system, LiH, and we analyze (i) the effect of the ab initio multiple spawning approximations on different observables and (ii) the convergence of the ab initio multiple spawning results towards numerically exact quantum dynamics upon a progressive relaxation of these approximations. We show that, despite the crude character of the approximations underlying ab initio multiple spawning for this low-dimensional system, the qualitative excited-state dynamics is adequately captured, and affordable corrections can further be applied to ameliorate the coupling between trajectory basis functions.

Matrix product operators, matrix product states, and ab initio density matrix renormalization group algorithms

NASA Astrophysics Data System (ADS)

Chan, Garnet Kin-Lic; Keselman, Anna; Nakatani, Naoki; Li, Zhendong; White, Steven R.

2016-07-01

Current descriptions of the ab initio density matrix renormalization group (DMRG) algorithm use two superficially different languages: an older language of the renormalization group and renormalized operators, and a more recent language of matrix product states and matrix product operators. The same algorithm can appear dramatically different when written in the two different vocabularies. In this work, we carefully describe the translation between the two languages in several contexts. First, we describe how to efficiently implement the ab initio DMRG sweep using a matrix product operator based code, and the equivalence to the original renormalized operator implementation. Next we describe how to implement the general matrix product operator/matrix product state algebra within a pure renormalized operator-based DMRG code. Finally, we discuss two improvements of the ab initio DMRG sweep algorithm motivated by matrix product operator language: Hamiltonian compression, and a sum over operators representation that allows for perfect computational parallelism. The connections and correspondences described here serve to link the future developments with the past and are important in the efficient implementation of continuing advances in ab initio DMRG and related algorithms.

Predicting vapor-liquid phase equilibria with augmented ab initio interatomic potentials

NASA Astrophysics Data System (ADS)

Vlasiuk, Maryna; Sadus, Richard J.

2017-06-01

The ability of ab initio interatomic potentials to accurately predict vapor-liquid phase equilibria is investigated. Monte Carlo simulations are reported for the vapor-liquid equilibria of argon and krypton using recently developed accurate ab initio interatomic potentials. Seventeen interatomic potentials are studied, formulated from different combinations of two-body plus three-body terms. The simulation results are compared to either experimental or reference data for conditions ranging from the triple point to the critical point. It is demonstrated that the use of ab initio potentials enables systematic improvements to the accuracy of predictions via the addition of theoretically based terms. The contribution of three-body interactions is accounted for using the Axilrod-Teller-Muto plus other multipole contributions and the effective Marcelli-Wang-Sadus potentials. The results indicate that the predictive ability of recent interatomic potentials, obtained from quantum chemical calculations, is comparable to that of accurate empirical models. It is demonstrated that the Marcelli-Wang-Sadus potential can be used in combination with accurate two-body ab initio models for the computationally inexpensive and accurate estimation of vapor-liquid phase equilibria.

Brønsted acidity of protic ionic liquids: a modern ab initio valence bond theory perspective.

PubMed

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.

Bicanonical ab Initio Molecular Dynamics for Open Systems.

PubMed

Frenzel, Johannes; Meyer, Bernd; Marx, Dominik

2017-08-08

Performing ab initio molecular dynamics simulations of open systems, where the chemical potential rather than the number of both nuclei and electrons is fixed, still is a challenge. Here, drawing on bicanonical sampling ideas introduced two decades ago by Swope and Andersen [ J. Chem. Phys. 1995 , 102 , 2851 - 2863 ] to calculate chemical potentials of liquids and solids, an ab initio simulation technique is devised, which introduces a fictitious dynamics of two superimposed but otherwise independent periodic systems including full electronic structure, such that either the chemical potential or the average fractional particle number of a specific chemical species can be kept constant. As proof of concept, we demonstrate that solvation free energies can be computed from these bicanonical ab initio simulations upon directly superimposing pure bulk water and the respective aqueous solution being the two limiting systems. The method is useful in many circumstances, for instance for studying heterogeneous catalytic processes taking place on surfaces where the chemical potential of reactants rather than their number is controlled and opens a pathway toward ab initio simulations at constant electrochemical potential.

A walk through the approximations of ab initio multiple spawning.

PubMed

Mignolet, Benoit; Curchod, Basile F E

2018-04-07

Full multiple spawning offers an in principle exact framework for excited-state dynamics, where nuclear wavefunctions in different electronic states are represented by a set of coupled trajectory basis functions that follow classical trajectories. The couplings between trajectory basis functions can be approximated to treat molecular systems, leading to the ab initio multiple spawning method which has been successfully employed to study the photochemistry and photophysics of several molecules. However, a detailed investigation of its approximations and their consequences is currently missing in the literature. In this work, we simulate the explicit photoexcitation and subsequent excited-state dynamics of a simple system, LiH, and we analyze (i) the effect of the ab initio multiple spawning approximations on different observables and (ii) the convergence of the ab initio multiple spawning results towards numerically exact quantum dynamics upon a progressive relaxation of these approximations. We show that, despite the crude character of the approximations underlying ab initio multiple spawning for this low-dimensional system, the qualitative excited-state dynamics is adequately captured, and affordable corrections can further be applied to ameliorate the coupling between trajectory basis functions.

Ab initio interatomic potentials and the thermodynamic properties of fluids.

PubMed

Vlasiuk, Maryna; Sadus, Richard J

2017-07-14

Monte Carlo simulations with accurate ab initio interatomic potentials are used to investigate the key thermodynamic properties of argon and krypton in both vapor and liquid phases. Data are reported for the isochoric and isobaric heat capacities, the Joule-Thomson coefficient, and the speed of sound calculated using various two-body interatomic potentials and different combinations of two-body plus three-body terms. The results are compared to either experimental or reference data at state points between the triple and critical points. Using accurate two-body ab initio potentials, combined with three-body interaction terms such as the Axilrod-Teller-Muto and Marcelli-Wang-Sadus potentials, yields systematic improvements to the accuracy of thermodynamic predictions. The effect of three-body interactions is to lower the isochoric and isobaric heat capacities and increase both the Joule-Thomson coefficient and speed of sound. The Marcelli-Wang-Sadus potential is a computationally inexpensive way to utilize accurate two-body ab initio potentials for the prediction of thermodynamic properties. In particular, it provides a very effective way of extending two-body ab initio potentials to liquid phase properties.

Predicting vapor-liquid phase equilibria with augmented ab initio interatomic potentials.

PubMed

Vlasiuk, Maryna; Sadus, Richard J

2017-06-28

The ability of ab initio interatomic potentials to accurately predict vapor-liquid phase equilibria is investigated. Monte Carlo simulations are reported for the vapor-liquid equilibria of argon and krypton using recently developed accurate ab initio interatomic potentials. Seventeen interatomic potentials are studied, formulated from different combinations of two-body plus three-body terms. The simulation results are compared to either experimental or reference data for conditions ranging from the triple point to the critical point. It is demonstrated that the use of ab initio potentials enables systematic improvements to the accuracy of predictions via the addition of theoretically based terms. The contribution of three-body interactions is accounted for using the Axilrod-Teller-Muto plus other multipole contributions and the effective Marcelli-Wang-Sadus potentials. The results indicate that the predictive ability of recent interatomic potentials, obtained from quantum chemical calculations, is comparable to that of accurate empirical models. It is demonstrated that the Marcelli-Wang-Sadus potential can be used in combination with accurate two-body ab initio models for the computationally inexpensive and accurate estimation of vapor-liquid phase equilibria.

Matrix product operators, matrix product states, and ab initio density matrix renormalization group algorithms.

PubMed

Chan, Garnet Kin-Lic; Keselman, Anna; Nakatani, Naoki; Li, Zhendong; White, Steven R

2016-07-07

Current descriptions of the ab initio density matrix renormalization group (DMRG) algorithm use two superficially different languages: an older language of the renormalization group and renormalized operators, and a more recent language of matrix product states and matrix product operators. The same algorithm can appear dramatically different when written in the two different vocabularies. In this work, we carefully describe the translation between the two languages in several contexts. First, we describe how to efficiently implement the ab initio DMRG sweep using a matrix product operator based code, and the equivalence to the original renormalized operator implementation. Next we describe how to implement the general matrix product operator/matrix product state algebra within a pure renormalized operator-based DMRG code. Finally, we discuss two improvements of the ab initio DMRG sweep algorithm motivated by matrix product operator language: Hamiltonian compression, and a sum over operators representation that allows for perfect computational parallelism. The connections and correspondences described here serve to link the future developments with the past and are important in the efficient implementation of continuing advances in ab initio DMRG and related algorithms.

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

PubMed Central

Füsti-Molnár, László; Merz, Kenneth M.

2008-01-01

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

An eigenvalue approach to quantum plasmonics based on a self-consistent hydrodynamics method

NASA Astrophysics Data System (ADS)

Ding, Kun; Chan, C. T.

2018-02-01

Plasmonics has attracted much attention not only because it has useful properties such as strong field enhancement, but also because it reveals the quantum nature of matter. To handle quantum plasmonics effects, ab initio packages or empirical Feibelman d-parameters have been used to explore the quantum correction of plasmonic resonances. However, most of these methods are formulated within the quasi-static framework. The self-consistent hydrodynamics model offers a reliable approach to study quantum plasmonics because it can incorporate the quantum effect of the electron gas into classical electrodynamics in a consistent manner. Instead of the standard scattering method, we formulate the self-consistent hydrodynamics method as an eigenvalue problem to study quantum plasmonics with electrons and photons treated on the same footing. We find that the eigenvalue approach must involve a global operator, which originates from the energy functional of the electron gas. This manifests the intrinsic nonlocality of the response of quantum plasmonic resonances. Our model gives the analytical forms of quantum corrections to plasmonic modes, incorporating quantum electron spill-out effects and electrodynamical retardation. We apply our method to study the quantum surface plasmon polariton for a single flat interface.

Ab initio theory and modeling of water.

PubMed

Chen, Mohan; Ko, Hsin-Yu; Remsing, Richard C; Calegari Andrade, Marcos F; Santra, Biswajit; Sun, Zhaoru; Selloni, Annabella; Car, Roberto; Klein, Michael L; Perdew, John P; Wu, Xifan

2017-10-10

Water is of the utmost importance for life and technology. However, a genuinely predictive ab initio model of water has eluded scientists. We demonstrate that a fully ab initio approach, relying on the strongly constrained and appropriately normed (SCAN) density functional, provides such a description of water. SCAN accurately describes the balance among covalent bonds, hydrogen bonds, and van der Waals interactions that dictates the structure and dynamics of liquid water. Notably, SCAN captures the density difference between water and ice I h at ambient conditions, as well as many important structural, electronic, and dynamic properties of liquid water. These successful predictions of the versatile SCAN functional open the gates to study complex processes in aqueous phase chemistry and the interactions of water with other materials in an efficient, accurate, and predictive, ab initio manner.

Ab initio theory and modeling of water

PubMed Central

Chen, Mohan; Ko, Hsin-Yu; Remsing, Richard C.; Calegari Andrade, Marcos F.; Santra, Biswajit; Sun, Zhaoru; Selloni, Annabella; Car, Roberto; Klein, Michael L.; Perdew, John P.; Wu, Xifan

2017-01-01

Water is of the utmost importance for life and technology. However, a genuinely predictive ab initio model of water has eluded scientists. We demonstrate that a fully ab initio approach, relying on the strongly constrained and appropriately normed (SCAN) density functional, provides such a description of water. SCAN accurately describes the balance among covalent bonds, hydrogen bonds, and van der Waals interactions that dictates the structure and dynamics of liquid water. Notably, SCAN captures the density difference between water and ice Ih at ambient conditions, as well as many important structural, electronic, and dynamic properties of liquid water. These successful predictions of the versatile SCAN functional open the gates to study complex processes in aqueous phase chemistry and the interactions of water with other materials in an efficient, accurate, and predictive, ab initio manner. PMID:28973868

Automated property optimization via ab initio O(N) elongation method: Application to (hyper-)polarizability in DNA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Orimoto, Yuuichi, E-mail: orimoto.yuuichi.888@m.kyushu-u.ac.jp; Aoki, Yuriko; Japan Science and Technology Agency, CREST, 4-1-8 Hon-chou, Kawaguchi, Saitama 332-0012

An automated property optimization method was developed based on the ab initio O(N) elongation (ELG) method and applied to the optimization of nonlinear optical (NLO) properties in DNA as a first test. The ELG method mimics a polymerization reaction on a computer, and the reaction terminal of a starting cluster is attacked by monomers sequentially to elongate the electronic structure of the system by solving in each step a limited space including the terminal (localized molecular orbitals at the terminal) and monomer. The ELG-finite field (ELG-FF) method for calculating (hyper-)polarizabilities was used as the engine program of the optimization method,more » and it was found to show linear scaling efficiency while maintaining high computational accuracy for a random sequenced DNA model. Furthermore, the self-consistent field convergence was significantly improved by using the ELG-FF method compared with a conventional method, and it can lead to more feasible NLO property values in the FF treatment. The automated optimization method successfully chose an appropriate base pair from four base pairs (A, T, G, and C) for each elongation step according to an evaluation function. From test optimizations for the first order hyper-polarizability (β) in DNA, a substantial difference was observed depending on optimization conditions between “choose-maximum” (choose a base pair giving the maximum β for each step) and “choose-minimum” (choose a base pair giving the minimum β). In contrast, there was an ambiguous difference between these conditions for optimizing the second order hyper-polarizability (γ) because of the small absolute value of γ and the limitation of numerical differential calculations in the FF method. It can be concluded that the ab initio level property optimization method introduced here can be an effective step towards an advanced computer aided material design method as long as the numerical limitation of the FF method is taken into account.« less

Automated property optimization via ab initio O(N) elongation method: Application to (hyper-)polarizability in DNA.

PubMed

Orimoto, Yuuichi; Aoki, Yuriko

2016-07-14

An automated property optimization method was developed based on the ab initio O(N) elongation (ELG) method and applied to the optimization of nonlinear optical (NLO) properties in DNA as a first test. The ELG method mimics a polymerization reaction on a computer, and the reaction terminal of a starting cluster is attacked by monomers sequentially to elongate the electronic structure of the system by solving in each step a limited space including the terminal (localized molecular orbitals at the terminal) and monomer. The ELG-finite field (ELG-FF) method for calculating (hyper-)polarizabilities was used as the engine program of the optimization method, and it was found to show linear scaling efficiency while maintaining high computational accuracy for a random sequenced DNA model. Furthermore, the self-consistent field convergence was significantly improved by using the ELG-FF method compared with a conventional method, and it can lead to more feasible NLO property values in the FF treatment. The automated optimization method successfully chose an appropriate base pair from four base pairs (A, T, G, and C) for each elongation step according to an evaluation function. From test optimizations for the first order hyper-polarizability (β) in DNA, a substantial difference was observed depending on optimization conditions between "choose-maximum" (choose a base pair giving the maximum β for each step) and "choose-minimum" (choose a base pair giving the minimum β). In contrast, there was an ambiguous difference between these conditions for optimizing the second order hyper-polarizability (γ) because of the small absolute value of γ and the limitation of numerical differential calculations in the FF method. It can be concluded that the ab initio level property optimization method introduced here can be an effective step towards an advanced computer aided material design method as long as the numerical limitation of the FF method is taken into account.

The accuracy of ab initio calculations without ab initio calculations for charged systems: Kriging predictions of atomistic properties for ions in aqueous solutions

NASA Astrophysics Data System (ADS)

Di Pasquale, Nicodemo; Davie, Stuart J.; Popelier, Paul L. A.

2018-06-01

Using the machine learning method kriging, we predict the energies of atoms in ion-water clusters, consisting of either Cl- or Na+ surrounded by a number of water molecules (i.e., without Na+Cl- interaction). These atomic energies are calculated following the topological energy partitioning method called Interacting Quantum Atoms (IQAs). Kriging predicts atomic properties (in this case IQA energies) by a model that has been trained over a small set of geometries with known property values. The results presented here are part of the development of an advanced type of force field, called FFLUX, which offers quantum mechanical information to molecular dynamics simulations without the limiting computational cost of ab initio calculations. The results reported for the prediction of the IQA components of the energy in the test set exhibit an accuracy of a few kJ/mol, corresponding to an average error of less than 5%, even when a large cluster of water molecules surrounding an ion is considered. Ions represent an important chemical system and this work shows that they can be correctly taken into account in the framework of the FFLUX force field.

Extracting DNA words based on the sequence features: non-uniform distribution and integrity.

PubMed

Li, Zhi; Cao, Hongyan; Cui, Yuehua; Zhang, Yanbo

2016-01-25

DNA sequence can be viewed as an unknown language with words as its functional units. Given that most sequence alignment algorithms such as the motif discovery algorithms depend on the quality of background information about sequences, it is necessary to develop an ab initio algorithm for extracting the "words" based only on the DNA sequences. We considered that non-uniform distribution and integrity were two important features of a word, based on which we developed an ab initio algorithm to extract "DNA words" that have potential functional meaning. A Kolmogorov-Smirnov test was used for consistency test of uniform distribution of DNA sequences, and the integrity was judged by the sequence and position alignment. Two random base sequences were adopted as negative control, and an English book was used as positive control to verify our algorithm. We applied our algorithm to the genomes of Saccharomyces cerevisiae and 10 strains of Escherichia coli to show the utility of the methods. The results provide strong evidences that the algorithm is a promising tool for ab initio building a DNA dictionary. Our method provides a fast way for large scale screening of important DNA elements and offers potential insights into the understanding of a genome.

Ab Initio and Analytic Intermolecular Potentials for Ar-CF₄

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vayner, Grigoriy; Alexeev, Yuri; Wang, Jiangping

2006-03-09

Ab initio calculations at the CCSD(T) level of theory are performed to characterize the Ar + CF ₄ intermolecular potential. Extensive calculations, with and without a correction for basis set superposition error (BSSE), are performed with the cc-pVTZ basis set. Additional calculations are performed with other correlation consistent (cc) basis sets to extrapolate the Ar---CF₄potential energy minimum to the complete basis set (CBS) limit. Both the size of the basis set and BSSE have substantial effects on the Ar + CF₄ potential. Calculations with the cc-pVTZ basis set and without a BSSE correction, appear to give a good representation ofmore » the potential at the CBS limit and with a BSSE correction. In addition, MP2 theory is found to give potential energies in very good agreement with those determined by the much higher level CCSD(T) theory. Two analytic potential energy functions were determined for Ar + CF₄by fitting the cc-pVTZ calculations both with and without a BSSE correction. These analytic functions were written as a sum of two body potentials and excellent fits to the ab initio potentials were obtained by representing each two body interaction as a Buckingham potential.« less

Ab-Initio Description and Prediction of Properties of Carbon-Based and Other Non-Metallic Materials

NASA Technical Reports Server (NTRS)

Bagayoko, D.; Zhao, G. L.; Hasan, S.

2001-01-01

We have resolved the long-standing problem consisting of 30%-50% theoretical underestimates of the band gaps of non-metallic materials. We describe the Bagayoko, Zhao, and Williams (BZW) method that rigorously circumvents the basis-set and variational effect presumed to be a cause of these underestimates. We present ab-initio, computational results that are in agreement with experiment for diamond (C), silicon (Si), silicon carbides (3C-SiC and 4H-SiC), and other semiconductors (GaN, BaTiO3, AlN, ZnSe, ZnO). We illustrate the predictive capability of the BZW method in the case of the newly discovered cubic phase of silicon nitride (c-Si3N4) and of selected carbon nanotabes [(10,0), and (8,4)]. Our conclusion underscores the inescapable need for the BZW method in ab-initio calculations that employ a basis set in a variational approach. Current nanoscale trends amplify this need. We estimate that the potential impact of applications of the BZW method in advancing our understanding of nonmetallic materials, in informing experiment, and particularly in guiding device design and fabrication is simply priceless.

A full-dimensional ab initio potential energy surface and rovibrational energies of the Ar–HF complex

NASA Astrophysics Data System (ADS)

Huang, Jing; Zhou, Yanzi; Xie, Daiqian

2018-04-01

We report a new full-dimensional ab initio potential energy surface for the Ar-HF van der Waals complex at the level of coupled-cluster singles and doubles with noniterative inclusion of connected triples levels [CCSD(T)] using augmented correlation-consistent quintuple-zeta basis set (aV5Z) plus bond functions. Full counterpoise correction was employed to correct the basis-set superposition error. The hypersurface was fitted using artificial neural network method with a root mean square error of 0.1085 cm-1 for more than 8000 ab initio points. The complex was found to prefer a linear Ar-H-F equilibrium structure. The three-dimensional discrete variable representation method and the Lanczos propagation algorithm were then employed to calculate the rovibrational states without separating inter- and intra- molecular nuclear motions. The calculated vibrational energies of Ar-HF differ from the experiment values within about 1 cm-1 on the first four HF vibrational states, and the predicted pure rotational energies on (0000) and (1000) vibrational states are deviated from the observed value by about 1%, which shows the accuracy of our new PES.

Length-dependence of intramolecular electron transfer in σ-bonded rigid molecular rods: an ab initio molecular orbital study

NASA Astrophysics Data System (ADS)

Pati, Ranjit; Karna, Shashi P.

2002-01-01

The dependence of electron transfer (ET) coupling element, VAB, on the length of rigid-rod-like systems consisting of bicyclo[1.1.1]pentane (BCP), cubane (CUB), and bicyclo[2.2.2]octane (BCO) monomers, has been investigated with the use of ab initio Hartree-Fock (HF) method employing Marcus-Hush two-state (TS) model. The value of VAB decreases exponentially with increase in the number of the cage units of the σ-bonded molecules. The calculated decay constant, β, shows good agreement with previously reported data. For molecular length⩾15 Å, the value of VAB becomes negligibly small, suggesting complete suppression of the through bond direct tunneling contribution to ET process.

Experimental and ab initio molecular dynamics simulation studies of liquid Al60Cu40 alloy

NASA Astrophysics Data System (ADS)

Wang, S. Y.; Kramer, M. J.; Xu, M.; Wu, S.; Hao, S. G.; Sordelet, D. J.; Ho, K. M.; Wang, C. Z.

2009-04-01

X-ray diffraction and ab initio molecular dynamics simulation studies of molten Al60Cu40 have been carried out between 973 and 1323 K. The structures obtained from our simulated atomic models are fully consistent with the experimental results. The local structures of the models analyzed using Honeycutt-Andersen and Voronoi tessellation methods clearly demonstrate that as the temperatures of the liquid is lowered it becomes more ordered. While no one cluster-type dominates the local structure of this liquid, the most prevalent polyhedra in the liquid structure can be described as distorted icosahedra. No obvious correlations between the clusters observed in the liquid and known stable crystalline phases in this system were observed.

Collisional excitation of interstellar PO(X2Π) by He: new ab initio potential energy surfaces and scattering calculations

NASA Astrophysics Data System (ADS)

Lique, François; Jiménez-Serra, Izaskun; Viti, Serena; Marinakis, Sarantos

2018-01-01

We present the first ab initio potential energy surfaces (PESs) for the PO(X2Π)-He van der Waals system. The PESs were obtained using the open-shell partially spin-restricted coupled cluster approach with single, double and perturbative triple excitations [UCCSD(T)]. The augmented correlation-consistent polarized valence triple-zeta (aug-cc-pVTZ) basis set was employed supplemented by mid-bond functions. Integral and differential cross sections for the rotational excitation in PO-He collisions were calculated using the new PES and compared with results in similar systems. Finally, our work presents the first hyperfine-resolved cross sections for this system that are needed for accurate modelling in astrophysical environments.

Ab initio study of the chlorine nitrate protonation reaction - Implications for loss of ClONO2 in the stratosphere

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Rice, Julia E.

1993-01-01

Ab initio quantum mechanical methods, including coupled-cluster theory, are used to determine the equilibrium geometries, dipole moments, and harmonic vibrational frequencies of ClONO2, NO2(+), and four isomers of protonated ClONO2. It was found that, for the equilibrium structures and harmonic frequencies of ClONO2, HOCl, and NO2(+), the highest-level theoretical predictions are consistent with the available experimental information concerning the reactions of ClONO2 and HOCl with HCl on the surface of polar stratospheric clouds (PSCs). The study supports a recent hypothesis that the reaction of ClONO2 on the surface of PSCs is proton catalyzed, although the mechanism is different.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pigozzi, Giancarlo; Janczak-Rusch, Jolanta; Passerone, Daniele

2012-10-29

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

40 CFR 92.306 - Certification.

Code of Federal Regulations, 2010 CFR

2010-07-01

... certificate of conformity for such engine families. The certificate of conformity may be voided ab initio for..., and the certificate may be deemed void ab initio. (3) The manufacturer or remanufacturer (as...

40 CFR 92.306 - Certification.

Code of Federal Regulations, 2012 CFR

2012-07-01

... certificate of conformity for such engine families. The certificate of conformity may be voided ab initio for..., and the certificate may be deemed void ab initio. (3) The manufacturer or remanufacturer (as...

40 CFR 92.306 - Certification.

Code of Federal Regulations, 2013 CFR

2013-07-01

... certificate of conformity for such engine families. The certificate of conformity may be voided ab initio for..., and the certificate may be deemed void ab initio. (3) The manufacturer or remanufacturer (as...

40 CFR 92.306 - Certification.

Code of Federal Regulations, 2014 CFR

2014-07-01

... certificate of conformity for such engine families. The certificate of conformity may be voided ab initio for..., and the certificate may be deemed void ab initio. (3) The manufacturer or remanufacturer (as...

40 CFR 92.306 - Certification.

Code of Federal Regulations, 2011 CFR

2011-07-01

... certificate of conformity for such engine families. The certificate of conformity may be voided ab initio for..., and the certificate may be deemed void ab initio. (3) The manufacturer or remanufacturer (as...

Carbon diffusion in molten uranium: an ab initio molecular dynamics study

NASA Astrophysics Data System (ADS)

Garrett, Kerry E.; Abrecht, David G.; Kessler, Sean H.; Henson, Neil J.; Devanathan, Ram; Schwantes, Jon M.; Reilly, Dallas D.

2018-04-01

In this work we used ab initio molecular dynamics within the framework of density functional theory and the projector-augmented wave method to study carbon diffusion in liquid uranium at temperatures above 1600 K. The electronic interactions of carbon and uranium were described using the local density approximation (LDA). The self-diffusion of uranium based on this approach is compared with literature computational and experimental results for liquid uranium. The temperature dependence of carbon and uranium diffusion in the melt was evaluated by fitting the resulting diffusion coefficients to an Arrhenius relationship. We found that the LDA calculated activation energy for carbon was nearly twice that of uranium: 0.55 ± 0.03 eV for carbon compared to 0.32 ± 0.04 eV for uranium. Structural analysis of the liquid uranium-carbon system is also discussed.

Lithium cluster anions: photoelectron spectroscopy and ab initio calculations.

PubMed

Alexandrova, Anastassia N; Boldyrev, Alexander I; Li, Xiang; Sarkas, Harry W; Hendricks, Jay H; Arnold, Susan T; Bowen, Kit H

2011-01-28

Structural and energetic properties of small, deceptively simple anionic clusters of lithium, Li(n)(-), n = 3-7, were determined using a combination of anion photoelectron spectroscopy and ab initio calculations. The most stable isomers of each of these anions, the ones most likely to contribute to the photoelectron spectra, were found using the gradient embedded genetic algorithm program. Subsequently, state-of-the-art ab initio techniques, including time-dependent density functional theory, coupled cluster, and multireference configurational interactions methods, were employed to interpret the experimental spectra.

21 CFR 201.150 - Drugs; processing, labeling, or repacking.

Code of Federal Regulations, 2010 CFR

2010-04-01

... part thereof, from such establishment, become void ab initio if the drug comprising such shipment... ab initio with respect to the person who introduced such shipment or delivery into interstate...

21 CFR 201.150 - Drugs; processing, labeling, or repacking.

Code of Federal Regulations, 2013 CFR

2013-04-01

... part thereof, from such establishment, become void ab initio if the drug comprising such shipment... ab initio with respect to the person who introduced such shipment or delivery into interstate...

40 CFR 86.094-30 - Certification.

Code of Federal Regulations, 2014 CFR

2014-07-01

..., the Administrator may deem such certificate void ab initio. (4) In any case in which certification of... fraud or other misconduct as makes the certification invalid ab initio. (6) The manufacturer may request...

21 CFR 201.150 - Drugs; processing, labeling, or repacking.

Code of Federal Regulations, 2012 CFR

2012-04-01

... part thereof, from such establishment, become void ab initio if the drug comprising such shipment... ab initio with respect to the person who introduced such shipment or delivery into interstate...

21 CFR 201.150 - Drugs; processing, labeling, or repacking.

Code of Federal Regulations, 2011 CFR

2011-04-01

... part thereof, from such establishment, become void ab initio if the drug comprising such shipment... ab initio with respect to the person who introduced such shipment or delivery into interstate...

21 CFR 201.150 - Drugs; processing, labeling, or repacking.

Code of Federal Regulations, 2014 CFR

2014-04-01

... part thereof, from such establishment, become void ab initio if the drug comprising such shipment... ab initio with respect to the person who introduced such shipment or delivery into interstate...

40 CFR 94.208 - Certification.

Code of Federal Regulations, 2010 CFR

2010-07-01

... ab initio. (5) In any case in which certification of an engine is to be withheld, denied, revoked or... makes the certification invalid ab initio. (7) The manufacturer may request, within 30 days of receiving...

40 CFR 92.208 - Certification.

Code of Federal Regulations, 2013 CFR

2013-07-01

... such certificate void ab initio. (5) In any case in which certification of a locomotive or locomotive..., except in cases of such fraud or other misconduct that makes the certification invalid ab initio. (7) The...

40 CFR 94.208 - Certification.

Code of Federal Regulations, 2012 CFR

2012-07-01

... ab initio. (5) In any case in which certification of an engine is to be withheld, denied, revoked or... makes the certification invalid ab initio. (7) The manufacturer may request, within 30 days of receiving...

40 CFR 94.208 - Certification.

Code of Federal Regulations, 2011 CFR

2011-07-01

... ab initio. (5) In any case in which certification of an engine is to be withheld, denied, revoked or... makes the certification invalid ab initio. (7) The manufacturer may request, within 30 days of receiving...

40 CFR 92.208 - Certification.

Code of Federal Regulations, 2011 CFR

2011-07-01

... such certificate void ab initio. (5) In any case in which certification of a locomotive or locomotive..., except in cases of such fraud or other misconduct that makes the certification invalid ab initio. (7) The...

40 CFR 94.208 - Certification.

Code of Federal Regulations, 2013 CFR

2013-07-01

... ab initio. (5) In any case in which certification of an engine is to be withheld, denied, revoked or... makes the certification invalid ab initio. (7) The manufacturer may request, within 30 days of receiving...

40 CFR 92.208 - Certification.

Code of Federal Regulations, 2012 CFR

2012-07-01

... such certificate void ab initio. (5) In any case in which certification of a locomotive or locomotive..., except in cases of such fraud or other misconduct that makes the certification invalid ab initio. (7) The...

40 CFR 92.208 - Certification.

Code of Federal Regulations, 2014 CFR

2014-07-01

... such certificate void ab initio. (5) In any case in which certification of a locomotive or locomotive..., except in cases of such fraud or other misconduct that makes the certification invalid ab initio. (7) The...

40 CFR 94.208 - Certification.

Code of Federal Regulations, 2014 CFR

2014-07-01

... ab initio. (5) In any case in which certification of an engine is to be withheld, denied, revoked or... makes the certification invalid ab initio. (7) The manufacturer may request, within 30 days of receiving...

Evaluating High-Throughput Ab Initio Gene Finders to Discover Proteins Encoded in Eukaryotic Pathogen Genomes Missed by Laboratory Techniques

PubMed Central

Goodswen, Stephen J.; Kennedy, Paul J.; Ellis, John T.

2012-01-01

Next generation sequencing technology is advancing genome sequencing at an unprecedented level. By unravelling the code within a pathogen’s genome, every possible protein (prior to post-translational modifications) can theoretically be discovered, irrespective of life cycle stages and environmental stimuli. Now more than ever there is a great need for high-throughput ab initio gene finding. Ab initio gene finders use statistical models to predict genes and their exon-intron structures from the genome sequence alone. This paper evaluates whether existing ab initio gene finders can effectively predict genes to deduce proteins that have presently missed capture by laboratory techniques. An aim here is to identify possible patterns of prediction inaccuracies for gene finders as a whole irrespective of the target pathogen. All currently available ab initio gene finders are considered in the evaluation but only four fulfil high-throughput capability: AUGUSTUS, GeneMark_hmm, GlimmerHMM, and SNAP. These gene finders require training data specific to a target pathogen and consequently the evaluation results are inextricably linked to the availability and quality of the data. The pathogen, Toxoplasma gondii, is used to illustrate the evaluation methods. The results support current opinion that predicted exons by ab initio gene finders are inaccurate in the absence of experimental evidence. However, the results reveal some patterns of inaccuracy that are common to all gene finders and these inaccuracies may provide a focus area for future gene finder developers. PMID:23226328

Theoretical study of the dipole moments of selected alkaline-earth halides

NASA Technical Reports Server (NTRS)

Langhoff, S. R.; Bauschlicher, C. W., Jr.; Partridge, H.; Ahlrichs, R.

1986-01-01

Ab initio calculations at the self-consistent-field (SCF), singles-plus-doubles configuration-interaction (SDCI), and coupled-pair functional (CPF) level, are reported for the dipole moments and dipole derivatives of the X2Sigma(+) ground states of BeF, BeCl, MgF, MgCl, CaF, CaCl, and SrF. For comparison, analogous calculations are performed for the X1Sigma(+) state of KCl. The CPF results are found to be in remarkably better agreement with experiment than are the SCF and SDCI results. Apparently higher excitations are required to properly describe the radial extent along the bond axis of the remaining valence electron on the alkaline-earth metal.

Ab initio simulations of the dynamic ion structure factor of warm dense lithium

DOE PAGES

Witte, B. B. L.; Shihab, M.; Glenzer, S. H.; ...

2017-04-06

Here, we present molecular dynamics simulations based on finite-temperature density functional theory that determine self-consistently the dynamic ion structure factor and the electronic form factor in lithium. Our comprehensive data set allows for the calculation of the dispersion relation for collective excitations, the calculation of the sound velocity, and the determination of the ion feature from the total electronic form factor and the ion structure factor. The results are compared with available experimental x-ray and neutron scattering data. Good agreement is found for both the liquid metal and warm dense matter domain. Finally, we study the impact of possible targetmore » inhomogeneities on x-ray scattering spectra.« less

Ab initio simulations of the dynamic ion structure factor of warm dense lithium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Witte, B. B. L.; Shihab, M.; Glenzer, S. H.

Here, we present molecular dynamics simulations based on finite-temperature density functional theory that determine self-consistently the dynamic ion structure factor and the electronic form factor in lithium. Our comprehensive data set allows for the calculation of the dispersion relation for collective excitations, the calculation of the sound velocity, and the determination of the ion feature from the total electronic form factor and the ion structure factor. The results are compared with available experimental x-ray and neutron scattering data. Good agreement is found for both the liquid metal and warm dense matter domain. Finally, we study the impact of possible targetmore » inhomogeneities on x-ray scattering spectra.« less

77 FR 21154 - BNSF Railway Company-Abandonment Exemption-in Oklahoma County, OK

Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-09

... proceeding and reject BNSF's notice of exemption as void ab initio on the grounds that BNSF had provided... misleading information, the exemption is void ab initio. BNSF has filed a combined environmental and historic... DEPARTMENT OF TRANSPORTATION Surface Transportation Board [Docket No. AB 6 (Sub-No. 480X)] BNSF...

DSMC study of oxygen shockwaves based on high-fidelity vibrational relaxation and dissociation models

NASA Astrophysics Data System (ADS)

Borges Sebastião, Israel; Kulakhmetov, Marat; Alexeenko, Alina

2017-01-01

This work evaluates high-fidelity vibrational-translational (VT) energy relaxation and dissociation models for pure O2 normal shockwave simulations with the direct simulation Monte Carlo (DSMC) method. The O2-O collisions are described using ab initio state-specific relaxation and dissociation models. The Macheret-Fridman (MF) dissociation model is adapted to the DSMC framework by modifying the standard implementation of the total collision energy (TCE) model. The O2-O2 dissociation is modeled with this TCE+MF approach, which is calibrated with O2-O ab initio data and experimental equilibrium dissociation rates. The O2-O2 vibrational relaxation is modeled via the Larsen-Borgnakke model, calibrated to experimental VT rates. All the present results are compared to experimental data and previous calculations available in the literature. It is found that, in general, the ab initio dissociation model is better than the TCE model at matching the shock experiments. Therefore, when available, efficient ab initio models are preferred over phenomenological models. We also show that the proposed TCE + MF formulation can be used to improve the standard TCE model results when ab initio data are not available or limited.

Multiple time step integrators in ab initio molecular dynamics.

PubMed

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

2014-02-28

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

21 CFR 701.9 - Exemptions from labeling requirements.

Code of Federal Regulations, 2010 CFR

2010-04-01

..., become void ab initio if the cosmetic comprising such shipment, delivery, or part is adulterated or... a cosmetic under paragraph (a)(2) of this section shall become void ab initio with respect to the...

Extended Lagrangian Excited State Molecular Dynamics

DOE PAGES

Bjorgaard, Josiah August; Sheppard, Daniel Glen; Tretiak, Sergei; ...

2018-01-09

In this work, an extended Lagrangian framework for excited state molecular dynamics (XL-ESMD) using time-dependent self-consistent field theory is proposed. The formulation is a generalization of the extended Lagrangian formulations for ground state Born–Oppenheimer molecular dynamics [Phys. Rev. Lett. 2008 100, 123004]. The theory is implemented, demonstrated, and evaluated using a time-dependent semiempirical model, though it should be generally applicable to ab initio theory. The simulations show enhanced energy stability and a significantly reduced computational cost associated with the iterative solutions of both the ground state and the electronically excited states. Relaxed convergence criteria can therefore be used both formore » the self-consistent ground state optimization and for the iterative subspace diagonalization of the random phase approximation matrix used to calculate the excited state transitions. In conclusion, the XL-ESMD approach is expected to enable numerically efficient excited state molecular dynamics for such methods as time-dependent Hartree–Fock (TD-HF), Configuration Interactions Singles (CIS), and time-dependent density functional theory (TD-DFT).« less

Extended Lagrangian Excited State Molecular Dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bjorgaard, Josiah August; Sheppard, Daniel Glen; Tretiak, Sergei

In this work, an extended Lagrangian framework for excited state molecular dynamics (XL-ESMD) using time-dependent self-consistent field theory is proposed. The formulation is a generalization of the extended Lagrangian formulations for ground state Born–Oppenheimer molecular dynamics [Phys. Rev. Lett. 2008 100, 123004]. The theory is implemented, demonstrated, and evaluated using a time-dependent semiempirical model, though it should be generally applicable to ab initio theory. The simulations show enhanced energy stability and a significantly reduced computational cost associated with the iterative solutions of both the ground state and the electronically excited states. Relaxed convergence criteria can therefore be used both formore » the self-consistent ground state optimization and for the iterative subspace diagonalization of the random phase approximation matrix used to calculate the excited state transitions. In conclusion, the XL-ESMD approach is expected to enable numerically efficient excited state molecular dynamics for such methods as time-dependent Hartree–Fock (TD-HF), Configuration Interactions Singles (CIS), and time-dependent density functional theory (TD-DFT).« less

Extended Lagrangian Excited State Molecular Dynamics.

PubMed

Bjorgaard, J A; Sheppard, D; Tretiak, S; Niklasson, A M N

2018-02-13

An extended Lagrangian framework for excited state molecular dynamics (XL-ESMD) using time-dependent self-consistent field theory is proposed. The formulation is a generalization of the extended Lagrangian formulations for ground state Born-Oppenheimer molecular dynamics [Phys. Rev. Lett. 2008 100, 123004]. The theory is implemented, demonstrated, and evaluated using a time-dependent semiempirical model, though it should be generally applicable to ab initio theory. The simulations show enhanced energy stability and a significantly reduced computational cost associated with the iterative solutions of both the ground state and the electronically excited states. Relaxed convergence criteria can therefore be used both for the self-consistent ground state optimization and for the iterative subspace diagonalization of the random phase approximation matrix used to calculate the excited state transitions. The XL-ESMD approach is expected to enable numerically efficient excited state molecular dynamics for such methods as time-dependent Hartree-Fock (TD-HF), Configuration Interactions Singles (CIS), and time-dependent density functional theory (TD-DFT).

AFLOW-SYM: platform for the complete, automatic and self-consistent symmetry analysis of crystals.

PubMed

Hicks, David; Oses, Corey; Gossett, Eric; Gomez, Geena; Taylor, Richard H; Toher, Cormac; Mehl, Michael J; Levy, Ohad; Curtarolo, Stefano

2018-05-01

Determination of the symmetry profile of structures is a persistent challenge in materials science. Results often vary amongst standard packages, hindering autonomous materials development by requiring continuous user attention and educated guesses. This article presents a robust procedure for evaluating the complete suite of symmetry properties, featuring various representations for the point, factor and space groups, site symmetries and Wyckoff positions. The protocol determines a system-specific mapping tolerance that yields symmetry operations entirely commensurate with fundamental crystallographic principles. The self-consistent tolerance characterizes the effective spatial resolution of the reported atomic positions. The approach is compared with the most used programs and is successfully validated against the space-group information provided for over 54 000 entries in the Inorganic Crystal Structure Database (ICSD). Subsequently, a complete symmetry analysis is applied to all 1.7+ million entries of the AFLOW data repository. The AFLOW-SYM package has been implemented in, and made available for, public use through the automated ab initio framework AFLOW.

Clustering/anticlustering effects on the GeSi Raman spectra at moderate (Ge,Si) contents: Percolation scheme vs. ab initio calculations

NASA Astrophysics Data System (ADS)

Torres, V. J. B.; Hajj Hussein, R.; Pagès, O.; Rayson, M. J.

2017-02-01

We test a presumed ability behind the phenomenological percolation scheme used for the basic description of the multi-mode Raman spectra of mixed crystals at one dimension along the linear chain approximation, to determine, via the Raman intensities, the nature of the atom substitution, as to whether this is random or due to local clustering/anticlustering. For doing so, we focus on the model percolation-type GeySi1-y system characterized by six oscillators { 1 × ( G e - G e ) , 3 × ( G e - S i ) , 2 × ( S i - S i ) } and place the study around the critical compositions y ˜ (0.16, 0.71, and 0.84) corresponding to nearly matching of intensities between the like Raman modes from a given multiplet ( G e - S i triplet or S i - S i doublet). The interplay between the GeySi1-y Raman intensities predicted by the percolation scheme depending on a suitable order parameter κ of local clustering/anticlustering is found to be consistent with ab initio calculations of the GeySi1-y Raman spectra done with the Ab Initio Modeling PROgram code using large (64-, 216-, and 512-atoms) disordered cubic supercells matching the required ( y , κ ) values. The actual "percolation vs. ab initio" comparative insight at moderate/dilute-(Ge,Si) limits, with an emphasis on the κ -induced intra-bond transfer of oscillator strength, extends a pioneering one earlier achieved at an intermediate composition ( y ˜ 0.50) by using small (32-atom) supercells [O. Pagès et al., J. Appl. Phys. 114, 033513 (2013)], mainly concerned with the inter-bond transfer of oscillator strength, providing altogether a complete picture.

Magnetic Transitions in Iron Porphyrin Halides by Inelastic Neutron Scattering and Ab-initio Studies of Zero-Field Splittings

DOE PAGES

Stavretis, Shelby E.; Atanasov, Mihail; Podlesnyak, Andrey A.; ...

2015-10-02

Zero-field splitting (ZFS) parameters of nondeuterated metalloporphyrins [Fe(TPP)X] (X = F, Br, I; H 2TPP = tetraphenylporphyrin) are determined by inelastic neutron scattering (INS). The ZFS values are D = 4.49(9) cm –1 for tetragonal polycrystalline [Fe(TPP)F], and D = 8.8(2) cm –1, E = 0.1(2) cm –1 and D = 13.4(6) cm –1, E = 0.3(6) cm –1 for monoclinic polycrystalline [Fe(TPP)Br] and [Fe(TPP)I], respectively. Along with our recent report of the ZFS value of D = 6.33(8) cm –1 for tetragonal polycrystalline [Fe(TPP)Cl], these data provide a rare, complete determination of ZFS parameters in a metalloporphyrin halide series.more » The electronic structure of [Fe(TPP)X] (X = F, Cl, Br, I) has been studied by multireference ab initio methods: the complete active space self-consistent field (CASSCF) and the N-electron valence perturbation theory (NEVPT2) with the aim of exploring the origin of the large and positive zero-field splitting D of the 6A 1 ground state. D was calculated from wave functions of the electronic multiplets spanned by the d 5 configuration of Fe(III) along with spin–orbit coupling accounted for by quasi degenerate perturbation theory. Results reproduce trends of D from inelastic neutron scattering data increasing in the order from F, Cl, Br, to I. A mapping of energy eigenvalues and eigenfunctions of the S = 3/2 excited states on ligand field theory was used to characterize the σ- and π-antibonding effects decreasing from F to I. This is in agreement with similar results deduced from ab initio calculations on CrX 6 3- complexes and also with the spectrochemical series showing a decrease of the ligand field in the same directions. A correlation is found between the increase of D and decrease of the π- and σ-antibonding energies e λ X (λ = σ, π) in the series from X = F to I. Analysis of this correlation using second-order perturbation theory expressions in terms of angular overlap parameters rationalizes the experimentally deduced trend. Furthermore, D parameters from CASSCF and NEVPT2 results have been calibrated against those from the INS data, yielding a predictive power of these approaches. Methods to improve the quantitative agreement between ab initio calculated and experimental D and spectroscopic transitions for high-spin Fe(III) complexes are proposed.« less

Magnetic Transitions in Iron Porphyrin Halides by Inelastic Neutron Scattering and Ab Initio Studies of Zero-Field Splittings.

PubMed

Stavretis, Shelby E; Atanasov, Mihail; Podlesnyak, Andrey A; Hunter, Seth C; Neese, Frank; Xue, Zi-Ling

2015-10-19

Zero-field splitting (ZFS) parameters of nondeuterated metalloporphyrins [Fe(TPP)X] (X = F, Br, I; H₂TPP = tetraphenylporphyrin) have been directly determined by inelastic neutron scattering (INS). The ZFS values are D = 4.49(9) cm⁻¹ for tetragonal polycrystalline [Fe(TPP)F], and D = 8.8(2) cm⁻¹, E = 0.1(2) cm⁻¹ and D = 13.4(6) cm⁻¹, E = 0.3(6) cm⁻¹ for monoclinic polycrystalline [Fe(TPP)Br] and [Fe(TPP)I], respectively. Along with our recent report of the ZFS value of D = 6.33(8) cm⁻¹ for tetragonal polycrystalline [Fe(TPP)Cl], these data provide a rare, complete determination of ZFS parameters in a metalloporphyrin halide series. The electronic structure of [Fe(TPP)X] (X = F, Cl, Br, I) has been studied by multireference ab initio methods: the complete active space self-consistent field (CASSCF) and the N-electron valence perturbation theory (NEVPT2) with the aim of exploring the origin of the large and positive zero-field splitting D of the ⁶A₁ ground state. D was calculated from wave functions of the electronic multiplets spanned by the d⁵ configuration of Fe(III) along with spin–orbit coupling accounted for by quasi degenerate perturbation theory. Results reproduce trends of D from inelastic neutron scattering data increasing in the order from F, Cl, Br, to I. A mapping of energy eigenvalues and eigenfunctions of the S = 3/2 excited states on ligand field theory was used to characterize the σ- and π-antibonding effects decreasing from F to I. This is in agreement with similar results deduced from ab initio calculations on CrX₆³⁻ complexes and also with the spectrochemical series showing a decrease of the ligand field in the same directions. A correlation is found between the increase of D and decrease of the π- and σ-antibonding energies e(λ)(X) (λ = σ, π) in the series from X = F to I. Analysis of this correlation using second-order perturbation theory expressions in terms of angular overlap parameters rationalizes the experimentally deduced trend. D parameters from CASSCF and NEVPT2 results have been calibrated against those from the INS data, yielding a predictive power of these approaches. Methods to improve the quantitative agreement between ab initio calculated and experimental D and spectroscopic transitions for high-spin Fe(III) complexes are proposed.

An ab initio global potential-energy surface for NH2(A(2)A') and vibrational spectrum of the Renner-Teller A(2)A'-X(2)A" system.

PubMed

Zhou, Shulan; Li, Zheng; Xie, Daiqian; Lin, Shi Ying; Guo, Hua

2009-05-14

A global potential-energy surface for the first excited electronic state of NH(2)(A(2)A(')) has been constructed by three-dimensional cubic spline interpolation of more than 20,000 ab initio points, which were calculated at the multireference configuration-interaction level with the Davidson correction using the augmented correlation-consistent polarized valence quadruple-zeta basis set. The (J=0) vibrational energy levels for the ground (X(2)A(")) and excited (A(2)A(')) electronic states of NH(2) were calculated on our potential-energy surfaces with the diagonal Renner-Teller terms. The results show a good agreement with the experimental vibrational frequencies of NH(2) and its isotopomers.

Ab initio/DFT/GIAO-CCSD(T) calculational study of the t-butyl cation: comparison of experimental data with structures, energetics, IR vibrational frequencies, and 13C NMR chemical shifts indicating preferred C(s) conformation.

PubMed

Rasul, Golam; Chen, Jonathan L; Prakash, G K Surya; Olah, George A

2009-06-18

The C(s) conformation of the tert-butyl cation 3 was established to be the preferred global energy minimum using a combination of ab initio, DFT, and CCSD(T) methodology with correlation-consistent basis sets. The potential energy surface of methyl rotation involving the C(3v), C(s), and C(3h) forms, however, in accord with previous studies, is quite flat. The computed IR absorptions of 3 indicate that it has the greatest degree of electron donation from C-H bonds into the C(+)-C bonds. The experimental (13)C NMR chemical shifts also agree very well with the experimental data.

21 CFR 801.150 - Medical devices; processing, labeling, or repacking.

Code of Federal Regulations, 2010 CFR

2010-04-01

... such shipment or delivery, or any part thereof, from such establishment, become void ab initio if the...)(2) of this section shall become void ab initio with respect to the person who introduced such...

40 CFR 86.442-78 - Denial, revocation, or suspension of certification.

Code of Federal Regulations, 2010 CFR

2010-07-01

... ab initio. (d) In any case in which certification of a vehicle is proposed to be withheld, denied... fraud or other misconduct as makes the certification invalid ab initio. (f) The manufacturer may request...

40 CFR 86.442-78 - Denial, revocation, or suspension of certification.

Code of Federal Regulations, 2014 CFR

2014-07-01

... ab initio. (d) In any case in which certification of a vehicle is proposed to be withheld, denied... fraud or other misconduct as makes the certification invalid ab initio. (f) The manufacturer may request...

40 CFR 86.442-78 - Denial, revocation, or suspension of certification.

Code of Federal Regulations, 2012 CFR

2012-07-01

... ab initio. (d) In any case in which certification of a vehicle is proposed to be withheld, denied... fraud or other misconduct as makes the certification invalid ab initio. (f) The manufacturer may request...

40 CFR 86.442-78 - Denial, revocation, or suspension of certification.

Code of Federal Regulations, 2013 CFR

2013-07-01

... ab initio. (d) In any case in which certification of a vehicle is proposed to be withheld, denied... fraud or other misconduct as makes the certification invalid ab initio. (f) The manufacturer may request...

40 CFR 86.442-78 - Denial, revocation, or suspension of certification.

Code of Federal Regulations, 2011 CFR

2011-07-01

... ab initio. (d) In any case in which certification of a vehicle is proposed to be withheld, denied... fraud or other misconduct as makes the certification invalid ab initio. (f) The manufacturer may request...

21 CFR 501.100 - Animal food; exemptions from labeling.

Code of Federal Regulations, 2014 CFR

2014-04-01

... become void ab initio if the food comprising such shipment, delivery, or part is adulterated or... a food under paragraph (d)(2) of this section shall become void ab initio with respect to the person...

21 CFR 801.150 - Medical devices; processing, labeling, or repacking.

Code of Federal Regulations, 2014 CFR

2014-04-01

... such shipment or delivery, or any part thereof, from such establishment, become void ab initio if the...)(2) of this section shall become void ab initio with respect to the person who introduced such...

21 CFR 801.150 - Medical devices; processing, labeling, or repacking.

Code of Federal Regulations, 2011 CFR

2011-04-01

... such shipment or delivery, or any part thereof, from such establishment, become void ab initio if the...)(2) of this section shall become void ab initio with respect to the person who introduced such...

21 CFR 801.150 - Medical devices; processing, labeling, or repacking.

Code of Federal Regulations, 2012 CFR

2012-04-01

... such shipment or delivery, or any part thereof, from such establishment, become void ab initio if the...)(2) of this section shall become void ab initio with respect to the person who introduced such...

21 CFR 801.150 - Medical devices; processing, labeling, or repacking.

Code of Federal Regulations, 2013 CFR

2013-04-01

... such shipment or delivery, or any part thereof, from such establishment, become void ab initio if the...)(2) of this section shall become void ab initio with respect to the person who introduced such...

Many-body optimization using an ab initio monte carlo method.

PubMed

Haubein, Ned C; McMillan, Scott A; Broadbelt, Linda J

2003-01-01

Advances in computing power have made it possible to study solvated molecules using ab initio quantum chemistry. Inclusion of discrete solvent molecules is required to determine geometric information about solute/solvent clusters. Monte Carlo methods are well suited to finding minima in many-body systems, and ab initio methods are applicable to the widest range of systems. A first principles Monte Carlo (FPMC) method was developed to find minima in many-body systems, and emphasis was placed on implementing moves that increase the likelihood of finding minimum energy structures. Partial optimization and molecular interchange moves aid in finding minima and overcome the incomplete sampling that is unavoidable when using ab initio methods. FPMC was validated by studying the boron trifluoride-water system, and then the method was used to examine the methyl carbenium ion in water to demonstrate its application to solvation problems.

Carbon diffusion in molten uranium: an ab initio molecular dynamics study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Garrett, Kerry E.; Abrecht, David G.; Kessler, Sean H.

In this work we used ab initio molecular dynamics (AIMD) within the framework of density functional theory (DFT) and the projector-augmented wave (PAW) method to study carbon diffusion in liquid uranium at temperatures above 1600 K. The electronic interactions of carbon and uranium were described using the local density approximation (LDA). The self-diffusion of uranium based on this approach is compared with literature computational and experimental results for liquid uranium. The temperature dependence of carbon and uranium diffusion in the melt was evaluated by fitting the resulting diffusion coefficients to an Arrhenius relationship. We found that the LDA calculated activationmore » energy for carbon was nearly twice that of uranium: 0.55±0.03 eV for carbon compared to 0.32±0.04 eV for uranium. Structural analysis of the liquid uranium-carbon system is also discussed.« less

How important is self-consistency for the dDsC density dependent dispersion correction?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brémond, Éric; Corminboeuf, Clémence, E-mail: clemence.corminboeuf@epfl.ch; Golubev, Nikolay

2014-05-14

The treatment of dispersion interactions is ubiquitous but computationally demanding for seamless ab initio approaches. A highly popular and simple remedy consists in correcting for the missing interactions a posteriori by adding an attractive energy term summed over all atom pairs to standard density functional approximations. These corrections were originally based on atom pairwise parameters and, hence, had a strong touch of empiricism. To overcome such limitations, we recently proposed a robust system-dependent dispersion correction, dDsC, that is computed from the electron density and that provides a balanced description of both weak inter- and intramolecular interactions. From the theoretical pointmore » of view and for the sake of increasing reliability, we here verify if the self-consistent implementation of dDsC impacts ground-state properties such as interaction energies, electron density, dipole moments, geometries, and harmonic frequencies. In addition, we investigate the suitability of the a posteriori scheme for molecular dynamics simulations, for which the analysis of the energy conservation constitutes a challenging tests. Our study demonstrates that the post-SCF approach in an excellent approximation.« less

Adhesion of a bimetallic interface. Ph.D. Thesis - Case Western Reserve Univ.; [for Al, Mg, and Zn

NASA Technical Reports Server (NTRS)

Ferrante, J.

1978-01-01

The Hohenberg-Kohn and Kohn-Sham formalisms are used to examine binding (binding energy as a function of separation) for combinations of the simple metals Al(111), Zn(0001), Mg(0001), and Na(110) in contact. Similar metal contacts between Al, Zn, Mg, and Na are examined self-consistently in an ab initio calculation using the Kohn-Sham formalism. Crystallinity is included using the Aschroft pseudopotential via first order perturbation theory for the electron-ion interaction; and the ion-ion interaction is included exactly via a lattice sum. Binding energy was determined both in the local-density approximation and including gradient corrections to the exchange and correlation energy. Binding was found in all cases. In dissimilar metal contacts, interfacial bonding was greater than that in the weaker material predicting the possibility of metallic transfer. The nonzero position of the energy minimum in like metal contacts is explained in terms of consistency between the Ashcroft pseudopotential and the bulk charge density. Good agreement with experimental surface energies is obtained in the self-consistent calculation when nonlocal terms are included.

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

PubMed

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.

Ab initio treatment of fully open-shell medium-mass nuclei with the IM-SRG

NASA Astrophysics Data System (ADS)

Stroberg, Ragnar; Calci, Angelo; Holt, Jason; Navratil, Petr; Bogner, Scott; Hergert, Heiko; Roth, Robert; Schwenk, Achim

2016-09-01

The in-medium similarity renormalization group (IM-SRG) is a recently-developed theoretical many-body framework which - like the coupled cluster and the self-consistent Green's function approaches - allows for the treatment of medium-mass nuclei using interactions fit at the few-body level. I will give a brief overview of how the IM-SRG may be used to decouple a shell-model type valence space. I will then describe a recent development for the approximate treatment of residual 3N forces in the valence space which extends the reach of IM-SRG to essentially all medium-mass nuclei, and I will present some selected results spanning isotopic chains from beryllium (Z=4) to nickel (Z=28). Finally, I will discuss the consistent treatment of transition operators, highlighting the potential for future applications in electroweak physics.

Origins of Singlet Fission in Solid Pentacene from an ab initio Green's Function Approach

NASA Astrophysics Data System (ADS)

Refaely-Abramson, Sivan; da Jornada, Felipe H.; Louie, Steven G.; Neaton, Jeffrey B.

2017-12-01

We develop a new first-principles approach to predict and understand rates of singlet fission with an ab initio Green's-function formalism based on many-body perturbation theory. Starting with singlet and triplet excitons computed from a G W plus Bethe-Salpeter equation approach, we calculate the exciton-biexciton coupling to lowest order in the Coulomb interaction, assuming a final state consisting of two noninteracting spin-correlated triplets with finite center-of-mass momentum. For crystalline pentacene, symmetries dictate that the only purely Coulombic fission decay process from a bright singlet state requires a final state consisting of two inequivalent nearly degenerate triplets of nonzero, equal and opposite, center-of-mass momenta. For such a process, we predict a singlet lifetime of 30-70 fs, in very good agreement with experimental data, indicating that this process can dominate singlet fission in crystalline pentacene. Our approach is general and provides a framework for predicting and understanding multiexciton interactions in solids.

Ab initio description of continuum effects in A=11 exotic systems with chiral NN+3N forces

NASA Astrophysics Data System (ADS)

Calci, Angelo; Navratil, Petr; Roth, Robert; Dohet-Eraly, Jeremy; Quaglioni, Sofia; Hupin, Guillaume

2016-09-01

Based on the fundamental symmetries of QCD, chiral effective field theory (EFT) provides two- (NN), three- (3N) and many-nucleon interactions in a consistent and systematically improvable scheme. The rapid developments to construct divers families of chiral NN+3N interactions and the conceptual and technical improvements of ab initio many-body approaches pose a great opportunity for nuclear physics. By studying particular interesting phenomena in nuclear structure and reaction observables one can discriminate between different forces and study the predictive power of chiral EFT. The accurate description of the 11Be nucleus, in particular, the ground-state parity inversion and exceptionally strong E1 transition between its two bound states constitute an enormous challenge for the developments of nuclear forces and many-body approaches. We present a sensitivity analysis of structure and reaction observables to different NN+3N interactions in 11Be and n+10Be as well as the mirror p+10C scattering using the ab initio NCSM with continuum (NCSMC). Supported by the U.S. Department of Energy, Office of Science, Office of Nuclear Physics, under Work Proposal No. SCW1158. TRIUMF receives federal funding via a contribution agreement with the National Research Council of Canada.

Ab initio molecular dynamics simulations of ion-solid interactions in zirconate pyrochlores

DOE PAGES

Xiao, Haiyan Y.; Weber, William J.; Zhang, Yanwen; ...

2015-01-31

In this paper, an ab initio molecular dynamics method is employed to study low energy recoil events in zirconate pyrochlores (A 2Zr 2O 7, A = La, Nd and Sm). It shows that both cations and anions in Nd 2Zr 2O 7 and Sm 2Zr 2O 7 are generally more likely to be displaced than those in La 2Zr 2O 7. The damage end states mainly consist of Frenkel pair defects, and the Frenkel pair formation energies in Nd 2Zr 2O 7 and Sm 2Zr 2O 7 are lower than those in La 2Zr 2O 7. These results suggest thatmore » the order–disorder structural transition more easily occurs in Nd 2Zr 2O 7 and Sm 2Zr 2O 7 resulting in a defect-fluorite structure, which agrees well with experimental observations. Our calculations indicate that oxygen migration from 48f and 8b to 8a sites is dominant under low energy irradiation. A number of new defects, including four types of cation Frenkel pairs and six types of anion Frenkel pairs, are revealed by ab initio molecular dynamics simulations. The present findings may help to advance the fundamental understanding of the irradiation response behavior of zirconate pyrochlores.« less

Kinetic products in coordination networks: ab initio X-ray powder diffraction analysis.

PubMed

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 disciplines in coordination networks, especially porous coordination networks, the ability to determine crystal structures when the crystals are not suitable for single crystal X-ray analysis is of paramount importance. In this Account, we report the potential of kinetic control to synthesize new coordination networks and we describe ab initio XRPD structure determination to characterize these networks' crystal structures. We describe our recent work on selective instant synthesis to yield kinetically controlled porous coordination networks. We demonstrate that instant synthesis can selectively produce metastable networks that are not possible to synthesize by conventional solution chemistry. Using kinetic products, we provide mechanistic insights into thermally induced (573-723 K) (i.e., annealing method) structural transformations in porous coordination networks as well as examples of guest exchange/inclusion reactions. Finally, we describe a memory effect that allows the transfer of structural information from kinetic precursor structures to thermally stable structures through amorphous intermediate phases. We believe that ab initio XRPD structure determination will soon be used to investigate chemical processes that lead intrinsically to microcrystalline solids, which up to now have not been fully understood due to the unavailability of single crystals. For example, only recently have researchers used single-crystal X-ray diffraction to elucidate crystal-to-crystal chemical reactions taking place in the crystalline scaffold of coordination networks. The potential of ab initio X-ray powder diffraction analysis goes beyond single-crystal-to-single-crystal processes, potentially allowing members of this field to study intriguing in situ reactions, such as reactions within pores.

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

ERIC Educational Resources Information Center

Gesell, Laurence E.

1995-01-01

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

Concentration dependence of electrical resistivity of binary liquid alloy HgZn: Ab-initio study

NASA Astrophysics Data System (ADS)

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

2013-06-01

The electrical resistivity of HgZn liquid alloy has been made calculated using Troullier and Martins ab-initio pseudopotential as a function of concentration. Hard sphere diameters of Hg and Zn are obtained through the inter-ionic pair potential have been used to calculate partial structure factors. Considering the liquid alloy to be a ternary mixture Ziman's formula for calculating the resistivity of binary liquid alloys, modified for complex formation, has been used. These results suggest that ab-initio approach for calculating electrical resistivity is quite successful in explaining the electronic transport properties of binary Liquid alloys.

Heats of Segregation of BCC Binaries from Ab Initio and Quantum Approximate Calculations

NASA Technical Reports Server (NTRS)

Good, Brian S.

2003-01-01

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

Accurate ab initio quartic force fields for borane and BeH2

NASA Technical Reports Server (NTRS)

Martin, J. M. L.; Lee, Timothy J.

1992-01-01

The quartic force fields of BH3 and BeH2 have been computed ab initio using an augmented coupled cluster (CCSD(T)) method and basis sets of spdf and spdfg quality. For BH3, the computed spectroscopic constants are in very good agreement with recent experimental data, and definitively confirm misassignments in some older work, in agreement with recent ab initio studies. Using the computed spectroscopic constants, the rovibrational partition function for both molecules has been constructed using a modified direct numerical summation algorithm, and JANAF-style thermochemical tables are presented.

Analysis of fcc metals fracture behaviour: Fracture behaviour of fcc metals: brittle/ductile behaviour criteria : with ab-initio, embedded atom and pseudopotential parameterization for Au, Ir and Al. analysis for Au, Ir and Al.

NASA Astrophysics Data System (ADS)

Gornostyrev, Yu. N.; Katsnelson, M. I.; Mryasov, Oleg N.; Freeman, A. J.; Trefilov, M. V.

1998-03-01

Theoretical analysis of the fracture behaviour of fcc Au, Ir and Al have been performed within various brittle/ductile criteria (BDC) with ab-initio, embedded atom (EAM), and pseudopotential parameterizations. We systematically examined several important aspects of the fracture behaviour: (i) dislocation structure, (ii) energetics of the cleavage decohesion and (iii) character of the interatomic interactions. Unit dislocation structures were analyzed within a two dimensional generalization of the Peierls-Nabarro model with restoring forces determined from ab-initio total energy calculations and found to be split with well defined highly mobile partials for all considered metals. We find from ab-initio and pseudopotential that in contrast with most of fcc metals, cleavage decohesion curve for Al appreciably differs from UBER relation. Finally, using ab-initio, EAM and pseudopotential parameterizations, we demonstrate that (i) Au (as a typical example of a ductile metal) is well described within existing BDC's, (ii) anomalous cleavage-like crack propagation of Ir is driven predominantly by it's high elastic modulus and (iii) Al is not described within BDC due to it's long-range interatomic interactions (and hence requires adjustments of the brittle/ductile criteria).

Quantum wavepacket ab initio molecular dynamics: an approach for computing dynamically averaged vibrational spectra including critical nuclear quantum effects.

PubMed

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.

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

PubMed Central

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

2017-01-01

Abstract Motivation: 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. Results: 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. Availability and Implementation: Sphinx is available at http://opig.stats.ox.ac.uk/webapps/sphinx. Contact: deane@stats.ox.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:28453681

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

PubMed

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. © The Author 2017. Published by Oxford University Press.

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

NASA Astrophysics Data System (ADS)

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.

On the room-temperature phase diagram of high pressure hydrogen: an ab initio molecular dynamics perspective and a diffusion Monte Carlo study.

PubMed

Chen, Ji; Ren, Xinguo; Li, Xin-Zheng; Alfè, Dario; Wang, Enge

2014-07-14

The finite-temperature phase diagram of hydrogen in the region of phase IV and its neighborhood was studied using the ab initio molecular dynamics (MD) and the ab initio path-integral molecular dynamics (PIMD). The electronic structures were analyzed using the density-functional theory (DFT), the random-phase approximation, and the diffusion Monte Carlo (DMC) methods. Taking the state-of-the-art DMC results as benchmark, comparisons of the energy differences between structures generated from the MD and PIMD simulations, with molecular and dissociated hydrogens, respectively, in the weak molecular layers of phase IV, indicate that standard functionals in DFT tend to underestimate the dissociation barrier of the weak molecular layers in this mixed phase. Because of this underestimation, inclusion of the quantum nuclear effects (QNEs) in PIMD using electronic structures generated with these functionals leads to artificially dissociated hydrogen layers in phase IV and an error compensation between the neglect of QNEs and the deficiencies of these functionals in standard ab initio MD simulations exists. This analysis partly rationalizes why earlier ab initio MD simulations complement so well the experimental observations. The temperature and pressure dependencies for the stability of phase IV were also studied in the end and compared with earlier results.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jäger, Benjamin, E-mail: benjamin.jaeger@uni-rostock.de; Hellmann, Robert, E-mail: robert.hellmann@uni-rostock.de; Bich, Eckard

2016-03-21

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

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

PubMed

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

2016-03-21

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

N vacancy, self-interstitial diffusion, and Frenkel-pair formation/dissociation in TiN studied by ab-initio and classical molecular dynamics

NASA Astrophysics Data System (ADS)

Sangiovanni, Davide G.; Alling, Björn; Hultman, Lars; Abrikosov, Igor A.

2015-03-01

We use ab-initio and classical molecular dynamics (AIMD, CMD) to simulate diffusion of N vacancy and N self-interstitial point-defects in B1 TiN. The physical properties of TiN, important material system for thin film and coatings applications, are largely dictated by concentration and mobility of point defects. We determine N dilute-point-defect diffusion pathways, activation energies, attempt frequencies, and diffusion coefficients as a function of temperature. In addition, MD simulations reveal an unanticipated atomistic process, which controls the spontaneous formation of N-self-interstitial/N-vacancy pairs (Frenkel pairs) in defect-free TiN. This entails that a N lattice atom leaves its bulk position and bonds to a neighboring N lattice atom. In most cases, Frenkel-pair NI and NV recombine within a fraction of ns; 50% of these processes result in the exchange of two nitrogen lattice atoms. Occasionally, however, Frenkel-pair N-interstitial atoms permanently escape from the anion vacancy site, thus producing unpaired NI and NV point defects. The Knut and Alice Wallenberg foundation (Isotope Project, 2011.0094), the Swedish Research Council (VR) Linköping Linnaeus Initiative LiLi-NFM (Grant 2008-6572), and the Swedish Government Strategic Research (Grant MatLiU 2009-00971).

Nitrogen vacancy, self-interstitial diffusion, and Frenkel-pair formation/dissociation in B 1 TiN studied by ab initio and classical molecular dynamics with optimized potentials

NASA Astrophysics Data System (ADS)

Sangiovanni, D. G.; Alling, B.; Steneteg, P.; Hultman, L.; Abrikosov, I. A.

2015-02-01

We use ab initio and classical molecular dynamics (AIMD and CMD) based on the modified embedded-atom method (MEAM) potential to simulate diffusion of N vacancy and N self-interstitial point defects in B 1 TiN. TiN MEAM parameters are optimized to obtain CMD nitrogen point-defect jump rates in agreement with AIMD predictions, as well as an excellent description of Ti Nx(˜0.7

Ab initio prediction of fast non-equilibrium transport of nascent polarons in SrI2: a key to high-performance scintillation

NASA Astrophysics Data System (ADS)

Zhou, Fei; Sadigh, Babak; Erhart, Paul; Åberg, Daniel

2016-08-01

The excellent light yield proportionality of europium-doped strontium iodide (SrI2:Eu) has resulted in state-of-the-art γ-ray detectors with remarkably high-energy resolution, far exceeding that of most halide compounds. In this class of materials, the formation of self-trapped hole polarons is very common. However, polaron formation is usually expected to limit carrier mobilities and has been associated with poor scintillator light-yield proportionality and resolution. Here using a recently developed first-principles method, we perform an unprecedented study of polaron transport in SrI2, both for equilibrium polarons, as well as nascent polarons immediately following a self-trapping event. We propose a rationale for the unexpected high-energy resolution of SrI2. We identify nine stable hole polaron configurations, which consist of dimerised iodine pairs with polaron-binding energies of up to 0.5 eV. They are connected by a complex potential energy landscape that comprises 66 unique nearest-neighbour migration paths. Ab initio molecular dynamics simulations reveal that a large fraction of polarons is born into configurations that migrate practically barrier free at room temperature. Consequently, carriers created during γ-irradiation can quickly diffuse away reducing the chance for non-linear recombination, the primary culprit for non-proportionality and resolution reduction. We conclude that the flat, albeit complex, landscape for polaron migration in SrI2 is a key for understanding its outstanding performance. This insight provides important guidance not only for the future development of high-performance scintillators but also of other materials, for which large polaron mobilities are crucial such as batteries and solid-state ionic conductors.

Ab initio prediction of fast non-equilibrium transport of nascent polarons in SrI 2: a key to high-performance scintillation [First-principles study of hole polaron formation and migration in strontium iodide

DOE PAGES

Zhou, Fei; Sadigh, Babak; Aberg, Daniel; ...

2016-08-12

The excellent light yield proportionality of europium-doped strontium iodide (SrI 2:Eu) has resulted in state-of-the-art γ-ray detectors with remarkably high-energy resolution, far exceeding that of most halide compounds. In this class of materials, the formation of self-trapped hole polarons is very common. However, polaron formation is usually expected to limit carrier mobilities and has been associated with poor scintillator light-yield proportionality and resolution. Here using a recently developed first-principles method, we perform an unprecedented study of polaron transport in SrI 2, both for equilibrium polarons, as well as nascent polarons immediately following a self-trapping event. We propose a rationale formore » the unexpected high-energy resolution of SrI 2. We identify nine stable hole polaron configurations, which consist of dimerised iodine pairs with polaron-binding energies of up to 0.5 eV. They are connected by a complex potential energy landscape that comprises 66 unique nearest-neighbour migration paths. Ab initio molecular dynamics simulations reveal that a large fraction of polarons is born into configurations that migrate practically barrier free at room temperature. Consequently, carriers created during γ-irradiation can quickly diffuse away reducing the chance for nonlinear recombination, the primary culprit for non-proportionality and resolution reduction. We conclude that the flat, albeit complex, landscape for polaron migration in SrI 2 is a key for understanding its outstanding performance. This insight provides important guidance not only for the future development of high-performance scintillators but also of other materials, for which large polaron mobilities are crucial such as batteries and solid-state ionic conductors.« less

Nanocarbon synthesis by high-temperature oxidation of nanoparticles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nomura, Ken-ichi; Kalia, Rajiv K.; Li, Ying

High-temperature oxidation of silicon-carbide nanoparticles (nSiC) underlies a wide range of technologies from high-power electronic switches for efficient electrical grid and thermal protection of space vehicles to self-healing ceramic nanocomposites. Here, multimillion-atom reactive molecular dynamics simulations validated by ab initio quantum molecular dynamics simulations predict unexpected condensation of large graphene flakes during high-temperature oxidation of nSiC. Initial oxidation produces a molten silica shell that acts as an autocatalytic ‘nanoreactor’ by actively transporting oxygen reactants while protecting the nanocarbon product from harsh oxidizing environment. Percolation transition produces porous nanocarbon with fractal geometry, which consists of mostly sp 2 carbons with pentagonalmore » and heptagonal defects. Furthermore, this work suggests a simple synthetic pathway to high surface-area, low-density nanocarbon with numerous energy, biomedical and mechanical-metamaterial applications, including the reinforcement of self-healing composites.« less

Nanocarbon synthesis by high-temperature oxidation of nanoparticles

DOE PAGES

Nomura, Ken-ichi; Kalia, Rajiv K.; Li, Ying; ...

2016-04-20

High-temperature oxidation of silicon-carbide nanoparticles (nSiC) underlies a wide range of technologies from high-power electronic switches for efficient electrical grid and thermal protection of space vehicles to self-healing ceramic nanocomposites. Here, multimillion-atom reactive molecular dynamics simulations validated by ab initio quantum molecular dynamics simulations predict unexpected condensation of large graphene flakes during high-temperature oxidation of nSiC. Initial oxidation produces a molten silica shell that acts as an autocatalytic ‘nanoreactor’ by actively transporting oxygen reactants while protecting the nanocarbon product from harsh oxidizing environment. Percolation transition produces porous nanocarbon with fractal geometry, which consists of mostly sp 2 carbons with pentagonalmore » and heptagonal defects. Furthermore, this work suggests a simple synthetic pathway to high surface-area, low-density nanocarbon with numerous energy, biomedical and mechanical-metamaterial applications, including the reinforcement of self-healing composites.« less

Nanocarbon synthesis by high-temperature oxidation of nanoparticles

PubMed Central

Nomura, Ken-ichi; Kalia, Rajiv K.; Li, Ying; Nakano, Aiichiro; Rajak, Pankaj; Sheng, Chunyang; Shimamura, Kohei; Shimojo, Fuyuki; Vashishta, Priya

2016-01-01

High-temperature oxidation of silicon-carbide nanoparticles (nSiC) underlies a wide range of technologies from high-power electronic switches for efficient electrical grid and thermal protection of space vehicles to self-healing ceramic nanocomposites. Here, multimillion-atom reactive molecular dynamics simulations validated by ab initio quantum molecular dynamics simulations predict unexpected condensation of large graphene flakes during high-temperature oxidation of nSiC. Initial oxidation produces a molten silica shell that acts as an autocatalytic ‘nanoreactor’ by actively transporting oxygen reactants while protecting the nanocarbon product from harsh oxidizing environment. Percolation transition produces porous nanocarbon with fractal geometry, which consists of mostly sp2 carbons with pentagonal and heptagonal defects. This work suggests a simple synthetic pathway to high surface-area, low-density nanocarbon with numerous energy, biomedical and mechanical-metamaterial applications, including the reinforcement of self-healing composites. PMID:27095061

Multipole-Based Force Fields from ab Initio Interaction Energies and the Need for Jointly Refitting All Intermolecular Parameters.

PubMed

Kramer, Christian; Gedeck, Peter; Meuwly, Markus

2013-03-12

Distributed atomic multipole (MTP) moments promise significant improvements over point charges (PCs) in molecular force fields, as they (a) more realistically reproduce the ab initio electrostatic potential (ESP) and (b) allow to capture anisotropic atomic properties such as lone pairs, conjugated systems, and σ holes. The present work focuses on the question of whether multipolar electrostatics instead of PCs in standard force fields leads to quantitative improvements over point charges in reproducing intermolecular interactions. To this end, the interaction energies of two model systems, benzonitrile (BZN) and formamide (FAM) homodimers, are characterized over a wide range of dimer conformations. It is found that although with MTPs the monomer ab initio ESP can be captured better by about an order of magnitude compared to point charges (PCs), this does not directly translate into better describing ab initio interaction energies compared to PCs. Neither ESP-fitted MTPs nor refitted Lennard-Jones (LJ) parameters alone demonstrate a clear superiority of atomic MTPs. We show that only if both electrostatic and LJ parameters are jointly optimized in standard, nonpolarizable force fields, atomic are MTPs clearly beneficial for reproducing ab initio dimerization energies. After an exhaustive exponent scan, we find that for both BZN and FAM, atomic MTPs and a 9-6 LJ potential can reproduce ab initio interaction energies with ∼30% (RMSD 0.13 vs 0.18 kcal/mol) less error than point charges (PCs) and a 12-6 LJ potential. We also find that the improvement due to using MTPs with a 9-6 LJ potential is considerably more pronounced than with a 12-6 LJ potential (≈ 10%; RMSD 0.19 versus 0.21 kcal/mol).

Perspective: Ab initio force field methods derived from quantum mechanics

NASA Astrophysics Data System (ADS)

Xu, Peng; Guidez, Emilie B.; Bertoni, Colleen; Gordon, Mark S.

2018-03-01

It is often desirable to accurately and efficiently model the behavior of large molecular systems in the condensed phase (thousands to tens of thousands of atoms) over long time scales (from nanoseconds to milliseconds). In these cases, ab initio methods are difficult due to the increasing computational cost with the number of electrons. A more computationally attractive alternative is to perform the simulations at the atomic level using a parameterized function to model the electronic energy. Many empirical force fields have been developed for this purpose. However, the functions that are used to model interatomic and intermolecular interactions contain many fitted parameters obtained from selected model systems, and such classical force fields cannot properly simulate important electronic effects. Furthermore, while such force fields are computationally affordable, they are not reliable when applied to systems that differ significantly from those used in their parameterization. They also cannot provide the information necessary to analyze the interactions that occur in the system, making the systematic improvement of the functional forms that are used difficult. Ab initio force field methods aim to combine the merits of both types of methods. The ideal ab initio force fields are built on first principles and require no fitted parameters. Ab initio force field methods surveyed in this perspective are based on fragmentation approaches and intermolecular perturbation theory. This perspective summarizes their theoretical foundation, key components in their formulation, and discusses key aspects of these methods such as accuracy and formal computational cost. The ab initio force fields considered here were developed for different targets, and this perspective also aims to provide a balanced presentation of their strengths and shortcomings. Finally, this perspective suggests some future directions for this actively developing area.

Investigation of polarization effects in the gramicidin A channel from ab initio molecular dynamics simulations.

PubMed

Timko, Jeff; Kuyucak, Serdar

2012-11-28

Polarization is an important component of molecular interactions and is expected to play a particularly significant role in inhomogeneous environments such as pores and interfaces. Here we investigate the effects of polarization in the gramicidin A ion channel by performing quantum mechanics/molecular mechanics molecular dynamics (MD) simulations and comparing the results with those obtained from classical MD simulations with non-polarizable force fields. We consider the dipole moments of backbone carbonyl groups and channel water molecules as well as a number of structural quantities of interest. The ab initio results show that the dipole moments of the carbonyl groups and water molecules are highly sensitive to the hydrogen bonds (H-bonds) they participate in. In the absence of a K(+) ion, water molecules in the channel are quite mobile, making the H-bond network highly dynamic. A central K(+) ion acts as an anchor for the channel waters, stabilizing the H-bond network and thereby increasing their average dipole moments. In contrast, the K(+) ion has little effect on the dipole moments of the neighboring carbonyl groups. The weakness of the ion-peptide interactions helps to explain the near diffusion-rate conductance of K(+) ions through the channel. We also address the sampling issue in relatively short ab initio MD simulations. Results obtained from a continuous 20 ps ab initio MD simulation are compared with those generated by sampling ten windows from a much longer classical MD simulation and running each window for 2 ps with ab initio MD. Both methods yield similar results for a number of quantities of interest, indicating that fluctuations are fast enough to justify the short ab initio MD simulations.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marsalek, Ondrej; Markland, Thomas E., E-mail: tmarkland@stanford.edu

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 asmore » 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.« less

First-principles theory of anharmonicity and the inverse isotope effect in superconducting palladium-hydride compounds.

PubMed

Errea, Ion; Calandra, Matteo; Mauri, Francesco

2013-10-25

Palladium hydrides display the largest isotope effect anomaly known in the literature. Replacement of hydrogen with the heavier isotopes leads to higher superconducting temperatures, a behavior inconsistent with harmonic theory. Solving the self-consistent harmonic approximation by a stochastic approach, we obtain the anharmonic free energy, the thermal expansion, and the superconducting properties fully ab initio. We find that the phonon spectra are strongly renormalized by anharmonicity far beyond the perturbative regime. Superconductivity is phonon mediated, but the harmonic approximation largely overestimates the superconducting critical temperatures. We explain the inverse isotope effect, obtaining a -0.38 value for the isotope coefficient in good agreement with experiments, hydrogen anharmonicity being mainly responsible for the isotope anomaly.

Immediate estimation of correlation energy for molecular systems from the partial charges on atoms in the molecule

NASA Astrophysics Data System (ADS)

Kristyán, Sándor

1997-11-01

In the author's previous work (Chem. Phys. Lett. 247 (1995) 101 and Chem. Phys. Lett. 256 (1996) 229) a simple quasi-linear relationship was introduced between the number of electrons, N, participating in any molecular system and the correlation energy: -0.035 ( N - 1) > Ecorr[hartree] > - 0.045( N -1). This relationship was developed to estimate more accurately correlation energy immediately in ab initio calculations by using the partial charges of atoms in the molecule, easily obtained after Hartree-Fock self-consistent field (HF-SCF) calculations. The method is compared to the well-known B3LYP, MP2, CCSD and G2M methods. Correlation energy estimations for negatively (-1) charged atomic ions are also reported.

Gas-phase infrared spectrum of phosphorus (III) oxycyanide, OPCN: experimental and theoretical investigations

NASA Astrophysics Data System (ADS)

Allaf, Abdul. W.; Kassem, M.; Alibrahim, M.; Boustani, Ihsan

1999-03-01

An attempt was made to observe the gas-phase infrared spectrum of Phosphorus (III) oxycyanide, OPCN for the first time. This molecule was produced by an on-line process using phosphorus (III) oxychloride, OPCl as precursor passed over heated AgCN. The products were characterised by the infrared spectra of their vapours. The low resolution gas-phase Fourier transform infrared spectrum shows two bands centered at 2165 and 1385 cm -1. These bands are assigned to, ν1 (CN stretch) and ν2 (OP stretch), respectively. Ab initio self-consistent-field (SCF) molecular orbital (MO) and Møller-Plesset second order perturbation theory (MP2) calculations were performed to determine the geometry, total energy and vibrational frequencies of OPCN.

Structural, Electronic and Elastic Properties of Half-Heusler Alloys CrNiZ (Z = Al, Si, Ge and As)

NASA Astrophysics Data System (ADS)

Zitouni, A.; Benstaali, W.; Abbad, A.; Lantri, T.; Bouadjemi, B.; Aziz, Z.

2018-06-01

In the present work, a self-consistent ab-initio calculation using the full- potential linearized augmented plane wave (FP-LAPW) method within the framework of the spin-polarized density functional theory (DFT) was used to study the structural, electronic, magnetic and elastic properties of the half Heusler alloys CrNiZ (Z = Al, Si, Ge and As) in three phases ( α, β and γ phases). The generalized gradient approximation (GGA) described by Perdew-Burke-Ernzerhof (PBE) was used. The results obtained for the spin-polarized band structure and the density of states show a halfmetallic behavior for the four compounds. The elastic constants ( C ij ) show that our compounds are ductile, stiff and anisotropic.

Correlation study of sodium-atom chemisorption on the GaAs(110) surface

NASA Astrophysics Data System (ADS)

Song, K. M.; Khan, D. C.; Ray, A. K.

1994-01-01

Different possible adsorption sites of sodium atoms on a gallium arsenide surface have been investigated using ab initio self-consistent unrestricted Hartree-Fock total-energy cluster calculations with Hay-Wadt effective core potentials. The effects of electron correlation have been included by invoking the concepts of many-body perturbation theory and are found to be highly significant. We find that the Na-atom adsorption at a site modeled with an NaGa5As4H12 cluster is most favored energetically followed by Na adsorption at the site modeled with the NaGa4As5H12 cluster. The effects of charge transfer from Na to the GaAs surface as also possibilities of metallization are also analyzed and discussed.

Towards an ab initio theory for metal L-edge soft X-ray spectroscopy of molecular aggregates.

PubMed

Preuße, Marie; Bokarev, Sergey I; Aziz, Saadullah G; Kühn, Oliver

2016-11-01

The Frenkel exciton model was adapted to describe X-ray absorption and resonant inelastic scattering spectra of polynuclear transition metal complexes by means of the restricted active space self-consistent field method. The proposed approach allows to substantially decrease the requirements on computational resources if compared to a full supermolecular quantum chemical treatment. This holds true, in particular, in cases where the dipole approximation to the electronic transition charge density can be applied. The computational protocol was applied to the calculation of X-ray spectra of the hemin complex, which forms dimers in aqueous solution. The aggregation effects were found to be comparable to the spectral alterations due to the replacement of the axial ligand by solvent molecules.

Ab initio thermal rate calculations of HO + HO = O(3P) + H2O reaction and isotopologues.

PubMed

Nguyen, Thanh Lam; Stanton, John F

2013-04-04

The forward and reverse reactions, HO + HO ⇌ O((3)P) + H2O, which play roles in both combustion and laboratory studies, were theoretically characterized with a master equation approach to compute thermal reaction rate constants at both the low and high pressure limits. Our ab initio k(T) results for the title reaction and two isotopic variants agree very well with experiments (within 15%) over a wide temperature range. The calculated reaction rate shows a distinctly non-Arrhenius behavior and a strong curvature consistent with the experiment. This characteristic behavior is due to effects of positive barrier height and quantum mechanical tunneling. Tunneling is very important and contributes more than 70% of total reaction rate at room temperature. A prereactive complex is also important in the overall reaction scheme.

Ab initio molecular dynamics of the reactivity of vitamin C toward hydroxyl and HO₂/O⁻₂ radicals.

PubMed

Lespade, Laure

2017-11-21

Vitamin C is one of the most abundant exogenous antioxidants in the cell, and it is of the utmost importance to elucidate its mechanism of action against radicals. In this study, the reactivity of vitamin C toward OH and [Formula: see text] radicals in aqueous medium was analyzed by ab initio molecular dynamics using CPMD code. The simulations led to results similar to those of static studies or experiments for the pair of [Formula: see text] radicals but bring new insights for the reactivity with hydroxyl radical: the reaction takes place before the formation of an adduct and consists of two steps: first an electron is transferred to hydroxyl radical and then the ascorbyl radical loses a proton. Graphical Abstract Reactivity of vitamin C toward hydroxyl and [Formula: see text] radicals.

Comparison between phenomenological and ab-initio reaction and relaxation models in DSMC

NASA Astrophysics Data System (ADS)

Sebastião, Israel B.; Kulakhmetov, Marat; Alexeenko, Alina

2016-11-01

New state-specific vibrational-translational energy exchange and dissociation models, based on ab-initio data, are implemented in direct simulation Monte Carlo (DSMC) method and compared to the established Larsen-Borgnakke (LB) and total collision energy (TCE) phenomenological models. For consistency, both the LB and TCE models are calibrated with QCT-calculated O2+O data. The model comparison test cases include 0-D thermochemical relaxation under adiabatic conditions and 1-D normal shockwave calculations. The results show that both the ME-QCT-VT and LB models can reproduce vibrational relaxation accurately but the TCE model is unable to reproduce nonequilibrium rates even when it is calibrated to accurate equilibrium rates. The new reaction model does capture QCT-calculated nonequilibrium rates. For all investigated cases, we discuss the prediction differences based on the new model features.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Halasyamani, Shiv; Fennie, Craig

2016-11-03

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

7Be(p,gamma)8B S-factor from Ab Initio Wave Functions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Navratil, P; Bertulani, C A; Caurier, E

2006-10-12

There has been a significant progress in ab initio approaches to the structure of light nuclei. Starting from realistic two- and three-nucleon interactions the ab initio no-core shell model (NCSM) predicts low-lying levels in p-shell nuclei. It is a challenging task to extend ab initio methods to describe nuclear reactions. We present here a brief overview of the first steps taken toward nuclear reaction applications. In particular, we discuss our calculation of the {sup 7}Be(p,{gamma}){sup 8}B S-factor. We also present our first results of the {sup 3}He({alpha},{gamma}){sup 7}Be S-factor and of the S-factor of the mirror reaction {sup 3}H({alpha},{gamma}){sup 7}Li.more » The {sup 7}Be(p,{gamma}){sup 8}B and {sup 3}He({alpha},{gamma}){sup 7}Be reactions correspond to the most important uncertainties in solar model predictions of neutrino fluxes.« less

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Li; ye, Yeting; Fan, K. M.

2014-09-01

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

Ab initio Studies of Magnetism in the Iron Chalcogenides FeTe and FeSe

NASA Astrophysics Data System (ADS)

Hirayama, Motoaki; Misawa, Takahiro; Miyake, Takashi; Imada, Masatoshi

2015-09-01

The iron chalcogenides FeTe and FeSe belong to the family of iron-based superconductors. We study the magnetism in these compounds in the normal state using the ab initio downfolding scheme developed for strongly correlated electron systems. In deriving ab initio low-energy effective models, we employ the constrained GW method to eliminate the double counting of electron correlations originating from the exchange correlations already taken into account in the density functional theory. By solving the derived ab initio effective models, we reveal that the elimination of the double counting is important in reproducing the bicollinear antiferromagnetic order in FeTe, as is observed in experiments. We also show that the elimination of the double counting induces a unique degeneracy of several magnetic orders in FeSe, which may explain the absence of the magnetic ordering. We discuss the relationship between the degeneracy and the recently found puzzling phenomena in FeSe as well as the magnetic ordering found under pressure.

Coupling of ab initio density functional theory and molecular dynamics for the multiscale modeling of carbon nanotubes

NASA Astrophysics Data System (ADS)

Ng, T. Y.; Yeak, S. H.; Liew, K. M.

2008-02-01

A multiscale technique is developed that couples empirical molecular dynamics (MD) and ab initio density functional theory (DFT). An overlap handshaking region between the empirical MD and ab initio DFT regions is formulated and the interaction forces between the carbon atoms are calculated based on the second-generation reactive empirical bond order potential, the long-range Lennard-Jones potential as well as the quantum-mechanical DFT derived forces. A density of point algorithm is also developed to track all interatomic distances in the system, and to activate and establish the DFT and handshaking regions. Through parallel computing, this multiscale method is used here to study the dynamic behavior of single-walled carbon nanotubes (SWCNTs) under asymmetrical axial compression. The detection of sideways buckling due to the asymmetrical axial compression is reported and discussed. It is noted from this study on SWCNTs that the MD results may be stiffer compared to those with electron density considerations, i.e. first-principle ab initio methods.

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

PubMed

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

2016-11-01

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

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

PubMed

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

2016-01-01

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

Resolution of ab initio shapes determined from small-angle scattering

PubMed Central

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

2016-01-01

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

A coupled channel study of HN2 unimolecular decay based on a global ab initio potential surface

NASA Technical Reports Server (NTRS)

Koizumi, Hiroyasu; Schatz, George C.; Walch, Stephen P.

1991-01-01

The unimolecular decay lifetimes of several vibrational states of HN2 are determined on the basis of an accurate coupled channel dynamics study using a global analytical potential surface. The surface reproduces the ab initio points with an rms error of 0.08 kcal/mol for energies below 20 kcal/mol. Modifications to the potential that describe the effect of improving the basis set in the ab initio calculations are provided. Converged coupled channel calculations are performed for the ground rotational state of HN2 to determine the lifetimes of the lowest ten vibrational states. Only the ground vibrational state (000) and first excited bend (001) are found to have lifetimes longer than 1 ps. The lifetimes of these states are estimated at 3 x 10 to the -9th and 2 x 10 to the -10th s, respectively. Variation of these results with quality of the ab initio calculations is not more than a factor of 5.

A highly accurate ab initio potential energy surface for methane.

PubMed

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

2016-09-14

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

Ab-initio study of the energetics and thermodynamics of the reaction CH3H + O( 3P) → CF3H … O → CF3 + OH

NASA Astrophysics Data System (ADS)

Kreye, W. C.

1996-07-01

Ab-initio computations at 298.15 K were made of the activation quantities ΔH ‡, ΔS ‡, and ΔG ‡ and of the reaction quantities ΔHr and ΔSr for CF3H + O( 3P) → CF3H … O → .CF3.OH. CF 3H … O is the transition state (TS). GAUSSIAN92 was used and energies computed at a slightly modified Gaussian-2 level. Two potential surfaces for the TS had symmetries 3A' and 3A″. The two rate constants included a semi-classical, quantum-mechanical-tunneling transmission coefficient. The ab-initio ΔH ‡and ΔH r values were in excellent agreement (± 1 kcal/mol) with experiment; but the ΔS ‡, ΔG ‡, and ΔS r values yielded somewhat poorer agreement. Experimental and ab-initio structures were in excellent agreement.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

2015-09-14

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

Evaluation of Density Functionals and Basis Sets for Carbohydrates

USDA-ARS?s Scientific Manuscript database

Correlated ab initio wave function calculations using MP2/aug-cc-pVTZ model chemistry have been performed for three test sets of gas phase saccharide conformations to provide reference values for their relative energies. The test sets consist of 15 conformers of alpha and beta-D-allopyranose, 15 of ...

Quantum ring-polymer contraction method: Including nuclear quantum effects at no additional computational cost in comparison to ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

John, Christopher; Spura, Thomas; Habershon, Scott; Kühne, Thomas D.

2016-04-01

We present a simple and accurate computational method which facilitates ab initio path-integral molecular dynamics simulations, where the quantum-mechanical nature of the nuclei is explicitly taken into account, at essentially no additional computational cost in comparison to the corresponding calculation using classical nuclei. The predictive power of the proposed quantum ring-polymer contraction method is demonstrated by computing various static and dynamic properties of liquid water at ambient conditions using density functional theory. This development will enable routine inclusion of nuclear quantum effects in ab initio molecular dynamics simulations of condensed-phase systems.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sano, Yukio; Sano, Tomokazu

A quadratic equation for the temperature-independent Grueneisen coefficient {gamma} was derived by a method in which the Walsh-Christian and Mie-Grueneisen equations are combined. Some previously existing ab initio temperature Hugoniots for hexagonal close-packed solid Fe are inaccurate because the constant-volume specific heats on the Hugoniots CVH, which are related uniquely to the solutions of the quadratic equation, have values that are too small. A CVH distribution in the solid phase range was demonstrated to agree approximately with a previous ab initio distribution. In contrast, the corresponding {gamma} distribution was significantly different from the ab initio distribution in the lower pressuremore » region. The causes of these disagreements are clarified.« less

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

PubMed

Bryk, Taras; Klevets, Ivan

2012-12-14

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

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

PubMed

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

2015-02-01

AMPLE clusters and truncates ab initio protein structure predictions, producing search models for molecular replacement. Here, an interesting degree of complementarity is shown between targets solved using the different ab initio modelling programs QUARK and ROSETTA. Search models derived from either program collectively solve almost all of the all-helical targets in the test set. Initial solutions produced by Phaser after only 5 min perform surprisingly well, improving the prospects for in situ structure solution by AMPLE during synchrotron visits. Taken together, the results show the potential for AMPLE to run more quickly and successfully solve more targets than previously suspected.

Calcium ions in aqueous solutions: Accurate force field description aided by ab initio molecular dynamics and neutron scattering

NASA Astrophysics Data System (ADS)

Martinek, Tomas; Duboué-Dijon, Elise; Timr, Štěpán; Mason, Philip E.; Baxová, Katarina; Fischer, Henry E.; Schmidt, Burkhard; Pluhařová, Eva; Jungwirth, Pavel

2018-06-01

We present a combination of force field and ab initio molecular dynamics simulations together with neutron scattering experiments with isotopic substitution that aim at characterizing ion hydration and pairing in aqueous calcium chloride and formate/acetate solutions. Benchmarking against neutron scattering data on concentrated solutions together with ion pairing free energy profiles from ab initio molecular dynamics allows us to develop an accurate calcium force field which accounts in a mean-field way for electronic polarization effects via charge rescaling. This refined calcium parameterization is directly usable for standard molecular dynamics simulations of processes involving this key biological signaling ion.

Ab initio study of H + + H 2 collisions: Elastic/inelastic and charge transfer processes

NASA Astrophysics Data System (ADS)

Saieswari, A.; Kumar, Sanjay

2007-12-01

An ab initio full configuration interaction study has been undertaken to obtain the global potential energy surfaces for the ground and the first excited electronic state of the H + + H 2 system employing Dunning's cc-pVQZ basis set. Using the ab initio approach the corresponding quasi-diabatic potential energy surfaces and coupling potentials have been obtained. A time-independent quantum mechanical study has been also undertaken for both the inelastic and charge transfer processes at the experimental collision energy Ec.m. = 20.0 eV and the preliminary results show better agreement with the experimental data as compared to the earlier available theoretical studies.

Ab initio calculation of one-nucleon halo states

NASA Astrophysics Data System (ADS)

Rodkin, D. M.; Tchuvil'sky, Yu M.

2018-02-01

We develop an approach to microscopic and ab initio description of clustered systems, states with halo nucleon and one-nucleon resonances. For these purposes a basis combining ordinary shell-model components and cluster-channel terms is built up. The transformation of clustered wave functions to the uniform Slater-determinant type is performed using the concept of cluster coefficients. The resulting basis of orthonormalized wave functions is used for calculating the eigenvalues and the eigenvectors of Hamiltonians built in the framework of ab initio approaches. Calculations of resonance and halo states of 5He, 9Be and 9B nuclei demonstrate that the approach is workable and labor-saving.

40 CFR 86.096-7 - Maintenance of records; submittal of information; right of entry.

Code of Federal Regulations, 2010 CFR

2010-07-01

...] (ii) EPA may void ab initio a certificate for a 1994 or 1995 model year light-duty vehicle or light... Administrator upon request. (iii) Any voiding ab initio of a certificate under § 86.091-7(c)(6) and paragraph (h...

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

NASA Astrophysics Data System (ADS)

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.

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.

PubMed

Wang, Qingfeng Kee; Bowman, Joel M

2017-10-28

We report an ab initio, full-dimensional, potential energy surface (PES) for CO 2 -H 2 O, 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, D 0 , of 787 cm -1 is obtained using that ZPE, D e , and the rigorous ZPEs of the monomers. Using a benchmark D e , D 0 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 CO 2 hydrate clathrate CO 2 (H 2 O) 20 (5 12 water cage). A full normal-mode analysis of this hydrate clathrate is reported as are local-monomer VSCF/VCI calculations of the fundamentals of CO 2 .

Full-dimensional analytical potential energy surface describing the gas-phase Cl + C2H6 reaction and kinetics study of rate constants and kinetic isotope effects.

PubMed

Rangel, Cipriano; Espinosa-Garcia, Joaquin

2018-02-07

Within the Born-Oppenheimer approximation a full-dimensional analytical potential energy surface, PES-2017, was developed for the gas-phase hydrogen abstraction reaction between the chlorine atom and ethane, which is a nine body system. This surface presents a valence-bond/molecular mechanics functional form dependent on 60 parameters and is fitted to high-level ab initio calculations. This reaction presents little exothermicity, -2.30 kcal mol -1 , with a low height barrier, 2.44 kcal mol -1 , and intermediate complexes in the entrance and exit channels. We found that the energetic description was strongly dependent on the ab initio level used and it presented a very flat topology in the entrance channel, which represents a theoretical challenge in the fitting process. In general, PES-2017 reproduces the ab initio information used as input, which is merely a test of self-consistency. As a first test of the quality of the PES-2017, a theoretical kinetics study was performed in the temperature range 200-1400 K using two approaches, i.e. the variational transition-state theory and quasi-classical trajectory calculations, with spin-orbit effects. The rate constants show reasonable agreement with experiments in the whole temperature range, with the largest differences at the lowest temperatures, and this behaviour agrees with previous theoretical studies, thus indicating the inherent difficulties in the theoretical simulation of the kinetics of the title reaction. Different sources of error were analysed, such as the limitations of the PES and theoretical methods, recrossing effects, and the tunnelling effect, which is negligible in this reaction, and the manner in which the spin-orbit effects were included in this non-relativistic study. We found that the variation of spin-orbit coupling along the reaction path, and the influence of the reactivity of the excited Cl( 2 P 1/2 ) state, have relative importance, but do not explain the whole discrepancy. Finally, the activation energy and the kinetics isotope effects reproduce the experimental information.

40 CFR 80.607 - What are the requirements for obtaining an exemption for diesel fuel or ECA marine fuel used for...

Code of Federal Regulations, 2010 CFR

2010-07-01

... section, will cause the exemption to be void ab initio. (6) If any information required under paragraph (c... void ab initio, and may make the party liable for a violation of this subpart. (f) Effects of exemption...

40 CFR 90.108 - Certification.

Code of Federal Regulations, 2010 CFR

2010-07-01

... the certificate may be determined to be void ab initio. (2) The manufacturer shall bear the burden of... certificates that failure to meet these conditions may result in suspension or revocation or the voiding ab initio of the certificate. [60 FR 34598, July 3, 1995, as amended at 64 FR 15238, Mar. 30, 1999] ...

The Band Structure of Polymers: Its Calculation and Interpretation. Part 2. Calculation.

ERIC Educational Resources Information Center

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

1988-01-01

Details ab initio crystal orbital calculations using all-trans-polyethylene as a model. Describes calculations based on various forms of translational symmetry. Compares these calculations with ab initio molecular orbital calculations discussed in a preceding article. Discusses three major approximations made in the crystal case. (CW)

Ab initio calculations of the lattice dynamics of silver halides

NASA Astrophysics Data System (ADS)

Gordienko, A. B.; Kravchenko, N. G.; Sedelnikov, A. N.

2010-12-01

Based on ab initio pseudopotential calculations, the results of investigations of the lattice dynamics of silver halides AgHal (Hal = Cl, Br, I) are presented. Equilibrium lattice parameters, phonon spectra, frequency densities and effective atomic-charge values are obtained for all types of crystals under study.

40 CFR 90.108 - Certification.

Code of Federal Regulations, 2014 CFR

2014-07-01

... the certificate may be determined to be void ab initio. (2) The manufacturer shall bear the burden of... certificates that failure to meet these conditions may result in suspension or revocation or the voiding ab initio of the certificate. [60 FR 34598, July 3, 1995, as amended at 64 FR 15238, Mar. 30, 1999] ...

40 CFR 90.108 - Certification.

Code of Federal Regulations, 2011 CFR

2011-07-01

... the certificate may be determined to be void ab initio. (2) The manufacturer shall bear the burden of... certificates that failure to meet these conditions may result in suspension or revocation or the voiding ab initio of the certificate. [60 FR 34598, July 3, 1995, as amended at 64 FR 15238, Mar. 30, 1999] ...

40 CFR 90.108 - Certification.

Code of Federal Regulations, 2013 CFR

2013-07-01

... the certificate may be determined to be void ab initio. (2) The manufacturer shall bear the burden of... certificates that failure to meet these conditions may result in suspension or revocation or the voiding ab initio of the certificate. [60 FR 34598, July 3, 1995, as amended at 64 FR 15238, Mar. 30, 1999] ...

40 CFR 90.108 - Certification.

Code of Federal Regulations, 2012 CFR

2012-07-01

... the certificate may be determined to be void ab initio. (2) The manufacturer shall bear the burden of... certificates that failure to meet these conditions may result in suspension or revocation or the voiding ab initio of the certificate. [60 FR 34598, July 3, 1995, as amended at 64 FR 15238, Mar. 30, 1999] ...

Interlayer interactions in graphites.

PubMed

Chen, Xiaobin; Tian, Fuyang; Persson, Clas; Duan, Wenhui; Chen, Nan-xian

2013-11-06

Based on ab initio calculations of both the ABC- and AB-stacked graphites, interlayer potentials (i.e., graphene-graphene interaction) are obtained as a function of the interlayer spacing using a modified Möbius inversion method, and are used to calculate basic physical properties of graphite. Excellent consistency is observed between the calculated and experimental phonon dispersions of AB-stacked graphite, showing the validity of the interlayer potentials. More importantly, layer-related properties for nonideal structures (e.g., the exfoliation energy, cleave energy, stacking fault energy, surface energy, etc.) can be easily predicted from the interlayer potentials, which promise to be extremely efficient and helpful in studying van der Waals structures.

Accurate deuterium spectroscopy for fundamental studies

NASA Astrophysics Data System (ADS)

Wcisło, P.; Thibault, F.; Zaborowski, M.; Wójtewicz, S.; Cygan, A.; Kowzan, G.; Masłowski, P.; Komasa, J.; Puchalski, M.; Pachucki, K.; Ciuryło, R.; Lisak, D.

2018-07-01

We present an accurate measurement of the weak quadrupole S(2) 2-0 line in self-perturbed D2 and theoretical ab initio calculations of both collisional line-shape effects and energy of this rovibrational transition. The spectra were collected at the 247-984 Torr pressure range with a frequency-stabilized cavity ring-down spectrometer linked to an optical frequency comb (OFC) referenced to a primary time standard. Our line-shape modeling employed quantum calculations of molecular scattering (the pressure broadening and shift and their speed dependencies were calculated, while the complex frequency of optical velocity-changing collisions was fitted to experimental spectra). The velocity-changing collisions are handled with the hard-sphere collisional kernel. The experimental and theoretical pressure broadening and shift are consistent within 5% and 27%, respectively (the discrepancy for shift is 8% when referred not to the speed averaged value, which is close to zero, but to the range of variability of the speed-dependent shift). We use our high pressure measurement to determine the energy, ν0, of the S(2) 2-0 transition. The ab initio line-shape calculations allowed us to mitigate the expected collisional systematics reaching the 410 kHz accuracy of ν0. We report theoretical determination of ν0 taking into account relativistic and QED corrections up to α5. Our estimation of the accuracy of the theoretical ν0 is 1.3 MHz. We observe 3.4σ discrepancy between experimental and theoretical ν0.

Ab initio study of dynamical E × e Jahn-Teller and spin-orbit coupling effects in the transition-metal trifluorides TiF3, CrF3, and NiF3

NASA Astrophysics Data System (ADS)

Mondal, Padmabati; Opalka, Daniel; Poluyanov, Leonid V.; Domcke, Wolfgang

2012-02-01

Multiconfiguration ab initio methods have been employed to study the effects of Jahn-Teller (JT) and spin-orbit (SO) coupling in the transition-metal trifluorides TiF3, CrF3, and NiF3, which possess spatially doubly degenerate excited states (ME) of even spin multiplicities (M = 2 or 4). The ground states of TiF3, CrF3, and NiF3 are nondegenerate and exhibit minima of D3h symmetry. Potential-energy surfaces of spatially degenerate excited states have been calculated using the state-averaged complete-active-space self-consistent-field method. SO coupling is described by the matrix elements of the Breit-Pauli operator. Linear and higher order JT coupling constants for the JT-active bending and stretching modes as well as SO-coupling constants have been determined. Vibronic spectra of JT-active excited electronic states have been calculated, using JT Hamiltonians for trigonal systems with inclusion of SO coupling. The effect of higher order (up to sixth order) JT couplings on the vibronic spectra has been investigated for selected electronic states and vibrational modes with particularly strong JT couplings. While the weak SO couplings in TiF3 and CrF3 are almost completely quenched by the strong JT couplings, the stronger SO coupling in NiF3 is only partially quenched by JT coupling.

Ab initio many-body calculations of nucleon scattering on ^16O

NASA Astrophysics Data System (ADS)

Navratil, Petr; Quaglioni, Sofia; Roth, Robert

2008-10-01

We develop a new ab initio many-body approachootnotetextS. Quaglioni and P. Navratil, arXiv:0804.1560. capable of describing simultaneously both bound and scattering states in light nuclei, by combining the resonating-group methodootnotetextY. C. Tang et al., Phys. Rep. 47, 167 (1978); K. Langanke and H. Friedrich, Advances in Nuclear Physics, Plenum, New York, 1987. with the ab initio no-core shell model (NCSM).ootnotetextP. Navratil, J. P. Vary, and B. R. Barrett, Phys. Rev. Lett. 84, 5728 (2000); Phys. Rev. C 62, 054311 (2000). In this way, we complement a microscopic-cluster technique with the use of realistic interactions, and a microscopic and consistent description of the nucleon clusters, while preserving Pauli principle and translational symmetry. We will present results for low-energy nucleon scattering on ^16O and for A=17 bound states obtained using realistic nucleon-nucleon potentials. The ^16O wave functions are calculated within the importance-truncated NCSMootnotetextR. Roth and P. Navratil, Phys. Rev. Lett. 99, 092501 (2007). that allows the use of model spaces up to 18φ and ultimately enables to reach convergence of phase-shifts and other observables. Prepared by LLNL under Contract DE-AC52-07NA27344. Support from the U.S. DOE/SC/NP (Work Proposal No. SCW0498), and from the U. S. Department of Energy Grant DE-FC02-07ER41457 is acknowledged.

Analysis of PH3 spectra in the Octad range 2733-3660 cm-1

NASA Astrophysics Data System (ADS)

Nikitin, A. V.; Ivanova, Y. A.; Rey, M.; Tashkun, S. A.; Toon, G. C.; Sung, K.; Tyuterev, Vl. G.

2017-12-01

Improved analysis of positions and intensities of phosphine spectral lines in the Octad region 2733-3660 cm-1 is reported. Some 5768 positions and 1752 intensities were modelled with RMS deviations of 0.00185 cm-1 and 10.9%, respectively. Based on an ab initio potential energy surface, the full Hamiltonian of phosphine nuclear motion was reduced to an effective Hamiltonian using high-order Contact Transformations method adapted to polyads of symmetric top AB3-type molecules with a subsequent empirical optimization of parameters. More than 2000 new ro-vibrational lines were assigned that include transitions for all 13 vibrational Octad sublevels. This new fitting of measured positions and intensities considerably improved the accuracy of line parameters in the calculated database. A comparison of our results with experimental spectra of PNNL showed that the new set of line parameters from this work permits better simulation of observed cross-sections than the HITRAN2012 linelist. In the 2733-3660 cm-1 range, our integrated intensities show a good consistency with recent ab initio variational calculations.

Advanced ab initio relativistic calculations of transition probabilities for some O I and O III emission lines

NASA Astrophysics Data System (ADS)

Nguyen, T. V. B.; Chantler, C. T.; Lowe, J. A.; Grant, I. P.

2014-06-01

This work presents new ab initio relativistic calculations using the multiconfiguration Dirac-Hartree-Fock method of some O I and O III transition lines detected in B-type and Wolf-Rayet stars. Our results are the first able to be presented in both the length and velocity gauges, with excellent gauge convergence. Compared to previous experimental and theoretical uncertainties of up to 50 per cent, our accuracies appear to be in the range of 0.33-5.60 per cent, with gauge convergence up to 0.6 per cent. Similar impressive convergence of the calculated energies is also shown. Two sets of theoretical computations are compared with earlier tabulated measurements. Excellent agreement is obtained with one set of transitions but an interesting and consistent discrepancy exists between the current work and the prior literature, deserving of future experimental studies.

Spectroscopy of 50Sc and ab initio calculations of B (M 3 ) strengths

NASA Astrophysics Data System (ADS)

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.

Ab initio study of structural and mechanical property of solid molecular hydrogens

NASA Astrophysics Data System (ADS)

Ye, Yingting; Yang, Li; Yang, Tianle; Nie, Jinlan; Peng, Shuming; Long, Xinggui; Zu, Xiaotao; Du, Jincheng

2015-06-01

Ab initio calculations based on density functional theory (DFT) were performed to investigate the structural and the elastic properties of solid molecular hydrogens (H2). The influence of molecular axes of H2 on structural relative stabilities of hexagonal close-packed (hcp) and face-centered cubic (fcc) structured hydrogen molecular crystals were systematically investigated. Our results indicate that for hcp structures, disordered hydrogen molecule structure is more stable, while for fcc structures, Pa3 hydrogen molecular crystal is most stable. The cohesive energy of fcc H2 crystal was found to be lower than hcp. The mechanical properties of fcc and hcp hydrogen molecular crystals were obtained, with results consistent with previous theoretical calculations. In addition, the effects of zero point energy (ZPE) and van der Waals (vdW) correction on the cohesive energy and the stability of hydrogen molecular crystals were systematically studied and discussed.

Ab initio study on the dynamics of furfural at the liquid-solid interfaces

NASA Astrophysics Data System (ADS)

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

2013-03-01

Catalytic biomass conversion sometimes occurs at the liquid-solid interfaces. We report ab initio molecular dynamics simulations at finite temperatures for the catalytic reactions involving furfural at the water-Pd and water-Cu interfaces. We found that, during the dynamic process, the furan ring of furfural prefers to be parallel to the Pd surface and the aldehyde group tends to be away from the Pd surface. On the other hand, at the water-Cu(111) interface, furfural prefers to be tilted to the Cu surface while the aldehyde group is bonded to the surface. In both cases, interaction of liquid water and furfural is identified. The difference of dynamic process of furfural at the two interfaces suggests different catalytic reaction mechanisms for the conversion of furfural, consistent with the experimental investigations. Supported by DOE (DE-SC0004600). Simulations and calculations were performed on XSED's and NERSC's supercomputers

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

NASA Astrophysics Data System (ADS)

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

2013-03-01

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

Ab Initio Molecular Dynamics Studies of Pb m Sb n ( m + n ≤ 9) Alloy Clusters

NASA Astrophysics Data System (ADS)

Song, Bingyi; Xu, Baoqiang; Yang, Bin; Jiang, Wenlong; Chen, Xiumin; Xu, Na; Liu, Dachun; Dai, Yongnian

2017-10-01

Structure, stability, and dynamics of Pb m Sb n ( m + n ≤ 9) clusters were investigated using ab initio molecular dynamics. Size dependence of binding energies, the second-order energy difference of clusters, dissociation energy, HOMO-LUMO gaps, Mayer bond order, and the diffusion coefficient of Pb m Sb n clusters were discussed. Results suggest that Pb3Sb2, Pb4Sb2, and Pb5Sb4 ( n = 2 or 4) clusters have higher stability than other clusters, which is consistent with previous findings. In case of Pb-Sb alloy, the dynamics results show that Pb4Sb2 (Pb-22.71 wt pct Sb) can exist in gas phase at 1073 K (800 °C), which reasonably explains the azeotropic phenomenon, and the calculated values are in agreement with the experimental results (Pb-22 wt pct Sb).

Ab initio correlated study of the Al13H- anion: Isomers, their kinetic stability and vertical detachment energies

NASA Astrophysics Data System (ADS)

Moc, Jerzy

2012-01-01

We report correlated ab initio calculations for the Al13H- cluster anion isomers, their kinetic stability and vertical detachment energies (VDEs). Of the two most energetically favored anion structures involving H atom in terminal and threefold bridged sites of the icosahedral Al13-, the higher energy ‘threefold bridged' isomer is shown to be of low kinetic stability. Our results are consistent with the recent photoelectron spectroscopy (PE) study of Grubisic et al. who observed two distinct Al13H- isomers, one of them identified as ‘metastable'. The VDE energies computed at the CCSD(T)/aug-cc-pVTZ//MP2/aug-cc-pVDZ level for the ‘terminal' and ‘threefold bridged' Al13H- isomers of 3.21 and 2.32 eV are in good agreement with those determined in the PE study.

Ab initio theories for light nuclei and neutron stars

NASA Astrophysics Data System (ADS)

Gezerlis, Alexandros

2016-09-01

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

Ab initio calculation of the shear viscosity of neon in the liquid and hypercritical state over a wide pressure and temperature range

NASA Astrophysics Data System (ADS)

Eggenberger, Rolf; Gerber, Stefan; Huber, Hanspeter; Searles, Debra; Welker, Marc

1992-08-01

The shear viscosity is calculated ab initio for the liquid and hypercritical state, i.e. a previously published potential for Ne 2, obtained from ab initio calculations including electron correlation, is used in classical equilibrium molecular dynamics simulations to obtain the shear viscosity from a Green-Kubo integral. The quality of the results is quite uniform over a large pressure range up to 1000 MPa and a wide temperature range from 26 to 600 K. In most cases the calculated shear viscosity deviates by less than 10% from the experimental value, in general the error being only a few percent.

Ab initio determination of mode coupling in HSSH - The torsional splitting in the first excited S-S stretching state

NASA Technical Reports Server (NTRS)

Herbst, Eric; Winnewisser, G.; Yamada, K. M. T.; Defrees, D. J.; Mclean, A. D.

1989-01-01

A mechanism for the enhanced splitting detected in the millimeter-wave rotational spectra of the first excited S-S stretching state of HSSH (disulfane) has been studied. The mechanism, which involves a potential coupling between the first excited S-S stretching state and excited torsional states, has been investigated in part by the use of ab initio theory. Based on an ab initio potential surface, coupling matrix elements have been calculated, and the amount of splitting has then been estimated by second-order perturbation theory. The result, while not in quantitative agreement with the measured splitting, lends plausibility to the assumed mechanism.

Specific interactions between mycobacterial FtsZ protein and curcumin derivatives: Molecular docking and ab initio molecular simulations

NASA Astrophysics Data System (ADS)

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.

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

PubMed Central

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

2015-01-01

AMPLE clusters and truncates ab initio protein structure predictions, producing search models for molecular replacement. Here, an interesting degree of complementarity is shown between targets solved using the different ab initio modelling programs QUARK and ROSETTA. Search models derived from either program collectively solve almost all of the all-helical targets in the test set. Initial solutions produced by Phaser after only 5 min perform surprisingly well, improving the prospects for in situ structure solution by AMPLE during synchrotron visits. Taken together, the results show the potential for AMPLE to run more quickly and successfully solve more targets than previously suspected. PMID:25664744

Approaches to ab initio molecular replacement of α-helical transmembrane proteins.

PubMed

Thomas, Jens M H; Simkovic, Felix; Keegan, Ronan; Mayans, Olga; Zhang, Chengxin; Zhang, Yang; Rigden, Daniel J

2017-12-01

α-Helical transmembrane proteins are a ubiquitous and important class of proteins, but present difficulties for crystallographic structure solution. Here, the effectiveness of the AMPLE molecular replacement pipeline in solving α-helical transmembrane-protein structures is assessed using a small library of eight ideal helices, as well as search models derived from ab initio models generated both with and without evolutionary contact information. The ideal helices prove to be surprisingly effective at solving higher resolution structures, but ab initio-derived search models are able to solve structures that could not be solved with the ideal helices. The addition of evolutionary contact information results in a marked improvement in the modelling and makes additional solutions possible.

AB INITIO Molecular Dynamics Simulations of Water Under Static and Shock Compressed Conditions

NASA Astrophysics Data System (ADS)

Goldman, Nir; Fried, Laurence E.; Mundy, Christopher J.; Kuo, I.-F. William; Curioni, Alessandro; Reed, Evan J.

2007-12-01

We report herein a series of ab initio simulations of water under both static and shocked conditions. We have calculated the coherent x-ray scattering intensity of several phases of water under high pressure, using ab initio Density Functional Theory (DFT). We provide new atomic scattering form factors for water at extreme conditions, which take into account frequently neglected changes in ionic charge and electron delocalization. We have also simulated liquid water undergoing shock loading of velocities from 5-11 km/s using the Multi-Scale Shock Technique (MSST). We show that Density Functional Theory (DFT) molecular dynamics results compare extremely well to experiments on the water shock Hugoniot.

Elastic dipoles of point defects from atomistic simulations

NASA Astrophysics Data System (ADS)

Varvenne, Céline; Clouet, Emmanuel

2017-12-01

The interaction of point defects with an external stress field or with other structural defects is usually well described within continuum elasticity by the elastic dipole approximation. Extraction of the elastic dipoles from atomistic simulations is therefore a fundamental step to connect an atomistic description of the defect with continuum models. This can be done either by a fitting of the point-defect displacement field, by a summation of the Kanzaki forces, or by a linking equation to the residual stress. We perform here a detailed comparison of these different available methods to extract elastic dipoles, and show that they all lead to the same values when the supercell of the atomistic simulations is large enough and when the anharmonic region around the point defect is correctly handled. But, for small simulation cells compatible with ab initio calculations, only the definition through the residual stress appears tractable. The approach is illustrated by considering various point defects (vacancy, self-interstitial, and hydrogen solute atom) in zirconium, using both empirical potentials and ab initio calculations.

Electronic structure, dielectric response, and surface charge distribution of RGD (1FUV) peptide.

PubMed

Adhikari, Puja; Wen, Amy M; French, Roger H; Parsegian, V Adrian; Steinmetz, Nicole F; Podgornik, Rudolf; Ching, Wai-Yim

2014-07-08

Long and short range molecular interactions govern molecular recognition and self-assembly of biological macromolecules. Microscopic parameters in the theories of these molecular interactions are either phenomenological or need to be calculated within a microscopic theory. We report a unified methodology for the ab initio quantum mechanical (QM) calculation that yields all the microscopic parameters, namely the partial charges as well as the frequency-dependent dielectric response function, that can then be taken as input for macroscopic theories of electrostatic, polar, and van der Waals-London dispersion intermolecular forces. We apply this methodology to obtain the electronic structure of the cyclic tripeptide RGD-4C (1FUV). This ab initio unified methodology yields the relevant parameters entering the long range interactions of biological macromolecules, providing accurate data for the partial charge distribution and the frequency-dependent dielectric response function of this peptide. These microscopic parameters determine the range and strength of the intricate intermolecular interactions between potential docking sites of the RGD-4C ligand and its integrin receptor.

Approximate solution of the mode-mode coupling integral: Application to cytosine and its deuterated derivative.

PubMed

Rasheed, Tabish; Ahmad, Shabbir

2010-10-01

Ab initio Hartree-Fock (HF), density functional theory (DFT) and second-order Møller-Plesset (MP2) methods were used to perform harmonic and anharmonic calculations for the biomolecule cytosine and its deuterated derivative. The anharmonic vibrational spectra were computed using the vibrational self-consistent field (VSCF) and correlation-corrected vibrational self-consistent field (CC-VSCF) methods. Calculated anharmonic frequencies have been compared with the argon matrix spectra reported in literature. The results were analyzed with focus on the properties of anharmonic couplings between pair of modes. A simple and easy to use formula for calculation of mode-mode coupling magnitudes has been derived. The key element in present approach is the approximation that only interactions between pairs of normal modes have been taken into account, while interactions of triples or more are neglected. FTIR and Raman spectra of solid state cytosine have been recorded in the regions 400-4000 cm(-1) and 60-4000 cm(-1), respectively. Vibrational analysis and assignments are based on calculated potential energy distribution (PED) values. Copyright 2010 Elsevier B.V. All rights reserved.

A self-consistent transport model for molecular conduction based on extended Hückel theory with full three-dimensional electrostatics

NASA Astrophysics Data System (ADS)

Zahid, F.; Paulsson, M.; Polizzi, E.; Ghosh, A. W.; Siddiqui, L.; Datta, S.

2005-08-01

We present a transport model for molecular conduction involving an extended Hückel theoretical treatment of the molecular chemistry combined with a nonequilibrium Green's function treatment of quantum transport. The self-consistent potential is approximated by CNDO (complete neglect of differential overlap) method and the electrostatic effects of metallic leads (bias and image charges) are included through a three-dimensional finite element method. This allows us to capture spatial details of the electrostatic potential profile, including effects of charging, screening, and complicated electrode configurations employing only a single adjustable parameter to locate the Fermi energy. As this model is based on semiempirical methods it is computationally inexpensive and flexible compared to ab initio models, yet at the same time it is able to capture salient qualitative features as well as several relevant quantitative details of transport. We apply our model to investigate recent experimental data on alkane dithiol molecules obtained in a nanopore setup. We also present a comparison study of single molecule transistors and identify electronic properties that control their performance.

Self-consistent phonon calculations of lattice dynamical properties in cubic SrTiO3 with first-principles anharmonic force constants

NASA Astrophysics Data System (ADS)

Tadano, Terumasa; Tsuneyuki, Shinji

2015-08-01

We present an ab initio framework to calculate anharmonic phonon frequency and phonon lifetime that is applicable to severely anharmonic systems. We employ self-consistent phonon (SCPH) theory with microscopic anharmonic force constants, which are extracted from density functional calculations using the least absolute shrinkage and selection operator technique. We apply the method to the high-temperature phase of SrTiO3 and obtain well-defined phonon quasiparticles that are free from imaginary frequencies. Here we show that the anharmonic phonon frequency of the antiferrodistortive mode depends significantly on the system size near the critical temperature of the cubic-to-tetragonal phase transition. By applying perturbation theory to the SCPH result, phonon lifetimes are calculated for cubic SrTiO3, which are then employed to predict lattice thermal conductivity using the Boltzmann transport equation within the relaxation-time approximation. The presented methodology is efficient and accurate, paving the way toward a reliable description of thermodynamic, dynamic, and transport properties of systems with severe anharmonicity, including thermoelectric, ferroelectric, and superconducting materials.

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

PubMed

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.

Ground-state properties of Na2IrO3 determined from an ab initio Hamiltonian and its extensions containing Kitaev and extended Heisenberg interactions

NASA Astrophysics Data System (ADS)

Okubo, Tsuyoshi; Shinjo, Kazuya; Yamaji, Youhei; Kawashima, Naoki; Sota, Shigetoshi; Tohyama, Takami; Imada, Masatoshi

2017-08-01

We investigate the ground state properties of Na2IrO3 based on numerical calculations of the recently proposed ab initio Hamiltonian represented by Kitaev and extended Heisenberg interactions. To overcome the limitation posed by small tractable system sizes in the exact diagonalization study employed in a previous study [Y. Yamaji et al., Phys. Rev. Lett. 113, 107201 (2014), 10.1103/PhysRevLett.113.107201], we apply a two-dimensional density matrix renormalization group and an infinite-size tensor-network method. By calculating at much larger system sizes, we critically test the validity of the exact diagonalization results. The results consistently indicate that the ground state of Na2IrO3 is a magnetically ordered state with zigzag configuration in agreement with experimental observations and the previous diagonalization study. Applications of the two independent methods in addition to the exact diagonalization study further uncover a consistent and rich phase diagram near the zigzag phase beyond the accessibility of the exact diagonalization. For example, in the parameter space away from the ab initio value of Na2IrO3 controlled by the trigonal distortion, we find three phases: (i) an ordered phase with the magnetic moment aligned mutually in 120 degrees orientation on every third hexagon, (ii) a magnetically ordered phase with a 16-site unit cell, and (iii) an ordered phase with presumably incommensurate periodicity of the moment. It suggests that potentially rich magnetic structures may appear in A2IrO3 compounds for A other than Na. The present results also serve to establish the accuracy of the first-principles approach in reproducing the available experimental results thereby further contributing to finding a route to realize the Kitaev spin liquid.

Interaction of Al with O2 exposed Mo2BC

NASA Astrophysics Data System (ADS)

Bolvardi, Hamid; Music, Denis; Schneider, Jochen M.

2015-03-01

A Mo2BC(0 4 0) surface was exposed to O2. The gas interaction was investigated using ab initio molecular dynamics and X-ray photoelectron spectroscopy (XPS) of air exposed surfaces. The calculations suggest that the most dominating physical mechanism is dissociative O2 adsorption whereby Mosbnd O, Osbnd Mosbnd O and Mo2sbnd Csbnd O bond formation is observed. To validate these results, Mo2BC thin films were synthesized utilizing high power pulsed magnetron sputtering and air exposed surfaces were probed by XPS. MoO2 and MoO3 bond formation is observed and is consistent with here obtained ab initio data. Additionally, the interfacial interactions of O2 exposed Mo2BC(0 4 0) surface with an Al nonamer is studied with ab initio molecular dynamics to describe on the atomic scale the interaction between this surface and Al to mimic the interface present during cold forming processes of Al based alloys. The Al nonamer was disrupted and Al forms chemical bonds with oxygen contained in the O2 exposed Mo2BC(0 4 0) surface. Based on the comparison of here calculated adsorption energy with literature data, Alsbnd Al bonds are shown to be significantly weaker than the Alsbnd O bonds formed across the interface. Hence, Alsbnd Al bond rupture is expected for a mechanically loaded interface. Therefore the adhesion of a residual Al on the native oxide layer is predicted. This is consistent with experimental observations. The data presented here may also be relevant for other oxygen containing surfaces in a contact with Al or Al based alloys for example during forming operations.

Thermal Conductivity of Metallic Uranium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hin, Celine

This project has developed a modeling and simulation approaches to predict the thermal conductivity of metallic fuels and their alloys. We focus on two methods. The first method has been developed by the team at the University of Wisconsin Madison. They developed a practical and general modeling approach for thermal conductivity of metals and metal alloys that integrates ab-initio and semi-empirical physics-based models to maximize the strengths of both techniques. The second method has been developed by the team at Virginia Tech. This approach consists of a determining the thermal conductivity using only ab-initio methods without any fitting parameters. Bothmore » methods were complementary. The models incorporated both phonon and electron contributions. Good agreement with experimental data over a wide temperature range were found. The models also provided insight into the different physical factors that govern the thermal conductivity under different temperatures. The models were general enough to incorporate more complex effects like additional alloying species, defects, transmutation products and noble gas bubbles to predict the behavior of complex metallic alloys like U-alloy fuel systems under burnup. 3 Introduction Thermal conductivity is an important thermal physical property affecting the performance and efficiency of metallic fuels [1]. Some experimental measurement of thermal conductivity and its correlation with composition and temperature from empirical fitting are available for U, Zr and their alloys with Pu and other minor actinides. However, as reviewed in by Kim, Cho and Sohn [2], due to the difficulty in doing experiments on actinide materials, thermal conductivities of metallic fuels have only been measured at limited alloy compositions and temperatures, some of them even being negative and unphysical. Furthermore, the correlations developed so far are empirical in nature and may not be accurate when used for prediction at conditions far from those used in the original fitting. Moreover, as fuels burn up in the reactor and fission products are built up, thermal conductivity is also significantly changed [3]. Unfortunately, fundamental understanding of the effect of fission products is also currently lacking. In this project, we probe thermal conductivity of metallic fuels with ab initio calculations, a theoretical tool with the potential to yield better accuracy and predictive power than empirical fitting. This work will both complement experimental data by determining thermal conductivity in wider composition and temperature ranges than is available experimentally, and also develop mechanistic understanding to guide better design of metallic fuels in the future. So far, we focused on α-U perfect crystal, the ground-state phase of U metal. We focus on two methods. The first method has been developed by the team at the University of Wisconsin Madison. They developed a practical and general modeling approach for thermal conductivity of metals and metal alloys that integrates ab-initio and semi-empirical physics-based models to maximize the strengths of both techniques. The second method has been developed by the team at Virginia Tech. This approach consists of a determining the thermal conductivity using only ab-initio methods without any fitting parameters. Both methods were complementary and very helpful to understand the physics behind the thermal conductivity in metallic uranium and other materials with similar characteristics. In Section I, the combined model developed at UWM is explained. In Section II, the ab-initio method developed at VT is described along with the uranium pseudo-potential and its validation. Section III is devoted to the work done by Jianguo Yu at INL. Finally, we will present the performance of the project in terms of milestones, publications, and presentations.« less

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

ERIC Educational Resources Information Center

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

2016-01-01

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

Ab initio theory of noble gas atoms in bcc transition metals

DOE PAGES

Jiang, Chao; Zhang, Yongfeng; Gao, Yipeng; ...

2018-01-01

Systematic ab initio calculations based on density functional theory have been performed to gain fundamental understanding of the interactions between noble gas atoms (He, Ne, Ar and Kr) and bcc transition metals in groups 5B (V, Nb and Ta), 6B (Cr, Mo and W) and 8B (Fe).

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

ERIC Educational Resources Information Center

Halpern, Arthur M.

2011-01-01

A computational chemistry experiment is described in which students can use advanced ab initio quantum mechanical methods to test the ability of the London equation to account quantitatively for the attractive (dispersion) interactions between rare gas atoms. Using readily available electronic structure applications, students can calculate the…

Infrared Emission Spectrum of the Hydroxyl Radical: A Novel Experiment in Molecular Spectroscopy.

ERIC Educational Resources Information Center

Henderson, Giles; And Others

1982-01-01

Describes an experiment in which parameters from an "ab-initio" potential are used to calculate vibrational-rotational energy levels and construct a "stick spectrum" for the overtone emission of the hydroxyl radical. Provides background information on ab-initio spectrum, experimental procedures, and analysis of data. (Author/JN)

NSSEFF COMPUTATIONAL AND THEORETICAL DESIGN OF PHOTO AND MECHANORESPONSIVE MOLECULAR DEVICES

DTIC Science & Technology

2016-11-10

R. McGibbon, F. Liu, V.S. Pande and T.J. Martinez, "Discovering Chemistry with an Ab Initio Nanoreactor," Nature Chem. 6, 1044 (2014...Pande and T.J. Martinez, "Discovering Chemistry with an Ab Initio Nanoreactor," Nature Chem. 6, 1044 (2014). New discoveries, inventions, or patent

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

PubMed

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

2010-09-29

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

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

NASA Technical Reports Server (NTRS)

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.

Ab Initio structure prediction for Escherichia coli: towards genome-wide protein structure modeling and fold assignment

PubMed Central

Xu, Dong; Zhang, Yang

2013-01-01

Genome-wide protein structure prediction and structure-based function annotation have been a long-term goal in molecular biology but not yet become possible due to difficulties in modeling distant-homology targets. We developed a hybrid pipeline combining ab initio folding and template-based modeling for genome-wide structure prediction applied to the Escherichia coli genome. The pipeline was tested on 43 known sequences, where QUARK-based ab initio folding simulation generated models with TM-score 17% higher than that by traditional comparative modeling methods. For 495 unknown hard sequences, 72 are predicted to have a correct fold (TM-score > 0.5) and 321 have a substantial portion of structure correctly modeled (TM-score > 0.35). 317 sequences can be reliably assigned to a SCOP fold family based on structural analogy to existing proteins in PDB. The presented results, as a case study of E. coli, represent promising progress towards genome-wide structure modeling and fold family assignment using state-of-the-art ab initio folding algorithms. PMID:23719418

Ab initio parameterization of a charge optimized many-body forcefield for Si-SiO2: Validation and thermal transport in nanostructures.

PubMed

France-Lanord, Arthur; Soukiassian, Patrick; Glattli, Christian; Wimmer, Erich

2016-03-14

In an effort to extend the reach of current ab initio calculations to simulations requiring millions of configurations for complex systems such as heterostructures, we have parameterized the third-generation Charge Optimized Many-Body (COMB3) potential using solely ab initio total energies, forces, and stress tensors as input. The quality and the predictive power of the new forcefield are assessed by computing properties including the cohesive energy and density of SiO2 polymorphs, surface energies of alpha-quartz, and phonon densities of states of crystalline and amorphous phases of SiO2. Comparison with data from experiments, ab initio calculations, and molecular dynamics simulations using published forcefields including BKS (van Beest, Kramer, and van Santen), ReaxFF, and COMB2 demonstrates an overall improvement of the new parameterization. The computed temperature dependence of the thermal conductivity of crystalline alpha-quartz and the Kapitza resistance of the interface between crystalline Si(001) and amorphous silica is in excellent agreement with experiment, setting the stage for simulations of complex nanoscale heterostructures.

Ab initio and empirical energy landscapes of (MgF2)n clusters (n = 3, 4).

PubMed

Neelamraju, S; Schön, J C; Doll, K; Jansen, M

2012-01-21

We explore the energy landscape of (MgF(2))(3) on both the empirical and ab initio level using the threshold algorithm. In order to determine the energy landscape and the dynamics of the trimer we investigate not only the stable isomers but also the barriers separating these isomers. Furthermore, we study the probability flows in order to estimate the stability of all the isomers found. We find that there is reasonable qualitative agreement between the ab initio and empirical potential, and important features such as sub-basins and energetic barriers follow similar trends. However, we observe that the energies are systematically different for the less compact clusters, when comparing empirical and ab initio energies. Since the underlying motivation of this work is to identify the possible clusters present in the gas phase during a low-temperature atom beam deposition synthesis of MgF(2), we employ the same procedure to additionally investigate the energy landscape of the tetramer. For this case, however, we use only the empirical potential.

IR Spectra of (HCOOH)2 and (DCOOH)2: Experiment, VSCF/VCI, and Ab Initio Molecular Dynamics Calculations Using Full-Dimensional Potential and Dipole Moment Surfaces.

PubMed

Qu, Chen; Bowman, Joel M

2018-05-17

We report quantum VSCF/VCI and ab initio molecular dynamics (AIMD) calculations of the IR spectra of (HCOOH) 2 and (DCOOH) 2 , using full-dimensional, ab initio potential energy and dipole moment surfaces (PES and DMS). These surfaces are fits, using permutationally invariant polynomials, to 13 475 ab initio CCSD(T)-F12a electronic energies and MP2 dipole moments. Here "AIMD" means using these ab initio potential and dipole moment surfaces in the MD calculations. The VSCF/VCI calculations use all (24) normal modes for coupling, with a four-mode representation of the potential. The quantum spectra align well with jet-cooled and room-temperature experimental spectra over the spectral range 600-3600 cm -1 . Analyses of the complex O-H and C-H stretch bands are made based on the mixing of the VSCF/VCI basis functions. The comparisons of the AIMD IR spectra with both experimental and VSCF/VCI ones provide tests of the accuracy of the AIMD approach. These indicate good accuracy for simple bands but not for the complex O-H stretch band, which is upshifted from experimental and VSCF/VCI bands by roughly 300 cm -1 . In addition to testing the AIMD approach, the PES, DMS, and VSCF/VCI calculations for formic acid dimer provide opportunities for testing other methods to represent high-dimensional data and other methods that perform postharmonic vibrational calculations.

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.

PubMed

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

2017-02-14

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 16 O 3 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 ΔV = 6. A particular challenge was a correct description of the B-type bands (even ΔV 3 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 μm 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 ν 3 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.

Ab Initio Path Integral Molecular Dynamics Study of the Nuclear Quantum Effect on Out-of-Plane Ring Deformation of Hydrogen Maleate Anion.

PubMed

Kawashima, Yukio; Tachikawa, Masanori

2014-01-14

Ab initio path integral molecular dynamics (PIMD) simulation was performed to understand the nuclear quantum effect on the out-of-plane ring deformation of hydrogen maleate anion and investigate the existence of a stable structure with ring deformation, which was suggested in experimental observation (Fillaux et al., Chem. Phys. 1999, 120, 387-403). The isotope effect and the temperature effect are studied as well. We first investigated the nuclear quantum effect on the proton transfer. In static calculation and classical ab initio molecular dynamics simulations, the proton in the hydrogen bond is localized to either oxygen atom. On the other hand, the proton is located at the center of two oxygen atoms in quantum ab initio PIMD simulations. The nuclear quantum effect washes out the barrier of proton transfer. We next examined the nuclear quantum effect on the motion of hydrogen maleate anion. Principal component analysis revealed that the out-of-plane ring bending modes have dominant contribution to the entire molecular motion. In quantum ab initio PIMD simulations, structures with ring deformation were the global minimum for the deuterated isotope at 300 K. We analyzed the out-of-plane ring bending mode further and found that there are three minima along a ring distortion mode. We successfully found a stable structure with ring deformation of hydrogen maleate for the first time, to our knowledge, using theoretical calculation. The structures with ring deformation found in quantum simulation of the deuterated isotope allowed the proton transfer to occur more frequently than the planar structure. Static ab initio electronic structure calculation found that the structures with ring deformation have very small proton transfer barrier compared to the planar structure. We suggest that the "proton transfer driven" mechanism is the origin of stabilization for the structure with out-of-plane ring deformation.

Ab initio construction of magnetic phase diagrams in alloys: The case of Fe 1-xMn xPt

DOE PAGES

Pujari, B. S.; Larson, P.; Antropov, V. P.; ...

2015-07-28

A first-principles approach to the construction of concentration-temperature magnetic phase diagrams of metallic alloys is presented. The method employs self-consistent total energy calculations based on the coherent potential approximation for partially ordered and noncollinear magnetic states and is able to account for competing interactions and multiple magnetic phases. The application to the Fe 1–xMn xPt “magnetic chameleon” system yields the sequence of magnetic phases at T = 0 and the c-T magnetic phase diagram in good agreement with experiment, and a new low-temperature phase is predicted at the Mn-rich end. The importance of non-Heisenberg interactions for the description of themore » magnetic phase diagram is demonstrated.« less

Vacuum Ultraviolet Laser Probe of Chemical Dynamics of Aerospace Relevance

DTIC Science & Technology

2012-09-12

carbide cation”, J. Phys. Chem. A (invited), 113, 4242 (2009). 5. Kai-Chung Lau , Yih-Chung Chang, Chow-Sheng Lam , and C. Y. Ng, “High-level ab...Chem. A (invited), 113, 14321 (2009). 6. Kai-Chung Lau , Yih-Chung Chang, Chow-Sheng Lam , and C. Y. Ng, “High-level ab initio predictions of the...VI. Selected scientific findings 1. Kai-Chung Lau , Yih-Chung Chang, Xiaoyu Shi, and C. Y. Ng, “High-level ab initio predictions of the ionization

The application of ab initio calculations to molecular spectroscopy

NASA Technical Reports Server (NTRS)

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

1989-01-01

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

The application of ab initio calculations to molecular spectroscopy

NASA Technical Reports Server (NTRS)

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

1989-01-01

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

{bold {ital Ab initio}} studies of the structural and electronic properties of solid cubane

DOE Office of Scientific and Technical Information (OSTI.GOV)

Richardson, S.L.; Martins, J.L.

1998-12-01

In this paper, we report {ital ab initio} calculation of the structural and electronic properties of solid cubane (s-C{sub 8}H{sub 8}) in the local-density approximation. By using an {ital ab initio} constant pressure extended molecular dynamics method with variable cell shape proposed by Wentzcovitch, Martins, and Price, we compute a lattice parameter {ital a} and a bond angle {alpha} for the rhombohedral Bravais lattice and compare it with experimental x-ray data. We obtain bond lengths for the mononuclear C{sub 8}H{sub 8} unit of basis atoms, as well as a density of states and heat of formation. {copyright} {ital 1998} {italmore » The American Physical Society}« less

Einstein coefficients and oscillator strengths for low lying state of CO molecules

NASA Astrophysics Data System (ADS)

Swer, S.; Syiemiong, A.; Ram, M.; Jha, A. K.; Saxena, A.

2018-04-01

Einstein Coefficients and Oscillator Strengths for different state of CO molecule have been calculated using LEROY'S LEVEL program and MOLCAS ab initio code. Using the wave function derived from Morse potential and transition dipole moment obtained from ab initio calculation, The potential energy functions were computed for these states using the spectroscopic constants. The Morse potential of these states and electronic transition dipole moment of the transition calculated in a recent ab initio study have been used in LEVEL program to produce transition dipole matrix element for a large number of bands. Einstein Coefficients have also been used to compute the radiative lifetimes of several vibrational levels and the calculated values are compared with other theoretical results and experimental values.

Ab Initio and Analytic Intermolecular Potentials for Ar–CH3OH

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tasic, Uros; Alexeev, Yuri; Vayner, Grigoriy

2006-09-20

Ab initio calculations at the CCSD(T)/aug-cc-pVTZ level of theory were used to characterize the Ar–CH₃y6tOH intermolecular potential energy surface (PES). Potential energy curves were calculated for four different Ar + CH₃OH orientations and used to derive an analytic function for the intermolecular PES. A sum of Ar–C, Ar–O, Ar–H(C), and Ar–H(O) two-body potentials gives an excellent fit to these potential energy curves up to 100 kcal mol¯¹, and adding an additional r¯¹n term to the Buckingham two-body potential results in only a minor improvement in the fit. Three Ar–CH₃OH van der Waals minima were found from the CCSD(T)/aug-cc-pVTZ//MP2/aug-cc-pVTZ calculations. Themore » structure of the global minimum is in overall good agreement with experiment (X.-C. Tan, L. Sun and R. L. Kuczkowski, J. Mol. Spectrosc., 1995, 171, 248). It is T-shaped with the hydroxyl H-atom syn with respect to Ar. Extrapolated to the complete basis set (CBS) limit, the global minimum has a well depth of 0.72 kcal mol¯¹ with basis set superposition error (BSSE) correction. The aug-cc-pVTZ basis set gives a well depth only 0.10 kcal mol¯¹ smaller than this value. The well depths of the other two minima are within 0.16 kcal mol¯¹ of the global minimum. The analytic Ar–CH₃OH intermolecular potential also identifies these three minima as the only van der Waals minima and the structures predicted by the analytic potential are similar to the ab initio structures. The analytic potential identifies the same global minimum and the predicted well depths for the minima are within 0.05 kcal mol¯1 of the ab initio values. Combining this Ar–CH₃OH intermolecular potential with a potential for a OH-terminated alkylthiolate self-assembled monolayer surface (i.e., HO-SAM) provides a potential to model Ar + HO-SAM collisions.« less

An Ab Initio Study of Alkali-C60 Complexes

NASA Astrophysics Data System (ADS)

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

2003-03-01

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

Superior ab initio identification, annotation and characterisation of TEs and segmental duplications from genome assemblies.

PubMed

Zeng, Lu; Kortschak, R Daniel; Raison, Joy M; Bertozzi, Terry; Adelson, David L

2018-01-01

Transposable Elements (TEs) are mobile DNA sequences that make up significant fractions of amniote genomes. However, they are difficult to detect and annotate ab initio because of their variable features, lengths and clade-specific variants. We have addressed this problem by refining and developing a Comprehensive ab initio Repeat Pipeline (CARP) to identify and cluster TEs and other repetitive sequences in genome assemblies. The pipeline begins with a pairwise alignment using krishna, a custom aligner. Single linkage clustering is then carried out to produce families of repetitive elements. Consensus sequences are then filtered for protein coding genes and then annotated using Repbase and a custom library of retrovirus and reverse transcriptase sequences. This process yields three types of family: fully annotated, partially annotated and unannotated. Fully annotated families reflect recently diverged/young known TEs present in Repbase. The remaining two types of families contain a mixture of novel TEs and segmental duplications. These can be resolved by aligning these consensus sequences back to the genome to assess copy number vs. length distribution. Our pipeline has three significant advantages compared to other methods for ab initio repeat identification: 1) we generate not only consensus sequences, but keep the genomic intervals for the original aligned sequences, allowing straightforward analysis of evolutionary dynamics, 2) consensus sequences represent low-divergence, recently/currently active TE families, 3) segmental duplications are annotated as a useful by-product. We have compared our ab initio repeat annotations for 7 genome assemblies to other methods and demonstrate that CARP compares favourably with RepeatModeler, the most widely used repeat annotation package.

Five ab initio potential energy and dipole moment surfaces for hydrated NaCl and NaF. I. Two-body interactions.

PubMed

Wang, Yimin; Bowman, Joel M; Kamarchik, Eugene

2016-03-21

We report full-dimensional, ab initio-based potentials and dipole moment surfaces for NaCl, NaF, Na(+)H2O, F(-)H2O, and Cl(-)H2O. The NaCl and NaF potentials are diabatic ones that dissociate to ions. These are obtained using spline fits to CCSD(T)/aug-cc-pV5Z energies. In addition, non-linear least square fits using the Born-Mayer-Huggins potential are presented, providing accurate parameters based strictly on the current ab initio energies. The long-range behavior of the NaCl and NaF potentials is shown to go, as expected, accurately to the point-charge Coulomb interaction. The three ion-H2O potentials are permutationally invariant fits to roughly 20,000 coupled cluster CCSD(T) energies (awCVTZ basis for Na(+) and aVTZ basis for Cl(-) and F(-)), over a large range of distances and H2O intramolecular configurations. These potentials are switched accurately in the long range to the analytical ion-dipole interactions, to improve computational efficiency. Dipole moment surfaces are fits to MP2 data; for the ion-ion cases, these are well described in the intermediate- and long-range by the simple point-charge expression. The performance of these new fits is examined by direct comparison to additional ab initio energies and dipole moments along various cuts. Equilibrium structures, harmonic frequencies, and electronic dissociation energies are also reported and compared to direct ab initio results. These indicate the high fidelity of the new PESs.

Superior ab initio identification, annotation and characterisation of TEs and segmental duplications from genome assemblies

PubMed Central

Zeng, Lu; Kortschak, R. Daniel; Raison, Joy M.

2018-01-01

Transposable Elements (TEs) are mobile DNA sequences that make up significant fractions of amniote genomes. However, they are difficult to detect and annotate ab initio because of their variable features, lengths and clade-specific variants. We have addressed this problem by refining and developing a Comprehensive ab initio Repeat Pipeline (CARP) to identify and cluster TEs and other repetitive sequences in genome assemblies. The pipeline begins with a pairwise alignment using krishna, a custom aligner. Single linkage clustering is then carried out to produce families of repetitive elements. Consensus sequences are then filtered for protein coding genes and then annotated using Repbase and a custom library of retrovirus and reverse transcriptase sequences. This process yields three types of family: fully annotated, partially annotated and unannotated. Fully annotated families reflect recently diverged/young known TEs present in Repbase. The remaining two types of families contain a mixture of novel TEs and segmental duplications. These can be resolved by aligning these consensus sequences back to the genome to assess copy number vs. length distribution. Our pipeline has three significant advantages compared to other methods for ab initio repeat identification: 1) we generate not only consensus sequences, but keep the genomic intervals for the original aligned sequences, allowing straightforward analysis of evolutionary dynamics, 2) consensus sequences represent low-divergence, recently/currently active TE families, 3) segmental duplications are annotated as a useful by-product. We have compared our ab initio repeat annotations for 7 genome assemblies to other methods and demonstrate that CARP compares favourably with RepeatModeler, the most widely used repeat annotation package. PMID:29538441

Cooperative effects in the structuring of fluoride water clusters: Ab initio hybrid quantum mechanical/molecular mechanical model incorporating polarizable fluctuating charge solvent

NASA Astrophysics Data System (ADS)

Bryce, Richard A.; Vincent, Mark A.; Malcolm, Nathaniel O. J.; Hillier, Ian H.; Burton, Neil A.

1998-08-01

A new hybrid quantum mechanical/molecular mechanical model of solvation is developed and used to describe the structure and dynamics of small fluoride/water clusters, using an ab initio wave function to model the ion and a fluctuating charge potential to model the waters. Appropriate parameters for the water-water and fluoride-water interactions are derived, with the fluoride anion being described by density functional theory and a large Gaussian basis. The role of solvent polarization in determining the structure and energetics of F(H2O)4- clusters is investigated, predicting a slightly greater stability of the interior compared to the surface structure, in agreement with ab initio studies. An extended Lagrangian treatment of the polarizable water, in which the water atomic charges fluctuate dynamically, is used to study the dynamics of F(H2O)4- cluster. A simulation using a fixed solvent charge distribution indicates principally interior, solvated states for the cluster. However, a preponderance of trisolvated configurations is observed using the polarizable model at 300 K, which involves only three direct fluoride-water hydrogen bonds. Ab initio calculations confirm this trisolvated species as a thermally accessible state at room temperature, in addition to the tetrasolvated interior and surface structures. Extension of this polarizable water model to fluoride clusters with five and six waters gave less satisfactory agreement with experimental energies and with ab initio geometries. However, our results do suggest that a quantitative model of solvent polarization is fundamental for an accurate understanding of the properties of anionic water clusters.

The many-body Wigner Monte Carlo method for time-dependent ab-initio quantum simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sellier, J.M., E-mail: jeanmichel.sellier@parallel.bas.bg; Dimov, I.

2014-09-15

The aim of ab-initio approaches is the simulation of many-body quantum systems from the first principles of quantum mechanics. These methods are traditionally based on the many-body Schrödinger equation which represents an incredible mathematical challenge. In this paper, we introduce the many-body Wigner Monte Carlo method in the context of distinguishable particles and in the absence of spin-dependent effects. Despite these restrictions, the method has several advantages. First of all, the Wigner formalism is intuitive, as it is based on the concept of a quasi-distribution function. Secondly, the Monte Carlo numerical approach allows scalability on parallel machines that is practicallymore » unachievable by means of other techniques based on finite difference or finite element methods. Finally, this method allows time-dependent ab-initio simulations of strongly correlated quantum systems. In order to validate our many-body Wigner Monte Carlo method, as a case study we simulate a relatively simple system consisting of two particles in several different situations. We first start from two non-interacting free Gaussian wave packets. We, then, proceed with the inclusion of an external potential barrier, and we conclude by simulating two entangled (i.e. correlated) particles. The results show how, in the case of negligible spin-dependent effects, the many-body Wigner Monte Carlo method provides an efficient and reliable tool to study the time-dependent evolution of quantum systems composed of distinguishable particles.« less

Low-Resolution Structure of the Full-Length Barley (Hordeum vulgare) SGT1 Protein in Solution, Obtained Using Small-Angle X-Ray Scattering

PubMed Central

Taube, Michał; Pieńkowska, Joanna R.; Jarmołowski, Artur; Kozak, Maciej

2014-01-01

SGT1 is an evolutionarily conserved eukaryotic protein involved in many important cellular processes. In plants, SGT1 is involved in resistance to disease. In a low ionic strength environment, the SGT1 protein tends to form dimers. The protein consists of three structurally independent domains (the tetratricopeptide repeats domain (TPR), the CHORD- and SGT1-containing domain (CS), and the SGT1-specific domain (SGS)), and two less conserved variable regions (VR1 and VR2). In the present study, we provide the low-resolution structure of the barley (Hordeum vulgare) SGT1 protein in solution and its dimer/monomer equilibrium using small-angle scattering of synchrotron radiation, ab-initio modeling and circular dichroism spectroscopy. The multivariate curve resolution least-square method (MCR-ALS) was applied to separate the scattering data of the monomeric and dimeric species from a complex mixture. The models of the barley SGT1 dimer and monomer were formulated using rigid body modeling with ab-initio structure prediction. Both oligomeric forms of barley SGT1 have elongated shapes with unfolded inter-domain regions. Circular dichroism spectroscopy confirmed that the barley SGT1 protein had a modular architecture, with an α-helical TPR domain, a β-sheet sandwich CS domain, and a disordered SGS domain separated by VR1 and VR2 regions. Using molecular docking and ab-initio protein structure prediction, a model of dimerization of the TPR domains was proposed. PMID:24714665

Study of hydrogen-molecule guests in type II clathrate hydrates using a force-matched potential model parameterised from ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

Burnham, Christian J.; Futera, Zdenek; English, Niall J.

2018-03-01

The force-matching method has been applied to parameterise an empirical potential model for water-water and water-hydrogen intermolecular interactions for use in clathrate-hydrate simulations containing hydrogen guest molecules. The underlying reference simulations constituted ab initio molecular dynamics (AIMD) of clathrate hydrates with various occupations of hydrogen-molecule guests. It is shown that the resultant model is able to reproduce AIMD-derived free-energy curves for the movement of a tagged hydrogen molecule between the water cages that make up the clathrate, thus giving us confidence in the model. Furthermore, with the aid of an umbrella-sampling algorithm, we calculate barrier heights for the force-matched model, yielding the free-energy barrier for a tagged molecule to move between cages. The barrier heights are reasonably large, being on the order of 30 kJ/mol, and are consistent with our previous studies with empirical models [C. J. Burnham and N. J. English, J. Phys. Chem. C 120, 16561 (2016) and C. J. Burnham et al., Phys. Chem. Chem. Phys. 19, 717 (2017)]. Our results are in opposition to the literature, which claims that this system may have very low barrier heights. We also compare results to that using the more ad hoc empirical model of Alavi et al. [J. Chem. Phys. 123, 024507 (2005)] and find that this model does very well when judged against the force-matched and ab initio simulation data.

Strategic L2 Lexical Innovation: Case Study of a University-Level Ab Initio Learner of German.

ERIC Educational Resources Information Center

Ridley, Jennifer; Singleton, David

1995-01-01

This article presents a case study of one English-speaking ab initio learner of German. It found that in target language production tasks performed over a two-year period, the subject exhibited a particular tendency toward lexical innovation as a strategy to cope with the lack of target language lexical knowledge. (38 references) (MDM)

Approximate Quantum Dynamics using Ab Initio Classical Separable Potentials: Spectroscopic Applications.

PubMed

Hirshberg, Barak; Sagiv, Lior; Gerber, R Benny

2017-03-14

Algorithms for quantum molecular dynamics simulations that directly use ab initio methods have many potential applications. In this article, the ab initio classical separable potentials (AICSP) method is proposed as the basis for approximate algorithms of this type. The AICSP method assumes separability of the total time-dependent wave function of the nuclei and employs mean-field potentials that govern the dynamics of each degree of freedom. In the proposed approach, the mean-field potentials are determined by classical ab initio molecular dynamics simulations. The nuclear wave function can thus be propagated in time using the effective potentials generated "on the fly". As a test of the method for realistic systems, calculations of the stationary anharmonic frequencies of hydrogen stretching modes were carried out for several polyatomic systems, including three amino acids and the guanine-cytosine pair of nucleobases. Good agreement with experiments was found. The method scales very favorably with the number of vibrational modes and should be applicable for very large molecules, e.g., peptides. The method should also be applicable for properties such as vibrational line widths and line shapes. Work in these directions is underway.

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

PubMed

Yang, Lina; Minnich, Austin J

2017-03-14

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

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

PubMed Central

Yang, Lina; Minnich, Austin J.

2017-01-01

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

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

PubMed

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

2016-10-26

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

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

NASA Astrophysics Data System (ADS)

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

2016-05-01

Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-In alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Three liquid Hg-In alloys (Hg10In90, Hg30In70,. Hg50In50, Hg70In30, and Hg90Pb10) at 299 K are considered. The calculated results for liquid Hg (l-Hg) and lead (l-In) are also drawn. Along with the calculated results of considered five liquid alloys of Hg-In alloy. The results obtained from electronic properties namely total density of state and partial density of states help to find the local arrangement of Hg and In atoms and the presence of liquid state in the considered five alloys.

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

NASA Astrophysics Data System (ADS)

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

2015-05-01

Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-In alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Five liquid Hg-In mixtures (Hg10In90, Hg30In70, Hg50In50, Hg70In30 and Hg90In10) at 299K are considered. The radial distribution function g(r) and structure factor S(q) of considered alloys are compared with respective experimental results for liquid Hg (l-Hg) and (l-In). The radial distribution function g(r) shows the presence of short range order in the systems considered. Smooth curves of Bhatia-Thornton partial structure factors factor shows the presence of liquid state in the considered alloys.

Recent advances in jointed quantum mechanics and molecular mechanics calculations of biological macromolecules: schemes and applications coupled to ab initio calculations.

PubMed

Hagiwara, Yohsuke; Tateno, Masaru

2010-10-20

We review the recent research on the functional mechanisms of biological macromolecules using theoretical methodologies coupled to ab initio quantum mechanical (QM) treatments of reaction centers in proteins and nucleic acids. Since in most cases such biological molecules are large, the computational costs of performing ab initio calculations for the entire structures are prohibitive. Instead, simulations that are jointed with molecular mechanics (MM) calculations are crucial to evaluate the long-range electrostatic interactions, which significantly affect the electronic structures of biological macromolecules. Thus, we focus our attention on the methodologies/schemes and applications of jointed QM/MM calculations, and discuss the critical issues to be elucidated in biological macromolecular systems. © 2010 IOP Publishing Ltd

Ab initio NMR parameters of BrCH3 and ICH3 with relativistic and vibrational corrections

NASA Astrophysics Data System (ADS)

Uhlíková, Tereza; Urban, Štěpán

2018-05-01

This study is focused on two effects identified when NMR parameters are calculated based on first principles. These effects are 1. vibrational correction of properties when using ab initio optimized equilibrium geometry; 2. relativistic effects and limits of using the Flygare equation. These effects have been investigated and determined for nuclear spin-rotation constants and nuclear magnetic shieldings for the CH3Br and CH3I molecules. The most significant result is the difference between chemical shieldings determined based on the ab initio relativistic four-component Dirac-Coulomb Hamiltonian and chemical shieldings calculated using experimental values and the Flygare equation. This difference is approximately 320 ppm and 1290 ppm for 79Br and 127I in the CH3X molecule, respectively.

An ab-initio study of mechanical, dynamical and electronic properties of MgEu intermetallic

NASA Astrophysics Data System (ADS)

Kumar, S. Ramesh; Jaiganesh, G.; Jayalakshmi, V.

2018-04-01

The theoretical investigation on the mechanical, dynamical and electronic properties of MgEu in CsCl-type structure has been carried out through the ab-initio calculations within the framework of the density functional theory and the density functional perturbation theory. For the purpose, Vienna Ab initio Simulation Package and Phonopy packages were used. Our calculated ground-state properties of MgEu are in good agreement with other available results. Our computed elastic constants and phonon spectrum results suggest that MgEu is mechanically and dynamically stable up to 5 GPa. The thermodynamic quantities as a function of temperatures are also reported and discussed. The band structure, density of states and charge density also calculated to understand the electronic properties of MgEu.

Assessing the accuracy of improved force-matched water models derived from Ab initio molecular dynamics simulations.

PubMed

Köster, Andreas; Spura, Thomas; Rutkai, Gábor; Kessler, Jan; Wiebeler, Hendrik; Vrabec, Jadran; Kühne, Thomas D

2016-07-15

The accuracy of water models derived from ab initio molecular dynamics simulations by means on an improved force-matching scheme is assessed for various thermodynamic, transport, and structural properties. It is found that although the resulting force-matched water models are typically less accurate than fully empirical force fields in predicting thermodynamic properties, they are nevertheless much more accurate than generally appreciated in reproducing the structure of liquid water and in fact superseding most of the commonly used empirical water models. This development demonstrates the feasibility to routinely parametrize computationally efficient yet predictive potential energy functions based on accurate ab initio molecular dynamics simulations for a large variety of different systems. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

An ab initio molecular orbital study of the mechanism for the gas-phase water-mediated decomposition and the formation of hydrates of peroxyacetyl nitrate (PAN).

PubMed

Li, Yumin; Francisco, Joseph S

2005-08-31

There is uncertainty in the mechanism for the hydrolysis of peroxyacetyl nitrate (PAN), and experimental attempts to detect products of the direct reaction have been unsuccessful. Ab initio calculations are used to examine the energetics of water-mediated decomposition of gas-phase PAN into acetic acid and peroxynitric acid. On the basis of ab initio calculations, an alternative reaction mechanism for the decomposition of PAN is proposed. The calculations indicate that the barrier for one water addition to PAN is large. However, including additional water molecules reveals a substantially lower energy route. The calculations suggest that the formation of PAN hydrate complexes are energetically favorable and stable. Additional waters are increasingly efficient at stabilizing hydrated PAN.

Explicit polarization (X-Pol) potential using ab initio molecular orbital theory and density functional theory.

PubMed

Song, Lingchun; Han, Jaebeom; Lin, Yen-lin; Xie, Wangshen; Gao, Jiali

2009-10-29

The explicit polarization (X-Pol) method has been examined using ab initio molecular orbital theory and density functional theory. The X-Pol potential was designed to provide a novel theoretical framework for developing next-generation force fields for biomolecular simulations. Importantly, the X-Pol potential is a general method, which can be employed with any level of electronic structure theory. The present study illustrates the implementation of the X-Pol method using ab initio Hartree-Fock theory and hybrid density functional theory. The computational results are illustrated by considering a set of bimolecular complexes of small organic molecules and ions with water. The computed interaction energies and hydrogen bond geometries are in good accord with CCSD(T) calculations and B3LYP/aug-cc-pVDZ optimizations.

The multi-reference retaining the excitation degree perturbation theory: A size-consistent, unitary invariant, and rapidly convergent wavefunction based ab initio approach

NASA Astrophysics Data System (ADS)

Fink, Reinhold F.

2009-02-01

The retaining the excitation degree (RE) partitioning [R.F. Fink, Chem. Phys. Lett. 428 (2006) 461(20 September)] is reformulated and applied to multi-reference cases with complete active space (CAS) reference wave functions. The generalised van Vleck perturbation theory is employed to set up the perturbation equations. It is demonstrated that this leads to a consistent and well defined theory which fulfils all important criteria of a generally applicable ab initio method: The theory is proven numerically and analytically to be size-consistent and invariant with respect to unitary orbital transformations within the inactive, active and virtual orbital spaces. In contrast to most previously proposed multi-reference perturbation theories the necessary condition for a proper perturbation theory to fulfil the zeroth order perturbation equation is exactly satisfied with the RE partitioning itself without additional projectors on configurational spaces. The theory is applied to several excited states of the benchmark systems CH2 , SiH2 , and NH2 , as well as to the lowest states of the carbon, nitrogen and oxygen atoms. In all cases comparisons are made with full configuration interaction results. The multi-reference (MR)-RE method is shown to provide very rapidly converging perturbation series. Energy differences between states of similar configurations converge even faster.

Electronic Excitations of Alkali-Alkaline Earth Diatomic Molecules - Results from AB Initio Calculations

NASA Astrophysics Data System (ADS)

Pototschnig, Johann V.; Krois, Günter; Lackner, Florian; Ernst, Wolfgang E.

2014-06-01

Recently interest in polar diatomic molecules with a magnetic dipole moment has been growing. An example for such molecules is the combination of an alkali metal atom and an alkaline earth metal atom. These systems are quite small, containing only three valence electrons. Nevertheless calculations of excited states are challenging. Ab initio calculations for two sample systems, LiCa and RbSr, will be presented. The potential energy curves and transition dipole moments for the ground state and several excited states were determined, up to 25000 wn for LiCa and up to 22000 wn for RbSr. Multireference configuration interaction calculations (MRCI) based on complete active space self-consistent field wave functions (CASSCF) were used to determine the properties of the system as implemented in the MOLPRO software package. Effective core potentials (ECPs) and core polarization potentials (CCPs) were applied to reduce the computational effort, while retaining accuracy. The similarities and differences of the two systems will be discussed. In both systems the accurate description of the asymptotic values of the PECs corresponding to atomic D-states proved to be difficult. The results will be compared to recent experiments, showing that a combination of theory and experiment gives a reliable description of the systems. G. Krois, J.V. Pototschnig, F. Lackner and W.E. Ernst, J. Phys. Chem. A, 117, 13719-13731 (2013) H.-J. Werner and P. J. Knowles and G. Knizia and F. R. Manby and M. {Schütz} et al., MOLPRO, version 2010.1, see http://www.molpro.net/

Nonenzymatic and enzymatic hydrolysis of alkyl halides: A theoretical study of the SN2 reactions of acetate and hydroxide ions with alkyl chlorides

PubMed Central

Maulitz, Andreas H.; Lightstone, Felice C.; Zheng, Ya-Jun; Bruice, Thomas C.

1997-01-01

The SN2 displacements of chloride ion from CH3Cl, C2H5Cl, and C2H4Cl2 by acetate and hydroxide ions have been investigated, using ab initio molecular orbital theory at the HF/6–31+G(d), MP2/6–31+G(d), and MP4/6–31+G(d) levels of theory. The central barriers (calculated from the initial ion–molecule complex) of the reactions, the differences of the overall reaction energies, and the geometries of the transition states are compared. Essential stereochemical changes before and after the displacement reactions are described for selected cases. The gas phase reactions of hydroxide with CH3Cl, C2H5Cl, and C2H4Cl2 have no overall barrier, but there is a small overall barrier for the reactions of acetate with CH3Cl, C2H5Cl, and C2H4Cl2. A self-consistent reaction field solvation model was used to examine the SN2 reactions between methyl chloride and hydroxide ion and between 1,2-dichloroethane and acetate in solution. As expected, the reactions in polar solvent have a large barrier. However, the transition state structures determined by ab initio calculations change only slightly in the presence of a highly polar solvent as compared with the gas phase. We also calibrated the PM3 method for future study of an enzymatic SN2 displacement of halogen. PMID:9192609

Weak interactions in Graphane/BN systems under static electric fields—A periodic ab-initio study.

PubMed

Steinkasserer, Lukas Eugen Marsoner; Gaston, Nicola; Paulus, Beate

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.

Molecular Dynamics Simulations with Quantum Mechanics/Molecular Mechanics and Adaptive Neural Networks.

PubMed

Shen, Lin; Yang, Weitao

2018-03-13

Direct molecular dynamics (MD) simulation with ab initio quantum mechanical and molecular mechanical (QM/MM) methods is very powerful for studying the mechanism of chemical reactions in a complex environment but also very time-consuming. The computational cost of QM/MM calculations during MD simulations can be reduced significantly using semiempirical QM/MM methods with lower accuracy. To achieve higher accuracy at the ab initio QM/MM level, a correction on the existing semiempirical QM/MM model is an attractive idea. Recently, we reported a neural network (NN) method as QM/MM-NN to predict the potential energy difference between semiempirical and ab initio QM/MM approaches. The high-level results can be obtained using neural network based on semiempirical QM/MM MD simulations, but the lack of direct MD samplings at the ab initio QM/MM level is still a deficiency that limits the applications of QM/MM-NN. In the present paper, we developed a dynamic scheme of QM/MM-NN for direct MD simulations on the NN-predicted potential energy surface to approximate ab initio QM/MM MD. Since some configurations excluded from the database for NN training were encountered during simulations, which may cause some difficulties on MD samplings, an adaptive procedure inspired by the selection scheme reported by Behler [ Behler Int. J. Quantum Chem. 2015 , 115 , 1032 ; Behler Angew. Chem., Int. Ed. 2017 , 56 , 12828 ] was employed with some adaptions to update NN and carry out MD iteratively. We further applied the adaptive QM/MM-NN MD method to the free energy calculation and transition path optimization on chemical reactions in water. The results at the ab initio QM/MM level can be well reproduced using this method after 2-4 iteration cycles. The saving in computational cost is about 2 orders of magnitude. It demonstrates that the QM/MM-NN with direct MD simulations has great potentials not only for the calculation of thermodynamic properties but also for the characterization of reaction dynamics, which provides a useful tool to study chemical or biochemical systems in solution or enzymes.

Accurate Determination of Tunneling-Affected Rate Coefficients: Theory Assessing Experiment.

PubMed

Zuo, Junxiang; Xie, Changjian; Guo, Hua; Xie, Daiqian

2017-07-20

The thermal rate coefficients of a prototypical bimolecular reaction are determined on an accurate ab initio potential energy surface (PES) using ring polymer molecular dynamics (RPMD). It is shown that quantum effects such as tunneling and zero-point energy (ZPE) are of critical importance for the HCl + OH reaction at low temperatures, while the heavier deuterium substitution renders tunneling less facile in the DCl + OH reaction. The calculated RPMD rate coefficients are in excellent agreement with experimental data for the HCl + OH reaction in the entire temperature range of 200-1000 K, confirming the accuracy of the PES. On the other hand, the RPMD rate coefficients for the DCl + OH reaction agree with some, but not all, experimental values. The self-consistency of the theoretical results thus allows a quality assessment of the experimental data.

Calculated temperature dependence of elastic constants and phonon dispersion of hcp and bcc beryllium

NASA Astrophysics Data System (ADS)

Hahn, Steven; Arapan, Sergiu; Harmon, Bruce; Eriksson, Olle

2011-03-01

Conventional first principle methods for calculating lattice dynamics are unable to calculate high temperature thermophysical properties of materials containing modes that are entropically stabilized. In this presentation we use a relatively new approach called self-consistent ab initio lattice dynamics (SCAILD) to study the hcp to bcc transition (1530 K) in beryllium. The SCAILD method goes beyond the harmonic approximation to include phonon-phonon interactions and produces a temperature-dependent phonon dispersion. In the high temperature bcc structure, phonon-phonon interactions dynamically stabilize the N-point phonon. Fits to the calculated phonon dispersion were used to determine the temperature dependence of the elastic constants in the hcp and bcc phases. Work at the Ames Laboratory was supported by the Department of Energy-Basic Energy Sciences under Contract No. DE-AC02-07CH11358.

Electronic Structure, Dielectric Response, and Surface Charge Distribution of RGD (1FUV) Peptide

PubMed Central

Adhikari, Puja; Wen, Amy M.; French, Roger H.; Parsegian, V. Adrian; Steinmetz, Nicole F.; Podgornik, Rudolf; Ching, Wai-Yim

2014-01-01

Long and short range molecular interactions govern molecular recognition and self-assembly of biological macromolecules. Microscopic parameters in the theories of these molecular interactions are either phenomenological or need to be calculated within a microscopic theory. We report a unified methodology for the ab initio quantum mechanical (QM) calculation that yields all the microscopic parameters, namely the partial charges as well as the frequency-dependent dielectric response function, that can then be taken as input for macroscopic theories of electrostatic, polar, and van der Waals-London dispersion intermolecular forces. We apply this methodology to obtain the electronic structure of the cyclic tripeptide RGD-4C (1FUV). This ab initio unified methodology yields the relevant parameters entering the long range interactions of biological macromolecules, providing accurate data for the partial charge distribution and the frequency-dependent dielectric response function of this peptide. These microscopic parameters determine the range and strength of the intricate intermolecular interactions between potential docking sites of the RGD-4C ligand and its integrin receptor. PMID:25001596

Domain Wall Formation in Ferromagnetic Layers: An Ab Initio Study

NASA Astrophysics Data System (ADS)

Herper, Heike C.

Domain walls are an inherent feature of ferromagnetic (FM) films consisting of layers with different magnetic orientations. Since FM films are used in electrical devices the question of the influence of domain walls on, e.g., the magnetoresistance has attracted much interest. Besides discussing the resistance contribution of domain walls, it is appropriate to study different types of domain walls and their energy of formation. The behaviour of domain walls is usually discussed within model calculations. In the present paper it is done within an ab initio Green's function technique for layered systems, i.e., the fully relativistic, spin-polarized screened Korringa-Kohn Rostoker method. Results are presented for fcc Co layers covered by two semi-infinite fcc Pt(001) bulk systems or by bulk fcc Co(001), respectively. The resistance, which is caused by the different types of domain walls is discussed within a Kubo-Greenwood approach considering Co(001)/Co24/Co(001) as an example.

High-level ab initio enthalpies of formation of 2,5-dimethylfuran, 2-methylfuran, and furan.

PubMed

Feller, David; Simmie, John M

2012-11-29

A high-level ab initio thermochemical technique, known as the Feller-Petersen-Dixon method, is used to calculate the total atomization energies and hence the enthalpies of formation of 2,5-dimethylfuran, 2-methylfuran, and furan itself as a means of rationalizing significant discrepancies in the literature. In order to avoid extremely large standard coupled cluster theory calculations, the explicitly correlated CCSD(T)-F12b variation was used with basis sets up to cc-pVQZ-F12. After extrapolating to the complete basis set limit and applying corrections for core/valence, scalar relativistic, and higher order effects, the final Δ(f)H° (298.15 K) values, with the available experimental values in parentheses are furan -34.8 ± 3 (-34.7 ± 0.8), 2-methylfuran -80.3 ± 5 (-76.4 ± 1.2), and 2,5-dimethylfuran -124.6 ± 6 (-128.1 ± 1.1) kJ mol(-1). The theoretical results exhibit a compelling internal consistency.

Double-walled silicon nanotubes: an ab initio investigation

NASA Astrophysics Data System (ADS)

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.

Geometry of AN Isolated Dimer of Imidazole Characterised by Rotational Spectroscopy and AB Initio Calculations

NASA Astrophysics Data System (ADS)

Mullaney, John C.; Zaleski, Daniel P.; Tew, David Peter; Walker, Nick; Legon, Anthony

2016-06-01

An isolated, gas-phase dimer of imidazole is generated through laser vaporisation of a solid rod containing a 1:1 mixture of imidazole and copper in the presence of an argon buffer gas undergoing supersonic expansion. The complex is characterised through broadband rotational spectroscopy and is shown to have a twisted, hydrogen-bonded geometry. Calculations at the CCSD(T)(F12*)/cc-pVDZ-F12 level of theory confirm this to be the lowest-energy conformer of the imidazole dimer. The distance between the respective centres of mass of the imidazole monomer subunits is determined to be 5.2751(1) Å, and the twist angle γ describing rotation of one monomer with respect to the other about a line connecting the centres of mass of the monomers is determined to be 87.9(4)o. Four out of six intermolecular parameters in the model geometry are precisely determined from the experimental rotational constants and are consistent with results calculated ab initio.

Ab initio prediction of stable nanotwin double layers and 4O structure in Ni2MnGa

NASA Astrophysics Data System (ADS)

Zelený, Martin; Straka, Ladislav; Sozinov, Alexei; Heczko, Oleg

2016-12-01

The ab initio electronic structure calculations of the Ni2MnGa alloy indicate that the orthorhombic 4O structure exhibits the lowest energy compared to all known martensitic structures. The 4O structure is formed by nanotwin double layers, i.e., oppositely oriented nanotwins consisting of two (101) lattice planes of nonmodulated martensitic structure. It exhibits the lowest occupation of density of states at the Fermi level. The total energy 1.98 meV/atom below the energy of nonmodulated martensite is achieved within structural relaxation by shifting Mn and Ga atoms at the nanotwin boundaries. The same atomic shift can also be found in other martensitic nanotwinned or modulated structures such as 10M and 14M, which indicates the importance of the nanotwin double layer for the stability of these structures. Our discovery shows that the nanotwinning or modulation is a natural property of low-temperature martensitic phases in Ni-Mn-Ga alloys.

Five ab initio potential energy and dipole moment surfaces for hydrated NaCl and NaF. I. Two-body interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Yimin, E-mail: yimin.wang@emory.edu; Bowman, Joel M., E-mail: jmbowma@emory.edu; Kamarchik, Eugene, E-mail: eugene.kamarchik@gmail.com

2016-03-21

We report full-dimensional, ab initio-based potentials and dipole moment surfaces for NaCl, NaF, Na{sup +}H{sub 2}O, F{sup −}H{sub 2}O, and Cl{sup −}H{sub 2}O. The NaCl and NaF potentials are diabatic ones that dissociate to ions. These are obtained using spline fits to CCSD(T)/aug-cc-pV5Z energies. In addition, non-linear least square fits using the Born-Mayer-Huggins potential are presented, providing accurate parameters based strictly on the current ab initio energies. The long-range behavior of the NaCl and NaF potentials is shown to go, as expected, accurately to the point-charge Coulomb interaction. The three ion-H{sub 2}O potentials are permutationally invariant fits to roughly 20 000more » coupled cluster CCSD(T) energies (awCVTZ basis for Na{sup +} and aVTZ basis for Cl{sup −} and F{sup −}), over a large range of distances and H{sub 2}O intramolecular configurations. These potentials are switched accurately in the long range to the analytical ion-dipole interactions, to improve computational efficiency. Dipole moment surfaces are fits to MP2 data; for the ion-ion cases, these are well described in the intermediate- and long-range by the simple point-charge expression. The performance of these new fits is examined by direct comparison to additional ab initio energies and dipole moments along various cuts. Equilibrium structures, harmonic frequencies, and electronic dissociation energies are also reported and compared to direct ab initio results. These indicate the high fidelity of the new PESs.« less

Mirnacle: machine learning with SMOTE and random forest for improving selectivity in pre-miRNA ab initio prediction.

PubMed

Marques, Yuri Bento; de Paiva Oliveira, Alcione; Ribeiro Vasconcelos, Ana Tereza; Cerqueira, Fabio Ribeiro

2016-12-15

MicroRNAs (miRNAs) are key gene expression regulators in plants and animals. Therefore, miRNAs are involved in several biological processes, making the study of these molecules one of the most relevant topics of molecular biology nowadays. However, characterizing miRNAs in vivo is still a complex task. As a consequence, in silico methods have been developed to predict miRNA loci. A common ab initio strategy to find miRNAs in genomic data is to search for sequences that can fold into the typical hairpin structure of miRNA precursors (pre-miRNAs). The current ab initio approaches, however, have selectivity issues, i.e., a high number of false positives is reported, which can lead to laborious and costly attempts to provide biological validation. This study presents an extension of the ab initio method miRNAFold, with the aim of improving selectivity through machine learning techniques, namely, random forest combined with the SMOTE procedure that copes with imbalance datasets. By comparing our method, termed Mirnacle, with other important approaches in the literature, we demonstrate that Mirnacle substantially improves selectivity without compromising sensitivity. For the three datasets used in our experiments, our method achieved at least 97% of sensitivity and could deliver a two-fold, 20-fold, and 6-fold increase in selectivity, respectively, compared with the best results of current computational tools. The extension of miRNAFold by the introduction of machine learning techniques, significantly increases selectivity in pre-miRNA ab initio prediction, which optimally contributes to advanced studies on miRNAs, as the need of biological validations is diminished. Hopefully, new research, such as studies of severe diseases caused by miRNA malfunction, will benefit from the proposed computational tool.

Residue contacts predicted by evolutionary covariance extend the application of ab initio molecular replacement to larger and more challenging protein folds.

PubMed

Simkovic, Felix; Thomas, Jens M H; Keegan, Ronan M; Winn, Martyn D; Mayans, Olga; Rigden, Daniel J

2016-07-01

For many protein families, the deluge of new sequence information together with new statistical protocols now allow the accurate prediction of contacting residues from sequence information alone. This offers the possibility of more accurate ab initio (non-homology-based) structure prediction. Such models can be used in structure solution by molecular replacement (MR) where the target fold is novel or is only distantly related to known structures. Here, AMPLE, an MR pipeline that assembles search-model ensembles from ab initio structure predictions ('decoys'), is employed to assess the value of contact-assisted ab initio models to the crystallographer. It is demonstrated that evolutionary covariance-derived residue-residue contact predictions improve the quality of ab initio models and, consequently, the success rate of MR using search models derived from them. For targets containing β-structure, decoy quality and MR performance were further improved by the use of a β-strand contact-filtering protocol. Such contact-guided decoys achieved 14 structure solutions from 21 attempted protein targets, compared with nine for simple Rosetta decoys. Previously encountered limitations were superseded in two key respects. Firstly, much larger targets of up to 221 residues in length were solved, which is far larger than the previously benchmarked threshold of 120 residues. Secondly, contact-guided decoys significantly improved success with β-sheet-rich proteins. Overall, the improved performance of contact-guided decoys suggests that MR is now applicable to a significantly wider range of protein targets than were previously tractable, and points to a direct benefit to structural biology from the recent remarkable advances in sequencing.

Toward ab initio molecular dynamics modeling for sum-frequency generation spectra; an efficient algorithm based on surface-specific velocity-velocity correlation function.

PubMed

Ohto, Tatsuhiko; Usui, Kota; Hasegawa, Taisuke; Bonn, Mischa; Nagata, Yuki

2015-09-28

Interfacial water structures have been studied intensively by probing the O-H stretch mode of water molecules using sum-frequency generation (SFG) spectroscopy. This surface-specific technique is finding increasingly widespread use, and accordingly, computational approaches to calculate SFG spectra using molecular dynamics (MD) trajectories of interfacial water molecules have been developed and employed to correlate specific spectral signatures with distinct interfacial water structures. Such simulations typically require relatively long (several nanoseconds) MD trajectories to allow reliable calculation of the SFG response functions through the dipole moment-polarizability time correlation function. These long trajectories limit the use of computationally expensive MD techniques such as ab initio MD and centroid MD simulations. Here, we present an efficient algorithm determining the SFG response from the surface-specific velocity-velocity correlation function (ssVVCF). This ssVVCF formalism allows us to calculate SFG spectra using a MD trajectory of only ∼100 ps, resulting in the substantial reduction of the computational costs, by almost an order of magnitude. We demonstrate that the O-H stretch SFG spectra at the water-air interface calculated by using the ssVVCF formalism well reproduce those calculated by using the dipole moment-polarizability time correlation function. Furthermore, we applied this ssVVCF technique for computing the SFG spectra from the ab initio MD trajectories with various density functionals. We report that the SFG responses computed from both ab initio MD simulations and MD simulations with an ab initio based force field model do not show a positive feature in its imaginary component at 3100 cm(-1).

Residue contacts predicted by evolutionary covariance extend the application of ab initio molecular replacement to larger and more challenging protein folds

PubMed Central

Simkovic, Felix; Thomas, Jens M. H.; Keegan, Ronan M.; Winn, Martyn D.; Mayans, Olga; Rigden, Daniel J.

2016-01-01

For many protein families, the deluge of new sequence information together with new statistical protocols now allow the accurate prediction of contacting residues from sequence information alone. This offers the possibility of more accurate ab initio (non-homology-based) structure prediction. Such models can be used in structure solution by molecular replacement (MR) where the target fold is novel or is only distantly related to known structures. Here, AMPLE, an MR pipeline that assembles search-model ensembles from ab initio structure predictions (‘decoys’), is employed to assess the value of contact-assisted ab initio models to the crystallographer. It is demonstrated that evolutionary covariance-derived residue–residue contact predictions improve the quality of ab initio models and, consequently, the success rate of MR using search models derived from them. For targets containing β-structure, decoy quality and MR performance were further improved by the use of a β-strand contact-filtering protocol. Such contact-guided decoys achieved 14 structure solutions from 21 attempted protein targets, compared with nine for simple Rosetta decoys. Previously encountered limitations were superseded in two key respects. Firstly, much larger targets of up to 221 residues in length were solved, which is far larger than the previously benchmarked threshold of 120 residues. Secondly, contact-guided decoys significantly improved success with β-sheet-rich proteins. Overall, the improved performance of contact-guided decoys suggests that MR is now applicable to a significantly wider range of protein targets than were previously tractable, and points to a direct benefit to structural biology from the recent remarkable advances in sequencing. PMID:27437113

Ab initio potential-energy surfaces for complex, multichannel systems using modified novelty sampling and feedforward neural networks

NASA Astrophysics Data System (ADS)

Raff, L. M.; Malshe, M.; Hagan, M.; Doughan, D. I.; Rockley, M. G.; Komanduri, R.

2005-02-01

A neural network/trajectory approach is presented for the development of accurate potential-energy hypersurfaces that can be utilized to conduct ab initio molecular dynamics (AIMD) and Monte Carlo studies of gas-phase chemical reactions, nanometric cutting, and nanotribology, and of a variety of mechanical properties of importance in potential microelectromechanical systems applications. The method is sufficiently robust that it can be applied to a wide range of polyatomic systems. The overall method integrates ab initio electronic structure calculations with importance sampling techniques that permit the critical regions of configuration space to be determined. The computed ab initio energies and gradients are then accurately interpolated using neural networks (NN) rather than arbitrary parametrized analytical functional forms, moving interpolation or least-squares methods. The sampling method involves a tight integration of molecular dynamics calculations with neural networks that employ early stopping and regularization procedures to improve network performance and test for convergence. The procedure can be initiated using an empirical potential surface or direct dynamics. The accuracy and interpolation power of the method has been tested for two cases, the global potential surface for vinyl bromide undergoing unimolecular decomposition via four different reaction channels and nanometric cutting of silicon. The results show that the sampling methods permit the important regions of configuration space to be easily and rapidly identified, that convergence of the NN fit to the ab initio electronic structure database can be easily monitored, and that the interpolation accuracy of the NN fits is excellent, even for systems involving five atoms or more. The method permits a substantial computational speed and accuracy advantage over existing methods, is robust, and relatively easy to implement.

Decohesion models informed by first-principles calculations: The ab initio tensile test

NASA Astrophysics Data System (ADS)

Enrique, Raúl A.; Van der Ven, Anton

2017-10-01

Extreme deformation and homogeneous fracture can be readily studied via ab initio methods by subjecting crystals to numerical "tensile tests", where the energy of locally stable crystal configurations corresponding to elongated and fractured states are evaluated by means of density functional method calculations. The information obtained can then be used to construct traction curves of cohesive zone models in order to address fracture at the macroscopic scale. In this work, we perform an in depth analysis of traction curves and how ab initio calculations must be interpreted to rigorously parameterize an atomic scale cohesive zone model, using crystalline Ag as an example. Our analysis of traction curves reveal the existence of two qualitatively distinct decohesion criteria: (i) an energy criterion whereby the released elastic energy equals the energy cost of creating two new surfaces and (ii) an instability criterion that occurs at a higher and size independent stress than that of the energy criterion. We find that increasing the size of the simulation cell renders parts of the traction curve inaccessible to ab initio calculations involving the uniform decohesion of the crystal. We also find that the separation distance below which a crack heals is not a material parameter as has been proposed in the past. Finally, we show that a large energy barrier separates the uniformly stressed crystal from the decohered crystal, resolving a paradox predicted by a scaling law based on the energy criterion that implies that large crystals will decohere under vanishingly small stresses. This work clarifies confusion in the literature as to how a cohesive zone model is to be parameterized with ab initio "tensile tests" in the presence of internal relaxations.

Ab initio calculation of hyperfine splitting constants of molecules

NASA Astrophysics Data System (ADS)

Ohta, K.; Nakatsuji, H.; Hirao, K.; Yonezawa, T.

1980-08-01

Hyperfine splitting (hfs) constants of molecules, methyl, ethyl, vinyl, allyl, cyclopropyl, formyl, O3-, NH2, NO2, and NF2 radicals have been calculated by the pseudo-orbital (PO) theory, the unrestricted HF (UHF), projected UHF (PUHF) and single excitation (SE) CI theories. The pseudo-orbital (PO) theory is based on the symmetry-adapted-cluster (SAC) expansion proposed previously. Several contractions of the Gaussian basis sets of double-zeta accuracy have been examined. The UHF results were consistently too large to compare with experiments and the PUHF results were too small. For molecules studied here, the PO theory and SECI theory gave relatively close results. They were in fair agreement with experiments. The first-order spin-polarization self-consistency effect, which was shown to be important for atoms, is relatively small for the molecules. The present result also shows an importance of eliminating orbital-transformation dependence from conventional first-order perturbation calculations. The present calculations have explained well several important variations in the experimental hfs constants.

BAC-MP4 predictions of thermochemistry for the gas-phase tin compounds in the Sn-H-C-Cl system.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Allendorf, Mark D.; Melius, Carl F.

2004-09-01

In this work, the BAC-MP4 method is extended for the first time to compounds in the fourth row of the periodic table, resulting in a self-consistent set of thermochemical data for 56 tin-containing molecules in the Sn-H-C-Cl system. The BAC-MP4 method combines ab initio electronic structure calculations with empirical corrections to obtain accurate heats of formation. To obtain electronic energies for tin-containing species, the standard 6-31G(d,p) basis set used in BAC-MP4 calculations is augmented with a relativistic effective core potential to describe the electronic structure of the tin atom. Both stable compounds and radical species are included in this study.more » Trends within homologous series and calculated bond dissociation energies are consistent with previous BAC-MP4 predictions for group 14 compounds and the limited data available from the literature, indicating that the method is performing well for these compounds.« less

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

NASA Astrophysics Data System (ADS)

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

2014-04-01

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

Towards ab initio Calculations with the Dynamical Vertex Approximation

NASA Astrophysics Data System (ADS)

Galler, Anna; Kaufmann, Josef; Gunacker, Patrik; Pickem, Matthias; Thunström, Patrik; Tomczak, Jan M.; Held, Karsten

2018-04-01

While key effects of the many-body problem — such as Kondo and Mott physics — can be understood in terms of on-site correlations, non-local fluctuations of charge, spin, and pairing amplitudes are at the heart of the most fascinating and unresolved phenomena in condensed matter physics. Here, we review recent progress in diagrammatic extensions to dynamical mean-field theory for ab initio materials calculations. We first recapitulate the quantum field theoretical background behind the two-particle vertex. Next we discuss latest algorithmic advances in quantum Monte Carlo simulations for calculating such two-particle quantities using worm sampling and vertex asymptotics, before giving an introduction to the ab initio dynamical vertex approximation (AbinitioDΓA). Finally, we highlight the potential of AbinitioDΓA by detailing results for the prototypical correlated metal SrVO3.

Crossover of cation partitioning in olivines: a combination of ab initio and Monte Carlo study

NASA Astrophysics Data System (ADS)

Chatterjee, Swastika; Bhattacharyya, Sirshendu; Sengupta, Surajit; Saha-Dasgupta, Tanusri

2011-04-01

We report studies based on a combination of ab initio electronic structure and Monte Carlo (MC) technique on the problem of cation partitioning among inequivalent octahedral sites, M1 and M2 in mixed olivines containing Mg2+ and Fe2+ ions. Our MC scheme uses interactions derived out of ab initio, density functional calculations carried out on measured crystal structure data. Our results show that there is no reversal of the preference of Fe for M1 over M2 as a function of temperature. Our findings do not agree with the experimental findings of Redfern et al. (Phys Chem Miner 27:630-637, 2000), but are in agreement with those of Heinemann et al. (Eur J Mineral 18:673-689, 2006) and Morozov et al. (Eur J Mineral 17:495-500, 2005).

Determination of NMR chemical shifts for cholesterol crystals from first-principles

NASA Astrophysics Data System (ADS)

Kucukbenli, Emine; de Gironcoli, Stefano

2011-03-01

Solid State Nuclear Magnetic Resonance (NMR) is a powerful tool in crystallography when combined with theoretical predictions. So far, empirical calculations of spectra have been employed for an unambiguous identification. However, many complex systems are outside the scope of these methods. Our implementation of ultrasoft and projector augmented wave pseudopotentials within ab initio gauge including projector augmented plane wave (GIPAW) method in Quantum Espresso simulation package allows affordable calculations of NMR spectra for systems of thousands of electrons. We report here the first ab initio determination of NMR spectra for several crystal structures of cholesterol. Cholesterol crystals, the main component of human gallstones, are of interest to medical research as their structural properties can shed light on the pathologies of gallbladder. With our application we show that ab initio calculations can be employed to aid NMR crystallography.

Spectroscopic study of uracil, 1-methyluracil and 1-methyl-4-thiouracil: Hydrogen bond interactions in crystals and ab-initio molecular dynamics

NASA Astrophysics Data System (ADS)

Brela, Mateusz Z.; Boczar, Marek; Malec, Leszek M.; Wójcik, Marek J.; Nakajima, Takahito

2018-05-01

Hydrogen bond networks in uracil, 1-methyluracil and 1-methyl-4-thiouracil were studied by ab initio molecular dynamics as well as analysis of the orbital interactions. The power spectra calculated by ab initio molecular dynamics for atoms involved in hydrogen bonds were analyzed. We calculated spectra by using anharmonic approximation based on the autocorrelation function of the atom positions obtained from the Born-Oppenheimer simulations. Our results show the differences between hydrogen bond networks in uracil and its methylated derivatives. The studied methylated derivatives, 1-methyluracil as well as 1-methyl-4-thiouracil, form dimeric structures in the crystal phase, while uracil does not form that kind of structures. The presence of sulfur atom instead oxygen atom reflects weakness of the hydrogen bonds that build dimers.

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

PubMed

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

2014-09-16

Conspectus Molecular crystals are chemists' solids in the sense that their structures and properties can be understood in terms of those of the constituent molecules merely perturbed by a crystalline environment. They form a large and important class of solids including ices of atmospheric species, drugs, explosives, and even some organic optoelectronic materials and supramolecular assemblies. Recently, surprisingly simple yet extremely efficient, versatile, easily implemented, and systematically accurate electronic structure methods for molecular crystals have been developed. The methods, collectively referred to as the embedded-fragment scheme, divide a crystal into monomers and overlapping dimers and apply modern molecular electronic structure methods and software to these fragments of the crystal that are embedded in a self-consistently determined crystalline electrostatic field. They enable facile applications of accurate but otherwise prohibitively expensive ab initio molecular orbital theories such as Møller-Plesset perturbation and coupled-cluster theories to a broad range of properties of solids such as internal energies, enthalpies, structures, equation of state, phonon dispersion curves and density of states, infrared and Raman spectra (including band intensities and sometimes anharmonic effects), inelastic neutron scattering spectra, heat capacities, Gibbs energies, and phase diagrams, while accounting for many-body electrostatic (namely, induction or polarization) effects as well as two-body exchange and dispersion interactions from first principles. They can fundamentally alter the role of computing in the studies of molecular crystals in the same way ab initio molecular orbital theories have transformed research practices in gas-phase physical chemistry and synthetic chemistry in the last half century. In this Account, after a brief summary of formalisms and algorithms, we discuss applications of these methods performed in our group as compelling illustrations of their unprecedented power in addressing some of the outstanding problems of solid-state chemistry, high-pressure chemistry, or geochemistry. They are the structure and spectra of ice Ih, in particular, the origin of two peaks in the hydrogen-bond-stretching region of its inelastic neutron scattering spectra, a solid-solid phase transition from CO2-I to elusive, metastable CO2-III, pressure tuning of Fermi resonance in solid CO2, and the structure and spectra of solid formic acid, all at the level of second-order Møller-Plesset perturbation theory or higher.

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

NASA Technical Reports Server (NTRS)

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

1997-01-01

Thioperoxy (XSO or XOS) radicals exist in a variety of chemical environments, and they have as a consequence drawn some interest. HSO, an important species in the chemistry of the troposphere, has been examined both experimentally. The halogenated (X = F, Cl or Br) peroxy species and isovalent thioperoxy species have been studied less, but they too are potentially interesting because oxidized sulfur species and halogen sources are present in the atmosphere. Learning the fate of XSO and XOS radicals is important to understanding the atmospheric oxidation chemistry of sulfur compounds. Of these, FSO and ClSO are particularly interesting because they have been directly detected spectroscopically. Recent studies in our laboratory on the photochemistry of thionyl halides (X2SO; where X = F or Cl) have suggested new ways to generate XSO species. The laser-induced photodissociation of thionyl fluoride, F2SO, at 193 nm and thionyl chloride, ClSO, at 248 nm is characterized by a radical mechanism, X2SO -> XSO + X. The structure of FSO has been characterized experimentally by Endo et cd. employing microwave spectroscopy. Using the unrestricted Hartree-Fock (UHF) self-consistent field (SCF) method, Sakai and Morokuma computed the electronic structure of the ground (sup 2)A" and the first excited (sup 2)A' states of FSO. Electron correlation was not taken into account in their study. In a laser photodissociation experiment, Huber et al. identified ClSO mass spectromctrically. ClSO has also been detected in low temperature matrices by EPR and in the gas phase by far IR laser magnetic resonance. Although the structure of FSO is known in detail, the only study, experimental or theoretical, of CISO has been an ab initio HFSCF study by Hinchliffe. Electron correlation corrections were also excluded from this study. In order to better understand the isomerization and dissociation dynamics of the radical species, we have performed ab initio correlated studies of the potential energy surfaces (PES) of ClSO and its isomer ClOS at the QCISD(T)/6-31 G* level of theory. For FSO and FOS, more extensive QCISD/6-31 1G(2df) calculations have been possible, and the results are summarized here.

E2 and SN2 Reactions of X(-) + CH3CH2X (X = F, Cl); an ab Initio and DFT Benchmark Study.

PubMed

Bento, A Patrícia; Solà, Miquel; Bickelhaupt, F Matthias

2008-06-01

We have computed consistent benchmark potential energy surfaces (PESs) for the anti-E2, syn-E2, and SN2 pathways of X(-) + CH3CH2X with X = F and Cl. This benchmark has been used to evaluate the performance of 31 popular density functionals, covering local-density approximation, generalized gradient approximation (GGA), meta-GGA, and hybrid density-functional theory (DFT). The ab initio benchmark has been obtained by exploring the PESs using a hierarchical series of ab initio methods [up to CCSD(T)] in combination with a hierarchical series of Gaussian-type basis sets (up to aug-cc-pVQZ). Our best CCSD(T) estimates show that the overall barriers for the various pathways increase in the order anti-E2 (X = F) < SN2 (X = F) < SN2 (X = Cl) ∼ syn-E2 (X = F) < anti-E2 (X = Cl) < syn-E2 (X = Cl). Thus, anti-E2 dominates for F(-) + CH3CH2F, and SN2 dominates for Cl(-) + CH3CH2Cl, while syn-E2 is in all cases the least favorable pathway. Best overall agreement with our ab initio benchmark is obtained by representatives from each of the three categories of functionals, GGA, meta-GGA, and hybrid DFT, with mean absolute errors in, for example, central barriers of 4.3 (OPBE), 2.2 (M06-L), and 2.0 kcal/mol (M06), respectively. Importantly, the hybrid functional BHandH and the meta-GGA M06-L yield incorrect trends and qualitative features of the PESs (in particular, an erroneous preference for SN2 over the anti-E2 in the case of F(-) + CH3CH2F) even though they are among the best functionals as measured by their small mean absolute errors of 3.3 and 2.2 kcal/mol in reaction barriers. OLYP and B3LYP have somewhat higher mean absolute errors in central barriers (5.6 and 4.8 kcal/mol, respectively), but the error distribution is somewhat more uniform, and as a consequence, the correct trends are reproduced.

An environment-dependent semi-empirical tight binding model suitable for electron transport in bulk metals, metal alloys, metallic interfaces, and metallic nanostructures. I. Model and validation

NASA Astrophysics Data System (ADS)

Hegde, Ganesh; Povolotskyi, Michael; Kubis, Tillmann; Boykin, Timothy; Klimeck, Gerhard

2014-03-01

Semi-empirical Tight Binding (TB) is known to be a scalable and accurate atomistic representation for electron transport for realistically extended nano-scaled semiconductor devices that might contain millions of atoms. In this paper, an environment-aware and transferable TB model suitable for electronic structure and transport simulations in technologically relevant metals, metallic alloys, metal nanostructures, and metallic interface systems are described. Part I of this paper describes the development and validation of the new TB model. The new model incorporates intra-atomic diagonal and off-diagonal elements for implicit self-consistency and greater transferability across bonding environments. The dependence of the on-site energies on strain has been obtained by appealing to the Moments Theorem that links closed electron paths in the system to energy moments of angular momentum resolved local density of states obtained ab initio. The model matches self-consistent density functional theory electronic structure results for bulk face centered cubic metals with and without strain, metallic alloys, metallic interfaces, and metallic nanostructures with high accuracy and can be used in predictive electronic structure and transport problems in metallic systems at realistically extended length scales.

Exploring the Nature of the H[subscript 2] Bond. 2. Using Ab Initio Molecular Orbital Calculations to Obtain the Molecular Constants

ERIC Educational Resources Information Center

Halpern, Arthur M.; Glendening, Eric D.

2013-01-01

A project for students in an upper-level course in quantum or computational chemistry is described in which they are introduced to the concepts and applications of a high quality, ab initio treatment of the ground-state potential energy curve (PEC) for H[subscript 2] and D[subscript 2]. Using a commercial computational chemistry application and a…

An ab initio mechanism for efficient population of triplet states in cytotoxic sulfur substituted DNA bases: the case of 6-thioguanine.

PubMed

Martínez-Fernández, Lara; González, Leticia; Corral, Inés

2012-02-18

The deactivation mechanism of the cytotoxic 6-thioguanine, the 6-sulfur-substituted analogue of the canonical DNA base, is unveiled by ab initio calculations. Oxygen-by-sulfur substitution leads to efficient population of triplet states-the first step for generating singlet oxygen-which is responsible for its cytotoxicity. This journal is © The Royal Society of Chemistry 2012

The Opacity of TiO from a Coupled Electronic State Calculation Parameterized by ab initio and Experimental Data

NASA Technical Reports Server (NTRS)

Schwenke, David W.; Huo, Winifred (Technical Monitor)

1998-01-01

We have carried out ab initio electronic structure calculations of the spin-orbit and rotation-orbit couplings among the 14 lowest electronic states of TiO and used them to predict ro-vibrational energy levels. We report on the qualitative results as well as our progress in optimizing our Hamiltonian parameters in order to improve agreement with experimental line positions,

The Opacity of TiO from a Coupled Electronic State Calculation Parameterized by ab initio and Experimental Data

NASA Technical Reports Server (NTRS)

Schwenke, David W.; Huo, Winifred (Technical Monitor)

1998-01-01

We have carried out ab initio electronic structure calculations of the spin-orbit and rotation-orbit couplings among the 14 lowest electronic states of TiO and used them to predict ro-vibrational energy levels. We report on the qualitative results as well as our progress in optimizing our Hamiltonian parameters in order to improve agreement with experimental line positions.

State of the art for ab initio vs empirical potentials for HeH+ (2e-), BeH+ (4e-), BeH (5e-), Li2 (6e-) and BH (6e-)

NASA Astrophysics Data System (ADS)

Dattani, Nike

For large internuclear distances, the potential energy between two atoms is known analytically, based on constants that are calculated from atomic ab initio rather than molecular ab initio. This analytic form can be built into models for molecular potentials that are fitted to spectroscopic data. Such empirical potentials constitute the most accurate molecular potentials known. For HeH+, and BeH+, the long-range form of the potential is based only on the polarizabilities for He and H respectively, for which we have included up to 4th order QED corrections. For BeH, the best ab initio potential matches all but one observed vibrational spacing to < 1 cm- accuracy, and for Li2 the discrepancy in the spacings is < 0.08 cm-1 for all vibrational levels. But experimental methods such as photoassociation require the absolute energies, not spacings, and these are still several in several cm-1 disagreement. So empirical potentials are still the only reliable way to predict energies for few-electron systems. We also give predictions for various unobserved ''halo nucleonic molecules'' containing the ''halo'' isotopes: 6,8He, 11Li, 11,14Be and 8 , 17 , 19B.

GalaxyGPCRloop: Template-Based and Ab Initio Structure Sampling of the Extracellular Loops of G-Protein-Coupled Receptors.

PubMed

Won, Jonghun; Lee, Gyu Rie; Park, Hahnbeom; Seok, Chaok

2018-06-07

The second extracellular loops (ECL2s) of G-protein-coupled receptors (GPCRs) are often involved in GPCR functions, and their structures have important implications in drug discovery. However, structure prediction of ECL2 is difficult because of its long length and the structural diversity among different GPCRs. In this study, a new ECL2 conformational sampling method involving both template-based and ab initio sampling was developed. Inspired by the observation of similar ECL2 structures of closely related GPCRs, a template-based sampling method employing loop structure templates selected from the structure database was developed. A new metric for evaluating similarity of the target loop to templates was introduced for template selection. An ab initio loop sampling method was also developed to treat cases without highly similar templates. The ab initio method is based on the previously developed fragment assembly and loop closure method. A new sampling component that takes advantage of secondary structure prediction was added. In addition, a conserved disulfide bridge restraining ECL2 conformation was predicted and analytically incorporated into sampling, reducing the effective dimension of the conformational search space. The sampling method was combined with an existing energy function for comparison with previously reported loop structure prediction methods, and the benchmark test demonstrated outstanding performance.

A Complete and Accurate Ab Initio Repeat Finding Algorithm.

PubMed

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

2016-03-01

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

Ab initio modeling of point defects, self-diffusion, and incorporation of impurities in thorium

NASA Astrophysics Data System (ADS)

Daroca, D. Pérez

2017-02-01

Research on Generation-IV nuclear reactors has boosted the investigation of thorium as nuclear fuel. By means of first-principles calculations within the framework of density functional theory, structural properties and phonon dispersion curves of Th are obtained. These results agreed very well with previous ones. The stability and formation energies of vacancies, interstitial and divacancies are studied. It is found that vacancies are the energetically preferred defects. The incorporation energies of He, Xe, and Kr atoms in Th defects are analyzed. Self-diffusion, migration paths and activation energies are also calculated.

Nonadiabatic couplings in the collisional removal of O(2)(b (1)Sigma(g) (+),v) by O(2).

PubMed

Dayou, F; Hernández, M I; Campos-Martínez, J; Hernández-Lamoneda, R

2010-01-28

The effect of nonadiabatic couplings on the collisional removal of O(2)(b (1)Sigma(g) (+),v) by O(2)(X (3)Sigma(g) (-), v=0) is investigated. Two-dimensional adiabatic and quasidiabatic potential energy surfaces for the excited dimer states and the corresponding nonadiabatic radial couplings have been computed by means of ab initio calculations. Alternately, a two-state theoretical model, based on the Landau-Zener and Rosen-Zener-Demkov assumptions, has been employed to derive analytical forms for the nonadiabatic couplings and an adiabatic-to-diabatic transformation only depending on a reduced set of adiabatic energy terms. Compared to the ab initio results, the predictions of the model are found to be highly accurate. Quantum dynamics calculations for the removal of the first ten vibrational states of O(2)(b (1)Sigma(g) (+),v) indicate a clear dominant contribution of the vibration-electronic relaxation mechanism relative to the vibration-translation energy transfer. Although the present reduced-dimensionality model precludes any quantitative comparison with experiments, it is found that the removal probabilities for v=1-3 are qualitatively consistent with the experimental observations, once the vibrational structure of the fragments is corrected with spectroscopical terms. Besides, the model served to show how the computation of the adiabatic PESs just at the crossing seam was sufficient to describe the nonadiabatic dynamics related to a given geometrical arrangement. This implies considerable savings in the calculations which will eventually allow for larger accuracy in the ab initio calculations as well as higher dimensional treatments.

Algebraic diagrammatic construction formalism with three-body interactions

NASA Astrophysics Data System (ADS)

Raimondi, Francesco; Barbieri, Carlo

2018-05-01

Background: Self-consistent Green's function theory has recently been extended to the basic formalism needed to account for three-body interactions [Carbone, Cipollone, Barbieri, Rios, and Polls, Phys. Rev. C 88, 054326 (2013), 10.1103/PhysRevC.88.054326]. The contribution of three-nucleon forces has so far been included in ab initio calculations on nuclear matter and finite nuclei only as averaged two-nucleon forces. Purpose: We derive the working equations for all possible two- and three-nucleon terms that enter the expansion of the self-energy up to the third order, thus including the interaction-irreducible (i.e., not averaged) diagrams with three-nucleon forces that have been previously neglected. Methods: We employ the algebraic diagrammatic construction up to the third order as an organization scheme for generating a nonperturbative self-energy, in which ring (particle-hole) and ladder (particle-particle) diagrams are resummed to all orders. Results: We derive expressions of the static and dynamic self-energy up to the third order, by taking into account the set of diagrams required when either the skeleton or nonskeleton expansions of the single-particle propagator are assumed. A hierarchy of importance among different diagrams is revealed, and a particular emphasis is given to a third-order diagram [see Fig. 2(c)] that is expected to play a significant role among those featuring an interaction-irreducible three-nucleon force. Conclusion: A consistent formalism to resum at infinite order correlations induced by three-nucleon forces in the self-consistent Green's function theory is now available and ready to be implemented in the many-body solvers.

Ab Initio Studies of Shock-Induced Chemical Reactions of Inter-Metallics

NASA Astrophysics Data System (ADS)

Zaharieva, Roussislava; Hanagud, Sathya

2009-06-01

Shock-induced and shock assisted chemical reactions of intermetallic mixtures are studied by many researchers, using both experimental and theoretical techniques. The theoretical studies are primarily at continuum scales. The model frameworks include mixture theories and meso-scale models of grains of porous mixtures. The reaction models vary from equilibrium thermodynamic model to several non-equilibrium thermodynamic models. The shock-effects are primarily studied using appropriate conservation equations and numerical techniques to integrate the equations. All these models require material constants from experiments and estimates of transition states. Thus, the objective of this paper is to present studies based on ab initio techniques. The ab inito studies, to date, use ab inito molecular dynamics. This paper presents a study that uses shock pressures, and associated temperatures as starting variables. Then intermetallic mixtures are modeled as slabs. The required shock stresses are created by straining the lattice. Then, ab initio binding energy calculations are used to examine the stability of the reactions. Binding energies are obtained for different strain components super imposed on uniform compression and finite temperatures. Then, vibrational frequencies and nudge elastic band techniques are used to study reactivity and transition states. Examples include Ni and Al.

An ab initio study on the four electronically lowest-lying states of CH 2 using the state-averaged complete active space second-order configuration interaction method

NASA Astrophysics Data System (ADS)

Yamaguchi, Yukio; Schaefer, Henry F., III

1997-12-01

Four electronically lowest-lying ( X˜ 3B 1, ã 1A 1, b˜ 1B 1, and c˜ 1A 1) states of CH 2 have been investigated systematically using ab initio electronic structure theory. Complete active space (CAS) self-consistent-field (SCF) second-order configuration interaction (SOCI) and state-averaged (SA) CASSCF-SOCI levels of theory have been employed. The CASSCF reference wave function was constructed by minimizing the total energy of a specified state, while the SACASSCF reference wave function was obtained by minimizing the equally weighted total energy of the four ( X˜ 3B 1, ã 1A 1, b˜ 1B 1, and c˜ 1A 1) states. The third excited state ( c˜ 1A 1 or 2 1A 1) is of particular theoretical interest because it is represented by the second root of CASSCF and SOCI Hamiltonian matrices. Theoretical treatments of states not the lowest of their symmetry require special attention due to their tendency of variational collapse to the lower-lying state(s). For these four lowest-lying states total energies and physical properties including dipole moments, harmonic vibrational frequencies, and associated infrared (IR) intensities were determined and compared with the results from the configuration interaction with single and double excitations (CISD) method and available experimental values. The CASSCF-SOCI method should provide the most reliable energetics and physical properties in the present study owing to its fully variational nature in the molecular orbital (MO) and CI spaces for a given state. It is demonstrated that the SACASSCF-SOCI wave functions produce results which are quite consistent with those from the CASSCF-SOCI method. Thus significantly increased application of the SACASSCF-SOCI method to the excited states of a wide variety of molecular systems is expected.

Dynamics of dissociative electron attachment to ammonia

DOE PAGES

Rescigno, T. N.; Trevisan, C. S.; Orel, A. E.; ...

2016-05-12

We present that ab initio theoretical studies and momentum-imaging experiments are combined to provide a consistent picture of the dynamics of dissociative electron attachment to ammonia through its 5.5- and 10.5-eV resonance channels. The present study clarifies the character and symmetry of the anion states involved and the dynamics that leads to the observed fragment-ion channels, their branching ratios, and angular distributions.

Dynamics of dissociative electron attachment to ammonia

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rescigno, T. N.; Trevisan, C. S.; Orel, A. E.

We present that ab initio theoretical studies and momentum-imaging experiments are combined to provide a consistent picture of the dynamics of dissociative electron attachment to ammonia through its 5.5- and 10.5-eV resonance channels. The present study clarifies the character and symmetry of the anion states involved and the dynamics that leads to the observed fragment-ion channels, their branching ratios, and angular distributions.

Avoiding fractional electrons in subsystem DFT based ab-initio molecular dynamics yields accurate models for liquid water and solvated OH radical

DOE Office of Scientific and Technical Information (OSTI.GOV)

Genova, Alessandro, E-mail: alessandro.genova@rutgers.edu; Pavanello, Michele, E-mail: m.pavanello@rutgers.edu; Ceresoli, Davide, E-mail: davide.ceresoli@cnr.it

2016-06-21

In this work we achieve three milestones: (1) we present a subsystem DFT method capable of running ab-initio molecular dynamics simulations accurately and efficiently. (2) In order to rid the simulations of inter-molecular self-interaction error, we exploit the ability of semilocal frozen density embedding formulation of subsystem DFT to represent the total electron density as a sum of localized subsystem electron densities that are constrained to integrate to a preset, constant number of electrons; the success of the method relies on the fact that employed semilocal nonadditive kinetic energy functionals effectively cancel out errors in semilocal exchange–correlation potentials that aremore » linked to static correlation effects and self-interaction. (3) We demonstrate this concept by simulating liquid water and solvated OH{sup •} radical. While the bulk of our simulations have been performed on a periodic box containing 64 independent water molecules for 52 ps, we also simulated a box containing 256 water molecules for 22 ps. The results show that, provided one employs an accurate nonadditive kinetic energy functional, the dynamics of liquid water and OH{sup •} radical are in semiquantitative agreement with experimental results or higher-level electronic structure calculations. Our assessments are based upon comparisons of radial and angular distribution functions as well as the diffusion coefficient of the liquid.« less

Avoiding fractional electrons in subsystem DFT based ab-initio molecular dynamics yields accurate models for liquid water and solvated OH radical.

PubMed

Genova, Alessandro; Ceresoli, Davide; Pavanello, Michele

2016-06-21

In this work we achieve three milestones: (1) we present a subsystem DFT method capable of running ab-initio molecular dynamics simulations accurately and efficiently. (2) In order to rid the simulations of inter-molecular self-interaction error, we exploit the ability of semilocal frozen density embedding formulation of subsystem DFT to represent the total electron density as a sum of localized subsystem electron densities that are constrained to integrate to a preset, constant number of electrons; the success of the method relies on the fact that employed semilocal nonadditive kinetic energy functionals effectively cancel out errors in semilocal exchange-correlation potentials that are linked to static correlation effects and self-interaction. (3) We demonstrate this concept by simulating liquid water and solvated OH(•) radical. While the bulk of our simulations have been performed on a periodic box containing 64 independent water molecules for 52 ps, we also simulated a box containing 256 water molecules for 22 ps. The results show that, provided one employs an accurate nonadditive kinetic energy functional, the dynamics of liquid water and OH(•) radical are in semiquantitative agreement with experimental results or higher-level electronic structure calculations. Our assessments are based upon comparisons of radial and angular distribution functions as well as the diffusion coefficient of the liquid.

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

NASA Astrophysics Data System (ADS)

Bacca, Sonia

2016-04-01

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

Ab initio density functional theory investigation of structural and electronic properties of double-walled silicon carbide nanotubes

NASA Astrophysics Data System (ADS)

Moradian, Rostam; Behzad, Somayeh; Chegel, Raad

2009-12-01

By using ab initio density functional theory, the structural and electronic properties of (n,n)@(11,11) double-walled silicon carbide nanotubes (SiCNTs) are investigated. Our calculations reveal the existence of an energetically favorable double-walled nanotube whose interwall distance is about 4.3 Å. Interwall spacing and curvature difference are found to be essential for the electronic states around the Fermi level.

Vibrational spectra for uric acid and its D- and 15N-substituted analogues. Assignments for its normal modes from ab initio 3-21G force field.

NASA Astrophysics Data System (ADS)

Majoube, M.; Vergoten, G.

1993-03-01

FTR, Raman, FTIR spectra are obtained for polycrystalline uric acid and seven of its D-and 15N-substituted analogues. Assignments are given from a normal coordinate analysis carried out using a 3-21G ab initio force field. These are discussed by considering observed and calculated frequencies and D- and 15N-isotopic shifts.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

2015-05-15

Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-In alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Five liquid Hg-In mixtures (Hg{sub 10}In{sub 90}, Hg{sub 30}In{sub 70}, Hg{sub 50}In{sub 50}, Hg{sub 70}In{sub 30} and Hg{sub 90}In{sub 10}) at 299K are considered. The radial distribution function g(r) and structure factor S(q) of considered alloys are compared with respective experimental results for liquid Hg (l-Hg) and (l-In). The radial distribution function g(r) shows the presence of short range order in the systems considered. Smooth curves of Bhatia-Thornton partial structure factors factormore » shows the presence of liquid state in the considered alloys.« less

Kubo–Greenwood approach to conductivity in dense plasmas with average atom models

DOE PAGES

Starrett, C. E.

2016-04-13

In this study, a new formulation of the Kubo–Greenwood conductivity for average atom models is given. The new formulation improves upon previous treatments by explicitly including the ionic-structure factor. Calculations based on this new expression lead to much improved agreement with ab initio results for DC conductivity of warm dense hydrogen and beryllium, and for thermal conductivity of hydrogen. We also give and test a slightly modified Ziman–Evans formula for the resistivity that includes a non-free electron density of states, thus removing an ambiguity in the original Ziman–Evans formula. Again, results based on this expression are in good agreement withmore » ab initio simulations for warm dense beryllium and hydrogen. However, for both these expressions, calculations of the electrical conductivity of warm dense aluminum lead to poor agreement at low temperatures compared to ab initio simulations.« less

Ab initio study of the electrostatic multipole nature of torsional potentials in CH3SSCH3, CH3SSH, and HOOH

NASA Technical Reports Server (NTRS)

Sokalski, W. A.; Lai, J.; Luo, N.; Sun, S.; Shibata, M.; Ornstein, R.; Rein, R.

1991-01-01

The origin of torsional potentials in H3CSSCH3, H3CSSH, and HOOH and the anisotropy of the local charge distribution has been analyzed in terms of atomic multipoles calculated from the ab initio LCAO-MO-SCF wave function in the 6-31G* basis set. The results indicate that for longer -S-S-bonds the major contribution to these torsional barriers are electrostatic interactions of the atomic multipoles located on two atoms forming the rotated bond. This finding demonstrates the important role of electrostatic 1-2 interatomic interactions, usually neglected in conformational studies. It also opens the possibility to derive directly from accurate ab initio wave functions a simple nonempirical torsional potential involving atomic multipoles of two bonded atoms defining the torsional angle. For shorter -O-O- bonds, use of more precise models and inclusion of 1-3 interactions seems to be necessary.

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

NASA Astrophysics Data System (ADS)

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

2015-02-01

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

Symplectic no-core configuration interaction framework for ab initio nuclear structure. II. Structure of rotational states

NASA Astrophysics Data System (ADS)

Caprio, Mark A.; McCoy, Anna E.; Dytrych, Tomas

2017-09-01

Rotational band structure is readily apparent as an emergent phenomenon in ab initio nuclear many-body calculations of light nuclei, despite the incompletely converged nature of most such calculations at present. Nuclear rotation in light nuclei can be analyzed in terms of approximate dynamical symmetries of the nuclear many-body problem: in particular, Elliott's SU (3) symmetry of the three-dimensional harmonic oscillator and the symplectic Sp (3 , R) symmetry of three-dimensional phase space. Calculations for rotational band members in the ab initio symplectic no-core configuration interaction (SpNCCI) framework allow us to directly examine the SU (3) and Sp (3 , R) nature of rotational states. We present results for rotational bands in p-shell nuclei. Supported by the US DOE under Award No. DE-FG02-95ER-40934 and the Czech Science Foundation under Grant No. 16-16772S.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sharma, Nalini, E-mail: nalini-2808@yahoo.co.in; Ahluwalia, P. K.; Thakur, Anil

2016-05-23

Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-In alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Three liquid Hg-In alloys (Hg{sub 10}In{sub 90}, Hg{sub 30}In{sub 70,.} Hg{sub 50}In{sub 50}, Hg{sub 70}In{sub 30}, and Hg{sub 90}Pb{sub 10}) at 299 K are considered. The calculated results for liquid Hg (l-Hg) and lead (l-In) are also drawn. Along with the calculated results of considered five liquid alloys of Hg-In alloy. The results obtained from electronic properties namely total density of state and partial density of states help to find the localmore » arrangement of Hg and In atoms and the presence of liquid state in the considered five alloys.« less

Spectroscopic study of uracil, 1-methyluracil and 1-methyl-4-thiouracil: Hydrogen bond interactions in crystals and ab-initio molecular dynamics.

PubMed

Brela, Mateusz Z; Boczar, Marek; Malec, Leszek M; Wójcik, Marek J; Nakajima, Takahito

2018-05-15

Hydrogen bond networks in uracil, 1-methyluracil and 1-methyl-4-thiouracil were studied by ab initio molecular dynamics as well as analysis of the orbital interactions. The power spectra calculated by ab initio molecular dynamics for atoms involved in hydrogen bonds were analyzed. We calculated spectra by using anharmonic approximation based on the autocorrelation function of the atom positions obtained from the Born-Oppenheimer simulations. Our results show the differences between hydrogen bond networks in uracil and its methylated derivatives. The studied methylated derivatives, 1-methyluracil as well as 1-methyl-4-thiouracil, form dimeric structures in the crystal phase, while uracil does not form that kind of structures. The presence of sulfur atom instead oxygen atom reflects weakness of the hydrogen bonds that build dimers. Copyright © 2018 Elsevier B.V. All rights reserved.

Atomic defects in monolayer WSe2 tunneling FETs studied by systematic ab initio calculations

NASA Astrophysics Data System (ADS)

Wu, Jixuan; Fan, Zhiqiang; Chen, Jiezhi; Jiang, Xiangwei

2018-05-01

Atomic defects in monolayer WSe2 tunneling FETs (TFETs) are studied through systematic ab initio calculations aiming at performance predictions and enhancements. The effects of various defect positions and different passivation atoms are characterized in WSe2 TFETs by rigorous ab initio quantum transport simulations. It is suggested that the Se vacancy (VSe) defect located in the gate-controlled channel region tends to increase the OFF current (I off), whereas it can be well suppressed by oxygen passivation. It is demonstrated that chlorine (Cl) passivation at the source-side tunneling region can largely suppress I off, leading to an impressively improved on–off ratio (I on/I off) compared with that without any defect. However, it is also observed that randomly positioned atomic defects tend to induce significant fluctuation of the TFET output. Further discussions are made with focus on the performance-variability trade-off for robust circuit design.

Efficacy of the SU(3) scheme for ab initio large-scale calculations beyond the lightest nuclei

DOE PAGES

Dytrych, T.; Maris, P.; Launey, K. D.; ...

2016-06-22

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 SU3-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 significant memory savings are achieved in physically important applications. In particular, a well-chosen symmetry-adapted basis affords memory savings in calculations of states withmore » a fixed total angular momentum in large model spaces while exactly preserving translational invariance.« less

Ab initio NMR Confirmed Evolutionary Structure Prediction for Organic Molecular Crystals

NASA Astrophysics Data System (ADS)

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

2015-03-01

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

Ab initio results for intermediate-mass, open-shell nuclei

NASA Astrophysics Data System (ADS)

Baker, Robert B.; Dytrych, Tomas; Launey, Kristina D.; Draayer, Jerry P.

2017-01-01

A theoretical understanding of nuclei in the intermediate-mass region is vital to astrophysical models, especially for nucleosynthesis. Here, we employ the ab initio symmetry-adapted no-core shell model (SA-NCSM) in an effort to push first-principle calculations across the sd-shell region. The ab initio SA-NCSM's advantages come from its ability to control the growth of model spaces by including only physically relevant subspaces, which allows us to explore ultra-large model spaces beyond the reach of other methods. We report on calculations for 19Ne and 20Ne up through 13 harmonic oscillator shells using realistic interactions and discuss the underlying structure as well as implications for various astrophysical reactions. This work was supported by the U.S. NSF (OCI-0904874 and ACI -1516338) and the U.S. DOE (DE-SC0005248), and also benefitted from the Blue Waters sustained-petascale computing project and high performance computing resources provided by LSU.

Ab initio theoretical calculations of the electronic excitation energies of small water clusters.

PubMed

Tachikawa, Hiroto; Yabushita, Akihiro; Kawasaki, Masahiro

2011-12-14

A direct ab initio molecular dynamics method has been applied to a water monomer and water clusters (H(2)O)(n) (n = 1-3) to elucidate the effects of zero-point energy (ZPE) vibration on the absorption spectra of water clusters. Static ab initio calculations without ZPE showed that the first electronic transitions of (H(2)O)(n), (1)B(1)←(1)A(1), are blue-shifted as a function of cluster size (n): 7.38 eV (n = 1), 7.58 eV (n = 2) and 8.01 eV (n = 3). The inclusion of the ZPE vibration strongly affects the excitation energies of a water dimer, and a long red-tail appears in the range of 6.42-6.90 eV due to the structural flexibility of a water dimer. The ultraviolet photodissociation of water clusters and water ice surfaces is relevant to these results.

General Rule of Negative Effective Ueff System & Materials Design of High-Tc Superconductors by ab initio Calculations

NASA Astrophysics Data System (ADS)

Katayama-Yoshida, Hiroshi; Nakanishi, Akitaka; Uede, Hiroki; Takawashi, Yuki; Fukushima, Tetsuya; Sato, Kazunori

2014-03-01

Based upon ab initio electronic structure calculation, I will discuss the general rule of negative effective U system by (1) exchange-correlation-induced negative effective U caused by the stability of the exchange-correlation energy in Hund's rule with high-spin ground states of d5 configuration, and (2) charge-excitation-induced negative effective U caused by the stability of chemical bond in the closed-shell of s2, p6, and d10 configurations. I will show the calculated results of negative effective U systems such as hole-doped CuAlO2 and CuFeS2. Based on the total energy calculations of antiferromagnetic and ferromagnetic states, I will discuss the magnetic phase diagram and superconductivity upon hole doping. I also discuss the computational materials design method of high-Tc superconductors by ab initio calculation to go beyond LDA and multi-scale simulations.

A global ab initio potential for HCN/HNC, exact vibrational energies, and comparison to experiment

NASA Technical Reports Server (NTRS)

Bentley, Joseph A.; Bowman, Joel M.; Gazdy, Bela; Lee, Timothy J.; Dateo, Christopher E.

1992-01-01

An ab initio (i.e., from first principles) calculation of vibrational energies of HCN and HNC is reported. The vibrational calculations were done with a new potential derived from a fit to 1124 ab initio electronic energies which were calculated using the highly accurate CCSD(T) coupled-cluster method in conjunction with a large atomic natural orbital basis set. The properties of this potential are presented, and the vibrational calculations are compared to experiment for 54 vibrational transitions, 39 of which are for zero total angular momentum, J = 0, and 15 of which are for J = 1. The level of agreement with experiment is unprecedented for a triatomic with two nonhydrogen atoms, and demonstrates the capability of the latest computational methods to give reliable predictions on a strongly bound triatomic molecule at very high levels of vibrational excitation.

Linear free-energy relationships between a single gas-phase ab initio equilibrium bond length and experimental pKa values in aqueous solution.

PubMed

Alkorta, Ibon; Popelier, Paul L A

2015-02-02

Remarkably simple yet effective linear free energy relationships were discovered between a single ab initio computed bond length in the gas phase and experimental pKa values in aqueous solution. The formation of these relationships is driven by chemical features such as functional groups, meta/para substitution and tautomerism. The high structural content of the ab initio bond length makes a given data set essentially divide itself into high correlation subsets (HCSs). Surprisingly, all molecules in a given high correlation subset share the same conformation in the gas phase. Here we show that accurate pKa values can be predicted from such HCSs. This is achieved within an accuracy of 0.2 pKa units for 5 drug molecules. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Spectroscopic and Ab Initio Determination of the Ring-Twisting Potential Energy Function for 1,3-Cyclohexadiene

NASA Astrophysics Data System (ADS)

Autrey, Daniel; Choo, Jaebum; Laane, Jaan

2000-10-01

The ring-twisting vibration of 1,3-cyclohexadiene has been studied using Raman and infrared spectroscopy of the molecule in the vapor phase. The Raman spectrum shows five ring-twisting transitions in the 150 - 200 cm-1 region. The far-infrared spectrum shows only two transitions for this vibration, which is infrared forbidden in the C_2v (planar) approximation. Three ring-twisting combination bands were also observed off a fundamental vibration at 926.1 cm-1. A coordinate dependent kinetic energy expansion for the ring-twisting motion was calculated, and this was used to determine the ring-twisting potential function. Ab initio calculations were performed using Moller-Plesset perturbation theory (MP2) using different basis sets. The barrier to planarity of 1150 cm-1 was determined from the spectroscopic data. The various ab initio calculations gave barriers to planarity in the 1197 - 1593 cm-1 range.

Computational prediction of muon stopping sites using ab initio random structure searching (AIRSS)

NASA Astrophysics Data System (ADS)

Liborio, Leandro; Sturniolo, Simone; Jochym, Dominik

2018-04-01

The stopping site of the muon in a muon-spin relaxation experiment is in general unknown. There are some techniques that can be used to guess the muon stopping site, but they often rely on approximations and are not generally applicable to all cases. In this work, we propose a purely theoretical method to predict muon stopping sites in crystalline materials from first principles. The method is based on a combination of ab initio calculations, random structure searching, and machine learning, and it has successfully predicted the MuT and MuBC stopping sites of muonium in Si, diamond, and Ge, as well as the muonium stopping site in LiF, without any recourse to experimental results. The method makes use of Soprano, a Python library developed to aid ab initio computational crystallography, that was publicly released and contains all the software tools necessary to reproduce our analysis.

Ab initio study of MF2 (M=Mn, Fe, Co, Ni) rutile-type compounds using the periodic unrestricted Hartree-Fock approach

NASA Astrophysics Data System (ADS)

de P. R. Moreira, Ibério; Dovesi, Roberto; Roetti, Carla; Saunders, Victor R.; Orlando, Roberto

2000-09-01

The ab initio periodic unrestricted Hartree-Fock method has been applied in the investigation of the ground-state structural, electronic, and magnetic properties of the rutile-type compounds MF2 (M=Mn, Fe, Co, and Ni). All electron Gaussian basis sets have been used. The systems turn out to be large band-gap antiferromagnetic insulators; the optimized geometrical parameters are in good agreement with experiment. The calculated most stable electronic state shows an antiferromagnetic order in agreement with that resulting from neutron scattering experiments. The magnetic coupling constants between nearest-neighbor magnetic ions along the [001], [111], and [100] (or [010]) directions have been calculated using several supercells. The resulting ab initio magnetic coupling constants are reasonably satisfactory when compared with available experimental data. The importance of the Jahn-Teller effect in FeF2 and CoF2 is also discussed.

Nuclear shielding constants by density functional theory with gauge including atomic orbitals

NASA Astrophysics Data System (ADS)

Helgaker, Trygve; Wilson, Philip J.; Amos, Roger D.; Handy, Nicholas C.

2000-08-01

Recently, we introduced a new density-functional theory (DFT) approach for the calculation of NMR shielding constants. First, a hybrid DFT calculation (using 5% exact exchange) is performed on the molecule to determine Kohn-Sham orbitals and their energies; second, the constants are determined as in nonhybrid DFT theory, that is, the paramagnetic contribution to the constants is calculated from a noniterative, uncoupled sum-over-states expression. The initial results suggested that this semiempirical DFT approach gives shielding constants in good agreement with the best ab initio and experimental data; in this paper, we further validate this procedure, using London orbitals in the theory, having implemented DFT into the ab initio code DALTON. Calculations on a number of small and medium-sized molecules confirm that our approach produces shieldings in excellent agreement with experiment and the best ab initio results available, demonstrating its potential for the study of shielding constants of large systems.

Ab-initio calculations on melting of thorium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mukherjee, D., E-mail: debojyoti@barc.gov.in; Sahoo, B. D.; Joshi, K. D.

2016-05-23

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

Efficacy of the SU(3) scheme for ab initio large-scale calculations beyond the lightest nuclei

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dytrych, T.; Maris, Pieter; Launey, K. D.

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 ofmore » states with a fixed total angular momentum in large model spaces while exactly preserving translational invariance.« less

Ab initio ground and excited state potential energy surfaces for NO-Kr complex and dynamics of Kr solids with NO impurity

NASA Astrophysics Data System (ADS)

Castro-Palacios, Juan Carlos; Rubayo-Soneira, Jesús; Ishii, Keisaku; Yamashita, Koichi

2007-04-01

The intermolecular potentials for the NO(XΠ2)-Kr and NO(AΣ+2)-Kr systems have been calculated using highly accurate ab initio calculations. The spin-restricted coupled cluster method for the ground 1A'2 state [NO(XΠ2)-Kr ] and the multireference singles and doubles configuration interaction method for the excited 2A'2 state [NO(AΣ+2)-Kr], respectively, were used. The potential energy surfaces (PESs) show two linear wells and one that is almost in the perpendicular position. An analytical representation of the PESs has been constructed for the triatomic systems and used to carry out molecular dynamics (MD) simulations of the NO-doped krypton matrix response after excitation of NO. MD results are shown comparatively for three sets of potentials: (1) anisotropic ab initio potentials [NO molecule direction fixed during the dynamics and considered as a point (its center of mass)], (2) isotropic ab initio potentials (isotropic part in a Legendre polynomial expansion of the PESs), and (3) fitted Kr-NO potentials to the spectroscopic data. An important finding of this work is that the anisotropic and isotropic ab initio potentials calculated for the Kr-NO triatomic system are not suitable for describing the dynamics of structural relaxation upon Rydberg excitation of a NO impurity in the crystal. However, the isotropic ab initio potential in the ground state almost overlaps the published experimental potential, being almost independent of the angle asymmetry. This fact is also manifested in the radial distribution function around NO. However, in the case of the excited state the isotropic ab initio potential differs from the fitted potentials, which indicates that the Kr-NO interaction in the matrix is quite different because of the presence of the surrounding Kr atoms acting on the NO molecule. MD simulations for isotropic potentials reasonably reproduce the experimental observables for the femtosecond response and the bubble size but do not match spectroscopic results. A general overall view of the results suggests that, when the Kr-NO interaction takes place inside the matrix, potentials are rather symmetric and less repulsive than those for the triatomic system. pectroscopy, yields a mean absolute deviation of about 5cm-1 over the 22 levels. The dissociation energy with respect to the lowest vibrational energy is calculated within 30cm-1 of the experimental value of 12953±8cm-1. The reported agreement of the theoretical spectrum and dissociation energy with experiment is contingent upon the inclusion of the effects of core-generated electron correlation, spin-orbit coupling, and scalar relativity. The Dunham analysis [Phys. Rev. 41, 721 (1932)] of the spectrum is found to be very accurate. New values are given for the spectroscopic constants.

Carbonate-Bridged Lanthanoid Triangles: Single-Molecule Magnet Behavior, Inelastic Neutron Scattering, and Ab Initio Studies.

PubMed

Giansiracusa, Marcus J; Vonci, Michele; Van den Heuvel, Willem; Gable, Robert W; Moubaraki, Boujemaa; Murray, Keith S; Yu, Dehong; Mole, Richard A; Soncini, Alessandro; Boskovic, Colette

2016-06-06

Optimization of literature synthetic procedures has afforded, in moderate yield, homogeneous and crystalline samples of the five analogues Na11[{RE(OH2)}3CO3(PW9O34)2] (1-RE; RE = Y, Tb, Dy, Ho, and Er). Phase-transfer methods have allowed isolation of the mixed salts (Et4N)9Na2[{RE(OH2)}3CO3(PW9O34)2] (2-RE; RE = Y and Er). The isostructural polyanions in these compounds are comprised of a triangular arrangement of trivalent rare-earth ions bridged by a μ3-carbonate ligand and sandwiched between two trilacunary Keggin {PW9O34} polyoxometalate ligands. Alternating-current (ac) magnetic susceptibility studies of 1-Dy, 1-Er, and 2-Er reveal the onset of frequency dependence for the out-of-phase susceptibility in the presence of an applied magnetic field at the lowest measured temperatures. Inelastic neutron scattering (INS) spectra of 1-Ho and 1-Er exhibit transitions between the lowest-lying crystal-field (CF) split states of the respective J = 8 and (15)/2 ground-state spin-orbit multiplets of the Ho(III) and Er(III) ions. Complementary ab initio calculations performed for these two analogues allow excellent reproduction of the experimental magnetic susceptibility and low-temperature magnetization data and are in reasonable agreement with the experimental INS data. The ab initio calculations reveal that the slight difference in coordination environments of the three Ln(III) ions in each complex gives rise to differences in the CF splitting that are not insignificant. This theoretical result is consistent with the observation of multiple relaxation processes by ac magnetic susceptibility and the broadness of the measured INS peaks. The ab initio calculations also indicate substantial mixing of the MJ contributions to the CF split energy levels of each Ln(III) ion. Calculations indicate that the CF ground states of the Ho(III) centers in 1-Ho are predominantly comprised of contributions from small MJ, while those of the Er(III) centers in 1-Er are predominantly comprised of contributions from large MJ, giving rise to slow magnetic relaxation. Although no direct evidence for intramolecular RE···RE magnetic coupling is observed in either magnetic or INS studies, on the basis of the ab initio calculations, we find noncollinear magnetic axes in 1-Er that are coplanar with the erbium triangle and radially arranged with respect to the triangle's centroid; thus, we argue that the absence of magnetic coupling in this system arises from dipolar and antiferromagnetic superexchange interactions that cancel each other out.

An Accurate ab initio Quartic Force Field and Vibrational Frequencies for CH4 and Isotopomers

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Martin, Jan M. L.; Taylor, Peter R.

1995-01-01

A very accurate ab initio quartic force field for CH4 and its isotopomers is presented. The quartic force field was determined with the singles and doubles coupled-cluster procedure that includes a quasiperturbative estimate of the effects of connected triple excitations, CCSD(T), using the correlation consistent polarized valence triple zeta, cc-pVTZ, basis set. Improved quadratic force constants were evaluated with the correlation consistent polarized valence quadruple zeta, cc-pVQZ, basis set. Fundamental vibrational frequencies are determined using second-order perturbation theory anharmonic analyses. All fundamentals of CH4 and isotopomers for which accurate experimental values exist and for which there is not a large Fermi resonance, are predicted to within +/- 6 cm(exp -1). It is thus concluded that our predictions for the harmonic frequencies and the anharmonic constants are the most accurate estimates available. It is also shown that using cubic and quartic force constants determined with the correlation consistent polarized double zeta, cc-pVDZ, basis set in conjunction with the cc-pVQZ quadratic force constants and equilibrium geometry leads to accurate predictions for the fundamental vibrational frequencies of methane, suggesting that this approach may be a viable alternative for larger molecules. Using CCSD(T), core correlation is found to reduce the CH4 r(e), by 0.0015 A. Our best estimate for r, is 1.0862 +/- 0.0005 A.

Ab initio study of the ground and excited electronic states of the methyl radical

PubMed Central

Zanchet, A.; Bañares, L.; Senent, M. L.; García-Vela, A.

2016-01-01

The ground and some excited electronic states of the methyl radical have been characterized by means of highly correlated ab intio techniques. The specific excited states investigated are those involved in the dissociation of the radical, namely the 3s and 3pz Rydberg states, and the A1 and B1 valence states crossing them, respectively. The C-H dissociative coordinate and the HCH bending angle were considered in order to generate the first two-dimensional ab initio representation of the potential surfaces of the above electronic states of CH3, along with the nonadiabatic couplings between them. Spectroscopic constants and frequencies calculated for the ground and bound excited states agree well with most of the available experimental data. Implications of the shape of the excited potential surfaces and couplings for the dissociation pathways of CH3 are discussed in the light of recent experimental results for dissociation from low-lying vibrational states of CH3. Based on the ab initio data some predictions are made regarding methyl photodissociation from higher initial vibrational states. PMID:27892569

Generalized One-Band Model Based on Zhang-Rice Singlets for Tetragonal CuO.

PubMed

Hamad, I J; Manuel, L O; Aligia, A A

2018-04-27

Tetragonal CuO (T-CuO) has attracted attention because of its structure similar to that of the cuprates. It has been recently proposed as a compound whose study can give an end to the long debate about the proper microscopic modeling for cuprates. In this work, we rigorously derive an effective one-band generalized t-J model for T-CuO, based on orthogonalized Zhang-Rice singlets, and make an estimative calculation of its parameters, based on previous ab initio calculations. By means of the self-consistent Born approximation, we then evaluate the spectral function and the quasiparticle dispersion for a single hole doped in antiferromagnetically ordered half filled T-CuO. Our predictions show very good agreement with angle-resolved photoemission spectra and with theoretical multiband results. We conclude that a generalized t-J model remains the minimal Hamiltonian for a correct description of single-hole dynamics in cuprates.

Theoretical dissociation energies for ionic molecules

NASA Technical Reports Server (NTRS)

Langhoff, S. R.; Bauschlicher, C. W., Jr.; Partridge, H.

1986-01-01

Ab initio calculations at the self-consistent-field and singles plus doubles configuration-interaction level are used to determine accurate spectroscopic parameters for most of the alkali and alkaline-earth fluorides, chlorides, oxides, sulfides, hydroxides, and isocyanides. Numerical Hartree-Fock (NHF) calculations are performed on selected systems to ensure that the extended Slater basis sets employed for the diatomic systems are near the Hartree-Fock limit. Extended Gaussian basis sets of at least triple-zeta plus double polarization equality are employed for the triatomic system. With this model, correlation effects are relatively small, but invariably increase the theoretical dissociation energies. The importance of correlating the electrons on both the anion and the metal is discussed. The theoretical dissociation energies are critically compared with the literature to rule out disparate experimental values. Theoretical (sup 2)Pi - (sup 2)Sigma (sup +) energy separations are presented for the alkali oxides and sulfides.

Melting properties of Pt and its transport coefficients in liquid states under high pressures

NASA Astrophysics Data System (ADS)

Wang, Pan-Pan; Shao, Ju-Xiang; Cao, Qi-Long

2016-11-01

Molecular dynamics (MD) simulations of the melting and transport properties in liquid states of platinum for the pressure range (50-200 GPa) are reported. The melting curve of platinum is consistent with previous ab initio MD simulation results and the first-principles melting curve. Calculated results for the pressure dependence of fusion entropy and fusion volume show that the fusion entropy and the fusion volume decrease with increasing pressure, and the ratio of the fusion volume to fusion entropy roughly reproduces the melting slope, which has a moderate decrease along the melting line. The Arrhenius law well describes the temperature dependence of self-diffusion coefficients and viscosity under high pressure, and the diffusion activation energy decreases with increasing pressure, while the viscosity activation energy increases with increasing pressure. In addition, the entropy-scaling law, proposed by Rosenfeld under ambient pressure, still holds well for liquid Pt under high pressure conditions.

Transitioning NWChem to the Next Generation of Manycore Machines

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bylaska, Eric J.; Apra, Edoardo; Kowalski, Karol

The NorthWest Chemistry (NWChem) modeling software is a popular molecular chemistry simulation software that was designed from the start to work on massively parallel processing supercomputers[6, 28, 49]. It contains an umbrella of modules that today includes Self Consistent Field (SCF), second order Mller-Plesset perturbation theory (MP2), Coupled Cluster, multi-conguration selfconsistent eld (MCSCF), selected conguration interaction (CI), tensor contraction engine (TCE) many body methods, density functional theory (DFT), time-dependent density functional theory (TDDFT), real time time-dependent density functional theory, pseudopotential plane-wave density functional theory (PSPW), band structure (BAND), ab initio molecular dynamics, Car-Parrinello molecular dynamics, classical molecular dynamics (MD), QM/MM,more » AIMD/MM, GIAO NMR, COSMO, COSMO-SMD, and RISM solvation models, free energy simulations, reaction path optimization, parallel in time, among other capabilities[ 22]. Moreover new capabilities continue to be added with each new release.« less

GPU implementation of the linear scaling three dimensional fragment method for large scale electronic structure calculations

NASA Astrophysics Data System (ADS)

Jia, Weile; Wang, Jue; Chi, Xuebin; Wang, Lin-Wang

2017-02-01

LS3DF, namely linear scaling three-dimensional fragment method, is an efficient linear scaling ab initio total energy electronic structure calculation code based on a divide-and-conquer strategy. In this paper, we present our GPU implementation of the LS3DF code. Our test results show that the GPU code can calculate systems with about ten thousand atoms fully self-consistently in the order of 10 min using thousands of computing nodes. This makes the electronic structure calculations of 10,000-atom nanosystems routine work. This speed is 4.5-6 times faster than the CPU calculations using the same number of nodes on the Titan machine in the Oak Ridge leadership computing facility (OLCF). Such speedup is achieved by (a) carefully re-designing of the computationally heavy kernels; (b) redesign of the communication pattern for heterogeneous supercomputers.

Magnetic anisotropy of dysprosium(III) in a low-symmetry environment: a theoretical and experimental investigation.

PubMed

Bernot, Kevin; Luzon, Javier; Bogani, Lapo; Etienne, Mael; Sangregorio, Claudio; Shanmugam, Muralidharan; Caneschi, Andrea; Sessoli, Roberta; Gatteschi, Dante

2009-04-22

A mixed theoretical and experimental approach was used to determine the local magnetic anisotropy of the dysprosium(III) ion in a low-symmetry environment. The susceptibility tensor of the monomeric species having the formula [Dy(hfac)(3)(NIT-C(6)H(4)-OEt)(2)], which contains nitronyl nitroxide (NIT-R) radicals, was determined at various temperatures through angle-resolved magnetometry. These results are in agreement with ab initio calculations performed using the complete active space self-consistent field (CASSCF) method, validating the predictive power of this theoretical approach for complex systems containing rare-earth ions, even in low-symmetry environments. Susceptibility measurements performed with the applied field along the easy axis eventually permitted a detailed analysis of the temperature and field dependence of the magnetization, providing evidence that the Dy ion transmits an antiferromagnetic interaction between radicals but that the Dy-radical interaction is ferromagnetic.

Cd in SnO: Probing structural effects on the electronic structure of doped oxide semiconductors through the electric field gradient at the Cd nucleus

NASA Astrophysics Data System (ADS)

Errico, Leonardo A.; Rentería, Mario; Petrilli, Helena M.

2007-04-01

We perform an ab initio study of the electric field gradient (EFG) at the nucleus of Cd impurities at substitutional Sn sites in crystalline SnO. The full-potential linearized-augmented plane wave and the projector augmented wave methods used here allow us to treat the electronic structure of the doped system and the atomic relaxations introduced by the impurities in the host in a fully self-consistent way using a supercell approach in a state-of-the-art way. Effects of the impurity charge state on the electronic and structural properties are also discussed. Since the EFG is a very subtle quantity, its determination is very useful to probe ground-state properties such as the charge density. We show that the EFG is very sensitive to structural relaxations induced by the impurity. Our theoretical predictions are compared with available experimental results.

Stretch or contraction induced inversion of rectification in diblock molecular junctions

NASA Astrophysics Data System (ADS)

Zhang, Guang-Ping; Hu, Gui-Chao; Song, Yang; Xie, Zhen; Wang, Chuan-Kui

2013-09-01

Based on ab initio theory and nonequilibrium Green's function method, the effect of stretch or contraction on the rectification in diblock co-oligomer molecular diodes is investigated theoretically. Interestingly, an inversion of rectifying direction induced by stretching or contracting the molecular junctions, which is closely related to the number of the pyrimidinyl-phenyl units, is proposed. The analysis of the molecular projected self-consistent Hamiltonian and the evolution of the frontier molecular orbitals as well as transmission coefficients under external biases gives an inside view of the observed results. It reveals that the asymmetric molecular level shift and asymmetric evolution of orbital wave functions under biases are competitive mechanisms for rectification. The stretching or contracting induced inversion of the rectification is due to the conversion of the dominant mechanism. This work suggests a feasible technique to manipulate the rectification performance in molecular diodes by use of the mechanically controllable method.

A PRELIMINARY JUPITER MODEL

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hubbard, W. B.; Militzer, B.

In anticipation of new observational results for Jupiter's axial moment of inertia and gravitational zonal harmonic coefficients from the forthcoming Juno orbiter, we present a number of preliminary Jupiter interior models. We combine results from ab initio computer simulations of hydrogen–helium mixtures, including immiscibility calculations, with a new nonperturbative calculation of Jupiter's zonal harmonic coefficients, to derive a self-consistent model for the planet's external gravity and moment of inertia. We assume helium rain modified the interior temperature and composition profiles. Our calculation predicts zonal harmonic values to which measurements can be compared. Although some models fit the observed (pre-Juno) second-more » and fourth-order zonal harmonics to within their error bars, our preferred reference model predicts a fourth-order zonal harmonic whose absolute value lies above the pre-Juno error bars. This model has a dense core of about 12 Earth masses and a hydrogen–helium-rich envelope with approximately three times solar metallicity.« less

Studies of an Isolated 15N- 15N Spin Pair. Off-Angle Fast-Sample-Spinning NMR and Self-Consistent-Field Calculations for Diazo Systems

NASA Astrophysics Data System (ADS)

Challoner, Robin; Harris, Robin K.; Tossell, John A.

1997-05-01

An off-magic-angle spinning study of the nonassociated molecular solid, doubly15N-labeled 5-methyl-2-diazobenzenesulphonic acid hydrochloride (I) is reported. The validity of the off-magic-angle spinning approach under fast-spinning conditions is verified by average Hamiltonian theory. Ab initio SCF calculations were performed on the simpler molecule, C6H5N2+, to provide the shielding parameters, the dipolar coupling between the two nitrogen nuclei, and the electric field gradient existing at both the α-nitrogen and β-nitrogen sites. The calculated values are in good agreement with the shielding and effective dipolar coupling data elucidated in the present investigation, and with a previous study of the two singly15N-labeled isotopomers in which information concerning the electric field gradient at the α and β sites was deduced.

Generalized One-Band Model Based on Zhang-Rice Singlets for Tetragonal CuO

NASA Astrophysics Data System (ADS)

Hamad, I. J.; Manuel, L. O.; Aligia, A. A.

2018-04-01

Tetragonal CuO (T-CuO) has attracted attention because of its structure similar to that of the cuprates. It has been recently proposed as a compound whose study can give an end to the long debate about the proper microscopic modeling for cuprates. In this work, we rigorously derive an effective one-band generalized t -J model for T-CuO, based on orthogonalized Zhang-Rice singlets, and make an estimative calculation of its parameters, based on previous ab initio calculations. By means of the self-consistent Born approximation, we then evaluate the spectral function and the quasiparticle dispersion for a single hole doped in antiferromagnetically ordered half filled T-CuO. Our predictions show very good agreement with angle-resolved photoemission spectra and with theoretical multiband results. We conclude that a generalized t -J model remains the minimal Hamiltonian for a correct description of single-hole dynamics in cuprates.

Two-Level Chebyshev Filter Based Complementary Subspace Method: Pushing the Envelope of Large-Scale Electronic Structure Calculations.

PubMed

Banerjee, Amartya S; Lin, Lin; Suryanarayana, Phanish; Yang, Chao; Pask, John E

2018-06-12

We describe a novel iterative strategy for Kohn-Sham density functional theory calculations aimed at large systems (>1,000 electrons), applicable to metals and insulators alike. In lieu of explicit diagonalization of the Kohn-Sham Hamiltonian on every self-consistent field (SCF) iteration, we employ a two-level Chebyshev polynomial filter based complementary subspace strategy to (1) compute a set of vectors that span the occupied subspace of the Hamiltonian; (2) reduce subspace diagonalization to just partially occupied states; and (3) obtain those states in an efficient, scalable manner via an inner Chebyshev filter iteration. By reducing the necessary computation to just partially occupied states and obtaining these through an inner Chebyshev iteration, our approach reduces the cost of large metallic calculations significantly, while eliminating subspace diagonalization for insulating systems altogether. We describe the implementation of the method within the framework of the discontinuous Galerkin (DG) electronic structure method and show that this results in a computational scheme that can effectively tackle bulk and nano systems containing tens of thousands of electrons, with chemical accuracy, within a few minutes or less of wall clock time per SCF iteration on large-scale computing platforms. We anticipate that our method will be instrumental in pushing the envelope of large-scale ab initio molecular dynamics. As a demonstration of this, we simulate a bulk silicon system containing 8,000 atoms at finite temperature, and obtain an average SCF step wall time of 51 s on 34,560 processors; thus allowing us to carry out 1.0 ps of ab initio molecular dynamics in approximately 28 h (of wall time).

Exact ab initio transport coefficients in bcc Fe-X (X=Cr, Cu, Mn, Ni, P, Si) dilute alloys

NASA Astrophysics Data System (ADS)

Messina, Luca; Nastar, Maylise; Garnier, Thomas; Domain, Christophe; Olsson, Pär

2014-09-01

Defect-driven diffusion of impurities is the major phenomenon leading to formation of embrittling nanoscopic precipitates in irradiated reactor pressure vessel (RPV) steels. Diffusion depends strongly on the kinetic correlations that may lead to flux coupling between solute atoms and point defects. In this work, flux coupling phenomena such as solute drag by vacancies and radiation-induced segregation at defect sinks are systematically investigated for six bcc iron-based dilute binary alloys, containing Cr, Cu, Mn, Ni, P, and Si impurities, respectively. First, solute-vacancy interactions and migration energies are obtained by means of ab initio calculations; subsequently, self-consistent mean field theory is employed in order to determine the exact Onsager matrix of the alloys. This innovative multiscale approach provides a more complete treatment of the solute-defect interaction than previous multifrequency models. Solute drag is found to be a widespread phenomenon that occurs systematically in ferritic alloys and is enhanced at low temperatures (as for instance RPV operational temperature), as long as an attractive solute-vacancy interaction is present, and that the kinetic modeling of bcc alloys requires the extension of the interaction shell to the second-nearest neighbors. Drag occurs in all alloys except Fe(Cr); the transition from dragging to nondragging regime takes place for the other alloys around (Cu, Mn, Ni) or above (P, Si) the Curie temperature. As far as only the vacancy-mediated solute migration is concerned, Cr depletion at sinks is foreseen by the model, as opposed to the other impurities which are expected to enrich up to no less than 1000 K. The results of this study confirm the current interpretation of the hardening processes in ferritic-martensitic steels under irradiation.

Two-state model based on the block-localized wave function method

NASA Astrophysics Data System (ADS)

Mo, Yirong

2007-06-01

The block-localized wave function (BLW) method is a variant of ab initio valence bond method but retains the efficiency of molecular orbital methods. It can derive the wave function for a diabatic (resonance) state self-consistently and is available at the Hartree-Fock (HF) and density functional theory (DFT) levels. In this work we present a two-state model based on the BLW method. Although numerous empirical and semiempirical two-state models, such as the Marcus-Hush two-state model, have been proposed to describe a chemical reaction process, the advantage of this BLW-based two-state model is that no empirical parameter is required. Important quantities such as the electronic coupling energy, structural weights of two diabatic states, and excitation energy can be uniquely derived from the energies of two diabatic states and the adiabatic state at the same HF or DFT level. Two simple examples of formamide and thioformamide in the gas phase and aqueous solution were presented and discussed. The solvation of formamide and thioformamide was studied with the combined ab initio quantum mechanical and molecular mechanical Monte Carlo simulations, together with the BLW-DFT calculations and analyses. Due to the favorable solute-solvent electrostatic interaction, the contribution of the ionic resonance structure to the ground state of formamide and thioformamide significantly increases, and for thioformamide the ionic form is even more stable than the covalent form. Thus, thioformamide in aqueous solution is essentially ionic rather than covalent. Although our two-state model in general underestimates the electronic excitation energies, it can predict relative solvatochromic shifts well. For instance, the intense π →π* transition for formamide upon solvation undergoes a redshift of 0.3eV, compared with the experimental data (0.40-0.5eV).

An accurate full-dimensional potential energy surface for H-Au(111): Importance of nonadiabatic electronic excitation in energy transfer and adsorption.

PubMed

Janke, Svenja M; Auerbach, Daniel J; Wodtke, Alec M; Kandratsenka, Alexander

2015-09-28

We have constructed a potential energy surface (PES) for H-atoms interacting with fcc Au(111) based on fitting the analytic form of the energy from Effective Medium Theory (EMT) to ab initio energy values calculated with density functional theory. The fit used input from configurations of the H-Au system with Au atoms at their lattice positions as well as configurations with the Au atoms displaced from their lattice positions. It reproduces the energy, in full dimension, not only for the configurations used as input but also for a large number of additional configurations derived from ab initio molecular dynamics (AIMD) trajectories at finite temperature. Adiabatic molecular dynamics simulations on this PES reproduce the energy loss behavior of AIMD. EMT also provides expressions for the embedding electron density, which enabled us to develop a self-consistent approach to simulate nonadiabatic electron-hole pair excitation and their effect on the motion of the incident H-atoms. For H atoms with an energy of 2.7 eV colliding with Au, electron-hole pair excitation is by far the most important energy loss pathway, giving an average energy loss ≈3 times that of the adiabatic case. This increased energy loss enhances the probability of the H-atom remaining on or in the Au slab by a factor of 2. The most likely outcome for H-atoms that are not scattered also depends prodigiously on the energy transfer mechanism; for the nonadiabatic case, more than 50% of the H-atoms which do not scatter are adsorbed on the surface, while for the adiabatic case more than 50% pass entirely through the 4 layer simulation slab.

Acetonitrile-water hydrogen-bonded interaction: Matrix-isolation infrared and ab initio computation

NASA Astrophysics Data System (ADS)

Gopi, R.; Ramanathan, N.; Sundararajan, K.

2015-08-01

The 1:1 hydrogen-bonded complex of acetonitrile (CH3CN) and water (H2O) was trapped in Ar and N2 matrices and studied using infrared technique. Ab initio computations showed two types of complexes formed between CH3CN and H2O, a linear complex A with a Ctbnd N⋯H interaction between nitrogen of CH3CN and hydrogen of H2O and a cyclic complex B, in which the interactions are between the hydrogen of CH3CN with oxygen of H2O and hydrogen of H2O with π cloud of sbnd Ctbnd N of CH3CN. Vibrational wavenumber calculations revealed that both the complexes A and B were minima on the potential energy surface. Interaction energies computed at B3LYP/6-311++G(d,p) showed that linear complex A is more stable than cyclic complex B. Computations identified a blue shift of ∼11.5 cm-1 and a red shift of ∼6.5 cm-1 in the CN stretching mode for the complexes A and B, respectively. Experimentally, we observed a blue shift of ∼15.0 and ∼8.3 cm-1 in N2 and Ar matrices, respectively, in the CN stretching mode of CH3CN, which supports the formation of complex A. The Onsager Self Consistent Reaction Field (SCRF) model was used to explain the influence of matrices on the complexes A and B. To understand the nature of the interactions, Atoms in Molecules (AIM) and Natural Bond Orbital (NBO) analyses were carried out for the complexes A and B.

Ab initio Bogoliubov coupled cluster theory for open-shell nuclei

DOE PAGES

Signoracci, Angelo J.; Duguet, Thomas; Hagen, Gaute; ...

2015-06-29

Background: Ab initio many-body methods have been developed over the past 10 yr to address closed-shell nuclei up to mass A≈130 on the basis of realistic two- and three-nucleon interactions. A current frontier relates to the extension of those many-body methods to the description of open-shell nuclei. Several routes to address open-shell nuclei are currently under investigation, including ideas that exploit spontaneous symmetry breaking. Purpose: Singly open-shell nuclei can be efficiently described via the sole breaking of U(1) gauge symmetry associated with particle-number conservation as a way to account for their superfluid character. While this route was recently followed withinmore » the framework of self-consistent Green's function theory, the goal of the present work is to formulate a similar extension within the framework of coupled cluster theory. Methods: We formulate and apply Bogoliubov coupled cluster (BCC) theory, which consists of representing the exact ground-state wave function of the system as the exponential of a quasiparticle excitation cluster operator acting on a Bogoliubov reference state. Equations for the ground-state energy and the cluster amplitudes are derived at the singles and doubles level (BCCSD) both algebraically and diagrammatically. The formalism includes three-nucleon forces at the normal-ordered two-body level. The first BCC code is implemented in m scheme, which will permit the treatment of doubly open-shell nuclei via the further breaking of SU(2) symmetry associated with angular momentum conservation. Results: Proof-of-principle calculations in an N max=6 spherical harmonic oscillator basis for 16,18O and 18Ne in the BCCD approximation are in good agreement with standard coupled cluster results with the same chiral two-nucleon interaction, while 20O and 20Mg display underbinding relative to experiment. The breaking of U(1) symmetry, monitored by computing the variance associated with the particle-number operator, is relatively constant for all five nuclei, in both the Hartree-Fock-Bogoliubov and BCCD approximations. Conclusions: The newly developed many-body formalism increases the potential span of ab initio calculations based on single-reference coupled cluster techniques tremendously, i.e., potentially to reach several hundred additional midmass nuclei. The new formalism offers a wealth of potential applications and further extensions dedicated to the description of ground and excited states of open-shell nuclei. Short-term goals include the implementation of three-nucleon forces at the normal-ordered two-body level. Midterm extensions include the approximate treatment of triples corrections and the development of the equation-of-motion methodology to treat both excited states and odd nuclei. Long-term extensions include exact restoration of U(1) and SU(2) symmetries.« less

Investigations of Reactive Processes at Temperatures Relevant to the Hypersonic Flight Regime

DTIC Science & Technology

2014-10-31

molecule is constructed based on high- level ab-initio calculations and interpolated using the reproducible kernel Hilbert space (RKHS) method and...a potential energy surface (PES) for the ground state of the NO2 molecule is constructed based on high- level ab initio calculations and interpolated...between O(3P) and NO(2Π) at higher temperatures relevant to the hypersonic flight regime of reentering space- crafts. At a more fundamental level , we

GAUSSIAN 76: An ab initio Molecular Orbital Program

DOE R&D Accomplishments Database

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

1978-01-01

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

Ab initio calculations for the elastic properties of magnesium under pressure

NASA Astrophysics Data System (ADS)

Sin'Ko, G. V.; Smirnov, N. A.

2009-09-01

Results of ab initio calculations of the elastic constants for the hcp, bcc, double hcp (dhcp), and fcc magnesium in a wide range of pressures are presented. The calculated elastic constants are compared with available experimental and theoretical data. We discuss the effect of the electron topological transition that occurs when the hcp structure is compressed on results of calculations and consider possibility of observing the hcp→dhcp transition on the magnesium Hugoniot.

Discovering charge density functionals and structure-property relationships with PROPhet: A general framework for coupling machine learning and first-principles methods

DOE PAGES

Kolb, Brian; Lentz, Levi C.; Kolpak, Alexie M.

2017-04-26

Modern ab initio methods have rapidly increased our understanding of solid state materials properties, chemical reactions, and the quantum interactions between atoms. However, poor scaling often renders direct ab initio calculations intractable for large or complex systems. There are two obvious avenues through which to remedy this problem: (i) develop new, less expensive methods to calculate system properties, or (ii) make existing methods faster. This paper describes an open source framework designed to pursue both of these avenues. PROPhet (short for PROPerty Prophet) utilizes machine learning techniques to find complex, non-linear mappings between sets of material or system properties. Themore » result is a single code capable of learning analytical potentials, non-linear density functionals, and other structure-property or property-property relationships. These capabilities enable highly accurate mesoscopic simulations, facilitate computation of expensive properties, and enable the development of predictive models for systematic materials design and optimization. Here, this work explores the coupling of machine learning to ab initio methods through means both familiar (e.g., the creation of various potentials and energy functionals) and less familiar (e.g., the creation of density functionals for arbitrary properties), serving both to demonstrate PROPhet’s ability to create exciting post-processing analysis tools and to open the door to improving ab initio methods themselves with these powerful machine learning techniques.« less

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Geng, Hua Y., E-mail: huay.geng@gmail.com; Department of Chemistry and Chemical Biology, Cornell University, Baker Laboratory, Ithaca, NY 14853

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

Discovering charge density functionals and structure-property relationships with PROPhet: A general framework for coupling machine learning and first-principles methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kolb, Brian; Lentz, Levi C.; Kolpak, Alexie M.

Modern ab initio methods have rapidly increased our understanding of solid state materials properties, chemical reactions, and the quantum interactions between atoms. However, poor scaling often renders direct ab initio calculations intractable for large or complex systems. There are two obvious avenues through which to remedy this problem: (i) develop new, less expensive methods to calculate system properties, or (ii) make existing methods faster. This paper describes an open source framework designed to pursue both of these avenues. PROPhet (short for PROPerty Prophet) utilizes machine learning techniques to find complex, non-linear mappings between sets of material or system properties. Themore » result is a single code capable of learning analytical potentials, non-linear density functionals, and other structure-property or property-property relationships. These capabilities enable highly accurate mesoscopic simulations, facilitate computation of expensive properties, and enable the development of predictive models for systematic materials design and optimization. Here, this work explores the coupling of machine learning to ab initio methods through means both familiar (e.g., the creation of various potentials and energy functionals) and less familiar (e.g., the creation of density functionals for arbitrary properties), serving both to demonstrate PROPhet’s ability to create exciting post-processing analysis tools and to open the door to improving ab initio methods themselves with these powerful machine learning techniques.« less

Experimental and Ab Initio Studies of the HDO Absorption Spectrum in the 13165-13500 1/cm Spectral Region

NASA Technical Reports Server (NTRS)

Schwenke, David; Naumenko, Olga; Bertseva, Elena; Campargue, Alain; Arnold, James O. (Technical Monitor)

2000-01-01

The HDO absorption spectrum has been recorded in the 13165 - 13500 cm(exp-1) spectral region by Intracavity Laser Absorption Spectroscopy. The spectrum (615 lines), dominated by the 2n2 + 3n3 and n1+3n3 bands was assigned and modeled leading to the derivation of 196 accurate energy levels of the (103) and (023) vibrational states. Finally, 150 of these levels have been reproduced by an effective Hamiltonian involving two vibrational dark states interacting with the (023) and ( 103) bright states. The rms deviation achieved by variation of 28 parameters is 0.05-1 cm, compared to an averaged experimental uncertainty of 0.007-1 cm, indicating the limit of validity of the effective Hamiltonian approach for HDO at high vibrational excitation. The predictions of previous ab initio calculations of the HDO spectrum were extensively used in the assignment process. The particular spectral region under consideration has been used to test and discuss the improvements of new ab initio calculations recently performed on the basis of the same potential energy surface but with an improved dipole moment surface. The improvements concern both the energy levels and the line intensities. In particular, the strong hybrid character of the n1+3n3 band is very well accounted for by the the new ab initio calculations.

Atomistic characterization of SAM coatings as gate insulators in Si-based FET devices

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gala, F.; Zollo, G.

2014-06-19

Many nano-material systems are currently under consideration as possible candidates for gate dielectric insulators in both metal-oxide-semiconductor (MOSFET) and organic (OFET) field-effect transistors. In this contribution, the possibility of employing self-assembled monolayers (SAMs) of hydroxylated octadecyltrichlorosilane (OTS) chains on a (111) Si substrate as gate dielectrics is discussed; in particular ab initio theoretical simulations have been employed to study the structural properties, work function modifications, and the insulating properties of OTS thin film coatings on Si substrates.

Atomistic characterization of SAM coatings as gate insulators in Si-based FET devices

NASA Astrophysics Data System (ADS)

Gala, F.; Zollo, G.

2014-06-01

Many nano-material systems are currently under consideration as possible candidates for gate dielectric insulators in both metal-oxide-semiconductor (MOSFET) and organic (OFET) field-effect transistors. In this contribution, the possibility of employing self-assembled monolayers (SAMs) of hydroxylated octadecyltrichlorosilane (OTS) chains on a (111) Si substrate as gate dielectrics is discussed; in particular ab initio theoretical simulations have been employed to study the structural properties, work function modifications, and the insulating properties of OTS thin film coatings on Si substrates.

Recommended direct simulation Monte Carlo collision model parameters for modeling ionized air transport processes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Swaminathan-Gopalan, Krishnan; Stephani, Kelly A., E-mail: ksteph@illinois.edu

2016-02-15

A systematic approach for calibrating the direct simulation Monte Carlo (DSMC) collision model parameters to achieve consistency in the transport processes is presented. The DSMC collision cross section model parameters are calibrated for high temperature atmospheric conditions by matching the collision integrals from DSMC against ab initio based collision integrals that are currently employed in the Langley Aerothermodynamic Upwind Relaxation Algorithm (LAURA) and Data Parallel Line Relaxation (DPLR) high temperature computational fluid dynamics solvers. The DSMC parameter values are computed for the widely used Variable Hard Sphere (VHS) and the Variable Soft Sphere (VSS) models using the collision-specific pairing approach.more » The recommended best-fit VHS/VSS parameter values are provided over a temperature range of 1000-20 000 K for a thirteen-species ionized air mixture. Use of the VSS model is necessary to achieve consistency in transport processes of ionized gases. The agreement of the VSS model transport properties with the transport properties as determined by the ab initio collision integral fits was found to be within 6% in the entire temperature range, regardless of the composition of the mixture. The recommended model parameter values can be readily applied to any gas mixture involving binary collisional interactions between the chemical species presented for the specified temperature range.« less

Reductive half-reaction of aldehyde oxidoreductase toward acetaldehyde: Ab initio and free energy quantum mechanical/molecular mechanical calculations.

PubMed

Dieterich, Johannes M; Werner, Hans-Joachim; Mata, Ricardo A; Metz, Sebastian; Thiel, Walter

2010-01-21

Energy and free energy barriers for acetaldehyde conversion in aldehyde oxidoreductase are determined for three reaction pathways using quantum mechanical/molecular mechanical (QM/MM) calculations on the solvated enzyme. Ab initio single-point QM/MM energies are obtained at the stationary points optimized at the DFT(B3LYP)/MM level. These ab initio calculations employ local correlation treatments [LMP2 and LCCSD(T0)] in combination with augmented triple- and quadruple-zeta basis sets, and the final coupled cluster results include MP2-based corrections for basis set incompleteness and for the domain approximation. Free energy perturbation (FEP) theory is used to generate free energy profiles at the DFT(B3LYP)/MM level for the most important reaction steps by sampling along the corresponding reaction paths using molecular dynamics. The ab initio and FEP QM/MM results are combined to derive improved estimates of the free energy barriers, which differ from the corresponding DFT(B3LYP)/MM energy barriers by about 3 kcal mol(-1). The present results confirm the qualitative mechanistic conclusions from a previous DFT(B3LYP)/MM study. Most favorable is a three-step Lewis base catalyzed mechanism with an initial proton transfer from the cofactor to the Glu869 residue, a subsequent nucleophilic attack that yields a tetrahedral intermediate (IM2), and a final rate-limiting hydride transfer. The competing metal center activated pathway has the same final step but needs to overcome a higher barrier in the initial step on the route to IM2. The concerted mechanism has the highest free energy barrier and can be ruled out. While confirming the qualitative mechanistic scenario proposed previously on the basis of DFT(B3LYP)/MM energy profiles, the present ab initio and FEP QM/MM calculations provide corrections to the barriers that are important when aiming at high accuracy.

Spin-orbit coupled potential energy surfaces and properties using effective relativistic coupling by asymptotic representation.

PubMed

Ndome, Hameth; Eisfeld, Wolfgang

2012-08-14

A new method has been reported recently [H. Ndome, R. Welsch, and W. Eisfeld, J. Chem. Phys. 136, 034103 (2012)] that allows the efficient generation of fully coupled potential energy surfaces (PESs) including derivative and spin-orbit (SO) coupling. The method is based on the diabatic asymptotic representation of the molecular fine structure states and an effective relativistic coupling operator and therefore is called effective relativistic coupling by asymptotic representation (ERCAR). The resulting diabatic spin-orbit coupling matrix is constant and the geometry dependence of the coupling between the eigenstates is accounted for by the diabatization. This approach allows to generate an analytical model for the fully coupled PESs without performing any ab initio SO calculations (except perhaps for the atoms) and thus is very efficient. In the present work, we study the performance of this new method for the example of hydrogen iodide as a well-established test case. Details of the diabatization and the accuracy of the results are investigated in comparison to reference ab initio calculations. The energies of the adiabatic fine structure states are reproduced in excellent agreement with reference ab initio data. It is shown that the accuracy of the ERCAR approach mainly depends on the quality of the underlying ab initio data. This is also the case for dissociation and vibrational level energies, which are influenced by the SO coupling. A method is presented how one-electron operators and the corresponding properties can be evaluated in the framework of the ERCAR approach. This allows the computation of dipole and transition moments of the fine structure states in good agreement with ab initio data. The new method is shown to be very promising for the construction of fully coupled PESs for more complex polyatomic systems to be used in quantum dynamics studies.

Deuteron-induced nucleon transfer reactions within an ab initio framework: First application to p -shell nuclei

DOE PAGES

Raimondi, Francesco; Hupin, Guillaume; Navratil, Petr; ...

2016-05-10

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. Here, ab initio approaches have been successfully applied to describe the 3H(d,n) 4He and 3He(d,p) 4He fusion processes. 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. Asmore » 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. 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. 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. Deuteron stripping reactions with p-shell targets can now be computed ab initio, but calculations are very demanding. Finally, 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.« less

Deuteron-induced nucleon transfer reactions within an ab initio framework: First application to p -shell nuclei

DOE Office of Scientific and Technical Information (OSTI.GOV)

Raimondi, Francesco; Hupin, Guillaume; Navratil, Petr

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. Here, ab initio approaches have been successfully applied to describe the 3H(d,n) 4He and 3He(d,p) 4He fusion processes. 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. Asmore » 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. 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. 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. Deuteron stripping reactions with p-shell targets can now be computed ab initio, but calculations are very demanding. Finally, 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.« less

Multi-physics transient simulation of monolithic niobium dioxide-tantalum dioxide memristor-selector structures

NASA Astrophysics Data System (ADS)

Sevic, John F.; Kobayashi, Nobuhiko P.

2017-10-01

Self-assembled niobium dioxide (NbO2) thin-film selectors self-aligned to tantalum dioxide (TaO2) memristive memory cells are studied by a multi-physics transient solution of the heat equation coupled to the nonlinear current continuity equation. While a compact model can resolve the quasi-static bulk negative differential resistance (NDR), a self-consistent coupled transport formulation provides a non-equilibrium picture of NbO2-TaO2 selector-memristor operation ab initio. By employing the drift-diffusion transport approximation, a finite element method is used to study the dynamic electrothermal behavior of our experimentally obtained selector-memristor devices, showing that existing conditions are suitable for electroformation of NbO2 selector thin-films. Both transient and steady-state simulations support our theory, suggesting that the phase change due to insulator-metal transition is responsible for NbO2 selector NDR in our as-fabricated selector-memristor devices. Simulation results further suggest that TiN nano-via may play a central role in electroforming, as its dimensions and material properties establish the mutual electrothermal interaction between TiN nano-via and the selector-memristor.

Kinetic and ab initio theoretical study of hydrogen atom abstraction from thiols by thiyl radicals: Basis rate expressions for reactions of sulfur-centered radicals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alnajjar, M.S.; Garrossian, M.S.; Autrey, S.T.

1992-08-20

Arrhenius rate expressions were determined for the abstraction of hydrogen atom from thiophenol and hexanethiol by the octanethiyl radical at 25-100 {degrees}C in nonane. Octanethiyl radicals were produced by steady-state photolysis of octyl thiobenzoate. Analysis of octyl disulfide and octanethiyl radical. For hexanethiol, log (k{sub abs}/K{sub t}{sup 1/2}) = (2.94 {plus_minus} 0.29) - (3.84 {plus_minus}0.41)/0, and for thiophenol, log (k{sub abs}/k{sub 5}{sup 1/2}) = (2.56 {plus_minus} 0.19) - (2.88 {plus_minus} 0.28)/0;0=2.3RT kcal/mol. Combining these expressions with the Smoluchowski expression for self-termination of octanethiyl in nonane, log (k{sub t}{sup 1/2}) = 5.96 - 1.335/0, which employs experimental diffusion coefficients of octanethiolmore » and a spin selection factor {sigma} = 1, yields, for thiophenol, log (k{sub abs}/M{sup {minus}1}s{sup {minus}1}) = (8.52 {plus_minus} 0.18) = (4.22 {plus_minus} 0.27)/0, and for hexanethiol, log (k{sub abs}/M{sup {minus}1} s{sup {minus}1}) = (8.90 {plus_minus} 0.29) = (5.18 {plus_minus} 0.41)/0 (errors are 2{sigma}). The rate of disappearance of octanethiyl/diphenylketyl radical pairs in SDS micelles, determined by nanosecond optical spectroscopy, was found to be unchanged in a 700-G magnetic field, providing evidence for rapid intersystem crossing of sulfur-centered radical pairs and support for the assignment of {sigma} = 1 above. Ab initio electronic structure calculations on the reaction HS{sup {lg_bullet}} + HSH {r_arrow} HSH + {sup {lg_bullet}}SH, performed at SCF and correlated levels, predict an activation barrier of {Delta}H{sub 298} {sup {double_dagger}}= 4.6 kcal/mol, in close agreement with the experimental barrier for the octanethiyl + hexanethiol reactions. 43 refs., 5 figs., 4 tabs.« less

Ab initio molecular dynamics simulations of liquid water using high quality meta-GGA functionals

DOE PAGES

Ruiz Pestana, Luis; Mardirossian, Narbe; Head-Gordon, Martin; ...

2017-02-27

We have used ab initio molecular dynamics (AIMD) to characterize water properties using two meta-generalized gradient approximation (meta-GGA) functionals, M06-L-D3 and B97M-rV, and compared their performance against a standard GGA corrected for dispersion, revPBE-D3, at ambient conditions (298 K, and 1 g cm –3 or 1 atm). Simulations of the equilibrium density, radial distribution functions, self-diffusivity, the infrared spectrum, liquid dipole moments, and characterizations of the hydrogen bond network show that all three functionals have overcome the problem of the early AIMD simulations that erroneously found ambient water to be highly structured, but they differ substantially among themselves in agreementmore » with experiment on this range of water properties. We show directly using water cluster data up through the pentamer that revPBE-D3 benefits from a cancellation of its intrinsic functional error by running classical trajectories, whereas the meta-GGA functionals are demonstrably more accurate and would require the simulation of nuclear quantum effects to realize better agreement with all cluster and condensed phase properties.« less

Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model.

PubMed

Laury, Marie L; Wang, Lee-Ping; Pande, Vijay S; Head-Gordon, Teresa; Ponder, Jay W

2015-07-23

A set of improved parameters for the AMOEBA polarizable atomic multipole water model is developed. An automated procedure, ForceBalance, is used to adjust model parameters to enforce agreement with ab initio-derived results for water clusters and experimental data for a variety of liquid phase properties across a broad temperature range. The values reported here for the new AMOEBA14 water model represent a substantial improvement over the previous AMOEBA03 model. The AMOEBA14 model accurately predicts the temperature of maximum density and qualitatively matches the experimental density curve across temperatures from 249 to 373 K. Excellent agreement is observed for the AMOEBA14 model in comparison to experimental properties as a function of temperature, including the second virial coefficient, enthalpy of vaporization, isothermal compressibility, thermal expansion coefficient, and dielectric constant. The viscosity, self-diffusion constant, and surface tension are also well reproduced. In comparison to high-level ab initio results for clusters of 2-20 water molecules, the AMOEBA14 model yields results similar to AMOEBA03 and the direct polarization iAMOEBA models. With advances in computing power, calibration data, and optimization techniques, we recommend the use of the AMOEBA14 water model for future studies employing a polarizable water model.